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annotate 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
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1 """
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2 Copyright 2023 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University.
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3
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4 Distributed under the MIT license.
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
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7 """
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8
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9 import argparse
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10 import csv
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11 import imghdr
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12 import os
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13 import pathlib
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14 import shutil
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15 import tempfile
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18 hyperparameters = [
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19 ('AF_scale', float),
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20 ('c2f_region_analysis/min_atom_radius', float),
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21 ('c2f_region_analysis_min_norm_energy_improvement', float),
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22 ('c2f_region_analysis_max_atom_norm_energy', float),
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23 ('c2f_region_analysis_max_cluster_marker_irregularity', float),
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24 ('dsm_alpha', float),
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25 ('dsm_AF_alpha', float),
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26 ('global_energy_minimization_betai', float),
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27 ('global_energy_minimization_AF_beta', float),
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28 ('postprocess_mask_max_distance', int),
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29 ('postprocess_mask_stdamp', float),
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30 ('postprocess_max_norm_energy', float),
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31 ('postprocess_min_contrast', float),
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32 ('postprocess_min_object_radius', float),
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33 ]
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34
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35
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36 def get_param_name(key):
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37 return key.replace('/', '_')
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38
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39
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40 def create_config(args):
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41 cfg = superdsm.config.Config()
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42 for key, _ in hyperparameters:
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43 value = getattr(args, get_param_name(key))
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44 if value is not None:
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45 cfg[key] = value
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46 return cfg
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47
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48
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49 def flatten_dict(d, sep='/'):
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50 result = {}
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51 for key, val in d.items():
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52 if isinstance(val, dict):
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53 for sub_key, sub_val in flatten_dict(val, sep=sep).items():
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54 result[f'{key}{sep}{sub_key}'] = sub_val
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55 else:
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56 result[key] = val
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57 return result
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58
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59
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60 if __name__ == "__main__":
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61 parser = argparse.ArgumentParser(description='Segmentation of cell nuclei in 2-D fluorescence microscopy images')
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62 parser.add_argument('image', type=str, help='Path to the input image')
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63 parser.add_argument('slots', type=int)
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64 parser.add_argument('--do-masks', type=str, default=None, help='Path to the file containing the segmentation masks')
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65 parser.add_argument('--do-cfg', type=str, default=None, help='Path to the file containing the configuration')
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66 parser.add_argument('--do-overlay', type=str, default=None, help='Path to the file containing the overlay of the segmentation results')
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67 parser.add_argument('--do-overlay-border', type=int)
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68 for key, ptype in hyperparameters:
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69 parser.add_argument('--' + get_param_name(key), type=ptype, default=None)
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70 args = parser.parse_args()
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71
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72 if args.slots >= 2:
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73 num_threads_per_process = 2
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74 num_processes = args.slots // num_threads_per_process
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75 else:
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76 num_threads_per_process = 1
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77 num_processes = 1
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78
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79 os.environ['MKL_NUM_THREADS'] = str(num_threads_per_process)
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80 os.environ['OPENBLAS_NUM_THREADS'] = str(num_threads_per_process)
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81
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82 import ray
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83 import superdsm.automation
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84 import superdsm.io
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85 import superdsm.render
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87 ray.init(num_cpus=num_processes, log_to_driver=True)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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88
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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89 with tempfile.TemporaryDirectory() as tmpdirname:
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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90 tmpdir = pathlib.Path(tmpdirname)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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91 img_ext = imghdr.what(args.image)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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92 img_filepath = tmpdir / f'input.{img_ext}'
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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93 shutil.copy(str(args.image), img_filepath)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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94
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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95 pipeline = superdsm.pipeline.create_default_pipeline()
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700ae37e5c69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 7db4b765fa5a1f526cc94cd1f65d963d1e047b27
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96 cfg = create_config(args)
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1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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97 img = superdsm.io.imread(img_filepath)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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98
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7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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99 if args.do_cfg:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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100 print(f'Writing config to: {args.do_cfg}')
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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101 cfg, _ = superdsm.automation.create_config(pipeline, cfg, img)
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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102 with open(args.do_cfg, 'w') as fp:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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103 tsv_out = csv.writer(fp, delimiter='\t')
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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104 tsv_out.writerow(['Hyperparameter', 'Value'])
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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105 for key, value in flatten_dict(cfg.entries).items():
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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106 tsv_out.writerow([key, value])
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1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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107
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7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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108 if args.do_overlay or args.do_masks:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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109 print('Performing segmentation')
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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110 data, cfg, _ = pipeline.process_image(img, cfg)
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1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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111
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7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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112 if args.do_overlay:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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113 print(f'Writing overlay to: {args.do_overlay}')
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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114 overlay = superdsm.render.render_result_over_image(data, border_width=args.do_overlay_border, normalize_img=False)
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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115 superdsm.io.imwrite(args.do_overlay, overlay)
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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116
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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117 if args.do_masks:
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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118 print(f'Writing masks to: {args.do_masks}')
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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119 masks = superdsm.render.rasterize_labels(data)
7fd8dba15bd3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit fea6c8161c4b3e6394fe035b12b69b73e6fa7d75
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120 superdsm.io.imwrite(args.do_masks, masks)