Mercurial > repos > thomaswollmann > overlay_segmentation_mask

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
author thomaswollmann
date Mon, 07 Jan 2019 05:38:10 -0500
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
parents:
diff changeset
1 import argparse
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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2 import sys
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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3 import os
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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4
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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5 import matplotlib
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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6 matplotlib.use('Agg')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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7 import matplotlib.pyplot as plt
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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9 #TODO make importable by python script
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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11 import skimage.io
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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12 import skimage.measure
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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14 parser = argparse.ArgumentParser()
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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15 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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16 parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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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
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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18 parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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19 parser.add_argument('--label', dest='label', action='store_true', help='plot label')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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20 parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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21 parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='thickness')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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22 parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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23 args = parser.parse_args()
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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24 img = skimage.io.imread(args.input_file.name)
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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25 label = skimage.io.imread(args.mask_file.name)
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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27 fig = plt.figure()
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
thomaswollmann
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28 ax = fig.add_axes([0, 0, 1, 1])
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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29 ax.axis('off')
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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31 if args.label:
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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32 for reg in skimage.measure.regionprops(label):
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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33 ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=args.label_color)
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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35 if args.greyscale:
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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36 plt.imshow(img, cmap=plt.cm.gray)
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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37 else:
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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38 plt.imshow(img)
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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39 plt.contour(label, linewidths=args.thickness, colors=args.stroke_color)
5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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5f83d67e30f1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f
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41 fig.canvas.print_png(args.out_file)