Mercurial > repos > imgteam > scale_image
view scale_image.py @ 5:85666e555698 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c86a1b93cb7732f7331a981d13465653cc1a2790
author | imgteam |
---|---|
date | Wed, 24 Apr 2024 08:13:13 +0000 |
parents | 3179853faae9 |
children |
line wrap: on
line source
import argparse import sys import giatools.io import numpy as np import skimage.io import skimage.transform import skimage.util from PIL import Image 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 = [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) # 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) 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, args.antialias)