R6289/div_thresh_overlay.py
05139327dccemaster

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)