# HG changeset patch # User imgteam # Date 1549741610 18000 # Node ID aacfbd7c4af65f6b68fa15f7bbb174fe6e4705a7 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581 diff -r 000000000000 -r aacfbd7c4af6 slice_image.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/slice_image.py Sat Feb 09 14:46:50 2019 -0500 @@ -0,0 +1,73 @@ +import argparse +import sys +import warnings +import numpy as np +import random +import os.path +import skimage.io +import skimage.util +import skimage.feature +from scipy.stats import entropy as scipy_entropy + +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: + img_raw = np.expand_dims(img_raw, 3) + + with warnings.catch_warnings(): # ignore FutureWarning + warnings.simplefilter("ignore") + patches_raw = skimage.util.view_as_windows(img_raw, (window_size, window_size, img_raw.shape[2]), step=stride) + patches_raw = patches_raw.reshape([-1, window_size, window_size, img_raw.shape[2]]) + + new_path = os.path.join(out_folder, "%d.tiff") + + #samples for thresholding the amount of slices + sample = random.sample(range(patches_raw.shape[0]), n_thresh) + + for i in range(0, patches_raw.shape[0]): + # TODO improve + sum_image = np.sum(patches_raw[i], 2)/img_raw.shape[2] + total_entr = np.var(sum_image.reshape([-1])) + + 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 == True: + 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') + else: + 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) diff -r 000000000000 -r aacfbd7c4af6 slice_image.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/slice_image.xml Sat Feb 09 14:46:50 2019 -0500 @@ -0,0 +1,66 @@ + + into smaller patches + + scikit-image + numpy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** + + Slices image into multiple smaller patches. + + + 10.1016/j.jbiotec.2017.07.019 + + diff -r 000000000000 -r aacfbd7c4af6 test-data/input.tiff Binary file test-data/input.tiff has changed diff -r 000000000000 -r aacfbd7c4af6 test-data/input_148.tiff Binary file test-data/input_148.tiff has changed diff -r 000000000000 -r aacfbd7c4af6 test-data/input_155.tiff Binary file test-data/input_155.tiff has changed diff -r 000000000000 -r aacfbd7c4af6 test-data/input_187.tiff Binary file test-data/input_187.tiff has changed diff -r 000000000000 -r aacfbd7c4af6 test-data/input_212.tiff Binary file test-data/input_212.tiff has changed diff -r 000000000000 -r aacfbd7c4af6 test-data/input_267.tiff Binary file test-data/input_267.tiff has changed