Radial plot scattergraph macro

[Michael Doube-2]

Dear list,

Here's a radial graph scatterplot macro that takes a csv list as input
(angle,length), then draws a scatterplot. It colours the points based on
how many neighbouring points lie within a given radius (in this example,
it's 20 pixels). Unfortunately, it goes really slowly, despite setting
batch mode - batch mode appears not to work in this script.

Any hints on how to make it go faster would be much appreciated.

Example data (c. 3000 points) here:  
ftp://wht-ogd-29.mds.qmw.ac.uk/pub/imagej/angles.csv

Cheers

Mike

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//Takes a CSV list of angles and values and draws a
//radial scattergraph
requires("1.37v");

//make it go faster
setBatchMode(true);

//Open the array file which must be a csv list in (angle, value \n) format
string = File.openAsString("");

//Split the CSV file into an array of lines
lines = split(string, "\n");

//initialise some variables
theta = newArray(lengthOf(lines));
r = newArray(lengthOf(lines));
rmax = 0;

//Find the maximum radius (to determine the outer boundary)
for (n=0; n<lengthOf(lines); n++){
    thetar= split(lines[n], "\,");
    theta[n] = parseFloat(thetar[0]);
    r[n] = parseFloat(thetar[1]);
    if (r[n] > rmax){
        rmax = r[n];
    }
}

radius = 500;
margin = 5;
image = 2*(radius+margin);

//Draw the new image
newImage("Untitled", "8-bit Black", 2*(radius+margin),2*(radius+margin), 1);
run("Orange Hot");
setColor(200);

//Draw the unit circle
drawOval(margin,margin,2*radius,2*radius);

//Draw axes
drawLine(0,radius+margin, 2*(radius+margin), radius+margin);  
drawLine(radius+margin,0, radius+margin, 2*(radius+margin));

//draw each point
for (n=0; n<lengthOf(lines); n++){
    setBatchMode(true);
    radtheta = theta[n]*2*PI / 360;
    unitr = r[n]/rmax;
    x = radius + margin + unitr*cos(radtheta)*radius;
    y = radius + margin - unitr*sin(radtheta)*radius;

//find out how many neighbours are within, say 20 pixels of our point
    neighbours = 0;
    for (p=0; p<lengthOf(lines); p++){
        setBatchMode(true);
        radtheta = theta[n]*2*PI / 360;
        punitr = r[p]/rmax;
        x1 = radius + margin + punitr*cos(radtheta)*radius;
        y1 = radius + margin - punitr*sin(radtheta)*radius;
        prox = sqrt((x-x1)*(x-x1)+(y-y1)*(y-y1));
       
        if(prox<20){
            neighbours=neighbours+1;
        }
    }

//find the colour of the pixel we will draw

    setColor(255);
//this bit needs to automatically spread the LUT to the observed densities.
//right now it doesn't.
    neighbours = neighbours / 3;
    if (neighbours<255){
    setColor(neighbours);
    print(neighbours);
    }
    fillRect(x,y,4,4);
}

//show us the plot
setBatchMode("exit and display");
-----------------

--
Michael Doube  BPhil BVSc MRCVS
PhD Student
Dental Institute
Queen Mary, University of London
New Rd
London  E1 1BB
United Kingdom

Phone [phone] ext 2681