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