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annotate cp_segmentation.py @ 0:1e7334a51725 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
author bgruening
date Thu, 29 Feb 2024 22:07:26 +0000
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children 32153c43126c
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1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
bgruening
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diff changeset
1 import argparse
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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2 import json
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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3 import os
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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4 import warnings
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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5
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6 import matplotlib.pyplot as plt
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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7 import numpy as np
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8 import skimage.io
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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9 from cellpose import models, plot, transforms
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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11
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12 def main(inputs, img_path, img_format, output_dir):
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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13 """
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14 Parameter
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15 ---------
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16 inputs : str
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17 File path to galaxy tool parameter
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18 img_path : str
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19 File path for the input image
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20 img_format : str
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21 One of the ['ome.tiff', 'tiff', 'png', 'jpg']
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22 output_dir : str
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23 Folder to save the outputs.
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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24 """
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25 warnings.simplefilter('ignore')
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27 with open(inputs, 'r') as param_handler:
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28 params = json.load(param_handler)
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30 gpu = params['use_gpu']
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31 model_type = params['model_type']
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32 chan = params['chan']
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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33 chan2 = params['chan2']
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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34 chan_first = params['chan_first']
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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35 if chan is None:
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36 channels = None
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37 else:
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38 channels = [int(chan), int(chan2) if chan2 is not None else None]
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39
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40 options = params['options']
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41
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42 img = skimage.io.imread(img_path)
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43
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44 print(f"Image shape: {img.shape}")
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45 # transpose to Ly x Lx x nchann and reshape based on channels
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46 if img_format.endswith('tiff'):
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47 img = np.transpose(img, (1, 2, 0))
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48 img = transforms.reshape(img, channels=channels, chan_first=chan_first)
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49
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50 print(f"Image shape: {img.shape}")
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51 model = models.Cellpose(gpu=gpu, model_type=model_type)
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52 masks, flows, styles, diams = model.eval(img, channels=channels, **options)
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53
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54 # save masks to tiff
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55 with warnings.catch_warnings():
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56 warnings.simplefilter("ignore")
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57 skimage.io.imsave(os.path.join(output_dir, 'cp_masks.tif'),
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58 masks.astype(np.uint16))
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59
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60 # make segmentation show #
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61 if params['show_segmentation']:
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62 img = skimage.io.imread(img_path)
1e7334a51725 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 06dd9637975e3b9d6d27a3d5a773c85e9a52baf2
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63 # uniform image
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64 if img_format.endswith('tiff'):
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65 img = np.transpose(img, (1, 2, 0))
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66 img = transforms.reshape(img, channels=channels, chan_first=chan_first)
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67
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68 maski = masks
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69 flowi = flows[0]
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70 fig = plt.figure(figsize=(12, 3))
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71 # can save images (set save_dir=None if not)
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72 plot.show_segmentation(fig, img, maski, flowi, channels=channels)
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73 fig.savefig(os.path.join(output_dir, 'segm_show.png'), dpi=300)
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74 plt.close(fig)
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75
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76
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77 if __name__ == '__main__':
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78 aparser = argparse.ArgumentParser()
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79 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
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80 aparser.add_argument("-p", "--img_path", dest="img_path")
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81 aparser.add_argument("-f", "--img_format", dest="img_format")
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82 aparser.add_argument("-O", "--output_dir", dest="output_dir")
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83 args = aparser.parse_args()
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84
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85 main(args.inputs, args.img_path, args.img_format, args.output_dir)