Mailman 3 March 2004 - SciPy-User

blitz++ and numarray
by Faheem Mitha March 29, 2004

March 29, 2004

Hi, I'm considering the use of the Blitz++ C++ library (http://www.oonumerics.org/blitz/) along with numarray/Numeric. I want to pass an array down to C++ and then manipulate it using Blitz++. My current thinking is to use the Numeric interface to pass down the array, and then copy it to a blitz++ array object. This seems straightforward except I am a little concerned about those reference counting issues, which I don't properly understand (I'm a Python beginner). I do get the impression that it is mainly an issue if I am working with Python objects in C/C++ code, though, and I am mostly going to try to avoid doing so by declaring C++ objects within the C++ code and working with those as much as possible. Other possibilities include somehow using the Boost.Python package, though I am not sure how. One advantage of this is that it apparently takes care of the reference counting issue. However, I don't want to learn yet another API. Also, weave.blitz() from SciPy looks relevant/useful, but this automatically generates its own C++ code, and I'd prefer to write my own. Can anyone suggested a good basic tutorial which discusses the issues of reference counting in a C/C++ API context? I have tried reading the official documentation and will continue to do so, but something gentler would be useful. Comments, suggestions gratefully appreciated. Please cc me on any reply to faheem(a)email.unc.edu. Thanks in advance. Faheem.

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(no subject)
by nwagner＠mecha.uni-stuttgart.de March 27, 2004

March 27, 2004

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special's Bessel functions and *plt
by el corto March 23, 2004

March 23, 2004

Hi I'm using Python 2.3, PythonWin, SciPy-0.2.1_253.3724.win32, Scipy_core-0.2.2_alpha_104.1488.win32 (for those who are interested in version numbers) When I plot the Bessel function scipy.special.jv(n,x) (where x can be complex) with gplt from scipy.special import * x=arange(-10,10,.1) from scipy import gplt gplt.plot(x,jv(3,x)) I get some "cuts" at -4 and +4 where the curve isn't smooth. When I try to give complex arguments like gplt.plot(x,jv(3,x+0j)) gplt refuses to plot and shows some errors which means that it isn't able to handle complex y-values as jv(3,x+0j) gives complex and jv(3,x) real values. Trying the same with xplt from scipy import xplt xplt.plot(x,jv(3,x)) shows the same cuts as with gplt but xplt.plot(x,jv(3,x+0j)) does not due to xplt.plot's the ability of handling complex y-values (ignoring imaginary parts). Do these "cuts" mean that jv(3,x) is unable to evaluate the correct function values when fed with a real x or is it a problem with the plotting routines anyway (with jv(3,x)) ?? ============ Another strange thing: Plotting the Bessel function scipy.special.jn(n,x) (where x must be real, gives real y-values) with gplt from scipy.special import * x=arange(-10,10,.1) from scipy import gplt gplt.plot(x,jn(2,x)) shows also some kind of "cut" at x = 0 down to y = -1 as it evaluates jn(2,0) -1.#IND (what doest "#IND" mean !!??) where the function value should be 0 at x = 0 which is evaluated and plotted correctly in Maple. Plotting the same with xplt from scipy import xplt xplt.plot(x,jn(2,x)) shows no such "peak" at x = 0. Why is that even though jn(2,0) evaluates to a wrong function value ? Thanx in advance for any hints about this. bye. -- +++ NEU bei GMX und erstmalig in Deutschland: TÜV-geprüfter Virenschutz +++ 100% Virenerkennung nach Wildlist. Infos: http://www.gmx.net/virenschutz

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Building fortran libraries using scipy_distutils
by Berthold Höllmann March 22, 2004

March 22, 2004

Hello, How (if at all) can I add command line switches for the fortran compiler when building libraries from scipy_distutils using 'libraries'? Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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How to build debugging versions of extensions using scipy distutils
by Berthold Höllmann March 19, 2004

March 19, 2004

Hello, How can I build debugging version of extension modules (especially f2py/Fortan modules) using scipy_distutils? Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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Books
by Sebastian Stark March 18, 2004

March 18, 2004

Can someone recommend a good book on using python in scientific environments, specifically with SciPy? Are there any at all? I already have a couple of books (nutshell, cookbook, learning python) but would need some more specific reading material about numerical programming and related stuff. Thanks, Sebastian -- Sebastian Stark -- http://www.kyb.tuebingen.mpg.de/~stark Max Planck Institute for Biological Cybernetics Spemannstr. 38, 72076 Tuebingen Phone: +49 7071 601 555 -- Fax: +49 7071 601 552

