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skimage.exposure

Image intensity adjustment, e.g., histogram equalization, etc.

`adjust_gamma`	Performs Gamma Correction on the input image.
`adjust_log`	Performs Logarithmic correction on the input image.
`adjust_sigmoid`	Performs Sigmoid Correction on the input image.
`cumulative_distribution`	Return cumulative distribution function (cdf) for the given image.
`equalize_adapthist`	Contrast Limited Adaptive Histogram Equalization (CLAHE).
`equalize_hist`	Return image after histogram equalization.
`histogram`	Return histogram of image.
`is_low_contrast`	Determine if an image is low contrast.
`match_histograms`	Adjust an image so that its cumulative histogram matches that of another.
`rescale_intensity`	Return image after stretching or shrinking its intensity levels.

skimage.exposure.adjust_gamma(image, gamma=1, gain=1) [source]

Performs Gamma Correction on the input image.

Also known as Power Law Transform. This function transforms the input image pixelwise according to the equation O = I**gamma after scaling each pixel to the range 0 to 1.

Parameters:

imagendarray: Input image.
gammafloat, optional: Non negative real number. Default value is 1.
gainfloat, optional: The constant multiplier. Default value is 1.

Returns:

outndarray: Gamma corrected output image.

See also

adjust_log

Notes

For gamma greater than 1, the histogram will shift towards left and the output image will be darker than the input image.

For gamma less than 1, the histogram will shift towards right and the output image will be brighter than the input image.

References

[1]

https://en.wikipedia.org/wiki/Gamma_correction

Examples

>>> from skimage import data, exposure, img_as_float
>>> image = img_as_float(data.moon())
>>> gamma_corrected = exposure.adjust_gamma(image, 2)
>>> # Output is darker for gamma > 1
>>> image.mean() > gamma_corrected.mean()
True

Gamma and log contrast adjustment

Explore 3D images (of cells)

skimage.exposure.adjust_log(image, gain=1, inv=False) [source]

Performs Logarithmic correction on the input image.

This function transforms the input image pixelwise according to the equation O = gain*log(1 + I) after scaling each pixel to the range 0 to 1. For inverse logarithmic correction, the equation is O = gain*(2**I - 1).

Parameters:

imagendarray: Input image.
gainfloat, optional: The constant multiplier. Default value is 1.
invfloat, optional: If True, it performs inverse logarithmic correction, else correction will be logarithmic. Defaults to False.

Returns:

outndarray: Logarithm corrected output image.

See also

adjust_gamma

References

[1]

http://www.ece.ucsb.edu/Faculty/Manjunath/courses/ece178W03/EnhancePart1.pdf

Gamma and log contrast adjustment

skimage.exposure.adjust_sigmoid(image, cutoff=0.5, gain=10, inv=False) [source]

Performs Sigmoid Correction on the input image.

Also known as Contrast Adjustment. This function transforms the input image pixelwise according to the equation O = 1/(1 + exp*(gain*(cutoff - I))) after scaling each pixel to the range 0 to 1.

Parameters:

imagendarray: Input image.
cutofffloat, optional: Cutoff of the sigmoid function that shifts the characteristic curve in horizontal direction. Default value is 0.5.
gainfloat, optional: The constant multiplier in exponential’s power of sigmoid function. Default value is 10.
invbool, optional: If True, returns the negative sigmoid correction. Defaults to False.

Returns:

outndarray: Sigmoid corrected output image.

See also

adjust_gamma

References

[1]

Gustav J. Braun, “Image Lightness Rescaling Using Sigmoidal Contrast Enhancement Functions”, http://markfairchild.org/PDFs/PAP07.pdf

skimage.exposure.cumulative_distribution(image, nbins=256) [source]

Return cumulative distribution function (cdf) for the given image.

Parameters:

imagearray: Image array.
nbinsint, optional: Number of bins for image histogram.

Returns:

img_cdfarray: Values of cumulative distribution function.
bin_centersarray: Centers of bins.

See also

histogram

References

[1]

https://en.wikipedia.org/wiki/Cumulative_distribution_function

Examples

>>> from skimage import data, exposure, img_as_float
>>> image = img_as_float(data.camera())
>>> hi = exposure.histogram(image)
>>> cdf = exposure.cumulative_distribution(image)
>>> all(cdf[0] == np.cumsum(hi[0])/float(image.size))
True

Histogram matching

Gamma and log contrast adjustment

Histogram Equalization

Local Histogram Equalization

Explore 3D images (of cells)

skimage.exposure.equalize_adapthist(image, kernel_size=None, clip_limit=0.01, nbins=256) [source]

Contrast Limited Adaptive Histogram Equalization (CLAHE).

