Mercurial > repos > imgteam > detection_viz
annotate detection_viz.py @ 4:99433164b593 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author | imgteam |
---|---|
date | Mon, 13 Nov 2023 22:11:04 +0000 |
parents | cb2d9de888a1 |
children |
rev | line source |
---|---|
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
1 import argparse |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
2 import csv |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
3 |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
4 import matplotlib |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
5 import matplotlib.pyplot as plt |
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
6 import skimage.io |
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
7 |
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
8 |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
9 matplotlib.use('Agg') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
10 |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
11 |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
12 def plot_circles(file_name, ax, color, stroke_size, radius): |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
13 resfile = open(file_name, 'rb') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
14 rd = csv.reader(resfile, delimiter=',') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
15 for row in rd: |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
16 circ = plt.Circle((int(row[1]), int(row[0])), lw=stroke_size, radius=radius, color=color, fill=False) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
17 ax.add_patch(circ) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
18 resfile.close() |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
19 |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
20 |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
21 def detection_viz(input_file, output_file, tp=None, fn=None, fp=None, stroke_size=3, circle_radius=50): |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
22 img = skimage.io.imread(input_file) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
23 |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
24 fig = plt.figure(figsize=(40, 40)) |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
25 ax = fig.add_axes([0, 0, 1, 1]) |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
26 ax.axis('off') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
27 |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
28 plt.imshow(img) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
29 if tp is not None: |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
30 plot_circles(tp, ax, '#00FF00', stroke_size, circle_radius) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
31 if fn is not None: |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
32 plot_circles(fn, ax, 'red', stroke_size, circle_radius) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
33 if fp is not None: |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
34 plot_circles(fp, ax, 'darkorange', stroke_size, circle_radius) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
35 |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
36 fig.canvas.print_png(output_file, dpi=1800) |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
37 |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
38 |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
39 if __name__ == "__main__": |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
40 parser = argparse.ArgumentParser() |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
41 parser.add_argument('input_file', type=argparse.FileType('r'), help='original file') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
42 # output file should not be of type argparse.FileType('w') sine it is created immediately in this case which leads to an error in renaming |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
43 parser.add_argument('out_file_str', type=str, help='string of output file name') |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
44 parser.add_argument('--tp', dest='input_tp_file', type=argparse.FileType('r'), help='input TP file') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
45 parser.add_argument('--fn', dest='input_fn_file', type=argparse.FileType('r'), help='input FN file') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
46 parser.add_argument('--fp', dest='input_fp_file', type=argparse.FileType('r'), help='input FP file') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
47 parser.add_argument('--stroke_size', dest='thickness', default=3, type=float, help='stroke thickness') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
48 parser.add_argument('--circle_radius', dest='circle_radius', type=float, default=50, help='circle radius') |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
49 args = parser.parse_args() |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
50 |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
51 tp = None |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
52 if args.input_tp_file: |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
53 tp = args.input_tp_file.name |
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
54 fn = None |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
55 if args.input_fn_file: |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
56 fn = args.input_fn_file.name |
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
57 fp = None |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
58 if args.input_fp_file: |
4
99433164b593
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents:
3
diff
changeset
|
59 fp = args.input_fp_file.name |
0
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
60 |
3f738d5d91bf
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff
changeset
|
61 detection_viz(args.input_file.name, args.out_file_str, tp=tp, fn=fn, fp=fp, stroke_size=args.thickness, circle_radius=args.circle_radius) |