ANN: mahotas 0.9.7

[Luis Pedro Coelho]

Hi list,

Last month there was no mahotas release (because of the holidays at the
end of last year, development slowed down), but here is this month's
version: 0.9.7

This version adds a bunch of small features. Most interesting is Bernsen
local thresholding.

Full ChangeLog:

* 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)


Mahotas
-------

Mahotas is a computer vision library. Algorithms operate on numpy
arrays, but are implemented in C++ for speed (efficiency is a major
concern of mahotas).

It includes algorithms such as watershed, morphological operations,
feature computation (Haralick features, Zernike moments, and SURF), and
other tidbits.


License: MIT

Release: http://pypi.python.org/pypi/mahotas
Repository: http://github.com/luispedro/mahotas
API Docs: http://packages.python.org/mahotas/
Mailing List: http://groups.google.com/group/pythonvision
General webpage: http://luispedro.org/software/mahotas
--
Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org

[Dana Zinatbakhsh]

Hi Luis,

Thanks for maintaining the library. I just downloaded mahotas on debian
(stable). Processor: i7(AMD64), running python 2.6.6 and ipython 0.10.
I tried installing mahotas and received an error printout that seemed to be
several pages in length (it appears to be a compile time error; receiving
many messages from what seemed to be gcc). I attempted easy_install, pip
and just running setup.py, both normally, under virtual_env, and using
sudo. The error messege culminated in this:

/usr/lib/pymodules/python2.6/numpy/core/include/numpy/__multiarray_api.h:1187:
warning: ‘int _import_array()’ defined but not used

error: Command "g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2
-Wall -fPIC -I/usr/lib/pymodules/python2.6/numpy/core/include
-I/usr/include/python2.6 -c mahotas/_histogram.cpp -o
build/temp.linux-x86_64-2.6/mahotas/_histogram.o" failed with exit status 1

Just wanted to know if there was a known hack/patch for this. I would
eventually like to have the library used in a script to be ran on a Windows
7 machine as well.

Thanks!

[Luis Pedro Coelho]

Mmmm...

Unfortunately, I think I would need the full error message to be able to
tell you more.

*

On Windows, I recommend the well-maintained versions of Christoph Gohlke

http://www.lfd.uci.edu/~gohlke/pythonlibs/

HTH
Luis

Post by Dana Zinatbakhsh
Hi Luis,
Thanks for maintaining the library. I just downloaded mahotas on debian
(stable). Processor: i7(AMD64), running python 2.6.6 and ipython 0.10.
I tried installing mahotas and received an error printout that seemed to
be several pages in length (it appears to be a compile time error;
receiving many messages from what seemed to be gcc). I attempted
easy_install, pip and just running setup.py, both normally, under
warning: ‘int _import_array()’ defined but not used
error: Command "g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
-O2 -Wall -fPIC -I/usr/lib/pymodules/python2.6/numpy/core/include
-I/usr/include/python2.6 -c mahotas/_histogram.cpp -o
build/temp.linux-x86_64-2.6/mahotas/_histogram.o" failed with exit status 1
Just wanted to know if there was a known hack/patch for this. I would
eventually like to have the library used in a script to be ran on a
Windows 7 machine as well.
Thanks!
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[Dana Zinatbakhsh]

I will try it on windows this weekend and I will send you the full error
report attached soon.

Thanks!

Post by Luis Pedro Coelho
Mmmm...
Unfortunately, I think I would need the full error message to be able to
tell you more.
*
On Windows, I recommend the well-maintained versions of Christoph Gohlke
http://www.lfd.uci.edu/~**gohlke/pythonlibs/<http://www.lfd.uci.edu/%7Egohlke/pythonlibs/>
HTH
Luis

Post by Dana Zinatbakhsh
Hi Luis,
Thanks for maintaining the library. I just downloaded mahotas on debian
(stable). Processor: i7(AMD64), running python 2.6.6 and ipython 0.10.
I tried installing mahotas and received an error printout that seemed to
be several pages in length (it appears to be a compile time error;
receiving many messages from what seemed to be gcc). I attempted
easy_install, pip and just running setup.py, both normally, under
/usr/lib/pymodules/python2.6/**numpy/core/include/numpy/__**
warning: ‘int _import_array()’ defined but not used
error: Command "g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
-O2 -Wall -fPIC -I/usr/lib/pymodules/python2.**6/numpy/core/include
-I/usr/include/python2.6 -c mahotas/_histogram.cpp -o
build/temp.linux-x86_64-2.6/**mahotas/_histogram.o" failed with exit
status 1
Just wanted to know if there was a known hack/patch for this. I would
eventually like to have the library used in a script to be ran on a
Windows 7 machine as well.
Thanks!
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[Jose Aristizabal]

Hi Luis,

I'm really new using Python, I do really appreciate what you've done here,
but I dont know how to upgrade mahotas I have v0.9.6 and working on windows
64 bits over Python27

Regards,

Jose.

Post by Luis Pedro Coelho
Hi list,
Last month there was no mahotas release (because of the holidays at the
end of last year, development slowed down), but here is this month's
version: 0.9.7
This version adds a bunch of small features. Most interesting is Bernsen
local thresholding.
* 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)
Mahotas
-------
Mahotas is a computer vision library. Algorithms operate on numpy arrays,
but are implemented in C++ for speed (efficiency is a major concern of
mahotas).
It includes algorithms such as watershed, morphological operations,
feature computation (Haralick features, Zernike moments, and SURF), and
other tidbits.
License: MIT
Release: http://pypi.python.org/pypi/**mahotas<http://pypi.python.org/pypi/mahotas>
Repository: http://github.com/luispedro/**mahotas<http://github.com/luispedro/mahotas>
API Docs: http://packages.python.org/**mahotas/<http://packages.python.org/mahotas/>
Mailing List: http://groups.google.com/**group/pythonvision<http://groups.google.com/group/pythonvision>
General webpage: http://luispedro.org/software/**mahotas<http://luispedro.org/software/mahotas>
--
Luis Pedro Coelho | Institute for Molecular Medicine |
http://luispedro.org
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[Anthony Oliver]

Jose,

You can easily upgrade using pip. If you don't have pip installed on
windows you can do so by using:
easy_install pip
pip install --upgrade
https://github.com/luispedro/mahotas/archive/release-0.9.7.zip

If you can't seem to run easy_install you may also have to install
setuptools if you haven't already:
http://pypi.python.org/pypi/setuptools





CTO
Sight Machine
Anthony Oliver
www.sightmachine.com

Post by Dana Zinatbakhsh
Hi Luis,
I'm really new using Python, I do really appreciate what you've done here,
but I dont know how to upgrade mahotas I have v0.9.6 and working on windows
64 bits over Python27
Regards,
Jose.

Post by Luis Pedro Coelho
Hi list,
Last month there was no mahotas release (because of the holidays at the
end of last year, development slowed down), but here is this month's
version: 0.9.7
This version adds a bunch of small features. Most interesting is Bernsen
local thresholding.
* 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)
Mahotas
-------
Mahotas is a computer vision library. Algorithms operate on numpy arrays,
but are implemented in C++ for speed (efficiency is a major concern of
mahotas).
It includes algorithms such as watershed, morphological operations,
feature computation (Haralick features, Zernike moments, and SURF), and
other tidbits.
License: MIT
Release: http://pypi.python.org/pypi/**mahotas<http://pypi.python.org/pypi/mahotas>
Repository: http://github.com/luispedro/**mahotas<http://github.com/luispedro/mahotas>
API Docs: http://packages.python.org/**mahotas/<http://packages.python.org/mahotas/>
Mailing List: http://groups.google.com/**group/pythonvision<http://groups.google.com/group/pythonvision>
General webpage: http://luispedro.org/software/**mahotas<http://luispedro.org/software/mahotas>
--
Luis Pedro Coelho | Institute for Molecular Medicine |
http://luispedro.org
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[Jose Aristizabal]

Thanks for your help, I really appreciate it.

Post by Anthony Oliver
Jose,
You can easily upgrade using pip. If you don't have pip installed on
easy_install pip
pip install --upgrade
https://github.com/luispedro/mahotas/archive/release-0.9.7.zip
If you can't seem to run easy_install you may also have to install
http://pypi.python.org/pypi/setuptools
CTO
Sight Machine
Anthony Oliver
www.sightmachine.com

Post by Dana Zinatbakhsh
Hi Luis,
I'm really new using Python, I do really appreciate what you've done
here, but I dont know how to upgrade mahotas I have v0.9.6 and working on
windows 64 bits over Python27
Regards,
Jose.

Post by Luis Pedro Coelho
Hi list,
Last month there was no mahotas release (because of the holidays at the
end of last year, development slowed down), but here is this month's
version: 0.9.7
This version adds a bunch of small features. Most interesting is Bernsen
local thresholding.
* 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)
Mahotas
-------
Mahotas is a computer vision library. Algorithms operate on numpy
arrays, but are implemented in C++ for speed (efficiency is a major concern
of mahotas).
It includes algorithms such as watershed, morphological operations,
feature computation (Haralick features, Zernike moments, and SURF), and
other tidbits.
License: MIT
Release: http://pypi.python.org/pypi/**mahotas<http://pypi.python.org/pypi/mahotas>
Repository: http://github.com/luispedro/**mahotas<http://github.com/luispedro/mahotas>
API Docs: http://packages.python.org/**mahotas/<http://packages.python.org/mahotas/>
Mailing List: http://groups.google.com/**group/pythonvision<http://groups.google.com/group/pythonvision>
General webpage: http://luispedro.org/software/**mahotas<http://luispedro.org/software/mahotas>
--
Luis Pedro Coelho | Institute for Molecular Medicine |
http://luispedro.org
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