images_to_frames_stack.py

#@File (label="Images folder", style="directory") imgdir
#@String (label="Images extension", value=".tif") ext
#@Boolean (label="Save the stack?") save
#@String (visibility=MESSAGE, value="Select save if you want to keep to stack containing the images to be traced on disk.") msg


# Bootstrap to extend modules search path #
from sys import path
import os.path
from java.lang.System import getProperty
jython_scripts = os.path.join(getProperty('user.home'), 'Jython_scripts')
path.append(jython_scripts)
#=========================================#

from IBPlib.ij.Utils.Files import buildList
from  IBPlib.ij.Utils import ThreadedFileSaver

from ij import (IJ, ImagePlus, ImageStack)
from ij.plugin import ZProjector

def images_to_frames_stack(imgdir, savestack=False):
	'''
	Method for preparing a stack of frames using images inside the input folder.
	When savestack is true it saves the resulting stack to the images folder while opening the stack.
	'''
	title = "tracing_stack.tiff" # Title of the final image stack.
	imgdir = imgdir.getPath()
	imglist = buildList(imgdir, ext)
	if not imglist:
		raise IOError("No {0} were found in {0}.".format(ext, imgdir))
	method = "max"
	implist = []
	for img in imglist:
		imp = ImagePlus(img)
		if imp.isStack():
			imp = ZProjector.run(imp, method)
		implist.append(imp)
	stack = ImageStack(
		implist[0].getWidth(),
		implist[0].getHeight())
	[stack.addSlice(img.getProcessor()) for img in implist]
	stackimp = ImagePlus(title, stack)
	IJ.run(stackimp, "Properties...", "slices=1 frames={0}".format(stackimp.getStackSize()))
	if savestack:
		IJ.log("# Saving tracing stack...")
		save_string = os.path.join(imgdir, title)
		fs = ThreadedFileSaver.ThreadedFileSaver(stackimp, save_string, "saveAsTiff")
		fs.start()
	stackimp.show()


if __name__ in ("__builtin__", "__main__"):
	images_to_frames_stack(imgdir, save)