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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:01:10 -0500
parents 5e21d7342593
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5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
1 import argparse
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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2 import sys
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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3 import skimage.io
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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4 from skimage.morphology import watershed
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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5 from skimage.feature import peak_local_max
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f8f7987586b7 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 0
diff changeset
6 from scipy import ndimage as ndi
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5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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7 import skimage.util
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
diff changeset
8
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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9 if __name__ == "__main__":
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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10 parser = argparse.ArgumentParser(description='Split binaryimage by watershed')
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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11 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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12 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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13 parser.add_argument('min_distance', type=int, default=100, help='Minimum distance to next object')
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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14 args = parser.parse_args()
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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16 img_in = skimage.io.imread(args.input_file.name)
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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17 distance = ndi.distance_transform_edt(img_in)
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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18 local_maxi = peak_local_max(distance,
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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19 indices=False,
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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20 min_distance=args.min_distance,
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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21 labels=img_in)
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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22 markers = ndi.label(local_maxi)[0]
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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23 res = watershed(-distance, markers, mask=img_in)
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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25 res = skimage.util.img_as_uint(res)
5e21d7342593 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_split_binaryimage_by_watershed/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents:
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26 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")