Mailman 3 January 2007 - NumPy-Discussion

Re: [Numpy-discussion] [Matplotlib-users] installing numpy, matplotlib, scipy from source on a Mac
by belinda thom Jan. 10, 2007

Jan. 10, 2007

Hi Chris, Robert, ...?, I'm glad you reminded me to make sure the path was right, b/c this time, I had forgotten to run the "Update Shell" command that came w/ MacPython2.4. This gave me: lrwxr-xr-x 1 root wheel 67 Jan 7 14:29 /usr/local/bin/pydoc@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/pydoc lrwxr-xr-x 1 root wheel 70 Jan 7 14:29 /usr/local/bin/pydoc2.4@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/ pydoc2.4 lrwxr-xr-x 1 root wheel 68 Jan 7 14:29 /usr/local/bin/python@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/python lrwxr-xr-x 1 root wheel 71 Jan 7 14:29 /usr/local/bin/python2.4@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/ python2.4 lrwxr-xr-x 1 root wheel 69 Jan 7 14:29 /usr/local/bin/pythonw@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/pythonw lrwxr-xr-x 1 root wheel 72 Jan 7 14:29 /usr/local/bin/pythonw2.4@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/ pythonw2.4 lrwxr-xr-x 1 root wheel 70 Jan 7 14:29 /usr/local/bin/smtpd.py@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/ smtpd.py lrwxr-xr-x 1 root wheel 73 Jan 7 14:29 /usr/local/bin/smtpd2.4.py@ - > ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/ smtpd2.4.py Nevertheless, the python I was using in the prior email looks like the same as what I'm using w/these path updates, that is, assuming version strings are enough to know: From prior run: Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin New run: Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin As you'd suspected, it is indeed the case that: diff pythonw python reports no differences. So, I went back and retried the plotting w/wx as a backend and discovered that wx FAILS with PYTHONW and PYTHON (appended). If you saw how many notes I've collected on the different installs I've tried you'd laugh (except that its not funny). Its no wonder I can't keep all this stuff straight. (When I first embarked on this exercise several months ago, I tried macports; everything seemed to work fine, but the Wx backend failed---I remember something about a bitmap, so it was likely the same error I'm having now; and unfortunately w/the macports python, the tk/tcl stuff didn't come wrapped, so TkAgg was not an option). After an email w/Robert, I switched to MacPython. As a result, I now have TkAgg working (and its using Aqua instead of that awful, klunky looking Tk stuff). Fortunately (ha!), I have three versions of this stuff installed on 3 different Macs (a G4, a G5, and an Intel). So I can say with safety that, using TkAgg backend, here's what's still not working: 1) Using macpython matplotlib, numpy, and scipy packages, you can't run scipy.test(); complaint: RuntimeError: module compiled against version 1000002 of C-API but this version of numpy is 1000009 2) Using superpak, everything (except ipython) worked out of the box, PROVIDED I had already installed the necessary fortran pieces (I used g77v3.4-bin.tar.gz, found somewhere on the scipy site). 3) Using Robert's install-from-source method (this install used gfortran.bin.tar.gz, with the caveat that the expected WXAgg doesn't work) Machines 2 and 3 are enough to get me back to the real work I have to do. But it is obvious there's several real issues for Mac users who wish to use the scipy/numpy/matplotlib route. This coming summer I may have more time to devote to this stuff, and since it really irks me that there isn't a clean way to do this, I may end up figuring out how to make the needed binaries myself. In the meantime, I thought I'd never wish I was still using Windows... Thanks to everyone for