segmentation/clitkExtractPatientFilter.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 CLITKEXTRACTPATIENTFILTER_TXX
  20 #define CLITKEXTRACTPATIENTFILTER_TXX
  21
  22 // clitk
  23 #include "clitkImageCommon.h"
  24 #include "clitkSetBackgroundImageFilter.h"
  25 #include "clitkDecomposeAndReconstructImageFilter.h"
  26 #include "clitkAutoCropFilter.h"
  27
  28 // itk
  29 #include "itkBinaryThresholdImageFilter.h"
  30 #include "itkConnectedComponentImageFilter.h"
  31 #include "itkRelabelComponentImageFilter.h"
  32 #include "itkBinaryMorphologicalClosingImageFilter.h"
  33 #include "itkBinaryMorphologicalOpeningImageFilter.h"
  34 #include "itkBinaryBallStructuringElement.h"
  35 #include "itkCastImageFilter.h"
  36
  37 //--------------------------------------------------------------------
  38 template <class TInputImageType, class TOutputImageType>
  39 clitk::ExtractPatientFilter<TInputImageType, TOutputImageType>::
  40 ExtractPatientFilter():
  41   clitk::FilterBase(),
  42   itk::ImageToImageFilter<TInputImageType, TOutputImageType>()
  43 {
  44   this->SetNumberOfRequiredInputs(1);
  45   SetBackgroundValue(0); // Must be zero
  46   SetForegroundValue(1);
  47
  48   // Step 1: Threshold + CC + sort (Find low density areas)
  49   SetUpperThreshold(-300);
  50   SetLowerThreshold(-1000);
  51   UseLowerThresholdOff();
  52
  53   // Step 2: DecomposeAndReconstructImageFilter (optional)
  54   DecomposeAndReconstructDuringFirstStepOff();
  55   InternalImageSizeType r;
  56   r.Fill(1);
  57   SetRadius1(r);
  58   SetMaximumNumberOfLabels1(2);
  59   SetNumberOfNewLabels1(1);
  60
  61   // Step 3: Remove the air (largest area).
  62
  63   // Step 4: 2nd DecomposeAndReconstructImageFilter
  64   DecomposeAndReconstructDuringSecondStepOff();
  65   SetRadius2(r);
  66   SetMaximumNumberOfLabels2(2);
  67   SetNumberOfNewLabels2(1);
  68
  69   // Step 5: Only keep label corresponding (Keep patient's labels)
  70   SetFirstKeep(1);
  71   SetLastKeep(1);
  72
  73   // Step 4: OpenClose (option)
  74   FinalOpenCloseOn();
  75   AutoCropOff();
  76 }
  77 //--------------------------------------------------------------------
  78
  79
  80 //--------------------------------------------------------------------
  81 template <class TInputImageType, class TOutputImageType>
  82 void
  83 clitk::ExtractPatientFilter<TInputImageType, TOutputImageType>::
  84 SetInput(const TInputImageType * image)
  85 {
  86   this->SetNthInput(0, const_cast<TInputImageType *>(image));
  87 }
  88 //--------------------------------------------------------------------
  89
  90
  91 //--------------------------------------------------------------------
  92 template <class TInputImageType, class TOutputImageType>
  93 template<class ArgsInfoType>
  94 void
  95 clitk::ExtractPatientFilter<TInputImageType, TOutputImageType>::
  96 SetArgsInfo(ArgsInfoType arg)
  97 {
  98   SetVerboseOption_GGO(arg);
  99   SetVerboseStep_GGO(arg);
 100   SetWriteStep_GGO(arg);
 101   SetVerboseWarningOff_GGO(arg);
 102
 103   SetUpperThreshold_GGO(arg);
 104   SetLowerThreshold_GGO(arg);
 105
 106   SetDecomposeAndReconstructDuringFirstStep_GGO(arg);
 107   SetRadius1_GGO(arg);
 108   SetMaximumNumberOfLabels1_GGO(arg);
 109   SetNumberOfNewLabels1_GGO(arg);
 110
 111   SetDecomposeAndReconstructDuringSecondStep_GGO(arg);
 112   SetRadius2_GGO(arg);
 113   SetMaximumNumberOfLabels2_GGO(arg);
 114   SetNumberOfNewLabels2_GGO(arg);
 115
 116   SetFirstKeep_GGO(arg);
 117   SetLastKeep_GGO(arg);
 118
 119   SetFinalOpenClose_GGO(arg);
 120   SetAutoCrop_GGO(arg);
 121 }
 122 //--------------------------------------------------------------------
 123
 124
 125 //--------------------------------------------------------------------
