Simple radial profile analysis for Fiji with Jython

radial_profile.py

# Example of Fiji script for calculating a radial profile.

from ij import IJ
from ij.process import ImageStatistics as IS
from ij.gui import Roi, OvalRoi


# Get mean pixel intensity in a specified donut-shaped area
def get_mean_in_donut(imp, cx, cy, min_r, max_r):
    options = IS.MEAN | IS.MEDIAN | IS.MIN_MAX | IS.AREA
    ip = imp.getProcessor()
    # Define two ROIs. One is outer diameter. Another is inner diameter.
    roi_small = OvalRoi(cx-min_r, cy-min_r, min_r*2+1, min_r*2+1)
    roi_big = OvalRoi(cx-max_r, cy-max_r, max_r*2+1, max_r*2+1)
    imp.setRoi(roi_small)
    stats_small = IS.getStatistics(ip, options, imp.getCalibration())
    imp.setRoi(roi_big)
    stats_big = IS.getStatistics(ip, options, imp.getCalibration())
    # Subtract integrated intensity of inner circle from that of outer circle, and divide it by the area.
    return (stats_big.mean * stats_big.area - stats_small.mean * stats_small.area) / (stats_big.area - stats_small.area)


# Getting a radial profile.
def get_radialprofile(imp, cx, cy, rmax, num_bin):
    r_interval = rmax / num_bin
    rs = [(i*r_interval, (i+1)*r_interval) for i in range(num_bin)]
    return [get_mean_in_donut(imp, cx, cy, r[0], r[1]) for r in rs]

# Starting point of the script
imp = IJ.getImage()
if not imp is None:
    profile = get_radialprofile(imp, 300, 200, 100, 10)
    print ",".join(map(str, profile))