.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/applications/plot_rank_filters.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_applications_plot_rank_filters.py>`
        to download the full example code or to run this example in your browser via Binder

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_applications_plot_rank_filters.py:


============
Rank filters
============

Rank filters are non-linear filters using local gray-level ordering to
compute the filtered value. This ensemble of filters share a common base:
the local gray-level histogram is computed on the neighborhood of a pixel
(defined by a 2D structuring element). If the filtered value is taken as the
middle value of the histogram, we get the classical median filter.

Rank filters can be used for several purposes, such as:

* image quality enhancement,
  e.g., image smoothing, sharpening

* image pre-processing,
  e.g., noise reduction, contrast enhancement

* feature extraction,
  e.g., border detection, isolated point detection

* image post-processing,
  e.g., small object removal, object grouping, contour smoothing

Some well-known filters (e.g., morphological dilation and morphological
erosion) are specific cases of rank filters [1]_.

In this example, we will see how to filter a gray-level image using some of the
linear and non-linear filters available in skimage. We use the ``camera`` image
from `skimage.data` for all comparisons.

.. [1] Pierre Soille, On morphological operators based on rank filters, Pattern
       Recognition 35 (2002) 527-535, :DOI:`10.1016/S0031-3203(01)00047-4`

.. GENERATED FROM PYTHON SOURCE LINES 36-57

.. code-block:: default


    import numpy as np
    import matplotlib.pyplot as plt

    from skimage.util import img_as_ubyte
    from skimage import data
    from skimage.exposure import histogram

    noisy_image = img_as_ubyte(data.camera())
    hist, hist_centers = histogram(noisy_image)

    fig, ax = plt.subplots(ncols=2, figsize=(10, 5))

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].axis('off')

    ax[1].plot(hist_centers, hist, lw=2)
    ax[1].set_title('Gray-level histogram')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_001.png
   :alt: Gray-level histogram
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 58-64

Noise removal
=============

Some noise is added to the image: 1% of pixels are randomly set to 255, 1%
are randomly set to 0. The **median** filter is applied to remove the
noise.

.. GENERATED FROM PYTHON SOURCE LINES 65-95

.. code-block:: default


    from skimage.filters.rank import median
    from skimage.morphology import disk, ball

    rng = np.random.default_rng()
    noise = rng.random(noisy_image.shape)
    noisy_image = img_as_ubyte(data.camera())
    noisy_image[noise > 0.99] = 255
    noisy_image[noise < 0.01] = 0

    fig, axes = plt.subplots(2, 2, figsize=(10, 10), sharex=True, sharey=True)
    ax = axes.ravel()

    ax[0].imshow(noisy_image, vmin=0, vmax=255, cmap=plt.cm.gray)
    ax[0].set_title('Noisy image')

    ax[1].imshow(median(noisy_image, disk(1)), vmin=0, vmax=255, cmap=plt.cm.gray)
    ax[1].set_title('Median $r=1$')

    ax[2].imshow(median(noisy_image, disk(5)), vmin=0, vmax=255, cmap=plt.cm.gray)
    ax[2].set_title('Median $r=5$')

    ax[3].imshow(median(noisy_image, disk(20)), vmin=0, vmax=255, cmap=plt.cm.gray)
    ax[3].set_title('Median $r=20$')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_002.png
   :alt: Noisy image, Median $r=1$, Median $r=5$, Median $r=20$
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 96-113

The added noise is efficiently removed, as the image defaults are small (1-\
pixel wide), a small filter radius is sufficient. As the radius
increases, objects with bigger sizes get filtered as well, such as the
camera tripod. The median filter is often used for noise removal because it
preserves borders. For example, consider noise which is located only on a
few pixels in the entire image, as is the case with salt-and-pepper noise
[2]_: the median filter will ignore the noisy pixels, for they will appear
as outliers; thus, it will not change significantly the median of a group of
local pixels, in contrast to what a moving average filter would do.

.. [2] https://en.wikipedia.org/wiki/Salt-and-pepper_noise

Image smoothing
===============

The example hereunder shows how a local **mean** filter smooths the camera
man image.

.. GENERATED FROM PYTHON SOURCE LINES 114-132

.. code-block:: default


    from skimage.filters.rank import mean

    loc_mean = mean(noisy_image, disk(10))

    fig, ax = plt.subplots(ncols=2, figsize=(10, 5), sharex=True, sharey=True)

    ax[0].imshow(noisy_image, vmin=0, vmax=255, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(loc_mean, vmin=0, vmax=255, cmap=plt.cm.gray)
    ax[1].set_title('Local mean $r=10$')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_003.png
   :alt: Original, Local mean $r=10$
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_003.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 133-142

One may be interested in smoothing an image while preserving important
borders (median filters already achieved this). Here, we use the
**bilateral** filter that restricts the local neighborhood to pixels with
gray levels similar to the central one.

.. note::

    A different implementation is available for color images in
    :func:`skimage.restoration.denoise_bilateral`.

.. GENERATED FROM PYTHON SOURCE LINES 143-169

.. code-block:: default


    from skimage.filters.rank import mean_bilateral

    noisy_image = img_as_ubyte(data.camera())

    bilat = mean_bilateral(noisy_image.astype(np.uint16), disk(20), s0=10, s1=10)

    fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(10, 10),
                             sharex='row', sharey='row')
    ax = axes.ravel()

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(bilat, cmap=plt.cm.gray)
    ax[1].set_title('Bilateral mean')

    ax[2].imshow(noisy_image[100:250, 350:450], cmap=plt.cm.gray)

    ax[3].imshow(bilat[100:250, 350:450], cmap=plt.cm.gray)

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_004.png
   :alt: Original, Bilateral mean
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_004.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 170-184

One can see that the large continuous part of the image (e.g. sky) is
smoothed whereas other details are preserved.

Contrast enhancement
====================

We compare here how the global histogram equalization is applied locally.

The equalized image [3]_ has a roughly linear cumulative distribution
function for each pixel neighborhood. The local version [4]_ of
histogram equalization emphasizes every local gray-level variation.

.. [3] https://en.wikipedia.org/wiki/Histogram_equalization
.. [4] https://en.wikipedia.org/wiki/Adaptive_histogram_equalization

.. GENERATED FROM PYTHON SOURCE LINES 184-222

.. code-block:: default


    from skimage import exposure
    from skimage.filters import rank

    noisy_image = img_as_ubyte(data.camera())

    # equalize globally and locally
    glob = exposure.equalize_hist(noisy_image) * 255
    loc = rank.equalize(noisy_image, disk(20))

    # extract histogram for each image
    hist = np.histogram(noisy_image, bins=np.arange(0, 256))
    glob_hist = np.histogram(glob, bins=np.arange(0, 256))
    loc_hist = np.histogram(loc, bins=np.arange(0, 256))

    fig, axes = plt.subplots(nrows=3, ncols=2, figsize=(12, 12))
    ax = axes.ravel()

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].axis('off')

    ax[1].plot(hist[1][:-1], hist[0], lw=2)
    ax[1].set_title('Histogram of gray values')

    ax[2].imshow(glob, cmap=plt.cm.gray)
    ax[2].axis('off')

    ax[3].plot(glob_hist[1][:-1], glob_hist[0], lw=2)
    ax[3].set_title('Histogram of gray values')

    ax[4].imshow(loc, cmap=plt.cm.gray)
    ax[4].axis('off')

    ax[5].plot(loc_hist[1][:-1], loc_hist[0], lw=2)
    ax[5].set_title('Histogram of gray values')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_005.png
   :alt: Histogram of gray values, Histogram of gray values, Histogram of gray values
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_005.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 223-229

Another way to maximize the number of gray-levels used for an image is to
apply a local auto-leveling, i.e. the gray-value of a pixel is
proportionally remapped between local minimum and local maximum.

The following example shows how local auto-level enhances the camara man
picture.

.. GENERATED FROM PYTHON SOURCE LINES 229-249

.. code-block:: default


    from skimage.filters.rank import autolevel

    noisy_image = img_as_ubyte(data.camera())

    auto = autolevel(noisy_image.astype(np.uint16), disk(20))

    fig, ax = plt.subplots(ncols=2, figsize=(10, 5), sharex=True, sharey=True)

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(auto, cmap=plt.cm.gray)
    ax[1].set_title('Local autolevel')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_006.png
   :alt: Original, Local autolevel
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_006.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 250-255

This filter is very sensitive to local outliers. One can
moderate this using the percentile version of the auto-level filter
which uses given percentiles (one inferior, one superior) in place
of local minimum and maximum. The example below illustrates how the
percentile parameters influence the local auto-level result.

.. GENERATED FROM PYTHON SOURCE LINES 255-299

.. code-block:: default


    from skimage.filters.rank import autolevel_percentile

    image = data.camera()

    footprint = disk(20)
    loc_autolevel = autolevel(image, footprint=footprint)
    loc_perc_autolevel0 = autolevel_percentile(
        image, footprint=footprint, p0=.01, p1=.99
    )
    loc_perc_autolevel1 = autolevel_percentile(
        image, footprint=footprint, p0=.05, p1=.95
    )
    loc_perc_autolevel2 = autolevel_percentile(
        image, footprint=footprint, p0=.1, p1=.9
    )
    loc_perc_autolevel3 = autolevel_percentile(
        image, footprint=footprint, p0=.15, p1=.85
    )

    fig, axes = plt.subplots(nrows=3, ncols=2, figsize=(10, 10),
                             sharex=True, sharey=True)
    ax = axes.ravel()

    title_list = ['Original',
                  'auto_level',
                  'auto-level 1%',
                  'auto-level 5%',
                  'auto-level 10%',
                  'auto-level 15%']
    image_list = [image,
                  loc_autolevel,
                  loc_perc_autolevel0,
                  loc_perc_autolevel1,
                  loc_perc_autolevel2,
                  loc_perc_autolevel3]

    for i in range(0, len(image_list)):
        ax[i].imshow(image_list[i], cmap=plt.cm.gray, vmin=0, vmax=255)
        ax[i].set_title(title_list[i])
        ax[i].axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_007.png
   :alt: Original, auto_level, auto-level 1%, auto-level 5%, auto-level 10%, auto-level 15%
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_007.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 300-303

The morphological contrast enhancement filter replaces the central pixel by
the local maximum if the original pixel value is closest to local maximum,
otherwise by the minimum local.

.. GENERATED FROM PYTHON SOURCE LINES 303-329

.. code-block:: default


    from skimage.filters.rank import enhance_contrast

    noisy_image = img_as_ubyte(data.camera())

    enh = enhance_contrast(noisy_image, disk(5))

    fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(10, 10),
                             sharex='row', sharey='row')
    ax = axes.ravel()

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(enh, cmap=plt.cm.gray)
    ax[1].set_title('Local morphological contrast enhancement')

    ax[2].imshow(noisy_image[100:250, 350:450], cmap=plt.cm.gray)

    ax[3].imshow(enh[100:250, 350:450], cmap=plt.cm.gray)

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_008.png
   :alt: Original, Local morphological contrast enhancement
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_008.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 330-332

The percentile version of the local morphological contrast enhancement uses
percentile *p0* and *p1* instead of the local minimum and maximum.

.. GENERATED FROM PYTHON SOURCE LINES 332-358

.. code-block:: default


    from skimage.filters.rank import enhance_contrast_percentile

    noisy_image = img_as_ubyte(data.camera())

    penh = enhance_contrast_percentile(noisy_image, disk(5), p0=.1, p1=.9)

    fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(10, 10),
                             sharex='row', sharey='row')
    ax = axes.ravel()

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(penh, cmap=plt.cm.gray)
    ax[1].set_title('Local percentile morphological\n contrast enhancement')

    ax[2].imshow(noisy_image[100:250, 350:450], cmap=plt.cm.gray)

    ax[3].imshow(penh[100:250, 350:450], cmap=plt.cm.gray)

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_009.png
   :alt: Original, Local percentile morphological  contrast enhancement
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_009.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 359-374

Image threshold
===============

The Otsu threshold method [5]_ can be applied locally using the local gray-\
level distribution. In the example below, for each pixel, an "optimal"
threshold is determined by maximizing the variance between two classes of
pixels of the local neighborhood defined by a structuring element.

These algorithms can be used on both 2D and 3D images.

The example compares local thresholding with global thresholding, which is
provided by :func:`skimage.filters.threshold_otsu`. Note that the former is
much slower than the latter.

.. [5] https://en.wikipedia.org/wiki/Otsu's_method

.. GENERATED FROM PYTHON SOURCE LINES 375-414

.. code-block:: default


    from skimage.filters.rank import otsu
    from skimage.filters import threshold_otsu
    from skimage import exposure

    p8 = data.page()

    radius = 10
    footprint = disk(radius)

    # t_loc_otsu is an image
    t_loc_otsu = otsu(p8, footprint)
    loc_otsu = p8 >= t_loc_otsu

    # t_glob_otsu is a scalar
    t_glob_otsu = threshold_otsu(p8)
    glob_otsu = p8 >= t_glob_otsu

    fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(12, 12),
                             sharex=True, sharey=True)
    ax = axes.ravel()

    fig.colorbar(ax[0].imshow(p8, cmap=plt.cm.gray), ax=ax[0])
    ax[0].set_title('Original')

    fig.colorbar(ax[1].imshow(t_loc_otsu, cmap=plt.cm.gray), ax=ax[1])
    ax[1].set_title(f'Local Otsu ($r={radius}$)')

    ax[2].imshow(p8 >= t_loc_otsu, cmap=plt.cm.gray)
    ax[2].set_title('Original >= local Otsu')

    ax[3].imshow(glob_otsu, cmap=plt.cm.gray)
    ax[3].set_title(f'Global Otsu ($t={t_glob_otsu}$)')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_010.png
   :alt: Original, Local Otsu ($r=10$), Original >= local Otsu, Global Otsu ($t=157$)
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_010.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 415-416

The example below performs the same comparison, using a 3D image this time.

.. GENERATED FROM PYTHON SOURCE LINES 416-453

.. code-block:: default


    brain = exposure.rescale_intensity(data.brain().astype(float))

    radius = 5
    neighborhood = ball(radius)

    # t_loc_otsu is an image
    t_loc_otsu = rank.otsu(brain, neighborhood)
    loc_otsu = brain >= t_loc_otsu

    # t_glob_otsu is a scalar
    t_glob_otsu = threshold_otsu(brain)
    glob_otsu = brain >= t_glob_otsu

    fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(12, 12),
                             sharex=True, sharey=True)
    ax = axes.ravel()

    slice_index = 3

    fig.colorbar(ax[0].imshow(brain[slice_index], cmap=plt.cm.gray), ax=ax[0])
    ax[0].set_title('Original')

    fig.colorbar(ax[1].imshow(t_loc_otsu[slice_index], cmap=plt.cm.gray), ax=ax[1])
    ax[1].set_title(f'Local Otsu ($r={radius}$)')

    ax[2].imshow(brain[slice_index] >= t_loc_otsu[slice_index], cmap=plt.cm.gray)
    ax[2].set_title('Original >= local Otsu')

    ax[3].imshow(glob_otsu[slice_index], cmap=plt.cm.gray)
    ax[3].set_title(f'Global Otsu ($t={t_glob_otsu}$)')

    for a in ax:
        a.axis('off')

    fig.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_011.png
   :alt: Original, Local Otsu ($r=5$), Original >= local Otsu, Global Otsu ($t=0.287109375$)
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_011.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/skimage/filters/rank/generic.py:282: UserWarning:

    Possible precision loss converting image of type float64 to uint8 as required by rank filters. Convert manually using skimage.util.img_as_ubyte to silence this warning.





.. GENERATED FROM PYTHON SOURCE LINES 454-456

The following example shows how local Otsu thresholding handles a global
level shift applied to a synthetic image.

.. GENERATED FROM PYTHON SOURCE LINES 456-479

.. code-block:: default


    n = 100
    theta = np.linspace(0, 10 * np.pi, n)
    x = np.sin(theta)
    m = (np.tile(x, (n, 1)) * np.linspace(0.1, 1, n) * 128 + 128).astype(np.uint8)

    radius = 10
    t = rank.otsu(m, disk(radius))

    fig, ax = plt.subplots(ncols=2, figsize=(10, 5),
                           sharex=True, sharey=True)

    ax[0].imshow(m, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(m >= t, cmap=plt.cm.gray)
    ax[1].set_title(f'Local Otsu ($r={radius}$)')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_012.png
   :alt: Original, Local Otsu ($r=10$)
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_012.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 480-488

Image morphology
================

Local maximum and local minimum are the base operators for gray-level
morphology.

Here is an example of the classical morphological gray-level filters:
opening, closing and morphological gradient.

.. GENERATED FROM PYTHON SOURCE LINES 488-519

.. code-block:: default


    from skimage.filters.rank import maximum, minimum, gradient

    noisy_image = img_as_ubyte(data.camera())

    opening = maximum(minimum(noisy_image, disk(5)), disk(5))
    closing = minimum(maximum(noisy_image, disk(5)), disk(5))
    grad = gradient(noisy_image, disk(5))

    # display results
    fig, axes = plt.subplots(nrows=2, ncols=2, figsize=(10, 10),
                             sharex=True, sharey=True)
    ax = axes.ravel()

    ax[0].imshow(noisy_image, cmap=plt.cm.gray)
    ax[0].set_title('Original')

    ax[1].imshow(closing, cmap=plt.cm.gray)
    ax[1].set_title('Gray-level closing')

    ax[2].imshow(opening, cmap=plt.cm.gray)
    ax[2].set_title('Gray-level opening')

    ax[3].imshow(grad, cmap=plt.cm.gray)
    ax[3].set_title('Morphological gradient')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_013.png
   :alt: Original, Gray-level closing, Gray-level opening, Morphological gradient
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_013.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 520-536

Feature extraction
===================

Local histograms can be exploited to compute local entropy, which is
related to the local image complexity. Entropy is computed using base 2
logarithm, i.e., the filter returns the minimum number of bits needed to
encode local gray-level distribution.

:func:`skimage.filters.rank.entropy` returns the local entropy on a given
structuring element. The following example applies this filter
on 8- and 16-bit images.

.. note::

    To better use the available image bit, the function returns 10x entropy
    for 8-bit images and 1000x entropy for 16-bit images.

.. GENERATED FROM PYTHON SOURCE LINES 537-559

.. code-block:: default


    from skimage import data
    from skimage.filters.rank import entropy
    from skimage.morphology import disk
    import numpy as np
    import matplotlib.pyplot as plt

    image = data.camera()

    fig, ax = plt.subplots(ncols=2, figsize=(12, 6), sharex=True, sharey=True)

    fig.colorbar(ax[0].imshow(image, cmap=plt.cm.gray), ax=ax[0])
    ax[0].set_title('Image')

    fig.colorbar(ax[1].imshow(entropy(image, disk(5)), cmap=plt.cm.gray), ax=ax[1])
    ax[1].set_title('Entropy')

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_014.png
   :alt: Image, Entropy
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_014.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 560-570

Implementation
==============

The central part of the `skimage.filters.rank` filters is built on a sliding
window that updates the local gray-level histogram. This approach limits the
algorithm complexity to O(n) where n is the number of image pixels. The
complexity is also limited with respect to the structuring element size.

In the following, we compare the performance of different implementations
available in `skimage`.

.. GENERATED FROM PYTHON SOURCE LINES 571-609

.. code-block:: default


    from time import time

    from scipy.ndimage import percentile_filter
    from skimage.morphology import dilation
    from skimage.filters.rank import median, maximum


    def exec_and_timeit(func):
        """Decorator that returns both function results and execution time."""
        def wrapper(*arg):
            t1 = time()
            res = func(*arg)
            t2 = time()
            ms = (t2 - t1) * 1000.0
            return (res, ms)
        return wrapper


    @exec_and_timeit
    def cr_med(image, footprint):
        return median(image=image, footprint=footprint)


    @exec_and_timeit
    def cr_max(image, footprint):
        return maximum(image=image, footprint=footprint)


    @exec_and_timeit
    def cm_dil(image, footprint):
        return dilation(image=image, footprint=footprint)


    @exec_and_timeit
    def ndi_med(image, n):
        return percentile_filter(image, 50, size=n * 2 - 1)








.. GENERATED FROM PYTHON SOURCE LINES 610-616

Comparison between

* `skimage.filters.rank.maximum`
* `skimage.morphology.dilation`

on increasing structuring element size:

.. GENERATED FROM PYTHON SOURCE LINES 616-638

.. code-block:: default


    a = data.camera()

    rec = []
    e_range = range(1, 20, 2)
    for r in e_range:
        elem = disk(r + 1)
        rc, ms_rc = cr_max(a, elem)
        rcm, ms_rcm = cm_dil(a, elem)
        rec.append((ms_rc, ms_rcm))

    rec = np.asarray(rec)

    fig, ax = plt.subplots(figsize=(10, 10), sharey=True)
    ax.set_title('Performance with respect to element size')
    ax.set_ylabel('Time (ms)')
    ax.set_xlabel('Element radius')
    ax.plot(e_range, rec)
    ax.legend(['filters.rank.maximum', 'morphology.dilate'])

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_015.png
   :alt: Performance with respect to element size
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_015.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 639-640

and increasing image size:

.. GENERATED FROM PYTHON SOURCE LINES 640-663

.. code-block:: default


    r = 9
    elem = disk(r + 1)

    rec = []
    s_range = range(100, 1000, 100)
    for s in s_range:
        a = (rng.random((s, s)) * 256).astype(np.uint8)
        (rc, ms_rc) = cr_max(a, elem)
        (rcm, ms_rcm) = cm_dil(a, elem)
        rec.append((ms_rc, ms_rcm))

    rec = np.asarray(rec)

    fig, ax = plt.subplots()
    ax.set_title('Performance with respect to image size')
    ax.set_ylabel('Time (ms)')
    ax.set_xlabel('Image size')
    ax.plot(s_range, rec)
    ax.legend(['filters.rank.maximum', 'morphology.dilate'])

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_016.png
   :alt: Performance with respect to image size
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_016.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 664-670

Comparison between:

* `skimage.filters.rank.median`
* `scipy.ndimage.percentile_filter`

on increasing structuring element size:

.. GENERATED FROM PYTHON SOURCE LINES 670-690

.. code-block:: default


    a = data.camera()

    rec = []
    e_range = range(2, 30, 4)
    for r in e_range:
        elem = disk(r + 1)
        rc, ms_rc = cr_med(a, elem)
        rndi, ms_ndi = ndi_med(a, r)
        rec.append((ms_rc, ms_ndi))

    rec = np.asarray(rec)

    fig, ax = plt.subplots()
    ax.set_title('Performance with respect to element size')
    ax.plot(e_range, rec)
    ax.legend(['filters.rank.median', 'scipy.ndimage.percentile'])
    ax.set_ylabel('Time (ms)')
    ax.set_xlabel('Element radius')




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_017.png
   :alt: Performance with respect to element size
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_017.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    Text(0.5, 23.52222222222222, 'Element radius')



.. GENERATED FROM PYTHON SOURCE LINES 691-692

Comparison of outcome of the two methods:

.. GENERATED FROM PYTHON SOURCE LINES 692-706

.. code-block:: default


    fig, ax = plt.subplots(ncols=2, figsize=(10, 5), sharex=True, sharey=True)

    ax[0].set_title('filters.rank.median')
    ax[0].imshow(rc, cmap=plt.cm.gray)

    ax[1].set_title('scipy.ndimage.percentile')
    ax[1].imshow(rndi, cmap=plt.cm.gray)

    for a in ax:
        a.axis('off')

    plt.tight_layout()




.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_018.png
   :alt: filters.rank.median, scipy.ndimage.percentile
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_018.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 707-708

on increasing image size:

.. GENERATED FROM PYTHON SOURCE LINES 708-732

.. code-block:: default


    r = 9
    elem = disk(r + 1)

    rec = []
    s_range = [100, 200, 500, 1000]
    for s in s_range:
        a = (rng.random((s, s)) * 256).astype(np.uint8)
        (rc, ms_rc) = cr_med(a, elem)
        rndi, ms_ndi = ndi_med(a, r)
        rec.append((ms_rc, ms_ndi))

    rec = np.asarray(rec)

    fig, ax = plt.subplots()
    ax.set_title('Performance with respect to image size')
    ax.plot(s_range, rec)
    ax.legend(['filters.rank.median', 'scipy.ndimage.percentile'])
    ax.set_ylabel('Time (ms)')
    ax.set_xlabel('Image size')

    plt.tight_layout()

    plt.show()



.. image-sg:: /auto_examples/applications/images/sphx_glr_plot_rank_filters_019.png
   :alt: Performance with respect to image size
   :srcset: /auto_examples/applications/images/sphx_glr_plot_rank_filters_019.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 57.498 seconds)


.. _sphx_glr_download_auto_examples_applications_plot_rank_filters.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example


    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://mybinder.org/v2/gh/scikit-image/scikit-image/v0.22.x?filepath=notebooks/auto_examples/applications/plot_rank_filters.ipynb
        :alt: Launch binder
        :width: 150 px



    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_rank_filters.py <plot_rank_filters.py>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_rank_filters.ipynb <plot_rank_filters.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_