Mailman 3 September 2005 - SciPy-User

Re: io.read_array slow
by Jordan H. Mantha Sept. 29, 2005

Sept. 29, 2005

Christian Kristukat wrote: >Hi, > I noticed that io.read_array is really slow compared to a python >while/readline/split loop (about 5 times slower). I believe to remember >that at some time it was written in C but when I looked at the source of >scipy 0.3.2 it seems to be pure python. Is there a evident reason why it >must be that slow or are there maybe plans to rewrite it in C? > Regards, >Christian I have noticed this too. I was wrote a fitting script that reads in a 3 column data file that has 502,000 rows. I first started with io.read_array and it took > 10 min. to get the array in. I was reading "Python Scripting for Computational Science" by Hans Petter Langtangen and used the following: data = array([float(x) for x in infile.read().split()], Float) data.shape = (len(data)/3,3) and it cut down the time to read in the data to ~ 5 s. This was a dramatic speed up for me. I know that io.read_array can handle more complicated cases, but it doesn't always seem to be the best solution for reading in data. --Jordan Mantha

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mdp question
by Ramon Crehuet Sept. 29, 2005

Sept. 29, 2005

Hi all, I am using mdp to perform a PCA on some (dummy) variables. I can get the principal components but I do not know how to get the "explained variance" or change the number of output components. Here is my input: import mdp from scipy import array x=array([[1.51, -2.10, 1.91], [-2.10, 0.45, -1.25], [1.59, -0.51, 0.50], [0.45, -0.93, 1.51], [0.04, -0.49,-0.09], [-0.78, 1.89,-1.55], [-0.62,0.00, -0.42]]) pca=mdp.nodes.PCANode() pca.train(x) pca.stop_training() mat=pca.get_projmatrix() # works fine. x=pca.execute(x,1) #works fine, too. print pca.get_explained_variance() # This gives "None" pca.set_output_dim(1) # and this raises an exception: Traceback (most recent call last): File "/home/ramon/python/pca.py", line 21, in -toplevel- pca.set_output_dim(1) File "/usr/lib/python2.3/site-packages/mdp/nodes/pca_nodes.py", line 32, in set_output_dim raise TrainingFinishedException, errstr NameError: global name 'TrainingFinishedException' is not defined Could someone tell me what I am doing wrong? By the way, does anybody know of an implementation of the partial least squares algorithm? Thanks for your help. Ramon

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splrep problem...
by emmanuel pecontal Sept. 29, 2005

Sept. 29, 2005

Hello, I am trying to use the splrep function to fit data with a B-spline. It works well when the knots are computed by the routine (ie task=0). But when I provide the knots myself I have a segmentation error. And if I provide the knots list computed by splrep in a previous call with task=0, I have the same behaviour. For example: a = arange(100)*2*pi/10. tck = interpolate.splrep(a,sin(a),s=1) tck = interpolate.splrep(a,sin(a),task=-1,t=tck[0]) -> segmentation error Does someone has an idea of what is happening? -- Emmanuel Pécontal CRAL - Observatoire de Lyon 9, Av. Charles Andre F-69561 Saint Genis Laval Cedex tel (33) (0)4.78.86.83.76 - fax (33) (0)4.78.86.83.86 email : pecontal(a)obs.univ-lyon1.fr

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How to wrap numarray with pygrid in python?
by philopensource＠hotmail.com Sept. 29, 2005

Sept. 29, 2005

Hi everyone, My problem is : I have a multidimensionnal numarray.array and i need to display it in a spreadsheet (like pygrid). I need to wrap numarray with pygrig. Although i read some tutorial how to create python wrapper. (Perhaps with swig). Can anybody help me or tell me where to find some ressources? Thanks a lot, Philippe Collet

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build error on itanium2
by Benjamin Rutt Sept. 28, 2005

Sept. 28, 2005

I'm trying to build scipy from source; I've installed f2py, lapack and blas first, and set BLAS and LAPACK. I seem to be getting the following error, on Itanium2. Reading play/unix/README.fpu revealed some discussion; should I be enabling FPU_IGNORE? And if so, how? Or, could I try not building xplt somehow? Thank you. gcc: Lib/xplt/src/play/unix/fpuset.c Lib/xplt/src/play/unix/fpuset.c:304:2: #error <read play/unix/README.fpu for help> Lib/xplt/src/play/unix/fpuset.c:304:2: #error <read play/unix/README.fpu for he lp> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstric t-prototypes -fPIC -Ibuild/temp.linux-ia64-2.4/config_pygist -ILib/xplt/src/gis t -ILib/xplt/src/play -ILib/xplt/src/play/unix -I/usr/X11R6/include -I/usr/X11R 6/include -I/home/ac/rutt/.upak/installed/python-2.4/include/python2.4 -c Lib/x plt/src/play/unix/fpuset.c -o build/temp.linux-ia64-2.4/Lib/xplt/src/play/unix/ fpuset.o -DGISTPATH="\"/home/ac/rutt/.upak/installed/python-2.4/lib/python2.4/s ite-packages/scipy/xplt/gistdata\""" failed with exit status 1

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pyvtk
by Rob Sept. 28, 2005

Sept. 28, 2005

Is this list a proper place to be discussing pyvtk? I have found no other. Thanks, Rob.

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Installation on dual opteron ...
by Arnd Baecker Sept. 28, 2005

Sept. 28, 2005

Hi, we are trying to install scipy on a dual opteron machine (presently running SUSE Linux 10.0 OSS beta). Because there is no fortran compiler installed (and it seems there is none for that beta?), we started to compile the relevant bits from scratch. There are several problems, so before we start reporting them in detail ;-), I would like to ask some general questions: - I have read the thread started by Stephen Walton http://aspn.activestate.com/ASPN/Mail/Message/scipy-dev/2817873 and would like to know, if the patches by Ravikiran Rajagopa (including the c versions of d1mach.f, r1mach.f and i1mach.f, posted in http://aspn.activestate.com/ASPN/Mail/Message/scipy-dev/2820689) have been applied to svn? - Would you recommend to use - gcc, Branch status 2005-09-13 (frozen for 4.0.2 release) or - or GCC 3.4.4 (released 2005-05-18) instead of gcc 4.0.1? (Would choosing gcc 3.4.4 have any negative impact on 64Bit performance?) - And more generally: is there any progress concerning Arrays >2GB with python/Numeric or numarray (as mentioned by Perry Greenfield http://www.scipy.net/pipermail/scipy-user/2005-February/004079.html The machine has 2x16 GB RAM and it would be nice to be able to use them... Many thanks in advance, Arnd and Jan Short notes on the installation: - gcc 4.0.1 (via http://gcc.gnu.org/) Compile command: ../gcc-4.0.1/configure --prefix=/scr/python --enable-shared \ --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu \ --enable-languages=c,c++,f95,objc - export CFLAGS=-fPIC - Python 2.4.1 - ATLAS: atlas3.7.11.tar.bz2 (Linux_HAMMER64SSE3_2) added: full Lapack version (following http://www.scipy.org/documentation/buildatlas4scipy.txt) - BLAS: gfortran -fno-second-underscore -O2 -fPIC -c *.f - LAPACK: make.inc.LINUX, In OPTS variable replace '-fno-f2c -O3' with '-O2 -fPIC' - ATLAS: make xconfig ./xconfig -F f "-fomit-frame-pointer -O -fno-second-underscore -fPIC" -b $BLAS make config - 64 Bit - Posix threads - don't stop - use express setup? [y]: - Enter f77 compiler [g77]: gfortran Enter F77 Flags [-fomit-frame-pointer -O -m64]: - Tune the Level 1 BLAS? [y]: One Problem is that the tests make sanity_test arch=Linux_HAMMER64SSE3_2 make ptsanity_test arch=Linux_HAMMER64SSE3_2 fail - ipython - fftw - f2py2e - scipy: svn co http://svn.scipy.org/svn/scipy/trunk scipy # Checked out revision 1270. cd scipy svn co http://svn.scipy.org/svn/scipy_core/trunk/ scipy_core # Install scipy_distutils: cd scipy_core/scipy_distutils python setup.py install # get system info: python scipy_core/scipy_distutils/system_info.py > ../scipy_systeminfo.txt F77=gfortran python setup.py install | tee ../scipy_install_log.txt

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Selecting items from an array
by Noel O'Boyle Sept. 27, 2005

Sept. 27, 2005

Newbie question: I'm trying to select items from a vector using a mask. For example: X = array([100,56,44,99]) mask = ([0,1,0,1]) I want to create: newX = array([56,99]) i.e. only those elements of X for which mask is true. scipy.take will do this but I need to find the indices of all of the 1's in mask. It must be possible to do this with scipy, but how? Regards, Noel

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making odeint shut up
by alford＠wuphys.wustl.edu Sept. 27, 2005

Sept. 27, 2005

Does anyone know how to stop odeint from displaying error messages like this: lsoda-- at current t (=r1), mxstep (=i1) steps taken on this call before reaching tout in above message, i1 = 500 in above message, r1 = 0.8840344508730E-01 Excess work done on this call (perhaps wrong Dfun type). I would like to tell it to send them to a different output channel (so they don't get mixed up with my print statements), or just suppress them altogether.

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Scipy with Python 2.4 on Windows
by Sylvain Gerbier Sept. 26, 2005

Sept. 26, 2005

Hi everybody, Need help here ... does anybody install scipy on a windows computer with Python 2.4 ? If yes, can he/she tells me how to do it ? I am not so much familiar with the build procedure but can learn ... If nobody have done it, I actually only use the io.savemat function from the scipy library. Does anybody know how I can find a turnaround to save a file with the matlab format without using the scipy library ? Thanks for your help. Sylvain

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