Fiji script: Crop confocal images (2 channels)

crop_confocal.py

from ij import IJ,ImagePlus
from ij.process import ColorProcessor
from ij.plugin import ContrastEnhancer
import csv

folder = "/Volumes/Macintosh HD/Google Drive/Groves/Scope 7/20141126 Immunostaining/"

def crop(imp,x,y,w,h):
    imp.setRoi(x,y,w,h)
    st = imp.getStack()
    n = st.getSize()
    m = n / 2      
    return st.crop(x,y,0,w,h,n),st

def process(count,imp,x,y,w,h):
    st,orig = crop(imp,x,y,w,h);
    imp2 = ImagePlus("stack",st)
    IJ.run(imp2,"Stack to Hyperstack...", "order=xyzct channels=2 slices=29 frames=1 display=Color");
    imp3 = IJ.getImage()
    imp3.setC(2);
    ContrastEnhancer().stretchHistogram(imp3.getStack().getProcessor(1),0.35)
    IJ.run(imp3,"Cyan","");
    #imp3.show()
    IJ.save(imp3,folder+"01A 02 confocal/out_"+str(count)+".tiff")


# Assume the CSV file has five columns: file id, x, y, width, height
infile = folder + '01A rois.csv'
csvfile = open(infile, 'rb')
maxProcess = 1000

try:
    # reader is used for reading a csv line by line.
    reader = csv.reader(csvfile)
    reader.next()   # Skip the title row
    count = 0
    prev = None
    imp = None
    for row in reader:
        if len(row) >= 5:
            count += 1
            if count > maxProcess:
               break
            if prev != row[0]:
                IJ.run('Close All')
                path = folder + "01 FC4 of 1125/02 tirf and confocal/confocal_"+row[0]+"/Pos0"
                print(path)
                print(count)
                IJ.run("Image Sequence...", "open=["+path+"] sort");
                imp = IJ.getImage()
                prev = row[0]
                process(count, imp, *map(int, row[1:5]))
            else:
                print(count)
                prev = row[0]
                process(count, imp, *map(int, row[1:5]))
            
# finally block is executed in the end no matter if an error occurs or not.
finally:
    csvfile.close()
    IJ.run('Close All')