X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkRelativePositionList.txx;h=4f4702b981c809b6705f1102bd1b4cebc32ac95d;hb=2d9ef51e893a0b5b93d44a88594c9c76e4b61239;hp=aff21e41618eb80a373a85bd66cadc0d33ed677b;hpb=adeedbea1fbf8bc34e2c9565867b992ad13ccc57;p=clitk.git

diff --git a/segmentation/clitkRelativePositionList.txx b/segmentation/clitkRelativePositionList.txx
index aff21e4..4f4702b 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();
 }
 //--------------------------------------------------------------------
 
@@ -77,7 +94,6 @@ Read(std::string filename) {
       if (!is) stop = true;
       else {
         std::getline(is, s);
-        // DD(s);
         if (s.find("object") != std::string::npos) stop=true;
         else ss << s << std::endl;
         if (!is) stop = true;
@@ -88,19 +104,23 @@ 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
+      // Create a struct to store options. I use two step to allow to
+      // fill the args values with de default and then check
+      // automatically the options.
       ArgsInfoType args_info;
-      args_info.input_given = 1;
-      args_info.input_arg = new char[1];
-      args_info.output_given = 1;
-      args_info.output_arg = new char[1];
       std::vector<char> writable(tmpfilename.size() + 1);
       std::copy(tmpfilename.begin(), tmpfilename.end(), writable.begin());
-      cmdline_parser_clitkRelativePosition_configfile(&writable[0], &args_info, 1, 1, 0);
-      
-      // Store the args
+      char ** argv = new char*[1];
+      argv[0] = new char[1];
+      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
@@ -138,39 +158,76 @@ 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++) {
-    std::string text = "["+s+"] limits "+
-      mArgsInfoList[i].orientation_arg[0]+" "+
-      mArgsInfoList[i].object_arg+" "+
-      toString(mArgsInfoList[i].threshold_arg);
+
+    // clitk::PrintMemory(true, "Start"); 
+    std::string text = "["+s+"] limits ";
+    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";
     }
     else text += " 3D";
+    text += " spacing=" + toString(mArgsInfoList[i].spacing_arg);
 
     StartNewStep(text);  
     typename RelPosFilterType::Pointer relPosFilter;
 
-    // DD(mArgsInfoList[i].sliceBySlice_flag);
+    // Is it slice by slice or 3D ?
     if (mArgsInfoList[i].sliceBySlice_flag) {
-      relPosFilter = SliceRelPosFilterType::New();
-      dynamic_cast<SliceRelPosFilterType*>(&*relPosFilter)->SetDirection(2);
+      typename SliceRelPosFilterType::Pointer f = SliceRelPosFilterType::New();
+      relPosFilter = f;
+      SetFilterOptions(relPosFilter, mArgsInfoList[i]);  
+      f->SetDirection(2);
+      // Set SbS specific options
+      f->SetUniqueConnectedComponentBySliceFlag(mArgsInfoList[i].uniqueCCL_flag);
+      f->SetObjectCCLSelectionFlag(mArgsInfoList[i].uniqueObjectCCL_flag);
+      f->IgnoreEmptySliceObjectFlagOn();
+      //f->SetObjectCCLSelectionDimension(0);
+      //f->SetObjectCCLSelectionDirection(-1);
+      //f->SetAutoCropFlag(false);
+      // Print if needed
+      if (mArgsInfoList[i].verboseOptions_flag) f->PrintOptions();
     }
     else {
       relPosFilter = clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::New();
+      SetFilterOptions(relPosFilter, mArgsInfoList[i]);  
+      // Print if needed
+      if (mArgsInfoList[i].verboseOptions_flag) relPosFilter->PrintOptions();
     }
-    relPosFilter->VerboseStepFlagOff();
-    relPosFilter->WriteStepFlagOff();
-    relPosFilter->SetVerboseImageSizeFlag(GetVerboseImageSizeFlag());
-    relPosFilter->SetInput(m_working_input);
-    SetFilterOptions(relPosFilter, mArgsInfoList[i]);    
-    //relPosFilter->PrintOptions();
+
+    // Set input
+    relPosFilter->SetInput(m_working_input);  
+  
+    // Run the filter
     relPosFilter->Update();
     m_working_input = relPosFilter->GetOutput();  
     StopCurrentStep<ImageType>(m_working_input);
+
+    // 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();
+    }
+    
   }
 }
 //--------------------------------------------------------------------
@@ -192,33 +249,41 @@ GenerateData()
 template <class TImageType>
 void
 clitk::RelativePositionList<TImageType>::
-SetFilterOptions(typename RelPosFilterType::Pointer filter, 
-                 ArgsInfoType & options) {
+SetFilterOptions(typename RelPosFilterType::Pointer filter, ArgsInfoType & options) {
 
-  if (options.orientation_given != 1) {
-    DD("ERRROR DEBUG TODO no more than 1 orientation yet");
-    exit(0);
+  if (options.orientation_given > 1) {
+    clitkExceptionMacro("Error in the RelPos options. I need a single --orientation (for the moment)."
+                        << " Current options are for obj = '" << options.object_arg
+                        << "', threshold = " << options.threshold_arg << std::endl);
   }
 
   ImagePointer object = GetAFDB()->template GetImage<ImageType>(options.object_arg);
   filter->SetInputObject(object);
+  filter->WriteStepFlagOff();
+  filter->SetVerboseImageSizeFlag(GetVerboseImageSizeFlag());
   filter->SetFuzzyThreshold(options.threshold_arg);
   filter->SetInverseOrientationFlag(options.inverse_flag); // MUST BE BEFORE AddOrientationTypeString
-  for(uint i=0; i<options.orientation_given; i++) 
-    filter->AddOrientationTypeString(options.orientation_arg[i]);
+
+  if (options.orientation_given == 1)  {
+    for(uint i=0; i<options.orientation_given; i++) 
+      filter->AddOrientationTypeString(options.orientation_arg[i]);
+  }
+  else {
+    if (options.angle1_given && options.angle2_given) {
+      filter->AddAnglesInDeg(options.angle1_arg, options.angle2_arg);
+    }
+    else {
+      clitkExceptionMacro("Error in the RelPos options. I need --orientation or (--angle1 and --angle2)."
+                          << " Current options are for obj = '" << options.object_arg
+                          << "', threshold = " << options.threshold_arg << std::endl);
+    }
+  }
   filter->SetIntermediateSpacing(options.spacing_arg);
   if (options.spacing_arg == -1) filter->IntermediateSpacingFlagOff();
-  filter->IntermediateSpacingFlagOn();
-  
-  if (options.sliceBySlice_flag) {
-    SliceRelPosFilterType * f = dynamic_cast<SliceRelPosFilterType*>(&*filter);
-    f->SetUniqueConnectedComponentBySliceFlag(options.uniqueCCL_flag);
-    f->SetObjectCCLSelectionFlag(options.uniqueObjectCCL_flag);
-    f->IgnoreEmptySliceObjectFlagOn();
-    //filter->SetObjectCCLSelectionDimension(0);
-    //filter->SetObjectCCLSelectionDirection(-1);
-    //filter->SetAutoCropFlag(false);
-  }
+  else filter->IntermediateSpacingFlagOn();
+  filter->SetVerboseStepFlag(options.verboseStep_flag);
   filter->SetAutoCropFlag(!options.noAutoCrop_flag); 
 }
 //--------------------------------------------------------------------
+
+