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

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4cd0dc9de7c8d8e4a4a27038a2d10f64e5fd8175..0c65b285c2ad73dad25ea45ee59dd8b76fd00002 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,3 +23,4 @@ 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}/scripts ${PROJECT_BINARY_DIR}/scripts)

diff --git a/cmake/build_opt.cmake b/cmake/build_opt.cmake
index a8f10ee13386e604411783e7e1c6b06304d5d5fa..d7c60aa12268f5e0054119ea358ecb6feb856f5f 100644 (file)
--- a/cmake/build_opt.cmake
+++ b/cmake/build_opt.cmake
@@ -34,21 +34,3 @@ IF(BUILD_TESTING)
   ADD_SUBDIRECTORY(${CLITK_SOURCE_DIR}/tests ${PROJECT_BINARY_DIR}/tests)
 ENDIF(BUILD_TESTING)
 
-#=========================================================
-# Install scripts when running make install
-SET(SCRIPTS 
-  ${CLITK_SOURCE_DIR}/scripts/calculate_motion_amplitude.sh
-  ${CLITK_SOURCE_DIR}/scripts/midp_common.sh
-  ${CLITK_SOURCE_DIR}/scripts/registration.sh
-  ${CLITK_SOURCE_DIR}/scripts/create_midP.sh
-  ${CLITK_SOURCE_DIR}/scripts/create_midP-2.0.sh        
-  ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D.sh          
-  ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D_pattern.sh  
-  ${CLITK_SOURCE_DIR}/scripts/create_midP_masks.sh  
-  ${CLITK_SOURCE_DIR}/scripts/create_midP_masks-2.0.sh  
-  ${CLITK_SOURCE_DIR}/scripts/pts_to_landmarks.sh
-  ${CLITK_SOURCE_DIR}/scripts/create_mhd_3D.sh
-  ${CLITK_SOURCE_DIR}/scripts/dicom_info.sh
-)
-
-INSTALL (FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)

diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
new file mode 100644 (file)
index 0000000..41ace96
--- /dev/null
+++ b/scripts/CMakeLists.txt
@@ -0,0 +1,19 @@
+#=========================================================
+# Install scripts when running make install
+SET(SCRIPTS 
+  ${CLITK_SOURCE_DIR}/scripts/calculate_motion_amplitude.sh
+  ${CLITK_SOURCE_DIR}/scripts/calculate_contour_stats.sh
+  ${CLITK_SOURCE_DIR}/scripts/midp_common.sh
+  ${CLITK_SOURCE_DIR}/scripts/registration.sh
+  ${CLITK_SOURCE_DIR}/scripts/create_midP.sh
+  ${CLITK_SOURCE_DIR}/scripts/create_midP-2.0.sh        
+  ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D.sh          
+  ${CLITK_SOURCE_DIR}/scripts/create_mhd_4D_pattern.sh  
+  ${CLITK_SOURCE_DIR}/scripts/create_midP_masks.sh  
+  ${CLITK_SOURCE_DIR}/scripts/create_midP_masks-2.0.sh  
+  ${CLITK_SOURCE_DIR}/scripts/pts_to_landmarks.sh
+  ${CLITK_SOURCE_DIR}/scripts/create_mhd_3D.sh
+  ${CLITK_SOURCE_DIR}/scripts/dicom_info.sh
+)
+
+INSTALL (FILES ${SCRIPTS} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)

diff --git a/scripts/calculate_contour_stats.sh b/scripts/calculate_contour_stats.sh
new file mode 100755 (executable)
index 0000000..b15caa8
--- /dev/null
+++ b/scripts/calculate_contour_stats.sh
@@ -0,0 +1,121 @@
+#! /bin/bash +x 
+
+select_contour_gui()
+{
+  local roi_list=$@
+  roi=`zenity --list --title="Available Contours" --column="Please choose a contour:" $roi_list`
+  case $? in
+    0)
+    if [ -z $roi ]
+    then
+      zenity --warning --text="You must choose one contour."
+      select_contour $roi_list
+    else
+      rtstruct_roi_name=$roi
+    fi;;
+    1)
+    if zenity --question --text="Do you really wish to quit?"
+    then
+      exit
+    else
+      select_contour $roi_list
+    fi;;
+    -1)
+      zenity --error --text="Unexpected error. Please relaunch the application."
+      exit;;
+  esac
+}
+
+select_contour()
+{
+  local roi_list=$@
+  echo "Available Contours:" 
+  for r in $roi_list; do
+    echo $r
+  done
+
+  echo "Please choose a contour number:"
+  read rtstruct_roi_number
+}
+
+select_roi()
+{
+  rtstruct_roi_name_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0026" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Name] \|]//'` )
+  rtstruct_roi_number_list=( `clitkDicomInfo ${rtstruct_file} | grep "3006|0022" | cut -d '[' -f 4 | sed 's/| V 3006|0026[LO] [ROI Number] \|]//'` )
+  rtstruct_roi_list=( )
+  for i in $(seq 0 1 $(( ${#rtstruct_roi_name_list[@]} - 1 ))); do
+    rtstruct_roi_list[$i]=${rtstruct_roi_number_list[$i]}:${rtstruct_roi_name_list[$i]}
+  done
+
+  if [ $gui_mode = 1 ]; then
+    select_contour_gui ${rtstruct_roi_list[@]}
+    rtstruct_roi=`echo ${rtstruct_roi_name} | cut -d ':' -f 1`
+    rtstruct_roi_name=`echo ${rtstruct_roi_name} | cut -d ':' -f 2`
+  else
+    select_contour ${rtstruct_roi_list[@]}
+    rtstruct_roi=$rtstruct_roi_number
+    rtstruct_roi_name=${rtstruct_roi_name_list[$(( $rtstruct_roi_number - 1))]}
+  fi
+}
+
+############# main 
+
+if echo $* | grep "\-h"; then
+  echo Usage: calculate_motion_amplitude.sh { RTSTRUCT_FILE REFERENCE_IMAGE | --gui }
+
+  exit 0
+fi
+
+
+rtstruct_roi=0
+
+if echo $* | grep "\-\-gui" > /dev/null 2>&1; then
+  if [ $# != 1 ]; then
+    echo Invalid arguments. Type \'`basename $0` -h\' for help
+    exit -1
+  fi
+
+  gui_mode=1
+  rtstruct_file=`zenity --file-selection --title="Select RT Struct file."`
+  select_roi
+  rtstruct_ref_image=`zenity --file-selection --title="Select Reference Image."`
+else
+  if [ $# != 2 ]; then
+    echo Invalid arguments. Type \'`basename $0` -h\' for help
+    exit -1
+  fi
+
+  gui_mode=0
+  rtstruct_file=$1
+  rtstruct_ref_image=$2
+  select_roi
+fi
+
+
+#echo "Processing \"${rtstruct_roi_list[$roi_struct]}\"..."
+# create ROI mask from rtstruct
+roi_mask=roi_${rtstruct_roi_name}.mhd
+clitkDicomRTStruct2Image -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
+if cat /tmp/err.txt | grep -q "No ROI"; then
+  echo Invalid contour number.
+  exit -3
+fi
+
+# guarantees the same sampling for roi mask and vector image
+roi_mask2=resampled_${roi_mask}
+clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${rtstruct_ref_image}
+
+# calculate stats
+clitkImageStatistics -i ${rtstruct_ref_image} -m ${roi_mask2} --verbose 2> /dev/null | tail -n 8 > /tmp/result.txt
+
+if [ $gui_mode = 1 ]; then
+  cat /tmp/result.txt | zenity --text-info --title "Restuls for \"${rtstruct_roi_name}\""
+else
+  echo "Restuls for \"${rtstruct_roi_name}\""
+  cat /tmp/result.txt 
+fi
+
+rm `basename $roi_mask .mhd`.{mhd,raw}
+rm `basename $roi_mask2 .mhd`.{mhd,raw}
+rm /tmp/err.txt
+rm /tmp/result.txt

diff --git a/vv/vvMainWindow.cxx b/vv/vvMainWindow.cxx
index bbbb2d8f4d89979c1f42bdd1a91eb306cfdc0174..303ab3a8b60e1ddb8dcfadfe9ecb6e5fc00b299d 100644 (file)
--- a/vv/vvMainWindow.cxx
+++ b/vv/vvMainWindow.cxx
@@ -2779,19 +2779,19 @@ void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
     w2i->Update();
     vtkImageData *image = w2i->GetOutput();
 
-    const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
+    std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
 
     // Image
     vtkImageWriter *imgwriter = NULL;
-    if (!strcmp(ext, ".bmp"))
+    if (ext==".bmp")
       imgwriter = vtkBMPWriter::New();
-    else if (!strcmp(ext, ".tif"))
+    else if (ext==".tif")
       imgwriter = vtkTIFFWriter::New();
-    else if (!strcmp(ext, ".ppm"))
+    else if (ext==".ppm")
       imgwriter = vtkPNMWriter::New();
-    else if (!strcmp(ext, ".png"))
+    else if (ext==".png")
       imgwriter = vtkPNGWriter::New();
-    else if (!strcmp(ext, ".jpg"))
+    else if (ext==".jpg")
       imgwriter = vtkJPEGWriter::New();
 
     // Snapshot image if not null
@@ -2805,7 +2805,7 @@ void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
     // Video
     vtkGenericMovieWriter *vidwriter = NULL;
 #if CLITK_EXPERIMENTAL == 1
-    if (!strcmp(ext, ".gif")) {
+    if (ext==".gif") {
       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
       vidwriter = gif;
 
@@ -2824,7 +2824,7 @@ void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
     }
 #endif
 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
-    if (!strcmp(ext, ".avi")) {
+    if (ext==".avi") {
       vtkAVIWriter *mpg = vtkAVIWriter::New();
       vidwriter = mpg;
       mpg->SetQuality(2);
@@ -2837,7 +2837,7 @@ void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
     }
 #endif
 #ifdef VTK_USE_FFMPEG_ENCODER
-    if (!strcmp(ext, ".avi")) {
+    if (ext==".avi") {
       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
       vidwriter = mpg;
       mpg->SetQuality(2);
@@ -2851,7 +2851,7 @@ void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
     }
 #endif
 #ifdef VTK_USE_MPEG2_ENCODER
-    if (!strcmp(ext, ".mpg")) {
+    if (ext==".mpg") {
       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
       vidwriter = mpg;
     }

diff --git a/vv/vvSlicer.cxx b/vv/vvSlicer.cxx
index d2a6ba71a24b842dae55db5ad2f6baaf09ee1dc7..714d3d97568743c8bd7e8313bb31249fafe24f54 100644 (file)
--- a/vv/vvSlicer.cxx
+++ b/vv/vvSlicer.cxx
@@ -1241,8 +1241,14 @@ double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, doubl
 //----------------------------------------------------------------------------
 void vvSlicer::Render()
 {
-  if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay && !this->mFusion) {
+  if (this->mFusion) {
+    legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
+    legend->UseOpacityOn();
+    legend->SetVisibility(1);
+  }
+  else if (this->GetWindowLevel()->GetLookupTable()) {// && !this->mOverlay && !this->mFusion) {
     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
+    legend->UseOpacityOff();
     legend->SetVisibility(1);
   } else legend->SetVisibility(0);
 

diff --git a/vv/vvSlicerManager.cxx b/vv/vvSlicerManager.cxx
index d9ed42e2deb448f541eaf97993db3f0eb6b1c483..2373abab970f69a17df88871a0051470ebe371a9 100644 (file)
--- a/vv/vvSlicerManager.cxx
+++ b/vv/vvSlicerManager.cxx
@@ -1236,15 +1236,17 @@ void vvSlicerManager::SetColorMap(int colormap)
     double v[4];
     
     // set color table transparency
+    double alpha_range=(double)mFusionThresOpacity/10;
     double range_end = frange[0] + (double)mFusionThresOpacity*(frange[1] - frange[0])/100;
-    double curr_value = frange[0];
+    double curr_value = fusRange[0];
     int nvalues = fusLUT->GetNumberOfTableValues();
-    //for (double i = frange[0]; i <= alpha_range_end; i++) {
     for (double i = 0; curr_value < range_end; i++) {  
       fusLUT->GetTableValue(i, v);
       v[3] = 0;
+      //if (curr_value >= -alpha_range && curr_value <= alpha_range) v[3] = pow(fabs(curr_value/alpha_range),2);
+      //else v[3] = 1;
       fusLUT->SetTableValue(i, v);
-      curr_value += (frange[1] - frange[0])/nvalues;
+      curr_value += (fusRange[1] - fusRange[0])/nvalues;
     }
   }
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {