+++ /dev/null
-"clitk related standards
-"
-set cindent
-set softtabstop=0 "disable
-set expandtab
-"set cino={.5s,e-.5s,^-.5s
-set shiftwidth=2
-
-set makeprg=${HOME}/workspace/cvs/clitk3/fast_make.sh
-set grepprg=clgrep
#=========================================================
# CLITK = Command Line ITK
-PROJECT(clitk)
+project(clitk)
cmake_minimum_required(VERSION 2.8)
cmake_policy(VERSION 2.8)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
+ cmake_policy(SET CMP0007 NEW)
endif(COMMAND cmake_policy)
-IF(NOT DEFINED CLITK_SOURCE_DIR)
- SET(CLITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
-ENDIF(NOT DEFINED CLITK_SOURCE_DIR)
+if(NOT DEFINED CLITK_SOURCE_DIR)
+ set(CLITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
+endif(NOT DEFINED CLITK_SOURCE_DIR)
+# Default build type
+IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE Release CACHE STRING
+ "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+ FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)
#=========================================================
-SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-IF(MSVC)
- SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj" )
- SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /bigobj" )
-ENDIF(MSVC)
+if(MSVC)
+ set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj" )
+ set( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /bigobj" )
+endif(MSVC)
#=========================================================
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/common.cmake)
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/dependencies.cmake)
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/build_opt.cmake)
+include(${CLITK_SOURCE_DIR}/cmake/common.cmake)
+include(${CLITK_SOURCE_DIR}/cmake/dependencies.cmake)
+include(${CLITK_SOURCE_DIR}/cmake/build_opt.cmake)
#=========================================================
#=========================================================
SET(vvPacsConnection true)
# Select what is compiled
-ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/common ${PROJECT_BINARY_DIR}/common)
-ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/tools ${PROJECT_BINARY_DIR}/tools)
-ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/segmentation ${PROJECT_BINARY_DIR}/segmentation)
-ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/registration ${PROJECT_BINARY_DIR}/registration)
+add_subdirectory(${CLITK_SOURCE_DIR}/common ${PROJECT_BINARY_DIR}/common)
+add_subdirectory(${CLITK_SOURCE_DIR}/tools ${PROJECT_BINARY_DIR}/tools)
+add_subdirectory(${CLITK_SOURCE_DIR}/segmentation ${PROJECT_BINARY_DIR}/segmentation)
+add_subdirectory(${CLITK_SOURCE_DIR}/registration ${PROJECT_BINARY_DIR}/registration)
+add_subdirectory(${CLITK_SOURCE_DIR}/cluster_tools ${PROJECT_BINARY_DIR}/cluster_tools)
-MACRO(SET_IF_NOT_SET var val)
- IF(NOT DEFINED "${var}")
- SET("${var}" "${val}")
- ENDIF(NOT DEFINED "${var}")
-ENDMACRO(SET_IF_NOT_SET)
+macro(SET_IF_NOT_SET var val)
+ if(NOT DEFINED "${var}")
+ set("${var}" "${val}")
+ endif(NOT DEFINED "${var}")
+endmacro(SET_IF_NOT_SET)
# Those are set for running a classical make Experimental
SET_IF_NOT_SET(CTEST_DROP_METHOD "http")
#
# Build the documentation
#
-INCLUDE (${CMAKE_ROOT}/Modules/Documentation.cmake)
+include(${CMAKE_ROOT}/Modules/Documentation.cmake)
-IF (BUILD_DOXYGEN)
+if(BUILD_DOXYGEN)
#
# Configure the script and the doxyfile, then add target
#
- CONFIGURE_FILE(${CLITK_SOURCE_DIR}/Doxygen/doxygen.config.in
+ configure_file(${CLITK_SOURCE_DIR}/Doxygen/doxygen.config.in
${PROJECT_BINARY_DIR}/Doxygen/doxygen.config)
- CONFIGURE_FILE(${CLITK_SOURCE_DIR}/Doxygen/itkdoxygen.pl.in
+ configure_file(${CLITK_SOURCE_DIR}/Doxygen/itkdoxygen.pl.in
${PROJECT_BINARY_DIR}/Doxygen/itkdoxygen.pl)
- ADD_CUSTOM_TARGET(Documentation
+ add_custom_target(Documentation
COMMAND ${DOXYGEN_EXECUTABLE} ${PROJECT_BINARY_DIR}/Doxygen/doxygen.config
MAIN_DEPENDENCY ${PROJECT_BINARY_DIR}/Doxygen/doxygen.config
DEPENDS ${PROJECT_BINARY_DIR}/Doxygen/itkdoxygen.pl
WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/Doxygen
)
-ENDIF (BUILD_DOXYGEN)
+endif(BUILD_DOXYGEN)
--- /dev/null
+if(CLITK_BUILD_TOOLS)
+ #=========================================================
+ # Install scripts when running make install
+ set(SCRIPTS
+ gate_job_cluster.job
+ gate_make_merge_release.sh
+ gate_make_release.sh
+ gate_power_merge.sh
+ gate_run_submit_cluster.sh
+ gate_upload_release.sh
+ mergeDosePerEnergyFile.sh
+ mergeStatFile.py
+ mergeStatFile.sh
+ gate_run_submit_cluster_nomove.sh
+ gate_job_cluster_nomove.job
+ check_tmp_cluster.sh
+ )
+
+ install(FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
+
+endif(CLITK_BUILD_TOOLS)
--- /dev/null
+#! /bin/bash
+
+for i in 1 $(seq 4 20) $(seq 30 36)
+do
+ echo
+ echo "Files on host linux${i}.dg.creatis.insa-lyon.fr "
+ #ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "find /tmp -user $1 -exec rm -fr {} \; "
+ ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "find /tmp -user $1 2>/dev/null"
+#ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "rm -fr /tmp/tmp.*/core* /tmp/tmp.*/mac /tmp/tmp.*/data /tmp/tmp.*/output/*root"
+#ssh -o "StrictHostKeyChecking no" linux${i}.dg.creatis.insa-lyon.fr "mv /tmp/tmp.* data/gate/hybrid_analog_mc/liver/hybrid_emlivermore/rr/rayleigh/run.O6VN"
+done
+
--- /dev/null
+#! /usr/local/bin/bash -lx
+#
+# MACRODIR
+# MACROFILE
+# RELEASEDIR
+# OUTPUTDIR
+# INDEX
+# INDEXMAX
+# PARAM
+#
+#$ -P "P_creatis"
+#$ -l vmem=2G
+#$ -l fsize=1G
+#$ -l ct=30:00:00
+#$ -j yes
+#$ -r no
+
+
+function error {
+echo "ERROR: $1"
+exit 1
+}
+
+function warning {
+echo "WARNING: $1"
+}
+
+test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
+set -u
+
+echo "Checking"
+uname -a
+echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
+echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
+echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
+echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
+echo "JOB_ID=${JOB_ID}"
+echo "INDEX=${INDEX}"
+echo "INDEXMAX=${INDEX}"
+echo "PARAM=${PARAM}"
+
+if test "$RELEASEDIR" = "NONE"
+then
+ echo Using $(which Gate)
+ ldd $(which Gate)
+else
+ test -d "${RELEASEDIR}" || error "can't find release"
+ md5sum ${RELEASEDIR}/Gate
+ test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
+
+ echo "Finding libraries"
+ ROOTLIBS="${RELEASEDIR}/libCore.so:${RELEASEDIR}/libCint.so:${RELEASEDIR}/libRIO.so:${RELEASEDIR}/libNet.so:${RELEASEDIR}/libHist.so:${RELEASEDIR}/libGraf.so:${RELEASEDIR}/libGraf3d.so:${RELEASEDIR}/libGpad.so:${RELEASEDIR}/libTree.so:${RELEASEDIR}/libRint.so:${RELEASEDIR}/libPostscript.so:${RELEASEDIR}/libMatrix.so:${RELEASEDIR}/libPhysics.so:${RELEASEDIR}/libMathCore.so:${RELEASEDIR}/libThread.so:"
+ echo "ROOTLIBS=${ROOTLIBS}"
+ G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
+ echo "G4LIBS=${G4LIBS}"
+ CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
+ echo "CLHEPLIBS=${CLHEPLIBS}"
+ GATELIBS=""
+ test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
+ echo "GATELIBS=${GATELIBS}"
+fi
+test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
+
+
+echo "Copying inputs"
+LOCALMACRODIR=$(mktemp -d)
+trap "mv output ${OUTPUTDIR}/output.${JOB_ID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
+cd ${LOCALMACRODIR}
+cp -r -L "${MACRODIR}"/{data,mac} .
+mkdir output
+
+# Enforce one thread
+ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+
+echo "Lauching macro"
+date
+if test "$RELEASEDIR" = "NONE"
+then
+ Gate ${PARAM} ${MACROFILE} || error "gate failed"
+else
+ LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
+ G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
+ G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
+ G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
+ G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
+ G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
+ G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
+ G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
+ G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
+ /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
+ ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
+ || error "gate failed"
+fi
+
+date
+echo "Copying data back"
+ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
+rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
+
+echo "Cleanup"
+rm -r ${LOCALMACRODIR}
+date
+
+echo "Success!!!"
#PBS -r n
#PBS -l walltime=100:00:00
#PBS -j oe
-
-#env
-#pwd
-#exit 1
+#PBS -l mem=3Gb
function error {
date
if test "$RELEASEDIR" = "NONE"
then
- Gate ${PARAM} ${MACROFILE} || error "gate failed"
+ echo Gate ${PARAM} ${MACROFILE}
+ eval Gate ${PARAM} ${MACROFILE} || error "gate failed"
else
LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
--- /dev/null
+#!/bin/bash
+#
+# MACRODIR
+# MACROFILE
+# RELEASEDIR
+# OUTPUTDIR
+# INDEX
+# INDEXMAX
+# PARAM
+#
+#PBS -r n
+#PBS -l walltime=5:00:00
+#PBS -j oe
+#PBS -l mem=5Gb
+
+
+function error {
+echo "ERROR: $1"
+exit 1
+}
+
+function warning {
+echo "WARNING: $1"
+}
+
+test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
+set -u
+
+echo "Checking"
+uname -a
+echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
+echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
+echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
+echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
+echo "PBS_JOBID=${PBS_JOBID}"
+echo "INDEX=${INDEX}"
+echo "INDEXMAX=${INDEX}"
+echo "PARAM=${PARAM}"
+
+if test "$RELEASEDIR" = "NONE"
+then
+ echo Using $(which Gate)
+ ldd $(which Gate)
+else
+ test -d "${RELEASEDIR}" || error "can't find release"
+ md5sum ${RELEASEDIR}/Gate
+ test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
+
+ echo "Finding libraries"
+ ROOTLIBS="${RELEASEDIR}/libCore.so:${RELEASEDIR}/libCint.so:${RELEASEDIR}/libRIO.so:${RELEASEDIR}/libNet.so:${RELEASEDIR}/libHist.so:${RELEASEDIR}/libGraf.so:${RELEASEDIR}/libGraf3d.so:${RELEASEDIR}/libGpad.so:${RELEASEDIR}/libTree.so:${RELEASEDIR}/libRint.so:${RELEASEDIR}/libPostscript.so:${RELEASEDIR}/libMatrix.so:${RELEASEDIR}/libPhysics.so:${RELEASEDIR}/libMathCore.so:${RELEASEDIR}/libThread.so:"
+ echo "ROOTLIBS=${ROOTLIBS}"
+ G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
+ echo "G4LIBS=${G4LIBS}"
+ CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
+ echo "CLHEPLIBS=${CLHEPLIBS}"
+ GATELIBS=""
+ test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
+ echo "GATELIBS=${GATELIBS}"
+fi
+test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
+
+
+echo "Copying/linking inputs"
+LOCALMACRODIR=$(mktemp -d)
+trap "mv output ${OUTPUTDIR}/output.${PBS_JOBID%%.*} ; rm -rf ${LOCALMACRODIR} ; exit 1" 1 2 3 15
+cd ${LOCALMACRODIR}
+## below line seems not to be trapped correctly
+cp -r -L "${MACRODIR}"/mac .
+ln -s "${MACRODIR}"/data ./data
+mkdir output
+
+# Enforce one thread
+ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+
+echo "Lauching macro"
+date
+if test "$RELEASEDIR" = "NONE"
+then
+ Gate ${PARAM} ${MACROFILE} || error "gate failed"
+else
+ LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
+ G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
+ G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
+ G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
+ G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
+ G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
+ G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
+ G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
+ G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
+ /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
+ ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
+ || error "gate failed"
+fi
+
+echo "Copying data back"
+mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
+
+echo "Cleanup"
+unlink "${LOCALMACRODIR}"/data
+rm -rf "${LOCALMACRODIR}"
+
+echo "Success!!!"
--- /dev/null
+#!/bin/bash
+
+set -u
+set -e
+
+function error {
+echo "ERROR: $1"
+echo "$(basename $0)"
+exit 1
+}
+
+function get_deps {
+targetbinary=${1}
+targetdir=${2}
+test -d ${targetdir} || error "${targetdir} isn't a directory"
+ldd ${targetbinary} | while read library; do
+ libfile="$(echo ${library} | awk -F' ' '/=> \// {print $3}')"
+ test $libfile || continue # didn't macht regex
+ test -f "${targetdir}/$(basename ${libfile})" && continue # already exists
+ cp "${libfile}" "${targetdir}"
+ get_deps "${libfile}" "${targetdir}"
+done
+}
+
+function package_target {
+targetname="${1}"
+which "${targetname}" > /dev/null || error "cant locate ${targetname}"
+targetbin="$(which ${targetname})"
+echo "${targetname} executable is ${targetbin}"
+
+echo "Getting libraries"
+targetdir="$(mktemp -d)"
+get_deps "${targetbin}" "${targetdir}"
+
+echo "Removing unused libraries"
+rm -f ${targetdir}/libdl.so*
+rm -f ${targetdir}/libm.so*
+rm -f ${targetdir}/libstdc++.so*
+rm -f ${targetdir}/libgcc_s.so*
+rm -f ${targetdir}/libpthread.so*
+rm -f ${targetdir}/libc.so*
+
+echo "Copying binary"
+cp "${targetbin}" .
+for filename in $(find ${targetdir} -name '*.so*'); do cp ${filename} . ; done
+
+echo "Cleaning up"
+rm -r "${targetdir}"
+}
+
+filenames=("clitkImageArithm" "clitkMergeRootFiles" "clitkMergeAsciiDoseActor" "clitkImageUncertainty" "mergeStatFile.sh" "gate_power_merge.sh")
+
+for input in "${filenames[@]}"; do
+ package_target "${input}" || error "error while packaging ${input}"
+done
+
+echo "Making release"
+tar -czvf merge_release.tar.gz ** \
+ || usage "can't create release zip"
+
+
+
echo "pii data is ${G4PIIDATA}"
echo "Cleaning previous build"
-rm -fr $(basename ${G4NEUTRONHPDATA})
-rm -fr $(basename ${G4LEVELGAMMADATA})
-rm -fr $(basename ${G4RADIOACTIVEDATA})
-rm -fr $(basename ${G4ABLADATA})
-rm -fr $(basename ${G4LEDATA})
-rm -fr $(basename ${G4REALSURFACEDATA})
+# rm -fr $(basename ${G4NEUTRONHPDATA})
+# rm -fr $(basename ${G4LEVELGAMMADATA})
+# rm -fr $(basename ${G4RADIOACTIVEDATA})
+# rm -fr $(basename ${G4ABLADATA})
+# rm -fr $(basename ${G4LEDATA})
+# rm -fr $(basename ${G4REALSURFACEDATA})
rm -fr test_libs gate_shared_libs.tar.gz gate_release.tar.gz
echo "Copying libraries"
|| usage "can't create release zip"
chmod -w gate_release.tar.gz
-
-
--- /dev/null
+mkdir run.merge
+for i in $(ls -d results.????)
+do
+ ln -s ../$i run.merge/output_${i}
+done
+gate_power_merge.sh run.merge
+
#!/usr/bin/env bash
-set -u
+set -u
function error {
-echo "ERROR: $1"
-exit 1
+ echo "ERROR: $1"
+ exit 1
}
warning_count=0
function warning {
-let "warning_count++"
-echo "MERGE_WARNING: $1"
+ let "warning_count++"
+ echo "MERGE_WARNING: $1"
}
function start_bar {
-count_max="${1:?"provide count max"}"
+ count_max="${1:?"provide count max"}"
}
function update_bar {
-local count="${1:?"provide count"}"
-local message="${2:?"provide message"}"
-local percent=$(echo "100*${count}/${count_max}" | bc)
-#printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
-printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
+ local count="${1:?"provide count"}"
+ local message="${2:?"provide message"}"
+ local percent=$(echo "100*${count}/${count_max}" | bc)
+ #printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
+ printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
}
function end_bar {
-unset count_max
-#echo -ne '\n'
+ unset count_max
+ #echo -ne '\n'
}
function check_interfile {
-local input_interfile="${1:?"provide input interfile"}"
+ local input_interfile="${1:?"provide input interfile"}"
-grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
+ grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
-local header_byte_size=$(awk -F' ' '
+ local header_byte_size=$(awk -F' ' '
BEGIN { zsize = 0; }
/matrix size/ && $3 == "[1]" { xsize = $5; }
/matrix size/ && $3 == "[2]" { ysize = $5; }
/number of bytes per pixel/ { byte_per_pixel = $7; }
END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
-local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
+ local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
-test -f "${raw_interfile}" || return 1
-test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
+ test -f "${raw_interfile}" || return 1
+ test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
}
function write_mhd_header {
-local input_interfile="${1:?"provide input interfile"}"
-local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
+ local input_interfile="${1:?"provide input interfile"}"
+ local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
-check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
+ check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
-local header_start='ObjectType = Image
+ local header_start='ObjectType = Image
NDims = 3
AcquisitionDate = none
BinaryData = True
DistanceUnits = mm
AnatomicalOrientation = RIP'
-echo "${header_start}" > "${output_mhd}"
+ echo "${header_start}" > "${output_mhd}"
-awk -F' ' '
+ awk -F' ' '
/scaling factor/ && $4 == "[1]" { xspacing = $6; }
/scaling factor/ && $4 == "[2]" { yspacing = $6; }
END { print "ElementSpacing = " xspacing " " yspacing " 1"; }' "${input_interfile}" >> "${output_mhd}"
-awk -F' ' '
+ awk -F' ' '
BEGIN { zsize = 0; }
/matrix size/ && $3 == "[1]" { xsize = $5; }
/matrix size/ && $3 == "[2]" { ysize = $5; }
/number of projections/ { zsize += $5; }
END { print "DimSize = " xsize " " ysize " " zsize; }' "${input_interfile}" >> "${output_mhd}"
-awk -F' := ' '
+ awk -F' := ' '
/number format/ { format = $2; }
/number of bytes per pixel/ { byte_per_pixel = $2 }
END {
print "ElementType = MET_INT";
}' "${input_interfile}" >> "${output_mhd}"
-awk -F' := ' '
+ awk -F' := ' '
/name of data file/ { print "ElementDataFile = " $2; }' "${input_interfile}" >> "${output_mhd}"
}
test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
function merge_root {
-local merged="$1"
-shift
-echo " ${indent}entering root merger"
-echo " ${indent}merger is ${rootMerger}"
-echo " ${indent}creating ${merged}"
-#echo "######## $#"
-#echo "######## $*"
-
-if test $# -eq 1
-then
- echo " ${indent}just one partial file => just copy it"
- cp "$1" "${merged}"
- return
-fi
-
-local count=0
-local arguments=" -o ${merged}"
-while test $# -gt 0
-do
- local partial="$1"
+ local merged="$1"
shift
- let count++
- local arguments=" -i ${partial} ${arguments}"
-done
-${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
-echo " ${indent}merged ${count} files"
+ echo " ${indent}entering root merger"
+ echo " ${indent}merger is ${rootMerger}"
+ echo " ${indent}creating ${merged}"
+ #echo "######## $#"
+ #echo "######## $*"
+
+ if test $# -eq 1
+ then
+ echo " ${indent}just one partial file => just copy it"
+ cp "$1" "${merged}"
+ return
+ fi
+
+ local count=0
+ local arguments=" -o ${merged}"
+ while test $# -gt 0
+ do
+ local partial="$1"
+ shift
+ let count++
+ local arguments=" -i ${partial} ${arguments}"
+ done
+ ${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
+ echo " ${indent}merged ${count} files"
}
statMerger="mergeStatFile.py"
test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
function merge_stat {
-local merged="$1"
-shift
-echo " ${indent}entering stat merger"
-echo " ${indent}merger is ${statMerger}"
-echo " ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
- local partial="$1"
+ local merged="$1"
shift
- let count++
-
- if test ! -f "${merged}"
- then
- update_bar ${count} "copying first partial result ${partial}"
- cp "${partial}" "${merged}"
- continue
- fi
+ echo " ${indent}entering stat merger"
+ echo " ${indent}merger is ${statMerger}"
+ echo " ${indent}creating ${merged}"
+ local count=0
+ start_bar $#
+ while test $# -gt 0
+ do
+ local partial="$1"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ continue
+ fi
- update_bar ${count} "adding ${partial}"
- ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
-done
-end_bar
-echo " ${indent}merged ${count} files"
+ update_bar ${count} "adding ${partial}"
+ ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
+ done
+ end_bar
+ echo " ${indent}merged ${count} files"
}
doseMerger="mergeDosePerEnegryFile.sh"
test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
function merge_dose {
-local merged="$1"
-shift
-echo " ${indent}entering dose merger"
-echo " ${indent}merger is ${doseMerger}"
-echo " ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
- local partial="$1"
+ local merged="$1"
shift
- let count++
-
- if test ! -f "${merged}"
- then
- update_bar ${count} "copying first partial result ${partial}"
- cp "${partial}" "${merged}"
- continue
- fi
+ echo " ${indent}entering dose merger"
+ echo " ${indent}merger is ${doseMerger}"
+ echo " ${indent}creating ${merged}"
+ local count=0
+ start_bar $#
+ while test $# -gt 0
+ do
+ local partial="$1"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ continue
+ fi
- update_bar ${count} "adding ${partial}"
- ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
-done
-end_bar
-echo " ${indent}merged ${count} files"
+ update_bar ${count} "adding ${partial}"
+ ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+ done
+ end_bar
+ echo " ${indent}merged ${count} files"
}
txtImageMerger="clitkMergeAsciiDoseActor"
test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
function merge_txt_image {
-local merged="$1"
-shift
-echo " ${indent}entering text image merger"
-echo " ${indent}merger is ${txtImageMerger}"
-echo " ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
- local partial="$1"
+ local merged="$1"
shift
- let count++
-
- if test ! -f "${merged}"
- then
- update_bar ${count} "copying first partial result ${partial}"
- cp "${partial}" "${merged}"
- continue
- fi
+ echo " ${indent}entering text image merger"
+ echo " ${indent}merger is ${txtImageMerger}"
+ echo " ${indent}creating ${merged}"
+ local count=0
+ start_bar $#
+ while test $# -gt 0
+ do
+ local partial="$1"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ continue
+ fi
- update_bar ${count} "adding ${partial}"
- local header="$(cat "${merged}" | head -n 6)"
- local tmp="$(mktemp)"
- ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
- echo "${header}" > "${merged}"
- grep -v '## Merge' "${tmp}" >> "${merged}"
- rm "${tmp}"
-done
-end_bar
-echo " ${indent}merged ${count} files"
+ update_bar ${count} "adding ${partial}"
+ local header="$(cat "${merged}" | head -n 6)"
+ local tmp="$(mktemp)"
+ ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
+ echo "${header}" > "${merged}"
+ grep -v '## Merge' "${tmp}" >> "${merged}"
+ rm "${tmp}"
+ done
+ end_bar
+ echo " ${indent}merged ${count} files"
}
hdrImageMerger="clitkImageArithm"
test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
function merge_hdr_image {
-local merged="$1"
-local merged_bin="${merged%.*}.img"
-shift
-echo " ${indent}entering hdr image merger"
-echo " ${indent}merger is ${hdrImageMerger}"
-echo " ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
- local partial="$1"
- local partial_bin="${partial%.*}.img"
+ local merged="$1"
+ local merged_bin="${merged%.*}.img"
shift
- let count++
-
- if test ! -f "${merged}"
- then
- update_bar ${count} "copying first partial result ${partial}"
- cp "${partial}" "${merged}"
- cp "${partial_bin}" "${merged_bin}"
- continue
- fi
+ echo " ${indent}entering hdr image merger"
+ echo " ${indent}merger is ${hdrImageMerger}"
+ echo " ${indent}creating ${merged}"
+ local count=0
+ start_bar $#
+ while test $# -gt 0
+ do
+ local partial="$1"
+ local partial_bin="${partial%.*}.img"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ cp "${partial_bin}" "${merged_bin}"
+ continue
+ fi
- update_bar ${count} "adding ${partial}"
- ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
-done
-end_bar
-echo " ${indent}merged ${count} files"
+ update_bar ${count} "adding ${partial}"
+ ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
+ done
+ end_bar
+ echo " ${indent}merged ${count} files"
}
mhdImageMerger="clitkImageArithm"
test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
function merge_mhd_image {
-local merged="$1"
-local merged_bin="${merged%.*}.raw"
-shift
-echo " ${indent}entering mhd image merger"
-echo " ${indent}merger is ${mhdImageMerger}"
-echo " ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
- local partial="$1"
- local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
+ local merged="$1"
+ local merged_bin="${merged%.*}.raw"
+ local last_character=${merged#${merged%?}}
shift
- let count++
-
- if test ! -f "${merged}"
- then
- update_bar ${count} "copying first partial result ${partial}"
- cp "${partial}" "${merged}"
- cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
- continue
- fi
+ echo " ${indent}entering mhd image merger"
+ echo " ${indent}merger is ${mhdImageMerger}"
+ echo " ${indent}creating ${merged}"
+ local count=0
+ start_bar $#
+ while test $# -gt 0
+ do
+ local partial="$1"
+ local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
+ shift
+ let count++
+
+ if test ! -f "${merged}"
+ then
+ update_bar ${count} "copying first partial result ${partial}"
+ cp "${partial}" "${merged}"
+ if test "$last_character" = "d"
+ then
+ cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ fi
+ continue
+ fi
- update_bar ${count} "adding ${partial}"
- ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
- mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
- sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
-done
-end_bar
-echo " ${indent}merged ${count} files"
+ update_bar ${count} "adding ${partial}"
+ ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
+ if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
+ then
+ mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+ sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
+ fi
+ done
+ end_bar
+ echo " ${indent}merged ${count} files"
}
function merge_dispatcher {
local outputfile="${1:?"provide output filename"}"
echo "merging ${outputfile}"
- local partialoutputfiles="$(find "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
if test ${nboutputdirs} -ne ${nboutputfiles}
then
warning "missing files"
- return
+ if ! test "${2}" == "--force"
+ then
+ return
+ fi
fi
local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
return
fi
- if test "${firstpartialoutputextension}" == "mhd"
+ if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
then
echo "${indent}this is a mhd image"
local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
error "unknown file type"
}
+function merge_dispatcher_uncertainty {
+ local indent=" ** "
+ local outputfile="${1:?"provide output filename"}"
+
+ local partialoutputfiles="$(find -L "${rundir}" -mindepth 2 -type f -name "${outputfile}")"
+ local nboutputfiles="$(echo "${partialoutputfiles}" | wc -l)"
+ if test ${nboutputdirs} -ne ${nboutputfiles}
+ then
+ warning "missing files"
+ if ! test "${2}" == "--force"
+ then
+ return
+ fi
+ fi
+
+ local firstpartialoutputfile="$(echo "${partialoutputfiles}" | head -n 1)"
+ local firstpartialoutputextension="${firstpartialoutputfile##*.}"
+
+ if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
+ then
+ if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
+ then
+ echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
+ ## search for sum
+ local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+ summed_merged_file=${mergedfile//-Uncertainty/}
+ if [ ! -f ${summed_merged_file} ];
+ then
+ warning "${summed_merged_file} does not exist. Error, no uncertainty computed"
+ return;
+ fi
+ echo "${indent}${summed_merged_file} found"
+ ## search for Squared
+ squared_merged_file=${mergedfile//-Uncertainty/-Squared}
+ if [ ! -f ${squared_merged_file} ];
+ then
+ warning "${squared_merged_file} does not exist. Error, no uncertainty computed"
+ return;
+ fi
+ echo "${indent}${squared_merged_file} found"
+ ## search for NumberOfEvent
+ totalEvents=0;
+ for outputfile in $(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+ do
+ #echo $outputfile
+ if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
+ then
+ totalEvents="$(grep "NumberOfEvents" "${outputdir}/${outputfile}" | cut -d' ' -f4)"
+ echo "${indent}Find the NumberOfEvent in $outputfile: ${totalEvents}"
+ fi
+ done
+
+ if test ${totalEvents} -gt 0
+ then
+ uncerImageMerger="clitkImageUncertainty"
+ test -x "./clitkImageUncertainty" && uncerImageMerger="./clitkImageUncertainty"
+ ${uncerImageMerger} -i ${summed_merged_file} -s ${squared_merged_file} -o ${mergedfile} -n ${totalEvents}
+ else
+ warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
+ return;
+ fi
+ else
+ error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
+ fi
+ fi
+
+}
+
echo "!!!! this is $0 v0.3k !!!!"
+echo "Usage: gate_power_merge.sh run.dir [--force]"
+echo " where --force allows to merge files even if the file is missing in some output directories"
rundir="${1?"provide run dir"}"
+force=${2:-""}
rundir="$(echo "${rundir}" | sed 's|/*$||')"
-nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
+nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' -o -type l -name 'output*' | wc -l)"
test ${nboutputdirs} -gt 0 || error "no output dir found"
echo "found ${nboutputdirs} partial output dirs"
fi
outputdir="$(basename "${outputdir}")"
echo "output dir is ${outputdir}"
+
test -d "${outputdir}" && rm -r "${outputdir}"
mkdir "${outputdir}"
+for outputfile in $(find -L "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+do
+ merge_dispatcher "${outputfile}" "${force}"
+done
-for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+echo ""
+echo "Merging done. Special case for statistical uncertainty"
+for outputfile in $(find -L "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
do
- merge_dispatcher "${outputfile}"
+ merge_dispatcher_uncertainty "${outputfile}" "${force}"
done
if [ -f "${rundir}/params.txt" ]
then
- echo "copying params file"
- cp "${rundir}/params.txt" "${outputdir}/params.txt"
+ echo "copying params file"
+ cp "${rundir}/params.txt" "${outputdir}/params.txt"
+fi
+
+if [ -d "${rundir}/mac" ]
+then
+ echo "copying mac folder"
+ cp -r "${rundir}/mac" "${outputdir}/mac"
fi
echo "these was ${warning_count} warning(s)"
-#!/usr/bin/env bash
+#! /usr/local/bin/bash -lx
set -u
SCRIPTNAME="$(basename "${0}")"
echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
echo "default releasesuffix = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)"
+ echo "default paramtogate = \"\" (use \"\" around params and \\ in front of commas)"
}
# -------------------------------------------------
test $# -eq 0 && usage && exit 0
-SCRIPTDIR="${HOME}/git/gate-tests/bin"
RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"}
RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}"
-JOBFILE="$(dirname $0)/gate_job_cluster.job"
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+ JOBFILE="$(dirname $0)/gate_job_ccin2p3.job"
+else
+ JOBFILE="$(dirname $0)/gate_job_cluster.job"
+fi
echo "Checking stuff"
test -f ${JOBFILE} || error "can't find job file ${JOBFILE}"
test -d ${MACRODIR}/mac && test -d ${MACRODIR}/data || error "invalid path"
MACROFILE=${1:?"provide relative macro path"}
test -f ${MACRODIR}/${MACROFILE} || error "invalid macro"
-OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+ OUTPUTDIR=$(mktemp -d -p "${MACRODIR}" run.XXXX || error "can't create temp dir")
+ ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr mkdir -p "cc/$(basename ${OUTPUTDIR})"
+else
+ OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+fi
test -d ${OUTPUTDIR} || error "can't locate output dir"
RUNID=${OUTPUTDIR##*.}
NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
NJOBSMAX=${NJOBS}
-PARAM="${4:-""}"
+PARAM="${4:-\"\"}"
echo "Lets roll!!"
echo "runid is ${RUNID}"
echo "macro = ${MACROFILE}" >> "${PARAMFILE}"
test -z "${PARAM}" || echo "param = ${PARAM}" >> "${PARAMFILE}"
+# Copy macros files (for log)
+mkdir ${OUTPUTDIR}/mac
+cp ${MACROFILE} ${OUTPUTDIR}/mac
+files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2`
+for i in $files
+do
+ cp $i ${OUTPUTDIR}/mac
+done
+
while test $NJOBS -gt 0; do
if test "${QSUB}" = "noqsub"
- then
+ then
echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
- PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} SCRIPTDIR=${SCRIPTDIR} OUTPUTDIR=${OUTPUTDIR} RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+ PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR} RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+ elif test "$(dnsdomainname)" = "in2p3.fr"
+ then
+ PROJECTGROUP=creatis
+ qsub -o "${OUTPUTDIR}" \
+ -N "gate.${RUNID}" \
+ -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+ "${JOBFILE}" || error "submission error"
else
- qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
- -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},SCRIPTDIR=${SCRIPTDIR},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+ qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
+ -v "PARAM=${PARAM},INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
"${JOBFILE}" || error "submission error"
fi
done
echo "runid is ${RUNID}"
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+ rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" ${OUTPUTDIR}/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})" --exclude '.__afs*' --exclude "${OUTPUTDIR}/gatejob.*.o*"
+fi
--- /dev/null
+#! /bin/bash
+
+set -u
+SCRIPTNAME="$(basename "${0}")"
+
+# -------------------------------------------------
+function error {
+ echo "ERROR: $1"
+ usage
+ exit 1
+}
+# -------------------------------------------------
+
+DEFAULTRELEASESUFFIX="NONE"
+DEFAULTNUMBEROFJOBS="10"
+
+# -------------------------------------------------
+function usage {
+ echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
+ echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
+ echo "default releasesuffix = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)"
+ echo "default paramtogate = \"\" (use \"\" around params and \\ in front of commas)"
+}
+# -------------------------------------------------
+
+test $# -eq 0 && usage && exit 0
+
+RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"}
+RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}"
+JOBFILE="$(dirname $0)/gate_job_cluster_nomove.job"
+
+echo "Checking stuff"
+test -f ${JOBFILE} || error "can't find job file ${JOBFILE}"
+if test "${RELEASESUFFIX}" = "${DEFAULTRELEASESUFFIX}"
+then
+ RELEASEDIR="NONE"
+ which Gate 2>&1 >/dev/null || error "there is no Gate in the PATH"
+else
+ test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}"
+fi
+MACRODIR=$(pwd)
+test -d ${MACRODIR}/mac && test -d ${MACRODIR}/data || error "invalid path"
+MACROFILE=${1:?"provide relative macro path"}
+test -f ${MACRODIR}/${MACROFILE} || error "invalid macro"
+OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+test -d ${OUTPUTDIR} || error "can't locate output dir"
+RUNID=${OUTPUTDIR##*.}
+NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
+NJOBSMAX=${NJOBS}
+PARAM="${4:-\"\"}"
+
+echo "Lets roll!!"
+echo "runid is ${RUNID}"
+
+QSUB=$(which qsub 2> /dev/null)
+# echo "qsub is $(which qsub)"
+test -z "${QSUB}" && QSUB="noqsub"
+if test "${QSUB}" = "noqsub"
+then
+ echo "qsub is not found. Simply run Gate on multiple cores."
+fi
+
+test -z "${PARAM}" && echo "no param" || echo "param is ${PARAM}"
+if test "$RELEASESUFFIX" = "$DEFAULTRELEASESUFFIX"
+then
+ echo "Gate is $(which Gate)"
+else
+ echo "Gate release is $(basename ${RELEASEDIR})"
+fi
+echo "submitting ${NJOBS} jobs"
+
+PARAMFILE="${OUTPUTDIR}/params.txt"
+echo "njobs = ${NJOBS}" >> "${PARAMFILE}"
+echo "macro = ${MACROFILE}" >> "${PARAMFILE}"
+test -z "${PARAM}" || echo "param = ${PARAM}" >> "${PARAMFILE}"
+
+# Copy macros files (for log)
+mkdir ${OUTPUTDIR}/mac
+cp ${MACROFILE} ${OUTPUTDIR}/mac
+files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2`
+for i in $files
+do
+ cp $i ${OUTPUTDIR}/mac
+done
+
+while test $NJOBS -gt 0; do
+
+ if test "${QSUB}" = "noqsub"
+ then
+ echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
+ PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR} RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+ else
+ qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
+ -v "PARAM=${PARAM},INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+ "${JOBFILE}" || error "submission error"
+ fi
+
+ let NJOBS--
+done
+
+echo "runid is ${RUNID}"
keys = {}
for line in open(filename,"r").readlines():
match = linere.match(line)
- assert(match is not None)
+ #assert(match is not None)
+ if match is None:
+ continue
groups = match.groups()
if groups[0] not in mergedlines:
continue
keys = merge_keys(ikeys,jkeys)
output = format_keys(keys)
open(sys.argv[6],"w").write(output)
-
# Attempt to find gengetopt. If not found, compile it.
-FIND_PROGRAM(GENGETOPT gengetopt)
-IF (GENGETOPT STREQUAL "GENGETOPT-NOTFOUND")
- GET_FILENAME_COMPONENT(CLITK_CMAKE_DIR ${CMAKE_CURRENT_LIST_FILE} PATH)
- ADD_SUBDIRECTORY(${CLITK_CMAKE_DIR}/../utilities/gengetopt ${CMAKE_CURRENT_BINARY_DIR}/gengetopt)
-ELSE(GENGETOPT STREQUAL "GENGETOPT-NOTFOUND")
- ADD_EXECUTABLE(gengetopt IMPORTED)
- SET_PROPERTY(TARGET gengetopt PROPERTY IMPORTED_LOCATION ${GENGETOPT})
-ENDIF(GENGETOPT STREQUAL "GENGETOPT-NOTFOUND")
+find_program(GENGETOPT gengetopt)
+if(GENGETOPT STREQUAL "GENGETOPT-NOTFOUND")
+ get_filename_component(CLITK_CMAKE_DIR ${CMAKE_CURRENT_LIST_FILE} PATH)
+ add_subdirectory(${CLITK_CMAKE_DIR}/../utilities/gengetopt ${CMAKE_CURRENT_BINARY_DIR}/gengetopt)
+else(GENGETOPT STREQUAL "GENGETOPT-NOTFOUND")
+ add_executable(gengetopt IMPORTED)
+ set_property(TARGET gengetopt PROPERTY IMPORTED_LOCATION ${GENGETOPT})
+endif(GENGETOPT STREQUAL "GENGETOPT-NOTFOUND")
-MACRO (WRAP_GGO GGO_SRCS)
- FOREACH(GGO_FILE ${ARGN})
- GET_FILENAME_COMPONENT(GGO_BASEFILENAME ${GGO_FILE} NAME_WE)
- GET_FILENAME_COMPONENT(GGO_FILE_ABS ${GGO_FILE} ABSOLUTE)
- SET(GGO_H ${GGO_BASEFILENAME}_ggo.h)
- SET(GGO_C ${GGO_BASEFILENAME}_ggo.c)
- SET(GGO_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${GGO_H} ${CMAKE_CURRENT_BINARY_DIR}/${GGO_C})
- ADD_CUSTOM_COMMAND(OUTPUT ${GGO_OUTPUT}
+macro(WRAP_GGO GGO_SRCS)
+ foreach(GGO_FILE ${ARGN})
+ get_filename_component(GGO_BASEFILENAME ${GGO_FILE} NAME_WE)
+ get_filename_component(GGO_FILE_ABS ${GGO_FILE} ABSOLUTE)
+ set(GGO_H ${GGO_BASEFILENAME}_ggo.h)
+ set(GGO_C ${GGO_BASEFILENAME}_ggo.c)
+ set(GGO_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${GGO_H} ${CMAKE_CURRENT_BINARY_DIR}/${GGO_C})
+ add_custom_command(OUTPUT ${GGO_OUTPUT}
COMMAND gengetopt
ARGS < ${GGO_FILE_ABS}
--output-dir=${CMAKE_CURRENT_BINARY_DIR}
--include-getopt
DEPENDS ${GGO_FILE_ABS}
)
- SET(${GGO_SRCS} ${${GGO_SRCS}} ${GGO_OUTPUT})
- INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
- ENDFOREACH(GGO_FILE)
- SET_SOURCE_FILES_PROPERTIES(${${GGO_SRCS}} PROPERTIES GENERATED TRUE)
- IF(CMAKE_COMPILER_IS_GNUCXX)
- FIND_PROGRAM(DEFAULT_GCC gcc)
- EXEC_PROGRAM(${DEFAULT_GCC} ARGS "-dumpversion" OUTPUT_VARIABLE GCCVER)
- IF("${GCCVER}" VERSION_GREATER "4.5.2")
- SET_SOURCE_FILES_PROPERTIES(${${GGO_SRCS}} PROPERTIES COMPILE_FLAGS "-Wno-unused-but-set-variable")
- ENDIF("${GCCVER}" VERSION_GREATER "4.5.2")
- ENDIF(CMAKE_COMPILER_IS_GNUCXX)
-ENDMACRO (WRAP_GGO)
+ set(${GGO_SRCS} ${${GGO_SRCS}} ${GGO_OUTPUT})
+ include_directories(${CMAKE_CURRENT_BINARY_DIR})
+ endforeach(GGO_FILE)
+ set_source_files_properties(${${GGO_SRCS}} PROPERTIES GENERATED TRUE)
+ if(CMAKE_COMPILER_IS_GNUCXX)
+ find_program(DEFAULT_GCC gcc)
+ exec_program(${DEFAULT_GCC} ARGS "-dumpversion" OUTPUT_VARIABLE GCCVER)
+ if("${GCCVER}" VERSION_GREATER "4.5.2")
+ set_source_files_properties(${${GGO_SRCS}} PROPERTIES COMPILE_FLAGS "-Wno-unused-but-set-variable")
+ endif("${GCCVER}" VERSION_GREATER "4.5.2")
+ endif(CMAKE_COMPILER_IS_GNUCXX)
+endmacro(WRAP_GGO)
# It tries to find the root-config script which gives you all the needed information.
# If the system variable ROOTSYS is set this is straight forward.
# If not the module uses the pathes given in ROOT_CONFIG_SEARCHPATH.
-# If you need an other path you should add this path to this varaible.
+# If you need an other path you should add this path to this varaible.
# The root-config script is then used to detect basically everything else.
# This module defines a number of key variables and macros.
-MESSAGE(STATUS "Looking for Root...")
+message(STATUS "Looking for Root...")
-SET(ROOT_DEFINITIONS "")
+set(ROOT_DEFINITIONS "")
-SET(ROOT_INSTALLED_VERSION_TOO_OLD FALSE)
+set(ROOT_INSTALLED_VERSION_TOO_OLD FALSE)
-SET(ROOT_CONFIG_EXECUTABLE ROOT_CONFIG_EXECUTABLE-NOTFOUND)
+set(ROOT_CONFIG_EXECUTABLE ROOT_CONFIG_EXECUTABLE-NOTFOUND)
-FIND_PROGRAM(ROOT_CONFIG_EXECUTABLE NAMES root-config PATHS)
-
-IF (${ROOT_CONFIG_EXECUTABLE} MATCHES "ROOT_CONFIG_EXECUTABLE-NOTFOUND")
- MESSAGE( FATAL_ERROR "ROOT not installed in the searchpath and ROOTSYS is not set. Please
+find_program(ROOT_CONFIG_EXECUTABLE NAMES root-config PATHS)
+
+if(${ROOT_CONFIG_EXECUTABLE} MATCHES "ROOT_CONFIG_EXECUTABLE-NOTFOUND")
+ message( FATAL_ERROR "ROOT not installed in the searchpath and ROOTSYS is not set. Please
set ROOTSYS or add the path to your ROOT installation in the Macro FindROOT.cmake in the
subdirectory cmake/modules.")
-ELSE (${ROOT_CONFIG_EXECUTABLE} MATCHES "ROOT_CONFIG_EXECUTABLE-NOTFOUND")
- MESSAGE(STATUS "root-config found")
- STRING(REGEX REPLACE "(^.*)/bin/root-config" "\\1" test ${ROOT_CONFIG_EXECUTABLE})
- SET( ENV{ROOTSYS} ${test})
+else(${ROOT_CONFIG_EXECUTABLE} MATCHES "ROOT_CONFIG_EXECUTABLE-NOTFOUND")
+ message(STATUS "root-config found")
+ string(REGEX REPLACE "(^.*)/bin/root-config" "\\1" test ${ROOT_CONFIG_EXECUTABLE})
+ set( ENV{ROOTSYS} ${test})
set( ROOTSYS ${test})
-ENDIF (${ROOT_CONFIG_EXECUTABLE} MATCHES "ROOT_CONFIG_EXECUTABLE-NOTFOUND")
+endif(${ROOT_CONFIG_EXECUTABLE} MATCHES "ROOT_CONFIG_EXECUTABLE-NOTFOUND")
+
+
+if(ROOT_CONFIG_EXECUTABLE)
-
-IF (ROOT_CONFIG_EXECUTABLE)
-
- SET(ROOT_FOUND FALSE)
+ set(ROOT_FOUND FALSE)
- EXEC_PROGRAM(${ROOT_CONFIG_EXECUTABLE} ARGS "--version" OUTPUT_VARIABLE ROOTVERSION)
+ exec_program(${ROOT_CONFIG_EXECUTABLE} ARGS "--version" OUTPUT_VARIABLE ROOTVERSION)
- MESSAGE(STATUS "Looking for Root... - found $ENV{ROOTSYS}/bin/root")
- MESSAGE(STATUS "Looking for Root... - version ${ROOTVERSION} ")
+ message(STATUS "Looking for Root... - found $ENV{ROOTSYS}/bin/root")
+ message(STATUS "Looking for Root... - version ${ROOTVERSION} ")
# we need at least version 5.00/00
- IF (NOT ROOT_MIN_VERSION)
- SET(ROOT_MIN_VERSION "5.00/00")
- ENDIF (NOT ROOT_MIN_VERSION)
-
+ if(NOT ROOT_MIN_VERSION)
+ set(ROOT_MIN_VERSION "5.00/00")
+ endif(NOT ROOT_MIN_VERSION)
+
# now parse the parts of the user given version string into variables
- STRING(REGEX REPLACE "^([0-9]+)\\.[0-9][0-9]+\\/[0-9][0-9]+" "\\1" req_root_major_vers "${ROOT_MIN_VERSION}")
- STRING(REGEX REPLACE "^[0-9]+\\.([0-9][0-9])+\\/[0-9][0-9]+.*" "\\1" req_root_minor_vers "${ROOT_MIN_VERSION}")
- STRING(REGEX REPLACE "^[0-9]+\\.[0-9][0-9]+\\/([0-9][0-9]+)" "\\1" req_root_patch_vers "${ROOT_MIN_VERSION}")
-
+ string(REGEX REPLACE "^([0-9]+)\\.[0-9][0-9]+\\/[0-9][0-9]+" "\\1" req_root_major_vers "${ROOT_MIN_VERSION}")
+ string(REGEX REPLACE "^[0-9]+\\.([0-9][0-9])+\\/[0-9][0-9]+.*" "\\1" req_root_minor_vers "${ROOT_MIN_VERSION}")
+ string(REGEX REPLACE "^[0-9]+\\.[0-9][0-9]+\\/([0-9][0-9]+)" "\\1" req_root_patch_vers "${ROOT_MIN_VERSION}")
+
# and now the version string given by qmake
- STRING(REGEX REPLACE "^([0-9]+)\\.[0-9][0-9]+\\/[0-9][0-9]+.*" "\\1" found_root_major_vers "${ROOTVERSION}")
- STRING(REGEX REPLACE "^[0-9]+\\.([0-9][0-9])+\\/[0-9][0-9]+.*" "\\1" found_root_minor_vers "${ROOTVERSION}")
- STRING(REGEX REPLACE "^[0-9]+\\.[0-9][0-9]+\\/([0-9][0-9]+).*" "\\1" found_root_patch_vers "${ROOTVERSION}")
+ string(REGEX REPLACE "^([0-9]+)\\.[0-9][0-9]+\\/[0-9][0-9]+.*" "\\1" found_root_major_vers "${ROOTVERSION}")
+ string(REGEX REPLACE "^[0-9]+\\.([0-9][0-9])+\\/[0-9][0-9]+.*" "\\1" found_root_minor_vers "${ROOTVERSION}")
+ string(REGEX REPLACE "^[0-9]+\\.[0-9][0-9]+\\/([0-9][0-9]+).*" "\\1" found_root_patch_vers "${ROOTVERSION}")
- IF (found_root_major_vers LESS 5)
- MESSAGE( FATAL_ERROR "Invalid ROOT version \"${ROOTERSION}\", at least major version 4 is required, e.g. \"5.00/00\"")
- ENDIF (found_root_major_vers LESS 5)
+ if(found_root_major_vers LESS 5)
+ message( FATAL_ERROR "Invalid ROOT version \"${ROOTERSION}\", at least major version 4 is required, e.g. \"5.00/00\"")
+ endif(found_root_major_vers LESS 5)
# compute an overall version number which can be compared at once
- MATH(EXPR req_vers "${req_root_major_vers}*10000 + ${req_root_minor_vers}*100 + ${req_root_patch_vers}")
- MATH(EXPR found_vers "${found_root_major_vers}*10000 + ${found_root_minor_vers}*100 + ${found_root_patch_vers}")
-
- IF (found_vers LESS req_vers)
- SET(ROOT_FOUND FALSE)
- SET(ROOT_INSTALLED_VERSION_TOO_OLD TRUE)
- ELSE (found_vers LESS req_vers)
- SET(ROOT_FOUND TRUE)
- ENDIF (found_vers LESS req_vers)
+ math(EXPR req_vers "${req_root_major_vers}*10000 + ${req_root_minor_vers}*100 + ${req_root_patch_vers}")
+ math(EXPR found_vers "${found_root_major_vers}*10000 + ${found_root_minor_vers}*100 + ${found_root_patch_vers}")
+
+ if(found_vers LESS req_vers)
+ set(ROOT_FOUND FALSE)
+ set(ROOT_INSTALLED_VERSION_TOO_OLD TRUE)
+ else(found_vers LESS req_vers)
+ set(ROOT_FOUND TRUE)
+ endif(found_vers LESS req_vers)
-ENDIF (ROOT_CONFIG_EXECUTABLE)
+endif(ROOT_CONFIG_EXECUTABLE)
-#MESSAGE("root found = "${ROOT_FOUND})
+#message("root found = "${ROOT_FOUND})
-IF (ROOT_FOUND)
+if(ROOT_FOUND)
# ask root-config for the library dir
# Set ROOT_LIBRARY_DIR
- EXEC_PROGRAM( ${ROOT_CONFIG_EXECUTABLE}
+ exec_program( ${ROOT_CONFIG_EXECUTABLE}
ARGS "--libdir"
OUTPUT_VARIABLE ROOT_LIBRARY_DIR_TMP )
- IF(EXISTS "${ROOT_LIBRARY_DIR_TMP}")
- SET(ROOT_LIBRARY_DIR ${ROOT_LIBRARY_DIR_TMP} )
- ELSE(EXISTS "${ROOT_LIBRARY_DIR_TMP}")
- MESSAGE("Warning: ROOT_CONFIG_EXECUTABLE reported ${ROOT_LIBRARY_DIR_TMP} as library path,")
- MESSAGE("Warning: but ${ROOT_LIBRARY_DIR_TMP} does NOT exist, ROOT must NOT be installed correctly.")
- ENDIF(EXISTS "${ROOT_LIBRARY_DIR_TMP}")
-
+ if(EXISTS "${ROOT_LIBRARY_DIR_TMP}")
+ set(ROOT_LIBRARY_DIR ${ROOT_LIBRARY_DIR_TMP} )
+ else(EXISTS "${ROOT_LIBRARY_DIR_TMP}")
+ message("Warning: ROOT_CONFIG_EXECUTABLE reported ${ROOT_LIBRARY_DIR_TMP} as library path,")
+ message("Warning: but ${ROOT_LIBRARY_DIR_TMP} does NOT exist, ROOT must NOT be installed correctly.")
+ endif(EXISTS "${ROOT_LIBRARY_DIR_TMP}")
+
# ask root-config for the binary dir
- EXEC_PROGRAM(${ROOT_CONFIG_EXECUTABLE}
+ exec_program(${ROOT_CONFIG_EXECUTABLE}
ARGS "--bindir"
OUTPUT_VARIABLE root_bins )
- SET(ROOT_BINARY_DIR ${root_bins})
+ set(ROOT_BINARY_DIR ${root_bins})
# ask root-config for the include dir
- EXEC_PROGRAM( ${ROOT_CONFIG_EXECUTABLE}
- ARGS "--incdir"
+ exec_program( ${ROOT_CONFIG_EXECUTABLE}
+ ARGS "--incdir"
OUTPUT_VARIABLE root_headers )
- SET(ROOT_INCLUDE_DIR ${root_headers})
+ set(ROOT_INCLUDE_DIR ${root_headers})
# CACHE INTERNAL "")
# ask root-config for the library varaibles
- EXEC_PROGRAM( ${ROOT_CONFIG_EXECUTABLE}
-# ARGS "--noldflags --noauxlibs --libs"
- ARGS "--glibs"
+ exec_program( ${ROOT_CONFIG_EXECUTABLE}
+# ARGS "--noldflags --noauxlibs --libs"
+ ARGS "--glibs"
OUTPUT_VARIABLE root_flags )
-# STRING(REGEX MATCHALL "([^ ])+" root_libs_all ${root_flags})
-# STRING(REGEX MATCHALL "-L([^ ])+" root_library ${root_flags})
+# string(REGEX MATCHALL "([^ ])+" root_libs_all ${root_flags})
+# string(REGEX MATCHALL "-L([^ ])+" root_library ${root_flags})
# REMOVE_FROM_LIST(root_flags "${root_libs_all}" "${root_library}")
- SET(ROOT_LIBRARIES ${root_flags})
+ set(ROOT_LIBRARIES ${root_flags})
# Make variables changeble to the advanced user
- MARK_AS_ADVANCED( ROOT_LIBRARY_DIR ROOT_INCLUDE_DIR ROOT_DEFINITIONS)
+ mark_as_advanced( ROOT_LIBRARY_DIR ROOT_INCLUDE_DIR ROOT_DEFINITIONS)
# Set ROOT_INCLUDES
- SET( ROOT_INCLUDES ${ROOT_INCLUDE_DIR})
+ set( ROOT_INCLUDES ${ROOT_INCLUDE_DIR})
- SET(LD_LIBRARY_PATH ${LD_LIBRARY_PATH} ${ROOT_LIBRARY_DIR})
+ set(LD_LIBRARY_PATH ${LD_LIBRARY_PATH} ${ROOT_LIBRARY_DIR})
#######################################
#
- # Check the executables of ROOT
- # ( rootcint )
+ # Check the executables of ROOT
+ # ( rootcint )
#
#######################################
- FIND_PROGRAM(ROOT_CINT_EXECUTABLE
+ find_program(ROOT_CINT_EXECUTABLE
NAMES rootcint
PATHS ${ROOT_BINARY_DIR}
NO_DEFAULT_PATH
)
-ENDIF (ROOT_FOUND)
+endif(ROOT_FOUND)
-#MESSAGE("icici")
+#message("icici")
###########################################
#
#
###########################################
-MACRO (ROOT_GENERATE_DICTIONARY_OLD )
-
- set(INFILES "")
+macro(ROOT_GENERATE_DICTIONARY_OLD )
+
+ set(INFILES "")
foreach (_current_FILE ${ARGN})
- IF (${_current_FILE} MATCHES "^.*\\.h$")
- IF (${_current_FILE} MATCHES "^.*Link.*$")
+ if(${_current_FILE} MATCHES "^.*\\.h$")
+ if(${_current_FILE} MATCHES "^.*Link.*$")
set(LINKDEF_FILE ${_current_FILE})
- ELSE (${_current_FILE} MATCHES "^.*Link.*$")
+ else(${_current_FILE} MATCHES "^.*Link.*$")
set(INFILES ${INFILES} ${_current_FILE})
- ENDIF (${_current_FILE} MATCHES "^.*Link.*$")
- ELSE (${_current_FILE} MATCHES "^.*\\.h$")
- IF (${_current_FILE} MATCHES "^.*\\.cxx$")
+ endif(${_current_FILE} MATCHES "^.*Link.*$")
+ else(${_current_FILE} MATCHES "^.*\\.h$")
+ if(${_current_FILE} MATCHES "^.*\\.cxx$")
set(OUTFILE ${_current_FILE})
- ELSE (${_current_FILE} MATCHES "^.*\\.cxx$")
- set(INCLUDE_DIRS ${INCLUDE_DIRS} -I${_current_FILE})
- ENDIF (${_current_FILE} MATCHES "^.*\\.cxx$")
- ENDIF (${_current_FILE} MATCHES "^.*\\.h$")
-
+ else(${_current_FILE} MATCHES "^.*\\.cxx$")
+ set(INCLUDE_DIRS ${INCLUDE_DIRS} -I${_current_FILE})
+ endif(${_current_FILE} MATCHES "^.*\\.cxx$")
+ endif(${_current_FILE} MATCHES "^.*\\.h$")
+
endforeach (_current_FILE ${ARGN})
-
-# MESSAGE("INFILES: ${INFILES}")
-# MESSAGE("OutFILE: ${OUTFILE}")
-# MESSAGE("LINKDEF_FILE: ${LINKDEF_FILE}")
-# MESSAGE("INCLUDE_DIRS: ${INCLUDE_DIRS}")
- STRING(REGEX REPLACE "(^.*).cxx" "\\1.h" bla "${OUTFILE}")
-# MESSAGE("BLA: ${bla}")
- SET (OUTFILES ${OUTFILE} ${bla})
+# message("INFILES: ${INFILES}")
+# message("OutFILE: ${OUTFILE}")
+# message("LINKDEF_FILE: ${LINKDEF_FILE}")
+# message("INCLUDE_DIRS: ${INCLUDE_DIRS}")
- ADD_CUSTOM_COMMAND(OUTPUT ${OUTFILES}
+ string(REGEX REPLACE "(^.*).cxx" "\\1.h" bla "${OUTFILE}")
+# message("BLA: ${bla}")
+ set(OUTFILES ${OUTFILE} ${bla})
+
+ add_custom_command(OUTPUT ${OUTFILES}
COMMAND ${ROOT_CINT_EXECUTABLE}
ARGS -f ${OUTFILE} -c -DHAVE_CONFIG_H ${INCLUDE_DIRS} ${INFILES} ${LINKDEF_FILE} DEPENDS ${INFILES})
-# MESSAGE("ROOT_CINT_EXECUTABLE has created the dictionary ${OUTFILE}")
+# message("ROOT_CINT_EXECUTABLE has created the dictionary ${OUTFILE}")
-ENDMACRO (ROOT_GENERATE_DICTIONARY_OLD)
+endmacro(ROOT_GENERATE_DICTIONARY_OLD)
###########################################
#
#
###########################################
-MACRO (ROOT_GENERATE_DICTIONARY INFILES LINKDEF_FILE OUTFILE INCLUDE_DIRS_IN)
-
+macro(ROOT_GENERATE_DICTIONARY INFILES LINKDEF_FILE OUTFILE INCLUDE_DIRS_IN)
+
set(INCLUDE_DIRS)
foreach (_current_FILE ${INCLUDE_DIRS_IN})
- set(INCLUDE_DIRS ${INCLUDE_DIRS} -I${_current_FILE})
+ set(INCLUDE_DIRS ${INCLUDE_DIRS} -I${_current_FILE})
endforeach (_current_FILE ${INCLUDE_DIRS_IN})
-
-# MESSAGE("INFILES: ${INFILES}")
-# MESSAGE("OutFILE: ${OUTFILE}")
-# MESSAGE("LINKDEF_FILE: ${LINKDEF_FILE}")
-# MESSAGE("INCLUDE_DIRS: ${INCLUDE_DIRS}")
- STRING(REGEX REPLACE "^(.*)\\.(.*)$" "\\1.h" bla "${OUTFILE}")
-# MESSAGE("BLA: ${bla}")
- SET (OUTFILES ${OUTFILE} ${bla})
+# message("INFILES: ${INFILES}")
+# message("OutFILE: ${OUTFILE}")
+# message("LINKDEF_FILE: ${LINKDEF_FILE}")
+# message("INCLUDE_DIRS: ${INCLUDE_DIRS}")
+
+ string(REGEX REPLACE "^(.*)\\.(.*)$" "\\1.h" bla "${OUTFILE}")
+# message("BLA: ${bla}")
+ set(OUTFILES ${OUTFILE} ${bla})
- ADD_CUSTOM_COMMAND(OUTPUT ${OUTFILES}
+ add_custom_command(OUTPUT ${OUTFILES}
COMMAND ${ROOT_CINT_EXECUTABLE}
ARGS -f ${OUTFILE} -c -DHAVE_CONFIG_H ${INCLUDE_DIRS} ${INFILES} ${LINKDEF_FILE} DEPENDS ${INFILES})
-ENDMACRO (ROOT_GENERATE_DICTIONARY)
+endmacro(ROOT_GENERATE_DICTIONARY)
-#MESSAGE("la")
+#message("la")
#=========================================================
#Support for the CTest dashboard testing system
-OPTION(BUILD_TESTING "Build the testing tree" OFF)
-IF (BUILD_TESTING)
- OPTION(CLITK_BUILD_TESTING "Test ITK" ON)
- INCLUDE(CTest)
-ENDIF(BUILD_TESTING)
+option(BUILD_TESTING "Build the testing tree" OFF)
+if(BUILD_TESTING)
+ option(CLITK_BUILD_TESTING "Test ITK" ON)
+ include(CTest)
+endif(BUILD_TESTING)
#=========================================================
#=========================================================
# If the user choose to build documentation, then search for Doxygen executables.
-OPTION(BUILD_DOXYGEN "Build Doxygen Documentation" OFF)
-IF(BUILD_DOXYGEN)
- FIND_PACKAGE(Doxygen)
- ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/Doxygen ${PROJECT_BINARY_DIR}/Doxygen)
-ENDIF(BUILD_DOXYGEN)
+option(BUILD_DOXYGEN "Build Doxygen Documentation" OFF)
+if(BUILD_DOXYGEN)
+ find_package(Doxygen)
+ add_subdirectory(${CLITK_SOURCE_DIR}/Doxygen ${PROJECT_BINARY_DIR}/Doxygen)
+endif(BUILD_DOXYGEN)
#=========================================================
# Compilation options
-OPTION(CLITK_EXPERIMENTAL "Enable experimental software and features" OFF)
-OPTION(CLITK_BUILD_TOOLS "Build command-line tools" OFF)
-OPTION(CLITK_BUILD_SEGMENTATION "Build command-line segmentation tools" OFF)
-OPTION(CLITK_BUILD_REGISTRATION "Build command-line registration tools" OFF)
+option(CLITK_EXPERIMENTAL "Enable experimental software and features" OFF)
+mark_as_advanced(CLITK_EXPERIMENTAL)
+option(CLITK_BUILD_TOOLS "Build command-line tools" OFF)
+option(CLITK_BUILD_SEGMENTATION "Build command-line segmentation tools" OFF)
+option(CLITK_BUILD_REGISTRATION "Build command-line registration tools" OFF)
-OPTION(CLITK_BUILD_VV "Build vv the 4D visualizer (requires VTK and QT)" ON)
-IF (CLITK_BUILD_VV)
- ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/vv ${PROJECT_BINARY_DIR}/vv)
-ENDIF(CLITK_BUILD_VV)
+option(CLITK_BUILD_VV "Build vv the 4D visualizer (requires VTK and QT)" ON)
+
+if(CLITK_BUILD_VV)
+ if(VTK_VERSION VERSION_LESS 6.0.0)
+ set(vv_QT_VERSION "4" CACHE INTERNAL "Expected Qt version")
+ else()
+ if(VTK_QT_VERSION VERSION_LESS 5)
+ set(vv_QT_VERSION "4" CACHE INTERNAL "Expected Qt version")
+ else()
+ set(vv_QT_VERSION "5" CACHE INTERNAL "Expected Qt version")
+ endif()
+ endif()
+
+ add_subdirectory(${CLITK_SOURCE_DIR}/vv ${PROJECT_BINARY_DIR}/vv)
+endif(CLITK_BUILD_VV)
#=========================================================
# Build test when vv has been compiled
-IF(BUILD_TESTING)
- ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/tests ${PROJECT_BINARY_DIR}/tests)
-ENDIF(BUILD_TESTING)
+if(BUILD_TESTING)
+ add_subdirectory(${CLITK_SOURCE_DIR}/tests ${PROJECT_BINARY_DIR}/tests)
+endif(BUILD_TESTING)
#=========================================================
-MACRO (DD in)
- MESSAGE(${in}=${${in}})
-ENDMACRO(DD)
+macro(DD in)
+ message(${in}=${${in}})
+endmacro(DD)
#=========================================================
#=========================================================
endif (NOT CMAKE_BUILD_TYPE)
#=========================================================
-INCLUDE_DIRECTORIES(${CLITK_SOURCE_DIR}/itk
+include_directories(${CLITK_SOURCE_DIR}/itk
${CLITK_SOURCE_DIR}/filters
${CLITK_SOURCE_DIR}/segmentation
${CLITK_SOURCE_DIR}/registration
${CLITK_SOURCE_DIR}/tools
${CLITK_SOURCE_DIR}/common
${PROJECT_BINARY_DIR})
-SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
-SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
-LINK_DIRECTORIES(${PROJECT_BINARY_DIR}/lib)
-INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/tools) #For _ggo.h includes from other directories
-INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/segmentation) #For _ggo.h includes from other directories
-INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/registration) #For _ggo.h includes from other directories
+set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
+set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+link_directories(${PROJECT_BINARY_DIR}/lib)
+include_directories(${PROJECT_BINARY_DIR}/tools) #For _ggo.h includes from other directories
+include_directories(${PROJECT_BINARY_DIR}/segmentation) #For _ggo.h includes from other directories
+include_directories(${PROJECT_BINARY_DIR}/registration) #For _ggo.h includes from other directories
#=========================================================
#=========================================================
# Building in the source tree is forbidden
-IF(PROJECT_BINARY_DIR STREQUAL ${PROJECT_SOURCE_DIR})
- MESSAGE(FATAL_ERROR "Building in the source tree is not allowed ! Quit; remove the file 'CMakeCache.txt' and the folder 'CMakeFiles' an
+if(PROJECT_BINARY_DIR STREQUAL ${PROJECT_SOURCE_DIR})
+ message(FATAL_ERROR "Building in the source tree is not allowed ! Quit; remove the file 'CMakeCache.txt' and the folder 'CMakeFiles' an
d build outside the sources (for example 'mkdir build ; cmake <CLITK_DIR>'.")
-ENDIF(PROJECT_BINARY_DIR STREQUAL ${PROJECT_SOURCE_DIR})
+endif(PROJECT_BINARY_DIR STREQUAL ${PROJECT_SOURCE_DIR})
#=========================================================
#=========================================================
# Remove some MS Visual c++ flags
-IF(MSVC)
- ADD_DEFINITIONS(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE -D_SCL_SECURE_NO_WARNINGS)
-ENDIF(MSVC)
+if(MSVC)
+ add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE -D_SCL_SECURE_NO_WARNINGS)
+endif(MSVC)
#=========================================================
#=========================================================
# Find ITK (required)
-FIND_PACKAGE(ITK)
-IF(ITK_FOUND)
- INCLUDE("${ITK_USE_FILE}")
-ELSE(ITK_FOUND)
- MESSAGE(FATAL_ERROR "Cannot build without ITK. Please set ITK_DIR.")
-ENDIF(ITK_FOUND)
+find_package(ITK)
+if(ITK_FOUND)
+ include("${ITK_USE_FILE}")
+else(ITK_FOUND)
+ message(FATAL_ERROR "Cannot build without ITK. Please set ITK_DIR.")
+endif(ITK_FOUND)
#=========================================================
#=========================================================
# Find VTK (required)
-FIND_PACKAGE(VTK REQUIRED)
-IF(VTK_FOUND)
- INCLUDE("${VTK_USE_FILE}")
- IF(VTK_VERSION VERSION_LESS 5.8.0)
- SET ( VTK_LIBRARIES
+find_package(VTK REQUIRED)
+if(VTK_FOUND)
+ include("${VTK_USE_FILE}")
+ if(VTK_VERSION VERSION_LESS 5.8.0)
+ set( VTK_LIBRARIES
vtkCommon
vtkRendering
vtkIO
vtkImaging
vtkHybrid
)
- ENDIF(VTK_VERSION VERSION_LESS 5.8.0)
- IF(VTK_VERSION VERSION_LESS 5.6.0)
- SET ( VTK_LIBRARIES
+ endif(VTK_VERSION VERSION_LESS 5.8.0)
+ if(VTK_VERSION VERSION_LESS 5.6.0)
+ set( VTK_LIBRARIES
${VTK_LIBRARIES}
vtkQVTK
)
- ENDIF(VTK_VERSION VERSION_LESS 5.6.0)
-ELSE(VTK_FOUND)
- MESSAGE(FATAL_ERROR "Please set VTK_DIR.")
-ENDIF(VTK_FOUND)
+ endif(VTK_VERSION VERSION_LESS 5.6.0)
+else(VTK_FOUND)
+ message(FATAL_ERROR "Please set VTK_DIR.")
+endif(VTK_FOUND)
#=========================================================
#=========================================================
# Find gengetopt, will create a target exe if not found
-SET(CMAKE_MODULE_PATH "${CLITK_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
-FIND_PACKAGE(Gengetopt)
+set(CMAKE_MODULE_PATH "${CLITK_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+find_package(Gengetopt)
#=========================================================
#=========================================================
# Find libstatgrab is installed, add clitkMemoryUsage.cxx in the library
-IF (NOT DEFINED CLITK_MEMORY_INFO OR CLITK_MEMORY_INFO)
- FIND_LIBRARY(LIBSTATGRAB NAMES statgrab PATHS)
- IF (${LIBSTATGRAB} MATCHES "LIBSTATGRAB-NOTFOUND")
-# MESSAGE("Install libstatgrab (http://www.i-scream.org/libstatgrab/) for memory usage information")
- SET(CLITK_MEMORY_INFO OFF)
- ELSE (${LIBSTATGRAB} MATCHES "LIBSTATGRAB-NOTFOUND")
- SET(CLITK_MEMORY_INFO ON)
- ENDIF (${LIBSTATGRAB} MATCHES "LIBSTATGRAB-NOTFOUND")
-ENDIF()
+if(NOT DEFINED CLITK_MEMORY_INFO OR CLITK_MEMORY_INFO)
+ find_library(LIBSTATGRAB NAMES statgrab PATHS)
+ if(${LIBSTATGRAB} MATCHES "LIBSTATGRAB-NOTFOUND")
+# message("Install libstatgrab (http://www.i-scream.org/libstatgrab/) for memory usage information")
+ set(CLITK_MEMORY_INFO OFF)
+ else(${LIBSTATGRAB} MATCHES "LIBSTATGRAB-NOTFOUND")
+ set(CLITK_MEMORY_INFO ON)
+ endif(${LIBSTATGRAB} MATCHES "LIBSTATGRAB-NOTFOUND")
+endif()
#=========================================================
#=========================================================
### Check if ITK was compiled with SYSTEM_GDCM = ON
-SET(CLITK_USE_SYSTEM_GDCM FALSE)
-IF(ITK_VERSION_MAJOR LESS "4")
- IF(ITK_USE_SYSTEM_GDCM)
- SET(CLITK_USE_SYSTEM_GDCM TRUE)
- ENDIF(ITK_USE_SYSTEM_GDCM)
-ELSE(ITK_VERSION_MAJOR LESS "4")
- SET(GDCM_INCLUDE_INSTALL ".*include/gdcm-.*")
- SET(GDCM_INCLUDE_BUILD ".*/Source/MediaStorageAndFileFormat")
- IF(NOT ITKGDCM_INCLUDE_DIRS MATCHES ${GDCM_INCLUDE_BUILD})
- SET(CLITK_USE_SYSTEM_GDCM TRUE)
- ENDIF()
-ENDIF(ITK_VERSION_MAJOR LESS "4")
+set(CLITK_USE_SYSTEM_GDCM FALSE)
+# ITK4 creates a target for each gdcm library when it compiles GDCM
+get_target_property(GDCMDICTTARG gdcmDICT TYPE )
+if(NOT GDCMDICTTARG)
+ set(CLITK_USE_SYSTEM_GDCM TRUE)
+endif()
-#DD(CLITK_USE_SYSTEM_GDCM)
#=========================================================
# make clitk libraries*
-CONFIGURE_FILE(clitkConfiguration.h.in ${PROJECT_BINARY_DIR}/clitkConfiguration.h)
+configure_file(clitkConfiguration.h.in ${PROJECT_BINARY_DIR}/clitkConfiguration.h)
-SET(clitkCommon_SRC
- clitkCommon.cxx
+set(clitkCommon_SRC
+ clitkCommon.cxx
clitkListOfPair.cxx
clitkTimer.cxx
clitkImageCommon.cxx
clitkIO.cxx
clitkGateAsciiImageIO.cxx
clitkGateAsciiImageIOFactory.cxx
- clitkVoxImageIO.cxx
+ clitkVoxImageIO.cxx
clitkVoxImageIOFactory.cxx
- clitkVfImageIO.cxx
+ clitkVfImageIO.cxx
clitkVfImageIOFactory.cxx
- clitkXdrImageIOReader.cxx
- clitkXdrImageIOWriter.cxx
+ clitkXdrImageIOReader.cxx
+ clitkXdrImageIOWriter.cxx
clitkXdrImageIOFactory.cxx
- rtkHisImageIO.cxx
+ rtkHisImageIO.cxx
rtkHisImageIOFactory.cxx
rtkHndImageIO.cxx
rtkHndImageIOFactory.cxx
rtkImagXImageIO.cxx
rtkImagXImageIOFactory.cxx
rtkImagXXMLFileReader.cxx
- clitkEsrfHstImageIO.cxx
+ clitkEsrfHstImageIO.cxx
clitkEsrfHstImageIOFactory.cxx
clitkEsrfHstXMLFileReader.cxx
clitkDicomRTDoseIO.cxx
vvImageReader.cxx
vvImageWriter.cxx
)
-IF(CLITK_PRIVATE_FEATURES)
- SET(clitkCommon_SRC ${clitkCommon_SRC}
+if(CLITK_PRIVATE_FEATURES)
+ set(clitkCommon_SRC ${clitkCommon_SRC}
${PROJECT_SOURCE_DIR}/private_features/clitkUsfImageIO.cxx
${PROJECT_SOURCE_DIR}/private_features/clitkUsfImageIOFactory.cxx
${PROJECT_SOURCE_DIR}/private_features/clitkUSVoxImageIO.cxx
${PROJECT_SOURCE_DIR}/private_features/clitkSvlImageIO.cxx
${PROJECT_SOURCE_DIR}/private_features/clitkSvlImageIOFactory.cxx
)
-ENDIF(CLITK_PRIVATE_FEATURES)
+endif(CLITK_PRIVATE_FEATURES)
### Declare clitkCommon library
-ADD_LIBRARY(clitkCommon STATIC ${clitkCommon_SRC})
+add_library(clitkCommon STATIC ${clitkCommon_SRC})
-IF(CLITK_MEMORY_INFO)
- TARGET_LINK_LIBRARIES(clitkCommon statgrab)
-ENDIF(CLITK_MEMORY_INFO)
+if(CLITK_MEMORY_INFO)
+ target_link_libraries(clitkCommon statgrab)
+endif(CLITK_MEMORY_INFO)
#=========================================================
-IF (CLITK_USE_SYSTEM_GDCM)
- FIND_PACKAGE(GDCM REQUIRED)
+if(CLITK_USE_SYSTEM_GDCM)
+ find_package(GDCM REQUIRED)
include(${GDCM_USE_FILE})
- TARGET_LINK_LIBRARIES(clitkCommon vtkgdcm gdcmDICT gdcmMSFF gdcmMEXD)
-ENDIF()
+ target_link_libraries(clitkCommon vtkgdcm gdcmDICT gdcmMSFF gdcmMEXD)
+endif()
#=========================================================
-TARGET_LINK_LIBRARIES(clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES})
+target_link_libraries(clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES})
-ADD_LIBRARY(clitkDicomRTStruct STATIC
+add_library(clitkDicomRTStruct STATIC
clitkDicomRT_Contour.cxx
clitkDicomRT_ROI.cxx
clitkDicomRT_StructureSet.cxx
clitkDicomRTStruct2ImageFilter.cxx
)
-TARGET_LINK_LIBRARIES(clitkDicomRTStruct clitkCommon)
+target_link_libraries(clitkDicomRTStruct clitkCommon)
-#ADD_LIBRARY(clitkCommonShared SHARED ${clitkCommon_SRC})
-#SET_TARGET_PROPERTIES(clitkCommonShared PROPERTIES COMPILE_FLAGS -fPIC)
+#add_library(clitkCommonShared SHARED ${clitkCommon_SRC})
+#set_target_properties(clitkCommonShared PROPERTIES COMPILE_FLAGS -fPIC)
}
//------------------------------------------------------------------
+//------------------------------------------------------------------
+// Convert a pixel type without casting
+template<>
+double clitk::PixelTypeDownCast(const double & x)
+{
+ return x;
+}
+//------------------------------------------------------------------
+
//------------------------------------------------------------------
double clitk::rad2deg(const double anglerad)
{
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
#include <fstream>
// Include for "rusage"
-#include <ctime>
+#include <ctime>
#if defined(unix) || defined(__APPLE__)
# include <sys/time.h>
# include <sys/resource.h>
typedef unsigned char uchar;
typedef unsigned short ushort;
typedef unsigned int uint;
-
+
#define CLITK_TRY_CATCH_EXIT(func) \
try { \
func; \
std::cout << "Unknown excpetion" << std::endl; \
exit(-3); \
}
-
+
//--------------------------------------------------------------------
// when everything goes wrong
#define WHEREAMI "[ " << __FILE__ << " ] line " << __LINE__
-#define FATAL(a) std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0);
-
+#define FATAL(a) { std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0); }
+
//--------------------------------------------------------------------
// GGO with modified struct name
#define GGO(ggo_filename, args_info) \
cmdline_parser_##ggo_filename##2(argc, argv, &args_info, 1, 1, 0); \
if (args_info.config_given) \
cmdline_parser_##ggo_filename##_configfile (args_info.config_arg, &args_info, 0, 0, 1); \
- else cmdline_parser_##ggo_filename(argc, argv, &args_info);
+ else cmdline_parser_##ggo_filename(argc, argv, &args_info);
//--------------------------------------------------------------------
// skip line with #
//--------------------------------------------------------------------
// Return filename extension
std::string GetExtension(const std::string& filename);
-
+
//--------------------------------------------------------------------
// Convert float, double ... to string
template<class T> std::string toString(const T & t);
template<class T> std::string toStringVector(const T * t, const int n);
template<class T> std::string toStringVector(const T & t, const int n);
template<class T> std::string toStringVector(const std::vector<T> & t);
- template <class T> bool fromString(T& t,
- const std::string& s,
+ template <class T> bool fromString(T& t,
+ const std::string& s,
std::ios_base& (*f)(std::ios_base&)=std::dec);
//--------------------------------------------------------------------
TPixelDown PixelTypeDownCast(const TPixelUp & x);
template<>
float PixelTypeDownCast(const double & x);
+ template<>
+ double PixelTypeDownCast(const double & x);
//--------------------------------------------------------------------
// Return the indexes of sorted values in a vector
// Return the name of a type as a string
template<class TPixel>
std::string GetTypeAsString();
-
+
//--------------------------------------------------------------------
// Convert radian / degree
double rad2deg(double anglerad);
std::string CreateListOfTypes(bool last=true) {
return GetTypeAsString<T1>();
}
-
+
template<class T1, class T2>
std::string CreateListOfTypes(bool last=true) {
if (last) return CreateListOfTypes<T1>()+" and "+CreateListOfTypes<T2>();
else return CreateListOfTypes<T1>()+", "+CreateListOfTypes<T2>();
}
-
+
template<class T1, class T2, class T3>
std::string CreateListOfTypes(bool last=true) {
if (last) return CreateListOfTypes<T1,T2>(false)+" and "+CreateListOfTypes<T3>();
else return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+", "+CreateListOfTypes<T8>();
}
//--------------------------------------------------------------------
-
+
//--------------------------------------------------------------------
void FindAndReplace(std::string & line, const std::string & tofind, const std::string & replacement);
void FindAndReplace(std::string & line, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
- const itk::ContinuousIndex<double, 3> pointInPlane,
+ double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
+ const itk::ContinuousIndex<double, 3> pointInPlane,
const itk::ContinuousIndex<double, 3> normalPlane);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Convert a map to a vector
- template <typename M, typename V>
+ template <typename M, typename V>
void MapToVecFirst(const M & m, V & v);
- template <typename M, typename V>
+ template <typename M, typename V>
void MapToVecSecond(const M & m, V & v);
//--------------------------------------------------------------------
} // end namespace
#endif /* end #define CLITKCOMMON_H */
-
ImageTypesManager(FilterType * f) { mFilter = f; }
virtual void DoIt(int dim, int ncomp, std::string pixelname) {
- // std::cout << "ImageTypesManager DoIt " << dim << " " << pixelname << std::endl;
+ //std::cout << "ImageTypesManager DoIt " << dim << " " << pixelname << std::endl;
if (mMapOfImageTypeToFunction[dim][ncomp][pixelname])
mMapOfImageTypeToFunction[dim][ncomp][pixelname]->Execute();
}
template<class T>
void _print_container(T const& a)
{ for(typename T::const_iterator i=a.begin();i!=a.end();++i) { std::cout << *i << " "; };}
-#define DDS(a) { std::cout << #a " = [ "; _print_container(a) ; std::cout << " ]" << std::endl;std::cout.flush():}
+#define DDS(a) { std::cout << #a " = [ "; _print_container(a) ; std::cout << " ]" << std::endl;std::cout.flush();}
#endif
#include "clitkImageCommon.h"
// vtk
+#include <vtkVersion.h>
#include <vtkPolyDataToImageStencil.h>
#include <vtkSmartPointer.h>
#include <vtkImageStencil.h>
// Create new output image
mBinaryImage = vtkSmartPointer<vtkImageData>::New();
+#if VTK_MAJOR_VERSION <= 5
mBinaryImage->SetScalarTypeToUnsignedChar();
+#endif
mBinaryImage->SetOrigin(&origin[0]);
mBinaryImage->SetSpacing(&mSpacing[0]);
mBinaryImage->SetExtent(0, extend[0],
0, extend[1],
0, extend[2]);
+#if VTK_MAJOR_VERSION <= 5
mBinaryImage->AllocateScalars();
+#else
+ mBinaryImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+#endif
memset(mBinaryImage->GetScalarPointer(), 0,
mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
// Extrude
vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
+#if VTK_MAJOR_VERSION <= 5
extrude->SetInput(mesh);
+#else
+ extrude->SetInputData(mesh);
+#endif
///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
extrude->SetVector(0, 0, -mSpacing[2]);
//http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
sts->SetTolerance(0);
sts->SetInformationInput(mBinaryImage);
+#if VTK_MAJOR_VERSION <= 5
sts->SetInput(extrude->GetOutput());
+#else
+ sts->SetInputConnection(extrude->GetOutputPort(0));
+#endif
//sts->SetInput(mesh);
vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
+#if VTK_MAJOR_VERSION <= 5
stencil->SetStencil(sts->GetOutput());
+#else
+ stencil->SetStencilConnection(sts->GetOutputPort(0));
+#endif
+#if VTK_MAJOR_VERSION <= 5
stencil->SetInput(mBinaryImage);
+#else
+ stencil->SetInputData(mBinaryImage);
+#endif
stencil->ReverseStencilOn();
stencil->Update();
=========================================================================*/
#ifndef CLITKDICOMRTSTRUCT2IMAGEFILTER_H
-#define CLITKDICOMRT_TRUCT2IMAGEFILTER_H
+#define CLITKDICOMRTSTRUCT2IMAGEFILTER_H
#include "clitkDicomRT_ROI.h"
#include "clitkImageCommon.h"
#include <vtkImageClip.h>
#include <vtkMarchingSquares.h>
#include <vtkPolyDataWriter.h>
+#include <vtkVersion.h>
#if GDCM_MAJOR_VERSION == 2
#include "gdcmAttribute.h"
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetROINumber(int number)
+{
+ mNumber = number;
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
const std::string & clitk::DicomRT_ROI::GetName() const
{
#if GDCM_MAJOR_VERSION == 2
bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
{
- FATAL("Error : compile vv with itk4 + external gdcm");
+ //FATAL("Error : compile vv with itk4 + external gdcm");
// Keep dicom item
mItemInfo = itemInfo;
mItemContour = itemContour;
{
vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
for(unsigned int i=0; i<mListOfContours.size(); i++) {
- append->AddInput(mListOfContours[i]->GetMesh());
+#if VTK_MAJOR_VERSION <= 5
+ append->AddInput(mListOfContours[i]->GetMesh());
+#else
+ append->AddInputData(mListOfContours[i]->GetMesh());
+#endif
}
append->Update();
// Get initial extend for the clipping
vtkSmartPointer<vtkImageClip> clipper = vtkSmartPointer<vtkImageClip>::New();
+#if VTK_MAJOR_VERSION <= 5
clipper->SetInput(image);
+#else
+ clipper->SetInputData(image);
+#endif
+
int* extent = image->GetExtent();
DDV(extent, 6);
// std::vector<int> extend;
vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
+#if VTK_MAJOR_VERSION <= 5
squares->SetInput(image);
+#else
+ squares->SetInputData(image);
+#endif
squares->SetImageRange(extent[0], extent[1], extent[2], extent[3], i, i);
squares->SetValue(1, 1.0);
squares->Update();
vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
for(unsigned int i=0; i<n; i++) {
+#if VTK_MAJOR_VERSION <= 5
append->AddInput(contours[i]);
+#else
+ append->AddInputData(contours[i]);
+#endif
}
append->Update();
// Write vtk
vtkPolyDataWriter * w = vtkPolyDataWriter::New();
+#if VTK_MAJOR_VERSION <= 5
w->SetInput(mMesh);
+#else
+ w->SetInputData(mMesh);
+#endif
w->SetFileName("toto.vtk");
w->Write();
std::string filename);
int GetROINumber() const;
+ void SetROINumber(int);
const std::string & GetName() const;
const std::string & GetFilename() const;
const std::vector<double> & GetDisplayColor() const;
//--------------------------------------------------------------------
void clitk::DicomRT_StructureSet::Read(const std::string & filename)
{
-#if CLITK_USE_SYSTEM_GDCM == 1
- vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
- reader->SetFileName(filename.c_str());
- reader->Update();
-
- // Get global information
- vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
- mStudyID = p->GetStudyInstanceUID();
- mStudyDate = p->GetStructureSetDate();
- mLabel = p->GetStructureSetLabel();
- mName = p->GetStructureSetName();
- mTime = p->GetStructureSetTime();
-
- int n = p->GetNumberOfStructureSetROIs();
- for(unsigned int i=0; i<n; i++) {
- // Get the roi number
- int roinumber = p->GetStructureSetROINumber(i);
- // Create the roi
- DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
- roi->Read(reader, i);
- // Insert in the map
- mROIs[roinumber] = roi;
- }
- return;
-#endif // END version with system gdcm (vtkGDCMPolyDataReader)
-
- // Open DICOM
-#if GDCM_MAJOR_VERSION == 2
- FATAL("Error : compile vv with itk4 + external gdcm");
-
- // Read gdcm file
- mReader = new gdcm::Reader;
- mReader->SetFileName(filename.c_str());
- mReader->Read();
- mFile = &(mReader->GetFile());
- const gdcm::DataSet & ds = mFile->GetDataSet();
+//Try to avoid to use extern GDCM library
+
+ //check the RS file is available before conversion
+ gdcm::Reader RTreader;
+ RTreader.SetFileName( filename.c_str() );
+ if( !RTreader.Read() )
+ {
+ std::cout << "Problem reading file: " << filename << std::endl;
+ return;
+ }
+
+ const gdcm::DataSet& ds = RTreader.GetFile().GetDataSet();
- // Check file type
- //Verify if the file is a RT-Structure-Set dicom file
gdcm::MediaStorage ms;
- ms.SetFromFile(*mFile);
- if( ms != gdcm::MediaStorage::RTStructureSetStorage )
- {
- std::cerr << "Error. the file " << filename
- << " is not a Dicom Struct ? (must have a SOP Class UID [0008|0016] = 1.2.840.10008.5.1.4.1.1.481.3 ==> [RT Structure Set Storage])"
- << std::endl;
- exit(0);
- }
+ ms.SetFromFile( RTreader.GetFile() );
+
+ // (3006,0020) SQ (Sequence with explicit length #=4) # 370, 1 StructureSetROISequence
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ if( !ds.FindDataElement( tssroisq ) )
+ {
+ std::cout << "Problem locating 0x3006,0x0020 - Is this a valid RT Struct file?" << std::endl;
+ return;
+ }
+ gdcm::Tag troicsq(0x3006,0x0039);
+ if( !ds.FindDataElement( troicsq ) )
+ {
+ std::cout << "Problem locating 0x3006,0x0039 - Is this a valid RT Struct file?" << std::endl;
+ return;
+ }
- gdcm::Attribute<0x8,0x60> modality;
- modality.SetFromDataSet( ds );
- if( modality.GetValue() != "RTSTRUCT" )
- {
- std::cerr << "Error. the file " << filename
- << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])"
- << std::endl;
- exit(0);
- }
+ const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = roicsq.GetValueAsSQ();
+ if( !sqi || !sqi->GetNumberOfItems() )
+ {
+ return;
+ }
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> ssqi = ssroisq.GetValueAsSQ();
+ if( !ssqi || !ssqi->GetNumberOfItems() )
+ {
+ return;
+ }
+
// Read global info
gdcm::Attribute<0x20,0x10> studyid;
studyid.SetFromDataSet( ds );
// Temporary store the list of items
std::map<int, gdcm::Item*> mMapOfROIInfo;
std::map<int, gdcm::Item*> mMapOfROIContours;
-
-std::map<int, clitk::DicomRT_ROI::Pointer> mROIs;
- std::map<int, std::string> mMapOfROIName;
-#if GDCM_MAJOR_VERSION == 2
- gdcm::Reader * mReader;
- gdcm::SmartPointer<gdcm::SequenceOfItems> mROIInfoSequenceOfItems;
- gdcm::SmartPointer<gdcm::SequenceOfItems> mROIContoursSequenceOfItems;
-#endif
- gdcm::File * mFile;
-
+
//----------------------------------
// Read all ROI Names and number
// 0x3006,0x0020 = [ Structure Set ROI Sequence ]
- gdcm::Tag tssroisq(0x3006,0x0020);
- const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ //gdcm::Tag tssroisq(0x3006,0x0020);
+ //const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
mROIInfoSequenceOfItems = ssroisq.GetValueAsSQ();
gdcm::SmartPointer<gdcm::SequenceOfItems> & roi_seq = mROIInfoSequenceOfItems;
assert(roi_seq); // TODO error message
//----------------------------------
// Read all ROI item
// 0x3006,0x0039 = [ ROI Contour Sequence ]
- gdcm::Tag troicsq(0x3006,0x0039);
- const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+ //gdcm::Tag troicsq(0x3006,0x0039);
+ //const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
gdcm::SmartPointer<gdcm::SequenceOfItems> roi_contour_seq = roicsq.GetValueAsSQ();
mROIContoursSequenceOfItems = roi_contour_seq;
assert(roi_contour_seq); // TODO error message
for(std::map<int, gdcm::Item*>::iterator i = mMapOfROIInfo.begin(); i != mMapOfROIInfo.end(); i++) {
int nb = i->first;//ReadROINumber(i);//mROIIndex[i];
// Create the roi
- DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
- roi->Read(mMapOfROIInfo[nb], mMapOfROIContours[nb]);
- // mListOfROI.push_back(roi);
- // mMapOfROIIndex[nb] = i;
- mROIs[nb] = roi;
- }
-
- //----------------------------------------------------------------------------------------
- //----------------------------------------------------------------------------------------
- //----------------------------------------------------------------------------------------
-#else
- mFile = new gdcm::File;
- mFile->SetFileName(filename.c_str());
- mFile->SetMaxSizeLoadEntry(16384); // Needed ...
- mFile->SetLoadMode(gdcm::LD_NOSHADOW); // don't load shadow tags (in order to save memory)
- mFile->Load();
-
- // Check file type
- //Verify if the file is a RT-Structure-Set dicom file
- if (!gdcm::Util::DicomStringEqual(mFile->GetEntryValue(0x0008,0x0016),"1.2.840.10008.5.1.4.1.1.481.3")) { //SOP clas UID
- std::cerr << "Error. the file " << filename
- << " is not a Dicom Struct ? (must have a SOP Class UID [0008|0016] = 1.2.840.10008.5.1.4.1.1.481.3 ==> [RT Structure Set Storage])"
- << std::endl;
- exit(0);
- }
- if (!gdcm::Util::DicomStringEqual(mFile->GetEntryValue(0x0008,0x0060),"RTSTRUCT")) { //SOP clas UID
- std::cerr << "Error. the file " << filename
- << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])"
- << std::endl;
- exit(0);
- }
-
- // Read global info
- mStudyID = mFile->GetValEntry(0x0020,0x0010)->GetValue();
- mStudyTime = mFile->GetValEntry(0x008,0x0020)->GetValue();
- mStudyDate = mFile->GetValEntry(0x008,0x0030)->GetValue();
- mLabel = mFile->GetValEntry(0x3006,0x002)->GetValue();
- if (!mFile->GetValEntry(0x3006,0x004)) {
- mName = "Anonymous";
- }
- else {
- mName = mFile->GetValEntry(0x3006,0x004)->GetValue();
- }
- mTime = mFile->GetValEntry(0x3006,0x009)->GetValue();
-
- //----------------------------------
- // Read all ROI Names and number
- // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
- gdcm::SeqEntry * roi_seq=mFile->GetSeqEntry(0x3006,0x0020);
- assert(roi_seq); // TODO error message
- for (gdcm::SQItem* r=roi_seq->GetFirstSQItem(); r!=0; r=roi_seq->GetNextSQItem()) {
- std::string name = r->GetEntryValue(0x3006,0x0026); // 0x3006,0x0026 = [ROI Name]
- int nb = atoi(r->GetEntryValue(0x3006,0x0022).c_str()); // 0x3006,0x0022 = [ROI Number]
- // Check if such a number already exist
- if (mMapOfROIName.find(nb) != mMapOfROIName.end()) {
- std::cerr << "WARNING. A Roi already exist with the number "
- << nb << ". I replace." << std::endl;
- }
- // Add in map
- mMapOfROIName[nb] = name;
- }
-
- //----------------------------------
- // Read all ROI
- // 0x3006,0x0039 = [ ROI Contour Sequence ]
- gdcm::SeqEntry * roi_contour_seq=mFile->GetSeqEntry(0x3006,0x0039);
- assert(roi_contour_seq); // TODO error message
- int n=0;
- for (gdcm::SQItem* r=roi_contour_seq->GetFirstSQItem(); r!=0; r=roi_contour_seq->GetNextSQItem()) {
- DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
- roi->Read(mMapOfROIName, r);
- mROIs[roi->GetROINumber()] = roi;
- n++;
+ mROIs[nb] = DicomRT_ROI::New();
+ mROIs[nb]->Read(mMapOfROIInfo[nb], mMapOfROIContours[nb]);
}
+
+ return;
-#endif
}
//--------------------------------------------------------------------
//-------------------------------------------------------------------
template<unsigned int Dimension>
typename itk::Matrix<double, Dimension+1, Dimension+1>
-createMatrixFromElastixFile(std::vector<std::string> & filename, bool verbose=true) {
+createMatrixFromElastixFile(std::string& filename, bool verbose=true) {
if (Dimension != 3) {
FATAL("Only 3D yet" << std::endl);
}
- typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
+ typename itk::Matrix<double, Dimension+1, Dimension+1> matrix, init;
itk::Euler3DTransform<double>::Pointer mat = itk::Euler3DTransform<double>::New();
itk::Euler3DTransform<double>::Pointer previous;
- for(uint j=0; j<filename.size(); j++) {
-
- // Open file
- if (verbose) std::cout << "Read elastix parameters in " << filename[j] << std::endl;
- std::ifstream is;
- clitk::openFileForReading(is, filename[j]);
-
- // Check Transform
- std::string s;
- bool b = GetElastixValueFromTag(is, "Transform ", s);
- if (!b) {
- FATAL("Error must read 'Transform' in " << filename[j] << std::endl);
- }
- if (s != "EulerTransform") {
- FATAL("Sorry only 'EulerTransform'" << std::endl);
- }
- // FIXME check
- // (InitialTransformParametersFilename[j] "NoInitialTransform")
+ // Open file
+ if (verbose) std::cout << "Read elastix parameters in " << filename << std::endl;
+ std::ifstream is;
+ clitk::openFileForReading(is, filename);
- // Get CenterOfRotationPoint
- GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
- if (!b) {
- FATAL("Error must read 'CenterOfRotationPoint' in " << filename[j] << std::endl);
- }
- std::vector<std::string> cor;
- GetValuesFromValue(s, cor);
- itk::Euler3DTransform<double>::CenterType c;
- for(uint i=0; i<3; i++)
- c[i] = atof(cor[i].c_str());
- mat->SetCenter(c);
-
- // Get Transformparameters
- GetElastixValueFromTag(is, "ComputeZYX ", s); // space is needed
- mat->SetComputeZYX( s==std::string("true") );
-
- // Get Transformparameters
- GetElastixValueFromTag(is, "TransformParameters ", s); // space is needed
- if (!b) {
- FATAL("Error must read 'TransformParameters' in " << filename[j] << std::endl);
- }
- std::vector<std::string> results;
- GetValuesFromValue(s, results);
-
- // construct a stream from the string
- itk::Euler3DTransform<double>::ParametersType p;
- p.SetSize(6);
- for(uint i=0; i<3; i++)
- p[i] = atof(results[i].c_str()); // Rotation
- for(uint i=0; i<3; i++)
- p[i+3] = atof(results[i+3].c_str()); // Translation
- mat->SetParameters(p);
-
- if (verbose) {
- std::cout << "Rotation (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
- std::cout << "Center of rot (phy) : " << c[0] << " " << c[1] << " " << c[2] << std::endl;
- std::cout << "Translation (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
- }
+ // Check Transform
+ std::string s;
+ bool b = GetElastixValueFromTag(is, "Transform ", s);
+ if (!b) {
+ FATAL("Error must read 'Transform' in " << filename << std::endl);
+ }
+ if (s != "EulerTransform") {
+ FATAL("Sorry only 'EulerTransform'" << std::endl);
+ }
- // Compose with previous if needed
- if (j!=0) {
- mat->Compose(previous);
- if (verbose) {
- std::cout << "Composed rotation (deg) : " << rad2deg(mat->GetAngleX()) << " " << rad2deg(mat->GetAngleY()) << " " << rad2deg(mat->GetAngleZ()) << std::endl;
- std::cout << "Composed center of rot (phy) : " << mat->GetCenter() << std::endl;
- std::cout << "Compsoed translation (phy) : " << mat->GetTranslation() << std::endl;
- }
- }
- // previous = mat->Clone(); // ITK4
- previous = itk::Euler3DTransform<double>::New();
- previous->SetParameters(mat->GetParameters());
- previous->SetCenter(c);
- previous->SetComputeZYX(mat->GetComputeZYX());
+ // Get previous
+ b = GetElastixValueFromTag(is, "InitialTransformParametersFileName ", s);
+ if(s == "NoInitialTransform")
+ init.SetIdentity();
+ else
+ init = createMatrixFromElastixFile<Dimension>(s, verbose);
+
+ // Get CenterOfRotationPoint
+ GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
+ if (!b) {
+ FATAL("Error must read 'CenterOfRotationPoint' in " << filename << std::endl);
+ }
+ std::vector<std::string> cor;
+ GetValuesFromValue(s, cor);
+ itk::Euler3DTransform<double>::CenterType c;
+ for(uint i=0; i<3; i++)
+ c[i] = atof(cor[i].c_str());
+ mat->SetCenter(c);
+
+ // Get Transformparameters
+ GetElastixValueFromTag(is, "ComputeZYX ", s); // space is needed
+ mat->SetComputeZYX( s==std::string("true") );
+
+ // Get Transformparameters
+ GetElastixValueFromTag(is, "TransformParameters ", s); // space is needed
+ if (!b) {
+ FATAL("Error must read 'TransformParameters' in " << filename << std::endl);
}
+ std::vector<std::string> results;
+ GetValuesFromValue(s, results);
+
+ // construct a stream from the string
+ itk::Euler3DTransform<double>::ParametersType p;
+ p.SetSize(6);
+ for(uint i=0; i<3; i++)
+ p[i] = atof(results[i].c_str()); // Rotation
+ for(uint i=0; i<3; i++)
+ p[i+3] = atof(results[i+3].c_str()); // Translation
+ mat->SetParameters(p);
+
+ if (verbose) {
+ std::cout << "Rotation (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
+ std::cout << "Center of rot (phy) : " << c[0] << " " << c[1] << " " << c[2] << std::endl;
+ std::cout << "Translation (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
+ }
+
+ previous = itk::Euler3DTransform<double>::New();
+ previous->SetParameters(mat->GetParameters());
+ previous->SetCenter(c);
+ previous->SetComputeZYX(mat->GetComputeZYX());
mat = previous;
for(uint i=0; i<3; i++)
matrix[2][3] = mat->GetOffset()[2];
matrix[3][3] = 1;
- return matrix;
+ return matrix*init;
}
}
//-------------------------------------------------------------------
typedef FilterBase Self;
// Run-time type information (and related methods)
- itkTypeMacro(FilterBase, Object);
+ virtual const char *GetNameOfClass() const
+ {
+ return "FilterBase";
+ }
// Needed by itkSetMacro (cannot inherit from itkObject because of
// multiple inheritance)
#include "clitkUSVoxImageIOFactory.h"
#include "clitkSvlImageIOFactory.h"
#endif
-#if ITK_VERSION_MAJOR >= 4
- #include "itkGDCMImageIOFactory.h"
-#endif
+#include <itkBMPImageIOFactory.h>
+#include <itkGDCMImageIOFactory.h>
+#include <itkGiplImageIOFactory.h>
+#include <itkJPEGImageIOFactory.h>
+#include <itkMetaImageIOFactory.h>
+#include <itkPNGImageIOFactory.h>
+#include <itkStimulateImageIOFactory.h>
+#include <itkTIFFImageIOFactory.h>
+#include <itkVTKImageIOFactory.h>
//--------------------------------------------------------------------
// Register factories
void clitk::RegisterClitkFactories()
{
-#if ITK_VERSION_MAJOR >= 4
std::list< itk::ObjectFactoryBase * > fl = itk::GDCMImageIOFactory::GetRegisteredFactories();
for (std::list< itk::ObjectFactoryBase * >::iterator it = fl.begin(); it != fl.end(); ++it)
if (dynamic_cast<itk::GDCMImageIOFactory *>(*it))
itk::GDCMImageIOFactory::UnRegisterFactory(*it);
break;
}
-#endif
+
+ std::list< itk::ObjectFactoryBase * > flpng = itk::PNGImageIOFactory::GetRegisteredFactories();
+ for (std::list< itk::ObjectFactoryBase * >::iterator it = flpng.begin(); it != flpng.end(); ++it)
+ if (dynamic_cast<itk::PNGImageIOFactory *>(*it))
+ {
+ itk::PNGImageIOFactory::UnRegisterFactory(*it);
+ break;
+ }
#if CLITK_PRIVATE_FEATURES
clitk::UsfImageIOFactory::RegisterOneFactory();
clitk::USVoxImageIOFactory::RegisterOneFactory();
#endif
clitk::GateAsciiImageIOFactory::RegisterOneFactory();
clitk::DicomRTDoseIOFactory::RegisterOneFactory();
-#if ITK_VERSION_MAJOR <= 3
- itk::ImageIOFactory::RegisterBuiltInFactories();
-#endif
clitk::VoxImageIOFactory::RegisterOneFactory();
clitk::VfImageIOFactory::RegisterOneFactory();
clitk::XdrImageIOFactory::RegisterOneFactory();
rtk::ImagXImageIOFactory::RegisterOneFactory();
rtk::XRadImageIOFactory::RegisterOneFactory();
clitk::EsrfHstImageIOFactory::RegisterOneFactory();
-#if ITK_VERSION_MAJOR >= 4
+ itk::BMPImageIOFactory::RegisterOneFactory();
itk::GDCMImageIOFactory::RegisterOneFactory();
-#endif
+ itk::GiplImageIOFactory::RegisterOneFactory();
+ itk::JPEGImageIOFactory::RegisterOneFactory();
+ itk::MetaImageIOFactory::RegisterOneFactory();
+ itk::PNGImageIOFactory::RegisterOneFactory();
+ itk::StimulateImageIOFactory::RegisterOneFactory();
+ itk::TIFFImageIOFactory::RegisterOneFactory();
+ itk::VTKImageIOFactory::RegisterOneFactory();
} ////
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
Main authors : XX XX XX
- Authors belongs to:
+ Authors belongs to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
//--------------------------------------------------------------------
template<class PixelType>
class Image2DicomRTStructFilter: public clitk::FilterBase {
-
+
public:
Image2DicomRTStructFilter();
~Image2DicomRTStructFilter();
typedef typename clitk::DicomRT_StructureSet::Pointer DicomRTStructPointer;
// Set inputs
- itkSetMacro(InputFilenames, std::vector<std::string> );
+ virtual void SetInputFilenames (const std::vector<std::string> _arg)
+ {
+ if ( this->m_InputFilenames != _arg )
+ {
+ this->m_InputFilenames = _arg;
+ this->Modified();
+ }
+ }
itkSetMacro(StructureSetFilename, std::string);
itkSetMacro(DicomFolder, std::string);
itkSetMacro(OutputFilename, std::string);
void SetROIType(std::string type);
itkSetMacro(ThresholdValue, PixelType);
itkSetMacro(SkipInitialStructuresFlag, bool);
-
+
// Run filter
- void Update();
-
+ void Update();
+
protected:
std::string m_StructureSetFilename;
std::string m_DicomFolder;
#include <itkVTKImageToImageFilter.h>
// gdcm
+#include <vtkRTStructSetProperties.h>
+#include <vtkGDCMPolyDataReader.h>
#include <vtkGDCMPolyDataWriter.h>
//--------------------------------------------------------------------
// Copy previous contours
for (unsigned int i = 0; i < numMasks-m; ++i) {
+#if VTK_MAJOR_VERSION <= 5
writer->SetInput(i, reader->GetOutput(i));
+#else
+ writer->SetInputData(i, reader->GetOutput(i));
+#endif
std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
roiNames->InsertValue(i, theString);
theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
// Add new ones
for (unsigned int i = numMasks-m; i < numMasks; ++i) {
+#if VTK_MAJOR_VERSION <= 5
writer->SetInput(i, meshes[i-numMasks+m]);
+#else
+ writer->SetInputData(i, meshes[i-numMasks+m]);
+#endif
roiNames->InsertValue(i, m_ROINames[i-numMasks+m]);
roiAlgorithms->InsertValue(i, "CLITK_CREATED");
roiTypes->InsertValue(i, m_ROIType);
for(unsigned int i=0; i< dim-1; i++)
os << inputSize[i] << "x";
os << inputSize[dim-1]
- << " ";
+ << " ";
for(unsigned int i=0; i< dim-1; i++)
os << inputSpacing[i] << "x";
os << inputSpacing[dim-1]
- << " ";
+ << " ";
for(unsigned int i=0; i< dim-1; i++)
os << inputOrigin[i] << "x";
os << inputOrigin[dim-1] << " ";
===========================================================================**/
#include "clitkMatrix.h"
+#include <algorithm>
//--------------------------------------------------------------------
namespace clitk {
#define clitkMatrix_h
#include <itkMatrix.h>
+#define VTK_EXCLUDE_STRSTREAM_HEADERS
#include <vtkMatrix4x4.h>
#include <vtkSmartPointer.h>
mElapsed += (mEnd.ru_utime.tv_usec - mBegin.ru_utime.tv_usec)+
(mEnd.ru_utime.tv_sec - mBegin.ru_utime.tv_sec)*1000000;
}
+ else
#elif defined(_WIN32)
QueryPerformanceCounter((LARGE_INTEGER*)&mEnd);
if (accumulate) {
mElapsed += ((mEnd-mBegin)*1000000)/(long double)mFrequency;
}
+ else
#endif
- else {
+ {
mNumberOfCall--;
}
}
// #endif // If UNIX
#endif /* end #define CLITKTIMER_CXX */
-
//From portdefs.h
#if defined(unix) || defined(__APPLE__)
#define O_BINARY 0
-#define setmode(a,b) 0
+//#define setmode(a,b) 0 // comment by ds
#endif
#ifndef __LARGE__
#ifndef _WIN32
# include <unistd.h>
#endif
-#if !defined(unix) && !defined(__APPLE__)
-#include <io.h>
+#ifdef _WIN32
+# include <io.h>
#endif
#include <fcntl.h>
#include <errno.h>
for (i=0; i<GetNumberOfDimensions(); i++) {
if (!raw) {
- sprintf(temp, "dim%d=%d\n", i+1, GetDimensions(i));
+ sprintf(temp, "dim%d=%lu\n", i+1, GetDimensions(i));
slen = strlen(temp);
if (!checked_write(f, temp, slen, buffer)) {
free(pCompressed);
<< "\"");
}
datalen = edf_datatype_table[k].sajzof;
- switch(k) {
+ switch(edf_datatype_table[k].value) {
case U_CHAR_DATATYPE:
SetComponentType(itk::ImageIOBase::UCHAR);
break;
SetComponentType(itk::ImageIOBase::INT);
break;
case U_L_INT_DATATYPE:
- SetComponentType(itk::ImageIOBase::ULONG);
+ SetComponentType(itk::ImageIOBase::UINT);
break;
case L_INT_DATATYPE:
- SetComponentType(itk::ImageIOBase::LONG);
+ SetComponentType(itk::ImageIOBase::INT);
break;
case FLOAT_DATATYPE:
SetComponentType(itk::ImageIOBase::FLOAT);
double spacing = 1.;
if ( (p = edf_findInHeader(header, "optic_used") ) )
+ {
spacing = atof(p);
+ if(spacing == 0.)
+ spacing = 1.;
+ }
+
free(header);
gzclose(inp);
else if itkReadRawBytesAfterSwappingMacro( unsigned char, UCHAR )
else if itkReadRawBytesAfterSwappingMacro( unsigned int, UINT )
else if itkReadRawBytesAfterSwappingMacro( int, INT )
- else if itkReadRawBytesAfterSwappingMacro( unsigned int, ULONG )
- else if itkReadRawBytesAfterSwappingMacro( int, LONG )
+ else if itkReadRawBytesAfterSwappingMacro( unsigned int, UINT )
+ else if itkReadRawBytesAfterSwappingMacro( int, INT )
else if itkReadRawBytesAfterSwappingMacro( float, FLOAT )
else if itkReadRawBytesAfterSwappingMacro( double, DOUBLE );
}
//--------------------------------------------------------------------
// Write Image Information
-void rtk::EdfImageIO::WriteImageInformation(bool keepOfStream)
+void rtk::EdfImageIO::WriteImageInformation( bool itkNotUsed(keepOfStream) )
{
}
//--------------------------------------------------------------------
// Write Image Information
-bool rtk::EdfImageIO::CanWriteFile(const char* FileNameToWrite)
+bool rtk::EdfImageIO::CanWriteFile( const char* itkNotUsed(FileNameToWrite) )
{
return false;
}
//--------------------------------------------------------------------
// Write Image
-void rtk::EdfImageIO::Write(const void * buffer)
+void rtk::EdfImageIO::Write( const void * itkNotUsed(buffer) )
{
} ////
};
/* Note - compatibility:
- Unsigned8 = 1, Signed8, Unsigned16, Signed16,
- Unsigned32, Signed32, Unsigned64, Signed64,
- FloatIEEE32, DoubleIEEE64
+ Unsigned8 = 1,Signed8, Unsigned16, Signed16,
+ Unsigned32, Signed32, Unsigned64, Signed64,
+ FloatIEEE32, DoubleIEEE64
*/
/***************************************************************************
// * of the matrix in the data file.)
// */
//enum EdfRasterAxes {
- // RASTER_AXES_XrightYdown, // matricial format: rows, columns
- // RASTER_AXES_XrightYup // cartesian coordinate system
+ //RASTER_AXES_XrightYdown, // matricial format: rows, columns
+ //RASTER_AXES_XrightYup // cartesian coordinate system
// // other 6 combinations not available (not needed until now)
//};
}
//--------------------------------------------------------------------
-bool rtk::HisImageIO::CanWriteFile(const char* FileNameToWrite)
+bool rtk::HisImageIO::CanWriteFile( const char* itkNotUsed(FileNameToWrite) )
{
- return CanReadFile(FileNameToWrite);
+ return false;
}
//--------------------------------------------------------------------
// Write Image
-void rtk::HisImageIO::Write(const void* buffer)
+void rtk::HisImageIO::Write( const void* itkNotUsed(buffer) )
{
- std::ofstream file(m_FileName.c_str(), std::ios::out | std::ios::binary);
-
- if ( file.fail() )
- itkGenericExceptionMacro(<< "Could not open file (for writing): " << m_FileName);
-
- m_HeaderSize = HEADER_INFO_SIZE + 32;
- char szHeader[HEADER_INFO_SIZE + 32] = {
- 0x00, 0x70, 0x44, 0x00, 0x64, 0x00, 0x64, 0x00, 0x20, 0x00, 0x20, 0x00, 0x01, 0x00, 0x01, 0x00,
- 0x00, 0x04, 0x00, 0x04, 0x01, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x6A, 0x18, 0x41,
- 0x04, 0x00, 0x40, 0x5F, 0x48, 0x01, 0x40, 0x00, 0x86, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00, 0x08, 0x63, 0x13, 0x00, 0xE8, 0x51, 0x13, 0x00, 0x5C, 0xE7, 0x12, 0x00,
- 0xFE, 0x2A, 0x49, 0x5F, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00
- };
-
- /* Fill into the header the essentials
- The 'iheader' in previous module is fixed to 0x20, and is included in szHeader.
- The 'ulx' and 'uly' are fixed to 0x01, so that 'brx' and 'bry' reflect the dimensions of
- the image.
- */
- const unsigned int ndim = GetNumberOfDimensions();
- if ( (ndim < 2) || (ndim > 3) )
- itkExceptionMacro( <<"Only 2D or 3D support");
-
- szHeader[16] = (char)(GetDimensions(0) % 256); // X-size lsb
- szHeader[17] = (char)(GetDimensions(0) / 256); // X-size msb
- szHeader[18] = (char)(GetDimensions(1) % 256); // Y-size lsb
- szHeader[19] = (char)(GetDimensions(1) / 256); // Y-size msb
- if (ndim == 3) {
- szHeader[20] = (char)(GetDimensions(0) % 256); // NbFrames lsb
- szHeader[21] = (char)(GetDimensions(0) / 256); // NbFrames msb
- }
-
- switch (GetComponentType())
- {
- case itk::ImageIOBase::USHORT:
- szHeader[32] = 4;
- break;
- //case AVS_TYPE_INTEGER:
- // szHeader[32] = 8;
- // break;
- //case AVS_TYPE_REAL:
- // szHeader[32] = 16;
- // break;
- default:
- itkExceptionMacro(<< "Unsupported field type");
- break;
- }
-
- file.write(szHeader, m_HeaderSize);
- file.write( (const char *)buffer, GetImageSizeInBytes() );
- file.close();
} ////
{
FILE *fp;
- itk::uint32_t* buf = (itk::uint32_t*)buffer;
+ itk::uint32_t *buf = (itk::uint32_t*)buffer;
unsigned char *pt_lut;
- itk::uint32_t a;
+ itk::uint32_t a;
unsigned char v;
int lut_idx, lut_off;
size_t num_read;
char dc;
short ds;
long dl, diff=0;
- itk::uint32_t i;
+ itk::uint32_t i;
fp = fopen (m_FileName.c_str(), "rb");
if (fp == NULL)
if(pixelType=="Type_float")
SetComponentType(itk::ImageIOBase::FLOAT);
- if(dic["dimensions"].GetPointer()==NULL)
+ if( dic["dimensions"].GetPointer() == NULL )
SetNumberOfDimensions(3);
else
SetNumberOfDimensions( ( dynamic_cast<MetaDataIntType *>(dic["dimensions"].GetPointer() )->GetMetaDataObjectValue() ) );
{
SetDimensions(2, dynamic_cast<MetaDataIntType *>(dic["z"].GetPointer() )->GetMetaDataObjectValue() );
SetSpacing(2, dynamic_cast<MetaDataDoubleType *>(dic["spacing_z"].GetPointer() )->GetMetaDataObjectValue() );
+ if(GetSpacing(2) == 0)
+ SetSpacing(2, 1);
}
- std::istringstream iss(
- dynamic_cast<MetaDataStringType*>(dic["matrixTransform"].GetPointer() )->GetMetaDataObjectValue() );
itk::Matrix<double, 4, 4> matrix;
- for(unsigned int j=0; j<4; j++)
- for(unsigned int i=0; i<4; i++)
- iss >> matrix[j][i];
- matrix /= matrix[3][3];
+ if(dic["matrixTransform"].GetPointer() == NULL)
+ matrix.SetIdentity();
+ else
+ {
+ std::istringstream iss(
+ dynamic_cast<MetaDataStringType*>(dic["matrixTransform"].GetPointer() )->GetMetaDataObjectValue() );
+ for(unsigned int j=0; j<4; j++)
+ for(unsigned int i=0; i<4; i++)
+ iss >> matrix[j][i];
+ matrix /= matrix[3][3];
+ }
std::vector<double> direction;
for(unsigned int i=0; i<GetNumberOfDimensions(); i++)
//--------------------------------------------------------------------
// Write Image Information
-void rtk::ImagXImageIO::WriteImageInformation(bool keepOfStream)
+void rtk::ImagXImageIO::WriteImageInformation( bool itkNotUsed(keepOfStream) )
{
}
//--------------------------------------------------------------------
// Write Image Information
-bool rtk::ImagXImageIO::CanWriteFile(const char* FileNameToWrite)
+bool rtk::ImagXImageIO::CanWriteFile( const char* itkNotUsed(FileNameToWrite) )
{
return false;
}
//--------------------------------------------------------------------
// Write Image
-void rtk::ImagXImageIO::Write(const void * buffer)
+void rtk::ImagXImageIO::Write( const void * itkNotUsed(buffer) )
{
} ////
-
} // end namespace
#endif
-
1,
itk::CreateObjectFunction<ImagXImageIO>::New() );
}
-
itkFactorylessNewMacro(Self);
/** Run-time type information (and related methods). */
- itkTypeMacro(EsrfHstImageIOFactory, ObjectFactoryBase);
+ itkTypeMacro(ImagXImageIOFactory, ObjectFactoryBase);
/** Register one factory of this type */
static void RegisterOneFactory(void) {
} // end namespace
#endif
-
+++ /dev/null
-/*=========================================================================
- *
- * Copyright RTK Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-
-#ifndef __rtkImagXLookupTableImageFilter_h
-#define __rtkImagXLookupTableImageFilter_h
-
-#include "rtkLookupTableImageFilter.h"
-#include <itkNumericTraits.h>
-
-namespace rtk
-{
-
-/** \class ImagXLookupTableImageFilter
- * \brief Lookup table for ImagX data.
- *
- * The lookup table converts the raw values measured by the panel to the
- * logarithm of the value divided by the maximum numerical value. This could
- * be improved with a calibration of the air value.
- *
- * \author Simon Rit
- *
- * \ingroup ImageToImageFilter
- */
-template <class TInputImage, class TOutputImage>
-class ITK_EXPORT ImagXLookupTableImageFilter : public LookupTableImageFilter<TInputImage, TOutputImage>
-{
-
-public:
- /** Standard class typedefs. */
- typedef ImagXLookupTableImageFilter Self;
- typedef LookupTableImageFilter<TInputImage, TOutputImage> Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- typedef typename TInputImage::PixelType InputImagePixelType;
- typedef typename TOutputImage::PixelType OutputImagePixelType;
- typedef typename Superclass::FunctorType::LookupTableType LookupTableType;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ImagXLookupTableImageFilter, LookupTableImageFilter);
-protected:
- ImagXLookupTableImageFilter();
- virtual ~ImagXLookupTableImageFilter() {
- }
-
-private:
- ImagXLookupTableImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-};
-
-} // end namespace rtk
-
-template <class TInputImage, class TOutputImage>
-rtk::ImagXLookupTableImageFilter<TInputImage, TOutputImage>::ImagXLookupTableImageFilter()
-{
- // Create the lut
- typename LookupTableType::Pointer lut = LookupTableType::New();
- typename LookupTableType::SizeType size;
- size[0] = itk::NumericTraits<InputImagePixelType>::max()-itk::NumericTraits<InputImagePixelType>::min()+1;
- lut->SetRegions( size );
- lut->Allocate();
-
- OutputImagePixelType logRef = log(OutputImagePixelType(size[0]) );
-
- // Iterate and set lut
- itk::ImageRegionIteratorWithIndex<LookupTableType> it( lut, lut->GetBufferedRegion() );
- it.GoToBegin();
- while( !it.IsAtEnd() )
- {
- it.Set( logRef - log(it.GetIndex()[0]+1.) );
- ++it;
- }
-
- // Set the lut to member and functor
- this->SetLookupTable(lut);
-}
-
-#endif
+++ /dev/null
-/*=========================================================================
- *
- * Copyright RTK Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-
-#ifndef __rtkImagXRawToAttenuationImageFilter_h
-#define __rtkImagXRawToAttenuationImageFilter_h
-
-#include <itkImageToImageFilter.h>
-#include <itkCropImageFilter.h>
-
-#include "rtkImagXLookupTableImageFilter.h"
-#include "rtkBoellaardScatterCorrectionImageFilter.h"
-
-/** \class ImagXRawToAttenuationImageFilter
- * \brief Convert raw ImagX data to attenuation images
- *
- * TODO
- *
- * \author Simon Rit
- *
- * \ingroup ImageToImageFilter
- */
-namespace rtk
-{
-
-template<class TInputImage, class TOutputImage=TInputImage>
-class ITK_EXPORT ImagXRawToAttenuationImageFilter :
- public itk::ImageToImageFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ImagXRawToAttenuationImageFilter Self;
- typedef itk::ImageToImageFilter<TInputImage, TOutputImage> Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Some convenient typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ImagXRawToAttenuationImageFilter, itk::ImageToImageFilter);
-protected:
- ImagXRawToAttenuationImageFilter();
- ~ImagXRawToAttenuationImageFilter(){
- }
-
- /** Apply changes to the input image requested region. */
- virtual void GenerateInputRequestedRegion();
-
- void GenerateOutputInformation();
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to other filters. */
- void GenerateData();
-
-private:
- //purposely not implemented
- ImagXRawToAttenuationImageFilter(const Self&);
- void operator=(const Self&);
-
- typedef itk::CropImageFilter<InputImageType, InputImageType> CropFilterType;
- typedef rtk::BoellaardScatterCorrectionImageFilter<InputImageType, InputImageType> ScatterFilterType;
- typedef rtk::ImagXLookupTableImageFilter<InputImageType, OutputImageType> LookupTableFilterType;
-
- typename LookupTableFilterType::Pointer m_LookupTableFilter;
- typename CropFilterType::Pointer m_CropFilter;
- typename ScatterFilterType::Pointer m_ScatterFilter;
-}; // end of class
-
-} // end namespace rtk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "rtkImagXRawToAttenuationImageFilter.txx"
-#endif
-
-#endif
+++ /dev/null
-/*=========================================================================
- *
- * Copyright RTK Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-
-#ifndef __rtkImagXRawToAttenuationImageFilter_txx
-#define __rtkImagXRawToAttenuationImageFilter_txx
-
-#include <itkImageFileWriter.h>
-
-namespace rtk
-{
-
-template<class TInputImage, class TOutputImage>
-void
-ImagXRawToAttenuationImageFilter<TInputImage, TOutputImage>
-::GenerateInputRequestedRegion()
-{
- typename Superclass::InputImagePointer inputPtr =
- const_cast< TInputImage * >( this->GetInput() );
- if ( !inputPtr )
- return;
-
- m_CropFilter->SetInput(inputPtr); //SR: this is most likely useless
- m_LookupTableFilter->GetOutput()->SetRequestedRegion(this->GetOutput()->GetRequestedRegion() );
- m_LookupTableFilter->GetOutput()->PropagateRequestedRegion();
-}
-
-template <class TInputImage, class TOutputImage>
-ImagXRawToAttenuationImageFilter<TInputImage, TOutputImage>
-::ImagXRawToAttenuationImageFilter()
-{
- m_CropFilter = CropFilterType::New();
- m_ScatterFilter = ScatterFilterType::New();
- m_LookupTableFilter = LookupTableFilterType::New();
-
- //Permanent internal connections
- m_ScatterFilter->SetInput( m_CropFilter->GetOutput() );
- m_LookupTableFilter->SetInput( m_ScatterFilter->GetOutput() );
-
- //Default filter parameters
- typename CropFilterType::SizeType border = m_CropFilter->GetLowerBoundaryCropSize();
- border[0] = 4;
- border[1] = 4;
- m_CropFilter->SetBoundaryCropSize(border);
-}
-
-template<class TInputImage, class TOutputImage>
-void
-ImagXRawToAttenuationImageFilter<TInputImage, TOutputImage>
-::GenerateOutputInformation()
-{
- m_CropFilter->SetInput(this->GetInput() );
- m_LookupTableFilter->UpdateOutputInformation();
- this->GetOutput()->SetOrigin( m_LookupTableFilter->GetOutput()->GetOrigin() );
- this->GetOutput()->SetSpacing( m_LookupTableFilter->GetOutput()->GetSpacing() );
- this->GetOutput()->SetDirection( m_LookupTableFilter->GetOutput()->GetDirection() );
- this->GetOutput()->SetLargestPossibleRegion( m_LookupTableFilter->GetOutput()->GetLargestPossibleRegion() );
-}
-
-template<class TInputImage, class TOutputImage>
-void
-ImagXRawToAttenuationImageFilter<TInputImage, TOutputImage>
-::GenerateData()
-{
- m_CropFilter->SetInput(this->GetInput() );
- m_LookupTableFilter->Update();
- this->GraftOutput( m_LookupTableFilter->GetOutput() );
-}
-
-} // end namespace rtk
-#endif
void
ImagXXMLFileReader::
-EndElement(const char *name)
+EndElement( const char *itkNotUsed(name) )
{
}
{
std::string line;
std::getline(is, line);
- if(line.find('[')!=std::string::npos)
+ if(line.find('[') != std::string::npos)
{
unsigned int pos1 = line.find('[');
unsigned int pos2 = line.find(']');
section = line.substr(pos1+1, pos2-pos1-1);
}
- if(line.find('=')!=std::string::npos)
+ if(line.find('=') != std::string::npos)
{
unsigned int pos = line.find('=');
std::string paramName = line.substr(0,pos);
SetDimensions(2, atoi(paramValue.c_str()));
else if(paramName == std::string("CBCT.DimensionalAttributes.DataSize"))
{
- if(atoi(paramValue.c_str())==3)
+ if(atoi(paramValue.c_str()) == 3)
SetComponentType(itk::ImageIOBase::FLOAT);
- if(atoi(paramValue.c_str())==6)
+ if(atoi(paramValue.c_str()) == 6)
SetComponentType(itk::ImageIOBase::USHORT);
}
else if(paramName == std::string("CBCT.DimensionalAttributes.PixelDimension_I_cm"))
//--------------------------------------------------------------------
// Write Image Information
-void rtk::XRadImageIO::WriteImageInformation(bool keepOfStream)
+void rtk::XRadImageIO::WriteImageInformation(bool itkNotUsed(keepOfStream))
{
}
//--------------------------------------------------------------------
// Write Image Information
-bool rtk::XRadImageIO::CanWriteFile(const char* FileNameToWrite)
+bool rtk::XRadImageIO::CanWriteFile(const char* itkNotUsed(FileNameToWrite))
{
return false;
}
//--------------------------------------------------------------------
// Write Image
-void rtk::XRadImageIO::Write(const void * buffer)
+void rtk::XRadImageIO::Write(const void * itkNotUsed(buffer))
{
} ////
extractedRegion.SetIndex(start);
typename FilterType::Pointer filter = FilterType::New();
-#if ITK_VERSION_MAJOR == 4
filter->SetDirectionCollapseToSubmatrix();
-#endif
filter->SetExtractionRegion(extractedRegion);
filter->SetInput(input);
filter->ReleaseDataFlagOn();
vv_image->AddItkImage<ItkImageType>(filter->GetOutput());
+ vv_image->ComputeScalarRangeBase<PixelType, Dim-1>(filter->GetOutput());
}
vv_image->SetTimeSpacing(input->GetSpacing()[Dim-1]);
vv_image->SetTimeOrigin(input->GetOrigin()[Dim-1]);
if (time_sequence) //The time sequence case: create a series of VTK images
ReadTimeSequence<Dim,PixelType>(vv_image, input, time_sequence);
- else //Dim == 1,2,3 and not time_sequence
+ else { //Dim == 1,2,3 and not time_sequence
vv_image->AddItkImage<InputImageType>(input);
-
+ vv_image->ComputeScalarRangeBase<PixelType, Dim>(input);
+ }
return vv_image;
}
};
// vtk
#include <vtkImageData.h>
#include <vtkTransform.h>
+#include <vtkDataObject.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
+#include <vtkVersion.h>
// std
#include <cassert>
mTimeSpacing = 1;
mTimeOrigin = 0;
mImageDimension = 0;
+ mrange[0] = std::numeric_limits<int>::max();;//min
+ mrange[1] = std::numeric_limits<int>::min();;//max
}
//--------------------------------------------------------------------
// mItkToVtkConverters is therefore not being updated, but
// up to here it's not being used anyway...
mImageDimension = 0;
+#if VTK_MAJOR_VERSION <= 5
int* extent = input->GetWholeExtent();
+#else
+ int* extent = input->GetInformation()->Get(vtkDataObject::DATA_EXTENT());
+#endif
if (extent[4] != extent[5])
mImageDimension = 3;
else if (extent[3] != extent[4])
//--------------------------------------------------------------------
void vvImage::GetScalarRange(double* range)
{
- assert(mVtkImages.size());
- double * temp = mVtkImages[0]->GetScalarRange();
- range[0]=temp[0];
- range[1]=temp[1];
- for (unsigned int i=1; i<mVtkImages.size(); i++) {
- temp = mVtkImages[i]->GetScalarRange();
- if (temp[0] < range[0]) range[0]=temp[0];
- if (temp[1] > range[1]) range[1]=temp[1];
- }
+ range[0]=mrange[0];
+ range[1]=mrange[1];
}
//--------------------------------------------------------------------
#include <vector>
#include <itkObjectFactory.h>
#include <itkProcessObject.h>
+#include <itkMinimumMaximumImageCalculator.h>
+#include <itkCastImageFilter.h>
#define VTK_EXCLUDE_STRSTREAM_HEADERS
#include <vtkSmartPointer.h>
typedef itk::SmartPointer<Self> Pointer;
typedef itk::ProcessObject::Pointer ConverterPointer;
itkNewMacro(Self);
+
+ struct DimensionDispatchBase {};
+ template< unsigned int VDimension >
+ struct DimensionDispatch:public DimensionDispatchBase {};
void Init();
void Reset();
int GetNumberOfDimensions() const;
int GetNumberOfSpatialDimensions();
void GetScalarRange(double* range);
+ template<class TPixelType, unsigned int VImageDimension> void ComputeScalarRangeBase(itk::Image<TPixelType,VImageDimension> *input);
+ template<class TPixelType, unsigned int VImageDimension> void ComputeScalarRange(DimensionDispatchBase, itk::Image<TPixelType,VImageDimension> *input);
+ template<class TPixelType, unsigned int VImageDimension> void ComputeScalarRange(DimensionDispatch< 1 >, itk::Image<TPixelType,VImageDimension> *input);
unsigned long GetActualMemorySize();
std::vector<double> GetSpacing();
std::vector<double> GetOrigin() const;
double mTimeOrigin;
double mTimeSpacing;
unsigned int mImageDimension;
+ double mrange[2];
};
//------------------------------------------------------------------------------
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================*/
#include <itkImageToVTKImageFilter.h>
+#include <itkPixelTraits.h>
//--------------------------------------------------------------------
template<class TItkImageType>
// Update input before conversion to enable exceptions thrown by the ITK pipeline.
// Otherwise, vtkImageImport catches the exception for us.
input->Update();
-
+
// Convert from ITK object to VTK object
mImageDimension = TItkImageType::ImageDimension;
typedef itk::ImageToVTKImageFilter <TItkImageType> ConverterType;
matrix->Identity();
for(unsigned int i=0; i<input->GetImageDimension(); i++) {
for(unsigned int j=0; j<input->GetImageDimension(); j++) {
+#if VTK_MAJOR_VERSION <= 6
(*matrix)[i][j] = input->GetDirection()[i][j];
// Direction is used around the image origin in ITK
(*matrix)[i][3] -= (*matrix)[i][j] * input->GetOrigin()[j];
+#else
+ (*matrix).SetElement(i, j, input->GetDirection()[i][j]);
+ // Direction is used around the image origin in ITK
+ (*matrix).SetElement(i, 3, (*matrix).GetElement(i,3) - (*matrix).GetElement(i,j) * input->GetOrigin()[j]);
+#endif
}
+#if VTK_MAJOR_VERSION <= 6
(*matrix)[i][3] += input->GetOrigin()[i];
+#else
+ (*matrix).SetElement(i, 3, (*matrix).GetElement(i,3) + input->GetOrigin()[i]);
+#endif
}
// GetDirection provides the forward transform, vtkImageReslice wants the inverse
mDictionary.push_back(&(input->GetMetaDataDictionary()));
}
//--------------------------------------------------------------------
+
+/** Dispatch the computation of scalar range between vector and scalar image */
+template<class TPixelType, unsigned int VImageDimension>
+void vvImage::ComputeScalarRangeBase(itk::Image<TPixelType,VImageDimension> *input)
+{
+ itkStaticConstMacro(Dimension1, unsigned int, itk::PixelTraits< TPixelType >::Dimension);
+ ComputeScalarRange(DimensionDispatch< Dimension1 >(), input);
+}
+
+//--------------------------------------------------------------------
+/** Compute the scalar range for a vector pixel type */
+/** TO DO*/
+template<class TPixelType, unsigned int VImageDimension>
+void vvImage::ComputeScalarRange(DimensionDispatchBase, itk::Image<TPixelType,VImageDimension> *input)
+{
+}
+
+//--------------------------------------------------------------------
+/** Compute the scalar range for a scalar pixel type */
+template<class TPixelType, unsigned int VImageDimension>
+void vvImage::ComputeScalarRange(DimensionDispatch< 1 >, itk::Image<TPixelType,VImageDimension> *input)
+{
+ typedef typename itk::Image<TPixelType,VImageDimension> TItkImageType;
+ typedef itk::MinimumMaximumImageCalculator <TItkImageType> ImageCalculatorFilterType;
+
+ typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New ();
+ TPixelType tempMin, tempMax;
+ double tempRange[2];
+ imageCalculatorFilter->SetImage(input);
+ imageCalculatorFilter->Compute();
+ tempMin= imageCalculatorFilter->GetMinimum();
+ tempMax= imageCalculatorFilter->GetMaximum();
+
+ tempRange[0] = (double) tempMin;
+ tempRange[1] = (double) tempMax;
+
+ if (tempRange[0] < mrange[0]) mrange[0]=tempRange[0];
+ if (tempRange[1] > mrange[1]) mrange[1]=tempRange[1];
+}
+//--------------------------------------------------------------------
f.open(filename.c_str());
if(!itkMatRead && f.is_open()) {
itkMatRead = true;
- std::vector<std::string> l;
- l.push_back(filename);
- itkMat = clitk::createMatrixFromElastixFile<3>(l, true);
+ itkMat = clitk::createMatrixFromElastixFile<3>(filename, true);
}
f.close();
else
std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
- if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
+ if (mLastError.size()==0) {
//ReadNkiImageTransform();
ReadMatImageTransform();
}
reader->SetFileName(*i);
try {
mImage->AddItkImage<InputImageType>(reader->GetOutput());
+ mImage->ComputeScalarRangeBase<InputPixelType, VImageDimension-1>(reader->GetOutput());
} catch ( itk::ExceptionObject & err ) {
std::cerr << "Error while reading " << mInputFilenames[0].c_str()
<< " " << err << std::endl;
filter->SetExtractionRegion(extractedRegion);
filter->SetInput(reader->GetOutput());
filter->ReleaseDataFlagOn();
-#if ITK_VERSION_MAJOR == 4
filter->SetDirectionCollapseToSubmatrix();
-#endif
try {
mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
+ mImage->ComputeScalarRangeBase<InputPixelType, VImageDimension-1>(filter->GetOutput());
} catch ( itk::ExceptionObject & err ) {
std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
<< "(slice #" << mSlice << ") " << err << std::endl;
* This filter is implemented using the propagation algorithm
*/
-#if ITK_VERSION_MAJOR == 4
template <class TInputImage, class TOutputImage, class TtNorm=Functor::Minimum<
typename TOutputImage::PixelType,
typename TOutputImage::PixelType,
typename TOutputImage::PixelType> >
-#else
- template <class TInputImage, class TOutputImage, class TtNorm=Function::Minimum<
- typename TOutputImage::PixelType,
- typename TOutputImage::PixelType,
- typename TOutputImage::PixelType> >
-#endif
class ITK_EXPORT RelativePositionPropImageFilter :
public ImageToImageFilter< TInputImage, TOutputImage >
{
#include <itkBinaryErodeImageFilter.h>
#include <itkBinaryBallStructuringElement.h>
#include <itkAddImageFilter.h>
-#if ITK_VERSION_MAJOR >= 4
- #include <itkDivideImageFilter.h>
-#else
- #include <itkDivideByConstantImageFilter.h>
-#endif
+#include <itkDivideImageFilter.h>
// itk [Bloch et al]
#include "RelativePositionPropImageFilter.h"
// Divide by the number of relpos
if (GetNumberOfAngles() != 1) {
-#if ITK_VERSION_MAJOR >= 4
typedef itk::DivideImageFilter<FloatImageType, FloatImageType, FloatImageType> DivideFilter;
typename DivideFilter::Pointer divideFilter = DivideFilter::New();
divideFilter->SetConstant2(GetNumberOfAngles());
-#else
- typedef itk::DivideByConstantImageFilter<FloatImageType, float, FloatImageType> DivideFilter;
- typename DivideFilter::Pointer divideFilter = DivideFilter::New();
- divideFilter->SetConstant(GetNumberOfAngles());
-#endif
divideFilter->SetInput(m_FuzzyMap);
divideFilter->Update();
m_FuzzyMap = divideFilter->GetOutput();
void BeforeThreadedGenerateData(void );
// Threaded Generate Data
-#if ITK_VERSION_MAJOR >= 4
void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, int threadId );
-#endif
-
//------------------------------------------------
//Member data
//-----------------------------------------------------------------------
template <class InputImageType, class OutputImageType>
void
- BackProjectImageFilter<InputImageType, OutputImageType>
-#if ITK_VERSION_MAJOR >= 4
- ::ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, itk::ThreadIdType threadId )
-#else
- ::ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, int threadId )
-#endif
+ BackProjectImageFilter<InputImageType, OutputImageType>::ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, itk::ThreadIdType threadId )
{
//Projection pointer
InputImageConstPointer inputPtr=this->GetInput();
======================================================================-====*/
#ifndef CLITKBINARYIMAGETOMESHFILTER_H
-#define CLITKMESHTOBINARYIMAGEFILTER_H
+#define CLITKBINARYIMAGETOMESHFILTER_H
// clitk
#include "clitkCommon.h"
// Get extend
vtkSmartPointer<vtkImageClip> clipper = vtkSmartPointer<vtkImageClip>::New();
+#if VTK_MAJOR_VERSION <= 5
clipper->SetInput(input_vtk);
+#else
+ clipper->SetInputData(input_vtk);
+#endif
int* extent = input_vtk->GetExtent();
// Loop on slices
// std::vector<vtkSmartPointer<vtkPolyData> > contours;
for(uint i=0; i<n; i++) {
vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
+#if VTK_MAJOR_VERSION <= 5
squares->SetInput(input_vtk);
+#else
+ squares->SetInputData(input_vtk);
+#endif
squares->SetImageRange(extent[0], extent[1], extent[2], extent[3], i, i);
squares->SetNumberOfContours(1);
squares->SetValue(0, m_ThresholdValue);
// Strip (needed)
vtkSmartPointer<vtkStripper> vs = vtkSmartPointer<vtkStripper>::New();
+#if VTK_MAJOR_VERSION <= 5
vs->SetInput(squares->GetOutput());
+#else
+ vs->SetInputData(squares->GetOutput());
+#endif
vs->Update();
m = vs->GetOutput();
// only add if lines>0
if (m->GetNumberOfLines() > 0) {
+#if VTK_MAJOR_VERSION <= 5
append->AddInput(m);//contours[i]);
+#else
+ append->AddInputData(m);//contours[i]);
+#endif
}
}
append->Update();
//========================================================================================
//Threaded execution should implement generate threaded data
-#if ITK_VERSION_MAJOR >= 4
- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
-#endif
+ void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId );
bool m_Verbose;
PixelType m_EdgePaddingValue;
//=========================================================================================================================
//update the output for the outputRegionForThread
-#if ITK_VERSION_MAJOR >= 4
template<class InputImageType, class OutputImageType>
void ComposeVFFilter<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId )
-#else
- template<class InputImageType, class OutputImageType>
- void ComposeVFFilter<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId )
-#endif
{
//Get pointer to the output
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
// clitk
#include "clitkBoundingBoxUtils.h"
+#include "clitkImageCommon.h"
// itk
#include <itkImageToImageFilter.h>
namespace clitk {
-
+
//--------------------------------------------------------------------
/*
Perform various cropping operation on a image
*/
//--------------------------------------------------------------------
-
+
template <class ImageType>
class ITK_EXPORT CropLikeImageFilter: public itk::ImageToImageFilter<ImageType, ImageType> {
public:
typedef itk::ImageToImageFilter<ImageType, ImageType> Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
-
+
/** Method for creation through the object factory. */
itkNewMacro(Self);
-
+
/** Run-time type information (and related methods). */
itkTypeMacro(CropLikeImageFilter, ImageToImageFilter);
// Set Background if 'like' is greater than input
itkSetMacro(BackgroundValue, PixelType);
- itkGetConstMacro(BackgroundValue, PixelType);
+ itkGetConstMacro(BackgroundValue, PixelType);
/** ImageDimension constants */
itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
protected:
CropLikeImageFilter();
virtual ~CropLikeImageFilter() {}
-
+
virtual void GenerateOutputInformation();
virtual void GenerateData();
virtual void GenerateInputRequestedRegion();
-
+
PixelType m_BackgroundValue;
RegionType m_OutputRegion;
RegionType m_Region;
PointType m_Origin;
const itk::ImageBase<ImageDimension> * m_LikeImage;
std::vector<bool> m_CropAlongThisDimension;
-
+
PointType m_StartPoint; // start point in physical world
- IndexType m_StartSourceIndex; // start index in "source" image
- IndexType m_StartDestIndex; // start index in "destination" image
-
+ IndexType m_StartSourceIndex; // start index in "source" image
+ IndexType m_StartDestIndex; // start index in "destination" image
+
PointType m_StopPoint; // stop point in physical world
- IndexType m_StopSourceIndex; // stop index in "source" image
- IndexType m_StopDestIndex; // stop index in "destination" image
-
+ IndexType m_StopSourceIndex; // stop index in "source" image
+ IndexType m_StopDestIndex; // stop index in "destination" image
+
private:
CropLikeImageFilter(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
-
+
}; // end class
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- // Convenient function
+ // Convenient function
template<class ImageType>
typename ImageType::Pointer
ResizeImageLike(const ImageType * input,
- const itk::ImageBase<ImageType::ImageDimension> * like,
+ const itk::ImageBase<ImageType::ImageDimension> * like,
typename ImageType::PixelType BG);
template<class ImageType>
typename ImageType::Pointer
ResizeImageLike(const ImageType * input,
- typename itk::ImageBase<ImageType::ImageDimension>::RegionType * like,
+ typename itk::ImageBase<ImageType::ImageDimension>::RegionType * like,
typename ImageType::PixelType BG);
template<class ImageType>
typename ImageType::Pointer
- ResizeImageLike(const ImageType * input,
- typename itk::BoundingBox<unsigned long, ImageType::ImageDimension>::Pointer bb,
+ ResizeImageLike(const ImageType * input,
+ typename itk::BoundingBox<unsigned long, ImageType::ImageDimension>::Pointer bb,
typename ImageType::PixelType BG);
const OutputImageRegionType &srcRegion);
-#if ITK_VERSION_MAJOR >= 4
void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
-#endif
InputImageRegionType m_ExtractionRegion;
OutputImageRegionType m_OutputImageRegion;
*/
template <class TInputImage, class TOutputImage>
void
-ExtractImageFilter<TInputImage,TOutputImage>
-#if ITK_VERSION_MAJOR >= 4
-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId)
-#else
-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId)
-#endif
+ExtractImageFilter<TInputImage,TOutputImage>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId)
{
itkDebugMacro(<<"Actually executing");
m_size[GetDirection()] = 0;
m_region.SetSize(m_size);
int start = m_index[GetDirection()];
-#if ITK_VERSION_MAJOR >= 4
this->SetNumberOfIndexedInputs(m_NumberOfSlices);
-#else
- this->SetNumberOfOutputs(m_NumberOfSlices);
-#endif
//--------------------------------------------------------------------
// loop ExtractImageFilter with region updated, push_back
m_index[GetDirection()] = start + i;
m_region.SetIndex(m_index);
extract->SetExtractionRegion(m_region);
-#if ITK_VERSION_MAJOR == 4
extract->SetDirectionCollapseToSubmatrix();
-#endif
extract->Update();
this->SetNthOutput(i, extract->GetOutput());
}
//the actual processing
void BeforeThreadedGenerateData();
-#if ITK_VERSION_MAJOR >= 4
void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
-#endif
//member data
typename WeightsImageType::Pointer m_Weights;
//=========================================================================================================================
//update the output for the outputRegionForThread
template<class InputImageType, class OutputImageType>
-#if ITK_VERSION_MAJOR >= 4
void HelperClass1<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId )
-#else
-void HelperClass1<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId )
-#endif
{
// std::cout << "HelperClass1::ThreadedGenerateData - IN " << threadId << std::endl;
//Get pointer to the input
typedef typename OutputImageType::PixelType DisplacementType;
DisplacementType displacement;
inputIt.GoToBegin();
-
+
typename OutputImageType::SizeType size = outputPtr->GetLargestPossibleRegion().GetSize();
//define some temp variables
overlap *= 1.0 - distance[dim];
}
upper >>= 1;
-
+
if (neighIndex[dim] >= size[dim])
neighIndex[dim] = size[dim] - 1;
}
//the actual processing
-#if ITK_VERSION_MAJOR >= 4
void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
-#endif
//member data
typename WeightsImageType::Pointer m_Weights;
//Empty constructor
template<class InputImageType, class OutputImageType > HelperClass2<InputImageType, OutputImageType>::HelperClass2()
{
- m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero;
+ PixelType zero;
+ for(unsigned int i=0;i <PixelType::Dimension; i++) zero[i] = 0.0;
+ m_EdgePaddingValue=zero;
+ //m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero;
}
//=========================================================================================================================
//update the output for the outputRegionForThread
-#if ITK_VERSION_MAJOR >= 4
template<class InputImageType, class OutputImageType > void HelperClass2<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, itk::ThreadIdType threadId )
-#else
-template<class InputImageType, class OutputImageType > void HelperClass2<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId )
-#endif
{
// std::cout << "HelperClass2::ThreadedGenerateData - IN " << threadId << std::endl;
-
+
//Get pointer to the input
typename InputImageType::ConstPointer inputPtr = this->GetInput();
++inputIt;
}//end while
-
+
// std::cout << "HelperClass2::ThreadedGenerateData - OUT " << threadId << std::endl;
-
+
}//end member
template <class InputImageType, class OutputImageType>
InvertVFFilter<InputImageType, OutputImageType>::InvertVFFilter()
{
- m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero; //no other reasonable value?
+
+ //m_EdgePaddingValue=itk::NumericTraits<PixelType>::Zero; //no other reasonable value?
+ PixelType zero;
+ for(unsigned int i=0;i <PixelType::Dimension; i++) zero[i] = 0.0;
+ m_EdgePaddingValue=zero; //no other reasonable value?
+
m_ThreadSafe=false;
m_Verbose=false;
}
//Set the output
this->SetNthOutput(0, helper2->GetOutput());
-
+
//std::cout << "InvertVFFilter::GenerateData - OUT" << std::endl;
}
#include <vtkLinearExtrusionFilter.h>
#include <vtkImageStencil.h>
#include <vtkMetaImageWriter.h>
+#include <vtkVersion.h>
#include "itkVTKImageImport.h"
#include "vtkImageExport.h"
{
// GO
vtkSmartPointer<vtkImageData> binary_image=vtkSmartPointer<vtkImageData>::New();
+#if VTK_MAJOR_VERSION <= 5
binary_image->SetScalarTypeToUnsignedChar();
// Set spacing
// Allocate data
binary_image->AllocateScalars();
+#else
+ // Set spacing
+ PointType samp_origin = m_LikeImage->GetOrigin();
+ SpacingType spacing=m_LikeImage->GetSpacing();
+ double * spacing2 = new double[3];
+ spacing2[0] = spacing[0];
+ spacing2[1] = spacing[1];
+ spacing2[2] = spacing[2];
+ binary_image->SetSpacing(spacing2);
+
+ // Set origin
+ /// Put the origin on a voxel to avoid small skips
+ binary_image->SetOrigin(samp_origin[0], samp_origin[1], samp_origin[2]);
+
+ // Compute image bounds
+ binary_image->SetExtent(0,m_LikeImage->GetLargestPossibleRegion().GetSize()[0],
+ 0,m_LikeImage->GetLargestPossibleRegion().GetSize()[1],
+ 0,m_LikeImage->GetLargestPossibleRegion().GetSize()[2]
+ );
+
+ // Allocate data
+ binary_image->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+#endif
memset(binary_image->GetScalarPointer(),0,
binary_image->GetDimensions()[0]*binary_image->GetDimensions()[1]*binary_image->GetDimensions()[2]*sizeof(unsigned char));
if (m_Extrude)
{
vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
+#if VTK_MAJOR_VERSION <= 5
extrude->SetInput(m_Mesh);
+#else
+ extrude->SetInputData(m_Mesh);
+#endif
// We extrude in the -slice_spacing direction to respect the FOCAL convention
extrude->SetVector(0, 0, -m_LikeImage->GetSpacing()[2]);
+#if VTK_MAJOR_VERSION <= 5
sts->SetInput(extrude->GetOutput());
+#else
+ sts->SetInputConnection(extrude->GetOutputPort());
+#endif
// When extrude ScaleFactor indicate the extrusion scaling (default = 1)
/*
*/
}
else
+#if VTK_MAJOR_VERSION <= 5
sts->SetInput(m_Mesh);
+#else
+ sts->SetInputData(m_Mesh);
+#endif
// Stencil
vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
+#if VTK_MAJOR_VERSION <= 5
stencil->SetStencil(sts->GetOutput());
stencil->SetInput(binary_image);
+#else
+ stencil->SetStencilData(sts->GetOutput());
+ stencil->SetInputData(binary_image);
+#endif
// Convert VTK to ITK
vtkImageExport * m_Exporter = vtkImageExport::New();
m_Importer->SetBufferPointerCallback( m_Exporter->GetBufferPointerCallback());
m_Importer->SetCallbackUserData( m_Exporter->GetCallbackUserData());
+#if VTK_MAJOR_VERSION <= 5
m_Exporter->SetInput( stencil->GetOutput() );
+#else
+ m_Exporter->SetInputData( stencil->GetOutput() );
+#endif
m_Importer->Update();
// writeImage<ImageType>(m_Importer->GetOutput(), "f.mhd");
#include "itkConnectedComponentImageFilter.h"
#include "itkStatisticsImageFilter.h"
#include "itkCastImageFilter.h"
-#if ITK_VERSION_MAJOR >= 4
- #include "itkTestingComparisonImageFilter.h"
-#else
- #include "itkDifferenceImageFilter.h"
-#endif
+#include "itkTestingComparisonImageFilter.h"
#include "itkThresholdImageFilter.h"
namespace clitk
typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
typedef itk::BinaryBallStructuringElement<InternalPixelType,InputImageDimension > KernelType;
typedef clitk::ConditionalBinaryDilateImageFilter<InternalImageType, InternalImageType , KernelType> ConditionalBinaryDilateImageFilterType;
-#if ITK_VERSION_MAJOR >= 4
typedef itk::Testing::ComparisonImageFilter<InternalImageType, InternalImageType> DifferenceImageFilterType;
-#else
- typedef itk::DifferenceImageFilter<InternalImageType, InternalImageType> DifferenceImageFilterType;
-#endif
typedef itk::CastImageFilter<InternalImageType, OutputImageType> OutputCastImageFilterType;
typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> SetBackgroundImageFilterType;
typedef typename OutputImageType::PixelType OutputImagePixelType;
typedef typename OutputImageType::SpacingType OutputImageSpacingType;
typedef typename OutputImageType::SizeType OutputImageSizeType;
+ typedef typename OutputImageType::PointType OutputImageOriginType;
+ typedef typename OutputImageType::DirectionType OutputImageDirectionType;
typedef itk::AffineTransform<double, InputImageType::ImageDimension> TransformType;
typedef typename InputImageType::SpacingType GaussianSigmaType;
itkGetMacro(OutputSpacing, OutputImageSpacingType);
itkSetMacro(OutputSize, OutputImageSizeType);
itkGetMacro(OutputSize, OutputImageSizeType);
+ itkSetMacro(OutputOrigin, OutputImageOriginType);
+ itkGetMacro(OutputOrigin, OutputImageOriginType);
+ itkSetMacro(OutputDirection, OutputImageDirectionType);
+ itkGetMacro(OutputDirection, OutputImageDirectionType);
itkGetMacro(InterpolationType, InterpolationTypeEnumeration);
itkSetMacro(InterpolationType, InterpolationTypeEnumeration);
itkGetMacro(GaussianFilteringEnabled, bool);
int m_BSplineOrder;
int m_BLUTSamplingFactor;
OutputImageSizeType m_OutputSize;
- OutputImageSpacingType m_OutputSpacing;
+ OutputImageSpacingType m_OutputSpacing;
+ OutputImageOriginType m_OutputOrigin;
+ OutputImageDirectionType m_OutputDirection;
typename TransformType::Pointer m_Transform;
GaussianSigmaType m_GaussianSigma;
OutputImagePixelType m_DefaultPixelValue;
//--------------------------------------------------------------------
template <class InputImageType, class OutputImageType>
clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputImageType>()
+ResampleImageWithOptionsFilter():itk::ImageToImageFilter<InputImageType, OutputImageType>()
{
static const unsigned int dim = InputImageType::ImageDimension;
this->SetNumberOfRequiredInputs(1);
m_OutputSpacing[i] = -1;
m_GaussianSigma[i] = -1;
}
+ m_OutputOrigin.Fill(0);
+ m_OutputDirection.SetIdentity();
m_VerboseOptions = false;
SetDefaultPixelValue(0);
}
template <class InputImageType, class OutputImageType>
void
clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-SetInput(const InputImageType * image)
+SetInput(const InputImageType * image)
{
// Process object is not const-correct so the const casting is required.
this->SetNthInput(0, const_cast<InputImageType *>(image));
template <class InputImageType, class OutputImageType>
void
clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-GenerateInputRequestedRegion()
+GenerateInputRequestedRegion()
{
// call the superclass's implementation of this method
Superclass::GenerateInputRequestedRegion();
template <class InputImageType, class OutputImageType>
void
clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-GenerateOutputInformation()
+GenerateOutputInformation()
{
static const unsigned int dim = InputImageType::ImageDimension;
if (m_OutputIsoSpacing != -1) { // apply isoSpacing
for(unsigned int i=0; i<dim; i++) {
m_OutputSpacing[i] = m_OutputIsoSpacing;
- // floor() is used to intentionally reduce the number of slices
- // because, from a clinical point of view, it's better to
+ // floor() is used to intentionally reduce the number of slices
+ // because, from a clinical point of view, it's better to
// remove data than to add data that privously didn't exist.
if(inputSpacing[i]*m_OutputSpacing[i]<0)
itkExceptionMacro( << "Input and output spacings don't have the same signs, can't cope with that" );
m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
}
- } else {
+ }
+ else if(m_OutputSpacing[0]==-1 || m_OutputSize[0]==0){
if (m_OutputSpacing[0] != -1) { // apply spacing, compute size
for(unsigned int i=0; i<dim; i++) {
- if(inputSpacing[i]*m_OutputSpacing[i]<0)
+ if(inputSpacing[i]*m_OutputSpacing[i]<0) {
itkExceptionMacro( << "Input and output spacings don't have the same signs, can't cope with that" );
- // see comment above for the use of floor()
- m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
+ }
+ // see comment above for the use of floor()
+ m_OutputSize[i] = (int)floor(inputSize[i]*inputSpacing[i]/m_OutputSpacing[i]);
}
- } else {
+ }
+ else {
if (m_OutputSize[0] != 0) { // apply size, compute spacing
for(unsigned int i=0; i<dim; i++) {
m_OutputSpacing[i] = (double)inputSize[i]*inputSpacing[i]/(double)m_OutputSize[i];
}
- } else { // copy input size/spacing ... (no resampling)
+ }
+ else { // copy input size/spacing ... (no resampling)
m_OutputSize = inputSize;
m_OutputSpacing = inputSpacing;
}
//--------------------------------------------------------------------
template <class InputImageType, class OutputImageType>
-void
+void
clitk::ResampleImageWithOptionsFilter<InputImageType, OutputImageType>::
-GenerateData()
+GenerateData()
{
-
+
// Get input pointer
InputImagePointer input = dynamic_cast<InputImageType*>(itk::ProcessObject::GetInput(0));
static const unsigned int dim = InputImageType::ImageDimension;
}
// Compute origin based on image corner
- typename FilterType::OriginPointType origin = input->GetOrigin();
for(unsigned int i=0; i<OutputImageType::ImageDimension; i++) {
- origin[i] -= 0.5 * input->GetSpacing()[i];
- origin[i] += 0.5 * m_OutputSpacing[i];
+ m_OutputOrigin[i] -= 0.5 * input->GetSpacing()[i];
+ m_OutputOrigin[i] += 0.5 * m_OutputSpacing[i];
}
// Instance of the transform object to be passed to the resample
filter->SetTransform(m_Transform);
filter->SetSize(m_OutputSize);
filter->SetOutputSpacing(m_OutputSpacing);
- filter->SetOutputOrigin(origin);
+ filter->SetOutputOrigin(m_OutputOrigin);
filter->SetDefaultPixelValue(m_DefaultPixelValue);
- filter->SetNumberOfThreads(this->GetNumberOfThreads());
- filter->SetOutputDirection(input->GetDirection()); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
+ filter->SetNumberOfThreads(this->GetNumberOfThreads());
+ filter->SetOutputDirection(m_OutputDirection); // <-- NEEDED if we want to keep orientation (in case of PermutAxes for example)
// Select interpolator
switch (m_InterpolationType) {
filter->Update();
// Set output
- // DD("before Graft");
-
- //this->GraftOutput(filter->GetOutput());
- this->SetNthOutput(0, filter->GetOutput());
-
- // DD("after Graft");
+ this->GraftOutput(filter->GetOutput());
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class InputImageType>
-typename InputImageType::Pointer
-clitk::ResampleImageSpacing(typename InputImageType::Pointer input,
- typename InputImageType::SpacingType spacing,
+typename InputImageType::Pointer
+clitk::ResampleImageSpacing(typename InputImageType::Pointer input,
+ typename InputImageType::SpacingType spacing,
int interpolationType)
{
typedef clitk::ResampleImageWithOptionsFilter<InputImageType> ResampleFilterType;
InputIterator inIt( this->GetInput(), this->GetInput()->GetBufferedRegion() );
OutputIterator outIt( this->GetOutput(), this->GetOutput()->GetBufferedRegion() );
- inIt = inIt.Begin();
- outIt = outIt.Begin();
+ inIt.GoToBegin();
+ outIt.GoToBegin();
OutputPixelType v;
while ( !outIt.IsAtEnd() ) {
for (unsigned int i=0; i< VectorDimension; i++) {
*
* \sa ImageToImageFilter::ThreadedGenerateData(),
* ImageToImageFilter::GenerateData() */
-#if ITK_VERSION_MAJOR >= 4
void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
- int threadId );
-#endif
private:
FlexibleBinaryFunctorImageFilter(const Self&); //purposely not implemented
template <class TInputImage1, class TInputImage2, class TOutputImage, class TFunction >
void
FlexibleBinaryFunctorImageFilter<TInputImage1, TInputImage2, TOutputImage, TFunction>
-::ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread,
-#if ITK_VERSION_MAJOR >= 4
- itk::ThreadIdType threadId )
-#else
- int threadId)
-#endif
+::ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId )
{
const unsigned int dim = Input1ImageType::ImageDimension;
VTKImageToImageFilter<TOutputImage>
::SetInput( vtkImageData * inputImage )
{
+#if VTK_MAJOR_VERSION <= 5
m_Exporter->SetInput( inputImage );
+#else
+ m_Exporter->SetInputData( inputImage );
+#endif
}
cp $i ${i/FooImage/$1}
if test "$(uname)" = "Darwin"
then
- sed -i "" "s/FooImage/$1/ig" ${i/FooImage/$1}
+ echo $(pwd)
+ echo sed -i "" "s/FooImage/$1/g" ${i/FooImage/$1}
+ sed -i "" "s/FooImage/$1/g" ${i/FooImage/$1}
else
sed -i "s/FooImage/$1/ig" ${i/FooImage/$1}
fi
# Add Libraries used in vv and clitk to avoid recompilation
WRAP_GGO(clitkAffineRegistration_GGO_C clitkAffineRegistration.ggo)
-ADD_LIBRARY(clitkAffineRegistrationLib
+add_library(clitkAffineRegistrationLib
clitkAffineRegistrationGenericFilter.cxx
${clitkAffineRegistration_GGO_C}
clitkLBFGSBOptimizer.cxx
#=========================================================
-IF(CLITK_BUILD_REGISTRATION)
+if(CLITK_BUILD_REGISTRATION)
############################## registration algorithms
- ADD_EXECUTABLE(clitkAffineRegistration clitkAffineRegistration.cxx)
- TARGET_LINK_LIBRARIES(clitkAffineRegistration clitkAffineRegistrationLib clitkCommon)
- SET(REGISTRATION_INSTALL clitkAffineRegistration)
+ add_executable(clitkAffineRegistration clitkAffineRegistration.cxx)
+ target_link_libraries(clitkAffineRegistration clitkAffineRegistrationLib clitkCommon)
+ set(REGISTRATION_INSTALL clitkAffineRegistration)
WRAP_GGO(clitkDemonsDeformableRegistration_GGO_C clitkDemonsDeformableRegistration.ggo)
- ADD_EXECUTABLE(clitkDemonsDeformableRegistration clitkDemonsDeformableRegistration.cxx ${clitkDemonsDeformableRegistration_GGO_C} clitkDemonsDeformableRegistrationGenericFilter.cxx)
- TARGET_LINK_LIBRARIES(clitkDemonsDeformableRegistration clitkCommon)
- SET(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkDemonsDeformableRegistration)
+ add_executable(clitkDemonsDeformableRegistration clitkDemonsDeformableRegistration.cxx ${clitkDemonsDeformableRegistration_GGO_C} clitkDemonsDeformableRegistrationGenericFilter.cxx)
+ target_link_libraries(clitkDemonsDeformableRegistration clitkCommon)
+ set(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkDemonsDeformableRegistration)
WRAP_GGO(clitkBLUTDIR_GGO_C clitkBLUTDIR.ggo)
- ADD_EXECUTABLE(clitkBLUTDIR clitkBLUTDIR.cxx clitkBLUTDIRGenericFilter.cxx ${clitkBLUTDIR_GGO_C} clitkLBFGSBOptimizer.cxx )
- TARGET_LINK_LIBRARIES(clitkBLUTDIR clitkCommon)
- SET(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkBLUTDIR)
+ add_executable(clitkBLUTDIR clitkBLUTDIR.cxx clitkBLUTDIRGenericFilter.cxx ${clitkBLUTDIR_GGO_C} clitkLBFGSBOptimizer.cxx )
+ target_link_libraries(clitkBLUTDIR clitkCommon)
+ set(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkBLUTDIR)
############################## registration-related tools to process points, bsplines, vf and image pyramids
WRAP_GGO(clitkCalculateTRE_GGO_C clitkCalculateTRE.ggo)
- ADD_EXECUTABLE(clitkCalculateTRE clitkCalculateTRE.cxx clitkCalculateTREGenericFilter.cxx ${clitkCalculateTRE_GGO_C})
- TARGET_LINK_LIBRARIES(clitkCalculateTRE clitkCommon)
- SET(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkCalculateTRE)
+ add_executable(clitkCalculateTRE clitkCalculateTRE.cxx clitkCalculateTREGenericFilter.cxx ${clitkCalculateTRE_GGO_C})
+ target_link_libraries(clitkCalculateTRE clitkCommon)
+ set(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkCalculateTRE)
WRAP_GGO(clitkMatrixTransformToVF_GGO_C clitkMatrixTransformToVF.ggo)
- ADD_EXECUTABLE(clitkMatrixTransformToVF clitkMatrixTransformToVF.cxx clitkMatrixTransformToVFGenericFilter.cxx ${clitkMatrixTransformToVF_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMatrixTransformToVF clitkCommon)
- SET(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkMatrixTransformToVF)
+ add_executable(clitkMatrixTransformToVF clitkMatrixTransformToVF.cxx clitkMatrixTransformToVFGenericFilter.cxx ${clitkMatrixTransformToVF_GGO_C})
+ target_link_libraries(clitkMatrixTransformToVF clitkCommon)
+ set(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkMatrixTransformToVF)
WRAP_GGO(clitkConvertBSplineDeformableTransformToVF_GGO_C clitkConvertBSplineDeformableTransformToVF.ggo)
- ADD_EXECUTABLE(clitkConvertBSplineDeformableTransformToVF clitkConvertBSplineDeformableTransformToVF.cxx clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx ${clitkConvertBSplineDeformableTransformToVF_GGO_C})
- TARGET_LINK_LIBRARIES(clitkConvertBSplineDeformableTransformToVF clitkCommon)
- SET(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkConvertBSplineDeformableTransformToVF)
+ add_executable(clitkConvertBSplineDeformableTransformToVF clitkConvertBSplineDeformableTransformToVF.cxx clitkConvertBSplineDeformableTransformToVFGenericFilter.cxx ${clitkConvertBSplineDeformableTransformToVF_GGO_C})
+ target_link_libraries(clitkConvertBSplineDeformableTransformToVF clitkCommon)
+ set(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkConvertBSplineDeformableTransformToVF)
- INSTALL (TARGETS ${REGISTRATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
+ install(TARGETS ${REGISTRATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
-ENDIF(CLITK_BUILD_REGISTRATION)
+endif(CLITK_BUILD_REGISTRATION)
typedef typename InputImageType::PixelType PixelType;
//typedef typename InputImageType::ImageDimension Dimension;
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
bool threadsGiven=m_ArgsInfo.threads_given;
int threads=m_ArgsInfo.threads_arg;
-#endif
//Coordinate Representation
typedef double TCoordRep;
typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
if (movingMask) metric->SetMovingImageMask(movingMask);
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
if (threadsGiven) metric->SetNumberOfThreads( threads );
-#else
- if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
-#endif
//============================================================================
// Initialize using image moments.
if (m_Verbose) std::cout << "Starting the registration now..." << std::endl;
try {
-#if ITK_VERSION_MAJOR < 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR <= 2)
- registration->StartRegistration();
-#else
registration->Update();
-#endif
} catch ( itk::ExceptionObject & err ) {
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
#include "clitkBLUTDIRGenericFilter.h"
#include "clitkBLUTDIRCommandIterationUpdateDVF.h"
#include "itkCenteredTransformInitializer.h"
-
+#if ITK_VERSION_MAJOR >= 4
+# if ITK_VERSION_MINOR < 6
+# include "itkTransformToDisplacementFieldSource.h"
+# else
+# include "itkTransformToDisplacementFieldFilter.h"
+# endif
+#else
+# include "itkTransformToDeformationFieldSource.h"
+#endif
+
namespace clitk
{
// Crop the fixedImage to the bounding box to facilitate multi-resolution
typedef itk::ExtractImageFilter<FixedImageType,FixedImageType> ExtractImageFilterType;
typename ExtractImageFilterType::Pointer extractImageFilter=ExtractImageFilterType::New();
-#if ITK_VERSION_MAJOR == 4
extractImageFilter->SetDirectionCollapseToSubmatrix();
-#endif
extractImageFilter->SetInput(fixedImage);
extractImageFilter->SetExtractionRegion(transformRegion);
extractImageFilter->Update();
typedef itk::ImageToImageMetric< FixedImageType, MovingImageType > MetricType;
typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
if (movingMask) metric->SetMovingImageMask(movingMask);
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
if (threadsGiven) {
metric->SetNumberOfThreads( threads );
if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
}
-#else
- if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
-#endif
-
//=======================================================
// Optimizer
try
{
-#if ITK_VERSION_MAJOR < 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR <= 2)
- registration->StartRegistration();
-#else
registration->Update();
-#endif
}
catch( itk::ExceptionObject & err )
{
typedef itk::Vector< float, SpaceDimension > DisplacementType;
typedef itk::Image< DisplacementType, InputImageType::ImageDimension > DisplacementFieldType;
#if ITK_VERSION_MAJOR >= 4
+# if ITK_VERSION_MINOR < 6
typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
-#else
- typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
+# else
+ typedef itk::TransformToDisplacementFieldFilter<DisplacementFieldType, double> ConvertorType;
+# endif
#endif
typename ConvertorType::Pointer filter= ConvertorType::New();
filter->SetNumberOfThreads(1);
else
transform->SetBulkTransform(NULL);
filter->SetTransform(regTransform);
+#if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 6)
+ filter->SetReferenceImage(fixedImage);
+#else
filter->SetOutputParametersFromImage(fixedImage);
+#endif
filter->Update();
typename DisplacementFieldType::Pointer field = filter->GetOutput();
#include "itkLabelGeometryImageFilter.h"
#include "itkImageDuplicator.h"
#include "itkExtractImageFilter.h"
-#if ITK_VERSION_MAJOR >= 4
- #include "itkTransformToDisplacementFieldSource.h"
-#else
- #include "itkTransformToDeformationFieldSource.h"
-#endif
namespace clitk
{
/** Standard parameters container. */
typedef typename Superclass::ParametersType ParametersType;
-#if ITK_VERSION_MAJOR >= 4
typedef typename Superclass::NumberOfParametersType NumberOfParametersType;
-#endif
/** Standard Jacobian container. */
typedef typename Superclass::JacobianType JacobianType;
}
/** Compute the Jacobian Matrix of the transformation at one point */
-#if ITK_VERSION_MAJOR >= 4
virtual void ComputeJacobianWithRespectToParameters (const InputPointType &p, JacobianType &jacobian) const;
virtual void ComputeJacobianWithRespectToPosition (const InputPointType &p, JacobianType &jacobian) const
{
itkExceptionMacro( "ComputeJacobianWithRespectToPosition not yet implemented for " << this->GetNameOfClass() );
}
-#else
- virtual const JacobianType& GetJacobian(const InputPointType &point ) const;
-#endif
/** Return the number of parameters that completely define the Transfom */
-#if ITK_VERSION_MAJOR >= 4
virtual NumberOfParametersType GetNumberOfParameters(void) const;
-#else
- virtual unsigned int GetNumberOfParameters(void) const;
-#endif
/** Return the number of parameters per dimension */
unsigned int GetNumberOfParametersPerDimension(void) const;
// VD Add MultipleBSplineDeformableTransform as friend to facilitate wrapping
friend class MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>;
-#if ITK_VERSION_MAJOR >= 4
mutable JacobianType m_SharedDataBSplineJacobian;
-#endif
-
}; //class BSplineDeformableTransform
} // namespace itk
-#if ITK_TEMPLATE_TXX
+#ifndef ITK_MANUAL_INSTANTIATION
# include "clitkBSplineDeformableTransform.txx"
#endif
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
#ifndef __clitkBSplineDeformableTransform_txx
-#define __clitkBSplineDeformableTransform_tx
+#define __clitkBSplineDeformableTransform_txx
#include "clitkBSplineDeformableTransform.h"
//itk
// Constructor with default arguments
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
- BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
- ::BSplineDeformableTransform():Superclass(0)
-#else
- ::BSplineDeformableTransform():Superclass(OutputDimension,0)
-#endif
+ BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::BSplineDeformableTransform():Superclass(0)
{
unsigned int i;
// Get the number of parameters
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
typename BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::NumberOfParametersType
-#else
- unsigned int
-#endif
BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
::GetNumberOfParameters(void) const
{
m_CoefficientImage = m_WrappedImage;
//JV Wrap jacobian into OutputDimension X Vectorial images
-#if ITK_VERSION_MAJOR >= 4
this->m_SharedDataBSplineJacobian.set_size( OutputDimension, this->GetNumberOfParameters() );
-#else
- this->m_Jacobian.set_size( OutputDimension, this->GetNumberOfParameters() );
-#endif
// Use memset to set the memory
-#if ITK_VERSION_MAJOR >= 4
JacobianPixelType * jacobianDataPointer = reinterpret_cast<JacobianPixelType *>(this->m_SharedDataBSplineJacobian.data_block());
-#else
- JacobianPixelType * jacobianDataPointer = reinterpret_cast<JacobianPixelType *>(this->m_Jacobian.data_block());
-#endif
+
memset(jacobianDataPointer, 0, OutputDimension*numberOfPixels*sizeof(JacobianPixelType));
m_LastJacobianIndex = m_ValidRegion.GetIndex();
m_NeedResetJacobian = false;
// JV weights are identical as for transformpoint, could be done simultaneously in metric!!!!
// Compute the Jacobian in one position
-#if ITK_VERSION_MAJOR >= 4
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
void
BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
jacobian = m_SharedDataBSplineJacobian;
}
-#else
- template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
- const
- typename BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
- ::JacobianType &
- BSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
- ::GetJacobian( const InputPointType & point ) const
- {
- // Can only compute Jacobian if parameters are set via
- // SetParameters or SetParametersByValue
- // if( m_InputParametersPointer == NULL )
- // {
- // itkExceptionMacro( <<"Cannot compute Jacobian: parameters not set" );
- // }
-
- if (m_NeedResetJacobian)
- ResetJacobian();
- //========================================================
- // For each dimension, copy the weight to the support region
- //========================================================
-
- // Check if inside mask
- if(m_Mask && !(m_Mask->IsInside(point) ) )
- {
- // Outside: no (deformable) displacement
- return this->m_Jacobian;
- }
-
- //Get index
- this->TransformPointToContinuousIndex( point, m_Index );
-
- // NOTE: if the support region does not lie totally within the grid
- // we assume zero displacement and return the input point
- if ( !this->InsideValidRegion( m_Index ) )
- {
- return this->m_Jacobian;
- }
-
- //Compute interpolation weights
- const WeightsDataType *weights=NULL;
- m_VectorInterpolator->EvaluateWeightsAtContinuousIndex( m_Index, &weights, m_LastJacobianIndex);
- m_SupportRegion.SetIndex( m_LastJacobianIndex );
-
- //Reset the iterators
- unsigned int j = 0;
- for ( j = 0; j < OutputDimension; j++ )
- m_Iterator[j] = IteratorType( m_JacobianImage[j], m_SupportRegion);
-
- // For each dimension, copy the weight to the support region
- while ( ! (m_Iterator[0]).IsAtEnd() )
- {
- //copy weight to jacobian image
- for ( j = 0; j < OutputDimension; j++ )
- {
- m_ZeroVector[j]=*weights;
- (m_Iterator[j]).Set( m_ZeroVector);
- m_ZeroVector[j]=itk::NumericTraits<JacobianValueType>::Zero;
- ++(m_Iterator[j]);
- }
- // go to next coefficient in the support region
- weights++;
- }
- m_NeedResetJacobian = true;
-
- // Return the result
- return this->m_Jacobian;
-
- }
-#endif
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
#include "clitkBSplineDeformableTransform.h"
#include "itkBSplineDeformableTransform.h"
#if ITK_VERSION_MAJOR >= 4
-#include "itkTransformToDisplacementFieldSource.h"
-#else
-#include "itkTransformToDeformationFieldSource.h"
+# if ITK_VERSION_MINOR < 6
+# include "itkTransformToDisplacementFieldSource.h"
+# else
+# include "itkTransformToDisplacementFieldFilter.h"
+# endif
#endif
namespace clitk
typedef itk::Transform< double, TDVFType::ImageDimension, TDVFType::ImageDimension> GenericTransformType;
#if ITK_VERSION_MAJOR >= 4
+# if ITK_VERSION_MINOR < 6
typedef itk::TransformToDisplacementFieldSource<OutputImageType, double> ConvertorType;
-#else
- typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
+# else
+ typedef itk::TransformToDisplacementFieldFilter<OutputImageType, double> ConvertorType;
+# endif
#endif
itkNewMacro(Self);
#include "clitkConvertBLUTCoeffsToVFFilter.txx"
-#endif // clitkConvertBLUTCoeffsToVFFilter_h
\ No newline at end of file
+#endif // clitkConvertBLUTCoeffsToVFFilter_h
//#include "clitkConvertBSplineDeformableTransformToVFGenericFilter.h"
#include "clitkVectorImageToImageFilter.h"
-#if ITK_VERSION_MAJOR >= 4
-#include "itkTransformToDisplacementFieldSource.h"
-#else
-#include "itkTransformToDeformationFieldSource.h"
-#endif
#include "itkBSplineDeformableTransform.h"
namespace clitk
typedef clitk::VectorImageToImageFilter<BLUTCoefficientImageType, typename ITKTransformType::ImageType> FilterType;
typename FilterType::Pointer component_filter[BLUTCoefficientImageType::ImageDimension];
-
-#if ITK_VERSION_MAJOR >= 4
typename ITKTransformType::CoefficientImageArray coefficient_images;
-#else
- typename ITKTransformType::ImagePointer coefficient_images[BLUTCoefficientImageType::ImageDimension];
-#endif
for (unsigned int i=0; i < BLUTCoefficientImageType::ImageDimension; i++) {
component_filter[i] = FilterType::New();
coefficient_images[i] = component_filter[i]->GetOutput();
}
-#if ITK_VERSION_MAJOR >= 4
// RP: 16/01/2013
// ATTENTION: Apparently, there's a bug in the SetCoefficientImages function of ITK 4.x
// I needed to use SetParametersByValue instead.
m_ITKTransform->SetGridRegion(input->GetLargestPossibleRegion());
m_ITKTransform->SetGridSpacing(input->GetSpacing());
m_ITKTransform->SetParametersByValue(params);
-#else
- m_ITKTransform->SetCoefficientImage(coefficient_images);
-#endif
m_GenericTransform = m_ITKTransform;
}
+#if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 6)
+ m_Filter->SetReferenceImage(output);
+#else
m_Filter->SetOutputOrigin(output->GetOrigin());
m_Filter->SetOutputSpacing(output->GetSpacing());
m_Filter->SetOutputSize(output->GetLargestPossibleRegion().GetSize());
+#endif
m_Filter->SetTransform(m_GenericTransform);
m_Filter->Update();
if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint , jacobian);
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
-
const RealType fixedValue = ti.Value();
this->m_NumberOfPixelsCounted++;
if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
-
const RealType fixedValue = ti.Value();
this->m_NumberOfPixelsCounted++;
return OutputCovariantVectorType();
}
-#if ITK_VERSION_MAJOR >= 4
virtual void ComputeJacobianWithRespectToParameters (const InputPointType &p, JacobianType &jacobian) const
{
itkExceptionMacro( << "DeformationFieldTransform doesn't declare ComputeJacobianWithRespectToParameters" );
{
itkExceptionMacro( << "DeformationFieldTransform doesn't declare ComputeJacobianWithRespectToPosition" );
}
-#else
- virtual const JacobianType& GetJacobian(const InputPointType &point ) const
- {
- itkExceptionMacro( << "DeformationFieldTransform doesn't declare GetJacobian" );
- return this->m_Jacobian;
- }
-#endif
protected:
DeformationFieldTransform();
// Constructor
template<class TScalarType, unsigned int InputDimension, unsigned int OutputDimension, unsigned int SpaceDimension>
- DeformationFieldTransform<TScalarType, InputDimension, OutputDimension, SpaceDimension>
-#if ITK_VERSION_MAJOR >= 4
- ::DeformationFieldTransform():Superclass(1)
-#else
- ::DeformationFieldTransform():Superclass(OutputDimension,1)
-#endif
+ DeformationFieldTransform<TScalarType, InputDimension, OutputDimension, SpaceDimension>::DeformationFieldTransform():Superclass(1)
+
{
m_DeformationField=NULL;
m_Interpolator=DefaultInterpolatorType::New();
//find the multiresolution filter
// typedef typename RegistrationFilterType::FixedImageType InternalImageType;
// typedef typename RegistrationFilterType::MovingImageType MovingImageType;
-#if ITK_VERSION_MAJOR >= 4
typedef typename RegistrationFilterType::DisplacementFieldType DisplacementFieldType;
-#else
- typedef typename RegistrationFilterType::DeformationFieldType DisplacementFieldType;
-#endif
typedef clitk::MultiResolutionPDEDeformableRegistration<FixedImageType, MovingImageType, DisplacementFieldType> MultiResolutionRegistrationType;
typedef CommandResolutionLevelUpdate<MultiResolutionRegistrationType> LevelObserver;
//JV TODO
// pdeFilter->SetMaximumError(m_ArgsInfo.maxError_arg);
// pdeFilter->SetMaximumKernelWidth(m_ArgsInfo.maxError_arg);
-#if ITK_VERSION_MAJOR >= 4
pdeFilter->SetSmoothDisplacementField(!m_ArgsInfo.fluid_flag);
-#else
- pdeFilter->SetSmoothDeformationField(!m_ArgsInfo.fluid_flag);
-#endif
pdeFilter->SetSmoothUpdateField(m_ArgsInfo.fluid_flag);
pdeFilter->SetUseImageSpacing( m_ArgsInfo.spacing_flag );
typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType > WarpFilterType;
typename WarpFilterType::Pointer warp = WarpFilterType::New();
-#if ITK_VERSION_MAJOR >= 4
warp->SetDisplacementField( deformationField );
-#else
- warp->SetDeformationField( deformationField );
-#endif
warp->SetInput( movingImageReader->GetOutput() );
warp->SetOutputOrigin( fixedImage->GetOrigin() );
warp->SetOutputSpacing( fixedImage->GetSpacing() );
typename FixedImageType::Pointer m_FixedImage;
typename FixedImageMaskType::ConstPointer m_FixedImageMask;
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
FixedImagePixelType m_FixedImageSamplesIntensityThreshold;
bool m_UseFixedImageSamplesIntensityThreshold;
-#endif
-
};
} // end namespace clitk
m_Maximize=false;
m_Verbose=false;
m_FixedImageRegionGiven=false;
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
m_FixedImageSamplesIntensityThreshold=0;
m_UseFixedImageSamplesIntensityThreshold=false;
-#endif
m_FixedImageMask=NULL;
}
m_Metric->SetFixedImageRegion(m_FixedImageRegion);
//m_Metric->SetFixedImageRegion(mask_region);
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
-
//============================================================================
// Set the lower intensity threshold
if (m_ArgsInfo.intThreshold_given) {
if (m_Verbose) std::cout<<"number of mask pixels "<<totalNumberOfMaskPixels<<std::endl;
}
-
-#else
- if (m_Verbose) std::cout<<"Not setting the fixed image intensity threshold or the fraction of samples to use (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
-
-
-#endif
//============================================================================
//return the pointer
return m_Metric;
bool m_OptimizerInitialized;
InternalOptimizerType * m_VnlOptimizer;
-#if ITK_VERSION_MAJOR > 3
mutable std::ostringstream m_StopConditionDescription;
-#else
- mutable itk::OStringStream m_StopConditionDescription;
-#endif
BoundValueType m_LowerBound;
BoundValueType m_UpperBound;
BoundSelectionType m_BoundSelection;
//itk include
#include "itkLightObject.h"
#if ITK_VERSION_MAJOR >= 4
- #include "itkTransformToDisplacementFieldSource.h"
-#else
- #include "itkTransformToDeformationFieldSource.h"
+# if ITK_VERSION_MINOR < 6
+# include "itkTransformToDisplacementFieldSource.h"
+# else
+# include "itkTransformToDisplacementFieldFilter.h"
+# endif
#endif
#include "itkAffineTransform.h"
// Filter
#if ITK_VERSION_MAJOR >= 4
+# if ITK_VERSION_MINOR < 6
typedef itk::TransformToDisplacementFieldSource<OutputImageType, double> ConvertorType;
-#else
- typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
+# else
+ typedef itk::TransformToDisplacementFieldFilter<OutputImageType, double> ConvertorType;
+# endif
#endif
+
typename ConvertorType::Pointer filter= ConvertorType::New();
// Output image info
reader2->Update();
typename OutputImageType::Pointer image=reader2->GetOutput();
- filter->SetOutputParametersFromImage(image);
+#if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 6)
+ filter->SetReferenceImage(image);
+ filter->UseReferenceImageOn();
+#else
+ filter->SetOutputParametersFromImage(image);
+#endif
}
else
{
typename OutputImageType::SizeType size;
for(i=0;i<Dimension;i++)
size[i]=m_ArgsInfo.size_arg[i];
- filter->SetOutputSize(size);
- }
+#if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 6)
+ filter->SetSize(size);
+#else
+ filter->SetOutputSize(size);
+#endif
+ }
}
// Transform
if( tempField.IsNull() )
{
-#if ITK_VERSION_MAJOR >= 4
m_RegistrationFilter->SetInitialDisplacementField( NULL );
-#else
- m_RegistrationFilter->SetInitialDeformationField( NULL );
-#endif
}
else
{
tempField = m_FieldExpander->GetOutput();
tempField->DisconnectPipeline();
-#if ITK_VERSION_MAJOR >= 4
m_RegistrationFilter->SetInitialDisplacementField( tempField );
-#else
- m_RegistrationFilter->SetInitialDeformationField( tempField );
-#endif
-
}
// setup registration filter and pyramids
/** Standard parameters container. */
typedef typename Superclass::ParametersType ParametersType;
-#if ITK_VERSION_MAJOR >= 4
typedef typename Superclass::NumberOfParametersType NumberOfParametersType;
-#endif
/** Standard Jacobian container. */
typedef typename Superclass::JacobianType JacobianType;
}
/** Compute the Jacobian Matrix of the transformation at one point */
-#if ITK_VERSION_MAJOR >= 4
virtual void ComputeJacobianWithRespectToParameters (const InputPointType &p, JacobianType &jacobian) const;
virtual void ComputeJacobianWithRespectToPosition (const InputPointType &p, JacobianType &jacobian) const
{
itkExceptionMacro( "ComputeJacobianWithRespectToPosition not yet implemented for " << this->GetNameOfClass() );
}
-#else
- virtual const JacobianType& GetJacobian(const InputPointType &point ) const;
-#endif
/** Return the number of parameters that completely define the Transfom */
-#if ITK_VERSION_MAJOR >= 4
virtual NumberOfParametersType GetNumberOfParameters(void) const;
-#else
- virtual unsigned int GetNumberOfParameters(void) const;
-#endif
/** Return the number of parameters per dimension */
unsigned int GetNumberOfParametersPerDimension(void) const;
std::vector<ParametersType> m_parameters;
mutable std::vector<CoefficientImagePointer> m_CoefficientImages;
mutable int m_LastJacobian;
-#if ITK_VERSION_MAJOR >= 4
mutable JacobianType m_SharedDataBSplineJacobian;
-#endif
void InitJacobian();
// FIXME it seems not used
} // namespace clitk
-#if ITK_TEMPLATE_TXX
+#ifndef ITK_MANUAL_INSTANTIATION
# include "clitkMultipleBSplineDeformableTransform.txx"
#endif
{
// Constructor with default arguments
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
- MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
- ::MultipleBSplineDeformableTransform() : Superclass(0)
-#else
- ::MultipleBSplineDeformableTransform() : Superclass(OutputDimension, 0)
-#endif
+ MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::MultipleBSplineDeformableTransform() : Superclass(0)
{
m_nLabels = 1;
m_labels = 0;
#undef LOOP_ON_LABELS
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
inline typename MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::NumberOfParametersType
-#else
- inline unsigned int
-#endif
MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
::GetNumberOfParameters(void) const
{
return m_trans[lidx]->DeformablyTransformPoint(inputPoint);
}
-#if ITK_VERSION_MAJOR >= 4
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
inline void
MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
jacobian = this->m_SharedDataBSplineJacobian;
}
-#else
- template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
- inline const typename MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::JacobianType &
- MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
- ::GetJacobian( const InputPointType & point ) const
- {
- if (m_LastJacobian != -1)
- m_trans[m_LastJacobian]->ResetJacobian();
-
- int lidx = 0;
- if (m_labels)
- lidx = m_labelInterpolator->Evaluate(point) - 1;
- if (lidx == -1)
- {
- m_LastJacobian = lidx;
- return this->m_Jacobian;
- }
-
- m_trans[lidx]->GetJacobian(point);
- m_LastJacobian = lidx;
-
- return this->m_Jacobian;
- }
-#endif
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
inline void
MultipleBSplineDeformableTransform<TCoordRep, NInputDimensions,NOutputDimensions>::InitJacobian()
{
unsigned numberOfParameters = this->GetNumberOfParameters();
-#if ITK_VERSION_MAJOR >= 4
this->m_SharedDataBSplineJacobian.set_size(OutputDimension, numberOfParameters);
JacobianPixelType * jacobianDataPointer = reinterpret_cast<JacobianPixelType *>(this->m_SharedDataBSplineJacobian.data_block());
-#else
- this->m_Jacobian.set_size(OutputDimension, numberOfParameters);
- JacobianPixelType * jacobianDataPointer = reinterpret_cast<JacobianPixelType *>(this->m_Jacobian.data_block());
-#endif
memset(jacobianDataPointer, 0, numberOfParameters * sizeof (JacobianPixelType));
unsigned tot = 0;
// This line can be removed once the optimized versions
// gets integrated into the main directories.
