X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.txx;h=3bb57b8ffb0cf290dc18c3fe2892fc84ebe52696;hb=16f9cff32207e43328678cdb17a0bccc3441b6cb;hp=4baee45296f5555d49b1748195b19d3757106e13;hpb=c5669e2c629b8248e22d8892c6576ada7a14cc25;p=clitk.git diff --git a/segmentation/clitkExtractLungFilter.txx b/segmentation/clitkExtractLungFilter.txx index 4baee45..3bb57b8 100644 --- a/segmentation/clitkExtractLungFilter.txx +++ b/segmentation/clitkExtractLungFilter.txx @@ -65,6 +65,7 @@ ExtractLungFilter(): SetUpperThresholdForTrachea(-900); SetMultiplierForTrachea(5); SetThresholdStepSizeForTrachea(64); + SetNumberOfSlicesToSkipBeforeSearchingSeed(0); // Step 3 default values SetNumberOfHistogramBins(500); @@ -136,6 +137,7 @@ SetArgsInfo(ArgsInfoType mArgsInfo) SetUpperThreshold_GGO(mArgsInfo); SetLowerThreshold_GGO(mArgsInfo); + SetNumberOfSlicesToSkipBeforeSearchingSeed_GGO(mArgsInfo); SetLabelizeParameters1_GGO(mArgsInfo); if (!mArgsInfo.remove1_given) { GetLabelizeParameters1()->AddLabelToRemove(2); @@ -228,57 +230,8 @@ GenerateOutputInformation() //-------------------------------------------------------------------- //-------------------------------------------------------------------- - StartNewStepOrStop("Find the trachea"); - if (m_Seeds.size() == 0) { // try to find seed - // 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]-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."); - StopCurrentStep(); - } + StartNewStepOrStop("Search for the trachea"); + SearchForTrachea(); //-------------------------------------------------------------------- //-------------------------------------------------------------------- @@ -319,7 +272,7 @@ GenerateOutputInformation() working_image = SetBackground (working_image, trachea_tmp, 1, -1); - // Dilate the trachea + // Dilate the trachea static const unsigned int Dim = ImageType::ImageDimension; typedef itk::BinaryBallStructuringElement KernelType; KernelType structuringElement; @@ -420,7 +373,7 @@ GenerateOutputInformation() working_image = decomposeAndReconstructFilter->GetOutput(); } - // Retain labels (lungs) + // 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); @@ -443,61 +396,64 @@ GenerateOutputInformation() // Try to extract bifurcation in the trachea (bronchi) // STILL EXPERIMENTAL - if (GetFindBronchialBifurcations()) { - StartNewStepOrStop("Find bronchial bifurcations"); - // Step 1 : extract skeleton - // Define the thinning filter - typedef itk::BinaryThinningImageFilter3D ThinningFilterType; - typename ThinningFilterType::Pointer thinningFilter = ThinningFilterType::New(); - thinningFilter->SetInput(trachea); - thinningFilter->Update(); - typename MaskImageType::Pointer skeleton = thinningFilter->GetOutput(); - writeImage(skeleton, "skeleton.mhd"); - - // Step 2 : tracking - DD("tracking"); + if (m_Seeds.size() != 0) { // if ==0 ->no trachea found + + if (GetFindBronchialBifurcations()) { + StartNewStepOrStop("Find bronchial bifurcations"); + // Step 1 : extract skeleton + // Define the thinning filter + typedef itk::BinaryThinningImageFilter3D ThinningFilterType; + typename ThinningFilterType::Pointer thinningFilter = ThinningFilterType::New(); + thinningFilter->SetInput(trachea); + thinningFilter->Update(); + typename MaskImageType::Pointer skeleton = thinningFilter->GetOutput(); + writeImage(skeleton, "skeleton.mhd"); + + // Step 2 : tracking + DD("tracking"); - // Step 2.1 : find first point for tracking - typedef itk::ImageRegionConstIteratorWithIndex IteratorType; - IteratorType it(skeleton, skeleton->GetLargestPossibleRegion()); - it.GoToReverseBegin(); - while ((!it.IsAtEnd()) && (it.Get() == GetBackgroundValue())) { - --it; - } - if (it.IsAtEnd()) { - this->SetLastError("ERROR: first point in the skeleton not found ! Abort"); - return; - } - DD(skeleton->GetLargestPossibleRegion().GetIndex()); - typename MaskImageType::IndexType index = it.GetIndex(); - DD(index); + // Step 2.1 : find first point for tracking + typedef itk::ImageRegionConstIteratorWithIndex IteratorType; + IteratorType it(skeleton, skeleton->GetLargestPossibleRegion()); + it.GoToReverseBegin(); + while ((!it.IsAtEnd()) && (it.Get() == GetBackgroundValue())) { + --it; + } + if (it.IsAtEnd()) { + this->SetLastError("ERROR: first point in the skeleton not found ! Abort"); + return; + } + DD(skeleton->GetLargestPossibleRegion().GetIndex()); + typename MaskImageType::IndexType index = it.GetIndex(); + DD(index); - // Step 2.2 : initialize neighborhooditerator - typedef itk::NeighborhoodIterator NeighborhoodIteratorType; - typename NeighborhoodIteratorType::SizeType radius; - radius.Fill(1); - NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion()); - DD(nit.GetSize()); - DD(nit.Size()); + // Step 2.2 : initialize neighborhooditerator + typedef itk::NeighborhoodIterator NeighborhoodIteratorType; + typename NeighborhoodIteratorType::SizeType radius; + radius.Fill(1); + NeighborhoodIteratorType nit(radius, skeleton, skeleton->GetLargestPossibleRegion()); + DD(nit.GetSize()); + DD(nit.Size()); - // Find first label number (must be different from BG and FG) - typename MaskImageType::PixelType label = GetForegroundValue()+1; - while ((label == GetBackgroundValue()) || (label == GetForegroundValue())) { label++; } - DD(label); - - // Track from the first point - std::vector listOfBifurcations; - TrackFromThisIndex(listOfBifurcations, skeleton, index, label); - DD("end track"); - DD(listOfBifurcations.size()); - writeImage(skeleton, "skeleton2.mhd"); - - for(unsigned int i=0; iTransformIndexToPhysicalPoint(listOfBifurcations[i].index, p); - DD(p); - } + // Find first label number (must be different from BG and FG) + typename MaskImageType::PixelType label = GetForegroundValue()+1; + while ((label == GetBackgroundValue()) || (label == GetForegroundValue())) { label++; } + DD(label); + + // Track from the first point + std::vector listOfBifurcations; + TrackFromThisIndex(listOfBifurcations, skeleton, index, label); + DD("end track"); + DD(listOfBifurcations.size()); + writeImage(skeleton, "skeleton2.mhd"); + + for(unsigned int i=0; iTransformIndexToPhysicalPoint(listOfBifurcations[i].index, p); + DD(p); + } + } } } //-------------------------------------------------------------------- @@ -507,7 +463,8 @@ GenerateOutputInformation() template void clitk::ExtractLungFilter:: -GenerateData() { +GenerateData() +{ // Do not put some "startnewstep" here, because the object if // modified and the filter's pipeline it do two times. But it is // required to quit if MustStop was set before. @@ -526,7 +483,8 @@ clitk::ExtractLungFilter:: TrackFromThisIndex(std::vector & listOfBifurcations, MaskImagePointer skeleton, MaskImageIndexType index, - MaskImagePixelType label) { + MaskImagePixelType label) +{ DD("TrackFromThisIndex"); DD(index); DD((int)label); @@ -577,5 +535,173 @@ TrackFromThisIndex(std::vector & listOfBifurcations, } //-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +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 (GetVerboseStep()) { + 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; + } + } + } + return (m_Seeds.size() != 0); +} +//-------------------------------------------------------------------- + +//-------------------------------------------------------------------- +template +void +clitk::ExtractLungFilter:: +TracheaRegionGrowing() +{ + // 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]); + // DD(m_Seeds[i]); + } + f->Update(); + + // take first (main) connected component + writeImage(f->GetOutput(), "t1.mhd"); + trachea_tmp = Labelize(f->GetOutput(), + GetBackgroundValue(), + true, + GetMinimalComponentSize()); + writeImage(trachea_tmp, "t2.mhd"); + trachea_tmp = KeepLabels(trachea_tmp, + GetBackgroundValue(), + GetForegroundValue(), + 1, 1, false); + writeImage(trachea_tmp, "t3.mhd"); +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +template +double +clitk::ExtractLungFilter:: +ComputeTracheaVolume() +{ + typedef itk::ImageRegionConstIterator IteratorType; + IteratorType iter(trachea_tmp, trachea_tmp->GetLargestPossibleRegion()); + iter.GoToBegin(); + double volume = 0.0; + while (!iter.IsAtEnd()) { + if (iter.Get() == this->GetForegroundValue()) volume++; + ++iter; + } + + double voxelsize = trachea_tmp->GetSpacing()[0]*trachea_tmp->GetSpacing()[1]*trachea_tmp->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(); // assume mm3 + if ((volume > 10000) && (volume < 55000 )) { // it is ok + // Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ] + if (GetVerboseStep()) { + std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl; + } + stop = true; + } + else { + if (GetVerboseStep()) { + 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(); + } + } + } + + if (volume != 0.0) { + // Set output + StopCurrentStep(trachea_tmp); + } + else { // Trachea not found + this->SetWarning("* WARNING * No seed found for trachea."); + StopCurrentStep(); + } +} +//-------------------------------------------------------------------- + #endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX