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Matlab / Python

14
Does sombody in here know how i can set an wariable in matlab from python.

I have found numpy an pymat, but i can not find out how to use it.

Im using python 2.5 and matlab 2006b.
Apr 18 '07 #1
9 10600
bartonc
6,596 Expert 4TB
Does sombody in here know how i can set an wariable in matlab from python.

I have found numpy an pymat, but i can not find out how to use it.

Im using python 2.5 and matlab 2006b.
I'm guessing that you have already seen this page.
Apr 18 '07 #2
lskov
14
Yes i have alredy seen it. But i cant find a solusion to my problem.

When im trying to run setup.py install i got an error message.

WINDOWS SPECIFIC ISSUE? Unable to remove c:\docume~1\lasko\locals~1\temp\tmpzzkifo; please delete it manually
[Error 13] The process cannot access the file because it is being used by another process: 'c:\\docume~1\\lasko\\locals~1\\temp\\tmpzzkifo'

running install
running build
running build_py
running build_ext

If i remove the file and trying to run the script again i create the file again and send the same error message.
Apr 18 '07 #3
bartonc
6,596 Expert 4TB
Yes i have alredy seen it. But i cant find a solusion to my problem.

When im trying to run setup.py install i got an error message.

WINDOWS SPECIFIC ISSUE? Unable to remove c:\docume~1\lasko\locals~1\temp\tmpzzkifo; please delete it manually
[Error 13] The process cannot access the file because it is being used by another process: 'c:\\docume~1\\lasko\\locals~1\\temp\\tmpzzkifo'

running install
running build
running build_py
running build_ext

If i remove the file and trying to run the script again i create the file again and send the same error message.
is this pymat or numpy that you are trying to install using the setup.py script?
Apr 18 '07 #4
lskov
14
It is mlabwrap-1.0
Apr 18 '07 #5
bartonc
6,596 Expert 4TB
It is mlabwrap-1.0
I'm guessing that you are on windows and don't have Visual Studio installed and are having a hard time reading this:
Expand|Select|Wrap|Line Numbers
  1. ==============
  2. mlabwrap v1.0
  3. ==============
  4.  
  5. :copyright: 2003-2007 Alexander Schmolck
  6. :date: 2007-04-10
  7.  
  8. ..
  9.  
  10.  
  11. .. contents:: 
  12.  
  13. Description
  14. -----------
  15. A high-level python to `Matlab(tm)`_ bridge. Let's Matlab look like a normal
  16. python library.
  17.  
  18.     Thanks for your terrific work on this very-useful Python tool!
  19.  
  20.     -- George A. Blaha, Senior Systems Engineer, 
  21.        Raytheon Integrated Defense Systems
  22.  
  23.  
  24.  
  25. .. _Matlab(tm): 
  26.    http://www.mathworks.com
  27.  
  28.  
  29.  
  30. News
  31. ----
  32.  
  33. **2007-04-10** 1.0final is out! Compared to the last beta, setup.py should now
  34. work better under windows (Borland C++ support, inter alia). Also included is
  35. a work-around for an ipython bug that causes spurious error message when using
  36. mlabwrap with some versions of ipython. 
  37.  
  38. This is the last version with optional Numeric support. Future versions of
  39. mlabwrap will be hosted as a scikits project on scipy (see
  40. <http://www.scipy.org/MlabWrap>), require numpy and adopt the scipy package
  41. structure (i.e. ``import mlabwrap`` -> ``import scikits.mlabwrap``), which
  42. also implies a change from distutils to setuptools. 
  43.  
  44. The source-forge hosted `project mailing list`_ will remain the prefered place
  45. for users who seek support or want to provide feedback.
  46.  
  47. **Compatibility Note:** Since matlab is becoming increasingly less
  48. ``double``-centric, the default conversion rules might change in post 1.0
  49. mlabwrap; so whilst using ``mlab.plot([1,2,3])`` rather than
  50. ``mlab.plot(array([1.,2.,3.]))`` is fine for interactive use as in the
  51. tutorial below, the latter is recommended for production code.
  52.  
  53.  
  54. License
  55. -------
  56.  
  57. mlabwrap is under MIT license, see LICENSE.txt. mlabraw is under a BSD-style
  58. license, see the mlabraw.cpp.
  59.  
  60. Installation
  61. ------------
  62.  
  63. If you're lucky (linux, Matlab binary in ``PATH`` and the Matlab libraries in
  64. ``LD_LIBRARY_PATH``)::
  65.  
  66.   python setup.py install
  67.  
  68. If the Matlab libraries are not in your ``LD_LIBRARY_PATH`` the above command
  69. will print out a message how to rectify this (you will need to enter something
  70. like ``export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/MatlabR14/bin/glnx86`` in
  71. the shell (assuming you're using bash or zsh); and adding that line to your
  72. ``~/.bashrc`` (or equivalent) is presumably a good idea).
  73.  
  74. If things do go awry, see Troubleshooting_.
  75.  
  76. Although I myself use only linux, mlabwrap should work with python>=2.3 (even
  77. python 2.2, with minor coaxing) and either numpy_ (recommended) or Numeric
  78. (obsolete) installed and Matlab 6, 6.5 or 7 under unix(tm), OS X (tm) and
  79. windows (see `OS X`) on 32- or 64-bit machines.
  80.  
  81. Documentation
  82. -------------
  83. - for lazy people
  84.  
  85.   >>> from mlabwrap import mlab; mlab.plot([1,2,3],'-o')
  86.  
  87.   .. image:: ugly-plot.png
  88.      :alt: ugly-plot
  89.  
  90. - a slightly prettier example
  91.  
  92.   >>> from mlabwrap import mlab; from numpy import *
  93.   >>> xx = arange(-2*pi, 2*pi, 0.2)
  94.   >>> mlab.surf(subtract.outer(sin(xx),cos(xx)))
  95.  
  96.   .. image:: surface-plot.png
  97.      :alt: surface-plot
  98.  
  99. - for a complete description:
  100.   see the doc_ dir or just run ``pydoc mlabwrap``
  101.  
  102.   .. _doc: doc/html/index.html
  103.  
  104. - for people who like tutorials:
  105.   see below
  106.  
  107.  
  108. Tutorial
  109. --------
  110.  
  111. [This is adapted from an email I wrote someone who asked me about mlabwrap.]
  112.  
  113. Legend: [...] = omitted output
  114.  
  115. Let's say you want to do use Matlab(tm) to calculate the singular value
  116. decomposition of a matrix.  So first you import the `mlab` pseudo-module and
  117. Numeric:
  118.  
  119.  
  120. >>> from mlabwrap import mlab
  121. >>> import numpy
  122.  
  123. Now you want to find out what the right function is, so you simply do:
  124.  
  125. >>> mlab.lookfor('singular value')
  126. GSVD   Generalized Singular Value Decompostion.
  127. SVD    Singular value decomposition.
  128. [...]
  129.  
  130. Then you look up what `svd` actually does, just as you'd look up the
  131. docstring of a python function:
  132.  
  133. >>> help(mlab.svd)
  134. mlab_command(*args, **kwargs)
  135.  SVD    Singular value decomposition.
  136.     [U,S,V] = SVD(X) produces a diagonal matrix S, of the same
  137.     dimension as X and with nonnegative diagonal elements in
  138. [...]
  139.  
  140. Then you try it out:
  141.  
  142. >>> mlab.svd(array([[1,2], [1,3]]))
  143. array([[ 3.86432845],
  144.       [ 0.25877718]])
  145.  
  146. Notice that we only got 'U' back -- that's because python hasn't got something
  147. like Matlab's multiple value return. Since Matlab functions can have
  148. completely different behavior depending on how many output parameters are
  149. requested, you have to specify explicitly if you want more than 1. So to get
  150. 'U' and also 'S' and 'V' you'd do:
  151.  
  152. >>> U, S, V = mlab.svd([[1,2],[1,3]], nout=3)
  153.  
  154. The only other possible catch is that Matlab (to a good approximation)
  155. basically represents everything as a double matrix. So there are no
  156. scalars, or 'flat' vectors. They correspond to 1x1 and 1xN matrices
  157. respectively. So, when you pass a flat vector or a scalar to a
  158. mlab-function, it is autoconverted. Also, integer values are automatically
  159. converted to double floats. Here is an example:
  160.  
  161. >>> mlab.abs(-1)
  162. array([       [ 1.]])
  163.  
  164. Strings also work as expected:
  165.  
  166. >>> mlab.upper('abcde')
  167. 'ABCDE'
  168.  
  169. However, although matrices and strings should cover most needs and can be
  170. directly converted, Matlab functions can also return structs or indeed
  171. classes and other types that cannot be converted into python
  172. equivalents. However, rather than just giving up, mlabwrap just hides
  173. this fact from the user by using proxies:
  174. E.g. to create a netlab_ neural net with 2 input, 3 hidden and 1 output node:
  175.  
  176. >>> net = mlab.mlp(2,3,1,'logistic')
  177.  
  178. Looking at `net` reveals that is a proxy:
  179.  
  180. >>> net
  181. <MLabObjectProxy of matlab-class: 'struct'; internal name: 'PROXY_VAL0__';
  182. has parent: no>
  183.     type: 'mlp'
  184.      nin: 3
  185.  nhidden: 3
  186.     nout: 3
  187.     nwts: 24
  188.    outfn: 'linear'
  189.       w1: [3x3 double]
  190.       b1: [0.0873 -0.0934 0.3629]
  191.       w2: [3x3 double]
  192.       b2: [-0.6681 0.3572 0.8118]
  193.  
  194. When `net` or other proxy objects a passed to mlab functions, they are
  195. automatically converted into the corresponding Matlab-objects. So to obtain
  196. a trained network on the 'xor'-problem, one can simply do:
  197.  
  198. >>> net = mlab.mlptrain(net, [[1,1], [0,0], [1,0], [0,1]], [0,0,1,1], 1000)
  199.  
  200. And test with:
  201.  
  202. >>> mlab.mlpfwd(net2, [[1,0]])
  203. array([       [ 1.]])
  204. >>> mlab.mlpfwd(net2, [[1,1]])
  205. array([       [  7.53175454e-09]])
  206.  
  207. As previously mentioned, normally you shouldn't notice at all when you are
  208. working with proxy objects; they can even be pickled (!), although that is
  209. still somewhat experimental.
  210.  
  211. mlabwrap also offers proper error handling and exceptions! So trying to
  212. pass only one input to a net with 2 input nodes raises an Exception:
  213.  
  214.  
Apr 18 '07 #6
bartonc
6,596 Expert 4TB
Here's the other half:
Expand|Select|Wrap|Line Numbers
  1. >>> mlab.mlpfwd(net2, 1)
  2. Traceback (most recent call last):
  3. [...]
  4. mlabraw.error: Error using ==> mlpfwd
  5. Dimension of inputs 1 does not match number of model inputs 2
  6. Warning messages (and messages to stdout) are also displayed:
  7. >>> mlab.log(0)
  8. Warning: Log of zero.
  9. array([       [             -inf]])
  10.  
  11. Comparison to other existing modules
  12. ------------------------------------
  13. To get a vague impression just *how* high-level all this, consider attempting to
  14. do something similar to the first example with pymat (upon which the
  15. underlying mlabraw interface to Matlab(TM) is based).
  16. this:
  17. >>> A, B, C = mlab.svd([[1,2],[1,3]], 0, nout=3)
  18. becomes this:
  19. >>> session = pymat.open()
  20. >>> pymat.put(session, "X", [[1,2], [1,3]])
  21. >>> pymat.put(session, "cheap", 0)
  22. >>> pymat.eval(session, '[A, B, C] = svd(X, cheap)')
  23. >>> A = pymat.get(session, 'A')
  24. >>> B = pymat.get(session, 'B')
  25. >>> C = pymat.get(session, 'C')
  26.  
  27. Plus, there is virtually no error-reporting at all, if something goes wrong in
  28. the `eval` step, you'll only notice because the subsequent `get` mysteriously
  29. fails. And of course something more fancy like the netlab example above (which
  30. uses proxies to represent matlab class instances in python) would be
  31. impossible to accomplish in pymat in a similar manner.
  32.  
  33. However *should* you need low-level access, then that is equally available
  34. (and *with* error reporting); basically just replace ``pymat`` with
  35. ``mlabraw`` above and use ``mlab._session`` as session), i.e
  36. >>> from mlabwrap import mlab
  37. >>> import mlabraw
  38. >>> pymat.put(mlab._session, "X", [[1,2], [1,3]])
  39. [...]
  40. Before you resort to this you should ask yourself if it's really a good idea;
  41. the inherent overhead associated with Matlab's C interface appears to be quite
  42. high, so the additional python overhead shouldn't normally matter much -- if
  43. efficiency becomes an issue it's probably better to try to chunk together
  44. several matlab commands in an ``.m``-file in order to reduce the number of
  45. matlab calls.
  46.  
  47. What's Missing?
  48. ---------------
  49. - Handling of as arrays of (array) rank 3 or more as well as
  50.   non-double/complex arrays (currently everything is converted to
  51.   double/complex for passing to Matlab and passing non-double/complex from
  52.   Matlab is not not supported). Both should be reasonably easy to implement,
  53.   but I currently don't need them.
  54. - Better support for cells.
  55.  
  56. Implementation Notes
  57. --------------------
  58. So how does it all work?
  59. I've got a C extension module (a heavily bug-fixed and somewhat modified
  60. version of pymat, an open-source, low-level python-matlab interface) to take
  61. care of opening Matlab sessions, sending Matlab commands as strings to a
  62. running Matlab session and and converting Numeric arrays (and sequences and
  63. strings...) to Matlab matrices and vice versa. On top of this I then built a
  64. pure python module that with various bells and whistles gives the impression
  65. of providing a Matlab "module".
  66.  
  67. This is done by a class that manages a single Matlab session (of which
  68. `mlab` is an instance) and creates methods with docstrings
  69. on-the-fly. Thus, on the first call of ``mlab.abs(1)``, the wrapper looks
  70. whether there already is a matching function in the cache. If not, the
  71. docstring for ``abs`` is looked up in Matlab and Matlab's flimsy
  72. introspection abilities are used to determine the number of output
  73. arguments (0 or more), then a function with the right docstring is
  74. dynamically created and assigned to ``mlab.abs``. This function takes care
  75. of the conversion of all input parameters and the return values, using
  76. proxies where necessary. Proxy are a bit more involved and the proxy
  77. pickling scheme uses Matlab's `save` command to create a binary version of
  78. the proxy's contents which is then pickled, together with the proxy object
  79. by python itself. Hope that gives a vague idea, for more info study the
  80. source.
  81.  
  82. Troubleshooting
  83. ---------------
  84.  
  85. matlab not in path
  86. ''''''''''''''''''
  87. ``setup.py`` will call ``matlab`` in an attempt to query the version and other
  88. information relevant for installation, so it has to be in your ``PATH``
  89. *unless* you specify everything by hand in ``setup.py``. Of course to be able
  90. to use ``mlabwrap`` in any way ``matlab`` will have to be in your path anyway
  91. (unless that is you set the environment variable ``MLABRAW_CMD_STR`` that
  92. specifies how exactly Matlab(tm) should be called).
  93.  
  94. Library path not set
  95. ''''''''''''''''''''
  96.  
  97. If on importing mlabwrap you get somthing like this::
  98.  
  99.  ImportError: libeng.so: cannot open shared object file: No such file or directory
  100.  
  101. then chances are that the relevant Matlab libraries are not in you library
  102. path. You can rectify this situation in a number of ways; let's assume your
  103. running linux and that the libraries are in ``/opt/matlab/bin/glnx86/``
  104. (**NOTE**: *this used to be ``/opt/matlab/extern/lib/glnx86/`` in versions
  105. before 7; confusingly enough the directory still exists, but the required
  106. libraries no longer reside there!*) 
  107.  
  108. 1. As a normal user, you can append the path to LD_LIBRARY_PATH (under bash)::
  109.  
  110.     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/matlab/bin/glnx86/
  111.  
  112. 2. As root, you can either add the Matlab library path to ``/etc/ld.so.conf``
  113.    and run ``ldconfig``
  114.  
  115. 3. Or, ugly but also works: just copy or symlink all the libraries to
  116.    ``/usr/lib`` or something else that's in your library path.
  117.  
  118. Can't open engine
  119. '''''''''''''''''
  120. If you see something like ``mlabraw.error: Unable to start MATLAB(TM) engine``
  121. then you may be using an incompatible C++ compiler (or version). Try if you
  122. can get the ``engdemo.c`` file to work that comes with your Matlab
  123. installation -- copy it to a directory where you have write access and do
  124. (assuming Matlab is installed in /opt/MatlabR14 and you're running unix,
  125. otherwise modify as requird)::
  126.  
  127.   mex -f /opt/MatlabR14/bin/engopts.sh engdemo.c
  128.   ./engdemo
  129.  
  130. if you get ``Can't start MATLAB engine`` chances are you're trying to use a
  131. compiler version that's not in Mathworks's `list of compatible compilers`_ or
  132. something else with your compiler/Matlab installation is broken that needs to
  133. be resolved before you can successfully build mlabwrap. Chances are that you
  134. or you institution pays a lot of money to the Mathworks, so they should be
  135. happy to give you some tech support. Here's what some user who recently
  136. (2007-02-04) got Matlab 7.04's mex support to work under Ubuntu Edgy after an
  137. exchange with support reported back; apart from installing gcc-3.2.3, he did
  138. the following::
  139.  
  140.   The code I'd run (from within Matlab) is...
  141.   > mex -setup;     # then select: 2 - gcc Mex options
  142.   > optsfile = [matlabroot '/bin/engopts.sh'];
  143.   > mex -v -f optsfile 'engdemo.c';
  144.   > !./engdemo;
  145.  
  146. Old Matlab version
  147. ''''''''''''''''''
  148. If you get something like this on ``python setup.py install``::
  149.  
  150.  mlabraw.cpp:634: `engGetVariable' undeclared (first use this function)
  151.  
  152. Then you're presumably using an old version of Matlab (i.e. < 6.5);
  153. ``setup.py`` ought to have detected this though (try adjusting
  154. ``MATLAB_VERSION`` by hand a write me a bug report).
  155.  
  156.  
  157. OS X
  158. ''''
  159. Josh Marshall tried it under OS X and sent me the following notes (thanks!).
  160.  
  161. Notes on running
  162. ................
  163.  
  164. - Before running python, run::
  165.  
  166.       export  DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH$:/Applications/MATLAB701/bin/mac/
  167.       export MLABRAW_CMD_STR=/Applications/MATLAB701/bin/matlab
  168.  
  169. - As far as graphics commands go, the python interpreter will need to  be run
  170.   from within the X11 xterm to be able to display anything to the  screen.
  171.   ie, the command for lazy people
  172.  
  173.   >>> from mlabwrap import mlab; mlab.plot([1,2,3],'-o')
  174.  
  175.   won't work unless python is run from an xterm, and the matlab startup
  176.   string is
  177.   changed to::
  178.  
  179.       export MLABRAW_CMD_STR="/Applications/MATLAB701/bin/matlab -nodesktop"
  180.  
  181. Windows
  182. '''''''
  183. I'm thankfully not using windows myself, but I try to keep mlabwrap working
  184. under windows, for which I depend on the feedback from windows users. 
  185.  
  186. Since there are several popular C++ compilers under windows, you might have to
  187. tell setup.py which one you'd like to use (unless it's VC 7).
  188.  
  189. George A. Blaha sent me a patch for Borland C++ support; search for "Borland
  190. C++" in setup.py and follow the instructions.
  191.  
  192. Dylan T Walker writes mingw32 will also work fine, but for some reason
  193. (distuils glitch?) the following invocation is required::
  194.  
  195.     > setup.py build --compiler=mingw32
  196.     > setup.py install --skip-build
  197.  
  198.  
  199. Support and Feedback
  200. --------------------
  201.  
  202. Private email is OK, but the preferred way is via the `project mailing list`_
  203.  
  204. .. _project mailing list:
  205.    http://lists.sourceforge.net/lists/listinfo/mlabwrap-user
  206.  
  207. Download
  208. --------
  209.  
  210. <http://sourceforge.net/projects/mlabwrap/>
  211.  
  212. (P.S. the activity stats are bogus -- look at the release dates).
  213.  
  214. Credits
  215. -------
  216.  
  217. Andrew Sterian for writing pymat without which this module would never have
  218. existed. 
  219.  
  220. Matthew Brett contributed numpy compatibility and nice setup.py improvements
  221. (which I adapted a bit) to further reduce the need for manual user
  222. intervention for installation. 
  223.  
  224. I'm only using linux myself -- so I gratefully acknowledge the help of Windows
  225. and OS X users to get things running smoothly under these OSes as well;
  226. particularly those who provided patches to setup.py or mlabraw.cpp (Joris van
  227. Zwieten, George A. Blaha and others).
  228.  
  229. Matlab is a registered trademark of `The Mathworks`_.
  230.  
  231. .. _The Mathworks: 
  232.    http://www.mathworks.com
  233.  
  234. .. _numpy:
  235.    http://numpy.scipy.org
  236.  
  237. .. _netlab:
  238.    http://www.ncrg.aston.ac.uk/netlab/
  239.  
  240. .. _list of compatible compilers:
  241.    http://www.mathworks.com/support/tech-notes/1600/1601.html
  242.  
  243. .. image:: http://sourceforge.net/sflogo.php?group_id=124293&amp;type=5
  244.    :alt: sourceforge-logo
  245.    :target: http://sourceforge.net/projects/mlabwrap/
  246.  
  247.  
Apr 18 '07 #7
bartonc
6,596 Expert 4TB
It is mlabwrap-1.0
I just found PyMat.

I hope MatLab users find this useful.
Jun 18 '07 #8
jlm699
314 100+
I'm trying to play around with mlabwrap but I'm getting an Import Error which is not discussed in the documentation, nor can I find anyone else that has the same problem on web searches. The error is

Expand|Select|Wrap|Line Numbers
  1. import mlabwrap
  2. Traceback (most recent call last):
  3.   File "<input>", line 1, in ?
  4.   File "C:\Python24\Lib\site-packages\mlabwrap.py", line 193, in ?
  5.     import mlabraw
  6. ImportError: DLL load failed: The specified module could not be found.
  7. import mlabraw
  8. Traceback (most recent call last):
  9.   File "<input>", line 1, in ?
  10. ImportError: DLL load failed: The specified module could not be found.
  11.  
Can anybody please help me?

Advanced Thanks,
James
Aug 29 '07 #9
jlm699
314 100+
It would seem that a simple reboot fixed the problem...

I'm sorry that mostly all of my posts follow the general pattern of me realizing my mistake before I get an answer.

Moderators and Administrators: Please feel free to delete my previous two posts as they are completely useless, my apologies.
Aug 29 '07 #10

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