Fiji image statistics example

statistics-fiji.py

from ij import IJ
from ij.process import ImageStatistics as IS
import os
 
options = IS.MEAN | IS.MEDIAN | IS.MIN_MAX | IS.AREA
 
 
def getStatistics(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
 
 
# Folder to read all images from:
filename = "input.tif"
roi1 = [56,55,13,13]
roi2 = [51,82,15,7]
roi3 = [92,58,7,13]
 
 
def getFrameStat(imp,i):
	imp.setSlice(i)
	mean, median, min, max,area = getStatistics(imp)
	return mean,median,min,max,area
 
imp = IJ.openImage(filename)
if imp is None:
    print "Could not open image from file:", filename
else:
#      mean, median, min, max = getStatistics(imp)
    n = imp.getNFrames()
    for i in range(1,n+1):
        imp.setRoi(*roi1)
        mean,median,min,max,area = getFrameStat(imp,i)
        imp.setRoi(*roi2)
        mean2,median2,min2,max2,area2 = getFrameStat(imp,i)
        imp.setRoi(*roi3)
        mean3,median3,min3,max3,area3 = getFrameStat(imp,i)
        print mean,"\t",mean2,"\t",mean3