Mercurial > repos > imgteam > coordinates_of_roi

comparison coordinates_of_roi.py @ 3:02a686fc1654 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
author imgteam
date Mon, 25 Mar 2019 11:15:39 -0400
parents 24d9bd16c953
children 00175f4a2bbb
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2:24d9bd16c953 3:02a686fc1654
12 y = [] 12 y = []
13 img_height = data.shape[0] 13 img_height = data.shape[0]
14 img_width = data.shape[1] 14 img_width = data.shape[1]
15 for j in range(img_width): 15 for j in range(img_width):
16 for i in range(img_height): 16 for i in range(img_height):
17 if white_obj == False: 17 if white_obj == False:
18 if data[i,j] <= threshold: 18 if data[i,j] <= threshold:
19 x.append(i + offset[0]) 19 x.append(i + offset[0])
20 y.append(j + offset[1]) 20 y.append(j + offset[1])
21 elif data[i,j] >= threshold: 21 elif data[i,j] >= threshold:
22 x.append(i + offset[0]) 22 x.append(i + offset[0])
29 29
30 if __name__=="__main__": 30 if __name__=="__main__":
31 parser = argparse.ArgumentParser(description = "Create a csv table with Coordinates of the ROI") 31 parser = argparse.ArgumentParser(description = "Create a csv table with Coordinates of the ROI")
32 parser.add_argument("im", help = "Paste path to out.png (output created by transformation)") 32 parser.add_argument("im", help = "Paste path to out.png (output created by transformation)")
33 parser.add_argument("pixel_table", help = "Paste path to file in which list with all pixles > threshold should be saved") 33 parser.add_argument("pixel_table", help = "Paste path to file in which list with all pixles > threshold should be saved")
34 parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0)
35 parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
36 parser.add_argument("--white_obj", dest = "white_obj", default=False, help = "If set objects in image are white otherwise black", action = "store_true") 34 parser.add_argument("--white_obj", dest = "white_obj", default=False, help = "If set objects in image are white otherwise black", action = "store_true")
37 parser.add_argument("--threshold", dest = "threshold", default = 0.5, help = "Enter desired threshold value", type = float) 35 parser.add_argument("--threshold", dest = "threshold", default = 0.5, help = "Enter desired threshold value", type = float)
38 36
39 args = parser.parse_args() 37 args = parser.parse_args()
40 # with warnings.catch_warnings(): 38 # with warnings.catch_warnings():
41 # warnings.simplefilter("ignore") 39 # warnings.simplefilter("ignore")
42 get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold, [args.offset_x, args.offset_y]) 40 get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold)