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

[clitk.git] / segmentation / clitkRelativePositionList.txx

diff --git a/segmentation/clitkRelativePositionList.txx b/segmentation/clitkRelativePositionList.txx
index e0258d5e71fb560e166c81d1a86a6608c6fe1bcb..d5c8d25f6181a596fbbf6d1e609af3fa6da0dde7 100644 (file)
--- 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();
 }
 //--------------------------------------------------------------------
 
@@ -87,6 +104,8 @@ Read(std::string filename) {
       std::ofstream os;
       openFileForWriting(os, tmpfilename);
       os << text;
+      os << "input = nothing" << std::endl;
+      os << "output = nothing" << std::endl;
       os.close();
 
       // Create a struct to store options. I use two step to allow to
@@ -97,14 +116,11 @@ Read(std::string filename) {
       std::copy(tmpfilename.begin(), tmpfilename.end(), writable.begin());
       char ** argv = new char*[1];
       argv[0] = new char[1];
-      cmdline_parser_clitkRelativePosition2(1, argv, &args_info, 1, 1, 0);
-      args_info.input_given = 1;
-      args_info.input_arg = new char[1];
-      args_info.output_given = 1;
-      args_info.output_arg = new char[1];
-      cmdline_parser_clitkRelativePosition_configfile(&writable[0], &args_info, 0, 0, 1);
-      
-      // Store the args
+      struct cmdline_parser_clitkRelativePosition_params params;
+      params.override = 0;
+      params.initialize = 1;
+      params.check_required = 0;
+      cmdline_parser_clitkRelativePosition_configfile(&writable[0], &args_info, 1, 1, 1);
       mArgsInfoList.push_back(args_info);
       
       // Delete the temporary file
@@ -142,10 +158,20 @@ 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 ";
     if (mArgsInfoList[i].orientation_given) text += std::string(mArgsInfoList[i].orientation_arg[0])+" ";
@@ -157,6 +183,7 @@ GenerateOutputInformation() {
       text += " slice by slice";
     }
     else text += " 3D";
+    text += " spacing=" + toString(mArgsInfoList[i].spacing_arg);
 
     StartNewStep(text);  
     typename RelPosFilterType::Pointer relPosFilter;
@@ -171,6 +198,7 @@ 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 +219,17 @@ 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;
+    }
+    
   }
 }
 //--------------------------------------------------------------------
@@ -224,6 +262,7 @@ SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & optio
   ImagePointer object = GetAFDB()->template GetImage<ImageType>(options.object_arg);
   filter->SetInputObject(object);
   filter->WriteStepFlagOff();
+  if (options.writeStep_flag) filter->WriteStepFlagOn();
   filter->SetVerboseImageSizeFlag(GetVerboseImageSizeFlag());
   filter->SetFuzzyThreshold(options.threshold_arg);
   filter->SetInverseOrientationFlag(options.inverse_flag); // MUST BE BEFORE AddOrientationTypeString
@@ -249,3 +288,5 @@ SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & optio
   filter->SetAutoCropFlag(!options.noAutoCrop_flag); 
 }
 //--------------------------------------------------------------------
+
+