An algorithm for local contrast enhancement, that uses histograms computed over different tile regions of the image. Local details can therefore be enhanced even in regions that are darker or lighter than most of the image.

Parameters:

image(M[, …][, C]) ndarray: Input image.
kernel_sizeint or array_like, optional: Defines the shape of contextual regions used in the algorithm. If iterable is passed, it must have the same number of elements as image.ndim (without color channel). If integer, it is broadcasted to each image dimension. By default, kernel_size is 1/8 of image height by 1/8 of its width.
clip_limitfloat, optional: Clipping limit, normalized between 0 and 1 (higher values give more contrast).
nbinsint, optional: Number of gray bins for histogram (“data range”).

Returns:

out(M[, …][, C]) ndarray: Equalized image with float64 dtype.

See also

equalize_hist, rescale_intensity

Notes

For color images, the following steps are performed:
- The image is converted to HSV color space
- The CLAHE algorithm is run on the V (Value) channel
- The image is converted back to RGB space and returned
For RGBA images, the original alpha channel is removed.

Changed in version 0.17: The values returned by this function are slightly shifted upwards because of an internal change in rounding behavior.

References

[1]

http://tog.acm.org/resources/GraphicsGems/

[2]

https://en.wikipedia.org/wiki/CLAHE#CLAHE

Histogram Equalization

3D adaptive histogram equalization

skimage.exposure.equalize_hist(image, nbins=256, mask=None) [source]

Return image after histogram equalization.

Parameters:

imagearray: Image array.
nbinsint, optional: Number of bins for image histogram. Note: this argument is ignored for integer images, for which each integer is its own bin.
maskndarray of bools or 0s and 1s, optional: Array of same shape as image. Only points at which mask == True are used for the equalization, which is applied to the whole image.

Returns:

outfloat array: Image array after histogram equalization.

Notes

This function is adapted from [1] with the author’s permission.

References

[1]

http://www.janeriksolem.net/histogram-equalization-with-python-and.html

[2]

https://en.wikipedia.org/wiki/Histogram_equalization

Histogram Equalization

Local Histogram Equalization

3D adaptive histogram equalization

Visual image comparison

Explore 3D images (of cells)

Rank filters

skimage.exposure.histogram(image, nbins=256, source_range='image', normalize=False, *, channel_axis=None) [source]

Return histogram of image.

Unlike numpy.histogram, this function returns the centers of bins and does not rebin integer arrays. For integer arrays, each integer value has its own bin, which improves speed and intensity-resolution.

If channel_axis is not set, the histogram is computed on the flattened image. For color or multichannel images, set channel_axis to use a common binning for all channels. Alternatively, one may apply the function separately on each channel to obtain a histogram for each color channel with separate binning.

Parameters:

imagearray: Input image.
nbinsint, optional: Number of bins used to calculate histogram. This value is ignored for integer arrays.
source_rangestring, optional: ‘image’ (default) determines the range from the input image. ‘dtype’ determines the range from the expected range of the images of that data type.
normalizebool, optional: If True, normalize the histogram by the sum of its values.
channel_axisint or None, optional: If None, the image is assumed to be a grayscale (single channel) image. Otherwise, this parameter indicates which axis of the array corresponds to channels.

Returns:

histarray: The values of the histogram. When channel_axis is not None, hist will be a 2D array where the first axis corresponds to channels.
bin_centersarray: The values at the center of the bins.

See also

cumulative_distribution

Examples

>>> from skimage import data, exposure, img_as_float
>>> image = img_as_float(data.camera())
>>> np.histogram(image, bins=2)
(array([ 93585, 168559]), array([0. , 0.5, 1. ]))
>>> exposure.histogram(image, nbins=2)
(array([ 93585, 168559]), array([0.25, 0.75]))

Histogram matching

Comparing edge-based and region-based segmentation

Rank filters

skimage.exposure.is_low_contrast(image, fraction_threshold=0.05, lower_percentile=1, upper_percentile=99, method='linear') [source]

Determine if an image is low contrast.

Parameters:

imagearray-like: The image under test.
fraction_thresholdfloat, optional: The low contrast fraction threshold. An image is considered low- contrast when its range of brightness spans less than this fraction of its data type’s full range. [1]
lower_percentilefloat, optional: Disregard values below this percentile when computing image contrast.
upper_percentilefloat, optional: Disregard values above this percentile when computing image contrast.
methodstr, optional: The contrast determination method. Right now the only available option is “linear”.

Returns:

outbool: True when the image is determined to be low contrast.

Notes

For boolean images, this function returns False only if all values are the same (the method, threshold, and percentile arguments are ignored).

References

[1]

https://scikit-image.org/docs/dev/user_guide/data_types.html

Examples

>>> image = np.linspace(0, 0.04, 100)
>>> is_low_contrast(image)
True
>>> image[-1] = 1
>>> is_low_contrast(image)
True
>>> is_low_contrast(image, upper_percentile=100)
False

skimage.exposure.match_histograms(image, reference, *, channel_axis=None) [source]

Adjust an image so that its cumulative histogram matches that of another.

The adjustment is applied separately for each channel.

Parameters:

imagendarray: Input image. Can be gray-scale or in color.
referencendarray: Image to match histogram of. Must have the same number of channels as image.
channel_axisint or None, optional: If None, the image is assumed to be a grayscale (single channel) image. Otherwise, this parameter indicates which axis of the array corresponds to channels.

Returns:

matchedndarray: Transformed input image.

Raises:

ValueError: Thrown when the number of channels in the input image and the reference differ.

References

[1]

http://paulbourke.net/miscellaneous/equalisation/

Histogram matching

skimage.exposure.rescale_intensity(image, in_range='image', out_range='dtype') [source]

Return image after stretching or shrinking its intensity levels.

The desired intensity range of the input and output, in_range and out_range respectively, are used to stretch or shrink the intensity range of the input image. See examples below.

Parameters:

imagearray

Image array.

in_range, out_rangestr or 2-tuple, optional

Min and max intensity values of input and output image. The possible values for this parameter are enumerated below.

‘image’: Use image min/max as the intensity range.
‘dtype’: Use min/max of the image’s dtype as the intensity range.
dtype-name: Use intensity range based on desired dtype. Must be valid key in DTYPE_RANGE.
2-tuple: Use range_values as explicit min/max intensities.

Returns:

outarray: Image array after rescaling its intensity. This image is the same dtype as the input image.

See also

equalize_hist

Notes

Changed in version 0.17: The dtype of the output array has changed to match the input dtype, or float if the output range is specified by a pair of values.

Examples

By default, the min/max intensities of the input image are stretched to the limits allowed by the image’s dtype, since in_range defaults to ‘image’ and out_range defaults to ‘dtype’:

>>> image = np.array([51, 102, 153], dtype=np.uint8)
>>> rescale_intensity(image)
array([  0, 127, 255], dtype=uint8)

It’s easy to accidentally convert an image dtype from uint8 to float:

>>> 1.0 * image
array([ 51., 102., 153.])

Use rescale_intensity to rescale to the proper range for float dtypes:

>>> image_float = 1.0 * image
>>> rescale_intensity(image_float)
array([0. , 0.5, 1. ])

To maintain the low contrast of the original, use the in_range parameter:

>>> rescale_intensity(image_float, in_range=(0, 255))
array([0.2, 0.4, 0.6])

If the min/max value of in_range is more/less than the min/max image intensity, then the intensity levels are clipped:

>>> rescale_intensity(image_float, in_range=(0, 102))
array([0.5, 1. , 1. ])

If you have an image with signed integers but want to rescale the image to just the positive range, use the out_range parameter. In that case, the output dtype will be float:

>>> image = np.array([-10, 0, 10], dtype=np.int8)
>>> rescale_intensity(image, out_range=(0, 127))
array([  0. ,  63.5, 127. ])

To get the desired range with a specific dtype, use .astype():

>>> rescale_intensity(image, out_range=(0, 127)).astype(np.int8)
array([  0,  63, 127], dtype=int8)

If the input image is constant, the output will be clipped directly to the output range: >>> image = np.array([130, 130, 130], dtype=np.int32) >>> rescale_intensity(image, out_range=(0, 127)).astype(np.int32) array([127, 127, 127], dtype=int32)

Adapting gray-scale filters to RGB images

Separate colors in immunohistochemical staining

Histogram Equalization

Robust matching using RANSAC

Phase Unwrapping

Histogram of Oriented Gradients

Filling holes and finding peaks

Random walker segmentation

Extrema

Explore 3D images (of cells)

Rank filters

© 2019 the scikit-image team
Licensed under the BSD 3-clause License.
https://scikit-image.org/docs/0.25.x/api/skimage.exposure.html