Full API Documentation¶

A package for computer vision in Python.

Main Features¶

features: Compute global and local features (several submodules, include SURF and Haralick features)
convolve: Convolution and wavelets
morph: Morphological features. Most are available at the mahotas level, include erode(), dilate()...
watershed: Seeded watershed implementation
imread/imsave: read/write image

Documentation: https://mahotas.readthedocs.io/

Citation:

Coelho, Luis Pedro, 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software, 1:e3, DOI: http://dx.doi.org/10.5334/jors.ac

mahotas.as_rgb(r, g, b)¶

Returns an RGB image with r in the red channel, g in the green, and b in the blue. The channels are contrast stretched.

If any of the channels is None, that channel is set to zero. The same can be achieved by passing 0 as that channels value. In fact, passing a number as a channel value will set the whole channel to that value.

Parameters:

r,g,b : array-like or int, optional

The channels can be of any type or None. At least one must be not None and all must have the same shape.

Returns:

rgb : ndarray

RGB ndarray

Examples

This shows a nice looking picture:

z1 = np.linspace(0, np.pi)
X,Y = np.meshgrid(z1, z1)
red = np.sin(X)
green = np.cos(4*Y)
blue = X*Y

plt.imshow(mahotas.as_rgb(red, green, blue))

Notice that the scaling on the blue channel is so different from the other channels (from 0..2500 compared with 0..1), but as_rgb stretches each channel independently.

mahotas.bbox(img, border={0}, as_slice={False})¶

Calculate the bounding box of image img.

Parameters:

img : ndarray

Any integer image type

Returns:

min1,max1,min2,max2 : int,int,int,int

These are such that img[min1:max1, min2:max2] contains all non-zero pixels. Returned when as_slice is false (the default)

s : slice

A slice representation of the bounding box. Returned when as_slice is true

mahotas.border(labeled, i, j, Bc={3x3 cross}, out={np.zeros(labeled.shape, bool)}, always_return=True)¶

Compute the border region between i and j regions.

A pixel is on the border if it has value i (or j) and a pixel in its neighbourhood (defined by Bc) has value j (or i).

Parameters:

labeled : ndarray of integer type

input labeled array

i : integer

j : integer

Bc : structure element, optional

out : ndarray of same shape as labeled, dtype=bool, optional

where to store the output. If None, a new array is allocated

always_return : bool, optional

if false, then, in the case where there is no pixel on the border, returns None. Otherwise (the default), it always returns an array even if it is empty.

Returns:

border_img : boolean ndarray

Pixels are True exactly where there is a border between i and j in labeled

mahotas.borders(labeled, Bc={3x3 cross}, out={np.zeros(labeled.shape, bool)})¶

Compute border pixels

A pixel is on a border if it has value i and a pixel in its neighbourhood (defined by Bc) has value j, with i != j.

Parameters:

labeled : ndarray of integer type

input labeled array

Bc : structure element, optional

out : ndarray of same shape as labeled, dtype=bool, optional

where to store the output. If None, a new array is allocated

mode : {‘reflect’, ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’ [default], ‘ignore’}

How to handle borders

Returns:

border_img : boolean ndarray

Pixels are True exactly where there is a border in labeled

mahotas.bwperim(bw, n=4)¶

Find the perimeter of objects in binary images.

A pixel is part of an object perimeter if its value is one and there is at least one zero-valued pixel in its neighborhood.

By default the neighborhood of a pixel is 4 nearest pixels, but if n is set to 8 the 8 nearest pixels will be considered.

Parameters:

bw : ndarray

A black-and-white image (any other image will be converted to black & white)

n : int, optional

Connectivity. Must be 4 or 8 (default: 4)

mode : {‘reflect’, ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’ [default], ‘ignore’}

How to handle borders

Returns:

perim : ndarray

A boolean image

See also

borders: function This is a more generic function

mahotas.cdilate(f, g, Bc={3x3 cross}, n=1)¶

Conditional dilation

cdilate creates the image y by dilating the image f by the structuring element Bc conditionally to the image g. This operator may be applied recursively n times.

Parameters:

f : Gray-scale (uint8 or uint16) or binary image.

g : Conditioning image. (Gray-scale or binary).

Bc : Structuring element (default: 3x3 cross)

n : Number of iterations (default: 1)

Returns:

y : Image

mahotas.center_of_mass(img, labels=None)¶

Returns the center of mass of img.

If labels is given, then it returns L centers of mass, one for each region identified by labels (including region 0).

Parameters:

img : ndarray

labels : ndarray, optional

A labeled array (i.e., an array of integers of the same shape as img such that each “object” is identified by areas with different values).

Returns:

coords : ndarray

The exact shape of the output depends on whether the labels argument was used. If labels is None, then the return value is a 1-ndarray of coordinates (size = len(img.shape)); otherwise, the return value is a 2-ndarray of coordinates (shape = (labels.max()+1, len(img.shape)).

mahotas.cerode(f, g, Bc={3x3 cross}, out={np.empty_as(A)})¶

Conditional morphological erosion.

The type of operation depends on the dtype of A! If boolean, then the erosion is binary, else it is greyscale erosion. In the case of greyscale erosion, the smallest value in the domain of Bc is interpreted as -Inf.

Parameters:

f : ndarray

input image

g : ndarray

conditional image

Bc : ndarray, optional

Structuring element. By default, use a cross (see get_structuring_elem for details on the default).

