ImageJ TiFF Stack Reader

tif.py

import sys,os,csv
from pylab import *
from PIL import Image
import time
#from mayavi import mlab

#returns a list (length = 3)  of channels, each of which is a list (length = Z stack depth) of images
def getImages(fN):
	returnArr= [ [], [], [] ]
	tiff = Image.open(fN)
	i = 0
	while True:
		try:
			tiff.seek(i)
			npa = ndarray((tiff.size[1],tiff.size[0]),uint64,array(tiff.getdata()))
			returnArr[i%2].append(npa)
			i += 1
		except EOFError:
		    break
	return returnArr

#given a list of images, displays them
def showImages(inList):
	ion()
	#close()
	for p in inList:
		fig = figure()
		imshow(p,figure=fig,cmap='RdBu')
		colorbar()
		fig.canvas.draw()
		pause(0.01)
		#fig.canvas.flush_events()
	ioff()
	return 0

#given a list of images, computes statistics on them
def getStats(zS):
	zA = array(zS)
	zAF = array(zA.flatten())

	rStats = {}
	tzAF = zAF[zAF > 140]
	rStats['num140'] = tzAF.shape[0]
	rStats['prct140'] = 100 * tzAF.shape[0]/(1.0*zAF.shape[0])
	rStats['mean140'] = mean(tzAF)
	rStats['sum140'] = sum(tzAF)

	autoThresh = sorted(zAF)[int(zAF.shape[0]*0.95)]
	rStats['threshAuto'] = autoThresh
	tzAF = zAF[zAF > autoThresh]
	rStats['numAuto'] = tzAF.shape[0]
	rStats['prctAuto'] = 100 * tzAF.shape[0]/(1.0*zAF.shape[0])
	rStats['meanAuto'] = mean(tzAF)
	rStats['sumAuto'] = sum(tzAF)

	rStats['min'] = min(zAF)
	rStats['sum'] = sum(zAF)
	rStats['mean'] = mean(zAF)
	rStats['max'] = max(zAF)
	rStats['maxStack'] = where(zA == zA.max())[0][0]
	return rStats

if __name__ == "__main__":
	dirToProc = "./"
	statNames = sorted(getStats(array([0xffffff])).keys(), key=lambda sName: sName[::-1]) #use reverse sorted names
	
	if len(sys.argv) > 1:
		dirToProc = sys.argv[1]

	if dirToProc[-1] != '/':
		dirToProc += '/'

	if not os.path.isdir(dirToProc):
		raise IOError(dirToProc + " is not a valid directory") 

	with open(dirToProc + 'stats.csv','wb') as outFile:
		csvOut = csv.writer(outFile)
		csvOut.writerow(['Filename'] + statNames)
		for f in os.listdir(dirToProc):
			fb, e = os.path.splitext(f)
			if e != '.tif':
				continue
				#if '-' not in f:
				#continue
			try:
				zStack = getImages(dirToProc + f)
				#showImages(zStack[1])
				stats = getStats(zStack[1])		#only use the second channel

				csvOut.writerow([f] + [str(stats[n]) for n in statNames])
			except:
				pass