comparison auto_threshold.py @ 8:699a5e9146b3 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit c86a1b93cb7732f7331a981d13465653cc1a2790

7:e5c8e7e72373

See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
"""

import argparse

import numpy as np
import skimage.filters
import skimage.io
import skimage.util
import tifffile

th_methods = {
    'manual': lambda thres, **kwargs: thres,

    'otsu': lambda img_raw, **kwargs: skimage.filters.threshold_otsu(img_raw),

    'loc_mean': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='mean')
}


def do_thresholding(in_fn, out_fn, th_method, block_size, offset, threshold, invert_output=False):
    img = skimage.io.imread(in_fn)
    img = np.squeeze(img)
    assert img.ndim == 2

    th = offset + th_methods[th_method](img_raw=img, bz=block_size, thres=threshold)
    res = img > th

8:699a5e9146b3

See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
"""

import argparse

import giatools.io
import numpy as np
import skimage.filters
import skimage.util
import tifffile


th_methods = {
    'manual': lambda thres, **kwargs: thres,

    'otsu': lambda img_raw, **kwargs: skimage.filters.threshold_otsu(img_raw),

    'loc_mean': lambda img_raw, bz, **kwargs: skimage.filters.threshold_local(img_raw, bz, method='mean')
}


def do_thresholding(in_fn, out_fn, th_method, block_size, offset, threshold, invert_output=False):
    img = giatools.io.imread(in_fn)
    img = np.squeeze(img)
    assert img.ndim == 2

    th = offset + th_methods[th_method](img_raw=img, bz=block_size, thres=threshold)
    res = img > th