Mailman 3 September 2006 - SciPy-User

Fitting a distribution to some data
by Jose Luis Gomez Dans 06 Sep '06

06 Sep '06

Hi, I am trying to fit a distribution to some data points (actually, I want to test which distribution is best to model the data). Moreover, I want to estimate the distributions parameters. I am sure that the stats module has many functions to help me with this, but I am not sure I understand how to use them. As a test, I create some RVs using say y=stats.distributions.norm.rvs ( size=100). I can then find the mean and standard deviation using (mu,sigma)=stats.distributions.norm.fit(y) which works fine. However, some methods do not work. For example, the pdf(self,x..) method returns an array of 0s, and similarly for the cdf() method. However, the _pdf() and _cdf() methods give the desired result. Is this a bug? Am I suppossed to use the underscore methods or the public methods? Also, is there some example of how to use kstest? it might be related, but if I try to test the previous data, I get the following error: stats.kstest(y,'norm',args=(mu,sigma)) --------------------------------------------------------------------------- exceptions.TypeError Traceback (most recent call last) /home/ggjlgd/<ipython console> /usr/lib/python2.4/site-packages/scipy/stats/stats.py in kstest(rvs, cdf, args, N) 1721 # D = max(D1,D2) 1722 D = D1 -> 1723 return D, distributions.ksone.sf(D,N) 1724 1725 def chisquare(f_obs, f_exp=None): /usr/lib/python2.4/site-packages/scipy/stats/distributions.py in sf(self, x, *args, **kwds) 521 output = zeros(shape(cond),'d') 522 insert(output,(1-cond0)*(cond1==cond1),self.badvalue) --> 523 insert(output,cond2,1.0) 524 goodargs = argsreduce(cond, *((x,)+args)) 525 insert(output,cond,self._sf(*goodargs)) /usr/lib/python2.4/site-packages/numpy/lib/function_base.py in insert(arr, obj, values, axis) 1190 1191 obj = asarray(obj, dtype=intp) -> 1192 numnew = len(obj) 1193 index1 = obj + arange(numnew) 1194 index2 = setdiff1d(arange(numnew+N),index1) TypeError: len() of unsized object Am I doing something wrong here? Is it a bug? My versions are Scipy: 0.5.0.2178 Numpy: 1.0b5 and I run on Kubuntu Dapper on Linux. I use Andrew Straw's packages. Thanks Jose -- "Feel free" – 10 GB Mailbox, 100 FreeSMS/Monat ... Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail

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Fw: Scientific computing and data visualization.
by Fie Pye 06 Sep '06

06 Sep '06

Hallo I would like to have a high class open source tools for scientific computing and powerful 2D and 3D data visualisation. Therefore I chose python, numpy and scipy as a base. Now I am in search for a visualisation tool. I tried matplotlib and py_opendx with OpenDx. OpenDx seems to me very good but the project py_opendx looks like closed. After py_opendx instalation and subsequent testing I got an error that needs discussion with author or an experienced user. Unfortunately a mail to author returned as undeliverable. Does anybody now about suitable visualisation tool? Does anybody have an experience with OpenDx and py_opendx instalation? Thanks for your response. fiepye

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Re: [SciPy-user] Problem with Windows Scipy 0.5
by Tony Triolo 06 Sep '06

06 Sep '06

David, Thanks for the info. The naming convention you mentioned, i.e., adding the numpy version which was used for compiling scipy to the filename, would have saved me some time and effort. Oh well... The enthought edition worked well on both my WinXP and Win2000 machines. I am now happily on my way. Thanks again. -Tony > Hi Tony! > > You have to use a (C-API) compatible Numpy version which should be > numpy-1.0b1.win32-py2.4.exe for your scipy download. ...but it seems > like this is no longer available on SF for download. If you don't want > to compile yourself you may also give http://code.enthought.com/enthon/ > a try. > > The download page on the wiki is not pointing out this C-API > compatibility issue clearly. To avoid confusion it would be good to add > the numpy version which was used for compiling scipy into the name of > the binary in the future. E.g. > scipy-0.5.0-numpy1.0.1b1-win32-py2.4.exe > > Regards, > David > > > ------------------------------ > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.org > http://projects.scipy.org/mailman/listinfo/scipy-user > > > End of SciPy-user Digest, Vol 37, Issue 1 > ***************************************** >

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Genetic Algorithm Module * ga
by Clinton Evans 06 Sep '06

06 Sep '06

I have fixed the ga module sufficiently to run the example code and run my old code. I am not an "official" scipy developer so I can't post it to subversion. However, if anyone wants a copy, please let me know. Clinton

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test failures in 0.5.1
by Erick Tryzelaar 06 Sep '06

