NifTK
16.4.1 - 0798f20
CMIC's Translational Medical Imaging Platform
|
Class to segment the breast mask from MRI for modelling purposes. More...
Public Types | |
typedef BreastMaskSegmForBreastDensity | Self |
typedef BreastMaskSegmentationFromMRI < ImageDimension, InputPixelType > | Superclass |
typedef SmartPointer< Self > | Pointer |
typedef SmartPointer< const Self > | ConstPointer |
typedef Superclass::InternalImageType | InternalImageType |
typedef Superclass::AxialImageType | AxialImageType |
typedef Superclass::PointSetType | PointSetType |
typedef Superclass::PointDataIterator | PointDataIterator |
typedef Superclass::RealType | RealType |
typedef Superclass::IteratorType | IteratorType |
typedef Superclass::VectorType | VectorType |
typedef Superclass::LineIteratorType | LineIteratorType |
typedef Superclass::SliceIteratorType | SliceIteratorType |
typedef Superclass::ConnectedSurfaceVoxelFilterType | ConnectedSurfaceVoxelFilterType |
typedef Superclass::ThresholdingFilterType | ThresholdingFilterType |
Public Types inherited from itk::BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType > | |
enum | enumBreastSideType { BOTH_BREASTS, LEFT_BREAST, RIGHT_BREAST } |
Breast side. More... | |
typedef BreastMaskSegmentationFromMRI | Self |
typedef Object | Superclass |
typedef SmartPointer< Self > | Pointer |
typedef SmartPointer< const Self > | ConstPointer |
typedef float | RealType |
typedef itk::Image < InputPixelType, ImageDimension > | InternalImageType |
typedef itk::Image< RealType, SliceDimension > | AxialImageType |
typedef itk::Vector< RealType, DataDimension > | VectorType |
typedef itk::Image< VectorType, ParametricDimension > | VectorImageType |
typedef itk::PointSet < VectorType, ParametricDimension > | PointSetType |
typedef PointSetType::PointsContainer | PointsContainer |
typedef PointsContainer::Iterator | PointsIterator |
typedef PointSetType::PointDataContainer | PointDataContainer |
typedef PointDataContainer::Iterator | PointDataIterator |
typedef itk::ImageRegionIterator < InternalImageType > | IteratorType |
typedef itk::ImageRegionIteratorWithIndex < InternalImageType > | IteratorWithIndexType |
typedef itk::ImageSliceIteratorWithIndex < InternalImageType > | SliceIteratorType |
typedef itk::ImageLinearIteratorWithIndex < InternalImageType > | LineIteratorType |
typedef itk::ImageDuplicator < InternalImageType > | DuplicatorType |
typedef itk::Image < InputPixelType, SliceDimension > | InputSliceType |
typedef itk::BasicImageFeaturesImageFilter < InputSliceType, InputSliceType > | BasicImageFeaturesFilterType |
typedef itk::SliceBySliceImageFilter < InternalImageType, InternalImageType > | SliceBySliceImageFilterType |
typedef itk::RegionGrowSurfacePoints < InternalImageType, InternalImageType > | ConnectedSurfaceVoxelFilterType |
typedef itk::CurvatureAnisotropicDiffusionImageFilter < InternalImageType, InternalImageType > | SmoothingFilterType |
typedef itk::GradientMagnitudeRecursiveGaussianImageFilter < InternalImageType, InternalImageType > | GradientFilterType |
typedef itk::SigmoidImageFilter < InternalImageType, InternalImageType > | SigmoidFilterType |
typedef itk::FastMarchingImageFilter < InternalImageType, InternalImageType > | FastMarchingFilterType |
typedef itk::BinaryThresholdImageFilter < InternalImageType, InternalImageType > | ThresholdingFilterType |
typedef itk::LewisGriffinRecursiveGaussianImageFilter < InternalImageType, InternalImageType > | DerivativeFilterType |
typedef DerivativeFilterType::Pointer | DerivativeFilterPointer |
typedef itk::MaximumImageFilter < InternalImageType, InternalImageType > | MaxImageFilterType |
typedef itk::ConnectedThresholdImageFilter < InternalImageType, InternalImageType > | ConnectedFilterType |
Static Public Member Functions | |
static Pointer | New () |
Protected Member Functions | |
BreastMaskSegmForBreastDensity () | |
Constructor. More... | |
~BreastMaskSegmForBreastDensity () | |
Destructor. More... | |
void | MaskThePectoralMuscleAndLateralChestSkinSurface (bool flgIncludeChestSkinSurface, RealType rYHeightOffset, typename PointSetType::Pointer &pecPointSet, unsigned long &iPointPec) |
Mask the pectoral muscle using a B-Spline surface. More... | |
Protected Member Functions inherited from itk::BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType > | |
BreastMaskSegmentationFromMRI () | |
Constructor. More... | |
virtual | ~BreastMaskSegmentationFromMRI () |
Destructor. More... | |
virtual void | Initialise (void) |
Initialise the segmentor. More... | |
virtual void | CreateBIFs (void) |
Create the BIF Image. More... | |
void | SmoothTheInputImages (void) |
Smooth the structural and FatSat images. More... | |
InternalImageType::Pointer | ScanLineMaxima (typename InternalImageType::Pointer image, typename InternalImageType::RegionType region, unsigned int direction, bool flgForward) |
Scan an image in a particular direction and replace voxels with scanned maximum intensity. More... | |
InternalImageType::Pointer | GreyScaleCloseImage (typename InternalImageType::Pointer image, typename InternalImageType::RegionType region, unsigned int direction, const std::string label) |
Scan an image in a particular direction and replace voxels with closed intensities. More... | |
InternalImageType::Pointer | GreyScaleCloseImage (typename InternalImageType::Pointer image, typename InternalImageType::RegionType region, const char *strSide) |
Scan an image in all directions and replace voxels with closed intensities. More... | |
void | GreyScaleClosing (void) |
Scan rows and columns in the image to fill in the center of the breast. More... | |
void | CalculateTheMaximumImage (void) |
Calculate the maximum image. More... | |
void | EnsureMaxImageHasOnlyPositiveIntensities (void) |
Ensure the maximum image contains only positive intensities. More... | |
void | SmoothMaxImageToIncreaseSeparationOfTheBackground (void) |
Smooth the image to increase separation of the background. More... | |
void | SegmentForegroundFromBackground (void) |
Segment the backgound using itkForegroundFromBackgroundImageThresholdCalculator. More... | |
void | SegmentBackground (void) |
Segment the backgound using the maximum image histogram. More... | |
void | ComputeElevationOfAnteriorSurface (bool flgCoilCrop=false) |
Compute a 2D map of the height of the patient's anterior skin surface. More... | |
InternalImageType::IndexType | FindSurfacePoint (typename InternalImageType::IndexType idxNipple, float deltaXinMM, float deltaZinMM) |
Find a point in the surface offset from the nipple. More... | |
void | FindBreastLandmarks (void) |
Find the nipple and mid-sternum landmarks. More... | |
PointSetType::Pointer | SegmentThePectoralMuscle (RealType rYHeightOffset, unsigned long &iPointPec, bool flgIncludeNippleSeeds=false) |
Segment the Pectoral Muscle. More... | |
void | CropTheMaskAccordingToEstimateOfCoilExtentInCoronalPlane (void) |
Discard anything not within the skin elevation mask. More... | |
void | MaskWithBSplineBreastSurface (RealType rYHeightOffset) |
Discard anything not within a B-Spline fitted to the breast skin surface. More... | |
void | MaskBreastWithSphere (void) |
Mask with a sphere centered on each breast. More... | |
void | SmoothMask (void) |
Smooth the mask and threshold to round corners etc. More... | |
void | ExtractLargestObject (enumBreastSideType breastSide) |
Extract the largest object. More... | |
double | DistanceBetweenVoxels (typename InternalImageType::IndexType p, typename InternalImageType::IndexType q) |
std::string | ModifySuffix (std::string filename, std::string strInsertBeforeSuffix) |
std::string | GetBreastSide (std::string &fileOutput, enumBreastSideType breastSide) |
InternalImageType::Pointer | GetBreastSide (typename InternalImageType::Pointer inImage, enumBreastSideType breastSide) |
bool | WriteImageToFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, enumBreastSideType breastSide) |
bool | WriteImageToFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, bool flgLeft=false, bool flgRight=false) |
bool | WriteBinaryImageToUCharFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, enumBreastSideType breastSide) |
bool | WriteBinaryImageToUCharFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, bool flgLeft, bool flgRight) |
bool | WriteBinaryImageToUCharFileOrVTKSurfaceFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, bool flgLeft, bool flgRight) |
Based on the file extension it will be decided wheter a vtk surface is written or an image is saved. More... | |
void | WriteHistogramToFile (std::string fileOutput, vnl_vector< double > &xHistIntensity, vnl_vector< double > &yHistFrequency, unsigned int nBins) |
void | polyDataInfo (vtkPolyData *polyData) |
void | WriteImageToVTKSurfaceFile (typename InternalImageType::Pointer image, std::string &fileOutput, enumBreastSideType breastSide, bool flgVerbose, float finalSegmThreshold) |
InternalImageType::Pointer | MaskImageFromBSplineFittedSurface (const typename PointSetType::Pointer &pointSet, const typename InternalImageType::RegionType ®ion, const typename InternalImageType::PointType &origin, const typename InternalImageType::SpacingType &spacing, const typename InternalImageType::DirectionType &direction, const RealType rYHeightOffset, const int splineOrder, const RealType controlPointSpacingInMM, const int numOfLevels, bool correctSurfaceOffest) |
Class to segment the breast mask from MRI for modelling purposes.
typedef Superclass::AxialImageType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::AxialImageType |
typedef Superclass::ConnectedSurfaceVoxelFilterType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::ConnectedSurfaceVoxelFilterType |
typedef SmartPointer<const Self> itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::ConstPointer |
typedef Superclass::InternalImageType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::InternalImageType |
typedef Superclass::IteratorType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::IteratorType |
typedef Superclass::LineIteratorType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::LineIteratorType |
typedef Superclass::PointDataIterator itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::PointDataIterator |
typedef SmartPointer<Self> itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::Pointer |
typedef Superclass::PointSetType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::PointSetType |
typedef Superclass::RealType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::RealType |
typedef BreastMaskSegmForBreastDensity itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::Self |
typedef Superclass::SliceIteratorType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::SliceIteratorType |
typedef BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType > itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::Superclass |
typedef Superclass::ThresholdingFilterType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::ThresholdingFilterType |
typedef Superclass::VectorType itk::BreastMaskSegmForBreastDensity< ImageDimension, InputPixelType >::VectorType |
|
protected |
Constructor.
|
protected |
Destructor.
|
virtual |
Execute the segmentation.
Implements itk::BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType >.
|
virtual |
Reimplemented from itk::BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType >.
|
protected |
Mask the pectoral muscle using a B-Spline surface.
|
static |