segmentation/clitkExtractBonesFilter.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 CLITKEXTRACTBONESSFILTER_TXX
  20 #define CLITKEXTRACTBONESSFILTER_TXX
  21
  22 // clitk
  23 #include "clitkImageCommon.h"
  24 #include "clitkSetBackgroundImageFilter.h"
  25 #include "clitkSegmentationUtils.h"
  26 #include "clitkAutoCropFilter.h"
  27
  28 // itk
  29 #include "itkBinaryThresholdImageFilter.h"
  30 #include "itkConnectedComponentImageFilter.h"
  31 #include "itkRelabelComponentImageFilter.h"
  32 #include "itkNeighborhoodConnectedImageFilter.h"
  33
  34 //--------------------------------------------------------------------
  35 template <class TInputImageType, class TOutputImageType>
  36 clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
  37 ExtractBonesFilter():
  38   clitk::FilterBase(),
  39   itk::ImageToImageFilter<TInputImageType, TOutputImageType>()
  40 {
  41   // Default global options
  42   this->SetNumberOfRequiredInputs(1);
  43   SetBackgroundValue(0); // Must be zero
  44   SetForegroundValue(1);
  45
  46   SetMinimalComponentSize(100);
  47   SetUpperThreshold1(1500);
  48   SetLowerThreshold1(100);
  49   SetFullConnectivity(false);
  50
  51   SetUpperThreshold2(1500);
  52   SetLowerThreshold2(10);
  53   InputImageSizeType s;
  54   s.Fill(1);
  55   SetRadius2(s);
  56   SetSampleRate2(0);
  57   AutoCropOff();
  58 }
  59 //--------------------------------------------------------------------
  60
  61
  62 //--------------------------------------------------------------------
  63 template <class TInputImageType, class TOutputImageType>
  64 void
  65 clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
  66 SetInput(const TInputImageType * image)
  67 {
  68   this->SetNthInput(0, const_cast<TInputImageType *>(image));
  69 }
  70 //--------------------------------------------------------------------
  71
  72
  73 //--------------------------------------------------------------------
  74 template <class TInputImageType, class TOutputImageType>
  75 template<class ArgsInfoType>
  76 void
  77 clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
  78 SetArgsInfo(ArgsInfoType mArgsInfo)
  79 {
  80   SetVerboseOption_GGO(mArgsInfo);
  81   SetVerboseStep_GGO(mArgsInfo);
  82   SetWriteStep_GGO(mArgsInfo);
  83   SetVerboseWarningOff_GGO(mArgsInfo);
  84
  85   SetMinimalComponentSize_GGO(mArgsInfo);
  86   SetUpperThreshold1_GGO(mArgsInfo);
  87   SetLowerThreshold1_GGO(mArgsInfo);
  88   SetFullConnectivity_GGO(mArgsInfo);
  89
  90   SetUpperThreshold2_GGO(mArgsInfo);
  91   SetLowerThreshold2_GGO(mArgsInfo);
  92   SetRadius2_GGO(mArgsInfo);
  93   SetSampleRate2_GGO(mArgsInfo);
  94   SetAutoCrop_GGO(mArgsInfo);
  95 }
  96 //--------------------------------------------------------------------
  97
  98
  99 //--------------------------------------------------------------------
 100 template <class TInputImageType, class TOutputImageType>
 101 void
 102 clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
 103 GenerateOutputInformation() {
 104   // Get input pointers
 105   InputImagePointer input   = dynamic_cast<TInputImageType*>(itk::ProcessObject::GetInput(0));
 106   //  InputImagePointer input = dynamic_cast<TInputImageType*>(itk::ProcessObject::GetInput(0));
 107   Superclass::GenerateOutputInformation();
 108   OutputImagePointer outputImage = this->GetOutput(0);
 109   outputImage->SetRegions(input->GetLargestPossibleRegion());
 110
 111   // typedefs
 112   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
 113   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> BinarizeFilterType;
 114   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 115   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 116   typedef clitk::SetBackgroundImageFilter<InternalImageType,InternalImageType, InternalImageType> SetBackgroundFilterType;
 117   typedef itk::CastImageFilter<InternalImageType,OutputImageType> CastImageFilterType;
 118   typedef itk::ImageFileWriter<OutputImageType> WriterType;
 119
 120   //--------------------------------------------------------------------
 121   //--------------------------------------------------------------------
 122   StartNewStep("Initial Labeling");
 123
 124   typename InternalImageType::Pointer firstLabelImage;
 125
 126   //---------------------------------
 127   // Binarize the image
 128   //---------------------------------
 129   typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 130   binarizeFilter->SetInput(input);
 131   binarizeFilter->SetLowerThreshold(GetLowerThreshold1());
 132   binarizeFilter->SetUpperThreshold(GetUpperThreshold1());
 133   binarizeFilter->SetInsideValue(this->GetForegroundValue());
 134   binarizeFilter->SetOutsideValue(this->GetBackgroundValue());
 135
 136   //---------------------------------
 137   // Label the connected components
 138   //---------------------------------
 139   typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 140   connectFilter->SetInput(binarizeFilter->GetOutput());
 141   connectFilter->SetBackgroundValue(this->GetBackgroundValue());
 142   connectFilter->SetFullyConnected(GetFullConnectivity());
 143
 144   //---------------------------------
