Batch processing template for Fiji with Jython

batch.py

# Example of Fiji script for batch processing.

import csv


# Stub
# You can put whatever opearations you want to apply.
def get_radialprofile(imp, cx, cy, r, num_bin)
    return None


def process(filename, cx, cy, r, num_bin):
    imp = IJ.openImage(filename)
    if imp is None:
        print "Could not open image from file:", filename
        return None
    else:
        return get_radialprofile(imp, cx, cy, r, num_bin)

# Assume the CSV file has five columns: file path, cx, cy, r, # of bins
infile = 'recipe.csv'

# Open a csv file. csvfile keeps a "file handle".
csvfile = open(infile, 'rb')
# Any error happening inside try block does not stop the execution of script.
try:
    # reader is used for reading a csv line by line.
    reader = csv.reader(csvfile)
    reader.next()   # Skip the first row
    for row in reader:
        if len(row) >= 5:
            # '*' operator expands a list to arguments to a function.
            profile = process(row[0], *map(int, row[1:5]))
            print ",".join(map(str, profile))
# finally block is executed in the end no matter if an error occurs or not.
finally:
    csvfile.close()