div_thresh_overlay.py
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	from skimage import io
	import numpy as np
	import cv2

	#path = 'div_2_170608_fly1_007/div_l1000g0'
	#path = 'div_4_170609_fly1_000/div_l1000g0'
	path = 'div_1_170426_fly1_013/div_l1000g0'

	paths = ['/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l100g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l200g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l300g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l400g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l500g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l600g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l700g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l800g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l900g10',
	'/mnt/internal_hdd/aymanns/Chen2018/divergence/div_2_170608_fly1_007/div_l1000g10']

	for path in paths:

	div = io.imread(path+'/div_out.tif')

	#wapred1 = io.imread(path+'/warped1.tif')

	mask = np.where(div<-1.2)

	z = np.zeros(div.shape,dtype=np.uint8)
	z[mask] = 255
	io.imsave(path+'/thresh_div.tif',z.astype(np.float32))

	artefact = False
	for i in range(len(z)):
	#print(z[i])
	output = cv2.connectedComponentsWithStats(z[i],8,cv2.CV_32S)
	#print(output[2])
	stats = output[2]
	if np.any(stats[1:,cv2.CC_STAT_AREA]>20):
	print(i,stats)
	artefact = True
	break

	print(path,artefact)