distanceMatrixToMesh

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

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

Categories: Graphs, Visualisation

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

distanceMatrixToMesh often follows after

multiplyImageAndScalar (1)
generateDistanceMatrix (1)

Usage in ImageJ macro

Ext.CLIJ2_distanceMatrixToMesh(Image pointlist, Image distance_matrix, Image mesh_destination, Number maximum_distance);

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 pointlist = clij2.push(pointlistImagePlus);
ClearCLBuffer distance_matrix = clij2.push(distance_matrixImagePlus);
mesh_destination = clij2.create(pointlist);
float maximum_distance = 1.0;

// Execute operation on GPU
clij2.distanceMatrixToMesh(pointlist, distance_matrix, mesh_destination, maximum_distance);

// show result
mesh_destinationImagePlus = clij2.pull(mesh_destination);
mesh_destinationImagePlus.show();

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

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
pointlist = clij2.pushMat(pointlist_matrix);
distance_matrix = clij2.pushMat(distance_matrix_matrix);
mesh_destination = clij2.create(pointlist);
maximum_distance = 1.0;

% Execute operation on GPU
clij2.distanceMatrixToMesh(pointlist, distance_matrix, mesh_destination, maximum_distance);

% show result
mesh_destination = clij2.pullMat(mesh_destination)

% cleanup memory on GPU
clij2.release(pointlist);
clij2.release(distance_matrix);
clij2.release(mesh_destination);

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
pointlist_sequence = getSequence();
pointlist = clij2.pushSequence(pointlist_sequence);
distance_matrix_sequence = getSequence();
distance_matrix = clij2.pushSequence(distance_matrix_sequence);
mesh_destination = clij2.create(pointlist);
maximum_distance = 1.0;

// Execute operation on GPU
clij2.distanceMatrixToMesh(pointlist, distance_matrix, mesh_destination, maximum_distance);

// show result
mesh_destination_sequence = clij2.pullSequence(mesh_destination)
Icy.addSequence(mesh_destination_sequence);
// cleanup memory on GPU
clij2.release(pointlist);
clij2.release(distance_matrix);
clij2.release(mesh_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.distance_matrix_to_mesh(pointlist, distance_matrix, mesh_destination, maximum_distance)

Example notebooks

spots_pointlists_matrices_tables

Example scripts

spots_pointlists_matrices_tables.ijm

Back to CLIJ2 reference Back to CLIJ2 documentation

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