pymat-users — Mailing list for users of PyMat

[Pymat-users] Further pymat development.

[Ilya O. <vr...@gm...>]

Hello.

I've updated PyMat - incapsulated all functionality inside of object
added many more
exceptions and refactored the code.

Is there any way I could become one of maintainers of given library?
I desire this since given project wasn't developed since 2002, as far
as I can understand and by strange coincidence I need Python-Matlab
interface anyway - I need matlab for my current research project (that
will continue for about a year from now) for running SUGGAR[1] and I
would really prefer to do everything else using Python.

I could provide binary builds for Windows. And probably for Linux, if
somebody requests.

[1] http://sourceforge.net/projects/mems/

---
Ilya O.

Re: [Pymat-users] Trying to implement the array interface

[Michael H. <mh...@al...>]

Mark Asbach wrote:
> I'm currently extending the Python wrapper for the Open Computer Vision
> Library (opencv) with the goal to interface numerical libraries as
> seemless as possible. [...]
> - Gnuplot (1.7): uses Numeric, so doesn't work as well

Gnuplot.py version 1.8 uses numpy.  Maybe that will help?

Michael

Re: [Pymat-users] [Numpy-discussion] Trying to implement the array interface

[Gael V. <gae...@no...>]

On Wed, Jan 14, 2009 at 12:17:40PM +0100, Mark Asbach wrote:
> - Added an __array_interface__ property to the Python side of OpenCV data 
> structures (matrices and images) [...]

> - Added parsing the __array_interface__ of Python objects passed to OpenCV 
> methods. [...]

> I've tried using the following packages with OpenCV this way:
> - numpy (1.0.4): everything works as expected. This is the most important 
> library for OpenCV users, so this is a good sign. [...]

_Fantastic_! I read from this e-mail that you are having a few
difficulties moving forward, but what you have already achieved is
really fantastic and will definitely be very useful to many people.

Sorry, I can't help you with the problems you are having, but I wanted to
thank you for this effort.

Gaël

[Pymat-users] Trying to implement the array interface

[Mark A. <as...@ie...>]

Hi there,

I'm currently extending the Python wrapper for the Open Computer  
Vision Library (opencv) with the goal to interface numerical libraries  
as seemless as possible. Unfortunately, it doesn't seem to be that  
easy ;-)

What I've done so far:

- Added an __array_interface__ property to the Python side of OpenCV  
data structures (matrices and images) that uses version 3 of the  
interface definition and supplies the keys 'version', 'shape',  
'typestr', 'data' and in some cases 'strides' when we have non- 
continuos memory layout. I think, I'm compatible to http://numpy.scipy.org/array_interface.shtml 
  .
- Added parsing the __array_interface__ of Python objects passed to  
OpenCV methods. I'm a bit unsure of how to use the C/C++ side (array  
struct) and if I can expect it to be there (for example: I don't  
provide one with OpenCV). Since I intend to keep OpenCV independent of  
numpy, calling functions from numpy.h is not an option, as far as I  
can see.

The stuff described above is in the head revision of OpenCV,  
accessible via "svn co https://opencvlibrary.svn.sourceforge.net/svnroot/opencvlibrary/trunk/opencv 
".

I've tried using the following packages with OpenCV this way:
- numpy (1.0.4): everything works as expected. This is the most  
important library for OpenCV users, so this is a good sign.
- pylab/matplotlib (0.91.2): seems to use numpy / scipy-core.  
Everything okay.
- PIL (1.1.6): the array interface (Python side) doesn't adhere to the  
definition -> no 'version' key, 'data' is string, not a tuple holding  
the pointer. What to do with this?
- Numeric (24.2): I can create arrays from OpenCV datatypes and print  
them. Converting to other types however always yields 'Cannot convert  
scalar to float' or 'a float is required'. Strange :-/ Numeric.array  
instances also don't carry an __array_interface__. I can however  
convert by using numpy.arrays as intermediate step.
- Gnuplot (1.7): uses Numeric, so doesn't work as well
- pymat: didn't check. Seems to use Numeric, test results cover  
Numeric 23 and Matlab 6.5 only, so this package might be dead?
- numarray: didn't check. Is there still any relevance of this package?

Best,
Mark

-- 
Mark Asbach
Institut für Nachrichtentechnik, RWTH Aachen University
http://www.ient.rwth-aachen.de/cms/team/m_asbach

[Pymat-users] The version of Pymat

[yunzhi c. <sj...@ya...>]

Hi,

I have installed Python 2.5 and MATLAB 7.1. I wonder which version of Pymat should I use?

