Mahotas
Python Computer Vision Library
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.
Examples
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 numpy as np import mahotas import pylab img = mahotas.imread('test.jpeg') T_otsu = mahotas.thresholding.otsu(img) seeds,_ = mahotas.label(img > T_otsu) labeled = mahotas.cwatershed(img.max() - img, 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 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 = mahotas.distance(f) p.imshow(dmap) p.show()
(This is under mahotas/demos/distance.py
).
How to invoke thresholding functions:
import mahotas import numpy as np from pylab import imshow, gray, show, subplot from os import path photo = mahotas.imread('luispedro.org', as_grey=True) photo = photo.astype(np.uint8) T_otsu = mahotas.otsu(photo) thresholded_otsu = (photo > T_otsu) T_rc = mahotas.rc(photo) thresholded_rc = (photo > T_rc)
Install
You will need python (naturally), numpy, and a C++ compiler. Then you should be able to either
Download the source and then run:
python setup.py install
or use one of:
pip install mahotas easy_install mahotas
You can test your instalation by running:
python -c "import mahotas; mahotas.test()"
If you compiled from source, you need to do this in another directory (or
compile locally, which can be accomplished with python setup.py build
--build-lib=.
).
If something fails, you can obtain more detail by running it again in verbose mode:
python -c "import mahotas; mahotas.test(verbose=True)"
Visual Studio
For compiling from source in Visual Studio, use:
python setup.py build_ext -c msvc python setup.py install
Citation
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
Development happens on github (http://github.com/luispedro/mahotas).
You can set the DEBUG
environment variable before compilation to get a
debug compile. 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. The debug modes are pretty slow as they add 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.
Travis Build Status
Links & Contacts
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.
Recent Changes
1.1.0 (February 12 2014)
- 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
1.0.4 (2013-12-15)
- Add mahotas.demos.load()
- Add stretch_rgb() function
- Add demos to mahotas namespace
- Fix SLIC superpixels
1.0.3 (2013-10-06)
- 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)
1.0.2 (July 10 2013)
- Fix requirements filename
1.0.1 (July 9 2013)
- 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
1.0 (May 21 2013)
- Make matplotlib a soft dependency
- Add demos.image_path() function
- Add citation() function
- Fix a few corner cases in texture analysis
- Integrate with travis
- Update citation (include DOI)
See the ChangeLog for older version.