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comparison slice_image.py @ 1:445a3246ceac draft default tip

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 09:59:42 +0000
parents 694d3a83e6f9
children
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0:694d3a83e6f9 1:445a3246ceac
6 import os.path 6 import os.path
7 import skimage.io 7 import skimage.io
8 import skimage.util 8 import skimage.util
9 import skimage.feature 9 import skimage.feature
10 from scipy.stats import entropy as scipy_entropy 10 from scipy.stats import entropy as scipy_entropy
11 11
12 def slice_image(input_file, out_folder, label=None, label_out_folder=None, window_size=64, 12 def slice_image(input_file, out_folder, label=None, label_out_folder=None, window_size=64,
13 stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None): 13 stride=1, bg_thresh=1, limit_slices=False, n_thresh=5000, seed=None):
14 #TODO NOT Implemented:process labels 14 #TODO NOT Implemented:process labels
15 # --> label and label_out_folder useless so far 15 # --> label and label_out_folder useless so far
16 16
17 # primarily for testing purposes: 17 # primarily for testing purposes:
18 if seed is not None: 18 if seed is not None:
19 random.seed(seed) 19 random.seed(seed)