fiji_radialprofile.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
import csv

options = IS.MEAN | IS.MEDIAN | IS.MIN_MAX | IS.AREA


def get_mean_in_donut(imp, cx, cy, min_r, max_r):
    global options
    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.
    return (stats_big.mean * stats_big.area - stats_small.mean * stats_small.area) / (stats_big.area - stats_small.area)


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]


def process(filename, cx, cy, r, num_bin):
    imp = IJ.openImage(filename)
    if imp is None:
        print "Could not open image from file:", filename
        return None
    else:
        return get_radialprofile(imp, cx, cy, r, num_bin)


# CSV file with five columns: file path, cx, cy, r, # of bins
infile = '/Users/hiroyuki/Documents/PycharmProjects/test/recipe.csv'

csvfile = open(infile, 'rb')
try:
    reader = csv.reader(csvfile)
    reader.next()   # Skip the first row
    for row in reader:
        if len(row) >= 5:
            profile = process(row[0], *map(int,row[1:5]))   # '*' operator expands a list to arguments to a function.
            print ",".join(map(str,profile))
        else:
            pass
finally:
    csvfile.close()