Mailman 3 September 2010 - SciPy-User

ask scipy
by Dan Lussier Sept. 10, 2010

Sept. 10, 2010

Hi, I am having trouble logging in to Ask Scipy using my GoogleID. On both Safari and Firefox on Mac I cannot get the input field to switch over to take GoodID input. The same appears to be true for Yahoo, while the other options are working well. Just wanted to pass it along.

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adding two pseudoinverse matrixes
by Jose Borreguero Sept. 10, 2010

Sept. 10, 2010

Dear Scipy users, I have to solve for Z in the following equation Z^(-1) = A^(-1) - B^(-1), where A and B are covariance matrices with zero determinant. I have never used pseudoinverse matrixes, could anybody please point to me any cautions I have to take when solving this equation for Z? The brute force approach linalg.pinv( linalg.pinv(A) - lingal.pinv(B) ) gives me a matrix with all entries equal to 'infinity'. -Jose Borreguero

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Making Python Lazy
by Lorenzo Isella Sept. 10, 2010

Sept. 10, 2010

Dear All, I hope this is not too off-topic. I am wondering if there is any possibility to make a Python code lazy i.e. to prevent it from calculating quantities which are not used in the code. As an example: you are in a rush to modify your code and at the end it ends up with "dead branches", let's say an array which is calculated but not used in any following calculations, not printed on screen, not stored in a file etc... It would be nice to teach Python to automagically skip its calculation when I run the script (at least in a non-interactive way). I know that such a situation is probably the result of bad programming habits, but it may arise all the same. If I understand correctly, what I am asking for is something different from garbage collection, which would take place, if ever, only after the array has been calculated. Any suggestions (or clarifications if I am on the wrong track) are appreciated. Cheers Lorenzo

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MemoryError with tsfromtxt
by Timmie Sept. 9, 2010

Sept. 9, 2010

Hello, using scikits.timeseries.tsfromtxt I got the following error: File "C:\Python26\lib\site-packages\scikits\timeseries\extras.py", line 504, in tsfromtxt mrec = genfromtxt(fname, **kwargs) File "C:\Python26\lib\site-packages\scikits\timeseries\_preview.py", line 1221, in genfromtxt append_to_rows(tuple(values)) MemoryError Where does this come from? And what could I do to mitigate it? Thanks in advance! Regards, Timmie

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ANN: Python(x,y) 2.6.5.3
by Pierre Raybaut Sept. 9, 2010

Sept. 9, 2010

Hi all, I am pleased to announce that Python(x,y) 2.6.5.3 has been released. Python(x,y) is a free Python distribution providing a ready-to-use scientific development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces (and development framework), Eclipse integrated development environment and Spyder interactive development environment. Its purpose is to help scientific programmers used to interpreted languages (such as MATLAB or IDL) or compiled languages (C/C++ or Fortran) to switch to Python. Changes history Version 2.6.5.3 (09/07/2010) Updated * Enthought Tool Suite 3.4.1 * VTK 5.6.0 Version 2.6.5.2 (09/06/2010) Added * guidata 1.2.1 - Automatically generated graphical user interfaces for easy data set edition and display * guiqwt 2.0.3 - Efficient curve/image plotting and other GUI tools for scientific data processing software development * Veusz 1.9 - Scientific plotting application designed to create publication quality output with a friendly interface * pyhdf 0.8.1 - Python interface to HDF4 files (Hierarchical Data Format version 4) Updated * xy 1.2.1 * Spyder 1.1.5 * Matplotlib 1.0.0 * Enthought Tool Suite 3.4.1 * VTK 5.6.0 * pyopencv 2.1.0.wr1.1.0 * NetworkX 1.3 * MDP 2.6 * Parallel Python 1.6.0 * Cython 0.13 * Sphinx 1.0.3 * docutils 0.7 * jinja2 2.5.2 * pylint 0.21.2 * winpdb 1.4.8 * Pydev 1.6.1 * Console 2.0.146.1 * SciTE 2.21 * SWIG 2.0.0 Cheers, Pierre

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Austin Job Posting
by Dharhas Pothina Sept. 9, 2010

Sept. 9, 2010

Hi All, We have a new full time position open in the Surface Water Resources division at the Texas Water Development Board that may be of interest to folks on this mailing list. This person will primarily working under me developing and maintaining software and procedures to manage and analyze various types of surface water data collected across our division. Most of the work will be using python/numpy/scipy. A description of the position and details on how to apply can be found on our website at http://www.twdb.state.tx.us/about/employment_opportunities/Employopport.asp (Scroll Down to Position # 11-01 Environmental Data Analyst). The actual responsibilities of the position and the skills we are looking for are flexible so I encourage potential applicants to call or email me if they have questions about the position. Actual applications need to be made following the procedures outlined on our website. Please circulate this email as you see fit. Thanks - dharhas Dharhas Pothina, Ph.D., P.E. Special Projects Lead Surface Water Resources Division Texas Water Development Board 1700 North Congress Ave. P.O. Box 13231 Austin, TX 78711-3231 Tel: (512) 936-0818 Fax: (512) 936-0816 dharhas.pothina(a)twdb.state.tx.us www.twdb.state.tx.us

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Weave.inline with multiple processors
by johnl Sept. 9, 2010

Sept. 9, 2010

Hello. I'm a long-time scipy user, but I'm new to this list. I'm having an issue that I haven't been able to find a solution to. I have several python functions with C code embedded using weave.inline. When the code is run, the functions are called by multiple processes. The first time the code is run, this causes a problem as all the processes try to compile the C code simultaneously leading to a broken object file. Any suggestions for fixing this would be appreciated. Thank you, J. David Lee

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Pb with Extending ndimage in C
by moscardi Sept. 9, 2010

Sept. 9, 2010

Hi scipy-users, I try to use the geometric_transform function from scipy.ndimage with a mapping function written in C in order to accelerate execution time of my code. For that, I try to use the tutorial " Extending ndimage in C" (http://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html#ndimage-cca…) but I have any difficulties with it. The given example (which implement a simple shift function) doesn't work : ########################################################################### static int _shift_function(int *output_coordinates, double* input_coordinates, int output_rank, int input_rank, void *callback_data) { int ii; /* get the shift from the callback data pointer: */ double shift = *(double*)callback_data; /* calculate the coordinates: */ for(ii = 0; ii < irank; ii++) icoor[ii] = ocoor[ii] - shift; /* return OK status: */ return 1; } ########################################################################### ***************************************************************************** gcc example.c --shared -lpython -o example.so Compile error : example.c: In function ‘_shift_function’: example.c:12: error: ‘irank’ undeclared (first use in this function) example.c:12: error: (Each undeclared identifier is reported only once example.c:12: error: for each function it appears in.) example.c:13: error: ‘icoor’ undeclared (first use in this function) example.c:13: error: ‘ocoor’ undeclared (first use in this function) ***************************************************************************** So I replace : icoor ocoor irank by : input_coordinates output_coordinates input_rank So my code is : ########################################################################### static int _shift_function(int *output_coordinates, double* input_coordinates, int output_rank, int input_rank, void *callback_data) { int ii; /* get the shift from the callback data pointer: */ double shift = *(double*)callback_data; /* calculate the coordinates: */ for(ii = 0; ii < input_rank; ii++) input_coordinates[ii] = output_coordinates[ii] - shift; /* return OK status: */ return 1; } ########################################################################### I run this code, but the result is not the same as the example : >>> a = np.arange(12.).reshape((4, 3)) >>> fnc= example.shift_function(0.5) >>> print ndimage.geometric_transform(a, fnc) array([[ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.]]) instead of : [[ 0. 0. 0. ] [ 0. 1.3625 2.7375] [ 0. 4.8125 6.1875] [ 0. 8.2625 9.6375]] Could someone please suggest what I need to get this working? Thanks, Eric

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element-wise exponentiation
by Marcel Blattner Sept. 9, 2010

Sept. 9, 2010

Hi I have a beginners question. I have to exponentiate each element of a sparse lil-matrix. I did: a,b = A.nonzero() for i in range(a.size): A[a[i],b[i]] = A[a[i],b[i]]**0.2 Is there a way to do something like A**0.2 like in numpy? Cheers

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Re: Making Python Lazy
by Pablo Angulo Sept. 9, 2010

Sept. 9, 2010

Do you know about generators and generator expressions? http://en.wikipedia.org/wiki/Generator_%28computer_science%29#Python > From: Lorenzo Isella <lorenzo.isella(a)gmail.com> > Subject: [SciPy-User] Making Python Lazy > > Dear All, > I hope this is not too off-topic. > I am wondering if there is any possibility to make a Python code lazy > i.e. to prevent it from calculating quantities which are not used in the > code. > As an example: you are in a rush to modify your code and at the end it > ends up with "dead branches", let's say an array which is calculated but > not used in any following calculations, not printed on screen, not > stored in a file etc... > It would be nice to teach Python to automagically skip its calculation > when I run the script (at least in a non-interactive way). > I know that such a situation is probably the result of bad programming > habits, but it may arise all the same. > If I understand correctly, what I am asking for is something different > from garbage collection, which would take place, if ever, only after the > array has been calculated. > Any suggestions (or clarifications if I am on the wrong track) are > appreciated. > Cheers > > Lorenzo > > > ------------------------------ >

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