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.

For the remaining labels_1, the value will be between 0 and 1 indicating the overlap as measured by the Jaccard Index. Major parts of this operation run on the CPU.

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.

generateJaccardIndexMatrix often follows after

pushString (2)

generateJaccardIndexMatrix is often followed by

maximumXProjection (1)

Usage in ImageJ macro

Ext.CLIJ2_generateJaccardIndexMatrix(Image label_map1, Image label_map2, Image jaccard_index_matrix_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 label_map1 = clij2.push(label_map1ImagePlus);
ClearCLBuffer label_map2 = clij2.push(label_map2ImagePlus);
jaccard_index_matrix_destination = clij2.create(label_map1);

// Execute operation on GPU
clij2.generateJaccardIndexMatrix(label_map1, label_map2, jaccard_index_matrix_destination);

// show result
jaccard_index_matrix_destinationImagePlus = clij2.pull(jaccard_index_matrix_destination);
jaccard_index_matrix_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(label_map1);
clij2.release(label_map2);
clij2.release(jaccard_index_matrix_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
label_map1 = clij2.pushMat(label_map1_matrix);
label_map2 = clij2.pushMat(label_map2_matrix);
jaccard_index_matrix_destination = clij2.create(label_map1);

% Execute operation on GPU
clij2.generateJaccardIndexMatrix(label_map1, label_map2, jaccard_index_matrix_destination);

% show result
jaccard_index_matrix_destination = clij2.pullMat(jaccard_index_matrix_destination)

% cleanup memory on GPU
clij2.release(label_map1);
clij2.release(label_map2);
clij2.release(jaccard_index_matrix_destination);

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
label_map1_sequence = getSequence();
label_map1 = clij2.pushSequence(label_map1_sequence);
label_map2_sequence = getSequence();
label_map2 = clij2.pushSequence(label_map2_sequence);
jaccard_index_matrix_destination = clij2.create(label_map1);

// Execute operation on GPU
clij2.generateJaccardIndexMatrix(label_map1, label_map2, jaccard_index_matrix_destination);

// show result
jaccard_index_matrix_destination_sequence = clij2.pullSequence(jaccard_index_matrix_destination)
Icy.addSequence(jaccard_index_matrix_destination_sequence);
// cleanup memory on GPU
clij2.release(label_map1);
clij2.release(label_map2);
clij2.release(jaccard_index_matrix_destination);

Example scripts

jaccard_matrix.ijm

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