segmentation/clitkStructuresExtractionFilter.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 // clitk
  20 #include "clitkStructuresExtractionFilter.h"
  21
  22 //--------------------------------------------------------------------
  23 template <class TImageType>
  24 clitk::StructuresExtractionFilter<TImageType>::
  25 StructuresExtractionFilter():
  26   clitk::FilterBase(),
  27   clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
  28   itk::ImageToImageFilter<TImageType, MaskImageType>()
  29 {
  30   SetBackgroundValue(0);
  31   SetForegroundValue(1);
  32 }
  33 //--------------------------------------------------------------------
  34
  35
  36 //--------------------------------------------------------------------
  37 template <class TImageType>
  38 void
  39 clitk::StructuresExtractionFilter<TImageType>::
  40 AddRelativePositionListFilename(std::string s) {
  41   mListOfRelativePositionListFilename.push_back(s);
  42 }
  43 //--------------------------------------------------------------------
  44
  45
  46 //--------------------------------------------------------------------
  47 template <class TImageType>
  48 typename clitk::StructuresExtractionFilter<TImageType>::MaskImagePointer
  49 clitk::StructuresExtractionFilter<TImageType>::
  50 ApplyRelativePositionList(std::string name, MaskImageType * input, bool overlap)
  51 {
  52   // Create all RelativePositionList
  53   for(unsigned int i=0; i<mListOfRelativePositionListFilename.size(); i++) {
  54     RelPosListPointer rpl = RelPosListType::New();
  55     rpl->SetDisplayUsedStructuresOnlyFlag(this->GetDisplayUsedStructuresOnlyFlag());
  56     rpl->SetAFDB(GetAFDB());
  57     rpl->Read(mListOfRelativePositionListFilename[i]);
  58     std::string s = rpl->GetInputName();
  59     mMapOfRelativePositionList[s] = rpl;
  60   }
  61
  62   RelPosListPointer relpos;
  63   if (mMapOfRelativePositionList.find(name) == mMapOfRelativePositionList.end()) {
  64     std::cerr << "Warning: I do not find '" << name << "' in the RelativePositionList." << std::endl;
  65     //DD("Not find !"); // do nothing
  66   }
  67   else {
  68     relpos = mMapOfRelativePositionList[name];
  69     relpos->SetVerboseStepFlag(GetVerboseStepFlag());
  70     relpos->SetCurrentStepBaseId(GetCurrentStepBaseId());
  71     relpos->SetCurrentStepId(GetCurrentStepId());
  72     relpos->SetCurrentStepNumber(GetCurrentStepNumber());
  73     relpos->SetWriteStepFlag(GetWriteStepFlag());
  74     relpos->SetInput(input);
  75     if (!this->GetDisplayUsedStructuresOnlyFlag() && overlap) {
  76       std::string n = name.substr(8,3);
  77       MaskImagePointer ref = this->GetAFDB()->template GetImage <MaskImageType>(n+"_Ref");
  78       relpos->SetReferenceImageForOverlapMeasure(ref);
  79     }
  80     relpos->Update();
  81     input = relpos->GetOutput();
  82
  83     SetCurrentStepNumber(relpos->GetCurrentStepNumber());
  84   }
  85   return input;
  86 }
  87 //--------------------------------------------------------------------
  88