Cropping and showing images

crop_and_show.py

import requests
import keyring
import json
import csv

gist_images = 'XXXX'
gist_rois = 'YYYY'

username = 'ZZZZ'
password = keyring.get_password('Github API', username)
r = requests.get('https://api.github.com/gists/'+gist_images, auth=(username, password))
r2 = requests.get('https://api.github.com/gists/'+gist_rois, auth=(username, password))

def get_content(r):
	obj = json.loads(r.content)
	files = obj['files']
	k,file = files.items()[0]
	return file['content']

def parse_csv(str,convert=False):
	reader = csv.reader(str.splitlines(),delimiter='\t')
	hd = reader.next()
	print hd
	res = []
	for row in reader:
		r = {}
		for i, col in enumerate(row):
			if col != '':
				r[hd[i]] = float(col) if convert else col
		res.append(r)
	return res

def show_all(filelist, rois):
	for i,f in enumerate(filelist):
		idx = i + 1
		import matplotlib.pyplot as plt
		import tifffile
		img = tifffile.imread(f)
		rois2 = filter(lambda a: a['Slice'] == idx, rois)
		for r in rois2:
			img2 = img[r['BY']:r['BY']+r['Height'],r['BX']:r['BX']+r['Width']]
			plt.imshow(img2,cmap='gray')
			plt.show()

def main():
	filelist = get_content(r).splitlines()
	rois = parse_csv(get_content(r2), convert=True)
	show_all(filelist,rois)


main()