// meshTouchingNeighbors.ijm

//

// This macro shows how to generate a mesh between

// all points which are neighbors.

//

// Author: Robert Haase

// October 2019

// ---------------------------------------------

run("Close All");

// Get test data

run("Blobs (25K)");

input = getTitle();

getDimensions(width, height, channels, slices, frames);

blurred = "Blurred";

// Init GPU

run("CLIJ2 Macro Extensions", "cl_device=");

Ext.CLIJ2_clear();

// push images to GPU

Ext.CLIJ2_push(input);

// cleanup ImageJ

run("Close All");

// Blur in GPU

Ext.CLIJ2_gaussianBlur3D(input, blurred, 5, 5, 1);

Ext.CLIJ2_pull(blurred);

detected_spots = "detected_spots";

Ext.CLIJ2_detectMaximaBox(blurred, detected_spots, 3);

Ext.CLIJ2_pullBinary(detected_spots);

// get spot positions as pointlist

pointlist = "pointlist";

Ext.CLIJ2_spotsToPointList(detected_spots, pointlist);

Ext.CLIJ2_getSize(pointlist);

number_of_detected_spots = getResult("Width", nResults() - 1);

IJ.log("number of spots: " + number_of_detected_spots);

labelled_spots = "labelled_spots";

//Ext.CLIJ_copy(detected_spots, labelled_spots);

//Ext.CLIJ_set(labelled_spots, 0);

Ext.CLIJ2_connectedComponentsLabeling(detected_spots, labelled_spots);

Ext.CLIJ2_pull(labelled_spots);

temp = "temp";

for (i = 0; i < 20; i++) {

//print("hll wrld");

Ext.CLIJ2_onlyzeroOverwriteMaximumDiamond(labelled_spots, temp);

Ext.CLIJ2_onlyzeroOverwriteMaximumDiamond(temp, labelled_spots);

//Ext.CLIJ_maximum2DSphere(labelled_spots, temp, 1, 1);

//Ext.CLIJ_maximum2DSphere(temp, labelled_spots, 1, 1);

}

touch_matrix = "touch_matrix";

Ext.CLIJ2_generateTouchMatrix(labelled_spots, touch_matrix);

Ext.CLIJ2_pull(labelled_spots);

// empty results table

run("Clear Results");

// we build a table with 2+n rows:

// x and y of the points and n rows with indices to closes points.

// as every points is the closest to itself, row number 3 will always be 0, 1, 3, 4 ...

Ext.CLIJ2_image2DToResultsTable(pointlist);

Ext.CLIJ2_image2DToResultsTable(touch_matrix);

mesh = "mesh";

Ext.CLIJ2_create2D(mesh, width, height, 32);

Ext.CLIJ2_set(mesh, 0);

print("points: " + number_of_detected_spots);

for (p = 0; p < number_of_detected_spots; p++) {

x1 = getResult("X" + (p), 0);

y1 = getResult("X" + (p), 1);

// we start at 1 (and not at 0) because we

// don't want to draw line from the point

// to itself

for (q = p; q < number_of_detected_spots; q++) {

touching = getResult("X" + (p+1), 3 + q);

if (touching > 0) {

//print("hhh");

x2 = getResult("X" + (q), 0);

y2 = getResult("X" + (q), 1);

thickness = 1;

Ext.CLIJ2_drawLine(mesh, x1, y1, 0, x2, y2, 0, thickness, q);

}

}

}

// Get results back from GPU

Ext.CLIJ2_pull(labelled_spots);

Ext.CLIJ2_pull(touch_matrix);

Ext.CLIJ2_pull(mesh);

// Cleanup by the end

Ext.CLIJ2_clear();

Ext.CLIJ2_reportMemory();