Mahotas: Computer Vision Library
Project description
Python Computer Vision Library
This 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.
There is a manuscript about mahotas, which will hopefully evolve into a journal publication later.
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 from scipy import ndimage import mahotas import pylab img = mahotas.imread('test.jpeg') T_otsu = mahotas.thresholding.otsu(img) seeds,_ = ndimage.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 something fails, you can obtain more detail by running it again in verbose mode:
python -c "import mahotas; mahotas.test(verbose=True)"
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.
Contacts
For bugfixes, feel free to use my email: luis@luispedro.org
For more general with achieving certain tasks in Python, the pythonvision mailing list is a much better venue and generates a public discussion log for others in the future.
Recent Changes
0.99 (May 4 2013)
Make matplotlib a soft dependency
Add demos.image_path() function
Add citation() function
This version is 1.0 beta.
0.9.8 (April 22 2013)
Use matplotlib as IO backend (fallback only)
Compute dense SURF features
Fix sobel edge filtering (post-processing)
Faster 1D convultions (including faster Gaussian filtering)
Location independent tests (run mahotas.tests.run() anywhere)
Add labeled.is_same_labeling function
Post filter SLIC for smoother regions
Fix compilation warnings on several platforms
0.9.7 (February 03 2013)
Add haralick_features function
Add out parameter to morph functions which were missing it
Fix erode() & dilate() with empty structuring elements
Special case binary erosion/dilation in C-Arrays
Fix long-standing warning in TAS on zero inputs
Add verbose argument to tests.run()
Add circle_se to morph
Allow loc(max|min) to take floating point inputs
Add Bernsen local thresholding (bernsen and gbernsen functions)
0.9.6 (December 02 2012)
Fix distance() of non-boolean images (issue #24 on github)
Fix encoding issue on PY3 on Mac OS (issue #25 on github)
Add relabel() function
Add remove_regions() function in labeled module
Fix median_filter() on the borders (respect the mode argument)
Add mahotas.color module for conversion between colour spaces
Add SLIC Superpixels
Many improvements to the documentation
0.9.5 (November 05 2012)
Fix compilation in older G++
Faster Otsu thresholding
Python 3 support without 2to3
Add cdilate function
Add subm function
Add tophat transforms (functions tophat_close and tophat_open)
Add mode argument to euler() (patch by Karol M. Langner)
Add mode argument to bwperim() & borders() (patch by Karol M. Langner)
0.9.4 (October 10 2012)
Fix compilation on 32-bit machines (Patch by Christoph Gohlke)
0.9.3 (October 9 2012)
Fix interpolation (Report by Christoph Gohlke)
Fix second interpolation bug (Report and patch by Christoph Gohlke)
Update tests to newer numpy
Enhanced debug mode (compile with DEBUG=2 in environment)
Faster morph.dilate()
Add labeled.labeled_max & labeled.labeled_min (This also led to a refactoring of the labeled_* code)
Many documentation fixes
0.9.2 (September 1 2012)
Fix compilation on Mac OS X 10.8 (reported by Davide Cittaro)
Freeimage fixes on Windows by Christoph Gohlke
Slightly faster _filter implementaiton
0.9.1 (August 28 2012)
Python 3 support (you need to use 2to3)
Haar wavelets (forward and inverse transform)
Daubechies wavelets (forward and inverse transform)
Corner case fix in Otsu thresholding
Add soft_threshold function
Have polygon.convexhull return an ndarray (instead of a list)
Memory usage improvements in regmin/regmax/close_holes (first reported as issue #9 by thanasi)
0.9 (July 16 2012)
Auto-convert integer to double on gaussian_filter (previously, integer values would result in zero-valued outputs).
Check for integer types in (reg|loc)(max|min)
Use name out instead of output for output arguments. This matches Numpy better
Switched to MIT License
See the ChangeLog for older version.
Website: http://luispedro.org/software/mahotas
API Docs: http://packages.python.org/mahotas/
Mailing List: Use the pythonvision mailing list for questions, bug submissions, etc.
Author: Luis Pedro Coelho (with code by Zachary Pincus [from scikits.image], Peter J. Verveer [from scipy.ndimage], and Davis King [from dlib])
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