Mercurial > repos > imgteam > 2d_simple_filter
comparison filter_image.py @ 4:d51310ab328a draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
| author | imgteam |
|---|---|
| date | Wed, 24 Apr 2024 08:12:03 +0000 |
| parents | 6c4b22ef2b81 |
| children |
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| 3:6c4b22ef2b81 | 4:d51310ab328a |
|---|---|
| 1 import argparse | 1 import argparse |
| 2 | 2 |
| 3 import giatools.io | |
| 3 import scipy.ndimage as ndi | 4 import scipy.ndimage as ndi |
| 4 import skimage.io | 5 import skimage.io |
| 5 import skimage.util | 6 import skimage.util |
| 6 from skimage.morphology import disk | 7 from skimage.morphology import disk |
| 7 | 8 |
| 21 parser.add_argument('output', type=argparse.FileType('w'), help='Output file (TIFF)') | 22 parser.add_argument('output', type=argparse.FileType('w'), help='Output file (TIFF)') |
| 22 parser.add_argument('filter', choices=filters.keys(), help='Filter to be used') | 23 parser.add_argument('filter', choices=filters.keys(), help='Filter to be used') |
| 23 parser.add_argument('size', type=float, help='Size of the filter (e.g., radius, sigma)') | 24 parser.add_argument('size', type=float, help='Size of the filter (e.g., radius, sigma)') |
| 24 args = parser.parse_args() | 25 args = parser.parse_args() |
| 25 | 26 |
| 26 im = skimage.io.imread(args.input.name) | 27 im = giatools.io.imread(args.input.name) |
| 27 res = filters[args.filter](im, args.size) | 28 res = filters[args.filter](im, args.size) |
| 28 skimage.io.imsave(args.output.name, res, plugin='tifffile') | 29 skimage.io.imsave(args.output.name, res, plugin='tifffile') |