# HG changeset patch
# User imgteam
# Date 1729162034 0
# Node ID ba2b1a6f1b8423342abb1a755a77fa315b66728f
# Parent ac497ba6819dfa884ae0c42e2f6875403ff0c0c2
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
diff -r ac497ba6819d -r ba2b1a6f1b84 creators.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/creators.xml Thu Oct 17 10:47:14 2024 +0000
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diff -r ac497ba6819d -r ba2b1a6f1b84 scale_image.py
--- a/scale_image.py Mon Jul 22 04:59:15 2019 -0400
+++ b/scale_image.py Thu Oct 17 10:47:14 2024 +0000
@@ -1,37 +1,51 @@
import argparse
import sys
+
+import giatools.io
+import numpy as np
import skimage.io
import skimage.transform
-import scipy.misc
+import skimage.util
from PIL import Image
-
-def scale_image(input_file, output_file, scale, order=1):
- Image.MAX_IMAGE_PIXELS = 50000*50000
- img_in = skimage.io.imread(input_file)
- if order == 0:
- interp = 'nearest'
- elif order == 1:
- interp = 'bilinear'
- elif order == 2:
- interp = 'bicubic'
+
+def scale_image(input_file, output_file, scale, order, antialias):
+ Image.MAX_IMAGE_PIXELS = 50000 * 50000
+ im = giatools.io.imread(input_file)
+
+ # Parse `--scale` argument
if ',' in scale:
- scale = scale[1:-1].split(',')
- scale = [int(i) for i in scale]
- elif '.' in scale:
+ scale = [float(s.strip()) for s in scale.split(',')]
+ assert len(scale) <= im.ndim, f'Image has {im.ndim} axes, but scale factors were given for {len(scale)} axes.'
+ scale = scale + [1] * (im.ndim - len(scale))
+
+ else:
scale = float(scale)
- else:
- scale = int(scale)
- res = scipy.misc.imresize(img_in, scale, interp=interp)
+
+ # For images with 3 or more axes, the last axis is assumed to correspond to channels
+ if im.ndim >= 3:
+ scale = [scale] * (im.ndim - 1) + [1]
+
+ # Do the scaling
+ res = skimage.transform.rescale(im, scale, order, anti_aliasing=antialias, preserve_range=True)
+
+ # Preserve the `dtype` so that both brightness and range of values is preserved
+ if res.dtype != im.dtype:
+ if np.issubdtype(im.dtype, np.integer):
+ res = res.round()
+ res = res.astype(im.dtype)
+
+ # Save result
skimage.io.imsave(output_file, res)
if __name__ == "__main__":
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 (PNG)')
- parser.add_argument('scale', type=str, help='fraction scaling factor(float), percentage scaling factor(int), output size(tuple(height,width))') # integer option not implemented in galaxy wrapper
- parser.add_argument('order', type=int, default=1, help='interpolation method')
+ parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin)
+ parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin)
+ parser.add_argument('--scale', type=str, required=True)
+ parser.add_argument('--order', type=int, required=True)
+ parser.add_argument('--antialias', default=False, action='store_true')
args = parser.parse_args()
- scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)
+ scale_image(args.input_file.name, args.out_file.name, args.scale, args.order, args.antialias)
diff -r ac497ba6819d -r ba2b1a6f1b84 scale_image.xml
--- a/scale_image.xml Mon Jul 22 04:59:15 2019 -0400
+++ b/scale_image.xml Thu Oct 17 10:47:14 2024 +0000
@@ -1,62 +1,101 @@
-
- Scales image
+
+ with scikit-image
+
+ creators.xml
+ tests.xml
+ 0.18.3
+ 2
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+ operation_3443
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+ scikit-image
+ scikit-image
+
- pillow
- scikit-image
- numpy
- scipy
- tifffile
+ scikit-image
+ pillow
+ numpy
+ tifffile
+ giatools
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-
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+ python '$__tool_directory__/scale_image.py' '$input'
+
+ ./output.${input.ext}
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+ --scale '$scale'
+ --order $order
+ $antialias
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+ && mv ./output.${input.ext} ./output
+
+ ]]>
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- **What it does**
+
+ **Scales an image using one or more scaling factors.**
- This tool scales an image using the scaling factor.
+ The image is rescaled uniformly along all axes, or anistropically if multiple scale factors are given.
+
+ This operation preserves both the brightness of the image, and the range of values.
+
10.1016/j.jbiotec.2017.07.019
diff -r ac497ba6819d -r ba2b1a6f1b84 test-data/anisotropic.png
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diff -r ac497ba6819d -r ba2b1a6f1b84 test-data/out.png
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diff -r ac497ba6819d -r ba2b1a6f1b84 test-data/sample1.png
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diff -r ac497ba6819d -r ba2b1a6f1b84 test-data/uniform.png
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diff -r ac497ba6819d -r ba2b1a6f1b84 tests.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tests.xml Thu Oct 17 10:47:14 2024 +0000
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