mquant.txt

// vim: set filetype=javascript :

macro "mquant" {
    setBatchMode(true);
    mquant();
}

function mquant() {
    FS = File.separator();
    title =getTitle();
    path = getDirectory("image");
    selection_path = path+"selections"+FS;

    selections = getFileList(selection_path);

    close();
    open(path+title);

    f = File.open(path+"mquant_results.txt");
    print(f, "slice\tcell\tcen_x\tcen_y\tx\ty\tint");
    for (i=1;i<=nSlices();i++) {
        setSlice(i);
        roiManager("reset");
        roiManager("open",selection_path+i+".zip");
        nSels = roiManager("count");
        for (j=0;j<nSels;j++) {
            roiManager("select",j);
            List.setMeasurements;
            cx = List.getValue("X");
            cy = List.getValue("Y");
            // Pixels returned by getSelectionCoordinates are around outside of
            // visible selection.
            run("Enlarge...", "enlarge=-2 pixel");
            getSelectionCoordinates(x, y);
            for (k=0;k<x.length;k++) {
                this_bound = new Array(x[k],y[k]);
                if (k+1 != x.length) {
                    next_bound = new Array(x[k+1],y[k+1]);
                }
                // getSelectionCoordinates returns the set of pixels sufficient
                // to define the selection boundary.  We want to walk along the
                // entire boundary.  Either the 'x' or 'y' coordinate will be the
                // same from one boundary defining point to the next.
                if (this_bound[0] != next_bound[0]) {
                    pix = new Array(this_bound[0], next_bound[0]);
                } else if (this_bound[1] != next_bound[1]) {
                    pix = new Array(this_bound[1], next_bound[1]);
                }

                // Step through this array and get the maximum pixel value in a
                // 4-connected neighborhood.
                for (l=pix[0];l<pix[1];l++) {
                    I = maxOf(maxOf(maxOf(maxOf(getPixel(x[k],y[k]),getPixel(x[k]+1,y[k])),getPixel(x[k],y[k]+1)),getPixel(x[k]-1,y[k])),getPixel(x[k],y[k]-1));
                }
                print(f, i+"\t"+j+1+"\t"+cx+"\t"+cy+"\t"+x[k]+"\t"+y[k]+"\t"+I);
            }
        }
    }
    run("Select None");
    File.close(f);
}