X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractPatientFilter.txx;h=97f79c5e9050bdcf1b5b4d2275ad0a32e73c60f8;hb=aa424793243b9b210a0d009f5cb8031db985549a;hp=a04232b9d3a72119f973fa784cc9f2011aee6a52;hpb=765020625fbc092d283e221e36c83e60a1844cb7;p=clitk.git diff --git a/segmentation/clitkExtractPatientFilter.txx b/segmentation/clitkExtractPatientFilter.txx index a04232b..97f79c5 100644 --- a/segmentation/clitkExtractPatientFilter.txx +++ b/segmentation/clitkExtractPatientFilter.txx @@ -1,7 +1,7 @@ /*========================================================================= 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://www.centreleonberard.fr - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr @@ -35,6 +35,7 @@ #include "itkBinaryMorphologicalOpeningImageFilter.h" #include "itkBinaryBallStructuringElement.h" #include "itkCastImageFilter.h" +#include "itkConstantPadImageFilter.h" //-------------------------------------------------------------------- template @@ -47,6 +48,7 @@ ExtractPatientFilter(): this->SetNumberOfRequiredInputs(1); SetBackgroundValue(0); // Must be zero SetForegroundValue(1); + SetPrimaryOpeningRadius(0); // Step 1: Threshold + CC + sort (Find low density areas) SetUpperThreshold(-300); @@ -68,11 +70,11 @@ 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(); @@ -82,9 +84,9 @@ ExtractPatientFilter(): //-------------------------------------------------------------------- template -void +void clitk::ExtractPatientFilter:: -SetInput(const TInputImageType * image) +SetInput(const TInputImageType * image) { this->SetNthInput(0, const_cast(image)); } @@ -93,9 +95,9 @@ SetInput(const TInputImageType * image) //-------------------------------------------------------------------- template -void +void clitk::ExtractPatientFilter:: -GenerateOutputInformation() { +GenerateOutputInformation() { clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK @@ -108,40 +110,82 @@ GenerateOutputInformation() { // Get input pointers static const unsigned int Dim = InputImageType::ImageDimension; //input = dynamic_cast(itk::ProcessObject::GetInput(0)); - + //-------------------------------------------------------------------- //-------------------------------------------------------------------- - // Step 1: + // Step 1: StartNewStep("Find low densities areas"); - typedef itk::BinaryThresholdImageFilter BinarizeFilterType; + + // Pad images with air to prevent patient touching the image border + // But the lungs can touch the outside air. In such case, use primaryOpeningRadius with 1 kernel + typedef itk::ConstantPadImageFilter 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); + padFilter->Update(); + + typedef itk::BinaryThresholdImageFilter 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()); binarizeFilter ->SetOutsideValue(this->GetBackgroundValue()); + padFilter->GetOutput()->ReleaseData(); + working_image = binarizeFilter->GetOutput(); + + typedef itk::BinaryBallStructuringElement KernelType; + unsigned int radius = this->GetPrimaryOpeningRadius(); + if (radius > 0) + { + if (this->GetVerboseOptionFlag()) std::cout << ("Opening after threshold; R = ") << radius << std::endl; + KernelType kernel; + kernel.SetRadius(radius); + + typedef itk::BinaryMorphologicalOpeningImageFilter OpenFilterType2; + typename OpenFilterType2::Pointer openFilter2 = OpenFilterType2::New(); + openFilter2->SetInput(working_image); + openFilter2->SetBackgroundValue(0); + openFilter2->SetForegroundValue(1); + openFilter2->SetKernel(kernel); + openFilter2->Update(); + working_image->ReleaseData(); + working_image = openFilter2->GetOutput(); + } + if (this->GetVerboseOptionFlag()) std::cout << ("Labelling") << std::endl; // Connected component labeling typedef itk::ConnectedComponentImageFilter ConnectFilterType; typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New(); - connectFilter->SetInput(binarizeFilter->GetOutput()); + connectFilter->SetInput(working_image); connectFilter->SetBackgroundValue(this->GetBackgroundValue()); connectFilter->SetFullyConnected(false); - + connectFilter->Update(); + working_image->ReleaseData(); + working_image = connectFilter->GetOutput(); + + if (this->GetVerboseOptionFlag()) std::cout << ("RelabelComponentImageFilter") << std::endl; // Sort labels according to size typedef itk::RelabelComponentImageFilter RelabelFilterType; typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New(); relabelFilter->InPlaceOn(); relabelFilter->SetInput(connectFilter->GetOutput()); relabelFilter->Update(); + working_image->ReleaseData(); working_image = relabelFilter->GetOutput(); - + // End StopCurrentStep(working_image); //-------------------------------------------------------------------- //-------------------------------------------------------------------- - // [Optional] + // [Optional] if (GetDecomposeAndReconstructDuringFirstStep()) { StartNewStep("First Decompose & Reconstruct step"); typedef clitk::DecomposeAndReconstructImageFilter FilterType; @@ -155,40 +199,48 @@ GenerateOutputInformation() { f->SetFullyConnected(true); f->SetNumberOfNewLabels(GetNumberOfNewLabels1()); f->Update(); + working_image->ReleaseData(); working_image = f->GetOutput(); StopCurrentStep(working_image); } - + //-------------------------------------------------------------------- //-------------------------------------------------------------------- + if (this->GetVerboseOptionFlag()) std::cout << ("Remove the air (largest area)") << std::endl; StartNewStep("Remove the air (largest area)"); - typedef itk::BinaryThresholdImageFilter iBinarizeFilterType; + typedef itk::BinaryThresholdImageFilter iBinarizeFilterType; typename iBinarizeFilterType::Pointer binarizeFilter2 = iBinarizeFilterType::New(); binarizeFilter2->SetInput(working_image); binarizeFilter2->SetLowerThreshold(GetFirstKeep()); binarizeFilter2->SetUpperThreshold(GetLastKeep()); binarizeFilter2 ->SetInsideValue(0); binarizeFilter2 ->SetOutsideValue(1); - // binarizeFilter2 ->Update(); // NEEDED ? + binarizeFilter2 ->Update(); + working_image->ReleaseData(); + working_image = binarizeFilter2->GetOutput(); typename ConnectFilterType::Pointer connectFilter2 = ConnectFilterType::New(); - connectFilter2->SetInput(binarizeFilter2->GetOutput()); + connectFilter2->SetInput(working_image); connectFilter2->SetBackgroundValue(this->GetBackgroundValue()); connectFilter2->SetFullyConnected(false); + connectFilter2->Update(); + working_image->ReleaseData(); + working_image = connectFilter2->GetOutput(); typename RelabelFilterType::Pointer relabelFilter2 = RelabelFilterType::New(); - relabelFilter2->SetInput(connectFilter2->GetOutput()); + relabelFilter2->SetInput(working_image); relabelFilter2->Update(); + working_image->ReleaseData(); working_image = relabelFilter2->GetOutput(); - + // Keep main label working_image = KeepLabels - (working_image, GetBackgroundValue(), GetForegroundValue(), 1, 1, true); + (working_image, GetBackgroundValue(), GetForegroundValue(), 1, 1, true); StopCurrentStep(working_image); //-------------------------------------------------------------------- //-------------------------------------------------------------------- - // [Optional] + // [Optional] if (GetDecomposeAndReconstructDuringSecondStep()) { StartNewStep("Second Decompose & Reconstruct step"); typedef clitk::DecomposeAndReconstructImageFilter FilterType; @@ -202,6 +254,7 @@ GenerateOutputInformation() { f->SetFullyConnected(true); f->SetNumberOfNewLabels(GetNumberOfNewLabels2()); f->Update(); + working_image->ReleaseData(); working_image = f->GetOutput(); StopCurrentStep(working_image); } @@ -212,7 +265,6 @@ GenerateOutputInformation() { if (GetFinalOpenClose()) { StartNewStep("Final OpenClose"); // Open - typedef itk::BinaryBallStructuringElement KernelType; KernelType structuringElement; structuringElement.SetRadius(1); structuringElement.CreateStructuringElement(); @@ -221,7 +273,7 @@ GenerateOutputInformation() { openFilter->SetInput(working_image); openFilter->SetBackgroundValue(this->GetBackgroundValue()); openFilter->SetForegroundValue(this->GetForegroundValue()); - openFilter->SetKernel(structuringElement); + openFilter->SetKernel(structuringElement); // Close typedef itk::BinaryMorphologicalClosingImageFilter CloseFilterType; typename CloseFilterType::Pointer closeFilter = CloseFilterType::New(); @@ -230,18 +282,20 @@ GenerateOutputInformation() { closeFilter->SetForegroundValue(this->GetForegroundValue()); // closeFilter->SetBackgroundValue(SetBackgroundValue()); closeFilter->SetKernel(structuringElement); - closeFilter->Update(); + closeFilter->Update(); + working_image->ReleaseData(); working_image = closeFilter->GetOutput(); StopCurrentStep(working_image); } //-------------------------------------------------------------------- //-------------------------------------------------------------------- - // Final Cast + // Final Cast typedef itk::CastImageFilter CastImageFilterType; typename CastImageFilterType::Pointer caster= CastImageFilterType::New(); caster->SetInput(working_image); caster->Update(); + working_image->ReleaseData(); output = caster->GetOutput(); //-------------------------------------------------------------------- @@ -253,26 +307,39 @@ GenerateOutputInformation() { typename CropFilterType::Pointer cropFilter = CropFilterType::New(); cropFilter->SetInput(output); cropFilter->SetBackgroundValue(GetBackgroundValue()); - cropFilter->Update(); + cropFilter->Update(); + output->ReleaseData(); output = cropFilter->GetOutput(); StopCurrentStep(output); } + else + { + // Remove Padding region + typedef itk::CropImageFilter CropFilterType; + typename CropFilterType::Pointer cropFilter = CropFilterType::New(); + cropFilter->SetInput(output); + cropFilter->SetLowerBoundaryCropSize(bounds); + cropFilter->SetUpperBoundaryCropSize(bounds); + cropFilter->Update(); + output->ReleaseData(); + output = cropFilter->GetOutput(); + } } //-------------------------------------------------------------------- //-------------------------------------------------------------------- template -void +void clitk::ExtractPatientFilter:: 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