JACoP Fiji Colocalization Automation

JACoP_Auto_.py

from ij import IJ
from ij import WindowManager as wm
from ij import ImagePlus
import time

def open_file_dialogue(window_title="", path_restriction=None):
	"""
	Opens a file dialogue and returns the path to the chosen file.
	Returns None on an invalid file or dialogue cancellation (prints to log).
	window_title will appear in the file dialogue window title.
	path_restriction will restrict file choices to a certain directory
	This is a blocking function.
	"""
	od = OpenDialog(window_title, path_restriction)
	if od.getFileName():
		return od.getDirectory() + od.getFileName()
	else:
		print "Dialogue cancelled or no File?"
		return None

def open_img(filename):
	"""
	Opens and shows the selected image.
	Returns the image on success, otherwise it returns None and
	prints to the log.
	"""
	try:
		img = IJ.openImage(filename)
		img.show()
		return img
	except Exception:
		print "Couldn't open ImagePlus of %s" % filename
		return None

def init_files():
	"""
	Initializes our two image files for object colocalization.
	Presents dialogues and shows the selected files.
	Returns a pair - (dendrite_img, psd_img)
	"""
	fn_dendrite = open_file_dialogue("Choose your dendrite image (CaMKII extension)", None)
	fn_psd = open_file_dialogue("Choose your marker image (PSD extension)", None)

	dendrite_img = open_img(fn_dendrite)
	psd_img = open_img(fn_psd)

	return (dendrite_img, psd_img)

def clean_up(*args):
	"""
	Assumes these are all images.
	Closes/Hides them from the viewport so as to not interfere
	with future JACoP runs.
	"""
	for img in args:
		img.hide()
		img.changes = False  # prevents a file save dialogue from popping up
		img.close()

def fill_selection(img):
	# select our image (for the autocrop macro)
	IJ.selectWindow(img.getID())
	ip = img.getProcessor()
	ip.setRoi(img.getRoi())
	ip.setColor(0)	# sets to black
	ip.fillOutside(img.getRoi())
	IJ.run("Auto Crop")
	img.updateAndDraw()

def dendrite_select_wait(dendrite_img):
	"""
	Non-Blocking call to wait for user to select a dendrite.
	"""
	IJ.setTool("freehand")
	IJ.selectWindow(dendrite_img.getID())
	WaitForUserDialog("Select your dendrite in your CaMKII image.").show()

def crop_mask_selection(selected, other):
	"""
	Mask and crop out our images based on the selection in selected image.
	"""
	other.setRoi(selected.getRoi())
	fill_selection(selected)
	fill_selection(other)

def show_instructions():
	WaitForUserDialog("Check only object based methods. Set Image A to PSD and Image B to CaMKII. Set the appropriate thresholds. Finally, in obj. tab set geometrical centre, show full table, and work on centres-particle coincidence.").show()

def __main__():
	dendrite_img, psd_img = init_files()
	# TODO: Image subtraction step with calibration image
	
	# Get a selection 
	# TODO: Automatically highlight dendrite candidates and click to select.
	# Treat each dendrite selected as a seperate image.
	dendrite_select_wait(dendrite_img)
	crop_mask_selection(dendrite_img, psd_img)

	# TODO: Supply possible params here
	# thresholding should be manual
	jacop = IJ.runPlugIn("JACoP_", "")
	show_instructions()
	
	results = IJ.getLog()
	IJ.append(results, "./output-%s.log" % (time.asctime( time.localtime(time.time()) )))

	for im_id in wm.getIDList():
		if "(Geometrical centres)" in wm.getImage(im_id).getWindow().getTitle():
			IJ.save(wm.getImage(im_id), "./output-%s.tif" % (time.asctime( time.localtime(time.time()) )))
	
	clean_up(dendrite_img, psd_img)

__main__()