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