 126 template <class TInputImageType, class TOutputImageType>
 127 void
 128 clitk::ExtractPatientFilter<TInputImageType, TOutputImageType>::
 129 GenerateOutputInformation() {
 130
 131   Superclass::GenerateOutputInformation();
 132   input = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
 133
 134   // OutputImagePointer outputImage = this->GetOutput(0);
 135 //   outputImage->SetRegions(input->GetLargestPossibleRegion());
 136
 137   // Get input pointers
 138   static const unsigned int Dim = InputImageType::ImageDimension;
 139   //input = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
 140
 141   //--------------------------------------------------------------------
 142   //--------------------------------------------------------------------
 143   // Step 1:
 144   StartNewStep("Find low densities areas");
 145   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> BinarizeFilterType;
 146   typename BinarizeFilterType::Pointer binarizeFilter=BinarizeFilterType::New();
 147   binarizeFilter->SetInput(input);
 148   if (m_UseLowerThreshold) binarizeFilter->SetLowerThreshold(GetLowerThreshold());
 149   binarizeFilter->SetUpperThreshold(GetUpperThreshold());
 150   binarizeFilter ->SetInsideValue(this->GetForegroundValue());
 151   binarizeFilter ->SetOutsideValue(this->GetBackgroundValue());
 152
 153   // Connected component labeling
 154   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 155   typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 156   connectFilter->SetInput(binarizeFilter->GetOutput());
 157   connectFilter->SetBackgroundValue(this->GetBackgroundValue());
 158   connectFilter->SetFullyConnected(false);
 159
 160   // Sort labels according to size
 161   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 162   typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 163   relabelFilter->InPlaceOn();
 164   relabelFilter->SetInput(connectFilter->GetOutput());
 165   relabelFilter->Update();
 166   working_image = relabelFilter->GetOutput();
 167
 168   // End
 169   StopCurrentStep<InternalImageType>(working_image);
 170
 171   //--------------------------------------------------------------------
 172   //--------------------------------------------------------------------
 173   // [Optional]
 174   if (GetDecomposeAndReconstructDuringFirstStep()) {
 175     StartNewStep("First Decompose & Reconstruct step");
 176     typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
 177     typename FilterType::Pointer f = FilterType::New();
 178     f->SetInput(working_image);
 179     // f->SetVerbose(m_Verbose);
 180     f->SetRadius(GetRadius1());
 181     f->SetMaximumNumberOfLabels(GetMaximumNumberOfLabels1());
 182     f->SetBackgroundValue(this->GetBackgroundValue());
 183     f->SetForegroundValue(this->GetForegroundValue());
 184     f->SetFullyConnected(true);
 185     f->SetNumberOfNewLabels(GetNumberOfNewLabels1());
 186     f->Update();
 187     working_image = f->GetOutput();
 188     StopCurrentStep<InternalImageType>(working_image);
 189   }
 190
 191   //--------------------------------------------------------------------
 192   //--------------------------------------------------------------------
 193   StartNewStep("Remove the air (largest area)");
 194   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> iBinarizeFilterType;
 195   typename iBinarizeFilterType::Pointer binarizeFilter2 = iBinarizeFilterType::New();
 196   binarizeFilter2->SetInput(working_image);
 197   binarizeFilter2->SetLowerThreshold(this->GetForegroundValue());
 198   binarizeFilter2->SetUpperThreshold(this->GetForegroundValue());
 199   binarizeFilter2 ->SetInsideValue(this->GetBackgroundValue());
 200   binarizeFilter2 ->SetOutsideValue(this->GetForegroundValue());
 201   //  binarizeFilter2 ->Update(); // NEEDED ?