Returns:

conditionally_eroded : ndarray

eroded version of f conditioned on g

See also

erode: function Unconditional version of this function

dilate

mahotas.close(f, Bc={3x3 cross}, out={np.empty_like(f)})¶

Morphological closing.

close creates the image y by the morphological closing of the image f by the structuring element Bc. In the binary case, the closing by a structuring element Bc may be interpreted as the intersection of all the binary images that contain the image f and have a hole equal to a translation of Bc. In the gray-scale case, there is a similar interpretation taking the functions umbra.

Parameters:

f : ndarray

Gray-scale (uint8 or uint16) or binary image.

Bc : ndarray, optional

Structuring element. (Default: 3x3 elementary cross).

out : ndarray, optional

Output array

output : deprecated

Do not use

Returns:

y : ndarray

See also

open: function

mahotas.close_holes(ref, Bc=None)¶

closed = close_holes(ref, Bc=None):

Close Holes

Parameters:

ref : ndarray

Reference image. This should be a binary image.

Bc : structuring element, optional

Default: 3x3 cross

Returns:

closed : ndarray

superset of ref (i.e. with closed holes)

mahotas.convolve(f, weights, mode='reflect', cval=0.0, out={new array})¶

Convolution of f and weights

Convolution is performed in doubles to avoid over/underflow, but the result is then cast to f.dtype. This conversion may result in over/underflow when using small integer types or unsigned types (if the output is negative). Converting to a floating point representation avoids this issue:

c = convolve(f.astype(float), kernel)

Parameters:

f : ndarray

input. Any dimension is supported

weights : ndarray

weight filter. If not of the same dtype as f, it is cast

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape and dtype as f as well as be C-contiguous.

Returns:

convolved : ndarray of same dtype as f

mahotas.convolve1d(f, weights, axis, mode='reflect', cval=0.0, out={new array})¶

Convolution of f and weights along axis axis.

Convolution is performed in doubles to avoid over/underflow, but the result is then cast to f.dtype.

Parameters:

f : ndarray

input. Any dimension is supported

weights : 1-D ndarray

weight filter. If not of the same dtype as f, it is cast

axis : int

Axis along which to convolve

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape and dtype as f as well as be C-contiguous.

Returns:

convolved : ndarray of same dtype as f

See also

convolve: function generic convolution

mahotas.croptobbox(img, border=0)¶

Returns a version of img cropped to the image’s bounding box

Parameters:

img : ndarray

Integer image array

border : int, optional

whether to add a border (default no border)

Returns:

nimg : ndarray

A subimage of img.

Notes

Note that the border is on the bounding box, not on the final image! This means that if the image has a positive pixel on its margin, it will still be on the margin.

This ensures that the result is always a sub-image of the input.

mahotas.cwatershed(surface, markers, Bc=None, return_lines=False) W, WL = cwatershed(surface, markers, Bc=None, return_lines=True)¶

Seeded watershed in n-dimensions

This function computes the watershed transform on the input surface (which may actually be an n-dimensional volume).

This function requires initial seed points. A traditional way of initializing watershed is to use regional minima:

minima = mh.regmin(f)
markers,nr_markers = mh.label(minima)
W = cwatershed(f, minima)

Parameters:

surface : image

markers : image

initial markers (must be a labeled image, i.e., one where 0 represents the background and higher integers represent different regions)

Bc : ndarray, optional

structuring element (default: 3x3 cross)

return_lines : boolean, optional

whether to return separating lines (in addition to regions)

Returns:

W : integer ndarray (int64 ints)

Regions image (i.e., W[i,j] == region for pixel (i,j))

WL : Lines image (if return_lines==True)

mahotas.daubechies(f, code, inline=False)¶

Daubechies wavelet transform

This function works best if the image sizes are powers of 2!

Parameters:

f : ndarray

2-D image

code : str

One of ‘D2’, ‘D4’, ... ‘D20’

inline : bool, optional

Whether to write the results to the input image. By default, a new image is returned. Integer images are always converted to floating point and copied.

See also

haar: function Haar transform (equivalent to D2)

mahotas.dilate(A, Bc=None, out=None, output=None)¶

Morphological dilation.

The type of operation depends on the dtype of A! If boolean, then the dilation is binary, else it is greyscale dilation. In the case of greyscale dilation, the smallest value in the domain of Bc is interpreted as +Inf.

Parameters:

A : ndarray of bools

input array

Bc : ndarray, optional

Structuring element. By default, use a cross (see get_structuring_elem for details on the default).

out : ndarray, optional

output array. If used, this must be a C-array of the same dtype as A. Otherwise, a new array is allocated.

output : deprecated

Do not use

Returns:

dilated : ndarray

dilated version of A

See also

erode

mahotas.disk(radius, dim=2)¶

Return a binary disk structuring element of radius radius and dimension dim

Parameters:

radius : int

Radius (in pixels) of returned disk

dim : int, optional

Dimension of returned array (default: 2)

Returns:

D : boolean ndarray

mahotas.distance(bw, metric='euclidean2')¶

Computes the distance transform of image bw:

dmap[i,j] = min_{i', j'} { (i-i')**2 + (j-j')**2 | !bw[i', j'] }

That is, at each point, compute the distance to the background.

If there is no background, then a very high value will be returned in all pixels (this is a sort of infinity).

Parameters:

bw : ndarray

If boolean, False will denote the background and True the foreground. If not boolean, this will be interpreted as bw != 0 (this way you can use labeled images without any problems).

metric : str, optional

one of ‘euclidean2’ (default) or ‘euclidean’

Returns:

dmap : ndarray

distance map

References

For 2-D images, the following algorithm is used:

Felzenszwalb P, Huttenlocher D. Distance transforms of sampled functions. Cornell Computing and Information. 2004.

Available at: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.1647&rep=rep1&type=pdf.

For n-D images (with n > 2), a slower hand-craft method is used.

mahotas.dog(img, sigma1 = 2, thresh= None, just_filter = False)¶

Compute edges using the Difference of Gaussian (DoG) operator.

edges is a binary image of edges.

Parameters:

img : Any 2D-ndarray

sigma1 : the sigma value of the first Gaussian filter. The second filter

will have sigma value 1.001*sigma1

multiplier : the multiplier to get sigma2. sigma2 = sigma1 * multiplier

just_filter : boolean, optional

If true, then return the result of filtering the image with the DoG filters, no zero-crossing is detected (default is False).

Returns:

edges : ndarray

Binary image of edges, unless just_filter, in which case it will be an array of floating point values.

mahotas.erode(A, Bc={3x3 cross}, out={np.empty_as(A)})¶

Morphological erosion.

The type of operation depends on the dtype of A! If boolean, then the erosion is binary, else it is greyscale erosion. In the case of greyscale erosion, the smallest value in the domain of Bc is interpreted as -Inf.

Parameters:

A : ndarray

input image

Bc : ndarray, optional

Structuring element. By default, use a cross (see get_structuring_elem for details on the default).

out : ndarray, optional

output array. If used, this must be a C-array of the same dtype as A. Otherwise, a new array is allocated.

Returns:

erosion : ndarray

eroded version of A

See also

dilate

mahotas.euler(f, n=8)¶

Compute the Euler number of image f

The Euler number is also known as the Euler characteristic given that many other mathematical objects are also known as Euler numbers.

Parameters:

f : ndarray

A 2-D binary image

n : int, optional

Connectivity, one of (4,8). default: 8

mode : {‘reflect’, ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’ [default]}

How to handle borders

Returns:

euler_nr : int

Euler number

References

The following algorithm is used:

A Fast Algorithm for Computing the Euler Number of an Image and its VLSI Implementation, doi: 10.1109/ICVD.2000.812628

mahotas.find(f, template)¶

Match template to image exactly

coordinates = find(f, template)

The output is in the same format as the np.where function.

Parameters:

f : ndarray

input. Currently, only 2-dimensional images are supported.

template : ndarray

Template to match. Must be explicitly passed, no default.

Returns:

match : np.array

coordinates : np.array

These are the coordinates of the match. The format is similar to the output of np.where, but in an ndarray.

mahotas.fullhistogram(img)¶

Return a histogram with bins 0, 1, ..., ``img.max()``.

After calling this function, it will be true that hist[i] == (img == i).sum(), for all i.

Parameters:

img : array-like of an unsigned type

input image.

Returns:

hist : an dnarray of type np.uint32

This will be of size img.max() + 1.

Notes

Only handles unsigned integer arrays.

mahotas.gaussian_filter(array, sigma, order=0, mode='reflect', cval=0., out={np.empty_like(array)})¶

Multi-dimensional Gaussian filter.

Parameters:

array : ndarray

input array, any dimension is supported. If the array is an integer array, it will be converted to a double array.

sigma : scalar or sequence of scalars

standard deviation for Gaussian kernel. The standard deviations of the Gaussian filter are given for each axis as a sequence, or as a single number, in which case it is equal for all axes.

order : {0, 1, 2, 3} or sequence from same set, optional

The order of the filter along each axis is given as a sequence of integers, or as a single number. An order of 0 corresponds to convolution with a Gaussian kernel. An order of 1, 2, or 3 corresponds to convolution with the first, second or third derivatives of a Gaussian. Higher order derivatives are not implemented

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape as array as well as be C-contiguous. If array is an integer array, this must be a double array; otherwise, it must have the same type as array.

Returns:

filtered : ndarray

Filtered version of array

Notes

The multi-dimensional filter is implemented as a sequence of one-dimensional convolution filters. The intermediate arrays are stored in the same data type as the output. Therefore, for output types with a limited precision, the results may be imprecise because intermediate results may be stored with insufficient precision.

mahotas.gaussian_filter1d(array, sigma, axis=-1, order=0, mode='reflect', cval=0., out={np.empty_like(array)})¶

One-dimensional Gaussian filter.

Parameters:

array : ndarray

input array of a floating-point type

sigma : float

standard deviation for Gaussian kernel (in pixel units)

axis : int, optional

axis to operate on

order : {0, 1, 2, 3}, optional

An order of 0 corresponds to convolution with a Gaussian kernel. An order of 1, 2, or 3 corresponds to convolution with the first, second or third derivatives of a Gaussian. Higher order derivatives are not implemented

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape and dtype as array as well as be C-contiguous.

