Fiji script: Cropping by csv files of ROIs

crop_and_merge.py

from ij import IJ, ImagePlus, ImageStack, WindowManager

from ij.plugin import ContrastEnhancer,StackCombiner,ImageCalculator
from ij.process import ImageConverter, ImageProcessor
from time import sleep
import csv

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141103/05-A FC4 488 568/"


def crop(imp,x,y,w,h):
    imp.setRoi(x,y,w,h)
    ip = imp.getProcessor()
    return ip.crop(),imp


def process(count,imp1,imp2, x, y, w, h):
    output = folder+"out/test_"+str(count)+"_488.tiff"
    ip,imp = crop(imp1,x,y,w,h)
    ContrastEnhancer().stretchHistogram(ip,0.35)
    imp = ImagePlus("488",ip)
    IJ.save(imp,output)
    ImageConverter(imp).convertToRGB()
    ip = imp.getProcessor()
    
    output = folder+"out/test_"+str(count)+"_561.tiff"
    ip2,imp2 = crop(imp2,x,y,w,h)
    ContrastEnhancer().stretchHistogram(ip2,0.35)
    imp2 = ImagePlus("561",ip2)
    IJ.save(imp2,output)

    imp3 = ImageCalculator().run("Add create", imp,imp2);

    st = ImageStack(w,h)
    st.addSlice(ip)
    st2 = ImageStack(w,h)
    st2.addSlice(ip2)
    st3 = ImageStack(w,h)
    st3.addSlice(imp3.getProcessor())
    ip4 = StackCombiner().combineHorizontally(st,st2)             
    ip5 = StackCombiner().combineHorizontally(ip4,st3)             
    output = folder+"out/test_"+str(count)+"_merge.tiff"
    IJ.save(ImagePlus("merge",ip5),output)
 
# Assume the CSV file has five columns: file id, x, y, width, height
infile = folder + 'rois.csv'
 
csvfile = open(infile, 'rb')

try:
    # reader is used for reading a csv line by line.
    reader = csv.reader(csvfile)
    reader.next()   # Skip the first row
    count = 0
    prev = None
    imp = None
    imp2 = None
    for row in reader:
        if len(row) >= 5:
            count += 1
            if count > 4:
                pass
#                 break
            if prev != row[0]:
                IJ.run('Close All')
                imp = IJ.openImage(folder + "fixed_"+row[0]+"_488.tif")
                imp2 = IJ.openImage(folder + "fixed_"+row[0]+"_561.tif")
                process(count,imp,imp2, *map(int, row[1:5]))
            else:
                process(count,imp,imp2, *map(int, row[1:5]))
        	prev = row[0]
            
# finally block is executed in the end no matter if an error occurs or not.
finally:
    csvfile.close()