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CLIJ 1/2/x reference in category ‘matrix’

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for working with matrices.. Read more about CLIJs release cycle

Please note: CLIJ is deprecated. Make the transition to CLIJ2.

Method is available in CLIJ (deprecated release)
Method is available in CLIJ2 (stable release)
Method is available in CLIJx (experimental release)
Method is available in clEsperanto (experimental)

Categories: Binary, Filter, Graphs, Labels, Math, Matrices, Measurements, Projections, Transformations, Detection, CLIc

[A], B,[C],[D], E, F,[G], H, I, J, K, L,[M],[N], O,[P], Q, R,[S],[T], U, V,[W], X, Y, Z

A

Converts a adjacency matrix in a touch matrix.

averageDistanceOfNClosestPoints

Determines the average of the n closest points for every point in a distance matrix.

averageDistanceOfNFarOffPoints

Determines the average of the n far off (most distant) points for every point in a distance matrix.

averageDistanceOfTouchingNeighbors

Takes a touch matrix and a distance matrix to determine the average distance of touching neighbors for every object.

C

colorDeconvolution (Experimental)

Computes the color deconvolution of an 8bit RGB stack color image with a given 3x3 matrix of color vectors. Note: The input image has to be a stack with three z-slices corresponding to the red, green and blue channel.)

countTouchingNeighbors

Takes a touch matrix as input and delivers a vector with number of touching neighbors per label as a vector.

D

distanceMap

Generates a distance map from a binary image.

distanceMatrixToMesh

Generates a mesh from a distance matric and a list of point coordinates.

G

generateAngleMatrix (Experimental)

Computes the angle in radians between all point coordinates given in two point lists.

generateBinaryOverlapMatrix

Takes two labelmaps with n and m labels and generates a (n+1)*(m+1) matrix where all pixels are set to 0 exept those where labels overlap between the label maps.

generateDistanceMatrix

Computes the distance between all point coordinates given in two point lists.

generateDistanceMatrixAlongAxis (Experimental)

Computes the distance in X, Y or Z (specified with parameter axis) between all point coordinates given in two point lists.

generateGreyValueCooccurrenceMatrixBox (Experimental)

Takes an image and an intensity range to determine a grey value co-occurrence matrix.

generateIntegerGreyValueCooccurrenceCountMatrixHalfBox (Experimental)

Takes an image and assumes its grey values are integers. It builds up a grey-level co-occurrence matrix of neighboring (west, south-west, south, south-east, in 3D 9 pixels on the next plane) pixel intensities.

generateIntegerGreyValueCooccurrenceCountMatrixHalfDiamond (Experimental)

Takes an image and assumes its grey values are integers. It builds up a grey-level co-occurrence matrix of neighboring (left, bottom, back) pixel intensities.

generateJaccardIndexMatrix

Takes two labelmaps with n and m labels_2 and generates a (n+1)*(m+1) matrix where all labels_1 are set to 0 exept those where labels_2 overlap between the label maps.

generateNNearestNeighborsMatrix

Produces a touch-matrix where the n nearest neighbors are marked as touching neighbors.

generateProximalNeighborsMatrix

Produces a touch-matrix where the neighbors within a given distance range are marked as touching neighbors.

generateTouchCountMatrix

Takes a label map with n labels and generates a (n+1)*(n+1) matrix where all pixels are set the number of pixels where labels touch (diamond neighborhood).

generateTouchMatrix

Takes a labelmap with n labels and generates a (n+1)*(n+1) matrix where all pixels are set to 0 exept those where labels are touching.

M

matrixEqual

Checks if all elements of a matrix are different by less than or equal to a given tolerance.

maximumDistanceOfTouchingNeighbors

Takes a touch matrix and a distance matrix to determine the maximum distance of touching neighbors for every object.

maximumOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the maximum value among touching neighbors for every object.

meanOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the mean value among touching neighbors for every object.

medianOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the median value among touching neighbors for every object.

minimumDistanceOfTouchingNeighbors

Takes a touch matrix and a distance matrix to determine the shortest distance of touching neighbors for every object.

minimumOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the minimum value among touching neighbors for every object.

modeOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the most popular integer value among touching neighbors for every object. TODO: This only works for values between 0 and 255 for now.

N

nClosestDistances

Determine the n point indices with shortest distance for all points in a distance matrix.

nClosestPoints

Determine the n point indices with shortest distance for all points in a distance matrix.

neighborsOfNeighbors

Determines neighbors of neigbors from touch matrix and saves the result as a new touch matrix.

P

pointIndexListToTouchMatrix

Takes a list of point indices to generate a touch matrix (a.k.a. adjacency graph matrix) out of it.

S

setWhereXequalsY

Sets all pixel values a of a given image A to a constant value v in case its coordinates x == y.

setWhereXgreaterThanY

Sets all pixel values a of a given image A to a constant value v in case its coordinates x > y.

setWhereXsmallerThanY

Sets all pixel values a of a given image A to a constant value v in case its coordinates x < y.

shortestDistances

Determine the shortest distance from a distance matrix.

standardDeviationOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the standard deviation value among touching neighbors for every object.

T

Converts a touch matrix in an adjacency matrix

touchMatrixToMesh

Takes a pointlist with dimensions nd with n point coordinates in d dimensions and a touch matrix of size nn to draw lines from all points to points if the corresponding pixel in the touch matrix is 1.

W

writeVTKLineListToDisc (Experimental)

Takes a point list image representing n points (n2 for 2D points, n3 for 3D points) and a corresponding touch matrix , sized (n+1)*(n+1), and exports them in VTK format.

40 methods listed.