some segmentation tools (most from jef)

[clitk.git] / segmentation / clitkConnectedComponentLabelingGenericFilter.txx

diff --git a/segmentation/clitkConnectedComponentLabelingGenericFilter.txx b/segmentation/clitkConnectedComponentLabelingGenericFilter.txx
new file mode 100644 (file)
index 0000000..caf5cdf
--- /dev/null
+++ b/segmentation/clitkConnectedComponentLabelingGenericFilter.txx
@@ -0,0 +1,120 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - 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"
+
+// itk
+#include "itkConnectedComponentImageFilter.h"
+#include "itkRelabelComponentImageFilter.h"
+  
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::ConnectedComponentLabelingGenericFilter():
+  ImageToImageGenericFilter<Self>("ConnectedComponentLabeling") 
+{
+  //  InitializeImageType<2>();
+  InitializeImageType<3>();
+  //InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::InitializeImageType() 
+{  
+  ADD_IMAGE_TYPE(Dim, uchar);
+  ADD_IMAGE_TYPE(Dim, short);
+  // ADD_IMAGE_TYPE(Dim, int);
+  // ADD_IMAGE_TYPE(Dim, float);
+}
+//--------------------------------------------------------------------
+  
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
+{
+  mArgsInfo=a;
+  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);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+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());
+
+  // Write/Save results
+  typename OutputImageType::Pointer output = relabelFilter->GetOutput();
+  this->template SetNextOutput<OutputImageType>(output); 
+}
+//--------------------------------------------------------------------
+
+#endif //#define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX