X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractPatientFilter.txx;h=00e31653afce00e5ea32c5a91a1218fbe39251fa;hb=e2b60b0a571c065a2fdfc2fba9ad174c39130299;hp=bf84ef79de31c6a8077005af82034aa005371b09;hpb=5668d4a49a5a6b68dc80fa28f0f82b54187cb70c;p=clitk.git

diff --git a/segmentation/clitkExtractPatientFilter.txx b/segmentation/clitkExtractPatientFilter.txx
index bf84ef7..00e3165 100644
--- a/segmentation/clitkExtractPatientFilter.txx
+++ b/segmentation/clitkExtractPatientFilter.txx
@@ -1,9 +1,9 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKEXTRACTPATIENTFILTER_TXX
 #define CLITKEXTRACTPATIENTFILTER_TXX
@@ -24,6 +24,8 @@
 #include "clitkSetBackgroundImageFilter.h"
 #include "clitkDecomposeAndReconstructImageFilter.h"
 #include "clitkAutoCropFilter.h"
+#include "clitkMemoryUsage.h"
+#include "clitkSegmentationUtils.h"
 
 // itk
 #include "itkBinaryThresholdImageFilter.h"
@@ -33,6 +35,7 @@
 #include "itkBinaryMorphologicalOpeningImageFilter.h"
 #include "itkBinaryBallStructuringElement.h"
 #include "itkCastImageFilter.h"
+#include "itkConstantPadImageFilter.h"
 
 //--------------------------------------------------------------------
 template <class TInputImageType>
@@ -66,11 +69,11 @@ ExtractPatientFilter():
   SetRadius2(r);
   SetMaximumNumberOfLabels2(2);
   SetNumberOfNewLabels2(1);
-  
+
   // Step 5: Only keep label corresponding (Keep patient's labels)
   SetFirstKeep(1);
   SetLastKeep(1);
-  
+
   // Step 4: OpenClose (option)
   FinalOpenCloseOff();
   AutoCropOn();
@@ -80,9 +83,9 @@ ExtractPatientFilter():
 
 //--------------------------------------------------------------------
 template <class TInputImageType>
-void 
+void
 clitk::ExtractPatientFilter<TInputImageType>::
-SetInput(const TInputImageType * image) 
+SetInput(const TInputImageType * image)
 {
   this->SetNthInput(0, const_cast<TInputImageType *>(image));
 }
@@ -91,47 +94,11 @@ SetInput(const TInputImageType * image)
 
 //--------------------------------------------------------------------
 template <class TInputImageType>
-template<class ArgsInfoType>
-void 
+void
 clitk::ExtractPatientFilter<TInputImageType>::
-SetArgsInfo(ArgsInfoType arg)
-{
-  SetVerboseOption_GGO(arg);
-  SetVerboseStep_GGO(arg);
-  SetWriteStep_GGO(arg);
-  SetVerboseWarningOff_GGO(arg);
-
-  SetOutputPatientFilename_GGO(arg);
-
-  SetUpperThreshold_GGO(arg);
-  SetLowerThreshold_GGO(arg);
-
-  SetDecomposeAndReconstructDuringFirstStep_GGO(arg);
-  SetRadius1_GGO(arg);
-  SetMaximumNumberOfLabels1_GGO(arg);
-  SetNumberOfNewLabels1_GGO(arg);
-
-  SetDecomposeAndReconstructDuringSecondStep_GGO(arg);
-  SetRadius2_GGO(arg);
-  SetMaximumNumberOfLabels2_GGO(arg);
-  SetNumberOfNewLabels2_GGO(arg);
-  
-  SetFirstKeep_GGO(arg);
-  SetLastKeep_GGO(arg);
+GenerateOutputInformation() {
 
-  SetFinalOpenClose_GGO(arg);
-  SetAutoCrop_GGO(arg);
-
-  SetAFDBFilename_GGO(arg);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TInputImageType>
-void 
-clitk::ExtractPatientFilter<TInputImageType>::
-GenerateOutputInformation() { 
+  clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK
 
   Superclass::GenerateOutputInformation();
   input = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
@@ -142,14 +109,27 @@ GenerateOutputInformation() {
   // Get input pointers
   static const unsigned int Dim = InputImageType::ImageDimension;
   //input = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
-    
+
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
-  // Step 1: 
+  // Step 1:
   StartNewStep("Find low densities areas");
-  typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> BinarizeFilterType;  
+
+  // Pad images with air to prevent patient touching the image border
+  typedef itk::ConstantPadImageFilter<InputImageType, InputImageType> PadFilterType;
+  typename PadFilterType::Pointer padFilter = PadFilterType::New();
+  padFilter->SetInput(input);
+  padFilter->SetConstant(GetUpperThreshold() - 1);
+  typename InputImageType::SizeType bounds;
+  for (unsigned i = 0; i < Dim - 1; ++i)
+    bounds[i] = 1;
+  bounds[Dim - 1] = 0;
+  padFilter->SetPadLowerBound(bounds);
+  padFilter->SetPadUpperBound(bounds);
+
+  typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> BinarizeFilterType;
   typename BinarizeFilterType::Pointer binarizeFilter=BinarizeFilterType::New();
-  binarizeFilter->SetInput(input);
+  binarizeFilter->SetInput(padFilter->GetOutput());
   if (m_UseLowerThreshold) binarizeFilter->SetLowerThreshold(GetLowerThreshold());
   binarizeFilter->SetUpperThreshold(GetUpperThreshold());
   binarizeFilter ->SetInsideValue(this->GetForegroundValue());
@@ -161,7 +141,7 @@ GenerateOutputInformation() {
   connectFilter->SetInput(binarizeFilter->GetOutput());
   connectFilter->SetBackgroundValue(this->GetBackgroundValue());
   connectFilter->SetFullyConnected(false);
-  
+
   // Sort labels according to size
   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
   typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
@@ -169,13 +149,13 @@ GenerateOutputInformation() {
   relabelFilter->SetInput(connectFilter->GetOutput());
   relabelFilter->Update();
   working_image = relabelFilter->GetOutput();
-  
+
   // End
   StopCurrentStep<InternalImageType>(working_image);
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
-  // [Optional] 
+  // [Optional]
   if (GetDecomposeAndReconstructDuringFirstStep()) {
     StartNewStep("First Decompose & Reconstruct step");
     typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
@@ -192,11 +172,11 @@ GenerateOutputInformation() {
     working_image = f->GetOutput();
     StopCurrentStep<InternalImageType>(working_image);
   }
-  
+
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
   StartNewStep("Remove the air (largest area)");
-  typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> iBinarizeFilterType;  
+  typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> iBinarizeFilterType;
   typename iBinarizeFilterType::Pointer binarizeFilter2 = iBinarizeFilterType::New();
   binarizeFilter2->SetInput(working_image);
   binarizeFilter2->SetLowerThreshold(GetFirstKeep());
@@ -214,15 +194,15 @@ GenerateOutputInformation() {
   relabelFilter2->SetInput(connectFilter2->GetOutput());
   relabelFilter2->Update();
   working_image = relabelFilter2->GetOutput();
-  
+
   // Keep main label
   working_image = KeepLabels<InternalImageType>
-    (working_image, GetBackgroundValue(), GetForegroundValue(), 1, 1, true);  
+    (working_image, GetBackgroundValue(), GetForegroundValue(), 1, 1, true);
   StopCurrentStep<InternalImageType>(working_image);
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
-  // [Optional] 
+  // [Optional]
   if (GetDecomposeAndReconstructDuringSecondStep()) {
     StartNewStep("Second Decompose & Reconstruct step");
     typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
@@ -255,7 +235,7 @@ GenerateOutputInformation() {
     openFilter->SetInput(working_image);
     openFilter->SetBackgroundValue(this->GetBackgroundValue());
     openFilter->SetForegroundValue(this->GetForegroundValue());
-    openFilter->SetKernel(structuringElement);  
+    openFilter->SetKernel(structuringElement);
     // Close
     typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> CloseFilterType;
     typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
@@ -264,14 +244,14 @@ GenerateOutputInformation() {
     closeFilter->SetForegroundValue(this->GetForegroundValue());
     //  closeFilter->SetBackgroundValue(SetBackgroundValue());
     closeFilter->SetKernel(structuringElement);
-    closeFilter->Update();  
+    closeFilter->Update();
     working_image = closeFilter->GetOutput();
     StopCurrentStep<InternalImageType>(working_image);
   }
 
   //--------------------------------------------------------------------
   //--------------------------------------------------------------------
-  // Final Cast 
+  // Final Cast
   typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
   typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
   caster->SetInput(working_image);
@@ -287,26 +267,37 @@ GenerateOutputInformation() {
     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
     cropFilter->SetInput(output);
     cropFilter->SetBackgroundValue(GetBackgroundValue());
-    cropFilter->Update();   
+    cropFilter->Update();
     output = cropFilter->GetOutput();
     StopCurrentStep<MaskImageType>(output);
   }
+  else
+  {
+    // Remove Padding region
+    typedef itk::CropImageFilter<MaskImageType, MaskImageType> CropFilterType;
+    typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+    cropFilter->SetInput(output);
+    cropFilter->SetLowerBoundaryCropSize(bounds);
+    cropFilter->SetUpperBoundaryCropSize(bounds);
+    cropFilter->Update();
+    output = cropFilter->GetOutput();
+  }
 }
 //--------------------------------------------------------------------
 
 
 //--------------------------------------------------------------------
 template <class TInputImageType>
-void 
+void
 clitk::ExtractPatientFilter<TInputImageType>::
 GenerateData() {
   // Final Graft
   this->GraftOutput(output);
   // Store image filename into AFDB
-  GetAFDB()->SetImageFilename("patient", this->GetOutputPatientFilename());  
+  GetAFDB()->SetImageFilename("Patient", this->GetOutputPatientFilename());
   WriteAFDB();
 }
 //--------------------------------------------------------------------
-  
+
 
 #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX