generateNNearestNeighborsMatrix

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

Takes a distance matrix (e.g. derived from a pointlist of centroids) and marks for every column the n smallest distances as neighbors. The resulting matrix can be use as if it was a touch-matrix (a.k.a. adjacency graph matrix).

Inspired by a similar implementation in imglib2 [1]

Note: The implementation is limited to square matrices.

Parameters

distance_marix : Image touch_matrix_destination : Image n : int number of neighbors

References

[1] https://github.com/imglib/imglib2/blob/master/src/main/java/net/imglib2/interpolation/neighborsearch/InverseDistanceWeightingInterpolator.java

Categories: Graphs, Measurements

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_generateNNearestNeighborsMatrix(Image distance_matrix, Image touch_matrix_destination, Number n);

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);
touch_matrix_destination = clij2.create(distance_matrix);
int n = 10;

// Execute operation on GPU
clij2.generateNNearestNeighborsMatrix(distance_matrix, touch_matrix_destination, n);

// show result
touch_matrix_destinationImagePlus = clij2.pull(touch_matrix_destination);
touch_matrix_destinationImagePlus.show();

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
distance_matrix = clij2.pushMat(distance_matrix_matrix);
touch_matrix_destination = clij2.create(distance_matrix);
n = 10;

% Execute operation on GPU
clij2.generateNNearestNeighborsMatrix(distance_matrix, touch_matrix_destination, n);

% show result
touch_matrix_destination = clij2.pullMat(touch_matrix_destination)

% cleanup memory on GPU
clij2.release(distance_matrix);
clij2.release(touch_matrix_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_destination = clij2.create(distance_matrix);
n = 10;

// Execute operation on GPU
clij2.generateNNearestNeighborsMatrix(distance_matrix, touch_matrix_destination, n);

// show result
touch_matrix_destination_sequence = clij2.pullSequence(touch_matrix_destination)
Icy.addSequence(touch_matrix_destination_sequence);
// cleanup memory on GPU
clij2.release(distance_matrix);
clij2.release(touch_matrix_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.generate_n_nearest_neighbors_matrix(distance_matrix, touch_matrix_destination, n)

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