X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.h;h=6c50b1c2d96c85e3c9b8485d970d9ad6e0a261b3;hb=aa424793243b9b210a0d009f5cb8031db985549a;hp=c62afe527066816da79fd6bc43c2611bea7c9ed4;hpb=e0464c9f7bdde185755d60e9dead188291fc3550;p=clitk.git diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h index c62afe5..6c50b1c 100644 --- a/segmentation/clitkExtractLungFilter.h +++ b/segmentation/clitkExtractLungFilter.h @@ -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_H #define CLITKEXTRACTLUNGSFILTER_H @@ -24,6 +24,7 @@ #include "clitkDecomposeAndReconstructImageFilter.h" #include "clitkExplosionControlledThresholdConnectedImageFilter.h" #include "clitkSegmentationUtils.h" +#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h" // itk #include "itkStatisticsImageFilter.h" @@ -54,36 +55,18 @@ namespace clitk { */ //-------------------------------------------------------------------- - - //-------------------------------------------------------------------- -template -class Bifurcation -{ -public: - Bifurcation(IndexType _index, PixelType _l, PixelType _l1, PixelType _l2) { - index = _index; - _l = l; - _l1 = l1; - _l2 = l2; - } - IndexType index; - PixelType l; - PixelType l1; - PixelType l2; -}; - //-------------------------------------------------------------------- - - //-------------------------------------------------------------------- - template + template class ITK_EXPORT ExtractLungFilter: - public clitk::FilterBase, - public itk::ImageToImageFilter + public virtual clitk::FilterBase, + public clitk::FilterWithAnatomicalFeatureDatabaseManagement, + public itk::ImageToImageFilter > { public: /** Standard class typedefs. */ - typedef itk::ImageToImageFilter Superclass; + typedef itk::Image MaskImageType; + typedef itk::ImageToImageFilter Superclass; typedef ExtractLungFilter Self; typedef itk::SmartPointer Pointer; typedef itk::SmartPointer ConstPointer; @@ -103,17 +86,19 @@ public: typedef typename ImageType::PixelType InputImagePixelType; typedef typename ImageType::SizeType InputImageSizeType; typedef typename ImageType::IndexType InputImageIndexType; + typedef typename ImageType::PointType InputImagePointType; - typedef TMaskImageType MaskImageType; typedef typename MaskImageType::ConstPointer MaskImageConstPointer; typedef typename MaskImageType::Pointer MaskImagePointer; typedef typename MaskImageType::RegionType MaskImageRegionType; typedef typename MaskImageType::PixelType MaskImagePixelType; typedef typename MaskImageType::SizeType MaskImageSizeType; typedef typename MaskImageType::IndexType MaskImageIndexType; + typedef typename MaskImageType::PointType MaskImagePointType; itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension); - typedef int InternalPixelType; + // typedef int InternalPixelType; + typedef uchar InternalPixelType; typedef itk::Image InternalImageType; typedef typename InternalImageType::Pointer InternalImagePointer; typedef typename InternalImageType::IndexType InternalIndexType; @@ -121,14 +106,15 @@ public: /** Connect inputs */ void SetInput(const ImageType * image); - void SetInputPatientMask(MaskImageType * mask, MaskImagePixelType BG); itkSetMacro(PatientMaskBackgroundValue, MaskImagePixelType); itkGetConstMacro(PatientMaskBackgroundValue, MaskImagePixelType); - GGO_DefineOption(patientBG, SetPatientMaskBackgroundValue, MaskImagePixelType); - // Set all options at a time - template - void SetArgsInfo(ArgsInfoType arg); + // Output filename (for AFBD) + itkSetMacro(OutputLungFilename, std::string); + itkGetMacro(OutputLungFilename, std::string); + + itkSetMacro(OutputTracheaFilename, std::string); + itkGetMacro(OutputTracheaFilename, std::string); // Get output (only availabe after update !) typename MaskImageType::Pointer GetTracheaImage() { return trachea; } @@ -140,81 +126,109 @@ public: // For common segmentation processes itkSetMacro(MinimalComponentSize, int); itkGetConstMacro(MinimalComponentSize, int); - GGO_DefineOption(minSize, SetMinimalComponentSize, int); // Step 1 options RemoveAir itkSetMacro(UpperThreshold, InputImagePixelType); itkGetConstMacro(UpperThreshold, InputImagePixelType); - GGO_DefineOption(upper, SetUpperThreshold, InputImagePixelType); + itkSetMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int); + itkGetConstMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int); + itkSetMacro(LowerThreshold, InputImagePixelType); itkGetConstMacro(LowerThreshold, InputImagePixelType); itkSetMacro(UseLowerThreshold, bool); itkGetConstMacro(UseLowerThreshold, bool); itkBooleanMacro(UseLowerThreshold); - GGO_DefineOption_WithTest(lower, SetLowerThreshold, InputImagePixelType, UseLowerThreshold); void SetLabelizeParameters1(LabelParamType * a) { m_LabelizeParameters1 = a; } itkGetConstMacro(LabelizeParameters1, LabelParamType*); - GGO_DefineOption_LabelParam(1, SetLabelizeParameters1, LabelParamType); + + itkSetMacro(TracheaSeedAlgorithm, int); + itkGetConstMacro(TracheaSeedAlgorithm, int); // Step 2 options FindTrachea itkSetMacro(UpperThresholdForTrachea, InputImagePixelType); itkGetConstMacro(UpperThresholdForTrachea, InputImagePixelType); - GGO_DefineOption(upperThresholdForTrachea, SetUpperThresholdForTrachea, InputImagePixelType); itkSetMacro(MultiplierForTrachea, double); itkGetConstMacro(MultiplierForTrachea, double); - GGO_DefineOption(multiplierForTrachea, SetMultiplierForTrachea, double); itkSetMacro(ThresholdStepSizeForTrachea, InputImagePixelType); itkGetConstMacro(ThresholdStepSizeForTrachea, InputImagePixelType); - GGO_DefineOption(thresholdStepSizeForTrachea, SetThresholdStepSizeForTrachea, InputImagePixelType); - void AddSeed(InternalIndexType s); + // options FindTrachea2 + itkSetMacro(NumSlices, int); + itkGetConstMacro(NumSlices, int); + itkSetMacro(MaxElongation, double); + itkGetConstMacro(MaxElongation, double); + itkSetMacro(SeedPreProcessingThreshold, int); + itkGetConstMacro(SeedPreProcessingThreshold, int); + + void AddSeedInPixels(InternalIndexType s); + void AddSeed(InputImagePointType s); std::vector & GetSeeds() { return m_Seeds; } - GGO_DefineOption_Vector(seed, AddSeed, InternalIndexType, ImageType::ImageDimension, true); + + itkSetMacro(TracheaVolumeMustBeCheckedFlag, bool); + itkGetConstMacro(TracheaVolumeMustBeCheckedFlag, bool); + itkBooleanMacro(TracheaVolumeMustBeCheckedFlag); + + itkSetMacro(VerboseRegionGrowingFlag, bool); + itkGetConstMacro(VerboseRegionGrowingFlag, bool); + itkBooleanMacro(VerboseRegionGrowingFlag); + + itkSetMacro(RemoveSmallLabelBeforeSeparationFlag, bool); + itkGetConstMacro(RemoveSmallLabelBeforeSeparationFlag, bool); + itkBooleanMacro(RemoveSmallLabelBeforeSeparationFlag); // Step 3 options ExtractLung itkSetMacro(NumberOfHistogramBins, int); itkGetConstMacro(NumberOfHistogramBins, int); - GGO_DefineOption(bins, SetNumberOfHistogramBins, int); void SetLabelizeParameters2(LabelParamType* a) { m_LabelizeParameters2 = a; } itkGetConstMacro(LabelizeParameters2, LabelParamType*); - GGO_DefineOption_LabelParam(2, SetLabelizeParameters2, LabelParamType); // Step 4 options RemoveTrachea itkSetMacro(RadiusForTrachea, int); itkGetConstMacro(RadiusForTrachea, int); - GGO_DefineOption(radius, SetRadiusForTrachea, int); void SetLabelizeParameters3(LabelParamType * a) { m_LabelizeParameters3 = a; } itkGetConstMacro(LabelizeParameters3, LabelParamType*); - GGO_DefineOption_LabelParam(3, SetLabelizeParameters3, LabelParamType); - - // Step 5 options LungSeparation - // itkSetMacro(FinalOpenClose, bool); - // itkGetConstMacro(FinalOpenClose, bool); - // itkBooleanMacro(FinalOpenClose); - // Bronchial bifurcations - itkSetMacro(FindBronchialBifurcations, bool); - itkGetConstMacro(FindBronchialBifurcations, bool); - itkBooleanMacro(FindBronchialBifurcations); + // Step 5 final openclose + itkSetMacro(OpenCloseFlag, bool); + itkGetConstMacro(OpenCloseFlag, bool); + itkBooleanMacro(OpenCloseFlag); + itkSetMacro(OpenCloseRadius, int); + itkGetConstMacro(OpenCloseRadius, int); + + // Step 6 fill holes + itkSetMacro(FillHolesFlag, bool); + itkGetConstMacro(FillHolesFlag, bool); + itkBooleanMacro(FillHolesFlag); + + // Separate lungs + itkSetMacro(SeparateLungsFlag, bool); + itkGetConstMacro(SeparateLungsFlag, bool); + itkBooleanMacro(SeparateLungsFlag); + + // Step Auto Crop + itkSetMacro(AutoCrop, bool); + itkGetConstMacro(AutoCrop, bool); + itkBooleanMacro(AutoCrop); + protected: ExtractLungFilter(); virtual ~ExtractLungFilter() {} // Main members InputImageConstPointer input; - MaskImageConstPointer patient; + MaskImagePointer patient; InputImagePointer working_input; - typename InternalImageType::Pointer working_image; - typename InternalImageType::Pointer trachea_tmp; + std::string m_OutputLungFilename; + std::string m_OutputTracheaFilename; + MaskImagePointer working_mask; MaskImagePointer trachea; - MaskImagePointer output; unsigned int m_MaxSeedNumber; // Global options @@ -224,6 +238,8 @@ public: MaskImagePixelType m_BackgroundValue; MaskImagePixelType m_ForegroundValue; int m_MinimalComponentSize; + bool m_AutoCrop; + bool m_RemoveSmallLabelBeforeSeparationFlag; // Step 1 InputImagePixelType m_UpperThreshold; @@ -232,10 +248,18 @@ public: LabelParamType* m_LabelizeParameters1; // Step 2 + int m_TracheaSeedAlgorithm; InputImagePixelType m_UpperThresholdForTrachea; InputImagePixelType m_ThresholdStepSizeForTrachea; double m_MultiplierForTrachea; std::vector m_Seeds; + std::vector m_SeedsInMM; + int m_NumberOfSlicesToSkipBeforeSearchingSeed; + bool m_TracheaVolumeMustBeCheckedFlag; + bool m_VerboseRegionGrowingFlag; + int m_NumSlices; + double m_MaxElongation; + int m_SeedPreProcessingThreshold; // Step 3 int m_NumberOfHistogramBins; @@ -246,19 +270,27 @@ public: LabelParamType* m_LabelizeParameters3; // Step 5 - // bool m_FinalOpenClose; - - bool m_FindBronchialBifurcations; + bool m_OpenCloseFlag; + int m_OpenCloseRadius; + + // Step 6 + bool m_FillHolesFlag; + InputImageSizeType m_FillHolesDirections; + + bool m_SeparateLungsFlag; + // Main functions virtual void GenerateOutputInformation(); + virtual void GenerateInputRequestedRegion(); virtual void GenerateData(); + + // Functions for trachea extraction + bool SearchForTracheaSeed(int skip); + bool SearchForTracheaSeed2(int numberOfSlices); + void SearchForTrachea(); + void TracheaRegionGrowing(); + double ComputeTracheaVolume(); - typedef Bifurcation BifurcationType; - void TrackFromThisIndex(std::vector & listOfBifurcations, - MaskImagePointer skeleton, - MaskImageIndexType index, - MaskImagePixelType label); - private: ExtractLungFilter(const Self&); //purposely not implemented void operator=(const Self&); //purposely not implemented