segmentation/clitkConnectedComponentLabelingGenericFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 #ifndef CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX
  20 #define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX
  21
  22 // clitk
  23 #include "clitkImageCommon.h"
  24 #include "clitkSegmentationUtils.h"
  25
  26 // itk
  27 #include "itkConnectedComponentImageFilter.h"
  28 #include "itkRelabelComponentImageFilter.h"
  29
  30 //--------------------------------------------------------------------
  31 template<class ArgsInfoType>
  32 clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::ConnectedComponentLabelingGenericFilter():
  33   ImageToImageGenericFilter<Self>("ConnectedComponentLabeling")
  34 {
  35   InitializeImageType<2>();
  36   InitializeImageType<3>();
  37   //InitializeImageType<4>();
  38 }
  39 //--------------------------------------------------------------------
  40
  41
  42 //--------------------------------------------------------------------
  43 template<class ArgsInfoType>
  44 template<unsigned int Dim>
  45 void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::InitializeImageType()
  46 {
  47   ADD_IMAGE_TYPE(Dim, uchar);
  48   ADD_IMAGE_TYPE(Dim, short);
  49   // ADD_IMAGE_TYPE(Dim, int);
  50   ADD_IMAGE_TYPE(Dim, float);
  51 }
  52 //--------------------------------------------------------------------
  53
  54
  55 //--------------------------------------------------------------------
  56 template<class ArgsInfoType>
  57 void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
  58 {
  59   mArgsInfo=a;
  60   this->SetIOVerbose(mArgsInfo.verbose_flag);
  61   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  62   if (mArgsInfo.input_given)   this->AddInputFilename(mArgsInfo.input_arg);
  63   if (mArgsInfo.output_given)  this->SetOutputFilename(mArgsInfo.output_arg);
  64 }
  65 //--------------------------------------------------------------------
  66
  67
  68 //--------------------------------------------------------------------
  69 // Update with the number of dimensions and the pixeltype
  70 //--------------------------------------------------------------------
  71 template<class ArgsInfoType>
  72 template<class ImageType>
  73 void clitk::ConnectedComponentLabelingGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
  74 {
  75   // Reading input
  76   typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
  77
  78   // Output image type
  79   typedef itk::Image<int, ImageType::ImageDimension> OutputImageType;
  80   //PrintMemory(true, "initial");
  81
  82   typename OutputImageType::Pointer output;
  83   {
  84     typename OutputImageType::Pointer temp;
  85     {
  86       // Create CCL filter
  87       typedef itk::ConnectedComponentImageFilter<ImageType, OutputImageType> ConnectFilterType;
  88       typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
  89       // connectFilter->ReleaseDataFlagOn(); // release earlier
  90       connectFilter->SetInput(input);
  91       connectFilter->SetBackgroundValue(mArgsInfo.inputBG_arg);
  92       connectFilter->SetFullyConnected(mArgsInfo.full_flag);
  93       //          connectFilter->SetNumberOfThreads(8);
  94       connectFilter->Update();
  95       temp = connectFilter->GetOutput();
  96       // PrintMemory(true, "after udpate");
  97     }
  98     // PrintMemory(true, "after CCL block");
  99     // DD(input->GetReferenceCount());
 100     // DD(temp->GetReferenceCount());
 101
 102     // Sort by size and remove too small area.
 103     typedef itk::RelabelComponentImageFilter<OutputImageType, OutputImageType> RelabelFilterType;
 104     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 105     //    relabelFilter->SetInput(connectFilter->GetOutput());
 106     relabelFilter->SetInput(temp);
 107     relabelFilter->SetMinimumObjectSize(mArgsInfo.minSize_arg);
 108     relabelFilter->Update();
 109
 110     // DD(mArgsInfo.inputBG_arg);
 111     // DD(mArgsInfo.full_flag);
 112     // DD(mArgsInfo.minSize_arg);
 113
 114     // Set information
 115     const std::vector<typename RelabelFilterType::ObjectSizeType> & a
 116       = relabelFilter->GetSizeOfObjectsInPixels();
 117     m_SizeOfObjectsInPixels.resize(a.size());
 118     for(unsigned int i=0; i<a.size(); i++) m_SizeOfObjectsInPixels[i] = a[i];
 119     m_SizeOfObjectsInPhysicalUnits = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
 120     m_OriginalNumberOfObjects = relabelFilter->GetOriginalNumberOfObjects();
 121     // DD(m_OriginalNumberOfObjects);
 122     // DD(m_SizeOfObjectsInPhysicalUnits.size());
 123
 124     output = relabelFilter->GetOutput();
 125   }
 126   // PrintMemory(true, "after block");
 127
 128   // Write/Save results
 129   this->template SetNextOutput<OutputImageType>(output);
 130   // PrintMemory(true, "end filter ");
 131 }
 132 //--------------------------------------------------------------------
 133
 134 #endif //#define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX