X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.txx;h=1a945917be9149b76617dfca22c40de34f533db6;hb=cf35c87a6dd45a7daf171d2adca9766846a0f127;hp=2c7be4c3546fb80629a7b25af8667981582e27e5;hpb=e008d74b0ecdc4ca2eaae8c429901a78f9ef5c31;p=clitk.git diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx index 2c7be4c..1a94591 100644 --- a/segmentation/clitkExtractLungFilter.txx +++ b/segmentation/clitkExtractLungFilter.txx @@ -3,7 +3,7 @@ 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 CLITKEXTRACTLUNGSFILTER_TXX #define CLITKEXTRACTLUNGSFILTER_TXX @@ -22,27 +22,40 @@ // clitk #include "clitkImageCommon.h" #include "clitkSetBackgroundImageFilter.h" -#include "clitkSegmentationFunctions.h" +#include "clitkSegmentationUtils.h" #include "clitkAutoCropFilter.h" +#include "clitkCropLikeImageFilter.h" +#include "clitkFillMaskFilter.h" +#include "clitkMemoryUsage.h" // itk #include "itkBinaryThresholdImageFilter.h" #include "itkConnectedComponentImageFilter.h" #include "itkRelabelComponentImageFilter.h" #include "itkOtsuThresholdImageFilter.h" +#include "itkBinaryThinningImageFilter3D.h" +#include "itkImageIteratorWithIndex.h" +#include "itkBinaryMorphologicalOpeningImageFilter.h" +#include "itkBinaryMorphologicalClosingImageFilter.h" //-------------------------------------------------------------------- -template -clitk::ExtractLungFilter:: +template +clitk::ExtractLungFilter:: ExtractLungFilter(): clitk::FilterBase(), - itk::ImageToImageFilter() + clitk::FilterWithAnatomicalFeatureDatabaseManagement(), + itk::ImageToImageFilter() { + SetNumberOfSteps(10); + m_MaxSeedNumber = 500; + // Default global options - this->SetNumberOfRequiredInputs(2); + this->SetNumberOfRequiredInputs(1); SetPatientMaskBackgroundValue(0); SetBackgroundValue(0); // Must be zero SetForegroundValue(1); + SetMinimalComponentSize(100); + VerboseRegionGrowingFlagOff(); // Step 1 default values SetUpperThreshold(-300); @@ -58,6 +71,8 @@ ExtractLungFilter(): SetUpperThresholdForTrachea(-900); SetMultiplierForTrachea(5); SetThresholdStepSizeForTrachea(64); + SetNumberOfSlicesToSkipBeforeSearchingSeed(0); + TracheaVolumeMustBeCheckedFlagOn(); // Step 3 default values SetNumberOfHistogramBins(500); @@ -74,37 +89,33 @@ ExtractLungFilter(): p3->SetLastKeep(2); p3->UseLastKeepOff(); SetLabelizeParameters3(p3); + + // Step 5 + OpenCloseFlagOff(); + SetOpenCloseRadius(1); + + // Step 6 + FillHolesFlagOn(); + AutoCropOn(); } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -template -void -clitk::ExtractLungFilter:: -SetInput(const TInputImageType * image) -{ - this->SetNthInput(0, const_cast(image)); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template +template void -clitk::ExtractLungFilter:: -SetInputPatientMask(TMaskImageType * image, MaskImagePixelType bg ) +clitk::ExtractLungFilter:: +SetInput(const ImageType * image) { - this->SetNthInput(1, const_cast(image)); - SetPatientMaskBackgroundValue(bg); + this->SetNthInput(0, const_cast(image)); } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -template +template void -clitk::ExtractLungFilter:: +clitk::ExtractLungFilter:: AddSeed(InternalIndexType s) { m_Seeds.push_back(s); @@ -113,179 +124,133 @@ AddSeed(InternalIndexType s) //-------------------------------------------------------------------- -template -template -void -clitk::ExtractLungFilter:: -SetArgsInfo(ArgsInfoType mArgsInfo) -{ - SetVerboseOption_GGO(mArgsInfo); - SetVerboseStep_GGO(mArgsInfo); - SetWriteStep_GGO(mArgsInfo); - SetVerboseWarningOff_GGO(mArgsInfo); - - SetUpperThreshold_GGO(mArgsInfo); - SetLowerThreshold_GGO(mArgsInfo); - SetLabelizeParameters1_GGO(mArgsInfo); - if (!mArgsInfo.remove1_given) { - GetLabelizeParameters1()->AddLabelToRemove(2); - if (GetVerboseOption()) VerboseOption("remove1", 2); - } - - SetUpperThresholdForTrachea_GGO(mArgsInfo); - SetMultiplierForTrachea_GGO(mArgsInfo); - SetThresholdStepSizeForTrachea_GGO(mArgsInfo); - AddSeed_GGO(mArgsInfo); - - SetNumberOfHistogramBins_GGO(mArgsInfo); - SetLabelizeParameters2_GGO(mArgsInfo); - - SetRadiusForTrachea_GGO(mArgsInfo); - SetLabelizeParameters3_GGO(mArgsInfo); -} -//-------------------------------------------------------------------- - - -//-------------------------------------------------------------------- -template +template void -clitk::ExtractLungFilter:: +clitk::ExtractLungFilter:: GenerateOutputInformation() { - input = dynamic_cast(itk::ProcessObject::GetInput(0)); + clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK Superclass::GenerateOutputInformation(); -// MaskImagePointer output = this->GetOutput(0); + + // Read DB + LoadAFDB(); // Get input pointers - input = dynamic_cast(itk::ProcessObject::GetInput(0)); - patient = dynamic_cast(itk::ProcessObject::GetInput(1)); + input = dynamic_cast(itk::ProcessObject::GetInput(0)); + patient = GetAFDB()->template GetImage ("Patient"); + PrintMemory(GetVerboseMemoryFlag(), "After reading patient"); // OK + + //-------------------------------------------------------------------- + //-------------------------------------------------------------------- + // Crop input like patient image (must have the same spacing) + // It copy the input if the same are the same + StartNewStep("Copy and crop input image to 'patient' extends"); + typedef clitk::CropLikeImageFilter CropImageFilter; + typename CropImageFilter::Pointer cropFilter = CropImageFilter::New(); + // cropFilter->ReleaseDataFlagOn(); // NO=seg fault !! + cropFilter->SetInput(input); + cropFilter->SetCropLikeImage(patient); + cropFilter->Update(); + working_input = cropFilter->GetOutput(); + // cropFilter->Delete(); // NO !!!! if yes, sg fault, Cropfilter is buggy !?? + StopCurrentStep(working_input); + PrintMemory(GetVerboseMemoryFlag(), "After crop"); // OK, slightly more than a copy of input - // Check image - if (!HasSameSizeAndSpacing(input, patient)) { - this->SetLastError("* ERROR * the images (input and patient mask) must have the same size & spacing"); - return; - } - //-------------------------------------------------------------------- //-------------------------------------------------------------------- StartNewStep("Set background to initial image"); - working_input = SetBackground - (input, patient, GetPatientMaskBackgroundValue(), -1000); - StopCurrentStep(working_input); + working_input = SetBackground + (working_input, patient, GetPatientMaskBackgroundValue(), -1000, true); + StopCurrentStep(working_input); + PrintMemory(GetVerboseMemoryFlag(), "After set bg"); // OK, additional mem = 0 + + /* + // We do not need patient mask anymore, release memory + GetAFDB()->template ReleaseImage("Patient"); + DD(patient->GetReferenceCount()); + PrintMemory(GetVerboseMemoryFlag(), "After delete patient"); // OK, additional mem = 0 + patient->Delete(); + PrintMemory(GetVerboseMemoryFlag(), "After delete patient"); // OK, additional mem = 0 + */ //-------------------------------------------------------------------- //-------------------------------------------------------------------- StartNewStep("Remove Air"); + // Check threshold + if (m_UseLowerThreshold) { + if (m_LowerThreshold > m_UpperThreshold) { + clitkExceptionMacro("lower threshold cannot be greater than upper threshold."); + } + } // Threshold to get air - typedef itk::BinaryThresholdImageFilter InputBinarizeFilterType; - typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New(); + typedef itk::BinaryThresholdImageFilter InputBinarizeFilterType; + typename InputBinarizeFilterType::Pointer binarizeFilter = InputBinarizeFilterType::New(); binarizeFilter->SetInput(working_input); if (m_UseLowerThreshold) binarizeFilter->SetLowerThreshold(m_LowerThreshold); + // binarizeFilter->CanRunInPlace() is false binarizeFilter->SetUpperThreshold(m_UpperThreshold); - binarizeFilter ->SetInsideValue(this->GetForegroundValue()); - binarizeFilter ->SetOutsideValue(this->GetBackgroundValue()); + binarizeFilter->SetInsideValue(this->GetForegroundValue()); + binarizeFilter->SetOutsideValue(this->GetBackgroundValue()); binarizeFilter->Update(); - working_image = binarizeFilter->GetOutput(); - + working_mask = binarizeFilter->GetOutput(); + PrintMemory(GetVerboseMemoryFlag(), "After Binarizefilter"); // OK, additional mem is one mask image + // Labelize and keep right labels - working_image = Labelize(working_image, GetBackgroundValue(), true, GetMinimalComponentSize()); - working_image = RemoveLabels - (working_image, GetBackgroundValue(), GetLabelizeParameters1()->GetLabelsToRemove()); - typename InternalImageType::Pointer air = KeepLabels - (working_image, + working_mask = + Labelize + (working_mask, GetBackgroundValue(), true, GetMinimalComponentSize()); + PrintMemory(GetVerboseMemoryFlag(), "After Labelize"); // BUG ? additional mem around 1 time the input ? + + working_mask = RemoveLabels + (working_mask, GetBackgroundValue(), GetLabelizeParameters1()->GetLabelsToRemove()); + PrintMemory(GetVerboseMemoryFlag(), "After RemoveLabels"); // OK additional mem = 0 + + working_mask = KeepLabels + (working_mask, GetBackgroundValue(), GetForegroundValue(), GetLabelizeParameters1()->GetFirstKeep(), GetLabelizeParameters1()->GetLastKeep(), GetLabelizeParameters1()->GetUseLastKeep()); + PrintMemory(GetVerboseMemoryFlag(), "After KeepLabels to create the 'air'"); // Set Air to BG - working_input = SetBackground - (working_input, air, this->GetForegroundValue(), this->GetBackgroundValue()); + working_input = SetBackground + (working_input, working_mask, this->GetForegroundValue(), this->GetBackgroundValue(), true); + PrintMemory(GetVerboseMemoryFlag(), "After SetBackground"); // End - StopCurrentStep(working_input); + StopCurrentStep(working_input); //-------------------------------------------------------------------- //-------------------------------------------------------------------- - StartNewStep("Find the trachea"); - if (m_Seeds.size() == 0) { // try to find seed - // Search seed (parameters = UpperThresholdForTrachea) - static const unsigned int Dim = InputImageType::ImageDimension; - typename InternalImageType::RegionType sliceRegion = working_input->GetLargestPossibleRegion(); - typename InternalImageType::SizeType sliceRegionSize = sliceRegion.GetSize(); - typename InternalImageType::IndexType sliceRegionIndex = sliceRegion.GetIndex(); - sliceRegionIndex[Dim-1]=sliceRegionSize[Dim-1]-5; - sliceRegionSize[Dim-1]=5; - sliceRegion.SetSize(sliceRegionSize); - sliceRegion.SetIndex(sliceRegionIndex); - - typedef itk::ImageRegionConstIterator IteratorType; - IteratorType it(working_input, sliceRegion); - it.GoToBegin(); - while (!it.IsAtEnd()) { - if(it.Get() < GetUpperThresholdForTrachea() ) { - AddSeed(it.GetIndex()); - } - ++it; - } - } - - if (m_Seeds.size() != 0) { - // Explosion controlled region growing - typedef clitk::ExplosionControlledThresholdConnectedImageFilter ImageFilterType; - typename ImageFilterType::Pointer f= ImageFilterType::New(); - f->SetInput(working_input); - f->SetVerbose(false); - f->SetLower(-2000); - f->SetUpper(GetUpperThresholdForTrachea()); - f->SetMinimumLowerThreshold(-2000); - f->SetMaximumUpperThreshold(0); - f->SetAdaptLowerBorder(false); - f->SetAdaptUpperBorder(true); - f->SetMinimumSize(5000); - f->SetReplaceValue(1); - f->SetMultiplier(GetMultiplierForTrachea()); - f->SetThresholdStepSize(GetThresholdStepSizeForTrachea()); - f->SetMinimumThresholdStepSize(1); - for(unsigned int i=0; iAddSeed(m_Seeds[i]); - } - f->Update(); - trachea_tmp = f->GetOutput(); - // Set output - StopCurrentStep(trachea_tmp); - - } - else { // Trachea not found - this->SetWarning("* WARNING * No seed found for trachea."); - // Set output - StopCurrentStep(); - } + StartNewStep("Search for the trachea"); + SearchForTrachea(); + PrintMemory(GetVerboseMemoryFlag(), "After SearchForTrachea"); //-------------------------------------------------------------------- //-------------------------------------------------------------------- StartNewStep("Extract the lung with Otsu filter"); // Automated Otsu thresholding and relabeling - typedef itk::OtsuThresholdImageFilter OtsuThresholdImageFilterType; + typedef itk::OtsuThresholdImageFilter OtsuThresholdImageFilterType; typename OtsuThresholdImageFilterType::Pointer otsuFilter=OtsuThresholdImageFilterType::New(); otsuFilter->SetInput(working_input); otsuFilter->SetNumberOfHistogramBins(GetNumberOfHistogramBins()); otsuFilter->SetInsideValue(this->GetForegroundValue()); otsuFilter->SetOutsideValue(this->GetBackgroundValue()); otsuFilter->Update(); - working_image = otsuFilter->GetOutput(); + working_mask = otsuFilter->GetOutput(); // Set output - StopCurrentStep(working_image); + StopCurrentStep(working_mask); + PrintMemory(GetVerboseMemoryFlag(), "After Otsufilter"); //-------------------------------------------------------------------- //-------------------------------------------------------------------- StartNewStep("Select labels"); // Keep right labels - working_image = LabelizeAndSelectLabels - (working_image, + working_mask = LabelizeAndSelectLabels + (working_mask, GetBackgroundValue(), GetForegroundValue(), false, @@ -293,43 +258,46 @@ GenerateOutputInformation() GetLabelizeParameters2()); // Set output - StopCurrentStep(working_image); + StopCurrentStep(working_mask); + PrintMemory(GetVerboseMemoryFlag(), "After LabelizeAndSelectLabels"); //-------------------------------------------------------------------- //-------------------------------------------------------------------- if (m_Seeds.size() != 0) { // if ==0 ->no trachea found StartNewStep("Remove the trachea"); // Set the trachea - working_image = SetBackground - (working_image, trachea_tmp, 1, -1); + working_mask = SetBackground + (working_mask, trachea, 1, -1, true); + PrintMemory(GetVerboseMemoryFlag(), "After SetBackground"); - // Dilate the trachea - static const unsigned int Dim = InputImageType::ImageDimension; + // Dilate the trachea + static const unsigned int Dim = ImageType::ImageDimension; typedef itk::BinaryBallStructuringElement KernelType; KernelType structuringElement; structuringElement.SetRadius(GetRadiusForTrachea()); structuringElement.CreateStructuringElement(); - typedef clitk::ConditionalBinaryDilateImageFilter ConditionalBinaryDilateImageFilterType; + typedef clitk::ConditionalBinaryDilateImageFilter ConditionalBinaryDilateImageFilterType; typename ConditionalBinaryDilateImageFilterType::Pointer dilateFilter = ConditionalBinaryDilateImageFilterType::New(); dilateFilter->SetBoundaryToForeground(false); dilateFilter->SetKernel(structuringElement); dilateFilter->SetBackgroundValue (1); dilateFilter->SetForegroundValue (-1); - dilateFilter->SetInput (working_image); + dilateFilter->SetInput (working_mask); dilateFilter->Update(); - working_image = dilateFilter->GetOutput(); + working_mask = dilateFilter->GetOutput(); + PrintMemory(GetVerboseMemoryFlag(), "After dilate"); // Set trachea with dilatation - trachea_tmp = SetBackground - (trachea_tmp, working_image, -1, this->GetForegroundValue()); + trachea = SetBackground + (trachea, working_mask, -1, this->GetForegroundValue(), true); // Remove the trachea - working_image = SetBackground - (working_image, working_image, -1, this->GetBackgroundValue()); + working_mask = SetBackground + (working_mask, working_mask, -1, this->GetBackgroundValue(), true); // Label - working_image = LabelizeAndSelectLabels - (working_image, + working_mask = LabelizeAndSelectLabels + (working_mask, GetBackgroundValue(), GetForegroundValue(), false, @@ -337,61 +305,107 @@ GenerateOutputInformation() GetLabelizeParameters3()); // Set output - StopCurrentStep(working_image); + StopCurrentStep(working_mask); } - //-------------------------------------------------------------------- //-------------------------------------------------------------------- - typedef clitk::AutoCropFilter CropFilterType; - typename CropFilterType::Pointer cropFilter = CropFilterType::New(); + PrintMemory(GetVerboseMemoryFlag(), "before autocropfilter"); if (m_Seeds.size() != 0) { // if ==0 ->no trachea found - StartNewStep("Croping trachea"); - cropFilter->SetInput(trachea_tmp); - cropFilter->Update(); // Needed - typedef itk::CastImageFilter CastImageFilterType; - typename CastImageFilterType::Pointer caster= CastImageFilterType::New(); - caster->SetInput(cropFilter->GetOutput()); - caster->Update(); - trachea = caster->GetOutput(); + if (GetAutoCrop()) + trachea = clitk::AutoCrop(trachea, GetBackgroundValue()); StopCurrentStep(trachea); + PrintMemory(GetVerboseMemoryFlag(), "after delete trachea"); + } + PrintMemory(GetVerboseMemoryFlag(), "after delete trachea"); + + //-------------------------------------------------------------------- + //-------------------------------------------------------------------- + StartNewStep("Cropping lung"); + PrintMemory(GetVerboseMemoryFlag(), "Before Autocropfilter"); + if (GetAutoCrop()) + working_mask = clitk::AutoCrop(working_mask, GetBackgroundValue()); + StopCurrentStep(working_mask); + + //-------------------------------------------------------------------- + //-------------------------------------------------------------------- + // Final OpenClose + if (GetOpenCloseFlag()) { + StartNewStep("Open/Close"); + PrintMemory(GetVerboseMemoryFlag(), "Before OpenClose"); + + // Structuring element + typedef itk::BinaryBallStructuringElement KernelType; + KernelType structuringElement; + structuringElement.SetRadius(GetOpenCloseRadius()); + structuringElement.CreateStructuringElement(); + + // Open + typedef itk::BinaryMorphologicalOpeningImageFilter OpenFilterType; + typename OpenFilterType::Pointer openFilter = OpenFilterType::New(); + openFilter->SetInput(working_mask); + openFilter->SetBackgroundValue(GetBackgroundValue()); + openFilter->SetForegroundValue(GetForegroundValue()); + openFilter->SetKernel(structuringElement); + + // Close + typedef itk::BinaryMorphologicalClosingImageFilter CloseFilterType; + typename