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comparison run-superdsm.py @ 3:7fd8dba15bd3 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
author imgteam
date Thu, 16 Nov 2023 12:29:41 +0000
parents 244f67290d28
children dc5f72f6b1e9
comparison
equal deleted inserted replaced
2:244f67290d28 3:7fd8dba15bd3
5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT 5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
6 6
7 """ 7 """
8 8
9 import argparse 9 import argparse
10 import csv
10 import imghdr 11 import imghdr
11 import os 12 import os
12 import pathlib 13 import pathlib
13 import shutil 14 import shutil
14 import tempfile 15 import tempfile
43 if value is not None: 44 if value is not None:
44 cfg[key] = value 45 cfg[key] = value
45 return cfg 46 return cfg
46 47
47 48
49 def flatten_dict(d, sep='/'):
50 result = {}
51 for key, val in d.items():
52 if isinstance(val, dict):
53 for sub_key, sub_val in flatten_dict(val, sep=sep).items():
54 result[f'{key}{sep}{sub_key}'] = sub_val
55 else:
56 result[key] = val
57 return result
58
59
48 if __name__ == "__main__": 60 if __name__ == "__main__":
49 parser = argparse.ArgumentParser(description='Segmentation of cell nuclei in 2-D fluorescence microscopy images') 61 parser = argparse.ArgumentParser(description='Segmentation of cell nuclei in 2-D fluorescence microscopy images')
50 parser.add_argument('image', help='Path to the input image') 62 parser.add_argument('image', type=str, help='Path to the input image')
51 parser.add_argument('cfg', help='Path to the file containing the configuration')
52 parser.add_argument('masks', help='Path to the file containing the segmentation masks')
53 parser.add_argument('overlay', help='Path to the file containing the overlay of the segmentation results')
54 parser.add_argument('seg_border', type=int)
55 parser.add_argument('slots', type=int) 63 parser.add_argument('slots', type=int)
64 parser.add_argument('--do-masks', type=str, default=None, help='Path to the file containing the segmentation masks')
65 parser.add_argument('--do-cfg', type=str, default=None, help='Path to the file containing the configuration')
66 parser.add_argument('--do-overlay', type=str, default=None, help='Path to the file containing the overlay of the segmentation results')
67 parser.add_argument('--do-overlay-border', type=int)
56 for key, ptype in hyperparameters: 68 for key, ptype in hyperparameters:
57 parser.add_argument('--' + get_param_name(key), type=ptype, default=None) 69 parser.add_argument('--' + get_param_name(key), type=ptype, default=None)
58 args = parser.parse_args() 70 args = parser.parse_args()
59 71
60 if args.slots >= 2: 72 if args.slots >= 2:
81 shutil.copy(str(args.image), img_filepath) 93 shutil.copy(str(args.image), img_filepath)
82 94
83 pipeline = superdsm.pipeline.create_default_pipeline() 95 pipeline = superdsm.pipeline.create_default_pipeline()
84 cfg = create_config(args) 96 cfg = create_config(args)
85 img = superdsm.io.imread(img_filepath) 97 img = superdsm.io.imread(img_filepath)
86 data, cfg, _ = superdsm.automation.process_image(pipeline, cfg, img)
87 98
88 with open(args.cfg, 'w') as fp: 99 if args.do_cfg:
89 cfg.dump_json(fp) 100 print(f'Writing config to: {args.do_cfg}')
101 cfg, _ = superdsm.automation.create_config(pipeline, cfg, img)
102 with open(args.do_cfg, 'w') as fp:
103 tsv_out = csv.writer(fp, delimiter='\t')
104 tsv_out.writerow(['Hyperparameter', 'Value'])
105 for key, value in flatten_dict(cfg.entries).items():
106 tsv_out.writerow([key, value])
90 107
91 overlay = superdsm.render.render_result_over_image(data, border_width=args.seg_border, normalize_img=False) 108 if args.do_overlay or args.do_masks:
92 superdsm.io.imwrite(args.overlay, overlay) 109 print('Performing segmentation')
110 data, cfg, _ = pipeline.process_image(img, cfg)
93 111
94 masks = superdsm.render.rasterize_labels(data) 112 if args.do_overlay:
95 superdsm.io.imwrite(args.masks, masks) 113 print(f'Writing overlay to: {args.do_overlay}')
114 overlay = superdsm.render.render_result_over_image(data, border_width=args.do_overlay_border, normalize_img=False)
115 superdsm.io.imwrite(args.do_overlay, overlay)
116
117 if args.do_masks:
118 print(f'Writing masks to: {args.do_masks}')
119 masks = superdsm.render.rasterize_labels(data)
120 superdsm.io.imwrite(args.do_masks, masks)