Increase number of decimal for fusion and overlay

[clitk.git] / segmentation / clitkConnectedComponentLabelingGenericFilter.txx

diff --git a/segmentation/clitkConnectedComponentLabelingGenericFilter.txx b/segmentation/clitkConnectedComponentLabelingGenericFilter.txx
index caf5cdf4534e4a9ef37470162ff9cfeafd230e9f..cb38852edfdaa53acf89af280b0dbad16167a017 100644 (file)
--- a/segmentation/clitkConnectedComponentLabelingGenericFilter.txx
+++ b/segmentation/clitkConnectedComponentLabelingGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,13 +14,14 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX
 #define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX
 
 // clitk
 #include "clitkImageCommon.h"
+#include "clitkSegmentationUtils.h"
 
 // itk
 #include "itkConnectedComponentImageFilter.h"
@@ -31,7 +32,7 @@ template<class ArgsInfoType>
 clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::ConnectedComponentLabelingGenericFilter():
   ImageToImageGenericFilter<Self>("ConnectedComponentLabeling") 
 {
-  //  InitializeImageType<2>();
+  InitializeImageType<2>();
   InitializeImageType<3>();
   //InitializeImageType<4>();
 }
@@ -45,8 +46,9 @@ void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::InitializeIma
 {  
   ADD_IMAGE_TYPE(Dim, uchar);
   ADD_IMAGE_TYPE(Dim, short);
+  ADD_IMAGE_TYPE(Dim, ushort);
   // ADD_IMAGE_TYPE(Dim, int);
-  // ADD_IMAGE_TYPE(Dim, float);
+  ADD_IMAGE_TYPE(Dim, float);
 }
 //--------------------------------------------------------------------
   
@@ -56,10 +58,10 @@ template<class ArgsInfoType>
 void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
 {
   mArgsInfo=a;
-  SetIOVerbose(mArgsInfo.verbose_flag);
+  this->SetIOVerbose(mArgsInfo.verbose_flag);
   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
-  if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
-  if (mArgsInfo.output_given)  SetOutputFilename(mArgsInfo.output_arg);
+  if (mArgsInfo.input_given)   this->AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  this->SetOutputFilename(mArgsInfo.output_arg);
 }
 //--------------------------------------------------------------------
 
@@ -71,49 +73,62 @@ template<class ArgsInfoType>
 template<class ImageType>
 void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
 { 
-  DD("UpdateWithInputImageType");
-
   // Reading input
   typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
 
   // Output image type
   typedef itk::Image<int, ImageType::ImageDimension> OutputImageType;
-
-  // Create CCL filter
-  DD("CCL");
-  typedef itk::ConnectedComponentImageFilter<ImageType, OutputImageType> ConnectFilterType;
-  typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
-  connectFilter->SetInput(input);
-  connectFilter->SetBackgroundValue(mArgsInfo.inputBG_arg);
-  connectFilter->SetFullyConnected(mArgsInfo.full_flag);
-
-  // TODO SetBackgroud to zero forr relabel ?
-
-
-  // Sort by size and remove too small area.
-  typedef itk::RelabelComponentImageFilter<OutputImageType, OutputImageType> RelabelFilterType;
-  typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
-  //  relabelFilter->InPlaceOn();
-  relabelFilter->SetInput(connectFilter->GetOutput());
-  relabelFilter->SetMinimumObjectSize(mArgsInfo.minSize_arg);
-  relabelFilter->Update();
-
-  DD(mArgsInfo.inputBG_arg);
-  DD(mArgsInfo.full_flag);
-  DD(mArgsInfo.minSize_arg);
-  
-  // Set information
-  const std::vector<typename RelabelFilterType::ObjectSizeType> & a = relabelFilter->GetSizeOfObjectsInPixels();
-  m_SizeOfObjectsInPixels.resize(a.size());
-  for(unsigned int i=0; i<a.size(); i++) m_SizeOfObjectsInPixels[i] = a[i];
-  m_SizeOfObjectsInPhysicalUnits = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
-  m_OriginalNumberOfObjects = relabelFilter->GetOriginalNumberOfObjects();
-  DD(m_OriginalNumberOfObjects);
-  DD(m_SizeOfObjectsInPhysicalUnits.size());
+  //PrintMemory(true, "initial");
+
+  typename OutputImageType::Pointer output;
+  {
+    typename OutputImageType::Pointer temp;
+    {
+      // Create CCL filter
+      typedef itk::ConnectedComponentImageFilter<ImageType, OutputImageType> ConnectFilterType;
+      typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+      // connectFilter->ReleaseDataFlagOn(); // release earlier
+      connectFilter->SetInput(input);
+      connectFilter->SetBackgroundValue(mArgsInfo.inputBG_arg);
+      connectFilter->SetFullyConnected(mArgsInfo.full_flag);
+      //          connectFilter->SetNumberOfThreads(8);
+      connectFilter->Update();
+      temp = connectFilter->GetOutput();
+      // PrintMemory(true, "after udpate");
+    }
+    // PrintMemory(true, "after CCL block");
+    // DD(input->GetReferenceCount());
+    // DD(temp->GetReferenceCount());
+    
+    // Sort by size and remove too small area.
+    typedef itk::RelabelComponentImageFilter<OutputImageType, OutputImageType> RelabelFilterType;
+    typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+    //    relabelFilter->SetInput(connectFilter->GetOutput());
+    relabelFilter->SetInput(temp);
+    relabelFilter->SetMinimumObjectSize(mArgsInfo.minSize_arg);
+    relabelFilter->Update();
+    
+    // DD(mArgsInfo.inputBG_arg);
+    // DD(mArgsInfo.full_flag);
+    // DD(mArgsInfo.minSize_arg);
+    
+    // Set information
+    const std::vector<typename RelabelFilterType::ObjectSizeType> & a 
+      = relabelFilter->GetSizeOfObjectsInPixels();
+    m_SizeOfObjectsInPixels.resize(a.size());
+    for(unsigned int i=0; i<a.size(); i++) m_SizeOfObjectsInPixels[i] = a[i];
+    m_SizeOfObjectsInPhysicalUnits = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
+    m_OriginalNumberOfObjects = relabelFilter->GetOriginalNumberOfObjects();
+    // DD(m_OriginalNumberOfObjects);
+    // DD(m_SizeOfObjectsInPhysicalUnits.size());
+    
+    output = relabelFilter->GetOutput();
+  }
+  // PrintMemory(true, "after block");
 
   // Write/Save results
-  typename OutputImageType::Pointer output = relabelFilter->GetOutput();
   this->template SetNextOutput<OutputImageType>(output); 
+  // PrintMemory(true, "end filter ");
 }
 //--------------------------------------------------------------------