CloseFilterType::Pointer closeFilter = CloseFilterType::New(); + closeFilter->SetInput(openFilter->GetOutput()); + closeFilter->SetSafeBorder(true); + closeFilter->SetForegroundValue(GetForegroundValue()); + closeFilter->SetKernel(structuringElement); + closeFilter->Update(); + working_mask = closeFilter->GetOutput(); } //-------------------------------------------------------------------- //-------------------------------------------------------------------- - StartNewStep("Croping lung"); - cropFilter = CropFilterType::New(); // Needed to reset pipeline - cropFilter->SetInput(working_image); - cropFilter->Update(); - working_image = cropFilter->GetOutput(); - StopCurrentStep(working_image); + // Fill Lungs + if (GetFillHolesFlag()) { + StartNewStep("Fill Holes"); + PrintMemory(GetVerboseMemoryFlag(), "Before Fill Holes"); + typedef clitk::FillMaskFilter FillMaskFilterType; + typename FillMaskFilterType::Pointer fillMaskFilter = FillMaskFilterType::New(); + fillMaskFilter->SetInput(working_mask); + fillMaskFilter->AddDirection(2); + //fillMaskFilter->AddDirection(1); + fillMaskFilter->Update(); + working_mask = fillMaskFilter->GetOutput(); + StopCurrentStep(working_mask); + } //-------------------------------------------------------------------- //-------------------------------------------------------------------- StartNewStep("Separate Left/Right lungs"); + PrintMemory(GetVerboseMemoryFlag(), "Before Separate"); // Initial label - working_image = Labelize(working_image, - GetBackgroundValue(), - false, - GetMinimalComponentSize()); + working_mask = Labelize(working_mask, + GetBackgroundValue(), + false, + GetMinimalComponentSize()); + + PrintMemory(GetVerboseMemoryFlag(), "After Labelize"); // Count the labels - typedef itk::StatisticsImageFilter StatisticsImageFilterType; + typedef itk::StatisticsImageFilter StatisticsImageFilterType; typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New(); - statisticsImageFilter->SetInput(working_image); + statisticsImageFilter->SetInput(working_mask); statisticsImageFilter->Update(); unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum(); - working_image = statisticsImageFilter->GetOutput(); + working_mask = statisticsImageFilter->GetOutput(); + + PrintMemory(GetVerboseMemoryFlag(), "After count label"); // Decompose the first label - static const unsigned int Dim = InputImageType::ImageDimension; + static const unsigned int Dim = ImageType::ImageDimension; if (initialNumberOfLabels<2) { // Structuring element radius - typename InputImageType::SizeType radius; + typename ImageType::SizeType radius; for (unsigned int i=0;i DecomposeAndReconstructFilterType; + typedef clitk::DecomposeAndReconstructImageFilter DecomposeAndReconstructFilterType; typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New(); - decomposeAndReconstructFilter->SetInput(working_image); + decomposeAndReconstructFilter->SetInput(working_mask); decomposeAndReconstructFilter->SetVerbose(false); decomposeAndReconstructFilter->SetRadius(radius); decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2); @@ -402,38 +416,238 @@ GenerateOutputInformation() decomposeAndReconstructFilter->SetFullyConnected(true); decomposeAndReconstructFilter->SetNumberOfNewLabels(1); decomposeAndReconstructFilter->Update(); - working_image = decomposeAndReconstructFilter->GetOutput(); + working_mask = decomposeAndReconstructFilter->GetOutput(); } + PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter"); - // Retain labels (lungs) - typedef itk::ThresholdImageFilter ThresholdImageFilterType; + // Retain