06 Sep '06

Hello, I just installed 0.5.1, and I got these errors. Any idea what's going on? -e ====================================================================== ERROR: check loadmat case cellnest ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/local/lib/python2.4/site-packages/scipy/io/tests/test_mio.py", line 80, in cc self._check_case(name, expected) File "/opt/local/lib/python2.4/site-packages/scipy/io/tests/test_mio.py", line 75, in _check_case self._check_level(k_label, expected, matdict[k]) File "/opt/local/lib/python2.4/site-packages/scipy/io/tests/test_mio.py", line 33, in _check_level self._check_level(level_label, ev, actual[i]) File "/opt/local/lib/python2.4/site-packages/scipy/io/tests/test_mio.py", line 30, in _check_level assert len(expected) == len(actual), "Different list lengths at %s" % label TypeError: len() of unsized object ====================================================================== FAIL: check loadmat case vec ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/local/lib/python2.4/site-packages/scipy/io/tests/test_mio.py", line 80, in cc self._check_case(name, expected) File "/opt/local/lib/python2.4/site-packages/scipy/io/tests/test_mio.py", line 74, in _check_case assert k in matdict, "Missing key at %s" % k_label AssertionError: Missing key at Test 'vec', file:/opt/local/lib/python2.4/site-packages/scipy/io/tests/./data/testvec_4_GLNX86.mat, variable fit_params ====================================================================== FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple) ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/local/lib/python2.4/site-packages/scipy/lib/blas/tests/test_blas.py", line 76, in check_dot assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j) File "/opt/local/lib/python2.4/site-packages/numpy/testing/utils.py", line 156, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: ACTUAL: (-1.998720645904541+5.8724710243597094e-37j) DESIRED: (-9+2j) ====================================================================== FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple) ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/local/lib/python2.4/site-packages/scipy/linalg/tests/test_blas.py", line 75, in check_dot assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j) File "/opt/local/lib/python2.4/site-packages/numpy/testing/utils.py", line 156, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: ACTUAL: (-1.998720645904541+5.8724710243597094e-37j) DESIRED: (-9+2j) ---------------------------------------------------------------------- Ran 1569 tests in 12.867s FAILED (failures=3, errors=1)

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Correlation
by PGM 06 Sep '06

06 Sep '06

Folks, I'd need to compute the cross-correlation of two series. For the 1D case, I use numpy.correlate and select the last half of the result to get what I want. I need to work with 2Darrays, either by row, or by colum, or on the flattened array. I'm a bit at loss about what commands to use: scipy.signal.signaltools does not allow to work per axis. Any comments will be welcome Thanks in advance P.

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small bug in filter_design.py
by Scott Ransom 05 Sep '06

05 Sep '06

Hi All, There is a small bug in the initial conditions parameter in ellipap() in the filter_design.py module: File "/users/sransom/lib/python2.3/site-packages/scipy/signal/filter_design.py", line 1049, in ellipap disp=0) File "/users/sransom/lib/python2.3/site-packages/scipy/optimize/optimize.py", line 140, in fmin N = len(x0) TypeError: len() of unsized object Here is the "fix": 1048c1048 < m = optimize.fmin(kratio, 0.5, args=(krat,), maxfun=250, maxiter=250, --- > m = optimize.fmin(kratio, [0.5], args=(krat,), maxfun=250, maxiter=250, Scott -- Scott M. Ransom Address: NRAO Phone: (434) 296-0320 520 Edgemont Rd. email: sransom(a)nrao.edu Charlottesville, VA 22903 USA GPG Fingerprint: 06A9 9553 78BE 16DB 407B FFCA 9BFA B6FF FFD3 2989

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Triangulation of L-shaped domains
by Nils Wagner 05 Sep '06

05 Sep '06

Hi all, I have installed delaunay from the sandbox. How can I triangulate L-shaped domains ? My first try is somewhat unsatisfactory (delaunay.png) ? How can I remove the unwanted triangles down to the right ? Nils

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Interpolate 1D
by Maik Trömel 05 Sep '06

05 Sep '06

Hello list, when I try to use scipy.interpolate.interpolate.interp1d( olddims[-1], a, kind='cubic' ) I get an ERROR: File "/usr/lib/python2.3/site-packages/scipy/interpolate/interpolate.py", line 118, in __init__ raise NotImplementedError, "Only linear supported for now. Use "\ NotImplementedError: Only linear supported for now. Use fitpack routines for other types. But under http://www.scipy.org/doc/api_docs/scipy.interpolate.interpolate.interp1d.ht… kind = 'cubic' is listed. Whats wrong with the command? Or is cubic not implemented yet? Thanks for your help! Greetings Maik

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global fitting of data sets with some parameters linked
by babu 05 Sep '06

05 Sep '06

Hello I have data sets and would like to fit them globally with common parameters. Is there a way to do this using existing scipy modules leastsq. Any pointers for algo and suggestions are welcome. Thanks Babu.

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