#include "itkConfigure.h"
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "clitkOptNormalizedCorrelationImageToImageMetric.h"
-#else
-
-#include "itkImageToImageMetric.h"
-#include "itkCovariantVector.h"
-#include "itkPoint.h"
-
-
-namespace clitk
-{
-
-template < class TFixedImage, class TMovingImage >
-class ITK_EXPORT NormalizedCorrelationImageToImageMetric :
- public itk::ImageToImageMetric< TFixedImage, TMovingImage>
-{
-public:
-
- /** Standard class typedefs. */
- typedef NormalizedCorrelationImageToImageMetric Self;
- typedef itk::ImageToImageMetric<TFixedImage, TMovingImage > Superclass;
-
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(NormalizedCorrelationImageToImageMetric, itk::Object);
-
-
- /** Types transferred from the base class */
- typedef typename Superclass::RealType RealType;
- typedef typename Superclass::TransformType TransformType;
- typedef typename Superclass::TransformPointer TransformPointer;
- typedef typename Superclass::TransformParametersType TransformParametersType;
- typedef typename Superclass::TransformJacobianType TransformJacobianType;
- typedef typename Superclass::GradientPixelType GradientPixelType;
- typedef typename Superclass::OutputPointType OutputPointType;
- typedef typename Superclass::InputPointType InputPointType;
-
- typedef typename Superclass::MeasureType MeasureType;
- typedef typename Superclass::DerivativeType DerivativeType;
- typedef typename Superclass::FixedImageType FixedImageType;
- typedef typename Superclass::MovingImageType MovingImageType;
- typedef typename Superclass::FixedImageConstPointer FixedImageConstPointer;
- typedef typename Superclass::MovingImageConstPointer MovingImageConstPointer;
-
-
- /** Get the derivatives of the match measure. */
- void GetDerivative( const TransformParametersType & parameters,
- DerivativeType & Derivative ) const;
-
- /** Get the value for single valued optimizers. */
- MeasureType GetValue( const TransformParametersType & parameters ) const;
-
- /** Get value and derivatives for multiple valued optimizers. */
- void GetValueAndDerivative( const TransformParametersType & parameters,
- MeasureType& Value, DerivativeType& Derivative ) const;
-
- /** Set/Get SubtractMean boolean. If true, the sample mean is subtracted
- * from the sample values in the cross-correlation formula and
- * typically results in narrower valleys in the cost fucntion.
- * Default value is false. */
- itkSetMacro( SubtractMean, bool );
- itkGetConstReferenceMacro( SubtractMean, bool );
- itkBooleanMacro( SubtractMean );
-
-protected:
- NormalizedCorrelationImageToImageMetric();
- virtual ~NormalizedCorrelationImageToImageMetric() {};
- void PrintSelf(std::ostream& os, itk::Indent indent) const;
-
-private:
- NormalizedCorrelationImageToImageMetric(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_SubtractMean;
-
-};
-
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkNormalizedCorrelationImageToImageMetric.txx"
-#endif
-
-#endif // opt
#endif // _clitkNormalizedCorrelationImageToImageMetric.txx
// gets integrated into the main directories.
#include "itkConfigure.h"
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "clitkOptNormalizedCorrelationImageToImageMetric.txx"
-#else
-
-
-#include "clitkNormalizedCorrelationImageToImageMetric.h"
-
-#include "itkImageRegionConstIteratorWithIndex.h"
-
-
-namespace clitk
-{
-
-/*
- * Constructor
- */
-template <class TFixedImage, class TMovingImage>
-NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
-::NormalizedCorrelationImageToImageMetric()
-{
- m_SubtractMean = false;
-}
-
-/*
- * Get the match Measure
- */
-template <class TFixedImage, class TMovingImage>
-typename NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>::MeasureType
-NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
-::GetValue( const TransformParametersType & parameters ) const
-{
-
- FixedImageConstPointer fixedImage = this->m_FixedImage;
-
- if( !fixedImage ) {
- itkExceptionMacro( << "Fixed image has not been assigned" );
- }
-
- typedef itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;
-
- FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );
-
- typename FixedImageType::IndexType index;
-
- MeasureType measure;
-
- this->m_NumberOfPixelsCounted = 0;
-
- this->SetTransformParameters( parameters );
-
- typedef typename itk::NumericTraits< MeasureType >::AccumulateType AccumulateType;
-
- AccumulateType sff = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType smm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sfm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sf = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sm = itk::NumericTraits< AccumulateType >::Zero;
-
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
- sff += fixedValue * fixedValue;
- smm += movingValue * movingValue;
- sfm += fixedValue * movingValue;
- if ( this->m_SubtractMean ) {
- sf += fixedValue;
- sm += movingValue;
- }
- this->m_NumberOfPixelsCounted++;
- }
-
- ++ti;
- }
-
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sff -= ( sf * sf / this->m_NumberOfPixelsCounted );
- smm -= ( sm * sm / this->m_NumberOfPixelsCounted );
- sfm -= ( sf * sm / this->m_NumberOfPixelsCounted );
- }
-
- const RealType denom = -1.0 * vcl_sqrt(sff * smm );
-
- if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) {
- measure = sfm / denom;
- } else {
- measure = itk::NumericTraits< MeasureType >::Zero;
- }
-
- return measure;
-
-}
-
-
-
-
-
-/*
- * Get the Derivative Measure
- */
-template < class TFixedImage, class TMovingImage>
-void
-NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
-::GetDerivative( const TransformParametersType & parameters,
- DerivativeType & derivative ) const
-{
-
- if( !this->GetGradientImage() ) {
- itkExceptionMacro(<<"The gradient image is null, maybe you forgot to call Initialize()");
- }
-
- FixedImageConstPointer fixedImage = this->m_FixedImage;
-
- if( !fixedImage ) {
- itkExceptionMacro( << "Fixed image has not been assigned" );
- }
-
- const unsigned int dimension = FixedImageType::ImageDimension;
-
- typedef itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;
-
- FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );
-
- typename FixedImageType::IndexType index;
-
- this->m_NumberOfPixelsCounted = 0;
-
- this->SetTransformParameters( parameters );
-
- typedef typename itk::NumericTraits< MeasureType >::AccumulateType AccumulateType;
-
- AccumulateType sff = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType smm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sfm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sf = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sm = itk::NumericTraits< AccumulateType >::Zero;
-
- const unsigned int ParametersDimension = this->GetNumberOfParameters();
- derivative = DerivativeType( ParametersDimension );
- derivative.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeF = DerivativeType( ParametersDimension );
- derivativeF.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeM = DerivativeType( ParametersDimension );
- derivativeM.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- ti.GoToBegin();
- // First compute the sums
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
- sff += fixedValue * fixedValue;
- smm += movingValue * movingValue;
- sfm += fixedValue * movingValue;
- if ( this->m_SubtractMean ) {
- sf += fixedValue;
- sm += movingValue;
- }
- this->m_NumberOfPixelsCounted++;
- }
-
- ++ti;
- }
-
- // Compute contributions to derivatives
- ti.GoToBegin();
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if ( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if ( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
-
-#if ITK_VERSION_MAJOR >= 4
- TransformJacobianType jacobian;
- this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
-
- // Get the gradient by NearestNeighboorInterpolation:
- // which is equivalent to round up the point components.
- typedef typename OutputPointType::CoordRepType CoordRepType;
- typedef itk::ContinuousIndex<CoordRepType,MovingImageType::ImageDimension>
- MovingImageContinuousIndexType;
-
- MovingImageContinuousIndexType tempIndex;
- this->m_MovingImage->TransformPhysicalPointToContinuousIndex( transformedPoint, tempIndex );
-
- typename MovingImageType::IndexType mappedIndex;
- mappedIndex.CopyWithRound( tempIndex );
-
- const GradientPixelType gradient =
- this->GetGradientImage()->GetPixel( mappedIndex );
-
- for(unsigned int par=0; par<ParametersDimension; par++) {
- RealType sumF = itk::NumericTraits< RealType >::Zero;
- RealType sumM = itk::NumericTraits< RealType >::Zero;
- for(unsigned int dim=0; dim<dimension; dim++) {
- const RealType differential = jacobian( dim, par ) * gradient[dim];
- sumF += fixedValue * differential;
- sumM += movingValue * differential;
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sumF -= differential * sf / this->m_NumberOfPixelsCounted;
- sumM -= differential * sm / this->m_NumberOfPixelsCounted;
- }
- }
- derivativeF[par] += sumF;
- derivativeM[par] += sumM;
- }
- }
-
- ++ti;
- }
-
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sff -= ( sf * sf / this->m_NumberOfPixelsCounted );
- smm -= ( sm * sm / this->m_NumberOfPixelsCounted );
- sfm -= ( sf * sm / this->m_NumberOfPixelsCounted );
- }
-
- const RealType denom = -1.0 * vcl_sqrt(sff * smm );
-
- if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = ( derivativeF[i] - (sfm/smm)* derivativeM[i] ) / denom;
- }
- } else {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = itk::NumericTraits< MeasureType >::Zero;
- }
- }
-
-}
-
-
-/*
- * Get both the match Measure and theDerivative Measure
- */
-template <class TFixedImage, class TMovingImage>
-void
-NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
-::GetValueAndDerivative(const TransformParametersType & parameters,
- MeasureType & value, DerivativeType & derivative) const
-{
-
-
- if( !this->GetGradientImage() ) {
- itkExceptionMacro(<<"The gradient image is null, maybe you forgot to call Initialize()");
- }
-
- FixedImageConstPointer fixedImage = this->m_FixedImage;
-
- if( !fixedImage ) {
- itkExceptionMacro( << "Fixed image has not been assigned" );
- }
-
- const unsigned int dimension = FixedImageType::ImageDimension;
-
- typedef itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;
-
- FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );
-
- typename FixedImageType::IndexType index;
-
- this->m_NumberOfPixelsCounted = 0;
-
- this->SetTransformParameters( parameters );
-
- typedef typename itk::NumericTraits< MeasureType >::AccumulateType AccumulateType;
-
- AccumulateType sff = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType smm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sfm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sf = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sm = itk::NumericTraits< AccumulateType >::Zero;
-
- const unsigned int ParametersDimension = this->GetNumberOfParameters();
- derivative = DerivativeType( ParametersDimension );
- derivative.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeF = DerivativeType( ParametersDimension );
- derivativeF.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeM = DerivativeType( ParametersDimension );
- derivativeM.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeM1 = DerivativeType( ParametersDimension );
- derivativeM1.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- ti.GoToBegin();
- // First compute the sums
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
- sff += fixedValue * fixedValue;
- smm += movingValue * movingValue;
- sfm += fixedValue * movingValue;
- if ( this->m_SubtractMean ) {
- sf += fixedValue;
- sm += movingValue;
- }
- this->m_NumberOfPixelsCounted++;
- }
-
- ++ti;
- }
-
-
- // Compute contributions to derivatives
- ti.GoToBegin();
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
-
-#if ITK_VERSION_MAJOR >= 4
- TransformJacobianType jacobian;
- this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
-
- // Get the gradient by NearestNeighboorInterpolation:
- // which is equivalent to round up the point components.
- typedef typename OutputPointType::CoordRepType CoordRepType;
- typedef itk::ContinuousIndex<CoordRepType,MovingImageType::ImageDimension>
- MovingImageContinuousIndexType;
-
- MovingImageContinuousIndexType tempIndex;
- this->m_MovingImage->TransformPhysicalPointToContinuousIndex( transformedPoint, tempIndex );
-
- typename MovingImageType::IndexType mappedIndex;
- mappedIndex.CopyWithRound( tempIndex );
-
- const GradientPixelType gradient =
- this->GetGradientImage()->GetPixel( mappedIndex );
-
- for(unsigned int par=0; par<ParametersDimension; par++) {
- RealType sumF = itk::NumericTraits< RealType >::Zero;
- RealType sumM = itk::NumericTraits< RealType >::Zero;
- for(unsigned int dim=0; dim<dimension; dim++) {
- const RealType differential = jacobian( dim, par ) * gradient[dim];
- sumF += fixedValue * differential;
- sumM += movingValue * differential;
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sumF -= differential * sf / this->m_NumberOfPixelsCounted;
- sumM -= differential * sm / this->m_NumberOfPixelsCounted;
- }
- }
- derivativeF[par] += sumF;
- derivativeM[par] += sumM;
- }
- }
- ++ti;
- }
-
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sff -= ( sf * sf / this->m_NumberOfPixelsCounted );
- smm -= ( sm * sm / this->m_NumberOfPixelsCounted );
- sfm -= ( sf * sm / this->m_NumberOfPixelsCounted );
- }
-
- const RealType denom = -1.0 * vcl_sqrt(sff * smm );
-
- if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = ( derivativeF[i] - (sfm/smm)* derivativeM[i] ) / denom;
- }
- value = sfm / denom;
- } else {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = itk::NumericTraits< MeasureType >::Zero;
- }
- value = itk::NumericTraits< MeasureType >::Zero;
- }
-
-
-
-}
-
-template < class TFixedImage, class TMovingImage>
-void
-NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
-::PrintSelf(std::ostream& os, itk::Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
- os << indent << "SubtractMean: " << m_SubtractMean << std::endl;
-}
-
-} // end namespace itk
-
-
-#endif // opt
-
#endif // _clitkNormalizedCorrelationImageToImageMetric.txx
// gets integrated into the main directories.
#include "itkConfigure.h"
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h"
-#else
-
-#include "itkImageToImageMetric.h"
-#include "itkCovariantVector.h"
-#include "itkPoint.h"
-
-
-namespace clitk
-{
-
-template < class TFixedImage, class TMovingImage >
-class ITK_EXPORT NormalizedCorrelationImageToImageMetricFor3DBLUTFFD :
- public itk::ImageToImageMetric< TFixedImage, TMovingImage>
-{
-public:
-
- /** Standard class typedefs. */
- typedef NormalizedCorrelationImageToImageMetricFor3DBLUTFFD Self;
- typedef itk::ImageToImageMetric<TFixedImage, TMovingImage > Superclass;
-
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(NormalizedCorrelationImageToImageMetricFor3DBLUTFFD, itk::Object);
-
-
- /** Types transferred from the base class */
- typedef typename Superclass::RealType RealType;
- typedef typename Superclass::TransformType TransformType;
- typedef typename Superclass::TransformPointer TransformPointer;
- typedef typename Superclass::TransformParametersType TransformParametersType;
- typedef typename Superclass::TransformJacobianType TransformJacobianType;
- typedef typename Superclass::GradientPixelType GradientPixelType;
- typedef typename Superclass::OutputPointType OutputPointType;
- typedef typename Superclass::InputPointType InputPointType;
-
- typedef typename Superclass::MeasureType MeasureType;
- typedef typename Superclass::DerivativeType DerivativeType;
- typedef typename Superclass::FixedImageType FixedImageType;
- typedef typename Superclass::MovingImageType MovingImageType;
- typedef typename Superclass::FixedImageConstPointer FixedImageConstPointer;
- typedef typename Superclass::MovingImageConstPointer MovingImageConstPointer;
-
-
- /** Get the derivatives of the match measure. */
- void GetDerivative( const TransformParametersType & parameters,
- DerivativeType & Derivative ) const;
-
- /** Get the value for single valued optimizers. */
- MeasureType GetValue( const TransformParametersType & parameters ) const;
-
- /** Get value and derivatives for multiple valued optimizers. */
- void GetValueAndDerivative( const TransformParametersType & parameters,
- MeasureType& Value, DerivativeType& Derivative ) const;
-
- /** Set/Get SubtractMean boolean. If true, the sample mean is subtracted
- * from the sample values in the cross-correlation formula and
- * typically results in narrower valleys in the cost fucntion.
- * Default value is false. */
- itkSetMacro( SubtractMean, bool );
- itkGetConstReferenceMacro( SubtractMean, bool );
- itkBooleanMacro( SubtractMean );
-
-protected:
- NormalizedCorrelationImageToImageMetricFor3DBLUTFFD();
- virtual ~NormalizedCorrelationImageToImageMetricFor3DBLUTFFD() {};
- void PrintSelf(std::ostream& os, itk::Indent indent) const;
-
-private:
- NormalizedCorrelationImageToImageMetricFor3DBLUTFFD(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_SubtractMean;
-
-};
-
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx"
-#endif
-
-#endif // opt
-
#endif // _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx
// This line can be removed once the optimized versions
// gets integrated into the main directories.
#include "itkConfigure.h"
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx"
-#else
-
-
-#include "clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h"
-
-#include "itkImageRegionConstIteratorWithIndex.h"
-
-
-namespace clitk
-{
-
-/*
- * Constructor
- */
-template <class TFixedImage, class TMovingImage>
-NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::NormalizedCorrelationImageToImageMetricFor3DBLUTFFD()
-{
- m_SubtractMean = false;
-}
-
-/*
- * Get the match Measure
- */
-template <class TFixedImage, class TMovingImage>
-typename NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>::MeasureType
-NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValue( const TransformParametersType & parameters ) const
-{
-
- FixedImageConstPointer fixedImage = this->m_FixedImage;
-
- if( !fixedImage ) {
- itkExceptionMacro( << "Fixed image has not been assigned" );
- }
-
- typedef itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;
-
- FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );
-
- typename FixedImageType::IndexType index;
-
- MeasureType measure;
-
- this->m_NumberOfPixelsCounted = 0;
-
- this->SetTransformParameters( parameters );
-
- typedef typename itk::NumericTraits< MeasureType >::AccumulateType AccumulateType;
-
- AccumulateType sff = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType smm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sfm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sf = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sm = itk::NumericTraits< AccumulateType >::Zero;
-
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
- sff += fixedValue * fixedValue;
- smm += movingValue * movingValue;
- sfm += fixedValue * movingValue;
- if ( this->m_SubtractMean ) {
- sf += fixedValue;
- sm += movingValue;
- }
- this->m_NumberOfPixelsCounted++;
- }
-
- ++ti;
- }
-
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sff -= ( sf * sf / this->m_NumberOfPixelsCounted );
- smm -= ( sm * sm / this->m_NumberOfPixelsCounted );
- sfm -= ( sf * sm / this->m_NumberOfPixelsCounted );
- }
-
- const RealType denom = -1.0 * vcl_sqrt(sff * smm );
-
- if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) {
- measure = sfm / denom;
- } else {
- measure = itk::NumericTraits< MeasureType >::Zero;
- }
-
- return measure;
-
-}
-
-
-
-
-
-/*
- * Get the Derivative Measure
- */
-template < class TFixedImage, class TMovingImage>
-void
-NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetDerivative( const TransformParametersType & parameters,
- DerivativeType & derivative ) const
-{
-
- if( !this->GetGradientImage() ) {
- itkExceptionMacro(<<"The gradient image is null, maybe you forgot to call Initialize()");
- }
-
- FixedImageConstPointer fixedImage = this->m_FixedImage;
-
- if( !fixedImage ) {
- itkExceptionMacro( << "Fixed image has not been assigned" );
- }
-
- const unsigned int dimension = FixedImageType::ImageDimension;
-
- typedef itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;
-
- FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );
-
- typename FixedImageType::IndexType index;
-
- this->m_NumberOfPixelsCounted = 0;
-
- this->SetTransformParameters( parameters );
-
- typedef typename itk::NumericTraits< MeasureType >::AccumulateType AccumulateType;
-
- AccumulateType sff = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType smm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sfm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sf = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sm = itk::NumericTraits< AccumulateType >::Zero;
-
- const unsigned int ParametersDimension = this->GetNumberOfParameters();
- derivative = DerivativeType( ParametersDimension );
- derivative.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeF = DerivativeType( ParametersDimension );
- derivativeF.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeM = DerivativeType( ParametersDimension );
- derivativeM.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- ti.GoToBegin();
- // First compute the sums
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
- sff += fixedValue * fixedValue;
- smm += movingValue * movingValue;
- sfm += fixedValue * movingValue;
- if ( this->m_SubtractMean ) {
- sf += fixedValue;
- sm += movingValue;
- }
- this->m_NumberOfPixelsCounted++;
- }
-
- ++ti;
- }
-
- // Compute contributions to derivatives
- ti.GoToBegin();
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if ( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if ( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
-
-#if ITK_VERSION_MAJOR >= 4
- TransformJacobianType jacobian;
- this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
-
- // Get the gradient by NearestNeighboorInterpolation:
- // which is equivalent to round up the point components.
- typedef typename OutputPointType::CoordRepType CoordRepType;
- typedef itk::ContinuousIndex<CoordRepType,MovingImageType::ImageDimension>
- MovingImageContinuousIndexType;
-
- MovingImageContinuousIndexType tempIndex;
- this->m_MovingImage->TransformPhysicalPointToContinuousIndex( transformedPoint, tempIndex );
-
- typename MovingImageType::IndexType mappedIndex;
- mappedIndex.CopyWithRound( tempIndex );
-
- const GradientPixelType gradient =
- this->GetGradientImage()->GetPixel( mappedIndex );
-
- for(unsigned int par=0; par<ParametersDimension; par++) {
- RealType sumF = itk::NumericTraits< RealType >::Zero;
- RealType sumM = itk::NumericTraits< RealType >::Zero;
- for(unsigned int dim=0; dim<dimension; dim++) {
- const RealType differential = jacobian( dim, par ) * gradient[dim];
- sumF += fixedValue * differential;
- sumM += movingValue * differential;
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sumF -= differential * sf / this->m_NumberOfPixelsCounted;
- sumM -= differential * sm / this->m_NumberOfPixelsCounted;
- }
- }
- derivativeF[par] += sumF;
- derivativeM[par] += sumM;
- }
- }
-
- ++ti;
- }
-
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sff -= ( sf * sf / this->m_NumberOfPixelsCounted );
- smm -= ( sm * sm / this->m_NumberOfPixelsCounted );
- sfm -= ( sf * sm / this->m_NumberOfPixelsCounted );
- }
-
- const RealType denom = -1.0 * vcl_sqrt(sff * smm );
-
- if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = ( derivativeF[i] - (sfm/smm)* derivativeM[i] ) / denom;
- }
- } else {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = itk::NumericTraits< MeasureType >::Zero;
- }
- }
-
-}
-
-
-/*
- * Get both the match Measure and theDerivative Measure
- */
-template <class TFixedImage, class TMovingImage>
-void
-NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValueAndDerivative(const TransformParametersType & parameters,
- MeasureType & value, DerivativeType & derivative) const
-{
-
-
- if( !this->GetGradientImage() ) {
- itkExceptionMacro(<<"The gradient image is null, maybe you forgot to call Initialize()");
- }
-
- FixedImageConstPointer fixedImage = this->m_FixedImage;
-
- if( !fixedImage ) {
- itkExceptionMacro( << "Fixed image has not been assigned" );
- }
-
- const unsigned int dimension = FixedImageType::ImageDimension;
-
- typedef itk::ImageRegionConstIteratorWithIndex<FixedImageType> FixedIteratorType;
-
- FixedIteratorType ti( fixedImage, this->GetFixedImageRegion() );
-
- typename FixedImageType::IndexType index;
-
- this->m_NumberOfPixelsCounted = 0;
-
- this->SetTransformParameters( parameters );
-
- typedef typename itk::NumericTraits< MeasureType >::AccumulateType AccumulateType;
-
- AccumulateType sff = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType smm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sfm = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sf = itk::NumericTraits< AccumulateType >::Zero;
- AccumulateType sm = itk::NumericTraits< AccumulateType >::Zero;
-
- const unsigned int ParametersDimension = this->GetNumberOfParameters();
- derivative = DerivativeType( ParametersDimension );
- derivative.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeF = DerivativeType( ParametersDimension );
- derivativeF.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeM = DerivativeType( ParametersDimension );
- derivativeM.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- DerivativeType derivativeM1 = DerivativeType( ParametersDimension );
- derivativeM1.Fill( itk::NumericTraits<typename DerivativeType::ValueType>::Zero );
-
- ti.GoToBegin();
- // First compute the sums
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
- sff += fixedValue * fixedValue;
- smm += movingValue * movingValue;
- sfm += fixedValue * movingValue;
- if ( this->m_SubtractMean ) {
- sf += fixedValue;
- sm += movingValue;
- }
- this->m_NumberOfPixelsCounted++;
- }
-
- ++ti;
- }
-
-
- // Compute contributions to derivatives
- ti.GoToBegin();
- while(!ti.IsAtEnd()) {
-
- index = ti.GetIndex();
-
- InputPointType inputPoint;
- fixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- if( this->m_FixedImageMask && !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++ti;
- continue;
- }
-
- OutputPointType transformedPoint = this->m_Transform->TransformPoint( inputPoint );
-
- if( this->m_MovingImageMask && !this->m_MovingImageMask->IsInside( transformedPoint ) ) {
- ++ti;
- continue;
- }
-
- if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
- const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
- const RealType fixedValue = ti.Get();
-
-#if ITK_VERSION_MAJOR >= 4
- TransformJacobianType jacobian;
- this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
-
- // Get the gradient by NearestNeighboorInterpolation:
- // which is equivalent to round up the point components.
- typedef typename OutputPointType::CoordRepType CoordRepType;
- typedef itk::ContinuousIndex<CoordRepType,MovingImageType::ImageDimension>
- MovingImageContinuousIndexType;
-
- MovingImageContinuousIndexType tempIndex;
- this->m_MovingImage->TransformPhysicalPointToContinuousIndex( transformedPoint, tempIndex );
-
- typename MovingImageType::IndexType mappedIndex;
- mappedIndex.CopyWithRound( tempIndex );
-
- const GradientPixelType gradient =
- this->GetGradientImage()->GetPixel( mappedIndex );
-
- for(unsigned int par=0; par<ParametersDimension; par++) {
- RealType sumF = itk::NumericTraits< RealType >::Zero;
- RealType sumM = itk::NumericTraits< RealType >::Zero;
- for(unsigned int dim=0; dim<dimension; dim++) {
- const RealType differential = jacobian( dim, par ) * gradient[dim];
- sumF += fixedValue * differential;
- sumM += movingValue * differential;
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sumF -= differential * sf / this->m_NumberOfPixelsCounted;
- sumM -= differential * sm / this->m_NumberOfPixelsCounted;
- }
- }
- derivativeF[par] += sumF;
- derivativeM[par] += sumM;
- }
- }
- ++ti;
- }
-
- if ( this->m_SubtractMean && this->m_NumberOfPixelsCounted > 0 ) {
- sff -= ( sf * sf / this->m_NumberOfPixelsCounted );
- smm -= ( sm * sm / this->m_NumberOfPixelsCounted );
- sfm -= ( sf * sm / this->m_NumberOfPixelsCounted );
- }
-
- const RealType denom = -1.0 * vcl_sqrt(sff * smm );
-
- if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = ( derivativeF[i] - (sfm/smm)* derivativeM[i] ) / denom;
- }
- value = sfm / denom;
- } else {
- for(unsigned int i=0; i<ParametersDimension; i++) {
- derivative[i] = itk::NumericTraits< MeasureType >::Zero;
- }
- value = itk::NumericTraits< MeasureType >::Zero;
- }
-
-
-
-}
-
-template < class TFixedImage, class TMovingImage>
-void
-NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::PrintSelf(std::ostream& os, itk::Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
- os << indent << "SubtractMean: " << m_SubtractMean << std::endl;
-}
-
-} // end namespace itk
-
-
-#endif // opt
-
#endif // _clitkNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx
#ifndef __clitkOptNormalizedCorrelationImageToImageMetric_h
#define __clitkOptNormalizedCorrelationImageToImageMetric_h
-#if ITK_VERSION_MAJOR >= 4
- #include "itkImageToImageMetric.h"
-#else
- #include "itkOptImageToImageMetric.h"
-#endif
+#include "itkImageToImageMetric.h"
#include "itkCovariantVector.h"
#include "itkPoint.h"
#include "itkIndex.h"
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING
this->GetValueMultiThreadedInitiate();
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING
this->GetValueMultiThreadedInitiate();
}
// Jacobian should be evaluated at the unmapped (fixed image) point.
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
transform->ComputeJacobianWithRespectToParameters(fixedImagePoint, jacobian);
-#else
- const TransformJacobianType & jacobian = transform
- ->GetJacobian( fixedImagePoint );
-#endif
for(unsigned int par=0; par<this->m_NumberOfParameters; par++) {
RealType sumF = itk::NumericTraits< RealType >::Zero;
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
//We need the sums and the value to be calculated first
value=this->ComputeSums(parameters);
#ifndef __clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD_h
#define __clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD_h
-#if ITK_VERSION_MAJOR >= 4
- #include "itkImageToImageMetric.h"
-#else
- #include "itkOptImageToImageMetric.h"
-#endif
+#include "itkImageToImageMetric.h"
#include "itkCovariantVector.h"
#include "itkPoint.h"
#include "itkIndex.h"
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING
this->GetValueMultiThreadedInitiate();
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING
this->GetValueMultiThreadedInitiate();
}
// Jacobian should be evaluated at the unmapped (fixed image) point.
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
transform->ComputeJacobianWithRespectToParameters( fixedImagePoint, jacobian );
-#else
- const TransformJacobianType & jacobian = transform->GetJacobian( fixedImagePoint );
-#endif
// for(unsigned int par=0; par<this->m_NumberOfParameters; par++)
// {
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
//We need the sums and the value to be calculated first
value=this->ComputeSums(parameters);
return OutputCovariantVectorType();
}
-#if ITK_VERSION_MAJOR >= 4
virtual void ComputeJacobianWithRespectToParameters (const InputPointType &p, JacobianType &jacobian) const
{
itkExceptionMacro( << "PointListTransform doesn't declare ComputeJacobianWithRespectToParameters" );
{
itkExceptionMacro( << "PointListTransform doesn't declare ComputeJacobianWithRespectToPosition" );
}
-#else
- virtual const JacobianType& GetJacobian(const InputPointType &point ) const
- {
- itkExceptionMacro( << "PointListTransform doesn't declare GetJacobian" );
- return this->m_Jacobian;
- }
-#endif
protected:
PointListTransform();
// Constructor
template<class TScalarType, unsigned int NDimensions, unsigned int NOutputDimensions>
- PointListTransform<TScalarType, NDimensions, NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
- ::PointListTransform():Superclass(1)
-#else
- ::PointListTransform():Superclass(NOutputDimensions,1)
-#endif
+ PointListTransform<TScalarType, NDimensions, NOutputDimensions>::PointListTransform():Superclass(1)
{
m_PointLists.resize(0);
m_PointList.resize(1);
/** Standard parameters container. */
typedef typename Superclass::ParametersType ParametersType;
-#if ITK_VERSION_MAJOR >= 4
typedef typename Superclass::NumberOfParametersType NumberOfParametersType;
-#endif
/** Standard Jacobian container. */
typedef typename Superclass::JacobianType JacobianType;
}
/** Compute the Jacobian Matrix of the transformation at one point */
-#if ITK_VERSION_MAJOR >= 4
virtual void ComputeJacobianWithRespectToParameters (const InputPointType &p, JacobianType &jacobian) const;
virtual void ComputeJacobianWithRespectToPosition (const InputPointType &p, JacobianType &jacobian) const
{
itkExceptionMacro( "ComputeJacobianWithRespectToPosition not yet implemented for " << this->GetNameOfClass() );
}
-#else
- virtual const JacobianType& GetJacobian(const InputPointType &point ) const;
-#endif
/** Return the number of parameters that completely define the Transfom */
-#if ITK_VERSION_MAJOR >= 4
virtual NumberOfParametersType GetNumberOfParameters(void) const;
-#else
- virtual unsigned int GetNumberOfParameters(void) const;
-#endif
//JV Return the padded number of parameters
virtual unsigned int GetPaddedNumberOfParameters(void) const;
// JV Shape
unsigned int m_TransformShape;
-#if ITK_VERSION_MAJOR >= 4
mutable JacobianType m_SharedDataBSplineJacobian;
-#endif
}; //class ShapedBLUTSpatioTemporalDeformableTransform
} // namespace itk
-#if ITK_TEMPLATE_TXX
+#ifndef ITK_MANUAL_INSTANTIATION
# include "clitkShapedBLUTSpatioTemporalDeformableTransform.txx"
#endif
// Constructor with default arguments
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
- ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
- ::ShapedBLUTSpatioTemporalDeformableTransform():Superclass(0)
-#else
- ::ShapedBLUTSpatioTemporalDeformableTransform():Superclass(OutputDimension,0)
-#endif
+ ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::ShapedBLUTSpatioTemporalDeformableTransform():Superclass(0)
{
unsigned int i;
// Get the number of parameters
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
typename ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>::NumberOfParametersType
-#else
- unsigned int
-#endif
ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
::GetNumberOfParameters(void) const
{
//=====================================
//JV Wrap jacobian into OutputDimension X Vectorial images
//=====================================
-#if ITK_VERSION_MAJOR >= 4
this->m_SharedDataBSplineJacobian.set_size( OutputDimension, this->GetNumberOfParameters() );
-#else
- this->m_Jacobian.set_size( OutputDimension, this->GetNumberOfParameters() );
-#endif
// Use memset to set the memory
// JV four rows of three comps of parameters
-#if ITK_VERSION_MAJOR >= 4
JacobianPixelType * jacobianDataPointer = reinterpret_cast<JacobianPixelType *>(this->m_SharedDataBSplineJacobian.data_block());
-#else
- JacobianPixelType * jacobianDataPointer = reinterpret_cast<JacobianPixelType *>(this->m_Jacobian.data_block());
-#endif
memset(jacobianDataPointer, 0, OutputDimension*numberOfPixels*sizeof(JacobianPixelType));
for (unsigned int j=0; j<OutputDimension; j++)
// JV weights are identical as for transformpoint, could be done simultaneously in metric!!!!
// Compute the Jacobian in one position
template<class TCoordRep, unsigned int NInputDimensions, unsigned int NOutputDimensions>
-#if ITK_VERSION_MAJOR >= 4
void
ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
::ComputeJacobianWithRespectToParameters( const InputPointType & point, JacobianType & jacobian) const
-#else
- const
- typename ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
- ::JacobianType &
- ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep, NInputDimensions, NOutputDimensions>
- ::GetJacobian( const InputPointType & point ) const
-#endif
{
//========================================================
if(m_Mask && !(m_Mask->IsInside(point) ) )
{
// Outside: no (deformable) displacement
-#if ITK_VERSION_MAJOR >= 4
jacobian = m_SharedDataBSplineJacobian;
return;
-#else
- return this->m_Jacobian;
-#endif
}
// Get index
// we assume zero displacement and return the input point
if ( !this->InsideValidRegion( m_Index ) )
{
-#if ITK_VERSION_MAJOR >= 4
jacobian = m_SharedDataBSplineJacobian;
return;
-#else
- return this->m_Jacobian;
-#endif
}
// Compute interpolation weights
}
// Return the result
-#if ITK_VERSION_MAJOR >= 4
jacobian = m_SharedDataBSplineJacobian;
-#else
- return this->m_Jacobian;
-#endif
}
// This line can be removed once the optimized versions
// gets integrated into the main directories.
#include "itkConfigure.h"
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h"
-#else
-
-#include "itkImageToImageMetric.h"
-#include "itkCovariantVector.h"
-#include "itkPoint.h"
-#include "itkIndex.h"
-#include "itkBSplineKernelFunction.h"
-#include "itkBSplineDerivativeKernelFunction.h"
-#include "itkCentralDifferenceImageFunction.h"
-#include "itkBSplineInterpolateImageFunction.h"
-#include "itkBSplineDeformableTransform.h"
-#include "itkArray2D.h"
-
-namespace itk
-{
-
-/** \class MattesMutualInformationImageToImageMetricFor3DBLUTFFD
- * \brief Computes the mutual information between two images to be
- * registered using the method of Mattes et al.
- *
- * MattesMutualInformationImageToImageMetricFor3DBLUTFFD computes the mutual
- * information between a fixed and moving image to be registered.
- *
- * This class is templated over the FixedImage type and the MovingImage
- * type.
- *
- * The fixed and moving images are set via methods SetFixedImage() and
- * SetMovingImage(). This metric makes use of user specified Transform and
- * Interpolator. The Transform is used to map points from the fixed image to
- * the moving image domain. The Interpolator is used to evaluate the image
- * intensity at user specified geometric points in the moving image.
- * The Transform and Interpolator are set via methods SetTransform() and
- * SetInterpolator().
- *
- * If a BSplineInterpolationFunction is used, this class obtain
- * image derivatives from the BSpline interpolator. Otherwise,
- * image derivatives are computed using central differencing.
- *
- * \warning This metric assumes that the moving image has already been
- * connected to the interpolator outside of this class.
- *
- * The method GetValue() computes of the mutual information
- * while method GetValueAndDerivative() computes
- * both the mutual information and its derivatives with respect to the
- * transform parameters.
- *
- * The calculations are based on the method of Mattes et al [1,2]
- * where the probability density distribution are estimated using
- * Parzen histograms. Since the fixed image PDF does not contribute
- * to the derivatives, it does not need to be smooth. Hence,
- * a zero order (box car) BSpline kernel is used
- * for the fixed image intensity PDF. On the other hand, to ensure
- * smoothness a third order BSpline kernel is used for the
- * moving image intensity PDF.
- *
- * On Initialize(), the FixedImage is uniformly sampled within
- * the FixedImageRegion. The number of samples used can be set
- * via SetNumberOfSpatialSamples(). Typically, the number of
- * spatial samples used should increase with the image size.
- *
- * The option UseAllPixelOn() disables the random sampling and uses
- * all the pixels of the FixedImageRegion in order to estimate the
- * joint intensity PDF.
- *
- * During each call of GetValue(), GetDerivatives(),
- * GetValueAndDerivatives(), marginal and joint intensity PDF's
- * values are estimated at discrete position or bins.
- * The number of bins used can be set via SetNumberOfHistogramBins().
- * To handle data with arbitray magnitude and dynamic range,
- * the image intensity is scale such that any contribution to the
- * histogram will fall into a valid bin.
- *
- * One the PDF's have been contructed, the mutual information
- * is obtained by doubling summing over the discrete PDF values.
- *
- *
- * Notes:
- * 1. This class returns the negative mutual information value.
- * 2. This class in not thread safe due the private data structures
- * used to the store the sampled points and the marginal and joint pdfs.
- *
- * References:
- * [1] "Nonrigid multimodality image registration"
- * D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank
- * Medical Imaging 2001: Image Processing, 2001, pp. 1609-1620.
- * [2] "PET-CT Image Registration in the Chest Using Free-form Deformations"
- * D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank
- * IEEE Transactions in Medical Imaging. Vol.22, No.1,
- January 2003. pp.120-128.
- * [3] "Optimization of Mutual Information for MultiResolution Image
- * Registration"
- * P. Thevenaz and M. Unser
- * IEEE Transactions in Image Processing, 9(12) December 2000.
- *
- * \ingroup RegistrationMetrics
- * \ingroup ThreadUnSafe
- */
-template <class TFixedImage,class TMovingImage >
-class ITK_EXPORT MattesMutualInformationImageToImageMetricFor3DBLUTFFD :
- public ImageToImageMetric< TFixedImage, TMovingImage >
-{
-public:
-
- /** Standard class typedefs. */
- typedef MattesMutualInformationImageToImageMetricFor3DBLUTFFD Self;
- typedef ImageToImageMetric< TFixedImage, TMovingImage > Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(MattesMutualInformationImageToImageMetricFor3DBLUTFFD, ImageToImageMetric);
-
- /** Types inherited from Superclass. */
- typedef typename Superclass::TransformType TransformType;
- typedef typename Superclass::TransformPointer TransformPointer;
- typedef typename Superclass::TransformJacobianType TransformJacobianType;
- typedef typename Superclass::InterpolatorType InterpolatorType;
- typedef typename Superclass::MeasureType MeasureType;
- typedef typename Superclass::DerivativeType DerivativeType;
- typedef typename Superclass::ParametersType ParametersType;
- typedef typename Superclass::FixedImageType FixedImageType;
- typedef typename Superclass::MovingImageType MovingImageType;
- typedef typename Superclass::FixedImageConstPointer FixedImageConstPointer;
- typedef typename Superclass::MovingImageConstPointer MovingImageCosntPointer;
- typedef typename Superclass::InputPointType InputPointType;
- typedef typename Superclass::OutputPointType OutputPointType;
-
- typedef typename Superclass::CoordinateRepresentationType
- CoordinateRepresentationType;
-
- /** Index and Point typedef support. */
- typedef typename FixedImageType::IndexType FixedImageIndexType;
- typedef typename FixedImageIndexType::IndexValueType FixedImageIndexValueType;
- typedef typename MovingImageType::IndexType MovingImageIndexType;
- typedef typename TransformType::InputPointType FixedImagePointType;
- typedef typename TransformType::OutputPointType MovingImagePointType;
-
- /** The moving image dimension. */
- itkStaticConstMacro( MovingImageDimension, unsigned int,
- MovingImageType::ImageDimension );
-
- /**
- * Initialize the Metric by
- * (1) making sure that all the components are present and plugged
- * together correctly,
- * (2) uniformly select NumberOfSpatialSamples within
- * the FixedImageRegion, and
- * (3) allocate memory for pdf data structures. */
- virtual void Initialize(void) throw ( ExceptionObject );
-
- /** Get the derivatives of the match measure. */
- void GetDerivative( const ParametersType& parameters,
- DerivativeType & Derivative ) const;
-
- /** Get the value. */
- MeasureType GetValue( const ParametersType& parameters ) const;
-
- /** Get the value and derivatives for single valued optimizers. */
- void GetValueAndDerivative( const ParametersType& parameters,
- MeasureType& Value,
- DerivativeType& Derivative ) const;
-
- /** Number of spatial samples to used to compute metric */
- itkSetClampMacro( NumberOfSpatialSamples, unsigned long,
- 1, NumericTraits<unsigned long>::max() );
- itkGetConstReferenceMacro( NumberOfSpatialSamples, unsigned long);
-
- /** Number of bins to used in the histogram. Typical value is 50. */
- itkSetClampMacro( NumberOfHistogramBins, unsigned long,
- 1, NumericTraits<unsigned long>::max() );
- itkGetConstReferenceMacro( NumberOfHistogramBins, unsigned long);
-
- /** Reinitialize the seed of the random number generator that selects the
- * sample of pixels used for estimating the image histograms and the joint
- * histogram. By nature, this metric is not deterministic, since at each run
- * it may select a different set of pixels. By initializing the random number
- * generator seed to the same value you can restore determinism. On the other
- * hand, calling the method ReinitializeSeed() without arguments will use the
- * clock from your machine in order to have a very random initialization of
- * the seed. This will indeed increase the non-deterministic behavior of the
- * metric. */
- void ReinitializeSeed();
- void ReinitializeSeed(int);
-
- /** Select whether the metric will be computed using all the pixels on the
- * fixed image region, or only using a set of randomly selected pixels. */
- itkSetMacro(UseAllPixels,bool);
- itkGetConstReferenceMacro(UseAllPixels,bool);
- itkBooleanMacro(UseAllPixels);
-
- /** This variable selects the method to be used for computing the Metric
- * derivatives with respect to the Transform parameters. Two modes of
- * computation are available. The choice between one and the other is a
- * trade-off between computation speed and memory allocations. The two modes
- * are described in detail below:
- *
- * UseExplicitPDFDerivatives = True
- * will compute the Metric derivative by first calculating the derivatives of
- * each one of the Joint PDF bins with respect to each one of the Transform
- * parameters and then accumulating these contributions in the final metric
- * derivative array by using a bin-specific weight. The memory required for
- * storing the intermediate derivatives is a 3D array of doubles with size
- * equals to the product of (number of histogram bins)^2 times number of
- * transform parameters. This method is well suited for Transform with a small
- * number of parameters.
- *
- * UseExplicitPDFDerivatives = False will compute the Metric derivative by
- * first computing the weights for each one of the Joint PDF bins and caching
- * them into an array. Then it will revisit each one of the PDF bins for
- * computing its weighted contribution to the full derivative array. In this
- * method an extra 2D array is used for storing the weights of each one of
- * the PDF bins. This is an array of doubles with size equals to (number of
- * histogram bins)^2. This method is well suited for Transforms with a large
- * number of parameters, such as, BSplineDeformableTransforms. */
- itkSetMacro(UseExplicitPDFDerivatives,bool);
- itkGetConstReferenceMacro(UseExplicitPDFDerivatives,bool);
- itkBooleanMacro(UseExplicitPDFDerivatives);
-
- /** This boolean flag is only relevant when this metric is used along
- * with a BSplineDeformableTransform. The flag enables/disables the
- * caching of values computed when a physical point is mapped through
- * the BSplineDeformableTransform. In particular it will cache the
- * values of the BSpline weights for that points, and the indexes
- * indicating what BSpline-grid nodes are relevant for that specific
- * point. This caching is made optional due to the fact that the
- * memory arrays used for the caching can reach large sizes even for
- * moderate image size problems. For example, for a 3D image of
- * 256^3, using 20% of pixels, these arrays will take about 1
- * Gigabyte of RAM for storage. The ratio of computing time between
- * using the cache or not using the cache can reach 1:5, meaning that
- * using the caching can provide a five times speed up. It is
- * therefore, interesting to enable the caching, if enough memory is
- * available for it. The caching is enabled by default, in order to
- * preserve backward compatibility with previous versions of ITK. */
- itkSetMacro(UseCachingOfBSplineWeights,bool);
- itkGetConstReferenceMacro(UseCachingOfBSplineWeights,bool);
- itkBooleanMacro(UseCachingOfBSplineWeights);
-
-protected:
-
- MattesMutualInformationImageToImageMetricFor3DBLUTFFD();
- virtual ~MattesMutualInformationImageToImageMetricFor3DBLUTFFD() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** \class FixedImageSpatialSample
- * A fixed image spatial sample consists of the fixed domain point
- * and the fixed image value at that point. */
- /// @cond
- class FixedImageSpatialSample
- {
- public:
- FixedImageSpatialSample():FixedImageValue(0.0) {
- FixedImagePointValue.Fill(0.0);
- }
- ~FixedImageSpatialSample() {};
-
- FixedImagePointType FixedImagePointValue;
- double FixedImageValue;
- unsigned int FixedImageParzenWindowIndex;
- };
- /// @endcond
-
- /** FixedImageSpatialSample typedef support. */
- typedef std::vector<FixedImageSpatialSample>
- FixedImageSpatialSampleContainer;
-
- /** Container to store a set of points and fixed image values. */
- FixedImageSpatialSampleContainer m_FixedImageSamples;
-
- /** Uniformly select a sample set from the fixed image domain. */
- virtual void SampleFixedImageDomain(
- FixedImageSpatialSampleContainer& samples);
-
- /** Gather all the pixels from the fixed image domain. */
- virtual void SampleFullFixedImageDomain(
- FixedImageSpatialSampleContainer& samples);
-
- /** Transform a point from FixedImage domain to MovingImage domain.
- * This function also checks if mapped point is within support region. */
- virtual void TransformPoint( unsigned int sampleNumber,
- const ParametersType& parameters,
- MovingImagePointType& mappedPoint,
- bool& sampleWithinSupportRegion,
- double& movingImageValue ) const;
-
-private:
-
- //purposely not implemented
- MattesMutualInformationImageToImageMetricFor3DBLUTFFD(const Self&);
- //purposely not implemented
- void operator=(const Self&);
-
-
- /** The marginal PDFs are stored as std::vector. */
- typedef float PDFValueType;
- typedef std::vector<PDFValueType> MarginalPDFType;
-
- /** The fixed image marginal PDF. */
- mutable MarginalPDFType m_FixedImageMarginalPDF;
-
- /** The moving image marginal PDF. */
- mutable MarginalPDFType m_MovingImageMarginalPDF;
-
- /** Helper array for storing the values of the JointPDF ratios. */
- typedef double PRatioType;
- typedef Array2D< PRatioType > PRatioArrayType;
- mutable PRatioArrayType m_PRatioArray;
-
- /** Helper variable for accumulating the derivative of the metric. */
- mutable DerivativeType m_MetricDerivative;
-
- /** Typedef for the joint PDF and PDF derivatives are stored as ITK Images. */
- typedef Image<PDFValueType,2> JointPDFType;
- typedef JointPDFType::IndexType JointPDFIndexType;
- typedef JointPDFType::PixelType JointPDFValueType;
- typedef JointPDFType::RegionType JointPDFRegionType;
- typedef JointPDFType::SizeType JointPDFSizeType;
- typedef Image<PDFValueType,3> JointPDFDerivativesType;
- typedef JointPDFDerivativesType::IndexType JointPDFDerivativesIndexType;
- typedef JointPDFDerivativesType::PixelType JointPDFDerivativesValueType;
- typedef JointPDFDerivativesType::RegionType JointPDFDerivativesRegionType;
- typedef JointPDFDerivativesType::SizeType JointPDFDerivativesSizeType;
-
- /** The joint PDF and PDF derivatives. */
- typename JointPDFType::Pointer m_JointPDF;
- typename JointPDFDerivativesType::Pointer m_JointPDFDerivatives;
-
- unsigned long m_NumberOfSpatialSamples;
- unsigned long m_NumberOfParameters;
-
- /** Variables to define the marginal and joint histograms. */
- unsigned long m_NumberOfHistogramBins;
- double m_MovingImageNormalizedMin;
- double m_FixedImageNormalizedMin;
- double m_MovingImageTrueMin;
- double m_MovingImageTrueMax;
- double m_FixedImageBinSize;
- double m_MovingImageBinSize;
-
- /** Typedefs for BSpline kernel and derivative functions. */
- typedef BSplineKernelFunction<3> CubicBSplineFunctionType;
- typedef BSplineDerivativeKernelFunction<3> CubicBSplineDerivativeFunctionType;
-
- /** Cubic BSpline kernel for computing Parzen histograms. */
- typename CubicBSplineFunctionType::Pointer m_CubicBSplineKernel;
- typename CubicBSplineDerivativeFunctionType::Pointer
- m_CubicBSplineDerivativeKernel;
-
- /** Precompute fixed image parzen window indices. */
- virtual void ComputeFixedImageParzenWindowIndices(
- FixedImageSpatialSampleContainer& samples );
-
- /**
- * Types and variables related to image derivative calculations.
- * If a BSplineInterpolationFunction is used, this class obtain
- * image derivatives from the BSpline interpolator. Otherwise,
- * image derivatives are computed using central differencing.
- */
- typedef CovariantVector< double,
- itkGetStaticConstMacro(MovingImageDimension) >
- ImageDerivativesType;
-
- /** Compute image derivatives at a point. */
- virtual void ComputeImageDerivatives( const MovingImagePointType& mappedPoint,
- ImageDerivativesType& gradient ) const;
-
- /** Boolean to indicate if the interpolator BSpline. */
- bool m_InterpolatorIsBSpline;
-
- /** Typedefs for using BSpline interpolator. */
- typedef
- BSplineInterpolateImageFunction<MovingImageType,
- CoordinateRepresentationType>
- BSplineInterpolatorType;
-
- /** Pointer to BSplineInterpolator. */
- typename BSplineInterpolatorType::Pointer m_BSplineInterpolator;
-
- /** Typedefs for using central difference calculator. */
- typedef CentralDifferenceImageFunction<MovingImageType,
- CoordinateRepresentationType>
- DerivativeFunctionType;
-
- /** Pointer to central difference calculator. */
- typename DerivativeFunctionType::Pointer m_DerivativeCalculator;
-
-
- /** Compute PDF derivative contribution for each parameter. */
- virtual void ComputePDFDerivatives( unsigned int sampleNumber,
- int movingImageParzenWindowIndex,
- const ImageDerivativesType&
- movingImageGradientValue,
- double cubicBSplineDerivativeValue
- ) const;
-
- /**
- * Types and variables related to BSpline deformable transforms.
- * If the transform is of type third order BSplineDeformableTransform,
- * then we can speed up the metric derivative calculation by
- * only inspecting the parameters within the support region
- * of a mapped point.
- */
-
- /** Boolean to indicate if the transform is BSpline deformable. */
- bool m_TransformIsBSpline;
-
- /** The number of BSpline parameters per image dimension. */
- long m_NumParametersPerDim;
-
- /**
- * The number of BSpline transform weights is the number of
- * of parameter in the support region (per dimension ). */
- unsigned long m_NumBSplineWeights;
-
- /** The fixed image dimension. */
- itkStaticConstMacro( FixedImageDimension, unsigned int,
- FixedImageType::ImageDimension );
-
- /**
- * Enum of the deformabtion field spline order.
- */
- enum { DeformationSplineOrder = 3 };
-
- /**
- * Typedefs for the BSplineDeformableTransform.
- */
- typedef BSplineDeformableTransform<
- CoordinateRepresentationType,
- ::itk::GetImageDimension<FixedImageType>::ImageDimension,
- DeformationSplineOrder> BSplineTransformType;
- typedef typename BSplineTransformType::WeightsType
- BSplineTransformWeightsType;
- typedef typename BSplineTransformType::ParameterIndexArrayType
- BSplineTransformIndexArrayType;
-
- /**
- * Variables used when transform is of type BSpline deformable.
- */
- typename BSplineTransformType::Pointer m_BSplineTransform;
-
- /**
- * Cache pre-transformed points, weights, indices and
- * within support region flag.
- */
- typedef typename BSplineTransformWeightsType::ValueType WeightsValueType;
- typedef Array2D<WeightsValueType> BSplineTransformWeightsArrayType;
- typedef typename BSplineTransformIndexArrayType::ValueType IndexValueType;
- typedef Array2D<IndexValueType> BSplineTransformIndicesArrayType;
- typedef std::vector<MovingImagePointType> MovingImagePointArrayType;
- typedef std::vector<bool> BooleanArrayType;
-
- BSplineTransformWeightsArrayType m_BSplineTransformWeightsArray;
- BSplineTransformIndicesArrayType m_BSplineTransformIndicesArray;
- MovingImagePointArrayType m_PreTransformPointsArray;
- BooleanArrayType m_WithinSupportRegionArray;
-
- typedef FixedArray<unsigned long,
- ::itk::GetImageDimension<FixedImageType>::ImageDimension>
- ParametersOffsetType;
- ParametersOffsetType m_ParametersOffset;
-
- bool m_UseAllPixels;
-
- virtual void PreComputeTransformValues();
-
- bool m_ReseedIterator;
- int m_RandomSeed;
-
- // Selection of explicit or implicit computation of PDF derivatives
- // with respect to Transform parameters.
- bool m_UseExplicitPDFDerivatives;
-
- // Variables needed for optionally caching values when using a BSpline transform.
- bool m_UseCachingOfBSplineWeights;
- mutable BSplineTransformWeightsType m_Weights;
- mutable BSplineTransformIndexArrayType m_Indices;
-
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx"
-#endif
-
-#endif
-
#endif
// gets integrated into the main directories.
#include "itkConfigure.h"
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx"
-#else
-
-
-#include "itkMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h"
-#include "itkBSplineInterpolateImageFunction.h"
-#include "itkCovariantVector.h"
-#include "itkImageRandomConstIteratorWithIndex.h"
-#include "itkImageRegionConstIterator.h"
-#include "itkImageRegionIterator.h"
-#include "itkImageIterator.h"
-#include "vnl/vnl_math.h"
-#include "itkBSplineDeformableTransform.h"
-
-namespace itk
-{
-
-
-/**
- * Constructor
- */
-template < class TFixedImage, class TMovingImage >
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::MattesMutualInformationImageToImageMetricFor3DBLUTFFD()
-{
-
- m_NumberOfSpatialSamples = 500;
- m_NumberOfHistogramBins = 50;
-
- this->SetComputeGradient(false); // don't use the default gradient for now
-
- m_InterpolatorIsBSpline = false;
- m_TransformIsBSpline = false;
-
- // Initialize PDFs to NULL
- m_JointPDF = NULL;
- m_JointPDFDerivatives = NULL;
-
- m_UseExplicitPDFDerivatives = true;
-
- typename BSplineTransformType::Pointer transformer =
- BSplineTransformType::New();
- this->SetTransform (transformer);
-
- typename BSplineInterpolatorType::Pointer interpolator =
- BSplineInterpolatorType::New();
- this->SetInterpolator (interpolator);
-
- // Initialize memory
- m_MovingImageNormalizedMin = 0.0;
- m_FixedImageNormalizedMin = 0.0;
- m_MovingImageTrueMin = 0.0;
- m_MovingImageTrueMax = 0.0;
- m_FixedImageBinSize = 0.0;
- m_MovingImageBinSize = 0.0;
- m_CubicBSplineDerivativeKernel = NULL;
- m_BSplineInterpolator = NULL;
- m_DerivativeCalculator = NULL;
- m_NumParametersPerDim = 0;
- m_NumBSplineWeights = 0;
- m_BSplineTransform = NULL;
- m_NumberOfParameters = 0;
- m_UseAllPixels = false;
- m_ReseedIterator = false;
- m_RandomSeed = -1;
- m_UseCachingOfBSplineWeights = true;
-}
-
-
-/**
- * Print out internal information about this class
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
-
- Superclass::PrintSelf(os, indent);
-
- os << indent << "NumberOfSpatialSamples: ";
- os << m_NumberOfSpatialSamples << std::endl;
- os << indent << "NumberOfHistogramBins: ";
- os << m_NumberOfHistogramBins << std::endl;
- os << indent << "UseAllPixels: ";
- os << m_UseAllPixels << std::endl;
-
- // Debugging information
- os << indent << "NumberOfParameters: ";
- os << m_NumberOfParameters << std::endl;
- os << indent << "FixedImageNormalizedMin: ";
- os << m_FixedImageNormalizedMin << std::endl;
- os << indent << "MovingImageNormalizedMin: ";
- os << m_MovingImageNormalizedMin << std::endl;
- os << indent << "MovingImageTrueMin: ";
- os << m_MovingImageTrueMin << std::endl;
- os << indent << "MovingImageTrueMax: ";
- os << m_MovingImageTrueMax << std::endl;
- os << indent << "FixedImageBinSize: ";
- os << m_FixedImageBinSize << std::endl;
- os << indent << "MovingImageBinSize: ";
- os << m_MovingImageBinSize << std::endl;
- os << indent << "InterpolatorIsBSpline: ";
- os << m_InterpolatorIsBSpline << std::endl;
- os << indent << "TransformIsBSpline: ";
- os << m_TransformIsBSpline << std::endl;
- os << indent << "UseCachingOfBSplineWeights: ";
- os << m_UseCachingOfBSplineWeights << std::endl;
- os << indent << "UseExplicitPDFDerivatives: ";
- os << m_UseExplicitPDFDerivatives << std::endl;
-
-}
-
-
-/**
- * Initialize
- */
-template <class TFixedImage, class TMovingImage>
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::Initialize(void) throw ( ExceptionObject )
-{
- this->Superclass::Initialize();
-
- // Cache the number of transformation parameters
- m_NumberOfParameters = this->m_Transform->GetNumberOfParameters();
-
- /**
- * Compute the minimum and maximum for the FixedImage over
- * the FixedImageRegion.
- *
- * NB: We can't use StatisticsImageFilter to do this because
- * the filter computes the min/max for the largest possible region
- */
- double fixedImageMin = NumericTraits<double>::max();
- double fixedImageMax = NumericTraits<double>::NonpositiveMin();
-
- typedef ImageRegionConstIterator<FixedImageType> FixedIteratorType;
- FixedIteratorType fixedImageIterator(
- this->m_FixedImage, this->GetFixedImageRegion() );
-
- for ( fixedImageIterator.GoToBegin();
- !fixedImageIterator.IsAtEnd(); ++fixedImageIterator ) {
-
- double sample = static_cast<double>( fixedImageIterator.Get() );
-
- if ( sample < fixedImageMin ) {
- fixedImageMin = sample;
- }
-
- if ( sample > fixedImageMax ) {
- fixedImageMax = sample;
- }
- }
-
-
- /**
- * Compute the minimum and maximum for the entire moving image
- * in the buffer.
- */
- double movingImageMin = NumericTraits<double>::max();
- double movingImageMax = NumericTraits<double>::NonpositiveMin();
-
- typedef ImageRegionConstIterator<MovingImageType> MovingIteratorType;
- MovingIteratorType movingImageIterator(
- this->m_MovingImage, this->m_MovingImage->GetBufferedRegion() );
-
- for ( movingImageIterator.GoToBegin();
- !movingImageIterator.IsAtEnd(); ++movingImageIterator) {
- double sample = static_cast<double>( movingImageIterator.Get() );
-
- if ( sample < movingImageMin ) {
- movingImageMin = sample;
- }
-
- if ( sample > movingImageMax ) {
- movingImageMax = sample;
- }
- }
-
- m_MovingImageTrueMin = movingImageMin;
- m_MovingImageTrueMax = movingImageMax;
-
- itkDebugMacro( " FixedImageMin: " << fixedImageMin <<
- " FixedImageMax: " << fixedImageMax << std::endl );
- itkDebugMacro( " MovingImageMin: " << movingImageMin <<
- " MovingImageMax: " << movingImageMax << std::endl );
-
-
- /**
- * Compute binsize for the histograms.
- *
- * The binsize for the image intensities needs to be adjusted so that
- * we can avoid dealing with boundary conditions using the cubic
- * spline as the Parzen window. We do this by increasing the size
- * of the bins so that the joint histogram becomes "padded" at the
- * borders. Because we are changing the binsize,
- * we also need to shift the minimum by the padded amount in order to
- * avoid minimum values filling in our padded region.
- *
- * Note that there can still be non-zero bin values in the padded region,
- * it's just that these bins will never be a central bin for the Parzen
- * window.
- *
- */
- const int padding = 2; // this will pad by 2 bins
-
- m_FixedImageBinSize = ( fixedImageMax - fixedImageMin ) /
- static_cast<double>( m_NumberOfHistogramBins - 2 * padding );
- m_FixedImageNormalizedMin = fixedImageMin / m_FixedImageBinSize -
- static_cast<double>( padding );
-
- m_MovingImageBinSize = ( movingImageMax - movingImageMin ) /
- static_cast<double>( m_NumberOfHistogramBins - 2 * padding );
- m_MovingImageNormalizedMin = movingImageMin / m_MovingImageBinSize -
- static_cast<double>( padding );
-
-
- itkDebugMacro( "FixedImageNormalizedMin: " << m_FixedImageNormalizedMin );
- itkDebugMacro( "MovingImageNormalizedMin: " << m_MovingImageNormalizedMin );
- itkDebugMacro( "FixedImageBinSize: " << m_FixedImageBinSize );
- itkDebugMacro( "MovingImageBinSize; " << m_MovingImageBinSize );
-
- if( m_UseAllPixels ) {
- m_NumberOfSpatialSamples =
- this->GetFixedImageRegion().GetNumberOfPixels();
- }
-
- /**
- * Allocate memory for the fixed image sample container.
- */
- m_FixedImageSamples.resize( m_NumberOfSpatialSamples );
-
-
- /**
- * Allocate memory for the marginal PDF and initialize values
- * to zero. The marginal PDFs are stored as std::vector.
- */
- m_FixedImageMarginalPDF.resize( m_NumberOfHistogramBins, 0.0 );
- m_MovingImageMarginalPDF.resize( m_NumberOfHistogramBins, 0.0 );
-
- /**
- * Allocate memory for the joint PDF and joint PDF derivatives.
- * The joint PDF and joint PDF derivatives are store as itk::Image.
- */
- m_JointPDF = JointPDFType::New();
-
- // Instantiate a region, index, size
- JointPDFRegionType jointPDFRegion;
- JointPDFIndexType jointPDFIndex;
- JointPDFSizeType jointPDFSize;
-
- // Deallocate the memory that may have been allocated for
- // previous runs of the metric.
- this->m_JointPDFDerivatives = NULL; // by destroying the dynamic array
- this->m_PRatioArray.SetSize( 1, 1 ); // and by allocating very small the static ones
- this->m_MetricDerivative = DerivativeType( 1 );
-
- //
- // Now allocate memory according to the user-selected method.
- //
- if( this->m_UseExplicitPDFDerivatives ) {
- this->m_JointPDFDerivatives = JointPDFDerivativesType::New();
- JointPDFDerivativesRegionType jointPDFDerivativesRegion;
- JointPDFDerivativesIndexType jointPDFDerivativesIndex;
- JointPDFDerivativesSizeType jointPDFDerivativesSize;
-
- // For the derivatives of the joint PDF define a region starting from {0,0,0}
- // with size {m_NumberOfParameters,m_NumberOfHistogramBins,
- // m_NumberOfHistogramBins}. The dimension represents transform parameters,
- // fixed image parzen window index and moving image parzen window index,
- // respectively.
- jointPDFDerivativesIndex.Fill( 0 );
- jointPDFDerivativesSize[0] = m_NumberOfParameters;
- jointPDFDerivativesSize[1] = m_NumberOfHistogramBins;
- jointPDFDerivativesSize[2] = m_NumberOfHistogramBins;
-
- jointPDFDerivativesRegion.SetIndex( jointPDFDerivativesIndex );
- jointPDFDerivativesRegion.SetSize( jointPDFDerivativesSize );
-
- // Set the regions and allocate
- m_JointPDFDerivatives->SetRegions( jointPDFDerivativesRegion );
- m_JointPDFDerivatives->Allocate();
- } else {
- /** Allocate memory for helper array that will contain the pRatios
- * for each bin of the joint histogram. This is part of the effort
- * for flattening the computation of the PDF Jacobians.
- */
- this->m_PRatioArray.SetSize( this->m_NumberOfHistogramBins, this->m_NumberOfHistogramBins );
- this->m_MetricDerivative = DerivativeType( this->GetNumberOfParameters() );
- }
-
- // For the joint PDF define a region starting from {0,0}
- // with size {m_NumberOfHistogramBins, m_NumberOfHistogramBins}.
- // The dimension represents fixed image parzen window index
- // and moving image parzen window index, respectively.
- jointPDFIndex.Fill( 0 );
- jointPDFSize.Fill( m_NumberOfHistogramBins );
-
- jointPDFRegion.SetIndex( jointPDFIndex );
- jointPDFRegion.SetSize( jointPDFSize );
-
- // Set the regions and allocate
- m_JointPDF->SetRegions( jointPDFRegion );
- m_JointPDF->Allocate();
-
-
- /**
- * Setup the kernels used for the Parzen windows.
- */
- m_CubicBSplineKernel = CubicBSplineFunctionType::New();
- m_CubicBSplineDerivativeKernel = CubicBSplineDerivativeFunctionType::New();
-
-
- if( m_UseAllPixels ) {
- /**
- * Take all the pixels within the fixed image region)
- * to create the sample points list.
- */
- this->SampleFullFixedImageDomain( m_FixedImageSamples );
- } else {
- /**
- * Uniformly sample the fixed image (within the fixed image region)
- * to create the sample points list.
- */
- this->SampleFixedImageDomain( m_FixedImageSamples );
- }
-
- /**
- * Pre-compute the fixed image parzen window index for
- * each point of the fixed image sample points list.
- */
- this->ComputeFixedImageParzenWindowIndices( m_FixedImageSamples );
-
- /**
- * Check if the interpolator is of type BSplineInterpolateImageFunction.
- * If so, we can make use of its EvaluateDerivatives method.
- * Otherwise, we instantiate an external central difference
- * derivative calculator.
- *
- * TODO: Also add it the possibility of using the default gradient
- * provided by the superclass.
- *
- */
- m_InterpolatorIsBSpline = true;
-
- BSplineInterpolatorType * testPtr = dynamic_cast<BSplineInterpolatorType *>(
- this->m_Interpolator.GetPointer() );
- if ( !testPtr ) {
- m_InterpolatorIsBSpline = false;
-
- m_DerivativeCalculator = DerivativeFunctionType::New();
-
-#ifdef ITK_USE_ORIENTED_IMAGE_DIRECTION
- m_DerivativeCalculator->UseImageDirectionOn();
-#endif
-
- m_DerivativeCalculator->SetInputImage( this->m_MovingImage );
-
- m_BSplineInterpolator = NULL;
- itkDebugMacro( "Interpolator is not BSpline" );
- } else {
- m_BSplineInterpolator = testPtr;
-
-#ifdef ITK_USE_ORIENTED_IMAGE_DIRECTION
- m_BSplineInterpolator->UseImageDirectionOn();
-#endif
-
- m_DerivativeCalculator = NULL;
- itkDebugMacro( "Interpolator is BSpline" );
- }
-
- /**
- * Check if the transform is of type BSplineDeformableTransform.
- *
- * If so, several speed up features are implemented.
- * [1] Precomputing the results of bulk transform for each sample point.
- * [2] Precomputing the BSpline weights for each sample point,
- * to be used later to directly compute the deformation vector
- * [3] Precomputing the indices of the parameters within the
- * the support region of each sample point.
- */
- m_TransformIsBSpline = true;
-
- BSplineTransformType * testPtr2 = dynamic_cast<BSplineTransformType *>(
- this->m_Transform.GetPointer() );
- if( !testPtr2 ) {
- m_TransformIsBSpline = false;
- m_BSplineTransform = NULL;
- itkDebugMacro( "Transform is not BSplineDeformable" );
- } else {
- m_BSplineTransform = testPtr2;
- m_NumParametersPerDim =
- m_BSplineTransform->GetNumberOfParametersPerDimension();
- m_NumBSplineWeights = m_BSplineTransform->GetNumberOfWeights();
- itkDebugMacro( "Transform is BSplineDeformable" );
- }
-
- if( this->m_TransformIsBSpline ) {
- // First, deallocate memory that may have been used from previous run of the Metric
- this->m_BSplineTransformWeightsArray.SetSize( 1, 1 );
- this->m_BSplineTransformIndicesArray.SetSize( 1, 1 );
- this->m_PreTransformPointsArray.resize( 1 );
- this->m_WithinSupportRegionArray.resize( 1 );
- this->m_Weights.SetSize( 1 );
- this->m_Indices.SetSize( 1 );
-
-
- if( this->m_UseCachingOfBSplineWeights ) {
- m_BSplineTransformWeightsArray.SetSize(
- m_NumberOfSpatialSamples, m_NumBSplineWeights );
- m_BSplineTransformIndicesArray.SetSize(
- m_NumberOfSpatialSamples, m_NumBSplineWeights );
- m_PreTransformPointsArray.resize( m_NumberOfSpatialSamples );
- m_WithinSupportRegionArray.resize( m_NumberOfSpatialSamples );
-
- this->PreComputeTransformValues();
- } else {
- this->m_Weights.SetSize( this->m_NumBSplineWeights );
- this->m_Indices.SetSize( this->m_NumBSplineWeights );
- }
-
- for ( unsigned int j = 0; j < FixedImageDimension; j++ ) {
- m_ParametersOffset[j] = j *
- m_BSplineTransform->GetNumberOfParametersPerDimension();
- }
- }
-
-}
-
-
-/**
- * Uniformly sample the fixed image domain using a random walk
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::SampleFixedImageDomain( FixedImageSpatialSampleContainer& samples )
-{
-
- // Set up a random interator within the user specified fixed image region.
- typedef ImageRandomConstIteratorWithIndex<FixedImageType> RandomIterator;
- RandomIterator randIter( this->m_FixedImage, this->GetFixedImageRegion() );
-
- randIter.SetNumberOfSamples( m_NumberOfSpatialSamples );
- randIter.GoToBegin();
-
- typename FixedImageSpatialSampleContainer::iterator iter;
- typename FixedImageSpatialSampleContainer::const_iterator end=samples.end();
-
- if( this->m_FixedImageMask ) {
-
- InputPointType inputPoint;
-
- iter=samples.begin();
- int count = 0;
- int samples_found = 0;
- int maxcount = m_NumberOfSpatialSamples * 10;
- while( iter != end ) {
-
- if ( count > maxcount ) {
-#if 0
- itkExceptionMacro(
- "Drew too many samples from the mask (is it too small?): "
- << maxcount << std::endl );
-#else
-samples.resize(samples_found);
-// this->SetNumberOfSpatialSamples(sample_found);
-break;
-#endif
- }
- count++;
-
- // Get sampled index
- FixedImageIndexType index = randIter.GetIndex();
- // Check if the Index is inside the mask, translate index to point
- this->m_FixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- // If not inside the mask, ignore the point
- if( !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++randIter; // jump to another random position
- continue;
- }
-
- // Get sampled fixed image value
- (*iter).FixedImageValue = randIter.Get();
- // Translate index to point
- (*iter).FixedImagePointValue = inputPoint;
- samples_found++;
- // Jump to random position
- ++randIter;
- ++iter;
- }
- } else {
- for( iter=samples.begin(); iter != end; ++iter ) {
- // Get sampled index
- FixedImageIndexType index = randIter.GetIndex();
- // Get sampled fixed image value
- (*iter).FixedImageValue = randIter.Get();
- // Translate index to point
- this->m_FixedImage->TransformIndexToPhysicalPoint( index,
- (*iter).FixedImagePointValue );
- // Jump to random position
- ++randIter;
-
- }
- }
-}
-
-/**
- * Sample the fixed image domain using all pixels in the Fixed image region
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::SampleFullFixedImageDomain( FixedImageSpatialSampleContainer& samples )
-{
-
- // Set up a region interator within the user specified fixed image region.
- typedef ImageRegionConstIteratorWithIndex<FixedImageType> RegionIterator;
- RegionIterator regionIter( this->m_FixedImage, this->GetFixedImageRegion() );
-
- regionIter.GoToBegin();
-
- typename FixedImageSpatialSampleContainer::iterator iter;
- typename FixedImageSpatialSampleContainer::const_iterator end=samples.end();
-
- if( this->m_FixedImageMask ) {
- InputPointType inputPoint;
-
- iter=samples.begin();
- unsigned long nSamplesPicked = 0;
-
- while( iter != end && !regionIter.IsAtEnd() ) {
- // Get sampled index
- FixedImageIndexType index = regionIter.GetIndex();
- // Check if the Index is inside the mask, translate index to point
- this->m_FixedImage->TransformIndexToPhysicalPoint( index, inputPoint );
-
- // If not inside the mask, ignore the point
- if( !this->m_FixedImageMask->IsInside( inputPoint ) ) {
- ++regionIter; // jump to next pixel
- continue;
- }
-
- // Get sampled fixed image value
- (*iter).FixedImageValue = regionIter.Get();
- // Translate index to point
- (*iter).FixedImagePointValue = inputPoint;
-
- ++regionIter;
- ++iter;
- ++nSamplesPicked;
- }
-
- // If we picked fewer samples than the desired number,
- // resize the container
- if (nSamplesPicked != this->m_NumberOfSpatialSamples) {
- this->m_NumberOfSpatialSamples = nSamplesPicked;
- samples.resize(this->m_NumberOfSpatialSamples);
- }
- } else { // not restricting sample throwing to a mask
-
- // cannot sample more than the number of pixels in the image region
- if ( this->m_NumberOfSpatialSamples
- > this->GetFixedImageRegion().GetNumberOfPixels()) {
- this->m_NumberOfSpatialSamples
- = this->GetFixedImageRegion().GetNumberOfPixels();
- samples.resize(this->m_NumberOfSpatialSamples);
- }
-
- for( iter=samples.begin(); iter != end; ++iter ) {
- // Get sampled index
- FixedImageIndexType index = regionIter.GetIndex();
- // Get sampled fixed image value
- (*iter).FixedImageValue = regionIter.Get();
- // Translate index to point
- this->m_FixedImage->TransformIndexToPhysicalPoint( index,
- (*iter).FixedImagePointValue );
- ++regionIter;
- }
- }
-}
-
-/**
- * Uniformly sample the fixed image domain using a random walk
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::ComputeFixedImageParzenWindowIndices(
- FixedImageSpatialSampleContainer& samples )
-{
-
- typename FixedImageSpatialSampleContainer::iterator iter;
- typename FixedImageSpatialSampleContainer::const_iterator end=samples.end();
-
- for( iter=samples.begin(); iter != end; ++iter ) {
-
- // Determine parzen window arguments (see eqn 6 of Mattes paper [2]).
- double windowTerm =
- static_cast<double>( (*iter).FixedImageValue ) / m_FixedImageBinSize -
- m_FixedImageNormalizedMin;
- unsigned int pindex = static_cast<unsigned int>( vcl_floor(windowTerm ) );
-
- // Make sure the extreme values are in valid bins
- if ( pindex < 2 ) {
- pindex = 2;
- } else if ( pindex > (m_NumberOfHistogramBins - 3) ) {
- pindex = m_NumberOfHistogramBins - 3;
- }
-
- (*iter).FixedImageParzenWindowIndex = pindex;
-
- }
-
-}
-
-/**
- * Get the match Measure
- */
-template < class TFixedImage, class TMovingImage >
-typename MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::MeasureType
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValue( const ParametersType& parameters ) const
-{
-
- // Reset marginal pdf to all zeros.
- // Assumed the size has already been set to NumberOfHistogramBins
- // in Initialize().
- for ( unsigned int j = 0; j < m_NumberOfHistogramBins; j++ ) {
- m_FixedImageMarginalPDF[j] = 0.0;
- m_MovingImageMarginalPDF[j] = 0.0;
- }
-
- // Reset the joint pdfs to zero
- m_JointPDF->FillBuffer( 0.0 );
-
- // Set up the parameters in the transform
- this->m_Transform->SetParameters( parameters );
-
-
- // Declare iterators for iteration over the sample container
- typename FixedImageSpatialSampleContainer::const_iterator fiter;
- typename FixedImageSpatialSampleContainer::const_iterator fend =
- m_FixedImageSamples.end();
-
- unsigned long nSamples=0;
- unsigned long nFixedImageSamples=0;
-
-
- for ( fiter = m_FixedImageSamples.begin(); fiter != fend; ++fiter ) {
-
- // Get moving image value
- MovingImagePointType mappedPoint;
- bool sampleOk;
- double movingImageValue;
-
- this->TransformPoint( nFixedImageSamples, parameters, mappedPoint,
- sampleOk, movingImageValue );
-
- ++nFixedImageSamples;
-
- if( sampleOk ) {
-
- ++nSamples;
-
- /**
- * Compute this sample's contribution to the marginal and
- * joint distributions.
- *
- */
-
- // Determine parzen window arguments (see eqn 6 of Mattes paper [2])
- double movingImageParzenWindowTerm =
- movingImageValue / m_MovingImageBinSize - m_MovingImageNormalizedMin;
- unsigned int movingImageParzenWindowIndex =
- static_cast<unsigned int>( vcl_floor(movingImageParzenWindowTerm ) );
-
- // Make sure the extreme values are in valid bins
- if ( movingImageParzenWindowIndex < 2 ) {
- movingImageParzenWindowIndex = 2;
- } else if ( movingImageParzenWindowIndex > (m_NumberOfHistogramBins - 3) ) {
- movingImageParzenWindowIndex = m_NumberOfHistogramBins - 3;
- }
-
-
- // Since a zero-order BSpline (box car) kernel is used for
- // the fixed image marginal pdf, we need only increment the
- // fixedImageParzenWindowIndex by value of 1.0.
- m_FixedImageMarginalPDF[(*fiter).FixedImageParzenWindowIndex] +=
- static_cast<PDFValueType>( 1 );
-
- /**
- * The region of support of the parzen window determines which bins
- * of the joint PDF are effected by the pair of image values.
- * Since we are using a cubic spline for the moving image parzen
- * window, four bins are affected. The fixed image parzen window is
- * a zero-order spline (box car) and thus effects only one bin.
- *
- * The PDF is arranged so that moving image bins corresponds to the
- * zero-th (column) dimension and the fixed image bins corresponds
- * to the first (row) dimension.
- *
- */
-
- // Pointer to affected bin to be updated
- JointPDFValueType *pdfPtr = m_JointPDF->GetBufferPointer() +
- ( (*fiter).FixedImageParzenWindowIndex
- * m_JointPDF->GetOffsetTable()[1] );
-
- // Move the pointer to the first affected bin
- int pdfMovingIndex = static_cast<int>( movingImageParzenWindowIndex ) - 1;
- pdfPtr += pdfMovingIndex;
-
- for (; pdfMovingIndex <= static_cast<int>( movingImageParzenWindowIndex )
- + 2;
- pdfMovingIndex++, pdfPtr++ ) {
-
- // Update PDF for the current intensity pair
- double movingImageParzenWindowArg =
- static_cast<double>( pdfMovingIndex ) -
- static_cast<double>( movingImageParzenWindowTerm );
-
- *(pdfPtr) += static_cast<PDFValueType>(
- m_CubicBSplineKernel->Evaluate( movingImageParzenWindowArg ) );
-
- } //end parzen windowing for loop
-
- } //end if-block check sampleOk
- } // end iterating over fixed image spatial sample container for loop
-
- itkDebugMacro( "Ratio of voxels mapping into moving image buffer: "
- << nSamples << " / " << m_NumberOfSpatialSamples
- << std::endl );
-
- if( nSamples < m_NumberOfSpatialSamples / 16 ) {
- itkExceptionMacro( "Too many samples map outside moving image buffer: "
- << nSamples << " / " << m_NumberOfSpatialSamples
- << std::endl );
- }
-
- this->m_NumberOfPixelsCounted = nSamples;
-
-
- /**
- * Normalize the PDFs, compute moving image marginal PDF
- *
- */
- typedef ImageRegionIterator<JointPDFType> JointPDFIteratorType;
- JointPDFIteratorType jointPDFIterator ( m_JointPDF,
- m_JointPDF->GetBufferedRegion() );
-
- jointPDFIterator.GoToBegin();
-
- // Compute joint PDF normalization factor
- // (to ensure joint PDF sum adds to 1.0)
- double jointPDFSum = 0.0;
-
- while( !jointPDFIterator.IsAtEnd() ) {
- jointPDFSum += jointPDFIterator.Get();
- ++jointPDFIterator;
- }
-
- if ( jointPDFSum == 0.0 ) {
- itkExceptionMacro( "Joint PDF summed to zero" );
- }
-
-
- // Normalize the PDF bins
- jointPDFIterator.GoToEnd();
- while( !jointPDFIterator.IsAtBegin() ) {
- --jointPDFIterator;
- jointPDFIterator.Value() /= static_cast<PDFValueType>( jointPDFSum );
- }
-
-
- // Normalize the fixed image marginal PDF
- double fixedPDFSum = 0.0;
- for( unsigned int bin = 0; bin < m_NumberOfHistogramBins; bin++ ) {
- fixedPDFSum += m_FixedImageMarginalPDF[bin];
- }
-
- if ( fixedPDFSum == 0.0 ) {
- itkExceptionMacro( "Fixed image marginal PDF summed to zero" );
- }
-
- for( unsigned int bin=0; bin < m_NumberOfHistogramBins; bin++ ) {
- m_FixedImageMarginalPDF[bin] /= static_cast<PDFValueType>( fixedPDFSum );
- }
-
-
- // Compute moving image marginal PDF by summing over fixed image bins.
- typedef ImageLinearIteratorWithIndex<JointPDFType> JointPDFLinearIterator;
- JointPDFLinearIterator linearIter( m_JointPDF,
- m_JointPDF->GetBufferedRegion() );
-
- linearIter.SetDirection( 1 );
- linearIter.GoToBegin();
- unsigned int movingIndex1 = 0;
-
- while( !linearIter.IsAtEnd() ) {
-
- double sum = 0.0;
-
- while( !linearIter.IsAtEndOfLine() ) {
- sum += linearIter.Get();
- ++linearIter;
- }
-
- m_MovingImageMarginalPDF[movingIndex1] = static_cast<PDFValueType>(sum);
-
- linearIter.NextLine();
- ++movingIndex1;
-
- }
-
- /**
- * Compute the metric by double summation over histogram.
- */
-
- // Setup pointer to point to the first bin
- JointPDFValueType * jointPDFPtr = m_JointPDF->GetBufferPointer();
-
- // Initialze sum to zero
- double sum = 0.0;
-
- for( unsigned int fixedIndex = 0;
- fixedIndex < m_NumberOfHistogramBins;
- ++fixedIndex ) {
-
- double fixedImagePDFValue = m_FixedImageMarginalPDF[fixedIndex];
-
- for( unsigned int movingIndex = 0;
- movingIndex < m_NumberOfHistogramBins;
- ++movingIndex, jointPDFPtr++ ) {
-
- double movingImagePDFValue = m_MovingImageMarginalPDF[movingIndex];
- double jointPDFValue = *(jointPDFPtr);
-
- // check for non-zero bin contribution
- if( jointPDFValue > 1e-16 && movingImagePDFValue > 1e-16 ) {
-
- double pRatio = vcl_log(jointPDFValue / movingImagePDFValue );
- if( fixedImagePDFValue > 1e-16) {
- sum += jointPDFValue * ( pRatio - vcl_log(fixedImagePDFValue ) );
- }
-
- } // end if-block to check non-zero bin contribution
- } // end for-loop over moving index
- } // end for-loop over fixed index
-
- return static_cast<MeasureType>( -1.0 * sum );
-
-}
-
-
-/**
- * Get the both Value and Derivative Measure
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValueAndDerivative(
- const ParametersType& parameters,
- MeasureType& value,
- DerivativeType& derivative) const
-{
-
- // Set output values to zero
- value = NumericTraits< MeasureType >::Zero;
-
- if( this->m_UseExplicitPDFDerivatives ) {
- m_JointPDFDerivatives->FillBuffer( 0.0 );
- derivative = DerivativeType( this->GetNumberOfParameters() );
- derivative.Fill( NumericTraits< MeasureType >::Zero );
- } else {
- this->m_MetricDerivative.Fill( NumericTraits< MeasureType >::Zero );
- this->m_PRatioArray.Fill( 0.0 );
- }
-
- // Reset marginal pdf to all zeros.
- // Assumed the size has already been set to NumberOfHistogramBins
- // in Initialize().
- for ( unsigned int j = 0; j < m_NumberOfHistogramBins; j++ ) {
- m_FixedImageMarginalPDF[j] = 0.0;
- m_MovingImageMarginalPDF[j] = 0.0;
- }
-
- // Reset the joint pdfs to zero
- m_JointPDF->FillBuffer( 0.0 );
-
-
- // Set up the parameters in the transform
- this->m_Transform->SetParameters( parameters );
-
-
- // Declare iterators for iteration over the sample container
- typename FixedImageSpatialSampleContainer::const_iterator fiter;
- typename FixedImageSpatialSampleContainer::const_iterator fend =
- m_FixedImageSamples.end();
-
- unsigned long nSamples=0;
- unsigned long nFixedImageSamples=0;
-
- for ( fiter = m_FixedImageSamples.begin(); fiter != fend; ++fiter ) {
-
- // Get moving image value
- MovingImagePointType mappedPoint;
- bool sampleOk;
- double movingImageValue;
-
-
- this->TransformPoint( nFixedImageSamples, parameters, mappedPoint,
- sampleOk, movingImageValue );
-
- if( sampleOk ) {
- ++nSamples;
-
- // Get moving image derivative at the mapped position
- ImageDerivativesType movingImageGradientValue;
- this->ComputeImageDerivatives( mappedPoint, movingImageGradientValue );
-
-
- /**
- * Compute this sample's contribution to the marginal
- * and joint distributions.
- *
- */
-
- // Determine parzen window arguments (see eqn 6 of Mattes paper [2])
- double movingImageParzenWindowTerm =
- movingImageValue / m_MovingImageBinSize - m_MovingImageNormalizedMin;
- unsigned int movingImageParzenWindowIndex =
- static_cast<unsigned int>( vcl_floor(movingImageParzenWindowTerm ) );
-
- // Make sure the extreme values are in valid bins
- if ( movingImageParzenWindowIndex < 2 ) {
- movingImageParzenWindowIndex = 2;
- } else if ( movingImageParzenWindowIndex > (m_NumberOfHistogramBins - 3) ) {
- movingImageParzenWindowIndex = m_NumberOfHistogramBins - 3;
- }
-
-
- // Since a zero-order BSpline (box car) kernel is used for
- // the fixed image marginal pdf, we need only increment the
- // fixedImageParzenWindowIndex by value of 1.0.
- m_FixedImageMarginalPDF[(*fiter).FixedImageParzenWindowIndex] +=
- static_cast<PDFValueType>( 1 );
-
- /**
- * The region of support of the parzen window determines which bins
- * of the joint PDF are effected by the pair of image values.
- * Since we are using a cubic spline for the moving image parzen
- * window, four bins are effected. The fixed image parzen window is
- * a zero-order spline (box car) and thus effects only one bin.
- *
- * The PDF is arranged so that moving image bins corresponds to the
- * zero-th (column) dimension and the fixed image bins corresponds
- * to the first (row) dimension.
- *
- */
-
- // Pointer to affected bin to be updated
- JointPDFValueType *pdfPtr = m_JointPDF->GetBufferPointer() +
- ( (*fiter).FixedImageParzenWindowIndex * m_NumberOfHistogramBins );
-
- // Move the pointer to the fist affected bin
- int pdfMovingIndex = static_cast<int>( movingImageParzenWindowIndex ) - 1;
- pdfPtr += pdfMovingIndex;
-
- for (; pdfMovingIndex <= static_cast<int>( movingImageParzenWindowIndex )
- + 2;
- pdfMovingIndex++, pdfPtr++ ) {
- // Update PDF for the current intensity pair
- double movingImageParzenWindowArg =
- static_cast<double>( pdfMovingIndex ) -
- static_cast<double>(movingImageParzenWindowTerm);
-
- *(pdfPtr) += static_cast<PDFValueType>(
- m_CubicBSplineKernel->Evaluate( movingImageParzenWindowArg ) );
-
- if( this->m_UseExplicitPDFDerivatives ) {
- // Compute the cubicBSplineDerivative for later repeated use.
- double cubicBSplineDerivativeValue =
- m_CubicBSplineDerivativeKernel->Evaluate(
- movingImageParzenWindowArg );
-
- // Compute PDF derivative contribution.
- this->ComputePDFDerivatives( nFixedImageSamples,
- pdfMovingIndex,
- movingImageGradientValue,
- cubicBSplineDerivativeValue );
- }
-
- } //end parzen windowing for loop
-
- } //end if-block check sampleOk
-
- ++nFixedImageSamples;
-
- } // end iterating over fixed image spatial sample container for loop
-
- itkDebugMacro( "Ratio of voxels mapping into moving image buffer: "
- << nSamples << " / " << m_NumberOfSpatialSamples
- << std::endl );
-
- if( nSamples < m_NumberOfSpatialSamples / 16 ) {
- itkExceptionMacro( "Too many samples map outside moving image buffer: "
- << nSamples << " / " << m_NumberOfSpatialSamples
- << std::endl );
- }
-
- this->m_NumberOfPixelsCounted = nSamples;
-
- /**
- * Normalize the PDFs, compute moving image marginal PDF
- *
- */
- typedef ImageRegionIterator<JointPDFType> JointPDFIteratorType;
- JointPDFIteratorType jointPDFIterator ( m_JointPDF,
- m_JointPDF->GetBufferedRegion() );
-
- jointPDFIterator.GoToBegin();
-
-
- // Compute joint PDF normalization factor
- // (to ensure joint PDF sum adds to 1.0)
- double jointPDFSum = 0.0;
-
- while( !jointPDFIterator.IsAtEnd() ) {
- jointPDFSum += jointPDFIterator.Get();
- ++jointPDFIterator;
- }
-
- if ( jointPDFSum == 0.0 ) {
- itkExceptionMacro( "Joint PDF summed to zero" );
- }
-
-
- // Normalize the PDF bins
- jointPDFIterator.GoToEnd();
- while( !jointPDFIterator.IsAtBegin() ) {
- --jointPDFIterator;
- jointPDFIterator.Value() /= static_cast<PDFValueType>( jointPDFSum );
- }
-
-
- // Normalize the fixed image marginal PDF
- double fixedPDFSum = 0.0;
- for( unsigned int bin = 0; bin < m_NumberOfHistogramBins; bin++ ) {
- fixedPDFSum += m_FixedImageMarginalPDF[bin];
- }
-
- if ( fixedPDFSum == 0.0 ) {
- itkExceptionMacro( "Fixed image marginal PDF summed to zero" );
- }
-
- for( unsigned int bin=0; bin < m_NumberOfHistogramBins; bin++ ) {
- m_FixedImageMarginalPDF[bin] /= static_cast<PDFValueType>( fixedPDFSum );
- }
-
-
- // Compute moving image marginal PDF by summing over fixed image bins.
- typedef ImageLinearIteratorWithIndex<JointPDFType> JointPDFLinearIterator;
- JointPDFLinearIterator linearIter(
- m_JointPDF, m_JointPDF->GetBufferedRegion() );
-
- linearIter.SetDirection( 1 );
- linearIter.GoToBegin();
- unsigned int movingIndex1 = 0;
-
- while( !linearIter.IsAtEnd() ) {
-
- double sum = 0.0;
-
- while( !linearIter.IsAtEndOfLine() ) {
- sum += linearIter.Get();
- ++linearIter;
- }
-
- m_MovingImageMarginalPDF[movingIndex1] = static_cast<PDFValueType>(sum);
-
- linearIter.NextLine();
- ++movingIndex1;
-
- }
-
- double nFactor = 1.0 / ( m_MovingImageBinSize
- * static_cast<double>( nSamples ) );
-
- if( this->m_UseExplicitPDFDerivatives ) {
- // Normalize the joint PDF derivatives by the test image binsize and nSamples
- typedef ImageRegionIterator<JointPDFDerivativesType>
- JointPDFDerivativesIteratorType;
- JointPDFDerivativesIteratorType jointPDFDerivativesIterator (
- m_JointPDFDerivatives,
- m_JointPDFDerivatives->GetBufferedRegion()
- );
-
- jointPDFDerivativesIterator.GoToBegin();
-
- while( !jointPDFDerivativesIterator.IsAtEnd() ) {
- jointPDFDerivativesIterator.Value() *= nFactor;
- ++jointPDFDerivativesIterator;
- }
- }
-
- /**
- * Compute the metric by double summation over histogram.
- */
-
- // Setup pointer to point to the first bin
- JointPDFValueType * jointPDFPtr = m_JointPDF->GetBufferPointer();
-
- // Initialize sum to zero
- double sum = 0.0;
-
- for( unsigned int fixedIndex = 0;
- fixedIndex < m_NumberOfHistogramBins;
- ++fixedIndex ) {
- double fixedImagePDFValue = m_FixedImageMarginalPDF[fixedIndex];
-
- for( unsigned int movingIndex = 0; movingIndex < m_NumberOfHistogramBins;
- ++movingIndex, jointPDFPtr++ ) {
- double movingImagePDFValue = m_MovingImageMarginalPDF[movingIndex];
- double jointPDFValue = *(jointPDFPtr);
-
- // check for non-zero bin contribution
- if( jointPDFValue > 1e-16 && movingImagePDFValue > 1e-16 ) {
-
- double pRatio = vcl_log(jointPDFValue / movingImagePDFValue );
-
- if( fixedImagePDFValue > 1e-16) {
- sum += jointPDFValue * ( pRatio - vcl_log(fixedImagePDFValue ) );
- }
-
- if( this->m_UseExplicitPDFDerivatives ) {
- // move joint pdf derivative pointer to the right position
- JointPDFValueType * derivPtr = m_JointPDFDerivatives->GetBufferPointer()
- + ( fixedIndex * m_JointPDFDerivatives->GetOffsetTable()[2] )
- + ( movingIndex * m_JointPDFDerivatives->GetOffsetTable()[1] );
-
- for( unsigned int parameter=0; parameter < m_NumberOfParameters; ++parameter, derivPtr++ ) {
- // Ref: eqn 23 of Thevenaz & Unser paper [3]
- derivative[parameter] -= (*derivPtr) * pRatio;
- } // end for-loop over parameters
- } else {
- this->m_PRatioArray[fixedIndex][movingIndex] = pRatio * nFactor;
- }
- } // end if-block to check non-zero bin contribution
- } // end for-loop over moving index
- } // end for-loop over fixed index
-
- if( !(this->m_UseExplicitPDFDerivatives ) ) {
- // Second pass: This one is done for accumulating the contributions
- // to the derivative array.
-
- nFixedImageSamples = 0;
-
- for ( fiter = m_FixedImageSamples.begin(); fiter != fend; ++fiter ) {
-
- // Get moving image value
- MovingImagePointType mappedPoint;
- bool sampleOk;
- double movingImageValue;
-
- this->TransformPoint( nFixedImageSamples, parameters, mappedPoint,
- sampleOk, movingImageValue );
-
- if( sampleOk ) {
- // Get moving image derivative at the mapped position
- ImageDerivativesType movingImageGradientValue;
- this->ComputeImageDerivatives( mappedPoint, movingImageGradientValue );
-
-
- /**
- * Compute this sample's contribution to the marginal
- * and joint distributions.
- *
- */
-
- // Determine parzen window arguments (see eqn 6 of Mattes paper [2]).
- double movingImageParzenWindowTerm =
- movingImageValue / m_MovingImageBinSize - m_MovingImageNormalizedMin;
- unsigned int movingImageParzenWindowIndex =
- static_cast<unsigned int>( vcl_floor(movingImageParzenWindowTerm ) );
-
- // Make sure the extreme values are in valid bins
- if ( movingImageParzenWindowIndex < 2 ) {
- movingImageParzenWindowIndex = 2;
- } else if ( movingImageParzenWindowIndex > (m_NumberOfHistogramBins - 3) ) {
- movingImageParzenWindowIndex = m_NumberOfHistogramBins - 3;
- }
-
-
- // Move the pointer to the fist affected bin
- int pdfMovingIndex = static_cast<int>( movingImageParzenWindowIndex ) - 1;
-
- for (; pdfMovingIndex <= static_cast<int>( movingImageParzenWindowIndex )
- + 2;
- pdfMovingIndex++ ) {
-
- // Update PDF for the current intensity pair
- double movingImageParzenWindowArg =
- static_cast<double>( pdfMovingIndex ) -
- static_cast<double>(movingImageParzenWindowTerm);
-
- // Compute the cubicBSplineDerivative for later repeated use.
- double cubicBSplineDerivativeValue =
- m_CubicBSplineDerivativeKernel->Evaluate(
- movingImageParzenWindowArg );
-
- // Compute PDF derivative contribution.
- this->ComputePDFDerivatives( nFixedImageSamples,
- pdfMovingIndex,
- movingImageGradientValue,
- cubicBSplineDerivativeValue );
-
-
- } //end parzen windowing for loop
-
- } //end if-block check sampleOk
-
- ++nFixedImageSamples;
-
- } // end iterating over fixed image spatial sample container for loop
-
-
- derivative = this->m_MetricDerivative;
- }
-
- value = static_cast<MeasureType>( -1.0 * sum );
-}
-
-
-/**
- * Get the match measure derivative
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetDerivative( const ParametersType& parameters,
- DerivativeType & derivative ) const
-{
- MeasureType value;
- // call the combined version
- this->GetValueAndDerivative( parameters, value, derivative );
-}
-
-
-/**
- * Compute image derivatives using a central difference function
- * if we are not using a BSplineInterpolator, which includes
- * derivatives.
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::ComputeImageDerivatives(
- const MovingImagePointType& mappedPoint,
- ImageDerivativesType& gradient ) const
-{
-
- if( m_InterpolatorIsBSpline ) {
- // Computed moving image gradient using derivative BSpline kernel.
- gradient = m_BSplineInterpolator->EvaluateDerivative( mappedPoint );
- } else {
- // For all generic interpolator use central differencing.
- gradient = m_DerivativeCalculator->Evaluate( mappedPoint );
- }
-
-}
-
-
-/**
- * Transform a point from FixedImage domain to MovingImage domain.
- * This function also checks if mapped point is within support region.
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::TransformPoint(
- unsigned int sampleNumber,
- const ParametersType& parameters,
- MovingImagePointType& mappedPoint,
- bool& sampleOk,
- double& movingImageValue ) const
-{
-
- if ( !m_TransformIsBSpline ) {
- // Use generic transform to compute mapped position
- mappedPoint = this->m_Transform->TransformPoint(
- m_FixedImageSamples[sampleNumber].FixedImagePointValue );
-
- // Check if mapped point inside image buffer
- sampleOk = this->m_Interpolator->IsInsideBuffer( mappedPoint );
- } else {
-
- if( this->m_UseCachingOfBSplineWeights ) {
- // If the transform is BSplineDeformable, we can use the precomputed
- // weights and indices to obtained the mapped position
- //
- const WeightsValueType * weights =
- m_BSplineTransformWeightsArray[sampleNumber];
- const IndexValueType * indices =
- m_BSplineTransformIndicesArray[sampleNumber];
- mappedPoint.Fill( 0.0 );
-
- if ( m_WithinSupportRegionArray[sampleNumber] ) {
- for ( unsigned int k = 0; k < m_NumBSplineWeights; k++ ) {
- for ( unsigned int j = 0; j < FixedImageDimension; j++ ) {
- mappedPoint[j] += weights[k] *
- parameters[ indices[k] + m_ParametersOffset[j] ];
- }
- }
- }
-
- for( unsigned int j = 0; j < FixedImageDimension; j++ ) {
- mappedPoint[j] += m_PreTransformPointsArray[sampleNumber][j];
- }
-
- // Check if mapped point inside image buffer
- sampleOk = this->m_Interpolator->IsInsideBuffer( mappedPoint );
-
- // Check if mapped point is within the support region of a grid point.
- // This is neccessary for computing the metric gradient
- sampleOk = sampleOk && m_WithinSupportRegionArray[sampleNumber];
- } else {
- // If not caching values, we invoke the Transform to recompute the
- // mapping of the point.
- this->m_BSplineTransform->TransformPoint(
- this->m_FixedImageSamples[sampleNumber].FixedImagePointValue,
- mappedPoint, this->m_Weights, this->m_Indices, sampleOk);
-
- // Check if mapped point inside image buffer
- sampleOk = sampleOk && this->m_Interpolator->IsInsideBuffer( mappedPoint );
- }
-
- }
-
- // If user provided a mask over the Moving image
- if ( this->m_MovingImageMask ) {
- // Check if mapped point is within the support region of the moving image
- // mask
- sampleOk = sampleOk && this->m_MovingImageMask->IsInside( mappedPoint );
- }
-
-
- if ( sampleOk ) {
- movingImageValue = this->m_Interpolator->Evaluate( mappedPoint );
-
- if ( movingImageValue < m_MovingImageTrueMin ||
- movingImageValue > m_MovingImageTrueMax ) {
- // need to throw out this sample as it will not fall into a valid bin
- sampleOk = false;
- }
- }
-}
-
-
-/**
- * Compute PDF derivatives contribution for each parameter
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::ComputePDFDerivatives(
- unsigned int sampleNumber,
- int pdfMovingIndex,
- const ImageDerivativesType& movingImageGradientValue,
- double cubicBSplineDerivativeValue ) const
-{
-
- const int pdfFixedIndex =
- m_FixedImageSamples[sampleNumber].FixedImageParzenWindowIndex;
-
- JointPDFValueType * derivPtr = NULL;
- double precomputedWeight = 0.0;
-
- if( this->m_UseExplicitPDFDerivatives ) {
- // Update bins in the PDF derivatives for the current intensity pair
- derivPtr = m_JointPDFDerivatives->GetBufferPointer() +
- ( pdfFixedIndex * m_JointPDFDerivatives->GetOffsetTable()[2] ) +
- ( pdfMovingIndex * m_JointPDFDerivatives->GetOffsetTable()[1] );
- } else {
- // Recover the precomputed weight for this specific PDF bin
- precomputedWeight = this->m_PRatioArray[pdfFixedIndex][pdfMovingIndex];
- }
-
- if( !m_TransformIsBSpline ) {
-
- /**
- * Generic version which works for all transforms.
- */
-
- // Compute the transform Jacobian.
- typedef typename TransformType::JacobianType JacobianType;
-#if ITK_VERSION_MAJOR >= 4
- JacobianType jacobian;
- this->m_Transform->ComputeJacobianWithRespectToParameters( m_FixedImageSamples[sampleNumber].FixedImagePointValue, jacobian );
-#else
- const JacobianType & jacobian =
- this->m_Transform->GetJacobian( m_FixedImageSamples[sampleNumber].FixedImagePointValue );
-#endif
-
- for ( unsigned int mu = 0; mu < m_NumberOfParameters; mu++ ) {
- double innerProduct = 0.0;
- for ( unsigned int dim = 0; dim < FixedImageDimension; dim++ ) {
- innerProduct += jacobian[dim][mu] * movingImageGradientValue[dim];
- }
-
- const double derivativeContribution = innerProduct * cubicBSplineDerivativeValue;
-
- if( this->m_UseExplicitPDFDerivatives ) {
- *(derivPtr) -= derivativeContribution;
- ++derivPtr;
- } else {
- this->m_MetricDerivative[mu] += precomputedWeight * derivativeContribution;
- }
- }
-
- } else {
- const WeightsValueType * weights = NULL;
- const IndexValueType * indices = NULL;
-
- if( this->m_UseCachingOfBSplineWeights ) {
- /**
- * If the transform is of type BSplineDeformableTransform,
- * we can obtain a speed up by only processing the affected parameters.
- * Note that these pointers are just pointing to pre-allocated rows
- * of the caching arrays. There is therefore, no need to free this
- * memory.
- */
- weights = m_BSplineTransformWeightsArray[sampleNumber];
- indices = m_BSplineTransformIndicesArray[sampleNumber];
- } else {
-#if ITK_VERSION_MAJOR >= 4
- m_BSplineTransform->ComputeJacobianFromBSplineWeightsWithRespectToPosition(
- m_FixedImageSamples[sampleNumber].FixedImagePointValue, m_Weights, m_Indices );
-#else
- m_BSplineTransform->GetJacobian(
- m_FixedImageSamples[sampleNumber].FixedImagePointValue, m_Weights, m_Indices );
-#endif
- }
-
- for( unsigned int dim = 0; dim < FixedImageDimension; dim++ ) {
-
- double innerProduct;
- int parameterIndex;
-
- for( unsigned int mu = 0; mu < m_NumBSplineWeights; mu++ ) {
-
- /* The array weights contains the Jacobian values in a 1-D array
- * (because for each parameter the Jacobian is non-zero in only 1 of the
- * possible dimensions) which is multiplied by the moving image
- * gradient. */
- if( this->m_UseCachingOfBSplineWeights ) {
- innerProduct = movingImageGradientValue[dim] * weights[mu];
- parameterIndex = indices[mu] + m_ParametersOffset[dim];
- } else {
- innerProduct = movingImageGradientValue[dim] * this->m_Weights[mu];
- parameterIndex = this->m_Indices[mu] + this->m_ParametersOffset[dim];
- }
-
- const double derivativeContribution = innerProduct * cubicBSplineDerivativeValue;
-
- if( this->m_UseExplicitPDFDerivatives ) {
- JointPDFValueType * ptr = derivPtr + parameterIndex;
- *(ptr) -= derivativeContribution;
- } else {
- this->m_MetricDerivative[parameterIndex] += precomputedWeight * derivativeContribution;
- }
-
- } //end mu for loop
- } //end dim for loop
-
- } // end if-block transform is BSpline
-
-}
-
-
-// Method to reinitialize the seed of the random number generator
-template < class TFixedImage, class TMovingImage > void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::ReinitializeSeed()
-{
- Statistics::MersenneTwisterRandomVariateGenerator::GetInstance()->SetSeed();
-}
-
-// Method to reinitialize the seed of the random number generator
-template < class TFixedImage, class TMovingImage > void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::ReinitializeSeed(int seed)
-{
- Statistics::MersenneTwisterRandomVariateGenerator::GetInstance()->SetSeed(
- seed);
-}
-
-
-/**
- * Cache pre-transformed points, weights and indices.
- * This method is only called if the flag UseCachingOfBSplineWeights is ON.
- */
-template < class TFixedImage, class TMovingImage >
-void
-MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::PreComputeTransformValues()
-{
- // Create all zero dummy transform parameters
- ParametersType dummyParameters( this->m_Transform->GetNumberOfParameters() );
- dummyParameters.Fill( 0.0 );
- this->m_Transform->SetParameters( dummyParameters );
-
- // Cycle through each sampled fixed image point
- BSplineTransformWeightsType weights( m_NumBSplineWeights );
- BSplineTransformIndexArrayType indices( m_NumBSplineWeights );
- bool valid;
- MovingImagePointType mappedPoint;
-
- // Declare iterators for iteration over the sample container
- typename FixedImageSpatialSampleContainer::const_iterator fiter;
- typename FixedImageSpatialSampleContainer::const_iterator fend =
- m_FixedImageSamples.end();
- unsigned long counter = 0;
-
- for( fiter = m_FixedImageSamples.begin(); fiter != fend; ++fiter, counter++ ) {
- m_BSplineTransform->TransformPoint(
- m_FixedImageSamples[counter].FixedImagePointValue,
- mappedPoint, weights, indices, valid );
-
- for( unsigned long k = 0; k < m_NumBSplineWeights; k++ ) {
- m_BSplineTransformWeightsArray[counter][k] = weights[k];
- m_BSplineTransformIndicesArray[counter][k] = indices[k];
- }
-
- m_PreTransformPointsArray[counter] = mappedPoint;
- m_WithinSupportRegionArray[counter] = valid;
-
- }
-
-}
-
-
-} // end namespace itk
-
-
-#endif
-
#endif
// gets integrated into the main directories.
#include "itkConfigure.h"
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h"
-#else
-
-#include "itkImageToImageMetric.h"
-#include "itkCovariantVector.h"
-#include "itkPoint.h"
-
-
-namespace itk
-{
-/** \class MeanSquaresImageToImageMetricFor3DBLUTFFD
- * \brief Computes similarity between two objects to be registered
- *
- * This Class is templated over the type of the fixed and moving
- * images to be compared.
- *
- * This metric computes the sum of squared differences between pixels in
- * the moving image and pixels in the fixed image. The spatial correspondance
- * between both images is established through a Transform. Pixel values are
- * taken from the Moving image. Their positions are mapped to the Fixed image
- * and result in general in non-grid position on it. Values at these non-grid
- * position of the Fixed image are interpolated using a user-selected Interpolator.
- *
- * \ingroup RegistrationMetrics
- */
-template < class TFixedImage, class TMovingImage >
-class ITK_EXPORT MeanSquaresImageToImageMetricFor3DBLUTFFD :
- public ImageToImageMetric< TFixedImage, TMovingImage>
-{
-public:
-
- /** Standard class typedefs. */
- typedef MeanSquaresImageToImageMetricFor3DBLUTFFD Self;
- typedef ImageToImageMetric<TFixedImage, TMovingImage > Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(MeanSquaresImageToImageMetricFor3DBLUTFFD, ImageToImageMetric);
-
-
- /** Types transferred from the base class */
- typedef typename Superclass::RealType RealType;
- typedef typename Superclass::TransformType TransformType;
- typedef typename Superclass::TransformPointer TransformPointer;
- typedef typename Superclass::TransformParametersType TransformParametersType;
- typedef typename Superclass::TransformJacobianType TransformJacobianType;
- typedef typename Superclass::GradientPixelType GradientPixelType;
- typedef typename Superclass::GradientImageType GradientImageType;
- typedef typename Superclass::InputPointType InputPointType;
- typedef typename Superclass::OutputPointType OutputPointType;
-
- typedef typename Superclass::MeasureType MeasureType;
- typedef typename Superclass::DerivativeType DerivativeType;
- typedef typename Superclass::FixedImageType FixedImageType;
- typedef typename Superclass::MovingImageType MovingImageType;
- typedef typename Superclass::FixedImageConstPointer FixedImageConstPointer;
- typedef typename Superclass::MovingImageConstPointer MovingImageConstPointer;
-
-
- /** Get the derivatives of the match measure. */
- void GetDerivative( const TransformParametersType & parameters,
- DerivativeType & derivative ) const;
-
- /** Get the value for single valued optimizers. */
- MeasureType GetValue( const TransformParametersType & parameters ) const;
-
- /** Get value and derivatives for multiple valued optimizers. */
- void GetValueAndDerivative( const TransformParametersType & parameters,
- MeasureType& Value, DerivativeType& Derivative ) const;
-
-#ifdef ITK_USE_CONCEPT_CHECKING
- /** Begin concept checking */
- itkConceptMacro(MovingPixelTypeHasNumericTraitsCheck,
- (Concept::HasNumericTraits<typename TMovingImage::PixelType>));
- itkConceptMacro(MovingRealTypeAdditivieOperatorsCheck,
- (Concept::AdditiveOperators<
- typename NumericTraits<typename TMovingImage::PixelType>::RealType>));
- itkConceptMacro(MovingRealTypeMultiplyOperatorCheck,
- (Concept::MultiplyOperator<
- typename NumericTraits<typename TMovingImage::PixelType>::RealType>));
-
- /** End concept checking */
-#endif
-
-protected:
- MeanSquaresImageToImageMetricFor3DBLUTFFD();
- virtual ~MeanSquaresImageToImageMetricFor3DBLUTFFD() {};
-
-private:
- MeanSquaresImageToImageMetricFor3DBLUTFFD(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkMeanSquaresImageToImageMetricFor3DBLUTFFD.txx"
-#endif
-
-#endif
-
#endif
// gets integrated into the main directories.
#include "itkConfigure.h"
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
#include "itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx"
-#else
#include "itkMeanSquaresImageToImageMetricFor3DBLUTFFD.h"
#include "itkImageRegionConstIteratorWithIndex.h"
if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
const RealType fixedValue = ti.Value();
this->m_NumberOfPixelsCounted++;
if( this->m_Interpolator->IsInsideBuffer( transformedPoint ) ) {
const RealType movingValue = this->m_Interpolator->Evaluate( transformedPoint );
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
this->m_Transform->ComputeJacobianWithRespectToParameters( inputPoint, jacobian );
-#else
- const TransformJacobianType & jacobian =
- this->m_Transform->GetJacobian( inputPoint );
-#endif
const RealType fixedValue = ti.Value();
this->m_NumberOfPixelsCounted++;
#ifndef __itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD_h
#define __itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD_h
-#if ITK_VERSION_MAJOR >= 4
- #include "itkImageToImageMetric.h"
-#else
- #include "itkOptImageToImageMetric.h"
-#endif
+#include "itkImageToImageMetric.h"
#include "itkCovariantVector.h"
#include "itkPoint.h"
#include "itkIndex.h"
#include "vnl/vnl_math.h"
#include "itkStatisticsImageFilter.h"
-#include "vnl/vnl_vector.txx"
-#include "vnl/vnl_c_vector.txx"
+#include "vnl/vnl_vector.h"
+#include "vnl/vnl_c_vector.h"
namespace itk
{
{
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING
this->GetValueMultiThreadedInitiate();
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING ON SAMPLES
this->GetValueAndDerivativeMultiThreadedInitiate();
transform = this->m_Transform;
}
-#if ITK_VERSION_MAJOR >= 4
JacobianType jacobian;
transform->ComputeJacobianWithRespectToParameters(this->m_FixedImageSamples[sampleNumber].point, jacobian);
-#else
- const JacobianType& jacobian =
- transform->GetJacobian( this->m_FixedImageSamples[sampleNumber].point );
-#endif
// for ( unsigned int mu = 0; mu < this->m_NumberOfParameters; mu++ )
// {
indicesHelper = &(this->m_BSplineTransformIndices);
}
-#if ITK_VERSION_MAJOR >= 4
this->m_BSplineTransform->ComputeJacobianFromBSplineWeightsWithRespectToPosition(
this->m_FixedImageSamples[sampleNumber].point,
*weightsHelper, *indicesHelper );
-#else
- this->m_BSplineTransform->GetJacobian(
- this->m_FixedImageSamples[sampleNumber].point,
- *weightsHelper, *indicesHelper );
-#endif
}
for( unsigned int dim = 0; dim < Superclass::FixedImageDimension; dim++ ) {
#ifndef __itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD_h
#define __itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD_h
-#if ITK_VERSION_MAJOR >= 4
- #include "itkImageToImageMetric.h"
-#else
- #include "itkOptImageToImageMetric.h"
-#endif
+#include "itkImageToImageMetric.h"
#include "itkCovariantVector.h"
#include "itkPoint.h"
#include "itkIndex.h"
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// MUST BE CALLED TO INITIATE PROCESSING
this->GetValueMultiThreadedInitiate();
}
// Jacobian should be evaluated at the unmapped (fixed image) point.
-#if ITK_VERSION_MAJOR >= 4
TransformJacobianType jacobian;
transform->ComputeJacobianWithRespectToParameters(this->m_FixedImageSamples[fixedImageSample].point, jacobian);
-#else
- const TransformJacobianType & jacobian = transform ->GetJacobian( this->m_FixedImageSamples[fixedImageSample].point );
-#endif
//double sum;
unsigned int par, dim;
for( par=0; par<this->m_NumberOfParameters; par+=3) {
// Set up the parameters in the transform
this->m_Transform->SetParameters( parameters );
-#if ITK_VERSION_MAJOR < 4
- this->m_Parameters = parameters;
-#endif
// Reset the joint pdfs to zero
memset( m_ThreaderMSE,
#=========================================================
# Add Libraries used in vv and clitk to avoid recompilation
-FOREACH(clitkTool clitkExtractLung clitkExtractPatient clitkConnectedComponentLabeling clitkRegionGrowing)
+foreach(clitkTool clitkExtractLung clitkExtractPatient clitkConnectedComponentLabeling clitkRegionGrowing)
WRAP_GGO(${clitkTool}_GGO_C ${clitkTool}.ggo)
- SET(GGO_C_FILES ${GGO_C_FILES} ${${clitkTool}_GGO_C})
-ENDFOREACH(clitkTool)
-ADD_LIBRARY(clitkSegmentationGgoLib
+ set(GGO_C_FILES ${GGO_C_FILES} ${${clitkTool}_GGO_C})
+endforeach(clitkTool)
+add_library(clitkSegmentationGgoLib
clitkFilterWithAnatomicalFeatureDatabaseManagement.cxx
clitkAnatomicalFeatureDatabase.cxx
clitkSliceBySliceRelativePositionFilter_uchar.cxx
#=========================================================
-IF(CLITK_BUILD_SEGMENTATION)
+if(CLITK_BUILD_SEGMENTATION)
WRAP_GGO(clitkConnectedComponentLabeling_GGO_C clitkConnectedComponentLabeling.ggo)
- ADD_EXECUTABLE(clitkConnectedComponentLabeling clitkConnectedComponentLabeling.cxx ${clitkConnectedComponentLabeling_GGO_C})
- TARGET_LINK_LIBRARIES(clitkConnectedComponentLabeling clitkCommon)
- SET(SEGMENTATION_INSTALL clitkConnectedComponentLabeling)
+ add_executable(clitkConnectedComponentLabeling clitkConnectedComponentLabeling.cxx ${clitkConnectedComponentLabeling_GGO_C})
+ target_link_libraries(clitkConnectedComponentLabeling clitkCommon)
+ set(SEGMENTATION_INSTALL clitkConnectedComponentLabeling)
- ADD_EXECUTABLE(clitkExtractPatient clitkExtractPatient.cxx ${clitkExtractPatient_GGO_C})
- TARGET_LINK_LIBRARIES(clitkExtractPatient clitkCommon clitkSegmentationGgoLib)
- SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractPatient)
+ add_executable(clitkExtractPatient clitkExtractPatient.cxx ${clitkExtractPatient_GGO_C})
+ target_link_libraries(clitkExtractPatient clitkCommon clitkSegmentationGgoLib)
+ set(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractPatient)
- ADD_EXECUTABLE(clitkExtractLung clitkExtractLung.cxx ${clitkExtractLung_GGO_C})
- TARGET_LINK_LIBRARIES(clitkExtractLung clitkSegmentationGgoLib clitkCommon)
- SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractLung)
+ add_executable(clitkExtractLung clitkExtractLung.cxx ${clitkExtractLung_GGO_C})
+ target_link_libraries(clitkExtractLung clitkSegmentationGgoLib clitkCommon)
+ set(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractLung)
WRAP_GGO(clitkExtractBones_GGO_C clitkExtractBones.ggo)
- ADD_EXECUTABLE(clitkExtractBones clitkExtractBones.cxx ${clitkExtractBones_GGO_C})
- TARGET_LINK_LIBRARIES(clitkExtractBones clitkCommon clitkSegmentationGgoLib)
- SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractBones)
+ add_executable(clitkExtractBones clitkExtractBones.cxx ${clitkExtractBones_GGO_C})
+ target_link_libraries(clitkExtractBones clitkCommon clitkSegmentationGgoLib)
+ set(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractBones)
WRAP_GGO(clitkMorphoMath_GGO_C clitkMorphoMath.ggo)
- ADD_EXECUTABLE(clitkMorphoMath clitkMorphoMath.cxx ${clitkMorphoMath_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMorphoMath clitkCommon)
- SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMorphoMath)
+ add_executable(clitkMorphoMath clitkMorphoMath.cxx ${clitkMorphoMath_GGO_C})
+ target_link_libraries(clitkMorphoMath clitkCommon)
+ set(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMorphoMath)
WRAP_GGO(clitkDecomposeAndReconstruct_GGO_C clitkDecomposeAndReconstruct.ggo)
- ADD_EXECUTABLE(clitkDecomposeAndReconstruct clitkDecomposeAndReconstruct.cxx clitkDecomposeAndReconstructGenericFilter.cxx ${clitkDecomposeAndReconstruct_GGO_C})
- TARGET_LINK_LIBRARIES(clitkDecomposeAndReconstruct clitkCommon)
- SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkDecomposeAndReconstruct)
+ add_executable(clitkDecomposeAndReconstruct clitkDecomposeAndReconstruct.cxx clitkDecomposeAndReconstructGenericFilter.cxx ${clitkDecomposeAndReconstruct_GGO_C})
+ target_link_libraries(clitkDecomposeAndReconstruct clitkCommon)
+ set(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkDecomposeAndReconstruct)
WRAP_GGO(clitkMotionMask_GGO_C clitkMotionMask.ggo)
- ADD_EXECUTABLE(clitkMotionMask clitkMotionMask.cxx clitkMotionMaskGenericFilter.cxx ${clitkMotionMask_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMotionMask clitkCommon)
- SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMotionMask)
-
+ add_executable(clitkMotionMask clitkMotionMask.cxx clitkMotionMaskGenericFilter.cxx ${clitkMotionMask_GGO_C})
+ target_link_libraries(clitkMotionMask clitkCommon)
+ set(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMotionMask)
+
WRAP_GGO(clitkRegionGrowing_GGO_C clitkRegionGrowing.ggo)
- ADD_EXECUTABLE(clitkRegionGrowing clitkRegionGrowing.cxx ${clitkRegionGrowing_GGO_C} ${clitkRelativePosition_GGO_C})
- TARGET_LINK_LIBRARIES(clitkRegionGrowing clitkCommon)
+ add_executable(clitkRegionGrowing clitkRegionGrowing.cxx ${clitkRegionGrowing_GGO_C} ${clitkRelativePosition_GGO_C})
+ target_link_libraries(clitkRegionGrowing clitkCommon)
- INSTALL (TARGETS ${SEGMENTATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
+ install(TARGETS ${SEGMENTATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
-ENDIF(CLITK_BUILD_SEGMENTATION)
+endif(CLITK_BUILD_SEGMENTATION)
-# ADD_EXECUTABLE(ScalarImageMarkovRandomField1 ScalarImageMarkovRandomField1.cxx)
-# TARGET_LINK_LIBRARIES(ScalarImageMarkovRandomField1 clitkCommon ITKStatistics)
-# ADD_EXECUTABLE(ScalarImageKmeansClassifier ScalarImageKmeansClassifier.cxx)
-# TARGET_LINK_LIBRARIES(ScalarImageKmeansClassifier clitkCommon ITKStatistics)
+# add_executable(ScalarImageMarkovRandomField1 ScalarImageMarkovRandomField1.cxx)
+# target_link_libraries(ScalarImageMarkovRandomField1 clitkCommon ITKStatistics)
+# add_executable(ScalarImageKmeansClassifier ScalarImageKmeansClassifier.cxx)
+# target_link_libraries(ScalarImageKmeansClassifier clitkCommon ITKStatistics)
//--------------------------------------------------------------------
void clitk::AnatomicalFeatureDatabase::SetPoint3D(std::string tag, PointType3D & p)
{
-#if ITK_VERSION_MAJOR > 3
std::ostringstream value;
-#else
- ::itk::OStringStream value;
-#endif
value << p[0] << " " << p[1] << " " << p[2];
m_MapOfTag[tag] = value.str();
}
opening->Update();
typename SlicerFilterType::Pointer slicer = SlicerFilterType::New();
-#if ITK_VERSION_MAJOR >= 4
slicer->SetDirectionCollapseToIdentity();
-#endif
slicer->SetInput(opening->GetOutput());
// label result
for (unsigned int j = 0; j < nlables; j++) {
shape = label_map->GetNthLabelObject(j);
if (shape->Size() > 150 && shape->Size() <= max_size) {
-#if ITK_VERSION_MAJOR < 4
- double e = 1 - 1/shape->GetBinaryElongation();
-#else
double e = 1 - 1/shape->GetElongation();
-#endif
//double area = 1 - r->Area() ;
if (e < max_elongation) {
nshapes++;
start2D[m_Directions[i]]=sliceIndex;
desiredRegion.SetIndex( start2D );
extractFilter->SetExtractionRegion( desiredRegion );
-#if ITK_VERSION_MAJOR == 4
extractFilter->SetDirectionCollapseToSubmatrix();
-#endif
extractFilter->Update( );
typename ImageSliceType::Pointer slice= extractFilter->GetOutput();
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
// clitk include
#include "clitkIO.h"
#include "clitkImageCommon.h"
-#include "clitkMorphoMath_ggo.h"
#include "clitkConditionalBinaryErodeImageFilter.h"
#include "clitkConditionalBinaryDilateImageFilter.h"
//--------------------------------------------------------------------
template<class ImageType>
- class ITK_EXPORT MorphoMathFilter:
- public clitk::FilterBase,
- public itk::ImageToImageFilter<ImageType, ImageType>
+ class ITK_EXPORT MorphoMathFilter:
+ public clitk::FilterBase,
+ public itk::ImageToImageFilter<ImageType, ImageType>
{
-
- public:
+
+ public:
/** Standard class typedefs. */
typedef itk::ImageToImageFilter<ImageType, ImageType> Superclass;
typedef MorphoMathFilter<ImageType> Self;
typedef itk::SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
- itkNewMacro(Self);
-
+ itkNewMacro(Self);
+
/** Run-time type information (and related methods). */
itkTypeMacro(AddRelativePositionConstraintToLabelImageFilter, ImageToImageFilter);
FILTERBASE_INIT;
/** Some convenient typedefs. */
typedef typename ImageType::ConstPointer ImageConstPointer;
typedef typename ImageType::Pointer ImagePointer;
- typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::RegionType RegionType;
typedef typename ImageType::PixelType PixelType;
typedef typename ImageType::SpacingType SpacingType;
typedef typename ImageType::SizeType SizeType;
typedef typename ImageType::PointType PointType;
typedef float InternalPixelType;
typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
-
+
/** ImageDimension constants */
itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
typedef itk::Image<float, ImageDimension> FloatImageType;
/** Operation types */
typedef enum { Erode = 0, Dilate = 1,
- Close = 2, Open = 3,
+ Close = 2, Open = 3,
CondErode = 4, CondDilate = 5
} OperationTypeEnumeration;
-
+
/** Options */
itkGetConstMacro(VerboseFlag, bool);
itkSetMacro(VerboseFlag, bool);
itkSetMacro(ForegroundValue, PixelType);
void SetOperationType(int type);
-
+
itkGetConstMacro(RadiusInMM, PointType);
void SetRadiusInMM(PointType & p);
itkGetConstMacro(BoundaryToForegroundFlag, bool);
itkSetMacro(BoundaryToForegroundFlag, bool);
itkBooleanMacro(BoundaryToForegroundFlag);
-
+
itkGetConstMacro(ExtendSupportFlag, bool);
itkSetMacro(ExtendSupportFlag, bool);
itkBooleanMacro(ExtendSupportFlag);
-
+
protected:
MorphoMathFilter();
virtual ~MorphoMathFilter();
MorphoMathFilter(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
};
-
+
} // end namespace clitk
#ifndef ITK_MANUAL_INSTANTIATION
#include "clitkMorphoMathFilter.txx"
#endif
-
+
#endif //#define CLITKMORPHOMATHFILTER_H
// try to guess ideal ellipse axes from the lungs' bounding box and centroid
// with some hard-coded "magic" constants...
-#if ITK_VERSION_MAJOR >= 4
typename LabelType::RegionType lung_bbox = label->GetBoundingBox();
-#else
- typename LabelType::RegionType lung_bbox = label->GetRegion();
-#endif
+
axes[0] = 0.95*lung_bbox.GetSize()[0]*spacing[0]/2;
axes[1] = 0.3*lung_bbox.GetSize()[1]*spacing[1]/2;
axes[2] = 1.25*fabs(lung_centroid[2] - center[2]);
IteratorType it(ball.GetRadius(),
input,
input->GetLargestPossibleRegion());
-#if ITK_VERSION_MAJOR < 4
- typename BallType::ConstIterator nit;
- unsigned idx = 0;
- for (nit = ball.Begin(); nit != ball.End(); ++nit, ++idx)
- {
- if (*nit)
- {
- it.ActivateOffset(it.GetOffset(idx));
- }
- else
- {
- it.DeactivateOffset(it.GetOffset(idx));
- }
- }
-#else
it.CreateActiveListFromNeighborhood(ball);
it.NeedToUseBoundaryConditionOff();
-#endif
it.SetLocation(seeds[0]);
for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
set(build_type ${CMAKE_BUILD_TYPE})
#=========================================================
-MACRO (DD in)
- MESSAGE(${in}=${${in}})
-ENDMACRO(DD)
+macro(DD in)
+ message(${in}=${${in}})
+endmacro(DD)
#=========================================================
project(SuperBuild_VV)
find_package(Git REQUIRED)
+if( 1 EQUAL 1)
#=========================================================
# QT
-SET(QtWinSpecFiles "${source_prefix}/qt/mkspecs/win32-msvc2003/qmake.conf";
- "${source_prefix}/qt/mkspecs/win32-msvc2005/qmake.conf";
- "${source_prefix}/qt/mkspecs/win32-msvc2008/qmake.conf";
- "${source_prefix}/qt/mkspecs/win32-msvc2010/qmake.conf")
+if(WIN32)
+set(QtWinSpecFiles "${source_prefix}/qt/mkspecs/win32-msvc2003/qmake.conf;${source_prefix}/qt/mkspecs/win32-msvc2005/qmake.conf;${source_prefix}/qt/mkspecs/win32-msvc2008/qmake.conf;${source_prefix}/qt/mkspecs/win32-msvc2010/qmake.conf")
+set(WINPATCH "sed -i \"s/\\-MD/-MT/g\" ${QtWinSpecFiles}")
+else()
+set(WINPATCH "")
+endif()
ExternalProject_Add(
QT
SOURCE_DIR ${source_prefix}/qt
- GIT_REPOSITORY git://gitorious.org/qt/qt.git
- GIT_TAG v4.8.3
- PATCH_COMMAND sed -i "s/\\-MD/-MT/g" ${QtWinSpecFiles}
+ GIT_REPOSITORY git://code.qt.io/qt/qt.git
+ GIT_TAG v4.8.6
+ PATCH_COMMAND ${WINPATCH}
CONFIGURE_COMMAND ${source_prefix}/qt/configure -confirm-license
- -static
+ -static
-fast
-opensource
-release
-no-glib
INSTALL_COMMAND ""
)
-SET(qmake_executable "${build_prefix}/QT/bin/qmake")
+set(qmake_executable "${build_prefix}/QT/bin/qmake")
+set(VTK_DEPEND_QT QT)
+
+else()
+ find_package(qt4 REQUIRED)
+ set(VTK_DEPEND_QT "")
+endif()
#=========================================================
#=========================================================
# VTK
-SET(VTK_CMAKE_CXX_STANDARD_LIBRARIES "${CMAKE_CXX_STANDARD_LIBRARIES}")
-IF(MSVC)
- SET(VTK_CMAKE_CXX_STANDARD_LIBRARIES "${VTK_CMAKE_CXX_STANDARD_LIBRARIES} Imm32.lib Winmm.lib Ws2_32.lib")
-ENDIF(MSVC)
+set(VTK_CMAKE_CXX_STANDARD_LIBRARIES "${CMAKE_CXX_STANDARD_LIBRARIES}")
+if(MSVC)
+ set(VTK_CMAKE_CXX_STANDARD_LIBRARIES "${VTK_CMAKE_CXX_STANDARD_LIBRARIES} Imm32.lib Winmm.lib Ws2_32.lib")
+endif(MSVC)
ExternalProject_Add(
- VTK
- DEPENDS QT
+ VTK
+ DEPENDS ${VTK_DEPEND_QT}
SOURCE_DIR ${source_prefix}/vtk
GIT_REPOSITORY git://vtk.org/VTK.git
- GIT_TAG v5.10.0
+ GIT_TAG release-5.10
INSTALL_COMMAND ""
CMAKE_ARGS
-DQT_QMAKE_EXECUTABLE:FILEPATH=${qmake_executable}
-DVTK_USE_QVTK_QTOPENGL:BOOL=ON
-DCMAKE_CXX_STANDARD_LIBRARIES:STRING=${VTK_CMAKE_CXX_STANDARD_LIBRARIES}
)
-SET(VTK_DIR ${build_prefix}/VTK)
+set(VTK_DIR ${build_prefix}/VTK)
#=========================================================
#=========================================================
ExternalProject_Add(
GDCM
SOURCE_DIR ${source_prefix}/gdcm
- GIT_REPOSITORY git://git.code.sf.net/p/gdcm/gdcm
- GIT_TAG v2.2.3
+ GIT_REPOSITORY git://git.code.sf.net/p/gdcm/gdcm
+ GIT_TAG v2.2.4
INSTALL_COMMAND ""
CMAKE_ARGS
- -DQT_QMAKE_EXECUTABLE:FILEPATH=${qmake_executable}
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
-DCMAKE_C_FLAGS_MINSIZEREL:STRING=${CMAKE_C_FLAGS_MINSIZEREL}
-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
-DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_PREFIX}
-DCMAKE_BUILD_TYPE:STRING=${build_type}
)
-SET(GDCM_DIR ${build_prefix}/GDCM)
+set(GDCM_DIR ${build_prefix}/GDCM)
#=========================================================
#=========================================================
ITK
SOURCE_DIR ${source_prefix}/itk
GIT_REPOSITORY git://itk.org/ITK.git
- GIT_TAG v4.4.0
+ GIT_TAG v4.5.2
INSTALL_COMMAND ""
CMAKE_ARGS
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
-DBUILD_EXAMPLES:BOOL=OFF
-DBUILD_TESTING:BOOL=OFF
)
-SET(ITK_DIR ${build_prefix}/ITK)
+set(ITK_DIR ${build_prefix}/ITK)
#=========================================================
#=========================================================
# VV
-SET(VV_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
+set(VV_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
if(MSVC)
- SET(VV_CMAKE_CXX_FLAGS "${VV_CMAKE_CXX_FLAGS} /bigobj")
+ set(VV_CMAKE_CXX_FLAGS "${VV_CMAKE_CXX_FLAGS} /bigobj")
endif(MSVC)
-SET(VV_CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS})
+set(VV_CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS})
if(CMAKE_COMPILER_IS_GNUCXX)
- SET(VV_CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+ set(VV_CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
endif(CMAKE_COMPILER_IS_GNUCXX)
-SET(MAKE_COMMAND "make")
+set(MAKE_COMMAND "make")
if(MSVC)
- SET(MAKE_COMMAND "nmake")
+ set(MAKE_COMMAND "nmake")
endif(MSVC)
ExternalProject_Add(
VV
- DEPENDS QT VTK ITK GDCM
+ DEPENDS ${VTK_DEPEND_QT} VTK ITK GDCM
SOURCE_DIR ${source_prefix}/vv
GIT_REPOSITORY git://git.creatis.insa-lyon.fr/clitk
- INSTALL_COMMAND ${MAKE_COMMAND} package
+ INSTALL_DIR ${install_prefix}
+ INSTALL_COMMAND make install
CMAKE_ARGS
-DQT_QMAKE_EXECUTABLE:FILEPATH=${qmake_executable}
-DGDCM_DIR:PATH=${GDCM_DIR}
-DCMAKE_BUILD_TYPE:STRING=${build_type}
-DBUILD_SHARED_LIBS:BOOL=OFF
-DBUILD_TESTING:BOOL=OFF
- -DCLITK_BUILD_REGISTRATION:BOOL=ON
- -DCLITK_BUILD_SEGMENTATION:BOOL=ON
- -DCLITK_BUILD_TOOLS:BOOL=ON
- -DCLITK_BUILD_EXPERIMENTAL:BOOL=ON
)
#=========================================================
#=========================================================
#=========================================================
# Data tests path
-FIND_PATH(CLITK_TEST_DATA_PATH Lung3D.mhd)
-IF(NOT ${CLITK_TEST_DATA_PATH} MATCHES "NOTFOUND$")
- SET(CLITK_TEST_DATA_PATH "${CLITK_TEST_DATA_PATH}/")
-ENDIF()
-ADD_DEFINITIONS(-DCLITK_TEST_DATA_PATH="${CLITK_TEST_DATA_PATH}")
+find_path(CLITK_TEST_DATA_PATH Lung3D.mhd)
+if(NOT ${CLITK_TEST_DATA_PATH} MATCHES "NOTFOUND$")
+ set(CLITK_TEST_DATA_PATH "${CLITK_TEST_DATA_PATH}/")
+endif()
+add_definitions(-DCLITK_TEST_DATA_PATH="${CLITK_TEST_DATA_PATH}")
#=========================================================
#=========================================================
-SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/tests/bin)
-SET(BUILDNAME ${CMAKE_SYSTEM_NAME}${CMAKE_OSX_ARCHITECTURES} CACHE INTERNAL DOCSTRING)
+set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/tests/bin)
+set(BUILDNAME ${CMAKE_SYSTEM_NAME}${CMAKE_OSX_ARCHITECTURES} CACHE INTERNAL DOCSTRING)
#=========================================================
#=========================================================
# Enabled options to test
-IF(CLITK_BUILD_TOOLS)
- ADD_SUBDIRECTORY(tools)
-ENDIF()
-#IF(CLITK_BUILD_VV)
-# ADD_SUBDIRECTORY(vv)
-#ENDIF()
-# IF(CLITK_BUILD_SEGMENTATION)
-# ADD_SUBDIRECTORY(segmentation)
-# ENDIF()
-#
-# IF(CLITK_BUILD_REGISTATION)
-# ADD_SUBDIRECTORY(registration)
-# ENDIF()
-#ADD_SUBDIRECTORY(common)
+if(CLITK_BUILD_TOOLS)
+ add_subdirectory(tools)
+endif()
+#if(CLITK_BUILD_VV)
+# add_subdirectory(vv)
+#endif()
+# if(CLITK_BUILD_SEGMENTATION)
+# add_subdirectory(segmentation)
+# endif()
+#
+# if(CLITK_BUILD_REGISTATION)
+# add_subdirectory(registration)
+# endif()
+#add_subdirectory(common)
#=========================================================
${PROJECT_SOURCE_DIR}/tools
)
-SET(BUILDNAME ${BUILDNAME}_tools CACHE INTERNAL DOCSTRING)
-ADD_DEFINITIONS(-DCLITK_TEST_TOOLS_PATH=\"${PROJECT_BINARY_DIR}/bin/\")
-SET (srcs
+set(BUILDNAME ${BUILDNAME}_tools CACHE INTERNAL DOCSTRING)
+add_definitions(-DCLITK_TEST_TOOLS_PATH=\"${PROJECT_BINARY_DIR}/bin/\")
+set(srcs
toolTestRunner.cxx
)
-ADD_EXECUTABLE(toolTestRunner ${srcs})
-TARGET_LINK_LIBRARIES(toolTestRunner ${ITK_LIBRARIES})
-SET(exe ${EXECUTABLE_OUTPUT_PATH}/toolTestRunner)
-SET(p ${CLITK_TEST_DATA_PATH})
+add_executable(toolTestRunner ${srcs})
+target_link_libraries(toolTestRunner ${ITK_LIBRARIES})
+set(exe ${EXECUTABLE_OUTPUT_PATH}/toolTestRunner)
+set(p ${CLITK_TEST_DATA_PATH})
#=========================================================
# clitkImageInfo
-ADD_TEST(clitkImageInfo_4d ${exe} clitkImageInfo ${p}Deformation4D.mhd ${p}Deformation4D_ref.info)
-ADD_TEST(clitkImageInfo_3d ${exe} clitkImageInfo ${p}Lung3D.mhd ${p}Lung3D_ref.info)
+add_test(clitkImageInfo_4d ${exe} clitkImageInfo ${p}Deformation4D.mhd ${p}Deformation4D_ref.info)
+add_test(clitkImageInfo_3d ${exe} clitkImageInfo ${p}Lung3D.mhd ${p}Lung3D_ref.info)
#=========================================================
# clitkGetSpacing
-ADD_TEST(clitkGetSpacing_4d ${exe} clitkGetSpacing -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.spacing)
-ADD_TEST(clitkGetSpacing_3d ${exe} clitkGetSpacing -i ${p}Lung3D.mhd ${p}Lung3D_ref.spacing)
+add_test(clitkGetSpacing_4d ${exe} clitkGetSpacing -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.spacing)
+add_test(clitkGetSpacing_3d ${exe} clitkGetSpacing -i ${p}Lung3D.mhd ${p}Lung3D_ref.spacing)
#=========================================================
# clitkGetOrigin
-ADD_TEST(clitkGetOrigin_4d ${exe} clitkGetOrigin -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.origin)
-ADD_TEST(clitkGetOrigin_3d ${exe} clitkGetOrigin -i ${p}Lung3D.mhd ${p}Lung3D_ref.origin)
+add_test(clitkGetOrigin_4d ${exe} clitkGetOrigin -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.origin)
+add_test(clitkGetOrigin_3d ${exe} clitkGetOrigin -i ${p}Lung3D.mhd ${p}Lung3D_ref.origin)
#=========================================================
# clitkGetSize
-ADD_TEST(clitkGetSize_4d ${exe} clitkGetSize -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.size)
-ADD_TEST(clitkGetSize_3d ${exe} clitkGetSize -i ${p}Lung3D.mhd ${p}Lung3D_ref.size)
+add_test(clitkGetSize_4d ${exe} clitkGetSize -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.size)
+add_test(clitkGetSize_3d ${exe} clitkGetSize -i ${p}Lung3D.mhd ${p}Lung3D_ref.size)
#=========================================================
# clitkGetDirection
-ADD_TEST(clitkGetDirection_4d ${exe} clitkGetDirection -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.direction)
-ADD_TEST(clitkGetDirection_3d ${exe} clitkGetDirection -i ${p}Lung3D.mhd ${p}Lung3D_ref.direction)
+add_test(clitkGetDirection_4d ${exe} clitkGetDirection -i ${p}Deformation4D.mhd ${p}Deformation4D_ref.direction)
+add_test(clitkGetDirection_3d ${exe} clitkGetDirection -i ${p}Lung3D.mhd ${p}Lung3D_ref.direction)
#=========================================================
# clitkBinarize
-ADD_TEST(clitkBinarizeBGl0.1356_4d ${exe} clitkBinarizeImage -i ${p}Deformation4D.mhd --mode BG -l 0.1356 -o Deformation4D_ref.binarizeBGl0.1356.mhd ${p}Deformation4D_ref.binarizeBGl0.1356.mhd)
-ADD_TEST(clitkBinarizeFGl0.1556_3d ${exe} clitkBinarizeImage -i ${p}Lung3D.mhd --mode FG -l 0.1556 -o Lung3D_ref.binarizeFGl0.1556.mhd ${p}Lung3D_ref.binarizeFGl0.1556.mhd)
+add_test(clitkBinarizeBGl0.1356_4d ${exe} clitkBinarizeImage -i ${p}Deformation4D.mhd --mode BG -l 0.1356 -o Deformation4D_ref.binarizeBGl0.1356.mhd ${p}Deformation4D_ref.binarizeBGl0.1356.mhd)
+add_test(clitkBinarizeFGl0.1556_3d ${exe} clitkBinarizeImage -i ${p}Lung3D.mhd --mode FG -l 0.1556 -o Lung3D_ref.binarizeFGl0.1556.mhd ${p}Lung3D_ref.binarizeFGl0.1556.mhd)
#=========================================================
# clitkImageArithm
-ADD_TEST(clitkImageArithm0_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 0 -o Lung3D_ref.arithm0.mhd ${p}Lung3D_ref.arithm0.mhd)
-ADD_TEST(clitkImageArithm1_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 1 -o Lung3D_ref.arithm1.mhd ${p}Lung3D_ref.arithm1.mhd)
-ADD_TEST(clitkImageArithm2_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 2 -o Lung3D_ref.arithm2.mhd ${p}Lung3D_ref.arithm2.mhd)
-ADD_TEST(clitkImageArithm3_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 3 -o Lung3D_ref.arithm3.mhd ${p}Lung3D_ref.arithm3.mhd)
-ADD_TEST(clitkImageArithm4_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 4 -o Lung3D_ref.arithm4.mhd ${p}Lung3D_ref.arithm4.mhd)
-ADD_TEST(clitkImageArithm5_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 5 -o Lung3D_ref.arithm5.mhd ${p}Lung3D_ref.arithm5.mhd)
-ADD_TEST(clitkImageArithm6_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 6 -o Lung3D_ref.arithm6.mhd ${p}Lung3D_ref.arithm6.mhd)
+add_test(clitkImageArithm0_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 0 -o Lung3D_ref.arithm0.mhd ${p}Lung3D_ref.arithm0.mhd)
+add_test(clitkImageArithm1_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 1 -o Lung3D_ref.arithm1.mhd ${p}Lung3D_ref.arithm1.mhd)
+add_test(clitkImageArithm2_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 2 -o Lung3D_ref.arithm2.mhd ${p}Lung3D_ref.arithm2.mhd)
+add_test(clitkImageArithm3_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 3 -o Lung3D_ref.arithm3.mhd ${p}Lung3D_ref.arithm3.mhd)
+add_test(clitkImageArithm4_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 4 -o Lung3D_ref.arithm4.mhd ${p}Lung3D_ref.arithm4.mhd)
+add_test(clitkImageArithm5_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 5 -o Lung3D_ref.arithm5.mhd ${p}Lung3D_ref.arithm5.mhd)
+add_test(clitkImageArithm6_3d ${exe} clitkImageArithm -i ${p}Lung3D.mhd -j ${p}Lung3D.mhd -t 6 -o Lung3D_ref.arithm6.mhd ${p}Lung3D_ref.arithm6.mhd)
-ADD_TEST(clitkImageArithm0_4d ${exe} clitkImageArithm -i ${p}Deformation4D.mhd -j ${p}Deformation4D.mhd -t 0 -o Deformation4D_ref.arithm0.mhd ${p}Deformation4D_ref.arithm0.mhd)
-ADD_TEST(clitkImageArithm2_4d ${exe} clitkImageArithm -i ${p}Deformation4D.mhd -j ${p}Deformation4D.mhd -t 2 -o Deformation4D_ref.arithm2.mhd ${p}Deformation4D_ref.arithm2.mhd)
+add_test(clitkImageArithm0_4d ${exe} clitkImageArithm -i ${p}Deformation4D.mhd -j ${p}Deformation4D.mhd -t 0 -o Deformation4D_ref.arithm0.mhd ${p}Deformation4D_ref.arithm0.mhd)
+add_test(clitkImageArithm2_4d ${exe} clitkImageArithm -i ${p}Deformation4D.mhd -j ${p}Deformation4D.mhd -t 2 -o Deformation4D_ref.arithm2.mhd ${p}Deformation4D_ref.arithm2.mhd)
#=========================================================
# clitkCropImage
-ADD_TEST(clitkCropImage_3d ${exe} clitkCropImage -i ${p}Lung3D.mhd -b 1,4,0,2,2,3 -o Lung3D_ref.cropImage.1.4.0.2.2.3.mhd ${p}Lung3D_ref.cropImage.1.4.0.2.2.3.mhd)
+add_test(clitkCropImage_3d ${exe} clitkCropImage -i ${p}Lung3D.mhd -b 1,4,0,2,2,3 -o Lung3D_ref.cropImage.1.4.0.2.2.3.mhd ${p}Lung3D_ref.cropImage.1.4.0.2.2.3.mhd)
#=========================================================
#clitkMorphoMath
-ADD_TEST(clitkMorphoMath0_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t0.mhd ${p}Lung3D_ref.morphoMath.t0.mhd)
-ADD_TEST(clitkMorphoMath1_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t1.mhd ${p}Lung3D_ref.morphoMath.t1.mhd)
-ADD_TEST(clitkMorphoMath2_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t2.mhd ${p}Lung3D_ref.morphoMath.t2.mhd)
-ADD_TEST(clitkMorphoMath3_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t3.mhd ${p}Lung3D_ref.morphoMath.t3.mhd)
-ADD_TEST(clitkMorphoMath4_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t4.mhd ${p}Lung3D_ref.morphoMath.t4.mhd)
-ADD_TEST(clitkMorphoMath5_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t5.mhd ${p}Lung3D_ref.morphoMath.t5.mhd)
+add_test(clitkMorphoMath0_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t0.mhd ${p}Lung3D_ref.morphoMath.t0.mhd)
+add_test(clitkMorphoMath1_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t1.mhd ${p}Lung3D_ref.morphoMath.t1.mhd)
+add_test(clitkMorphoMath2_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t2.mhd ${p}Lung3D_ref.morphoMath.t2.mhd)
+add_test(clitkMorphoMath3_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t3.mhd ${p}Lung3D_ref.morphoMath.t3.mhd)
+add_test(clitkMorphoMath4_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t4.mhd ${p}Lung3D_ref.morphoMath.t4.mhd)
+add_test(clitkMorphoMath5_3d ${exe} clitkMorphoMath -i ${p}Lung3D.mhd -o Lung3D_ref.morphoMath.t5.mhd ${p}Lung3D_ref.morphoMath.t5.mhd)
-ADD_TEST(clitkMorphoMath0_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t0.mhd ${p}Deformation4D_ref.morphoMath.t0.mhd)
-ADD_TEST(clitkMorphoMath1_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t1.mhd ${p}Deformation4D_ref.morphoMath.t1.mhd)
-ADD_TEST(clitkMorphoMath2_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t2.mhd ${p}Deformation4D_ref.morphoMath.t2.mhd)
-ADD_TEST(clitkMorphoMath3_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t3.mhd ${p}Deformation4D_ref.morphoMath.t3.mhd)
-ADD_TEST(clitkMorphoMath4_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t4.mhd ${p}Deformation4D_ref.morphoMath.t4.mhd)
-ADD_TEST(clitkMorphoMath5_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t5.mhd ${p}Deformation4D_ref.morphoMath.t5.mhd)
+add_test(clitkMorphoMath0_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t0.mhd ${p}Deformation4D_ref.morphoMath.t0.mhd)
+add_test(clitkMorphoMath1_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t1.mhd ${p}Deformation4D_ref.morphoMath.t1.mhd)
+add_test(clitkMorphoMath2_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t2.mhd ${p}Deformation4D_ref.morphoMath.t2.mhd)
+add_test(clitkMorphoMath3_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t3.mhd ${p}Deformation4D_ref.morphoMath.t3.mhd)
+add_test(clitkMorphoMath4_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t4.mhd ${p}Deformation4D_ref.morphoMath.t4.mhd)
+add_test(clitkMorphoMath5_4d ${exe} clitkMorphoMath -i ${p}Deformation4D.mhd -o Deformation4D_ref.morphoMath.t5.mhd ${p}Deformation4D_ref.morphoMath.t5.mhd)
#=========================================================
#clitkSetBackground
-ADD_TEST(clitkSetBackground_4d ${exe} clitkSetBackground -i ${p}Deformation4D.mhd -m ${p}Deformation4D.mhd -o Deformation4D_ref.setBackground.mhd ${p}Deformation4D_ref.setBackground.mhd)
-ADD_TEST(clitkSetBackground_3d ${exe} clitkSetBackground -i ${p}Lung3D.mhd -m ${p}Lung3D.mhd -o Lung3D_ref.setBackground.mhd ${p}Lung3D_ref.setBackground.mhd)
+add_test(clitkSetBackground_4d ${exe} clitkSetBackground -i ${p}Deformation4D.mhd -m ${p}Deformation4D.mhd -o Deformation4D_ref.setBackground.mhd ${p}Deformation4D_ref.setBackground.mhd)
+add_test(clitkSetBackground_3d ${exe} clitkSetBackground -i ${p}Lung3D.mhd -m ${p}Lung3D.mhd -o Lung3D_ref.setBackground.mhd ${p}Lung3D_ref.setBackground.mhd)
#clitkWarpImage
-ADD_TEST(clitkWarpImage_3d ${exe} clitkWarpImage -i ${p}00-P.mhd --vf ${p}vf50-P_1.mhd -o 00-P_ref.warpImage.mhd ${p}00-P_ref.warpImage.mhd)
+add_test(clitkWarpImage_3d ${exe} clitkWarpImage -i ${p}00-P.mhd --vf ${p}vf50-P_1.mhd -o 00-P_ref.warpImage.mhd ${p}00-P_ref.warpImage.mhd)
-UNSET(exe)
-UNSET(p)
+unset(exe)
+unset(p)
#=========================================================
# Add Libraries used in vv and clitk to avoid recompilation
WRAP_GGO(clitkCropImage_GGO_C clitkCropImage.ggo)
-ADD_LIBRARY(clitkCropImageLib clitkCropImageGenericFilter.cxx ${clitkCropImage_GGO_C})
+add_library(clitkCropImageLib clitkCropImageGenericFilter.cxx ${clitkCropImage_GGO_C})
WRAP_GGO(clitkImageConvert_GGO_C clitkImageConvert.ggo)
-ADD_LIBRARY(clitkImageConvertLib clitkImageConvertGenericFilter.cxx ${clitkImageConvert_GGO_C})
+add_library(clitkImageConvertLib clitkImageConvertGenericFilter.cxx ${clitkImageConvert_GGO_C})
WRAP_GGO(clitkBinarizeImage_GGO_C clitkBinarizeImage.ggo)
-ADD_LIBRARY(clitkBinarizeImageLib clitkBinarizeImageGenericFilter.cxx ${clitkBinarizeImage_GGO_C})
+add_library(clitkBinarizeImageLib clitkBinarizeImageGenericFilter.cxx ${clitkBinarizeImage_GGO_C})
+
+WRAP_GGO(clitkProfileImage_GGO_C clitkProfileImage.ggo)
+add_library(clitkProfileImageLib clitkProfileImageGenericFilter.cxx ${clitkProfileImage_GGO_C})
WRAP_GGO(clitkImageArithm_GGO_C clitkImageArithm.ggo)
-ADD_LIBRARY(clitkImageArithmImageLib clitkImageArithmGenericFilter.cxx ${clitkImageArithm_GGO_C})
+add_library(clitkImageArithmImageLib clitkImageArithmGenericFilter.cxx ${clitkImageArithm_GGO_C})
WRAP_GGO(clitkVectorArithm_GGO_C clitkVectorArithm.ggo)
-ADD_LIBRARY(clitkVectorArithmLib clitkVectorArithmGenericFilter.cxx ${clitkVectorArithm_GGO_C})
+add_library(clitkVectorArithmLib clitkVectorArithmGenericFilter.cxx ${clitkVectorArithm_GGO_C})
WRAP_GGO(clitkResampleImage_GGO_C clitkResampleImage.ggo)
-ADD_LIBRARY(clitkResampleImageLib clitkResampleImageGenericFilter.cxx ${clitkResampleImage_GGO_C})
+add_library(clitkResampleImageLib clitkResampleImageGenericFilter.cxx ${clitkResampleImage_GGO_C})
WRAP_GGO(clitkMIP_GGO_C clitkMIP.ggo)
-ADD_LIBRARY(clitkMIPLib clitkMIPGenericFilter.cxx ${clitkMIP_GGO_C})
+add_library(clitkMIPLib clitkMIPGenericFilter.cxx ${clitkMIP_GGO_C})
WRAP_GGO(clitkMedianImageFilter_GGO_C clitkMedianImageFilter.ggo)
-ADD_LIBRARY(clitkMedianImageFilterLib clitkMedianImageGenericFilter.cxx ${clitkMedianImageFilter_GGO_C})
+add_library(clitkMedianImageFilterLib clitkMedianImageGenericFilter.cxx ${clitkMedianImageFilter_GGO_C})
#=========================================================
-IF (CLITK_BUILD_TOOLS)
+if(CLITK_BUILD_TOOLS)
+
WRAP_GGO(clitkDicomInfo_GGO_C clitkDicomInfo.ggo)
- ADD_EXECUTABLE(clitkDicomInfo clitkDicomInfo.cxx ${clitkDicomInfo_GGO_C})
- TARGET_LINK_LIBRARIES(clitkDicomInfo clitkCommon)
+ add_executable(clitkDicomInfo clitkDicomInfo.cxx ${clitkDicomInfo_GGO_C})
+ target_link_libraries(clitkDicomInfo clitkCommon)
# set_target_properties(clitkDicomInfo
# PROPERTIES
# LINK_INTERFACE_LIBRARIES ""
# )
- SET(TOOLS_INSTALL clitkDicomInfo)
+ set(TOOLS_INSTALL clitkDicomInfo)
WRAP_GGO(clitkDicom2Image_GGO_C clitkDicom2Image.ggo)
- ADD_EXECUTABLE(clitkDicom2Image clitkDicom2Image.cxx ${clitkDicom2Image_GGO_C})
- TARGET_LINK_LIBRARIES(clitkDicom2Image clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicom2Image)
+ add_executable(clitkDicom2Image clitkDicom2Image.cxx ${clitkDicom2Image_GGO_C})
+ target_link_libraries(clitkDicom2Image clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicom2Image)
WRAP_GGO(clitkDicomWave2Text_GGO_C clitkDicomWave2Text.ggo)
- ADD_EXECUTABLE(clitkDicomWave2Text clitkDicomWave2Text.cxx ${clitkDicomWave2Text_GGO_C})
- TARGET_LINK_LIBRARIES(clitkDicomWave2Text clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomWave2Text)
+ add_executable(clitkDicomWave2Text clitkDicomWave2Text.cxx ${clitkDicomWave2Text_GGO_C})
+ target_link_libraries(clitkDicomWave2Text clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomWave2Text)
WRAP_GGO(clitkImageInfo_GGO_C clitkImageInfo.ggo)
- ADD_EXECUTABLE(clitkImageInfo clitkImageInfo.cxx ${clitkImageInfo_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImageInfo clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageInfo)
-
- ADD_EXECUTABLE(clitkImageConvert clitkImageConvert.cxx)
- TARGET_LINK_LIBRARIES(clitkImageConvert clitkImageConvertLib clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageConvert)
-
- ADD_EXECUTABLE(clitkBinarizeImage clitkBinarizeImage.cxx)
- TARGET_LINK_LIBRARIES(clitkBinarizeImage clitkBinarizeImageLib clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinarizeImage)
+ add_executable(clitkImageInfo clitkImageInfo.cxx ${clitkImageInfo_GGO_C})
+ target_link_libraries(clitkImageInfo clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageInfo)
+
+ add_executable(clitkImageConvert clitkImageConvert.cxx)
+ target_link_libraries(clitkImageConvert clitkImageConvertLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageConvert)
+
+ add_executable(clitkBinarizeImage clitkBinarizeImage.cxx)
+ target_link_libraries(clitkBinarizeImage clitkBinarizeImageLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinarizeImage)
+
+ add_executable(clitkProfileImage clitkProfileImage.cxx)
+ target_link_libraries(clitkProfileImage clitkProfileImageLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkProfileImage)
WRAP_GGO(clitkVFResample_GGO_C clitkVFResample.ggo)
- ADD_EXECUTABLE(clitkVFResample clitkVFResample.cxx clitkVFResampleGenericFilter.cxx ${clitkVFResample_GGO_C})
- TARGET_LINK_LIBRARIES(clitkVFResample clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFResample)
+ add_executable(clitkVFResample clitkVFResample.cxx clitkVFResampleGenericFilter.cxx ${clitkVFResample_GGO_C})
+ target_link_libraries(clitkVFResample clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFResample)
WRAP_GGO(clitkVFInterpolate_GGO_C clitkVFInterpolate.ggo)
- ADD_EXECUTABLE(clitkVFInterpolate clitkVFInterpolate.cxx clitkVFInterpolateGenericFilter.cxx ${clitkVFInterpolate_GGO_C})
- TARGET_LINK_LIBRARIES(clitkVFInterpolate clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFInterpolate)
+ add_executable(clitkVFInterpolate clitkVFInterpolate.cxx clitkVFInterpolateGenericFilter.cxx ${clitkVFInterpolate_GGO_C})
+ target_link_libraries(clitkVFInterpolate clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFInterpolate)
WRAP_GGO(clitkImageCreate_GGO_C clitkImageCreate.ggo)
- ADD_EXECUTABLE(clitkImageCreate clitkImageCreate.cxx ${clitkImageCreate_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImageCreate clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageCreate)
+ add_executable(clitkImageCreate clitkImageCreate.cxx ${clitkImageCreate_GGO_C})
+ target_link_libraries(clitkImageCreate clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageCreate)
WRAP_GGO(clitkZeroVF_GGO_C clitkZeroVF.ggo)
- ADD_EXECUTABLE(clitkZeroVF clitkZeroVF.cxx ${clitkZeroVF_GGO_C} clitkZeroVFGenericFilter.cxx)
- TARGET_LINK_LIBRARIES(clitkZeroVF clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkZeroVF)
+ add_executable(clitkZeroVF clitkZeroVF.cxx ${clitkZeroVF_GGO_C} clitkZeroVFGenericFilter.cxx)
+ target_link_libraries(clitkZeroVF clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkZeroVF)
WRAP_GGO(clitkSplitImage_GGO_C clitkSplitImage.ggo)
- ADD_EXECUTABLE(clitkSplitImage clitkSplitImage.cxx clitkSplitImageGenericFilter.cxx ${clitkSplitImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkSplitImage clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSplitImage)
+ add_executable(clitkSplitImage clitkSplitImage.cxx clitkSplitImageGenericFilter.cxx ${clitkSplitImage_GGO_C})
+ target_link_libraries(clitkSplitImage clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSplitImage)
WRAP_GGO(clitkWriteDicomSeries_GGO_C clitkWriteDicomSeries.ggo)
- ADD_EXECUTABLE(clitkWriteDicomSeries clitkWriteDicomSeries.cxx ${clitkWriteDicomSeries_GGO_C})
- TARGET_LINK_LIBRARIES(clitkWriteDicomSeries clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkWriteDicomSeries)
+ add_executable(clitkWriteDicomSeries clitkWriteDicomSeries.cxx ${clitkWriteDicomSeries_GGO_C})
+ target_link_libraries(clitkWriteDicomSeries clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkWriteDicomSeries)
WRAP_GGO(clitkMedianTemporalDimension_GGO_C clitkMedianTemporalDimension.ggo)
- ADD_EXECUTABLE(clitkMedianTemporalDimension clitkMedianTemporalDimension.cxx
+ add_executable(clitkMedianTemporalDimension clitkMedianTemporalDimension.cxx
${clitkMedianTemporalDimension_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMedianTemporalDimension clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMedianTemporalDimension)
+ target_link_libraries(clitkMedianTemporalDimension clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMedianTemporalDimension)
WRAP_GGO(clitkWarpImage_GGO_C clitkWarpImage.ggo)
- ADD_EXECUTABLE(clitkWarpImage clitkWarpImage.cxx ${clitkWarpImage_GGO_C} clitkWarpImageGenericFilter.cxx)
- TARGET_LINK_LIBRARIES(clitkWarpImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkWarpImage)
+ add_executable(clitkWarpImage clitkWarpImage.cxx ${clitkWarpImage_GGO_C} clitkWarpImageGenericFilter.cxx)
+ target_link_libraries(clitkWarpImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkWarpImage)
WRAP_GGO(clitkInvertVF_GGO_C clitkInvertVF.ggo)
- ADD_EXECUTABLE(clitkInvertVF clitkInvertVF.cxx ${clitkInvertVF_GGO_C})
- TARGET_LINK_LIBRARIES(clitkInvertVF clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkInvertVF)
+ add_executable(clitkInvertVF clitkInvertVF.cxx ${clitkInvertVF_GGO_C})
+ target_link_libraries(clitkInvertVF clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkInvertVF)
WRAP_GGO(clitkAffineTransform_GGO_C clitkAffineTransform.ggo)
- ADD_EXECUTABLE(clitkAffineTransform clitkAffineTransform.cxx ${clitkAffineTransform_GGO_C})
- TARGET_LINK_LIBRARIES(clitkAffineTransform clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAffineTransform)
+ add_executable(clitkAffineTransform clitkAffineTransform.cxx ${clitkAffineTransform_GGO_C})
+ target_link_libraries(clitkAffineTransform clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAffineTransform)
WRAP_GGO(clitkElastixTransformToMatrix_GGO_C clitkElastixTransformToMatrix.ggo)
- ADD_EXECUTABLE(clitkElastixTransformToMatrix clitkElastixTransformToMatrix.cxx ${clitkElastixTransformToMatrix_GGO_C})
- TARGET_LINK_LIBRARIES(clitkElastixTransformToMatrix clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkElastixTransformToMatrix)
+ add_executable(clitkElastixTransformToMatrix clitkElastixTransformToMatrix.cxx ${clitkElastixTransformToMatrix_GGO_C})
+ target_link_libraries(clitkElastixTransformToMatrix clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkElastixTransformToMatrix)
WRAP_GGO(clitkMatrixToElastixTransform_GGO_C clitkMatrixToElastixTransform.ggo)
- ADD_EXECUTABLE(clitkMatrixToElastixTransform clitkMatrixToElastixTransform.cxx ${clitkMatrixToElastixTransform_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMatrixToElastixTransform clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMatrixToElastixTransform)
+ add_executable(clitkMatrixToElastixTransform clitkMatrixToElastixTransform.cxx ${clitkMatrixToElastixTransform_GGO_C})
+ target_link_libraries(clitkMatrixToElastixTransform clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMatrixToElastixTransform)
+
+ WRAP_GGO(clitkMatrixMultiply_GGO_C clitkMatrixMultiply.ggo)
+ add_executable(clitkMatrixMultiply clitkMatrixMultiply.cxx ${clitkMatrixMultiply_GGO_C})
+ target_link_libraries(clitkMatrixMultiply clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMatrixMultiply)
WRAP_GGO(clitkMatrixInverse_GGO_C clitkMatrixInverse.ggo)
- ADD_EXECUTABLE(clitkMatrixInverse clitkMatrixInverse.cxx ${clitkMatrixInverse_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMatrixInverse clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMatrixInverse)
+ add_executable(clitkMatrixInverse clitkMatrixInverse.cxx ${clitkMatrixInverse_GGO_C})
+ target_link_libraries(clitkMatrixInverse clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMatrixInverse)
WRAP_GGO(clitkSetBackground_GGO_C clitkSetBackground.ggo)
- ADD_EXECUTABLE(clitkSetBackground clitkSetBackground.cxx clitkSetBackgroundGenericFilter.cxx ${clitkSetBackground_GGO_C})
- TARGET_LINK_LIBRARIES(clitkSetBackground clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSetBackground)
+ add_executable(clitkSetBackground clitkSetBackground.cxx clitkSetBackgroundGenericFilter.cxx ${clitkSetBackground_GGO_C})
+ target_link_libraries(clitkSetBackground clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSetBackground)
WRAP_GGO(clitkGammaIndex_GGO_C clitkGammaIndex.ggo)
- ADD_EXECUTABLE(clitkGammaIndex clitkGammaIndex.cxx ${clitkGammaIndex_GGO_C})
- TARGET_LINK_LIBRARIES(clitkGammaIndex clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGammaIndex)
+ add_executable(clitkGammaIndex clitkGammaIndex.cxx ${clitkGammaIndex_GGO_C})
+ target_link_libraries(clitkGammaIndex clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGammaIndex)
- ADD_EXECUTABLE(clitkImageArithm clitkImageArithm.cxx)
- TARGET_LINK_LIBRARIES(clitkImageArithm clitkImageArithmImageLib clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageArithm)
+ add_executable(clitkImageArithm clitkImageArithm.cxx)
+ target_link_libraries(clitkImageArithm clitkImageArithmImageLib clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageArithm)
- ADD_EXECUTABLE(clitkVectorArithm clitkVectorArithm.cxx)
- TARGET_LINK_LIBRARIES(clitkVectorArithm clitkVectorArithmLib clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVectorArithm)
+ add_executable(clitkVectorArithm clitkVectorArithm.cxx)
+ target_link_libraries(clitkVectorArithm clitkVectorArithmLib clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVectorArithm)
WRAP_GGO(clitkUnsharpMask_GGO_C clitkUnsharpMask.ggo)
- ADD_EXECUTABLE(clitkUnsharpMask clitkUnsharpMask.cxx ${clitkUnsharpMask_GGO_C})
- TARGET_LINK_LIBRARIES(clitkUnsharpMask clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkUnsharpMask)
-
- WRAP_GGO(clitkFooImage_GGO_C clitkFooImage.ggo)
- ADD_EXECUTABLE(clitkFooImage clitkFooImage.cxx ${clitkFooImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkFooImage clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkFooImage)
+ add_executable(clitkUnsharpMask clitkUnsharpMask.cxx ${clitkUnsharpMask_GGO_C})
+ target_link_libraries(clitkUnsharpMask clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkUnsharpMask)
- #WRAP_GGO(clitkMedianImageFilter_GGO_C clitkMedianImageFilter.ggo)
- #ADD_EXECUTABLE(clitkMedianImageFilter clitkMedianImageFilter.cxx ${clitkMedianImageFilter_GGO_C})
- #TARGET_LINK_LIBRARIES(clitkMedianImageFilter clitkMedianImageFilterLib clitkCommon)
- #SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMedianImageFilter)
+ WRAP_GGO(clitkMedianImageFilter_GGO_C clitkMedianImageFilter.ggo)
+ add_executable(clitkMedianImageFilter clitkMedianImageFilter.cxx ${clitkMedianImageFilter_GGO_C})
+ target_link_libraries(clitkMedianImageFilter clitkMedianImageFilterLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMedianImageFilter)
- ADD_EXECUTABLE(clitkResampleImage clitkResampleImage.cxx)
- TARGET_LINK_LIBRARIES(clitkResampleImage clitkResampleImageLib clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkResampleImage)
+ add_executable(clitkResampleImage clitkResampleImage.cxx)
+ target_link_libraries(clitkResampleImage clitkResampleImageLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkResampleImage)
WRAP_GGO(clitkMinMaxMask_GGO_C clitkMinMaxMask.ggo)
- ADD_EXECUTABLE(clitkMinMaxMask clitkMinMaxMask.cxx ${clitkMinMaxMask_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMinMaxMask clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMinMaxMask)
+ add_executable(clitkMinMaxMask clitkMinMaxMask.cxx ${clitkMinMaxMask_GGO_C})
+ target_link_libraries(clitkMinMaxMask clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMinMaxMask)
WRAP_GGO(clitkAutoCrop_GGO_C clitkAutoCrop.ggo)
- ADD_EXECUTABLE(clitkAutoCrop clitkAutoCrop.cxx ${clitkAutoCrop_GGO_C})
- TARGET_LINK_LIBRARIES(clitkAutoCrop clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAutoCrop)
+ add_executable(clitkAutoCrop clitkAutoCrop.cxx ${clitkAutoCrop_GGO_C})
+ target_link_libraries(clitkAutoCrop clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAutoCrop)
WRAP_GGO(clitkDicomRTStruct2Image_GGO_C clitkDicomRTStruct2Image.ggo)
- ADD_EXECUTABLE(clitkDicomRTStruct2Image clitkDicomRTStruct2Image.cxx ${clitkDicomRTStruct2Image_GGO_C})
- TARGET_LINK_LIBRARIES(clitkDicomRTStruct2Image clitkDicomRTStruct)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTStruct2Image)
+ add_executable(clitkDicomRTStruct2Image clitkDicomRTStruct2Image.cxx ${clitkDicomRTStruct2Image_GGO_C})
+ target_link_libraries(clitkDicomRTStruct2Image clitkDicomRTStruct)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTStruct2Image)
- IF(CLITK_USE_SYSTEM_GDCM)
+ if(CLITK_USE_SYSTEM_GDCM)
WRAP_GGO(clitkImage2DicomRTStruct_GGO_C clitkImage2DicomRTStruct.ggo)
- ADD_EXECUTABLE(clitkImage2DicomRTStruct clitkImage2DicomRTStruct.cxx ${clitkImage2DicomRTStruct_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImage2DicomRTStruct clitkDicomRTStruct)
- ENDIF()
+ add_executable(clitkImage2DicomRTStruct clitkImage2DicomRTStruct.cxx ${clitkImage2DicomRTStruct_GGO_C})
+ target_link_libraries(clitkImage2DicomRTStruct clitkDicomRTStruct)
+ endif()
WRAP_GGO(clitkComposeVF_GGO_C clitkComposeVF.ggo)
- ADD_EXECUTABLE(clitkComposeVF clitkComposeVFGenericFilter.cxx clitkComposeVF.cxx ${clitkComposeVF_GGO_C})
- TARGET_LINK_LIBRARIES(clitkComposeVF clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkComposeVF)
+ add_executable(clitkComposeVF clitkComposeVFGenericFilter.cxx clitkComposeVF.cxx ${clitkComposeVF_GGO_C})
+ target_link_libraries(clitkComposeVF clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkComposeVF)
WRAP_GGO(clitkMergeSequence_GGO_C clitkMergeSequence.ggo)
- ADD_EXECUTABLE(clitkMergeSequence clitkMergeSequence.cxx clitkMergeSequenceGenericFilter.cxx ${clitkMergeSequence_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMergeSequence clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMergeSequence)
+ add_executable(clitkMergeSequence clitkMergeSequence.cxx clitkMergeSequenceGenericFilter.cxx ${clitkMergeSequence_GGO_C})
+ target_link_libraries(clitkMergeSequence clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMergeSequence)
WRAP_GGO(clitkBackProjectImage_GGO_C clitkBackProjectImage.ggo)
- ADD_EXECUTABLE(clitkBackProjectImage clitkBackProjectImage.cxx clitkBackProjectImageGenericFilter.cxx ${clitkBackProjectImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkBackProjectImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBackProjectImage)
+ add_executable(clitkBackProjectImage clitkBackProjectImage.cxx clitkBackProjectImageGenericFilter.cxx ${clitkBackProjectImage_GGO_C})
+ target_link_libraries(clitkBackProjectImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBackProjectImage)
- ADD_EXECUTABLE(clitkCropImage clitkCropImage.cxx ${clitkCropImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkCropImage clitkCropImageLib clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCropImage)
+ add_executable(clitkCropImage clitkCropImage.cxx ${clitkCropImage_GGO_C})
+ target_link_libraries(clitkCropImage clitkCropImageLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCropImage)
# WRAP_GGO(clitkExtractSlice_GGO_C clitkExtractSlice.ggo)
- # ADD_EXECUTABLE(clitkExtractSlice clitkExtractSlice.cxx clitkExtractSliceGenericFilter.cxx ${clitkExtractSlice_GGO_C})
- # TARGET_LINK_LIBRARIES(clitkExtractSlice clitkCommon)
- #SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkExtractSlice)
+ # add_executable(clitkExtractSlice clitkExtractSlice.cxx clitkExtractSliceGenericFilter.cxx ${clitkExtractSlice_GGO_C})
+ # target_link_libraries(clitkExtractSlice clitkCommon)
+ #set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkExtractSlice)
WRAP_GGO(clitkFlipImage_GGO_C clitkFlipImage.ggo)
- ADD_EXECUTABLE(clitkFlipImage clitkFlipImage.cxx clitkFlipImageGenericFilter.cxx ${clitkFlipImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkFlipImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkFlipImage)
+ add_executable(clitkFlipImage clitkFlipImage.cxx clitkFlipImageGenericFilter.cxx ${clitkFlipImage_GGO_C})
+ target_link_libraries(clitkFlipImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkFlipImage)
WRAP_GGO(clitkMirrorPadImage_GGO_C clitkMirrorPadImage.ggo)
- ADD_EXECUTABLE(clitkMirrorPadImage clitkMirrorPadImage.cxx clitkMirrorPadImageGenericFilter.cxx ${clitkMirrorPadImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMirrorPadImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMirrorPadImage)
+ add_executable(clitkMirrorPadImage clitkMirrorPadImage.cxx clitkMirrorPadImageGenericFilter.cxx ${clitkMirrorPadImage_GGO_C})
+ target_link_libraries(clitkMirrorPadImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMirrorPadImage)
WRAP_GGO(clitkImageMoment_GGO_C clitkImageMoment.ggo)
- ADD_EXECUTABLE(clitkImageMoment clitkImageMoment.cxx clitkImageMomentGenericFilter.cxx ${clitkImageMoment_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImageMoment clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageMoment)
+ add_executable(clitkImageMoment clitkImageMoment.cxx clitkImageMomentGenericFilter.cxx ${clitkImageMoment_GGO_C})
+ target_link_libraries(clitkImageMoment clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageMoment)
WRAP_GGO(clitkImageStatistics_GGO_C clitkImageStatistics.ggo)
- ADD_EXECUTABLE(clitkImageStatistics clitkImageStatistics.cxx clitkImageStatisticsGenericFilter.cxx ${clitkImageStatistics_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImageStatistics clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageStatistics)
+ add_executable(clitkImageStatistics clitkImageStatistics.cxx clitkImageStatisticsGenericFilter.cxx ${clitkImageStatistics_GGO_C})
+ target_link_libraries(clitkImageStatistics clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageStatistics)
WRAP_GGO(clitkVFConvert_GGO_C clitkVFConvert.ggo)
- ADD_EXECUTABLE(clitkVFConvert clitkVFConvert.cxx clitkVFConvertGenericFilter.cxx ${clitkVFConvert_GGO_C})
- TARGET_LINK_LIBRARIES(clitkVFConvert clitkCommon )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFConvert)
+ add_executable(clitkVFConvert clitkVFConvert.cxx clitkVFConvertGenericFilter.cxx ${clitkVFConvert_GGO_C})
+ target_link_libraries(clitkVFConvert clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVFConvert)
WRAP_GGO(clitkImageToVectorImage_GGO_C clitkImageToVectorImage.ggo)
- ADD_EXECUTABLE(clitkImageToVectorImage clitkImageToVectorImage.cxx clitkImageToVectorImageGenericFilter.cxx ${clitkImageToVectorImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkImageToVectorImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageToVectorImage)
+ add_executable(clitkImageToVectorImage clitkImageToVectorImage.cxx clitkImageToVectorImageGenericFilter.cxx ${clitkImageToVectorImage_GGO_C})
+ target_link_libraries(clitkImageToVectorImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageToVectorImage)
WRAP_GGO(clitkVectorImageToImage_GGO_C clitkVectorImageToImage.ggo)
- ADD_EXECUTABLE(clitkVectorImageToImage clitkVectorImageToImage.cxx clitkVectorImageToImageGenericFilter.cxx ${clitkVectorImageToImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkVectorImageToImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVectorImageToImage)
+ add_executable(clitkVectorImageToImage clitkVectorImageToImage.cxx clitkVectorImageToImageGenericFilter.cxx ${clitkVectorImageToImage_GGO_C})
+ target_link_libraries(clitkVectorImageToImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkVectorImageToImage)
- ADD_EXECUTABLE(clitkMIP clitkMIP.cxx clitkMIPGenericFilter.cxx)
- TARGET_LINK_LIBRARIES(clitkMIP clitkMIPLib clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMIP)
+ add_executable(clitkMIP clitkMIP.cxx clitkMIPGenericFilter.cxx)
+ target_link_libraries(clitkMIP clitkMIPLib clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMIP)
- WRAP_GGO(clitkTransformLandmarks_GGO_C clitkTransformLandmarks.ggo)
- ADD_EXECUTABLE(clitkTransformLandmarks clitkTransformLandmarks.cxx ${clitkTransformLandmarks_GGO_C})
- TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkTransformLandmarks)
+ WRAP_GGO(clitkSum_GGO_C clitkSum.ggo)
+ add_executable(clitkSum clitkSum.cxx ${clitkSum_GGO_C})
+ target_link_libraries(clitkSum clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkSum)
- WRAP_GGO(clitkDice_GGO_C clitkDice.ggo)
- ADD_EXECUTABLE(clitkDice clitkDice.cxx ${clitkDice_GGO_C})
- TARGET_LINK_LIBRARIES(clitkDice clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES} )
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDice)
+ WRAP_GGO(clitkTransformLandmarks_GGO_C clitkTransformLandmarks.ggo)
+ add_executable(clitkTransformLandmarks clitkTransformLandmarks.cxx ${clitkTransformLandmarks_GGO_C})
+ target_link_libraries(clitkTransformLandmarks clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkTransformLandmarks)
WRAP_GGO(clitkMaskLandmarks_GGO_C clitkMaskLandmarks.ggo)
- ADD_EXECUTABLE(clitkMaskLandmarks clitkMaskLandmarks.cxx ${clitkMaskLandmarks_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMaskLandmarks clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMaskLandmarks)
+ add_executable(clitkMaskLandmarks clitkMaskLandmarks.cxx ${clitkMaskLandmarks_GGO_C})
+ target_link_libraries(clitkMaskLandmarks clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMaskLandmarks)
WRAP_GGO(clitkJacobianImage_GGO_C clitkJacobianImage.ggo)
- ADD_EXECUTABLE(clitkJacobianImage clitkJacobianImage.cxx clitkJacobianImageGenericFilter.cxx ${clitkJacobianImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkJacobianImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkJacobianImage)
+ add_executable(clitkJacobianImage clitkJacobianImage.cxx clitkJacobianImageGenericFilter.cxx ${clitkJacobianImage_GGO_C})
+ target_link_libraries(clitkJacobianImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkJacobianImage)
WRAP_GGO(clitkPadImage_GGO_C clitkPadImage.ggo)
- ADD_EXECUTABLE(clitkPadImage clitkPadImage.cxx clitkPadImageGenericFilter.cxx ${clitkPadImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkPadImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkPadImage)
+ add_executable(clitkPadImage clitkPadImage.cxx clitkPadImageGenericFilter.cxx ${clitkPadImage_GGO_C})
+ target_link_libraries(clitkPadImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkPadImage)
WRAP_GGO(clitkCatImage_GGO_C clitkCatImage.ggo)
- ADD_EXECUTABLE(clitkCatImage clitkCatImage.cxx ${clitkCatImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkCatImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCatImage)
+ add_executable(clitkCatImage clitkCatImage.cxx ${clitkCatImage_GGO_C})
+ target_link_libraries(clitkCatImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCatImage)
WRAP_GGO(clitkAnisotropicDiffusion_GGO_C clitkAnisotropicDiffusion.ggo)
- ADD_EXECUTABLE(clitkAnisotropicDiffusion clitkAnisotropicDiffusion.cxx
+ add_executable(clitkAnisotropicDiffusion clitkAnisotropicDiffusion.cxx
clitkAnisotropicDiffusionGenericFilter.cxx
${clitkAnisotropicDiffusion_GGO_C})
- TARGET_LINK_LIBRARIES(clitkAnisotropicDiffusion clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAnisotropicDiffusion)
+ target_link_libraries(clitkAnisotropicDiffusion clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAnisotropicDiffusion)
WRAP_GGO(clitkChangeImageInfo_GGO_C clitkChangeImageInfo.ggo)
- ADD_EXECUTABLE(clitkChangeImageInfo clitkChangeImageInfo.cxx
+ add_executable(clitkChangeImageInfo clitkChangeImageInfo.cxx
clitkChangeImageInfoGenericFilter.cxx
${clitkChangeImageInfo_GGO_C})
- TARGET_LINK_LIBRARIES(clitkChangeImageInfo clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkChangeImageInfo)
+ target_link_libraries(clitkChangeImageInfo clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkChangeImageInfo)
WRAP_GGO(clitkMergeAsciiDoseActor_GGO_C clitkMergeAsciiDoseActor.ggo)
- ADD_EXECUTABLE(clitkMergeAsciiDoseActor clitkMergeAsciiDoseActor.cxx ${clitkMergeAsciiDoseActor_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMergeAsciiDoseActor ITKCommon clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMergeAsciiDoseActor)
+ add_executable(clitkMergeAsciiDoseActor clitkMergeAsciiDoseActor.cxx ${clitkMergeAsciiDoseActor_GGO_C})
+ target_link_libraries(clitkMergeAsciiDoseActor ITKCommon clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMergeAsciiDoseActor)
+
+ WRAP_GGO(clitkImageUncertainty_GGO_C clitkImageUncertainty.ggo)
+ add_executable(clitkImageUncertainty clitkImageUncertainty.cxx clitkImageUncertainty_ggo.c)
+ target_link_libraries(clitkImageUncertainty clitkCommon ${ITK_LIBRARIES})
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageUncertainty)
+
+ WRAP_GGO(clitkNormalizeImageFilter_GGO_C clitkNormalizeImageFilter.ggo)
+ add_executable(clitkNormalizeImageFilter clitkNormalizeImageFilter.cxx ${clitkNormalizeImageFilter_GGO_C})
+ target_link_libraries(clitkNormalizeImageFilter clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkNormalizeImageFilter)
+
+ WRAP_GGO(clitkImageGradientMagnitude_GGO_C clitkImageGradientMagnitude.ggo)
+ add_executable(clitkImageGradientMagnitude clitkImageGradientMagnitude.cxx ${clitkImageGradientMagnitude_GGO_C})
+ target_link_libraries(clitkImageGradientMagnitude clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageGradientMagnitude)
+
+ WRAP_GGO(clitkImageLaplacian_GGO_C clitkImageLaplacian.ggo)
+ add_executable(clitkImageLaplacian clitkImageLaplacian.cxx ${clitkImageLaplacian_GGO_C})
+ target_link_libraries(clitkImageLaplacian clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageLaplacian)
+
+ WRAP_GGO(clitkImageIntensityWindowing_GGO_C clitkImageIntensityWindowing.ggo)
+ add_executable(clitkImageIntensityWindowing clitkImageIntensityWindowing.cxx ${clitkImageIntensityWindowing_GGO_C})
+ target_link_libraries(clitkImageIntensityWindowing clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageIntensityWindowing)
+
+ WRAP_GGO(clitkBlurImage_GGO_C clitkBlurImage.ggo)
+ add_executable(clitkBlurImage clitkBlurImage.cxx ${clitkBlurImage_GGO_C})
+ target_link_libraries(clitkBlurImage clitkCommon )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBlurImage)
#=========================================================
option(CLITK_USE_ROOT "Build experimental tools using root" OFF)
if (CLITK_USE_ROOT)
- FIND_PACKAGE(ROOT REQUIRED)
+ find_package(ROOT REQUIRED)
if(ROOT_FOUND)
- MESSAGE(STATUS "ROOT found : ${ROOT_LIBRARY_DIR} ${ROOT_INCLUDE_DIR} ${ROOT_LIBRARIES}")
- ELSE(ROOT_FOUND)
- MESSAGE(FATAL_ERROR
+ message(STATUS "ROOT found : ${ROOT_LIBRARY_DIR} ${ROOT_INCLUDE_DIR} ${ROOT_LIBRARIES}")
+ else(ROOT_FOUND)
+ message(FATAL_ERROR
"Cannot build without ROOT. Please set ROOTSYS environement variable.")
endif(ROOT_FOUND)
- INCLUDE_DIRECTORIES(${ROOT_INCLUDE_DIR})
- LINK_DIRECTORIES(${ROOT_LIBRARY_DIR})
+ include_directories(${ROOT_INCLUDE_DIR})
+ link_directories(${ROOT_LIBRARY_DIR})
WRAP_GGO(clitkMergeRootFiles_GGO_C clitkMergeRootFiles.ggo)
- ADD_EXECUTABLE(clitkMergeRootFiles clitkMergeRootFiles.cxx GateMergeManager.cc ${clitkMergeRootFiles_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMergeRootFiles ${ROOT_LIBRARIES})
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMergeRootFiles)
+ add_executable(clitkMergeRootFiles clitkMergeRootFiles.cxx GateMergeManager.cc ${clitkMergeRootFiles_GGO_C})
+ target_link_libraries(clitkMergeRootFiles ${ROOT_LIBRARIES})
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMergeRootFiles)
endif()
#=========================================================
#=========================================================
- IF(CLITK_EXPERIMENTAL)
+ if(CLITK_EXPERIMENTAL)
WRAP_GGO(clitkBinaryImageToMesh_GGO_C clitkBinaryImageToMesh.ggo)
- ADD_EXECUTABLE(clitkBinaryImageToMesh clitkBinaryImageToMesh.cxx ${clitkBinaryImageToMesh_GGO_C})
- TARGET_LINK_LIBRARIES(clitkBinaryImageToMesh clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinaryImageToMesh)
+ add_executable(clitkBinaryImageToMesh clitkBinaryImageToMesh.cxx ${clitkBinaryImageToMesh_GGO_C})
+ target_link_libraries(clitkBinaryImageToMesh clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinaryImageToMesh)
WRAP_GGO(clitkMeshToBinaryImage_GGO_C clitkMeshToBinaryImage.ggo)
- ADD_EXECUTABLE(clitkMeshToBinaryImage clitkMeshToBinaryImage.cxx ${clitkMeshToBinaryImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMeshToBinaryImage clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshToBinaryImage)
+ add_executable(clitkMeshToBinaryImage clitkMeshToBinaryImage.cxx ${clitkMeshToBinaryImage_GGO_C})
+ target_link_libraries(clitkMeshToBinaryImage clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshToBinaryImage)
WRAP_GGO(clitkMeshViewer_GGO_C clitkMeshViewer.ggo)
- ADD_EXECUTABLE(clitkMeshViewer clitkMeshViewer.cxx ${clitkMeshViewer_GGO_C})
- TARGET_LINK_LIBRARIES(clitkMeshViewer clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshViewer)
- ENDIF(CLITK_EXPERIMENTAL)
+ add_executable(clitkMeshViewer clitkMeshViewer.cxx ${clitkMeshViewer_GGO_C})
+ target_link_libraries(clitkMeshViewer clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshViewer)
+ endif(CLITK_EXPERIMENTAL)
#=========================================================
#=========================================================
- IF(ITK_VERSION_MAJOR VERSION_LESS 4)
- MESSAGE("clitkDicomRTPlan2Gate is not compatible with GDCM<2 (ITK<4). It will not be built.")
- ELSE(ITK_VERSION_MAJOR VERSION_LESS 4)
- WRAP_GGO(clitkDicomRTPlan2Gate_GGO_C clitkDicomRTPlan2Gate.ggo)
- ADD_EXECUTABLE(clitkDicomRTPlan2Gate clitkDicomRTPlan2Gate.cxx clitkDicomRTPlan2Gate_ggo.c)
- TARGET_LINK_LIBRARIES(clitkDicomRTPlan2Gate clitkCommon)
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTPlan2Gate)
- ENDIF(ITK_VERSION_MAJOR VERSION_LESS 4)
+ WRAP_GGO(clitkDice_GGO_C clitkDice.ggo)
+ add_executable(clitkDice clitkDice.cxx ${clitkDice_GGO_C})
+ target_link_libraries(clitkDice clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES} )
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDice)
+
+ WRAP_GGO(clitkDicomRTPlan2Gate_GGO_C clitkDicomRTPlan2Gate.ggo)
+ add_executable(clitkDicomRTPlan2Gate clitkDicomRTPlan2Gate.cxx clitkDicomRTPlan2Gate_ggo.c)
+ target_link_libraries(clitkDicomRTPlan2Gate clitkCommon)
+ set(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTPlan2Gate)
#=========================================================
- INSTALL (TARGETS ${TOOLS_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+ install(TARGETS ${TOOLS_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
-ENDIF(CLITK_BUILD_TOOLS)
+endif(CLITK_BUILD_TOOLS)
version "1.0"
purpose "Resample with or without affine transform of 2D, 3D, 4D images or vector fields"
-option "config" - "Config file" string no
-option "verbose" v "Verbose" flag off
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
section "I/O"
-option "input" i "Input image filename" string yes
-option "output" o "Output image filename" string yes
-option "like" l "Resample output this image (size, spacing,origin)" string no
-option "transform_grid" - "Apply affine transform to input grid for output's" flag off
+option "input" i "Input image filename" string yes
+option "output" o "Output image filename" string yes
+option "like" l "Resample output this image (size, spacing, origin, direction)" string no
+option "transform_grid" - "Apply affine transform to input grid for output's" flag off
section "Options"
-option "size" - "New output size if different from input" int no multiple
-option "spacing" - "New output spacing if different from input" double no multiple
-option "spacinglike" - "New output spacing like this image" string no
-option "origin" - "New output origin if different from input" double no multiple
-option "matrix" m "Affine matrix (homogene) filename" string no
-option "elastix" e "Read EulerTransform from elastix output file (combine if multiple)" string no multiple
-option "rotate" r "Rotation to apply (radians)" double no multiple
-option "translate" t "Translation to apply (mm)" double no multiple
-option "pad" - "Edge padding value" double no default="0.0"
+option "size" - "New output size if different from input" int no multiple
+option "spacing" - "New output spacing if different from input" double no multiple
+option "spacinglike" - "New output spacing like this image" string no
+option "origin" - "New output origin if different from input" double no multiple
+option "matrix" m "Affine matrix (homogene) filename" string no
+option "elastix" e "Read EulerTransform from elastix output file (combine if multiple)" string no
+option "rotate" r "Rotation to apply (radians)" double no multiple
+option "translate" t "Translation to apply (mm)" double no multiple
+option "pad" - "Edge padding value" double no default="0.0"
section "Interpolation"
-option "interp" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
-option "interpOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
-option "interpSF" - "Sampling factor if BLUT" int no default="20"
-option "interpVF" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
-option "interpVFOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
-option "interpVFSF" - "Sampling factor if BLUT" int no default="20"
+option "interp" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
+option "interpOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
+option "interpSF" - "Sampling factor if BLUT" int no default="20"
+option "interpVF" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1"
+option "interpVFOrder" - "Order if BLUT or BSpline (0-5)" int no default="3"
+option "interpVFSF" - "Sampling factor if BLUT" int no default="20"
}
else {
if (m_ArgsInfo.elastix_given) {
- std::vector<std::string> s;
- for(uint i=0; i<m_ArgsInfo.elastix_given; i++) s.push_back(m_ArgsInfo.elastix_arg[i]);
- matrix = createMatrixFromElastixFile<Dimension>(s, m_Verbose);
+ std::string filename(m_ArgsInfo.elastix_arg);
+ matrix = createMatrixFromElastixFile<Dimension>(filename, m_Verbose);
}
else
matrix.SetIdentity();
likeReader->SetFileName(m_ArgsInfo.like_arg);
likeReader->Update();
resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ resampler->SetOutputDirection(likeReader->GetOutput()->GetDirection());
} else if(m_ArgsInfo.transform_grid_flag) {
typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
gadFilter->SetConductanceParameter(mArgsInfo.conductance_arg);
gadFilter->Update();
this->template SetNextOutput<InputImageType>(gadFilter->GetOutput());
+ break;
case type_arg_Curvature:
cadFilter->SetInput(input);
cadFilter->SetNumberOfIterations(mArgsInfo.niterations_arg);
cadFilter->SetConductanceParameter(mArgsInfo.conductance_arg);
cadFilter->Update();
this->template SetNextOutput<InputImageType>(cadFilter->GetOutput());
+ break;
+ default:
+ itkGenericExceptionMacro("Unhandled type");
+ break;
}
}
//--------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkBlurImageGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief BlurImage an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkBlurImage_ggo.h"
+#include "clitkBlurImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkBlurImage, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::BlurImageGenericFilter<args_info_clitkBlurImage> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkBlurImage.ggo
+package "clitkBlurImage"
+version "1.0"
+purpose "Filter the input image with a Gaussian"
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string required
+option "output" o "Output image filename" string required
+
+option "variance" - "value of the gaussian variance (multiple values=number of image dimension) - default=1.0" double optional multiple
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKBlurImageGENERICFILTER_H
+#define CLITKBlurImageGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT BlurImageGenericFilter:
+ public ImageToImageGenericFilter<BlurImageGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ BlurImageGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef BlurImageGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(BlurImageGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkBlurImageGenericFilter.txx"
+#endif
+
+#endif // #define clitkBlurImageGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkBlurImageGenericFilter_txx
+#define clitkBlurImageGenericFilter_txx
+
+/* =================================================
+ * @file clitkBlurImageGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkDiscreteGaussianImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+BlurImageGenericFilter<args_info_type>::BlurImageGenericFilter():
+ ImageToImageGenericFilter<Self>("BlurImage")
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ //InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void BlurImageGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void BlurImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+BlurImageGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+ const unsigned int dim = InputImageType::ImageDimension;
+ double varianceArray[dim];
+
+ //std::cout<<"mArgsInfo.variance_given"<<mArgsInfo.variance_given<<std::endl;
+
+
+ //if (mArgsInfo.variance_given != dim) {
+ // std::cerr << "The number of variance parameters must be equal to the image dimension." << std::endl;
+ // return;
+ //}
+
+ if (mArgsInfo.variance_given && mArgsInfo.variance_given == dim) {
+ for (unsigned int i = 0; i < dim; i++) {
+ //std::cout<<"mArgsInfo.variance_arg[i]"<<mArgsInfo.variance_arg[i]<<std::endl;
+ varianceArray[i] = mArgsInfo.variance_arg[i];
+ }
+ } else {
+ for (unsigned int i = 0; i < dim; i++) {
+ varianceArray[i] = 1.0;
+ }
+ }
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ // Main filter
+ typedef typename InputImageType::PixelType PixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+
+ // Filter
+ typedef itk::DiscreteGaussianImageFilter<InputImageType, OutputImageType> DiscreteGaussianImageFilterType;
+ typename DiscreteGaussianImageFilterType::Pointer gaussianFilter=DiscreteGaussianImageFilterType::New();
+ gaussianFilter->SetInput(input);
+ gaussianFilter->SetVariance(varianceArray);
+ gaussianFilter->Update();
+
+ //std::cout<<"variance value="<<gaussianFilter->GetVariance()<<std::endl;
+
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(gaussianFilter->GetOutput());
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkBlurImageGenericFilter_txx
typename ImageType::PointType origin = output->GetOrigin();
typename ImageType::SpacingType spacing = output->GetSpacing();
if (mArgsInfo.verbose_flag) std::cout << "origin before crop " << origin << std::endl;
- for (unsigned int i = 0; i < output->GetImageDimension(); i++)
- origin[i] += index[i]*spacing[i];
+ input->TransformIndexToPhysicalPoint(index,origin);
if (mArgsInfo.verbose_flag) std::cout << "origin after crop " << origin << std::endl;
output->SetOrigin(origin);
#include "vvImageReader.h"
#include "vvImageWriter.h"
#include <gdcmFile.h>
+#include <vtkVersion.h>
#include <vtkImageChangeInformation.h>
#if GDCM_MAJOR_VERSION == 2
#include <gdcmImageHelper.h>
std::vector<int> size = image->GetSize();
origin[0] = -spacing[0]*size[0]/2.0;
origin[1] = -spacing[1]*size[1]/2.0;
+#if VTK_MAJOR_VERSION <= 5
modifier->SetInput(vtk_image);
+#else
+ modifier->SetInputData(vtk_image);
+#endif
modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
modifier->Update();
vvImage::Pointer focal_image = vvImage::New();
#include "clitkDicomRTStruct2ImageFilter.h"
#include "clitkDicomRT_StructureSet.h"
#include "clitkDicomRTStruct2Image_ggo.h"
+#include "clitkIO.h"
//--------------------------------------------------------------------
int main(int argc, char * argv[]) {
// Init command line
GGO(clitkDicomRTStruct2Image, args_info);
+ CLITK_INIT;
// Read and display information
clitk::DicomRT_StructureSet::Pointer s = clitk::DicomRT_StructureSet::New();
filter.SetCropMaskEnabled(args_info.crop_flag);
filter.SetImageFilename(args_info.image_arg); // Used to get spacing + origin
name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
- std::string n = std::string(args_info.output_arg).append
- (clitk::toString(num)).append
- ("_").append
- (name).append
- (".mhd");
+ std::string n;
+ if (args_info.mha_flag) {
+ n = std::string(args_info.output_arg).append
+ (clitk::toString(num)).append
+ ("_").append
+ (name).append
+ (".mha");
+ }
+ else {
+ n = std::string(args_info.output_arg).append
+ (clitk::toString(num)).append
+ ("_").append
+ (name).append
+ (".mhd");
+ }
if (args_info.verbose_flag) {
std::cout << num << " " << roi->GetName() << " num=" << num << " : " << n << std::endl;
}
option "crop" c "Crop binary mask" flag off
+option "mha" - "Write the RTStruct as a mha image to avoid special character problems" flag off
+
#option "roi" r "ROI to print (ID)" int no
#option "contour" c "contour to print (ID)" int no
#option "offset" o "to display points as image offsets" flag off
CLITK_INIT;
// Use static fct of AffineTransformGenericFilter
- std::vector<std::string> l;
- l.push_back(args_info.input_arg);
- itk::Matrix<double, 4, 4> m = clitk::createMatrixFromElastixFile<3>(l, args_info.verbose_flag);
+ std::string filename(args_info.input_arg);
+ itk::Matrix<double, 4, 4> m = clitk::createMatrixFromElastixFile<3>(filename,
+ args_info.verbose_flag);
// Print matrix
std::ofstream os;
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
-/* =================================================
- * @file clitkFooImageGenericFilter.txx
- * @author xxx <xxx@creatis.insa-lyon.fr>
- * @date 29 June 2029
- *
- * @brief FooImage an image
- *
- ===================================================*/
-
// clitk
#include "clitkFooImage_ggo.h"
#include "clitkFooImageGenericFilter.h"
option "input" i "Input image filename" string required
option "output" o "Output image filename" string required
-option "lower" l "Lower intensity (default=min), fg is greater than this value" double optional
-option "upper" u "Upper intensity (default=max), fg is lower than this value" double optional
-option "fg" - "Foreground (FG) or 'inside' value" double optional default="1"
-option "bg" - "Background (BG) or 'ouside' value" double optional default="0"
-option "mode" - "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both" default="both" optional
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
-#ifndef CLITKFooIMAGEGENERICFILTER_H
-#define CLITKFooIMAGEGENERICFILTER_H
+#ifndef clitkFooImageGenericFilter_h
+#define clitkFooImageGenericFilter_h
#include "clitkIO.h"
#include "clitkImageToImageGenericFilter.h"
#ifndef clitkFooImageGenericFilter_txx
#define clitkFooImageGenericFilter_txx
-/* =================================================
- * @file clitkFooImageGenericFilter.txx
- * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
- * @date 29 june 2009
- *
- * @brief
- *
- ===================================================*/
-
// itk include
#include "itkBinaryThresholdImageFilter.h"
#include "itkMaskImageFilter.h"
typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
thresholdFilter->SetInput(input);
- thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
-
- if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
- if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
-
- if (mArgsInfo.mode_arg == std::string("both")) {
- thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
- thresholdFilter->Update();
-
- typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
- this->template SetNextOutput<OutputImageType>(outputImage);
- } else {
- typename InputImageType::Pointer outputImage;
- thresholdFilter->SetOutsideValue(0);
- if (mArgsInfo.mode_arg == std::string("BG")) {
- typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
- typename maskFilterType::Pointer maskFilter = maskFilterType::New();
- maskFilter->SetInput1(input);
- maskFilter->SetInput2(thresholdFilter->GetOutput());
- maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
- maskFilter->Update();
- outputImage = maskFilter->GetOutput();
- } else {
- typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
- typename maskFilterType::Pointer maskFilter = maskFilterType::New();
- maskFilter->SetInput1(input);
- maskFilter->SetInput2(thresholdFilter->GetOutput());
- maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
- maskFilter->Update();
- outputImage = maskFilter->GetOutput();
- }
- // Write/Save results
- this->template SetNextOutput<InputImageType>(outputImage);
- }
+ // Set filter members
+
+ // Write/Save results
+ typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
+ this->template SetNextOutput<OutputImageType>(outputImage);
}
//--------------------------------------------------------------------
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================*/
+
+#include "clitkGammaIndex_ggo.h"
+#include "clitkIO.h"
+#include "clitkDD.h"
+
+#include <iostream>
+#include <cmath>
+#include <cassert>
+
#include <vtkPoints.h>
#include <vtkCellArray.h>
#include <vtkPointData.h>
#include <vtkPNGReader.h>
#include <vtkPolyData.h>
#include <vtkCellLocator.h>
-#include <iostream>
-#include <cmath>
-#include <cassert>
-using std::endl;
-using std::cout;
-#include "clitkGammaIndex_ggo.h"
-
-#include <clitkIO.h>
#include <vvImage.h>
#include <vvImageReader.h>
#include <vvImageWriter.h>
typedef itk::Image<double> OutputImageType;
typedef itk::ImageRegionIterator<OutputImageType> OutputImageIterator;
+using std::endl;
+using std::cout;
+
vtkImageData* loadImage(const std::string& filename)
{
vvImageReader::Pointer reader = vvImageReader::New();
// load reference
vtkImageData* reference = loadImage(reference_filename);
assert(reference);
-
+
// translate target with arguments values
// reference is translated instead of target so that the output space stay the same as target
{
vtkAbstractCellLocator *locator = vtkCellLocator::New();
locator->SetDataSet(data);
- data->Delete();
+ DD("here");
+ // data->Delete();
locator->CacheCellBoundsOn();
locator->AutomaticOn();
+ DD("BuildLocator");
locator->BuildLocator();
+ DD("end BuildLocator");
// load target
vtkImageData* target = loadImage(target_filename);
unsigned long over_one = 0;
OutputImageIterator iter(output,output->GetLargestPossibleRegion());
iter.GoToBegin();
+ DD("loop");
while (!iter.IsAtEnd()) {
double *point = target->GetPoint(kk);
double value = target->GetPointData()->GetScalars()->GetTuple1(kk);
return 0;
}
-
filter->SetInputFilenames(l);
filter->SetIOVerbose(args_info.verbose_flag);
filter->SetOutputFilename(output);
+ filter->SetVV(args_info.vv_flag);
+ filter->SetCorrectNegativeSpacingFlag(args_info.correct_flag);
filter->EnableWriteCompression(args_info.compression_flag);
if (args_info.type_given) filter->SetOutputPixelType(args_info.type_arg);
//-------------------------------------------------------------------=
#endif /* end #define CLITKIMAGECONVERT_CXX */
-
version "1.0"
purpose "Convert an image into another image.\n\tAllow to change the file format and/or the pixel type. \n\tKnown file formats 2D: jpeg png bmp tif mhd hdr vox dcm \n\tKnown file formats 3D: mhd vox hdr dcm\n\tKnown file formats 4D: mhd \n\tKnown images: 2D 3D or 4D, schar, uchar, short, ushort, int, float and double\n\nIf the -o option is not given, the last parameter of the command line is used as output."
-option "config" - "Config file" string no
-option "input" i "Input image filename" string no
-option "output" o "Output image filename" string no
-option "type" t "Output type (float, ushort ...)" string no
-option "verbose" v "Verbose" flag off
-option "compression" c "Compress output" flag off
+option "config" - "Config file" string no
+option "input" i "Input image filename" string no
+option "output" o "Output image filename" string no
+option "type" t "Output type (float, ushort ...)" string no
+option "verbose" v "Verbose" flag off
+option "compression" c "Compress output" flag off
+option "vv" - "Read image as in vv and save transform in meta information" flag off
+option "correct" - "Correct dicom with negative Z spacing" flag off
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
+
#ifndef CLITKIMAGECONVERTGENERICFILTER_CXX
#define CLITKIMAGECONVERTGENERICFILTER_CXX
#include "clitkImageConvertGenericFilter.h"
+#include "vvImageReader.h"
+#include "vvImageWriter.h"
+#include "itkFlipImageFilter.h"
+#include "itkGDCMImageIO.h"
+
+#include "gdcmReader.h"
+#include "gdcmAttribute.h"
+#include "gdcmPrinter.h"
+#include "gdcmDict.h"
+#include "gdcmStringFilter.h"
//--------------------------------------------------------------------
clitk::ImageConvertGenericFilter::ImageConvertGenericFilter():
mDisplayWarning = true;
mWarning = "";
mWarningOccur = false;
-
+ SetCorrectNegativeSpacingFlag(false);
+
InitializeImageType<2>();
InitializeImageType<3>();
InitializeImageType<4>();
}
}
- if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
+ if(mVV) {
+ if (mOutputPixelTypeName != "NotSpecified" || m_WriteCompression) {
+ std::cerr << "--vv is not compatible with --compression and --type options." << std::endl;
+ exit(-1);
+ }
+
+ vvImageReader::Pointer reader = vvImageReader::New();
+ reader->SetInputFilenames(m_InputFilenames);
+ reader->Update(vvImageReader::IMAGE);
+
+ vvImageWriter::Pointer writer = vvImageWriter::New();
+ writer->SetOutputFileName(m_OutputFilenames.front());
+ writer->SetSaveTransform(true);
+ writer->SetInput(reader->GetOutput());
+ writer->Update();
+ return;
+ }
+ else if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
+
+ // Get input image
typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
- this->SetNextOutput<InputImageType>(input);
+
+ if (mCorrectNegativeSpacingFlag) {
+ // Read dicom
+ gdcm::Reader reader;
+ reader.SetFileName(m_InputFilenames[0].c_str());
+ // if (!reader.CanReadFile(m_InputFilenames[0])) {
+ // std::cout << "Error: " << m_InputFilenames[0] << " is not a dicom file. Abort." << std::endl;
+ // exit(0);
+ // }
+ reader.Read();
+
+ // the dataset is the the set of element we are interested in:
+ gdcm::DataSet & ds = reader.GetFile().GetDataSet();
+
+ // Read the attribute SpacingBetweenSlices, check if negative and replace
+ gdcm::Attribute<0x0018,0x0088> SpacingBetweenSlices;
+ SpacingBetweenSlices.SetFromDataSet(ds);
+ double s = SpacingBetweenSlices.GetValue();
+ if (s >=0) {
+ std::cout << "Error: no negative spacing found SpacingBetweenSlices = " << s << " Abort. " << std::endl;
+ exit(0);
+ }
+ s = -s;
+
+ // Set spacing
+ typename InputImageType::SpacingType spacing = input->GetSpacing();
+ spacing[2] = s;
+ input->SetSpacing(spacing);
+
+ // Flip
+ typedef itk::FlipImageFilter< InputImageType > FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ typedef typename FilterType::FlipAxesArrayType FlipAxesArrayType;
+ FlipAxesArrayType flipArray;
+ flipArray[0] = false;
+ flipArray[1] = false;
+ flipArray[2] = true;
+ filter->SetFlipAxes(flipArray);
+ filter->SetInput(input);
+ filter->Update();
+
+ // Read the attribute Image Position (Patient)
+ gdcm::Tag DetectorInformationSequenceTag(0x0054,0x0022);
+ const gdcm::DataElement & DIS = ds.GetDataElement(DetectorInformationSequenceTag);
+ gdcm::SmartPointer<gdcm::SequenceOfItems> sqf = DIS.GetValueAsSQ();
+ gdcm::Item & item = sqf->GetItem(1);
+ gdcm::DataSet & ds_position = item.GetNestedDataSet();
+ gdcm::Attribute<0x0020,0x0032> ImagePositionPatient;
+ ImagePositionPatient.SetFromDataSet(ds_position);
+ double x = ImagePositionPatient.GetValue(0);
+ double y = ImagePositionPatient.GetValue(1);
+ double z = ImagePositionPatient.GetValue(2);
+
+ // Set offset
+ typename InputImageType::PointType origin = input->GetOrigin();
+ origin[0] = x;
+ origin[1] = y;
+ origin[2] = z;
+ input->SetOrigin(origin);
+
+ // Orientation
+ typename InputImageType::DirectionType direction = input->GetDirection();
+ direction[2][2] = -1;
+ input->SetDirection(direction);
+
+ // Empty meta info
+ itk::MetaDataDictionary dict;// = new itk::MetaDataDictionary;
+ input->SetMetaDataDictionary(dict);
+
+ this->SetNextOutput<InputImageType>(input);
+ }
+
} else {
- // "trick" to call independent versions of update according to the
+ // "trick" to call independent versions of update according to the
// pixel type (vector or scalar), using partial specializations
- if (!UpdateWithSelectiveOutputType<InputImageType, ImageConvertTraits<typename InputImageType::PixelType>::IS_VECTOR>::Run(*this, mOutputPixelTypeName))
+ if (!UpdateWithSelectiveOutputType<InputImageType, ImageConvertTraits<typename InputImageType::PixelType>::IS_VECTOR>::Run(*this, mOutputPixelTypeName))
exit(-1);
}
}
#endif /* end #define CLITKIMAGECONVERTGENERICFILTER_CXX */
-
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
* @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
* @date 05 May 2008 10:40:24
- * @brief
+ * @brief
===================================================================*/
namespace clitk {
-
+
template <class TPixel>
class ImageConvertTraits
{
}
};
- template < class TPixel, unsigned int Comp >
- class ImageConvertTraits< itk::Vector<TPixel, Comp> >
- {
- public:
- enum { IS_VECTOR = true };
+ template < class TPixel, unsigned int Comp >
+ class ImageConvertTraits< itk::Vector<TPixel, Comp> >
+ {
+ public:
+ enum { IS_VECTOR = true };
};
- class ImageConvertGenericFilter:
+ class ImageConvertGenericFilter:
public clitk::ImageToImageGenericFilter<ImageConvertGenericFilter> {
-
- public:
+
+ public:
// constructor - destructor
ImageConvertGenericFilter();
// New
itkNewMacro(Self);
-
+
// Members functions
std::string GetInputPixelTypeName() { return m_PixelTypeName; }
std::string GetOutputPixelTypeName() { return mOutputPixelTypeName; }
void SetOutputPixelType(std::string p) { mOutputPixelTypeName = p; }
+ void SetVV(bool b) { mVV = b; }
bool IsWarningOccur() { return mWarningOccur; }
std::string & GetWarning() { return mWarning; }
void EnableDisplayWarning(bool b) { mDisplayWarning = b; }
+ void SetCorrectNegativeSpacingFlag(bool b) { mCorrectNegativeSpacingFlag = b; }
//--------------------------------------------------------------------
// Main function called each time the filter is updated
- template<class InputImageType>
+ template<class InputImageType>
void UpdateWithInputImageType();
template<class PixelType, class OutputPixelType>
void CheckTypes(std::string inType, std::string outType);
-
+
protected:
template<unsigned int Dim> void InitializeImageType();
std::string mWarning;
bool mWarningOccur;
bool mDisplayWarning;
+ bool mVV;
+ bool mCorrectNegativeSpacingFlag;
private:
template <class InputImageType, bool isVector>
else
{
std::string list = CreateListOfTypes<float, double>();
- std::cerr << "Error, I don't know the vector output type '" << outputPixelType
+ std::cerr << "Error, I don't know the vector output type '" << outputPixelType
<< "'. " << std::endl << "Known types are " << list << "." << std::endl;
return false;
}
-
+
return true;
}
private:
-
- template <class OutputPixelType>
+
+ template <class OutputPixelType>
static void UpdateWithOutputType(ImageConvertGenericFilter& filter)
{
// Read
filter.SetNextOutput<OutputImageType>(cast_filter->GetOutput());
}
};
-
+
template <class InputImageType>
class UpdateWithSelectiveOutputType<InputImageType, true>
{
static bool Run(ImageConvertGenericFilter& filter, std::string outputPixelType)
{
/*
- // RP: future conversions?
+ // RP: future conversions?
if (IsSameType<char>(outputPixelType))
UpdateWithOutputVectorType<char>();
else if (IsSameType<uchar>(outputPixelType))
UpdateWithOutputVectorType<ushort>();
else if (IsSameType<int>(outputPixelType))
UpdateWithOutputVectorType<int>();
- else
+ else
*/
if (IsSameType<float>(outputPixelType))
UpdateWithOutputVectorType<float>(filter);
else
{
std::string list = CreateListOfTypes<float, double>();
- std::cerr << "Error, I don't know the vector output type '" << outputPixelType
+ std::cerr << "Error, I don't know the vector output type '" << outputPixelType
<< "'. " << std::endl << "Known types are " << list << "." << std::endl;
return false;
}
-
+
return true;
}
-
+
private:
-
- template <class OutputPixelType>
+
+ template <class OutputPixelType>
static void UpdateWithOutputVectorType(ImageConvertGenericFilter& filter)
{
// Read
// Warning
filter.CheckTypes<PixelType, OutputPixelType>(filter.GetInputPixelTypeName(), filter.GetOutputPixelTypeName());
-
+
// Cast
typedef itk::Image<itk::Vector<OutputPixelType, InputImageType::PixelType::Dimension>, InputImageType::ImageDimension> OutputImageType;
typedef itk::VectorCastImageFilter<InputImageType, OutputImageType> FilterType;
} // end namespace
#endif /* end #define CLITKIMAGECONVERTGENERICFILTER_H */
-
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkImageGradientMagnitudeGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief ImageGradientMagnitude an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkImageGradientMagnitude_ggo.h"
+#include "clitkImageGradientMagnitudeGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkImageGradientMagnitude, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::ImageGradientMagnitudeGenericFilter<args_info_clitkImageGradientMagnitude> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkImageGradientMagnitude.ggo
+package "clitkImageGradientMagnitude"
+version "1.0"
+purpose "Compute the gradient magnitude of the input image"
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string required
+option "mask" m "Mask input image filename" string optional
+option "output" o "Output image filename" string required
+option "normalize" n "Normalize the output image between 0 and 1" flag off
+option "gaussian_filter" g "Gaussian filtering - default sigma value=1.0" flag off
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKImageGradientMagnitudeGENERICFILTER_H
+#define CLITKImageGradientMagnitudeGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT ImageGradientMagnitudeGenericFilter:
+ public ImageToImageGenericFilter<ImageGradientMagnitudeGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ ImageGradientMagnitudeGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageGradientMagnitudeGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(ImageGradientMagnitudeGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+private:
+ bool m_NormalizeOutput;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkImageGradientMagnitudeGenericFilter.txx"
+#endif
+
+#endif // #define clitkImageGradientMagnitudeGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkImageGradientMagnitudeGenericFilter_txx
+#define clitkImageGradientMagnitudeGenericFilter_txx
+
+/* =================================================
+ * @file clitkImageGradientMagnitudeGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkGradientMagnitudeImageFilter.h"
+#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ ImageGradientMagnitudeGenericFilter<args_info_type>::ImageGradientMagnitudeGenericFilter():
+ ImageToImageGenericFilter<Self>("ImageGradientMagnitude")
+ {
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dim>
+ void ImageGradientMagnitudeGenericFilter<args_info_type>::InitializeImageType()
+ {
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ void ImageGradientMagnitudeGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+ {
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+ //
+ if (mArgsInfo.normalize_flag) {
+ this->m_NormalizeOutput = 1;
+ }
+ else {
+ this->m_NormalizeOutput = 0;
+ }
+ if (mArgsInfo.mask_given) {
+ this->AddInputFilename(mArgsInfo.mask_arg);
+ }
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<class InputImageType>
+ void
+ ImageGradientMagnitudeGenericFilter<args_info_type>::UpdateWithInputImageType()
+ {
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<unsigned char, OutputImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ typename MaskImageType::Pointer mask = NULL;
+ if(mArgsInfo.mask_given) {
+ mask = this->template GetInput<MaskImageType>(1);
+ }
+ else {
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(1);
+ }
+
+
+ // Create output image
+ typename OutputImageType::Pointer outputImage = OutputImageType::New();
+ outputImage->SetRegions(input->GetLargestPossibleRegion());
+ outputImage->SetOrigin(input->GetOrigin());
+ outputImage->SetSpacing(input->GetSpacing());
+ outputImage->Allocate();
+ outputImage->FillBuffer(0.0);
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+ // Filter
+ typename OutputImageType::Pointer outputGradientFilter;
+ if (mArgsInfo.gaussian_filter_flag == 0) {
+ typedef itk::GradientMagnitudeImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
+ typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
+ gradientFilter->SetInput(input);
+ gradientFilter->Update();
+ outputGradientFilter = gradientFilter->GetOutput();
+ }
+ else {
+ typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
+ typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
+ gradientFilter->SetInput(input);
+ gradientFilter->Update();
+ //std::cout<<"sigma value="<<gradientFilter->GetSigma()<<std::endl;
+ outputGradientFilter = gradientFilter->GetOutput();
+ }
+ // Set iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorType;
+ IteratorType it(outputGradientFilter, outputGradientFilter->GetLargestPossibleRegion());
+
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+
+ //typedef itk::MinimumMaximumImageCalculator <OutputImageType> ImageCalculatorFilterType;
+ //typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
+ //imageCalculatorFilter->SetImage(outputGradientFilter);
+ //imageCalculatorFilter->Compute();
+ typedef itk::LabelStatisticsImageFilter< OutputImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(outputGradientFilter);
+ labelStatisticsImageFilter->Update();
+
+ //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
+
+ float minImg = labelStatisticsImageFilter->GetMinimum(1);
+ //std::cout << "minImg: " << minImg << std::endl;
+ float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+ //std::cout << "maxImg: " << maxImg << std::endl;
+
+ it.GoToBegin();
+ ito.GoToBegin();
+ itm.GoToBegin();
+
+ while (!ito.IsAtEnd()) {
+ if(m_NormalizeOutput && itm.Get() == 1) {
+ ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
+ }
+ if (m_NormalizeOutput == 0 && itm.Get() == 1) {
+ ito.Set((float) it.Get());
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+
+ //typename OutputImageType::Pointer outputImage = outputGradientFilter;
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ //--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkImageGradientMagnitudeGenericFilter_txx
#include "clitkIO.h"
#include "clitkImageCommon.h"
#include "clitkCommon.h"
+#include "vvImageReader.h"
//====================================================================
int main(int argc, char * argv[])
else {
std::cerr << "*** Warning : I could not read '" << args_info.inputs[i] << "' ***" << std::endl;
}
- }
+
+ if (args_info.matrix_flag) {
+ vvImageReader::Pointer r = vvImageReader::New();
+ r->SetInputFilename(args_info.inputs[i]);
+ r->Update(vvImageReader::IMAGE);
+ vtkMatrix4x4 * m = r->GetOutput()->GetTransform()[0]->GetMatrix();
+ for(int i=0; i<4; i++) {
+ for(int j=0; j<4; j++)
+ std::cout << m->GetElement(i,j) << " ";
+ std::cout << std::endl;
+ }
+
+ // inverse
+ m->Invert();
+ for(int i=0; i<4; i++) {
+ for(int j=0; j<4; j++)
+ std::cout << m->GetElement(i,j) << " ";
+ std::cout << std::endl;
+ }
+
+ }
+ } // end for
+
// this is the end my friend
return 0;
option "long" l "Long line output (1 or 2)" int default = "1" no
option "verbose" v "Same as -l 1" flag off
option "name" n "Display filename" flag off
-
+option "matrix" m "Display matrix" flag off
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkImageIntensityWindowingGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief ImageIntensityWindowing an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkImageIntensityWindowing_ggo.h"
+#include "clitkImageIntensityWindowingGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkImageIntensityWindowing, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::ImageIntensityWindowingGenericFilter<args_info_clitkImageIntensityWindowing> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkImageIntensityWindowing.ggo
+package "clitkImageIntensityWindowing"
+version "1.0"
+purpose ""
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string required
+option "output" o "Output image filename" string required
+option "mask" m "Mask input image filename" string optional
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKImageIntensityWindowingGENERICFILTER_H
+#define CLITKImageIntensityWindowingGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT ImageIntensityWindowingGenericFilter:
+ public ImageToImageGenericFilter<ImageIntensityWindowingGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ ImageIntensityWindowingGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageIntensityWindowingGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(ImageIntensityWindowingGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkImageIntensityWindowingGenericFilter.txx"
+#endif
+
+#endif // #define clitkImageIntensityWindowingGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkImageIntensityWindowingGenericFilter_txx
+#define clitkImageIntensityWindowingGenericFilter_txx
+
+/* =================================================
+ * @file clitkImageIntensityWindowingGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkIntensityWindowingImageFilter.h"
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+ImageIntensityWindowingGenericFilter<args_info_type>::ImageIntensityWindowingGenericFilter():
+ ImageToImageGenericFilter<Self>("ImageIntensityWindowing")
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void ImageIntensityWindowingGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void ImageIntensityWindowingGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+ if (mArgsInfo.mask_given) {
+ this->AddInputFilename(mArgsInfo.mask_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+ImageIntensityWindowingGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<unsigned char, InputImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename OutputImageType::Pointer input = this->template GetInput<OutputImageType>(0);
+
+ typename MaskImageType::Pointer mask = NULL;
+ if(mArgsInfo.mask_given) {
+ mask = this->template GetInput<MaskImageType>(1);
+ }
+ else {
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(1);
+ }
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+ //
+ typedef itk::LabelStatisticsImageFilter< OutputImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(input);
+ labelStatisticsImageFilter->Update();
+ float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+ //std::cout << "maxImg: " << maxImg << std::endl;
+ // Filter
+ typedef itk::IntensityWindowingImageFilter <OutputImageType, OutputImageType> IntensityWindowingImageFilterType;
+ typename IntensityWindowingImageFilterType::Pointer filter = IntensityWindowingImageFilterType::New();
+ filter->SetInput(input);
+ filter->SetWindowMinimum(0.0);
+ filter->SetWindowMaximum(maxImg);
+ filter->SetOutputMinimum(0.0);
+ filter->SetOutputMaximum(1.0);
+ filter->Update();
+
+ // Set iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorType;
+ IteratorType it(filter->GetOutput(), filter->GetOutput()->GetLargestPossibleRegion());
+ //A little bit strange to do that but I think I need to do it.
+ // Create output image
+ typename OutputImageType::Pointer outputImage = OutputImageType::New();
+ outputImage->SetRegions(filter->GetOutput()->GetLargestPossibleRegion());
+ outputImage->SetOrigin(filter->GetOutput()->GetOrigin());
+ outputImage->SetSpacing(filter->GetOutput()->GetSpacing());
+ outputImage->Allocate();
+ outputImage->FillBuffer(-100.0);
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+ ito.GoToBegin();
+ itm.GoToBegin();
+
+ while (!ito.IsAtEnd()) {
+ if(itm.Get() > 0) {
+ ito.Set(it.Get());
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(outputImage);
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkImageIntensityWindowingGenericFilter_txx
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkImageLaplacianGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief ImageLaplacian an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkImageLaplacian_ggo.h"
+#include "clitkImageLaplacianGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkImageLaplacian, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::ImageLaplacianGenericFilter<args_info_clitkImageLaplacian> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkImageLaplacian.ggo
+package "clitkImageLaplacian"
+version "1.0"
+purpose "Compute the laplacian of the input image"
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string required
+option "mask" m "Mask input image filename" string optional
+option "output" o "Output image filename" string required
+option "normalize" n "Normalize the output image between 0 and 1" flag off
+option "gaussian_filter" g "Gaussian filtering - default sigma value=1.0" flag on
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKImageLaplacianGENERICFILTER_H
+#define CLITKImageLaplacianGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT ImageLaplacianGenericFilter:
+ public ImageToImageGenericFilter<ImageLaplacianGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ ImageLaplacianGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageLaplacianGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(ImageLaplacianGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkImageLaplacianGenericFilter.txx"
+#endif
+
+#endif // #define clitkImageLaplacianGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkImageLaplacianGenericFilter_txx
+#define clitkImageLaplacianGenericFilter_txx
+
+/* =================================================
+ * @file clitkImageLaplacianGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkCastImageFilter.h"
+#include "itkLaplacianImageFilter.h"
+#include "itkLaplacianRecursiveGaussianImageFilter.h"
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+ImageLaplacianGenericFilter<args_info_type>::ImageLaplacianGenericFilter():
+ ImageToImageGenericFilter<Self>("ImageLaplacian")
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void ImageLaplacianGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void ImageLaplacianGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+ if (mArgsInfo.mask_given) {
+ this->AddInputFilename(mArgsInfo.mask_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+ImageLaplacianGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> FloatImageType;
+ typedef itk::Image<unsigned char, FloatImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ //Cast input to float
+ typedef itk::CastImageFilter< InputImageType, FloatImageType > CastFilterType;
+ typename CastFilterType::Pointer castFilter = CastFilterType::New();
+ castFilter->SetInput(input);
+ castFilter->Update();
+
+ typename MaskImageType::Pointer mask = NULL;
+ if(mArgsInfo.mask_given) {
+ mask = this->template GetInput<MaskImageType>(1);
+ }
+ else {
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(1);
+ }
+
+
+ // Create output image
+ typename FloatImageType::Pointer outputImage = FloatImageType::New();
+ outputImage->SetRegions(input->GetLargestPossibleRegion());
+ outputImage->SetOrigin(input->GetOrigin());
+ outputImage->SetSpacing(input->GetSpacing());
+ outputImage->Allocate();
+ outputImage->FillBuffer(0.0);
+ // Set output iterator
+ typedef itk::ImageRegionIterator<FloatImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+ // Filter
+ typename FloatImageType::Pointer outputLaplacianFilter;
+ if (mArgsInfo.gaussian_filter_flag == 0) {
+ //std::cout<<"gaussian filter flag == 0"<<std::endl;
+ typedef itk::LaplacianImageFilter<FloatImageType, FloatImageType> LaplacianImageFilterType;
+ typename LaplacianImageFilterType::Pointer laplacianFilter=LaplacianImageFilterType::New();
+ laplacianFilter->SetInput(castFilter->GetOutput());
+ laplacianFilter->Update();
+ outputLaplacianFilter = laplacianFilter->GetOutput();
+ }
+ else {
+ //std::cout<<"gaussian filter flag == 1"<<std::endl;
+ typedef itk::LaplacianRecursiveGaussianImageFilter< FloatImageType, FloatImageType > LaplacianImageFilterType;
+ typename LaplacianImageFilterType::Pointer laplacianFilter=LaplacianImageFilterType::New();
+ laplacianFilter->SetInput(castFilter->GetOutput());
+ laplacianFilter->Update();
+ //std::cout<<"sigma value="<<laplacianFilter->GetSigma()<<std::endl;
+ outputLaplacianFilter = laplacianFilter->GetOutput();
+ }
+ // Set iterator
+ typedef itk::ImageRegionIterator<FloatImageType> IteratorType;
+ IteratorType it(outputLaplacianFilter, outputLaplacianFilter->GetLargestPossibleRegion());
+
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+
+ //typedef itk::MinimumMaximumImageCalculator <OutputImageType> ImageCalculatorFilterType;
+ //typename ImageCalculatorFilterType::Pointer imageCalculatorFilter = ImageCalculatorFilterType::New();
+ //imageCalculatorFilter->SetImage(gradientFilter->GetOutput());
+ //imageCalculatorFilter->Compute();
+ typedef itk::LabelStatisticsImageFilter< FloatImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(outputLaplacianFilter);
+ labelStatisticsImageFilter->Update();
+
+ //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
+
+ float minImg = labelStatisticsImageFilter->GetMinimum(1);
+ //std::cout << "minImg: " << minImg << std::endl;
+ float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+ //std::cout << "maxImg: " << maxImg << std::endl;
+
+ it.GoToBegin();
+ ito.GoToBegin();
+ itm.GoToBegin();
+
+ while (!ito.IsAtEnd()) {
+ if(mArgsInfo.normalize_flag && itm.Get() == 1) {
+ ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
+ }
+ if (mArgsInfo.normalize_flag == 0 && itm.Get() == 1) {
+ ito.Set((float) it.Get());
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+
+ //typename OutputImageType::Pointer outputImage = gradientFilter->GetOutput();
+ this->template SetNextOutput<FloatImageType>(outputImage);
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkImageLaplacianGenericFilter_txx
option "mask" m "Mask image filename (uchar)" string no
option "label" l "Label(s) in the mask image to consider" int no multiple default="1"
option "histogram" - "Compute histogram, allows median calculation" string no
+option "dvhistogram" - "Compute dose volume histogram" string no
option "bins" - "Number of histogram bins" int no default="100"
option "lower" - "Lower histogram bound" double no default="-1000"
option "upper" - "Upper histogram bound" double no default="1000"
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
m_InputFileName="";
}
//-----------------------------------------------------------
-
+
//-----------------------------------------------------------
// Update
int Dimension, Components;
std::string PixelType;
ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
+
if (m_ArgsInfo.channel_arg < -1 || m_ArgsInfo.channel_arg >= Components) {
std::cout << "Invalid image channel" << std::endl;
return;
}
-
+
if (m_ArgsInfo.mask_given) {
int maskDimension, maskComponents;
std::string maskPixelType;
}
}
-
+
// Call UpdateWithDim
if (Dimension==2) {
switch (Components) {
- case 1:
+ case 1:
UpdateWithDim<2,1>(PixelType);
break;
- case 2:
+ case 2:
UpdateWithDim<2,2>(PixelType);
break;
- case 3:
+ case 3:
UpdateWithDim<2,3>(PixelType);
break;
default:
}
else if (Dimension==3) {
switch (Components) {
- case 1:
+ case 1:
UpdateWithDim<3,1>(PixelType);
break;
- case 2:
+ case 2:
UpdateWithDim<3,2>(PixelType);
break;
- case 3:
+ case 3:
UpdateWithDim<3,3>(PixelType);
break;
default:
}
else if (Dimension==4) {
switch (Components) {
- case 1:
+ case 1:
UpdateWithDim<4,1>(PixelType);
break;
- case 2:
+ case 2:
UpdateWithDim<4,2>(PixelType);
break;
- case 3:
+ case 3:
UpdateWithDim<4,3>(PixelType);
break;
default:
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
// Update with the number of dimensions
//-------------------------------------------------------------------
template<unsigned int Dimension, unsigned int Components>
- void
+ void
ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
{
if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<" with " << Components << " channel(s)..."<<std::endl;
- if(PixelType == "short"){
+ if(PixelType == "short"){
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, signed short, Components>();
+ UpdateWithDimAndPixelType<Dimension, signed short, Components>();
}
- else if(PixelType == "unsigned_short"){
+ else if(PixelType == "unsigned_short"){
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
+ UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
}
-
- else if (PixelType == "unsigned_char"){
+
+ else if (PixelType == "unsigned_char"){
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
UpdateWithDimAndPixelType<Dimension, unsigned char, Components>();
}
-
- else if(PixelType == "double"){
+
+ else if(PixelType == "double"){
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, double, Components>();
+ UpdateWithDimAndPixelType<Dimension, double, Components>();
}
else {
if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
//-------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
//-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType, unsigned int Components>
- void
+ template <unsigned int Dimension, class PixelType, unsigned int Components>
+ void
ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
{
typedef unsigned char LabelPixelType;
typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
typedef itk::Image<LabelPixelType, Dimension> LabelImageType;
-
+
// Read the input
typedef itk::ImageFileReader<InputImageType> InputReaderType;
typename InputReaderType::Pointer reader = InputReaderType::New();
reader->SetFileName( m_InputFileName);
reader->Update();
typename InputImageType::Pointer input= reader->GetOutput();
-
+
typedef itk::NthElementImageAdaptor<InputImageType, PixelType> InputImageAdaptorType;
typedef itk::Image<PixelType, Dimension> OutputImageType;
typename InputImageAdaptorType::Pointer input_adaptor = InputImageAdaptorType::New();
input_adaptor->SetImage(input);
-
+
// Filter
typedef itk::LabelStatisticsImageFilter<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
// Due to a limitation of filter itk::LabelStatisticsImageFilter, InputImageType and LabelImageType
// must have the same image dimension. However, we want to support label images with Dl = Di - 1,
// so we need to replicate the label image as many times as the size along dimension Di.
- if (m_Verbose)
+ if (m_Verbose)
std::cout << "Replicating label image to match input image's dimension... " << std::endl;
-
+
typedef itk::Image<LabelPixelType, Dimension - 1> ReducedLabelImageType;
typedef itk::ImageFileReader<ReducedLabelImageType> LabelImageReaderType;
typedef itk::JoinSeriesImageFilter<ReducedLabelImageType, LabelImageType> JoinImageFilterType;
-
+
typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
labelImageReader->Update();
typename InputImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
for (unsigned int i = 0; i < size[Dimension - 1]; i++)
joinFilter->PushBackInput(labelImageReader->GetOutput());
-
+
joinFilter->Update();
labelImage = joinFilter->GetOutput();
}
typename ResamplerType::Pointer resampler = ResamplerType::New();
resampler->SetInput(labelImage);
resampler->SetOutputSpacing(input->GetSpacing());
+ resampler->SetOutputOrigin(labelImage->GetOrigin());
resampler->SetGaussianFilteringEnabled(false);
resampler->Update();
labelImage = resampler->GetOutput();
//writeImage<LabelImageType>(labelImage, "test1.mha");
-
+
typedef clitk::CropLikeImageFilter<LabelImageType> FilterType;
typename FilterType::Pointer crop = FilterType::New();
crop->SetInput(labelImage);
crop->SetCropLikeImage(input);
crop->Update();
- labelImage = crop->GetOutput();
+ labelImage = crop->GetOutput();
//writeImage<LabelImageType>(labelImage, "test2.mha");
}
else {
- std::cerr << "Mask image has a different size/spacing than input. Abort" << std::endl;
+ std::cerr << "Mask image has a different size/spacing than input. Abort. (Use option to resize)" << std::endl;
exit(-1);
}
}
}
}
- else {
+ else {
labelImage=LabelImageType::New();
+ labelImage->SetDirection(input->GetDirection());
labelImage->SetRegions(input->GetLargestPossibleRegion());
labelImage->SetOrigin(input->GetOrigin());
labelImage->SetSpacing(input->GetSpacing());
+ labelImage->SetDirection(input->GetDirection());
labelImage->Allocate();
labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
}
statisticsFilter->SetLabelInput(labelImage);
+ // Check/compute spacing
+ const typename LabelImageType::SpacingType& spacing = input->GetSpacing();
+ double spacing_cc = (spacing[0]*spacing[1]*spacing[2])/1000;
+ // std::cout<<"Spacing x : " << spacing[0]<<std::endl;
+ // std::cout<<"Spacing y : " << spacing[1]<<std::endl;
+ // std::cout<<"Spacing z : " << spacing[2]<<std::endl;
+ // std::cout <<"spacing_cc : " << spacing_cc << std::endl;
+
+
// For each Label
typename LabelImageType::PixelType label;
unsigned int numberOfLabels;
unsigned int firstComponent = 0, lastComponent = 0;
if (m_ArgsInfo.channel_arg == -1) {
- firstComponent = 0;
+ firstComponent = 0;
lastComponent = Components - 1;
}
else {
firstComponent = m_ArgsInfo.channel_arg;
lastComponent = m_ArgsInfo.channel_arg;
}
-
+
for (unsigned int c=firstComponent; c<=lastComponent; c++) {
if (m_Verbose) std::cout << std::endl << "Processing channel " << c << std::endl;
-
+
input_adaptor->SelectNthElement(c);
input_adaptor->Update();
-
+
for (unsigned int k=0; k< numberOfLabels; k++) {
label=m_ArgsInfo.label_arg[k];
std::cout<<std::endl;
if (m_Verbose) std::cout<<"-------------"<<std::endl;
- if (m_Verbose) std::cout<<"| Label: "<<label<<" |"<<std::endl;
+ if (m_Verbose) std::cout<<"| Label: "<< (int) label<<" |"<<std::endl;
if (m_Verbose) std::cout<<"-------------"<<std::endl;
// Histograms
statisticsFilter->SetUseHistograms(true);
statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
}
+
+ // DVH
+ if(m_ArgsInfo.dvhistogram_given)
+ {
+ statisticsFilter->SetUseHistograms(true);
+ statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
+ }
+
statisticsFilter->Update();
// Output
- if (m_Verbose) std::cout<<"N° of pixels: ";
- std::cout<<statisticsFilter->GetCount(label)<<std::endl;
-
+ if (m_Verbose) std::cout<<"N° of pixels: ";
+ std::cout<<statisticsFilter->GetCount(label)<<std::endl;
if (m_Verbose) std::cout<<"Mean: ";
- std::cout<<statisticsFilter->GetMean(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetMean(label)<<std::endl;
if (m_Verbose) std::cout<<"SD: ";
- std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
if (m_Verbose) std::cout<<"Variance: ";
- std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
if (m_Verbose) std::cout<<"Min: ";
- std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
if (m_Verbose) std::cout<<"Max: ";
- std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
if (m_Verbose) std::cout<<"Sum: ";
- std::cout<<statisticsFilter->GetSum(label)<<std::endl;
-
+ std::cout<<statisticsFilter->GetSum(label)<<std::endl;
+ if (m_Verbose) std::cout<<"Volume (cc): ";
+ std::cout<<statisticsFilter->GetCount(label)*spacing_cc<<std::endl;
if (m_Verbose) std::cout<<"Bounding box: ";
-
for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
- std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
+ std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
std::cout<<std::endl;
// Histogram
for( int i =0; i <m_ArgsInfo.bins_arg; i++)
histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
}
+
+ // DVH
+ if(m_ArgsInfo.dvhistogram_given)
+ {
+ typename StatisticsImageFilterType::HistogramPointer dvhistogram = statisticsFilter->GetHistogram(label);
+ double totalVolumeCC = ((statisticsFilter->GetCount(label))*spacing_cc);
+ double totalVolume = statisticsFilter->GetCount(label);
+
+ // Screen
+ std::cout<<"# Total volume : ";
+ std::cout<<totalVolume<<" [No. of voxels]"<<std::endl;
+ std::cout<<"# Total volume : ";
+ std::cout<<totalVolumeCC<<" [cc]"<<std::endl;
+ std::cout<<"# Dose mean: ";
+ std::cout<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
+ std::cout<<"# Dose min: ";
+ std::cout<<statisticsFilter->GetMinimum(label)<<" [Gy]"<<std::endl;
+ std::cout<<"# Dose max: ";
+ std::cout<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
+ std::cout<<" "<<std::endl;
+ std::cout<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
+ for( int i =0; i <m_ArgsInfo.bins_arg; i++)
+ {
+ double popCumulativeVolume = 0;
+ for(int j=0; j<i; j++)
+ {
+ popCumulativeVolume+=(dvhistogram->GetFrequency(j));
+ }
+ double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
+ double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
+ double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
+ double percentDiffVolume = dvhistogram->GetFrequency(i)*100/(statisticsFilter->GetCount(label));
+ std::cout<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<"\t "<<std::endl;
+ }
+
+ // Add to the file
+ std::ofstream dvhistogramFile(m_ArgsInfo.dvhistogram_arg);
+ dvhistogramFile<<"# Total volume : ";
+ dvhistogramFile<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
+ dvhistogramFile<<"# Total volume : ";
+ dvhistogramFile<<totalVolumeCC<<" [cc]"<<std::endl;
+ dvhistogramFile<<"# Dose mean: ";
+ dvhistogramFile<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
+ dvhistogramFile<<"# Dose min: ";
+ dvhistogramFile<<statisticsFilter->GetMinimum(label)<<" [Gy]"<<std::endl;
+ dvhistogramFile<<"# Dose max: ";
+ dvhistogramFile<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
+ dvhistogramFile<<" "<<std::endl;
+ dvhistogramFile<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
+ for( int i =0; i <m_ArgsInfo.bins_arg; i++)
+ {
+ double popCumulativeVolume = 0;
+ for(int j=0; j<i; j++)
+ {
+ popCumulativeVolume+=(dvhistogram->GetFrequency(j));
+ }
+ double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
+ double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label));
+ double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
+ double percentDiffVolume = ((dvhistogram->GetFrequency(i))*100)/(statisticsFilter->GetCount(label));
+ dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t "<<dvhistogram->GetFrequency(i)<<"\t "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t "<<ccCumulativeVolume<<std::endl;
+ }
+ }
}
}
return;
}
-
-
+
+
}//end clitk
#endif //#define clitkImageStatisticsGenericFilter_txx
* @brief
*
===================================================*/
-#if ITK_VERSION_MAJOR < 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR <= 2)
-# include "itkCompose3DVectorImageFilter.h"
-#else
# include "itkComposeImageFilter.h"
-#endif
namespace clitk
{
typedef itk::Image<itk::Vector<PixelType,3>, Dimension> OutputImageType;
// Filter
-#if ITK_VERSION_MAJOR < 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR <= 2)
- typedef itk::Compose3DVectorImageFilter<InputImageType,OutputImageType> ComposeFilterType;
-#else
typedef itk::ComposeImageFilter<InputImageType,OutputImageType> ComposeFilterType;
-#endif
typename ComposeFilterType::Pointer composeFilter=ComposeFilterType::New();
// Read the inputs
--- /dev/null
+/*=========================================================================
+
+ Program: clitk
+ Module: $RCSfile: clitkImageUncertainty.cxx,v $
+ Language: C++
+ Date: $Date: 2011/03/03 15:03:30 $
+ Version: $Revision: 1.3 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef CLITKIMAGEUNCERTAINTY_CXX
+#define CLITKIMAGEUNCERTAINTY_CXX
+
+/**
+ =================================================
+ * @file clitkImageUncertainty.cxx
+ * @author David Sarrut <david.sarrut@creatis.insa-lyon.fr>
+ * @date 04 Jul 2006 14:03:57
+ *
+ * @brief
+ *
+ *
+ =================================================*/
+
+// clitk include
+#include "clitkImageUncertainty_ggo.h"
+#include "clitkImageCommon.h"
+#include "clitkCommon.h"
+#include "clitkPortability.h"
+
+// itk include
+#include "itkImageRegionConstIterator.h"
+#include "itkImageRegionIterator.h"
+
+//====================================================================
+int main(int argc, char * argv[]) {
+
+ // init command line
+ GGO(clitkImageUncertainty, args_info);
+
+ // Declare main types
+ typedef float PixelType;
+ const unsigned int Dimension=3;
+ typedef itk::Image< PixelType, Dimension > ImageType;
+
+ // Read images
+ ImageType::Pointer input =
+ clitk::readImage<ImageType>(args_info.input_arg, args_info.verbose_flag);
+ ImageType::Pointer inputSquared =
+ clitk::readImage<ImageType>(args_info.inputSquared_arg, args_info.verbose_flag);
+
+ // Create Output
+ ImageType::Pointer output = ImageType::New();
+ output->SetRegions(input->GetLargestPossibleRegion());
+ output->CopyInformation(input);
+ output->Allocate();
+
+ // Loop
+ typedef itk::ImageRegionConstIterator<ImageType> ConstIteratorType;
+ ConstIteratorType pi(input, input->GetLargestPossibleRegion());
+ ConstIteratorType pii(inputSquared, inputSquared->GetLargestPossibleRegion());
+ pi.GoToBegin();
+ pii.GoToBegin();
+ typedef itk::ImageRegionIterator<ImageType> IteratorType;
+ IteratorType po(output, output->GetLargestPossibleRegion());
+ po.GoToBegin();
+
+ int NumberOfEvents = args_info.NumberOfEvents_arg;
+ while ( !pi.IsAtEnd() ) {
+ double squared = pii.Get();
+ double mean = pi.Get();
+ double uncert = sqrt((NumberOfEvents*squared - mean*mean) / (NumberOfEvents-1));
+ if(!args_info.absolute_flag)
+ uncert /= std::abs(mean);
+ if (!IsNormal(uncert)) uncert = args_info.default_arg;
+ po.Set(uncert);
+ ++pi;
+ ++pii;
+ ++po;
+ }
+
+ // Write output image
+ // DD(clitk::GetExtension(args_info.output_arg));
+ if (clitk::GetExtension(args_info.output_arg) != "txt") {
+ clitk::writeImage<ImageType>(output, args_info.output_arg, args_info.verbose_flag);
+ }
+ else {
+ std::ofstream os;
+ clitk::openFileForWriting(os, args_info.output_arg);
+ typedef itk::ImageRegionConstIterator<ImageType> IteratorType;
+ IteratorType pi(output, output->GetLargestPossibleRegion());
+ pi.GoToBegin();
+ os << "# Image size = " << output->GetLargestPossibleRegion().GetSize() << std::endl;
+ os << "# Image spacing = " << output->GetSpacing() << std::endl;
+ os << "# Number of events = " << NumberOfEvents << std::endl;
+ while (!pi.IsAtEnd()) {
+ os << pi.Get() << std::endl;
+ ++pi;
+ }
+ }
+}
+
+
+#endif /* end #define CLITKIMAGEUNCERTAINTY_CXX */
--- /dev/null
+# file clitkImageRescaleIntensity.ggo
+package "clitk"
+version "Compute the uncertainty of simulation outputs using Chetty's history-by-history's method"
+
+option "config" - "Config file" string no
+option "input" i "Input image filename" string yes
+option "inputSquared" s "Input squared image filename" string yes
+option "output" o "Output image filename" string yes
+option "NumberOfEvents" n "Number of events" int yes
+option "verbose" v "Verbose" flag off
+option "absolute" a "Absolute instead of the relative" flag off
+option "default" d "Default when input is 0." double no default="1."
//itk include
#include "itkLightObject.h"
-#if ITK_VERSION_MAJOR >= 4
- #include "itkInverseDisplacementFieldImageFilter.h"
-#else
- #include "itkInverseDeformationFieldImageFilter.h"
-#endif
+#include "itkInverseDisplacementFieldImageFilter.h"
namespace clitk
{
case 2: {
// Create the InverseDeformationFieldFilter
-#if ITK_VERSION_MAJOR >= 4
typedef itk::InverseDisplacementFieldImageFilter<InputImageType,OutputImageType> FilterType;
-#else
- typedef itk::InverseDeformationFieldImageFilter<InputImageType,OutputImageType> FilterType;
-#endif
typename FilterType::Pointer filter =FilterType::New();
filter->SetInput(input);
filter->SetOutputOrigin(input->GetOrigin());
//itk include
#include "itkLightObject.h"
-#if ITK_VERSION_MAJOR >= 4
- #include "itkInverseDisplacementFieldImageFilter.h"
-#else
- #include "itkInverseDeformationFieldImageFilter.h"
-#endif
+#include "itkInverseDisplacementFieldImageFilter.h"
namespace clitk
{
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// clitk
+#include "clitkMatrixMultiply_ggo.h"
+#include "clitkTransformUtilities.h"
+#include "clitkIO.h"
+#include "clitkMatrix.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+ // Init command line
+ GGO(clitkMatrixMultiply, args_info);
+ CLITK_INIT;
+
+ // Read matrix
+ itk::Matrix<double, 4, 4> matrix1, matrix2;
+ try {
+ matrix1 = clitk::ReadMatrix3D(args_info.input1_arg);
+ matrix2 = clitk::ReadMatrix3D(args_info.input2_arg);
+ }
+ catch (itk::ExceptionObject & err) {
+ std::cerr << "Error reading "
+ << args_info.input1_arg
+ << " and "
+ << args_info.input2_arg
+ << std::endl;
+ std::cerr << err.GetDescription() << std::endl;
+ exit(-1);
+ }
+
+ itk::Matrix<double, 4, 4> matrix(matrix2.GetVnlMatrix() * matrix1.GetVnlMatrix());
+
+ // Print matrix
+ std::ofstream os;
+ clitk::openFileForWriting(os, args_info.output_arg);
+ os << clitk::Get4x4MatrixDoubleAsString(matrix, 16);
+ os.close();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+package "clitkMatrixMultiply"
+version "1.0"
+purpose "Multiply two 4x4 matrices. In matrice notations, does input2*input"
+
+option "config" - "Config file" string optional
+option "input1" i "Input matrix filename" string required
+option "input2" j "Input matrix filename" string required
+option "output" o "Output matrix filename" string required
public:
//--------------------------------------------------------------------
- MedianImageGenericFilter();
+ MedianImageGenericFilter();
//--------------------------------------------------------------------
- typedef MedianImageGenericFilter Self;
+ typedef MedianImageGenericFilter Self;
+ typedef ImageToImageGenericFilter<MedianImageGenericFilter<args_info_type> > Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
// Main function called each time the filter is updated
template<class InputImageType>
void UpdateWithInputImageType();
-
-
-
protected:
template<unsigned int Dim> void InitializeImageType();
-
args_info_type mArgsInfo;
-
+
+ private:
+ MedianImageGenericFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
}; // end class
//--------------------------------------------------------------------
// typedef itk::Image<PixelType,InputImageType::ImageDimension> OutputImageType;
- // Main filter
- typedef itk::Image<PixelType, InputImageType::ImageDimension> OutputImageType;
- typename InputImageType::SizeType indexRadius;
-
// Filter
- typedef itk::MedianImageFilter<InputImageType, OutputImageType> MedianImageFilterType;
- typename MedianImageFilterType::Pointer thresholdFilter=MedianImageFilterType::New();
- thresholdFilter->SetInput(input);
-
- for (unsigned i = 0; i < InputImageType::ImageDimension; ++i)
- indexRadius[i]=mArgsInfo.radius_arg[i];
-
- // indexRadius[0] = 1;
- // indexRadius[1] = 1;
-
- thresholdFilter->SetRadius( indexRadius );
-
- typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
- thresholdFilter->Update();
+ typedef itk::MedianImageFilter<InputImageType, InputImageType> MedianImageFilterType;
+ typename MedianImageFilterType::Pointer medianFilter=MedianImageFilterType::New();
+ typename MedianImageFilterType::InputSizeType radius;
+ radius.Fill(1);
+ medianFilter->SetInput(input);
+
+ if(mArgsInfo.radius_given) {
+ for (unsigned i = 0; i < InputImageType::ImageDimension; ++i)
+ radius[i]=mArgsInfo.radius_arg[i];
+ }
+ //
+ std::cout<<"radius median filter= "<<radius<<std::endl;
+ //
+ medianFilter->SetRadius( radius );
+ medianFilter->Update();
// Write/Save results
- this->template SetNextOutput<OutputImageType>(outputImage);
+ typename InputImageType::Pointer outputImage = medianFilter->GetOutput();
+ this->template SetNextOutput<InputImageType>(outputImage);
}
//--------------------------------------------------------------------
=================================================
* @file clitkMergeRootFiles.cxx
* @author David Sarrut <david.sarrut@creatis.insa-lyon.fr>
- * @date 01 Apr 2009
- *
- * @brief
- *
+ * @author Brent Huisman <brent.huisman@insa-lyon.fr>
+ * @date 06 May 2014
+ *
+ * @brief
+ *
=================================================*/
#include "clitkMergeRootFiles_ggo.h"
#include "clitkCommon.h"
#include "GateMergeManager.hh"
-#include <string>
+#include <string>
#include <TROOT.h>
#include <TPluginManager.h>
#include <TFile.h>
#include <TH1.h>
#include <TH2.h>
#include <iostream>
+#include <TApplication.h>
using std::endl;
using std::cout;
-struct PetInputFile
-{
- string filename;
- double mean_time;
+struct PetInputFile {
+ string filename;
+ double mean_time;
};
-bool sort_pet_input_file(const PetInputFile& a, const PetInputFile& b)
-{
- return a.mean_time<b.mean_time;
+bool sort_pet_input_file(const PetInputFile &a, const PetInputFile &b) {
+ return a.mean_time < b.mean_time;
};
typedef std::vector<PetInputFile> PetInputFiles;
//-----------------------------------------------------------------------------
-int main(int argc, char * argv[]) {
-
- gROOT->GetPluginManager()->AddHandler("TVirtualStreamerInfo", "*",
- "TStreamerInfo", "RIO", "TStreamerInfo()");
-
- // init command line
- GGO(clitkMergeRootFiles, args_info);
-
- // Check parameters
- if (args_info.input_given < 2) {
- FATAL("Error, please provide at least two inputs files");
- }
-
- { // Detect Pet output
- bool all_pet_output = true;
- PetInputFiles pet_input_files;
- for (uint i=0; i<args_info.input_given; i++)
- {
- const char* filename = args_info.input_arg[i];
- PetInputFile input_file;
- input_file.filename = filename;
- TFile* handle = TFile::Open(filename,"READ");
- assert(handle);
- TTree* hits = dynamic_cast<TTree*>(handle->Get("Hits"));
- TTree* singles = dynamic_cast<TTree*>(handle->Get("Singles"));
- const bool is_pet_output = (hits!=NULL) && (singles!=NULL);
- cout << "testing " << filename << " is_pet_output " << is_pet_output;
-
- if (is_pet_output)
- {
- double time;
- double time_accum = 0;
- singles->SetBranchAddress("time",&time);
- size_t total = singles->GetEntries();
- for (size_t kk=0; kk<total; kk++)
- {
- singles->GetEntry(kk);
- time_accum += time;
- }
-
- input_file.mean_time = time_accum/total;
- pet_input_files.push_back(input_file);
- cout << " mean_time " << input_file.mean_time;
- }
-
- cout << endl;
-
- handle->Close();
- delete handle;
- all_pet_output &= is_pet_output;
- }
- cout << "all_pet_output " << all_pet_output << endl;
-
- if (all_pet_output)
- {
- GateMergeManager manager(args_info.fastmerge_given,args_info.verbose_arg,true,0,"");
-
- cout << "sorting input file using singles time" << endl;
- std::sort(pet_input_files.begin(),pet_input_files.end(),sort_pet_input_file);
-
- Strings input_filenames;
- for (PetInputFiles::const_iterator iter=pet_input_files.begin(); iter!=pet_input_files.end(); iter++)
- input_filenames.push_back(iter->filename);
-
- manager.StartMergingFromFilenames(input_filenames,args_info.output_arg);
- return 0;
- }
- }
-
-
- // Merge
- TFileMerger * merger = new TFileMerger;
- for (uint i=0; i<args_info.input_given; i++) merger->AddFile(args_info.input_arg[i]);
- merger->OutputFile(args_info.output_arg);
- merger->Merge();
-
- // this is the end my friend
- return 0;
+int main(int argc, char *argv[]) {
+ //this fixes a bug in TFileMerger. See http://root.cern.ch/phpBB3/viewtopic.php?t=18016.
+ TApplication app("app", 0, 0);
+
+ gROOT->GetPluginManager()->AddHandler("TVirtualStreamerInfo", "*",
+ "TStreamerInfo", "RIO", "TStreamerInfo()");
+
+ // init command line
+ GGO(clitkMergeRootFiles, args_info);
+
+ // Check parameters
+ if (args_info.input_given < 2) {
+ FATAL("Error, please provide at least two inputs files");
+ }
+
+ /* The following block does some bookkeeping necesary for files originating from a pet simulation.
+ Seems fixing some timing info, for coincidences between files perhaps.
+ It seems the files are later on reopened and merged, if the conditions were met.
+ It's not required for merging other .root files.
+ GateMergeManager reportedly exists specifically for the purpose of merging pet simulations. */
+ {
+ // Detect Pet output
+ bool all_pet_output = true;
+ PetInputFiles pet_input_files;
+ for (uint i = 0; i < args_info.input_given; i++) {
+ const char *filename = args_info.input_arg[i];
+ PetInputFile input_file;
+ input_file.filename = filename;
+ TFile *handle = TFile::Open(filename, "READ");
+ assert(handle);
+ TTree *hits = dynamic_cast<TTree *>(handle->Get("Hits"));
+ TTree *singles = dynamic_cast<TTree *>(handle->Get("Singles"));
+ const bool is_pet_output = (hits != NULL) && (singles != NULL);
+ cout << "testing " << filename << " is_pet_output " << is_pet_output;
+
+ //TTree *histos = dynamic_cast<TH1F *>(handle->Get("histo;1"));
+ //const bool is_hist_output = (histos != NULL);
+
+
+ if (is_pet_output) {
+ double time;
+ double time_accum = 0;
+ singles->SetBranchAddress("time", &time);
+ size_t total = singles->GetEntries();
+ for (size_t kk = 0; kk < total; kk++) {
+ singles->GetEntry(kk);
+ time_accum += time;
+ }
+
+ input_file.mean_time = time_accum / total;
+ pet_input_files.push_back(input_file);
+ cout << " mean_time " << input_file.mean_time;
+ }
+
+ cout << endl;
+
+ handle->Close();
+ delete handle;
+ //bitwise on booleans?
+ all_pet_output &= is_pet_output;
+ }
+ cout << "all_pet_output " << all_pet_output << endl;
+
+ if (all_pet_output) {
+ GateMergeManager manager(args_info.fastmerge_given, args_info.verbose_arg, true, 0, "");
+
+ cout << "sorting input file using singles time" << endl;
+ std::sort(pet_input_files.begin(), pet_input_files.end(), sort_pet_input_file);
+
+ Strings input_filenames;
+ for (PetInputFiles::const_iterator iter = pet_input_files.begin(); iter != pet_input_files.end(); iter++)
+ input_filenames.push_back(iter->filename);
+
+ manager.StartMergingFromFilenames(input_filenames, args_info.output_arg);
+ //if the file was PET, then we're done.
+ return 0;
+ }
+ }
+
+ //if the file was not PET, but a generic Rootfile, use TFileMerger.
+
+ // Merge
+ TFileMerger *merger = new TFileMerger;
+ for (uint i = 0; i < args_info.input_given; i++) merger->AddFile(args_info.input_arg[i]);
+ merger->OutputFile(args_info.output_arg);
+ bool whatbool = merger->Merge();
+
+ cout << "whatbool: " << whatbool << " no more whatbool" << endl;
+ // this is the end my friend
+ return 0;
+
}
//-----------------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkNormalizeImageFilterGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief NormalizeImageFilter an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkNormalizeImageFilter_ggo.h"
+#include "clitkNormalizeImageFilterGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkNormalizeImageFilter, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::NormalizeImageFilterGenericFilter<args_info_clitkNormalizeImageFilter> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkNormalizeImageFilter.ggo
+package "clitkNormalizeImageFilter"
+version "1.0"
+purpose ""
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string required
+option "output" o "Output image filename" string required
+option "mask" m "Mask input image filename" string optional
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKNormalizeImageFilterGENERICFILTER_H
+#define CLITKNormalizeImageFilterGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT NormalizeImageFilterGenericFilter:
+ public ImageToImageGenericFilter<NormalizeImageFilterGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ NormalizeImageFilterGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef NormalizeImageFilterGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(NormalizeImageFilterGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkNormalizeImageFilterGenericFilter.txx"
+#endif
+
+#endif // #define clitkNormalizeImageFilterGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkNormalizeImageFilterGenericFilter_txx
+#define clitkNormalizeImageFilterGenericFilter_txx
+
+/* =================================================
+ * @file clitkNormalizeImageFilterGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ NormalizeImageFilterGenericFilter<args_info_type>::NormalizeImageFilterGenericFilter():
+ ImageToImageGenericFilter<Self>("NormalizeImageFilter")
+ {
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dim>
+ void NormalizeImageFilterGenericFilter<args_info_type>::InitializeImageType()
+ {
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ void NormalizeImageFilterGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+ {
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+ if (mArgsInfo.mask_given) {
+ this->AddInputFilename(mArgsInfo.mask_arg);
+ }
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //--------------------------------------------------------------------
+ template<class args_info_type>
+ template<class InputImageType>
+ void
+ NormalizeImageFilterGenericFilter<args_info_type>::UpdateWithInputImageType()
+ {
+
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<unsigned char, OutputImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ typename MaskImageType::Pointer mask = NULL;
+ if(mArgsInfo.mask_given) {
+ mask = this->template GetInput<MaskImageType>(1);
+ }
+ else {
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(1);
+ }
+
+ // Create output image
+ typename OutputImageType::Pointer outputImage = OutputImageType::New();
+ outputImage->SetRegions(input->GetLargestPossibleRegion());
+ outputImage->SetOrigin(input->GetOrigin());
+ outputImage->SetSpacing(input->GetSpacing());
+ outputImage->Allocate();
+ outputImage->FillBuffer(0.0);
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+ // Filter
+ // Set iterator
+ typedef itk::ImageRegionIterator<InputImageType> IteratorType;
+ IteratorType it(input, input->GetLargestPossibleRegion());
+
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+
+ typedef itk::LabelStatisticsImageFilter< InputImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(input);
+ labelStatisticsImageFilter->Update();
+
+ //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
+
+ float minImg = labelStatisticsImageFilter->GetMinimum(1);
+ //std::cout << "minImg= " << minImg << std::endl;
+ float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+ //std::cout << "maxImg= " << maxImg << std::endl;
+
+ it.GoToBegin();
+ ito.GoToBegin();
+ itm.GoToBegin();
+
+ while (!ito.IsAtEnd()) {
+ if(itm.Get() == 1) {
+ ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+ //
+ //
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ //--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkNormalizeImageFilterGenericFilter_txx
SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing();
if (spacing != like_spacing) {
std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
- return ERR_NOT_SAME_SPACING;
+ return PAD_ERR_NOT_SAME_SPACING;
}
SizeType size = input->GetLargestPossibleRegion().GetSize(), like_size = like_image->GetLargestPossibleRegion().GetSize();
if (auxl < 0 || auxu < 0) {
std::cerr << "Like-image's bounding box must be larger than input's" << std::endl;
- return ERR_NOT_LIKE_LARGER;
+ return PAD_ERR_NOT_LIKE_LARGER;
}
padLower[i] = (PadBoundType)auxl;
if (mArgsInfo.verbose_flag)
std::cout << "PadLike - OUT" << std::endl;
- return ERR_SUCCESS;
+ return PAD_ERR_SUCCESS;
}
} //end clitk
#include "clitkImageToImageGenericFilter.h"
#include "clitkPadImage_ggo.h"
-
//--------------------------------------------------------------------
namespace clitk
{
public:
enum
{
- ERR_SUCCESS = 0,
- ERR_NOT_SAME_SPACING = -1,
- ERR_NOT_LIKE_LARGER = -2
+ PAD_ERR_SUCCESS = 0,
+ PAD_ERR_NOT_SAME_SPACING = -1,
+ PAD_ERR_NOT_LIKE_LARGER = -2
};
//--------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+/* =================================================
+ * @file clitkPointRigidRegistrationGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief PointRigidRegistration an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkPointRigidRegistration_ggo.h"
+
+
+//paste from RigidRegistration
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImage.h"
+#include "itkVector.h"
+#include "itkResampleImageFilter.h"
+#include "itkLandmarkBasedTransformInitializer.h"
+#include "itkRigid2DTransform.h"
+#include "itkVersorRigid3DTransform.h"
+#include <iostream>
+
+
+#include "itkMatrix.h"
+#include "itkArray.h"
+//#include "itkPoint.h"
+#include "clitkImageCommon.h"
+#include "clitkCommon.h"
+//#define VTK_EXCLUDE_STRSTREAM_HEADERS
+#include <vtkMatrix4x4.h>
+#include <vtkSmartPointer.h>
+
+//for open file for reading
+#include "clitkIO.h"
+#include "clitkImageCommon.h"
+#include "clitkCommon.h"
+
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkPointRigidRegistration, args_info);
+ CLITK_INIT;
+
+
+
+
+ // Iinit itk
+ // read input file
+ //open stream to reading
+ std::ifstream is;
+ clitk::openFileForReading(is, args_info.input_arg);
+
+
+
+ //reading first line of input file to chck thw dimension of data
+ double x = 0;
+ //clitk::skipComment(is);
+ is >> x;
+
+ typedef unsigned char PixelType;
+
+
+
+
+
+ unsigned int Dimension_temp = (unsigned int)x;
+
+
+
+ if (Dimension_temp==2)
+ {
+ const unsigned int Dimension = 2;
+ typedef itk::Image< PixelType, Dimension > ImageType;
+ typedef float VectorComponentType;
+ typedef itk::Vector< VectorComponentType, Dimension > VectorType;
+ //Typ LandmarkBasedTransormInitializer
+ typedef itk::Rigid2DTransform< double > Rigid2DTransformType;
+ typedef itk::LandmarkBasedTransformInitializer< Rigid2DTransformType,ImageType, ImageType>
+ LandmarkBasedTransformInitializerType;
+
+ LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
+
+ // Create source and target landmarks.
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer LandmarkContainerType;
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointType LandmarkPointType;
+
+ LandmarkContainerType imageLandmarks;
+ LandmarkContainerType trackerLandmarks;
+
+ LandmarkPointType imagePoint;
+ LandmarkPointType trackerPoint;
+
+ is >> x;
+
+
+ while (is && !is.eof()) {
+ imagePoint[0] = x;
+ is >> imagePoint[1];
+
+
+ is >> trackerPoint[0];
+ is >> trackerPoint[1];
+
+ imageLandmarks.push_back(imagePoint );
+ trackerLandmarks.push_back(trackerPoint );
+
+
+ is >> x;
+ }
+
+ is.close();
+
+ landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
+ landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
+
+ Rigid2DTransformType::Pointer transform = Rigid2DTransformType::New();
+
+ transform->SetIdentity();
+
+ landmarkBasedTransformInitializer->SetTransform(transform);
+ landmarkBasedTransformInitializer->InitializeTransform();
+
+ Rigid2DTransformType::MatrixType matrix = transform->GetMatrix();
+ Rigid2DTransformType::OffsetType offset = transform->GetOffset();
+
+ // Write result
+ std::ofstream out;
+ clitk::openFileForWriting(out, args_info.output_arg);
+
+ out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << offset[0] << std::endl;
+ out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << offset[1] << std::endl;
+ out << 0.0 << ' ' << 0.0 << ' ' << 1.0;
+ out.close();
+
+
+
+ // Write result
+ if (args_info.error_arg != 0)
+ {
+ std::ofstream error;
+ clitk::openFileForWriting(error, args_info.error_arg);
+
+
+ //imagePoints
+ int nImagePoints = imageLandmarks.size();
+ double imagePoints[3][nImagePoints];
+ double trackerPoints[3][nImagePoints];
+ double imagePointstoTrackerCoordinate[3][nImagePoints];
+ double FRE = 0;
+ double PointEuclideanDistance = 0;
+ double SumofPointsEuclideanDistance = 0;
+
+
+ for(int n= 0; n < imageLandmarks.size(); n++)
+ {
+ for(int j= 0; j < 2; j++)
+ {
+ imagePoints[j][n] = imageLandmarks[n][j];
+ trackerPoints[j][n] = trackerLandmarks[n][j];
+
+
+
+
+// imagePoints[j][n] = trackerLandmarks[n][j];
+// trackerPoints[j][n] = imageLandmarks[n][j];
+ imagePointstoTrackerCoordinate[j][n] = 0;
+
+ }
+ imagePoints[2][n] = 1.0;
+ trackerPoints[2][n] = 1.0;
+ imagePointstoTrackerCoordinate[2][n] = 0;
+ }
+
+
+ //transformation matrix
+ double RigidTransformationImagetoTracker[4][4];
+
+
+ for(int i = 0; i < 2; i++)
+ for(int j = 0; j < 2; j++)
+ RigidTransformationImagetoTracker[i][j] = matrix[i][j];
+
+
+ for(int i = 0; i < 2; i++)
+ RigidTransformationImagetoTracker[i][2] = offset[i];
+
+ RigidTransformationImagetoTracker[2][0] = 0.0;
+ RigidTransformationImagetoTracker[2][1] = 0.0;
+ RigidTransformationImagetoTracker[2][2] = 1.0;
+
+
+ //writing results
+ error << "ImagePoints: CorrespondingTrackerPoints: ImagePointstoTrackerCoordinateSystem: PointsDistanceafterRigidRegistration:" << std::endl;
+
+
+
+
+
+ //Calculate FRE
+
+ for(int n= 0; n < imageLandmarks.size(); n++)
+ {
+
+
+ //Calculate imagePointstoTrackerCoordinate
+ for(int i = 0; i < 3; i++)
+ {
+
+ for(int k = 0; k < 3; k++)
+ {
+ imagePointstoTrackerCoordinate[i][n] = imagePointstoTrackerCoordinate[i][n] + RigidTransformationImagetoTracker[i][k]*imagePoints[k][n];
+
+ }
+
+ }
+
+
+ //writing results
+
+ for(int i = 0; i < 2; i++)
+ error << imagePoints[i][n] << ' ';
+
+ error << " ";
+
+ for(int i = 0; i < 2; i++)
+ error << trackerPoints[i][n] << ' ';
+
+ error << " ";
+
+ for(int i = 0; i < 2; i++)
+ error << imagePointstoTrackerCoordinate[i][n] << ' ';
+
+
+
+ //calculate PointEuclideanDistance
+ PointEuclideanDistance = 0;
+ for(int i=0; i < 2;i++)
+ {
+ PointEuclideanDistance = PointEuclideanDistance + std::pow((trackerPoints[i][n] - imagePointstoTrackerCoordinate[i][n]),2);
+ }
+ PointEuclideanDistance = std::sqrt(PointEuclideanDistance);
+ error << " " << PointEuclideanDistance << " ";
+
+ SumofPointsEuclideanDistance = SumofPointsEuclideanDistance + std::pow(PointEuclideanDistance,2);
+
+
+
+
+
+
+ error << std::endl;
+
+
+
+
+
+ } //end loop via points
+
+ error << std::endl;
+ SumofPointsEuclideanDistance = std::sqrt(SumofPointsEuclideanDistance/nImagePoints);
+ error << "Fiducial Registration Error: " << SumofPointsEuclideanDistance;
+ error.close();
+
+ } //end if (args_info.error_arg != null)
+ } //end Dimension == 2 case
+ else if (Dimension_temp==3)
+ {
+
+ const unsigned int Dimension = 3;
+ typedef itk::Image< PixelType, Dimension > ImageType;
+ typedef float VectorComponentType;
+ typedef itk::Vector< VectorComponentType, Dimension > VectorType;
+ //Typ LandmarkBasedTransormInitializer
+ typedef itk::VersorRigid3DTransform< double > Rigid3DTransformType;
+ typedef itk::LandmarkBasedTransformInitializer< Rigid3DTransformType,ImageType, ImageType>
+ LandmarkBasedTransformInitializerType;
+
+ LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer = LandmarkBasedTransformInitializerType::New();
+
+ // Create source and target landmarks.
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer LandmarkContainerType;
+ typedef LandmarkBasedTransformInitializerType::LandmarkPointType LandmarkPointType;
+
+ LandmarkContainerType imageLandmarks;
+ LandmarkContainerType trackerLandmarks;
+ LandmarkContainerType imageLandmarksTotrackerCoordinate;
+
+
+ LandmarkPointType imagePoint;
+ LandmarkPointType trackerPoint;
+
+ is >> x;
+
+ while (is && !is.eof()) {
+ imagePoint[0] = x;
+ is >> imagePoint[1];
+ is >> imagePoint[2];
+
+ is >> trackerPoint[0];
+ is >> trackerPoint[1];
+ is >> trackerPoint[2];
+
+ imageLandmarks.push_back(imagePoint );
+ trackerLandmarks.push_back(trackerPoint );
+
+ is >> x;
+ }
+
+ is.close();
+
+ landmarkBasedTransformInitializer->SetFixedLandmarks( imageLandmarks);
+ landmarkBasedTransformInitializer->SetMovingLandmarks( trackerLandmarks);
+
+ Rigid3DTransformType::Pointer transform = Rigid3DTransformType::New();
+
+ transform->SetIdentity();
+
+ landmarkBasedTransformInitializer->SetTransform(transform);
+ landmarkBasedTransformInitializer->InitializeTransform();
+
+ Rigid3DTransformType::MatrixType matrix = transform->GetMatrix();
+ Rigid3DTransformType::OffsetType offset = transform->GetOffset();
+
+ // Write result
+ std::ofstream out;
+ clitk::openFileForWriting(out, args_info.output_arg);
+
+ out << matrix[0][0] << ' ' << matrix[0][1] << ' ' << matrix[0][2] << ' '<< offset[0] << std::endl;
+ out << matrix[1][0] << ' ' << matrix[1][1] << ' ' << matrix[1][2] << ' '<< offset[1] << std::endl;
+ out << matrix[2][0] << ' ' << matrix[2][1] << ' ' << matrix[2][2] << ' '<< offset[2] << std::endl;
+ out << 0.0 << ' ' << 0.0 << ' ' << 0.0 << ' ' << 1.0;
+ out.close();
+
+
+ if (args_info.error_arg != 0)
+ {
+ // Write result
+ std::ofstream error;
+ clitk::openFileForWriting(error, args_info.error_arg);
+
+
+ //imagePoints
+ int nImagePoints = imageLandmarks.size();
+ double imagePoints[4][nImagePoints];
+ double trackerPoints[4][nImagePoints];
+ double imagePointstoTrackerCoordinate[4][nImagePoints];
+ double FRE = 0;
+ double PointEuclideanDistance = 0;
+ double SumofPointsEuclideanDistance = 0;
+
+
+ for(int n= 0; n < imageLandmarks.size(); n++)
+ {
+ for(int j= 0; j < 3; j++)
+ {
+ imagePoints[j][n] = imageLandmarks[n][j];
+ trackerPoints[j][n] = trackerLandmarks[n][j];
+
+
+
+
+// imagePoints[j][n] = trackerLandmarks[n][j];
+// trackerPoints[j][n] = imageLandmarks[n][j];
+ imagePointstoTrackerCoordinate[j][n] = 0;
+
+ }
+ imagePoints[3][n] = 1.0;
+ trackerPoints[3][n] = 1.0;
+ imagePointstoTrackerCoordinate[3][n] = 0;
+ }
+
+
+ //transformation matrix
+ double RigidTransformationImagetoTracker[4][4];
+
+
+ for(int i = 0; i < 3; i++)
+ for(int j = 0; j < 3; j++)
+ RigidTransformationImagetoTracker[i][j] = matrix[i][j];
+
+
+ for(int i = 0; i < 3; i++)
+ RigidTransformationImagetoTracker[i][3] = offset[i];
+
+ RigidTransformationImagetoTracker[3][0] = 0.0;
+ RigidTransformationImagetoTracker[3][1] = 0.0;
+ RigidTransformationImagetoTracker[3][2] = 0.0;
+ RigidTransformationImagetoTracker[3][3] = 1.0;
+
+ //writing results
+ error << "ImagePoints: CorrespondingTrackerPoints: ImagePointstoTrackerCoordinateSystem: PointsDistanceafterRigidRegistration:" << std::endl;
+
+
+
+
+
+ //Calculate FRE
+
+ for(int n= 0; n < imageLandmarks.size(); n++)
+ {
+
+
+ //Calculate imagePointstoTrackerCoordinate
+ for(int i = 0; i < 4; i++)
+ {
+
+ for(int k = 0; k < 4; k++)
+ {
+ imagePointstoTrackerCoordinate[i][n] = imagePointstoTrackerCoordinate[i][n] + RigidTransformationImagetoTracker[i][k]*imagePoints[k][n];
+
+ }
+
+ }
+
+
+ //writing results
+
+ for(int i = 0; i < 3; i++)
+ error << imagePoints[i][n] << ' ';
+
+ error << " ";
+
+ for(int i = 0; i < 3; i++)
+ error << trackerPoints[i][n] << ' ';
+
+ error << " ";
+
+ for(int i = 0; i < 3; i++)
+ error << imagePointstoTrackerCoordinate[i][n] << ' ';
+
+
+
+ //calculate PointEuclideanDistance
+ PointEuclideanDistance = 0;
+ for(int i=0; i < 3;i++)
+ {
+ PointEuclideanDistance = PointEuclideanDistance + std::pow((trackerPoints[i][n] - imagePointstoTrackerCoordinate[i][n]),2);
+ }
+ PointEuclideanDistance = std::sqrt(PointEuclideanDistance);
+ error << " " << PointEuclideanDistance << " ";
+
+ SumofPointsEuclideanDistance = SumofPointsEuclideanDistance + std::pow(PointEuclideanDistance,2);
+
+
+
+
+
+
+ error << std::endl;
+
+
+
+
+
+ } //end loop via points
+
+ error << std::endl;
+ SumofPointsEuclideanDistance = std::sqrt(SumofPointsEuclideanDistance/nImagePoints);
+ error << "Fiducial Registration Error: " << SumofPointsEuclideanDistance;
+ error.close();
+
+
+ } //end if (args_info.error_arg != null)
+ } //end Dimension == 3 case
+ else
+ {
+ is.close();
+ return EXIT_FAILURE;
+
+ }
+
+
+
+
+
+
+
+ return EXIT_SUCCESS;
+}// end main
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkPointRigidRegistration.ggo
+package "clitkPointRigidRegistration"
+version "1.0"
+purpose "Finding the rigid transformation between two cartesian coordinate systems\n
+based on corresponding points positions"
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+
+
+option "input" i "Corresponding points' positions filename" string required
+option "output" o "Output transformation filename" string required
+option "error" e "Output error filename" string optional
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// clitk
+#include "clitkProfileImage_ggo.h"
+#include "clitkProfileImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkProfileImage, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::ProfileImageGenericFilter FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+
+ CLITK_TRY_CATCH_EXIT(filter->Update());
+
+ return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkProfileImage.ggo
+package "clitkProfileImage"
+version "1.0"
+purpose "Save the profile between 2 points of the input image in the output text file"
+
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string yes
+option "output" o "Output texte filename" string yes
+option "point1" f "First point (mm)" double yes multiple(-4)
+option "point2" s "Second point (mm)" double yes multiple(-4)
+
+
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkProfileImageGenericFilter_cxx
+#define clitkProfileImageGenericFilter_cxx
+
+/* =================================================
+ * @file clitkProfileImageGenericFilter.cxx
+ * @author Thomas Baudier <thomas.baudier@creatis.insa-lyon.fr>
+ * @date 22 dec 2015
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "clitkProfileImageGenericFilter.h"
+
+// itk include
+#include <itkLineIterator.h>
+#include <itkPoint.h>
+
+#include <clitkCommon.h>
+
+
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+ProfileImageGenericFilter::ProfileImageGenericFilter():
+ ImageToImageGenericFilter<Self>("ProfileImage")
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<unsigned int Dim>
+void ProfileImageGenericFilter::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vtkFloatArray* ProfileImageGenericFilter::GetArrayX()
+{
+ return(mArrayX);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vtkFloatArray* ProfileImageGenericFilter::GetArrayY()
+{
+ return(mArrayY);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+vtkFloatArray* ProfileImageGenericFilter::GetCoord()
+{
+ return(mCoord);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void ProfileImageGenericFilter::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+ if (mArgsInfo.verbose_given)
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_given && mArgsInfo.imagetypes_flag)
+ this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ SetOutputFilename(mArgsInfo.output_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class InputImageType>
+void
+ProfileImageGenericFilter::UpdateWithInputImageType()
+{
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+ typedef typename InputImageType::PixelType PixelType;
+ typedef typename InputImageType::IndexType IndexType;
+
+ mArrayX = vtkSmartPointer<vtkFloatArray>::New();
+ mArrayY = vtkSmartPointer<vtkFloatArray>::New();
+ mCoord = vtkSmartPointer<vtkFloatArray>::New();
+ mCoord->SetNumberOfComponents(InputImageType::ImageDimension);
+
+ /*typename InputImageType::Pointer outputImage;
+ outputImage = InputImageType::New();
+
+ outputImage->SetRegions(input->GetLargestPossibleRegion());
+ outputImage->Allocate();
+ outputImage->FillBuffer(0); */
+
+ //Iterator
+ IndexType pointBegin, pointEnd;
+
+ for (int i = 0; i < mArgsInfo.point1_given; ++i) {
+ pointBegin[i] = mArgsInfo.point1_arg[i];
+ pointEnd[i] = mArgsInfo.point2_arg[i];
+ }
+
+ itk::LineConstIterator<InputImageType> itProfile(input, pointBegin, pointEnd);
+ itProfile.GoToBegin();
+ int lineNumber(1);
+ double *tuple;
+ double distance;
+ tuple = new double[InputImageType::ImageDimension];
+ itk::Point<double, InputImageType::ImageDimension> transformedFirstPoint;
+ itk::Point<double, InputImageType::ImageDimension> transformedCurrentPoint;
+
+ input->TransformIndexToPhysicalPoint(itProfile.GetIndex(), transformedFirstPoint);
+
+ while (!itProfile.IsAtEnd())
+ {
+ // Fill in the table the intensity value
+ mArrayY->InsertNextTuple1(itProfile.Get());
+
+ for (int i=0; i<InputImageType::ImageDimension; ++i) {
+ tuple[i] = itProfile.GetIndex()[i];
+ }
+
+ input->TransformIndexToPhysicalPoint(itProfile.GetIndex(), transformedCurrentPoint);
+ distance = transformedFirstPoint.EuclideanDistanceTo(transformedCurrentPoint);
+
+ // Fill in the table the distance value
+ mArrayX->InsertNextTuple1(distance);
+
+ // Fille in the table the voxel coordinate value
+ mCoord->InsertNextTuple(tuple);
+ ++lineNumber;
+ ++itProfile;
+ }
+
+ /*
+ itk::LineIterator<InputImageType> otProfile(outputImage, pointBegin, pointEnd);
+ otProfile.GoToBegin();
+ while (!otProfile.IsAtEnd())
+ {
+ otProfile.Set(1.0);
+ ++otProfile;
+ }
+
+ this->template SetNextOutput<InputImageType>(outputImage): */
+
+ delete [] tuple;
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkProfileImageGenericFilter_cxx
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#ifndef clitkProfileImageGenericFilter_h
+#define clitkProfileImageGenericFilter_h
+
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkProfileImage_ggo.h"
+
+#include <vtkIntArray.h>
+#include <vtkFloatArray.h>
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ class ITK_EXPORT ProfileImageGenericFilter:
+ public ImageToImageGenericFilter<ProfileImageGenericFilter>
+ {
+
+ public:
+ //--------------------------------------------------------------------
+ typedef ProfileImageGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef args_info_clitkProfileImage args_info_type;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(ProfileImageGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+ vtkFloatArray* GetArrayX();
+ vtkFloatArray* GetArrayY();
+ vtkFloatArray* GetCoord();
+
+ protected:
+ ProfileImageGenericFilter();
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+
+ vtkSmartPointer<vtkFloatArray> mArrayX;
+ vtkSmartPointer<vtkFloatArray> mArrayY;
+ vtkSmartPointer<vtkFloatArray> mCoord;
+
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#endif // #define clitkProfileImageGenericFilter_h
// Init command line
GGO(clitkResampleImage, args_info);
+ CLITK_INIT;
// Filter
typedef clitk::ResampleImageGenericFilter FilterType;
static const unsigned int dim = OutputImageType::ImageDimension;
typename OutputImageType::SpacingType spacing;
typename OutputImageType::SizeType size;
+ typename OutputImageType::PointType origin;
+ typename OutputImageType::DirectionType direction;
if (mArgsInfo.like_given) {
itk::ImageIOBase::Pointer header = clitk::readImageHeader(mArgsInfo.like_arg);
for(unsigned int i=0; i<dim; i++){
spacing[i] = header->GetSpacing(i);
size[i] = header->GetDimensions(i);
+ origin[i] = header->GetOrigin(i);
+ }
+ for(unsigned int i=0; i<dim; i++) {
+ for(unsigned int j=0;j<dim;j++) {
+ direction(i,j) = header->GetDirection(i)[j];
+ }
}
filter->SetOutputSpacing(spacing);
filter->SetOutputSize(size);
+ filter->SetOutputOrigin(origin);
+ filter->SetOutputDirection(direction);
}
else {
std::cerr << "*** Warning : I could not read '" << mArgsInfo.like_arg << "' ***" << std::endl;
size[i] = mArgsInfo.size_arg[i];
filter->SetOutputSize(size);
}
+ for(unsigned int i=0; i<dim; i++){
+ origin[i] = input->GetOrigin()[i];
+ }
+ for(unsigned int i=0; i<dim; i++) {
+ for(unsigned int j=0;j<dim;j++) {
+ direction(i,j) = input->GetDirection()[i][j];
+ }
+ }
+ filter->SetOutputOrigin(origin);
+ filter->SetOutputDirection(direction);
}
// Set temporal dimension
size[mSplitDimension]=0;
typename ImageType::RegionType extracted_region;
extracted_region.SetSize(size);
-#if ITK_VERSION_MAJOR >= 4
- filter->SetDirectionCollapseToSubmatrix();
-#endif
+ filter->SetDirectionCollapseToIdentity();
filter->SetExtractionRegion(extracted_region);
filter->Update();
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// clitk
+#include "clitkSum_ggo.h"
+#include "clitkSumGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkSum, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::SumGenericFilter<args_info_clitkSum> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ try {
+ filter->Update();
+ } catch(std::runtime_error e) {
+ std::cout << e.what() << std::endl;
+ }
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkSum.ggo
+package "clitkSum"
+version "1.0"
+purpose ""
+
+option "config" - "Config file" string optional
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string required
+option "output" o "Output image filename" string required
+option "dimension" d "Dimension along which to sum" int yes
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkSumGenericFilter_h
+#define clitkSumGenericFilter_h
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT SumGenericFilter:
+ public ImageToImageGenericFilter<SumGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ SumGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef SumGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(SumGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkSumGenericFilter.txx"
+#endif
+
+#endif // #define clitkSumGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkSumGenericFilter_txx
+#define clitkSumGenericFilter_txx
+
+// itk include
+#include <itkSumProjectionImageFilter.h>
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+SumGenericFilter<args_info_type>::SumGenericFilter():
+ ImageToImageGenericFilter<Self>("Sum")
+{
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void SumGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void SumGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+SumGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ // Main filter
+ typedef typename InputImageType::PixelType PixelType;
+ const int Dim = InputImageType::ImageDimension;
+ typedef itk::Image<PixelType,Dim> ImageType;
+ typedef itk::Image<PixelType,Dim-1> OutputImageType;
+
+ // Filter
+ typedef itk::SumProjectionImageFilter<ImageType,OutputImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetProjectionDimension(mArgsInfo.dimension_arg);
+ filter->SetInput(input);
+ filter->Update();
+ this->template SetNextOutput<OutputImageType>(filter->GetOutput());
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkSumGenericFilter_txx
//----------------------------------------
// Update
//----------------------------------------
-#if ITK_VERSION_MAJOR >= 4
void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, itk::ThreadIdType threadId );
-#else
- void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, int threadId );
-#endif
//----------------------------------------
// Data members
// Generate Data
//-------------------------------------------------------------------
template<class InputImageType, class OutputImageType>
- void
-#if ITK_VERSION_MAJOR >= 4
- VectorImageToImageFilter<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, itk::ThreadIdType threadId)
-#else
- VectorImageToImageFilter<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, int threadId)
-#endif
+ void VectorImageToImageFilter<InputImageType, OutputImageType>::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, itk::ThreadIdType threadId)
{
// Iterators
typename OutputImageType::Pointer output=this->GetOutput();
//Backward mapping
typedef itk::WarpImageFilter<InputImageType, InputImageType, DeformationFieldType> BackwardWarpFilterType;
typename BackwardWarpFilterType::Pointer backwardWarpFilter= BackwardWarpFilterType::New();
-#if ITK_VERSION_MAJOR >= 4
backwardWarpFilter->SetDisplacementField( deformationField );
-#else
- backwardWarpFilter->SetDeformationField( deformationField );
-#endif
backwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
backwardWarpFilter->SetOutputSpacing( deformationField->GetSpacing() );
backwardWarpFilter->SetOutputOrigin( input->GetOrigin() );
option "newSeriesUID" e "Write the series with a new series UID (ignored if given in key/tag option)" flag off
option "newStudyUID" u "Write the series with a new study UID (ignored if given in key/tag option; forces newSeriesUID = true)" flag off
option "useSizeAsReference" s "Use the size of the dicom image as reference for an occasional resampling" flag off
+option "preserve" p "Preserve private tags and keep original UID (eg: Xio)" flag off
// Read the series
typename ReaderType::Pointer reader = ReaderType::New();
+ if (m_ArgsInfo.preserve_flag) {
+#if GDCM_MAJOR_VERSION >= 2
+ gdcmIO->LoadPrivateTagsOn();
+ gdcmIO->KeepOriginalUIDOn();
+#endif
+ }
reader->SetImageIO( gdcmIO );
reader->SetFileNames( filenames_in );
try {
-INCLUDE(../../cmake/common.cmake)
+include(../../cmake/common.cmake)
-ADD_LIBRARY(clitkCxImage STATIC
+add_library(clitkCxImage STATIC
ximaenc.cpp
ximatran.cpp
ximath.cpp
ximasel.cpp
xmemfile.cpp
)
-INCLUDE_DIRECTORIES(.)
+include_directories(.)
# Gengetopt: http://www.gnu.org/software/gengetopt/
-ADD_DEFINITIONS(-DPACKAGE=\"gengetopt\")
-ADD_DEFINITIONS(-DVERSION=\"2.22.4\")
-ADD_DEFINITIONS(-DHAVE_SSTREAM)
-ADD_DEFINITIONS(-DHAVE_NAMESPACES)
+add_definitions(-DPACKAGE=\"gengetopt\")
+add_definitions(-DVERSION=\"2.22.4\")
+add_definitions(-DHAVE_SSTREAM)
+add_definitions(-DHAVE_NAMESPACES)
# Remove compiler warnings
-STRING(REPLACE "/W3" "/w" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-STRING(REPLACE "/W3" "/w" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
-STRING(REPLACE "-Wall" "-w" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-STRING(REPLACE "-Wall" "-w" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+string(REPLACE "/W3" "/w" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+string(REPLACE "/W3" "/w" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+string(REPLACE "-Wall" "-w" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+string(REPLACE "-Wall" "-w" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
# MSVC specific issues
-IF(MSVC)
- ADD_DEFINITIONS(-DHAVE_STRING_H)
- ADD_DEFINITIONS(-DYY_NO_UNISTD_H)
- ADD_DEFINITIONS(-Disatty=!)
-ENDIF(MSVC)
+if(MSVC)
+ add_definitions(-DHAVE_STRING_H)
+ add_definitions(-DYY_NO_UNISTD_H)
+ add_definitions(-Disatty=!)
+endif(MSVC)
-ADD_EXECUTABLE(gengetopt
+add_executable(gengetopt
./cmdline.c
./ggos.cpp
./scanner.cc
./yyerror.cc
./parser.cc)
-INCLUDE_DIRECTORIES(.)
-INCLUDE_DIRECTORIES(skels)
-#INCLUDE_DIRECTORIES(includes)
+include_directories(.)
+include_directories(skels)
+#include_directories(includes)
# To avoid warning with some version
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
+ cmake_policy(SET CMP0007 NEW)
endif(COMMAND cmake_policy)
#=========================================================
OPTION(CLITK_USE_PACS_CONNECTION "USE PACS CONNECTION" OFF)
#=========================================================
#List of vv tools to compile
-SET(vv_TOOLS
+set(vv_TOOLS
vvToolMedianFilter
vvToolRigidReg
vvToolCropImage
vvToolConvert ## with dummy vvToolConvert.ui
vvToolROIManager
vvToolSegmentation
+ vvToolProfile
## these ones are for tests (not working)
+ # vvToolTest
# vvToolFoo
# vvToolFooWithWidgetBase
# vvToolPlastimatch
- # vvToolConnectedComponentLabeling
+ # vvToolConnectedComponentLabeling
## these ones are old ones
# vvToolExtractPatient
# vvToolExtractLung
# dependencies of the tools
# Future issues : when tool depend on other tools ... how to manage that ?
# >> add the relevant $_LIBS variable to the tool that has dependencies?
-SET(vvToolBinarize_LIBS clitkBinarizeImageLib)
-SET(vvToolResample_LIBS clitkResampleImageLib)
-SET(vvToolConvert_LIBS clitkImageConvertLib)
-SET(vvToolExtractPatient_LIBS clitkSegmentationGgoLib)
-SET(vvToolExtractLung_LIBS clitkSegmentationGgoLib)
-SET(vvToolCropImage_LIBS clitkCropImageLib)
-SET(vvToolMIP_LIBS clitkMIPLib)
-SET(vvToolMedianFilter_LIBS clitkMedianImageFilterLib)
-SET(vvToolImageArithm_LIBS clitkImageArithmImageLib)
-SET(vvToolROIManager_LIBS clitkDicomRTStruct)
+set(vvToolBinarize_LIBS clitkBinarizeImageLib)
+set(vvToolProfile_LIBS clitkProfileImageLib)
+set(vvToolResample_LIBS clitkResampleImageLib)
+set(vvToolConvert_LIBS clitkImageConvertLib)
+set(vvToolExtractPatient_LIBS clitkSegmentationGgoLib)
+set(vvToolExtractLung_LIBS clitkSegmentationGgoLib)
+set(vvToolCropImage_LIBS clitkCropImageLib)
+set(vvToolMIP_LIBS clitkMIPLib)
+set(vvToolMedianFilter_LIBS clitkMedianImageFilterLib)
+set(vvToolImageArithm_LIBS clitkImageArithmImageLib)
+set(vvToolROIManager_LIBS clitkDicomRTStruct)
#=========================================================
# List of vv source files
# in COMMON_WITH_UI -> must have .h and .cxx and .ui
-SET(vv_COMMON_WITH_UI
+set(vv_COMMON_WITH_UI
vvInfoPanel
- vvMainWindow
- vvLinkPanel
- vvOverlayPanel
- vvLandmarksPanel
- vvProgressDialog
+ vvMainWindow
+ vvLinkPanel
+ vvOverlayPanel
+ vvLandmarksPanel
+ vvProgressDialog
vvSegmentationDialog
vvSurfaceViewerDialog
vvDeformationDialog
vvStructSelector
vvIntensityValueSlider
vvLabelImageLoaderWidget
- vvToolWidgetBase
+ vvToolWidgetBase
vvToolSimpleInputSelectorWidget
vvToolInputSelectorWidget
vvRegisterForm
)
# All others sources
-SET(vv_SRCS
+set(vv_SRCS
vvQProgressDialogITKCommand.cxx
vvQDicomSeriesSelector.cxx
QTreePushButton.cxx
#=========================================================
# Qt related commands
-FIND_PACKAGE(Qt4 REQUIRED)
+if(vv_QT_VERSION VERSION_GREATER "4")
+ find_package(Qt5Widgets REQUIRED)
+ find_package(Qt5Network REQUIRED)
+ find_package(Qt5Designer REQUIRED)
+else()
+ find_package(Qt4 REQUIRED)
+endif()
-QT4_WRAP_CPP(vv_SRCS
- vvMainWindowBase.h
- QTreePushButton.h
- vvDocumentation.h
- vvHelpDialog.h
- vvQDicomSeriesSelector.h
- vvSlicerManager.h
- vvStructureSetActor.h
- vvROIActor.h
- vvToolCreatorBase.h
- )
+if(vv_QT_VERSION VERSION_GREATER "4")
+ link_directories(${QT5Widgets_LIBRARIES})
+ link_directories(${QT5Network_LIBRARIES})
+ link_directories(${QT5Designer_LIBRARIES})
+else()
+ link_directories(${QT_LIBRARY_DIR})
+endif()
-QT4_WRAP_UI(vv_UI_CXX
- qt_ui/vvHelpDialog.ui
- qt_ui/vvDocumentation.ui
- qt_ui/vvDicomSeriesSelector.ui
-qt_ui/vvDummyWindow.ui #For testing
-#qt_ui/vvPacsConnection.ui
- # qt_ui/vvPacsSettingsDialog.ui
-)
+if(vv_QT_VERSION VERSION_GREATER "4")
+ qt5_wrap_cpp(vv_SRCS
+ vvMainWindowBase.h
+ QTreePushButton.h
+ vvDocumentation.h
+ vvHelpDialog.h
+ vvQDicomSeriesSelector.h
+ vvSlicerManager.h
+ vvSlicer.h
+ vvStructureSetActor.h
+ vvROIActor.h
+ vvToolCreatorBase.h
+ )
+else()
+ QT4_WRAP_CPP(vv_SRCS
+ vvMainWindowBase.h
+ QTreePushButton.h
+ vvDocumentation.h
+ vvHelpDialog.h
+ vvQDicomSeriesSelector.h
+ vvSlicerManager.h
+ vvSlicer.h
+ vvStructureSetActor.h
+ vvROIActor.h
+ vvToolCreatorBase.h
+ )
+endif()
-QT4_ADD_RESOURCES(vv_SRCS vvIcons.qrc)
+if(vv_QT_VERSION VERSION_GREATER "4")
+ qt5_wrap_ui(vv_UI_CXX
+ qt_ui/vvHelpDialog.ui
+ qt_ui/vvDocumentation.ui
+ qt_ui/vvDicomSeriesSelector.ui
+ qt_ui/vvDummyWindow.ui #For testing
+ )
+else()
+ QT4_WRAP_UI(vv_UI_CXX
+ qt_ui/vvHelpDialog.ui
+ qt_ui/vvDocumentation.ui
+ qt_ui/vvDicomSeriesSelector.ui
+ qt_ui/vvDummyWindow.ui #For testing
+ )
+endif()
+
+if(vv_QT_VERSION VERSION_GREATER "4")
+ QT5_add_resources(vv_SRCS vvIcons.qrc)
+else()
+ QT4_ADD_RESOURCES(vv_SRCS vvIcons.qrc)
+endif()
# Add DICOM SERVER gui selector if the adequate GDCM is available
-IF(CLITK_USE_PACS_CONNECTION)
+if(CLITK_USE_PACS_CONNECTION)
SET(vv_SRCS ${vv_SRCS}
- vvQPacsConnection.cxx
- vvPacsSettingsDialog.cxx
- vvDicomServerQueryFactory.cxx
- )
- QT4_WRAP_CPP(vv_SRCS vvQPacsConnection.h
- vvPacsSettingsDialog.h)
- QT4_WRAP_UI(vv_UI_CXX
- qt_ui/vvPacsConnection.ui
- qt_ui/vvPacsSettingsDialog.ui)
-ENDIF(CLITK_USE_PACS_CONNECTION)
-
-# Add the autotools in the header vvToolsList.h for initialization of the dummy
-# variables in vv.cxx for the tools contained in vvLib
-if(${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt IS_NEWER_THAN ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h)
- file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h)
- foreach(tool ${vv_TOOLS})
- FILE(APPEND ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h "#include \"${tool}.h\"\n")
- FILE(APPEND ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h "extern const vvToolCreator<${tool}> *dummy${tool};\n")
- FILE(APPEND ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h "const vvToolCreator<${tool}> *dummy${tool}2 = dummy${tool};\n\n")
+ vvQPacsConnection.cxx
+ vvPacsSettingsDialog.cxx
+ vvDicomServerQueryFactory.cxx
+ )
+ if(vv_QT_VERSION VERSION_GREATER "4")
+ qt5_wrap_cpp(vv_SRCS vvQPacsConnection.h
+ vvPacsSettingsDialog.h)
+ qt5_wrap_ui(vv_UI_CXX
+ qt_ui/vvPacsConnection.ui
+ qt_ui/vvPacsSettingsDialog.ui)
+ else()
+ QT4_WRAP_CPP(vv_SRCS vvQPacsConnection.h
+ vvPacsSettingsDialog.h)
+ QT4_WRAP_UI(vv_UI_CXX
+ qt_ui/vvPacsConnection.ui
+ qt_ui/vvPacsSettingsDialog.ui)
+ endif()
+endif(CLITK_USE_PACS_CONNECTION)
+
+ # Add the autotools in the header vvToolsList.h for initialization of the dummy
+ # variables in vv.cxx for the tools contained in vvLib
+ if(${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt IS_NEWER_THAN ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h)
+ file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h)
+ foreach(tool ${vv_TOOLS})
+ file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h "#include \"${tool}.h\"\n")
+ file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h "extern const vvToolCreator<${tool}> *dummy${tool};\n")
+ file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h "const vvToolCreator<${tool}> *dummy${tool}2 = dummy${tool};\n\n")
+ endforeach(tool)
+ endif(${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt IS_NEWER_THAN ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h)
+
+ # Add the autotools and the common files ui
+ foreach(tool ${vv_TOOLS} ${vv_COMMON_WITH_UI})
+ set(vv_SRCS ${vv_SRCS} ${tool}.cxx)
+ if(vv_QT_VERSION VERSION_GREATER "4")
+ QT5_WRAP_CPP(vv_SRCS ${tool}.h)
+ QT5_WRAP_UI(vv_UI_CXX qt_ui/${tool}.ui)
+ else()
+ QT4_WRAP_CPP(vv_SRCS ${tool}.h)
+ QT4_WRAP_UI(vv_UI_CXX qt_ui/${tool}.ui)
+ endif()
endforeach(tool)
-endif(${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt IS_NEWER_THAN ${CMAKE_CURRENT_BINARY_DIR}/vvToolsList.h)
-
-# Add the autotools and the common files ui
-foreach(tool ${vv_TOOLS} ${vv_COMMON_WITH_UI})
- SET(vv_SRCS ${vv_SRCS} ${tool}.cxx)
- QT4_WRAP_CPP(vv_SRCS ${tool}.h)
- QT4_WRAP_UI(vv_UI_CXX qt_ui/${tool}.ui)
-endforeach(tool)
-
-# Add the common source files
-foreach(tool ${vv_COMMON})
- SET(vv_SRCS ${vv_SRCS} ${tool}.cxx)
- QT4_WRAP_CPP(vv_SRCS ${tool}.h)
-endforeach(tool)
-
-# if Windows and Qt was built as a static lib then don't set QT_DLL flag
-SET(QT_STATIC 0)
-IF (WIN32)
- IF(EXISTS ${QT_LIBRARY_DIR}/QtCore.prl)
- FILE(READ ${QT_LIBRARY_DIR}/QtCore.prl QT_CORE_PRL)
- IF(${QT_CORE_PRL} MATCHES "static")
- SET(QT_STATIC 1)
- ENDIF(${QT_CORE_PRL} MATCHES "static")
- ENDIF(EXISTS ${QT_LIBRARY_DIR}/QtCore.prl)
-ENDIF(WIN32)
-IF(NOT QT_STATIC)
- ADD_DEFINITIONS(-DQT_DLL)
-ENDIF(NOT QT_STATIC)
-
-ADD_DEFINITIONS(-DQT_THREAD_SUPPORT)
+
+ # Add the common source files
+ foreach(tool ${vv_COMMON})
+ set(vv_SRCS ${vv_SRCS} ${tool}.cxx)
+ if(vv_QT_VERSION VERSION_GREATER "4")
+ QT5_WRAP_CPP(vv_SRCS ${tool}.h)
+ else()
+ QT4_WRAP_CPP(vv_SRCS ${tool}.h)
+ endif()
+ endforeach(tool)
+
+ # if Windows and Qt was built as a static lib then don't set QT_DLL flag
+ set(QT_STATIC 0)
+ if(WIN32)
+ if(vv_QT_VERSION VERSION_GREATER "4")
+ if(EXISTS ${Qt5Widgets_LIBRARIES}/QtCore.prl)
+ file(READ ${Qt5Widgets_LIBRARIES}/QtCore.prl QT_CORE_PRL)
+ if(${QT_CORE_PRL} MATCHES "static")
+ set(QT_STATIC 1)
+ endif(${QT_CORE_PRL} MATCHES "static")
+ endif(EXISTS ${Qt5Widgets_LIBRARIES}/QtCore.prl)
+ else()
+ if(EXISTS ${QT_LIBRARY_DIR}/QtCore.prl)
+ file(READ ${QT_LIBRARY_DIR}/QtCore.prl QT_CORE_PRL)
+ if(${QT_CORE_PRL} MATCHES "static")
+ set(QT_STATIC 1)
+ endif(${QT_CORE_PRL} MATCHES "static")
+ endif(EXISTS ${QT_LIBRARY_DIR}/QtCore.prl)
+ endif()
+ endif(WIN32)
+ if(NOT QT_STATIC)
+ add_definitions(-DQT_DLL)
+ endif(NOT QT_STATIC)
-INCLUDE_DIRECTORIES(
- ${QT_INCLUDES}
- ${QT_INCLUDE_DIR}
- ${QT_QTGUI_INCLUDE_DIR}
- ${QT_QTCORE_INCLUDE_DIR}
- ${CMAKE_CURRENT_BINARY_DIR}
- ${CMAKE_CURRENT_SOURCE_DIR}
-)
+ add_definitions(-DQT_THREAD_SUPPORT)
+ if(vv_QT_VERSION VERSION_GREATER "4")
+ include_directories(
+ ${Qt5Widgets_INCLUDE_DIRS}
+ ${Qt5Gui_INCLUDE_DIRS}
+ ${Qt5Core_INCLUDE_DIRS}
+ ${Qt5Network_INCLUDE_DIRS}
+ ${Qt5Designer_INCLUDE_DIRS}
+ ${CMAKE_CURRENT_BINARY_DIR}
+ ${CMAKE_CURRENT_SOURCE_DIR}
+ )
+ else()
+ include_directories(
+ ${QT_INCLUDES}
+ ${QT_INCLUDE_DIR}
+ ${QT_QTGUI_INCLUDE_DIR}
+ ${QT_QTCORE_INCLUDE_DIR}
+ ${CMAKE_CURRENT_BINARY_DIR}
+ ${CMAKE_CURRENT_SOURCE_DIR}
+ )
+ endif()
#=========================================================
#=========================================================
#support for parallel deformable registration with OpenMP
-IF(NOT APPLE)
-IF(CMAKE_COMPILER_IS_GNUCC)
- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
-ENDIF(CMAKE_COMPILER_IS_GNUCC)
-ENDIF(NOT APPLE)
+if(NOT APPLE)
+if(CMAKE_COMPILER_IS_GNUCC)
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
+endif(CMAKE_COMPILER_IS_GNUCC)
+endif(NOT APPLE)
#=========================================================
#=========================================================
-INCLUDE_DIRECTORIES(
+include_directories(
../common
../tools
../segmentation
)
-LINK_DIRECTORIES(${QT_LIBRARY_DIR})
-
#=========================================================
#Add each tool's dependencies
foreach(tool ${vv_TOOLS})
- SET(toolLibs ${toolLibs} ${${tool}_LIBS})
+ set(toolLibs ${toolLibs} ${${tool}_LIBS})
endforeach(tool)
#=========================================================
#Add Foundation Libraries (this should be after our libraries, since we depend
#on them)
-SET(foundationLibraries clitkCommon ${ITK_LIBRARIES} QVTK vtkHybrid)
+if(VTK_VERSION VERSION_GREATER "6.2.0")
+set(foundationLibraries clitkCommon ${ITK_LIBRARIES} ${VTK_LIBRARIES})
+else()
+set(foundationLibraries clitkCommon ${ITK_LIBRARIES} QVTK vtkHybrid)
+endif()
#=========================================================
# Use CxImage to create animated gifs
-IF(CLITK_EXPERIMENTAL)
- SET(vvCxImage clitkCxImage)
- SET(vv_SRCS ${vv_SRCS} vvAnimatedGIFWriter.cxx)
- INCLUDE_DIRECTORIES(${CLITK_SOURCE_DIR}/utilities/CxImage)
- ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/utilities/CxImage ${PROJECT_BINARY_DIR}/utilities/CxImage)
-ENDIF(CLITK_EXPERIMENTAL)
+if(CLITK_EXPERIMENTAL)
+ set(vvCxImage clitkCxImage)
+ set(vv_SRCS ${vv_SRCS} vvAnimatedGIFWriter.cxx)
+ include_directories(${CLITK_SOURCE_DIR}/utilities/CxImage)
+ add_subdirectory(${CLITK_SOURCE_DIR}/utilities/CxImage ${PROJECT_BINARY_DIR}/utilities/CxImage)
+endif(CLITK_EXPERIMENTAL)
#=========================================================
+#-----------------------------------------------------------------------------
+# Avoid linker bug in Mac OS 10.5
+# See http://wiki.finkproject.org/index.php/Fink:Packaging:Preparing_for_10.5#OpenGL_Bug
+#
+if(APPLE)
+ find_library(CoreFoundation_LIBRARY CoreFoundation REQUIRED)
+ find_library(ApplicationServices_LIBRARY ApplicationServices REQUIRED)
+ find_library(SystemConfiguration_LIBRARY SystemConfiguration REQUIRED)
+ find_library(Security_LIBRARY Security REQUIRED)
+ set(APPLE_FRAMEWORKS ${CoreFoundation_LIBRARY}
+ ${ApplicationServices_LIBRARY}
+ ${SystemConfiguration_LIBRARY}
+ ${Security_LIBRARY}
+ )
+ message(STATUS "===== ${APPLE_FRAMEWORKS}")
+endif()
#=========================================================
#Create binary and libs for tests
-SET(vvExternalLibs ${QT_QTNETWORK_LIBRARY} clitkSegmentationGgoLib ${toolLibs} ${foundationLibraries} ${vvCxImage})
-# QtNetwork is required by vvRegisterForm
+if(vv_QT_VERSION VERSION_GREATER "4")
+set(vvExternalLibs clitkSegmentationGgoLib ${toolLibs} ${foundationLibraries} ${vvCxImage} Qt5::Widgets Qt5::Network Qt5::Designer ${APPLE_FRAMEWORKS})
+else()
+set(vvExternalLibs clitkSegmentationGgoLib ${toolLibs} ${foundationLibraries} ${vvCxImage} ${QT_LIBRARIES} ${APPLE_FRAMEWORKS})
+endif()
+# QtNetwork is required by vvRegisterForm ${QT_QTNETWORK_LIBRARY}
+
+#-----------------------------------------------------------------------------
+# For retina displays, see
+# http://public.kitware.com/pipermail/vtkusers/2015-February/090117.html
+if(APPLE)
+ set(vv_SRCS ${vv_SRCS} vvOSXHelper.mm)
+endif()
-ADD_LIBRARY(vvLib ${vv_SRCS} ${vv_UI_CXX})
-TARGET_LINK_LIBRARIES(vvLib ${vvExternalLibs})
+add_library(vvLib ${vv_SRCS} ${vv_UI_CXX})
+target_link_libraries(vvLib ${vvExternalLibs})
-IF(WIN32)
- ADD_EXECUTABLE(vv WIN32 vv.cxx vvIcon.rc)
-ELSE(WIN32)
- ADD_EXECUTABLE(vv vv.cxx)
-ENDIF(WIN32)
+if(WIN32)
+ add_executable(vv WIN32 vv.cxx vvIcon.rc)
+else(WIN32)
+ add_executable(vv vv.cxx)
+endif(WIN32)
-TARGET_LINK_LIBRARIES(vv vvLib)
+target_link_libraries(vv vvLib)
#=========================================================
# Install options (also used by CPack)
-INSTALL (TARGETS vv DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
+install(TARGETS vv DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
#=========================================================
#=========================================================
# CPack options
-SET(CPACK_PACKAGE_NAME "vv")
-SET(CPACK_SOURCE_PACKAGE_FILE_NAME "vv-src")
-SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "vv, the 4D slicer : let's jump into a new dimension !")
-SET(CPACK_PACKAGE_VENDOR "Creatis-CLB")
-SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/ReadMe.txt")
-SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/License.txt")
-SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
-IF(NIGHTLY)
- SET(CPACK_PACKAGE_INSTALL_DIRECTORY "vv-nightly")
-ELSE(NIGHTLY)
- SET(CPACK_PACKAGE_INSTALL_DIRECTORY "vv")
-ENDIF(NIGHTLY)
-SET(CPACK_STRIP_FILES TRUE)
+set(CPACK_PACKAGE_NAME "vv")
+set(CPACK_SOURCE_PACKAGE_FILE_NAME "vv-src")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "vv, the 4D slicer : let's jump into a new dimension !")
+set(CPACK_PACKAGE_VENDOR "Creatis-CLB")
+set(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/ReadMe.txt")
+set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/License.txt")
+set(CPACK_PACKAGE_VERSION_MAJOR "1")
+set(CPACK_PACKAGE_VERSION_MINOR "3")
+set(CPACK_PACKAGE_VERSION_PATCH "0")
+if(NIGHTLY)
+ set(CPACK_PACKAGE_INSTALL_DIRECTORY "vv-nightly")
+else(NIGHTLY)
+ set(CPACK_PACKAGE_INSTALL_DIRECTORY "vv")
+endif(NIGHTLY)
+set(CPACK_STRIP_FILES TRUE)
-IF(WIN32)
+if(WIN32)
# There is a bug in NSI that does not handle full unix paths properly. Make
# sure there is at least one set of four (4) backlasshes.
- SET(CPACK_NSIS_MUI_ICON "${CMAKE_CURRENT_SOURCE_DIR}\\\\icons\\\\ducky.ico")
- SET(CPACK_NSIS_INSTALLED_ICON_NAME "vv.exe")
-IF(NIGHTLY)
- SET(CPACK_NSIS_DISPLAY_NAME "vv - The 4D slicer (nightly)")
-ELSE(NIGHTLY)
- SET(CPACK_NSIS_DISPLAY_NAME "vv - The 4D slicer")
-ENDIF(NIGHTLY)
- SET(CPACK_NSIS_HELP_LINK "http://www.creatis.insa-lyon.fr/rio/vv")
- SET(CPACK_NSIS_URL_INFO_ABOUT "http://www.creatis.insa-lyon.fr/rio")
- SET(CPACK_NSIS_CONTACT "vv@creatis.insa-lyon.fr")
- SET(CPACK_NSIS_CREATE_ICONS_EXTRA "CreateShortCut \\\"$SMPROGRAMS\\\\$STARTMENU_FOLDER\\\\vv.lnk\\\" \\\"$INSTDIR\\\\bin\\\\vv.exe\\\" ")
- SET(CPACK_NSIS_DELETE_ICONS_EXTRA "Delete \\\"$SMPROGRAMS\\\\$MUI_TEMP\\\\vv.lnk\\\" ")
- #SET(CPACK_NSIS_MODIFY_PATH ON) SR: buggy, wait for cmake updates for a fix
- #SET(CPACK_BINARY_ZIP ON)
-ELSE(WIN32)
- SET(CPACK_GENERATOR "STGZ")
- SET(CPACK_SOURCE_GENERATOR "TGZ")
-ENDIF(WIN32)
-INCLUDE(CPack)
+ set(CPACK_NSIS_MUI_ICON "${CMAKE_CURRENT_SOURCE_DIR}\\\\icons\\\\ducky.ico")
+ set(CPACK_NSIS_INSTALLED_ICON_NAME "vv.exe")
+if(NIGHTLY)
+ set(CPACK_NSIS_DISPLAY_NAME "vv - The 4D slicer (nightly)")
+else(NIGHTLY)
+ set(CPACK_NSIS_DISPLAY_NAME "vv - The 4D slicer")
+endif(NIGHTLY)
+ set(CPACK_NSIS_HELP_LINK "http://www.creatis.insa-lyon.fr/rio/vv")
+ set(CPACK_NSIS_URL_INFO_ABOUT "http://www.creatis.insa-lyon.fr/rio")
+ set(CPACK_NSIS_CONTACT "vv@creatis.insa-lyon.fr")
+ set(CPACK_NSIS_CREATE_ICONS_EXTRA "CreateShortCut \\\"$SMPROGRAMS\\\\$STARTMENU_FOLDER\\\\vv.lnk\\\" \\\"$INSTDIR\\\\bin\\\\vv.exe\\\" ")
+ set(CPACK_NSIS_DELETE_ICONS_EXTRA "Delete \\\"$SMPROGRAMS\\\\$MUI_TEMP\\\\vv.lnk\\\" ")
+ #set(CPACK_NSIS_MODIFY_PATH ON) SR: buggy, wait for cmake updates for a fix
+ #set(CPACK_BINARY_ZIP ON)
+else(WIN32)
+ set(CPACK_GENERATOR "STGZ")
+ set(CPACK_SOURCE_GENERATOR "TGZ")
+endif(WIN32)
+include(CPack)
#=========================================================
#=========================================================
configure_file(vvConfiguration.h.in vvConfiguration.h)
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
<string>Form</string>
</property>
<layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0" colspan="2">
+ <item row="0" column="0" colspan="-1">
<widget class="QLabel" name="nameLabel">
<property name="text">
<string><html><head><meta name="qrichtext" content="1" /><style type="text/css">
<x>0</x>
<y>0</y>
<width>1008</width>
- <height>21</height>
+ <height>27</height>
</rect>
</property>
<property name="defaultUp">
<property name="text">
<string>Open image(s)</string>
</property>
+ <property name="shortcut">
+ <string>Ctrl+O</string>
+ </property>
<property name="iconVisibleInMenu">
<bool>true</bool>
</property>
<property name="text">
<string>Navigation Help</string>
</property>
- <property name="shortcut">
- <string>F1</string>
- </property>
<property name="iconVisibleInMenu">
<bool>true</bool>
</property>
+ <property name="priority">
+ <enum>QAction::NormalPriority</enum>
+ </property>
</action>
<action name="actionOpen_Dicom_Struct">
<property name="icon">
<string>Save</string>
</property>
</widget>
- <widget class="QWidget" name="layoutWidget">
+ <widget class="QWidget" name="layoutWidget1">
<property name="geometry">
<rect>
<x>0</x>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>vvToolProfile</class>
+ <widget class="QWidget" name="vvToolProfile">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>505</width>
+ <height>452</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Profile image</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <layout class="QGridLayout" name="gridLayout_2">
+ <property name="horizontalSpacing">
+ <number>6</number>
+ </property>
+ <item row="2" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_3">
+ <item>
+ <widget class="QPushButton" name="mSelectPoint2Button">
+ <property name="text">
+ <string>Select point 2</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="Point2">
+ <property name="text">
+ <string>Center of voxel2 (vox):</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item row="2" column="3">
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QLabel" name="mPosPoint2Label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>200</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item row="3" column="3">
+ <layout class="QHBoxLayout" name="horizontalLayout_6">
+ <item>
+ <widget class="QToolButton" name="mCancelPointsButton">
+ <property name="text">
+ <string>Cancel</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="mSaveProfileButton">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Save Profile</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_7">
+ <item>
+ <widget class="QPushButton" name="mSelectPoint1Button">
+ <property name="text">
+ <string>Select point 1</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="Point1">
+ <property name="text">
+ <string>Center of voxel1 (vox):</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="3">
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QLabel" name="mPosPoint1Label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>200</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="text">
+ <string/>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <widget class="Line" name="line_2">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QVTKWidget" name="ProfileWidget" native="true">
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>300</height>
+ </size>
+ </property>
+ <property name="mouseTracking">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>QVTKWidget</class>
+ <extends>QWidget</extends>
+ <header>QVTKWidget.h</header>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>
</sizepolicy>
</property>
<property name="text">
- <string> </string>
+ <string/>
</property>
</widget>
</item>
</property>
</spacer>
</item>
+ <item>
+ <widget class="QPushButton" name="mRemoveButton">
+ <property name="text">
+ <string>1</string>
+ </property>
+ <property name="icon">
+ <iconset resource="../vvIcons.qrc">
+ <normaloff>:/common/icons/standardbutton-cancel-16.png</normaloff>:/common/icons/standardbutton-cancel-16.png</iconset>
+ </property>
+ </widget>
+ </item>
<item>
<widget class="QLabel" name="mROInameLabel_3">
<property name="sizePolicy">
<bool>false</bool>
</property>
<property name="text">
- <string/>
+ <string>All</string>
</property>
<property name="icon">
<iconset resource="../vvIcons.qrc">
- <normaloff>:/common/icons/exit.png</normaloff>:/common/icons/exit.png</iconset>
+ <normaloff>:/common/icons/standardbutton-cancel-16.png</normaloff>:/common/icons/standardbutton-cancel-16.png</iconset>
</property>
</widget>
</item>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>vvToolTest</class>
+ <widget class="QWidget" name="vvToolTest">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>433</width>
+ <height>222</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Test sphere</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="Line" name="line_3">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>
<rect>
<x>0</x>
<y>0</y>
- <width>179</width>
+ <width>194</width>
<height>62</height>
</rect>
</property>
<property name="orientation">
<enum>Qt::Vertical</enum>
</property>
- <widget class="vvToolInputSelectorWidget" name="mToolInputSelectionWidget" native="true"/>
+ <widget class="vvToolInputSelectorWidget" name="mToolInputSelectionWidget" native="true">
+ <property name="maximumSize">
+ <size>
+ <width>16777215</width>
+ <height>200</height>
+ </size>
+ </property>
+ </widget>
<widget class="QWidget" name="mToolWidget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
#include "vtkObjectFactory.h"
#include "vtkStreamingDemandDrivenPipeline.h"
#include "vtkDataSetAttributes.h"
-
-#include <vtkstd/string>
+#include <vtkVersion.h>
+#include <vtkAlgorithm.h>
#include <sys/stat.h>
//----------------------------------------------------------------------------
-vtkCxxRevisionMacro(vtkVOXImageWriter, "DummyRevision");
vtkStandardNewMacro(vtkVOXImageWriter);
//----------------------------------------------------------------------------
void vtkVOXImageWriter::Write( )
{
this->SetErrorCode(vtkErrorCode::NoError);
-
+#if VTK_MAJOR_VERSION <= 5
this->GetInput()->UpdateInformation();
-
+#else
+ this->UpdateInformation();
+#endif
// Error checking
if (this->GetInput() == NULL ) {
vtkErrorMacro(<<"Write:Please specify an input!");
}
int nDims = 3;
+#if VTK_MAJOR_VERSION <= 5
int * ext = this->GetInput()->GetWholeExtent();
+#else
+ int * ext = this->GetInformation()->Get(vtkDataObject::DATA_EXTENT());
+#endif
if ( ext[4] == ext[5] ) {
nDims = 2;
if ( ext[2] == ext[3] ) {
origin[1] += ext[2] * spacing[1];
origin[2] += ext[4] * spacing[2];
+#if VTK_MAJOR_VERSION <= 5
this->GetInput()->SetUpdateExtent(ext[0], ext[1],
ext[2], ext[3],
ext[4], ext[5]);
this->GetInput()->UpdateData();
-
-
+#else
+ this->SetUpdateExtent(ext);
+ this->Update();
+#endif
this->SetFileDimensionality(nDims);
this->InvokeEvent(vtkCommand::StartEvent);
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
===========================================================================**/
-#ifndef __vtkVoxImageWriter_h
+#ifndef __vtkVOXImageWriter_h
#define __vtkVOXImageWriter_h
#include "vtkImageWriter.h"
#include <string>
class vtkVOXImageWriter : public vtkImageWriter
{
public:
- vtkTypeRevisionMacro(vtkVOXImageWriter,vtkImageWriter);
+ vtkTypeMacro(vtkVOXImageWriter,vtkImageWriter);
void PrintSelf(ostream& os, vtkIndent indent);
// Description:
#include <QDesktopWidget>
#include <QDir>
+#if VTK_MAJOR_VERSION > 5
+#include <vtkAutoInit.h>
+ VTK_MODULE_INIT(vtkInteractionStyle);
+ VTK_MODULE_INIT(vtkRenderingOpenGL);
+ VTK_MODULE_INIT(vtkRenderingFreeType);
+#define vtkRenderingContext2D_AUTOINIT 1(vtkRenderingContextOpenGL)
+#endif
+
+
#include "clitkIO.h"
#include "vvMainWindow.h"
#include "vvReadState.h"
const std::string open_mode_names[] = {"base", "overlay", "fusion", "vf", "contour", "fusionSequence"};
if(open_mode==O_BASE)
window.LoadImages(sequence_filenames, vvImageReader::MERGEDWITHTIME);
- else if (open_mode==O_OVERLAY)
+ else if (open_mode==O_OVERLAY && window.CheckAddedImage(n_image_loaded-1, "overlay"))
window.AddOverlayImage(n_image_loaded-1,sequence_filenames,vvImageReader::MERGEDWITHTIME);
else if (open_mode==O_LANDMARKS)
window.AddLandmarks(n_image_loaded-1,sequence_filenames);
- else if (open_mode==O_FUSION)
+ else if (open_mode==O_FUSION && window.CheckAddedImage(n_image_loaded-1, "fusion") && window.CheckAddedImage(n_image_loaded-1, "fusionSequence"))
window.AddFusionImage(n_image_loaded-1,sequence_filenames,vvImageReader::MERGEDWITHTIME);
else {
std::cerr << "Sequences are not managed for opening " << open_mode_names[open_mode] << std::endl;
<< std::endl
<< "These last options must follow a file name since they overlay something on an image:" << std::endl
<< "--vf file \t Overlay the vector field in file." << std::endl
- << "--overlay file \t Overlay the image in file with complementary colors." << std::endl
- << "--fusion file \t Overlay the image in file with alpha blending and colormap." << std::endl
+ << "--overlay [--sequence] file(s) \t Overlay the image in file with complementary colors." << std::endl
+ << "--fusion [--sequence] file(s) \t Overlay the image in file with alpha blending and colormap." << std::endl
//<< "--roi file \t Overlay binary mask images. Option may be repeated on a single base image." << std::endl
<< "--contour file \t Overlay DICOM RT-STRUCT contours." << std::endl
<< "--landmarks [--sequence] file(s) \t Overlay the landmarks in file(s) (.txt or .pts)." << std::endl;
first_of_wl_set = n_image_loaded-1;
}
}
- else if (open_mode==O_VF)
+ else if (open_mode==O_VF && window.CheckAddedImage(n_image_loaded-1, "vector"))
window.AddField(current.c_str(), n_image_loaded-1);
- else if (open_mode==O_OVERLAY)
+ else if (open_mode==O_OVERLAY && window.CheckAddedImage(n_image_loaded-1, "overlay"))
window.AddOverlayImage(n_image_loaded-1,image,vvImageReader::IMAGE);
else if (open_mode==O_CONTOUR)
window.AddDCStructContour(n_image_loaded-1,current.c_str());
- else if (open_mode==O_FUSION)
+ else if (open_mode==O_FUSION && window.CheckAddedImage(n_image_loaded-1, "fusion") && window.CheckAddedImage(n_image_loaded-1, "fusionSequence"))
window.AddFusionImage(n_image_loaded-1,image,vvImageReader::IMAGE);
else if (open_mode==O_LANDMARKS)
window.AddLandmarks(n_image_loaded-1,image);
#include "vvAnimatedGIFWriter.h"
#include "clitkDD.h"
-#include "ximagif.h"
-
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
#include <vtkImageData.h>
#include <vtkImageQuantizeRGBToIndex.h>
#include <vtkImageAppend.h>
#include <vtkObjectFactory.h>
#include <vtkLookupTable.h>
+#include "ximagif.h"
+
//---------------------------------------------------------------------------
vtkStandardNewMacro(vvAnimatedGIFWriter);
void vvAnimatedGIFWriter::Write()
{
// get the data
+#if VTK_MAJOR_VERSION <= 5
this->GetInput()->UpdateInformation();
int *wExtent = this->GetInput()->GetWholeExtent();
this->GetInput()->SetUpdateExtent(wExtent);
this->GetInput()->Update();
+#else
+ this->UpdateInformation();
+ int *wExtent = this->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT());
+ this->SetUpdateExtent(wExtent);
+ this->Update();
+#endif
RGBslices.push_back( vtkSmartPointer<vtkImageData>::New() );
RGBslices.back()->ShallowCopy(this->GetInput());
+#if VTK_MAJOR_VERSION <= 5
RGBvolume->AddInput(RGBslices.back());
+#else
+ RGBvolume->AddInputData(RGBslices.back());
+#endif
}
//---------------------------------------------------------------------------
// Quantize to 8 bit colors
vtkSmartPointer<vtkImageQuantizeRGBToIndex> quant = vtkSmartPointer<vtkImageQuantizeRGBToIndex>::New();
quant->SetNumberOfColors(256);
+#if VTK_MAJOR_VERSION <= 5
quant->SetInput(RGBvolume->GetOutput());
+#else
+ quant->SetInputConnection(RGBvolume->GetOutputPort());
+#endif
quant->Update();
// Convert to 8 bit image
vtkSmartPointer<vtkImageCast> cast = vtkSmartPointer<vtkImageCast>::New();
+#if VTK_MAJOR_VERSION <= 5
cast->SetInput( quant->GetOutput() );
+#else
+ cast->SetInputConnection( quant->GetOutputPort() );
+#endif
cast->SetOutputScalarTypeToUnsignedChar();
cast->Update();
#include "vvBinaryImageOverlayActor.h"
#include "vvImage.h"
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
#include <vtkImageActor.h>
#include <vtkCamera.h>
#include <vtkRenderer.h>
#include <vtkProperty.h>
#include <vtkImageMapToRGBA.h>
#include <vtkLookupTable.h>
+#include <vtkImageMapper3D.h>
//------------------------------------------------------------------------------
vvBinaryImageOverlayActor::vvBinaryImageOverlayActor()
-{
+{
mTSlice = -1;
mSlice = 0;
mColor.resize(3);
//------------------------------------------------------------------------------
vvBinaryImageOverlayActor::~vvBinaryImageOverlayActor()
-{
+{
mImageActorList.clear();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::RemoveActors()
-{
+{
for (unsigned int i = 0; i < mImageActorList.size(); i++) {
if (mSlicer != 0) {
if (mSlicer != NULL) {
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::SetColor(double r, double g, double b)
-{
+{
mColor[0] = r;
mColor[1] = g;
mColor[2] = b;
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::SetSlicer(vvSlicer * slicer)
-{
+{
mSlicer = slicer;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::Initialize(bool IsVisible)
-{
+{
if (!mSlicer) {
std::cerr << "ERROR. Please use setSlicer before setSlicer in vvBinaryImageOverlayActor." << std::endl;
exit(0);
for (unsigned int numImage = 0; numImage < mSlicer->GetImage()->GetVTKImages().size(); numImage++) {
// how many intensity ?
vtkSmartPointer<vtkImageMapToRGBA> mOverlayMapper = vtkSmartPointer<vtkImageMapToRGBA>::New();
- mOverlayMapper->SetInput(mImage->GetVTKImages()[0]); // DS TODO : to change if it is 4D !!!
+ if (mImage->IsTimeSequence())
+ {
+ #if VTK_MAJOR_VERSION <= 5
+ mOverlayMapper->SetInput(mImage->GetVTKImages()[numImage]);
+#else
+ mOverlayMapper->SetInputData(mImage->GetVTKImages()[numImage]);
+#endif
+ }
+ else {
+#if VTK_MAJOR_VERSION <= 5
+ mOverlayMapper->SetInput(mImage->GetVTKImages()[0]);
+#else
+ mOverlayMapper->SetInputData(mImage->GetVTKImages()[0]);
+#endif
+ }
double range[2];
- mImage->GetVTKImages()[0]->GetScalarRange(range);
+ if (mImage->IsTimeSequence())
+ {
+ mImage->GetVTKImages()[numImage]->GetScalarRange(range);
+ }
+ else {
+ mImage->GetVTKImages()[0]->GetScalarRange(range);
+ }
int n = range[1]-range[0]+1;
mColorLUT->SetRange(range[0],range[1]);
mColorLUT->SetNumberOfTableValues(n);
mOverlayMapper->SetLookupTable(mColorLUT);
vtkSmartPointer<vtkImageActor> mOverlayActor = vtkSmartPointer<vtkImageActor>::New();
+#if VTK_MAJOR_VERSION <= 5
mOverlayActor->SetInput(mOverlayMapper->GetOutput());
+#else
+ mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
+#endif
mOverlayActor->SetPickable(0);
mOverlayActor->SetVisibility(IsVisible);
//mOverlayActor->SetOpacity(1.0);
mMapperList.push_back(mOverlayMapper);
mImageActorList.push_back(mOverlayActor);
- mSlicer->GetRenderer()->AddActor(mOverlayActor);
+ mSlicer->GetRenderer()->AddActor(mImageActorList[numImage]);
}
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::SetOpacity(double d)
-{
+{
mAlpha = d;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::SetImage(vvImage::Pointer image, double bg, bool modeBG)
-{
+{
mImage = image;
if (modeBG) {
mBackgroundValue = bg;
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::HideActors()
-{
+{
if (!mSlicer) return;
mSlice = mSlicer->GetSlice();
for(unsigned int i=0; i<mImageActorList.size(); i++) {
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::ShowActors()
-{
+{
if (!mSlicer) return;
mSlice = mSlicer->GetSlice();
mTSlice = mSlicer->GetTSlice();
- // for(unsigned int i=0; i<mSquaresActorList.size(); i++) {
mImageActorList[mTSlice]->VisibilityOn();
UpdateSlice(0, mSlice);
- //}
// Caller MUST call Render
//mSlicer->Render();
}
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::UpdateColor()
-{
+{
mColorLUT->SetTableValue(1, mColor[0], mColor[1], mColor[2], mAlpha); // FG
for (unsigned int numImage = 0; numImage < mSlicer->GetImage()->GetVTKImages().size(); numImage++) {
// how many intensity ?
mOverlayMapper->SetLookupTable(mColorLUT);
vtkImageActor * mOverlayActor = mImageActorList[numImage];
+#if VTK_MAJOR_VERSION <= 5
mOverlayActor->SetInput(mOverlayMapper->GetOutput());
+#else
+ mOverlayActor->SetInputData(mOverlayMapper->GetOutput());
+#endif
}
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvBinaryImageOverlayActor::UpdateSlice(int slicer, int slice, bool force)
-{
+{
if (!mSlicer) return;
if (!force) {
int orientation = mSlicer->GetOrientation();
int maskExtent[6];
ComputeExtent(orientation, mSlice, imageExtent, maskExtent);
- ComputeExtent(maskExtent, maskExtent, mSlicer->GetImage()->GetFirstVTKImageData(), mImage->GetFirstVTKImageData());
+ ComputeExtent(maskExtent, maskExtent, mSlicer->GetImage()->GetVTKImages()[mTSlice], mImage->GetVTKImages()[mTSlice]);
+#if VTK_MAJOR_VERSION <= 5
mSlicer->ClipDisplayedExtent(maskExtent, mMapperList[mTSlice]->GetInput()->GetWholeExtent());
+#else
+ mSlicer->ClipDisplayedExtent(maskExtent, mMapperList[mTSlice]->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
+#endif
+ HideActors();
+ mImageActorList[mTSlice]->VisibilityOn();
SetDisplayExtentAndCameraPosition(orientation, mSlice, maskExtent, mImageActorList[mTSlice], mDepth);
// set previous slice
int slice,
int * inExtent,
int * outExtent)
-{
+{
switch (orientation) {
case vtkImageViewer2::SLICE_ORIENTATION_XY:
for(int i=0; i<4; i++) outExtent[i] = inExtent[i];
//----------------------------------------------------------------------------
void vvBinaryImageOverlayActor::ComputeExtent(int * inExtent, int * outExtent, vtkImageData * image, vtkImageData * overlay)
-{
+{
for(int i=0; i<3; i++) {
double a = (image->GetOrigin()[i] + inExtent[i*2]*image->GetSpacing()[i] -
overlay->GetOrigin()[i]) / overlay->GetSpacing()[i];
int * extent,
vtkImageActor * actor,
double position)
-{
+{
/* FIXME
Error according to camera orientation
*/
#include "vtkVOXImageWriter.h"
#include <vtkImageData.h>
+#include <vtkVersion.h>
#include "clitkCommon.h"
#include "vvSlicerManager.h"
for (unsigned int i=0; i<images.size(); i++) {
std::stringstream filename;
filename << temp_dir << "/temp_" << i << ".vox";
+#if VTK_MAJOR_VERSION <= 5
vox->SetInput(images[i]);
+#else
+ vox->SetInputData(images[i]);
+#endif
vox->SetFileName(filename.str().c_str());
if (i==refimage)
ref_file=filename.str();
===========================================================================**/
#include "vvGlyph2D.h"
+#include <vtkVersion.h>
#include "vtkCell.h"
#include "vtkDataSet.h"
#include "vtkFloatArray.h"
#include "vtkTransform.h"
#include "vtkUnsignedCharArray.h"
-vtkCxxRevisionMacro(vvGlyph2D, "DummyRevision");
vtkStandardNewMacro(vvGlyph2D);
vvGlyph2D::vvGlyph2D()
defaultPointIds[0] = 0;
defaultPointIds[1] = 1;
defaultSource->SetPoints(defaultPoints);
- defaultSource->InsertNextCell(VTK_LINE, 2, defaultPointIds);
+ defaultSource->InsertNextCell(VTK_LINE, 2, defaultPointIds);
+#if VTK_MAJOR_VERSION <= 5
defaultSource->SetUpdateExtent(0, 1, 0);
this->SetSource(defaultSource);
+#else
+ this->SetUpdateExtent(0, 1, 0);
+ this->SetSourceData(defaultSource);
+#endif
defaultSource->Delete();
defaultSource = NULL;
defaultPoints->Delete();
class vvGlyph2D : public vtkGlyph3D
{
public:
- vtkTypeRevisionMacro(vvGlyph2D,vtkGlyph3D);
+ vtkTypeMacro(vvGlyph2D,vtkGlyph3D);
void PrintSelf(ostream& os, vtkIndent indent);
// Description
#include "vtkPolyData.h"
#include "vtkUnsignedCharArray.h"
-vtkCxxRevisionMacro(vvGlyphSource, "DummyRevision");
vtkStandardNewMacro(vvGlyphSource);
{
public:
static vvGlyphSource *New();
- vtkTypeRevisionMacro(vvGlyphSource,vtkGlyphSource2D);
+ vtkTypeMacro(vvGlyphSource,vtkGlyphSource2D);
void PrintSelf(ostream& os, vtkIndent indent);
void SetGlyphTypeToSpecificArrow() {
<file>icons/8b.png</file>
<file>icons/1b.png</file>
<file>icons/binarize.png</file>
+ <file>icons/profile.png</file>
<file>icons/resample.png</file>
<file>icons/crop.png</file>
<file>icons/splashscreen2.png</file>
#include "vvImageContour.h"
#include "vvImage.h"
+#include <vtkVersion.h>
#include <vtkImageActor.h>
#include <vtkCamera.h>
#include <vtkRenderer.h>
#include <vtkImageData.h>
#include <vtkPolyDataMapper.h>
#include <vtkProperty.h>
+#include <vtkInformation.h>
//------------------------------------------------------------------------------
vvImageContour::vvImageContour()
-{
+{
mTSlice = -1;
mSlice = 0;
mHiddenImageIsUsed = false;
//------------------------------------------------------------------------------
vvImageContour::~vvImageContour()
-{
+{
mSquaresActorList.clear();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvImageContour::RemoveActors()
-{
+{
for (unsigned int i = 0; i < mSquaresActorList.size(); i++) {
if (mSlicer != 0) {
if (mSlicer!= NULL) {
//------------------------------------------------------------------------------
-void vvImageContour::SetSlicer(vvSlicer * slicer) {
+void vvImageContour::SetSlicer(vvSlicer * slicer)
+{
mSlicer = slicer;
// Create an actor for each time slice
for (unsigned int numImage = 0; numImage < mSlicer->GetImage()->GetVTKImages().size(); numImage++) {
//------------------------------------------------------------------------------
-void vvImageContour::SetImage(vvImage::Pointer image) {
+void vvImageContour::SetImage(vvImage::Pointer image)
+{
for (unsigned int numImage = 0; numImage < image->GetVTKImages().size(); numImage++) {
+#if VTK_MAJOR_VERSION <= 5
mClipperList[numImage]->SetInput(image->GetVTKImages()[numImage]);
+#else
+ mClipperList[numImage]->SetInputData(image->GetVTKImages()[numImage]);
+#endif
}
mHiddenImageIsUsed = true;
mHiddenImage = image;
//------------------------------------------------------------------------------
-void vvImageContour::SetPreserveMemoryModeEnabled(bool b) {
+void vvImageContour::SetPreserveMemoryModeEnabled(bool b)
+{
// FastCache mode work only if threshold is always the same
if (mDisplayModeIsPreserveMemory == b) return;
mDisplayModeIsPreserveMemory = b;
//------------------------------------------------------------------------------
-void vvImageContour::SetColor(double r, double g, double b) {
+void vvImageContour::SetColor(double r, double g, double b)
+{
for(unsigned int i=0; i<mSquaresActorList.size(); i++) {
mSquaresActorList[i]->GetProperty()->SetColor(r,g,b);
+ mSquaresActorList[i]->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
}
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvImageContour::SetLineWidth(double w)
-{
+{
for(unsigned int i=0; i<mSquaresActorList.size(); i++) {
mSquaresActorList[i]->GetProperty()->SetLineWidth(w);
}
//------------------------------------------------------------------------------
-void vvImageContour::HideActors() {
+void vvImageContour::HideActors()
+{
if (!mSlicer) return;
mSlice = mSlicer->GetSlice();
for(unsigned int i=0; i<mSquaresActorList.size(); i++) {
//------------------------------------------------------------------------------
-void vvImageContour::ShowActors() {
+void vvImageContour::ShowActors()
+{
if (!mSlicer) return;
mSlice = mSlicer->GetSlice();
mTSlice = mSlicer->GetTSlice();
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvImageContour::Update(double value) {
+void vvImageContour::Update(double value)
+{
if (!mSlicer) return;
if (mPreviousValue == value) {
if (mPreviousSlice == mSlicer->GetSlice()) {
//------------------------------------------------------------------------------
-void vvImageContour::UpdateWithPreserveMemoryMode() {
+void vvImageContour::UpdateWithPreserveMemoryMode()
+{
// Only change actor visibility if tslice change
mPreviousTslice = mTSlice;
mTSlice = mSlicer->GetTSlice();
if (mPreviousTslice != mTSlice) {
if (mPreviousTslice != -1) mSquaresActorList[mPreviousTslice]->VisibilityOff();
}
-
- mSlicer->Render();
+
+ //mSlicer->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvImageContour::InitializeCacheMode() {
+void vvImageContour::InitializeCacheMode()
+{
clitkExceptionMacro("TODO : not implemented yet");
mPreviousSlice = mPreviousOrientation = 0;
int dim = mSlicer->GetImage()->GetNumberOfDimensions();
//------------------------------------------------------------------------------
-int vvImageContour::ComputeCurrentOrientation() {
+int vvImageContour::ComputeCurrentOrientation()
+{
// Get extent of image in the slicer
int* extent = mSlicer->GetImageActor()->GetDisplayExtent();
//------------------------------------------------------------------------------
-void vvImageContour::UpdateWithFastCacheMode() {
+void vvImageContour::UpdateWithFastCacheMode()
+{
clitkExceptionMacro("TODO : not implemented yet");
// Compute orientation
//------------------------------------------------------------------------------
-void vvImageContour::CreateNewActor(int numImage) {
+void vvImageContour::CreateNewActor(int numImage)
+{
vtkSmartPointer<vtkActor> squaresActor = vtkSmartPointer<vtkActor>::New();
vtkSmartPointer<vtkImageClip> clipper = vtkSmartPointer<vtkImageClip>::New();
vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
vtkSmartPointer<vtkPolyDataMapper> squaresMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
- if (mHiddenImageIsUsed)
+ if (mHiddenImageIsUsed) {
+#if VTK_MAJOR_VERSION <= 5
clipper->SetInput(mHiddenImage->GetVTKImages()[0]);
- else
+#else
+ clipper->SetInputData(mHiddenImage->GetVTKImages()[0]);
+#endif
+ } else {
+#if VTK_MAJOR_VERSION <= 5
clipper->SetInput(mSlicer->GetImage()->GetVTKImages()[numImage]);
-
+#else
+ clipper->SetInputData(mSlicer->GetImage()->GetVTKImages()[numImage]);
+#endif
+ }
+#if VTK_MAJOR_VERSION <= 5
squares->SetInput(clipper->GetOutput());
squaresMapper->SetInput(squares->GetOutput());
+#else
+ squares->SetInputConnection(clipper->GetOutputPort(0));
+ squaresMapper->SetInputConnection(squares->GetOutputPort(0));
+#endif
squaresMapper->ScalarVisibilityOff();
squaresActor->SetMapper(squaresMapper);
squaresActor->GetProperty()->SetColor(1.0,0,0);
+ squaresActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
squaresActor->SetPickable(0);
squaresActor->VisibilityOff();
mSlicer->GetRenderer()->AddActor(squaresActor);
vtkPolyDataMapper * mapper,
vtkMarchingSquares * squares,
vtkImageClip * clipper,
- double threshold, int orientation, int slice) {
+ double threshold, int orientation, int slice)
+{
// Set parameter for the MarchigSquare
squares->SetValue(0, threshold);
-
+ squares->Update();
// Get image extent
int* extent = mSlicer->GetImageActor()->GetDisplayExtent();
extent2 = extent;
actor->VisibilityOn();
}
-
+
clipper->SetOutputWholeExtent(extent2[0],extent2[1],extent2[2],
extent2[3],extent2[4],extent2[5]);
-
+
if (mHiddenImageIsUsed) delete extent2;
// Move the actor to be visible
// DD(mDepth);
// position[orientation] = -mDepth;
// actor->SetPosition(position);
-
mapper->Update();
}
//------------------------------------------------------------------------------
jacobian_filter->SetUseImageSpacingOn();
vf_connector->SetInput(mVF->GetVTKImages()[num]);
warp_filter->SetInput(input[num]);
-#if ITK_VERSION_MAJOR >= 4
warp_filter->SetDisplacementField(vf_connector->GetOutput());
-#else
- warp_filter->SetDeformationField(vf_connector->GetOutput());
-#endif
jacobian_filter->SetInput(vf_connector->GetOutput());
warp_filter->SetOutputSpacing(input[num]->GetSpacing());
warp_filter->SetOutputOrigin(input[num]->GetOrigin());
#define VVINTENSITYVALUESLIDER_H
// qt
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include <QDialog>
#include <vtkRendererCollection.h>
#include "clitkCommon.h"
-
-vtkCxxRevisionMacro(vvInteractorStyleNavigator, "DummyRevision");
vtkStandardNewMacro(vvInteractorStyleNavigator);
//----------------------------------------------------------------------------
{
public:
static vvInteractorStyleNavigator *New();
- vtkTypeRevisionMacro(vvInteractorStyleNavigator, vtkInteractorStyle);
+ vtkTypeMacro(vvInteractorStyleNavigator, vtkInteractorStyle);
void PrintSelf(ostream& os, vtkIndent indent);
// Description:
#include "vvImage.h"
// qt
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include <QDialog>
#include "ui_vvLabelImageLoaderWidget.h"
#include <string>
#include <locale.h>
+#include <vtkVersion.h>
#include "vtkPolyData.h"
#include "vtkPoints.h"
#include "vtkFloatArray.h"
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+void vvLandmarks::RemoveLandmarkWithLabel(vtkStdString label, int time)
+{
+ if (label != "P1" && label != "P2")
+ return;
+ // erase a vtkPoint by shifiting the array .
+ // not a problem here because there are no
+ // pologyons linking the points
+ int t = time;//mLandmarks[index].coordinates[3];
+ int npoints = mPoints[t]->GetNumberOfPoints();
+
+ //search of the index corresponding to the label
+ int index(0);
+ while (mLabels[t]->GetValue(index) != label)
+ ++index;
+
+ for (int i = index; i < npoints - 1; i++) {
+ mPoints[t]->InsertPoint(i, mPoints[t]->GetPoint(i+1));
+ std::string str_i; // string which will contain the result
+ std::ostringstream convert; // stream used for the conversion
+ convert << i; // insert the textual representation of 'i' in the characters in the stream
+ str_i = convert.str(); // set 'str_i' to the contents of the stream
+ mLabels[t]->SetValue(i,mLabels[t]->GetValue(i+1));
+ }
+ mPoints[t]->SetNumberOfPoints(npoints-1);
+ mLabels[t]->SetNumberOfValues(npoints-1);
+ mLabels[t]->Modified();
+ mPolyData->Modified();
+
+ mLandmarks[t].erase(mLandmarks[t].begin() + index);
+ mIds[t]->RemoveLastTuple();
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
void vvLandmarks::RemoveLandmark(int index)
{
mPolyData->GetPointData()->SetScalars(mIds[time]);
mPolyData->GetPointData()->AddArray(mLabels[time]);
mPolyData->Modified();
+#if VTK_MAJOR_VERSION <= 5
mPolyData->Update();
+#else
+ //mPolyData->Update();
+#endif
mTime = time;
}
}
void AddLandmark(float x,float y,float z,float t,double value);
void RemoveLastLandmark();
+ void RemoveLandmarkWithLabel(vtkStdString, int);
void RemoveLandmark(int index);
void RemoveAll();
float* GetCoordinates(int index);
double GetPixelValue(int index);
std::string GetComments(int index);
+ vtkStringArray* GetLabels() { return mLabels[mTime]; }
unsigned int GetNumberOfPoints() { return (unsigned int) mLandmarks[mTime].size(); }
//int GetNumberOfSources(){return mText.size();}
#include "vtkUnsignedCharArray.h"
#include <cassert>
-vtkCxxRevisionMacro(vvLandmarksGlyph, "DummyRevision");
vtkStandardNewMacro(vvLandmarksGlyph);
#define vtkfont_width 9
class vvLandmarksGlyph : public vtkTextSource
{
public:
- vtkTypeRevisionMacro(vvLandmarksGlyph,vtkTextSource);
+ vtkTypeMacro(vvLandmarksGlyph,vtkTextSource);
void PrintSelf(ostream& os, vtkIndent indent);
// Description:
#include <QtGui>
#include <Qt>
+#include <QFileDialog>
#include "QTreePushButton.h"
#include "vvLandmarks.h"
//====================================================================
vvLandmarksPanel::vvLandmarksPanel(QWidget * parent):QWidget(parent)
-{
+{
setupUi(this);
tableWidget->verticalHeader()->hide();
}
void vvLandmarksPanel::Load()
-{
+{
QString file = QFileDialog::getOpenFileName(this,tr("Load Landmarks"),
mCurrentPath.c_str(),tr("Landmarks ( *.txt *.pts)"));
if (!file.isEmpty()) {
}
bool vvLandmarksPanel::LoadFromFile(std::vector<std::string> files)
-{
+{
if (!mCurrentLandmarks->LoadFile(files))
return false;
- SetCurrentLandmarks(mCurrentLandmarks,2);
+ SetCurrentLandmarks(mCurrentLandmarks,0);
emit UpdateRenderWindows();
return true;
}
void vvLandmarksPanel::Save()
-{
+{
QString file = QFileDialog::getSaveFileName(this,
tr("Save Landmarks"),
mCurrentPath.c_str(),tr("Landmarks ( *.txt)"));
}
void vvLandmarksPanel::SelectPoint()
-{
+{
if (tableWidget->rowCount() > 0) {
QList<QTableWidgetItem *> items = tableWidget->selectedItems();
if (!items.empty()) {
void vvLandmarksPanel::RemoveSelectedPoints()
-{
+{
if (tableWidget->rowCount() > 0) {
QList<QTableWidgetItem *> items = tableWidget->selectedItems();
if (items.empty()) {
}
void vvLandmarksPanel::RemoveAllPoints()
-{
+{
mCurrentLandmarks->RemoveAll();
tableWidget->clearContents();
tableWidget->setRowCount(0);
}
void vvLandmarksPanel::AddPoint()
-{
+{
AddPoint(mCurrentLandmarks->GetNumberOfPoints()-1);
}
void vvLandmarksPanel::AddPoint(int landmarksIndex)
-{
+{
int rowIndex = tableWidget->rowCount();
// DD(rowIndex);
tableWidget->setRowCount(rowIndex+1);
}
void vvLandmarksPanel::SetCurrentLandmarks(vvLandmarks* lm,int time)
-{
+{
if (time != lm->GetTime())
return;
-
loadButton->setEnabled(1);
saveButton->setEnabled(1);
removeButton->setEnabled(1);
tableWidget->clearContents();
tableWidget->setRowCount(0);
for (unsigned int i = 0; i < mCurrentLandmarks->GetNumberOfPoints(); i++) {
- AddPoint(i);
+ if ((mCurrentLandmarks->GetLabels()->GetValue(i) != "P1") && (mCurrentLandmarks->GetLabels()->GetValue(i) != "P2"))
+ AddPoint(i);
}
//if (time > 1)
//tableWidget->setColumnHidden(4,1);
}
void vvLandmarksPanel::SetCurrentImage(std::string filename)
-{
+{
QString image = "<b>CurrentImage : </b>";
image += vtksys::SystemTools::GetFilenameWithoutLastExtension(filename).c_str();
nameLabel->setText(image);
}
void vvLandmarksPanel::CommentsChanged(int row, int column)
-{
+{
if (column == 6) {
mCurrentLandmarks->ChangeComments(row,std::string(tableWidget->item(row,column)->text().toStdString()));
tableWidget->resizeColumnsToContents();
#include "QTreePushButton.h"
#include <QUrl>
#include <QSettings>
+#include <QShortcut>
// VV include
#include "vvMainWindow.h"
#endif
#include "clitkConfiguration.h"
#include "clitkMatrix.h"
+#ifdef Q_OS_OSX
+# include "vvOSXHelper.h"
+#endif
// ITK include
#include <itkImage.h>
#include <itkNumericSeriesFileNames.h>
// VTK include
+#include <vtkImageMapper3D.h>
+#include <vtkInformation.h>
+#include <vtkVersion.h>
#include <vtkImageData.h>
#include <vtkImageActor.h>
#include <vtkCornerAnnotation.h>
#define COLUMN_IMAGE_NAME 7
#ifdef CLITK_PRIVATE_FEATURES
-#define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
+#define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
#else
-#define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
+#define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
#endif
//------------------------------------------------------------------------------
vvMainWindow::vvMainWindow():vvMainWindowBase()
-{
+{
setupUi(this); // this sets up the GUI
+
setDicomClient();
+
+ //Qt::WindowFlags flags = windowFlags();
+ //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
+
mInputPathName = "";
mMenuTools = menuTools;
// mMenuSegmentation = menuSegmentation;
contextActions.resize(0);
QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
tr("O&pen new Image"));
- actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
contextActions.push_back(actionOpen_new_image);
contextMenu.addSeparator();
tr("Reset transformation to identity"));
connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
- // TRIAL DS
- /*
- QMenu * m = new QMenu(menubar);
- m->setTitle("TOTO");
- // m->setObjectName(QString::fromUtf8("TOTOTO"));
- contextMenu.addMenu(m);
- QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
- tr("BIDON"));
- QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
- tr("BIDON2"));
- m->addAction(a);
- m->addAction(b);
- connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
- */
-
//init the DataTree
mSlicerManagers.resize(0);
connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
+
+ QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
+ shortcutHelp->setContext(Qt::ApplicationShortcut);
+ QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
+
connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
SOViewWidget->hide();
SEViewWidget->hide();
+#ifdef Q_OS_OSX
+ disableGLHiDPI(NOViewWidget->winId());
+ disableGLHiDPI(NEViewWidget->winId());
+ disableGLHiDPI(SOViewWidget->winId());
+ disableGLHiDPI(SEViewWidget->winId());
+#endif
+
//Recently opened files
std::list<std::string> recent_files = GetRecentlyOpenedImages();
recentlyOpenedFilesMenu=NULL;
vvToolManager::GetInstance()->InsertToolsInMenu(this);
vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
+//#ifndef CLITK_EXPERIMENTAL
+//#define CLITK_EXPERIMENTAL 0
+//#endif
+#ifdef CLITK_EXPERIMENTAL
if (!CLITK_EXPERIMENTAL)
menuExperimental->menuAction()->setVisible(false);
-
+#endif
QTimer * timerMemory = new QTimer(this);
//timerMemory->setInterval(5);
connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
timerMemory->start(2000);
-
}
+
//------------------------------------------------------------------------------
void vvMainWindow::show()
-{
+{
vvMainWindowBase::show();
PopupRegisterForm(true);
}
//------------------------------------------------------------------------------
void vvMainWindow::UpdateMemoryUsage()
-{
+{
// clitk::PrintMemory(true);
if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
//------------------------------------------------------------------------------
void vvMainWindow::createRecentlyOpenedFilesMenu()
-{
+{
recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
//------------------------------------------------------------------------------
void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
-{
+{
if(recentlyOpenedFilesMenu==NULL) {
createRecentlyOpenedFilesMenu();
} else {
//------------------------------------------------------------------------------
void vvMainWindow::ComputeMidPosition()
-{
+{
bool ok;
int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
- int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
- mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
+ int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
+mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
if (ok) {
vvMidPosition midp;
midp.slicer_manager = mSlicerManagers[index];
//------------------------------------------------------------------------------
void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
-{
+{
QTreeWidgetItem *item = new QTreeWidgetItem();
item->setData(0,Qt::UserRole,"filename.vtk");
item->setData(1,Qt::UserRole,tr("contour"));
brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
brush.setStyle(Qt::SolidPattern);
item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
- // item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
+ item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
for (int j = 1; j <= 4; j++)
item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
//------------------------------------------------------------------------------
void vvMainWindow::OpenVTKContour()
-{
+{
if (mSlicerManagers.size() > 0) {
QString Extensions = "Images ( *.vtk *.obj)";
Extensions += ";;All Files (*)";
//------------------------------------------------------------------------------
void vvMainWindow::AddDCStructContour(int index, QString file)
-{
+{
vvMeshReader reader;
reader.SetFilename(file.toStdString());
vvStructSelector selector;
//------------------------------------------------------------------------------
void vvMainWindow::OpenDCStructContour()
-{
+{
if (mSlicerManagers.size() > 0) {
QString Extensions = "Dicom Files ( *.dcm RS*)";
Extensions += ";;All Files (*)";
//------------------------------------------------------------------------------
void vvMainWindow::ComputeDeformableRegistration()
-{
+{
if (mSlicerManagers.size() > 0) {
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
vvDeformationDialog dialog(index,mSlicerManagers);
//------------------------------------------------------------------------------
void vvMainWindow::WarpImage()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
if (!mSlicerManagers[index]->GetVF().IsNull()) {
bool ok;
- int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
+ int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
if (ok) {
WarpImage(mSlicerManagers[index],ref);
//------------------------------------------------------------------------------
void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
-{
+{
if (!selected_slicer->GetVF().IsNull()) {
QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
QFileInfo info(selected_slicer->GetFileName().c_str());
//------------------------------------------------------------------------------
vvMainWindow::~vvMainWindow()
-{
+{
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
if (mSlicerManagers[i] != NULL)
delete mSlicerManagers[i];
}
+ delete documentation;
+ delete help_dialog;
+ delete dicomSeriesSelector;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
QTabWidget * vvMainWindow::GetTab()
-{
+{
return tabWidget;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::MergeImages()
-{
+{
QString Extensions = EXTENSIONS;
Extensions += ";;All Files (*)";
QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
//------------------------------------------------------------------------------
void vvMainWindow::SliceImages()
-{
+{
QString Extensions = EXTENSIONS;
Extensions += ";;All Files (*)";
//------------------------------------------------------------------------------
void vvMainWindow::MergeImagesWithTime()
-{
+{
QString Extensions = EXTENSIONS;
Extensions += ";;All Files (*)";
QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
//------------------------------------------------------------------------------
void vvMainWindow::OpenDicom()
-{
+{
std::vector<std::string> files;
//std::cout << "dicomSeriesSelector " << std::endl;
//------------------------------------------------------------------------------
void vvMainWindow::OpenImages()
-{
+{
QString Extensions = EXTENSIONS;
Extensions += ";;All Files (*)";
}
//------------------------------------------------------------------------------
void vvMainWindow::OpenRecentImage()
-{
+{
QAction * caller = qobject_cast<QAction*>(sender());
std::vector<std::string> images;
images.push_back(caller->text().toStdString());
//------------------------------------------------------------------------------
void vvMainWindow::OpenImageWithTime()
-{
+{
QString Extensions = EXTENSIONS;
Extensions += ";;All Files (*)";
//------------------------------------------------------------------------------
void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
-{
+{
//Separate the way to open images and dicoms
int fileSize;
if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
// Change filename if an image with the same already exist
int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
- if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
+ if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
- else {
+ } else {
SetImageSucceed = imageManager->SetImages(files,filetype, number);
}
-
if (!SetImageSucceed) {
QApplication::restoreOverrideCursor();
QString error = "Cannot open file \n";
QMessageBox::information(this,tr("Reading problem"),error);
delete imageManager;
} else {
+
mSlicerManagers.push_back(imageManager);
//create an item in the tree with good settings
connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
-
InitSlicers();
numberofsuccesulreads++;
}
}
}
+
if (numberofsuccesulreads) {
NOViewWidget->show();
NEViewWidget->show();
//------------------------------------------------------------------------------
void vvMainWindow::UpdateTree()
-{
+{
DataTree->resizeColumnToContents(COLUMN_TREE);
DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
//------------------------------------------------------------------------------
void vvMainWindow::CurrentImageChanged(std::string id)
-{
+{
if (id == mCurrentSelectedImageId) return; // Do nothing
int selected = 0;
for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
mSlicerManagers[selected]->GetTSlice());
landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
-
+
emit SelectedImageHasChanged(mSlicerManagers[selected]);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::CurrentPickedImageChanged(std::string id)
-{
+{
if (id == mCurrentPickedImageId) return; // Do nothing
int selected = 0;
for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
//------------------------------------------------------------------------------
void vvMainWindow::ImageInfoChanged()
-{
+{
contextActions[6]->setEnabled(1);
contextActions[5]->setEnabled(1);
actionSave_As->setEnabled(1);
// infoPanel->setOrigin(GetVectorDoubleAsString(origin));
// infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
// infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
-//
+//
// landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
// mSlicerManagers[index]->GetTSlice());
// landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
// landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
-//
+//
// overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
// for (int i = 0; i < 4; i++) {
// if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
//------------------------------------------------------------------------------
void vvMainWindow::ShowDocumentation()
-{
+{
documentation->show();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::PopupRegisterForm(bool checkCanPush)
-{
+{
vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
if(!checkCanPush) {
registerForm->show();
//------------------------------------------------------------------------------
void vvMainWindow::ShowHelpDialog()
-{
+{
help_dialog->show();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::ChangeViewMode()
-{
+{
typedef struct _SIZE{
QSplitter* splitter;
QList<int> size1, size2;
//------------------------------------------------------------------------------
QString vvMainWindow::GetSizeInBytes(unsigned long size)
-{
+{
QString result = "";// QString::number(size);
//result += " bytes (";
if (size > 1000000000) {
//------------------------------------------------------------------------------
QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
-{
+{
QString result;
for (unsigned int i= 0; i < vectorDouble.size(); i++) {
if (i != 0)
//------------------------------------------------------------------------------
QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
-{
+{
QString result;
for (unsigned int i= 0; i < vectorInt.size(); i++) {
if (i != 0)
//------------------------------------------------------------------------------
//this actually returns the SlicerManager index!
int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
-{
+{
QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
//------------------------------------------------------------------------------
QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
-{
+{
QString id = sm->GetId().c_str();
for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
//------------------------------------------------------------------------------
void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
-{
+{
if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
return;
clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
// Children
- std::map<std::string, int> actorTypeCounts;
+ std::map<std::string, int> actorTypeCounts;
for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
//------------------------------------------------------------------------------
void vvMainWindow::InitSlicers()
-{
+{
if (mSlicerManagers.size()) {
mSlicerManagers.back()->GenerateDefaultLookupTable();
-
mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
+#if VTK_MAJOR_VERSION <= 5
+ mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
+#endif
}
}
//------------------------------------------------------------------------------
void vvMainWindow::InitDisplay()
-{
+{
if (mSlicerManagers.size()) {
//BE CAREFUL : this is absolutely necessary to set the interactor style
//in order to have the same style instanciation for all SlicerManagers in
bool AlreadySelected = false;
for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
-
//select the image only if previous are not selected
if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
mSlicerManagers[i]->UpdateSlicer(j,1);
AlreadySelected = true;
} else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
- if (DataTree->selectedItems().size() == 0)
+ if (DataTree->selectedItems().size() == 0) {
DataTree->topLevelItem(i)->setSelected(1);
+ }
DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
mSlicerManagers[i]->UpdateSlicer(j,1);
DisplaySliders(i,j);
//------------------------------------------------------------------------------
void vvMainWindow::DisplaySliders(int slicer, int window)
-{
+{
if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
return;
//------------------------------------------------------------------------------
void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
-{
+{
int index = GetSlicerIndexFromItem(item);
if (DataTree->topLevelItem(index) != item) {
if (DataTree->topLevelItem(index)->child(child) == item) break;
}
if (overlay_type=="fusionSequence") {
- //removing the overlay sequence in a fusion sequence visualization mode
+ //removing the overlay sequence in a fusion sequence visualization mode
//reset the transforms
overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
//------------------------------------------------------------------------------
void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
-{
+{
// int index = GetSlicerIndexFromItem(item);
// QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
// if (item->data(1,Qt::UserRole).toString() == "vector")
else if (role == "fusionSequence") {
//both versions of the secondary sequence must be updated.
mSlicerManagers[index]->ReloadFusionSequence();
- mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
+ mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
}
else {
mSlicerManagers[index]->Reload();
//if we update the secondary sequence, then the overlay of the main sequence should also be updated
- if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
+ if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
}
// Update view and info
ImageInfoChanged();
//------------------------------------------------------------------------------
void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
-{
+{
infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
-{
+{
overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
-{
+{
overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::FusionChanged(int visibility, double value)
-{
+{
overlayPanel->getCurrentFusionInfo(visibility,value);
}
//------------------------------------------------------------------------------
//or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
//when ImageInfoChanged() is called
void vvMainWindow::WindowLevelChanged()
-{
+{
// Base image
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
if(index==-1) return;
mSlicerManagers[index]->GetFusionLevel());
if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
- mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
+ mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
mSlicerManagers[index]->GetFusionSequenceNbFrames(),
mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
}
mSlicerManagers[ind]->GetFusionWindow(),
mSlicerManagers[ind]->GetFusionLevel());
overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
- mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
+ mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
}
//------------------------------------------------------------------------------
void vvMainWindow::WindowLevelEdited()
-{
+{
presetComboBox->setCurrentIndex(WL_USER);
UpdateWindowLevel();
}
//------------------------------------------------------------------------------
void vvMainWindow::SetWindowLevel(double w, double l)
-{
+{
windowSpinBox->setValue(w);
levelSpinBox->setValue(l);
presetComboBox->setCurrentIndex(WL_USER);
//------------------------------------------------------------------------------
void vvMainWindow::UpdateWindowLevel()
-{
+{
if (DataTree->selectedItems().size()) {
if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
colorMapComboBox->setCurrentIndex(5);
//------------------------------------------------------------------------------
void vvMainWindow::UpdateSlicingPreset()
-{
+{
if (DataTree->selectedItems().size()) {
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
//------------------------------------------------------------------------------
void vvMainWindow::UpdateColorMap()
-{
+{
if (DataTree->selectedItems().size()) {
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
}
//------------------------------------------------------------------------------
void vvMainWindow::SwitchWindowLevel()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
int window = mSlicerManagers[index]->GetColorWindow();
presetComboBox->setCurrentIndex(WL_USER);
//------------------------------------------------------------------------------
void vvMainWindow::ApplyWindowLevelToAllImages()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
if(index==-1) return;
double window = mSlicerManagers[index]->GetColorWindow();
double level = mSlicerManagers[index]->GetColorLevel();
+ double fusWindow = mSlicerManagers[index]->GetFusionWindow();
+ double fusLevel = mSlicerManagers[index]->GetFusionLevel();
+
+ double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
+ double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
+
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
if (mSlicerManagers[i] == NULL)
continue;
mSlicerManagers[i]->SetColorWindow(window);
mSlicerManagers[i]->SetColorLevel(level);
mSlicerManagers[i]->SetPreset(WL_USER);
+ mSlicerManagers[i]->SetFusionWindow(fusWindow);
+ mSlicerManagers[i]->SetFusionLevel(fusLevel);
+ mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
+ mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
mSlicerManagers[i]->Render();
}
}
//------------------------------------------------------------------------------
void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
-{
+{
for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
if (mSlicerManagers[i] == NULL)
continue;
+ SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
mSlicerManagers[i]->SetColorWindow(window);
mSlicerManagers[i]->SetPreset(WL_USER);
mSlicerManagers[i]->Render();
//------------------------------------------------------------------------------
void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
-{
+{
for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
if (mSlicerManagers[i] == NULL)
continue;
+ SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
mSlicerManagers[i]->SetColorLevel(level);
mSlicerManagers[i]->SetPreset(WL_USER);
mSlicerManagers[i]->Render();
//------------------------------------------------------------------------------
void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
-{
+{
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
if (mSlicerManagers[i]->GetId() == id) {
mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
//------------------------------------------------------------------------------
void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
-{
+{
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
if (id == mSlicerManagers[i]->GetId()) {
mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
//------------------------------------------------------------------------------
void vvMainWindow::ShowContextMenu(QPoint point)
-{
+{
if (!DataTree->selectedItems().size()) {
contextActions[1]->setEnabled(0);
contextActions[2]->setEnabled(0);
//------------------------------------------------------------------------------
void vvMainWindow::CloseImage()
-{
+{
CloseImage(DataTree->selectedItems()[0],0);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::ReloadImage()
-{
+{
ReloadImage(DataTree->selectedItems()[0],0);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::SelectOverlayImage()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
+ if (!(CheckAddedImage(index, "overlay")))
+ return;
+
+ QString Extensions = EXTENSIONS;
+ Extensions += ";;All Files (*)";
+ QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
+ if (files.isEmpty())
+ return;
+
+ std::vector<std::string> vecFileNames;
+ for (int i = 0; i < files.size(); i++) {
+ vecFileNames.push_back(files[i].toStdString());
+ }
+
+ AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
+}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+bool vvMainWindow::CheckAddedImage(int index, QString imageType)
+{
//check if one overlay image is added
for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
- if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
+ if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
QString error = "Cannot add more than one compared image\n";
error += "Please remove first ";
error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
QMessageBox::information(this,tr("Problem adding compared image !"),error);
- return;
- }
-
- QString Extensions = EXTENSIONS;
- Extensions += ";;All Files (*)";
- QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
- if (files.isEmpty())
- return;
-
- std::vector<std::string> vecFileNames;
- for (int i = 0; i < files.size(); i++) {
- vecFileNames.push_back(files[i].toStdString());
+ return false;
}
- AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
+ return true;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
-{
+{
QString file(fileNames[0].c_str());
if (QFile::exists(file))
{
item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
qApp->processEvents();
+#if VTK_MAJOR_VERSION > 5
+ for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
+ mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
+#endif
for (int j = 1; j <= 4; j++) {
item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
//------------------------------------------------------------------------------
void vvMainWindow::AddROI(int index, QString file)
-{
+{
/*
// Get slice manager
//------------------------------------------------------------------------------
void vvMainWindow::SelectFusionImage()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
- //check if one fusion image is added
- for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
- if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
- (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
- QString error = "Cannot add more than one fusion image\n";
- error += "Please remove first ";
- error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
- QMessageBox::information(this,tr("Problem adding fusion image !"),error);
- return;
- }
+ if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
+ return;
- QString Extensions = EXTENSIONS;
- Extensions += ";;All Files (*)";
- QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
- if (files.isEmpty())
- return;
+ QString Extensions = EXTENSIONS;
+ Extensions += ";;All Files (*)";
+ QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
+ if (files.isEmpty())
+ return;
- std::vector<std::string> vecFileNames;
- for (int i = 0; i < files.size(); i++) {
- vecFileNames.push_back(files[i].toStdString());
- }
- AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
+ std::vector<std::string> vecFileNames;
+ for (int i = 0; i < files.size(); i++) {
+ vecFileNames.push_back(files[i].toStdString());
+ }
+ AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::ResetTransformationToIdentity()
-{
+{
std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
//------------------------------------------------------------------------------
void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
-{
+{
QString file(fileNames[0].c_str());
if (QFile::exists(file))
{
item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
qApp->processEvents();
-
+#if VTK_MAJOR_VERSION > 5
+ for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
+ mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
+#endif
for (int j = 1; j <= 4; j++) {
item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
-{
+{
if (!landmarksPanel->LoadFromFile(files))
QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
-
+
landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
}
//------------------------------------------------------------------------------
void vvMainWindow::OpenField()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
- //check if a vector field has already been added
- for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
- if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
- QString error = "Cannot add more than one vector field\n";
- error += "Please remove first ";
- error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
- QMessageBox::information(this,tr("Problem adding vector field!"),error);
- return;
- }
+
+ if (!(CheckAddedImage(index, "vector")))
+ return;
- QString Extensions = "Images ( *.mhd)";
- Extensions += ";;Images ( *.mha)";
- Extensions += ";;VF Images ( *.vf)";
- Extensions += ";;nii Images ( *.nii)";
- Extensions += ";;nrrd Images ( *.nrrd)";
- Extensions += ";;nhdr Images ( *.nhdr)";
- Extensions += ";;All Files (*)";
- QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
- if (!file.isEmpty())
- AddField(file,index);
+ QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
+ // Extensions += ";;Images ( *.mha)";
+ // Extensions += ";;VF Images ( *.vf)";
+ // Extensions += ";;nii Images ( *.nii)";
+ // Extensions += ";;nrrd Images ( *.nrrd)";
+ // Extensions += ";;nhdr Images ( *.nhdr)";
+ Extensions += ";;All Files (*)";
+ QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
+ if (!file.isEmpty())
+ AddField(file,index);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
-{
+{
//create an item in the tree with good settings
QTreeWidgetItem *item = new QTreeWidgetItem();
item->setData(0,Qt::UserRole,filename.toStdString().c_str());
//------------------------------------------------------------------------------
void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
-{
+{
QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
vvSlicerManager* imageManager = mSlicerManagers[index];
if (imageManager->SetVF(vf,file.toStdString())) {
AddFieldEntry(file,index,false);
+#if VTK_MAJOR_VERSION > 5
+ for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
+ mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
+#endif
} else {
QString error = "Cannot import the vector field for this image.\n";
error += imageManager->GetLastError().c_str();
//------------------------------------------------------------------------------
void vvMainWindow::AddField(QString file,int index)
-{
+{
if (QFile::exists(file)) {
mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
//------------------------------------------------------------------------------
void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
for (int i = 0; i < 4; i++) {
//------------------------------------------------------------------------------
void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
mSlicerManagers[index]->SetOverlayColor(color);
//------------------------------------------------------------------------------
void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
mSlicerManagers[index]->SetFusionColorMap(colormap);
//------------------------------------------------------------------------------
void vvMainWindow::SelectFusionSequence()
-{
+{
//get the index of the slicer manager of the main sequence (CT)
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
- //check if one overlay image is already associated
- for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
- if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
- (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
- QString error = "Cannot add more than one compared image\n";
- error += "Please remove first ";
- error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
- QMessageBox::information(this,tr("Problem adding compared image !"),error);
- return;
- }
- QString Extensions = EXTENSIONS;
- Extensions += ";;All Files (*)";
- QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
- if (files.isEmpty())
- return;
+ if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
+ return;
- std::vector<std::string> vecFileNames;
- for (int i = 0; i < files.size(); i++) {
- vecFileNames.push_back(files[i].toStdString());
- }
+ QString Extensions = EXTENSIONS;
+ Extensions += ";;All Files (*)";
+ QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
+ if (files.isEmpty())
+ return;
- //associate the secondary sequence (US) to the main one
- AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
+ std::vector<std::string> vecFileNames;
+ for (int i = 0; i < files.size(); i++) {
+ vecFileNames.push_back(files[i].toStdString());
+ }
+
+ //associate the secondary sequence (US) to the main one
+ AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvMainWindow::SelectFusionSequenceCorrespondances() {
-
+void vvMainWindow::SelectFusionSequenceCorrespondances()
+{
//make sure the index is right?
//in the end, I should attach the temporal data to the right sequence!
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
bool signalOK = true;
unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
-std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
+ std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
std::vector<unsigned> temporalCorrespondances;
if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
for (unsigned i=0 ; i<tmpVect.size() ; i++) {
}
else { //first part of the file -> index in secondary seq.
if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
- else { signalOK=false; break; } //pointing outside the secondary sequence...
- }
+ else { signalOK=false; break; } //pointing outside the secondary sequence...
+ }
}
}
else {signalOK=false;}
//when this function is called index is the slicer manager index corresponding to the main sequence (CT)
//the files behind fileNames points to the data for the secondary sequence
void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
-{
+{
QString file(fileNames[0].c_str());
if (QFile::exists(file))
{
item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
qApp->processEvents();
+#if VTK_MAJOR_VERSION > 5
+ for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
+ mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
+#endif
for (int j = 1; j <= 4; j++) {
item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
}
//------------------------------------------------------------------------------
//fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
- if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
+ if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
//check if the focus moved to the linked sequence, and in this case, select the master sequence instead
if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
}
int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
if (secondaryIndex==-1) return; //this should never happen
- if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
- (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
+ if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
+ (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
{return;} //this should never happen, raise an exception?
if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
//and set it!
mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
- //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
+ //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
}
//------------------------------------------------------------------------------
void vvMainWindow::SaveAs()
-{
+{
if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
return;
//------------------------------------------------------------------------------
void vvMainWindow::SaveCurrentState()
-{
+{
QString Extensions = "XML Files(*.xml)";
QString fileName = QFileDialog::getSaveFileName(this,
tr("Save Current Window State"),
//------------------------------------------------------------------------------
void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
-{
+{
vvSaveState save_state;
save_state.Run(this, stateFile);
}
//------------------------------------------------------------------------------
void vvMainWindow::ReadSavedState()
-{
+{
QString Extensions = "XML Files(*.xml)";
QString fileName = QFileDialog::getOpenFileName(this,
tr("Load Window State"),
//------------------------------------------------------------------------------
void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
-{
+{
vvReadState read_state;
read_state.Run(this, stateFile);
}
//------------------------------------------------------------------------------
void vvMainWindow::LinkAllImages()
-{
+{
linkPanel->linkAll();
}
//------------------------------------------------------------------------------
void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
-{
+{
if (!fromPanel) {
// delegate to linkPanel if call came from elsewhere...
linkPanel->addLinkFromIds(image1, image2);
//------------------------------------------------------------------------------
void vvMainWindow::RemoveLink(QString image1,QString image2)
-{
+{
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
mSlicerManagers[i]->RemoveLink(image2.toStdString());
//------------------------------------------------------------------------------
void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
-{
+{
if(mSlicerManagers.size()==1)
return;
}
//------------------------------------------------------------------------------
void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
-{
+{
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
//i is the SlicerManager that is in charge of this slicer.
if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
//if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
- if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
- overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
+ if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
+ overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
}
else { //if this is the primary sequence that has been modified
- if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
+ if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
//WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
int estimatedValue=0;
//estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
- estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
+ estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
//TODO: at the moment, there is a loop in TSlice modifications
//modifying sequence 1 causes seq 2 to update, which in turns update seq1...
