Merge branch 'master' of /home/dsarrut/clitk3.server

diff --combined tools/CMakeLists.txt
index e79de4027db17c788f7207fe923c51a8e6768403,f5a62b443880ceb3c3c4dc18575b5f73d3a4e710..7fe9c8451762519f9e4602d86bd8fd0b1eba7886
--- 1/tools/CMakeLists.txt
--- 2/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@@ -157,15 -157,10 +157,15 @@@ IF (CLITK_BUILD_TOOLS
    TARGET_LINK_LIBRARIES(clitkAutoCrop clitkCommon ${ITK_LIBRARIES} )
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkAutoCrop)
  
 -  WRAP_GGO(clitkDicomRTStruct2BinaryImage_GGO_C clitkDicomRTStruct2BinaryImage.ggo)
 -  ADD_EXECUTABLE(clitkDicomRTStruct2BinaryImage clitkDicomRTStruct2BinaryImage.cxx ${clitkDicomRTStruct2BinaryImage_GGO_C})
 -  TARGET_LINK_LIBRARIES(clitkDicomRTStruct2BinaryImage clitkDicomRTStruct clitkCommon ${ITK_LIBRARIES} )
 -  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTStruct2BinaryImage)
 +  WRAP_GGO(clitkDicomRTStruct2Image_GGO_C clitkDicomRTStruct2Image.ggo)
 +  ADD_EXECUTABLE(clitkDicomRTStruct2Image clitkDicomRTStruct2Image.cxx ${clitkDicomRTStruct2Image_GGO_C})
 +  TARGET_LINK_LIBRARIES(clitkDicomRTStruct2Image clitkDicomRTStruct clitkCommon ${ITK_LIBRARIES} )
 +  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTStruct2Image)
 +
 +  WRAP_GGO(clitkImage2DicomRTStruct_GGO_C clitkImage2DicomRTStruct.ggo)
 +  ADD_EXECUTABLE(clitkImage2DicomRTStruct clitkImage2DicomRTStruct.cxx ${clitkImage2DicomRTStruct_GGO_C})
 +  TARGET_LINK_LIBRARIES(clitkImage2DicomRTStruct clitkDicomRTStruct clitkCommon ${ITK_LIBRARIES} )
 +  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImage2DicomRTStruct)
  
    WRAP_GGO(clitkImageLog_GGO_C clitkImageLog.ggo)
    ADD_EXECUTABLE(clitkImageLog clitkImageLog.cxx ${clitkImageLog_GGO_C})
@@@ -330,7 -325,7 +330,7 @@@
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkJacobianImage)
    
    WRAP_GGO(clitkPadImage_GGO_C clitkPadImage.ggo)
-   ADD_EXECUTABLE(clitkPadImage clitkPadImage.cxx ${clitkPadImage_GGO_C})
+   ADD_EXECUTABLE(clitkPadImage clitkPadImage.cxx clitkPadImageGenericFilter.cxx ${clitkPadImage_GGO_C})
    TARGET_LINK_LIBRARIES(clitkPadImage clitkCommon ${ITK_LIBRARIES})
    SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkPadImage)
  

diff --combined vv/vvToolStructureSetManager.cxx
index 542e50c734e5ca07f3cbc11aed071072b676279a,b4243596907338d5b1ccdff5ece3e6950a9e5a9f..f625e4cd46ef0945fa3c40df9036a2be50e547ee
--- 1/vv/vvToolStructureSetManager.cxx
--- 2/vv/vvToolStructureSetManager.cxx
+++ b/vv/vvToolStructureSetManager.cxx
@@@ -202,19 -202,11 +202,19 @@@ void vvToolStructureSetManager::AddRoiI
  //------------------------------------------------------------------------------
  void vvToolStructureSetManager::UpdateStructureSetInTreeWidget(int index, clitk::DicomRT_StructureSet * s) {
    // Insert ROI
 +  /*
    const std::vector<clitk::DicomRT_ROI::Pointer> & rois = s->GetListOfROI();
    for(unsigned int i=0; i<rois.size(); i++) {
      if (mMapROIToTreeWidget.find(rois[i]) == mMapROIToTreeWidget.end())
        AddRoiInTreeWidget(rois[i], mTree); // replace mTree with ss if several SS
    }
 +  */
 +  clitk::DicomRT_StructureSet::ROIConstIteratorType iter;
 +  for(iter = s->GetROIs().begin(); iter != s->GetROIs().end(); iter++) {
 +    clitk::DicomRT_ROI::Pointer roi = iter->second;
 +    if (mMapROIToTreeWidget.find(roi) == mMapROIToTreeWidget.end())
 +      AddRoiInTreeWidget(roi, mTree); // replace mTree with ss if several SS
 +  }
  }
  //------------------------------------------------------------------------------
  
@@@ -256,7 -248,7 +256,7 @@@ void vvToolStructureSetManager::OpenBin
    mCurrentStructureSetActor = mStructureSetActorsList[index].data();
    mCurrentStructureSetIndex = index;
    // Open images
-   QString Extensions = "Images files ( *.mhd *.hdr *.his)";
+   QString Extensions = "Images files ( *.mha *.mhd *.hdr *.his)";
    Extensions += ";;All Files (*)";
    QStringList filename =
      QFileDialog::getOpenFileNames(this,tr("Open binary image"),
@@@ -342,14 -334,14 +342,14 @@@ void vvToolStructureSetManager::AddImag
    int n = mCurrentStructureSet->AddBinaryImageAsNewROI(binaryImage, filename);
    mLoadedROIIndex.push_back(n);
    if (m_modeBG) 
 -    mCurrentStructureSet->GetROI(n)->SetBackgroundValueLabelImage(BG);
 +    mCurrentStructureSet->GetROIFromROINumber(n)->SetBackgroundValueLabelImage(BG);
    else 
 -    mCurrentStructureSet->GetROI(n)->SetForegroundValueLabelImage(BG);
 +    mCurrentStructureSet->GetROIFromROINumber(n)->SetForegroundValueLabelImage(BG);
    
    // Change color
    if (n<mDefaultLUTColor->GetNumberOfTableValues ()) {
      double * color = mDefaultLUTColor->GetTableValue(n % mDefaultLUTColor->GetNumberOfTableValues ());
 -    mCurrentStructureSet->GetROI(n)->SetDisplayColor(color[0], color[1], color[2]);
 +    mCurrentStructureSet->GetROIFromROINumber(n)->SetDisplayColor(color[0], color[1], color[2]);
    }
    
    // Add a new roi actor