Collection of static utility functions for classification and image processing. More...

#include <mitkCLUtil.h>

Public Types
enum	MorphologicalDimensions { Axial , Coronal , Sagittal , All }
	Specifies the anatomical plane for morphological operations. More...

Static Public Member Functions
static void	CreateCheckerboardMask (mitk::Image::Pointer image, mitk::Image::Pointer &outimage)
	Create a checkerboard mask from the given image. More...

static void	InterpolateCheckerboardPrediction (mitk::Image::Pointer checkerboard_prediction, mitk::Image::Pointer &checkerboard_mask, mitk::Image::Pointer &outimage)
	Interpolate a prediction using a checkerboard pattern. More...

static void	CountVoxel (mitk::Image::Pointer image, std::map< unsigned int, unsigned int > &map)
	Count voxels per label in an image. More...

static void	CountVoxel (mitk::Image::Pointer image, unsigned int label, unsigned int &count)
	Count the number of voxels with a specific label value. More...

static void	CountVoxel (mitk::Image::Pointer image, unsigned int &count)
	Count the total number of non-zero voxels. More...

static void	SumVoxelForLabel (mitk::Image::Pointer image, const mitk::Image::Pointer &source, unsigned int label, double &val)
	Sum intensity values from a source image for voxels matching a given label. More...

static void	SqSumVoxelForLabel (mitk::Image::Pointer image, const mitk::Image::Pointer &source, unsigned int label, double &val)
	Sum squared intensity values from a source image for voxels matching a given label. More...

static void	LogicalAndImages (const Image::Pointer &image1, const Image::Pointer &image2, Image::Pointer &outimage)
	Compute the logical AND of two binary images. More...

static void	GaussianFilter (mitk::Image::Pointer image, mitk::Image::Pointer &smoothed, double sigma)
	Apply a Gaussian smoothing filter to an image. More...

static void	DifferenceOfGaussianFilter (mitk::Image::Pointer image, mitk::Image::Pointer &smoothed, double sigma1, double sigma2)
	Compute the Difference of Gaussians (DoG) of an image. More...

static void	LaplacianOfGaussianFilter (mitk::Image::Pointer image, mitk::Image::Pointer &smoothed, double sigma1)
	Compute the Laplacian of Gaussian (LoG) of an image. More...

static void	HessianOfGaussianFilter (mitk::Image::Pointer image, std::vector< mitk::Image::Pointer > &out, double sigma)
	Compute the Hessian of Gaussian for an image. More...

static void	LocalHistogram (mitk::Image::Pointer image, std::vector< mitk::Image::Pointer > &out, int Bins, int NeighbourhoodSize)
	Compute local histograms for each voxel in an image. More...

template<typename TMatrixElementType >
static mitk::Image::Pointer	Transform (const Eigen::Matrix< TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic > &matrix, const mitk::Image::Pointer &mask)
	Transform an Eigen matrix back to an MITK image using a mask. More...

template<typename TMatrixElementType >
static Eigen::Matrix< TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic >	Transform (const mitk::Image::Pointer &img, const mitk::Image::Pointer &mask)
	Transform an MITK image into an Eigen column matrix using a mask. More...

static void	DilateBinary (mitk::Image::Pointer &sourceImage, mitk::Image::Pointer &resultImage, int radius, MorphologicalDimensions d)
	Dilate a binary image using a ball structuring element. More...

static void	ErodeBinary (mitk::Image::Pointer &sourceImage, mitk::Image::Pointer &resultImage, int radius, MorphologicalDimensions d)
	Erode a binary image using a ball structuring element. More...

static void	ClosingBinary (mitk::Image::Pointer &sourceImage, mitk::Image::Pointer &resultImage, int radius, MorphologicalDimensions d)
	Perform morphological closing on a binary image. More...

static void	MergeLabels (mitk::Image::Pointer &img, const std::map< unsigned int, unsigned int > &map)
	Merge labels in a label image according to a mapping. More...

static void	ConnectedComponentsImage (mitk::Image::Pointer &image, mitk::Image::Pointer &mask, mitk::Image::Pointer &outimage, unsigned int &num_components)
	Compute connected components of a label image. More...

static void	GrabLabel (mitk::Image::Pointer &image, mitk::Image::Pointer &outimage, unsigned int label)
	Extract a single label from a label image into a binary mask. More...

static void	InsertLabel (mitk::Image::Pointer &image, mitk::Image::Pointer &maskImage, unsigned int label)
	Insert a label value into an output image at positions defined by a mask. More...

static void	ErodeGrayscale (mitk::Image::Pointer &image, unsigned int radius, mitk::CLUtil::MorphologicalDimensions d, mitk::Image::Pointer &outimage)
	Perform grayscale erosion using a ball structuring element. More...

static void	DilateGrayscale (mitk::Image::Pointer &image, unsigned int radius, mitk::CLUtil::MorphologicalDimensions d, mitk::Image::Pointer &outimage)
	Perform grayscale dilation using a ball structuring element. More...

static void	FillHoleGrayscale (mitk::Image::Pointer &image, mitk::Image::Pointer &outimage)
	Fill holes in a grayscale image. More...

static void	ProbabilityMap (const mitk::Image::Pointer &sourceImage, double mean, double std_dev, mitk::Image::Pointer &resultImage)
	Create a probability map based on Gaussian distribution parameters. More...

template<class TImageType >
static void	itkCountVoxel (TImageType *image, std::map< unsigned int, unsigned int > &map)

template<class TImageType >
static void	itkCountVoxel (TImageType *image, typename TImageType::PixelType label, unsigned int &count)

template<typename TImageType >
static void	itkCountVoxel (TImageType *mask, unsigned int &n_numSamples)

template<class TImageType1 , class TImageType2 >
static void	itkSampleLabel (TImageType1 image, TImageType2 output, double acceptrate, unsigned int label)

template<class TImageType >
static void	itkSampleLabel (TImageType *image, mitk::Image::Pointer &output, unsigned int n_samples_drawn)

Detailed Description

Collection of static utility functions for classification and image processing.

CLUtil provides convenience methods for voxel counting, morphological operations, image filtering (Gaussian, DoG, LoG, Hessian), label manipulation, and conversion between Eigen matrices and MITK images.

See also: AbstractGlobalImageFeature; AbstractClassifier

Definition at line 39 of file mitkCLUtil.h.

Member Enumeration Documentation

◆ MorphologicalDimensions

enum mitk::CLUtil::MorphologicalDimensions

Specifies the anatomical plane for morphological operations.

Enumerator
Axial	Axial (transverse) plane.
Coronal	Coronal (frontal) plane.
Sagittal	Sagittal plane.
All	All three dimensions (3D operation).

Definition at line 45 of file mitkCLUtil.h.

Member Function Documentation

◆ ClosingBinary()

static void mitk::CLUtil::ClosingBinary	(	mitk::Image::Pointer &	sourceImage,
		mitk::Image::Pointer &	resultImage,
		int	radius,
		MorphologicalDimensions	d
	)

static

Perform morphological closing on a binary image.

Parameters

sourceImage	The input binary image.
resultImage	The closed output image.
radius	Radius of the structuring element in voxels.
d	The anatomical dimension(s) for the operation.

◆ ConnectedComponentsImage()

static void mitk::CLUtil::ConnectedComponentsImage	(	mitk::Image::Pointer &	image,
		mitk::Image::Pointer &	mask,
		mitk::Image::Pointer &	outimage,
		unsigned int &	num_components
	)

static

Compute connected components of a label image.

Parameters

image	The input label image.
mask	Optional mask restricting the region. Can be nullptr.
outimage	The output image with unique labels per connected component.
num_components	The number of connected components found.

◆ CountVoxel() [1/3]

static void mitk::CLUtil::CountVoxel	(	mitk::Image::Pointer	image,
		std::map< unsigned int, unsigned int > &	map
	)

static

Count voxels per label in an image.

Parameters

[in]	image	The label image.
[out]	map	Map from label value to voxel count.

Referenced by Transform().

◆ CountVoxel() [2/3]

static void mitk::CLUtil::CountVoxel	(	mitk::Image::Pointer	image,
		unsigned int &	count
	)

static

Count the total number of non-zero voxels.

Parameters

[in]	image	The input image.
[out]	count	The total count of voxels with value > 0.

◆ CountVoxel() [3/3]

static void mitk::CLUtil::CountVoxel	(	mitk::Image::Pointer	image,
		unsigned int	label,
		unsigned int &	count
	)

static

Count the number of voxels with a specific label value.

Parameters

[in]	image	The label image.
[in]	label	The label value to count.
[out]	count	The number of voxels with the given label.

◆ CreateCheckerboardMask()

static void mitk::CLUtil::CreateCheckerboardMask	(	mitk::Image::Pointer	image,
		mitk::Image::Pointer &	outimage
	)

static

Create a checkerboard mask from the given image.

Parameters

[in]	image	The input image.
[out]	outimage	The resulting checkerboard mask.

◆ DifferenceOfGaussianFilter()

static void mitk::CLUtil::DifferenceOfGaussianFilter	(	mitk::Image::Pointer	image,
		mitk::Image::Pointer &	smoothed,
		double	sigma1,
		double	sigma2
	)

static

Compute the Difference of Gaussians (DoG) of an image.

The result is the difference between two Gaussian-smoothed images with sigmas sigma1 and sigma2.

Parameters

[in]	image	The input image.
[out]	smoothed	The DoG output image.
[in]	sigma1	Standard deviation of the first Gaussian.
[in]	sigma2	Standard deviation of the second Gaussian.

◆ DilateBinary()

static void mitk::CLUtil::DilateBinary	(	mitk::Image::Pointer &	sourceImage,
		mitk::Image::Pointer &	resultImage,
		int	radius,
		MorphologicalDimensions	d
	)

static

Dilate a binary image using a ball structuring element.

Parameters

sourceImage	The input binary image.
resultImage	The dilated output image.
radius	Radius of the structuring element in voxels.
d	The anatomical dimension(s) for the operation.

◆ DilateGrayscale()

static void mitk::CLUtil::DilateGrayscale	(	mitk::Image::Pointer &	image,
		unsigned int	radius,
		mitk::CLUtil::MorphologicalDimensions	d,
		mitk::Image::Pointer &	outimage
	)

static

Perform grayscale dilation using a ball structuring element.

Parameters

image	The input image.
radius	Radius of the structuring element in voxels.
d	The anatomical dimension(s) for the operation.
outimage	The dilated output image.

◆ ErodeBinary()

static void mitk::CLUtil::ErodeBinary	(	mitk::Image::Pointer &	sourceImage,
		mitk::Image::Pointer &	resultImage,
		int	radius,
		MorphologicalDimensions	d
	)

static

Erode a binary image using a ball structuring element.

Parameters

sourceImage	The input binary image.
resultImage	The eroded output image.
radius	Radius of the structuring element in voxels.
d	The anatomical dimension(s) for the operation.

◆ ErodeGrayscale()

static void mitk::CLUtil::ErodeGrayscale	(	mitk::Image::Pointer &	image,
		unsigned int	radius,
		mitk::CLUtil::MorphologicalDimensions	d,
		mitk::Image::Pointer &	outimage
	)

static

Perform grayscale erosion using a ball structuring element.

Parameters

image	The input image.
radius	Radius of the structuring element in voxels.
d	The anatomical dimension(s) for the operation.
outimage	The eroded output image.

◆ FillHoleGrayscale()

static void mitk::CLUtil::FillHoleGrayscale	(	mitk::Image::Pointer &	image,
		mitk::Image::Pointer &	outimage
	)

static

Fill holes in a grayscale image.

Parameters

image	The input image.
outimage	The output image with holes filled.

◆ GaussianFilter()

static void mitk::CLUtil::GaussianFilter	(	mitk::Image::Pointer	image,
		mitk::Image::Pointer &	smoothed,
		double	sigma
	)

static

Apply a Gaussian smoothing filter to an image.

Parameters

[in]	image	The input image.
[out]	smoothed	The smoothed output image.
[in]	sigma	Standard deviation of the Gaussian kernel.

◆ GrabLabel()

static void mitk::CLUtil::GrabLabel	(	mitk::Image::Pointer &	image,
		mitk::Image::Pointer &	outimage,
		unsigned int	label
	)

static

Extract a single label from a label image into a binary mask.

Parameters

image	The input label image.
outimage	The output binary image (1 where label matches, 0 otherwise).
label	The label value to extract.

◆ HessianOfGaussianFilter()

static void mitk::CLUtil::HessianOfGaussianFilter	(	mitk::Image::Pointer	image,
		std::vector< mitk::Image::Pointer > &	out,
		double	sigma
	)

static

Compute the Hessian of Gaussian for an image.

Produces multiple output images corresponding to the Hessian matrix components.

Parameters

[in]	image	The input image.
[out]	out	Vector of output images for each Hessian component.
[in]	sigma	Standard deviation of the Gaussian.

◆ InsertLabel()

static void mitk::CLUtil::InsertLabel	(	mitk::Image::Pointer &	image,
		mitk::Image::Pointer &	maskImage,
		unsigned int	label
	)

static

Insert a label value into an output image at positions defined by a mask.

Parameters

image	The output image to insert the label into (created if null).
maskImage	The mask defining where to insert the label.
label	The label value to insert.

◆ InterpolateCheckerboardPrediction()

static void mitk::CLUtil::InterpolateCheckerboardPrediction	(	mitk::Image::Pointer	checkerboard_prediction,
		mitk::Image::Pointer &	checkerboard_mask,
		mitk::Image::Pointer &	outimage
	)

static

Interpolate a prediction using a checkerboard pattern.

Parameters

[in]	checkerboard_prediction	The prediction computed on the checkerboard pattern.
[in,out]	checkerboard_mask	The checkerboard mask.
[out]	outimage	The interpolated full prediction.

◆ itkCountVoxel() [1/3]

template<class TImageType >

static void mitk::CLUtil::itkCountVoxel	(	TImageType *	image,
		std::map< unsigned int, unsigned int > &	map
	)

inlinestatic

Definition at line 355 of file mitkCLUtil.h.

◆ itkCountVoxel() [2/3]

template<class TImageType >

static void mitk::CLUtil::itkCountVoxel	(	TImageType *	image,
		typename TImageType::PixelType	label,
		unsigned int &	count
	)

inlinestatic

Definition at line 368 of file mitkCLUtil.h.

◆ itkCountVoxel() [3/3]

template<typename TImageType >

static void mitk::CLUtil::itkCountVoxel	(	TImageType *	mask,
		unsigned int &	n_numSamples
	)

inlinestatic

Definition at line 379 of file mitkCLUtil.h.

◆ itkSampleLabel() [1/2]

template<class TImageType >

static void mitk::CLUtil::itkSampleLabel	(	TImageType *	image,
		mitk::Image::Pointer &	output,
		unsigned int	n_samples_drawn
	)

inlinestatic

Definition at line 410 of file mitkCLUtil.h.

References mitk::CastToMitkImage().

◆ itkSampleLabel() [2/2]

template<class TImageType1 , class TImageType2 >

static void mitk::CLUtil::itkSampleLabel	(	TImageType1 *	image,
		TImageType2 *	output,
		double	acceptrate,
		unsigned int	label
	)

inlinestatic

Definition at line 391 of file mitkCLUtil.h.

◆ LaplacianOfGaussianFilter()

static void mitk::CLUtil::LaplacianOfGaussianFilter	(	mitk::Image::Pointer	image,
		mitk::Image::Pointer &	smoothed,
		double	sigma1
	)

static

Compute the Laplacian of Gaussian (LoG) of an image.

Parameters

[in]	image	The input image.
[out]	smoothed	The LoG output image.
[in]	sigma1	Standard deviation of the Gaussian.

◆ LocalHistogram()

static void mitk::CLUtil::LocalHistogram	(	mitk::Image::Pointer	image,
		std::vector< mitk::Image::Pointer > &	out,
		int	Bins,
		int	NeighbourhoodSize
	)

static

Compute local histograms for each voxel in an image.

Parameters

[in]	image	The input image.
[out]	out	Vector of output images, one per histogram bin.
[in]	Bins	Number of histogram bins.
[in]	NeighbourhoodSize	Size of the local neighbourhood.

◆ LogicalAndImages()

static void mitk::CLUtil::LogicalAndImages	(	const Image::Pointer &	image1,
		const Image::Pointer &	image2,
		Image::Pointer &	outimage
	)

static

Compute the logical AND of two binary images.

Parameters

[in]	image1	First binary image.
[in]	image2	Second binary image.
[out]	outimage	The resulting AND image.

◆ MergeLabels()

static void mitk::CLUtil::MergeLabels	(	mitk::Image::Pointer &	img,
		const std::map< unsigned int, unsigned int > &	map
	)

static

Merge labels in a label image according to a mapping.

Parameters

img	The label image to modify in place.
map	Map of source label to target label. Each occurrence of a source label is replaced by its target.

◆ ProbabilityMap()

static void mitk::CLUtil::ProbabilityMap	(	const mitk::Image::Pointer &	sourceImage,
		double	mean,
		double	std_dev,
		mitk::Image::Pointer &	resultImage
	)

static

Create a probability map based on Gaussian distribution parameters.

Parameters

sourceImage	The input intensity image.
mean	The mean of the Gaussian distribution.
std_dev	The standard deviation of the Gaussian distribution.
resultImage	The output probability map image.

◆ SqSumVoxelForLabel()

static void mitk::CLUtil::SqSumVoxelForLabel	(	mitk::Image::Pointer	image,
		const mitk::Image::Pointer &	source,
		unsigned int	label,
		double &	val
	)

static

Sum squared intensity values from a source image for voxels matching a given label.

Parameters

[in]	image	The label image.
[in]	source	The intensity source image.
[in]	label	The label value to select voxels.
[out]	val	The sum of squared intensities for the selected voxels.

◆ SumVoxelForLabel()

static void mitk::CLUtil::SumVoxelForLabel	(	mitk::Image::Pointer	image,
		const mitk::Image::Pointer &	source,
		unsigned int	label,
		double &	val
	)

static

Sum intensity values from a source image for voxels matching a given label.

Parameters

[in]	image	The label image.
[in]	source	The intensity source image.
[in]	label	The label value to select voxels.
[out]	val	The sum of intensities for the selected voxels.

◆ Transform() [1/2]

template<typename TMatrixElementType >

static mitk::Image::Pointer mitk::CLUtil::Transform	(	const Eigen::Matrix< TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic > &	matrix,
		const mitk::Image::Pointer &	mask
	)

inlinestatic

Transform an Eigen matrix back to an MITK image using a mask.

Non-zero voxels in the mask are filled with values from the matrix in order.

Template Parameters

TMatrixElementType Element type of the Eigen matrix.

Parameters

[in]	matrix	The Eigen matrix of shape [n_masked_voxels, 1].
[in]	mask	The mask image defining which voxels to populate.

Returns: The resulting MITK image.

Definition at line 186 of file mitkCLUtil.h.

References mitk::CastToItkImage(), CountVoxel(), mitk::GrabItkImageMemory(), MITK_ERROR, and mitk::Image::New().

◆ Transform() [2/2]

template<typename TMatrixElementType >

static Eigen::Matrix<TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic> mitk::CLUtil::Transform	(	const mitk::Image::Pointer &	img,
		const mitk::Image::Pointer &	mask
	)

inlinestatic

Transform an MITK image into an Eigen column matrix using a mask.

Extracts intensity values from masked (non-zero) voxels and stores them in a single-column Eigen matrix.

Template Parameters

TMatrixElementType Element type of the Eigen matrix.

Parameters

img	The input intensity image.
mask	The mask image defining which voxels to extract.

Returns: An Eigen matrix of shape [n_masked_voxels, 1].

Definition at line 235 of file mitkCLUtil.h.

References mitk::CastToItkImage(), and CountVoxel().

The documentation for this class was generated from the following file:

mitkCLUtil.h

Public Types

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ MorphologicalDimensions

Member Function Documentation

◆ ClosingBinary()

◆ ConnectedComponentsImage()

◆ CountVoxel() [1/3]

◆ CountVoxel() [2/3]

◆ CountVoxel() [3/3]

◆ CreateCheckerboardMask()

◆ DifferenceOfGaussianFilter()

◆ DilateBinary()

◆ DilateGrayscale()

◆ ErodeBinary()

◆ ErodeGrayscale()

◆ FillHoleGrayscale()

◆ GaussianFilter()

◆ GrabLabel()

◆ HessianOfGaussianFilter()

◆ InsertLabel()

◆ InterpolateCheckerboardPrediction()

◆ itkCountVoxel() [1/3]

◆ itkCountVoxel() [2/3]

◆ itkCountVoxel() [3/3]

◆ itkSampleLabel() [1/2]

◆ itkSampleLabel() [2/2]

◆ LaplacianOfGaussianFilter()

◆ LocalHistogram()

◆ LogicalAndImages()

◆ MergeLabels()

◆ ProbabilityMap()

◆ SqSumVoxelForLabel()

◆ SumVoxelForLabel()

◆ Transform() [1/2]

◆ Transform() [2/2]