//I disable control on seq1 at the moment.
//------------------------------------------------------------------------------
void vvMainWindow::NOHorizontalSliderMoved()
-{
+{
// if (mCurrentTime == NOHorizontalSlider->value()) return;
HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
// mCurrentTime = NOHorizontalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::NEHorizontalSliderMoved()
-{
+{
// if (mCurrentTime == NEHorizontalSlider->value()) return;
HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
// mCurrentTime = NEHorizontalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::SOHorizontalSliderMoved()
-{
+{
// if (mCurrentTime == SOHorizontalSlider->value()) return;
HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
// mCurrentTime = SOHorizontalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::SEHorizontalSliderMoved()
-{
+{
// if (mCurrentTime == SEHorizontalSlider->value()) return;
HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
// mCurrentTime = SEHorizontalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::NOVerticalSliderChanged()
-{
+{
static int value=-1;
if (value == NOVerticalSlider->value()) return;
else value = NOVerticalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::NEVerticalSliderChanged()
-{
+{
static int value=-1;
if (value == NEVerticalSlider->value()) return;
else value = NEVerticalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::SOVerticalSliderChanged()
-{
+{
static int value=-1;
if (value == SOVerticalSlider->value()) return;
else value = SOVerticalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::SEVerticalSliderChanged()
-{
+{
static int value=-1;
if (value == SEVerticalSlider->value()) return;
else value = SEVerticalSlider->value();
//------------------------------------------------------------------------------
void vvMainWindow::UpdateSlice(int slicer, int slice)
-{
+{
// DD("vvMainWindow::UpdateSlice");
// DD(slicer);
// DD(slice);
//------------------------------------------------------------------------------
void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
-{
+{
//FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
bool doUpdate=false;
if (code==-1) doUpdate=true;
//------------------------------------------------------------------------------
void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
-{
+{
//int position = int((min+max)/2);
int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
if (slicer == 0) {
//------------------------------------------------------------------------------
void vvMainWindow::SaveNOScreenshot()
-{
+{
SaveScreenshot(NOViewWidget);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::SaveNEScreenshot()
-{
+{
SaveScreenshot(NEViewWidget);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::SaveSOScreenshot()
-{
+{
SaveScreenshot(SOViewWidget);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::SaveSEScreenshot()
-{
+{
SaveScreenshot(SEViewWidget);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvMainWindow::SaveScreenshotAllSlices()
-{
+{
QVTKWidget *widget = NOViewWidget;
int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
// Change the slice
slicer->SetSlice(i); // -> change the slice of the current slicer
SM->UpdateSlice(0); // --> this one emit UpdateSlice
- QCoreApplication::flush(); // -> needed to force display of contours
+ QCoreApplication::flush(); // -> needed to force display of contours
- // Screenshot
+ // Screenshot
vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
windowToImageFilter->SetInput(renderWindow);
windowToImageFilter->SetMagnification(1);
if (i<100) num = "0"+num;
if (i<1000) num = "0"+num;
- fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
+ fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
+ "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
writer->SetFileName(fn.c_str());
+#if VTK_MAJOR_VERSION <= 5
writer->SetInput(windowToImageFilter->GetOutput());
+#else
+ writer->SetInputConnection(windowToImageFilter->GetOutputPort());
+#endif
writer->Write();
}
}
//------------------------------------------------------------------------------
void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
-{
+{
QString Extensions = "Images( *.png);;";
Extensions += "Images( *.jpg);;";
Extensions += "Images( *.bmp);;";
// Snapshot image if not null
if(imgwriter!=NULL) {
+#if VTK_MAJOR_VERSION <= 5
imgwriter->SetInput(image);
+#else
+ imgwriter->SetInputConnection(w2i->GetOutputPort());
+#endif
imgwriter->SetFileName(fileName.toStdString().c_str());
imgwriter->Write();
return;
// FPS
bool ok;
- int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
+ int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
tr("FPS:"), 5, 0, 1000, 1, &ok);
if(ok)
gif->SetRate(fps);
// Loops
- int loops = QInputDialog::getInteger(this, tr("Loops"),
+ int loops = QInputDialog::getInt(this, tr("Loops"),
tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
if(ok)
gif->SetLoops(loops);
vidwriter = mpg;
mpg->SetQuality(2);
bool ok;
- int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
+ int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
tr("FPS:"), 5, 0, 1024, 1, &ok);
if(!ok)
fps = 5;
vidwriter = mpg;
mpg->SetQuality(2);
bool ok;
- int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
+ int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
tr("FPS:"), 5, 0, 1024, 1, &ok);
if(!ok)
fps = 5;
// Take video if not null
if(vidwriter!=NULL){
+#if VTK_MAJOR_VERSION <= 5
vidwriter->SetInput(image);
+#else
+ vidwriter->SetInputConnection(w2i->GetOutputPort());
+#endif
vidwriter->SetFileName(fileName.toStdString().c_str());
vidwriter->Start();
int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
w2i->SetInput(widget->GetRenderWindow());
w2i->Update();
+#if VTK_MAJOR_VERSION <= 5
vidwriter->SetInput(w2i->GetOutput());
+#else
+ vidwriter->SetInputConnection(w2i->GetOutputPort());
+#endif
vidwriter->Write();
}
vidwriter->End();
//------------------------------------------------------------------------------
void vvMainWindow::GoToCursor()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
for (int column = 1; column < 5; column++) {
if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
//------------------------------------------------------------------------------
void vvMainWindow::GoToLandmark()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
for (int column = 1; column < 5; column++) {
if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
//------------------------------------------------------------------------------
void vvMainWindow::PlayPause()
-{
+{
if (playMode) {
playMode = 0;
playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
//------------------------------------------------------------------------------
void vvMainWindow::PlayNext()
-{
+{
if (playMode && !this->isHidden()) {
int image_number=DataTree->topLevelItemCount();
///Only play one slicer per SM, and only if the SM is being displayed
//------------------------------------------------------------------------------
void vvMainWindow::ShowLastImage()
-{
+{
if (mSlicerManagers.size() > 1) {
QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
+ //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
DisplayChanged(item,1);
}
}
//------------------------------------------------------------------------------
void vvMainWindow::UpdateRenderWindows()
-{
+{
for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
- mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
- mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
- mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
- mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
+ for (unsigned int j = 0; j < 4; ++j) {
+ mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
+ mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
+ }
}
if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
//------------------------------------------------------------------------------
void vvMainWindow::SegmentationOnCurrentImage()
-{
+{
int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
vvSegmentationDialog segmentation;
//------------------------------------------------------------------------------
void vvMainWindow::SurfaceViewerLaunch()
-{
+{
vvSurfaceViewerDialog surfaceViewer;
surfaceViewer.exec();
}
//------------------------------------------------------------------------------
int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
-{
+{
int number=0;
for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
vvSlicerManager * v = mSlicerManagers[l];
//------------------------------------------------------------------------------
vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
-{
+{
// Change filename if another image exist with the same name
int number = GetImageDuplicateFilenameNumber(filename);
connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
+
+ InitSlicers();
UpdateTree();
qApp->processEvents();
- InitSlicers();
- ShowLastImage();
InitDisplay();
+ ShowLastImage();
qApp->processEvents();
-
// End
ImageInfoChanged();
return slicer_manager;
//------------------------------------------------------------------------------
void vvMainWindow::UpdateCurrentSlicer()
-{
+{
int index = -1;
if (DataTree->selectedItems().size() > 0) {
index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
mSlicerManagerCurrentIndex = index;
}
//------------------------------------------------------------------------------
-
void LoadImages(std::vector<std::string> filenames, vvImageReader::LoadedImageType type);
vvSlicerManager * AddImage(vvImage::Pointer image,std::string filename);
void AddField(QString file,int index);
+ bool CheckAddedImage(int index, QString imageType);
void AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type);
void AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type);
void AddROI(int index, QString filename);
#include <itksys/SystemTools.hxx>
// vtk
+#include <vtkVersion.h>
#include <vtkSmartPointer.h>
#include <vtkFloatArray.h>
#include <vtkPointData.h>
double *bounds=mesh->GetBounds();
vtkSmartPointer<vtkImageData> binary_image=vtkSmartPointer<vtkImageData>::New();
+#if VTK_MAJOR_VERSION <= 5
binary_image->SetScalarTypeToUnsignedChar();
+#endif
///Use the smallest mask in which the mesh fits
// Add two voxels on each side to make sure the mesh fits
double * samp_origin=sample->GetOrigin();
binary_image->SetExtent(0,ceil((bounds[1]-origin[0])/spacing[0]+4),
0,ceil((bounds[3]-origin[1])/spacing[1]+4),
0,ceil((bounds[5]-origin[2])/spacing[2])+4);
+#if VTK_MAJOR_VERSION <= 5
binary_image->AllocateScalars();
+#else
+ binary_image->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+#endif
memset(binary_image->GetScalarPointer(),0,binary_image->GetDimensions()[0]*binary_image->GetDimensions()[1]*binary_image->GetDimensions()[2]*sizeof(unsigned char));
if (extrude) {
vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
+#if VTK_MAJOR_VERSION <= 5
extrude->SetInput(mesh);
+#else
+ extrude->SetInputData(mesh);
+#endif
///We extrude in the -slice_spacing direction to respect the FOCAL convention
extrude->SetVector(0, 0, -slice_spacing);
+#if VTK_MAJOR_VERSION <= 5
sts->SetInput(extrude->GetOutput());
- } else
+#else
+ sts->SetInputConnection(extrude->GetOutputPort());
+#endif
+ } else {
+#if VTK_MAJOR_VERSION <= 5
sts->SetInput(mesh);
+#else
+ sts->SetInputData(mesh);
+#endif
+ }
vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
+#if VTK_MAJOR_VERSION <= 5
stencil->SetStencil(sts->GetOutput());
stencil->SetInput(binary_image);
+#else
+ stencil->SetStencilConnection(sts->GetOutputPort());
+ stencil->SetInputData(binary_image);
+#endif
stencil->Update();
this->AddMask(stencil->GetOutput());
this->RemoveMeshes();
for (std::vector<vtkImageData*>::iterator i=masks.begin(); i!=masks.end(); i++) {
vtkSmartPointer<vtkMarchingCubes> marching = vtkSmartPointer<vtkMarchingCubes>::New();
+#if VTK_MAJOR_VERSION <= 5
marching->SetInput(*i);
+#else
+ marching->SetInputData(*i);
+#endif
marching->SetValue(0,0.5);
marching->Update();
this->AddMesh(marching->GetOutput());
===========================================================================**/
#include "vvMeshActor.h"
#include "clitkCommon.h"
+#include <vtkVersion.h>
#include <vtkPolyDataMapper.h>
#include <vtkMarchingSquares.h>
#include <vtkImageData.h>
mMarching=vtkMarchingSquares::New();
mTimeSlice=time_slice;
- if (static_cast<unsigned int>(time_slice)<mMesh->GetNumberOfMeshes())
+ if (static_cast<unsigned int>(time_slice)<mMesh->GetNumberOfMeshes()) {
+#if VTK_MAJOR_VERSION <= 5
mMarching->SetInput(mMesh->GetMask(time_slice));
- else
+#else
+ mMarching->SetInputData(mMesh->GetMask(time_slice));
+#endif
+ } else {
+#if VTK_MAJOR_VERSION <= 5
mMarching->SetInput(mMesh->GetMask(0));
+#else
+ mMarching->SetInputData(mMesh->GetMask(0));
+#endif
+ }
mMarching->SetValue(0,0.5);
//mMarching->Update();
mMapper=vtkPolyDataMapper::New();
+#if VTK_MAJOR_VERSION <= 5
mMapper->SetInput(mMarching->GetOutput());
+#else
+ mMapper->SetInputConnection(mMarching->GetOutputPort());
+#endif
//The following line allows to display the contour over the image
//(http://www.nabble.com/What-happens-when-two-actors-are-at-the-same-depth--td23175458.html)
vtkMapper::SetResolveCoincidentTopologyToPolygonOffset();
mActor->GetProperty()->EdgeVisibilityOn();
mActor->GetProperty()->SetEdgeColor(mMesh->r,mMesh->g,mMesh->b);
mActor->GetProperty()->SetLineWidth(2.);
+ mActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
}
void vvMeshActor::SetCutSlice(double slice)
void vvMeshActor::SetTimeSlice(int time)
{
mTimeSlice=time;
- if (static_cast<unsigned int>(time)<mMesh->GetNumberOfMasks())
+ if (static_cast<unsigned int>(time)<mMesh->GetNumberOfMasks()) {
+#if VTK_MAJOR_VERSION <= 5
mMarching->SetInput(mMesh->GetMask(time));
- else
+#else
+ mMarching->SetInputData(mMesh->GetMask(time));
+#endif
+ } else {
+#if VTK_MAJOR_VERSION <= 5
mMarching->SetInput(mMesh->GetMask(0));
+#else
+ mMarching->SetInputData(mMesh->GetMask(0));
+#endif
+ }
SetCutSlice(mCutSlice); //We need to find the new mask cut slice,
//since masks do not all have the same origin
}
#endif
// vtk
+#include <vtkVersion.h>
#include <vtkSmartPointer.h>
#include <vtkAppendPolyData.h>
#include <vtkCellArray.h>
{
std::vector<vvMesh::Pointer> result;
#if GDCM_MAJOR_VERSION == 2
-
-#if CLITK_USE_SYSTEM_GDCM == 0
-
- clitkExceptionMacro("ERROR ! You need to compile vv with itk4 + system_gdcm to use this function");
-
-#endif
-
gdcm::Reader reader;
reader.SetFileName(filename.c_str());
reader.Read();
ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
contour->GetLines()->InsertNextCell(2, ids);
}
+#if VTK_MAJOR_VERSION <= 5
append->AddInput(contour);
+#else
+ append->AddInputData(contour);
+#endif
}
else
if (contour_type == "POINT ")
typename FilterType::Pointer warp_filter = FilterType::New();
warp_filter->SetInput(input);
-#if ITK_VERSION_MAJOR >= 4
warp_filter->SetDisplacementField(resampler->GetOutput());
-#else
- warp_filter->SetDeformationField(resampler->GetOutput());
-#endif
warp_filter->SetOutputSpacing(input->GetSpacing());
warp_filter->SetOutputOrigin(input->GetOrigin());
warp_filter->SetOutputSize(input->GetLargestPossibleRegion().GetSize());
// Average
VFPixelType vector;
- VFPixelType zeroVector=itk::NumericTraits<VFPixelType>::Zero;
+ VFPixelType zeroVector;//=itk::NumericTraits<VFPixelType>::Zero;
+ for(unsigned int i=0;i <VFPixelType::Dimension; i++) zeroVector[i] = 0.0;
while (!(iterators[0]).IsAtEnd()) {
vector=zeroVector;
p_bar.setValue(progress);
p_bar.show();
}
-
--- /dev/null
+#ifndef _OSX_HELPER_
+#define _OSX_HELPER_
+
+// For retina displays, see
+// http://public.kitware.com/pipermail/vtkusers/2015-February/090117.html
+void disableGLHiDPI( long a_id );
+
+#endif
+
--- /dev/null
+#include <Cocoa/Cocoa.h>
+#include "vvOSXHelper.h"
+
+// For retina displays, see
+// http://public.kitware.com/pipermail/vtkusers/2015-February/090117.html
+void disableGLHiDPI( long a_id ){
+ NSView *view = reinterpret_cast<NSView*>( a_id );
+ [view setWantsBestResolutionOpenGLSurface:NO];
+}
+
if (disableFusionSignals)
return;
- fusionOpacitySpin->setValue(opacityHorizontalSlider->value());
+ fusionOpacitySpin->setValue(opacityHorizontalSlider->value());
fusionThresSpin->setValue(thresOpacityHorizontalSlider->value());
emit FusionPropertyUpdated(opacityHorizontalSlider->value(), thresOpacityHorizontalSlider->value(), fusionColorMapComboBox->currentIndex(),
void vvDicomSeriesSelector::BrowseButtonRelease()
{
QFileDialog dialog(this);
+ QStringList filters;
+ filters << "DICOM files (*.dcm)"
+ << "All files (*)";
dialog.setFileMode(QFileDialog::AnyFile);
- dialog.setFilter("DICOM files (*.dcm); All files (*)");
+ dialog.setNameFilters(filters);
+ //dialog.setFilter(tr("DICOM files (*.dcm); All files (*)"));
mFoldername = dialog.getExistingDirectory(this,
"Select a folder to find DICOM image",
mPreviousPath);
//gdcm::Tag tagsdc(8,1030);
//keys.push_back(std::make_pair(tagsdc, ""));
- //// Accession n°
+ //// Accession
//gdcm::Tag tagacc(8,50);
//keys.push_back(std::make_pair(tagacc, ""));
dirpath.mkdir(path);
}
bool didItWork = gdcm::CompositeNetworkFunctions::CMove(m_adress.c_str(),atoi(m_port.c_str()),
- gdcm::CompositeNetworkFunctions::ConstructQuery(mQFactory.getMoveQuery().theRoot, mQFactory.getMoveQuery().theLevel ,mQFactory.getMoveQuery().keys,true),
+ gdcm::CompositeNetworkFunctions::ConstructQuery(mQFactory.getMoveQuery().theRoot, mQFactory.getMoveQuery().theLevel ,mQFactory.getMoveQuery().keys, gdcm::eMove),
getDicomClientPort(), getDicomClientAETitle().c_str(), m_aetitle.c_str(), path.toStdString().c_str() );
gdcm::Directory theDir;
theDir.Load(path.toStdString().c_str());
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails(true);
- //ds gérer recursive moi-meme pour progress ...
+ //ds gerer recursive moi-meme pour progress ...
nameGenerator->SetInputDirectory(path.toStdString());
// insert in table
//------------------------------------------------------------------------------
vvROIActor::vvROIActor()
-{
+{
mIsVisible = true;
mIsContourVisible = false;
mOpacity = 0.5;
//------------------------------------------------------------------------------
vvROIActor::~vvROIActor()
-{
+{
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvROIActor::RemoveActors()
-{
+{
for(unsigned int i= 0; i<mOverlayActors.size(); i++) {
mOverlayActors[i]->RemoveActors();
}
}
Update(true);
- mImageContour.clear();
- mOverlayActors.clear();
+ //mImageContour.clear();
+ //mOverlayActors.clear();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvROIActor::SetROI(clitk::DicomRT_ROI * s)
-{
+{
mROI = s;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvROIActor::SetContourWidth(int n) {
+void vvROIActor::SetContourWidth(int n)
+{
mContourWidth = n;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvROIActor::SetSlicerManager(vvSlicerManager * s) {
+void vvROIActor::SetSlicerManager(vvSlicerManager * s)
+{
mSlicerManager = s;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvROIActor::UpdateImage()
-{
+{
mOverlayActors.clear();
mImageContour.clear();
Initialize(mDepth, mIsVisible);
//------------------------------------------------------------------------------
void vvROIActor::SetVisible(bool b)
-{
+{
mIsVisible = b;
if (!b) { // remove actor
for(unsigned int i= 0; i<mOverlayActors.size(); i++)
for(unsigned int i= 0; i<mOverlayActors.size(); i++)
mOverlayActors[i]->ShowActors();
}
- Update(); // No Render
+ //Update(); // No Render
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvROIActor::SetContourVisible(bool b) {
+void vvROIActor::SetContourVisible(bool b)
+{
mIsContourVisible = b;
if (!b) { // remove actor
for(unsigned int i= 0; i<mImageContour.size(); i++) {
mImageContour[i]->ShowActors();
}
}
- Update(); // No Render
+ //Update(); // No Render
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-bool vvROIActor::IsVisible() {
+bool vvROIActor::IsVisible()
+{
return mIsVisible;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-bool vvROIActor::IsContourVisible() {
+bool vvROIActor::IsContourVisible()
+{
return mIsContourVisible;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvROIActor::Initialize(double depth, bool IsVisible) {
+void vvROIActor::Initialize(double depth, bool IsVisible)
+{
if (mROI->GetImage()) {
mImageContour.clear();
mOverlayActors.clear();
mImageContour[i]->SetLineWidth(mContourWidth);
mImageContour[i]->SetPreserveMemoryModeEnabled(true);
mImageContour[i]->SetDepth(mDepth+0.5);
- mImageContour[i]->HideActors();
+ mImageContour[i]->ShowActors();
mOverlayActors.push_back(vvBinaryImageOverlayActor::New());
mOverlayActors[i]->Initialize(IsVisible);
mOverlayActors[i]->SetDepth(mDepth);
}
-
connect(mSlicerManager,SIGNAL(UpdateSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
- //connect(mSlicerManager,SIGNAL(UpdateTSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
+ connect(mSlicerManager,SIGNAL(UpdateTSlice(int,int,int)),this,SLOT(UpdateSlice(int, int, int)));
connect(mSlicerManager, SIGNAL(AVerticalSliderHasChanged(int, int)), SLOT(UpdateSlice(int, int)));
}
}
//------------------------------------------------------------------------------
void vvROIActor::SetDepth(double d)
-{
+{
mDepth = d;
if (!mSlicerManager) return;
for(int i=0; i<mSlicerManager->GetNumberOfSlicers(); i++) {
//------------------------------------------------------------------------------
void vvROIActor::Update(bool force)
-{
+{
if (!mSlicerManager) return;
for(int i=0; i<mSlicerManager->GetNumberOfSlicers(); i++) {
UpdateSlice(i, mSlicerManager->GetSlicer(i)->GetSlice(), force);
//------------------------------------------------------------------------------
-void vvROIActor::UpdateSlice(int slicer, int slices, bool force)
-{
+void vvROIActor::UpdateSlice(int slicer, int slices, int force)
+{
if (!mROI->GetImage()) return;
if ((!mIsVisible) && (!mIsContourVisible)) return;
if (!mSlicerManager) {
}
// Refresh overlays
- mOverlayActors[slicer]->UpdateSlice(slicer, slices, force);
+ if (mIsVisible) {
+ mOverlayActors[slicer]->UpdateSlice(slicer, slices, force);
+ }
+ //mSlicerManager->GetSlicer(slicer)->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvROIActor::SetOpacity(double d)
-{
+{
mOpacity = d;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvROIActor::SetContourColor(double r, double v, double b) {
+void vvROIActor::SetContourColor(double r, double v, double b)
+{
mContourColor[0] = r;
mContourColor[1] = v;
mContourColor[2] = b;
//------------------------------------------------------------------------------
-void vvROIActor::SetOverlayColor(double r, double v, double b) {
+void vvROIActor::SetOverlayColor(double r, double v, double b)
+{
if (mROI)
mROI->SetDisplayColor(r,v,b);
}
//------------------------------------------------------------------------------
-std::vector<double> & vvROIActor::GetContourColor() {
+std::vector<double> & vvROIActor::GetContourColor()
+{
return mContourColor;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-std::vector<double> & vvROIActor::GetOverlayColor() {
+std::vector<double> & vvROIActor::GetOverlayColor()
+{
return mROI->GetDisplayColor();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvROIActor::UpdateColor() {
+void vvROIActor::UpdateColor()
+{
for(unsigned int i=0; i<mOverlayActors.size(); i++) {
mOverlayActors[i]->SetOpacity(mOpacity);
mOverlayActors[i]->SetColor(mROI->GetDisplayColor()[0],
//------------------------------------------------------------------------------
double vvROIActor::GetOpacity()
-{
+{
return mOpacity;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvROIActor::SetSelected(bool b)
-{
+{
mIsSelected = b;
if (b) {
for(int i=0; i<mSlicerManager->GetNumberOfSlicers(); i++) {
//------------------------------------------------------------------------------
void vvROIActor::CopyParameters(QSharedPointer<vvROIActor> roi)
-{
+{
// Overlay
SetVisible(roi->IsVisible());
SetOpacity(roi->GetOpacity());
void RemoveActors();
public slots:
- void UpdateSlice(int slicer, int slices, bool force=false);
+ void UpdateSlice(int slicer, int slices, int force=0);
void UpdateColor();
void UpdateImage();
#include "vvRegisterForm.h"
#include <QNetworkRequest>
#include <QDir>
+#if QT_VERSION >= 0x050000
+#include <QUrlQuery>
+#endif
#include <QPalette>
#include "clitkConfiguration.h"
#include "vvConfiguration.h"
void vvRegisterForm::sendData(){
QUrl url2(url);
+
+#if QT_VERSION < 0x050000
url2.addQueryItem("name", firstName->text().toUtf8());
url2.addQueryItem("lastName", lastName->text().toUtf8());
url2.addQueryItem("email", email->text().toUtf8());
url2.addQueryItem("architecture", ARCHITECTURE);
url2.addQueryItem("adressing", QString::number(sizeof(char*)*8)+"-bit");
url2.addQueryItem("compilationDate", QString(__DATE__) + ", " + QString(__TIME__) );
-
+#else
+ QUrlQuery url2Query;
+
+ url2Query.addQueryItem("name", firstName->text().toUtf8());
+ url2Query.addQueryItem("lastName", lastName->text().toUtf8());
+ url2Query.addQueryItem("email", email->text().toUtf8());
+ url2Query.addQueryItem("group", group->text().toUtf8());
+ url2Query.addQueryItem("os", OS_NAME);
+ url2Query.addQueryItem("vvVersion", VV_VERSION);
+ url2Query.addQueryItem("architecture", ARCHITECTURE);
+ url2Query.addQueryItem("adressing", QString::number(sizeof(char*)*8)+"-bit");
+ url2Query.addQueryItem("compilationDate", QString(__DATE__) + ", " + QString(__TIME__) );
+ url2.setQuery(url2Query);
+#endif
+
manager->get(QNetworkRequest(url2));
}
void vvRegisterForm::accept(){
#include "vvInteractorStyleNavigator.h"
#include "vvSlicer.h"
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
#include "vtkMarchingCubes.h"
#include "vtkMarchingSquares.h"
#include "vtkImageClip.h"
#include <vtkPolyDataWriter.h>
#include <QMessageBox>
+#include <QFileDialog>
+
+#ifdef Q_OS_OSX
+# include "vvOSXHelper.h"
+#endif
//====================================================================
vvSegmentationDialog::vvSegmentationDialog(QWidget * parent, Qt::WindowFlags f)
erodeButton->setEnabled(0);
dilateButton->setEnabled(0);
infoLabel->setText("Select Up and Down threshold before clicking binarise !");
+
+#ifdef Q_OS_OSX
+ disableGLHiDPI(viewWidget->winId());
+#endif
}
vvSegmentationDialog::~vvSegmentationDialog()
clipping1Slider->setValue(range[0]);
clipping2Slider->setValue(range[1]);
+#if VTK_MAJOR_VERSION <= 5
mClipper->SetInput(mManager->GetSlicer(0)->GetInput());
+#else
+ mClipper->SetInputData(mManager->GetSlicer(0)->GetInput());
+#endif
mSquares1->SetValue(0,clipping1Slider->value());
mSquares2->SetValue(0,clipping2Slider->value());
+
+#if VTK_MAJOR_VERSION <= 5
mSquares1->SetInput(mClipper->GetOutput());
mSquares2->SetInput(mClipper->GetOutput());
mSquaresMapper1->SetInput(mSquares1->GetOutput());
mSquaresMapper2->SetInput(mSquares2->GetOutput());
+#else
+ mSquares1->SetInputData(mClipper->GetOutput());
+ mSquares2->SetInputData(mClipper->GetOutput());
+
+ mSquaresMapper1->SetInputData(mSquares1->GetOutput());
+ mSquaresMapper2->SetInputData(mSquares2->GetOutput());
+#endif
mSquaresMapper1->ScalarVisibilityOff();
mSquaresMapper2->ScalarVisibilityOff();
{
int slice = mManager->GetSlicer(0)->GetSlice();
int tslice = mManager->GetSlicer(0)->GetTSlice();
+#if VTK_MAJOR_VERSION <= 5
mClipper->SetInput(mManager->GetSlicer(0)->GetInput());
+#else
+ mClipper->SetInputData(mManager->GetSlicer(0)->GetInput());
+#endif
int* extent = mManager->GetSlicer(0)->GetImageActor()->GetDisplayExtent();
mClipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],extent[3],extent[4],extent[5]);
int i;
for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
int ext[6];
+#if VTK_MAJOR_VERSION <= 5
image->GetWholeExtent(ext);
+#else
+ image->GetExtent(ext);
+#endif
void *in1Ptr;
in1Ptr = image->GetScalarPointerForExtent(ext);
outputImage->SetExtent(ext);
outputImage->SetOrigin(image->GetOrigin());
outputImage->SetSpacing(image->GetSpacing());
+#if VTK_MAJOR_VERSION <= 5
outputImage->SetScalarTypeToUnsignedChar();
+#else
+ outputImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+#endif
outputImage->CopyAndCastFrom(image,ext);
+#if VTK_MAJOR_VERSION <= 5
outputImage->Update();
+#else
+ //outputImage->Update();
+#endif
image->DeepCopy(outputImage);
+#if VTK_MAJOR_VERSION <= 5
image->UpdateInformation();
image->PropagateUpdateExtent();
+#else
+ //image->UpdateInformation();
+ //image->PropagateUpdateExtent();
+#endif
vtkImageData* imageBin = vtkImageData::New();
imageBin->DeepCopy(image);
+#if VTK_MAJOR_VERSION <= 5
imageBin->Update();
+#else
+ //imageBin->Update();
+#endif
mBinaireImages.push_back(imageBin);
}
erode->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
+#if VTK_MAJOR_VERSION <= 5
erode->SetInput(image);
erode->Update();
+#else
+ erode->SetInputData(image);
+ //erode->Update();
+#endif
image->DeepCopy(erode->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
image->Update();
+#else
+ //image->Update();
+#endif
}
erode->Delete();
dilateButton->setEnabled(1);
dilate->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
+#if VTK_MAJOR_VERSION <= 5
dilate->SetInput(image);
+#else
+ dilate->SetInputData(image);
+#endif
vtkImageData* mask = mBinaireImages[numImage];
+#if VTK_MAJOR_VERSION <= 5
And->SetInput1(dilate->GetOutput());
And->SetInput2(mask);
+#else
+ And->SetInput1Data(dilate->GetOutput());
+ And->SetInput2Data(mask);
+#endif
And->Update();
image->DeepCopy(And->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
image->Update();
+#else
+ //image->Update();
+#endif
}
And->Delete();
dilate->Delete();
for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
+#if VTK_MAJOR_VERSION <= 5
seed->SetInput(image);
+#else
+ seed->SetInputData(image);
+#endif
seed->Update();
image->DeepCopy(seed->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
image->Update();
+#else
+ //image->Update();
+#endif
}
seed->Delete();
m3DExtractor->SetValue(0,0.5);
for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++) {
vtkActor* actor = vtkActor::New();
+#if VTK_MAJOR_VERSION <= 5
m3DExtractor->SetInput(mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage]);
+#else
+ m3DExtractor->SetInputData(mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage]);
+#endif
m3DExtractor->Update();
vtkPolyDataMapper* mapper = vtkPolyDataMapper::New();
+#if VTK_MAJOR_VERSION <= 5
mapper->SetInput(m3DExtractor->GetOutput());
+#else
+ mapper->SetInputData(m3DExtractor->GetOutput());
+#endif
m3DMappers.push_back(mapper);
actor->SetMapper(mapper);
"Mesh Files (*.vtk *.vtp)");
if (!fileName.isEmpty()) {
vtkSmartPointer<vtkPolyDataWriter> w = vtkSmartPointer<vtkPolyDataWriter>::New();
+#if VTK_MAJOR_VERSION <= 5
w->SetInput(m3DExtractor->GetOutput());
+#else
+ w->SetInputData(m3DExtractor->GetOutput());
+#endif
w->SetFileName(fileName.toStdString().c_str());
w->Write();
}
#include "vvGlyphSource.h"
#include "vvGlyph2D.h"
+#include <vtkVersion.h>
+#include <vtkExtentTranslator.h>
+#include <vtkAlgorithm.h>
+#include <vtkExecutive.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
#include <vtkTextProperty.h>
#include <vtkTextActor.h>
#include <vtkTextSource.h>
#include <vtkImageAccumulate.h>
#include <vtkImageReslice.h>
#if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
+# include <vtkOpenGLImageSliceMapper.h>
# include <vtkImageMapper3D.h>
# include <vtkImageSliceMapper.h>
#endif
-vtkCxxRevisionMacro(vvSlicer, "DummyRevision");
vtkStandardNewMacro(vvSlicer);
static void copyExtent(int* in, int* to){
- for(int i=0; i<6; ++i) to[i]=in[i];
+ for(int i=0; i<6; ++i)
+ {
+ to[i]=in[i];
+ }
}
//------------------------------------------------------------------------------
vvSlicer::vvSlicer()
-{
+{
mFusionSequenceCode = -1;
this->UnInstallPipeline();
mImage = NULL;
mReducedExtent = new int[6];
+ mRegisterExtent = NULL;
mCurrentTSlice = 0;
mCurrentFusionTSlice = 0;
mCurrentOverlayTSlice = 0;
crossCursor->SetRadius(2);
pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
+#if VTK_MAJOR_VERSION <= 5
pdm->SetInput(crossCursor->GetOutput());
+#else
+ pdm->SetInputConnection(crossCursor->GetOutputPort(0));
+#endif
pdmA = vtkSmartPointer<vtkActor2D>::New();
pdmA->SetMapper(pdm);
//------------------------------------------------------------------------------
vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
-{
+{
return mOverlayMapper.GetPointer();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vvBlendImageActor* vvSlicer::GetOverlayActor()
-{
+{
return mOverlayActor.GetPointer();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vtkImageMapToColors* vvSlicer::GetFusionMapper()
-{
+{
return mFusionMapper.GetPointer();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vtkImageActor* vvSlicer::GetFusionActor()
-{
+{
return mFusionActor.GetPointer();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vtkActor* vvSlicer::GetVFActor()
-{
+{
return mVFActor.GetPointer();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vtkCornerAnnotation* vvSlicer::GetAnnotation()
-{
+{
return ca.GetPointer();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::EnableReducedExtent(bool b)
-{
+{
mUseReducedExtent = b;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::SetReducedExtent(int * ext)
-{
+{
copyExtent(ext, mReducedExtent);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
-{
+{
mSurfaceCutActors.push_back(new vvMeshActor());
if (propagate)
//------------------------------------------------------------------------------
void vvSlicer::ToggleContourSuperposition()
-{
+{
for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
i!=mSurfaceCutActors.end(); i++)
(*i)->ToggleSuperposition();
//------------------------------------------------------------------------------
void vvSlicer::SetCursorColor(int r,int g, int b)
-{
+{
pdmA->GetProperty()->SetColor(r,g,b);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::SetCursorVisibility(bool s)
-{
+{
pdmA->SetVisibility(s);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
bool vvSlicer::GetCursorVisibility()
-{
+{
return pdmA->GetVisibility();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::SetCornerAnnotationVisibility(bool s)
-{
+{
ca->SetVisibility(s);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
bool vvSlicer::GetCornerAnnotationVisibility()
-{
+{
return ca->GetVisibility();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
vvSlicer::~vvSlicer()
-{
+{
for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
i!=mSurfaceCutActors.end(); i++)
delete (*i);
//------------------------------------------------------------------------------
double* vvSlicer::GetCurrentPosition()
-{
+{
return mCurrentBeforeSlicingTransform;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
-{
+{
mCurrentBeforeSlicingTransform[0]=x;
mCurrentBeforeSlicingTransform[1]=y;
mCurrentBeforeSlicingTransform[2]=z;
//------------------------------------------------------------------------------
void vvSlicer::SetImage(vvImage::Pointer image)
-{
+{
if (image->GetVTKImages().size()) {
mImage = image;
mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
mConcatenatedTransform->Concatenate(mSlicingTransform);
mImageReslice->SetResliceTransform(mConcatenatedTransform);
+#if VTK_MAJOR_VERSION <= 5
mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
+#else
+ mImageReslice->SetInputData(0, mImage->GetFirstVTKImageData());
+#endif
mImageReslice->UpdateInformation();
+#if VTK_MAJOR_VERSION <= 5
this->Superclass::SetInput(mImageReslice->GetOutput());
+#else
+ this->Superclass::SetInputConnection(mImageReslice->GetOutputPort());
+#endif
int extent[6];
+#if VTK_MAJOR_VERSION <= 5
this->GetInput()->GetWholeExtent(extent);
+#else
+ int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
+ copyExtent(ext, extent);
+#endif
// Prevent crash when reload -> change slice if outside extent
if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
// Make sure that the required part image has been computed
extent[SliceOrientation*2] = Slice;
- extent[SliceOrientation*2+1] = Slice;
+ extent[SliceOrientation*2+1] = Slice;
+#if VTK_MAJOR_VERSION <= 5
mImageReslice->GetOutput()->SetUpdateExtent(extent);
mImageReslice->GetOutput()->Update();
+#else
+ //mImageReslice->SetUpdateExtent(extent);
+ mImageReslice->Update();
+#endif
this->UpdateDisplayExtent();
//------------------------------------------------------------------------------
void vvSlicer::SetOverlay(vvImage::Pointer overlay)
-{
+{
if (overlay->GetVTKImages().size()) {
mOverlay = overlay;
mOverlayVisibility = true;
mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
+#if VTK_MAJOR_VERSION <= 5
mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
mImageReslice->UpdateInformation();
+#else
+ mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
+#endif
+ mOverlayReslice->Update();
if (!mOverlayMapper)
mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
+#if VTK_MAJOR_VERSION <= 5
mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
+#else
+ mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
+#endif
if (!mOverlayActor) {
mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
+#if VTK_MAJOR_VERSION <= 5
mOverlayActor->SetInput(mOverlayMapper->GetOutput());
+#else
+ mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
+#endif
mOverlayActor->SetPickable(0);
mOverlayActor->SetVisibility(true);
mOverlayActor->SetOpacity(0.5);
//------------------------------------------------------------------------------
void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
-{
+{
mFusionSequenceCode = fusionSequenceCode;
if (fusion->GetVTKImages().size()) {
mFusion = fusion;
mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
+#if VTK_MAJOR_VERSION <= 5
mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
mFusionReslice->UpdateInformation();
+#else
+ mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
+#endif
+ mFusionReslice->Update();
if (!mFusionMapper)
mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
lut->SetSaturationRange(0, 0);
lut->Build();
mFusionMapper->SetLookupTable(lut);
+#if VTK_MAJOR_VERSION <= 5
mFusionMapper->SetInput(mFusionReslice->GetOutput());
-
+#else
+ mFusionMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
+#endif
+
if (!mFusionActor) {
mFusionActor = vtkSmartPointer<vtkImageActor>::New();
+#if VTK_MAJOR_VERSION <= 5
mFusionActor->SetInput(mFusionMapper->GetOutput());
+#else
+ mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
+#endif
mFusionActor->SetPickable(0);
mFusionActor->SetVisibility(true);
mFusionActor->SetOpacity(0.7);
#if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
mFusionActor->GetMapper()->BorderOn();
#endif
+
this->GetRenderer()->AddActor(mFusionActor);
}
//------------------------------------------------------------------------------
bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
-{
+{
bool vis = false;
if (actor_type == "image")
vis = mImageVisibility;
//------------------------------------------------------------------------------
void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
-{
+{
if (actor_type == "image")
mImageVisibility = vis;
else if (actor_type == "vector")
//------------------------------------------------------------------------------
void vvSlicer::SetVF(vvImage::Pointer vf)
-{
+{
if (vf->GetVTKImages().size()) {
mVF = vf;
mVFVisibility = true;
mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
}
+#if VTK_MAJOR_VERSION <= 5
mVOIFilter->SetInput(vf->GetFirstVTKImageData());
mAAFilter->SetInput(mVOIFilter->GetOutput());
+#else
+ mVOIFilter->SetInputData(vf->GetFirstVTKImageData());
+ mAAFilter->SetInputConnection(mVOIFilter->GetOutputPort());
+#endif
///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
// Glyph the gradient vector (with arrows)
if (!mGlyphFilter)
mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
+#if VTK_MAJOR_VERSION <= 5
mGlyphFilter->SetInput(mAAFilter->GetOutput());
mGlyphFilter->SetSource(mArrow->GetOutput());
+#else
+ mGlyphFilter->SetInputConnection(mAAFilter->GetOutputPort());
+ mGlyphFilter->SetSourceConnection(mArrow->GetOutputPort());
+#endif
mGlyphFilter->ScalingOn();
mGlyphFilter->SetScaleModeToScaleByVector();
mGlyphFilter->OrientOn();
if (!mVFMapper)
mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+#if VTK_MAJOR_VERSION <= 5
mVFMapper->SetInput(mGlyphFilter->GetOutput());
+#else
+ mVFMapper->SetInputConnection(mGlyphFilter->GetOutputPort());
+#endif
mVFMapper->ImmediateModeRenderingOn();
mVFMapper->SetLookupTable(mVFColorLUT);
//------------------------------------------------------------------------------
void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
-{
+{
mLandmarks = landmarks;
if (landmarks) {
mLandClipper->SetClipFunction(mClipBox);
mLandClipper->InsideOutOn();
- mLandClipper->SetInput(mLandmarks->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
+ mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
+ mLandmarkTransform->SetInput(mLandmarks->GetOutput());
+ mConcatenatedTransform->Identity();
+ mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
+ mConcatenatedTransform->Concatenate(mSlicingTransform);
+ mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
+ mLandClipper->SetInput(mLandmarkTransform->GetOutput());
mLandGlyph->SetSource(mCross->GetOutput());
mLandGlyph->SetInput(mLandClipper->GetOutput());
+#else
+ mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
+ mLandmarkTransform->SetInputData(mLandmarks->GetOutput());
+ mConcatenatedTransform->Identity();
+ mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
+ mConcatenatedTransform->Concatenate(mSlicingTransform);
+ mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
+ mLandClipper->SetInputConnection(mLandmarkTransform->GetOutputPort());
+
+ mLandGlyph->SetSourceConnection(mCross->GetOutputPort());
+ mLandGlyph->SetInputConnection(mLandClipper->GetOutputPort());
+#endif
//mLandGlyph->SetIndexModeToScalar();
//mLandGlyph->SetRange(0,1);
//mLandGlyph->ScalingOff();
//mLandMapper->ScalarVisibilityOff();
mLandActor->SetMapper(mLandMapper);
+ mLandActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
mLandActor->GetProperty()->SetColor(255,10,212);
mLandActor->SetPickable(0);
mLandActor->SetVisibility(true);
this->UpdateDisplayExtent();
- this->GetRenderer()->AddActor(mLandActor);
}
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
//FIXME: this function leaks memory, we should fix it someday :)
void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
-{
+{
if (actor_type == "vector") {
Renderer->RemoveActor(mVFActor);
mGlyphFilter=NULL;
//------------------------------------------------------------------------------
void vvSlicer::SetVFSubSampling(int sub)
-{
+{
if (mVOIFilter) {
mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
mSubSampling = sub;
//------------------------------------------------------------------------------
void vvSlicer::SetVFScale(int scale)
-{
+{
mScale = scale;
if (mArrow)
mArrow->SetScale(mScale);
//------------------------------------------------------------------------------
void vvSlicer::SetVFWidth(int width)
-{
+{
mVFWidth = width;
if (mVFActor)
mVFActor->GetProperty()->SetLineWidth(mVFWidth);
//------------------------------------------------------------------------------
void vvSlicer::SetVFLog(int log)
-{
+{
mVFLog = log;
if (mGlyphFilter) {
mGlyphFilter->SetUseLog(mVFLog);
//------------------------------------------------------------------------------
void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
-{
+{
if (!updateLinkedImages) {
mCurrentTSlice = t;
- mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
+#if VTK_MAJOR_VERSION <= 5
+ mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
+#else
+ mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
+#endif
// Update transform
mConcatenatedTransform->Identity();
mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
UpdateDisplayExtent();
return;
}
-
if (t < 0)
mCurrentTSlice = 0;
else if ((unsigned int)t >= mImage->GetVTKImages().size())
mConcatenatedTransform->Concatenate(mSlicingTransform);
// Update image data
- mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
+#if VTK_MAJOR_VERSION <= 5
+ mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
+#else
+ mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
+#endif
if (mVF && mVFActor->GetVisibility()) {
if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
+#if VTK_MAJOR_VERSION <= 5
mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
+#else
+ mVOIFilter->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
+#endif
}
//update the overlay
if (mOverlay && mOverlayActor->GetVisibility()) {
if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
mCurrentOverlayTSlice = t;
+#if VTK_MAJOR_VERSION <= 5
mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
-
+#else
+ mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
+#endif
// Update overlay transform
mConcatenatedOverlayTransform->Identity();
mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
if (mFusion->GetVTKImages().size() > (unsigned int)t) {
mCurrentFusionTSlice = t;
+#if VTK_MAJOR_VERSION <= 5
mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
+#else
+ mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
+#endif
// Update fusion transform
mConcatenatedFusionTransform->Identity();
//------------------------------------------------------------------------------
void vvSlicer::SetFusionSequenceTSlice(int t)
-{
+{
if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
if (mFusion->GetVTKImages().size() > (unsigned int)t) {
mCurrentFusionTSlice = t;
+#if VTK_MAJOR_VERSION <= 5
mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
+#else
+ mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
+#endif
// Update fusion transform
mConcatenatedFusionTransform->Identity();
mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
//------------------------------------------------------------------------------
int vvSlicer::GetTSlice()
-{
+{
return mCurrentTSlice;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
int vvSlicer::GetMaxCurrentTSlice()
-{
+{
int t = mCurrentTSlice;
if(mOverlay)
t = std::max(t, mCurrentOverlayTSlice);
//------------------------------------------------------------------------------
int vvSlicer::GetFusionTSlice()
-{
+{
return mCurrentFusionTSlice;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
int vvSlicer::GetOverlayTSlice()
-{
+{
return mCurrentOverlayTSlice;
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvSlicer::SetSliceOrientation(int orientation)
-{
+{
//if 2D image, force to watch in Axial View
int extent[6];
- this->GetInput()->GetWholeExtent(extent);
+#if VTK_MAJOR_VERSION <= 5
+ this->GetInput()->GetWholeExtent(extent);
+#else
+ int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
+ copyExtent(ext, extent);
+#endif
+
if (extent[5]-extent[4] <= 2)
orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
int *range = this->GetSliceRange();
if (range)
this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
- mFirstSetSliceOrientation = false;
+#if VTK_MAJOR_VERSION <= 5
+ mFirstSetSliceOrientation = false;
+#endif
}
else if (this->Renderer && this->GetInput()) {
double s = mCursor[orientation];
}
this->UpdateOrientation();
+
this->UpdateDisplayExtent();
-
+
+ if (mFirstSetSliceOrientation) {
+ mFirstSetSliceOrientation = false;
+ }
+
if (this->Renderer && this->GetInput()) {
double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
this->Renderer->ResetCamera();
// In other words, we change the grid of the reslice in the same way as the grid
// of the displayed image in the slicing direction.
void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
-{
+{
// Reset autocrop and update output information
reslice->SetOutputOriginToDefault();
reslice->SetOutputSpacingToDefault();
+#if VTK_MAJOR_VERSION <= 5
reslice->GetOutput()->UpdateInformation();
+#else
+ reslice->UpdateInformation();
+#endif
// Ge new origin / spacing
double origin[3];
reslice->SetOutputOrigin(origin);
reslice->SetOutputSpacing(spacing);
reslice->UpdateInformation();
+#if VTK_MAJOR_VERSION <= 5
reslice->GetOutput()->UpdateInformation();
+#endif
}
//------------------------------------------------------------------------------
//----------------------------------------------------------------------------
-int * vvSlicer::GetExtent(){
+int * vvSlicer::GetExtent()
+{
int *w_ext;
if (mUseReducedExtent) {
w_ext = mReducedExtent;
- } else w_ext = GetInput()->GetWholeExtent();
+ }
+ else {
+#if VTK_MAJOR_VERSION <= 5
+ w_ext = GetInput()->GetWholeExtent();
+#else
+ w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
+#endif
+ }
return w_ext;
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
int vvSlicer::GetOrientation()
-{
+{
return this->SliceOrientation;
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::UpdateDisplayExtent()
-{
+{
+ emit UpdateDisplayExtentBegin(mSlicerNumber);
vtkImageData *input = this->GetInput();
if (!input || !this->ImageActor) {
return;
}
+
+#if VTK_MAJOR_VERSION <= 5
input->UpdateInformation();
+#else
+ mRegisterExtent = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
+#endif
this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
// Local copy of extent
int w_ext[6];
+#if VTK_MAJOR_VERSION <= 5
int* ext = GetExtent();
+#else
+ int* ext = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
+#endif
copyExtent(ext, w_ext);
+ if (mUseReducedExtent) {
+ copyExtent(mReducedExtent, w_ext);
+ }
// Set slice value
+
w_ext[ this->SliceOrientation*2 ] = this->Slice;
w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
// Image actor
this->ImageActor->SetVisibility(mImageVisibility);
this->ImageActor->SetDisplayExtent(w_ext);
+
#if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
// Fix for bug #1882
dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
if (mOverlay && mOverlayVisibility) {
AdjustResliceToSliceOrientation(mOverlayReslice);
int overExtent[6];
+#if VTK_MAJOR_VERSION <= 5
this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
+#else
+ this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mOverlayReslice->GetOutput(), overExtent);
+ bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
+#endif
mOverlayActor->SetVisibility(!out);
mOverlayActor->SetDisplayExtent( overExtent );
#if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
if (mFusion && mFusionVisibility) {
AdjustResliceToSliceOrientation(mFusionReslice);
int fusExtent[6];
+#if VTK_MAJOR_VERSION <= 5
this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
+#else
+ this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mFusionReslice->GetOutput(), fusExtent);
+ bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
+#endif
mFusionActor->SetVisibility(!out);
mFusionActor->SetDisplayExtent( fusExtent );
#if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
}
else if(mFusion)
mFusionActor->SetVisibility(false);
-
// Vector field actor
double* camera = Renderer->GetActiveCamera()->GetPosition();
double* image_bounds = ImageActor->GetBounds();
if (mVF && mVFVisibility) {
int vfExtent[6];
+#if VTK_MAJOR_VERSION <= 5
mVF->GetVTKImages()[0]->UpdateInformation();
this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
+#else
+ mVOIFilter->Update();
+ this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mVF->GetVTKImages()[0], vfExtent);
+ bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
+#endif
mVFActor->SetVisibility(!out);
mVOIFilter->SetVOI(vfExtent);
int orientation[3] = {1,1,1};
orientation[this->SliceOrientation] = 0;
mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
- mVFMapper->Update();
-
position[this->SliceOrientation] += offset;
mVFActor->SetPosition(position);
+ mVFActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
+ mVFMapper->Update();
+
}
else if(mVF)
mVFActor->SetVisibility(false);
+
+
+ double boundsT [6];
+ for(unsigned int i=0; i<6; i++)
+ boundsT[i] = ImageActor->GetBounds()[i];
+ boundsT[ this->SliceOrientation*2 ] = ImageActor->GetBounds()[ this->SliceOrientation*2 ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
+ boundsT[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
+
// Landmarks actor
if (mLandActor) {
if (mClipBox) {
- double bounds [6];
- for(unsigned int i=0; i<6; i++)
- bounds[i] = ImageActor->GetBounds()[i];
- bounds[ this->SliceOrientation*2 ] = ImageActor->GetBounds()[ this->SliceOrientation*2 ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
- bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
- mClipBox->SetBounds(bounds);
- UpdateLandmarks();
+ RemoveLandmarks();
}
position[this->SliceOrientation] = offset;
cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
}
}
+
+ if (mLandActor) {
+ if (mClipBox) {
+ DisplayLandmarks();
+ }
+ }
+ }
+ emit UpdateDisplayExtentEnd(mSlicerNumber);
+}
+//----------------------------------------------------------------------------
+
+//----------------------------------------------------------------------------
+void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
+ vtkImageData *targetImage, int targetExtent[6])
+{
+ double dExtents[6];
+ double *origin, *spacing;
+ origin = sourceImage->Get(vtkDataObject::ORIGIN());
+ spacing = sourceImage->Get(vtkDataObject::SPACING());
+ for(unsigned int i=0; i<6; i++) {
+ // From source voxel coordinates to world coordinates
+ dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
+
+ // From world coordinates to floating point target voxel coordinates
+ dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
+
+ // Round to current slice or larger extent
+ if(i/2==this->GetOrientation())
+ targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
+ else if(i%2==1)
+ targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
+ else
+ targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
}
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
-{
+{
bool out = false;
int maxBound = 6;
//----------------------------------------------------------------------------
void vvSlicer::UpdateOrientation()
-{
+{
// Set the camera position
vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
if (cam) {
//----------------------------------------------------------------------------
void vvSlicer::SetOpacity(double s)
-{
+{
this->GetImageActor()->SetOpacity(s);
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
-{
+{
this->Superclass::SetRenderWindow(rw);
this->SetupInteractor(rw->GetInteractor());
ca->SetImageActor(this->GetImageActor());
ca->SetWindowLevel(this->GetWindowLevel());
- ca->SetText(2, "<slice>");
ca->SetText(3, "<window>\n<level>");
double bounds[6];
bounds[3] = max;
bounds[4] = -max;
bounds[5] = max;
-
crossCursor->SetModelBounds(bounds);
+
this->GetRenderer()->AddActor(pdmA);
this->GetRenderer()->AddActor(ca);
this->GetRenderer()->ResetCamera();
//----------------------------------------------------------------------------
void vvSlicer::ResetCamera()
-{
+{
this->GetRenderer()->ResetCamera();
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::SetDisplayMode(bool i)
-{
+{
this->GetRenderer()->SetDraw(i);
if (i) UpdateDisplayExtent();
}
//----------------------------------------------------------------------------
void vvSlicer::FlipHorizontalView()
-{
+{
vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
if (cam) {
double *position = cam->GetPosition();
//----------------------------------------------------------------------------
void vvSlicer::FlipVerticalView()
-{
+{
vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
if (cam) {
FlipHorizontalView();
//----------------------------------------------------------------------------
void vvSlicer::SetColorWindow(double window)
-{
+{
vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
if ( LUT ) {
double level = this->GetWindowLevel()->GetLevel();
//----------------------------------------------------------------------------
void vvSlicer::SetColorLevel(double level)
-{
+{
vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
if ( LUT ) {
double window = this->GetWindowLevel()->GetWindow();
//----------------------------------------------------------------------------
double vvSlicer::GetOverlayColorWindow()
-{
+{
if(mOverlayMapper)
return mOverlayMapper->GetWindow();
else
//----------------------------------------------------------------------------
double vvSlicer::GetOverlayColorLevel()
-{
+{
if(mOverlayMapper)
return mOverlayMapper->GetLevel();
else
//----------------------------------------------------------------------------
void vvSlicer::SetOverlayColorWindow(double window)
-{
- mOverlayMapper->SetWindow(window);
+{
+ if(mOverlayMapper)
+ mOverlayMapper->SetWindow(window);
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::SetOverlayColorLevel(double level)
-{
- mOverlayMapper->SetLevel(level);
+{
+ if(mOverlayMapper)
+ mOverlayMapper->SetLevel(level);
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
// Returns the min an the max value in a 20%x20% region around the mouse pointer
void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
-{
+{
//Get mouse pointer position in view coordinates
double corner1[3];
double corner2[3];
if(iLocalExtents[i*2 ]>iLocalExtents[i*2+1])
std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
+
+#if VTK_MAJOR_VERSION > 5
+ for(int j=0;j<2; j++) {
+ if(iLocalExtents[i*2+j]< mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i])
+ iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i];
+
+ if(iLocalExtents[i*2+j]> mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1])
+ iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1];
+ }
+#endif
}
vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
+#if VTK_MAJOR_VERSION <= 5
voiFilter->SetInput(image);
+#else
+ voiFilter->SetInputData(image);
+#endif
voiFilter->SetVOI(iLocalExtents);
voiFilter->Update();
if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
}
vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
+#if VTK_MAJOR_VERSION <= 5
accFilter->SetInput(voiFilter->GetOutput());
+#else
+ accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
+#endif
accFilter->Update();
min = *(accFilter->GetMin());
//----------------------------------------------------------------------------
double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
-{
+{
ix = lrint(X);
iy = lrint(Y);
iz = lrint(Z);
-
+#if VTK_MAJOR_VERSION <= 5
if (ix < image->GetWholeExtent()[0] ||
ix > image->GetWholeExtent()[1] ||
iy < image->GetWholeExtent()[2] ||
iz < image->GetWholeExtent()[4] ||
iz > image->GetWholeExtent()[5] )
return std::numeric_limits<double>::quiet_NaN();
-
image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
image->Update();
+#else
+ if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
+ ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
+ iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
+ iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
+ iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
+ iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
+ return std::numeric_limits<double>::quiet_NaN();
+ //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
+ //image->Update();
+#endif
+
return image->GetScalarComponentAsDouble(ix, iy, iz, component);
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::Render()
-{
+{
if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
legend->UseOpacityOn();
} else legend->SetVisibility(0);
if (ca->GetVisibility()) {
- std::stringstream worldPos;
+
+ std::stringstream worldPos(" ");
double pt[3];
mConcatenatedTransform->TransformPoint(mCurrent, pt);
double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
-
+#if VTK_MAJOR_VERSION <= 5
if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
<< mCurrentTSlice
<< std::endl;
}
+#else
+ if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
+ X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
+ Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
+ Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
+ Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
+ Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
+
+ int ix, iy, iz;
+ double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
+
+ if(ImageActor->GetVisibility())
+ worldPos << "data value : " << value << std::endl;
+
+ worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
+ << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
+ << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
+ << mCurrentTSlice
+ << std::endl;
+ worldPos << "pixel : " << ix << ' '
+ << iy << ' '
+ << iz << ' '
+ << mCurrentTSlice
+ << std::endl;
+
+ }
+#endif
ca->SetText(1,worldPos.str().c_str());
+
+ std::stringstream slicePos;
+ slicePos << "Slice: " << this->GetSlice();
+ ca->SetText(2, slicePos.str().c_str());
}
if (pdmA->GetVisibility()) {
double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
-
+#if VTK_MAJOR_VERSION <= 5
if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
crossCursor->SetFocalPoint(x,y,z);
} else
crossCursor->SetFocalPoint(-1,-1,z);
+ crossCursor->Update();
}
+#else
+ vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
+ try {
+ mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
+ } catch (const std::bad_cast& e) {
+ std::cerr << e.what() << std::endl;
+ std::cerr << "Conversion error" << std::endl;
+ return;
+ }
+ if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
+ xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
+ yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
+ yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
+ zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
+ zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
+ vtkRenderer * renderer = this->Renderer;
+
+ renderer->WorldToView(x,y,z);
+ renderer->ViewToNormalizedViewport(x,y,z);
+ renderer->NormalizedViewportToViewport(x,y);
+ renderer->ViewportToNormalizedDisplay(x,y);
+ renderer->NormalizedDisplayToDisplay(x,y);
+ crossCursor->SetFocalPoint(x,y,z);
+ } else
+ crossCursor->SetFocalPoint(-1,-1,z);
+ crossCursor->Update();
+ }
+#endif
if (mOverlay && mOverlayActor->GetVisibility()) {
if(mLinkOverlayWindowLevel) {
mOverlayMapper->SetWindow(this->GetColorWindow());
mOverlayMapper->SetLevel(this->GetColorLevel());
}
+#if VTK_MAJOR_VERSION <= 5
mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
- mOverlayMapper->GetOutput()->Update();
+#else
+ mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
+#endif
mOverlayMapper->Update();
}
- if (mLandMapper)
- UpdateLandmarks();
+ if (mFusion && mFusionActor->GetVisibility()) {
+#if VTK_MAJOR_VERSION <= 5
+ mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
+#else
+ mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
+#endif
+ mFusionMapper->Update();
+ }
+ if (mLandMapper) {
+ RemoveLandmarks();
+ DisplayLandmarks();
+ }
- this->GetRenderWindow()->Render();
+ this->GetRenderWindow()->Render();
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::UpdateCursorPosition()
-{
+{
pdmA->SetVisibility(true);
mCursor[0] = mCurrent[0];
mCursor[1] = mCurrent[1];
//----------------------------------------------------------------------------
-void vvSlicer::UpdateLandmarks()
-{
- vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
+void vvSlicer::RemoveLandmarks()
+{
+ vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
if (pd->GetPoints()) {
- //mLandGlyph->SetRange(0,1);
- //mLandGlyph->Modified();
- //mLandGlyph->Update();
- mClipBox->Modified();
- mLandClipper->Update();
- mLandMapper->Update();
- //Let's add the captions
//First remove all captions:
for(unsigned int i=0;i<mLandLabelActors.size();i++) {
this->Renderer->RemoveActor2D(mLandLabelActors[i]);
//allActors2D->Remove (mLandLabelActors[i]);
}
mLandLabelActors.clear();
+ }
+}
+//----------------------------------------------------------------------------
+
+
+//----------------------------------------------------------------------------
+void vvSlicer::DisplayLandmarks()
+{
+
+ double bounds [6];
+ for(unsigned int i=0; i<6; i++)
+ bounds[i] = ImageActor->GetBounds()[i];
+ bounds[ this->SliceOrientation*2 ] = ImageActor->GetBounds()[ this->SliceOrientation*2 ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
+ bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
+ mClipBox->SetBounds(bounds);
+
+
+ vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
+ if (pd->GetPoints()) {
+ this->GetRenderer()->AddActor(mLandActor);
+ //mLandGlyph->SetRange(0,1);
+ //mLandGlyph->Modified();
+ //mLandGlyph->Update();
+ mClipBox->Modified();
+ mLandClipper->Update();
+ mLandMapper->Update();
//Next add the captions to the displayed points
for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
double *position = mLandClipper->GetOutput()->GetPoint(id);
//----------------------------------------------------------------------------
void vvSlicer::SetSlice(int slice)
-{
+{
int *range = this->GetSliceRange();
if (range) {
if (slice < range[0]) {
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
-int vvSlicer::GetTMax() {
+int vvSlicer::GetTMax()
+{
int tmax = (int)mImage->GetVTKImages().size() - 1;
if(mOverlay)
tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
//----------------------------------------------------------------------------
void vvSlicer::SetContourSlice()
-{
+{
if (mSurfaceCutActors.size() > 0)
for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
i!=mSurfaceCutActors.end(); i++) {
//----------------------------------------------------------------------------
void vvSlicer::ForceUpdateDisplayExtent()
-{
+{
this->UpdateDisplayExtent();
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
int* vvSlicer::GetDisplayExtent()
-{
+{
return this->GetImageActor()->GetDisplayExtent();
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
-{
+{
this->Superclass::PrintSelf(os, indent);
}
//----------------------------------------------------------------------------
+
//----------------------------------------------------------------------------
void vvSlicer::SetVFColor(double r, double g, double b)
-{
+{
double mVFColorHSV[3];
mVFColor[0] = r;
mVFColor[1] = g;
this->Render();
}
+//----------------------------------------------------------------------------
+
+
+//----------------------------------------------------------------------------
+void vvSlicer::SetRegisterExtent(int ext[6])
+{
+ copyExtent(ext, mRegisterExtent);
+}
+//----------------------------------------------------------------------------
+
+
+//----------------------------------------------------------------------------
+void vvSlicer::GetRegisterExtent(int ext[6])
+{
+ copyExtent(mRegisterExtent, ext);
+}
+//----------------------------------------------------------------------------
#include <iostream>
#include <vector>
+#include <QObject>
#include <QString> //TODO delete
#include <QMessageBox>
#include <vtkImageReslice.h>
#include <vtkImageMapToColors.h>
#include <vtkCaptionActor2D.h>
+#include <vtkTransformPolyDataFilter.h>
class vtkActor;
class vtkActor2D;
class vtkTransform;
class vtkImageReslice;
-class vvSlicer: public vtkImageViewer2
-{
+class vvSlicer: public QObject, public vtkImageViewer2 {
+
+Q_OBJECT
+
public:
static vvSlicer *New();
- vtkTypeRevisionMacro(vvSlicer,vtkImageViewer2);
+ vtkTypeMacro(vvSlicer,vtkImageViewer2);
void PrintSelf(ostream& os, vtkIndent indent);
void SetImage(vvImage::Pointer inputImages);
double* GetCursorPosition() {
return mCursor;
}
-
vtkTransform * GetSlicingTransform() { return mSlicingTransform; }
vtkTransform * GetConcatenatedTransform() { return mConcatenatedTransform; }
vtkTransform * GetConcatenatedFusionTransform() { return mConcatenatedFusionTransform; }
void GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform);
- void UpdateLandmarks();
+ void RemoveLandmarks();
+ void DisplayLandmarks();
void ForceUpdateDisplayExtent();
int* GetDisplayExtent();
return mVFColor;
}
void SetVFColor(double r, double g, double b);
-
+
//necessary to flag the secondary sequence
void SetFusionSequenceCode(int code) {mFusionSequenceCode=code;}
+ void SetRegisterExtent(int [6]);
+ void GetRegisterExtent(int [6]);
+
+ void SetSlicerNumber(const int nbSlicer) {mSlicerNumber = nbSlicer;}
+ int GetSlicerNumber() const {return mSlicerNumber;}
+
+signals:
+ void UpdateDisplayExtentBegin(int);
+ void UpdateDisplayExtentEnd(int);
+
protected:
vvSlicer();
~vvSlicer();
// ___|__|___ VTK world coordinates (mm) (never displayed) mCurrent
vtkSmartPointer<vtkTransform> mSlicingTransform;
+ vtkSmartPointer<vtkTransformPolyDataFilter> mLandmarkTransform;
vtkSmartPointer<vtkImageReslice> mImageReslice;
vtkSmartPointer<vtkTransform> mConcatenatedTransform;
vtkSmartPointer<vtkImageReslice> mOverlayReslice;
vtkSmartPointer<vtkScalarBarActor> legend;
std::vector<vvMeshActor*> mSurfaceCutActors;
+ int mSlicerNumber;
int mCurrentTSlice;
int mCurrentFusionTSlice;
int mCurrentOverlayTSlice;
double mVFColor[3];
bool mUseReducedExtent;
int * mReducedExtent;
- int * mInitialExtent;
+ int * mRegisterExtent;
bool mLinkOverlayWindowLevel;
bool showFusionLegend;
private:
void UpdateOrientation();
void UpdateDisplayExtent();
+ void ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
+ vtkImageData *targetImage, int targetExtent[6]);
void ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
vtkImageData *targetImage, int targetExtent[6]);
///Sets the surfaces to be cut on the image slice: update the vtkCutter
#include "vvMesh.h"\r
#include "vvBlendImageActor.h"\r
\r
+#include <vtkVersion.h>\r
+#include <vtkStreamingDemandDrivenPipeline.h>\r
+#include <vtkInformation.h>\r
#include <vtkImageActor.h>\r
#include <vtkImageData.h>\r
#include <vtkRenderWindow.h>\r
#include <QMessageBox>\r
//----------------------------------------------------------------------------\r
vvSlicerManager::vvSlicerManager(int numberOfSlicers)\r
-{\r
+{ \r
+\r
+ connect(this, SIGNAL(callAddLandmark(float,float,float,float)), this, SLOT(AddLandmark(float,float,float,float)));\r
+\r
mFileName = "";\r
mId = "";\r
mVFName = "";\r
mLandmarks = NULL;\r
mLinkedId.resize(0);\r
\r
- for ( int i = 0; i < numberOfSlicers; i++)\r
+ for ( int i = 0; i < numberOfSlicers; i++) {\r
mSlicers.push_back(vtkSmartPointer<vvSlicer>::New());\r
+ mSlicers[i]->SetSlicerNumber(i);\r
+ }\r
mSelectedSlicer = -1;\r
\r
mPreviousSlice.resize(numberOfSlicers, 0);\r
\r
//----------------------------------------------------------------------------\r
vvSlicerManager::~vvSlicerManager()\r
-{\r
+{ \r
if (mLandmarks)\r
delete mLandmarks;\r
}\r
\r
//------------------------------------------------------------------------------\r
void vvSlicerManager::SetFilename(std::string filename, int number)\r
-{\r
+{ \r
mFileName = filename;\r
mFileName = vtksys::SystemTools::GetFilenameName(mFileName);\r
mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->AddContour(contour,propagate);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::ToggleContourSuperposition()\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++)\r
mSlicers[i]->ToggleContourSuperposition();\r
}\r
\r
//----------------------------------------------------------------------------\r
std::string vvSlicerManager::GetListOfAbsoluteFilePathInOneString(const std::string &actorType)\r
-{\r
+{ \r
vvImageReader *reader = NULL;\r
\r
if(actorType=="image")\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::SetImage(std::string filename, vvImageReader::LoadedImageType type, int n, unsigned int slice)\r
-{\r
+{ \r
mType = type;\r
if (mReader.IsNull())\r
mReader = vvImageReader::New();\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetImage(vvImage::Pointer image)\r
-{\r
+{ \r
mImage=image;\r
for (unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetImage(image);\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::SetImages(std::vector<std::string> filenames, vvImageReader::LoadedImageType type, int n)\r
-{\r
+{ \r
mType = type;\r
std::string fileWithoutExtension = vtksys::SystemTools::GetFilenameWithoutExtension(filenames[0]);\r
if (type == vvImageReader::DICOM)\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::SetOverlay(std::vector<std::string> filenames,int dim, std::string component, vvImageReader::LoadedImageType type)\r
-{\r
+{ \r
mOverlayName = filenames[0];\r
mOverlayComponent = component;\r
if (dim > mImage->GetNumberOfDimensions()) {\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::SetFusion(std::vector<std::string> filenames,int dim, std::string component, vvImageReader::LoadedImageType type)\r
-{\r
+{ \r
mFusionName = filenames[0];\r
mFusionComponent = component;\r
if (dim > mImage->GetNumberOfDimensions()) {\r
//----------------------------------------------------------------------------\r
//this function is called by vvMainWindow::AddFusionSequence for the primary sequence (CT), while the given files constitute the secondary sequence.\r
bool vvSlicerManager::SetFusionSequence(std::vector<std::string> filenames, int dim, std::string component, vvImageReader::LoadedImageType type)\r
-{\r
+{ \r
mFusionSequenceInvolvementCode = 0;\r
\r
mFusionName = filenames[0];\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::SetVF(std::string filename)\r
-{\r
+{ \r
if (mVectorReader.IsNull())\r
mVectorReader = vvImageReader::New();\r
mVectorReader->SetInputFilename(filename);\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)\r
-{\r
+{ \r
if (vf->GetNumberOfDimensions() > mImage->GetNumberOfDimensions()) {\r
mLastError = "Sorry, vector field dimension cannot be greater then reference image.";\r
return false;\r
\r
//----------------------------------------------------------------------------\r
vvSlicer* vvSlicerManager::GetSlicer(int i)\r
-{\r
+{ \r
return mSlicers[i];\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateSlicer(int num, bool state)\r
-{\r
+{ \r
if (mSlicers[num]->GetImage()) {\r
mSlicers[num]->SetDisplayMode(state);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)\r
-{\r
+{ \r
mSlicers[i]->SetRenderWindow(i,RW);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* style)\r
-{\r
+{ \r
vvSlicerManagerCommand *smc = vvSlicerManagerCommand::New();\r
smc->SM = this;\r
smc->SetSlicerNumber(i);\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::LeftButtonReleaseEvent(int slicer)\r
-{\r
+{ \r
emit LeftButtonReleaseSignal(slicer);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::EmitMousePositionUpdated(int slicer)\r
-{\r
+{ \r
emit MousePositionUpdatedSignal(slicer);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::EmitKeyPressed(std::string KeyPress)\r
-{\r
+{ \r
emit KeyPressedSignal(KeyPress);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetSliceOrientation(int slicer, int orientation)\r
-{\r
+{ \r
mSlicers[slicer]->SetSliceOrientation(orientation);\r
emit UpdateOrientation(slicer, orientation);\r
}\r
\r
//----------------------------------------------------------------------------\r
int vvSlicerManager::GetTSlice()\r
-{\r
+{ \r
return mSlicers[0]->GetTSlice();\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetTSlice(int slice, bool updateLinkedImages)\r
-{\r
+{ \r
if (!updateLinkedImages) { //for fusionSequence, TMax / MaxCurrentTSlice are irrelevant.\r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetTSlice(slice, updateLinkedImages);\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetFusionSequenceTSlice(int slice)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetFusionSequenceTSlice(slice);\r
UpdateTSlice(i);\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetNextTSlice(int originating_slicer)\r
-{\r
+{ \r
int t = mSlicers[0]->GetMaxCurrentTSlice();\r
t++;\r
if (t > mSlicers[0]->GetTMax())\r
t = 0;\r
- //std::cout << "vvSlicerManager::SetNextTSlice" << std::endl;\r
emit UpdateTSlice(originating_slicer,t, mFusionSequenceInvolvementCode);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetPreviousTSlice(int originating_slicer)\r
-{\r
+{ \r
int t = mSlicers[0]->GetMaxCurrentTSlice();\r
t--;\r
if (t < 0)\r
t = mSlicers[0]->GetTMax();\r
- //std::cout << "vvSlicerManager::SetPreviousTSlice" << std::endl;\r
emit UpdateTSlice(originating_slicer,t, mFusionSequenceInvolvementCode);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::ToggleInterpolation()\r
-{\r
+{ \r
bool interpolate=!(mSlicers[0]->GetImageActor()->GetInterpolate());\r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->GetImageActor()->SetInterpolate(interpolate);\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)\r
-{\r
+{ \r
if (tslice < 0)\r
tslice = 0;\r
else if (tslice > mSlicers[slicer]->GetTMax())\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetColorWindow(double s)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetColorWindow(s);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetColorLevel(double s)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetColorLevel(s);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetOverlayColorWindow(double s)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetOverlayColorWindow(s);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetOverlayColorLevel(double s)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetOverlayColorLevel(s);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetLinkOverlayWindowLevel(bool b)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetLinkOverlayWindowLevel(b);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetCursorAndCornerAnnotationVisibility(int s)\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetCursorVisibility(s);\r
mSlicers[i]->SetCornerAnnotationVisibility(s);\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetOpacity(int i, double factor)\r
-{\r
+{ \r
mSlicers[i]->SetOpacity(1/factor);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateViews(int current,int slicer)\r
-{\r
+{ \r
double p[3], pt[3];\r
p[0] = mSlicers[slicer]->GetCurrentPosition()[0];\r
p[1] = mSlicers[slicer]->GetCurrentPosition()[1];\r
/mSlicers[slicer]->GetInput()->GetSpacing()[1];\r
double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])\r
/mSlicers[slicer]->GetInput()->GetSpacing()[2];\r
-\r
+#if VTK_MAJOR_VERSION <= 5\r
if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&\r
x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&\r
y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&\r
}\r
}\r
}\r
+#else\r
+int extentImageReslice[6];\r
+mSlicers[slicer]->GetRegisterExtent(extentImageReslice);\r
+ if (x >= extentImageReslice[0]-0.5 &&\r
+ x <= extentImageReslice[1]+0.5 &&\r
+ y >= extentImageReslice[2]-0.5 &&\r
+ y <= extentImageReslice[3]+0.5 &&\r
+ z >= extentImageReslice[4]-0.5 &&\r
+ z <= extentImageReslice[5]+0.5) {\r
+ mSlicers[slicer]->UpdateCursorPosition();\r
+ mSlicers[slicer]->SetCursorColor(10,212,255);\r
+ mSelectedSlicer = slicer;\r
+\r
+ switch (mSlicers[slicer]->GetSliceOrientation()) {\r
+ case vtkImageViewer2::SLICE_ORIENTATION_XY:\r
+ if (mSlicers[slicer]->GetSlice() != (int)lrint(z))\r
+ mSlicers[slicer]->SetSlice((int)lrint(z));\r
+ break;\r
+\r
+ case vtkImageViewer2::SLICE_ORIENTATION_XZ:\r
+ if (mSlicers[slicer]->GetSlice() != (int)lrint(y))\r
+ mSlicers[slicer]->SetSlice((int)lrint(y));\r
+ break;\r
+\r
+ case vtkImageViewer2::SLICE_ORIENTATION_YZ:\r
+ if (mSlicers[slicer]->GetSlice() != (int)lrint(x))\r
+ mSlicers[slicer]->SetSlice((int)lrint(x));\r
+ break;\r
+ }\r
+ mSlicers[slicer]->Render();\r
+\r
+ for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
+ if (i != (unsigned int)slicer\r
+ && mSlicers[i]->GetRenderer()->GetDraw()\r
+ && mSlicers[i]->GetRenderWindow()->GetSize()[0] > 2\r
+ && mSlicers[i]->GetRenderWindow()->GetSize()[1] > 2) {\r
+ mSlicers[i]->SetCurrentPosition(p[0], p[1], p[2], mSlicers[slicer]->GetMaxCurrentTSlice());\r
+ mSlicers[i]->UpdateCursorPosition();\r
+ if (current) { //do not display corner annotation if image is the one picked\r
+ mSlicers[i]->SetCurrentPosition(-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,\r
+ -VTK_DOUBLE_MAX, mSlicers[slicer]->GetMaxCurrentTSlice());\r
+ mSlicers[i]->SetCursorColor(255,10,212);\r
+ } else {\r
+ mSlicers[i]->SetCursorColor(150,10,282);\r
+ }\r
+ switch (mSlicers[i]->GetSliceOrientation()) {\r
+ case vtkImageViewer2::SLICE_ORIENTATION_XY:\r
+ if (mSlicers[i]->GetSlice() != (int)lrint(z))\r
+ mSlicers[i]->SetSlice((int)lrint(z));\r
+ break;\r
+\r
+ case vtkImageViewer2::SLICE_ORIENTATION_XZ:\r
+ if (mSlicers[i]->GetSlice() != (int)lrint(y))\r
+ mSlicers[i]->SetSlice((int)lrint(y));\r
+ break;\r
+\r
+ case vtkImageViewer2::SLICE_ORIENTATION_YZ:\r
+ if (mSlicers[i]->GetSlice() != (int)lrint(x))\r
+ mSlicers[i]->SetSlice((int)lrint(x));\r
+ break;\r
+ }\r
+ \r
+ mSlicers[i]->Render();\r
+ \r
+ UpdateSlice(i);\r
+ UpdateTSlice(i);\r
+ }\r
+ }\r
+ }\r
+#endif\r
}\r
//----------------------------------------------------------------------------\r
\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateLinked(int slicer)\r
-{\r
+{ \r
double p[3], pt[3];\r
p[0] = mSlicers[slicer]->GetCurrentPosition()[0];\r
p[1] = mSlicers[slicer]->GetCurrentPosition()[1];\r
double x = (pt[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0]) / mSlicers[slicer]->GetInput()->GetSpacing()[0];\r
double y = (pt[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1]) / mSlicers[slicer]->GetInput()->GetSpacing()[1];\r
double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2]) / mSlicers[slicer]->GetInput()->GetSpacing()[2];\r
-\r
+#if VTK_MAJOR_VERSION <= 5\r
if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&\r
x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&\r
y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&\r
}\r
}\r
}\r
+#else\r
+int extentImageReslice[6];\r
+mSlicers[slicer]->GetRegisterExtent(extentImageReslice);\r
+ if (x >= extentImageReslice[0]-0.5 &&\r
+ x <= extentImageReslice[1]+0.5 &&\r
+ y >= extentImageReslice[2]-0.5 &&\r
+ y <= extentImageReslice[3]+0.5 &&\r
+ z >= extentImageReslice[4]-0.5 &&\r
+ z <= extentImageReslice[5]+0.5) {\r
+ for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++) {\r
+ if (this->IsInvolvedInFusionSequence()) {\r
+ //this SlicerManager is involved in fusionSequence => do not synchronize the times\r
+ emit UpdateLinkManager(*i, slicer, p[0], p[1], p[2], -1);\r
+ }\r
+ else {\r
+ emit UpdateLinkManager(*i, slicer, p[0], p[1], p[2], mSlicers[slicer]->GetMaxCurrentTSlice());\r
+ }\r
+ }\r
+ }\r
+#endif\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateLinkedNavigation(vvSlicer *refSlicer, bool bPropagate)\r
-{\r
+{ \r
vtkCamera *refCam = refSlicer->GetRenderer()->GetActiveCamera();\r
\r
double refPosition[3];\r
\r
//----------------------------------------------------------------------------\r
double vvSlicerManager::GetColorWindow() const\r
-{\r
+{ \r
if (mSlicers.size())\r
return mSlicers[0]->GetColorWindow();\r
return -1;\r
\r
//----------------------------------------------------------------------------\r
double vvSlicerManager::GetColorLevel() const\r
-{\r
+{ \r
if (mSlicers.size())\r
return mSlicers[0]->GetColorLevel();\r
return -1;\r
\r
//----------------------------------------------------------------------------\r
double vvSlicerManager::GetOverlayColorWindow() const\r
-{\r
+{ \r
if (mSlicers.size())\r
return mSlicers[0]->GetOverlayColorWindow();\r
return -1;\r
\r
//----------------------------------------------------------------------------\r
double vvSlicerManager::GetOverlayColorLevel() const\r
-{\r
+{ \r
if (mSlicers.size())\r
return mSlicers[0]->GetOverlayColorLevel();\r
return -1;\r
\r
//----------------------------------------------------------------------------\r
bool vvSlicerManager::GetLinkOverlayWindowLevel() const\r
-{\r
+{ \r
if (mSlicers.size())\r
return mSlicers[0]->GetLinkOverlayWindowLevel();\r
return -1;\r
\r
//------------------------------------------------------------------------------\r
void vvSlicerManager::ResetTransformationToIdentity(const std::string actorType)\r
-{\r
+{ \r
if(actorType == "image")\r
for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)\r
this->GetImage()->GetTransform()[i]->Identity();\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::Render()\r
-{\r
+{ \r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->Render();\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::GenerateDefaultLookupTable()\r
-{\r
+{ \r
SetPreset(mPreset);\r
SetColorMap(mColorMap);\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::Reload()\r
-{\r
+{ \r
mReader->Update(mType);\r
mImage=mReader->GetOutput();\r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::ReloadFusion()\r
-{\r
+{ \r
mFusionReader->Update(mImage->GetNumberOfDimensions(),mFusionComponent.c_str(),mType);\r
\r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
//----------------------------------------------------------------------------\r
//the secondary sequence is being reloaded.\r
void vvSlicerManager::ReloadFusionSequence()\r
-{\r
+{ \r
// this is to keep the slice thickness, which needs to be artificially increased for visualization\r
double sp_x, sp_y, sp_z;\r
this->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::ReloadOverlay()\r
-{\r
+{ \r
mOverlayReader->Update(mImage->GetNumberOfDimensions(),mOverlayComponent.c_str(),mType);\r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::ReloadVF()\r
-{\r
+{ \r
mVectorReader->Update(vvImageReader::VECTORFIELD); //deletes the old images through the VF::Init() function\r
mVF=mVectorReader->GetOutput();\r
for ( unsigned int i = 0; i < mSlicers.size(); i++) {\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_index)\r
-{\r
+{ \r
if (actor_type =="overlay")\r
mOverlayReader = NULL;\r
\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::RemoveActors()\r
-{\r
+{ \r
///This method leaks a few objects. See RemoveActor for what a\r
///correct implementation would look like\r
//DS -> probably due to the reader (now released in the\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)\r
-{\r
+{ \r
// int view = mSlicers[slicer]->GetSliceOrientation();\r
// int slice = mSlicers[slicer]->GetSlice();\r
double x = mSlicers[slicer]->GetCursorPosition()[0];\r
mSlicers[slicer]->GetInput()->GetSpacing()[1];\r
double Z = (z - mSlicers[slicer]->GetInput()->GetOrigin()[2])/\r
mSlicers[slicer]->GetInput()->GetSpacing()[2];\r
+ double xyz[3], xyzTransform[3];\r
+ xyz[0] = x;\r
+ xyz[1] = y;\r
+ xyz[2] = z;\r
+ mSlicers[slicer]->GetConcatenatedTransform()->TransformPoint(xyz, xyzTransform);\r
+ double XTransform = (xyzTransform[0] - mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetOrigin()[0])/\r
+ mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetSpacing()[0];\r
+ double YTransform = (xyzTransform[1] - mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetOrigin()[1])/\r
+ mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetSpacing()[1];\r
+ double ZTransform = (xyzTransform[2] - mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetOrigin()[2])/\r
+ mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetSpacing()[2];\r
double value = -VTK_DOUBLE_MAX;\r
int displayVec = 0;\r
double xVec=0, yVec=0, zVec=0, valueVec=0;\r
int displayOver = 0;\r
int displayFus = 0;\r
double valueOver=0, valueFus=0;\r
- if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&\r
- X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&\r
- Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&\r
- Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&\r
- Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&\r
- Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {\r
+#if VTK_MAJOR_VERSION <= 5\r
+ if (XTransform >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&\r
+ XTransform <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&\r
+ YTransform >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&\r
+ YTransform <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&\r
+ ZTransform >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&\r
+ ZTransform <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {\r
\r
value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);\r
\r
}\r
\r
emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),\r
- x,y,z,X,Y,Z,value);\r
+ x,y,z,XTransform,YTransform,ZTransform,value);\r
emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);\r
emit UpdateOverlay(displayOver,valueOver,value);\r
emit UpdateFusion(displayFus,valueFus);\r
}\r
+#else\r
+int extentImageReslice[6];\r
+mSlicers[slicer]->GetRegisterExtent(extentImageReslice);\r
+ if (XTransform >= extentImageReslice[0] &&\r
+ XTransform <= extentImageReslice[1] &&\r
+ YTransform >= extentImageReslice[2] &&\r
+ YTransform <= extentImageReslice[3] &&\r
+ ZTransform >= extentImageReslice[4] &&\r
+ ZTransform <= extentImageReslice[5]) {\r
+\r
+ value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);\r
+\r
+ if (mSlicers[slicer]->GetVFActor() ) {\r
+ displayVec = 1;\r
+ unsigned int currentTime = mSlicers[slicer]->GetMaxCurrentTSlice();\r
+ vtkImageData *vf = NULL;\r
+\r
+ if (mSlicers[slicer]->GetVF()->GetVTKImages().size() > currentTime)\r
+ vf = mSlicers[slicer]->GetVF()->GetVTKImages()[currentTime];\r
+ else\r
+ vf = mSlicers[slicer]->GetVF()->GetVTKImages()[0];\r
+\r
+ if (vf) {\r
+ double Xvf = (x - vf->GetOrigin()[0])/ vf->GetSpacing()[0];\r
+ double Yvf = (y - vf->GetOrigin()[1])/ vf->GetSpacing()[1];\r
+ double Zvf = (z - vf->GetOrigin()[2])/ vf->GetSpacing()[2];\r
+ xVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 0);\r
+ yVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 1);\r
+ zVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 2);\r
+ valueVec = sqrt(xVec*xVec + yVec*yVec + zVec*zVec);\r
+ }\r
+ }\r
+ if (mSlicers[slicer]->GetOverlayActor() ) {\r
+ displayOver = 1;\r
+ vtkImageData *overlay = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetOverlayMapper()->GetInput());\r
+ double Xover = (x - overlay->GetOrigin()[0]) / overlay->GetSpacing()[0];\r
+ double Yover = (y - overlay->GetOrigin()[1]) / overlay->GetSpacing()[1];\r
+ double Zover = (z - overlay->GetOrigin()[2]) / overlay->GetSpacing()[2];\r
+ valueOver = this->GetScalarComponentAsDouble(overlay, Xover, Yover, Zover);\r
+ }\r
+\r
+ if ( mSlicers[slicer]->GetFusionActor() ) {\r
+ displayFus = 1;\r
+ vtkImageData *fusion = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetFusionMapper()->GetInput());\r
+ double Xover = (x - fusion->GetOrigin()[0]) / fusion->GetSpacing()[0];\r
+ double Yover = (y - fusion->GetOrigin()[1]) / fusion->GetSpacing()[1];\r
+ double Zover = (z - fusion->GetOrigin()[2]) / fusion->GetSpacing()[2];\r
+ valueFus = this->GetScalarComponentAsDouble(fusion, Xover, Yover, Zover);\r
+ }\r
+ else if (this->IsInvolvedInFusionSequence()) { \r
+ //if the cursor moves over the 'independent' version of the secondary sequence\r
+ //do not update the panel, just keep it as it is.\r
+ displayFus = 1;\r
+ valueFus = std::numeric_limits<double>::quiet_NaN();\r
+ }\r
+\r
+ emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),\r
+ x,y,z,XTransform,YTransform,ZTransform,value);\r
+ emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);\r
+ emit UpdateOverlay(displayOver,valueOver,value);\r
+ emit UpdateFusion(displayFus,valueFus);\r
+ }\r
+#endif\r
}\r
//----------------------------------------------------------------------------\r
\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::Activated()\r
-{\r
+{ \r
emit currentImageChanged(mId);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::Picked()\r
-{\r
+{ \r
emit currentPickedImageChanged(mId);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateWindowLevel()\r
-{\r
+{ \r
emit WindowLevelChanged();\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateSlice(int slicer)\r
-{\r
+{ \r
if (mPreviousSlice[slicer] == mSlicers[slicer]->GetSlice()) {\r
//DD("============= NOTHING");\r
return;\r
}\r
- //std::cout << "vvSlicerManager::UpdateSlice " << slicer << " " << mSlicers[slicer]->GetSlice() << std::endl;\r
emit UpdateSlice(slicer, mSlicers[slicer]->GetSlice());\r
mSlicers[slicer]->Render(); // DS <-- I add this, this could/must be the only Render ...\r
mPreviousSlice[slicer] = mSlicers[slicer]->GetSlice();\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateTSlice(int slicer)\r
-{\r
+{ \r
int slice = mSlicers[slicer]->GetSlice();\r
\r
int tslice = mSlicers[slicer]->GetMaxCurrentTSlice();\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::UpdateSliceRange(int slicer)\r
-{\r
+{ \r
emit UpdateSliceRange(slicer,\r
mSlicers[slicer]->GetSliceRange()[0], mSlicers[slicer]->GetSliceRange()[1],\r
0,mSlicers[slicer]->GetTMax());\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetSlicingPreset(SlicingPresetType preset)\r
-{\r
+{ \r
if(mSlicingPreset==preset)\r
return;\r
\r
return;\r
}\r
s->ForceUpdateDisplayExtent();\r
+#if VTK_MAJOR_VERSION <= 5\r
s->SetSlice((s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2+1]\r
+s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2])/2.0);\r
+#else\r
+ int extentImageReslice[6];\r
+ s->GetRegisterExtent(extentImageReslice);\r
+ s->SetSlice((extentImageReslice[s->GetSliceOrientation()*2+1]\r
+ +extentImageReslice[s->GetSliceOrientation()*2])/2.0);\r
+#endif\r
s->ResetCamera();\r
s->Render();\r
}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetPreset(int preset)\r
-{\r
+{ \r
\r
//vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());\r
double window = mSlicers[0]->GetColorWindow();\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetLocalColorWindowing(const int slicer, const bool bCtrlKey)\r
-{\r
+{ \r
double min, max;\r
if(bCtrlKey && this->mSlicers[slicer]->GetFusion()) {\r
int t = mSlicers[slicer]->GetFusionTSlice();\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::SetColorMap(int colormap)\r
-{\r
+{ \r
double range[2];\r
\r
range[0] = mSlicers[0]->GetInput()->GetScalarRange()[0];\r
\r
fusLUT->ForceBuild();\r
double v[4];\r
-\r
// set color table transparency\r
//double alpha_range=(double)mFusionThresOpacity/10;\r
double range_end = fusRange[0] + (double)mFusionThresOpacity*(fusRange[1] - fusRange[0])/100;\r
\r
//----------------------------------------------------------------------------\r
vvLandmarks* vvSlicerManager::GetLandmarks()\r
-{\r
+{ \r
if (mLandmarks == NULL) {\r
mLandmarks = new vvLandmarks(mSlicers[0]->GetTMax()+1);\r
for (unsigned int i = 0; i < mSlicers.size(); i++)\r
return mLandmarks;\r
}\r
//----------------------------------------------------------------------------\r
-\r
+void vvSlicerManager::AddNewLandmark(float x,float y,float z,float t)\r
+{ \r
+ emit callAddLandmark(x,y,z,t);\r
+}\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::AddLandmark(float x,float y,float z,float t)\r
-{\r
+{ \r
double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];\r
double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];\r
double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];\r
+#if VTK_MAJOR_VERSION <= 5\r
if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0]-0.5 &&\r
x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1]+0.5 &&\r
y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2]-0.5 &&\r
y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3]+0.5 &&\r
z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4]-0.5 &&\r
z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5) {\r
- double value = this->GetScalarComponentAsDouble(mSlicers[0]->GetInput(), x_index, y_index, z_index);\r
+ double value = this->GetScalarComponentAsDouble(mSlicers[mSelectedSlicer]->GetInput(), x_index, y_index, z_index); //Value in selected Slicer (not 0): bug #2848\r
this->GetLandmarks()->AddLandmark(x,y,z,t,value);\r
emit LandmarkAdded();\r
}\r
+#else\r
+ int extentImageReslice[6];\r
+ mSlicers[0]->GetRegisterExtent(extentImageReslice);\r
+ if (x_index >= extentImageReslice[0]-0.5 &&\r
+ x_index <= extentImageReslice[1]+0.5 &&\r
+ y_index >= extentImageReslice[2]-0.5 &&\r
+ y_index <= extentImageReslice[3]+0.5 &&\r
+ z_index >= extentImageReslice[4]-0.5 &&\r
+ z_index <= extentImageReslice[5]+0.5) {\r
+ double value = this->GetScalarComponentAsDouble(mSlicers[mSelectedSlicer]->GetInput(), x_index, y_index, z_index); //Value in selected Slicer (not 0): bug #2848\r
+ this->GetLandmarks()->AddLandmark(x,y,z,t,value);\r
+ emit LandmarkAdded();\r
+ }\r
+#endif\r
+}\r
+//----------------------------------------------------------------------------\r
+\r
+//----------------------------------------------------------------------------\r
+void vvSlicerManager::AddLandmarkProfile(float x,float y,float z,float t)\r
+{ \r
+ double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];\r
+ double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];\r
+ double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];\r
+#if VTK_MAJOR_VERSION <= 5\r
+ if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0]-0.5 &&\r
+ x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1]+0.5 &&\r
+ y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2]-0.5 &&\r
+ y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3]+0.5 &&\r
+ z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4]-0.5 &&\r
+ z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5) {\r
+ double value = this->GetScalarComponentAsDouble(mSlicers[mSelectedSlicer]->GetInput(), x_index, y_index, z_index); //Value in selected Slicer (not 0): bug #2848\r
+ this->GetLandmarks()->AddLandmark(x,y,z,t,value);\r
+ }\r
+#else\r
+ int extentImageReslice[6];\r
+ mSlicers[0]->GetRegisterExtent(extentImageReslice);\r
+ if (x_index >= extentImageReslice[0]-0.5 &&\r
+ x_index <= extentImageReslice[1]+0.5 &&\r
+ y_index >= extentImageReslice[2]-0.5 &&\r
+ y_index <= extentImageReslice[3]+0.5 &&\r
+ z_index >= extentImageReslice[4]-0.5 &&\r
+ z_index <= extentImageReslice[5]+0.5) {\r
+ double value = this->GetScalarComponentAsDouble(mSlicers[mSelectedSlicer]->GetInput(), x_index, y_index, z_index); //Value in selected Slicer (not 0): bug #2848\r
+ this->GetLandmarks()->AddLandmark(x,y,z,t,value);\r
+ }\r
+#endif\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::PrevImage(int slicer)\r
-{\r
+{ \r
emit ChangeImageWithIndexOffset(this, slicer, -1);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::NextImage(int slicer)\r
-{\r
+{ \r
emit ChangeImageWithIndexOffset(this, slicer, 1);\r
}\r
//----------------------------------------------------------------------------\r
\r
//----------------------------------------------------------------------------\r
void vvSlicerManager::VerticalSliderHasChanged(int slicer, int slice)\r
-{\r
+{ \r
emit AVerticalSliderHasChanged(slicer, slice);\r
}\r
\r
\r
//----------------------------------------------------------------------------\r
double vvSlicerManager::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int component)\r
-{\r
+{ \r
int ix, iy, iz;\r
return mSlicers[0]->GetScalarComponentAsDouble(image, X, Y, Z, ix, iy, iz, component);\r
}\r
void SetSlicingPreset(SlicingPresetType preset);
vvLandmarks *GetLandmarks();
- void AddLandmark(float x,float y,float z,float t);
+ void AddNewLandmark(float x,float y,float z,float t);
+ void AddLandmarkProfile(float x,float y,float z,float t);
void NextImage(int slicer);
void PrevImage(int slicer);
void VerticalSliderHasChanged(int slicer, int slice);
double GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int component=0);
+public slots:
+ void AddLandmark(float x,float y,float z,float t);
+
signals :
+ void callAddLandmark(float x,float y,float z,float t);
void currentImageChanged(std::string id);
void currentPickedImageChanged(std::string id);
void UpdatePosition(int visibility,double x, double y, double z, double X, double Y, double Z, double value);
#include "vtkTransform.h"
#include <cmath>
-
//------------------------------------------------------------------------------
vvSlicerManagerCommand::vvSlicerManagerCommand()
{
this->SM->SetLocalColorWindowing(VisibleInWindow, bCtrlKey);
return;
}
- if (KeyPress == "0") {
+ if (KeyPress == "0" || KeyPress == "KP_0") {
this->SM->SetPreset(WL_AUTO);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "1") {
+ if (KeyPress == "1" || KeyPress == "KP_1") {
this->SM->SetPreset(WL_HOUNSFIELD);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "2") {
+ if (KeyPress == "2" || KeyPress == "KP_2") {
this->SM->SetPreset(WL_SOFTTISSUE);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "3") {
+ if (KeyPress == "3" || KeyPress == "KP_3") {
this->SM->SetPreset(WL_LUNGS);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "4") {
+ if (KeyPress == "4" || KeyPress == "KP_4") {
this->SM->SetPreset(WL_BONES);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "5") {
+ if (KeyPress == "5" || KeyPress == "KP_5") {
this->SM->SetPreset(WL_HEAD);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "6") {
+ if (KeyPress == "6" || KeyPress == "KP_6") {
this->SM->SetColorMap(0);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "7") {
+ if (KeyPress == "7" || KeyPress == "KP_7") {
this->SM->SetColorMap(1);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "8") {
+ if (KeyPress == "8" || KeyPress == "KP_8") {
this->SM->SetColorMap(2);
this->SM->UpdateWindowLevel();
return;
}
- if (KeyPress == "9") {
+ if (KeyPress == "9" || KeyPress == "KP_9") {
this->SM->SetColorMap(3);
this->SM->UpdateWindowLevel();
return;
//>>>>>>> 921642d767beba2442dacc8fdb40dc36396e1b7d
if (newLandmark) {
- this->SM->AddLandmark(xWorld,yWorld,zWorld,
+ double pLand[3]; pLand[0] = xWorld; pLand[1] = yWorld; pLand[2] = zWorld;
+ double ptLand[3];
+ this->SM->GetSlicer(VisibleInWindow)->GetConcatenatedTransform()->TransformPoint(pLand, ptLand);
+ this->SM->AddNewLandmark(ptLand[0],ptLand[1],ptLand[2],
this->SM->GetSlicer(VisibleInWindow)->GetTSlice());
- this->SM->GetSlicer(VisibleInWindow)->UpdateLandmarks();
+ this->SM->GetSlicer(VisibleInWindow)->RemoveLandmarks();
+ //this->SM->GetSlicer(VisibleInWindow)->DisplayLandmarks();
this->SM->Render();
}
if (event == vtkCommand::PickEvent || event == vtkCommand::StartPickEvent) {
#include "vtkOBJReader.h"
#include "vtkInteractorStyle.h"
-
+#include <vtkVersion.h>
#include "vtkPolyDataMapper.h"
#include "vtkActor.h"
#include "vtkPolyData.h"
#include "vtkRenderer.h"
#include <QMessageBox>
+#include <QFileDialog>
+
+#ifdef Q_OS_OSX
+# include "vvOSXHelper.h"
+#endif
//----------------------------------------------------------------------------
class vvManagerCallback : public vtkCommand
mCurrentTime = 0;
connect(loadButton,SIGNAL(clicked()),this,SLOT(LoadSurface()));
+
+#ifdef Q_OS_OSX
+ disableGLHiDPI(renderWidget->winId());
+#endif
}
vvSurfaceViewerDialog::~vvSurfaceViewerDialog()
reader->Update();
mReaders.push_back(reader);
}
-
+#if VTK_MAJOR_VERSION <= 5
mMapper->SetInput(mReaders[mCurrentTime]->GetOutput());
+#else
+ mMapper->SetInputConnection(mReaders[mCurrentTime]->GetOutputPort());
+#endif
if (!mActor) {
mActor = vtkActor::New();
mCurrentTime++;
if (mCurrentTime >= mReaders.size())
mCurrentTime = 0;
+#if VTK_MAJOR_VERSION <= 5
mMapper->SetInput(mReaders[mCurrentTime]->GetOutput());
+#else
+ mMapper->SetInputConnection(mReaders[mCurrentTime]->GetOutputPort());
+#endif
mMapper->Modified();
renderWidget->GetRenderWindow()->Render();
}
mCurrentTime--;
if (mCurrentTime < 0)
mCurrentTime = (unsigned int) mReaders.size() - 1;
+#if VTK_MAJOR_VERSION <= 5
mMapper->SetInput(mReaders[mCurrentTime]->GetOutput());
+#else
+ mMapper->SetInputConnection(mReaders[mCurrentTime]->GetOutputPort());
+#endif
mMapper->Modified();
renderWidget->GetRenderWindow()->Render();
}
vtkPolyDataMapper* mMapper;
vtkActor* mActor;
vtkRenderer * mRenderer;
- unsigned int mCurrentTime;
+ int mCurrentTime;
}; // end class vvSurfaceViewerDialog
//====================================================================
#include <vtkImageClip.h>
#include <vtkRenderWindow.h>
+
//------------------------------------------------------------------------------
// Create the tool and automagically (I like this word) insert it in
// the main window menu.
//------------------------------------------------------------------------------
void vvToolBinarize::Initialize()
-{
+{
SetToolName("Binarize");
SetToolMenuName("Binarize");
SetToolIconFilename(":/common/icons/binarize.png");
:vvToolWidgetBase(parent,f),
vvToolBase<vvToolBinarize>(parent),
Ui::vvToolBinarize()
-{
+{
// GUI Initialization
Ui_vvToolBinarize::setupUi(mToolWidget);
mInteractiveDisplayIsEnabled = mCheckBoxInteractiveDisplay->isChecked();
//------------------------------------------------------------------------------
vvToolBinarize::~vvToolBinarize()
-{
+{
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolBinarize::InteractiveDisplayToggled(bool b)
-{
+{
mInteractiveDisplayIsEnabled = b;
if (!mInteractiveDisplayIsEnabled) {
RemoveVTKObjects();
//------------------------------------------------------------------------------
void vvToolBinarize::RemoveVTKObjects()
-{
+{
for(unsigned int i=0; i<mImageContour.size(); i++) {
mImageContour[i]->HideActors();
mImageContourLower[i]->HideActors();
//------------------------------------------------------------------------------
bool vvToolBinarize::close()
-{
+{
// RemoveVTKObjects();
return vvToolWidgetBase::close();
}
//------------------------------------------------------------------------------
-void vvToolBinarize::closeEvent(QCloseEvent *event) {
+void vvToolBinarize::closeEvent(QCloseEvent *event)
+{
RemoveVTKObjects();
event->accept();
}
//------------------------------------------------------------------------------
void vvToolBinarize::reject()
-{
+{
// DD("vvToolBinarize::reject");
RemoveVTKObjects();
return vvToolWidgetBase::reject();
//------------------------------------------------------------------------------
void vvToolBinarize::enableLowerThan(bool b)
-{
+{
if (!b) {
mThresholdSlider1->resetMaximum();
for(unsigned int i=0; i<mImageContour.size(); i++) {
//------------------------------------------------------------------------------
void vvToolBinarize::useFGBGtoggled(bool)
-{
+{
if (!mCheckBoxUseBG->isChecked() && !mCheckBoxUseFG->isChecked())
mCheckBoxUseBG->toggle();
}
// DD(m.size());
// }
void vvToolBinarize::InputIsSelected(vvSlicerManager * m)
-{
+{
mCurrentSlicerManager = m;
// Specific for this gui
mImageContour.push_back(vvImageContour::New());
mImageContour[i]->SetSlicer(mCurrentSlicerManager->GetSlicer(i));
mImageContour[i]->SetColor(1.0, 0.0, 0.0);
- mImageContour[i]->SetDepth(100); // to be in front of (whe used with ROI tool)
+ mImageContour[i]->SetDepth(0); // to be in front of (whe used with ROI tool)
mImageContourLower.push_back(vvImageContour::New());
mImageContourLower[i]->SetSlicer(mCurrentSlicerManager->GetSlicer(i));
mImageContourLower[i]->SetColor(0.0, 0.0, 1.0);
connect(mThresholdSlider2, SIGNAL(valueChanged(double)), this, SLOT(valueChangedT2(double)));
connect(mCurrentSlicerManager,SIGNAL(UpdateSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
- connect(mCurrentSlicerManager,SIGNAL(UpdateTSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
+ connect(mCurrentSlicerManager,SIGNAL(UpdateTSlice(int,int, int)),this,SLOT(UpdateSlice(int, int, int)));
connect(mCurrentSlicerManager,SIGNAL(UpdateOrientation(int,int)),this,SLOT(UpdateOrientation(int, int)));
// connect(mCurrentSlicerManager, SIGNAL(LeftButtonReleaseSignal(int)), SLOT(LeftButtonReleaseEvent(int)));
-
InteractiveDisplayToggled(mInteractiveDisplayIsEnabled);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolBinarize::UpdateOrientation(int slicer,int orientation)
-{
+{
Update(slicer);
}
//------------------------------------------------------------------------------
+
//------------------------------------------------------------------------------
-void vvToolBinarize::UpdateSlice(int slicer,int slices)
-{
+void vvToolBinarize::UpdateSlice(int slicer,int slices, int code)
+{
Update(slicer);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolBinarize::Update(int slicer)
-{
+{
if (!mInteractiveDisplayIsEnabled) return;
if (!mCurrentSlicerManager) close();
mImageContour[slicer]->Update(mThresholdSlider1->GetValue());
//------------------------------------------------------------------------------
void vvToolBinarize::GetArgsInfoFromGUI()
-{
+{
/* //KEEP THIS FOR READING GGO FROM FILE
int argc=1;
//------------------------------------------------------------------------------
void vvToolBinarize::apply()
-{
+{
if (!mCurrentSlicerManager) close();
QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
- GetArgsInfoFromGUI();
-
+ GetArgsInfoFromGUI();
+
// Main filter
clitk::BinarizeImageGenericFilter::Pointer filter =
clitk::BinarizeImageGenericFilter::New();
filter->SetArgsInfo(mArgsInfo);
filter->Update();
+
// Output
- vvImage::Pointer output = filter->GetOutputVVImage();
+ vvImage::Pointer output = filter->GetOutputVVImage();
std::ostringstream osstream;
osstream << "Binarized_" << mCurrentSlicerManager->GetSlicer(0)->GetFileName() << ".mhd";
AddImage(output,osstream.str());
//------------------------------------------------------------------------------
void vvToolBinarize::valueChangedT2(double v)
-{
+{
// DD("valueChangedT2");
if (mRadioButtonLowerThan->isChecked()) {
mThresholdSlider1->SetMaximum(v);
//------------------------------------------------------------------------------
void vvToolBinarize::valueChangedT1(double v)
-{
+{
// DD("valueChangedT1");
if (!mCurrentSlicerManager) close();
mThresholdSlider2->SetMinimum(v);
#ifndef VVTOOLBINARIZE_H
#define VVTOOLBINARIZE_H
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include "vvToolBase.h"
void valueChangedT1(double v);
void valueChangedT2(double v);
void UpdateOrientation(int slicer, int orientation);
- void UpdateSlice(int slicer,int slices);
+ void UpdateSlice(int slicer,int slices, int code=0);
void enableLowerThan(bool b);
void useFGBGtoggled(bool);
void InteractiveDisplayToggled(bool b);
#include <QSignalMapper>
// vtk
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
#include <vtkImageClip.h>
#include <vtkImageTranslateExtent.h>
#include <vtkImageData.h>
{
if(mCurrentSlicerManager){
// Reset extends
- for(int i=0; i<mExtentSize; i++){
+ for(int i=0; i<6; i++){
mReducedExtent[i] = mInitialExtent[i];
}
+ for(int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++)
+ mCurrentSlicerManager->GetSlicer(i)->EnableReducedExtent(false);
UpdateExtent();
}
+ mCurrentSlicerManager->GetImage()->GetTransform()[0]->SetMatrix(mConcatenedTransform);
+ for (int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ mCurrentSlicerManager->GetSlicer(i)->ResetCamera();
+ mCurrentSlicerManager->GetSlicer(i)->Render();
+ mCurrentSlicerManager->UpdateLinkedNavigation( mCurrentSlicerManager->GetSlicer(i) );
+ }
vvToolWidgetBase::closeEvent(event);
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolCropImage::reject()
{
- for(int i=0; i<mExtentSize; i++) mReducedExtent[i] = mInitialExtent[i];
+ for(int i=0; i<mExtentSize; i++)
+ mReducedExtent[i] = mInitialExtent[i];
+ for(int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++)
+ mCurrentSlicerManager->GetSlicer(i)->EnableReducedExtent(false);
UpdateExtent();
return vvToolWidgetBase::reject();
}
//------------------------------------------------------------------------------
void vvToolCropImage::InputIsSelected(vvSlicerManager * slicer)
{
+ //Save the current transformation
+ mConcatenedTransform = vtkSmartPointer<vtkMatrix4x4>::New();
+ mConcatenedTransform->DeepCopy(slicer->GetSlicer(0)->GetConcatenatedTransform()->GetMatrix());
+ vtkSmartPointer<vtkMatrix4x4> matrix = vtkSmartPointer<vtkMatrix4x4>::New();
+ matrix->Identity();
+ mCurrentSlicerManager->GetImage()->GetTransform()[0]->SetMatrix(matrix);
+ for (int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ mCurrentSlicerManager->GetSlicer(i)->ResetCamera();
+ mCurrentSlicerManager->GetSlicer(i)->Render();
+ mCurrentSlicerManager->UpdateLinkedNavigation( mCurrentSlicerManager->GetSlicer(i) );
+ }
+
// Change interface according to number of dimension
mExtentSize = 2*slicer->GetDimension();
if (slicer->GetDimension()<4) {
spin_zmin->setHidden(true);
spin_zmax->setHidden(true);
}
-
+#if VTK_MAJOR_VERSION <= 5
int *a = mCurrentImage->GetFirstVTKImageData()->GetWholeExtent();
+#else
+ int *a = mCurrentImage->GetFirstVTKImageData()->GetInformation()->Get(vtkDataObject::DATA_EXTENT());
+#endif
for(int i=0; i<6; i++){
mInitialExtent[i] = a[i];
mReducedExtent[i] = a[i];
}
// Set initial sliders values
- std::vector<int> imsize = mCurrentSlicerManager->GetImage()->GetSize();
+ int w_ext[6], imsize[3];
+ mCurrentSlicerManager->GetSlicer(0)->GetRegisterExtent(w_ext);
for(int dim=0; dim<slicer->GetDimension() && dim<3; ++dim){
+ imsize[dim] = w_ext[2*dim+1] - w_ext[2*dim] +1;
mSliders[dim*2]->setMaximum(imsize[dim]-1);
mSliders[dim*2+1]->setMaximum(imsize[dim]-1);
mSliders[dim*2+1]->setValue(imsize[dim]-1);
}
// We MUST reset initial extend to input image before using the
// filter to retrieve the correct image size
- for(int i=0; i<mExtentSize; i++) {
+ for(int i=0; i<6; i++) {
mReducedExtent[i] = mInitialExtent[i];
}
// Retrieve result and display it
vvImage::Pointer output = filter->GetOutputVVImage();
+ output->GetTransform()[0]->SetMatrix(mConcatenedTransform);
+
AddImage(output,croppedImageName.str());
// End
#define VVTOOLCROPIMAGE_H
//qt
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include <QDialog>
#include <QSlider>
#include "vvToolWidgetBase.h"
#include "vvMainWindowBase.h"
#include "ui_vvToolCropImage.h"
+//vtk
+#include <vtkTransform.h>
//------------------------------------------------------------------------------
class vvToolCropImage:
virtual void closeEvent(QCloseEvent *event);
std::vector<QSlider*> mSliders;
+ vtkSmartPointer<vtkMatrix4x4> mConcatenedTransform;
}; // end class vvToolCropImage
//------------------------------------------------------------------------------
===========================================================================**/
#ifndef VVTOOLImageArithm_H
#define VVTOOLImageArithm_H
+
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include "vvToolBase.h"
#define VVTOOLINPUTSELECTORWIDGET_H
// qt
+#include <QObject>
#include <QtDesigner/QDesignerExportWidget>
#include <QDialog>
#include <vvImage.h>
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include "vvToolBase.h"
#include "QWidget"
#ifndef VVTOOLMedianFilter_H
#define VVTOOLMedianFilter_H
+ #include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include "vvToolBase.h"
#include "QWidget"
#include "vvToolWidgetBase.h"
#include "ui_vvToolMedianFilter.h"
#include "clitkMedianImageFilter_ggo.h"
- #include <clitkMedianImageGenericFilter.h>
+ #include <clitkMedianImageGenericFilter.h>
//------------------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
+
+#include <QFileDialog>
+#include <QShortcut>
+
+#include <algorithm>
+
+// vv
+#include "vvToolProfile.h"
+#include "vvProgressDialog.h"
+#include "vvSlicerManager.h"
+#include "vvSlicer.h"
+#include "vvToolInputSelectorWidget.h"
+
+// vtk
+#include <vtkAxis.h>
+#include <vtkImageActor.h>
+#include <vtkCamera.h>
+#include <vtkImageClip.h>
+#include <vtkRenderWindow.h>
+#include <vtkChartXY.h>
+#include <vtkPlot.h>
+#include <vtkRendererCollection.h>
+#include <vtkRenderer.h>
+
+#include <vtkLine.h>
+#include <vtkCellArray.h>
+#include <vtkCellData.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkProperty.h>
+#include <vtkBox.h>
+#include <vtkInformation.h>
+
+#ifdef Q_OS_OSX
+# include "vvOSXHelper.h"
+#endif
+
+//------------------------------------------------------------------------------
+// Create the tool and automagically (I like this word) insert it in
+// the main window menu.
+ADD_TOOL(vvToolProfile);
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::Initialize()
+{
+ SetToolName("Profile");
+ SetToolMenuName("Intensity Profile");
+ SetToolIconFilename(":/common/icons/profile.png");
+ SetToolTip("Display the intensity profile between 2 points of the image.");
+ SetToolExperimental(false);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolProfile::vvToolProfile(vvMainWindowBase * parent, Qt::WindowFlags f)
+ :vvToolWidgetBase(parent,f),
+ vvToolBase<vvToolProfile>(parent),
+ Ui::vvToolProfile()
+{
+ // GUI Initialization
+ Ui_vvToolProfile::setupUi(mToolWidget);
+
+ QShortcut *shortcutPoint1 = new QShortcut(QKeySequence("Ctrl+1"), parent);
+ shortcutPoint1->setContext(Qt::ApplicationShortcut);
+ QObject::connect(shortcutPoint1, SIGNAL(activated()), this, SLOT(selectPoint1()));
+ QShortcut *shortcutPoint2 = new QShortcut(QKeySequence("Ctrl+2"), parent);
+ shortcutPoint2->setContext(Qt::ApplicationShortcut);
+ QObject::connect(shortcutPoint2, SIGNAL(activated()), this, SLOT(selectPoint2()));
+
+ // Connect signals & slots
+ connect(mSelectPoint1Button, SIGNAL(clicked()), this, SLOT(selectPoint1()));
+ connect(mSelectPoint2Button, SIGNAL(clicked()), this, SLOT(selectPoint2()));
+ connect(mCancelPointsButton, SIGNAL(clicked()), this, SLOT(cancelPoints()));
+ connect(mSaveProfileButton, SIGNAL(clicked()), this, SLOT(SaveAs()));
+
+ // Initialize some widget
+ ProfileWidget->hide();
+ mPoint1 = NULL;
+ mPoint2 = NULL;
+
+ mPoint1Selected = false;
+ mPoint2Selected = false;
+
+ mView = vtkSmartPointer<vtkContextView>::New();
+ vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
+ chart->SetAutoSize(false);
+ chart->SetRenderEmpty(true);
+ mView->GetScene()->AddItem(chart);
+ this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
+ this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
+ ProfileWidget->show();
+
+#ifdef Q_OS_OSX
+ disableGLHiDPI(ProfileWidget->winId());
+#endif
+
+ // Main filter
+ mFilter = clitk::ProfileImageGenericFilter::New();
+
+ // Set how many inputs are needed for this tool
+ AddInputSelector("Select one image", mFilter);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolProfile::~vvToolProfile()
+{
+ delete [] mPoint1;
+ delete [] mPoint2;
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::selectPoint1()
+{
+ QString position = "";
+
+ if(mCurrentSlicerManager) {
+ if (mPoint1Selected) {
+ ProfileWidget->hide();
+ vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
+ chart->SetAutoSize(false);
+ chart->SetRenderEmpty(true);
+ mView->GetScene()->ClearItems();
+ mView->GetScene()->AddItem(chart);
+ this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
+ this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
+ ProfileWidget->show();
+ mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P1", mPoint1[3]);
+ }
+
+ mPoint1Selected = false;
+
+ if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
+ double *pos;
+ pos = new double [4];
+ pos[0] = pos[1] = pos[2] = pos[3] = 0;
+
+ int i(0);
+ while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
+ pos[i] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetCursorPosition()[i];
+ ++i;
+ }
+ double posTransformed[3];
+ mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetConcatenatedTransform()->TransformPoint(pos, posTransformed);
+ i = 0;
+ while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
+ pos[i] = posTransformed[i];
+ mPoint1[i] = round((pos[i] - mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i])/mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i]);
+ pos[i] = mPoint1[i]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i]; //Ensure to be at the center of the voxel
+ position += QString::number(mPoint1[i],'f',0) + " ";
+ ++i;
+ }
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
+ pos[3] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetTSlice();
+ mPoint1[3] = pos[3];
+ position += QString::number(mPoint1[3],'f',0) + " ";
+ }
+ mPoint1Selected = true;
+ mCurrentSlicerManager->AddLandmarkProfile(pos[0], pos[1], pos[2], pos[3]);
+ mCurrentSlicerManager->GetLandmarks()->GetLabels()->SetNumberOfValues(mCurrentSlicerManager->GetLandmarks()->GetLabels()->GetNumberOfValues()-1);
+ mCurrentSlicerManager->GetLandmarks()->GetLabels()->Modified();
+ mCurrentSlicerManager->GetLandmarks()->GetLabels()->InsertNextValue("P1");
+ }
+ }
+ mPosPoint1Label->setText(position);
+ isPointsSelected();
+ mCurrentSlicerManager->Render();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::selectPoint2()
+{
+ QString position = "";
+
+ if(mCurrentSlicerManager) {
+ if (mPoint2Selected) {
+ ProfileWidget->hide();
+ vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
+ chart->SetAutoSize(false);
+ chart->SetRenderEmpty(true);
+ mView->GetScene()->ClearItems();
+ mView->GetScene()->AddItem(chart);
+ this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
+ this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
+ ProfileWidget->show();
+ mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P2", mPoint2[3]);
+ }
+
+ mPoint2Selected = false;
+
+ if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
+ double *pos;
+ pos = new double [4];
+ pos[0] = pos[1] = pos[2] = pos[3] = 0;;
+
+ int i(0);
+ while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
+ pos[i] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetCursorPosition()[i];
+ ++i;
+ }
+ double posTransformed[3];
+ mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetConcatenatedTransform()->TransformPoint(pos, posTransformed);
+ i = 0;
+ while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
+ pos[i] = posTransformed[i];
+ mPoint2[i] = round((pos[i] - mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i])/mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i]);
+ pos[i] = mPoint2[i]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i]; //Ensure to be at the center of the voxel
+ position += QString::number(mPoint2[i],'f',0) + " ";
+ ++i;
+ }
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
+ pos[3] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetTSlice();
+ mPoint2[3] = pos[3];
+ position += QString::number(mPoint2[3],'f',0) + " ";
+ }
+ mPoint2Selected = true;
+ mCurrentSlicerManager->AddLandmarkProfile(pos[0], pos[1], pos[2], pos[3]);
+ mCurrentSlicerManager->GetLandmarks()->GetLabels()->SetNumberOfValues(mCurrentSlicerManager->GetLandmarks()->GetLabels()->GetNumberOfValues()-1);
+ mCurrentSlicerManager->GetLandmarks()->GetLabels()->Modified();
+ mCurrentSlicerManager->GetLandmarks()->GetLabels()->InsertNextValue("P2");
+ }
+ }
+ mPosPoint2Label->setText(position);
+ isPointsSelected();
+ mCurrentSlicerManager->Render();
+}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+bool vvToolProfile::isPointsSelected()
+{
+ if (mPoint1Selected && mPoint2Selected) {
+ mSaveProfileButton->setEnabled(true);
+ computeProfile();
+ SetPoints();
+ for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ DisplayLine(i);
+ connect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentBegin(int)), this, SLOT(DeleteLine(int)));
+ connect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentEnd(int)), this, SLOT(DisplayLine(int)));
+ }
+ mCurrentSlicerManager->Render();
+ }
+ else {
+ mSaveProfileButton->setEnabled(false);
+ for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ disconnect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentBegin(int)), this, SLOT(DeleteLine(int)));
+ disconnect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentEnd(int)), this, SLOT(DisplayLine(int)));
+ mCurrentSlicerManager->GetSlicer(i)->GetRenderer()->RemoveActor(mLineActors[i]);
+ }
+
+ }
+ return (mPoint1Selected && mPoint2Selected);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::computeProfile()
+{
+ if (!mCurrentSlicerManager) close();
+ QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+ GetArgsInfoFromGUI();
+ ProfileWidget->hide();
+
+ // Main filter
+ mFilter->SetInputVVImage(mCurrentImage);
+ mFilter->SetArgsInfo(mArgsInfo);
+ mFilter->Update();
+
+ //Creation of the XY chart
+ vtkSmartPointer<vtkTable> table = vtkSmartPointer<vtkTable>::New();
+ vtkSmartPointer<vtkFloatArray> arrX = vtkSmartPointer<vtkFloatArray>::New();
+ vtkSmartPointer<vtkFloatArray> arrY = vtkSmartPointer<vtkFloatArray>::New();
+ arrX = mFilter->GetArrayX();
+ arrY = mFilter->GetArrayY();
+ arrX->SetName("Distance (mm)");
+ arrY->SetName("Intensity");
+
+ table->AddColumn(arrX);
+ table->AddColumn(arrY);
+
+ mView->GetRenderer()->SetBackground(1.0, 1.0, 1.0);
+
+ vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
+ chart->SetAutoSize(true);
+ mView->GetScene()->ClearItems();
+ mView->GetScene()->AddItem(chart);
+ vtkPlot *line = chart->AddPlot(vtkChart::LINE);
+#if VTK_MAJOR_VERSION <= 5
+ line->SetInput(table, 0, 1);
+#else
+ line->SetInputData(table, 0, 1);
+#endif
+ line->SetColor(0, 255, 0, 255);
+ line->SetWidth(1.0);
+ chart->GetAxis(vtkAxis::LEFT)->SetTitle("Intensity");
+ chart->GetAxis(vtkAxis::BOTTOM)->SetTitle("Distance (mm)");
+
+ this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
+ this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
+ ProfileWidget->show();
+
+ QApplication::restoreOverrideCursor();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::cancelPoints()
+{
+ if (mPoint1Selected)
+ mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P1", mPoint1[3]);
+ if (mPoint2Selected)
+ mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P2", mPoint2[3]);
+ ProfileWidget->hide();
+ vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
+ chart->SetAutoSize(false);
+ chart->SetRenderEmpty(true);
+ mView->GetScene()->ClearItems();
+ mView->GetScene()->AddItem(chart);
+ this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
+ this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
+ ProfileWidget->show();
+
+ QString position = "";
+ mPosPoint1Label->setText(position);
+ mPosPoint2Label->setText(position);
+ mPoint1Selected = false;
+ mPoint2Selected = false;
+ mSaveProfileButton->setEnabled(false);
+ isPointsSelected();
+ mCurrentSlicerManager->Render();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::RemoveVTKObjects()
+{
+ for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ mCurrentSlicerManager->GetSlicer(i)->GetRenderer()->RemoveActor(mLineActors[i]);
+ }
+
+ if (mPoint1Selected)
+ mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P1", mPoint1[3]);
+ if (mPoint2Selected)
+ mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P2", mPoint2[3]);
+
+
+ if (mCurrentSlicerManager)
+ mCurrentSlicerManager->Render();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+bool vvToolProfile::close()
+{
+ //RemoveVTKObjects();
+
+ connect(mCurrentSlicerManager, SIGNAL(callAddLandmark(float,float,float,float)), mCurrentSlicerManager, SLOT(AddLandmark(float,float,float,float)));
+ return vvToolWidgetBase::close();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::closeEvent(QCloseEvent *event)
+{
+ RemoveVTKObjects();
+ event->accept();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::reject()
+{
+ // DD("vvToolProfile::reject");
+ RemoveVTKObjects();
+ return vvToolWidgetBase::reject();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::InputIsSelected(vvSlicerManager * m)
+{
+ mCurrentSlicerManager = m;
+
+ mPoint1 = new double[4];
+ mPoint1[0] = mPoint1[1] = mPoint1[2] = mPoint1[3] = 0;
+ mPoint2 = new double[4];
+ mPoint2[0] = mPoint2[1] = mPoint2[2] = mPoint2[3] = 0;
+
+ mSaveProfileButton->setEnabled(false);
+ mTextFileName = "Profile.txt";
+ InitializeLine();
+
+ disconnect(mCurrentSlicerManager, SIGNAL(callAddLandmark(float,float,float,float)), mCurrentSlicerManager, SLOT(AddLandmark(float,float,float,float)));
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::GetArgsInfoFromGUI()
+{
+
+ /* //KEEP THIS FOR READING GGO FROM FILE
+ int argc=1;
+ std::string a = "toto";
+ char * const* argv = new char*;
+ //a.c_str();
+ struct cmdline_parser_params p;
+ p.check_required = 0;
+ int good = cmdline_parser_ext(argc, argv, &args_info, &p);
+ DD(good);
+ */
+ cmdline_parser_clitkProfileImage_init(&mArgsInfo); // Initialisation to default
+
+ mArgsInfo.verbose_flag = false;
+
+ mArgsInfo.point1_arg = mPoint1;
+ mArgsInfo.point2_arg = mPoint2;
+ mArgsInfo.point1_given = mCurrentSlicerManager->GetImage()->GetNumberOfDimensions();
+ mArgsInfo.point2_given = mCurrentSlicerManager->GetImage()->GetNumberOfDimensions();
+
+ // Required (even if not used)
+ mArgsInfo.input_given = 0;
+ mArgsInfo.output_given = 0;
+
+ mArgsInfo.input_arg = new char;
+ mArgsInfo.output_arg = new char;
+
+
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::apply()
+{
+ close();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::SaveAs()
+{
+ QStringList OutputListeFormat;
+ OutputListeFormat.clear();
+ OutputListeFormat.push_back(".txt");
+
+ QString Extensions = "AllFiles(*.*)";
+ for (int i = 0; i < OutputListeFormat.count(); i++) {
+ Extensions += ";;Text File ( *";
+ Extensions += OutputListeFormat[i];
+ Extensions += ")";
+ }
+ QString fileName = QFileDialog::getSaveFileName(this, tr("Save As"), mTextFileName.c_str(), Extensions);
+ if (!fileName.isEmpty()) {
+ std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
+ QString fileQFormat = fileformat.c_str();
+ if (OutputListeFormat.contains(fileformat.c_str()) || fileQFormat.isEmpty()) {
+ QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+ std::string action = "Saving";
+ vvProgressDialog progress("Saving "+fileName.toStdString());
+ qApp->processEvents();
+
+ if (!mCurrentSlicerManager || !isPointsSelected()) {
+ close();
+ return;
+ }
+
+ // Output
+ mTextFileName = fileName.toStdString();
+ if (fileQFormat.isEmpty())
+ mTextFileName += ".txt";
+ ofstream fileOpen(mTextFileName.c_str(), std::ofstream::trunc);
+
+ if(!fileOpen) {
+ cerr << "Error during saving" << endl;
+ QApplication::restoreOverrideCursor();
+ close();
+ return;
+ }
+
+ vtkSmartPointer<vtkFloatArray> arrX = vtkSmartPointer<vtkFloatArray>::New();
+ vtkSmartPointer<vtkFloatArray> arrY = vtkSmartPointer<vtkFloatArray>::New();
+ vtkSmartPointer<vtkFloatArray> coords = vtkSmartPointer<vtkFloatArray>::New();
+ arrX = mFilter->GetArrayX();
+ arrY = mFilter->GetArrayY();
+ coords = mFilter->GetCoord();
+ double *tuple;
+ tuple = new double[mCurrentSlicerManager->GetImage()->GetNumberOfDimensions()];
+ int i(0);
+ fileOpen << "The Bresenham algorithm is used to travel along the line. Values represent the center of each crossed voxel (in voxel and mm)" << endl;
+ fileOpen << "Id" << "\t" << "Value" << "\t" ;
+ fileOpen << "x(vox)" << "\t" << "y(vox)" << "\t";
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=3)
+ fileOpen << "z(vox)" << "\t";
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=4)
+ fileOpen << "t" << "\t";
+ fileOpen << "x(mm)" << "\t" << "y(mm)" << "\t";
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=3)
+ fileOpen << "z(mm)" << "\t";
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=4)
+ fileOpen << "t" << "\t";
+ fileOpen << endl;
+
+ while (i<arrX->GetNumberOfTuples()) {
+ fileOpen << i << "\t" << arrY->GetTuple(i)[0] << "\t" ;
+
+ coords->GetTuple(i, tuple);
+ for (int j=0; j<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() ; ++j) {
+ fileOpen << tuple[j] << "\t" ;
+ }
+ int j(0);
+ while (j<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && j<3) {
+ fileOpen << tuple[j]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[j]+mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[j] << "\t" ;
+ ++j;
+ }
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
+ fileOpen << tuple[3] << "\t" ;
+ }
+ fileOpen << endl;
+ ++i;
+ }
+
+ delete [] tuple;
+
+ fileOpen.close();
+ QApplication::restoreOverrideCursor();
+ } else {
+ QString error = fileformat.c_str();
+ error += " format unknown !!!\n";
+ QMessageBox::information(this,tr("Saving Problem"),error);
+ SaveAs();
+ }
+ }
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::DeleteLine(int slicer)
+{
+ if (!mPoint1Selected && !mPoint2Selected)
+ return;
+
+ if(mCurrentSlicerManager) {
+ if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
+ mCurrentSlicerManager->GetSlicer(slicer)->GetRenderer()->RemoveActor(mLineActors[slicer]);
+ }
+ }
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::DisplayLine(int slicer)
+{
+ if (!mPoint1Selected && !mPoint2Selected)
+ return;
+
+ if(mCurrentSlicerManager) {
+ if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
+ double currentSlice = (mCurrentSlicerManager->GetSlicer(slicer)->GetSlice()*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetInput()->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetInput()->GetOrigin()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] - mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] )/ mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()];
+ if (std::min(mPoint1[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()],mPoint2[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]) <= currentSlice && std::max(mPoint1[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()],mPoint2[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]) >= currentSlice) {
+ vtkSmartPointer<vtkBox> clippingBox = vtkSmartPointer<vtkBox>::New();
+ double extent[6];
+ for (int j=0; j<6; ++j) {
+ extent[j] = mCurrentSlicerManager->GetSlicer(slicer)->GetExtent()[j];
+ }
+ extent[2*mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] = mCurrentSlicerManager->GetSlicer(slicer)->GetImageActor()->GetBounds()[ mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()*2 ]-fabs(mCurrentSlicerManager->GetSlicer(slicer)->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]);
+ extent[2*mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()+1] = mCurrentSlicerManager->GetSlicer(slicer)->GetImageActor()->GetBounds()[ mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()*2+1 ]+fabs(mCurrentSlicerManager->GetSlicer(slicer)->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]);
+ clippingBox->SetBounds(extent);
+
+ vtkSmartPointer<vtkClipPolyData> clipper = vtkSmartPointer<vtkClipPolyData>::New();
+ clipper->SetClipFunction(clippingBox);
+#if VTK_MAJOR_VERSION <= 5
+ clipper->SetInput(mLinesPolyData);
+#else
+ mLineTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
+ mLineTransform->SetInputData(mLinesPolyData);
+ mLineTransform->SetTransform(mCurrentSlicerManager->GetSlicer(slicer)->GetConcatenatedTransform()->GetInverse());
+ clipper->SetInputConnection(mLineTransform->GetOutputPort());
+#endif
+ clipper->InsideOutOff();
+ clipper->Update();
+ vtkSmartPointer<vtkPolyDataMapper> lineMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
+#if VTK_MAJOR_VERSION <= 5
+ lineMapper->SetInput(clipper->GetOutput());
+#else
+ lineMapper->SetInputData(clipper->GetOutput());
+#endif
+
+ mLineActors[slicer]->SetMapper(lineMapper);
+ mLineActors[slicer]->GetProperty()->SetOpacity(0.995);
+
+ mCurrentSlicerManager->GetSlicer(slicer)->GetRenderer()->AddActor(mLineActors[slicer]);
+ }
+ }
+ }
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::InitializeLine()
+{
+ if(mCurrentSlicerManager) {
+
+ mLinesPolyData = vtkSmartPointer<vtkPolyData>::New();
+
+ vtkSmartPointer<vtkPoints> pts = vtkSmartPointer<vtkPoints>::New();
+ double pos[4];
+ pos[0] = pos[1] = pos[2] = pos[3] = 0;
+ pts->InsertNextPoint(pos);
+ pts->InsertNextPoint(pos);
+ mLinesPolyData->SetPoints(pts);
+
+ vtkSmartPointer<vtkCellArray> lines = vtkSmartPointer<vtkCellArray>::New();
+ vtkSmartPointer<vtkLine> line = vtkSmartPointer<vtkLine>::New();
+ line->GetPointIds()->SetId(0, 0); // the second 0 is the index of the 1st point in mLinesPolyData's points (pts)
+ line->GetPointIds()->SetId(1, 1); // the second 1 is the index of the 2nd point in mLinesPolyData's points (pts)
+ lines->InsertNextCell(line);
+ mLinesPolyData->SetLines(lines);
+
+ unsigned char red[3] = { 255, 0, 0 };
+ vtkSmartPointer<vtkUnsignedCharArray> colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
+ colors->SetNumberOfComponents(3);
+ colors->InsertNextTupleValue(red);
+ mLinesPolyData->GetCellData()->SetScalars(colors);
+
+ for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ mLineActors.push_back(vtkSmartPointer<vtkActor>::New());
+ }
+ }
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolProfile::SetPoints()
+{
+ if (!mPoint1Selected && !mPoint2Selected)
+ return;
+
+ if(mCurrentSlicerManager) {
+ if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
+ /*double *pos;
+ pos = new double [4];
+ pos[0] = pos[1] = pos[2] = pos[3] = 0;
+
+ int i(0);
+ while (i<3) {
+ pos[i] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetCursorPosition()[i];
+ ++i;
+ }
+ if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
+ pos[3] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetTSlice();
+ } */
+
+ double p0[4], p1[4];
+ p0[0] = mPoint1[0]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[0] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[0];
+ p0[1] = mPoint1[1]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[1] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[1];
+ p0[2] = mPoint1[2]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[2] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[2];
+ p0[3] = mPoint1[3];
+
+ p1[0] = mPoint2[0]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[0] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[0];
+ p1[1] = mPoint2[1]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[1] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[1];
+ p1[2] = mPoint2[2]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[2] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[2];
+ p1[3] = mPoint2[3];
+
+ vtkSmartPointer<vtkPoints> pts = mLinesPolyData->GetPoints();
+ pts->SetPoint(0,p0);
+ pts->SetPoint(1,p1);
+ }
+ }
+}
+//------------------------------------------------------------------------------
+
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef VVTOOLPROFILE_H
+#define VVTOOLPROFILE_H
+
+#include <QtGlobal>
+#include <QtDesigner/QDesignerExportWidget>
+
+#include "vvToolBase.h"
+#include "vvToolWidgetBase.h"
+#include "vvImageContour.h"
+#include "vvLandmarks.h"
+#include "ui_vvToolProfile.h"
+#include "vvBinaryImageOverlayActor.h"
+
+#include "clitkProfileImage_ggo.h"
+#include "clitkProfileImageGenericFilter.h"
+#include <vtkTable.h>
+#include <vtkContextView.h>
+#include <vtkContextScene.h>
+#include <vtkTransformPolyDataFilter.h>
+
+//------------------------------------------------------------------------------
+class vvToolProfile:
+ public vvToolWidgetBase,
+ public vvToolBase<vvToolProfile>,
+ private Ui::vvToolProfile
+{
+ Q_OBJECT
+ public:
+ vvToolProfile(vvMainWindowBase * parent=0, Qt::WindowFlags f=0);
+ ~vvToolProfile();
+
+ //-----------------------------------------------------
+ static void Initialize();
+ void InitializeLine();
+ void GetArgsInfoFromGUI();
+ virtual void InputIsSelected(vvSlicerManager * m);
+
+ bool isPointsSelected();
+ void computeProfile();
+ void SetPoints();
+
+ //-----------------------------------------------------
+ public slots:
+ virtual void apply();
+ virtual bool close();
+ virtual void reject();
+
+ void selectPoint1();
+ void selectPoint2();
+ void cancelPoints();
+ void SaveAs();
+ void DisplayLine(int);
+ void DeleteLine(int);
+
+ protected:
+ void RemoveVTKObjects();
+ virtual void closeEvent(QCloseEvent *event);
+ Ui::vvToolProfile ui;
+ args_info_clitkProfileImage mArgsInfo;
+
+ double* mPoint1;
+ double* mPoint2;
+ bool mPoint1Selected;
+ bool mPoint2Selected;
+ vtkSmartPointer<vtkContextView> mView;
+ clitk::ProfileImageGenericFilter::Pointer mFilter;
+ std::string mTextFileName;
+ std::vector<vtkSmartPointer<vtkActor> > mLineActors;
+ vtkSmartPointer<vtkPolyData> mLinesPolyData;
+ vtkSmartPointer<vtkTransformPolyDataFilter> mLineTransform;
+
+
+}; // end class vvToolProfile
+//------------------------------------------------------------------------------
+
+#endif
+
#include "vvImageWriter.h"
#include "vvROIActor.h"
#include "vvSlicer.h"
-#include "vvROIActor.h"
#include "vvMeshReader.h"
#include "vvStructSelector.h"
#include "vvToolManager.h"
#include <QColorDialog>
#include <QAbstractEventDispatcher>
#include <QXmlStreamReader>
-
+
// vtk
#include <vtkLookupTable.h>
#include <vtkRenderWindow.h>
ADD_TOOL(vvToolROIManager);
//------------------------------------------------------------------------------
+int vvToolROIManager::nbTotalROI = 0;
+
//------------------------------------------------------------------------------
vvToolROIManager::vvToolROIManager(vvMainWindowBase * parent, Qt::WindowFlags f):
- QWidget(parent->GetTab()),
+ QWidget(parent->GetTab()),
vvToolBase<vvToolROIManager>(parent),
Ui::vvToolROIManager()
-{
+{
// Store parent
mMainWindow = parent;
-
+
// Assume the initial tab ROI index is 2
mIndexFirstTab = 2;
mTree->clear();
mTree->header()->resizeSection(0, 30);
mGroupBoxROI->setEnabled(false);
-
+
// Disable "Load dicom" button -> not useful
frame_4->hide();
//------------------------------------------------------------------------------
vvToolROIManager::~vvToolROIManager()
-{
+{
mROIActorsList.clear();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
// STATIC
-void vvToolROIManager::Initialize() {
+void vvToolROIManager::Initialize()
+{
SetToolName("ROIManager");
SetToolMenuName("Open ROI (binary image or RT-STRUCT)");
SetToolIconFilename(":/common/icons/tool-roi.png");
//------------------------------------------------------------------------------
-void vvToolROIManager::InitializeNewTool(bool ReadStateFlag)
-{
+void vvToolROIManager::InitializeNewTool(bool ReadStateFlag)
+{
// Check if we need to start a new tool or read in the state file to load
if (ReadStateFlag == false) {
// Select the current image as the target
// Read all information in the XML
ReadXMLInformation();
-
- // Check that a ROI is not already present
+
+ // Check that a ROI is not already present
mInitialImageIndex += mImageIndex;
if (mInitialImageIndex >= mMainWindow->GetSlicerManagers().size()) {
QMessageBox::warning(this, "ROIManager tool", QString("Image index %1 not found, abort.").arg(mInitialImageIndex));
close();
return;
}
-
+
// Set the attached image
mCurrentSlicerManager = mMainWindow->GetSlicerManagers()[mInitialImageIndex];
}
// Tab insertion, check that another tool does not already exist for this image
- std::vector<vvToolBaseBase*> & tools =
+ std::vector<vvToolBaseBase*> & tools =
vvToolManager::GetInstance()->GetToolCreatorFromName(GetToolName())->GetListOfTool();
if (tools.size() > 0) {
for(uint i=0; i<tools.size()-1; i++) { // current tool is last
}
// Display tool in the correct tab
- QWidget * tab = qFindChild<QWidget*>(mMainWindow->GetTab(), "ROItab");
+ QWidget * tab = mMainWindow->GetTab()->findChild<QWidget*>("ROItab");
tab->layout()->addWidget(this);
-
+
// If not read in a file we start automatically the browser to load
// a roi file (binary image)
- if (ReadStateFlag) {
+ if (ReadStateFlag) {
mOpenFileBrowserFlag = false;
InputIsSelected(mCurrentSlicerManager);
mOpenFileBrowserFlag = true;
roi->GetROI()->GetDisplayColor()[2]*255));
brush.setStyle(Qt::SolidPattern);
w->setBackground(2, brush);
- w->setText(3, QString("%1").arg(roi->GetDepth()));
+ w->setText(3, QString("%1").arg(roi->GetDepth()));
roi->UpdateColor();
}
// Display the ROI
UpdateAllContours();
- UpdateAllROIStatus();
+ UpdateAllROIStatus();
// Connect event from mainwindow to this widget
- connect(mMainWindow, SIGNAL(AnImageIsBeingClosed(vvSlicerManager *)),
+ connect(mMainWindow, SIGNAL(AnImageIsBeingClosed(vvSlicerManager *)),
this, SLOT(AnImageIsBeingClosed(vvSlicerManager *)));
- connect(mMainWindow, SIGNAL(SelectedImageHasChanged(vvSlicerManager *)),
+ connect(mMainWindow, SIGNAL(SelectedImageHasChanged(vvSlicerManager *)),
this, SLOT(SelectedImageHasChanged(vvSlicerManager *)));
connect(mOpenBinaryButton, SIGNAL(clicked()), this, SLOT(Open()));
// connect(mOpenDicomButton, SIGNAL(clicked()), this, SLOT(OpenDicomImage()));
connect(mCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleROIToggled(bool)));
connect(mOpacitySlider, SIGNAL(valueChanged(int)), this, SLOT(OpacityChanged(int)));
connect(mChangeColorButton, SIGNAL(clicked()), this, SLOT(ChangeColor()));
- connect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
+ connect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
connect(mChangeContourColorButton, SIGNAL(clicked()), this, SLOT(ChangeContourColor()));
connect(mContourWidthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeContourWidth(int)));
connect(mDepthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeDepth(int)));
connect(mReloadButton, SIGNAL(clicked()), this, SLOT(ReloadCurrentROI()));
connect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
- connect(mContourCheckBoxShowAll, SIGNAL(toggled(bool)), this, SLOT(AllVisibleContourROIToggled(bool)));
+ connect(mContourCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleContourROIToggled(int)));
connect(mCloseButton, SIGNAL(clicked()), this, SLOT(close()));
+ connect(mRemoveButton, SIGNAL(clicked()), this, SLOT(RemoveROI()));
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolROIManager::InputIsSelected(vvSlicerManager *m)
-{
+{
// Initialization
mCurrentSlicerManager = m;
mCurrentImage = mCurrentSlicerManager->GetImage();
- // Refuse if non 3D image
- if (mCurrentImage->GetNumberOfDimensions() != 3) {
- QMessageBox::information(this,tr("Sorry only 3D yet"), tr("Sorry only 3D yet"));
- close();
- return;
- }
-
// Change gui
mLabelInputInfo->setText(QString("%1").arg(m->GetFileName().c_str()));
- // Auto display browser to select new contours
+ // Auto display browser to select new contours
if (mOpenFileBrowserFlag) Open();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolROIManager::AnImageIsBeingClosed(vvSlicerManager * m)
-{
- if (m == mCurrentSlicerManager) {
+{
+ if (m == mCurrentSlicerManager) {
close();
return;
}
}
//------------------------------------------------------------------------------
+void vvToolROIManager::RemoveROI()
+{
+
+ // Search the indice of the selected ROI
+ QList<QTreeWidgetItem *> l = mTree->selectedItems();
+ if (l.size() == 0)
+ return;
+
+ QTreeWidgetItem * w = l[0];
+ if (w == NULL) return;
+ if (w == 0) return;
+ if (mMapTreeWidgetToROI.find(w) == mMapTreeWidgetToROI.end()) {
+ return;
+ }
+
+ clitk::DicomRT_ROI * roi = mMapTreeWidgetToROI[w];
+ if (roi == NULL) return;
+
+ // Get selected roi actor
+ int n = roi->GetROINumber();
+
+ disconnect(mTree, SIGNAL(itemSelectionChanged()), this, SLOT(SelectedItemChangedInTree()));
+ mROIActorsList[n]->RemoveActors();
+ mROIActorsList.erase(mROIActorsList.begin()+n);
+ mROIList.erase(mROIList.begin()+n);
+ mTreeWidgetList.erase(mTreeWidgetList.begin()+n);
+
+ for (int i = n; i < mROIActorsList.size(); ++i) {
+ mROIList[i]->SetROINumber(i);
+ mTreeWidgetList[i].data()->setText(0, QString("%1").arg(mROIList[i]->GetROINumber()));
+ }
+ connect(mTree, SIGNAL(itemSelectionChanged()), this, SLOT(SelectedItemChangedInTree()));
+ for(int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ mCurrentSlicerManager->GetSlicer(i)->Render();
+ }
+}
+//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolROIManager::close()
-{
+{
disconnect(mTree, SIGNAL(itemSelectionChanged()), this, SLOT(SelectedItemChangedInTree()));
disconnect(mCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleROIToggled(bool)));
disconnect(mOpacitySlider, SIGNAL(valueChanged(int)), this, SLOT(OpacityChanged(int)));
disconnect(mChangeColorButton, SIGNAL(clicked()), this, SLOT(ChangeColor()));
- disconnect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
+ disconnect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
disconnect(mChangeContourColorButton, SIGNAL(clicked()), this, SLOT(ChangeContourColor()));
disconnect(mContourWidthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeContourWidth(int)));
disconnect(mDepthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeDepth(int)));
+ disconnect(mRemoveButton, SIGNAL(clicked()), this, SLOT(RemoveROI()));
// Remove actors
for (unsigned int i = 0; i < mROIActorsList.size(); i++) {
//------------------------------------------------------------------------------
-void vvToolROIManager::SelectedImageHasChanged(vvSlicerManager * m) {
-
+void vvToolROIManager::SelectedImageHasChanged(vvSlicerManager * m)
+{
if (mCurrentSlicerManager == NULL) return;
if (m == NULL) return;
- if (m != mCurrentSlicerManager) hide();
+ if (m != mCurrentSlicerManager) hide();
else {
show();
}
//------------------------------------------------------------------------------
-void vvToolROIManager::Open()
-{
+void vvToolROIManager::Open()
+{
// Open images
QString Extensions = "Images or Dicom-Struct files ( *.mha *.mhd *.hdr *.his *.dcm RS*)";
Extensions += ";;All Files (*)";
//------------------------------------------------------------------------------
-void vvToolROIManager::OpenBinaryImage(QStringList & filename)
-{
+void vvToolROIManager::OpenBinaryImage(QStringList & filename)
+{
if (filename.size() == 0) return;
-
+
vvProgressDialog p("Reading ROI ...", true);
p.SetCancelButtonEnabled(false);
QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
-
+
// For each selected file, open the image
- for(int i=0; i<filename.size(); i++) {
+ for(int i=0; i<filename.size(); i++) {
p.SetProgress(i, filename.size());
// Open Image
filenames.push_back(filename[i].toStdString());
reader->SetInputFilenames(filenames);
reader->Update(vvImageReader::IMAGE);
-
+
if (reader->GetLastError().size() != 0) {
std::cerr << "Error while reading " << filename[i].toStdString() << std::endl;
QString error = "Cannot open file \n";
QApplication::restoreOverrideCursor();
// Update the contours
- UpdateAllContours();
+ UpdateAllContours();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::OpenDicomImage(std::string filename)
-{
+void vvToolROIManager::OpenDicomImage(std::string filename)
+{
// GUI selector of roi
vvMeshReader reader;
reader.SetFilename(filename);
-
+
vvStructSelector selector;
selector.SetStructures(reader.GetROINames());
selector.SetPropagationCheckBoxFlag(false);
-
- if (selector.exec()) {
+
+ if (selector.exec()) {
vvProgressDialog p("Reading ROI...", true);
p.SetCancelButtonEnabled(false);
QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
// Loop on selected struct
std::vector<int> list = selector.getSelectedItems();
for (uint i=0; i<list.size(); i++) {
- p.SetProgress(i, list.size());
-
+ p.SetProgress(i, list.size());
+
clitk::DicomRTStruct2ImageFilter filter;
filter.SetCropMaskEnabled(true);
filter.SetImage(mCurrentImage);
- filter.SetROI(s->GetROIFromROINumber(list[i]));
+ filter.SetROI(s->GetROIFromROINumber(list[i]));
filter.SetWriteOutputFlag(false);
- filter.Update();
+ filter.Update();
// Get image
vvImage::Pointer binaryImage = vvImage::New();
binaryImage->AddVtkImage(filter.GetOutput());
-
+
// Add to gui
AddImage(binaryImage, s->GetROIFromROINumber(list[i])->GetName(), "", 0, true); // "" = no filename
mOpenedBinaryImageFilenames.push_back(filename.c_str());
QApplication::restoreOverrideCursor();
}
// Update the contours
- UpdateAllContours();
+ UpdateAllContours();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::AddImage(vvImage * binaryImage,
- std::string name,
- std::string filename,
- double BG, bool modeBG)
-{
+void vvToolROIManager::AddImage(vvImage * binaryImage,
+ std::string name,
+ std::string filename,
+ double BG, bool modeBG)
+{
// Check Dimension
int dim = mCurrentImage->GetNumberOfDimensions();
int bin_dim = binaryImage->GetNumberOfDimensions();
QMessageBox::information(this,tr("Reading problem"),os.str().c_str());
return;
}
-
+
// Compute roi index
- int n = mROIList.size();
+ int n = nbTotalROI;
+ ++nbTotalROI;
// Compute the name of the new ROI
// std::ostringstream oss;
// oss << vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
// std::string name = oss.str();
-
+
// Set color
std::vector<double> color;
color.push_back(1);
// Create ROI
clitk::DicomRT_ROI::Pointer roi = clitk::DicomRT_ROI::New();
- roi->SetFromBinaryImage(binaryImage, n, name, color, filename);
+ roi->SetFromBinaryImage(binaryImage, mROIList.size(), name, color, filename);
// Add a new roi to the list
mROIList.push_back(roi);
-
+
// Set BG or FG mode
- if (modeBG)
+ if (modeBG)
roi->SetBackgroundValueLabelImage(BG);
- else
+ else
roi->SetForegroundValueLabelImage(BG);
-
+
// Change color
if (n<mDefaultLUTColor->GetNumberOfTableValues ()) {
double * color = mDefaultLUTColor->GetTableValue(n % mDefaultLUTColor->GetNumberOfTableValues ());
roi->SetDisplayColor(color[0], color[1], color[2]);
}
-
+
// Add a new roi actor
QSharedPointer<vvROIActor> actor = QSharedPointer<vvROIActor>(new vvROIActor);
actor->SetBGMode(modeBG);
actor->SetSlicerManager(mCurrentSlicerManager);
actor->Initialize(n+1); // depth is n+1 to start at 1
mROIActorsList.push_back(actor);
-
+
// CheckBox for "All"
if (actor->IsVisible()) mNumberOfVisibleROI++;
if (actor->IsContourVisible()) mNumberOfVisibleContourROI++;
+ AllVisibleContourROIToggled(1);
// Add ROI in tree
mTreeWidgetList.push_back(QSharedPointer<QTreeWidgetItem>(new QTreeWidgetItem(mTree)));
QTreeWidgetItem * w = mTreeWidgetList.back().data();
w->setText(0, QString("%1").arg(roi->GetROINumber()));
w->setText(1, QString("%1").arg(roi->GetName().c_str()));
- w->setText(3, QString("%1").arg(actor->GetDepth()));
- QBrush brush(QColor(roi->GetDisplayColor()[0]*255,
- roi->GetDisplayColor()[1]*255,
+ w->setText(3, QString("%1").arg(actor->GetDepth()));
+ QBrush brush(QColor(roi->GetDisplayColor()[0]*255,
+ roi->GetDisplayColor()[1]*255,
roi->GetDisplayColor()[2]*255));
brush.setStyle(Qt::SolidPattern);
w->setBackground(2, brush);
mTree->resizeColumnToContents(0);
mTree->resizeColumnToContents(1);
- // Update
- UpdateAllROIStatus();
+ // Update
+ UpdateAllROIStatus();
+
+ if (mCurrentImage->GetNumberOfDimensions() > 3) {
+
+ //Modifications to avoid display bug with a 4D image
+ QSharedPointer<vvROIActor> CurrentROIActorTemp;
+ CurrentROIActorTemp = mCurrentROIActor;
+ mCurrentROIActor = actor;
+
+ int VisibleInWindow(0);
+ mCurrentSlicerManager->GetSlicer(VisibleInWindow)->SetCurrentPosition(-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,mCurrentSlicerManager->GetSlicer(VisibleInWindow)->GetMaxCurrentTSlice());
+ mCurrentSlicerManager->GetSlicer(VisibleInWindow)->Render();
+
+ VisibleROIToggled(false);
+ VisibleROIToggled(true);
+
+ mCurrentROIActor = CurrentROIActorTemp;
+
+ }
+
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::UpdateAllContours()
-{
+void vvToolROIManager::UpdateAllContours()
+{
if (mCurrentSlicerManager == NULL) return;
// Render loaded ROIs (the first is sufficient)
for(unsigned int i=0; i<mROIList.size(); i++) {
mROIActorsList[i]->Update();
}
- mCurrentSlicerManager->Render();
+ //mCurrentSlicerManager->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::UpdateAllROIStatus() {
+void vvToolROIManager::UpdateAllROIStatus()
+{
int nbVisible = 0;
+ int nbContourVisible = 0;
int nb = mROIList.size();
for(int i=0; i<nb; i++) {
if (mROIActorsList[i]->IsVisible()) {
nbVisible++;
}
+ if (mROIActorsList[i]->IsContourVisible()) {
+ nbContourVisible++;
+ }
}
// change the states
- disconnect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
- disconnect(mContourCheckBoxShowAll, SIGNAL(toggled(bool)), this, SLOT(AllVisibleContourROIToggled(bool)));
+ disconnect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
+ disconnect(mContourCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleContourROIToggled(int)));
if (nbVisible == nb) mCheckBoxShowAll->setCheckState(Qt::Checked);
else {
if (nbVisible == 0) mCheckBoxShowAll->setCheckState(Qt::Unchecked);
else mCheckBoxShowAll->setCheckState(Qt::PartiallyChecked);
}
- connect(mContourCheckBoxShowAll, SIGNAL(toggled(bool)), this, SLOT(AllVisibleContourROIToggled(bool)));
+ if (nbContourVisible == nb) mContourCheckBoxShowAll->setCheckState(Qt::Checked);
+ else {
+ if (nbContourVisible == 0) mContourCheckBoxShowAll->setCheckState(Qt::Unchecked);
+ else mContourCheckBoxShowAll->setCheckState(Qt::PartiallyChecked);
+ }
+ connect(mContourCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleContourROIToggled(int)));
connect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::SelectedItemChangedInTree() {
+void vvToolROIManager::SelectedItemChangedInTree()
+{
// Search which roi is selected
QList<QTreeWidgetItem *> l = mTree->selectedItems();
if (l.size() == 0) {
mCurrentROI = roi;
mCurrentROIActor = actor;
- // Warning -> avoid unuseful Render here by disconnect slider
+ // Warning -> avoid unuseful Render here by disconnect slider
// Update GUI
disconnect(mTree, SIGNAL(itemSelectionChanged()), this, SLOT(SelectedItemChangedInTree()));
disconnect(mCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleROIToggled(bool)));
disconnect(mOpacitySlider, SIGNAL(valueChanged(int)), this, SLOT(OpacityChanged(int)));
disconnect(mChangeColorButton, SIGNAL(clicked()), this, SLOT(ChangeColor()));
- disconnect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
+ disconnect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
disconnect(mChangeContourColorButton, SIGNAL(clicked()), this, SLOT(ChangeContourColor()));
disconnect(mContourWidthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeContourWidth(int)));
disconnect(mDepthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeDepth(int)));
+ disconnect(mRemoveButton, SIGNAL(clicked()), this, SLOT(RemoveROI()));
mROInameLabel->setText(roi->GetName().c_str());
mCheckBoxShow->setChecked(actor->IsVisible());
connect(mCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleROIToggled(bool)));
connect(mOpacitySlider, SIGNAL(valueChanged(int)), this, SLOT(OpacityChanged(int)));
connect(mChangeColorButton, SIGNAL(clicked()), this, SLOT(ChangeColor()));
- connect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
+ connect(mContourCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleContourROIToggled(bool)));
connect(mChangeContourColorButton, SIGNAL(clicked()), this, SLOT(ChangeContourColor()));
connect(mContourWidthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeContourWidth(int)));
connect(mDepthSpinBox, SIGNAL(valueChanged(int)), this, SLOT(ChangeDepth(int)));
+ connect(mRemoveButton, SIGNAL(clicked()), this, SLOT(RemoveROI()));
+
-
// Set the current color to the selected ROI name
mROInameLabel->setAutoFillBackground(true);// # This is important!!
// mROInameLabel->setStyleSheet("QLabel { background-color : red; color : blue; }");
(1-mCurrentROI->GetDisplayColor()[2])*255);
palette->setColor(QPalette::WindowText,colorFG);
palette->setColor(QPalette::Background, color);
- mROInameLabel->setPalette(*palette);
+ mROInameLabel->setPalette(*palette);
// Enable the group box (in case no selection before)
mGroupBoxROI->setEnabled(true);
//------------------------------------------------------------------------------
-void vvToolROIManager::VisibleROIToggled(bool b) {
+void vvToolROIManager::VisibleROIToggled(bool b)
+{
if (mCurrentROIActor == NULL) return;
if (b == mCurrentROIActor->IsVisible()) return; // nothing to do
mCurrentROIActor->SetVisible(b);
UpdateAllROIStatus();
- mCurrentSlicerManager->Render();
+ mCurrentSlicerManager->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::VisibleContourROIToggled(bool b) {
+void vvToolROIManager::VisibleContourROIToggled(bool b)
+{
if (mCurrentROIActor == NULL) return;
if (mCurrentROIActor->IsContourVisible() == b) return; // nothing to do
mCurrentROIActor->SetContourVisible(b);
mCurrentROIActor->UpdateColor();
- mCurrentSlicerManager->Render();
+ UpdateAllROIStatus();
+ mCurrentSlicerManager->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::OpacityChanged(int v) {
+void vvToolROIManager::OpacityChanged(int v)
+{
if (mCurrentROIActor == NULL) return;
mCurrentROIActor->SetOpacity((double)v/100.0);
mCurrentROIActor->UpdateColor();
- mCurrentSlicerManager->Render();
+ mCurrentSlicerManager->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::AllVisibleROIToggled(int b) {
+void vvToolROIManager::AllVisibleROIToggled(int b)
+{
+ disconnect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
bool status = false;
if ((mCheckBoxShowAll->checkState() == Qt::Checked) ||
(mCheckBoxShowAll->checkState() == Qt::PartiallyChecked)) status = true;
if (status) mCheckBoxShowAll->setCheckState(Qt::Checked);
else mCheckBoxShowAll->setCheckState(Qt::Unchecked);
mCheckBoxShow->setChecked(status);
- mCurrentSlicerManager->Render();
+ mCurrentSlicerManager->Render();
+ connect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::AllVisibleContourROIToggled(bool b) {
+void vvToolROIManager::AllVisibleContourROIToggled(int b)
+{
+ disconnect(mContourCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleContourROIToggled(int)));
bool status = false;
if ((mContourCheckBoxShowAll->checkState() == Qt::Checked) ||
(mContourCheckBoxShowAll->checkState() == Qt::PartiallyChecked)) status = true;
- // Update current
+ // Update current
for(uint i=0; i<mROIActorsList.size(); i++) {
mROIActorsList[i]->SetContourVisible(status);
}
if (status) mContourCheckBoxShowAll->setCheckState(Qt::Checked);
else mContourCheckBoxShowAll->setCheckState(Qt::Unchecked);
mContourCheckBoxShow->setChecked(status);
- mCurrentSlicerManager->Render();
+ mCurrentSlicerManager->Render();
+ connect(mContourCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleContourROIToggled(int)));
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
-void vvToolROIManager::ChangeColor() {
+void vvToolROIManager::ChangeColor()
+{
if (mCurrentROIActor == NULL) return;
QColor color;
color.setRgbF(mCurrentROIActor->GetROI()->GetDisplayColor()[0],
//------------------------------------------------------------------------------
-void vvToolROIManager::ChangeContourColor() {
+void vvToolROIManager::ChangeContourColor()
+{
if (mCurrentROIActor == NULL) return;
QColor color;
- color.setRgbF(mCurrentROIActor->GetContourColor()[0],
- mCurrentROIActor->GetContourColor()[1],
+ color.setRgbF(mCurrentROIActor->GetContourColor()[0],
+ mCurrentROIActor->GetContourColor()[1],
mCurrentROIActor->GetContourColor()[2]);
// QColorDialog d(color);
QColor c = QColorDialog::getColor(color, this, "Choose the contour color");
//------------------------------------------------------------------------------
-void vvToolROIManager::ChangeContourWidth(int n) {
+void vvToolROIManager::ChangeContourWidth(int n)
+{
if (mCurrentROIActor == NULL) return;
mCurrentROIActor->SetContourWidth(n);
mCurrentROIActor->UpdateColor();
//------------------------------------------------------------------------------
-void vvToolROIManager::ChangeDepth(int n) {
+void vvToolROIManager::ChangeDepth(int n)
+{
if (mCurrentROIActor == NULL) return;
mCurrentROIActor->SetDepth(n);
- // mCurrentROIActor->UpdateImage(); // FIXME
+ // mCurrentROIActor->UpdateImage(); // FIXME
mCurrentSlicerManager->Render();
QList<QTreeWidgetItem *> l = mTree->selectedItems();
QTreeWidgetItem * w = l[0];
//------------------------------------------------------------------------------
-void vvToolROIManager::ReloadCurrentROI() {
+void vvToolROIManager::ReloadCurrentROI()
+{
if (mCurrentROI->GetFilename() == "") {
return; // do nothing (contour from rt struct do not reload)
}
mCurrentROIActor->SetVisible(false);
mCurrentROIActor->SetContourVisible(false);
mCurrentSlicerManager->Render();
-
+
// Reload image
vvImageReader::Pointer reader = vvImageReader::New();
reader->SetInputFilename(mCurrentROI->GetFilename());
reader->Update(vvImageReader::IMAGE);
if (reader->GetLastError() != "") {
// No message just ignore (because can be from dicom)
- // QMessageBox::information(mMainWindowBase, tr("Sorry, error. Could not reload"),
+ // QMessageBox::information(mMainWindowBase, tr("Sorry, error. Could not reload"),
// reader->GetLastError().c_str());
return;
}
mCurrentROIActor->UpdateImage();
mCurrentROIActor->SetVisible(visible);
mCurrentROIActor->SetContourVisible(cvisible);
- mCurrentSlicerManager->Render();
+ mCurrentSlicerManager->Render();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolROIManager::SaveState(std::auto_ptr<QXmlStreamWriter> & m_XmlWriter)
-{
+{
// Get index of the image
int n = mMainWindow->GetSlicerManagers().size();
int index=-1;
m_XmlWriter->writeAttribute("Opacity", QString("%1").arg(roi->GetOpacity()));
m_XmlWriter->writeAttribute("Depth", QString("%1").arg(roi->GetDepth()));
m_XmlWriter->writeEndElement();
-
+
m_XmlWriter->writeStartElement("Contour");
m_XmlWriter->writeAttribute("Red", QString("%1").arg(roi->GetContourColor()[0]));
m_XmlWriter->writeAttribute("Green",QString("%1").arg(roi->GetContourColor()[1]));
//------------------------------------------------------------------------------
-void vvToolROIManager::ReadXMLInformation()
-{
+void vvToolROIManager::ReadXMLInformation()
+{
std::string value="";
mInitialImageIndex = -1;
- while (!(m_XmlReader->isEndElement() && value == GetToolName().toStdString())) {
+ while (!(m_XmlReader->isEndElement() && value == GetToolName().toStdString())) {
m_XmlReader->readNext();
value = m_XmlReader->qualifiedName().toString().toStdString();
-
- if (value == "Image_Index")
+
+ if (value == "Image_Index")
mInitialImageIndex = m_XmlReader->readElementText().toInt();
-
+
if (m_XmlReader->isStartElement()) {
if (value == "ROI") {
ReadXMLInformation_ROI();
- }
+ }
}
}
}
//------------------------------------------------------------------------------
-void vvToolROIManager::ReadXMLInformation_ROI()
-{
+void vvToolROIManager::ReadXMLInformation_ROI()
+{
QString s;
std::string value="";
QSharedPointer<vvROIActor> param = QSharedPointer<vvROIActor>(new vvROIActor);
int width = 1;
int depth=1;
- while (!(m_XmlReader->isEndElement() && value == "ROI")) {
+ while (!(m_XmlReader->isEndElement() && value == "ROI")) {
m_XmlReader->readNext();
value = m_XmlReader->qualifiedName().toString().toStdString();
if (value == "Image") {
s = m_XmlReader->readElementText();
}
-
+
if (value == "Overlay" && m_XmlReader->isStartElement()) {
QXmlStreamAttributes attributes = m_XmlReader->attributes();
if (!m_XmlReader->hasError())
}
param->SetOverlayColor(r,g,b);
param->SetVisible(visible);
- param->SetOpacity(opacity);
- param->SetDepth(depth);
+ param->SetOpacity(opacity);
+ param->SetDepth(depth);
param->SetContourColor(cr,cg,cb);
param->SetContourVisible(cvisible);
#ifndef VVTOOLROIMANAGER_H
#define VVTOOLROIMANAGER_H
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include <QSharedPointer>
void ChangeContourWidth(int n);
void ChangeDepth(int n);
void AllVisibleROIToggled(int b);
- void AllVisibleContourROIToggled(bool b);
+ void AllVisibleContourROIToggled(int b);
void ReloadCurrentROI();
void close();
+ void RemoveROI();
vvSlicerManager * GetCurrentSlicerManager() { return mCurrentSlicerManager; }
protected:
int mNumberOfVisibleROI;
int mNumberOfVisibleContourROI;
+ static int nbTotalROI;
vtkSmartPointer<vtkLookupTable> mDefaultLUTColor;
// Go !
mFilter->Update();
mOutput = mFilter->GetOutputVVImage();
+ mOutput->GetTransform()[0]->SetMatrix(mCurrentSlicerManager->GetSlicer(0)->GetConcatenatedTransform()->GetMatrix());
AddImage(mOutput,GetOutputFileName());
close();
}
// vv
#include "vvToolRigidReg.h"
#include "vvSlicer.h"
+#include <vvBlendImageActor.h>
// vtk
#include <vtkImageData.h>
#include <vtkSmartPointer.h>
+#include <vtkInformation.h>
#include <vtkTransform.h>
+#include <vtkImageActor.h>
+#include <vtkImageMapper3D.h>
+#include <vtkOpenGLImageSliceMapper.h>
// itk
#include <itkEuler3DTransform.h>
itk::Euler3DTransform<double>::Pointer euler;
euler = itk::Euler3DTransform<double>::New();
euler->SetCenter(center);
- euler->SetMatrix(rotMat);
+ try {
+#if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR > 6)
+ euler->SetMatrix(rotMat,0.00001);
+#else
+ euler->SetMatrix(rotMat);
+#endif
+ } catch (itk::ExceptionObject) {
+ QString warning = "The matrice is a non-orthogonal rotation matrix.\nThe manual registration doesn't work.";
+ QMessageBox msgBox(QMessageBox::Warning, tr("Reset transform"),warning, 0, this);
+ msgBox.addButton(tr("OK"), QMessageBox::AcceptRole);
+ if (msgBox.exec() == QMessageBox::AcceptRole) {
+ //SetTransform(mInitialMatrix);
+ vvToolWidgetBase::close();
+ }
+ }
euler->SetOffset(transVec);
// Modify GUI according to the new parameters
double rad = (checkBoxDegrees->checkState()==Qt::Checked)?180./itk::Math::pi:1.;
double angleDiff = euler->GetParameters()[i]-rotSBs[i]->value()/rad+2*itk::Math::pi;
angleDiff = angleDiff - 2*itk::Math::pi*itk::Math::Round<double,double>(angleDiff/(2*itk::Math::pi));
- if(angleDiff>1.e-4) {
+ if(abs(angleDiff)>1.e-4) {
rotSBs[i]->blockSignals(true);
rotSBs[i]->setValue( euler->GetParameters()[i]*rad );
rotSBs[i]->blockSignals(false);
}
//------------------------------------------------------------------------------
+//------------------------------------------------------------------------------
+void vvToolRigidReg::ExtentMax(const double pointExtent[8][4], double maxExtent[2][3])
+{
+ double max, min;
+ for (int i=0; i<3; ++i) {
+ max = pointExtent[0][i];
+ min = pointExtent[0][i];
+ for (int j=1; j<8; ++j) {
+ if (pointExtent[j][i] > max) {
+ max = pointExtent[j][i];
+ }
+ if (pointExtent[j][i] < min) {
+ min = pointExtent[j][i];
+ }
+ }
+ maxExtent[0][i] = min;
+ maxExtent[1][i] = max;
+ }
+}
+//------------------------------------------------------------------------------
+
//------------------------------------------------------------------------------
void vvToolRigidReg::Render()
{
- for (int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++)
- {
+for (int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
mCurrentSlicerManager->GetSlicer(i)->ForceUpdateDisplayExtent();
mCurrentSlicerManager->GetSlicer(i)->Render();
- }
+}
}
//------------------------------------------------------------------------------
Ui::vvToolRigidReg ui;
vvSlicerManager * mInput;
vtkSmartPointer<vtkMatrix4x4> mInitialMatrix;
+ void ExtentMax(const double [8][4], double [2][3]);
void SetTransform(vtkMatrix4x4 * matrix);
void GetSlidersAndSpinBoxes(std::vector<QSlider *>&transSliders, std::vector<QSlider *>&rotSliders,
std::vector<QDoubleSpinBox *>&transSBs, std::vector<QDoubleSpinBox *>&rotSBs);
#include <QMessageBox>
// vtk
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
#include "vtkImageContinuousErode3D.h"
#include "vtkImageContinuousDilate3D.h"
#include "vtkRenderWindow.h"
vtkImageContinuousErode3D* erode = vtkImageContinuousErode3D::New();
erode->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
vtkImageData* image = mCurrentMaskImage->GetVTKImages()[0];
+#if VTK_MAJOR_VERSION <= 5
erode->SetInput(image);
+#else
+ erode->SetInputData(image);
+#endif
erode->Update();
image->DeepCopy(erode->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
image->Update();
+#else
+ //image->Update();
+#endif
UpdateAndRenderNewMask();
erode->Delete();
QApplication::restoreOverrideCursor();
vtkImageContinuousDilate3D* dilate = vtkImageContinuousDilate3D::New();
dilate->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
vtkImageData* image = mCurrentMaskImage->GetVTKImages()[0];
+#if VTK_MAJOR_VERSION <= 5
dilate->SetInput(image);
+#else
+ dilate->SetInputData(image);
+#endif
dilate->Update();
image->DeepCopy(dilate->GetOutput());
+#if VTK_MAJOR_VERSION <= 5
image->Update();
+#else
+ //image->Update();
+#endif
UpdateAndRenderNewMask();
dilate->Delete();
QApplication::restoreOverrideCursor();
// mCurrentMousePositionInPixel[1] = Yover;
// mCurrentMousePositionInPixel[2] = Zover;
// DDV(mCurrentMousePositionInPixel, 3);
-
+#if VTK_MAJOR_VERSION <= 5
if (Xover >= image->GetWholeExtent()[0] &&
Xover <= image->GetWholeExtent()[1] &&
Yover >= image->GetWholeExtent()[2] &&
// DD("out of mask");
mCurrentLabelUnderMousePointer = 0; // BG is always 0 in CCL
}
+#else
+ if (Xover >= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] &&
+ Xover <= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] &&
+ Yover >= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] &&
+ Yover <= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] &&
+ Zover >= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] &&
+ Zover <= image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]) {
+ if (mCurrentState == State_Default) { // inside the mask
+ mCurrentLabelUnderMousePointer = 1;
+ return;
+ }
+ else { // inside the label image
+ vtkImageData * image = mCurrentCCLImage->GetFirstVTKImageData();
+ mCurrentLabelUnderMousePointer =
+ mCurrentSlicerManager->GetSlicer(0)->GetScalarComponentAsDouble(image, Xover, Yover, Zover, ix, iy, iz, 0);
+ return;
+ }
+ }
+ else {
+ // DD("out of mask");
+ mCurrentLabelUnderMousePointer = 0; // BG is always 0 in CCL
+ }
+#endif
}
//------------------------------------------------------------------------------
#ifndef VVTOOLSEGMENTATION_H
#define VVTOOLSEGMENTATION_H
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include "vvToolBase.h"
===========================================================================**/
#ifndef VVTOOLSIMPLEINPUTSELECTORWIDGET_H
#define VVTOOLSIMPLEINPUTSELECTORWIDGET_H
+
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include <QDialog>
#include "ui_vvToolSimpleInputSelectorWidget.h"
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
+
+// vv
+#include "vvToolTest.h"
+#include "vvSlicerManager.h"
+#include "vvSlicer.h"
+#include "vvToolInputSelectorWidget.h"
+
+// clitk
+#include "clitkBinarizeImageGenericFilter.h"
+
+// vtk
+#include <vtkImageActor.h>
+#include <vtkCamera.h>
+#include <vtkImageClip.h>
+#include <vtkRenderWindow.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkRenderer.h>
+#include <vtkSphereSource.h>
+#include <vtkProperty.h>
+
+#include <itkGDCMImageIO.h>
+
+//------------------------------------------------------------------------------
+// Create the tool and automagically (I like this word) insert it in
+// the main window menu.
+ADD_TOOL(vvToolTest);
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolTest::Initialize()
+{ cout << __func__ << endl;
+ SetToolName("Test");
+ SetToolMenuName("Test");
+ SetToolIconFilename(":/common/icons/binarize.png");
+ SetToolTip("try to display a sphere.");
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolTest::vvToolTest(vvMainWindowBase * parent, Qt::WindowFlags f)
+ :vvToolWidgetBase(parent,f),
+ vvToolBase<vvToolTest>(parent),
+ Ui::vvToolTest()
+{ cout << __func__ << endl;
+ // GUI Initialization
+
+ // Connect signals & slots
+
+ // Main filter
+ mFilter = clitk::BinarizeImageGenericFilter::New();
+
+ // Set how many inputs are needed for this tool
+ AddInputSelector("Select one image", mFilter);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolTest::~vvToolTest()
+{ cout << __func__ << endl;
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+/*
+void vvToolTest::InteractiveDisplayToggled(bool b)
+{ cout << __func__ << endl;
+ mInteractiveDisplayIsEnabled = b;
+ if (!mInteractiveDisplayIsEnabled) {
+ RemoveVTKObjects();
+ } else {
+ for(unsigned int i=0; i<mImageContour.size(); i++) {
+ mImageContour[i]->ShowActors();
+ if (mRadioButtonLowerThan->isChecked())
+ mImageContourLower[i]->ShowActors();
+ }
+ if (mCurrentSlicerManager)
+ mCurrentSlicerManager->Render();
+ }
+}
+*/
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+bool vvToolTest::close()
+{ cout << __func__ << endl;
+ return vvToolWidgetBase::close();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolTest::reject()
+{ cout << __func__ << endl;
+ // DD("vvToolBinarize::reject");
+ return vvToolWidgetBase::reject();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+
+void vvToolTest::InputIsSelected(vvSlicerManager * m)
+{ cout << __func__ << endl;
+ mCurrentSlicerManager = m;
+
+
+ vtkSmartPointer<vtkSphereSource> sphereSource =
+ vtkSmartPointer<vtkSphereSource>::New();
+ sphereSource->SetCenter(0, 0, 0);
+ //sphereSource->SetCenter(235.351, 175.781, 141.0);
+ sphereSource->SetRadius(10.0);
+ sphereSource->Update();
+ vtkSmartPointer<vtkPolyDataMapper> sphereMapper =
+ vtkSmartPointer<vtkPolyDataMapper>::New();
+ sphereMapper->SetInputConnection(sphereSource->GetOutputPort());
+ vtkSmartPointer<vtkActor> sphereActor =
+ vtkSmartPointer<vtkActor>::New();
+ sphereActor->SetMapper(sphereMapper);
+ sphereActor->GetProperty()->SetColor(1.0, 0.0, 0.0);
+ sphereActor->GetProperty()->SetOpacity(0.995);
+ sphereActor->SetPosition(235.351, 175.781, -10);
+
+
+ // VTK Renderer
+ vtkSmartPointer<vtkRenderer> sphereRenderer =
+ vtkSmartPointer<vtkRenderer>::New();
+ // Add Actor to renderer
+ for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ mCurrentSlicerManager->GetSlicer(i)->GetRenderer()->AddActor(sphereActor);
+ }
+ //sphereRenderer->AddActor(sphereActor); //mettre le vvSlicer
+
+ // VTK/Qt wedded
+ //this->qvtkWidgetLeft->GetRenderWindow()->AddRenderer(leftRenderer);
+
+
+
+
+
+ // VTK objects for interactive display
+ valueChangedT1();
+
+ //connect(mThresholdSlider1, SIGNAL(valueChanged(double)), this, SLOT(valueChangedT1()));
+
+ connect(mCurrentSlicerManager,SIGNAL(UpdateSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
+ connect(mCurrentSlicerManager,SIGNAL(UpdateTSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
+
+ connect(mCurrentSlicerManager,SIGNAL(UpdateOrientation(int,int)),this,SLOT(UpdateSlice(int, int)));
+
+ // connect(mCurrentSlicerManager, SIGNAL(LeftButtonReleaseSignal(int)), SLOT(LeftButtonReleaseEvent(int)));
+ //InteractiveDisplayToggled(mInteractiveDisplayIsEnabled);
+
+
+
+typedef signed short InputPixelType;
+const unsigned int Dimension = 3;
+typedef itk::Image< InputPixelType, Dimension > InputImageType;
+typedef itk::ImageFileReader< InputImageType > ReaderType;
+ReaderType::Pointer reader = ReaderType::New();
+reader->SetFileName( "/home/tbaudier/BJ13/RTSTRUCT/1.2.840.113704.1.111.4140.1439902720.30/20160201/160325.000000_/2.16.840.1.113669.1919.1454339005/2.16.840.1.113669.1919.1454339005/1.2.840.10008.5.1.4.1.1.481.3.1454339000.dcm" );
+typedef itk::GDCMImageIO ImageIOType;
+ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
+reader->SetImageIO( gdcmImageIO );
+try
+{
+reader->Update();
+}
+catch (itk::ExceptionObject & e)
+{
+std::cerr << "exception in file reader " << std::endl;
+std::cerr << e.GetDescription() << std::endl;
+std::cerr << e.GetLocation() << std::endl;
+return;
+}
+
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+// void vvToolBinarize::LeftButtonReleaseEvent(int slicer) {
+// DD("LeftButtonReleaseEvent");
+// for(int i=0; i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+// if (i == slicer);
+// mCurrentSlicerManager->GetSlicer(i)->GetRenderWindow()->Render();
+// }
+// }
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolTest::apply()
+{ cout << __func__ << endl;
+ if (!mCurrentSlicerManager) close();
+ QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+ //GetArgsInfoFromGUI();
+
+ // Main filter
+
+
+
+ // Output
+ QApplication::restoreOverrideCursor();
+ close();
+}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+void vvToolTest::UpdateSlice(int slicer,int slices)
+{ cout << __func__ << endl;
+ Update(slicer);
+}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+void vvToolTest::Update(int slicer)
+{ cout << __func__ << endl;
+ if (!mCurrentSlicerManager) close();
+ mCurrentSlicerManager->Render();
+ //mImageContour[slicer]->Update(mThresholdSlider1->GetValue());
+}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
+/* void vvToolTest::GetArgsInfoFromGUI()
+{ cout << __func__ << endl;
+
+ /* //KEEP THIS FOR READING GGO FROM FILE
+ int argc=1;
+ std::string a = "toto";
+ char * const* argv = new char*;
+ //a.c_str();
+ struct cmdline_parser_params p;
+ p.check_required = 0;
+ int good = cmdline_parser_ext(argc, argv, &args_info, &p);
+ DD(good);
+ */
+/* cmdline_parser_clitkBinarizeImage_init(&mArgsInfo); // Initialisation to default
+ bool inverseBGandFG = false;
+
+ mArgsInfo.lower_given = 1;
+ mArgsInfo.lower_arg = mThresholdSlider1->GetValue();
+ if (mRadioButtonLowerThan->isChecked()) {
+ mArgsInfo.upper_given = 1;
+ mArgsInfo.upper_arg = mThresholdSlider2->GetValue();
+ if (mArgsInfo.upper_arg<mArgsInfo.lower_arg) {
+ mArgsInfo.upper_given = 0;
+ DD("TODO : lower thres greater than greater thres ! Ignoring ");
+ }
+ }
+
+ mArgsInfo.fg_arg = mFGSlider->GetValue();
+ mArgsInfo.bg_arg = mBGSlider->GetValue();
+
+ if (inverseBGandFG) {
+ mArgsInfo.fg_arg = mFGSlider->GetValue();
+ mArgsInfo.bg_arg = mBGSlider->GetValue();
+ }
+ mArgsInfo.fg_given = 1;
+ mArgsInfo.bg_given = 1;
+
+ if (mCheckBoxUseBG->isChecked()) {
+ if (mCheckBoxUseFG->isChecked()) mArgsInfo.mode_arg = (char*)"both";
+ else mArgsInfo.mode_arg = (char*)"BG";
+ } else mArgsInfo.mode_arg = (char*)"FG";
+
+ mArgsInfo.verbose_flag = false;
+
+ // // Required (even if not used)
+ // mArgsInfo.input_given = 0;
+ // mArgsInfo.output_given = 0;
+
+ // mArgsInfo.input_arg = new char;
+ // mArgsInfo.output_arg = new char;
+} */
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolTest::valueChangedT1()
+{ cout << __func__ << endl;
+ // DD("valueChangedT1");
+ if (!mCurrentSlicerManager) close();
+ for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
+ //mImageContour[i]->Update(v);
+ }
+ mCurrentSlicerManager->Render();
+}
+//------------------------------------------------------------------------------
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef VVTOOLTEST_H
+#define VVTOOLTEST_H
+
+#include <QtUiPlugin/QDesignerExportWidget>
+
+#include "vvToolBase.h"
+#include "vvToolWidgetBase.h"
+#include "vvImageContour.h"
+#include "ui_vvToolTest.h"
+
+
+//------------------------------------------------------------------------------
+class vvToolTest:
+ public vvToolWidgetBase,
+ public vvToolBase<vvToolTest>,
+ private Ui::vvToolTest
+{
+ Q_OBJECT
+ public:
+ vvToolTest(vvMainWindowBase * parent=0, Qt::WindowFlags f=0);
+ ~vvToolTest();
+
+ //-----------------------------------------------------
+ static void Initialize();
+ //void GetArgsInfoFromGUI();
+ virtual void InputIsSelected(vvSlicerManager * m);
+
+ //-----------------------------------------------------
+ public slots:
+ virtual bool close();
+ virtual void reject();
+ virtual void apply();
+ void UpdateSlice(int slicer,int slices);
+ void valueChangedT1();
+
+ protected:
+ Ui::vvToolTest ui;
+
+ void Update(int slicer);
+
+}; // end class vvToolTest
+//------------------------------------------------------------------------------
+
+#endif
+
vvToolWidgetBase::vvToolWidgetBase(vvMainWindowBase * parent, Qt::WindowFlags f, bool initialize):
QWidget(parent, f),
Ui::vvToolWidgetBase()
-{
+{
mMainWindow = parent;
setAttribute(Qt::WA_DeleteOnClose);
if (initialize) Initialization();
//------------------------------------------------------------------------------
void vvToolWidgetBase::Initialization()
-{
+{
mCurrentSlicerManager = 0;
mIsInitialized = false;
mFilter = 0;
//------------------------------------------------------------------------------
vvToolWidgetBase::~vvToolWidgetBase()
-{
+{
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolWidgetBase::keyPressEvent(QKeyEvent *event)
-{
+{
if (event->key() == Qt::Key_Escape) {
reject();
event->accept();
//------------------------------------------------------------------------------
void vvToolWidgetBase::accept()
-{
+{
apply();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolWidgetBase::reject()
-{
+{
close();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolWidgetBase::AddInputSelector(QString s, clitk::ImageToImageGenericFilterBase * f, bool allowSkip)
-{
+{
int j=0;
mFilter = f;
mSlicerManagersCompatible.clear();
//------------------------------------------------------------------------------
void vvToolWidgetBase::AddInputSelector(QString s, bool allowSkip)
-{
+{
mSlicerManagersCompatible.clear();
for(unsigned int i=0; i<mMainWindow->GetSlicerManagers().size(); i++) {
mSlicerManagersCompatible.push_back(mMainWindow->GetSlicerManagers()[i]);
//------------------------------------------------------------------------------
void vvToolWidgetBase::HideInputSelector()
-{
+{
mToolInputSelectionWidget->hide();
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolWidgetBase::show()
-{
+{
if (!mIsInitialized) {
mToolInputSelectionWidget->Initialize();
mIsInitialized = true;
//------------------------------------------------------------------------------
void vvToolWidgetBase::closeEvent(QCloseEvent *event)
-{
+{
mIsAnotherToolWaitInput = false;
if (isWindow()) {
event->accept();//return QWidget::close();
//------------------------------------------------------------------------------
bool vvToolWidgetBase::close()
-{
+{
QApplication::restoreOverrideCursor();
return QWidget::close();
}
//------------------------------------------------------------------------------
void vvToolWidgetBase::AnImageIsBeingClosed(vvSlicerManager * m)
-{
+{
mToolInputSelectionWidget->AnImageIsBeingClosed(m);
if (m == mCurrentSlicerManager) {
close();
//------------------------------------------------------------------------------
void vvToolWidgetBase::SwapCurrentWidget()
-{
+{
mStaticWidgetForTab->setUpdatesEnabled(false);
QList<QObject*> l =mStaticWidgetForTab->children();
for(int i=1; i<l.size(); i++) {
//------------------------------------------------------------------------------
void vvToolWidgetBase::SelectedImageHasChanged(vvSlicerManager * m)
-{
+{
if (!isWindow()) { // When the tool is not in a window, it is in a tab : we only display if needed
if (mCurrentSlicerManager == NULL) return;
if (mToolWidget == NULL) return;
//------------------------------------------------------------------------------
void vvToolWidgetBase::InitializeInputs()
-{
+{
}
//------------------------------------------------------------------------------
//------------------------------------------------------------------------------
void vvToolWidgetBase::InputIsSelected()
-{
+{
mMainButtonBox->setEnabled(true);
std::vector<vvSlicerManager*> & l = mToolInputSelectionWidget->GetSelectedInputs();
mCurrentSlicerManager = l[0];
//------------------------------------------------------------------------------
void vvToolWidgetBase::InputIsSelected(vvSlicerManager * m)
-{
+{
std::cerr << "You MUST overwrite this method vvToolWidgetBase::InputIsSelected(vvSlicerManager * m) if you use one single input" << std::endl;
exit(0);
}
//------------------------------------------------------------------------------
void vvToolWidgetBase::InputIsSelected(std::vector<vvSlicerManager*> & l)
-{
+{
mMainButtonBox->setEnabled(true);
if (l.size() == 1) InputIsSelected(l[0]);
else {
#ifndef VVTOOLWIDGETBASE_H
#define VVTOOLWIDGETBASE_H
+#include <QtGlobal>
#include <QtDesigner/QDesignerExportWidget>
#include "ui_vvToolWidgetBase.h"
#include "clitkImageToImageGenericFilter.h"
int getDicomClientPort();
// get the directory where the dicom files will be stored during c-move action.
-std::string getCMoveDirectory()
+std::string getCMoveDirectory();
std::map <std::string,std::string > getDicomServer(QString nickname);
#endif
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff
