Mailman 3 July 2011 - SciPy-User

Power Spectral Density in SciPy, not pylab
by Gus Ishere 26 Nov '11

26 Nov '11

I see the psd() function within matplotlib pylab, and I realize that I can use it to get an array of Pxx,freqs. I don't need to make a figure though and I need to take the PSD of many time series (so it would be nice to do it in a vectorized way). Is there a PSD function within SciPy that allows me to select an axis in a n-dimensional array on which to do the PSD estimation, and then return an n-1 dimensional array? Thanks, Gustavo

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scipy.io.numpyio.fwrite replacement??
by Andres Luhamaa 12 Oct '11

12 Oct '11

Hi all, I try to upgrade code from scipy 0.7.2 to 0.9.0 and see that there is no more scipy.io.numpyio. I found two similar questions in the archive of this list without a reasonable answer (new in the list, so cannot replay to these). In particular I need scipy.io.numpyio.fwrite and I do not know how to replace it with something else. np.save seems to save in double, np.lib.format has some options, but nothing seems what I want. As I am not using python to read the data file, using some other file format like ".npy" or ".npz" is not an option. To illustrate what I want to get, to those familiar with fortran, the write sequence in fortran looks like this: open (filenum, file=filename,form='unformatted', & & access='DIRECT', status='unknown', RECL=lon) write (filenum,REC=IREC) data Any guidance really appreciated, Andres

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inverse function of a spline
by josef.pktd＠gmail.com 01 Oct '11

01 Oct '11

I have a function y = f(x) which is monotonically increasing (a cumulative distribution function) f is defined by piecewise polynomial interpolation, an interpolating spline on some points I would like to get the inverse function (ppf) x = f^{-1} (y) if the spline is of higher order than linear In the linear case it's trivial, because the inverse function is also just a piecewise linear interpolation. If I have a cubic spline, or any other smooth interpolator in scipy, is there a way to get the inverse function directly? I don't know much about general properties of splines, and would appreciate any hints, so I can avoid numerical inversion (fsolve or similar) Thanks, Josef

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Separate scales for left and right axis broken
by Christopher Peters 29 Sep '11

29 Sep '11

All, I am trying to run the code at http://pytseries.sourceforge.net/lib.plotting.examples.html#separate-scales… to generate separate scales for left and right axes for tsplot in scikits.timeseries.lib.plotlib, but I am getting an error. Package versions: Numpy: 1.5.1 Matplotlib: 1.0.1 Scikits Timeseries: 0.91.3 Code to test: import numpy as np print np.__version__ import numpy.ma as ma import matplotlib.pyplot as plt print matplotlib.__version__ import scikits.timeseries as ts print ts.__version__ import scikits.timeseries.lib.plotlib as tpl # generate some random data data1 = np.cumprod(1 + np.random.normal(0, 1, 300)/100) data2 = np.cumprod(1 + np.random.normal(0, 1, 300)/100)*100 start_date = ts.Date(freq='M', year=1982, month=1) series1 = ts.time_series(data1, start_date=start_date-50) series2 = ts.time_series(data2, start_date=start_date) fig = tpl.tsfigure() fsp = fig.add_tsplot(111) # plot series on left axis fsp.tsplot(series1, 'b-', label='<- left series') fsp.set_ylim(ma.min(series1.series), ma.max(series1.series)) # create right axis fsp_right = fsp.add_yaxis(position='right', yscale='log') # plot series on right axis fsp_right.tsplot(series2, 'r-', label='-> right series') fsp_right.set_ylim(ma.min(series2.series), ma.max(series2.series)) # setup legend fsp.legend( (fsp.lines[-1], fsp_right.lines[-1]), (fsp.lines[-1].get_label(), fsp_right.lines[-1].get_label()), ) plt.show() Traceback (most recent call last): File "<pyshell#75>", line 23, in <module> fsp_right = fsp.add_yaxis(position='right', yscale='log') File "C:\Python27\lib\site-packages\scikits\timeseries\lib\plotlib.py", line 1196, in add_yaxis fsp_alt_args = (fsp._rows, fsp._cols, fsp._num + 1) AttributeError: 'TimeSeriesPlot' object has no attribute '_rows' My guess is that the newest version of matplotlib (1.0.1) removed the _rows (_cols, and _num as well) attribute for the Subplot base class, but this was not propagated to plotlib.py. Looking at the revision log at http://projects.scipy.org/scikits/log/trunk/timeseries/scikits/timeseries/l… , it appears that 20 months ago there were some fixes for matplotlib version 0.99.0. It seems that this question was already posed by Dave Hirschfeld on 2010 Nov 8 (a post entitled "TimeSeries Plotting Broken?" at http://permalink.gmane.org/gmane.comp.python.scientific.devel/14645), but there were no replies. Any help on this would be greatly appreciated!

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scikits timeseries tofile
by Gar Brown 28 Sep '11

28 Sep '11

Hi All, While trying to write a timeseries object to file I the following error: File "C:\Python27\lib\site-packages\scikits\timeseries\tseries.py", line 1527, in tofile return scipy.io.write_array(fileobject, tmpfiller, **optpars) AttributeError: 'module' object has no attribute 'write_array' I noticed that the scipy.io.write_array function has been deprecated for some time, is there a fix or workaround for avoiding this error. I really like the time series functionality of scikits.timeseries timeseries version: __author__ = "Pierre GF Gerard-Marchant & Matt Knox ($Author: mattknox_ca $)" __revision__ = "$Revision: 2213 $" __date__ = '$Date: 2009-08-23 12:43:40 -0400 (Sun, 23 Aug 2009) $'

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computing local extrema
by fred 15 Sep '11

15 Sep '11

Hi, I would like to compute local extrema of an array (2D/3D), ie get a list of points (coords + value). How could I do this? Any hint? TIA. Cheers, -- Fred

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scipy.optimize named argument inconsistency
by Joon Ro 14 Sep '11

14 Sep '11

Hi, I just found that for some functions such as fmin_bfgs, the argument name for the objective function to be minimized is f, and for others such as fmin, it is func. I was wondering if this was intended, because I think it would be better to have consistent argument names across those functions. http://docs.scipy.org/doc/scipy/reference/optimize.html -Joon --

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Building SciPy on Debian with Intel compilers
by Klonuo Umom 17 Aug '11

17 Aug '11

Debian 6.0.1 Python 2.6.7 ifort 11.1 20100806 icc 11.1 20091130 mkl 10.3 After successfully building latest stable NumPy (1.6.1RC2) I tried to build SciPy (0.9.0) following two sources: http://new.scipy.org/building/linux.html http://blog.sun.tc/2010/11/numpy-and-scipy-with-intel-mkl-on-linux.html But I get this error: ------------------------------------------------ ... building 'qhull' library compiling C sources C compiler: icc -fPIC compile options: '-I/usr/include/python2.6 -I/usr/local/lib/python2.6/dist-packages/numpy/core/include -I/usr/local/lib/python2.6/dist-packages/numpy/core/include -c' icc: scipy/spatial/qhull/src/poly.c scipy/spatial/qhull/src/qhull_a.h(106): warning #77: this declaration has no storage class or type specifier template <typename T> ^ scipy/spatial/qhull/src/qhull_a.h(106): error: expected a ";" template <typename T> ^ scipy/spatial/qhull/src/qhull_a.h(115): warning #12: parsing restarts here after previous syntax error void qh_qhull(void); ^ compilation aborted for scipy/spatial/qhull/src/poly.c (code 2) scipy/spatial/qhull/src/qhull_a.h(106): warning #77: this declaration has no storage class or type specifier template <typename T> ^ scipy/spatial/qhull/src/qhull_a.h(106): error: expected a ";" template <typename T> ^ scipy/spatial/qhull/src/qhull_a.h(115): warning #12: parsing restarts here after previous syntax error void qh_qhull(void); ^ compilation aborted for scipy/spatial/qhull/src/poly.c (code 2) error: Command "icc -fPIC -I/usr/include/python2.6 -I/usr/local/lib/python2.6/dist-packages/numpy/core/include -I/usr/local/lib/python2.6/dist-packages/numpy/core/include -c scipy/spatial/qhull/src/poly.c -o build/temp.linux-i686-2.6/scipy/spatial/qhull/src/poly.o" failed with exit status 2 ------------------------------------------------ As Google did not return anything about this error, and I just installed Debian two days ago, without any Linux experience, I might miss something. Or what can cause this error? Thanks

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[ANN] Bottleneck 0.5.0 released
by Keith Goodman 13 Aug '11

13 Aug '11

Bottleneck is a collection of fast NumPy array functions written in Cython. It contains functions like median, nanmedian, nanargmax, move_max, rankdata. The fifth release of bottleneck adds four new functions, comes in a single source distribution instead of separate 32 and 64 bit versions, and contains bug fixes. J. David Lee wrote the C-code implementation of the double heap moving window median. New functions: - move_median(), moving window median - partsort(), partial sort - argpartsort() - ss(), sum of squares, faster version of scipy.stats.ss Changes: - Single source distribution instead of separate 32 and 64 bit versions - nanmax and nanmin now follow Numpy 1.6 (not 1.5.1) when input is all NaN Bug fixes: - #14 Support python 2.5 by importing `with` statement - #22 nanmedian wrong for particular ordering of NaN and non-NaN elements - #26 argpartsort, nanargmin, nanargmax returned wrong dtype on 64-bit Windows - #29 rankdata and nanrankdata crashed on 64-bit Windows download http://pypi.python.org/pypi/Bottleneck docs http://berkeleyanalytics.com/bottleneck code http://github.com/kwgoodman/bottleneck mailing list http://groups.google.com/group/bottle-neck mailing list 2 http://mail.scipy.org/mailman/listinfo/scipy-user

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Status of TimeSeries SciKit
by Paul Bilokon 07 Aug '11

07 Aug '11

Hi, I would like to find out about the status of the TimeSeries SciKit. It looks like it hasn't been updated for some years. Has the development ceased? Best wishes, Paul

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