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INSTALL-package
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INSTALL-package
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This directory contains files to build the python interfaces
to the functions of V2.5 SPAMS library already interfaced with matlab.
The interface consists of 4 files : spams.py myscipy_rand.py spams_wrap.py _spams_wrap.so
Note: myscipy_rand.py supplies a random generator for sparse matrix
for some old scipy distributions
WARNING : the API of spams.OMP and spams.OMPMask has changed since version V2.2
########################################
Interface building
Packages required: python-numpy, python-scipy, blas + lapack (preferably from atlas).
tar zxf spams-python-v2.5-svn2014-07-04.tar.gz
cd spams-python
python setup.py build
inst=<your-python-install-dir>
python setup.py install --prefix=$inst
Two documentations are installed in $inst/doc
- doc_spams.pdf and html/index.html : the detailed user documentation
- sphinx/index.html : the documentation of python function extracted by sphinx
################################
Linux :
carefully install atlas. For example on my ubuntu I had to do
apt-get install libatlas-dev libatlas3gf-base libatlas-3gf.so
If you don't have libblas.so and liblapack.so in /lib or /usr/lib,
you need to edit setup.py
MacOS:
the build has been tested with MacOS 10 (Lion) and required
packages were installed with 'port install' :
port install atlas;port install py26-numpy;install py26-scipy
I have added /opt/local/bin to my PATH
and specified the compiler by setting CC and CXX, for example:
export CC=/opt/local/bin/gcc-mp-4.3;export CXX=/opt/local/bin/g++-mp-4.3
Windows 32bits:
You need packages MinGW, python-2.7, and scipy + numpy for python-2.7
You will find binary distributions for MinGW on www.mingw.org,
python-2.7 on www.python.org,
numpy and scipy on www.numpy.org (or www.scipy.org).
If you want to run test_dictLearn.py, you must install
Python Imaging Library (PIL) : http://www.pythonware.com/products/pil/
Unfortunately, I did not find a binary distro for atlas.
` I use blas and lapack dlls fron the package R (2.15.1).
I found dlls for blas and lapcak on http://icl.cs.utk.edu/lapack-for-windows/lapack.
They work fine, but are slower.
To make a binary windows installer (spams-2.5.win32-py2.7.exe) :
- open a mingw console (msys.bat)
- extract files from the .tar.gz source distribution (tar zxf ...)
- enter directory spams-python
- execute ./win-build.sh
you will obtain spams-python-v2.5-svn2014-07-04.win32-py2.7.exe
Note : you may need to modify the script if you have different versions of python and R.
- when your installer is built, you may remove the package R.
Windows 64bits :
As I am a windows newbe, it was a nightmare for me to build a win64 distro
(the difficulty was to download the right version of each MS component).
According to http://mattptr.net/2010/07/28/building-python-extensions-in-a-modern-windows-environment/
(and to my experience) this can only be done with "Visual C++ 2008 express".
I worked on a virtual machine with a 64 bits windows7.
Here is what I exactly did.
- install MinGW (for the comfort of bash)
(http://sourceforge.net/projects/mingw/files/Installer/mingw-get-inst/mingw-get-inst-20120426/mingw-get-inst-20120426.exe)
- install python-2.7 + numpy +scipy for win64
(www.python.org and www.numpy.org)
- install R (2.15.1 ) from http://cran.r-project.org/, for blas and lapack libraries.
- install "Microsoft Visual C++ 2008 SP1 Redistributable Package (x64)"
(vcredist_x64.exe http://www.microsoft.com/fr-fr/download/details.aspx?id=2092)
- install "Microsoft Visual Studio 2008 Express with SP1"
(vcsetup.exe http://www.microsoft.com/fr-fr/download/details.aspx?id=14597)
- install (uncheck doc, samples, .NET dev)
"Microsoft Windows SDK for Windows 7 and .NET Framework 3.5 SP1"
(winsdk_web.exe http://www.microsoft.com/en-us/download/details.aspx?id=3138)
- install (select only "Windows Headers and Libraries")
"Microsoft Windows SDK for Windows 7 and .NET Framework 4"
(winsdk_web.exe http://www.microsoft.com/en-us/download/confirmation.aspx?id=8279)
- create a file "/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 9.0"/VC/bin/amd64/vcvarsamd64.bat
containing just the line
call "C:\Program Files\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 /Release
- get pexports and copy pexports.exe to C:/Windows/syatem32 or /c/mingw/bin
(http://sourceforge.net/projects/mingw/files/MinGW/Extension/pexports/)
- install a "Python Imaging Library" package (PIL), for example from
http://www.lfd.uci.edu/~gohlke/pythonlibs/
- untar the source package of spams-python
- cd spams-python
./win-build.sh
Ignore error "mt.exe not found"
The result should be spams-python-v2.5-svn2014-07-04.win-amd64-py2.7.exe
########################################
Testing the interface :
- Linux or Mac :
export PYTHONPATH=$inst/lib/python2.6/site-packages
cd $inst/test
python test_spams.py -h : to get help
python test_spams.py : will run all the tests
python test_spams.py linalg : test of linalg functions
python test_spams.py name1 name2 ... : run named tests
- Windows (binary install) :
cd C:\Python27\test
..\python.exe test_spams.py -h
..\python.exe test_spams.py
...
########################################
Using the interface :
setup your PYTHONPATH
import spams
The spams functions accept only numpy dense vectors or "Fortran" matrices and
scipy sparce matrices of csc type.
Examples :
-----
import numpy as np
import spams
X = np.asfortranarray(np.random.random((64,200)))
Y = np.asfortranarray(np.random.random((200,20000)))
Z = spams.CalcXY(X,Y)
----
import numpy as np
import scipy
import scipy.sparse
import spams
if not ('rand' in scipy.sparse.__dict__):
import myscipy as ssp
else:
import scipy.sparse as ssp
m=200; n = 200000; d= 0.05
A = ssp.rand(m,n,density=d,format='csc',dtype=np.float64)
B = spams.CalcAAt(A)
-----