fix_he_exhibit.py

#!/usr/bin/python

import argparse
import re
from shutil import copy
import os
import json

parser = argparse.ArgumentParser()
parser.add_argument('input',
                    type=str,
                    help='the file to parse the headers of ')

args = parser.parse_args()

with open(args.input, 'r') as f:
    input=f.read()

pattern = r'(Groups.+Name\"\:\ \")(.*?)(\"\,.*?,)(.*?\]\}\])'

to_insert =  ' "Colors": ["6000a0","d030d0"], "Channels": ["Hematoxylin","Eosin"]}]'

replacement_string = '\\1' + 'H&E' + '\\3' + to_insert

fix = re.sub(pattern, replacement_string, str(input))

newname = args.input + '.bak' 
copy(args.input, newname)

with open(args.input, 'w', encoding='utf-8') as f:
    f.write(fix)