Mailman 3 November 2007 - SciPy-User

Argos data
by David Huard 09 Nov '07

09 Nov '07

Hi, Is there someone working with Argos satellite data ? I'd need some utility to process the data files and wanted to know what are the existing tools. Thanks, David

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Introduction to Image Analysis
by Lorenzo Isella 09 Nov '07

09 Nov '07

Dear All, For my own personal interest, I would like to learn something about analyzing images with Python. The number of modules, scripts etc..."out there" can be a bit confusing, especially if you are starting from scratch. My purpose is to learn the ropes with some easy-going tutorial (if it relied on scipy it would be a huge plus for me). The interest comes from the fact that several job positions I would like to apply for imply dealing with satellite images (to detect common structures, take statistics etc...). Any suggestions? Kind Regards Lorenzo

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Re: [SciPy-user] genetic algorithms
by Gary Robinson 08 Nov '07

08 Nov '07

> scipy/sandbox/ga/ > > Nothing in the sandbox is built by default. See scipy/sandbox/setup.py for > instructions on enabling them. It's not in scipy/sandbox/setup.py. setup.py has the appropriate lines for 'montecarlo', 'spline', and others, but no 'ga'. Again, I have version = '0.6.0', according to scipy/version.py. -- Gary Robinson CTO Emergent Music, LLC garyrob(a)mac.com 207-942-3463 Company: http://www.goombah.com Blog: http://www.garyrobinson.net

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Undefined variable bug in scipy.stats.gaussian_kde.integrate_1d
by John Reid 08 Nov '07

08 Nov '07

I get the following error when calling scipy.stats.gaussian_kde.integrate_1d c:\apps\python25\lib\site-packages\scipy\stats\kde.py in integrate_box_1d(self, low, high) 204 raise ValueError("integrate_box_1d() only handles 1D pdfs") 205 --> 206 stdev = np.ravel(sqrt(self.covariance))[0] 207 208 normalized_low = ravel((low - self.dataset)/stdev) <type 'exceptions.NameError'>: global name 'np' is not defined > c:\apps\python25\lib\site-packages\scipy\stats\kde.py(206)integrate_box_1d() 205 --> 206 stdev = np.ravel(sqrt(self.covariance))[0] 207 I had a quick look at the source and I think perhaps np should be numpy. Also ravel is explicitly imported from numpy in the file. John.

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about MLab
by linda.s 08 Nov '07

08 Nov '07

I have quite a few codes written in Numeric. MLab comes with Numeric too. I got confused when I began to use numpy because it does not have MLab and does not have some same functions in Numeric. is there any smooth way to change the code developed in Numeric to numpy? Thanks, Linda

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Geostatistics with Scipy?
by Mark Bakker 08 Nov '07

08 Nov '07

Hello - I have been looking for some package that can doe Geostatistics with Scipy. Mostly Kriging of 2D data. I expect somebody has done something like this before. Does anybody know of some code somewhere? Thanks, Mark

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Where is the border between SciPy and ML algorithms?
by Willi Richert 08 Nov '07

08 Nov '07

Hi, the scipy.cluster module up to now contains already algorithms for Vector Quantization and Kmeans. In the docs it's said that SOMs are following. Now, after having followed the mails mentioning Orange and Elefant: Where do we draw the line? I'm asking, because a student of mine has implemented SWIG-Python-wrappers to the C++ implementations of diverse decision trees (continuous VFDT, C4.5 and some others), which work quite well. We would of course be glad if those would be included in standard SciPy. However, I'm not quite sure, what the current policy of the core SciPy developers is regarding non-core algorithms. Thanks in advance for any light on this topic, wr

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Re: [SciPy-user] Geostatistics with Scipy?
by Anand Patil 08 Nov '07

08 Nov '07

Mark Bakker wrote: > > Hello - > > I have been looking for some package that can doe Geostatistics with Scipy. > Mostly Kriging of 2D data. > > I expect somebody has done something like this before. > > Does anybody know of some code somewhere? > > Thanks, > > Mark Hi Mark, You could try the observe() function in my Gaussian process package at code.google.com/p/random-realizations. Don't tell anyone, I haven't released it yet. ;) Email me if you try it and need help. Anand

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genetic algorithms
by Gary Robinson 08 Nov '07

08 Nov '07

I've seen a few references to a GA module in scipy, as either scipy.ga or sandbox.ga. But I can't find it in scipy in either of those locations, or elsewhere. (I have version 0.6.) Is there still such a module? If so, where can I find it? BTW, while I'm at it, I'll mention that the INSTALL.TXT file for scipy specifies that you need to have 2.3.x or 2.4.x. I'm using it with 2.5 and it seems OK -- does it really need an earlier version or does that file need to be updated? Thanks, Gary -- Gary Robinson CTO Emergent Music, LLC garyrob(a)mac.com 207-942-3463 Company: http://www.goombah.com Blog: http://www.garyrobinson.net

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SciPy test fails..
by Lev Lafayette 07 Nov '07

07 Nov '07

Hey people, I've just installed NUMPY and SciPy on our cluster and the standard test fails. Can someone give me some pointers on what's wrong? The relevant sections of the test follows. Thanks in advance, Lev Found 128 tests for scipy.lib.blas.fblas **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** Found 7 tests for scipy.linalg.matfuncs Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '.../linsolve/umfpack/__init__.pyc'> /usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?) Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/umfpack.pyc'> /usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?) Found 0 tests for __main__ .../usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/cluster/vq.py:477: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization. warnings.warn("One of the clusters is empty. " exception raised as expected: One of the clusters is empty. Re-run kmean with a different initialization. ................................................Residual: 1.05006987327e-07 ..................../usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/interpolate/fitpack2.py:458: UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. warnings.warn(message) ...... Don't worry about a warning regarding the number of bytes read. ..zswap:n=3 ..................................................................................... **************************************************************** WARNING: cblas module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses fblas instead of cblas. **************************************************************** ...........................................................................................caxpy:n=4 ..zswap:n=3 .......... **************************************************************** WARNING: clapack module is empty ----------- See scipy/INSTALL.txt for troubleshooting. Notes: * If atlas library is not found by numpy/distutils/system_info.py, then scipy uses flapack instead of clapack. **************************************************************** ...Result may be inaccurate, approximate err = 1.73156859734e-08 ...Result may be inaccurate, approximate err = 7.73070496507e-12 ............................................................................................................/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/ndimage/interpolation.py:41: UserWarning: Mode "reflect" may yield incorrect results on boundaries. Please use "mirror" instead. warnings.warn('Mode "reflect" may yield incorrect results on ' ........................................................................................................................................................................................................................................................................................................F..F.........................................................Use minimum degree ordering on A'+A. .....................................Use minimum degree ordering on A'+A. .....................................Use minimum degree ordering on A'+A. ................................Use minimum degree ordering on A'+A. ....................................................................................................................................................................................................................................................................................................................................................0.2 0.2 0.2 ......0.2 ..0.2 0.2 0.2 0.2 0.2 .........................................................................................................................................................................................................Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ...... ====================================================================== FAIL: test_explicit (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/odr/tests/test_odr.py", line 49, in test_explicit np.array([ 1.2646548050648876e+03, -5.4018409956678255e+01, File "/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 1.26462971e+03, -5.42545890e+01, -8.64250389e-02]) y: array([ 1.26465481e+03, -5.40184100e+01, -8.78497122e-02]) ====================================================================== FAIL: test_multi (scipy.tests.test_odr.test_odr) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/scipy/odr/tests/test_odr.py", line 190, in test_multi np.array([ 4.3799880305938963, 2.4333057577497703, 8.0028845899503978, File "/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/numpy/testing/utils.py", line 230, in assert_array_almost_equal header='Arrays are not almost equal') File "/usr/local/python/2.4.4-gcc/lib/python2.4/site-packages/numpy/testing/utils.py", line 215, in assert_array_compare assert cond, msg AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4.31272063, 2.44289312, 7.76215871, 0.55995622, 0.46423343]) y: array([ 4.37998803, 2.43330576, 8.00288459, 0.51011472, 0.51739023]) ---------------------------------------------------------------------- Ran 1716 tests in 3.670s FAILED (failures=2)

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