labels ('1' is largset lung, so right. '2' is left) + typedef itk::ThresholdImageFilter ThresholdImageFilterType; typename ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New(); - thresholdFilter->SetInput(working_image); + thresholdFilter->SetInput(working_mask); thresholdFilter->ThresholdAbove(2); thresholdFilter->SetOutsideValue(this->GetBackgroundValue()); thresholdFilter->Update(); - working_image = thresholdFilter->GetOutput(); - StopCurrentStep (working_image); + working_mask = thresholdFilter->GetOutput(); + StopCurrentStep (working_mask); + PrintMemory(GetVerboseMemoryFlag(), "After Thresholdfilter"); + + // Update output info + // output = working_mask; + //this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion()); + + // this->GetOutput(0)->SetRegions(working_mask->GetLargestPossibleRegion()); + } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -template +template void -clitk::ExtractLungFilter:: -GenerateData() { - // Final Cast - typedef itk::CastImageFilter CastImageFilterType; - typename CastImageFilterType::Pointer caster= CastImageFilterType::New(); - caster->SetInput(working_image); - caster->Update(); - // Set output - //this->SetNthOutput(0, caster->GetOutput()); // -> no because redo filter otherwise - this->GraftOutput(caster->GetOutput()); - return; +clitk::ExtractLungFilter:: +GenerateInputRequestedRegion() { + // DD("GenerateInputRequestedRegion (nothing?)"); +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLungFilter:: +GenerateData() +{ + // Set the output + // this->GraftOutput(output); // not SetNthOutput + this->GraftOutput(working_mask); // not SetNthOutput + // Store image filenames into AFDB + GetAFDB()->SetImageFilename("Lungs", this->GetOutputLungFilename()); + GetAFDB()->SetImageFilename("Trachea", this->GetOutputTracheaFilename()); + WriteAFDB(); +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +bool +clitk::ExtractLungFilter:: +SearchForTracheaSeed(int skip) +{ + if (m_Seeds.size() == 0) { // try to find seed (if not zero, it is given by user) + // Restart the search until a seed is found, skipping more and more slices + bool stop = false; + while (!stop) { + // Search seed (parameters = UpperThresholdForTrachea) + static const unsigned int Dim = ImageType::ImageDimension; + typename InternalImageType::RegionType sliceRegion = working_input->GetLargestPossibleRegion(); + typename InternalImageType::SizeType sliceRegionSize = sliceRegion.GetSize(); + typename InternalImageType::IndexType sliceRegionIndex = sliceRegion.GetIndex(); + sliceRegionIndex[Dim-1]=sliceRegionSize[Dim-1]-skip-5; + sliceRegionSize[Dim-1]=5; + sliceRegion.SetSize(sliceRegionSize); + sliceRegion.SetIndex(sliceRegionIndex); + typedef itk::ImageRegionConstIterator IteratorType; + IteratorType it(working_input, sliceRegion); + it.GoToBegin(); + while (!it.IsAtEnd()) { + if(it.Get() < GetUpperThresholdForTrachea() ) { + AddSeed(it.GetIndex()); + // DD(it.GetIndex()); + } + ++it; + } + + // if we do not found : restart + stop = (m_Seeds.size() != 0); + if (!stop) { + if (GetVerboseStepFlag()) { + std::cout << "\t No seed found this time. I skip some slices and restart." << std::endl; + } + if (skip > 0.5 * working_input->GetLargestPossibleRegion().GetSize()[2]) { + // we want to skip more than a half of the image, it is probably a bug + std::cerr << "Number of slices to skip to find trachea to high = " << skip << std::endl; + stop = true; + } + skip += 5; + } + else { + // DD(m_Seeds[0]); + // DD(m_Seeds.size()); + } + } + } + return (m_Seeds.size() != 