Mailman 3 March 2006 - SciPy-User

Getting an RGB value from a colormap
by mike cantor March 7, 2006

March 7, 2006

Hi, I'd like to use the colormap interface in a different way than it's used in plotting images. I am plotting a series of curves (using regular old plot), each of which corresponds to the behavior of a biological circuit under a different level of "inducer", ranging from around 0-100. I want to assign the color of each line according to the inducer value, and I want to try out different colormaps to see which I like best. All I really want is a method that, for a given colormap (jet, pink, hot, hsv, etc), takes a number between 0,1 as input and returns the corresponding RGB value, which I can then use a 'color' argument in a plotting command. (I was sort of hoping that the colormap object itself would provide such a method but I couldn't find any description of it's interface). Any ideas? Thanks, -mike

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Re: [SciPy-user] SciPy-user Digest, Vol 31, Issue 8
by pierregm March 7, 2006

March 7, 2006

Paul, I'm running numpy/scipy on an Gentoo/AMD64 without glitches. I assume you have some troubles with lapack/blas & atlas ? I just followed the generic installation instructions from the wiki http://www.scipy.org/Installing_SciPy/BuildingGeneral I copied the blas.a and lapack.a I got in /usr/lib, and the numpy/scipy installation went fine. Not a very elegant method, but one that does the trick. But I'm surprised you have some 32b libraries in /usr/lib. Don't you have a /usr/lib32 in parallel to /usr/lib64, with lib pointing to lib64 only ? I remmbr having the same problem with SuSE (the reason why I switched to Gentoo). What are the libraries being accessed, in fact ? Sorry for not being more helpful -- Pierre GM

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64 bit support
by Paul Ray March 7, 2006

March 7, 2006

Hi, Does anyone have experience building SciPy on 64 bit linux boxes? Our machine is a dual Opteron, running something like RedHat Enterprise 4.2: xxi1 : 74>uname -a Linux xxi1.nrl.navy.mil 2.6.9-11.ELsmp #1 SMP Thu Jun 16 11:18:13 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux We've been running into problems with numpy/scipy looking for libraries in /usr/lib when it should be using /usr/lib64, so that a simple install with setup.py install doesn't work. It crashes when you run and it loads those 32 bit libraries. I think all I need to do is ensure that the library search paths include /usr/lib64 and / usr/X11R6/lib64 and NOT /usr/lib or /usr/X11R6/lib. What is the easy or "right" way to do this? Is there an option to setup.py? Should I make a site.cfg (and where should it reside?)? Should I edit system_info.py? I assume that this configuration is becoming more common as 64-bit processors show up in more machines, so I'm surprised that setup.py doesn't already figure it out and "do the right thing". Are we doing something boneheaded? Thanks, -- Paul

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unsupported operand type(s) for +: 'slice' and 'int'
by Nils Wagner March 7, 2006

March 7, 2006

Traceback (most recent call last): File "aispd.py", line 33, in ? M[:,j] = m_j File "/usr/lib64/python2.4/site-packages/scipy/sparse/sparse.py", line 1308, in __setitem__ self.indptr = resize1d(self.indptr, row+2) TypeError: unsupported operand type(s) for +: 'slice' and 'int' >>> M <420x420 sparse matrix of type '<type 'float64scalar'>' with 0 stored elements (space for 100) in Compressed Sparse Row format> >>> m_j <420x1 sparse matrix of type '<type 'float64scalar'>' with 10 stored elements (space for 1002) in Compressed Sparse Row format> How can I resolve this problem ? for i in arange(0,420): M[i,j] = m_j[i] seems to be not very efficient. Nils

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Addition of sparse matrices
by Nils Wagner March 7, 2006

March 7, 2006

Hi Robert, I am sorry but I cannot resolve my problem w.r.t. to addition of sparse matrices. I tried astype('d') and astype('D'). Please can you exemplify how to fix it. Thanks in advance Nils I think it works ok: $ python add.py 0.393709556483 0.393709570169 should be zero -1.36865185851e-08 1e-8 is the float precision... Try using doubles. r.

