Mailman 3 June 2010 - SciPy-User

incomplete beta function B(x; k+1, 0) ?
by josef.pktd＠gmail.com 27 Jun '10

27 Jun '10

Is there a incomplete beta function with a zero argument B(x; k+1, 0) available in scipy? >>> special.betainc( np.arange(5)+1, 0, 0.5) array([ NaN, NaN, NaN, NaN, NaN]) http://en.wikipedia.org/wiki/Logarithmic_distribution has an expression for the cdf of logseries, which is not in scipy.stats.distributions, but I don't find the right incomplete Beta function values. Josef

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mary, a masked array
by Keith Goodman 26 Jun '10

26 Jun '10

An outer join of two data objects (labeled arrays, larrys, in my case) can introduce missing values when one data object contains labels that are not in the other data object. For float data I fill the missing values with NaN. But I couldn't come up with a good fill value for int or bool data. Coverting int and bool to float is one way to go, but not ideal. The obvious solution is to use np.ma to mask the missing values. But my masking needs are modest so I coded up a quick proof of concept for a stripped down masked array class that is tailored to my needs. Here's what I came up with: http://github.com/kwgoodman/mary Comments and suggestions are welcomed. I'm not familiar with np.ma so I imagine there are many issues I haven't thought through.

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Re: [SciPy-User] corrcoef and dump
by R. Padraic Springuel 26 Jun '10

26 Jun '10

Each of the 15 arrays between which I want the calculations has 6,695,970 entries in it. I tried feeding corrcoef just two of the lists and while I don't get a MemoryError (the python exception), I do get a couple of these errors: Python(337) malloc: *** mmap(size=2678390784) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug They don't seem to make the program fail, however, as I still get a result from corrcoef. I found a function I'd written some time before to calculate the correlation coefficient that doesn't raise that error and its results agree with those from corrcoef, so there has to be an implementation thing going on here with memory usage. -- R. Padraic Springuel Research Assistant Department of Physics and Astronomy University of Maine Bennett 309 Office Hours: By Appointment Only

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solving linear algebra and substitute in diff equations reg.
by morovia morovia 26 Jun '10

26 Jun '10

Hello, I have 2 homogeneous linear algebraic equations and 4 differential equations. Solving the algebraic equations and substituting, I can eliminate 2 variables out of 6, resulting in 4 differential equations which can be written in matrix form for further analysis. Presently I am using the individual elements of the matrix to compute. I am wondering, whether this substitution and solving can be carried out directly through scipy. Or can sympy be used for this purpose. Thanks in advance, Best regards Morovia.

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Saving the world from economic collapse with Python?
by josef.pktd＠gmail.com 26 Jun '10

26 Jun '10

Just some pieces of information that numpy and scipy are popular http://www.activestate.com/blog/2010/06/must-have-python-packages-finance http://www.activestate.com/blog/2010/06/saving-world-economic-collapse-pyth… http://www.activestate.com/press-releases/activestate-adds-key-python-packa… Josef

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installation missing files, ICC compiler
by gintare statkute 25 Jun '10

25 Jun '10

Hello, I am not able to install ATLAS. 1) My computer has no ICC compiler and The ICC compiler from Intel seems too modern for my proccesor acording description. I try to use gcc-4.2 instead of ICC * working:/usr/ATLAS# /opt/pages/ATLAS/configure -b 64 --prefix=/opt/pages/ATLAS -Ss kern /usr/bin/gcc-4.2 -C ic gcc-4.2 -Fa alg -fPIC --with-netlib-lapack=$/opt/lapack-3.1.1/lapack_LINUX.a * I am getting error: *working:/usr/ATLAS# /opt/pages/ATLAS/configure -b 64 --prefix=/opt/pages/ATLAS -Ss kern /usr/bin/gcc-4.2 -C ic gcc-4.2 -Fa alg -fPIC --with-netlib-lapack=$/opt/lapack-3.1.1/lapack_LINUX.a * 2) Another error is about missing files: */usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory * Full code: *working:/usr/ATLAS# /opt/pages/ATLAS/configure -b 64 --prefix=/opt/pages/ATLAS -Ss kern /usr/bin/gcc-4.2 -C ic gcc-4.2 -Fa alg -fPIC --with-netlib-lapack=$/opt/lapack-3.1.1/lapack_LINUX.a make: `xconfig' is up to date. ./xconfig -d s /opt/pages/ATLAS/ -d b /usr/ATLAS -b 64 -Ss kern /usr/bin/gcc-4.2 -C ic gcc-4.2 -Fa alg -fPIC -Si lapackref 1 OS configured as Linux (1) Assembly configured as GAS_x8632 (1) Vector ISA Extension configured as SSE3 (2,28) Architecture configured as Core2 (15) Clock rate configured as 1667Mhz Maximum number of threads configured as 2 Parallel make command configured as '$(MAKE) -j 2' Cannot detect CPU throttling. rm -f config1.out make atlas_run atldir=/usr/ATLAS exe=xprobe_comp args="-v 0 -o atlconf.txt -O 1 -A 15 -Si nof77 0 -C ic 'gcc-4.2' -Fa ic '-fPIC' -C sm '/usr/bin/gcc-4.2' -Fa sm '-fPIC' -C dm '/usr/bin/gcc-4.2' -Fa dm '-fPIC' -C sk '/usr/bin/gcc-4.2' -Fa sk '-fPIC' -C dk '/usr/bin/gcc-4.2' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa if '-fPIC' -b 64" \ redir=config1.out make[1]: Entering directory `/usr/ATLAS' cd /usr/ATLAS ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 15 -Si nof77 0 -C ic 'gcc-4.2' -Fa ic '-fPIC' -C sm '/usr/bin/gcc-4.2' -Fa sm '-fPIC' -C dm '/usr/bin/gcc-4.2' -Fa dm '-fPIC' -C sk '/usr/bin/gcc-4.2' -Fa sk '-fPIC' -C dk '/usr/bin/gcc-4.2' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa if '-fPIC' -b 64 > config1.out In file included from /usr/include/features.h:354, from /usr/include/stdio.h:28, from /opt/pages/ATLAS//CONFIG/src/backend/comptestC.c:1: /usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory make[2]: *** [IRunCComp] Error 1 Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1 make[1]: Leaving directory `/usr/ATLAS' make: *** [IRun_comp] Error 2 xconfig: /opt/pages/ATLAS//CONFIG/src/config.c:125: ProbeComp: Assertion `!system(ln)' failed. /bin/sh: line 1: 24985 Aborted ./xconfig -d s /opt/pages/ATLAS/ -d b /usr/ATLAS -b 64 -Ss kern /usr/bin/gcc-4.2 -C ic gcc-4.2 -Fa alg -fPIC -Si lapackref 1 -D c -DATL_FULL_LAPACK xconfig exited with 134 working:/usr/ATLAS# /opt/pages/ATLAS/configure -b 64 --prefix=/opt/pages/ATLAS -Ss kern /usr/bin/gcc-4.2 -C ic gcc-4.2 -Fa alg -fPIC --with-netlib-lapack=$/opt/lapack-3.1.1/lapack_LINUX.a* regards, gintare statkute

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checklist script error
by Kevin 25 Jun '10

25 Jun '10

The entire output of that script upon attempting to run it is the following: Running tests: __main__.test_imports('setuptools', None) ... ERROR __main__.test_imports('IPython', None) ... MOD: IPython, version: 0.9.1 ok __main__.test_imports('numpy', None) ... MOD: numpy, version: 1.3.0 ok __main__.test_imports('scipy', None) ... MOD: scipy, version: 0.7.1 ok __main__.test_imports('scipy.io', None) ... MOD: scipy.io, version: *no info* ok __main__.test_imports('matplotlib', <function validate_mpl at 0x6d5f70>) ... MOD: matplotlib, version: 0.99.0 ok __main__.test_imports('pylab', None) ... MOD: pylab, version: *no info* ok __main__.test_imports('enthought.mayavi.api', None) ... ERROR __main__.test_loadtxt(array([[ 0., 1.], ... ok __main__.test_loadtxt(array([('M', 21, 72.0), ('F', 35, 58.0)], ... ok __main__.test_loadtxt(array([ 1., 3.]), array([ 1., 3.])) ... ok __main__.test_loadtxt(array([ 2., 4.]), array([ 2., 4.])) ... ok Simple plot generation. ... ok Plots with math ... ok ====================================================================== ERROR: __main__.test_imports('setuptools', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/stsci/pyssg/2.5.4/nose/case.py", line 183, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 95, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> ImportError: No module named setuptools ====================================================================== ERROR: __main__.test_imports('enthought.mayavi.api', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/stsci/pyssg/2.5.4/nose/case.py", line 183, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 95, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> ImportError: No module named enthought.mayavi.api ---------------------------------------------------------------------- Ran 14 tests in 10.766s FAILED (errors=2) Cleanup - removing temp directory: /Users/lindsay/tmp-testdata-etwtf9 *************************************************************************** TESTS FINISHED *************************************************************************** If the printout above did not finish in 'OK' but instead says 'FAILED', copy and send the *entire* output, including the system information below, for help. We'll do our best to assist you. You can send your message to the Scipy user mailing list: http://mail.scipy.org/mailman/listinfo/scipy-user but feel free to also CC directly: cburns at berkeley dot edu ================== System information ================== os.name : posix os.uname : ('Darwin', 'mooseman.home', '9.8.0', 'Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386', 'i386') platform : darwin platform+ : Darwin-9.8.0-i386-32bit prefix : /usr/stsci/pyssg/Python-2.5.4 exec_prefix : /usr/stsci/pyssg/Python-2.5.4 executable : /usr/stsci/pyssg/Python-2.5.4//bin/python version_info : (2, 5, 4, 'final', 0) version : 2.5.4 (r254:67916, Nov 6 2009, 11:35:14) [GCC 4.0.1 (Apple Inc. build 5465)] ==================

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Re: [SciPy-User] Autocorrelation function: Convolution vs FFT
by davide 25 Jun '10

25 Jun '10

Have a look to "Random data analysi" by Piersol and Bendat. Here is some code of mine. Still need some tweaks. To test it try to autocorrelate a long time history of a pure sine wave. Then compare the result with a cosine of the same frequency. def acorr( y, fs=1, maxlags=None, normed=True, full=False ): """ Get the auto-correlation function of a signal. Parameters ---------- y : a one dimensional array maxlags: the maximum number of time delay for which to compute the auto-correlation. normed : a boolean option. If true the normalized auto-correlation function is returned. fs : the sampling frequecy of the data full : if True also a time array is returned for plotting purposes Returns ------- rho : the auto-correlation function t : a time array. Only if full==True Example ------- t = np.arange(2**20) / 1000.0 y = np.sin(2*np.pi*100*t) rho = acorr( y, maxlags=1000 ) """ if not maxlags: maxlags = len(y)/2 if maxlags > len(y)/2: maxlags = len(y)/2 fs = float(fs) # pad with zeros x = np.hstack( (y, np.zeros(len(y))) ) # compute FFT trasform of signal sp = np.fft.rfft( x ) tmp = np.empty_like(sp) tmp = np.conj(sp, tmp) tmp = np.multiply(tmp, sp, tmp) rho = np.fft.irfft( tmp ) # divide by array length rho = np.divide(rho, len(y), rho)[:maxlags] # obtain the unbiased estimate tmp = len(y) / ( len(y) - np.arange(maxlags, dtype=np.float64) ) rho = np.multiply(rho, tmp, rho) if normed: rho = rho / rho[0] if full: t = np.arange(maxlags, dtype=np.float32) / fs return t, rho else: return rho

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SciPy crashes on loading scipy.stats
by Anil C R 25 Jun '10

25 Jun '10

SciPy crashes on loading the scipy.stats module on Win XP and Scipy version 0.7.1 Anil

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[ANN] Spyder v1.1.0 released
by Pierre Raybaut 24 Jun '10

24 Jun '10

Hi all, I'm pleased to announce here that Spyder version 1.1.0 has been released: http://packages.python.org/spyder Spyder (the Scientific PYthon Development EnviRonment) is a free open-source Python development environment providing MATLAB-like features in a simple and light-weighted software, available for Windows XP/Vista/7, GNU/Linux and MacOS X: * advanced code editing features (code analysis, ...) * interactive console with MATLAB-like workspace (with GUI-based list, dictionary, tuple, text and array editors -- screenshots: http://packages.python.org/spyder/console.html#the-workspace) and integrated matplotlib figures * external console to open an interpreter or run a script in a separate process (with a global variable explorer providing the same features as the interactive console's workspace) * code analysis with pyflakes and pylint * search in files features * object inspector: automatically retrieves docstrings or source code of the function/class called in the interactive/external console * online documentation viewer (pydoc) * integrated file/directories explorer * MATLAB-like path management * project management ...and more! Spyder is part of spyderlib, a Python module based on PyQt4 and QScintilla2 which provides powerful console-related PyQt4 widgets. Some of the major changes since v1.0.0 (433 commits!): * A lot of bugfixes! * IPython integration within the external console (still experimental) * QScintilla2 is now optional (a whole pure PyQt4 code editor -faster than its QScintilla's counterpart- has been implemented): brings code folding and code completion * Improved Matplotlib's figure options feature (added support for image parameters, added an "Apply" button) * Added: Project Explorer plugin (Pydev projects may be imported) * Added: Online help browser plugin (based on pydoc) * Editor new features: * Unlimited horizontal/vertical splitting: each new editor panel is a clone of the first panel, allowing comparing two parts of the same file * Unlimited independent editor windows creation * Flag vertical scrollbar area: shows warnings, TODOs, FIXMEs and occurrence highlighting of the whole file * External console: added import/export features to the variable explorer Cheers, Pierre

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