0); +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLungFilter:: +TracheaRegionGrowing() +{ + // Explosion controlled region growing + PrintMemory(GetVerboseMemoryFlag(), "Before ExplosionControlledThresholdConnectedImageFilter"); + typedef clitk::ExplosionControlledThresholdConnectedImageFilter ImageFilterType; + typename ImageFilterType::Pointer f= ImageFilterType::New(); + f->SetInput(working_input); + f->SetLower(-2000); + f->SetUpper(GetUpperThresholdForTrachea()); + f->SetMinimumLowerThreshold(-2000); + // f->SetMaximumUpperThreshold(0); // MAYBE TO CHANGE ??? + f->SetMaximumUpperThreshold(-800); // MAYBE TO CHANGE ??? + f->SetAdaptLowerBorder(false); + f->SetAdaptUpperBorder(true); + f->SetMinimumSize(5000); + f->SetReplaceValue(1); + f->SetMultiplier(GetMultiplierForTrachea()); + f->SetThresholdStepSize(GetThresholdStepSizeForTrachea()); + f->SetMinimumThresholdStepSize(1); + f->SetVerbose(GetVerboseRegionGrowingFlag()); + for(unsigned int i=0; iAddSeed(m_Seeds[i]); + // DD(m_Seeds[i]); + } + f->Update(); + PrintMemory(GetVerboseMemoryFlag(), "After RG update"); + + // take first (main) connected component + trachea = Labelize(f->GetOutput(), + GetBackgroundValue(), + true, + 1000);//GetMinimalComponentSize()); + PrintMemory(GetVerboseMemoryFlag(), "After Labelize"); + trachea = KeepLabels(trachea, + GetBackgroundValue(), + GetForegroundValue(), + 1, 1, false); + PrintMemory(GetVerboseMemoryFlag(), "After KeepLabels"); } //-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +double +clitk::ExtractLungFilter:: +ComputeTracheaVolume() +{ + typedef itk::ImageRegionConstIterator IteratorType; + IteratorType iter(trachea, trachea->GetLargestPossibleRegion()); + iter.GoToBegin(); + double volume = 0.0; + while (!iter.IsAtEnd()) { + if (iter.Get() == this->GetForegroundValue()) volume++; + ++iter; + } + double voxelsize = trachea->GetSpacing()[0]*trachea->GetSpacing()[1]*trachea->GetSpacing()[2]; + return volume*voxelsize; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLungFilter:: +SearchForTrachea() +{ + // Search for seed among n slices, skip some slices before starting + // if not found -> skip more and restart + + // when seed found : perform region growing + // compute trachea volume + // if volume not plausible -> skip more slices and restart + + bool stop = false; + double volume = 0.0; + int skip = GetNumberOfSlicesToSkipBeforeSearchingSeed(); + while (!stop) { + stop = SearchForTracheaSeed(skip); + if (stop) { + TracheaRegionGrowing(); + volume = ComputeTracheaVolume()/1000; // assume mm3, so divide by 1000 to get cc + if (GetWriteStepFlag()) { + writeImage(trachea, "step-trachea-"+toString(skip)+".mhd"); + } + if (GetTracheaVolumeMustBeCheckedFlag()) { + if ((volume > 10) && (volume < 65 )) { // depend on image size ... + // Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ] + if (GetVerboseStepFlag()) { + std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl; + } + stop = true; + } + else { + if (GetVerboseStepFlag()) { + std::cout << "\t The volume of the trachea (" << volume + << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds." + << std::endl; + } + skip += 5; + stop = false; + // empty the list of seed + m_Seeds.clear(); + } + } + else { + stop = true; + } + } + } + + if (volume != 0.0) { + // Set output + StopCurrentStep(trachea); + } + else { // Trachea not found + this->SetWarning("* WARNING * No seed found for trachea."); + StopCurrentStep(); + } +} +//-------------------------------------------------------------------- + #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX