Mailman 3 May 2009 - SciPy-User

scipy.signal issues in trak
by Tom K. 09 May '09

09 May '09

I am happy to submit a patch to firwin for the new highpass, bandpass, bandstop, and multi-band functionality that I coded up. But it appears that it may languish in trac like several other submitted features that have yet to be integrated in scipy.signal. E.g., fir2, fftfilt (submitted 5/07 and 1/09 respectively). Would it be helpful if I tried to integrate some of these and write tests for them, and then submit a combined patch? -- View this message in context: http://www.nabble.com/scipy.signal-issues-in-trak-tp23460546p23460546.html Sent from the Scipy-User mailing list archive at Nabble.com.

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'from scipy import linalg' fails
by Klubok, Igor 09 May '09

09 May '09

Good morning, I installed scipy 0.7.0 and numpy 1.3.0 on 64bit RedHat Linux 3 ES (kernel 2.4.21-37.Elsmp, AMD-based hardware) Since there was a known bug for incomplete blas packags on RedHat, I properly compiled lapack 3.1.1 and atlas 3.8.3 and installed the resultant files in /usr/local/lib/atlas dir. I set up an env var ATLAS=/usr/local/lib/atlas/lib prior to scipy build/install process. Here is an error message I get: % python2.5 >>> from scipy import linalg; Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/python2.5/lib/python2.5/site- packages/scipy/linalg/__init__.py", line 8, in <module> from basic import * File "/usr/local/python2.5/lib/python2.5/site-packages/scipy/linalg/basic.py" , line 389, in <module> import decomp File "/usr/local/python2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py ", line 23, in <module> from blas import get_blas_funcs File "/usr/local/python2.5/lib/python2.5/site-packages/scipy/linalg/blas.py", line 14, in <module> from scipy.linalg import fblas ImportError: /usr/local/python2.5/lib/python2.5/site-packages/scipy/linalg/fblas.so: undefined symbol: srotmg_ I would appreciate your advice on how to address this issue. Thank you, Igor Klubok DISCLAIMER: This e-mail message and any attachments are intended solely for the use of the individual or entity to which it is addressed and may contain information that is confidential or legally privileged. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately and permanently delete this message and any attachments.

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Size of the text in the legend box
by Mani chandra 07 May '09

07 May '09

Hi, How do I adjust the size of the text in the legend box for matplotlib? Thanks, Mani chandra

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when will scipy win32 for Python2.6 be ready
by Shawn GONG 07 May '09

07 May '09

hi, I am running Python2.6 and MS VS 2005 on Windows XP. I'd like to use scipy. When will scipy binary install for Python2.6 be ready? I tried to run "python setup.py install", but got error message saying: numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. Thanks, Shawn

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SciPy autotester fails on pilutil
by Tanja Gurzhiy 07 May '09

07 May '09

Hi all, I am currently busy with SciPy 0.7.0 installation (I have NumPy v1.3.0 installed and PIL v). If I run the scipy autotester (scipy.test()), I get the failure in testcase from scipy.misc ERROR: Failure: ImportError (No module named Image) ---------------------------------------------------------------------- Traceback (most recent call last): File "/scratch/sources/numpy/nose-0.10.4-install/lib/python2.5/site-packages/nose/loader.py", line 364, in loadTestsFromName addr.filename, addr.module) File "/scratch/sources/numpy/nose-0.10.4-install/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/scratch/sources/numpy/nose-0.10.4-install/lib/python2.5/site-packages/nose/importer.py", line 84, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/tgurzhiy/cadlib/scipy/misc/tests/test_pilutil.py", line 12, in <module> import scipy.misc.pilutil as pilutil File "/cadappl/python_scipy/0.7.0/python_scipy/lib/python2.5/site-packages/scipy/misc/pilutil.py", line 10, in <module> import Image ImportError: No module named Image In pilutil.py line 10 use import Image, the module Image is located in PIL. In my case PYTHONPATH includes only directory (~/cadlib) that includes PIL, NumPy, matloptlib and SciPy therefore module Image cannot be imported directly if scipy.test() is ran. As consequences of this error in pilutil, the functions from this file cannot be used (e.g., imread, imshow, etc.) >>> from scipy import misc >>> im = misc.lena() >>> im.shape (512, 512) >>> im1= misc.imresize(im,1.1) Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'module' object has no attribute 'imresize' Why scipy/misc/pilutil.py uses direct import Image and not import PIL.Image? The work-around could be to update my PYTHONPATH with ~/cadlib/PIL , but I think it is not what should be done. Correct me if I am wrong. Best regards, Tanja Gurzhiy Please find below the information about my system, platform, etc. 'from numpy.f2py.diagnose import run; run() os.name='posix' ------ sys.platform='sunos5' ------ sys.version: 2.5.1 (r251:54863, Aug 6 2008, 14:27:55) [GCC 3.4.3] ------ sys.prefix: /home/tgurzhiy/.caddata/python/python ------ sys.path='/usr/local/asm::/home/tgurzhiy/cadlib:/usr/local/asm/lib/python:/usr/local/asm/bin/python:/scratch/sources/numpy/nose-0.10.4-install/lib/python2.5/site-packages:/home/tgurzhiy/.caddata/python/python/lib/python25.zip:/home/tgurzhiy/.caddata/python/python/lib/python2.5:/home/tgurzhiy/.caddata/python/python/lib/python2.5/plat-sunos5:/home/tgurzhiy/.caddata/python/python/lib/python2.5/lib-tk:/home/tgurzhiy/.caddata/python/python/lib/python2.5/lib-dynload:/home/tgurzhiy/.caddata/python/python/lib/python2.5/site-packages' ------ Failed to import Numeric: No module named Numeric Failed to import numarray: No module named numarray Found new numpy version '1.3.0' in /home/tgurzhiy/cadlib/numpy/__init__.pyc Found f2py2e version '2' in /home/tgurzhiy/cadlib/numpy/f2py/f2py2e.pyc Found numpy.distutils version '0.4.0' in '/home/tgurzhiy/cadlib/numpy/distutils/__init__.pyc' ------ Importing numpy.distutils.fcompiler ... ok ------ Checking availability of supported Fortran compilers: GnuFCompiler instance properties: archiver = ['/home/tgurzhiy/cadbin/g77', '-cr'] compile_switch = '-c' compiler_f77 = ['/home/tgurzhiy/cadbin/g77', '-g', '-Wall', '-fno- second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = None compiler_fix = None libraries = ['g2c'] library_dirs = ['/home/cadappl/gcc/3.4.3/gcc/bin/../lib/gcc/sparc-sun- solaris2.8/3.4.3'] linker_exe = ['/home/tgurzhiy/cadbin/g77', '-g', '-Wall', '-g', '- Wall'] linker_so = ['/home/tgurzhiy/cadbin/g77', '-g', '-Wall', '-g', '- Wall', '-shared', '-mimpure-text'] object_switch = '-o ' ranlib = ['/home/tgurzhiy/cadbin/g77'] version = LooseVersion ('3.4.3') version_cmd = ['/home/tgurzhiy/cadbin/g77', '--version'] Fortran compilers found: --fcompiler=gnu GNU Fortran 77 compiler (3.4.3) Compilers available for this platform, but not found: --fcompiler=g95 G95 Fortran Compiler --fcompiler=gnu95 GNU Fortran 95 compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler Compilers not available on this platform: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=compaq Compaq Fortran Compiler --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for EM64T-based apps --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=none Fake Fortran compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler For compiler details, run 'config_fc --verbose' setup command. ------ Importing numpy.distutils.cpuinfo ... ok ------ CPU information: CPUInfoBase__get_nbits getNCPUs is_32bit is_cpusparcv9 is_sparcv9 is_sun4 ------

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Re: [SciPy-user] sparse SVD
by Kenneth Arnold 07 May '09

07 May '09

2009/4/9 Rob Patro <rob.patro(a)gmail.com>: > Is there any implementation of sparse SVD available in scipy? If not, > does anyone know of an implementation available in python at all? I'd > like to port a project on which I'm working from Matlab to Python, but > it is crucial that I am able to perform the SVD of large and *very* > sparse matrices. The Commonsense Computing Initiative at the MIT Media Lab (http://csc.media.mit.edu but probably best known for http://openmind.media.mit.edu) had a similar problem two years ago: we wanted to run an SVD on a large, sparse semantic network. So we build Divisi (http://divisi.media.mit.edu), which is based on numpy, but also: * wraps SVDLIBC (first with SWIG, now with Cython) (the SVD functionality is abstracted, so we could easily switch to something like cvxopt or ARPACK which I hadn't heard of) * has a data structure for sparse tensors (i.e., matrices with dim > 2) * has a layered model of views enabling: - labeling rows and columns with arbitrary Python objects - various forms of normalization - unfolding tensors into 2D for the higher-order SVD (HO-SVD) operation * supports various math with the SVD results * supports "blending" data from different sources * (in progress) can reason by association as well as similarity The result, refined over almost 2 years of work (by grad students) has powered nearly all of our group's research during this time. It's released under GPL, but other licensing is possible especially if your company sponsors the Media Lab. If you have the numpy headers, you should be able to just `easy_install divisi`. We've recently been working on distribution, so let us know if anything about that is broken. We think that significant chunks of this code would make a great addition to numpy/scipy. We don't have the resources to push integration ourselves, though, but we could certainly help anyone who is interested in assimilating our code. And in the mean time it should be useful to anyone wanting to run sparse SVDs. -Ken

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firwin for even order NOT linear phase; returns 0 coefficients
by Tom K. 07 May '09

07 May '09

This filter is not linear phase: signal.firwin(4,.3) --> array([ 0.02051616, 0.23560318, 0.50827748, 0.23560318]) These two filters are identical except that the 2nd has zeros at either end, the 1st has a zero at the beginning - neither filter is actually the length requested (19 and 19 instead of 20 and 21). In [46]: signal.firwin(20,.3) Out[46]: array([ 9.34176168e-19, 2.92890318e-03, 6.34234732e-03, 3.78304197e-03, -1.23878481e-02, -3.43265728e-02, -3.18598611e-02, 2.65312166e-02, 1.37863165e-01, 2.51347679e-01, 2.99555858e-01, 2.51347679e-01, 1.37863165e-01, 2.65312166e-02, -3.18598611e-02, -3.43265728e-02, -1.23878481e-02, 3.78304197e-03, 6.34234732e-03, 2.92890318e-03]) In [47]: signal.firwin(21,.3) Out[47]: array([ 9.34176168e-19, 2.92890318e-03, 6.34234732e-03, 3.78304197e-03, -1.23878481e-02, -3.43265728e-02, -3.18598611e-02, 2.65312166e-02, 1.37863165e-01, 2.51347679e-01, 2.99555858e-01, 2.51347679e-01, 1.37863165e-01, 2.65312166e-02, -3.18598611e-02, -3.43265728e-02, -1.23878481e-02, 3.78304197e-03, 6.34234732e-03, 2.92890318e-03, 9.34176168e-19]) Can anyone explain this behavior? I don't think either filter should end in zero. I suspect something funny about the way the windows are defined - like, they are designed for spectral analysis, not FIR filter design. -- View this message in context: http://www.nabble.com/firwin-for-even-order-NOT-linear-phase--returns-0-coe… Sent from the Scipy-User mailing list archive at Nabble.com.

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firwin upgrades
by Tom K. 07 May '09

07 May '09

Hi folks, About a month ago, a feature for high / pass / stop filters was requested in firwin (or somewhere in scipy.signal) (see http://projects.scipy.org/scipy/ticket/902). I'm looking at how that might be added and had a few alternatives I would like to run by the group: SUPPORT FOR OTHER FILTER TYPES - PROPOSALS 1) add "btype" kwarg after cutoff that may be any key of the band_dict mapping. Allow cutoff to be a list or 1D array, and make sure that the cutoff and btype arguments are consistent. h = firwin(N, .1) # lowpass h = firwin(N, .1, btype='high') # highpass h = firwin(N, [.1, .2]) # bandpass h = firwin(N, [.1, .2], btype='stop') # bandstop For this, I propose the btype defaults to None, and its value would be 'low' for length 1 cutoff, and 'pass' for length 2 cutoff, since I think bandpass filters are more common than bandstop (maybe I am wrong though). 2) Allow cutoff to be an arbitrary length list. Only need a boolean to indicate whether to start with a value of 0 at DC (the default), or start with a value of 1 at DC (for highpass and bandpass filters). I propose a new 'lowpass' boolean with default True for that in this option. For this, the calls would be e.g.: h = firwin(N, .1) # lowpass h = firwin(N, .1, lowpass=False) # highpass h = firwin(N, [.1, .2], lowpass=False) # bandpass h = firwin(N, [.1, .2]) # bandstop 3) Same as option 2), but instead of a new boolean argument, allow "0" as the first cutoff frequency: h = firwin(N, .1) # lowpass h = firwin(N, [0, .1]) # highpass h = firwin(N, [0, .1, .2]) # bandpass h = firwin(N, [.1, .2]) # bandstop In each of these cases, instead of scaling by 1./sum(h, axis=0), scale by the DTFT of the filter at the center of the first band. What are your preferences from the above (or, suggest an alternative)? NULL AT NYQUIST ISSUE Also, what do we want to do about having an even length filter with a passband at Nyquist (that is pi radians frequency)? All even length filters have a null at pi (because h[0]-h[1]+h[2]-h[3]... = 0 for linear phase, even length). If arguments indicate a passband at Nyquist (that is pi radians frequency), here are some options: a) issue a warning, increase length by 1, and return the longer filter [this is the behavior of another popular signal processing package] b) design the filter anyway, and issue either an error if noScale is False (since the scaling would cause a divide by 0 - see proposal below) or a warning if noScale is True. SUPPORT FOR NO SCALING Currently, the filter is scaled so that the DC value of the filter is unity. This filter no longer minimizes the integral of the square of the error because the scaling is not natural. I propose we provide a boolean "noScale" argument that will allow the filter to float according to the actual least-squares filter. How does that sound? -- View this message in context: http://www.nabble.com/firwin-upgrades-tp23246480p23246480.html Sent from the Scipy-User mailing list archive at Nabble.com.

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examples in docs
by josef.pktd＠gmail.com 05 May '09

05 May '09

Rob Falck just pointed out a nice set of examples for fmin_slsqp at http://projects.scipy.org/scipy/attachment/ticket/570/slsqp_test.py. What's the best way to include them in the docs? the tutorial? Is there a way to include or link to examples that are too long for a docstring? Josef

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How Do I Interpolate a Grid of Data
by Joseph Smidt 04 May '09

04 May '09

Hello, I am new to python and scipy. Lets say I have a file called grid.txt that looks like this ( x, y, f(x,y)): 1 1 0.6 3 1 0.8 7 1 2.3 1 3 0.3 3 3 1.5 7 3 1.3 1 7 2.6 3 7 2.8 7 7 1.3 How would I, using scipy, interpolate this so I get a value at any point on a new grid [0,10]x[0,10]? IE, I would like to take the above information and create some NXN array f so that I could say print f[1][2] or print f[9][10] say, and it would give me the interpolated value at that point. Thanks. Joseph Smidt -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Physics and Astronomy 4129 Frederick Reines Hall Irvine, CA 92697-4575 Office: 949-824-3269

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