fiji_stats.py

# Example of Fiji script for taking statistics of every stack in a stack file.
# Statistics of 3 ROIs are taken for every stack.

from ij import IJ
from ij.process import ImageStatistics as IS
# import os

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


def get_statistics(imp):
    # Return statistics for the given ImagePlus
    global options
    ip = imp.getProcessor()
    stats = IS.getStatistics(ip, options, imp.getCalibration())
    return stats.mean, stats.median, stats.min, stats.max, stats.area

filename = "image.tif"
rois = [[56, 55, 13, 13],
    [51, 82, 15, 7],
    [92, 58, 7, 13]]


def get_framestat(imp, i):
    imp.setSlice(i)
    mean, median, min, max,area = get_statistics(imp)
    return mean,median,min,max,area

# print "Processing", filename
imp = IJ.openImage(filename)
if imp is None:
    print "Could not open image from file:", filename
else:
    n = imp.getNFrames()
    for i in range(1,n+1):
        imp.setRoi(*rois[0])
        mean, median, min, max, area = get_framestat(imp,i)
        imp.setRoi(*rois[1])
        mean2, median2, min2, max2, area2 = get_framestat(imp,i)
        imp.setRoi(*rois[2])
        mean3, median3, min3, max3, area3 = get_framestat(imp,i)
        print mean, "\t", mean2, "\t", mean3