# segmentation.py

# ===============

#

# particle analysis on the GPU

#

# Author: Robert Haase, [email protected]

# October 2019

#########################################

from ij import IJ;

from net.haesleinhuepf.clij2 import CLIJ2;

IJ.run("Close All");

# load example image

imp = IJ.openImage("http://wsr.imagej.net/images/blobs.gif");

IJ.run(imp, "32-bit", "");

imp.show();

# init GPU

clij2 = CLIJ2.getInstance();

# push image to GPU

input = clij2.push(imp);

# reserve memory for output, same size and type as input

blurred = clij2.create(input);

thresholded = clij2.create(input);

labelled = clij2.create(input);

labelled_without_edges = clij2.create(input);

# blur, threshold and label the image

clij2.blur(input, blurred, 5, 5, 0);

clij2.automaticThreshold(blurred, thresholded, "Otsu");

clij2.connectedComponentsLabeling(thresholded, labelled);

clij2.excludeLabelsOnEdges(labelled, labelled_without_edges);

# show result

clij2.show(labelled_without_edges, "labelled_without_edges");

IJ.run("glasbey");

# clean up

clij2.clear();