Source code for ClearMap.ImageProcessing.Filter.Rank.Parametric

# -*- coding: utf-8 -*-
"""
Parameteric rank filters 

This module provides rank filters that depend on several parameters.
"""
__author__    = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__   = 'GPLv3 - GNU General Pulic License v3 (see LICENSE.txt)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__   = 'http://idisco.info'
__download__  = 'http://www.github.com/ChristophKirst/ClearMap2'


import numpy as np

from . import Rank as rnk

import pyximport;
pyximport.install(setup_args={"include_dirs":np.get_include()}, reload_support=True)

from . import ParametricCode as code


__all__ = ['nilblack', 'sauvola', 'contrast_limited_percentile', 'light_sheet_artifact_correction']


[docs] def nilblack(source, selem=None, sink=None, mask=None, k=0.0, **kwargs): """Local nilblack threshold of an image. The resulting binary mask is True if the greyvalue of the center pixel is greater than the local mean. Arguments --------- source : array Input array. selem : array Structure element. If None, use a cube of size 3. sink : array Output array. If None, a new array is allocated. mask : array Optional mask, if None, the complete source is used. Pixels on the mask are zero in the output. max_bin : int or None Maximal number of bins. k : float The factor between mean and standard deviation: threshold = mu + k * std Returns ------- sink : array The filtered array. """ return rnk._apply_code(code.nilblack, code.nilblack_masked, sink_dtype = bool, source=source, selem=selem, sink=sink, mask=mask, parameter_float=[k], **kwargs);
[docs] def sauvola(source, selem=None, sink=None, mask=None, k=0.0, R=1.0): """Local Sauvola threshold of an image. The resulting binary mask is True if the greyvalue of the center pixel is greater than the local mean. Arguments --------- source : array Input array. selem : array Structure element. If None, use a cube of size 3. sink : array Output array. If None, a new array is allocated. mask : array Optional mask, if None, the complete source is used. Pixels on the mask are zero in the output. max_bin : int or None Maximal number of bins. k, R : float The factors in the formula: threshold = mu + k * (std/R - 1) * (mu - max_bin) Returns ------- sink : array The filtered array. """ return rnk._apply_code(code.sauvola, code.sauvola_masked, sink_dtype = None, source=source, selem=selem, sink=sink, mask=mask, parameter_float=[k,R]);
[docs] def contrast_limited_percentile(source, selem=None, sink=None, mask=None, percentile=0.0, limit = None, contrast_limit = 0.1, **kwargs): """Local Sauvola threshold of an image. The resulting binary mask is True if the greyvalue of the center pixel is greater than the local mean. Arguments --------- source : array Input array. selem : array Structure element. If None, use a cube of size 3. sink : array Output array. If None, a new array is allocated. mask : array Optional mask, if None, the complete source is used. Pixels on the mask are zero in the output. max_bin : int or None Maximal number of bins. k, R : float The factors in the formula: threshold = mu + k * (std/R - 1) * (mu - max_bin) Returns ------- sink : array The filtered array. """ if limit is None: selem = rnk._initialize_selem(selem, source.ndim); n_selem = np.sum(selem); limit = int(np.round(contrast_limit * n_selem)); parameter_float = [percentile]; parameter_index = np.hstack([[limit], np.zeros(max_bin, dtype=int)]); return rnk._apply_code(code.clp, code.clp_masked, sink_dtype = float, source=source, selem=selem, sink=sink, mask=mask, parameter_index=parameter_index, parameter_float=parameter_float, **kwargs);
[docs] def light_sheet_artifact_correction(source, selem=None, sink=None, mask=None, percentiles = (0.0, 1.0), limit = None, contrast_limit = 0.5, **kwargs): """Local Sauvola threshold of an image. The resulting binary mask is True if the greyvalue of the center pixel is greater than the local mean. Arguments --------- source : array Input array. selem : array Structure element. If None, use a cube of size 3. sink : array Output array. If None, a new array is allocated. mask : array Optional mask, if None, the complete source is used. Pixels on the mask are zero in the output. max_bin : int or None Maximal number of bins. k, R : float The factors in the formula: threshold = mu + k * (std/R - 1) * (mu - max_bin) Returns ------- sink : array The filtered array. """ if limit is None: selem = rnk._initialize_selem(selem, source.ndim); n_selem = np.sum(selem); limit = int(np.round(contrast_limit * n_selem)); parameter_float = np.array(percentiles, dtype = float); parameter_index = np.hstack([[limit], np.zeros(max_bin, dtype=int)]); return rnk._apply_code(code.lsac, code.lsac_masked, sink_dtype = float, source=source, selem=selem, sink=sink, mask=mask, parameter_index=parameter_index, parameter_float=parameter_float, **kwargs);