X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSliceBySliceRelativePositionFilter.txx;h=0548146d2051ffe0b61289dc2d07fbf52d6af95b;hb=15e781be4b87a75be8fe01e56da5eb4435c97786;hp=36564cc945d9666ed672d088aceee39d6cdf59a7;hpb=cd0b3ebc56173699e23b90bc911e9caf8b7145c9;p=clitk.git

diff --git a/itk/clitkSliceBySliceRelativePositionFilter.txx b/itk/clitkSliceBySliceRelativePositionFilter.txx
index 36564cc..0548146 100644
--- a/itk/clitkSliceBySliceRelativePositionFilter.txx
+++ b/itk/clitkSliceBySliceRelativePositionFilter.txx
@@ -31,7 +31,16 @@ SliceBySliceRelativePositionFilter():
   clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>()
 {
   SetDirection(2);
-  UniqueConnectedComponentBySliceOff();
+  UniqueConnectedComponentBySliceFlagOff();
+  SetIgnoreEmptySliceObjectFlag(false);
+  UseTheLargestObjectCCLFlagOff();
+  this->VerboseStepFlagOff();
+  this->WriteStepFlagOff();
+  this->SetCombineWithOrFlag(false);
+  ObjectCCLSelectionFlagOff();
+  SetObjectCCLSelectionDimension(0);
+  SetObjectCCLSelectionDirection(1);
+  ObjectCCLSelectionIgnoreSingleCCLFlagOff();
 }
 //--------------------------------------------------------------------
 
@@ -64,19 +73,25 @@ SetInputObject(const ImageType * image)
 template <class ImageType>
 void 
 clitk::SliceBySliceRelativePositionFilter<ImageType>::
-PrintOptions() 
+PrintOptions(std::ostream & os) 
 {
-  DD(this->GetDirection());
-  DD((int)this->GetObjectBackgroundValue());
-  DDV(this->GetOrientationTypeString(), (uint)this->GetNumberOfAngles());
-  DD(this->GetResampleBeforeRelativePositionFilter());
-  DD(this->GetIntermediateSpacing());
-  DD(this->GetFuzzyThreshold());
-  DD(this->GetUniqueConnectedComponentBySlice());
-  DD(this->GetAutoCropFlag());
-  DD(this->GetInverseOrientationFlag());
-  DD(this->GetRemoveObjectFlag());
-  DD(this->GetCombineWithOrFlag());
+  os << "Slice direction = " << this->GetDirection() << std::endl
+     << "BG value        = " << this->GetBackgroundValue() << std::endl;
+  for(int i=0; i<this->GetNumberOfAngles(); i++)
+    os << "Orientation     = " << this->GetOrientationTypeString()[i] << std::endl;
+  os << "InverseOrientationFlag  = " << this->GetInverseOrientationFlag() << std::endl        
+     << "SpacingFlag     = " << this->GetIntermediateSpacingFlag() << std::endl
+     << "Spacing         = " << this->GetIntermediateSpacing() << std::endl
+     << "FuzzyThreshold  = " << this->GetFuzzyThreshold() << std::endl
+     << "UniqueConnectedComponentBySliceFlag  = " << this->GetUniqueConnectedComponentBySliceFlag() << std::endl
+     << "AutoCropFlag    = " << this->GetAutoCropFlag() << std::endl    
+     << "RemoveObjectFlag= " << this->GetRemoveObjectFlag() << std::endl    
+     << "CombineWithOrFlag = " << this->GetCombineWithOrFlag() << std::endl    
+     << "UseTheLargestObjectCCLFlag = " << this->GetUseTheLargestObjectCCLFlag() << std::endl    
+     << "ObjectCCLSelectionFlag = " << this->GetObjectCCLSelectionFlag() << std::endl    
+     << "ObjectCCLSelectionDimension = " << this->GetObjectCCLSelectionDimension() << std::endl    
+     << "ObjectCCLSelectionIgnoreSingleCCLFlag = " << this->GetObjectCCLSelectionIgnoreSingleCCLFlag() << std::endl    
+     << "IgnoreEmptySliceObjectFlag = " << this->GetIgnoreEmptySliceObjectFlag() << std::endl;    
 }
 //--------------------------------------------------------------------
 
@@ -128,8 +143,8 @@ GenerateOutputInformation()
   if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(m_working_object, input)) {
     this->StartNewStep("Pad object to the same size than input");
     m_working_object = clitk::ResizeImageLike<ImageType>(m_working_object, 
-                                                          input, 
-                                                          this->GetObjectBackgroundValue());
+                                                         input, 
+                                                         this->GetObjectBackgroundValue());
     this->template StopCurrentStep<ImageType>(m_working_object);
   }
   else {
@@ -171,39 +186,93 @@ GenerateOutputInformation()
   // Perform slice by slice relative position
   this->StartNewStep("Perform slice by slice relative position");
   for(unsigned int i=0; i<mInputSlices.size(); i++) {
-    // Select main CC in each object slice (required ?)
-    mObjectSlices[i] = Labelize<SliceType>(mObjectSlices[i], 0, true, 1);
-    mObjectSlices[i] = KeepLabels<SliceType>(mObjectSlices[i], 0, 1, 1, 1, true);
-
-    // Relative position
-    typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
-    typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
-    relPosFilter->VerboseStepFlagOff();
-    relPosFilter->WriteStepFlagOff();
-    relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-    relPosFilter->SetBackgroundValue(this->GetBackgroundValue());
-    relPosFilter->SetInput(mInputSlices[i]); 
-    relPosFilter->SetInputObject(mObjectSlices[i]); 
-    relPosFilter->SetRemoveObjectFlag(this->GetRemoveObjectFlag());
-    for(int j=0; j<this->GetNumberOfAngles(); j++) {
-      relPosFilter->AddOrientationTypeString(this->GetOrientationTypeString(j));
-    }
-    relPosFilter->SetInverseOrientationFlag(this->GetInverseOrientationFlag());
-    //relPosFilter->SetOrientationType(this->GetOrientationType());
-    relPosFilter->SetIntermediateSpacing(this->GetIntermediateSpacing());
-    relPosFilter->SetResampleBeforeRelativePositionFilter(this->GetResampleBeforeRelativePositionFilter());
-    relPosFilter->SetFuzzyThreshold(this->GetFuzzyThreshold());
-    relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
-    relPosFilter->SetCombineWithOrFlag(this->GetCombineWithOrFlag()); 
-    relPosFilter->Update();
-    mInputSlices[i] = relPosFilter->GetOutput();
-
-    // Select main CC if needed
-    if (GetUniqueConnectedComponentBySlice()) {
-      mInputSlices[i] = Labelize<SliceType>(mInputSlices[i], 0, true, 1);
-      mInputSlices[i] = KeepLabels<SliceType>(mInputSlices[i], 0, 1, 1, 1, true);
-    }
+    
+    // Count the number of CCL (allow to ignore empty slice)
+    int nb=0;
+    mObjectSlices[i] = LabelizeAndCountNumberOfObjects<SliceType>(mObjectSlices[i], 0, true, 1, nb);
+    if ((!GetIgnoreEmptySliceObjectFlag()) || (nb!=0)) {
+
+      // Select or not a single CCL ?
+      if (GetUseTheLargestObjectCCLFlag()) {
+        mObjectSlices[i] = KeepLabels<SliceType>(mObjectSlices[i], 0, 1, 1, 1, true);
+      }
+
+      // Select a single according to a position if more than one CCL
+      if (GetObjectCCLSelectionFlag()) {
+        // if several CCL, choose the most extrema according a direction, 
+        // if not -> should we consider this slice ? 
+        if (nb<2) {
+          if (GetObjectCCLSelectionIgnoreSingleCCLFlag()) {
+            mObjectSlices[i] = SetBackground<SliceType, SliceType>(mObjectSlices[i], mObjectSlices[i], 
+                                                                   1, this->GetBackgroundValue(), 
+                                                                   true);
+          }
+        }
+        int dim = GetObjectCCLSelectionDimension();
+        int direction = GetObjectCCLSelectionDirection();
+        std::vector<typename SliceType::PointType> centroids;
+        ComputeCentroids<SliceType>(mObjectSlices[i], this->GetBackgroundValue(), centroids);
+        uint index=1;
+        for(uint j=1; j<centroids.size(); j++) {
+          if (direction == 1) {
+            if (centroids[j][dim] > centroids[index][dim]) index = j;
+          }
+          else {
+            if (centroids[j][dim] < centroids[index][dim]) index = j;
+          }
+        }
+        for(uint v=1; v<centroids.size(); v++) {
+          if (v != index) {
+            mObjectSlices[i] = SetBackground<SliceType, SliceType>(mObjectSlices[i], mObjectSlices[i], 
+                                                                   (char)v, this->GetBackgroundValue(), 
+                                                                   true);
+          }
+        }
+      } // end GetbjectCCLSelectionFlag = true
 
+      // Relative position
+      typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
+      typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+
+      relPosFilter->VerboseStepFlagOff();
+      relPosFilter->WriteStepFlagOff();
+      relPosFilter->SetBackgroundValue(this->GetBackgroundValue());
+      relPosFilter->SetInput(mInputSlices[i]); 
+      relPosFilter->SetInputObject(mObjectSlices[i]); 
+      relPosFilter->SetRemoveObjectFlag(this->GetRemoveObjectFlag());
+      // This flag (InverseOrientation) *must* be set before
+      // AddOrientation because AddOrientation can change it.
+      relPosFilter->SetInverseOrientationFlag(this->GetInverseOrientationFlag());
+      for(int j=0; j<this->GetNumberOfAngles(); j++) {
+        relPosFilter->AddOrientationTypeString(this->GetOrientationTypeString(j));
+        //DD(this->GetOrientationTypeString(j));
+      }
+      //DD(this->GetInverseOrientationFlag());
+      //relPosFilter->SetOrientationType(this->GetOrientationType());
+      relPosFilter->SetIntermediateSpacing(this->GetIntermediateSpacing());
+      relPosFilter->SetIntermediateSpacingFlag(this->GetIntermediateSpacingFlag());
+      relPosFilter->SetFuzzyThreshold(this->GetFuzzyThreshold());
+      relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+      relPosFilter->SetCombineWithOrFlag(this->GetCombineWithOrFlag()); 
+      relPosFilter->Update();
+      mInputSlices[i] = relPosFilter->GetOutput();
+
+      // Select main CC if needed
+      if (GetUniqueConnectedComponentBySliceFlag()) {
+        mInputSlices[i] = Labelize<SliceType>(mInputSlices[i], 0, true, 1);
+        mInputSlices[i] = KeepLabels<SliceType>(mInputSlices[i], 0, 1, 1, 1, true);
+      }
+
+      /*
+      // Select unique CC according to the most in a given direction
+      if (GetUniqueConnectedComponentBySliceAccordingToADirection()) {
+        int nb;
+        mInputSlices[i] = LabelizeAndCountNumberOfObjects<SliceType>(mInputSlices[i], 0, true, 1, nb);
+        std::vector<typename ImageType::PointType> & centroids;
+        ComputeCentroids
+        }
+      */
+    }
   }
 
   // Join the slices