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