Mercurial > repos > imgteam > coordinates_of_roi

comparison coordinates_of_roi.py @ 1:ee045a6bbdef draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit 4efef27bbe105490fc125e3586024ebb51fa929f
author imgteam
date Fri, 22 Feb 2019 17:11:28 -0500
parents 0d30ffea8874
children 24d9bd16c953
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0:0d30ffea8874 1:ee045a6bbdef
8 data = skimage.io.imread(im) 8 data = skimage.io.imread(im)
9 if len(data.shape) == 3 and data.shape[-1] > 1: 9 if len(data.shape) == 3 and data.shape[-1] > 1:
10 data = skimage.color.rgb2grey(data) 10 data = skimage.color.rgb2grey(data)
11 x = [] 11 x = []
12 y = [] 12 y = []
13 for i in range(data.shape[0]): 13 img_height = data.shape[0]
14 for j in range(data.shape[1]): 14 img_width = data.shape[1]
15 for j in range(img_width):
16 for i in range(img_height):
15 if white_obj == False: 17 if white_obj == False:
16 if data[i,j] <= threshold: 18 if data[i,j] <= threshold:
17 x.append(j + offset[0]) 19 x.append(j + offset[0])
18 y.append(i + offset[1]) 20 y.append(img_height-(i+1) + offset[1])
19 elif data[i,j] >= threshold: 21 elif data[i,j] >= threshold:
20 x.append(j + offset[0]) 22 x.append(j + offset[0])
21 y.append(i + offset[1]) 23 y.append(img_height-(i+1) + offset[1])
22 24
23 df = pd.DataFrame() 25 df = pd.DataFrame()
24 df['x'] = x 26 df['x'] = x
25 df['y'] = y 27 df['y'] = y
26 df.to_csv(pixel_table, sep="\t", index = False) 28 df.to_csv(pixel_table, sep="\t", index = False)