Mailman 3 February 2007 - SciPy-User

savitzky golay filtering
by Meesters, Christian Feb. 20, 2007

Feb. 20, 2007

Hi I wanted to do a Savitzky Golay filtering on my data and came aross this piece of code: http://www.dalkescientific.com/writings/NBN/data/savitzky_golay.py Well, translating the necessary bits into current numpy/scipy code is driving me crazy. Can somebody give me a hint on the "M = ..."-line, please? (Or is there a better way to do this filtering with scipy?) TIA Christian

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Re: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
by Nick Fotopoulos Feb. 19, 2007

Feb. 19, 2007

On 2/19/07, scipy-user-request(a)scipy.org <scipy-user-request(a)scipy.org> wrote: > ------------------------------ > > Message: 3 > Date: Sun, 18 Feb 2007 17:09:15 -0600 > From: Robert Kern <robert.kern(a)gmail.com> > Subject: Re: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8 > To: SciPy Users List <scipy-user(a)scipy.org> > Message-ID: <45D8DC9B.9070005(a)gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Niklas Saers wrote: > > Hi guys, > > has anyone successfully compiled Scipy for Python 2.5 under Mac OS X > > 10.4.8? I notice that the binaries on the webpage only support up to > > Python 2.4 so I would like to build them. However, running "python > > setup.py build" I get: > > > > g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3- > > fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/ > > Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/ > > drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ > > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ > > temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ > > fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ > > lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so > > /sw/lib/odcctools590/bin/ld: Undefined symbols: > > It looks like you have the LDFLAGS environment variable defined. That > *overrides* all of the link flags, including the ones that distutils provides to > link against the Python libraries. Don't use LDFLAGS. Robert, At least for me, this is not the case. LDFLAGS is not set, but I get the same "ld: Undefined symbols" error, with both MacPython 2.4 and MacPython 2.5. The failing command is different than Nik's, though. Here is my failing command with MacPython 2.4: error: Command "/usr/local/bin/gfortran -Wall -bundle build/temp.macosx-10.3-fat-2.4/build/src.macosx-10.3-fat-2.4/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/drfft.o build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/zrfft.o build/temp.macosx-10.3-fat-2.4/Lib/fftpack/src/zfftnd.o build/temp.macosx-10.3-fat-2.4/build/src.macosx-10.3-fat-2.4/fortranobject.o -L/opt/lscsoft/non-lsc/lib -L/usr/local/lib/gcc/i386-apple-darwin8.8.1/4.3.0 -Lbuild/temp.macosx-10.3-fat-2.4 -ldfftpack -lfftw3 -lgfortran -o build/lib.macosx-10.3-fat-2.4/scipy/fftpack/_fftpack.so" failed with exit status 1 Numpy and scipy are fresh from SVN. gfortran is from hpc.sourceforge.net, OS is OSX 10.4, and architecture is Intel Any other ideas? Is there other useful information I could provide? My site.cfg and highlights of my python setup.py config are below. Many thanks, Nick ===================== [DEFAULT] search_static_first=true [fftw3] library_dirs = /opt/lscsoft/non-lsc/lib fftw3_libs = fftw3 include_dirs = /opt/lscsoft/non-lsc/include ===================== fftw3_info: FOUND: libraries = ['fftw3'] library_dirs = ['/opt/lscsoft/non-lsc/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/opt/lscsoft/non-lsc/include'] blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] mkl_info, djbfft_info, and umfpack_info are all NOT AVAILABLE, which seems fine by me.

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numpy/scipy on an Intel(R) Core(TM)2 CPU
by Nils Wagner Feb. 19, 2007

Feb. 19, 2007

Hi all, I am going to install numpy/scipy (svn version) on an Intel(R) Core(TM)2 CPU. And I would like to build everything from scratch (including BLAS/LAPACK/ATLAS). Which compiler options/flags should I use for BLAS/LAPACK in that case ? Which fortran compiler g77/gfortran is currently recommended to build numpy/scipy ? BTW, I am using openSUSE 10.2. Nils

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More elegant solution for binning lookup?
by Tom Bridgman Feb. 18, 2007

Feb. 18, 2007

I've browsed the numpy and scipy lists and available docs and haven't found an answer to this. SciPy v0.5.1, numpy v1.0rc3. I've got an array of samples through a region and a value 'R' where I want to find the proper bin in 'radius'. 'R' will generally not match any value in 'radius'. Here's the cleanest solution I found: >>> import scipy >>> import numpy >>> radius = scipy.arange(0.0, 1.5, 1.5/1000) >>> r=0.7274 >>> bin = numpy.nonzero(numpy.where(radius > r, 0, 1))[0][-1] >>> bin 484 >>> radius[484:486] array([ 0.726 , 0.7275]) But even this looks rather ugly and not very intuitive as to what I'm doing. Is there a function built-in to scipy or numpy for this? Thanks, Tom -- W.T. Bridgman, Ph.D. Physics & Astronomy

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Scipy on Python 2.5 / OS X 10.4.8
by Niklas Saers Feb. 18, 2007

Feb. 18, 2007

Hi guys, has anyone successfully compiled Scipy for Python 2.5 under Mac OS X 10.4.8? I notice that the binaries on the webpage only support up to Python 2.4 so I would like to build them. However, running "python setup.py build" I get: g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3- fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/ Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/ drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so /sw/lib/odcctools590/bin/ld: Undefined symbols: _PyArg_ParseTupleAndKeywords _PyCObject_AsVoidPtr _PyCObject_Type _PyComplex_Type _PyDict_SetItemString _PyErr_Clear _PyErr_Format _PyErr_NewException _PyErr_Occurred _PyErr_Print _PyErr_SetString _PyExc_ImportError _PyExc_RuntimeError _PyImport_ImportModule _PyInt_Type _PyModule_GetDict _PyNumber_Int _PyObject_GetAttrString _PySequence_Check _PySequence_GetItem _PyString_FromString _PyString_Type _PyType_IsSubtype _PyType_Type _Py_BuildValue _Py_InitModule4 __Py_NoneStruct _PyCObject_FromVoidPtr _PyDict_DelItemString _PyDict_GetItemString _PyDict_New _PyExc_AttributeError _PyExc_TypeError _PyExc_ValueError _PyMem_Free _PyObject_Str _PyObject_Type _PyString_AsString _PyString_ConcatAndDel _Py_FindMethod __PyObject_New _MAIN_ /sw/lib/odcctools590/bin/ld: Undefined symbols: _PyArg_ParseTupleAndKeywords _PyCObject_AsVoidPtr _PyCObject_Type _PyComplex_Type _PyDict_SetItemString _PyErr_Clear _PyErr_Format _PyErr_NewException _PyErr_Occurred _PyErr_Print _PyErr_SetString _PyExc_ImportError _PyExc_RuntimeError _PyImport_ImportModule _PyInt_Type _PyModule_GetDict _PyNumber_Int _PyObject_GetAttrString _PySequence_Check _PySequence_GetItem _PyString_FromString _PyString_Type _PyType_IsSubtype _PyType_Type _Py_BuildValue _Py_InitModule4 __Py_NoneStruct _PyCObject_FromVoidPtr _PyDict_DelItemString _PyDict_GetItemString _PyDict_New _PyExc_AttributeError _PyExc_TypeError _PyExc_ValueError _PyMem_Free _PyObject_Str _PyObject_Type _PyString_AsString _PyString_ConcatAndDel _Py_FindMethod __PyObject_New _MAIN_ error: Command "g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/ src.macosx-10.3-fat-2.5/Lib/fftpack/_fftpackmodule.o build/ temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfft.o build/ temp.macosx-10.3-fat-2.5/Lib/fftpack/src/drfft.o build/ temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so" failed with exit status 1 I have no idea of why it sais 10.3 rather than 10.4, but perhaps this is not the OS version? I use FFTW 2.1.5 after the website recommended the 2.1 branch for performance over 3.0 and I'm going to be using FFTs a lot Could anyone help me out? :-) Cheers Nik

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Re: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8
by Nick Fotopoulos Feb. 18, 2007

Feb. 18, 2007

On 2/16/07, scipy-user-request(a)scipy.org <scipy-user-request(a)scipy.org> wrote: > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 16 Feb 2007 11:15:35 +0100 > From: Niklas Saers <niklassaers(a)gmail.com> > Subject: [SciPy-user] Scipy on Python 2.5 / OS X 10.4.8 > To: SciPy Users List <scipy-user(a)scipy.org> > Message-ID: <D96375DC-3140-4B1A-8108-3BD0A52937BD(a)gmail.com> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi guys, > has anyone successfully compiled Scipy for Python 2.5 under Mac OS X > 10.4.8? I notice that the binaries on the webpage only support up to > Python 2.4 so I would like to build them. However, running "python > setup.py build" I get: > > g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3- > fat-2.5/Lib/fftpack/_fftpackmodule.o build/temp.macosx-10.3-fat-2.5/ > Lib/fftpack/src/zfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/ > drfft.o build/temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ > temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ > fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ > lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so > /sw/lib/odcctools590/bin/ld: Undefined symbols: > _PyArg_ParseTupleAndKeywords > _PyCObject_AsVoidPtr > _PyCObject_Type > _PyComplex_Type > _PyDict_SetItemString > _PyErr_Clear > _PyErr_Format > _PyErr_NewException > _PyErr_Occurred > _PyErr_Print > _PyErr_SetString > _PyExc_ImportError > _PyExc_RuntimeError > _PyImport_ImportModule > _PyInt_Type > _PyModule_GetDict > _PyNumber_Int > _PyObject_GetAttrString > _PySequence_Check > _PySequence_GetItem > _PyString_FromString > _PyString_Type > _PyType_IsSubtype > _PyType_Type > _Py_BuildValue > _Py_InitModule4 > __Py_NoneStruct > _PyCObject_FromVoidPtr > _PyDict_DelItemString > _PyDict_GetItemString > _PyDict_New > _PyExc_AttributeError > _PyExc_TypeError > _PyExc_ValueError > _PyMem_Free > _PyObject_Str > _PyObject_Type > _PyString_AsString > _PyString_ConcatAndDel > _Py_FindMethod > __PyObject_New > _MAIN_ > /sw/lib/odcctools590/bin/ld: Undefined symbols: > _PyArg_ParseTupleAndKeywords > _PyCObject_AsVoidPtr > _PyCObject_Type > _PyComplex_Type > _PyDict_SetItemString > _PyErr_Clear > _PyErr_Format > _PyErr_NewException > _PyErr_Occurred > _PyErr_Print > _PyErr_SetString > _PyExc_ImportError > _PyExc_RuntimeError > _PyImport_ImportModule > _PyInt_Type > _PyModule_GetDict > _PyNumber_Int > _PyObject_GetAttrString > _PySequence_Check > _PySequence_GetItem > _PyString_FromString > _PyString_Type > _PyType_IsSubtype > _PyType_Type > _Py_BuildValue > _Py_InitModule4 > __Py_NoneStruct > _PyCObject_FromVoidPtr > _PyDict_DelItemString > _PyDict_GetItemString > _PyDict_New > _PyExc_AttributeError > _PyExc_TypeError > _PyExc_ValueError > _PyMem_Free > _PyObject_Str > _PyObject_Type > _PyString_AsString > _PyString_ConcatAndDel > _Py_FindMethod > __PyObject_New > _MAIN_ > error: Command "g95 -L/sw/lib build/temp.macosx-10.3-fat-2.5/build/ > src.macosx-10.3-fat-2.5/Lib/fftpack/_fftpackmodule.o build/ > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfft.o build/ > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/drfft.o build/ > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zrfft.o build/ > temp.macosx-10.3-fat-2.5/Lib/fftpack/src/zfftnd.o build/ > temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/ > fortranobject.o -Lbuild/temp.macosx-10.3-fat-2.5 -ldfftpack -o build/ > lib.macosx-10.3-fat-2.5/scipy/fftpack/_fftpack.so" failed with exit > status 1 > > I have no idea of why it sais 10.3 rather than 10.4, but perhaps this > is not the OS version? I use FFTW 2.1.5 after the website recommended > the 2.1 branch for performance over 3.0 and I'm going to be using > FFTs a lot > > Could anyone help me out? :-) I just wanted to chime in that I have had the same problem on a PPC Mac and on an Intel Mac. My workaround with the iBook (PPC) was to compile Python 2.5 from source. I'll probably do the same on my MBP (Intel), but that's rather inconvenient. It'd make me quite happy if someone could help Nik and I. As an aside, on my MBP, I am testing (for work) the Python 2.3 that shipped with OSX 10.4. Despite the numerous warnings I've found online not to use it, I have found that numpy, scipy, and matplotlib work just fine with 2.3, but I will have to do The Readline Fix in order to make interactive sessions at the command-line usable. Thanks, Nick

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bose-einstein distribution ?
by Gary Pajer Feb. 17, 2007

Feb. 17, 2007

Does the Bose-Einstein distribution exist in scipy.stats? (Perhaps as a name I don't recognize, or a special case of another distribution?) -gary

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str(numpy.inf)
by Samuel GARCIA Feb. 16, 2007

Feb. 16, 2007

Hi list, I have this problem str(numpy.inf) under linux give 'inf' str(numpy.inf) under win32 give '1.#INF' It is a problem for me because with a GUI in LineEdit, for example, the end user who have to enter a float can enter inf under linux but not under win32. Any idea to solve this ? Thanks a lot. Sam -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Samuel Garcia Universite Claude Bernard LYON 1 CNRS - UMR5020, Laboratoire des Neurosciences et Systemes Sensoriels 50, avenue Tony Garnier 69366 LYON Cedex 07 FRANCE Tél : 04 37 28 74 64 Fax : 04 37 28 76 01 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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lsq problem
by Tommy Grav Feb. 15, 2007

Feb. 15, 2007

I need to fit a gaussian profile to a set of points and would like to use scipy (or numpy) to do the least square fitting if possible. I am however unsure if the proper routines are available, so I thought I would ask to get some hints to get going in the right direction. The input are two 1-dimensional arrays x and flux, together with a function def Gaussian(a,b,c,x1): return a*exp(-(pow(x1,2)/pow(c,2))) - c I would like to find the values of (a,b,c), such that the difference between the gaussian and fluxes are minimalized. Would scipy.linalg.lstsq be the right function to use, or is this problem not linear? (I know I could find out this particular problem with a little research, but I am under a little time pressure and I can not for the life of me remember my old math classes). If the problem is not linear, is there another function that can be used or do I have to code up my own lstsq function to solve the problem? Thanks in advance for any hints to the answers. Cheers Tommy

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problem with signal.residue
by Ryan Krauss Feb. 14, 2007

Feb. 14, 2007

I think I have found a small bug in signal.residue and may have found a simple solution. The problem seems to come from polydiv requiring that the numerator polynomial be of degree at most 1 less than the denominator. If I have a denominator of s^2+3*s+2, the numerator must have an s coefficient (even if that coefficient is 0) for signal.residue to work: In [75]: a Out[75]: array([1, 3, 2]) In [76]: signal.residue([1],a) --------------------------------------------------------------------------- exceptions.ValueError Traceback (most recent cal last) C:\Python24\<ipython console> C:\Python24\Lib\site-packages\scipy\signal\signaltools.py in residue(b, a, tol, rtype) 1054 1055 b,a = map(asarray,(b,a)) -> 1056 k,b = polydiv(b,a) 1057 p = roots(a) 1058 r = p*0.0 C:\Python24\Lib\site-packages\numpy\lib\polynomial.py in polydiv(u, v) 399 n = len(v) - 1 400 scale = 1. / v[0] --> 401 q = NX.zeros((m-n+1,), float) 402 r = u.copy() 403 for k in range(0, m-n+1): ValueError: negative dimensions are not allowed In [77]: signal.residue([0,1],a) Out[77]: (array([ 1.+0.j, -1.+0.j]), array([-1.+0.j, -2.+0.j]), array([], dtype=float64)) I think the simple solution is to replace line 1056 with these four lines: if len(b)<len(a): k=[] else: k,b = polydiv(b,a) where the last line above is the old line 1056. Basically, specify that there is no k term if the len of b is less than the len of a. Is this too simple? What do I do to actually submit this if it is the right solution? Ryan

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