X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSliceBySliceRelativePositionFilter.txx;h=db3c677c0e8701c2a424676fcd72117e26576b12;hb=4d169a2b4d862ed8bb9155b358776ffe08154c76;hp=449ffff9f5a06162a5ed1b11b387a9ade104e549;hpb=4efd93f02e07c2d8fe45f29f9579cabe27a93c1a;p=clitk.git

diff --git a/itk/clitkSliceBySliceRelativePositionFilter.txx b/itk/clitkSliceBySliceRelativePositionFilter.txx
index 449ffff..db3c677 100644
--- a/itk/clitkSliceBySliceRelativePositionFilter.txx
+++ b/itk/clitkSliceBySliceRelativePositionFilter.txx
@@ -42,6 +42,7 @@ SliceBySliceRelativePositionFilter():
   SetObjectCCLSelectionDimension(0);
   SetObjectCCLSelectionDirection(1);
   ObjectCCLSelectionIgnoreSingleCCLFlagOff();
+  VerboseSlicesFlagOff();
 }
 //--------------------------------------------------------------------
 
@@ -95,7 +96,9 @@ PrintOptions(std::ostream & os)
      << "ObjectCCLSelectionFlag = " << this->GetObjectCCLSelectionFlag() << std::endl    
      << "ObjectCCLSelectionDimension = " << this->GetObjectCCLSelectionDimension() << std::endl    
      << "ObjectCCLSelectionIgnoreSingleCCLFlag = " << this->GetObjectCCLSelectionIgnoreSingleCCLFlag() << std::endl    
-     << "IgnoreEmptySliceObjectFlag = " << this->GetIgnoreEmptySliceObjectFlag() << std::endl;    
+     << "IgnoreEmptySliceObjectFlag = " << this->GetIgnoreEmptySliceObjectFlag() << std::endl
+     << "(RP) FastFlag              = " << this->GetFastFlag() << std::endl
+     << "(RP) Radius                = " << this->GetRadius() << std::endl;
 }
 //--------------------------------------------------------------------
 
@@ -127,7 +130,7 @@ GenerateOutputInformation()
     PrintOptions();
   }
 
-  if (this->GetFuzzyMapOnlyFlag()) this->ComputeFuzzyMapFlagOn();
+  //  if (this->GetFuzzyMapOnlyFlag()) this->ComputeFuzzyMapFlagOn();
 
   // Get input pointer
   input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
@@ -179,6 +182,13 @@ GenerateOutputInformation()
     m_working_object = clitk::ResizeImageLike<ImageType>(m_working_object, 
                                                          m_working_input, 
                                                          this->GetObjectBackgroundValue());
+    
+    // Index can be negative in some cases, and lead to problem with
+    // some filter. So we correct it.
+    m_working_input = clitk::RemoveNegativeIndexFromRegion<ImageType>(m_working_input);
+    m_working_object = clitk::RemoveNegativeIndexFromRegion<ImageType>(m_working_object);
+
+    // End
     this->template StopCurrentStep<ImageType>(m_working_input);  
   }
   
@@ -221,7 +231,7 @@ GenerateOutputInformation()
 
   //--------------------------------------------------------------------
   // Perform slice by slice relative position
-  this->StartNewStep("Perform slice by slice relative position");
+  this->StartNewStep("Perform slice by slice relative position ("+toString(mInputSlices.size())+")");
   for(unsigned int i=0; i<mInputSlices.size(); i++) {
     
     // Count the number of CCL (allow to ignore empty slice)
@@ -229,7 +239,7 @@ GenerateOutputInformation()
     mObjectSlices[i] = LabelizeAndCountNumberOfObjects<SliceType>(mObjectSlices[i], 0, true, 1, nb);
 
     // If no object and empty slices and if we need the full fuzzy map, create a dummy one.
-    if ((nb==0) && (this->GetComputeFuzzyMapFlag())) {
+    if ((nb==0) && (this->GetFuzzyMapOnlyFlag())) {
       typename FloatSliceType::Pointer one = FloatSliceType::New();
       one->CopyInformation(mObjectSlices[0]);
       one->SetRegions(mObjectSlices[0]->GetLargestPossibleRegion());
@@ -281,17 +291,18 @@ GenerateOutputInformation()
         // Relative position
         typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
         typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
-
         relPosFilter->VerboseStepFlagOff();
+        if (GetVerboseSlicesFlag()) {
+          std::cout << "Slice " << i << std::endl;
+          relPosFilter->VerboseStepFlagOn();
+        }
         relPosFilter->WriteStepFlagOff();
         // relPosFilter->VerboseMemoryFlagOn();
-        relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId()+"-"+toString(i));
-        
+        relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId()+"-"+toString(i));        
         relPosFilter->SetBackgroundValue(this->GetBackgroundValue());
         relPosFilter->SetInput(mInputSlices[i]); 
         relPosFilter->SetInputObject(mObjectSlices[i]); 
-        relPosFilter->SetRemoveObjectFlag(this->GetRemoveObjectFlag());
-        
+        relPosFilter->SetRemoveObjectFlag(this->GetRemoveObjectFlag());        
         // This flag (InverseOrientation) *must* be set before
         // AddOrientation because AddOrientation can change it.
         relPosFilter->SetInverseOrientationFlag(this->GetInverseOrientationFlag());
@@ -303,16 +314,17 @@ GenerateOutputInformation()
         relPosFilter->SetFuzzyThreshold(this->GetFuzzyThreshold());
         relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
         relPosFilter->SetCombineWithOrFlag(this->GetCombineWithOrFlag()); 
-
         // should we stop after fuzzy map ?
         relPosFilter->SetFuzzyMapOnlyFlag(this->GetFuzzyMapOnlyFlag());
-        relPosFilter->SetComputeFuzzyMapFlag(this->GetComputeFuzzyMapFlag());
-      
+        //        relPosFilter->SetComputeFuzzyMapFlag(this->GetComputeFuzzyMapFlag());      
+        relPosFilter->SetFastFlag(this->GetFastFlag());
+        relPosFilter->SetRadius(this->GetRadius());
+
         // Go !
         relPosFilter->Update();
 
         // If we stop after the fuzzy map, store the fuzzy slices
-        if (this->GetComputeFuzzyMapFlag()) {
+        if (this->GetFuzzyMapOnlyFlag()) {
           mFuzzyMapSlices[i] = relPosFilter->GetFuzzyMap();
           // writeImage<FloatSliceType>(mFuzzyMapSlices[i], "slice_"+toString(i)+".mha");
         }
@@ -348,7 +360,7 @@ GenerateOutputInformation()
   this->template StopCurrentStep<ImageType>(m_working_input);
 
   // Join the fuzzy map if needed
-  if (this->GetComputeFuzzyMapFlag()) {
+  if (this->GetFuzzyMapOnlyFlag()) {
     this->m_FuzzyMap = clitk::JoinSlices<FloatImageType>(mFuzzyMapSlices, m_working_input, GetDirection());
     this->template StopCurrentStep<FloatImageType>(this->m_FuzzyMap);
     if (this->GetFuzzyMapOnlyFlag()) return;