Fiji script: Time lapse of stitched images (conversion from (multipos,frames) to (frames))

stitch_timelapse.py

# 02A: Make time lapse of stitched image.

from ij import IJ, ImagePlus, ImageStack, WindowManager

from ij.plugin import ContrastEnhancer,StackCombiner,ImageCalculator
from ij.process import ImageConverter, ImageProcessor
from java.awt.image import IndexColorModel
from time import sleep
import csv
from jarray import zeros

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141204 T cells short time fix with live imaging/"

positions = [["4-Pos_000_000", "4-Pos_000_001", "4-Pos_000_002", "4-Pos_000_003"], ["4-Pos_001_000", "4-Pos_001_001", "4-Pos_001_002", "4-Pos_001_003"],
				["4-Pos_002_000", "4-Pos_002_001", "4-Pos_002_002", "4-Pos_002_003"], ["4-Pos_003_000", "4-Pos_003_001", "4-Pos_003_002", "4-Pos_003_003"]]

frames = map(lambda n: "img_000000"+"%03d"%(n)+"_RICM_000.tif", range(100))


def mk_stack(ips,w,h):
	res = ImageStack(w,h)
	for ip in ips:
		res.addSlice(ip)
	return ImagePlus("frames",res)


def combine_multiple(w,h,ip):
    res = ImageStack(w,h)
    res.addSlice(ip[0])
    for ip in ip[1:]:
        st = ImageStack(w,h)
        st.addSlice(ip)
        res = StackCombiner().combineHorizontally(res,st)
    return res


def combine_multiple_v(w,h,ip):
    res = ImageStack(w,h)
#    print(ip[0])
    res.addSlice(ip[0])
    for ip in ip[1:]:
        st = ImageStack(w,h)
        st.addSlice(ip)
        res = StackCombiner().combineVertically(res,st)
    return res


#files: 2D list of file paths.
def stitch(files):
	w = 200
	h = 200
	xlen = len(files[0])
	rows = []
	for row in files:
		ips = []
		for f in row:
			imp = IJ.openImage(f)
			ip = imp.getProcessor()
			ips.append(ip.resize(w))
		st = combine_multiple(w,h,ips)
		rows.append(st.getProcessor(1))
	res = combine_multiple_v(w*xlen,h,rows).getProcessor(1)
#	ImagePlus("test",res).show()
	return res


def main():
	maxProcess = 1000
	count = 0
	imgs = []
	for fr in frames:
		count += 1
		print(count)
		if count > maxProcess:
			break
		files = [[folder + '02 FC1/tirf_2/' + pos + '/' + fr for pos in row] for row in positions]
		imgs.append(stitch(files))
	im = mk_stack(imgs,800,800)
	outpath = folder + "02A stitched frames/" + 'out.tif'
	print(outpath)
	IJ.save(im,outpath)


if __name__ == "__main__":
	main()