Mahotas is a library of fast computer vision algorithms (all implemented in C++) operates over numpy arrays for convenience.
- Notable algorithms:
- watershed.
- convex points calculations.
- hit & miss. thinning.
- Zernike & Haralick, LBP, and TAS features.
- freeimage based numpy image loading (requires freeimage libraries to be installed).
- Speeded-Up Robust Features (SURF), a form of local features.
- thresholding.
- convolution.
- Sobel edge detection.
- spline interpolation
Mahotas currently has over 100 functions for image processing and computer vision and it keeps growing.
The release schedule is roughly one release a month and each release brings new functionality and improved performance. The interface is very stable, though, and code written using a version of mahotas from years back will work just fine in the current version, except it will be faster (some interfaces are deprecated and will be removed after a few years, but in the meanwhile, you only get a warning). In a few unfortunate cases, there was a bug in the old code and your results will change for the better.
Please cite the mahotas paper (see details below under Citation) if you use it in a publication.
This is a simple example of loading a file (called test.jpeg) and calling watershed using above threshold regions as a seed (we use Otsu to define threshold).
# import using ``mh`` abbreviation which is common:
import mahotas as mh
# Load one of the demo images
im = mh.demos.load('nuclear')
# Automatically compute a threshold
T_otsu = mh.thresholding.otsu(im)
# Label the thresholded image (thresholding is done with numpy operations
seeds,nr_regions = mh.label(im > T_otsu)
# Call seeded watershed to expand the threshold
labeled = mh.cwatershed(im.max() - im, seeds)
Here is a very simple example of using mahotas.distance
(which computes a distance map):
import pylab as p
import numpy as np
import mahotas as mh
f = np.ones((256,256), bool)
f[200:,240:] = False
f[128:144,32:48] = False
# f is basically True with the exception of two islands: one in the lower-right
# corner, another, middle-left
dmap = mh.distance(f)
p.imshow(dmap)
p.show()
(This is under mahotas/demos/distance.py
).
How to invoke thresholding functions:
import mahotas as mh
import numpy as np
from pylab import imshow, gray, show, subplot
from os import path
# Load photo of mahotas' author in greyscale
photo = mh.demos.load('luispedro', as_grey=True)
# Convert to integer values (using numpy operations)
photo = photo.astype(np.uint8)
# Compute Otsu threshold
T_otsu = mh.otsu(photo)
thresholded_otsu = (photo > T_otsu)
# Compute Riddler-Calvard threshold
T_rc = mh.rc(photo)
thresholded_rc = (photo > T_rc)
# Now call pylab functions to display the image
gray()
subplot(2,1,1)
imshow(thresholded_otsu)
subplot(2,1,2)
imshow(thresholded_rc)
show()
As you can see, we rely on numpy/matplotlib for many operations.
You will need python (naturally), numpy, and a C++ compiler. Then you should be able to use:
pip install mahotas
You can test your instalation by running:
python -c "import mahotas; mahotas.test()"
If you run into issues, the manual has more extensive documentation on mahotas intallation
If you use mahotas on a published publication, please cite:
Luis Pedro Coelho Mahotas: Open source software for scriptable computer vision in Journal of Open Research Software, vol 1, 2013. [DOI]
In Bibtex format:
@article{mahotas,
author = {Luis Pedro Coelho},
title = {Mahotas: Open source software for scriptable computer vision},
journal = {Journal of Open Research Software},
year = {2013},
doi = {http://dx.doi.org/10.5334/jors.ac},
month = {July},
volume = {1}
}
You can access this information using the mahotas.citation()
function.
Development happens on github (http://github.com/luispedro/mahotas).
You can set the DEBUG
environment variable before compilation to get a debug version:
export DEBUG=1
python setup.py test
You can set it to the value 2
to get extra checks:
export DEBUG=2
python setup.py test
Be careful not to use this in production unless you are chasing a bug. Debug level 2 is very slow as it adds many runtime checks.
The Makefile
that is shipped with the source of mahotas can be useful too. make debug
will create a debug build. make fast
will create a non-debug build (you need to make clean
in between). make test
will run the test suite.
Documentation: http://mahotas.readthedocs.org/
Issue Tracker: github mahotas issues
Mailing List: Use the pythonvision mailing list for questions, bug submissions, etc. Or ask on stackoverflow (tag mahotas)
Main Author & Maintainer: Luis Pedro Coelho (follow on twitter or github).
Mahotas also includes code by Zachary Pincus [from scikits.image], Peter J. Verveer [from scipy.ndimage], and Davis King [from dlib], Christoph Gohlke, as well as others.
Presentation about mahotas for bioimage informatics
For more general discussion of computer vision in Python, the pythonvision mailing list is a much better venue and generates a public discussion log for others in the future. You can use it for mahotas or general computer vision in Python questions.
- Explicitly set numpy.include_dirs() in setup.py [patch by Andrew Stromnov]
- Export locmax|locmin at the mahotas namespace level
- Break away ellipse_axes from eccentricity code as it can be useful on its own
- Add
find()
function - Add
mean_filter()
function - Fix
cwatershed()
overflow possibility - Make labeled functions more flexible in accepting more types
- Fix crash in
close_holes()
with nD images (for n > 2) - Remove matplotlibwrap
- Use standard setuptools for building (instead of numpy.distutils)
- Add
overlay()
function
- Fix crash in close_holes() with nD images (for n > 2)
- Better error checking
- Fix interpolation of integer images using order 1
- Add resize_to & resize_rgb_to
- Add coveralls coverage
- Fix SLIC superpixels connectivity
- Add remove_regions_where function
- Fix hard crash in convolution
- Fix axis handling in convolve1d
- Add normalization to moments calculation
- Add mahotas.demos.load()
- Add stretch_rgb() function
- Add demos to mahotas namespace
- Fix SLIC superpixels
- Add border & as_slice arguments to bbox()
- Better error message in gaussian_filter
- Allow as_rgb() to take integer arguments
- Extend distance() to n-dimensions
- Update to newer Numpy APIs (remove direct access to PyArray members)
- Fix requirements filename
- Add lbp_transform() function
- Add rgb2sepia function
- Add mahotas.demos.nuclear_image() function
- Work around matplotlib.imsave's implementation of greyscale
- Fix Haralick bug (report & patch by Tony S Yu)
- Add count_binary1s() function
See the ChangeLog for older version.