Returns:

filtered : ndarray

Filtered version of array

mahotas.get_structuring_elem(A, Bc)¶

Retrieve appropriate structuring element

Parameters:

A : ndarray

array which will be operated on

Bc : None, int, or array-like

None:
Then Bc is taken to be 1

An integer:

There are two associated semantics:

connectivity

Bc[y,x] = [[ is |y - 1| + |x - 1| <= Bc_i ]]

count

Bc.sum() == Bc_i This is the more traditional meaning (when one writes that “4-connected”, this is what one has in mind).

Fortunately, the value itself allows one to distinguish between the two semantics and, if used correctly, no ambiguity should ever occur.

An array:
This should be of the same nr. of dimensions as A and will be passed through if of the right type. Otherwise, it will be cast.

Returns:

Bc_out : ndarray

Structuring element. This array will be of the same type as A, C-contiguous.

mahotas.haar(f, preserve_energy=True, inline=False)¶

Haar transform

Parameters:

f : 2-D ndarray

Input image

preserve_energy : bool, optional

Whether to normalise the result so that energy is preserved (the default).

inline : bool, optional

Whether to write the results to the input image. By default, a new image is returned. Integer images are always converted to floating point and copied.

See also

ihaar: function Reverse Haar transform

mahotas.hitmiss(input, Bc, out=np.zeros_like(input))¶

Hit & Miss transform

For a given pixel position, the hit&miss is True if, when Bc is overlaid on input, centered at that position, the 1 values line up with 1s, while the 0s line up with 0s (2s correspond to don’t care).

Parameters:

input : input ndarray

This is interpreted as a binary array.

Bc : ndarray

hit & miss template, values must be one of (0, 1, 2)

out : ndarray, optional

Used for output. Must be Boolean ndarray of same size as input

output : deprecated

Do not use

Returns:

filtered : ndarray

Examples

print(hitmiss(np.array([
            [0,0,0,0,0],
            [0,1,1,1,1],
            [0,0,1,1,1]]),
        np.array([
            [0,0,0],
            [2,1,1],
            [2,1,1]])))

prints::

    [[0 0 0 0 0]
     [0 0 1 1 0]
     [0 0 0 0 0]]

mahotas.idaubechies(f, code, inline=False)¶

Daubechies wavelet inverse transform

Parameters:

f : ndarray

2-D image

code : str

One of ‘D2’, ‘D4’, ... ‘D20’

inline : bool, optional

Whether to write the results to the input image. By default, a new image is returned. Integer images are always converted to floating point and copied.

See also

haar: function Haar transform (equivalent to D2)

mahotas.ihaar(f, preserve_energy=True, inline=False)¶

Reverse Haar transform

ihaar(haar(f)) is more or less equal to f (equal, except for possible rounding issues).

Parameters:

f : 2-D ndarray

Input image. If it is an integer image, it is converted to floating point (double).

preserve_energy : bool, optional

Whether to normalise the result so that energy is preserved (the default).

inline : bool, optional

Whether to write the results to the input image. By default, a new image is returned. Integer images are always converted to floating point and copied.

Returns:

f : ndarray

See also

haar: function Forward Haar transform

mahotas.imread(filename, as_grey=False)¶

Read an image into a ndarray from a file.

This function depends on PIL (or Pillow) being installed.

Parameters:

filename : str

filename

as_grey : boolean, optional

Whether to convert to grey scale image (default: no)

mahotas.imresize(img, nsize, order=3)¶

Resizes image

This function works in two ways: if nsize is a tuple or list of integers, then the result will be of this size; otherwise, this function behaves the same as mh.interpolate.zoom

Parameters:

img : ndarray

nsize : float or tuple(float) or tuple(integers)

Size of return. Meaning depends on the type

float: img’.shape[i] = nsize * img.shape[i] tuple of float: img’.shape[i] = nsize[i] * img.shape[i] tuple of int: img’.shape[i] = nsize[i]

order : integer, optional

Spline order to use (default: 3)

Returns:

img’ : ndarray

See also

zoom: Similar function
scipy.misc.pilutil.imresize: Similar function

mahotas.imsave(filename, array)¶

Writes array into file filename

This function depends on PIL (or Pillow) being installed.

Parameters:

filename : str

path on file system

array : ndarray-like

mahotas.label(array, Bc={3x3 cross}, output={new array})¶

Label the array, which is interpreted as a binary array

This is also called connected component labeled, where the connectivity is defined by the structuring element Bc.

See: http://en.wikipedia.org/wiki/Connected-component_labeling

Parameters:

array : ndarray

This will be interpreted as binary array

Bc : ndarray, optional

This is the structuring element to use

out : ndarray, optional

Output array. Must be a C-array, of type np.int32

Returns:

labeled : ndarray

Labeled result

nr_objects : int

Number of objects

mahotas.labeled_sum(array, labeled, minlength=None)¶

Labeled sum. sum will be an array of size labeled.max() + 1, where sum[i] is equal to np.sum(array[labeled == i]).

Parameters:

array : ndarray of any type

labeled : int ndarray

Label map. This is the same type as returned from mahotas.label()

minlength : int, optional

Minimum size of return array. If labeled has fewer than minlength regions, 0s are added to the result. (optional)

Returns:

sums : 1-d ndarray of array.dtype

mahotas.laplacian_2D(array, alpha = 0.2)¶

2D Laplacian filter.

Parameters:

array : ndarray

input 2D array. If the array is an integer array, it will be converted to a double array.

alpha : scalar or sequence of scalars

controls the shape of Laplacian operator. Must be 0-1. A larger values makes the operator empahsize the diagonal direction.

