Mailman 3 March 2010 - SciPy-User

Easy to make ufuncs from scalar Fortran function?
by John Salvatier 05 Mar '10

05 Mar '10

Hello, Can anyone tell me if it is very difficult to make a numpy ufunc given a scalar function written in Fortran? I have read part of http://docs.scipy.org/doc/numpy/user/c-info.beyond-basics.html on creating ufuncs, is there anything else I should read? John

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changing signs
by josef.pktd＠gmail.com 05 Mar '10

05 Mar '10

http://boscoh.com/protein/a-sign-a-flipped-structure-and-a-scientific-flame… (link found at http://python.genedrift.org/2010/03/03/python-testing-beginner%E2%80%99s-gu… ) Just a reminder about test coverage Josef

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Re: [SciPy-User] [SciPy-user] Audiolab on Py2.6
by SteveRedmond 05 Mar '10

05 Mar '10

ninjasmith wrote: > > >> I made some tests and I am almost sure the problem is with this file: >> "C:\Python26\Lib\site-packages\scikits\audiolab\pysndfile\_sndfile.pyd". >> >> But I don´t know how to see its contents or fix the problem. >> >> Any more tips? (Please!) >> -- > > I have this problem as well, as far as I am aware its not fixed and is a > problem linking to the sndfile.dll. > I just want to echo that I have this problem too. I am using WinXP Home SP3 and a new full installation of Python(x,y)-2.6.2. The simplest attempt to import from _sndfile.pyd is causing audiolab to fail, e.g., a one line script, "from scikits.audiolab import Sndfile", results in the following error: Traceback (most recent call last): File "C:\Python26\lib\site-packages\scikits\audiolab\pysndfile\__init__.py", line 1, in <module> from _sndfile import Sndfile, Format, available_file_formats, available_encodings ImportError: DLL load failed: The specified procedure could not be found. I hope this is only a small and familiar glitch, and that David Cournapeau can get a round to it soon. Audiolab looked promising until this issue stopped me. SteveR -- View this message in context: http://old.nabble.com/Audiolab-on-Py2.6-tp26064218p27788613.html Sent from the Scipy-User mailing list archive at Nabble.com.

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Re: [SciPy-User] helmert implementation (7 parameters - geometric transformation)
by Massimo Di Stefano 05 Mar '10

05 Mar '10

Hi Charles, apologize me, i had only now a chance to answer your mail. i'm really gratefull for your help, now the code works perfectly and i'm really really happy for this ! i tried it with some points and all works fine :-) reading it i also learned some functions like : np.newaxis linalg.lstsq you gived me an awesome help, thanks!!! i've a question about the code, what does : # res = rhs - np.dot(A, sol) # in the code i added the equation to apply the transformation to an input file with coordinates to be converted : XYZ = np.loadtxt(str(inputf)) XYZsize = XYZ.shape[0] ENZglob = np.zeros((XYZsize,3),float) for i in np.arange(XYZsize): X = sol[0] + (1 + sol[6]) * ( XYZ[i,0] - sol[5] * XYZ[i,1] + sol[4] * XYZ[i,2] ) Y = sol[1] + (1 + sol[6]) * ( sol[5] * XYZ[i,0] + XYZ[i,1] - sol[3] * XYZ[i,2] ) Z = sol[2] + (1 + sol[6]) * ( -sol[4] * XYZ[i,0] + sol[3] * XYZ[i,1] + XYZ[i,2] ) ENZglob[i,:] = np.hstack((X,Y,Z)) np.savetxt(output,ENZglob) thanks again!!! regards, Massimo. Il giorno 03/mar/2010, alle ore 02.02, scipy-user-request(a)scipy.org ha scritto: > I've attached a script for the computation. Two things of note: the angles > in the pdf results are in degrees, the value of ? is pretty much in the > noise (the condition number of the matrix is 10^10), and the fit you get > with my version differs from the data by about 7mm. Note that the Helmert > parameters result from a linearization of the rotation matrix, see > Gauss-Newton for more about linearization and least squares, but in this > case I think the limiting factor is the accuracy of the coordinates, not the > linearization.

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interpolate.bispl{rep, ev} need some love, or I'm using them incorrectly...
by Kurt Smith 04 Mar '10

04 Mar '10

I've been trying to get interpolation working on a not-too-large array (512 X 512) using interpolate.interp2d, which is a nice wrapper for interpolate.bispl{rep,ev}. Apparently these routines are meant to work on smallish arrays (~ 50 X 50) and give me a segfault when I hand them anything about (200 X 200) or so. When they do work, they're prohibitively slow. My question is: what is the usecase for these bivariate spline routines? I've discovered ndimage.spline_filter and ndimage.map_coordinates -- these fit my purposes much better; fast and nice interface. What is the difference between the two approaches? Kurt

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scikits.audiolab NameError
by Nils Wagner 04 Mar '10

04 Mar '10

Hi all, I installed audiolab via git clone git://github.com/cournape/audiolab.git python setup.py install --prefix=$HOME/local How can I fix the backend problem wrt. alsa ? python -i test_sndfile.py /data/home/nwagner/local/lib/python2.5/site-packages/scikits.audiolab-0.11.0.dev-py2.5-linux-x86_64.egg/scikits/audiolab/soundio/play.py:48: UserWarning: Could not import alsa backend; most probably, you did not have alsa headers when building audiolab warnings.warn("Could not import alsa backend; most probably, " Traceback (most recent call last): File "test_sndfile.py", line 332, in <module> NumpyTest().run() NameError: name 'NumpyTest' is not defined AFAIK, NumpyTest is obsolete. Am I missing something ? Nils

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Signal to noise ratio
by Nils Wagner 04 Mar '10

04 Mar '10

Hi all, I have two questions concerning signal processing I have used scipy.stats.signaltonoise to compute the signal-to-noise ratio. The value is 0.0447. How can I judge it ? How can I filter out high frequencies using scipy ? How can I eliminate noise from the signal ? Nils

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Scipy failing -- undefined symbol: _ZNSt8ios_base4InitD1Ev
by Baker D.J. 04 Mar '10

04 Mar '10

Hello, I've just installed scipy on our Linux x86_64 machine using the Intel compilers and MKL. All is not well, however, since when I try to use scipy, for example... from scipy import linsolve, sparse I find that there is an unresolved symbol. That is, _ZNSt8ios_base4InitD1Ev. Using c++filt would appear to suggest that I need to add "-lstdc++" to my loader command. c++filt _ZNSt8ios_base4InitD1Ev std::ios_base::Init::~Init() I'm new to numpy and scipy, and so I'm working in the dark to some degree. I've tried modifying intelccompiler.py in the following way, and recompiling numpy and scipy (the idea being that some of the programs in the scipy build are cxx files) compiler_type = 'intel' cc_exe = 'icc -O3 -fPIC' cxx_exe = 'icpc -O3 -fPIC' def __init__ (self, verbose=0, dry_run=0, force=0): UnixCCompiler.__init__ (self, verbose,dry_run, force) compiler = self.cc_exe compiler_cxx = self.cxx_exe self.set_executables(compiler=compiler, compiler_so=compiler, compiler_cxx=compiler_cxx, linker_exe=compiler, linker_so=compiler_cxx + ' -shared -lstdc++') I rebuild scipy using the following command, however the above hasn't helped: python setup.py config --compiler=intel config_fc --fcompiler=intelem install --prefix=/local/software/rh53/scipy/0.7.1/intel Could someone please advise me how to ensure that the "-lstdc++" is successfully passed to the linker as and when I build scipy. This would really be appreciated. Best -- David.

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ValueError with ts.convert of scikits.timeseries
by Marco Tuckner 04 Mar '10

04 Mar '10

Hello, I encountered an error working with a recarray read from a ASCII file with ts.tsfromtxt [1]. The steps were conducted: 1) read in with ts.tsfromtxt ==> recarray with data with minutely frequency 2) missing dates were filed with ts.fill_missing_dates ==> complete series 3) convert into hourly frequency with ts.convert 4) an error occurs, see below. What could be the cause for this? My recarray have the following dtypes: dtype = [('f2', '<i4'), ('f3', '<f8'), ('f4', '<f8'), ('f5', '<i4'), ('f6', '<i4'), ('f7', '<f8'), ('f8', '<f8'), ('f9', '<f8'), ('f10', '<f8'), ('f11', '<f8'), ('f12', '<f8')], Another question related to this: How do I convert the recarrays returned by ts.tsfromtxt into a ndarray? I would like to transform the recarray in a form similar to what is returned data is loaded with np.loadtxt (and then pushed in a timeseries)? I would appreciate any help. Thanks in advance, Marco ##### Traceback ##### [C:scripts/eval]|103> run dataeval.py ------------------------------------------------------------------------ --- ValueError Traceback (most recent call last) C:\scripts\eval\dataeval.py in <module>() 42 myseries_filled_min = ts.fill_missing_dates(series) 43 ---> 44 myseries_hourly_mean = ts.convert(myseries_filled_min,'H',func=np.mean) C:\Python26\lib\site-packages\scikits\timeseries\tseries.pyc in convert(series, freq, func, position, *args, **kwargs) 2003 2004 if series.ndim == 1: -> 2005 obj = _convert1d(series, freq, func, position, *args, **kwargs) 2006 elif series.ndim == 2: 2007 base = _convert1d(series[:,0], freq, func, position, *args, **kwargs) C:\Python26\lib\site-packages\scikits\timeseries\tseries.pyc in _convert1d(series, freq, func, position, *args, **kwargs) 1913 1914 cdictresult = cseries.TS_convert(data_, from_freq, to_freq, position, -> 1915 int(start_date), mask_) 1916 start_date = Date(freq=to_freq, value=cdictresult['startindex']) 1917 data_ = masked_array(cdictresult['values'], mask=cdictresult['mask']) ValueError: data type must provide an itemsize WARNING: Failure executing file: <dataeval.py> ##### [1]: http://pytseries.sourceforge.net/core.timeseries.io.html

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segfaults with weave.inline
by pitam 04 Mar '10

04 Mar '10

Hi Pauli, Thanks, that resolved the issue. I also want to contribute to make a good documentation for weave. Hence, I will submit my code and explanations with the difficulties I had to the present wiki. However, the wiki right now lacks a section for arrays in weave.inline. Shall we create one? Pitam

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