 145   // Sort the labels according to size
 146   //---------------------------------
 147   typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 148   relabelFilter->SetInput(connectFilter->GetOutput());
 149   relabelFilter->SetMinimumObjectSize(GetMinimalComponentSize());
 150
 151   //---------------------------------
 152   // Keep the label
 153   //---------------------------------
 154   typename BinarizeFilterType::Pointer binarizeFilter2=BinarizeFilterType::New();
 155   binarizeFilter2->SetInput(relabelFilter->GetOutput());
 156   binarizeFilter2->SetLowerThreshold(1);
 157   binarizeFilter2->SetUpperThreshold(1);
 158   binarizeFilter2->SetInsideValue(this->GetForegroundValue());
 159   binarizeFilter2->SetOutsideValue(this->GetBackgroundValue());
 160   binarizeFilter2->Update();
 161
 162   firstLabelImage = binarizeFilter2->GetOutput();
 163
 164   //--------------------------------------------------------------------
 165   //--------------------------------------------------------------------
 166   StartNewStep("Neighborhood connected filter");
 167   typename InternalImageType::Pointer secondLabelImage;
 168
 169   //---------------------------------
 170   //Neighborhood connected RG
 171   //---------------------------------
 172   typedef itk::NeighborhoodConnectedImageFilter<InputImageType, InternalImageType>
 173     NeighborhoodConnectedImageFilterType;
 174   typename NeighborhoodConnectedImageFilterType::Pointer neighborhoodConnectedImageFilter=
 175     NeighborhoodConnectedImageFilterType::New();
 176
 177   // thresholds
 178   neighborhoodConnectedImageFilter->SetLower(GetLowerThreshold2());
 179   neighborhoodConnectedImageFilter->SetUpper(GetUpperThreshold2());
 180   neighborhoodConnectedImageFilter->SetReplaceValue(this->GetForegroundValue());
 181   neighborhoodConnectedImageFilter->SetRadius(GetRadius2());
 182   neighborhoodConnectedImageFilter->SetInput(input);
 183
 184   // Seeds from label image
 185   typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 186   IteratorType it(firstLabelImage, firstLabelImage->GetLargestPossibleRegion());
 187   typename InputImageType::IndexType index;
 188   unsigned int counter=0;
 189   while (!it.IsAtEnd())
 190     {
 191       if (it.Get()==this->GetForegroundValue())
 192         {
 193           counter++;
 194           index=it.GetIndex();
 195           neighborhoodConnectedImageFilter->AddSeed(index);
 196           ++it;
 197           unsigned int i=0;
 198           while (!it.IsAtEnd()  &&  i< (unsigned int) GetSampleRate2())
 199             {
 200               ++it;
 201               i++;
 202             }
 203         }
 204       else ++it;
 205     }
 206
 207   neighborhoodConnectedImageFilter->Update();
 208   secondLabelImage = neighborhoodConnectedImageFilter->GetOutput();
 209
 210   //--------------------------------------------------------------------
 211   //--------------------------------------------------------------------
 212   StartNewStep("Combine de images");
 213   typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType>
 214     SetBackgroundImageFilterType;
 215   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter=SetBackgroundImageFilterType::New();
 216   setBackgroundFilter->SetInput(firstLabelImage);
 217   setBackgroundFilter->SetInput2(secondLabelImage);
 218   setBackgroundFilter->SetMaskValue(this->GetForegroundValue());
 219   setBackgroundFilter->SetOutsideValue(this->GetForegroundValue());
 220   setBackgroundFilter->Update();
 221
 222   output = setBackgroundFilter->GetOutput();
 223
 224   //--------------------------------------------------------------------
 225   //--------------------------------------------------------------------
 226   // [Optional]
 227   if (GetAutoCrop()) {
 228     StartNewStep("AutoCrop");
 229     typedef clitk::AutoCropFilter<InternalImageType> CropFilterType;
 230     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 231     cropFilter->SetInput(output);
 232     cropFilter->SetBackgroundValue(GetBackgroundValue());
 233     cropFilter->Update();
 234     output = cropFilter->GetOutput();
 235     StopCurrentStep<InternalImageType>(output);
 236     outputImage->SetRegions(output->GetLargestPossibleRegion());
 237   }
 238
 239 }
 240 //--------------------------------------------------------------------
 241
 242
 243 //--------------------------------------------------------------------
 244 template <class TInputImageType, class TOutputImageType>
 245 void
 246 clitk::ExtractBonesFilter<TInputImageType, TOutputImageType>::
 247 GenerateData() {
 248
 249   //--------------------------------------------------------------------
 250   //--------------------------------------------------------------------
 251   // Final Cast
 252   typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
 253   typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
 254   caster->SetInput(output);
 255   caster->Update();
 256   //this->SetNthOutput(0, caster->GetOutput());
 257   this->GraftOutput(caster->GetOutput());
 258   return;
 259 }
 260 //--------------------------------------------------------------------
 261
 262
 263 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX