Mailman 3 October 2004 - SciPy-User

from scipy.xplt import *
by Nils Wagner 06 Oct '04

06 Oct '04

Hi Pearu, hi Travis, Sorry for the trouble with my problem. Finally I have used python setup.py install --force for installing scipy. It seems that --force solved my problems with Numeric 23.3. However with Numeric 23.5 from scipy.xplt import * still fails What is going on there ? Nils

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symeig
by David Grant 06 Oct '04

06 Oct '04

Would it be possible to add something like symeig to scipy? -------- Original Message -------- Subject: Re: [SciPy-user] First few eigenvectors of a numarray array Date: Fri, 3 Sep 2004 17:07:06 +0200 (CEST) From: p.berkes(a)biologie.hu-berlin.de Reply-To: SciPy Users List <scipy-user(a)scipy.net> To: SciPy Users List <scipy-user(a)scipy.net> Hi Stuart, in fact MDP contains a function (mdp.utils.symeig), which provides an interface to some LAPACK routines that are able to compute only the first eigenvectors of a matrix, given that it is symmetrical positive definite (which should be the case, since you're doing PCA). Pietro. On Fri, 3 Sep 2004, Gary Ruben wrote: > Hi Stuart, > > It may well not be relevant to your needs, but since you mentioned you were doing PCA, you might want to look at the MDP package which was announced on this list a few days ago. > http://mdp-toolkit.sourceforge.net/ > > Gary > > ----- Original Message ----- > From: Stuart Murdock <s.e.murdock(a)soton.ac.uk> > Date: Thu, 02 Sep 2004 19:50:57 +0000 > To: SciPy Users List <scipy-user(a)scipy.net> > Subject: Re: [SciPy-user] First few eigenvectors of a numarray array > > > Hi Dave > > > > David Grant wrote: > > > > > When you say "top 10" do you mean the eigenvalues with the largest or > > > smallest values? > > > > > > > Primarily I would be concerned with the eigenvectors associated with the > > largest eigenvalues as presently > > I am interested in Principal Component Analysis of biomolecular > > simulation trajectories. There are ways to approximate > > the top eigenvector / eigenvalue, then get the next and so on but I was > > wondering if there were any packages with those > > types of algorithms already implemented. > > > > Thanks > > > > Stuart > > > > > I would also be interested in knowing if there is any mathematical way > > > of doing this. Sometimes for example in molecular simulations you > > > only want to calculate the ground state energy, for example, and you > > > don't care about the rest... > > > > > > Dave > > > > > > > > > Stuart Murdock wrote: > > > > > >> Hi > > >> > > >> I have a 10000 by 10000 square numarray array which I have obtained > > >> using numarray. I need to obtain the first 10 eigenvalues and > > >> eigenvectors of this so I dont want to have to calculate all > > >> eigenvectors of the matrix. Is anyone aware of any pythonic packages > > >> which > > >> can calculate, lets say, the 10 eigenvectors corresponding to the top > > >> 10 eigenvalues of a numarray array. > > >> > > >> There are a few functions which calculate all of the eigenvectors e.g. > > >> > > >> eig > > >> eigenvectors > > >> > > >> but I only want to calculate the top few. > > >> > > >> Thanks > > >> > > >> Stuart > > >> > > > > > > > > >_______________________________________________ > > >SciPy-user mailing list > > >SciPy-user(a)scipy.net > > >http://www.scipy.net/mailman/listinfo/scipy-user > > > > > > > > > > > > -- > > > > Stuart Murdock Ph.D, > > Research Fellow, > > Dept. of Chemistry / E-Science, > > University of Southampton, > > Highfield, Southampton, > > SO17 1BJ, United Kingdom > > > > http://www.biosimgrid.org > > > > > > > > _______________________________________________ > > SciPy-user mailing list > > SciPy-user(a)scipy.net > > http://www.scipy.net/mailman/listinfo/scipy-user > > _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user -- David J. Grant <http://www.davidgrant.ca:81> Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=1621&t=64>

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Matrix Structure Plots in scipy ?
by Nils Wagner 06 Oct '04

06 Oct '04

Hi all, First of all I would like to thank Pearu for implementing Matrix Market I/O support ! The number of outputs is more than described in help (io.mmio) mmread(source) Reads the contents of the Matrix Market file 'filename' into the matrix 'A'. Inputs: source - Matrix Market filename (extension .mtx) or open file object. Outputs: a - sparse or full matrix Actually b,m,n,s = mmread('young1c') should be used. Is it possible to generate matrix structure plots in scipy ? http://math.nist.gov/MatrixMarket/structureplots.html BTW, there is another "important" matrix format namely matrices generated by NASTRAN (commercial Finite Element program).There exists already a tool that can read and write both dense and sparse matrices, either real or complex, either little or big endian, and either text (any precision) or binary. You can find the code by downloading http://savannah.nongnu.org/cgi-bin/viewcvs/tops/tops/usr/extra/op4tools/ Pearu, please can you manage the support of this format in scipy too ? I believe devoutly, that many users will appreciate this feature. Thanks in advance Nils

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scipy snapshots
by David Grant 05 Oct '04

05 Oct '04

Does anyone build more recent snapshots of scipy for python 2.3 in Windows? I'd really like to get one since mdp-toolkit requires a more recent version than 0.3 Thanks, David -- David J. Grant <http://www.davidgrant.ca:81> Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=1621&t=64>

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RPM building trouble
by Michael Reimpell 05 Oct '04

05 Oct '04

There are some troubles building rpm packages: With the scipy CVS (2004-10-03) version, "python setup.py bdist_rpm --fix-python" fails, because the file "scipy_base/_compiled_base.c" contains two includes (e.g. _scipy_mapping.c), that do not handle the path correctly (therefore _scipy_mapping.c is not found). With the SciPy_complete-0.3.tar.gz version, "python setup.py bdist_rpm --fix-python" fails, because SciPy_complete-0.3/scipy_core/setup.py is missing. Also, in order to build a rpm package from scipy CVS, the scipy_distutils rpm has to be installed, but this package confilcts with the scipy rpm itself, afterwards. Also, recent versions of f2py fail completely building rpms with "python setup.py bdits_rpm --fix-python", because of path problems in setup.py (complains about missing 'src'-directory). This is a known issue at least since F2PY-2.39.235_1693. After installing scipy I stumbled across the following issues: Following the plotting tutorial on "http://www.scipy.org/documentation/plottutorial.html", I had to use gui_thread.start(use_main=1) instead of gui_thread.start(). Also plt.title('some text') fails with: "Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/scipy/plt/interface.py", line 144, in title _active.title.text = name AttributeError: 'instancemethod' object has no attribute 'text'". In general plotting seems to be a bit unstable: sometimes no window appears at first, but it works after restarting python and trying again. I also had a problem with the linalg module: linalg.norm(A,'fro') fails with "Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/scipy/linalg/basic.py", line 273, in norm val = real((conjugate(x)*x).flat) NameError: global name 'real' is not defined", but linalg.norm(A,2) works without problems. Kind regards, Michael

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from scipy.xplt import * failed
by Nils Wagner 05 Oct '04

05 Oct '04

in version '0.3.1_285.4312' Python 2.3.3 (#1, Apr 6 2004, 01:47:39) [GCC 3.3.3 (SuSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy.xplt import * Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/scipy_base/ppimport.py", line 303, in __getattr__ module = self._ppimport_importer() File "/usr/lib/python2.3/site-packages/scipy_base/ppimport.py", line 262, in _ppimport_importer raise PPImportError,\ scipy_base.ppimport.PPImportError: Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy_base/ppimport.py", line 273, in _ppimport_importer module = __import__(name,None,None,['*']) File "/usr/lib/python2.3/site-packages/scipy/xplt/__init__.py", line 12, in ? from Mplot import * File "/usr/lib/python2.3/site-packages/scipy/xplt/Mplot.py", line 1015, in ? import colorbar File "/usr/lib/python2.3/site-packages/scipy/xplt/colorbar.py", line 9, in ? from slice3 import * File "/usr/lib/python2.3/site-packages/scipy/xplt/slice3.py", line 1581, in ? _poly_permutations4 = _construct3 (0) File "/usr/lib/python2.3/site-packages/scipy/xplt/slice3.py", line 1575, in _construct3 mask = find_mask (below, _node_edges3 [itype]) TypeError: Array can not be safely cast to required type Nils

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sqrtm
by Nils Wagner 05 Oct '04

05 Oct '04

Hi all, An entry for sqrtm in help (linalg) is missing. matrix Functions: expm --- matrix exponential using Pade approx. expm2 --- matrix exponential using Eigenvalue decomp. expm3 --- matrix exponential using Taylor-series expansion logm --- matrix logarithm cosm --- matrix cosine sinm --- matrix sine tanm --- matrix tangent coshm --- matrix hyperbolic cosine sinhm --- matrix hyperbolic sine tanhm --- matrix hyperbolic tangent signm --- matrix sign funm --- Evaluating an arbitrary matrix function. help(linalg.sqrtm) yields Help on function sqrtm in module scipy.linalg.matfuncs: sqrtm(A, disp=1) Matrix square root If disp is non-zero display warning if singular matrix. If disp is zero then return residual ||A-X*X||_F / ||A||_F Uses algorithm by Nicholas J. Higham How about help (linalg.iterative) help (linalg.iterative.*) where * = cg,cgs, qmr, gmres, bicg, bicgstab is already available. Nils

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Matrix square root
by Stuart Murdock 05 Oct '04

05 Oct '04

Hi I am trying to calculate the matrix square root (lets say B) of a Matrix (A) which is an array. A = array([[1,2],[3,4]]) such that A = matrixmultiply(B,B) are there any functions in SciPy to do that ? Thanks Stuart -- Stuart Murdock Ph.D, Research Fellow, Dept. of Chemistry / E-Science, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom http://www.biosimgrid.org

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Has anyone use the GA module in SciPy?
by Qingliang Li 04 Oct '04

04 Oct '04

Hi everyone, I am beginner using scipy. I have tryed several ways to install scipy in my computer(Fedora core1). But every times when run the example.py file ($python example.py) of GA module(in the /path/to/python_x.x/site-packages/scipy/ga/). It raises the following errors. What is the wrong with the GA module, or it is because I did not install the scipy in a correct way? Another question: I want to use the Genetic Algorithm in scipy, but it seems that there is not a instruction about the usage. Can someone help me? Any help will be appreciated. ^_^ Error goes like this when I run the file of example.py: Warning: The key "migrants" in not a valid setting. The valid settings are ['pop_size', 'p_replace', 'p_cross', 'p_mutate', 'p_deviation', 'gens', 'rand_seed', 'rand_alg', 'dbase', 'update_rate'] Warning: The key "num_pops" in not a valid setting. The valid settings are ['pop_size', 'p_replace', 'p_cross', 'p_mutate', 'p_deviation', 'gens', 'rand_seed', 'rand_alg', 'dbase', 'update_rate'] initializing... seed = 10161042 beigninning genome generation finished generation: 0.24 evals: 250 evaluation time: 0.03 gen: 0 max: 1.761510717868805 dev: 0.59021618153112299 eval time: 0.37 Traceback (most recent call last) ....... -- Qingliang Li Center for Theoretical Biology, Peking University, Beijing, P.R.China, 100871 Email: qlli(a)ctb.pku.edu.cn Tel: +86-010-6275-9669

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dead links on www.scipy.org
by Michael Reimpell 02 Oct '04

02 Oct '04

on: http://www.scipy.org/documentation/buildscipy.txt link: http://www.scipy.org/documentation/numarraydiscuss link: http://www.scipy.org/development/atlasbinaries/ Anyway, does someone provide a fedora apt repository for SciPy and its dependencies? Michael

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