Mailman 3 February 2007 - SciPy-Dev

Question about Kaiser Implementation in firwin
by Buehler, Eric (AGRE) 04 Oct '08

04 Oct '08

Hello, I have been using the signal.firwin FIR design tool and I have a question about the implementation. Scipy-0.4.8 Numpy-0.9.6 I am generating a kaiser window with the following parameters: N = 128 Cutoff = ~4e7 width = .3 All of the special kaiser generation parameters in the function follow Oppenheim and Schafer well. Even the sinc function for linear phase is follows exactly. However, the last line of the firwin function is causing me some heartburn. filter_design.py 1538 win = get_window(window,N,fftbins=1) 1539 alpha = N//2 1540 m = numpy.arange(0,N) 1541 h = win*special.sinc(cutoff*(m-alpha)) 1542 return h / sum(h) Line 1542 of filter_design.py, "return h / sum(h)", normalizes the function where it doesn't seem necessary, at least in the kaiser window case. Without the normalization, the kaiser window already returns a value of 1 at the zero frequency point. This normalization scales all of the data, making the window difficult to use in the frequency domain. Can someone point me to the rationale for this line? Looking at the code, this seems to be a pretty recent change (within the last year/year and a half). Thanks, Eric Buehler eric <dot> buehler <at> smiths-aerospace <dot> com ****************************************** The information contained in, or attached to, this e-mail, may contain confidential information and is intended solely for the use of the individual or entity to whom they are addressed and may be subject to legal privilege. If you have received this e-mail in error you should notify the sender immediately by reply e-mail, delete the message from your system and notify your system manager. Please do not copy it for any purpose, or disclose its contents to any other person. The views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of the company. The recipient should check this e-mail and any attachments for the presence of viruses. The company accepts no liability for any damage caused, directly or indirectly, by any virus transmitted in this email. ******************************************

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ZVODE, a Double Precision Complex ODE Solver
by Nils Wagner 19 Feb '08

19 Feb '08

This might be of interest. Nils From: Alan Hindmarsh <alanh(a)llnl.gov> Date: Wed, 6 Dec 2006 18:20:32 -0500 Subject: ZVODE, a Double Precision Complex ODE Solver Of the many solvers freely available for ODE initial value problems, there seem to be very few, if any, for the case of double precision complex dependent variables, even though there have been occasional user calls for this functionality. (Of course a complex system can be treated as a real system of twice the size, but direct treatment as a complex system is preferable.) I have provided such a solver: ZVODE. ZVODE is a straightforward modification of the Fortran ODE solver DVODE, for double precision real systems, making it part of a trio, SVODE/DVODE/ZVODE. ZVODE is available in two locations: (1) Netlib, in /ode (see file zvode.f), and (2) the LLNL CASC software site, www.llnl.gov/CASC/software.html (see VODE). The latter site also includes a demonstration program, zvdemo. Alan Hindmarsh Center for Applied Scientific Computing Lawrence Livermore National Laboratory

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Re: [SciPy-dev] Callback feature for iterative solvers
by Nils Wagner 04 May '07

04 May '07

Ed Schofield wrote: > > On 1/24/07, *Nils Wagner* <nwagner(a)iam.uni-stuttgart.de > <mailto:nwagner@iam.uni-stuttgart.de>> wrote: > > Hi Ed, > > Great ! > Thank you very much ! > It seems to work well with the exception of GMRES. > Please find attached a short test. > Am I missing something ? > > > No, I agree. It seems that there's something wrong with GMRES -- the > iter_ return parameter from gmresrevcom() is never incremented for > this example. I'm not familiar with the algorithm -- perhaps it really > does converge in one iteration? If not, it's just a bug. Could you > file a bug against gmres() in Tracker? > > -- Ed > Hi Ed, Done. Maybe you can add some comments. Again thank you very much for the new functionality !! http://projects.scipy.org/scipy/scipy/ticket/360 Cheers, Nils

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Proposal for more generic optimizers (posted before on scipy-user)
by Matthieu Brucher 18 Apr '07

18 Apr '07

Hi, I'm migratting toward Python for some weeks, but I do not find the tools I had to develop for my PhD in SciPy at the moment. I can't, for instance, find an elegant way to save the set of parameters used in an optimization for the standard algorithms. What is more, I think they can be more generic. What I did in C++, and I'd like your opinion about porting it in Python, was to define a standard optimizer with no iteration loop - iterate was a pure virtual method called by a optimize method -. This iteration loop was then defined for standard optimizer or damped optimizer. Each time, the parameters tested could be saved. Then, the step that had to be taken was an instance of a class that used a gradient step, a Newton step, ... and the same was used for the stoping criterion. The function was a class that defined value, gradient, hessian, ... if needed. For instance, a simplified instruction could have been : Optimizer* optimizer = StandardOptimizer</*some more parameters not relevant in Python*/(function, GradientStep(), SimpleCriterion(NbMaxIterations), step, saveParameters); optimizer->optimize(); optimizer->getOptimalParameters(); The "step" argument was a constant by which the computed step had to be multiplied, by default, it was 1. I know that this kind of writting is not as clear and lightweight as the current one, which is used by Matlab too. But perhaps giving more latitude to the user can be proposed with this system. If people want, I can try making a real Python example... Matthieu P.S. : sorry for the multiposting, I forgot that there were two ML for SciPy :(

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UMFPACKv4.4 and swig memory leak of type 'void *'
by Nils Wagner 10 Apr '07

10 Apr '07

Hi all, scipy.test(1,10) reports a lot of memory leaks, e.g. Getting factors of complex matrixswig/python detected a memory leak of type 'void *', no destructor found. Getting factors of real matrixswig/python detected a memory leak of type 'void *', no destructor found. Solve with UMFPACK: double precision complexswig/python detected a memory leak of type 'void *', no destructor found. swig/python detected a memory leak of type 'void *', no destructor found. ... ok Solve: single precision complexUse minimum degree ordering on A'+A. ... ok Solve with UMFPACK: double precisionswig/python detected a memory leak of type 'void *', no destructor found. swig/python detected a memory leak of type 'void *', no destructor found. ... ok Is this a swig problem ? I am using Numpy version 1.0.2.dev3562 Scipy version 0.5.3.dev2774 cat /proc/cpuinfo yields processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 15 model name : Intel(R) Core(TM)2 CPU 6300 @ 1.86GHz stepping : 6 cpu MHz : 1596.000 cache size : 2048 KB physical id : 0 siblings : 2 core id : 0 cpu cores : 2 fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx lm constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm bogomips : 3726.92 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: processor : 1 vendor_id : GenuineIntel cpu family : 6 model : 15 model name : Intel(R) Core(TM)2 CPU 6300 @ 1.86GHz stepping : 6 cpu MHz : 1596.000 cache size : 2048 KB physical id : 0 siblings : 2 core id : 1 cpu cores : 2 fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx lm constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm bogomips : 3724.17 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: amd_info: libraries = ['amd'] library_dirs = ['/usr/local/src/UMFPACKv4.4/AMD/Lib'] define_macros = [('SCIPY_AMD_H', None)] swig_opts = ['-I/usr/local/src/UMFPACKv4.4/AMD/Include'] include_dirs = ['/usr/local/src/UMFPACKv4.4/AMD/Include'] umfpack_info: libraries = ['umfpack', 'amd'] library_dirs = ['/usr/local/src/UMFPACKv4.4/UMFPACK/Lib', '/usr/local/src/UMFPACKv4.4/AMD/Lib'] define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)] swig_opts = ['-I/usr/local/src/UMFPACKv4.4/UMFPACK/Include', '-I/usr/local/src/UMFPACKv4.4/AMD/Include'] include_dirs = ['/usr/local/src/UMFPACKv4.4/UMFPACK/Include', '/usr/local/src/UMFPACKv4.4/AMD/Include'] rpm -qi swig Name : swig Relocations: (not relocatable) Version : 1.3.29 Vendor: SUSE LINUX Products GmbH, Nuernberg, Germany Release : 29 Build Date: Mon 27 Nov 2006 10:46:51 PM CET Install Date: Mon 19 Feb 2007 09:04:53 AM CET Build Host: lanner.suse.de Group : Development/Languages/C and C++ Source RPM: swig-1.3.29-29.src.rpm Size : 3602040 License: BSD License and BSD-like Signature : DSA/SHA1, Mon 27 Nov 2006 10:57:29 PM CET, Key ID a84edae89c800aca Packager : http://bugs.opensuse.org URL : http://www.swig.org Summary : Simplified Wrapper and Interface Generator Nils

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from scipy import * error on ppc
by Vincent Nijs 27 Feb '07

27 Feb '07

I get the following output on a G5 PPC, OS 10.4.8 when I do 'from scipy import *'. I am using the most recent Mac developer tools and gfortran. This is for todays SVN builds of numpy and scipy. Thanks, Vincent In [4]: from scipy import * --------------------------------------------------------------------------- exceptions.OverflowError Traceback (most recent call last) /Users/vrn953/<ipython console> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/scipy/io/__init__.py 10 from mio import * 11 from npfile import npfile ---> 12 from recaster import sctype_attributes, Recaster 13 from array_import import * 14 from data_store import * /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/scipy/io/recaster.py 47 pass 48 ---> 49 class Recaster(object): 50 ''' Class to recast arrays to one of acceptable scalar types 51 /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/scipy/io/recaster.py in Recaster() 59 ''' 60 ---> 61 _sctype_attributes = sctype_attributes() 62 _k = 2**10 63 _option_defaults = { /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/scipy/io/recaster.py in sctype_attributes() 13 t_list = sctypes[sc_type] 14 for T in t_list: ---> 15 F = finfo(T) 16 dt = dtype(T) 17 d_dict[T] = { /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/numpy/lib/getlimits.py in __new__(cls, dtype) 47 if obj is not None: 48 return obj ---> 49 obj = object.__new__(cls)._init(dtype) 50 for dt in dtypes: 51 cls._finfo_cache[dt] = obj /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/numpy/lib/getlimits.py in _init(self, dtype) 73 lambda v:array(_frz(v)[0], dtype), 74 lambda v: fmt % array(_frz(v)[0], dtype), ---> 75 'numpy %s precision floating point number' % precname) 76 77 for word in ['precision', 'iexp', /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-package s/numpy/lib/machar.py in __init__(self, float_conv, int_conv, float_to_float, float_to_str, title) 263 264 import math --> 265 self.precision = int(-math.log10(float_to_float(self.eps))) 266 ten = two + two + two + two + two 267 resolution = ten ** (-self.precision) OverflowError: math range error --

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no linalg module and failed check_integer test
by Jeremy Conlin 27 Feb '07

27 Feb '07

I just installed scipy from svn and I am having some problems. The most vexing is that I can no longer load the linalg package, at least I can't do anything with it. For example: Python 2.5 (r25:51918, Sep 19 2006, 08:49:13) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.pkgload('linalg') >>> help(scipy.linalg) Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'module' object has no attribute 'linalg' >>> A = scipy.ones((10,10)) >>> scipy.linalg.eig(A) Traceback (most recent call last): File "<stdin>", line 1, in <module> AttributeError: 'module' object has no attribute 'linalg' >>> I didn't notice any errors during the installation. I know this isn't a lot of information to go on, but does anyone know what the problem is? Secondly, and this might be related, when I run scipy.test(1,10) I get the error shown below. Could this be the cause of my linalg problem? Thanks in advance, Jeremy test_init (scipy.io.tests.test_npfile.test_npfile) ... ok test_parse_endian (scipy.io.tests.test_npfile.test_npfile) ... ok test_read_write_array (scipy.io.tests.test_npfile.test_npfile) ... ok test_read_write_raw (scipy.io.tests.test_npfile.test_npfile) ... ok test_remaining_bytes (scipy.io.tests.test_npfile.test_npfile) ... ok ====================================================================== ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/io/tests/test_array_import.py", line 55, in check_integer from scipy import stats File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/stats.py", line 190, in <module> import scipy.special as special File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/__init__.py", line 8, in <module> from basic import * File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/basic.py", line 8, in <module> from _cephes import * ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so, 2): Symbol not found: ___dso_handle Referenced from: /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so Expected in: dynamic lookup ---------------------------------------------------------------------- Ran 554 tests in 2.424s FAILED (errors=1) <unittest.TextTestRunner object at 0x2a49fb0>

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request to be added to editors list wiki page
by Matt Knox 27 Feb '07

27 Feb '07

I'm working on a wiki (http://www.scipy.org/TimeSeriesPackage) and need to edit/delete some attachments I have placed there. Could someone please add me to the editors list for the scipy wiki? My wiki username is "MattKnox". Thanks, - Matt Knox

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scipy license compatibility
by Matt Knox 22 Feb '07

22 Feb '07

Wondering if either of the following licenses are compatible with scipy: Academic Free License ("AFL") v. 3.0: http://opensource.org/licenses/afl-3.0.php EGENIX public license: http://www.egenix.com/files/python/mxLicense.html#Public I'm pretty sure the GNU GPL is not compatible, is that correct? Might be a good idea to have a list of compatible and incompatible open source licences somewhere on the web-site (I can start that myself actually if nobody objects) - Matt Knox

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sandbox.image
by Nils Wagner 22 Feb '07

22 Feb '07

Hi Robert K., I cannot build sanbox.image due to File "Lib/sandbox/setup.py", line 22, in configuration config.add_subpackage(p) File "/usr/lib64/python2.4/site-packages/numpy/distutils/misc_util.py", line 765, in add_subpackage caller_level = 2) File "/usr/lib64/python2.4/site-packages/numpy/distutils/misc_util.py", line 748, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.4/site-packages/numpy/distutils/misc_util.py", line 695, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "Lib/sandbox/image/setup.py", line 6, in configuration config.add_data_files("""ciexyz31_1.txt ciexyz64_1.txt ciexyzjv.txt File "/usr/lib64/python2.4/site-packages/numpy/distutils/misc_util.py", line 903, in add_data_files d,files = files[0] ValueError: too many values to unpack Cheers, Nils

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