Mercurial > repos > imgteam > binary2labelimage
changeset 3:9bb446db4a1e draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:10:33 +0000 |
| parents | 6e65fd971e13 |
| children | 984358e43242 |
| files | binary2label.py binary2label.xml |
| diffstat | 2 files changed, 13 insertions(+), 8 deletions(-) [+] |
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--- a/binary2label.py Wed Dec 18 05:01:27 2019 -0500 +++ b/binary2label.py Mon Nov 13 22:10:33 2023 +0000 @@ -1,17 +1,16 @@ import argparse import sys + import skimage.io +import skimage.util +from PIL import Image from skimage.measure import label -import numpy as np -import warnings -from PIL import Image -import skimage.util parser = argparse.ArgumentParser() parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') -parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') +parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') args = parser.parse_args() - + img_in = skimage.io.imread(args.input_file.name) > 0 res = label(img_in) res = skimage.util.img_as_uint(res)
--- a/binary2label.xml Wed Dec 18 05:01:27 2019 -0500 +++ b/binary2label.xml Mon Nov 13 22:10:33 2023 +0000 @@ -1,5 +1,11 @@ -<tool id="ip_binary_to_labelimage" name="Binary 2 Label" version="0.4"> - <description>Converts Binary to Label Image</description> +<tool id="ip_binary_to_labelimage" name="Convert binary image to label map" version="0.4-2"> + <description></description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">galaxy_image_analysis</xref> + </xrefs> <requirements> <requirement type="package" version="0.12.3">scikit-image</requirement> <requirement type="package" version="0.15.1">tifffile</requirement>