Returns:

filtered : ndarray

Filtered version of array

mahotas.locmax(f, Bc={3x3 cross}, out={np.empty(f.shape, bool)})¶

Local maxima

Parameters:

f : ndarray

Bc : ndarray, optional

structuring element

out : ndarray, optional

Used for output. Must be Boolean ndarray of same size as f

output : deprecated

Do not use

Returns:

filtered : ndarray

boolean image of same size as f.

See also

regmax: function Regional maxima. This is a stricter criterion than the local maxima as it takes the whole object into account and not just the neighbourhood defined by Bc:: 0 0 0 0 0 0 0 2 0 0 0 0 2 0 0 0 0 3 0 0 0 0 3 0 0 0 0 0 0 0 The top 2 is a local maximum because it has the maximal value in its neighbourhood, but it is not a regional maximum.
locmin: function Local minima

mahotas.locmin(f, Bc={3x3 cross}, out={np.empty(f.shape, bool)})¶

Local minima

Parameters:

f : ndarray

Bc : ndarray, optional

structuring element

out : ndarray, optional

Used for output. Must be Boolean ndarray of same size as f

output : deprecated

Do not use

Returns:

filtered : ndarray

boolean image of same size as f.

See also

locmax: function Regional maxima

mahotas.majority_filter(img, N=3, out={np.empty(img.shape, np.bool)})¶

Majority filter

filtered[y,x] is positive if the majority of pixels in the squared of size N centred on (y,x) are positive.

Parameters:

img : ndarray

input img (currently only 2-D images accepted)

N : int, optional

size of filter (must be odd integer), defaults to 3.

out : ndarray, optional

Used for output. Must be Boolean ndarray of same size as img

output : deprecated

Do not use

Returns:

filtered : ndarray

boolean image of same size as img.

mahotas.mean_filter(f, Bc, mode='ignore', cval=0.0, out=None)¶

Mean filter. The value at mean[i,j] will be the mean of the values in the neighbourhood defined by Bc.

Parameters:

f : ndarray

input. Any dimension is supported

Bc : ndarray

Defines the neighbourhood. Must be explicitly passed, no default.

mode : {‘reflect’, ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’ [ignore]}

How to handle borders. The default is to ignore points beyond the border, so that the means computed near the border include fewer elements.

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must be a double array with the same shape as f as well as be C-contiguous.

Returns:

mean : ndarray of type double and same shape as f

See also

median_filter: An alternative filtering method

mahotas.median_filter(f, Bc={square}, mode='reflect', cval=0.0, out={np.empty(f.shape, f.dtype})¶

Median filter

Parameters:

f : ndarray

input. Any dimension is supported

Bc : ndarray or int, optional

Defines the neighbourhood, default is a square of side 3.

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape and dtype as f as well as be C-contiguous.

Returns:

median : ndarray of same type and shape as f

median[i,j] is the median value of the points in f close to (i,j)

mahotas.moments(img, p0, p1, cm=(0, 0), convert_to_float=True)¶

Returns the p0-p1 moment of image img

The formula computed is

sum_{ij} { img[i,j] (i - c0)**p0 (j - c1)**p1 }

where cm = (c0,c1). If cm is not given, then (0,0) is used.

If image is of an integer type, then it is internally converted to np.float64, unlesss convert_to_float is False. The reason is that, otherwise, overflow is likely except for small images. Since this conversion takes longer than the computation, you can turn it off in case you are sure that your images are small enough for overflow to be an issue. Note that no conversion is made if img is of any floating point type.

Parameters:

img : 2-ndarray

An 2-d ndarray

p0 : float

Power for first dimension

p1 : float

Power for second dimension

cm : (int,int), optional

center of mass (default: 0,0)

convert_to_float : boolean, optional

whether to convert to floating point (default: True)

normalize : boolean, optional

whether to normalize to size of image (default: False)

Returns:

moment: float

floating point number

Notes

It only works for 2-D images

mahotas.open(f, Bc={3x3 cross}, out={np.empty_like(f)})¶

Morphological opening.

open creates the image y by the morphological opening of the image f by the structuring element Bc.

In the binary case, the opening by the structuring element Bc may be interpreted as the union of translations of b included in f. In the gray-scale case, there is a similar interpretation taking the functions umbra.

Parameters:

f : ndarray

Gray-scale (uint8 or uint16) or binary image.

Bc : ndarray, optional

Structuring element (default: 3x3 elementary cross).

out : ndarray, optional

Output array

output : deprecated

Do not use

Returns:

y : ndarray

See also

open: function

mahotas.otsu(img, ignore_zeros=False)¶

Calculate a threshold according to the Otsu method.

Example:

import mahotas as mh
import mahotas.demos

im = mahotas.demos.nuclear_image()
# im is stored as RGB, let's convert to single 2D format:
im = im.max(2)

#Now, we compute Otsu:
t = mh.otsu(im)

# finally, we use the value to form a binary image:
bin = (im > t)

See Wikipedia for details on methods: http://en.wikipedia.org/wiki/Otsu’s_method

Parameters:

img : an image as a numpy array.

This should be of an unsigned integer type.

ignore_zeros : Boolean

whether to ignore zero-valued pixels (default: False)

Returns:

T : integer

the threshold

mahotas.overlay(gray, red=None, green=None, blue=None, if_gray_dtype_not_uint8='stretch')¶

Create an image which is greyscale, but with possible boolean overlays.

Parameters:

gray: ndarray of type np.uint8

Should be a greyscale image of type np.uint8

red,green,blue : ndarray, optional

boolean arrays

if_gray_dtype_not_uint8 : str, optional

What to do if gray is not of type np.uint8, must be one of

‘stretch’ (default): the function stretch is called. ‘error’ : in this case, an error is raised

Returns:

overlaid : ndarray

Colour image

mahotas.rank_filter(f, Bc, rank, mode='reflect', cval=0.0, out=None)¶

Rank filter. The value at ranked[i,j] will be the rankth largest in the neighbourhood defined by Bc.

Parameters:

f : ndarray

input. Any dimension is supported

Bc : ndarray

Defines the neighbourhood. Must be explicitly passed, no default.

rank : integer

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape and dtype as f as well as be C-contiguous.

Returns:

ranked : ndarray of same type and shape as f

ranked[i,j] is the rankth value of the points in f close to (i,j)

See also

median_filter: A special case of rank_filter

mahotas.rc(img, ignore_zeros=False)¶

Calculate a threshold according to the Riddler-Calvard method.

Example:

import mahotas as mh
import mahotas.demos

im = mahotas.demos.nuclear_image()
# im is stored as RGB, let's convert to single 2D format:
im = im.max(2)

#Now, we compute a threshold:
t = mh.rc(im)

# finally, we use the value to form a binary image:
bin = (im > t)

Parameters:

img : ndarray

Image of any type

ignore_zeros : boolean, optional

Whether to ignore zero valued pixels (default: False)

Returns:

T : float

threshold

mahotas.regmax(f, Bc={3x3 cross}, out={np.empty(f.shape, bool)})¶

Regional maxima. This is a stricter criterion than the local maxima as it takes the whole object into account and not just the neighbourhood defined by Bc:

The top 2 is a local maximum because it has the maximal value in its neighbourhood, but it is not a regional maximum.

Parameters:

f : ndarray

Bc : ndarray, optional

structuring element

out : ndarray, optional

Used for output. Must be Boolean ndarray of same size as f

output : deprecated

Do not use

Returns:

filtered : ndarray

boolean image of same size as f.

See also

locmax: function Local maxima. The local maxima are a superset of the regional maxima

mahotas.regmin(f, Bc={3x3 cross}, out={np.empty(f.shape, bool)})¶

Regional minima. See the documentation for regmax for more details.

Parameters:

f : ndarray

Bc : ndarray, optional

structuring element

out : ndarray, optional

Used for output. Must be Boolean ndarray of same size as f

output : deprecated

Do not use

Returns:

filtered : ndarray

boolean image of same size as f.

See also

locmin: function Local minima

mahotas.sobel(img, just_filter=False)¶

Compute edges using Sobel’s algorithm

edges is a binary image of edges computed according to Sobel’s algorithm.

This implementation is tuned to match MATLAB’s implementation.

Parameters:

img : Any 2D-ndarray

just_filter : boolean, optional

If true, then return the result of filtering the image with the sobel filters, but do not threashold (default is False).

Returns:

edges : ndarray

Binary image of edges, unless just_filter, in which case it will be an array of floating point values.

mahotas.stretch(img, arg0=None, arg1=None, dtype=<type 'numpy.uint8'>)¶

img’ = stretch(img, [dtype=np.uint8]) img’ = stretch(img, max, [dtype=np.uint8]) img’ = stretch(img, min, max, [dtype=np.uint8])

Contrast stretch the image to the range [0, max] (first form) or [min, max] (second form). The method is simple linear stretching according to the formula:

p' = max * (p - img.min())/img.ptp() + min

Parameters:

img : ndarray

input image. It is not modified by this function

min : integer, optional

minimum value for output [default: 0]

max : integer, optional

maximum value for output [default: 255]

dtype : dtype of output,optional

[default: np.uint8]

Returns:

img’: ndarray

resulting image. ndarray of same shape as img and type dtype.

Notes

If max > 255, then it truncates the values if dtype is not specified.

mahotas.stretch_rgb(img, arg0=None, arg1=None, dtype=<type 'numpy.uint8'>)¶

Variation of stretch() function that works per-channel on an RGB image

Parameters:

img : ndarray

input image. It is not modified by this function

min : integer, optional

minimum value for output [default: 0]

max : integer, optional

maximum value for output [default: 255]

dtype : dtype of output,optional

[default: np.uint8]

Returns:

img’: ndarray

resulting image. ndarray of same shape as img and type dtype.

See also

stretch: function

mahotas.template_match(f, template, mode='reflect', cval=0.0, out=None, output=None)¶

Match template to image

match = template_match(f, template, mode=’reflect’, cval=0., out={np.empty_like(f)})

The value at match[i,j] will be the difference (in squared euclidean terms), between template and a same sized window on f centered on that point.

Note that the computation is performed using the same dtype as f. Thus is may overflow if the template is large.

Parameters:

f : ndarray

input. Any dimension is supported

template : ndarray

Template to match. Must be explicitly passed, no default.

mode : {‘reflect’ [default], ‘nearest’, ‘wrap’, ‘mirror’, ‘constant’, ‘ignore’}

How to handle borders

cval : double, optional

If mode is constant, which constant to use (default: 0.0)

out : ndarray, optional

Output array. Must have same shape and dtype as f as well as be C-contiguous.

Returns:

match : ndarray of same type and shape as f

match[i,j] is the squared euclidean distance between f[i-s0:i+s0,j-s1:j+s1] and template (for appropriately defined s0 and s1).

mahotas.thin(binimg)¶

Skeletonisation by thinning

Parameters:

binimg : ndarray

Binary input image

max_iter : int, optional

Maximum number of iterations (set to a negative number, the default, to run full skeletonization)

Returns:

skel : Skeletonised version of binimg

mahotas.wavelet_center(f, border=0, dtype=float, cval=0.0)¶

fc is a centered version of f with a shape that is composed of powers of 2.

Parameters:

f : ndarray

input image

border : int, optional

The border to use (default is no border)

dtype : type, optional

Type of fc

cval : float, optional

Which value to fill the border with (default is 0)

Returns:

fc : ndarray

See also

wavelet_decenter: function Reverse function

mahotas.wavelet_decenter(w, oshape, border=0)¶

Undoes the effect of wavelet_center

Parameters:

w : ndarray

Wavelet array

oshape : tuple

Desired shape

border : int, optional

The desired border. This must be the same value as was used for wavelet_center

Returns:

f : ndarray

This will have shape oshape

See also

wavelet_center: function Forward function

mahotas.features.eccentricity(bwimage)¶

Compute eccentricity

Parameters:

bwimage : ndarray

Interpreted as a boolean image

Returns:

r : float

Eccentricity measure

mahotas.features.ellipse_axes(bwimage)¶

Parameters of the ‘image ellipse’

semimajor,semiminor = ellipse_axes(bwimage)

Returns the parameters of the constant intensity ellipse with the same mass and second order moments as the original image.

Parameters:

bwimage : ndarray

Interpreted as a boolean image

Returns:

semimajor : float

semiminor : float

References

Prokop, RJ, and Reeves, AP. 1992. CVGIP: Graphical Models and Image Processing 54(5):438-460

mahotas.features.haralick(f, ignore_zeros=False, preserve_haralick_bug=False, compute_14th_feature=False, return_mean=False, return_mean_ptp=False, use_x_minus_y_variance=False, distance=1)¶

Compute Haralick texture features

Computes the Haralick texture features for the four 2-D directions or thirteen 3-D directions (depending on the dimensions of f).

ignore_zeros can be used to have the function ignore any zero-valued pixels (as background). If there are no-nonzero neighbour pairs in all directions, an exception is raised. Note that this can happen even with some non-zero pixels, e.g.:

would trigger an error when ignore_zeros=True as there are no horizontal non-zero pairs!

Parameters:

f : ndarray of integer type

input image. 2-D and 3-D images are supported.

distance: int, optional (default=1)

The distance to consider while computing the cooccurence matrix.

ignore_zeros : bool, optional

Whether to ignore zero pixels (default: False).

Returns:

feats : ndarray of np.double

A 4x13 or 4x14 feature vector (one row per direction) if f is 2D, 13x13 or 13x14 if it is 3D. The exact number of features depends on the value of compute_14th_feature Also, if either return_mean or return_mean_ptp is set, then a single dimensional array is returned.

Other Parameters:

preserve_haralick_bug : bool, optional

whether to replicate Haralick’s typo (default: False). You probably want to always set this to False unless you want to replicate someone else’s wrong implementation.

compute_14th_feature : bool, optional

whether to compute & return the 14-th feature

return_mean : bool, optional

When set, the function returns the mean across all the directions (default: False).

return_mean_ptp : bool, optional

When set, the function returns the mean and ptp (point-to-point, i.e., difference between max() and min()) across all the directions (default: False).

use_x_minus_y_variance : bool, optional

Feature 10 (index 9) has two interpretations, as the variance of |x-y| or as the variance of P(|x-y|). In order to achieve compatibility with other software and previous versions of mahotas, mahotas defaults to using VAR[P(\|x-y\|)]; if this argument is True, then it uses VAR[\|x-y\|] (default: False)

Notes

Haralick’s paper has a typo in one of the equations. This function implements the correct feature unless preserve_haralick_bug is True. The only reason why you’d want the buggy behaviour is if you want to match another implementation.

References

Cite the following reference for these features:

@article{Haralick1973,
    author = {Haralick, Robert M. and Dinstein, Its'hak and Shanmugam, K.},
    journal = {Ieee Transactions On Systems Man And Cybernetics},
    number = {6},
    pages = {610--621},
    publisher = {IEEE},
    title = {Textural features for image classification},
    url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4309314},
    volume = {3},
    year = {1973}
}

mahotas.features.lbp(image, radius, points, ignore_zeros=False)¶

Compute Linear Binary Patterns

The return value is a histogram of feature counts, where position i corresponds to the number of pixels that had code i. The codes are compressed so that impossible codes are not used. Therefore, this is the i``th feature, not just the feature with binary code ``i.

Parameters:

image : ndarray

input image (2-D numpy ndarray)

radius : number (integer or floating point)

radius (in pixels)

points : integer

nr of points to consider

ignore_zeros : boolean, optional

whether to ignore zeros (default: False)

Returns:

features : 1-D numpy ndarray

histogram of features. See above for a caveat on the interpretation of these.

References

Gray Scale and Rotation Invariant Texture Classification with Local Binary Patterns: Ojala, T. Pietikainen, M. Maenpaa, T. Lecture Notes in Computer Science (Springer) 2000, ISSU 1842, pages 404-420

mahotas.features.pftas(img, T={mahotas.threshold.otsu(img)})¶

Compute parameter free Threshold Adjacency Statistics

TAS were presented by Hamilton et al. in “Fast automated cell phenotype image classification” (http://www.biomedcentral.com/1471-2105/8/110)

The current version is an adapted version which is free of parameters. The thresholding is done by using Otsu’s algorithm (or can be pre-computed and passed in by setting T), the margin around the mean of pixels to be included is the standard deviation. This was first published by Coelho et al. in “Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature” (http://www.springerlink.com/content/60634778710577t0/)

Also returns a version computed on the negative of the binarisation defined by Hamilton et al.

Use tas() to get the original version of the features.

Parameters:

img : ndarray, 2D or 3D

input image

T : integer, optional

Threshold to use (default: compute with otsu)

Returns:

values : ndarray

A 1-D ndarray of feature values

mahotas.features.roundness(bw)¶

Roundness

Parameters:

bw : ndarray

Interpreted as a boolean image

Returns:

r : float

mahotas.features.tas(img)¶

Compute Threshold Adjacency Statistics

TAS were presented by Hamilton et al. in “Fast automated cell phenotype image classification” (http://www.biomedcentral.com/1471-2105/8/110)

Also returns a version computed on the negative of the binarisation defined by Hamilton et al.

See also pftas() for a variation without any hardcoded parameters.

Parameters:

img : ndarray, 2D or 3D

input image

Returns:

values : ndarray

A 1-D ndarray of feature values

See also

pftas: Parameter free TAS

mahotas.features.zernike(im, degree, radius, cm={center_of_mass(im)})¶

mahotas.features.zernike_moments(im, radius, degree=8, cm={center_of_mass(im)})¶

Zernike moments through degree. These are computed on a circle of radius radius centered around cm (or the center of mass of the image, if the cm argument is not used).

Returns a vector of absolute Zernike moments through degree for the image im.

Parameters:

im : 2-ndarray

input image

radius : integer

the maximum radius for the Zernike polynomials, in pixels. Note that the area outside the circle (centered on center of mass) defined by this radius is ignored.

degree : integer, optional

Maximum degree to use (default: 8)

cm : pair of floats, optional

the centre of mass to use. By default, uses the image’s centre of mass.

Returns:

zvalues : 1-ndarray of floats

Zernike moments

References

Teague, MR. (1980). Image Analysis via the General Theory of Moments. J. Opt. Soc. Am. 70(8):920-930.

mahotas.colors.rgb2gray(rgb_image, dtype=np.float)¶

Convert an RGB image to a grayscale image

The interpretation of RGB and greyscale values is very much object dependent (as anyone who has used an overhead projector which mangled their colour figures will have experienced). This function uses a typical method for conversion and will work acceptably well for typical use cases, but if you have strict requirements, consider implementing the conversion by yourself for fine control.

Parameters:

array : ndarray of shape (a,b,3)

dtype : dtype, optional

dtype of return

Returns:

grey : ndarray of dtype

mahotas.colors.rgb2grey(rgb_image, dtype=np.float)¶

Convert an RGB image to a grayscale image

The interpretation of RGB and greyscale values is very much object dependent (as anyone who has used an overhead projector which mangled their colour figures will have experienced). This function uses a typical method for conversion and will work acceptably well for typical use cases, but if you have strict requirements, consider implementing the conversion by yourself for fine control.

Parameters:

array : ndarray of shape (a,b,3)

dtype : dtype, optional

dtype of return

Returns:

grey : ndarray of dtype

mahotas.colors.rgb2lab(rgb, dtype={float})¶

Convert sRGB to L*a*b* coordinates

http://en.wikipedia.org/wiki/CIELAB

Parameters:

rgb : ndarray

Must be of shape (h,w,3)

dtype : dtype, optional

What dtype to return. Default will be floats

Returns:

lab : ndarray

mahotas.colors.rgb2sepia(rgb)¶

Parameters:

rgb : ndarray

Must be of shape (h,w,3)

Returns:

sepia : ndarray

Output is of same shape as rgb

mahotas.colors.rgb2xyz(rgb, dtype={float})¶

Convert RGB to XYZ coordinates

The input is interpreted as sRGB. See Wikipedia for more details:

http://en.wikipedia.org/wiki/SRGB

Parameters:

rgb : ndarray

dtype : dtype, optional

What dtype to return

Returns:

xyz : ndarray

See also

xyz2rgb: function The reverse function

mahotas.colors.xyz2lab(xyz, dtype={float})¶

Convert CIE XYZ to L*a*b* coordinates

http://en.wikipedia.org/wiki/CIELAB

Parameters:

xyz : ndarray

dtype : dtype, optional

What dtype to return. Default will be floats

Returns:

lab : ndarray

mahotas.colors.xyz2rgb(xyz, dtype={float})¶

Convert XYZ to sRGB coordinates

The output should be interpreted as sRGB. See Wikipedia for more details:

http://en.wikipedia.org/wiki/SRGB

Parameters:

xyz : ndarray

dtype : dtype, optional

What dtype to return. Default will be floats

Returns:

rgb : ndarray

See also

rgb2xyz: function The reverse function