Mailman 3 March 2006 - NumPy-Discussion

Cygwin
by Lalo 26 Mar '06

26 Mar '06

Hi, I tried to compile numpy 0.9.6 on a standard Cygwin installation but got some errors. Do I need to modify the site.cfg defaults? Thank you for your help. Lalo ------------------------------------------------------ Running from numpy source directory. /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['mkl', 'vml', 'guide'] found_libs=[] warnings.warn("Library error: libs=%s found_libs=%s" % \ /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['lapack', 'f77blas', 'cblas', 'atlas'] found_libs=[] warnings.warn("Library error: libs=%s found_libs=%s" % \ /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['lapack', 'f77blas', 'cblas', 'atlas'] found_libs=['/usr/lib/liblapack.a'] warnings.warn("Library error: libs=%s found_libs=%s" % \ /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['lapack', 'f77blas', 'cblas', 'atlas'] found_libs=['/usr/lib/liblapack.dll.a'] warnings.warn("Library error: libs=%s found_libs=%s" % \ /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:1264: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['blas'] found_libs=[] warnings.warn("Library error: libs=%s found_libs=%s" % \ /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['lapack_atlas'] found_libs=[] warnings.warn("Library error: libs=%s found_libs=%s" % \ /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:1183: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /home/lalo/tmp/numpy-0.9.6/numpy/distutils/system_info.py:531: UserWarning: Library error: libs=['lapack'] found_libs=[] warnings.warn("Library error: libs=%s found_libs=%s" % \ F2PY Version 2_2236 blas_opt_info: blas_mkl_info: NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS NOT AVAILABLE atlas_blas_info: NOT AVAILABLE blas_info: FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 lapack_opt_info: lapack_mkl_info: mkl_info: NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: numpy.distutils.system_info.atlas_info NOT AVAILABLE lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 running install running build running config_fc running build_src building py_modules sources building extension "numpy.core.multiarray" sources adding 'build/src/numpy/core/config.h' to sources. adding 'build/src/numpy/core/__multiarray_api.h' to sources. adding 'build/src/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files= ['build/src/numpy/core/src/scalartypes.inc', 'build/src/numpy/core/src/arraytypes.inc', 'build/src/numpy/core/config.h', 'build/src/numpy/core/__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build/src/numpy/core/config.h' to sources. adding 'build/src/numpy/core/__ufunc_api.h' to sources. adding 'build/src/numpy/core/src' to include_dirs. numpy.core - nothing done with h_files= ['build/src/numpy/core/src/scalartypes.inc', 'build/src/numpy/core/src/arraytypes.inc', 'build/src/numpy/core/config.h', 'build/src/numpy/core/__ufunc_api.h'] building extension "numpy.core._sort" sources adding 'build/src/numpy/core/config.h' to sources. adding 'build/src/numpy/core/__multiarray_api.h' to sources. numpy.core - nothing done with h_files= ['build/src/numpy/core/config.h', 'build/src/numpy/core/__multiarray_api.h'] building extension "numpy.core._dotblas" sources adding 'numpy/core/blasdot/_dotblas.c' to sources. building extension "numpy.lib._compiled_base" sources building extension "numpy.dft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources adding 'numpy/linalg/lapack_litemodule.c' to sources. building extension "numpy.random.mtrand" sources Could not locate executable gfortran Could not locate executable f95 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config gcc options: '-fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes' compile options: '-Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c' gcc: _configtest.c _configtest.c:7:2: #error No _WIN32 _configtest.c:7:2: #error No _WIN32 failure. removing: _configtest.c _configtest.o building data_files sources running build_py copying build/src/numpy/__config__.py -> build/lib.cygwin-1.5.19-i686-2.4/numpy copying build/src/numpy/distutils/__config__.py -> build/lib.cygwin-1.5.19-i686-2.4/numpy/distutils running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext building 'numpy.core.multiarray' extension compiling C sources gcc options: '-fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes' compile options: '-Ibuild/src/numpy/core/src -Inumpy/core/include -Ibuild/src/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c' gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.5.19-i686-2.4/numpy/core/src/multiarraymodule.o -L. -lpython2.4 -o build/lib.cygwin-1.5.19-i686-2.4/numpy/core/multiarray.dll /usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lpython2.4 collect2: ld returned 1 exit status /usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lpython2.4 collect2: ld returned 1 exit status error: Command "gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.5.19-i686-2.4/numpy/core/src/multiarraymodule.o -L. -lpython2.4 -o build/lib.cygwin-1.5.19-i686-2.4/numpy/core/multiarray.dll" failed with exit status 1

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Problem on install Numpy. Thanks~!
by Bill_Lang 26 Mar '06

26 Mar '06

Hi Numpy list members, Just now, I have run numpy-0.9.6r1.win32-py2.4.exe which was download from sourceforge. Then there is a new dictionary under "C:\Python24\Lib\site-packages\". And I checked the sys.path. the numby path is included in sys.path. But when I import numeric. There is a hint that "ImportError: No module named numeric". Is there anybody could help me to solve this problem? Thanks a lot~! BTW: I am a freshman of Python. Yet, I love Python now. Best wishes; Bill_Lang

3 2

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26 Mar '06

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1 0

Re: [SciPy-dev] masked_array drops fill_value
by Sasha 25 Mar '06

25 Mar '06

Please post questions about "ma" on numpy-discussion. I don't like per-array fill_value feature. I believe fill_value should be a mandatory argument to the filled method and default fill_values only used internally to avoid passing bad data to ufuncs. The behavior that you describe seem to be historical. I would like to hear from other people who rely on per-array fill values before making any change. On 3/25/06, Tim Leslie <tim.leslie(a)gmail.com> wrote: > Hi all, > > In ma.py the masked_array function the fill_value of the array passed in is > not used. The code currently looks like this: > > def masked_array (a, mask=nomask, fill_value=None): > """masked_array(a, mask=nomask) = > array(a, mask=mask, copy=0, fill_value=fill_value) > """ > return array(a, mask=mask, copy=0, fill_value=fill_value) > > > It seems to me that using the fill_value from a (if it is a MaskedArray) > would be the sane thing to do? Something like > > if fill_value == None and isinstance(a, MaskedArray): > fill_value = a.fill_value() > return array(a, mask=mask, copy=0, fill_value=fill_value) > > As it stands, all the ma functions such as transpose, reshape, etc lose the > fill_value which seems wrong to me. > > Tim > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-dev > > >

1 0

OS X - Universal MacPython - numpy install failure
by James Boyle 24 Mar '06

24 Mar '06

I am running OX 10.3.9. I installed python 2.4.2 using Universal MacPython 2.4.2.dmg. I am on a PowerPC G4. The Universal build is designed to install on the Mac PPC and Intel machines. When I run the numpy 0.9.6 install it apparently fails on the configure. The whole trace back is at the end of this posting. One thing that I noted was the line: gcc options: '-arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g' It appears that the configure routines think that I have two architectures - ppc and i386. At my low level of understanding, all I can do is speculate that the Universal install generates some confusion as to the actual cpu. Somewhere numpy is keying on information that is ambiguous in the universal install. I have installed Numeric, matplotlib and other packages without a problem. --Jim The trace back from >python setup.py build: Running from numpy source directory. Warning: not existing path in numpy/distutils: site.cfg F2PY Version 2_2236 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'] running build running config_fc running build_src building py_modules sources creating build creating build/src creating build/src/numpy creating build/src/numpy/distutils building extension "numpy.core.multiarray" sources creating build/src/numpy/core Generating build/src/numpy/core/config.h customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config gcc options: '-arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g' compile options: '-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -Inumpy/core/src -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -c' gcc: _configtest.c gcc: cannot specify -o with -c or -S and multiple compilations gcc: cannot specify -o with -c or -S and multiple compilations failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "setup.py", line 76, in ? setup_package() File "setup.py", line 69, in setup_package setup( **config.todict() ) File "/Volumes/IBM1/macPython/numpy-0.9.6/numpy/distutils/core.py", line 85, in setup return old_setup(**new_attr) File "/Library/Frameworks/Python.framework/Versions/2.4//lib/python2.4/ distutils/core.py", line 149, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.4//lib/python2.4/ distutils/dist.py", line 946, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.4//lib/python2.4/ distutils/dist.py", line 966, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.4//lib/python2.4/ distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.4//lib/python2.4/ distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.4//lib/python2.4/ distutils/dist.py", line 966, in run_command cmd_obj.run() File "/Volumes/IBM1/macPython/numpy-0.9.6/numpy/distutils/command/ build_src.py", line 84, in run self.build_sources() File "/Volumes/IBM1/macPython/numpy-0.9.6/numpy/distutils/command/ build_src.py", line 99, in build_sources self.build_extension_sources(ext) File "/Volumes/IBM1/macPython/numpy-0.9.6/numpy/distutils/command/ build_src.py", line 209, in build_extension_sources sources = self.generate_sources(sources, ext) File "/Volumes/IBM1/macPython/numpy-0.9.6/numpy/distutils/command/ build_src.py", line 267, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 37, in generate_config_h raise "ERROR: Failed to test configuration" ERROR: Failed to test configuration