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Re: [SciPy-user] Data types
by Tony Mannucci March 6, 2006

March 6, 2006

I am now learning that my installation may be lacking. Travis seemed to confirm that I was not necessarily making a completely silly mistake, so the next step would be to clean up the installation. I great deal of information can be provided according to the instructions in INSTALL.txt. It seems wrong to send that to everyone. Can that also be a ticket? -Tony > >Message: 5 >Date: Mon, 06 Mar 2006 00:44:35 -0700 >From: Travis Oliphant <oliphant.travis(a)ieee.org> >Subject: Re: [SciPy-user] Data types >To: SciPy Users List <scipy-user(a)scipy.net> >Message-ID: <440BE863.5050306(a)ieee.org> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Tony Mannucci wrote: >> Dear Scipy community, >> >> I cannot find a clear statement as to allowable data types, and how >> these are specified. I am trying to read in an array using >> read_array. One of the arguments of the function is "atype", to >> specify the dtype of the output array. I cannot figure out what >> format the tuple atype is in. >> >> >While SciPy builds for NumPy, it has not been "fully" adapted in that it >still uses a lot of Numeric idioms for data-types. > >The read_array code is still using the old concept of "typecode" which >is a one-character string (i.e. what dtype.char gives now). > >There may also still be bugs still in SciPy. >> If Numpy is like Numeric, then, according to "Python In A Nutshell", >> the array objects contain a single type. So, I cannot use several >> values, I would specify only one value for atype. This seems to >> differ from the scipy online documentation, suggesting atype could be >> a tuple. I realize the functionality is evolving. >> >In this case, the functionality was there but might have become broken >in the transition to NumPy (or the result of an old bug). You should be >able to specify a tuple for data-type. Most SciPy functions that take >data-types need to be made aware of the new concept of data type in NumPy. >> Along these lines, the following works: >> data = ARRIN.read_array('filename',columns=(0,2),atype='d') >> >> and appears to give a double precision array (as evidenced from >> data.dtype.char = 'd'). However, using a few other strings for atype >> does not work, e.g. 'I', or 'L', etc. >What do you get as the error? > >> Finally, the following does not seem to work: >> data = ARRIN.read_array('filename',columns=(2)) >> >> so reading a single column appears to cause a problem. The >>following DOES work: >> data = ARRIN.read_array('filename',columns=(0,2)) >> >> >It would be easiest if you opened a ticket and attached an example >file. Open tickets at > >http://projects.scipy.org/scipy/scipy/timeline > >Thanks, > >-Travis > -- Tony Mannucci Supervisor, Ionospheric and Atmospheric Remote Sensing Group Mail-Stop 138-308, Tel > (818) 354-1699 Jet Propulsion Laboratory, Fax > (818) 393-5115 California Institute of Technology, Email > Tony.Mannucci(a)jpl.nasa.gov 4800 Oak Grove Drive, http://genesis.jpl.nasa.gov Pasadena, CA 91109

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Question w.r.t. sparse matrices
by Nils Wagner March 6, 2006

March 6, 2006

Hi, Consider the sparse vector >>> x <420x1 sparse matrix of type '<type 'float64scalar'>' with 2 stored elements (space for 2) in Compressed Sparse Row format> >>> print x (3, 0) 1.0 (30, 0) 1.0 x.getnnz() yields the number of nonzero elements >>> x.getnnz() 2 How can I obtain the pattern of x ? I mean the indices of nonzero elements. Nils

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CSparse: software for upcoming book on sparse direct methods
by Nils Wagner March 6, 2006

March 6, 2006

This might be of interest. Nils From: Tim Davis <davis(a)cise.ufl.edu> Date: Tue, 28 Feb 2006 13:46:36 -0500 Subject: CSparse: software for upcoming book on sparse direct methods I would like to announce the release of a sparse matrix package, CSparse, that I've written for my upcoming book, "Direct Methods for Sparse Linear Systems," to appear in SIAM's Series on the Fundamentals of Algorithms sometime this year. It demonstrates a wide range of sparse matrix algorithms in as concise a code as possible (sparse LU with partial pivoting is only 165 lines, for example, not including the fill-reducing ordering). The algorithms are asymptotically optimal (in most cases), and have comparable performance with existing methods (with exception of the sparse LU, Cholesky, and QR factorizations). One section of the book provides an overview of a wide range of available software for sparse direct methods, with links to high-performance sparse LU, Cholesky, and QR factorization codes: http://www.cise.ufl.edu/research/sparse/codes A MATLAB interface is included (including a pretty color "spy", and an easy MATLAB interface to the UF Sparse Matrix Collection). See http://www.cise.ufl.edu/research/sparse/CSparse or http://www.cise.ufl.edu/research/sparse/CXSparse for an extended version (for complex matrices). Tim Davis University of Florida

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Re: [SciPy-user] CFD in scipy
by Howey, David A March 6, 2006

March 6, 2006

Check this out as well - not python, but open source CFD called openfoam http://www.opencfd.co.uk/ Dave -----Original Message----- From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of Ryan Krauss Sent: 09 February 2006 10:52 To: SciPy Users List Subject: Re: [SciPy-user] CFD in scipy I typed Python CFD into google and this is the first thing that came up: http://datamining.anu.edu.au/~ole/pypar/py4cfd.pdf On 2/9/06, nokophala(a)aim.com <nokophala(a)aim.com> wrote: > > > Hi, > Are there any success stories on the use of Scipy to do CFD or solve > the Navier-Stokes equations, simple or complex problems? I would like > to try some simple RTD distribution calculations for pulp/slurry flows > through mixed batch/continuous reactors, and other relatively simple > cases - but have no funds to do this so I cant buy advanced software yet. > > Thanks in advance, > Noko > ________________________________ > Check Out the new free AIM(R) Mail -- 2 GB of storage and > industry-leading spam and email virus protection. > > _______________________________________________ > 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

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Data types
by Tony Mannucci March 6, 2006

March 6, 2006

Dear Scipy community, I cannot find a clear statement as to allowable data types, and how these are specified. I am trying to read in an array using read_array. One of the arguments of the function is "atype", to specify the dtype of the output array. I cannot figure out what format the tuple atype is in. For example, the following does not work: import scipy.io.array_import as ARRIN data = ARRIN.read_array('filename',columns=(0,2),atype=('d','d')) Yet, if I omit the atype argument, and I do data.dtype.char, I get 'd'. In the read_array doc, it suggests using a "typecode". I don't know what are the allowable typecodes, or the type of a typecode (string? number? etc), and cannot seem to locate this from the Numpy book. If Numpy is like Numeric, then, according to "Python In A Nutshell", the array objects contain a single type. So, I cannot use several values, I would specify only one value for atype. This seems to differ from the scipy online documentation, suggesting atype could be a tuple. I realize the functionality is evolving. Along these lines, the following works: data = ARRIN.read_array('filename',columns=(0,2),atype='d') and appears to give a double precision array (as evidenced from data.dtype.char = 'd'). However, using a few other strings for atype does not work, e.g. 'I', or 'L', etc. Yet, these strings were found from Table 2.1 in the Numpy book. Finally, the following does not seem to work: data = ARRIN.read_array('filename',columns=(2)) so reading a single column appears to cause a problem. The following DOES work: data = ARRIN.read_array('filename',columns=(0,2)) Perhaps I have an incorrect version of the scipy/Numpy modules. I am working on OS X 10.4. Thanks! -Tony -- Tony Mannucci Supervisor, Ionospheric and Atmospheric Remote Sensing Group Mail-Stop 138-308, Tel > (818) 354-1699 Jet Propulsion Laboratory, Fax > (818) 393-5115 California Institute of Technology, Email > Tony.Mannucci(a)jpl.nasa.gov 4800 Oak Grove Drive, http://genesis.jpl.nasa.gov Pasadena, CA 91109

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