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   SetIOVerbose(mArgsInfo.verbose_flag);
  61   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  62   if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
  63   if (mArgsInfo.output_given)  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   DD("UpdateWithInputImageType");
  76
  77   // Reading input
  78   typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
  79
  80   // Output image type
  81   typedef itk::Image<int, ImageType::ImageDimension> OutputImageType;
  82   PrintMemory(true, "initial");
  83
  84   typename OutputImageType::Pointer output;
  85   {
  86     typename OutputImageType::Pointer temp;
  87     {
  88       // Create CCL filter
  89       typedef itk::ConnectedComponentImageFilter<ImageType, OutputImageType> ConnectFilterType;
  90       typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
  91       // connectFilter->ReleaseDataFlagOn(); // release earlier
  92       connectFilter->SetInput(input);
  93       connectFilter->SetBackgroundValue(mArgsInfo.inputBG_arg);
  94       connectFilter->SetFullyConnected(mArgsInfo.full_flag);
  95       //          connectFilter->SetNumberOfThreads(8);
  96       connectFilter->Update();
  97       temp = connectFilter->GetOutput();
  98       PrintMemory(true, "after udpate");
  99     }
 100     PrintMemory(true, "after CCL block");
 101     DD(input->GetReferenceCount());
 102     DD(temp->GetReferenceCount());
 103
 104     // Sort by size and remove too small area.
 105     typedef itk::RelabelComponentImageFilter<OutputImageType, OutputImageType> RelabelFilterType;
 106     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 107     //    relabelFilter->SetInput(connectFilter->GetOutput());
 108     relabelFilter->SetInput(temp);
 109     relabelFilter->SetMinimumObjectSize(mArgsInfo.minSize_arg);
 110     relabelFilter->Update();
 111
 112     DD(mArgsInfo.inputBG_arg);
 113     DD(mArgsInfo.full_flag);
 114     DD(mArgsInfo.minSize_arg);
 115
 116     // Set information
 117     const std::vector<typename RelabelFilterType::ObjectSizeType> & a
 118       = relabelFilter->GetSizeOfObjectsInPixels();
 119     m_SizeOfObjectsInPixels.resize(a.size());
 120     for(unsigned int i=0; i<a.size(); i++) m_SizeOfObjectsInPixels[i] = a[i];
 121     m_SizeOfObjectsInPhysicalUnits = relabelFilter->GetSizeOfObjectsInPhysicalUnits();
 122     m_OriginalNumberOfObjects = relabelFilter->GetOriginalNumberOfObjects();
 123     DD(m_OriginalNumberOfObjects);
 124     DD(m_SizeOfObjectsInPhysicalUnits.size());
 125
 126     output = relabelFilter->GetOutput();
 127   }
 128   PrintMemory(true, "after block");
 129
 130   // Write/Save results
 131   this->template SetNextOutput<OutputImageType>(output);
 132   PrintMemory(true, "end filter ");
 133 }
 134 //--------------------------------------------------------------------
 135
 136 #endif //#define CLITKCONNECTEDCOMPONENTLABELINGSGENERICFILTER_TXX