Mercurial > repos > imgteam > overlay_segmentation_mask

annotate overlay_segmentation_mask.py @ 1:8ad39f493587 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 05:03:51 -0400
parents 63b2a10b1001
children 22e573b7dcb1
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import sys
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import os
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import matplotlib
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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6 matplotlib.use('Agg')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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7 import matplotlib.pyplot as plt
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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9 #TODO make importable by python script
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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11 import skimage.io
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8ad39f493587 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
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12 import skimage.measure
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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14 parser = argparse.ArgumentParser()
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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16 parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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17 parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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18 parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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19 parser.add_argument('--label', dest='label', action='store_true', help='plot label')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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21 parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='thickness')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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22 parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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23 args = parser.parse_args()
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 img = skimage.io.imread(args.input_file.name)
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 label = skimage.io.imread(args.mask_file.name)
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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27 fig = plt.figure()
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 ax = fig.add_axes([0, 0, 1, 1])
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 ax.axis('off')
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 if args.label:
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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32 for reg in skimage.measure.regionprops(label):
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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33 ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=args.label_color)
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 if args.greyscale:
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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36 plt.imshow(img, cmap=plt.cm.gray)
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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37 else:
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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38 plt.imshow(img)
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 plt.contour(label, linewidths=args.thickness, colors=args.stroke_color)
63b2a10b1001 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40
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8ad39f493587 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 0
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41 fig.canvas.print_png(args.out_file)