# Batch extension for Kotas dot segmenting script PreProcessing!

# by Christoph Schiklenk (schiklen@embl.de)

# with help of Kota Miura, CMCI (miura@embl.de)

from os import listdir, makedirs

from os import path as pth

import re

from ij.plugin.filter import Filler as CO

from emblcmci.foci3Dtracker import PreprocessChromosomeDots as PPC

from ij.plugin import ChannelSplitter as CS

from ij.plugin import RGBStackMerge as StackMerge

from ij.io import DirectoryChooser, Opener

from ij.process import ImageConverter

from ij import IJ, WindowManager

G_saveSubFold = "ppcd"

G_saveFilePrefix = "ppcd_"

#- - - M A I N - - -

# select directory that is to be processed

path = DirectoryChooser("DotSeg Preprocess Batch Extension - Please choose directory containing the images").getDirectory()

saveFolder = pth.join(pth.split(pth.dirname(path))[0], G_saveSubFold)

# create list of match objects of .tiff files in directory

regEx = re.compile('(?!ppcd_)(?P<prefix>.+).tiff?$', re.IGNORECASE)

moFileList = [] # match object File list

for fileName in listdir(path):

if regEx.match(fileName): # if matches RE, add to list

moFileList.append(regEx.match(fileName))

if moFileList == []:

IJ.showMessage("Input Exception", "No unprocessed images found in the directory you selected.")

raise IOError("No unpocessed TIFFs found in this folder.")

for image in moFileList:

print "Processing cell " + image.group() + " (" + str(moFileList.index(image)+1) + "/" + str(len(moFileList)) + ")"

IJ.log("Processing cell " + image.group() + " (" + str(moFileList.index(image)+1) + "/" + str(len(moFileList)) + ")")

imp = Opener().openImage(path + image.group()) # open Image

#if imp.getBitDepth() != 8: # converting to 8 bit if

# ImageConverter(imp).convertToGray8()

roi = imp.roi

imps = CS.split(imp)

ppc = PPC()

for aimp in imps:

ppc.setImp(aimp)

ppc.run()

if roi != None:

aimp.setRoi(roi)

for n in range(1, aimp.getImageStackSize()+1):

aimp.getImageStack().getProcessor(n).fillOutside(roi)

aimp.killRoi()

final = StackMerge.mergeChannels(imps, False)

final.copyScale(imp) # copyscale from .copyscale

if not pth.exists(saveFolder):

makedirs(saveFolder)

fileName = G_saveFilePrefix + image.group('prefix')

IJ.saveAs(final, ".tiff", pth.join(saveFolder, fileName) ) # saveAs(ImagePlus imp, java.lang.String format, java.lang.String path)

print "Successfully saved", G_saveFilePrefix + image.group('prefix')

IJ.log("Successfully saved " + G_saveFilePrefix + image.group('prefix') + ".tif")

for win in WindowManager.getIDList():

imp = WindowManager.getImage(win)

imp.close()

print "Finished."

IJ.log("Finished pre-processing.")