Mercurial > repos > thomaswollmann > binary2labelimage

annotate binary2label.py @ 0:4f07ac917459 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
author thomaswollmann
date Sat, 11 Feb 2017 17:28:38 -0500
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4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
1 import argparse
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
2 import sys
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
3 import skimage.io
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
4 from skimage.measure import label
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
5 import numpy as np
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
6 import warnings
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
7 from PIL import Image
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
8
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
9 parser = argparse.ArgumentParser()
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
12 args = parser.parse_args()
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
13
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
diff changeset
14 img_in = skimage.io.imread(args.input_file.name) > 0
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
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15 res = label(img_in).astype(np.int32)
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
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16
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
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17 res = Image.fromarray(res)
4f07ac917459 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/\binary2labelimage commit 77f1ea5beca40d8b5851fe366e84c32d5df5d6f8
thomaswollmann
parents:
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18 res.save(args.out_file.name, "tiff")