 202
 203   typename ConnectFilterType::Pointer connectFilter2 = ConnectFilterType::New();
 204   connectFilter2->SetInput(binarizeFilter2->GetOutput());
 205   connectFilter2->SetBackgroundValue(this->GetBackgroundValue());
 206   connectFilter2->SetFullyConnected(false);
 207
 208   typename RelabelFilterType::Pointer relabelFilter2 = RelabelFilterType::New();
 209   relabelFilter2->SetInput(connectFilter2->GetOutput());
 210   relabelFilter2->Update();
 211   working_image = relabelFilter2->GetOutput();
 212   StopCurrentStep<InternalImageType>(working_image);
 213
 214   //--------------------------------------------------------------------
 215   //--------------------------------------------------------------------
 216   // [Optional]
 217   if (GetDecomposeAndReconstructDuringSecondStep()) {
 218     StartNewStep("Second Decompose & Reconstruct step");
 219     typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
 220     typename FilterType::Pointer f = FilterType::New();
 221     f->SetInput(working_image);
 222     // f->SetVerbose(m_Verbose);
 223     f->SetRadius(GetRadius2());
 224     f->SetMaximumNumberOfLabels(GetMaximumNumberOfLabels2());
 225     f->SetBackgroundValue(this->GetBackgroundValue());
 226     f->SetForegroundValue(this->GetForegroundValue());
 227     f->SetFullyConnected(true);
 228     f->SetNumberOfNewLabels(GetNumberOfNewLabels2());
 229     f->Update();
 230     working_image = f->GetOutput();
 231     StopCurrentStep<InternalImageType>(working_image);
 232   }
 233
 234   //--------------------------------------------------------------------
 235   //--------------------------------------------------------------------
 236   StartNewStep("Keep patient's labels");
 237   typename iBinarizeFilterType::Pointer binarizeFilter3 = iBinarizeFilterType::New();
 238   binarizeFilter3->SetInput(working_image);
 239   binarizeFilter3->SetLowerThreshold(GetFirstKeep());
 240   binarizeFilter3->SetUpperThreshold(GetLastKeep());
 241   binarizeFilter3 ->SetInsideValue(this->GetForegroundValue());
 242   binarizeFilter3 ->SetOutsideValue(this->GetBackgroundValue());
 243   binarizeFilter3->Update();
 244   working_image = binarizeFilter3->GetOutput();
 245   StopCurrentStep<InternalImageType>(working_image);
 246
 247   //--------------------------------------------------------------------
 248   //--------------------------------------------------------------------
 249   // [Optional]
 250   if (GetFinalOpenClose()) {
 251     StartNewStep("Final OpenClose");
 252     // Open
 253     typedef itk::BinaryBallStructuringElement<InternalPixelType,Dim> KernelType;
 254     KernelType structuringElement;
 255     structuringElement.SetRadius(1);
 256     structuringElement.CreateStructuringElement();
 257     typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> OpenFilterType;
 258     typename OpenFilterType::Pointer openFilter = OpenFilterType::New();
 259     openFilter->SetInput(working_image);
 260     openFilter->SetBackgroundValue(this->GetBackgroundValue());
 261     openFilter->SetForegroundValue(this->GetForegroundValue());
 262     openFilter->SetKernel(structuringElement);
 263     // Close
 264     typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> CloseFilterType;
 265     typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
 266     closeFilter->SetInput(openFilter->GetOutput());
 267     closeFilter->SetSafeBorder(true);
 268     closeFilter->SetForegroundValue(this->GetForegroundValue());
 269     //  closeFilter->SetBackgroundValue(SetBackgroundValue());
 270     closeFilter->SetKernel(structuringElement);
 271     closeFilter->Update();
 272     working_image = closeFilter->GetOutput();
 273     StopCurrentStep<InternalImageType>(working_image);
 274   }
 275
 276   //--------------------------------------------------------------------
 277   //--------------------------------------------------------------------
 278   // Final Cast
 279   typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
 280   typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
 281   caster->SetInput(working_image);
 282   caster->Update();
 283   output = caster->GetOutput();
 284
 285   //--------------------------------------------------------------------
 286   //--------------------------------------------------------------------
 287   // [Optional]
 288   if (GetAutoCrop()) {
 289   StartNewStep("AutoCrop");
 290     typedef clitk::AutoCropFilter<OutputImageType> CropFilterType;
 291     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 292     cropFilter->SetInput(output);
 293     cropFilter->SetBackgroundValue(GetBackgroundValue());
 294     cropFilter->Update();
 295     output = cropFilter->GetOutput();
 296     StopCurrentStep<OutputImageType>(output);
 297   }
 298 }
 299 //--------------------------------------------------------------------
 300
 301
 302 //--------------------------------------------------------------------
 303 template <class TInputImageType, class TOutputImageType>
 304 void
 305 clitk::ExtractPatientFilter<TInputImageType, TOutputImageType>::
 306 GenerateData() {
 307   //this->SetNthOutput(0, output); // -> no because redo filter otherwise
 308   this->GraftOutput(output);
 309 }
 310 //--------------------------------------------------------------------
 311
 312
 313 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX