Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 75f52c44af3ac5c5e3af2b0b07c5c7df068f541b..4cd0dc9de7c8d8e4a4a27038a2d10f64e5fd8175 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,18 +6,20 @@ if(COMMAND cmake_policy)
     cmake_policy(SET CMP0003 NEW)
 endif(COMMAND cmake_policy)
 PROJECT(clitk)
-SET(CLITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
+IF(NOT DEFINED CLITK_SOURCE_DIR)
+  SET(CLITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
+ENDIF(NOT DEFINED CLITK_SOURCE_DIR)
 #=========================================================
 
 #=========================================================
-INCLUDE(cmake/common.cmake)
-INCLUDE(cmake/dependencies.cmake)
-INCLUDE(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)
 #=========================================================
 #=========================================================
 
 # Select what is compiled
-ADD_SUBDIRECTORY(common)
-ADD_SUBDIRECTORY(tools)
-ADD_SUBDIRECTORY(segmentation)
-ADD_SUBDIRECTORY(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)

diff --git a/cmake/dependencies.cmake b/cmake/dependencies.cmake
index 225ddccb1bdba22c30df0354347852f2f3028697..078c5a4de21d50e1839019a5e469c3bf8789d4f6 100644 (file)
--- a/cmake/dependencies.cmake
+++ b/cmake/dependencies.cmake
@@ -13,6 +13,18 @@ ENDIF(ITK_FOUND)
 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
+      vtkFiltering
+      vtkGraphics
+      vtkWidgets
+      vtkImaging
+      vtkHybrid
+      )
+  ENDIF(VTK_VERSION VERSION_LESS 5.8.0)
 ELSE(VTK_FOUND)
   MESSAGE(FATAL_ERROR "Please set VTK_DIR.")
 ENDIF(VTK_FOUND)

diff --git a/common/CMakeLists.txt b/common/CMakeLists.txt
index b956dd9f71c6e1dcc76ce16d5e566535a32ef2f6..336e22558c7e8628aa2b27e32550c3676c026182 100644 (file)
--- a/common/CMakeLists.txt
+++ b/common/CMakeLists.txt
@@ -1,7 +1,3 @@
-#=========================================================
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/common.cmake)
-#=========================================================
-
 #=========================================================
 # make clitk libraries*
 CONFIGURE_FILE(clitkConfiguration.h.in ${PROJECT_BINARY_DIR}/clitkConfiguration.h)

diff --git a/registration/CMakeLists.txt b/registration/CMakeLists.txt
index 3ae919f718c800df9072d9f7595cda4aec897ef0..e02f2ff4c1acb2d7e395d136b8ef0c988ed317fd 100644 (file)
--- a/registration/CMakeLists.txt
+++ b/registration/CMakeLists.txt
@@ -1,10 +1,6 @@
 #ADD_LIBRARY(clitkLBGSB STATIC clitkLBGSBOptimizer.cxx)
 #=========================================================
 
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/common.cmake)
-
-#=========================================================
-
 # Add Libraries used in vv and clitk to avoid recompilation
 WRAP_GGO(clitkAffineRegistration_GGO_C clitkAffineRegistration.ggo)
 ADD_LIBRARY(clitkAffineRegistrationLib 

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index a422e4f07e5ad713e62074a45b53553cb8e52b66..1f18830311102decf806136bd23f1c7ef4ca9a97 100755 (executable)
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -38,7 +38,7 @@ registration()
   # with the specified preffix, which is interesting for debugging. 
   # if blank, it means that the original images (those without bands) 
   # will be used (see create_midP_masks-2.0.sh for details).
-  banded="banded_"
+  banded=""
 
   # params read from conf file
   params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
@@ -102,15 +102,29 @@ registration()
     fi
   done
 
-  # create (zero) vf from reference to reference
+  # create (zero) vf from reference to reference and associated images
+  vf_in=$vf_dir/vf_inside_${ref_phase_nb}_${ref_phase_nb}.mhd
+  vf_out=$vf_dir/vf_outside_${ref_phase_nb}_${ref_phase_nb}.mhd
   clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
+  clitkZeroVF -i $vf_ref -o $vf_in
+  clitkZeroVF -i $vf_ref -o $vf_out
+  abort_on_error registration $? clean_up_registration
+
+  motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
+  reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
+  reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
+  out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
+  clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
   abort_on_error registration $? clean_up_registration
 
   # create 4D vf
   create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
 
   # create 4D result image
   create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
   create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
 
   echo
@@ -134,7 +148,7 @@ midp()
   ########### calculate the midp wrt the reference phase
   phase_nb=$ref_phase_nb
   echo "Calculating midp_$phase_nb.mhd..."
-  vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+  vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
   midp=$midp_dir/midp_$phase_nb.mhd
   # average the vf's from reference phase to phase
   clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
@@ -157,7 +171,7 @@ midp()
   for i in $( seq 0 $((${#phase_files[@]} - 1))); do
     phase_file=${phase_files[$i]}
     phase_nb=${phase_nbs[$i]}
-    vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+    vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
     midp=$midp_dir/midp_$phase_nb.mhd
 
     if [ "$phase_nb" != "$ref_phase_nb" ]; then
@@ -175,7 +189,9 @@ midp()
     fi
   done
 
+  # create 4D midp
   create_mhd_4D_pattern.sh $midp_dir/midp_
+  create_mhd_4D_pattern.sh $midp_dir/vf_midp_
 
   echo "Calculating midp_avg.mhd..."
   clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
@@ -186,7 +202,7 @@ midp()
   abort_on_error midp $? clean_up_midp
 
   # clean-up
-  rm $midp_dir/vf_*
+  #rm $midp_dir/vf_*
       
   echo
   echo "-------- Mid-position done ! --------"

diff --git a/scripts/create_midP_masks-2.0.sh b/scripts/create_midP_masks-2.0.sh
index 7c84294d65f87cb234d4df68e8db77db46ace034..eb5983af70ab378ec4b97ae4a887273ce92109cf 100755 (executable)
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -43,7 +43,7 @@ extract_bones()
 extract_lungs()
 {
   echo "$phase_file -> Extracting lungs..."  
-  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs
+  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
 }
 
 

diff --git a/segmentation/CMakeLists.txt b/segmentation/CMakeLists.txt
index 058b2c7f831f669bec0b82accb8745d1987b173e..a2451a5741f6d6ce3b06a280060d120e9875ce1c 100644 (file)
--- a/segmentation/CMakeLists.txt
+++ b/segmentation/CMakeLists.txt
@@ -1,9 +1,5 @@
 #=========================================================
 
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/common.cmake)
-
-#=========================================================
-
 # Add Libraries used in vv and clitk to avoid recompilation
 FOREACH(clitkTool clitkExtractLung clitkExtractPatient)
     WRAP_GGO(${clitkTool}_GGO_C ${clitkTool}.ggo)

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 21a8101be396d3e353d599442d02f996f9c7304b..7b1a9fa7ec3b8d93dcf3d2a337907900d574ee6f 100644 (file)
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -1,7 +1,3 @@
-#=========================================================
-INCLUDE(${CLITK_SOURCE_DIR}/cmake/common.cmake)
-#=========================================================
-
 # 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})
@@ -126,7 +122,7 @@ IF (CLITK_BUILD_TOOLS)
 
   WRAP_GGO(clitkGammaIndex_GGO_C clitkGammaIndex.ggo)
   ADD_EXECUTABLE(clitkGammaIndex clitkGammaIndex.cxx ${clitkGammaIndex_GGO_C})
-  TARGET_LINK_LIBRARIES(clitkGammaIndex clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES} vtkIO)
+  TARGET_LINK_LIBRARIES(clitkGammaIndex clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES})
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkGammaIndex)
 
   ADD_EXECUTABLE(clitkImageArithm clitkImageArithm.cxx)
@@ -368,21 +364,17 @@ IF (CLITK_BUILD_TOOLS)
 
     WRAP_GGO(clitkBinaryImageToMesh_GGO_C clitkBinaryImageToMesh.ggo)
     ADD_EXECUTABLE(clitkBinaryImageToMesh clitkBinaryImageToMesh.cxx ${clitkBinaryImageToMesh_GGO_C})
-    TARGET_LINK_LIBRARIES(clitkBinaryImageToMesh ${ITK_LIBRARIES} vtkCommon vtkRendering)
+    TARGET_LINK_LIBRARIES(clitkBinaryImageToMesh ${ITK_LIBRARIES} ${VTK_LIBRARIES})
     SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBinaryImageToMesh)
 
     WRAP_GGO(clitkMeshToBinaryImage_GGO_C clitkMeshToBinaryImage.ggo)
     ADD_EXECUTABLE(clitkMeshToBinaryImage clitkMeshToBinaryImage.cxx ${clitkMeshToBinaryImage_GGO_C})
-    IF(VTK_VERSION VERSION_LESS 5.8.0)
-      TARGET_LINK_LIBRARIES(clitkMeshToBinaryImage clitkCommon ${ITK_LIBRARIES} vtkHybrid vtkIO)
-    ELSE(VTK_VERSION VERSION_LESS 5.8.0)
-      TARGET_LINK_LIBRARIES(clitkMeshToBinaryImage clitkCommon ${ITK_LIBRARIES} ${VTK_LIBRARIES})
-    ENDIF(VTK_VERSION VERSION_LESS 5.8.0)
+    TARGET_LINK_LIBRARIES(clitkMeshToBinaryImage clitkCommon ${ITK_LIBRARIES} ${VTK_LIBRARIES})
     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 vtkCommon vtkRendering)
+    TARGET_LINK_LIBRARIES(clitkMeshViewer ${VTK_LIBRARIES})
     SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshViewer)
   ENDIF(CLITK_EXPERIMENTAL)