annotate scale_image.py @ 3:d09507d3fb0e draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d

import argparse
import sys

import scipy.misc
import skimage.io
import skimage.transform
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'
    if ',' in scale:
        scale = scale[1:-1].split(',')
        scale = [int(i) for i in scale]
    elif '.' in scale:
        scale = float(scale)
    else:
        scale = int(scale)
    res = scipy.misc.imresize(img_in, scale, interp=interp)
    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')
    args = parser.parse_args()

    scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)