annotate run-superdsm.py @ 2:244f67290d28 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:35 +0000
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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 imghdr
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11 import os
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12 import pathlib
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13 import shutil
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14 import tempfile
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16
1
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17 hyperparameters = [
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18 ('AF_scale', float),
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19 ('c2f_region_analysis/min_atom_radius', float),
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20 ('c2f_region_analysis_min_norm_energy_improvement', float),
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21 ('c2f_region_analysis_max_atom_norm_energy', float),
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22 ('c2f_region_analysis_max_cluster_marker_irregularity', float),
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23 ('dsm_alpha', float),
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24 ('dsm_AF_alpha', float),
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25 ('global_energy_minimization_betai', float),
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26 ('global_energy_minimization_AF_beta', float),
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27 ('postprocess_mask_max_distance', int),
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28 ('postprocess_mask_stdamp', float),
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29 ('postprocess_max_norm_energy', float),
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30 ('postprocess_min_contrast', float),
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31 ('postprocess_min_object_radius', float),
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32 ]
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33
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34
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35 def get_param_name(key):
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36 return key.replace('/', '_')
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37
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38
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39 def create_config(args):
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40 cfg = superdsm.config.Config()
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41 for key, _ in hyperparameters:
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42 value = getattr(args, get_param_name(key))
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43 if value is not None:
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44 cfg[key] = value
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45 return cfg
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46
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47
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48 if __name__ == "__main__":
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49 parser = argparse.ArgumentParser(description='Segmentation of cell nuclei in 2-D fluorescence microscopy images')
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50 parser.add_argument('image', help='Path to the input image')
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51 parser.add_argument('cfg', help='Path to the file containing the configuration')
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52 parser.add_argument('masks', help='Path to the file containing the segmentation masks')
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53 parser.add_argument('overlay', help='Path to the file containing the overlay of the segmentation results')
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54 parser.add_argument('seg_border', type=int)
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55 parser.add_argument('slots', type=int)
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56 for key, ptype in hyperparameters:
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57 parser.add_argument('--' + get_param_name(key), type=ptype, default=None)
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58 args = parser.parse_args()
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59
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60 if args.slots >= 2:
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61 num_threads_per_process = 2
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62 num_processes = args.slots // num_threads_per_process
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63 else:
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64 num_threads_per_process = 1
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65 num_processes = 1
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66
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67 os.environ['MKL_NUM_THREADS'] = str(num_threads_per_process)
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68 os.environ['OPENBLAS_NUM_THREADS'] = str(num_threads_per_process)
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69
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70 import ray
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71 import superdsm.automation
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72 import superdsm.io
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73 import superdsm.render
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74
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75 ray.init(num_cpus=num_processes, log_to_driver=True)
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76
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77 with tempfile.TemporaryDirectory() as tmpdirname:
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78 tmpdir = pathlib.Path(tmpdirname)
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79 img_ext = imghdr.what(args.image)
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80 img_filepath = tmpdir / f'input.{img_ext}'
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81 shutil.copy(str(args.image), img_filepath)
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82
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83 pipeline = superdsm.pipeline.create_default_pipeline()
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84 cfg = create_config(args)
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85 img = superdsm.io.imread(img_filepath)
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86 data, cfg, _ = superdsm.automation.process_image(pipeline, cfg, img)
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88 with open(args.cfg, 'w') as fp:
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
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89 cfg.dump_json(fp)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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parents:
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90
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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91 overlay = superdsm.render.render_result_over_image(data, border_width=args.seg_border, normalize_img=False)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
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92 superdsm.io.imwrite(args.overlay, overlay)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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parents:
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93
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
imgteam
parents:
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94 masks = superdsm.render.rasterize_labels(data)
1b0fc671187f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/superdsm/ commit 4d66ff6e8a2a842e44e8d0d7102dfb3ac78dca7e
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95 superdsm.io.imwrite(args.masks, masks)