Yunzhi Cheng

       
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[Pymat-users] new version

[Thomas H. <mma...@ya...>]

Hello!

Where can I find the newest version of pymat?
How can I implement the Pymat Interface in Zope?


		
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[Pymat-users] neue Version

[Thomas H. <mma...@ya...>]

Hallo!

Wo finde ich denn eine neue Version von PyMat zum
downloaden.
Hat schon mal jemand Pymat im Zope integriert, wie
geht das??

Danke.


		
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[Pymat-users] Problem passing x = array([1, 2, 3, 4, 5]) to Matlab

[Varun P. <pur...@ya...>]

  Hi 
   
  I am a Masters student at UTD and have started learning Python.
  I had a really good experience at Pycon 2006.
   
  I am kinda stuck on a small issue of PyMat.
  I am tryin to pass a Numeric array to Matlab 7.0.1
  I am running Python 2.2 (as PyMat supports that) on Windows XP.
   
  The problem is that when i pass x = array([1, 2, 3, 4, 5]) to Matlab by using
   
  >>> import pymat
>>> from Numeric import * 
>>> x = array([1, 2, 3, 4, 5]) 
>>> H = pymat.open() 
>>> pymat.put(H, 'x', x) 

  the value of x is [1, 2, 3, 4, 5] in Python, but when it gets passed to Matlab, it becomes [0 0 0 0 0]  ... all zeros.
   
  Can anyone suggest what needs to be done.
   
  any help would be appreciated.
   
  - Varun


		
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[Pymat-users] hi every one

[mohamed h. <moh...@ho...>]

<html><div style='background-color:'><P class=MsoNormal dir=ltr style="MARGIN: 0cm 0cm 0pt; DIRECTION: ltr; unicode-bidi: embed; TEXT-ALIGN: left"><FONT face="Times New Roman" size=3>Hi every one </FONT></P>
<P class=MsoNormal dir=ltr style="MARGIN: 0cm 0cm 0pt; DIRECTION: ltr; unicode-bidi: embed; TEXT-ALIGN: left"><FONT face="Times New Roman" size=3>I'm an aerospace engineer and I'm working in my master degree in computational fluid dynamics. <SPAN style="mso-spacerun: yes">&nbsp;</SPAN>I 'm using matlab as my programming tool, but I'm now using a CFDRC package witch introduces python as a scripting language for automating the regular work. </FONT></P>
<P class=MsoNormal dir=ltr style="MARGIN: 0cm 0cm 0pt; DIRECTION: ltr; unicode-bidi: embed; TEXT-ALIGN: left"><FONT face="Times New Roman" size=3>I was searching for the tool to reuse my matalb work in the python environment so after searching I found that pymat is the best available tool </FONT></P>
<P class=MsoNormal dir=ltr style="MARGIN: 0cm 0cm 0pt; DIRECTION: ltr; unicode-bidi: embed; TEXT-ALIGN: left"><FONT size=3><FONT face="Times New Roman">So I'm using a version of CFDRC witch uses python 2.3 as a scripting language and I use matlab 6.5 where I already spent a lot of time building my codes in now I'm asking If anyone can help me by telling me the links to install pymat how, to install it and if there are pre requirements to take care of before installation <SPAN style="mso-spacerun: yes">&nbsp;</SPAN></FONT></FONT></P>
<P class=MsoNormal dir=ltr style="MARGIN: 0cm 0cm 0pt; DIRECTION: ltr; unicode-bidi: embed; TEXT-ALIGN: left"><FONT face="Times New Roman" size=3>Thanks every one and I appreciate your time for reading my message.</FONT></P></div></html>

Re: [Pymat-users] Linking not working after compilation

[Stephan R. <ste...@tu...>]

On Monday 12 September 2005 21:06, ro...@st... wrote:
> I havn't tried the lates matlab version under linux yet. I probably will
> have an attempt at it during this or next week.

I have later found a link from brainvisa (pymat-brainvisa.tar.gz) that said 
that matlab 7.0 is not working because of the dynamic linking issues. They 
have a derived package that compiled okay after some Makefile adjustments and 
also allows me to import the module. But then I am not able to open a 
connection to matlab and it gives me:

$ python -c "import pymat; pymat.open()"
Traceback (most recent call last):
  File "<string>", line 1, in ?
RuntimeError: Unable to start MATLAB engine

> Some tips:
> Are you running the cvs version?

No, but I can certainly try this.

> Try to compile by editing the test/testND script.

Okay.

> If it doesn't help I'll ask me again in a week.

Cool, I will.

BTW, the reason I am looking at pymat is that I want to use it to write unit 
tests for my matlab code. If you guys are interested I'll let you know about 
the results.

Regards,
Stephan
-- 
Stephan Richter
CBU Physics & Chemistry (B.S.) / Tufts Physics (Ph.D. student)
Web2k - Web Software Design, Development and Training

Re: [Pymat-users] Linking not working after compilation

[<ro...@st...>]

Hi Stephan,
I havn't tried the lates matlab version under linux yet. I probably will
have an attempt at it during this or next week.

Some tips:
Are you running the cvs version?
Try to compile by editing the test/testND script.

If it doesn't help I'll ask me again in a week.

Rolv

> Hi everyone,
>
> I just tried to compile pymat and I ran into some troubles. The first
> thing I
> had to do was to change setup.py and comment out the following lines like
> this:
>
> if sys.platform[:6] == 'linux2':
>     matlab_dir ='/opt/matlab'
>     matlab_plat = 'glnx86'
>     libraries = [
>         #'eng',
>         #'mat',
>         #'mx',
>         #'ut',
>         'stdc++'
>         ]
>
> After that the lib compiled and installed just fine. However, then the
> following fails:
>
> $ python -c "import pymat"
> Traceback (most recent call last):
>   File "<string>", line 1, in ?
>   File "/usr/lib/python2.4/site-packages/pymat/__init__.py", line 9, in ?
>     from pymat import *
> ImportError: /usr/lib/python2.4/site-packages/pymat/pymat.so: undefined
> symbol: mxCalloc
Hi Stephan,



>
> So it can clearly not find the mx.so library, right? Then I tried:
>
> $ export LD_LIBRARY_PATH=/opt/matlab/extern/lib/glnx86/
> $ python -c "import pymat"
>
> with the same result as above. I am using:
>
> Python 2.4
> GCC 3.4.3
> Matlab (the latest)
>
> Regards,
> Stephan
> --
> Stephan Richter
> CBU Physics & Chemistry (B.S.) / Tufts Physics (Ph.D. student)
> Web2k - Web Software Design, Development and Training
>
>
> -------------------------------------------------------
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>

[Pymat-users] Linking not working after compilation

[Stephan R. <ste...@tu...>]

Hi everyone,

I just tried to compile pymat and I ran into some troubles. The first thing I 
had to do was to change setup.py and comment out the following lines like 
this:

if sys.platform[:6] == 'linux2':
    matlab_dir ='/opt/matlab'
    matlab_plat = 'glnx86'
    libraries = [
        #'eng',
        #'mat',
        #'mx',
        #'ut',
        'stdc++'
        ]

After that the lib compiled and installed just fine. However, then the 
following fails:

$ python -c "import pymat"
Traceback (most recent call last):
  File "<string>", line 1, in ?
  File "/usr/lib/python2.4/site-packages/pymat/__init__.py", line 9, in ?
    from pymat import *
ImportError: /usr/lib/python2.4/site-packages/pymat/pymat.so: undefined 
symbol: mxCalloc

So it can clearly not find the mx.so library, right? Then I tried:

$ export LD_LIBRARY_PATH=/opt/matlab/extern/lib/glnx86/
$ python -c "import pymat"

with the same result as above. I am using:

Python 2.4
GCC 3.4.3
Matlab (the latest)

Regards,
Stephan
-- 
Stephan Richter
CBU Physics & Chemistry (B.S.) / Tufts Physics (Ph.D. student)
Web2k - Web Software Design, Development and Training

Re: [Pymat-users] Python 2.4

[<ro...@st...>]

Hi,

As far as I see there is no problem compiling pymat with python2.4 header
files.
Please check out from cvs since a fix was updated a few days ago.
There is a script called test/testND.py you could edit and try to run.

Rolv

>
> Hello,
>
> I currently use Python 2.4, and PyMat library would be very helpful for
> me.
> Unfortunately, It doesn't work with 2.4 version. Is there a new version
> that
> enable to use python 2.4 or a trick to make it compatible ?
>
> Tanks
>
>
>
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>
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[Pymat-users] Python 2.4

[<mle...@gr...>]

Hello,

I currently use Python 2.4, and PyMat library would be very helpful for me.
Unfortunately, It doesn't work with 2.4 version. Is there a new version that
enable to use python 2.4 or a trick to make it compatible ?

Tanks 



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[Pymat-users] pymat update

[<ro...@st...>]

Hi everybody,

'rank > 2 arrays' problem in pymat have been fixed.
Now multidimensional arrays can be passed to and from matlab,

The code and some tests can be found at:
http://www.simula.no/~rolv/pymat/

The file rolvpymat.cpp there have the original code commented out, so it
is easy to see what I did.
While pymat.cpp  file is the new pymat.cpp file with comments stripped.

I've tested it and it works. Could someone add the file to CVS?
The pymat version is now 1.2
(Thanks to Tal Tversky for showing me a fix to an earlier version of pymat)

Regards,
Rolv

[Pymat-users] pymat 3d support

[Tal T. <ta...@cs...>]

At some point about a year ago I tried fixing the 2-d limitation and
managed to get a version working that took arbitrary dimensional
arrays.  I don't remember how I did it exactly, but it wasn't
difficult.  Basically I read the documentation on how both Matlab and
python stored their arrays and figured out a way to change the code so
that you were transferring the array information instead of the array
dimension by dimension.  I believe both array representations
basically use a large flat array that stores the N-dimensional array
content and then a set of variables that store the information about
the number and size of the dimensions.

I never tested the code much or else I would have checked it back in.
By now, it's too late because the code base has changed too much from
the code that I originally altered.

Please let us know if you fix this.  Also, I'd be happy to help and to
send you my old code.

Cheers,
Tal Tversky
ta...@cs...

Rolv Erlend Bredesen writes:
 > Hi Guys,
 > I want the "rank > 2 arrays" limitation fixed.
 > If some of you have good hints I can look into it.
 > 
 > Sincerely Rolv
 > 
 > 
 > ---------- Forwarded message ----------
 > Date: Mon, 18 Oct 2004 10:25:55 -0400
 > From: Andrew Sterian <ste...@cl...>
 > To: ro...@st...
 > Subject: Re: pymat 3d support
 > 
 > Hi Rolv,
 > 
 > I don't really know how MATLAB works with higher dimension
 > arrays. I also haven't really used the python-MATLAB connection
 > in a long time. There is a new project on Sourceforge now
 > at http://sourceforge.net/projects/pymat that has some developers
 > that may be more informed.
 > 
 > ro...@st... wrote:
 > > Hi Andrew.
 > > I'm using python a  lot for numerical computing.
 > > Especially using matlab as a backend for plotting has been very useful.
 > >
 > > Now I want to fix this limitation of pymat:
 > >
 > > """
 > > The following limitations apply to the current version of PyMat:
 > >    1. Only 1-D and 2-D double-precision (real or complex) MATLAB arrays
 > > are supported (and single character strings). Matrices of higher
 > > dimension, structure arrays, cell arrays, etc. are not yet supported.
 > > """
 > >
 > > So I wonder if you could give me some hints on sending 3D, 4D and larger
 > > arrays into matlab through pymat.
 > >
 > > (know about the reshape/flatten trix)
 > >
 > > I already understand most of the code and have compiled it myself.
 > >
 > > Sincerely Rolv

[Pymat-users] pymat 3d support

[Rolv E. B. <ro...@st...>]

Hi Guys,
I want the "rank > 2 arrays" limitation fixed.
If some of you have good hints I can look into it.

Sincerely Rolv


---------- Forwarded message ----------
Date: Mon, 18 Oct 2004 10:25:55 -0400
From: Andrew Sterian <ste...@cl...>
To: ro...@st...
Subject: Re: pymat 3d support

Hi Rolv,

I don't really know how MATLAB works with higher dimension
arrays. I also haven't really used the python-MATLAB connection
in a long time. There is a new project on Sourceforge now
at http://sourceforge.net/projects/pymat that has some developers
that may be more informed.

ro...@st... wrote:
> Hi Andrew.
> I'm using python a  lot for numerical computing.
> Especially using matlab as a backend for plotting has been very useful.
>
> Now I want to fix this limitation of pymat:
>
> """
> The following limitations apply to the current version of PyMat:
>    1. Only 1-D and 2-D double-precision (real or complex) MATLAB arrays
> are supported (and single character strings). Matrices of higher
> dimension, structure arrays, cell arrays, etc. are not yet supported.
> """
>
> So I wonder if you could give me some hints on sending 3D, 4D and larger
> arrays into matlab through pymat.
>
> (know about the reshape/flatten trix)
>
> I already understand most of the code and have compiled it myself.
>
> Sincerely Rolv

-- 
Andrew Sterian, Assistant Professor
Padnos College of Engineering & Computing
Grand Valley State University
ste...@cl...|http://claymore.engineer.gvsu.edu/~steriana

[Pymat-users] problem compiling pymat - invalid conversion from `const maybelong*' to `int*'

[Roy Y. <yve...@um...>]

Hi:

I am compiling pymat and I get this error all over the place:

 invalid conversion from `const maybelong*' to `int*' (see below)

I am compiling using g++ (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5)


Any idea what I should do to solve that ?=20

Thanks
Roy

pymat.cpp: In function `mxArray* makeMxFromNumeric(const =
PyArrayObject*)':
pymat.cpp:216: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:216:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D char]'
pymat.cpp:219: duplicate case value
pymat.cpp:215: previously used here
pymat.cpp:220: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:220:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D unsigned char]'
pymat.cpp:224: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:224:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D signed char]'
pymat.cpp:228: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:228:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D short int]'
pymat.cpp:232: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:232:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D int]'
pymat.cpp:235: duplicate case value
pymat.cpp:231: previously used here
pymat.cpp:236: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:236:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D long int]'
pymat.cpp:240: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:240:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D float]'
pymat.cpp:244: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:244:   initializing argument 5 of `void copyNumeric2Mx(T*, =
int, int,
   double*, int*) [with T =3D double]'
pymat.cpp:248: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:248:   initializing argument 6 of `void copyCplxNumeric2Mx(T*, =
int,
   int, double*, double*, int*) [with T =3D float]'
pymat.cpp:252: invalid conversion from `const maybelong*' to `int*'
pymat.cpp:252:   initializing argument 6 of `void copyCplxNumeric2Mx(T*, =
int,
   int, double*, double*, int*) [with T =3D double]'
pymat.cpp: In function `mxArray* numeric2mx(const PyObject*)':
pymat.cpp:294: invalid conversion from `const PyObject*' to `PyObject*'

[Pymat-users] FASD project: Online survey launched

[<ben...@id...>]

Dear Open Source developer

I am doing a research project on "Fun and Software Development" in which I kindly invite you to participate.
You will find the online survey under http://fasd.ethz.ch/qsf/. The questionnaire consists of 53 questions and you will need about 15 minutes to complete it.

With the FASD project (Fun and Software Development) we want to define the motivational significance of fun when software developers decide to engage in Open Source projects. What is special about our research project is that a similar survey is planned with software developers in commercial firms. This procedure allows the immediate comparison between the involved individuals and the conditions of production of these two development models. Thus we hope to obtain substantial new insights to the phenomenon of Open Source Development.


With many thanks for your participation,
Benno Luthiger


PS:
The results of the survey will be published under http://www.isu.unizh.ch/fuehrung/blprojects/FASD/.
We have set up the mailing list fa...@we... for this study. Please see http://fasd.ethz.ch/qsf/mailinglist_en.html for registration to this mailing list.

_______________________________________________________________________

Benno Luthiger
Swiss Federal Institute of Technology Zurich
8092 Zurich

Mail: benno.luthiger(at)id.ethz.ch
_______________________________________________________________________

[Pymat-users] Adding engOutputBuffer

[Koen V. <ko...@ph...>]

Hi,

Recently, I tried to call Matlab from C, and started with the examples
provided by MathWorks. This wasn't a problem, so I moved to Python.
After spending some time trying to install PyMat, I got it to work as
well, but the Python equivalent of engOutputBuffer was missing. So,
since I never did any Python<->C programming and I'm always looking for
new things to try, I decided to add it.
I tried to copy the style in pymat.cpp. I'm not sure the thing is
correct in any way (should I do Py_INCREF(Pbuf)? I don't know...), but
it seemed to work when I tested it. See the attached file for the diff.
Again, note that I did this just to see if I could and it might not be
useful to anyone. But if you have any comments, I'd be happy to hear
them.

As a quick example, try to run:

import pymat
import array

h=pymat.open()
buf=array.array('c',250*['*'])
print buf
pymat.outputbuffer(h,buf)
pymat.eval(h,'a=1+1+1')
print buf
s=buf.tostring()
print s[0:s.find('\0')]
pymat.eval(h,'b=a^2')
s=buf.tostring()
print s[0:s.find('\0')]
pymat.outputbuffer(h,None)
pymat.eval(h,'c=b-a')
s=buf.tostring()
print s[0:s.find('\0')]
pymat.close(h)


Koen