X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkRelativePositionList.txx;h=8d89e9fd364320d058ec1ba6ad88950ea9e12e58;hb=796954f9fff960cee1599e5a8960e0f424931900;hp=973f79f1f2d39c4432fd844ca0d3e6a9e961a945;hpb=00f07c87d82d07e3a284ca2990d586f49d68f8e4;p=clitk.git

diff --git a/segmentation/clitkRelativePositionList.txx b/segmentation/clitkRelativePositionList.txx
index 973f79f..8d89e9f 100644
--- a/segmentation/clitkRelativePositionList.txx
+++ b/segmentation/clitkRelativePositionList.txx
@@ -16,11 +16,28 @@
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
   ======================================================================-====*/
 
+#include "clitkLabelImageOverlapMeasureFilter.h"
 
 //--------------------------------------------------------------------
 template <class TImageType>
 clitk::RelativePositionList<TImageType>::
-RelativePositionList() {
+RelativePositionList():  
+  clitk::FilterBase(),
+  clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+  itk::ImageToImageFilter<TImageType, TImageType>()
+{
+  ComputeOverlapFlagOff();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::RelativePositionList<TImageType>::
+SetReferenceImageForOverlapMeasure(ImagePointer ref) {
+  m_reference = ref;
+  ComputeOverlapFlagOn();
 }
 //--------------------------------------------------------------------
 
@@ -141,24 +158,37 @@ GenerateOutputInformation() {
 
   // Get input
   m_working_input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+  std::string s = GetInputName();
+
+  // Debug
+  if (GetDisplayUsedStructuresOnlyFlag()) {
+    for(uint i=0; i<mArgsInfoList.size(); i++) {
+      // Check if we only want to display structure name
+      AddUsedStructures(s, mArgsInfoList[i].object_arg);
+    }
+    return;
+  }
 
   // Loop on RelativePositionList of operations
-  std::string s = GetInputName();
   for(uint i=0; i<mArgsInfoList.size(); i++) {
+
     // clitk::PrintMemory(true, "Start"); 
-    std::string text = "["+s+"] limits ";
+    // remove _S in station name
+    std::string sname = s;
+    clitk::findAndReplace<std::string>(sname, "_S", " ");
+    std::string text = "["+sname+"] ";
     if (mArgsInfoList[i].orientation_given) text += std::string(mArgsInfoList[i].orientation_arg[0])+" ";
     else text = text+"("+toString(mArgsInfoList[i].angle1_arg)+" "+
            toString(mArgsInfoList[i].angle2_arg)+" "+
            (mArgsInfoList[i].inverse_flag?"true":"false")+") ";
     text = text+mArgsInfoList[i].object_arg+" "+toString(mArgsInfoList[i].threshold_arg);
     if (mArgsInfoList[i].sliceBySlice_flag) {
-      text += " slice by slice";
+      text += " SbS";
     }
     else text += " 3D";
-    text += " spacing=" + toString(mArgsInfoList[i].spacing_arg);
+    text += " sp=" + toString(mArgsInfoList[i].spacing_arg)+" ";
 
-    StartNewStep(text);  
+    StartNewStep(text, false); // no endl
     typename RelPosFilterType::Pointer relPosFilter;
 
     // Is it slice by slice or 3D ?
@@ -171,6 +201,7 @@ GenerateOutputInformation() {
       f->SetUniqueConnectedComponentBySliceFlag(mArgsInfoList[i].uniqueCCL_flag);
       f->SetObjectCCLSelectionFlag(mArgsInfoList[i].uniqueObjectCCL_flag);
       f->IgnoreEmptySliceObjectFlagOn();
+      f->SetVerboseSlicesFlag(mArgsInfoList[i].verboseSlices_flag);
       //f->SetObjectCCLSelectionDimension(0);
       //f->SetObjectCCLSelectionDirection(-1);
       //f->SetAutoCropFlag(false);
@@ -191,7 +222,16 @@ GenerateOutputInformation() {
     relPosFilter->Update();
     m_working_input = relPosFilter->GetOutput();  
     StopCurrentStep<ImageType>(m_working_input);
-    // clitk::PrintMemory(true, "End"); 
+
+    // Compute overlap with reference if needed
+    if (GetComputeOverlapFlag()) {
+      typedef clitk::LabelImageOverlapMeasureFilter<ImageType> FilterType;
+      typename FilterType::Pointer filter = FilterType::New();
+      filter->SetInput(0, m_working_input);
+      filter->SetInput(1, m_reference);
+      filter->Update();
+    }
+    std::cout << std::endl;    
   }
 }
 //--------------------------------------------------------------------
@@ -224,9 +264,12 @@ SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & optio
   ImagePointer object = GetAFDB()->template GetImage<ImageType>(options.object_arg);
   filter->SetInputObject(object);
   filter->WriteStepFlagOff();
+  filter->SetRadius(options.radius_arg);
+  if (options.writeStep_flag) filter->WriteStepFlagOn();
   filter->SetVerboseImageSizeFlag(GetVerboseImageSizeFlag());
   filter->SetFuzzyThreshold(options.threshold_arg);
   filter->SetInverseOrientationFlag(options.inverse_flag); // MUST BE BEFORE AddOrientationTypeString
+  filter->SetFastFlag(options.fastFlag_flag);
 
   if (options.orientation_given == 1)  {
     for(uint i=0; i<options.orientation_given; i++) 
@@ -249,3 +292,5 @@ SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & optio
   filter->SetAutoCropFlag(!options.noAutoCrop_flag); 
 }
 //--------------------------------------------------------------------
+
+