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.

Thus, afterwards number of labels and maximum label index are equal. This operation is mostly performed on the CPU.

Category: Labels

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_closeIndexGapsInLabelMap(Image labeling_input, Image labeling_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 labeling_input = clij2.push(labeling_inputImagePlus);
labeling_destination = clij2.create(labeling_input);

// Execute operation on GPU
clij2.closeIndexGapsInLabelMap(labeling_input, labeling_destination);

// show result
labeling_destinationImagePlus = clij2.pull(labeling_destination);
labeling_destinationImagePlus.show();

// cleanup memory on GPU
clij2.release(labeling_input);
clij2.release(labeling_destination);

Matlab

% init CLIJ and GPU
clij2 = init_clatlab();

% get input parameters
labeling_input = clij2.pushMat(labeling_input_matrix);
labeling_destination = clij2.create(labeling_input);

% Execute operation on GPU
clij2.closeIndexGapsInLabelMap(labeling_input, labeling_destination);

% show result
labeling_destination = clij2.pullMat(labeling_destination)

% cleanup memory on GPU
clij2.release(labeling_input);
clij2.release(labeling_destination);

Icy JavaScript

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

clij2 = CLICY.getInstance();

// get input parameters
labeling_input_sequence = getSequence();
labeling_input = clij2.pushSequence(labeling_input_sequence);
labeling_destination = clij2.create(labeling_input);

// Execute operation on GPU
clij2.closeIndexGapsInLabelMap(labeling_input, labeling_destination);

// show result
labeling_destination_sequence = clij2.pullSequence(labeling_destination)
Icy.addSequence(labeling_destination_sequence);
// cleanup memory on GPU
clij2.release(labeling_input);
clij2.release(labeling_destination);

clEsperanto Python (experimental)

import pyclesperanto_prototype as cle

cle.close_index_gaps_in_label_map(labeling_input, labeling_destination)

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