the time spent on this. And for posterity's sake, when you use matplotlib with Numeric, it also crashes. I've verified that behavior on Machines 1 and 2 above. --b 54 % pythonw Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. history mechanism set up >>> import pylab as P >>> import matplotlib as M >>> M.rcParams['interactive'] True >>> M.rcParams['backend'] 'WXAgg' >>> P.plot([1,2,3]) Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wx.py", line 1048, in _onPaint self.draw(repaint=False) <snip> draw_if_interactive() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wx.py", line 1172, in draw_if_interactive figManager.canvas.draw() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wxagg.py", line 63, in draw self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), None) MemoryError: _wxagg.convert_agg_to_wx_bitmap(): could not create the wx.Bitmap >> 55 % python Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. history mechanism set up >>> import pylab as P >>> import matplotlib as M >>> M.rcParams['interactive'] True >>> M.rcParams['backend'] 'WXAgg' >>> P.plot([1,2,3]) Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wx.py", line 1048, in _onPaint self.draw(repaint=False) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wxagg.py", line 63, in draw self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), None) MemoryError: _wxagg.convert_agg_to_wx_bitmap(): could not create the wx.Bitmap Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/pylab.py", line 2022, in plot <snip> File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wx.py", line 1172, in draw_if_interactive figManager.canvas.draw() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/ site-packages/matplotlib/backends/backend_wxagg.py", line 63, in draw self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), None) MemoryError: _wxagg.convert_agg_to_wx_bitmap(): could not create the wx.Bitmap >>> On Jan 10, 2007, at 3:06 PM, Christopher Barker wrote: > > > Robert Kern wrote: > >> Try running with pythonw. > > That's probably not it -- as of MacPython 2.4, pythonw ands python > are the same. > > belinda thom wrote: >> And running w/pythonw does what it should :-). > > OK, now I'm confused: > > $ ls -l /Library/Frameworks/Python.framework/Versions/2.4/bin/ > python2.4 > -rwxrwxr-x 1 root admin 39936 Apr 7 2006 /Library/Frameworks/ > Python.framework/Versions/2.4/bin/python2.4 > > $ ls -l /Library/Frameworks/Python.framework/Versions/2.4/bin/ > pythonw2.4 > -rwxrwxr-x 1 root admin 39936 Apr 7 2006 /Library/Frameworks/ > Python.framework/Versions/2.4/bin/pythonw2.4 > > Those two look like the same binaries to me -- and diff tells me > they are. > > Are you sure you're running the same python with "python" and > "pythonw"? Try running them on the command line alone and see what > you get. > >> File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ >> python2.4/site-packages/matplotlib/backends/backend_wxagg.py", >> line 63, in draw >> self.bitmap = _convert_agg_to_wx_bitmap(self.get_renderer(), >> None) >> MemoryError: _wxagg.convert_agg_to_wx_bitmap(): could not create >> the wx.Bitmap > > This looks like the error we usually get when you've built the > wxAgg extension against a different version of wx than the one > you're running. That's easy to do, as Apple has provided an old wx > with it's Python, it is often found by default by the MPL build > process. > > Search this list for the way to fix that, or, if you really can't > find it, I'll dig it up. > > -Chris > > > > > > > > > -- > Christopher Barker, Ph.D. > Oceanographer > > Emergency Response Division > NOAA/NOS/OR&R (206) 526-6959 voice > 7600 Sand Point Way NE (206) 526-6329 fax > Seattle, WA 98115 (206) 526-6317 main reception > > Chris.Barker(a)noaa.gov

1 0

Exported symbols and code reorganization.
by Charles R Harris Jan. 10, 2007

Jan. 10, 2007

Hi all, I've started some experiments at breaking up the large multiarraymodule.cand arrayobject.c files. As part of this I also looked at what symbols are currently exported by the *.so libraries. Most are just the usual three python symbols, but multiarray, mtrand, and fftpack_lite have extras. ./core/multiarray.so 000530b4 T _fini 0004d450 T _flat_copyinto 00005f58 T _init 000107e0 T count_new_axes_0d 0002c160 T initmultiarray I'm guessing the extras are unintended and should be made static. ./fft/fftpack_lite.so 00008284 T _fini 000008a4 T _init 00003570 T cfftb 00003530 T cfftf 00003800 T cffti 00001070 T fftpack_cfftb 00001220 T fftpack_cfftf 00000df0 T fftpack_rfftb 000013d0 T fftpack_rfftf 00000c30 T initfftpack_lite 00005e20 T rfftb 000039b0 T rfftb1 00006f30 T rfftf 00003680 T rffti Is there a good reason to make all those global? Is the library intended to be used as more than a module? ./random/mtrand.so 000294d4 T _fini 00002da4 T _init 00026ef0 T init_by_array 00023090 T initmtrand 00027020 T loggam 00026db0 T rk_altfill 00028360 T rk_beta 00028fc0 T rk_binomial 00028760 T rk_binomial_btpe 000279f0 T rk_binomial_inversion 000281d0 T rk_chisquare 00026d10 T rk_devfill 00026b40 T rk_double 000273a0 T rk_exponential 00028210 T rk_f 00026ba0 T rk_fill 00028440 T rk_gamma 00026c20 T rk_gauss 00027c70 T rk_geometric 00027bf0 T rk_geometric_inversion 00027180 T rk_geometric_search 00027240 T rk_gumbel 00029430 T rk_hypergeometric 00029090 T rk_hypergeometric_hrua 00027560 T rk_hypergeometric_hyp 00026ae0 T rk_interval 000272a0 T rk_laplace 000271f0 T rk_logistic 00028510 T rk_lognormal 00027470 T rk_logseries 00026ab0 T rk_long 00028480 T rk_negative_binomial 00028270 T rk_noncentral_chisquare 000282f0 T rk_noncentral_f 000284d0 T rk_normal 000273d0 T rk_pareto 00027970 T rk_poisson 00027410 T rk_poisson_mult 00027770 T rk_poisson_ptrs 00027dc0 T rk_power 00026970 T rk_random 00026e10 T rk_randomseed 00027700 T rk_rayleigh 000268f0 T rk_seed 00027f00 T rk_standard_cauchy 00027360 T rk_standard_exponential 00027f40 T rk_standard_gamma 00028120 T rk_standard_t 00027640 T rk_triangular 00026a80 T rk_ulong 00027320 T rk_uniform 00028550 T rk_vonmises 00027e50 T rk_wald 00027e10 T rk_weibull 00027cd0 T rk_zipf I'm guessing at least some of these should be private. The script that generates these lists is for i in $(find . -name "*.so") ; do echo $i && nm $i | grep \ T ; done ; executed in the package directory. That brings up the main question I have about how to break up the C files. I note that most of the functions in multiarraymodule.c, for instance, are part of the C-API, and are tagged as belonging to either the MULTIARRAY_API or the OBJECT_API. Apparently the build system scans for these tags and extracts the files somewhere. So, what is this API, is it available somewhere or is the code just copied somewhere convenient. As to breaking up the files, the scan only covers the code in the two current files, included code from broken out parts is not seen. This strikes me as a bit of a kludge, but I am sure there is a reason for it. Anyway, I assume the build system can be fixed, so that brings up the question of how to break up the files. The maximal strategy is to make every API functions, with it's helper functions, a separate file. This adds a *lot* of files, but it is straight forward and modular. A less drastic approach is to start by breaking multiarraymodule into four files: the converters, the two apis, and the module functions. My own preference is for the bunch of files, but I suspect some will object. Any comments? Chuck

4 10

Python EM Project
by lorenzo bolla Jan. 10, 2007

Jan. 10, 2007

Hi all, I'm not sure if I am slightly out of topic, but I can't find information anywhere else. Can someone tell me where the Python EM Project has gone? The website www.pythonemproject.com that used to host it is now a bunch of ads, property of DomainDrop. Also Robert Lytle, who seemed to be "responsible" for the project, cannot be contacted via e-mail. Thank you! Lorenzo

2 1

Getting 3-D array values from a 2-D array of indexes
by Jordan Dawe Jan. 9, 2007

Jan. 9, 2007

I have a 3D array A of shape (nz, ny, nx) and a 2D array B of shape (ny, nx) that contains integer indexes. I want to generate a 2D array C of shape (ny, nx) composed of the values of A at the z-indexes specified in B. Is there an easy way to do this? Jordan

3 2

reduction
by lorenzo bolla Jan. 9, 2007

Jan. 9, 2007

Hello all! I'm fairly new to Numpy and, while experimenting, I found a strange (i.e. not expected by me!) behaviour of arrays. I tried this (in comment what I get): x = arange(4) # x = array([0,1,2,3]) def myadd(x,y): # re-define the binary sum function return x + y reduce(myadd, x) # 6, as expected add.reduce(x) # 6, as expected def mysub(x,y): # re-define the binary diff function return x - y reduce(mysub, x) # -6, as expected subtract.reduce(x) # 2 ---> WHY? Can someone explain me this? Thank you in advance! lorenzo.

5 15

discussion about array.resize() -- compare to numarray
by Sebastian Haase Jan. 9, 2007

Jan. 9, 2007

Hi! I'm continuing my code conversion to numpy. Trying to track down a segmentation fault I found 1) ndimage crashed because I was feeding (nan,nan) as shift value ..... 2) but where did I get the nan from ? I just found that there is code like this: (*paraphrased*) size = N.array( [255] ) size.resize( 2 ) ... trying this interactively I get an exception: >>> a = N.array([5]) >>> a [5] >>> a.resize(2) Traceback (most recent call last): File "<input>", line 1, in ? ValueError: cannot resize an array that has been referenced or is referencing another array in this way. Use the resize function >>> N.__version__ '1.0.2.dev3487' in any case: inside the script it somehow generated a nan --- is there a bug in numpy !? I remember that there was some discussion about resize !? What should I add to the Scipy Wiki numarray page about this ? ( http://www.scipy.org/Converting_from_numarray ) Thanks, Sebastian Haase

10 27

defmatrix.sum
by Stefan van der Walt Jan. 9, 2007

Jan. 9, 2007

Hi all, I noticed that Tim Leslie picked up on the out=None in defmatrix.sum: def sum(self, axis=None, dtype=None, out=None): """Sum the matrix over the given axis. If the axis is None, sum over all dimensions. This preserves the orientation of the result as a row or column. """ return N.ndarray.sum(self, axis, dtype, out=None)._align(axis) Surely, that out=None should just be out? If out is specified, should sum() still return a value? Cheers Stéfan

2 1

Note to developers: Pyrex, Python 2.5, and exceptions
by Robert Kern Jan. 8, 2007

Jan. 8, 2007

The official distribution of Pyrex has not been completely updated for Python 2.5. The change of the base Exception to new-style classes causes errors in some of the code that Pyrex generates to handle exceptions. I've been using the branch of Pyrex that the lxml project maintains which includes a fix for this: http://codespeak.net/svn/lxml/pyrex/ When regenerating mtrand.c from mtrand.pyx, please use this version instead of the official version. Thank you. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco

1 0

Re: [Numpy-discussion] recompiling needed for binary module after numpy 1.0
by belinda thom Jan. 8, 2007

Jan. 8, 2007

Thanks for the Intel update. I'm doing the same for my PPC (Powerbook, G4, OS X 10.4.8), and have some failures in scipy's tests. Did you try doing: >>> import numpy as N >>> N.test() and >>> import scipy as S >>> S.test()? For me, the latter one fails (both install and S.test() I/O appended). > I just got a new MacBook Pro, core 2 duo. There is no > numpy/scipy fink distro for the intels yet so I tried out > Robert's suggestions above. I installed python 2.5 as > the base. I can confirm that all is working well for > numpy and scipy. > > Matplotlib compiled, but gave some odd warnings such > as > Perhaps I should attempt to install matplot lib at this point---I don't know. Any idea if the FAILUREs I'm seeing are a problem? Thx, --b Below, I paste the output from python setup.py install (for scipy) as well as the command I ran inside of python to check scipy's functionality. bthom(a)tweedledee.local [5:51pm] ~/Download/scipy-0.5.2 4 % sudo python setup.py install Password: mkl_info: libraries mkl,vml,guide not found in /Library/Frameworks/ Python.framework/Versions/2.4/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib libraries mkl,vml,guide not found in /opt/local/lib NOT AVAILABLE fftw3_info: libraries fftw3 not found in /Library/Frameworks/Python.framework/ Versions/2.4/lib libraries fftw3 not found in /usr/local/lib libraries fftw3 not found in /usr/lib libraries fftw3 not found in /opt/local/lib fftw3 not found NOT AVAILABLE fftw2_info: libraries rfftw,fftw not found in /Library/Frameworks/ Python.framework/Versions/2.4/lib libraries rfftw,fftw not found in /usr/local/lib libraries rfftw,fftw not found in /usr/lib libraries rfftw,fftw not found in /opt/local/lib fftw2 not found NOT AVAILABLE dfftw_info: libraries drfftw,dfftw not found in /Library/Frameworks/ Python.framework/Versions/2.4/lib libraries drfftw,dfftw not found in /usr/local/lib libraries drfftw,dfftw not found in /usr/lib libraries drfftw,dfftw not found in /opt/local/lib dfftw not found NOT AVAILABLE djbfft_info: NOT AVAILABLE blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/ vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] non-existing path in 'Lib/linsolve': 'tests' umfpack_info: libraries umfpack not found in /Library/Frameworks/ Python.framework/Versions/2.4/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib libraries umfpack not found in /opt/local/lib /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/numpy/distutils/system_info.py:401: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/ umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE non-existing path in 'Lib/maxentropy': 'doc' Warning: Subpackage 'Lib' configuration returned as 'scipy' running install running build running config_fc running build_src building py_modules sources building library "dfftpack" sources building library "linpack_lite" sources <snip> building library "specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.4' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.4' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources <snip> building extension "scipy.special._cephes" sources building extension "scipy.special.specfun" sources f2py options: ['--no-wrap-functions'] adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.4' to include_dirs. building extension "scipy.stats.statlib" sources f2py options: ['--no-wrap-functions'] adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.4' to include_dirs. building extension "scipy.stats.futil" sources f2py options: [] adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.4' to include_dirs. building extension "scipy.stats.mvn" sources f2py options: [] adding 'build/src.macosx-10.3-fat-2.4/fortranobject.c' to sources. adding 'build/src.macosx-10.3-fat-2.4' to include_dirs. adding 'build/src.macosx-10.3-fat-2.4/Lib/stats/mvn- f2pywrappers.f' to sources. building extension "scipy.ndimage._nd_image" sources building data_files sources running build_py copying build/src.macosx-10.3-fat-2.4/scipy/__config__.py -> build/ lib.macosx-10.3-fat-2.4/scipy running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler Could not locate executable g77 Could not locate executable f77 Could not locate executable f95 customize GnuFCompiler customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler customize GnuFCompiler customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_ext running install_lib creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy <snip> creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/lib/blas copying build/lib.macosx-10.3-fat-2.4/scipy/lib/blas/__init__.py -> / Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/scipy/lib/blas copying build/lib.macosx-10.3-fat-2.4/scipy/lib/blas/cblas.so -> / Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/scipy/lib/blas <snip> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/scipy/weave copying build/lib.macosx-10.3-fat-2.4/scipy/weave/wx_spec.py -> / Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/scipy/weave byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/__config__.py to __config__.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/__init__.py to __init__.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/__svn_version__.py to <snip> byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/slice_handler.py to slice_handler.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/standard_array_spec.py to standard_array_spec.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/swig2_spec.py to swig2_spec.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/swigptr.py to swigptr.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/swigptr2.py to swigptr2.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/vtk_spec.py to vtk_spec.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/weave_version.py to weave_version.pyc byte-compiling /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/wx_spec.py to wx_spec.pyc running install_data creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/sparse/tests copying Lib/sparse/tests/test_sparse.orig -> /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ sparse/tests/ <snip> creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/maxentropy/examples copying Lib/maxentropy/examples/bergerexamplesimulated.py -> /Library/ Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ scipy/maxentropy/examples/ copying Lib/maxentropy/examples/conditionalexample1.py -> /Library/ Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ scipy/maxentropy/examples/ copying Lib/maxentropy/examples/conditionalexample2.py -> /Library/ Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ scipy/maxentropy/examples/ copying Lib/maxentropy/examples/bergerexample.py -> /Library/ Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/ scipy/maxentropy/examples/ copying ./TOCHANGE.txt -> /Library/Frameworks/Python.framework/ Versions/2.4/lib/python2.4/site-packages/scipy copying ./DEVELOPERS.txt -> /Library/Frameworks/Python.framework/ Versions/2.4/lib/python2.4/site-packages/scipy copying ./THANKS.txt -> /Library/Frameworks/Python.framework/Versions/ 2.4/lib/python2.4/site-packages/scipy copying ./LICENSE.txt -> /Library/Frameworks/Python.framework/ Versions/2.4/lib/python2.4/site-packages/scipy copying ./LATEST.txt -> /Library/Frameworks/Python.framework/Versions/ 2.4/lib/python2.4/site-packages/scipy copying ./FORMAT_GUIDELINES.txt -> /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy copying ./INSTALL.txt -> /Library/Frameworks/Python.framework/ Versions/2.4/lib/python2.4/site-packages/scipy creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/linalg/tests copying Lib/linalg/tests/test_blas.py -> /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ linalg/tests/ <snip> site-packages/scipy/fftpack/tests/ creating /Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/weave/doc copying Lib/weave/doc/tutorial.html -> /Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/ doc/ bthom(a)tweedledee.local [5:52pm] ~/Download/scipy-0.5.2 5 % python Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy as S >>> S.test() Found 4 tests for scipy.io.array_import Found 1 tests for scipy.cluster.vq Found 128 tests for scipy.linalg.fblas <snip> Found 18 tests for scipy.fftpack.basic Found 4 tests for scipy.io.recaster Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '.../linsolve/umfpack/__init__.pyc'> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?) Found 4 tests for scipy.optimize.zeros Found 28 tests for scipy.io.mio Found 41 tests for scipy.linalg.basic Found 2 tests for scipy.maxentropy.maxentropy Found 358 tests for scipy.special.basic Found 128 tests for scipy.lib.blas.fblas Found 7 tests for scipy.linalg.matfuncs **************************************************************** 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 42 tests for scipy.lib.lapack Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/ umfpack.pyc'> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site- packages/scipy/linsolve/umfpack/tests/test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?) Found 1 tests for scipy.optimize.cobyla Found 16 tests for scipy.lib.blas Found 1 tests for scipy.integrate Found 14 tests for scipy.linalg.blas Found 4 tests for scipy.fftpack.helper Found 4 tests for scipy.signal.signaltools Found 0 tests for __main__ Don't worry about a warning regarding the number of bytes read. Warning: 1000000 bytes requested, 20 bytes read. <snip> .....Use minimum degree ordering on A'+A. ....................................../Library/Frameworks/ Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/ interpolate/fitpack2.py:457: 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) ........................................................................ ........................Ties preclude use of exact statistic. ..Ties preclude use of exact statistic. ........ **************************************************************** 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. **************************************************************** .......................F................................................ ............................................................ <snip> ...Result may be inaccurate, approximate err = 1.6582899877e-08 ...Result may be inaccurate, approximate err = 4.54747350886e-13 ......................................................F.......Residual: 1.05006926991e-07 . **************************************************************** 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. **************************************************************** .......F.............. ====================================================================== FAIL: test_smallest_same_kind (scipy.io.tests.test_recaster.test_recaster) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/io/tests/test_recaster.py", line 61, in test_smallest_same_kind assert C is not None, 'Got unexpected None from %s' % T AssertionError: Got unexpected None from <type 'numpy.float128'> ====================================================================== FAIL: check_dot (scipy.lib.tests.test_blas.test_fblas1_simple) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/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 "/Library/Frameworks/Python.framework/Versions/2.4/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: (-1.9987130165100098+4.5784586609566519e-37j) DESIRED: (-9+2j) ====================================================================== FAIL: check_dot (scipy.linalg.tests.test_blas.test_fblas1_simple) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.4/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 "/Library/Frameworks/Python.framework/Versions/2.4/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: (-1.9987130165100098+4.5784443116603772e-37j) DESIRED: (-9+2j) ---------------------------------------------------------------------- Ran 1596 tests in 14.230s FAILED (failures=3) <unittest.TextTestRunner object at 0x2cf6bb0> >>>

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More complex issues
by Tim Leslie Jan. 8, 2007

Jan. 8, 2007

Hi all, Sorry for the bad pun, but I'm getting myself confused trying to understand the expected behaviour of how complex values are handled throughout numpy. My current confusion is to do with the difference between how <type 'complex'> and <type 'numpy.complex128'> are handled. If someone could explain this difference that would be great. Cheers, Tim In [45]: z = N.complex128(1 + 2j) In [46]: N.float64(z) Out[46]: 1.0 In [47]: N.float64(1 + 2j) --------------------------------------------------------------------------- exceptions.TypeError Traceback (most recent call last) /home/timl/src/scipy/Lib/linsolve/<ipython console> TypeError: can't convert complex to float; use abs(z)

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