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A numerical agnostic extension
by Francesc Altet 24 Mar '06

24 Mar '06

Hi, After seeing the inspiring work of Andrew Straw on the implementation of a __array_struct__ Pyrex interface for the array protocol, I wasn't able to relax and finally implemented another extension (heavily based on Andrew's work) that takes Numeric/numarray/NumPy objects and exposes the same interface to access to their data and metadata from both Python and Pyrex (and hence, C) spaces. All this *without* a need to compile against a specific numerical package. I've created a new recipe for this extension in: http://www.scipy.org/Cookbook/A_Pyrex_Agnostic_Class I'm pretty excited about all the possibilities that opens this relatively small class: numerical agnosticism is closer than ever :-) -- >0,0< Francesc Altet http://www.carabos.com/ V V Cárabos Coop. V. Enjoy Data "-"

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Current SVN segfaults under VC7
by Tim Hochberg 24 Mar '06

24 Mar '06

I just updated from CVS and compiled using VC7. The resulting numpy segfaults immediately on import. Do not pass go, do not collect $200. It's been a couple of weeks probably since I updated from CVS, so I'm not sure where to start looking. I suppose I could start going back in time until it works again and then see what checkins broke it, but if anyone has any better ideas, let me know. -tim

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Newbie: Matrix form of segment-sphere intersection?
by Jim Carroll 24 Mar '06

24 Mar '06

Hi, I'm considering using matricies for some math that determines where segments intersect spheres. I have pairs of 3d coordinates P1, P2; P3, P4; P5, P6; ... Pn-1, Pn. one is inside a sphere, and the other is outside the same sphere. I want the point where segment joining the point intersects the sphere. The math is straightforward enough done in a function (for example: http://www.siggraph.org/education/materials/HyperGraph/raytrace/rtinter1.htm) Are matricies appropriate as a way of applying this sort of computation to a large number of points? Where can I find applicable tutorials or recipies? Thanks, -Jim

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Re: [Numpy-discussion] array, asarray as contiguous and friends
by Colin J. Williams 24 Mar '06

24 Mar '06

Tim Hochberg wrote: > Colin J. Williams wrote: > >> Tim Hochberg wrote: >> >>> >>> >>> I was just looking at the interface for array and asarray to see >>> what other stuff should go in the interface of the hypothetical >>> ascontiguous. There's 'dtype', which I knew about, and 'fortran', >>> which I didn't, but which makes sense. However, there's also >>> 'ndmin'. First off, it's not described in docstring for asarray, but >>> I was able to find it in the docstring for array without a problem. >>> Second, is it really necessary? It seems to be useful in an awfully >>> narrow set of circumstances, particularly since when you are padding >>> axes not everyone wants to pad to the left. >>> >>> It would seem to be more useful to ditch the ndmin and have some >>> sort of paddims function that was more full featured (padding to >>> either the left or the right at a minimum). I'm not entirely sure >>> what the best interface to such a beast would look like, but a >>> simple tactic would be to just provide leftpaddims and rightpaddims. >>> >>> If it's not allready clear by now (;), I prefer several narrow >>> interfaces to one broad one. >>> >>> -tim >>> >> >> >> >> What does ascontiguous do that copy doesn't? > > > What it doesn't do is always copy the argument. Just like asarray, it > returns it unchanged if it's contiguous. Fair enough. I guess that, for some array a, "b= ascontiguous(a)" saves a few keystrokes as compared with "b= a if a.flags.contiguous else a.copy()". The intent of the latter is clearer and probably burns fewer cycles. numarray has an iscontiguous method, which is a bit simpler than concerning the Python user with flags. > >> In numarray, transpose created a discontiguous array. copy() made >> the array contiguous. Is there sufficient benefit to justify another >> method? > > > I was proposing a function, not a method. The array object has plenty > of methods already. Since the function would only operate on ArrayType instances, would it not be better as a method? Colin W. > > -tim > >> >> Colin W. >> >> > >

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PyArray_ISSTRING
by Fred Clare 24 Mar '06

24 Mar '06

I am running NumPy 0.9.6 on Mac OS X. When I try to use the API function PyArray_ISSTRING I get: `PyArray_UCHAR' undeclared In fact I cannot see where PyArray_UCHAR is ever declared. Fred Clare

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