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

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx compatible with pyclesperanto.. 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

[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

absolute

Computes the absolute value of every individual pixel x in a given image.

absoluteDifference

Determines the absolute difference pixel by pixel between two images.

addImageAndScalar

Adds a scalar value s to all pixels x of a given image X.

addImagesWeighted

Calculates the sum of pairs of pixels x and y from images X and Y weighted with factors a and b.

B

binaryAnd

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary AND operator &. All pixel values except 0 in the input images are interpreted as 1.

binaryEdgeDetection

Determines pixels/voxels which are on the surface of binary objects and sets only them to 1 in the destination image. All other pixels are set to 0.

binaryNot

Computes a binary image (containing pixel values 0 and 1) from an image X by negating its pixel values x using the binary NOT operator !

binaryOr

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary OR operator |.

binarySubtract

Subtracts one binary image from another.

binaryXOr

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary operators AND &, OR | and NOT ! implementing the XOR operator.

bottomHatBox

Apply a bottom-hat filter for background subtraction to the input image.

bottomHatSphere

Applies a bottom-hat filter for background subtraction to the input image.

boundingBox

Determines the bounding box of all non-zero pixels in a binary image.

C

centerOfMass

Determines the center of mass of an image or image stack.

clInfo

Outputs information about available OpenCL devices.

closeIndexGapsInLabelMap

Analyses a label map and if there are gaps in the indexing (e.g. label 5 is not present) all subsequent labels will be relabelled.

connectedComponentsLabelingBox

Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

connectedComponentsLabelingDiamond

Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.

convolve

Convolve the image with a given kernel image.

copy

Copies an image.

copySlice

This method has two purposes: It copies a 2D image to a given slice z position in a 3D image stack or It copies a given slice at position z in an image stack to a 2D image.

create2D

Allocated memory for a new 2D image in the GPU memory.

create3D

Allocated memory for a new 3D image in the GPU memory.

crop2D

Crops a given rectangle out of a given image.

crop3D

Crops a given sub-stack out of a given image stack.

D

detectLabelEdges

Takes a labelmap and returns an image where all pixels on label edges are set to 1 and all other pixels to 0.

detectMaxima2DBox

Detects local maxima in a given square/cubic neighborhood.

detectMaxima3DBox

Detects local maxima in a given square/cubic neighborhood.

detectMaximaBox

Detects local maxima in a given square/cubic neighborhood.

differenceOfGaussian2D

Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.

differenceOfGaussian3D

Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.

dilateBox

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateSphere

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

divideImages

Divides two images X and Y by each other pixel wise.

drawBox

Draws a box at a given start point with given size. All pixels other than in the box are untouched. Consider using set(buffer, 0); in advance.

drawLine

Draws a line between two points with a given thickness.

drawSphere

Draws a sphere around a given point with given radii in x, y and z (if 3D).

E

equal

Determines if two images A and B equal pixel wise.

equalConstant

Determines if an image A and a constant b are equal.

erodeBox

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeSphere

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

excludeLabelsOnEdges

Removes all labels from a label map which touch the edges of the image (in X, Y and Z if the image is 3D).

exponential

Computes base exponential of all pixels values.

extendLabelingViaVoronoi

Takes a label map image and dilates the regions using a octagon shape until they touch.

F

flip2D

Flips an image in X and/or Y direction depending on boolean flags.

flip3D

Flips an image in X, Y and/or Z direction depending on boolean flags.

G

gaussianBlur2D

Computes the Gaussian blurred image of an image given two sigma values in X and Y.

gaussianBlur3D

Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z.

generateDistanceMatrix

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

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.

gradientX

Computes the gradient of gray values along X.

gradientY

Computes the gradient of gray values along Y.

gradientZ

Computes the gradient of gray values along Z.

greater

Determines if two images A and B greater pixel wise.

greaterConstant

Determines if two images A and B greater pixel wise.

greaterOrEqual

Determines if two images A and B greater or equal pixel wise.

greaterOrEqualConstant

Determines if two images A and B greater or equal pixel wise.

H

histogram

Determines the histogram of a given image.

I

invert

Computes the negative value of all pixels in a given image.

J

jaccardIndex

Determines the overlap of two binary images using the Jaccard index.

L

laplaceBox

Applies the Laplace operator (Box neighborhood) to an image.

logarithm

Computes base e logarithm of all pixels values.

M

mask

Computes a masked image by applying a binary mask to an image.

maskLabel

Computes a masked image by applying a label mask to an image.

maximum2DBox

Computes the local maximum of a pixels rectangular neighborhood.

maximum2DSphere

Computes the local maximum of a pixels ellipsoidal neighborhood.

maximum3DBox

Computes the local maximum of a pixels cube neighborhood.

maximum3DSphere

Computes the local maximum of a pixels spherical neighborhood.

maximumImageAndScalar

Computes the maximum of a constant scalar s and each pixel value x in a given image X.

maximumImages

Computes the maximum of a pair of pixel values x, y from two given images X and Y.

maximumOfAllPixels

Determines the maximum of all pixels in a given image.

maximumXProjection

Determines the maximum intensity projection of an image along X.

maximumYProjection

Determines the maximum intensity projection of an image along X.

maximumZProjection

Determines the maximum intensity projection of an image along Z.

mean2DBox

Computes the local mean average of a pixels rectangular neighborhood.

mean2DSphere

Computes the local mean average of a pixels ellipsoidal neighborhood.

mean3DBox

Computes the local mean average of a pixels cube neighborhood.

mean3DSphere

Computes the local mean average of a pixels spherical neighborhood.

meanOfAllPixels

Determines the mean average of all pixels in a given image.

meanSquaredError

Determines the mean squared error (MSE) between two images.

meanXProjection

Determines the mean average intensity projection of an image along X.

meanYProjection

Determines the mean average intensity projection of an image along Y.

meanZProjection

Determines the mean average intensity projection of an image along Z.

minimum2DBox

Computes the local minimum of a pixels rectangular neighborhood.

minimum2DSphere

Computes the local minimum of a pixels ellipsoidal neighborhood.

minimum3DBox

Computes the local minimum of a pixels cube neighborhood.

minimum3DSphere

Computes the local minimum of a pixels spherical neighborhood.

minimumImageAndScalar

Computes the minimum of a constant scalar s and each pixel value x in a given image X.

minimumImages

Computes the minimum of a pair of pixel values x, y from two given images X and Y.

minimumOfAllPixels

Determines the minimum of all pixels in a given image.

minimumOfMaskedPixels

Determines the minimum intensity in a masked image.

minimumXProjection

Determines the minimum intensity projection of an image along Y.

minimumYProjection

Determines the minimum intensity projection of an image along Y.

minimumZProjection

Determines the minimum intensity projection of an image along Z.

multiplyImageAndCoordinate

Multiplies all pixel intensities with the x, y or z coordinate, depending on specified dimension.

multiplyImageAndScalar

Multiplies all pixels value x in a given image X with a constant scalar s.

multiplyImages

Multiplies all pairs of pixel values x and y from two image X and Y.

multiplyMatrix

Multiplies two matrices with each other.

N

nonzeroMaximumBox

Apply a maximum filter (box shape) to the input image.

nonzeroMaximumDiamond

Apply a maximum filter (diamond shape) to the input image.

nonzeroMinimumBox

Apply a minimum filter (box shape) to the input image.

nonzeroMinimumDiamond

Apply a minimum filter (diamond shape) to the input image.

notEqual

Determines if two images A and B equal pixel wise.

notEqualConstant

Determines if two images A and B equal pixel wise.

O

onlyzeroOverwriteMaximumBox

Apply a local maximum filter to an image which only overwrites pixels with value 0.

onlyzeroOverwriteMaximumDiamond

Apply a local maximum filter to an image which only overwrites pixels with value 0.

P

paste2D

Pastes an image into another image at a given position.

paste3D

Pastes an image into another image at a given position.

power

Computes all pixels value x to the power of a given exponent a.

powerImages

Calculates x to the power of y pixel wise of two images X and Y.

pull

Copies an image specified by its name from GPU memory back to ImageJ and shows it.

push

Copies an image specified by its name to GPU memory in order to process it there later.

R

replaceIntensities

Replaces integer intensities specified in a vector image.

replaceIntensity

Replaces a specific intensity in an image with a given new value.

S

set

Sets all pixel values x of a given image X to a constant value v.

setColumn

Sets all pixel values x of a given column in X to a constant value v.

setImageBorders

Sets all pixel values at the image border to a given value.

setPlane

Sets all pixel values x of a given plane in X to a constant value v.

setRampX

Sets all pixel values to their X coordinate

setRampY

Sets all pixel values to their Y coordinate

setRampZ

Sets all pixel values to their Z coordinate

setRow

Sets all pixel values x of a given row in X to a constant value v.

smaller

Determines if two images A and B smaller pixel wise.

smallerConstant

Determines if two images A and B smaller pixel wise.

smallerOrEqual

Determines if two images A and B smaller or equal pixel wise.

smallerOrEqualConstant

Determines if two images A and B smaller or equal pixel wise.

sobel

Convolve the image with the Sobel kernel.

sorensenDiceCoefficient

Determines the overlap of two binary images using the Sorensen-Dice coefficent.

squaredDifference

Determines the squared difference pixel by pixel between two images.

standardDeviationZProjection

Determines the standard deviation intensity projection of an image stack along Z.

subtractImageFromScalar

Subtracts one image X from a scalar s pixel wise.

subtractImages

Subtracts one image X from another image Y pixel wise.

sumOfAllPixels

Determines the sum of all pixels in a given image.

sumXProjection

Determines the sum intensity projection of an image along Z.

sumYProjection

Determines the sum intensity projection of an image along Z.

sumZProjection

Determines the sum intensity projection of an image along Z.

T

thresholdOtsu

The automatic thresholder utilizes the Otsu threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

topHatBox

Applies a top-hat filter for background subtraction to the input image.

topHatSphere

Applies a top-hat filter for background subtraction to the input image.

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.

transposeXY

Transpose X and Y axes of an image.

transposeXZ

Transpose X and Z axes of an image.

transposeYZ

Transpose Y and Z axes of an image.

U

undefinedToZero

Copies all pixels instead those which are not a number (NaN) or infinity (inf), which are replaced by 0.

V

voronoiLabeling

Takes a binary image, labels connected components and dilates the regions using a octagon shape until they touch.

157 methods listed.