segmentation/clitkExtractLymphStationsFilter.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://oncora1.lyon.fnclcc.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 CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
  20 #define CLITKEXTRACTLYMPHSTATIONSFILTER_TXX
  21
  22 // clitk
  23 #include "clitkCommon.h"
  24 #include "clitkExtractLymphStationsFilter.h"
  25 #include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
  26 #include "clitkSegmentationUtils.h"
  27 #include "clitkAutoCropFilter.h"
  28 #include "clitkSegmentationUtils.h"
  29 #include "clitkSliceBySliceRelativePositionFilter.h"
  30
  31 // itk
  32 #include <itkStatisticsLabelMapFilter.h>
  33 #include <itkLabelImageToStatisticsLabelMapFilter.h>
  34 #include <itkRegionOfInterestImageFilter.h>
  35 #include <itkBinaryThresholdImageFilter.h>
  36 #include <itkImageSliceConstIteratorWithIndex.h>
  37 #include <itkImageSliceIteratorWithIndex.h>
  38 #include <itkBinaryThinningImageFilter.h>
  39
  40 // itk ENST
  41 #include "RelativePositionPropImageFilter.h"
  42
  43 //--------------------------------------------------------------------
  44 template <class TImageType>
  45 clitk::ExtractLymphStationsFilter<TImageType>::
  46 ExtractLymphStationsFilter():
  47   clitk::FilterBase(),
  48   clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
  49   itk::ImageToImageFilter<TImageType, MaskImageType>()
  50 {
  51   this->SetNumberOfRequiredInputs(1);
  52   SetBackgroundValue(0);
  53   SetForegroundValue(1);
  54
  55   // Station 7
  56   SetFuzzyThreshold(0.5);
  57   SetStation7Filename("station7.mhd");
  58 }
  59 //--------------------------------------------------------------------
  60
  61
  62 //--------------------------------------------------------------------
  63 template <class TImageType>
  64 template <class ArgsInfoType>
  65 void
  66 clitk::ExtractLymphStationsFilter<TImageType>::
  67 SetArgsInfo(ArgsInfoType & argsinfo) {
  68   DD("SetArgsInfo");
  69 }
  70 //--------------------------------------------------------------------
  71
  72
  73 //--------------------------------------------------------------------
  74 template <class TImageType>
  75 void
  76 clitk::ExtractLymphStationsFilter<TImageType>::
  77 GenerateOutputInformation() {
  78   // Get inputs
  79   LoadAFDB();
  80   m_Input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
  81   m_Support = GetAFDB()->template GetImage <MaskImageType>("mediastinum");
  82
  83   //
  84   typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BFilter;
  85   BFilter::Pointer merge = BFilter::New();
  86
  87   // Extract Station7
  88   ExtractStation_7();
  89   m_Output = m_Station7;
  90
  91   // Extract Station4RL
  92   ExtractStation_4RL();
  93
  94   writeImage<MaskImageType>(m_Station4RL, "s4rl.mhd");
  95   // writeImage<MaskImageType>(m_Output, "ouput.mhd");
  96   //writeImage<MaskImageType>(m_Working_Support, "ws.mhd");
  97   /*merge->SetInput1(m_Station7);
  98   merge->SetInput2(m_Station4RL); // support
  99   merge->SetOperationType(BFilter::AndNot); CHANGE OPERATOR
 100   merge->SetForegroundValue(4);
 101   merge->Update();
 102   m_Output = merge->GetOutput();
 103   */
 104 }
 105 //--------------------------------------------------------------------
 106
 107
 108 //--------------------------------------------------------------------
 109 template <class TImageType>
 110 void
 111 clitk::ExtractLymphStationsFilter<TImageType>::
 112 GenerateInputRequestedRegion() {
 113   DD("GenerateInputRequestedRegion (nothing?)");
 114 }
 115 //--------------------------------------------------------------------
 116
 117
 118 //--------------------------------------------------------------------
 119 template <class TImageType>
 120 void
 121 clitk::ExtractLymphStationsFilter<TImageType>::
 122 GenerateData() {
 123   DD("GenerateData, graft output");
 124
 125   // Final Step -> graft output (if SetNthOutput => redo)
 126   this->GraftOutput(m_Output);
 127 }
 128 //--------------------------------------------------------------------
 129
 130
 131 //--------------------------------------------------------------------
 132 template <class TImageType>
 133 void
 134 clitk::ExtractLymphStationsFilter<TImageType>::
 135 ExtractStation_7() {
 136   DD("ExtractStation_7");
 137   ExtractStation_7_SI_Limits();
 138   ExtractStation_7_RL_Limits();
 139   ExtractStation_7_Posterior_Limits();
 140 }
 141 //--------------------------------------------------------------------
 142
 143
 144 //--------------------------------------------------------------------
 145 template <class TImageType>
 146 void
 147 clitk::ExtractLymphStationsFilter<TImageType>::
 148 ExtractStation_4RL() {
 149   DD("ExtractStation_4RL");
 150   writeImage<MaskImageType>(m_Support, "essai.mhd"); // OK
 151
 152   /*
 153     WARNING ONLY 4R FIRST !!! (not same inf limits)
 154    */
 155
 156   ExtractStation_4RL_SI_Limits();
 157   ExtractStation_4RL_LR_Limits();
 158
 159 }
 160 //--------------------------------------------------------------------
 161
 162
 163
 164 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX