X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.h;h=6c50b1c2d96c85e3c9b8485d970d9ad6e0a261b3;hb=48727138e88f056b67312603560e600362346462;hp=3183457dde0a6eb7ff06d445670cb132523a2ae8;hpb=5668d4a49a5a6b68dc80fa28f0f82b54187cb70c;p=clitk.git diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h index 3183457..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 @@ -97,7 +97,8 @@ namespace clitk { 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; @@ -107,20 +108,13 @@ namespace clitk { void SetInput(const ImageType * image); itkSetMacro(PatientMaskBackgroundValue, MaskImagePixelType); itkGetConstMacro(PatientMaskBackgroundValue, MaskImagePixelType); - GGO_DefineOption(patientBG, SetPatientMaskBackgroundValue, MaskImagePixelType); // Output filename (for AFBD) itkSetMacro(OutputLungFilename, std::string); itkGetMacro(OutputLungFilename, std::string); - GGO_DefineOption(output, SetOutputLungFilename, std::string); itkSetMacro(OutputTracheaFilename, std::string); itkGetMacro(OutputTracheaFilename, std::string); - GGO_DefineOption(outputTrachea, SetOutputTracheaFilename, std::string); - - // Set all options at a time - template - void SetArgsInfo(ArgsInfoType arg); // Get output (only availabe after update !) typename MaskImageType::Pointer GetTracheaImage() { return trachea; } @@ -132,93 +126,109 @@ namespace clitk { // 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); - GGO_DefineOption(skipslices, SetNumberOfSlicesToSkipBeforeSearchingSeed, 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 final openclose - itkSetMacro(OpenClose, bool); - itkGetConstMacro(OpenClose, bool); - itkBooleanMacro(OpenClose); - GGO_DefineOption_Flag(openclose, SetOpenClose); + itkSetMacro(OpenCloseFlag, bool); + itkGetConstMacro(OpenCloseFlag, bool); + itkBooleanMacro(OpenCloseFlag); itkSetMacro(OpenCloseRadius, int); itkGetConstMacro(OpenCloseRadius, int); - GGO_DefineOption(opencloseRadius, SetOpenCloseRadius, int); // Step 6 fill holes - itkSetMacro(FillHoles, bool); - itkGetConstMacro(FillHoles, bool); - itkBooleanMacro(FillHoles); - GGO_DefineOption_Flag(doNotFillHoles, SetFillHoles); - + 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; std::string m_OutputLungFilename; std::string m_OutputTracheaFilename; - typename InternalImageType::Pointer working_image; - typename InternalImageType::Pointer trachea_tmp; + MaskImagePointer working_mask; MaskImagePointer trachea; - MaskImagePointer output; unsigned int m_MaxSeedNumber; // Global options @@ -228,6 +238,8 @@ namespace clitk { MaskImagePixelType m_BackgroundValue; MaskImagePixelType m_ForegroundValue; int m_MinimalComponentSize; + bool m_AutoCrop; + bool m_RemoveSmallLabelBeforeSeparationFlag; // Step 1 InputImagePixelType m_UpperThreshold; @@ -236,11 +248,18 @@ namespace clitk { 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; @@ -251,19 +270,23 @@ namespace clitk { LabelParamType* m_LabelizeParameters3; // Step 5 - bool m_OpenClose; + bool m_OpenCloseFlag; int m_OpenCloseRadius; // Step 6 - bool m_FillHoles; + 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();