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Error building statlib.so
by Christopher Fonnesbeck March 13, 2004

March 13, 2004

For some reason, stats/statlib refuses to build for me anymore. I did not make any changes to this file, yet on the last few build attempts I get the error below, which is obviously related to not seeing the python framework. However, I have the updated gnufcompiler.py, which contains the following for OSX: opt.extend(["-Wl,-framework","-Wl,Python","-lcc_dynamic","-bundle"]) So, I'm completely at a loss as to why these do not get appended to the compile options. Any ideas? Thanks, C. /usr/local/bin/g77 -lcc_dynamic build/temp.darwin-7.2.0-Power_Macintosh-2.3/usr/local/src/scipy/Lib/ stats/statlibmodule.o build/temp.darwin-7.2.0-Power_Macintosh-2.3/build/src/fortranobject.o -L/usr/local/lib/gcc/powerpc-apple-darwin7.0.0/3.4 -Lbuild/temp.darwin-7.2.0-Power_Macintosh-2.3 -lstatlib -lg2c -o build/lib.darwin-7.2.0-Power_Macintosh-2.3/stats/statlib.so /usr/bin/ld: Undefined symbols: _PyArg_ParseTuple _PyArg_ParseTupleAndKeywords _PyCObject_AsVoidPtr _PyCObject_Type _PyComplex_Type _PyDict_GetItemString _PyDict_SetItemString _PyErr_Clear _PyErr_NewException _PyErr_Occurred _PyErr_Print _PyErr_SetString _PyImport_ImportModule _PyInt_Type _PyModule_GetDict _PyNumber_Int _PyObject_GetAttrString _PyObject_IsTrue _PySequence_Check _PySequence_GetItem _PyString_FromString _PyString_Type _PyType_IsSubtype _PyType_Type _Py_BuildValue _Py_FatalError _Py_InitModule4 __Py_NoneStruct _PyDict_DelItemString _PyDict_New _PyErr_Format _PyExc_AttributeError _PyExc_RuntimeError _PyExc_TypeError _PyObject_Free _PyString_ConcatAndDel _Py_FindMethod __PyObject_New _MAIN__ collect2: ld returned 1 exit status error: Command "/usr/local/bin/g77 -lcc_dynamic build/temp.darwin-7.2.0-Power_Macintosh-2.3/usr/local/src/scipy/Lib/ stats/statlibmodule.o build/temp.darwin-7.2.0-Power_Macintosh-2.3/build/src/fortranobject.o -L/usr/local/lib/gcc/powerpc-apple-darwin7.0.0/3.4 -Lbuild/temp.darwin-7.2.0-Power_Macintosh-2.3 -lstatlib -lg2c -o build/lib.darwin-7.2.0-Power_Macintosh-2.3/stats/statlib.so" failed with exit status 1 C. -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia

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description of io is inconsistent with respect to loadmat
by Nils Wagner March 11, 2004

March 11, 2004

Hi all, The description of io is inconsistent with respect to loadmat. >>help (scipy.io) yields loadmat -- read a MATLAB (version <= 4) style mat file savemat -- write a MATLAB (version <= 4) style mat file >>help (scipy.io.loadmat) yields Both v4 (Level 1.0) and v5 matfiles are supported. Nils

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Failure in scipy.test()
by Nils Wagner March 10, 2004

March 10, 2004

Hi all, scipy.test() in latest cvs failed ====================================================================== FAIL: check_real (scipy_base.type_check.test_type_check.test_imag) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.3/site-packages/scipy_base/tests/test_type_check.py", line 31, in check_real assert_array_equal(0,imag(y)) File "/usr/local/lib/python2.3/site-packages/scipy_test/testing.py", line 641, in assert_array_equal assert len(shape(x))==len(shape(y)) and \ AssertionError: Arrays are not equal (shapes (), (10,) mismatch): Nils

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os x error on import
by John Hunter March 9, 2004

March 9, 2004

I am building CVS scipy on OS X 10.3. The build goes fine, and I can import scipy, or do "from scipy import array" w/o problems. I can "import scipy.signal" but if I do "help(scipy.signal)" or "from scipy.signal import buttord" I get Fatal Python error: Interpreter not initialized (version mismatch?) Abort I have python compiled from src in /usr/local/lib/python2.3 and the python framework is also installed. I wonder if the message is arising from the build using part of the framework when I just want to be using the python from src. >From the CVS root, I built scipy with > cd scipy_core > sudo python setup.py install # uses /usr/local/bin/python2.3 > cd .. > sudo python setup.py install Below is the head of the setup output; if anyone has any suggestions I'm much obliged. Thanks! John Hunter numpy_info: FOUND: define_macros = [('NUMERIC_VERSION', '"\\"23.1\\""')] include_dirs = ['/usr/local/include/python2.3'] SciPy Core Version 0.2.2_alpha_104.1544 **************************************************************** Using fortran_libraries setup option is depreciated --------------------------------------------------- Use libraries option instead. Yes, scipy_distutils now supports Fortran sources in libraries. **************************************************************** running install running build running config_fc running build_src building extension "scipy_base.fastumath" sources adding 'scipy_base/fastumathmodule.c' to sources. building extension "scipy_base._compiled_base" sources running build_py package init file '/Users/jdhunter/python/src/scipy/scipy_core/scipy_distutils/tests/__init__.py' not found (or not a regular file) package init file '/Users/jdhunter/python/src/scipy/scipy_core/scipy_base/tests/__init__.py' not found (or not a regular file) package init file 'weave/tests/__init__.py' not found (or not a regular file) package init file 'weave/tests/__init__.py' not found (or not a regular file) package init file '/Users/jdhunter/python/src/scipy/scipy_core/scipy_distutils/tests/__init__.py' not found (or not a regular file) package init file '/Users/jdhunter/python/src/scipy/scipy_core/scipy_base/tests/__init__.py' not found (or not a regular file) package init file 'weave/tests/__init__.py' not found (or not a regular file) package init file 'weave/tests/__init__.py' not found (or not a regular file) running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext distutils.unixccompiler.UnixCCompiler does not provide version_cmd and version_pattern attributes ******************************************************************************** distutils.unixccompiler.UnixCCompiler compiler_cxx = ['c++'] ranlib = ['ranlib'] linker_exe = ['gcc'] compiler_so = ['gcc', '-fno-strict-aliasing', '-Wno-long-double', '-no-cpp-precomp', '-mno-fused-madd', '-DNDEBUG', '-g', '-O3', '-Wall', '-Wstrict-prototypes'] archiver = ['ar', '-cr'] preprocessor = ['gcc', '-E'] linker_so = ['gcc', '-bundle', '-bundle_loader', '/usr/local/bin/python2.3'] compiler = ['gcc', '-fno-strict-aliasing', '-Wno-long-double', '-no-cpp-precomp', '-mno-fused-madd', '-DNDEBUG', '-g', '-O3', '-Wall', '-Wstrict-prototypes'] libraries = [] library_dirs = [] include_dirs = ['/usr/local/include/python2.3'] ******************************************************************************** running install_lib running install_data /usr/local/bin/python2.3 /Users/jdhunter/python/src/scipy/scipy_core/setup.py install fftw_info: NOT AVAILABLE dfftw_info: NOT AVAILABLE FFTW (http://www.fftw.org/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [fftw]) or by setting the FFTW environment variable. djbfft_info: NOT AVAILABLE DJBFFT (http://cr.yp.to/djbfft.html) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [djbfft]) or by setting the DJBFFT environment variable. blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-framework', 'Accelerate'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-framework', 'Accelerate'] creating build creating build/temp.darwin-7.2.0-Power_Macintosh-2.3 creating build/temp.darwin-7.2.0-Power_Macintosh-2.3/config_pygist ============= begin top level configuration ============= compiling '_configtest.c': /* check whether libm is broken */ #include <math.h> int main(int argc, char *argv[]) { return exp(-720.) > 1.0; /* typically an IEEE denormal */ } gcc options: '-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes' compile options: '-c' gcc: _configtest.c gcc _configtest.o -lm -o _configtest success! removing: _configtest.c _configtest.o _configtest compiling '_configtest.c': /* check whether libm is broken */ #include <math.h> int main(int argc, char *argv[]) { return exp(-720.) > 1.0; /* typically an IEEE denormal */ }

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