Include dependency graph for niftkGeneralSegmentorUtils.h:
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Go to the source code of this file.
Namespaces | |
| niftk | |
Functions | |
| void | niftk::GenerateOutlineFromBinaryImage (mitk::Image::Pointer image, int sliceAxis, int sliceIndex, int projectedSliceNumber, mitk::ContourModelSet *outputContourSet) |
| Used to generate a contour outline round a binary segmentation image, and refreshes the outputSurface. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKFillRegion (itk::Image< TPixel, VImageDimension > *itkImage, const typename itk::Image< TPixel, VImageDimension >::RegionType ®ion, TPixel fillValue) |
| Fills the itkImage region with the fillValue. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKClearImage (itk::Image< TPixel, VImageDimension > *itkImage) |
| Clears an image by setting all voxels to zero using ITKFillRegion. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKCopyImage (const itk::Image< TPixel, VImageDimension > *input, itk::Image< TPixel, VImageDimension > *output) |
| Copies an image from input to output, assuming input and output already allocated and of the same size. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKCopyRegion (const itk::Image< TPixel, VImageDimension > *input, int sliceAxis, int sliceIndex, itk::Image< TPixel, VImageDimension > *output) |
| Copies the region from input to output, assuming both images are the same size, and contain the region. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKCalculateSliceRegion (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, typename itk::Image< TPixel, VImageDimension >::RegionType &outputRegion) |
| Calculates the region corresponding to a single slice. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKCalculateSliceRegionAsVector (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, std::vector< int > &outputRegion) |
| Calculates the region corresponding to a single slice. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKClearSlice (itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex) |
| Clears a slice by setting all voxels to zero for a given slice and axis. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKFilterSeedsToCurrentSlice (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, mitk::PointSet *outputSeeds) |
| Takes the inputSeeds and filters them so that outputSeeds contains just those seeds contained within the current slice. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKRecalculateMinAndMaxOfSeedValues (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, double &min, double &max) |
| Called from RecalculateMinAndMaxOfSeedValues(), the actual method in ITK that recalculates the min and max intensity value of all the voxel locations given by the seeds. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKFilterInputPointSetToExcludeRegionOfInterest (const itk::Image< TPixel, VImageDimension > *itkImage, const typename itk::Image< TPixel, VImageDimension >::RegionType ®ionOfInterest, const mitk::PointSet *inputSeeds, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeedsNotInRegionOfInterest) |
| Takes the inputSeeds and copies them to outputCopyOfInputSeeds, and also copies seeds to outputNewSeedsNotInRegionOfInterest if the seed is not within the region of interest. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| bool | niftk::ITKSliceDoesHaveSeeds (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *seeds, int sliceAxis, int sliceIndex) |
| Will return true if the given slice has seeds within that slice. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| bool | niftk::ITKSliceIsEmpty (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, bool &outputSliceIsEmpty) |
| Creates a region of interest within itkImage corresponding to the given slice, and checks if it is empty returning true if it is all zero. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKUpdateRegionGrowing (const itk::Image< TPixel, VImageDimension > *itkImage, bool skipUpdate, const mitk::Image *workingImage, const mitk::PointSet *seeds, mitk::ContourModelSet *segmentationContours, mitk::ContourModelSet *drawContours, mitk::ContourModelSet *polyContours, int sliceAxis, int sliceIndex, double lowerThreshold, double upperThreshold, mitk::Image *outputRegionGrowingImage) |
| Called from UpdateRegionGrowing(), updates the interactive ITK single 2D slice region growing pipeline. Note: segmentationContours, drawContours and polyContours could be const pointers, but some const functions are missing from mitk::ContourModelSet. They are not modified from within this function (including transitive calls). More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKPropagateToRegionGrowingImage (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, int direction, double lowerThreshold, double upperThreshold, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeeds, std::vector< int > &outputRegion, mitk::Image *outputRegionGrowingImage) |
| Method takes all the input, and calculates the 3D propagated region (up or down or 3D), and stores it in the region growing node. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKPropagateUpOrDown (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *seeds, int sliceAxis, int sliceIndex, int direction, double lowerThreshold, double upperThreshold, mitk::Image *outputRegionGrowingImage) |
| Called from ITKPropagateToRegionGrowingImage to propagate up or down. More... | |
| template<typename TGreyScalePixel , unsigned int VImageDimension> | |
| void | niftk::ITKPropagateToSegmentationImage (const itk::Image< TGreyScalePixel, VImageDimension > *itkImage, mitk::Image *segmentedImage, mitk::Image *regionGrowingImage, OpPropagate *op) |
| Called from the ExecuteOperate (i.e. undo/redo framework) to actually apply the calculated propagated region to the current segmentation. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKGenerateOutlineFromBinaryImage (const itk::Image< TPixel, VImageDimension > *itkImage, int sliceAxis, int sliceIndex, int projectedSliceIndex, mitk::ContourModelSet *contourSet) |
| Called to extract a contour set from a binary image, as might be used for "See Prior", "See Next", or the outlining a binary segmentation. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKGetLargestMinimumDistanceSeedLocation (const itk::Image< TPixel, VImageDimension > *itkImage, TPixel foregroundPixelValue, typename itk::Image< TPixel, VImageDimension >::IndexType &outputSeedIndex, int &outputDistance) |
| Works out the largest minimum distance to the edge of the image data, filtered on a given foregroundPixelValue. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKAddNewSeedsToPointSet (const itk::Image< TPixel, VImageDimension > *itkImage, const typename itk::Image< TPixel, VImageDimension >::RegionType ®ionOfInterest, int sliceAxis, mitk::PointSet *outputNewSeeds) |
| For the given input itkImage (assumed to always be binary), and regionOfInterest, will iterate on a slice by slice basis, recalculating new seeds. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKPreprocessingOfSeedsForChangingSlice (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int oldSliceAxis, int oldSliceIndex, int newSliceAxis, int newSliceIndex, bool optimiseSeedPosition, bool newSliceIsEmpty, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeeds, std::vector< int > &outputRegion) |
| Does any pre-processing of seeds necessary to facilitate Undo/Redo for Threshold Apply, and also changing slice. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKPreprocessingForWipe (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *inputSeeds, int sliceAxis, int sliceIndex, int direction, mitk::PointSet *outputCopyOfInputSeeds, mitk::PointSet *outputNewSeeds, std::vector< int > &outputRegion) |
| Does any pre-processing necessary to facilitate Undo/Redo for Wipe commands, which in this case means computing a new list of seeds, and the region of interest to be wiped. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKDoWipe (itk::Image< TPixel, VImageDimension > *itkImage, mitk::PointSet *currentSeeds, OpWipe *op) |
| Does the wipe command for Wipe, Wipe+, Wipe-. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| bool | niftk::ITKImageHasNonZeroEdgePixels (const itk::Image< TPixel, VImageDimension > *itkImage) |
| Returns true if the image has non-zero edge pixels, and false otherwise. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKSliceDoesHaveUnenclosedSeeds (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *seeds, mitk::ContourModelSet *segmentationContours, mitk::ContourModelSet *polyToolContours, mitk::ContourModelSet *drawToolContours, const mitk::Image *workingImage, double lowerThreshold, double upperThreshold, bool useThresholds, int sliceAxis, int sliceIndex, bool &sliceDoesHaveUnenclosedSeeds) |
| Will return true if slice has unenclosed seeds, and false otherwise. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKFilterContours (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::Image *workingImage, const mitk::PointSet *seeds, mitk::ContourModelSet *segmentationContours, mitk::ContourModelSet *drawContours, mitk::ContourModelSet *polyContours, int sliceAxis, int sliceIndex, double lowerThreshold, double upperThreshold, bool isThresholding, mitk::ContourModelSet *outputCopyOfInputContours, mitk::ContourModelSet *outputContours) |
| Extracts a new contour set, for doing "Clean" operation. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKPropagateSeedsToNewSlice (const itk::Image< TPixel, VImageDimension > *itkImage, const mitk::PointSet *currentSeeds, mitk::PointSet *newSeeds, int sliceAxis, int oldSliceIndex, int newSliceIndex) |
| Given an image, and a set of seeds, will append new seeds in the new slice if necessary. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKDestroyPipeline (const itk::Image< TPixel, VImageDimension > *itkImage) |
| Completely removes the current 2D region growing pipeline that is stored in the map m_TypeToPipelineMap. More... | |
| template<typename TPixel , unsigned int VImageDimension> | |
| void | niftk::ITKInitialiseSeedsForSlice (const itk::Image< TPixel, VImageDimension > *itkImage, mitk::PointSet *seeds, int sliceAxis, int sliceIndex) |
| Creates seeds for each distinct 4-connected region for a given slice. More... | |
