comparison slice_image.py @ 3:1faa7e3c94ff draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f

2:f312d414f234

import skimage.feature
import skimage.io
import skimage.util


def slice_image(input_file, out_folder, label=None, label_out_folder=None, window_size=64,
                stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None):
    # TODO NOT Implemented:process labels
    # --> label and label_out_folder useless so far

    # primarily for testing purposes:
    if seed is not None:
        random.seed(seed)

    img_raw = skimage.io.imread(input_file)
    if len(img_raw.shape) == 2:

            if bg_thresh > 0:
                sum_image = skimage.util.img_as_uint(sum_image)
                g = skimage.feature.greycomatrix(sum_image, [1, 2], [0, np.pi / 2], nnormed=True, symmetric=True)
                hom = np.var(skimage.feature.greycoprops(g, prop='homogeneity'))
                if hom > bg_thresh:  # 0.0005
                    continue

            if limit_slices:
                if i in sample:
                    res = skimage.util.img_as_uint(patches_raw[i])  # Attention: precision loss

                skimage.io.imsave(new_path % i, res, plugin='tifffile')


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
    parser.add_argument('out_folder', help='out folder')
    parser.add_argument('--label', dest='label_file', default=None, help='auxiliary label file to split in the same way')
    parser.add_argument('--label_out_folder', dest='label_out_folder', default=None, help='label out folder')
    parser.add_argument('--stride', dest='stride', type=int, default=1, help='applied stride')
    parser.add_argument('--window_size', dest='window_size', type=int, default=64, help='size of resulting patches')
    parser.add_argument('--bg_thresh', dest='bg_thresh', type=float, default=0, help='skip patches without information using a treshold')
    parser.add_argument('--limit_slices', dest='limit_slices', type=bool, default=False, help='limit amount of slices')
    parser.add_argument('--n_thresh', dest='n_thresh', type=int, default=5000, help='amount of slices')
    parser.add_argument('--seed', dest='seed', type=int, default=None, help='seed for random choice of limited slices')
    args = parser.parse_args()

    slice_image(args.input_file.name, args.out_folder,
                label=args.label_file, label_out_folder=args.label_out_folder,
                stride=args.stride, window_size=args.window_size, bg_thresh=args.bg_thresh,
                limit_slices=args.limit_slices, n_thresh=args.n_thresh, seed=args.seed)

3:1faa7e3c94ff

import skimage.feature
import skimage.io
import skimage.util


def slice_image(input_file, out_folder, window_size=64, stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None):

    # Primarily for testing purposes
    if seed is not None:
        random.seed(seed)

    img_raw = skimage.io.imread(input_file)
    if len(img_raw.shape) == 2:

            if bg_thresh > 0:
                sum_image = skimage.util.img_as_uint(sum_image)
                g = skimage.feature.greycomatrix(sum_image, [1, 2], [0, np.pi / 2], nnormed=True, symmetric=True)
                hom = np.var(skimage.feature.greycoprops(g, prop='homogeneity'))
                if hom > bg_thresh:
                    continue

            if limit_slices:
                if i in sample:
                    res = skimage.util.img_as_uint(patches_raw[i])  # Attention: precision loss

                skimage.io.imsave(new_path % i, res, plugin='tifffile')


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('input_file', type=argparse.FileType('r'), help='Input file')
    parser.add_argument('out_folder', help='Output directory')
    parser.add_argument('--stride', dest='stride', type=int, default=1, help='Applied stride')
    parser.add_argument('--window_size', dest='window_size', type=int, default=64, help='Size of resulting patches')
    parser.add_argument('--bg_thresh', dest='bg_thresh', type=float, default=0, help='Skip background patches without information using a treshold')
    parser.add_argument('--n_thresh', dest='n_thresh', type=int, default=5000, help='Maximum number of slices to retain')
    parser.add_argument('--seed', dest='seed', type=int, default=None, help='Seed for random choice of slices')
    args = parser.parse_args()

    slice_image(
        args.input_file.name,
        args.out_folder,
        stride=args.stride,
        window_size=args.window_size,
        bg_thresh=args.bg_thresh,
        limit_slices=args.n_thresh > 0,
        n_thresh=args.n_thresh,
        seed=args.seed,
    )