Mailman 3 February 2006 - SciPy-User

io.loadmat
by Ryan Krauss Feb. 5, 2006

Feb. 5, 2006

I am having trouble loading Matlab .mat files that loaded just fine under the old scipy. Here is the error message: In [1]: test=scipy.io.loadmat('figure5') --------------------------------------------------------------------------- exceptions.TypeError Traceback (most recent call last) /home/ryan/thesis/actuator_modeling/<ipython console> /usr/lib/python2.4/site-packages/scipy/io/mio.py in loadmat(name, dict, appendmat, basename) 745 if not (0 in test_vals): # MATLAB version 5 format 746 fid.rewind() --> 747 thisdict = _loadv5(fid,basename) 748 if dict is not None: 749 dict.update(thisdict) /usr/lib/python2.4/site-packages/scipy/io/mio.py in _loadv5(fid, basename) 682 try: 683 var = var + 1 --> 684 el, varname = _get_element(fid) 685 if varname is None: 686 varname = '%s_%04d' % (basename,var) /usr/lib/python2.4/site-packages/scipy/io/mio.py in _get_element(fid) 642 fid.rewind(1) 643 # get the data tag --> 644 raw_tag = fid.read(1,'I') 645 646 # check for compressed /usr/lib/python2.4/site-packages/scipy/io/mio.py in read(self, count, stype, rtype, bs, c_is_b) 283 if count == 0: 284 return zeros(0,rtype) --> 285 retval = numpyio.fread(self, count, stype, rtype, bs) 286 if len(retval) == 1: 287 retval = retval[0] TypeError: argument 3 must be char, not type I attached the message in a previous message, but it was sent to a moderator because it is 600kb. I thought that was a reasonable attachment size, but I guess that message limit is 100kb. If anyone wants the file to try and help me with this, I will gladly send it off list or post it on my website. Thanks, Ryan

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Re: [SciPy-user] BLT for python.
by Bill Northcott Feb. 4, 2006

Feb. 4, 2006

On 04/02/2006, at 1:39 AM, Gary wrote: > > I have a few real-time (strip-chart-like) apps that use BLT. It works > well in real time. It's seems that BLT's not in development anymore, > so I keep waiting for the day when the apps won't run anymore. The > "z" > (latest) version of BLT is slightly broken under Linux, but there > is a > workaround. > The BLT developer, George Howlett, has put a lot of work recently into a version 3.0 of BLT which appears to have support for Aqua on MacOS X. There were quite a few commits to the cvs in November/ December. See http://sf.net/projects/blt Unfortunately as a Mac user myself, one of the Mac files is missing from the cvs, but the code might build under Windows or Linux. The 2.4z version will build on MacOS X with a few fixes which I have posted on the Sourceforge site, but it is far from bug free. George does not respond to email but maybe he reads it. So if a few more people show interest, he might get inspired. Bill Northcott

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compiling scipy on Fedora Core 4 -- undefined reference to PyInt_Type --follow-up
by David Mobley Feb. 3, 2006

Feb. 3, 2006

Following up on the below problems, I'm still trying to compile scipy 0.4.4under RedHat Fedora Core 4. I'm now using gcc 4.0.2 and atlas 3.6.0-8, blas 3.0-36, lapack 3.0-35, numpy 0.94, numarray 1.4.0, and Numeric 24.2. We've also tried on an Opteron (fedora core 4) with no success. I'm still getting the same error when I try to compile as before: > The first error is "In function 'int_from_pyobj': build/src/Lib/fftpack/_fftpackmodule.c:109: undefine d reference to 'PyInt_Type'. Any further suggestions? This is all because I'm hoping to install f2py (although I anticipate using scipy for other reasons later) to be able to interface with some fortran code I'm trying to use for my research relating to computational drug design. Anyway, any help will be greatly appreciated. I still suspect I've done something fundamental wrong, as it doesn't seem like this should be so difficult. Thanks, David On 2/2/06, David Mobley <dmobley(a)gmail.com> wrote: > > Dear All, > > > > I'm sure I've done something stupid, but I haven't been able to turn up > > anything useful with Google, so I need to appeal to the list for help. > > > > I'm trying to install scipy under RedHat Fedora Core 4 on a Xeon, and > the > > build crashes with a whole bunch of "undefined reference to..." errors > when > > it gets to the step of running g77 on various fft and fftpack object and > > shared object libraries. The first error is "In function > 'int_from_pyobj': > > build/src/Lib/fftpack/_fftpackmodule.c:109: undefined > > reference to 'PyInt_Type'. > > > > Can anyone help? I already have NumPy installed and in my PYTHONPATH, > and > > also turned up on the web various suggestions about using > lapack/blas/atlas > > even though they're not absolutely required, so I tried with those as > well > > as without them (first with just lapack and blas, then adding ATLAS) and > > encountered the same problem every time. > > > > Am I missing something eseential? > > > > Thanks very much, > > David Mobley > > > > _______________________________________________ > > SciPy-user mailing list > > SciPy-user(a)scipy.net > > http://www.scipy.net/mailman/listinfo/scipy-user > > > > > > > > Which version of scipy are you trying to build? tried the 0.4.4? > > be sure to yum update everything first. also the Numeric package > (python-numeric-23.7-2) for FC4 is kinda out of date, grab the latest > one from sourceforge. Be sure to upgrade your gcc to at least 4.0.2. > > I am using FC4 on a P4 machine, the following is what i have, not all > of them are needed. > > blas-3.0-36.fc4 > atlas-3.6.0-8.fc4 > lapack-3.0-36.fc4 > gcc-4.0.2-8.fc4 > python-numarray-1.3.3-4.fc4 > > fftw-2.1.5-8 > fftw3-3.0.1-3 > Numeric 24.2 > > scipy-0.4.4 > > > -- > iCy-fLaME > The body maybe wounded, but it is the mind that hurts. > > ------------------------------ > > Message: 9 > Date: Thu, 02 Feb 2006 11:30:54 -0800 > From: Gregory Novak <novak(a)ucolick.org> > Subject: [SciPy-user] What shape should arg 2 of integrate.trapz be? > To: SciPy Users List <scipy-user(a)scipy.net> > Message-ID: <m2acd94ky9.fsf(a)euterpe.local> > Content-Type: text/plain; charset=us-ascii > > If I do this: > > (Note: nrange is like arange, except you specify the number of samples > instead of dx). > > In [474]: x = nrange(-1,1,4) > In [475]: y = nrange(-1,1,5) > In [476]: z = reshape(arange(20.), (4,5)) > In [479]: shape(integrate.trapz(z,axis=0)) > Out[479]: (5,) > > the output is as I expect: I integrate away the (length 4) x dimension > and am left with an answer for each y value. > > However, if I try to specify the x axis, I get the following traceback: > > In [480]: shape(integrate.trapz(z,x,axis=0)) > > --------------------------------------------------------------------------- > /sw/lib/python2.3/site-packages/scipy/integrate/quadrature.py in trapz(y, > x, dx, axis) > 96 slice1[axis] = slice(1,None) > 97 slice2[axis] = slice(None,-1) > ---> 98 return add.reduce(d * (y[slice1]+y[slice2])/2.0,axis) > 99 > 100 def cumtrapz(y, x=None, dx=1.0, axis=-1): > > ValueError: frames are not aligned > > > I can make this work again by explicitly making the x array be 2dim > instead of 1dim: > > In [481]: shape(integrate.trapz(z,x[:,NewAxis],axis=0)) > Out[481]: (5,) > > The question is: Is this the desired behavior? It seems to me that > In[479] is well-specified and should give the correct result. Is > there some reason that one would want to pass in a multi-d array as > the grid for the independent variable? > > Thanks, > Greg > > > > ------------------------------ > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > > End of SciPy-user Digest, Vol 30, Issue 3 > ***************************************** >

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PCA and Scipy
by jaonary＠free.fr Feb. 3, 2006

Feb. 3, 2006

Hi all, I'd like to know if the principal component analysis is already implemented elsewhere in scipy. More generaly, how can I find the list of packages and modules in scipy, and the algo implemented? The link to the API documentation on the web site is not working. Thank you, Jaonary

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Re: [SciPy-user] PCA and Scipy
by Joe Harrington Feb. 3, 2006

Feb. 3, 2006

> I'd like to know if the principal component analysis is already implemented > elsewhere in scipy. If all else fails, and you are on Unix/Linux, try the brute-force approach: find path-to-scipy -type f -print | xargs egrep -i 'pca|principal components' If you don't find what you want in the SciPy package itself, be sure to check the Topical Software listing on the website, and google. Googling "PCA SciPy" shows there were several PCA-related mailing list posts in the past couple of years. --jh--

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BLT for python.
by Peter Jensen Feb. 2, 2006

Feb. 2, 2006

I am new to python, and I am writing a program to display simulation and measurements results. I have a raw version of the program which uses gnuplot and Tkinter, however I would like to make the graphs more interactive. Marker etc... I found BLT for python at : http://heim.ifi.uio.no/~hpl/Pmw.Blt/doc/ It looks very good Does anybody have experience with it. Should we add it to http://www.scipy.org/Wiki/Topical_Software ? I also looked at Chaco at : http://code.enthought.com/chaco/ Again. There is no link at : http://www.scipy.org/Wiki/Topical_Software I also looked a matplotlib, however it does not look well suited for interactive graphs e.g markers are only functional with wxwindows. For TK they are difficult to get to work properly. Any recommendations ?. Regards Peter

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What shape should arg 2 of integrate.trapz be?
by Gregory Novak Feb. 2, 2006

Feb. 2, 2006

If I do this: (Note: nrange is like arange, except you specify the number of samples instead of dx). In [474]: x = nrange(-1,1,4) In [475]: y = nrange(-1,1,5) In [476]: z = reshape(arange(20.), (4,5)) In [479]: shape(integrate.trapz(z,axis=0)) Out[479]: (5,) the output is as I expect: I integrate away the (length 4) x dimension and am left with an answer for each y value. However, if I try to specify the x axis, I get the following traceback: In [480]: shape(integrate.trapz(z,x,axis=0)) --------------------------------------------------------------------------- /sw/lib/python2.3/site-packages/scipy/integrate/quadrature.py in trapz(y, x, dx, axis) 96 slice1[axis] = slice(1,None) 97 slice2[axis] = slice(None,-1) ---> 98 return add.reduce(d * (y[slice1]+y[slice2])/2.0,axis) 99 100 def cumtrapz(y, x=None, dx=1.0, axis=-1): ValueError: frames are not aligned I can make this work again by explicitly making the x array be 2dim instead of 1dim: In [481]: shape(integrate.trapz(z,x[:,NewAxis],axis=0)) Out[481]: (5,) The question is: Is this the desired behavior? It seems to me that In[479] is well-specified and should give the correct result. Is there some reason that one would want to pass in a multi-d array as the grid for the independent variable? Thanks, Greg

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compiling scipy on Fedora Core 4 -- undefined reference to PyInt_Type
by David Mobley Feb. 2, 2006

Feb. 2, 2006

Dear All, I'm sure I've done something stupid, but I haven't been able to turn up anything useful with Google, so I need to appeal to the list for help. I'm trying to install scipy under RedHat Fedora Core 4 on a Xeon, and the build crashes with a whole bunch of "undefined reference to..." errors when it gets to the step of running g77 on various fft and fftpack object and shared object libraries. The first error is "In function 'int_from_pyobj': build/src/Lib/fftpack/_fftpackmodule.c:109: undefined reference to 'PyInt_Type'. Can anyone help? I already have NumPy installed and in my PYTHONPATH, and also turned up on the web various suggestions about using lapack/blas/atlas even though they're not absolutely required, so I tried with those as well as without them (first with just lapack and blas, then adding ATLAS) and encountered the same problem every time. Am I missing something eseential? Thanks very much, David Mobley

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scipy 0.4.4 problems with converters.blitz
by Christian Kristukat Feb. 2, 2006

Feb. 2, 2006

Hi, I've got problems getting inline code to work after having updated from 0.3.2 to 0.4.4. Automatic argument conversion with converters.blitz fails (try the array3d.py example) with this error message: In file included from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/compiler.h:31, from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/blitz.h:47, from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/array-impl.h:41, from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/array.h:32, from /home/ck/.python23_compiled/sc_9824b12a96792c10b5fdb725f9caa3c414.cpp:5: /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/bzconfig.h:39:32: blitz/gnu/bzconfig.h: No such file or directory In file included from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/blitz.h:47, from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/array-impl.h:41, from /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/array.h:32, from /home/ck/.python23_compiled/sc_9824b12a96792c10b5fdb725f9caa3c414.cpp:5: /usr/lib/python2.3/site-packages/scipy/weave/blitz/blitz/compiler.h:38:6: #error In <blitz/config.h>: A working template implementation is required by Blitz++ (you may need to rerun the compiler/bzconfig script) I've tried to install Blitz 0.9, so that at least weave can find the header file "gnu/bzconfig.h" but it didn't really help. Any ideas what is wrong? Regards, Christian

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Failed to plot array using gnuplot-py
by iCy-fLaME Feb. 1, 2006

Feb. 1, 2006

Not sure what is going on, dont even know if this is a glitch cause by gnuplot-py or scipy or python itself, but here is what i found out on my system. Fedora Core 4 gnuplot-4.0.0-7 gnuplot-py-1.7-1 SciPy 0.4.4 It wouldnt plot if i do this: ================================= from scipy import linspace import Gnuplot g = Gnuplot.Gnuplot(debug = 1) x = linspace(0, 1, 20).astype('f') # i.e. array(0.0, 0.05, 0.10, ... 1.0) y = linspace(0, 5, 20).astype('f') d = Gnuplot.Data(x, y) g.plot(d) ================================= However, if i convert the array into a list, then somehow it worked: ================================= from scipy import linspace import Gnuplot g = Gnuplot.Gnuplot(debug = 1) x = linspace(0, 1, 20).astype('f').tolist() y = linspace(0, 5, 20).astype('f').tolist() d = Gnuplot.Data(x, y) g.plot(d) ================================= -- iCy-fLaME The body maybe wounded, but it is the mind that hurts.

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