minimumDistanceOfTouchingNeighbors

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

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.

Usage in ImageJ macro

Ext.CLIJ2_minimumDistanceOfTouchingNeighbors(Image distance_matrix, Image touch_matrix, Image minimum_distancelist_destination);

Usage in object oriented programming languages

Java

// init CLIJ and GPU
import net.haesleinhuepf.clij2.CLIJ2;
import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
CLIJ2 clij2 = CLIJ2.getInstance();

// get input parameters
ClearCLBuffer distance_matrix = clij2.push(distance_matrixImagePlus);
ClearCLBuffer touch_matrix = clij2.push(touch_matrixImagePlus);
minimum_distancelist_destination = clij2.create(distance_matrix);

// Execute operation on GPU
clij2.minimumDistanceOfTouchingNeighbors(distance_matrix, touch_matrix, minimum_distancelist_destination);

// show result
minimum_distancelist_destinationImagePlus = clij2.pull(minimum_distancelist_destination);
minimum_distancelist_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(distance_matrix);
clij2.release(touch_matrix);
clij2.release(minimum_distancelist_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
distance_matrix = clij2.pushMat(distance_matrix_matrix);
touch_matrix = clij2.pushMat(touch_matrix_matrix);
minimum_distancelist_destination = clij2.create(distance_matrix);

% Execute operation on GPU
clij2.minimumDistanceOfTouchingNeighbors(distance_matrix, touch_matrix, minimum_distancelist_destination);

% show result
minimum_distancelist_destination = clij2.pullMat(minimum_distancelist_destination)

% cleanup memory on GPU
clij2.release(distance_matrix);
clij2.release(touch_matrix);
clij2.release(minimum_distancelist_destination);

Icy JavaScript

// init CLIJ and GPU
importClass(net.haesleinhuepf.clicy.CLICY);
importClass(Packages.icy.main.Icy);

clij2 = CLICY.getInstance();

// get input parameters
distance_matrix_sequence = getSequence();
distance_matrix = clij2.pushSequence(distance_matrix_sequence);
touch_matrix_sequence = getSequence();
touch_matrix = clij2.pushSequence(touch_matrix_sequence);
minimum_distancelist_destination = clij2.create(distance_matrix);

// Execute operation on GPU
clij2.minimumDistanceOfTouchingNeighbors(distance_matrix, touch_matrix, minimum_distancelist_destination);

// show result
minimum_distancelist_destination_sequence = clij2.pullSequence(minimum_distancelist_destination)
Icy.addSequence(minimum_distancelist_destination_sequence);
// cleanup memory on GPU
clij2.release(distance_matrix);
clij2.release(touch_matrix);
clij2.release(minimum_distancelist_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.minimum_distance_of_touching_neighbors(distance_matrix, touch_matrix, minimum_distancelist_destination)

Example notebooks

shape_descriptors_based_on_neighborhood_graphs.ipynb

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