Mailman 3 July 2007 - NumPy-Discussion

build on windows 64-bit platform
by Stefan van der Walt 28 Jul '07

28 Jul '07

Hi all, The build is still failing on winXP 64-bit, as shown on the buildbot page http://buildbot.scipy.org/Windows%20XP%20x86_64%20MSVC/builds/25/step-shell… with the error AttributeError: MSVCCompiler instance has no attribute '_MSVCCompiler__root' Could someone familiar with the MSVC compilers please take a look? Thanks Stéfan

3 8

PLEASE help with mpi4py
by Viktor Oudovenko 28 Jul '07

28 Jul '07

Dear Lisandro, I'd be very grateful is you could help us to understand why mpi4py does not work with MPI-1 . We've succeeded to build and run mpi4py with MPI-2 (mpd) only. We did not get thought for MPI-1 case and for MPI-2 (smpd). We are using SGE queuing system and for it we need weather MPI-1 or MPI-2 (smpd) working. What we've got so far plz see attachment where we are sending you 2 configuration files and 3 log files plus info file about python. The only conclusion we've come to is that to get MPI-1 working we need to recompile python. Python we used is the standard installation of OpenSuSE 10.2 . If you need any other information which we've missed to provide plz let us know. Thank you very much in advance for your help. Regards, viktor

1 0

Bug with MA and reduce?
by Ludwig M Brinckmann 27 Jul '07

27 Jul '07

I have ma.minimum.reduce return a minimum value that does not exist in the array. The following code prints -1 as the minimum of the MA, I believe it should be 1. import numpy shape = (100) data = numpy.ones(shape, numpy.int16) data[2:40] = 3 # dummy data data[45:70] = -999 # null values mask = numpy.ma.make_mask_none(data.shape) mask[data == -999] = True ma = numpy.ma.MaskedArray(data, mask = mask) min = numpy.ma.minimum.reduce(ma,0) print min Am I doing something really stupid here? Ludwig

2 2

numarray problem when compiling WrapITK external project PyBuffer
by Sven Prevrhal 27 Jul '07

27 Jul '07

(NumPy community, read on this only seems unrelated) I use NumPy 1.0.3 , MSVC 2005 Express, ITK CVS from 23Jul2007, WrapITK for Python only, wrap for the standard types plus signed short (imho that should be switched on by default because many DICOM images are in that type). BTW I had to include the /bigobj compiler switch in the CMakeLists.txt for ITK for that to work. ItkVtkGlue compiled, but PyBuffer gave errors: 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value and 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value at several occasions. At these line numbers, the numarray function import_array() is called. I checked the numarray code and import_array() is a #define that does not return a value: #define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return; } } I realize that's more a problem with numarray than PyBuffer. Since that's inline-used the compiler is probably thwarted by the return inside the macro. Consequently, if I replace the #define with a void to make it a real function call PyBuffer compiles just fine. Thanks, Sven Here is the whole build log: 1>------ Build started: Project: _BufferConversionPython, Configuration: Release Win32 ------ 1>Generating wrap_itkPyBuffer.xml 1>Generating wrap_itkPyBuffer.idx 1>Generating wrap_itkPyBufferPython.cxx 1>Generating wrap_BufferConversionPythonPython.cxx 1>create swig package BufferConversionPython 1> init module: itkPyBuffer 1>Compiling... 1>wrap_itkPyBufferPython.cxx 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned char,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<unsigned char,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<unsigned char,3>, 1> TPixel=unsigned char, 1> VImageDimension=3 1> ] 1> .\wrap_itkPyBufferPython.cxx(1542) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<unsigned char,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned char,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<unsigned char,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<unsigned char,3>, 1> TImage=itk::Image<unsigned char,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<float,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<float,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<float,3>, 1> TPixel=float, 1> VImageDimension=3 1> ] 1> .\wrap_itkPyBufferPython.cxx(1646) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<float,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<float,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<float,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<float,3>, 1> TImage=itk::Image<float,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<float,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<float,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<float,2>, 1> TPixel=float, 1> VImageDimension=2 1> ] 1> .\wrap_itkPyBufferPython.cxx(1750) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<float,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<float,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<float,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<float,2>, 1> TImage=itk::Image<float,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<unsigned short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<unsigned short,3>, 1> TPixel=unsigned short, 1> VImageDimension=3 1> ] 1> .\wrap_itkPyBufferPython.cxx(1854) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<unsigned short,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<unsigned short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<unsigned short,3>, 1> TImage=itk::Image<unsigned short,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned char,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<unsigned char,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<unsigned char,2>, 1> TPixel=unsigned char, 1> VImageDimension=2 1> ] 1> .\wrap_itkPyBufferPython.cxx(1958) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<unsigned char,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned char,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<unsigned char,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<unsigned char,2>, 1> TImage=itk::Image<unsigned char,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<unsigned short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<unsigned short,2>, 1> TPixel=unsigned short, 1> VImageDimension=2 1> ] 1> .\wrap_itkPyBufferPython.cxx(2062) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<unsigned short,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<unsigned short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<unsigned short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<unsigned short,2>, 1> TImage=itk::Image<unsigned short,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<short,3>, 1> TPixel=short, 1> VImageDimension=3 1> ] 1> .\wrap_itkPyBufferPython.cxx(2151) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<short,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<short,3> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<short,3>, 1> TImage=itk::Image<short,3> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(46) : error C2561: 'itk::PyBuffer<TImage>::GetArrayFromImage' : function must return a value 1> with 1> [ 1> TImage=itk::Image<short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(73) : see declaration of 'itk::PyBuffer<TImage>::GetArrayFromImage' 1> with 1> [ 1> TImage=itk::Image<short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(38) : while compiling class template member function 'PyObject *itk::PyBuffer<TImage>::GetArrayFromImage(itk::Image<TPixel,VImageDimension> *)' 1> with 1> [ 1> TImage=itk::Image<short,2>, 1> TPixel=short, 1> VImageDimension=2 1> ] 1> .\wrap_itkPyBufferPython.cxx(2240) : see reference to class template instantiation 'itk::PyBuffer<TImage>' being compiled 1> with 1> [ 1> TImage=itk::Image<short,2> 1> ] 1>c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\i tkPyBuffer.txx(77) : error C2561: 'itk::PyBuffer<TImage>::GetImageFromArray' : function must return a value 1> with 1> [ 1> TImage=itk::Image<short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.h(78) : see declaration of 'itk::PyBuffer<TImage>::GetImageFromArray' 1> with 1> [ 1> TImage=itk::Image<short,2> 1> ] 1> c:\users\sprevrha\src\insight\wrapping\wrapitk\externalprojects\pybuffer\itk PyBuffer.txx(75) : while compiling class template member function 'const itk::SmartPointer<TObjectType> itk::PyBuffer<TImage>::GetImageFromArray(PyObject *)' 1> with 1> [ 1> TObjectType=itk::Image<short,2>, 1> TImage=itk::Image<short,2> 1> ] 1>wrap_BufferConversionPythonPython.cxx 1>Generating Code... 1>Build log was saved at "file://c:\packages\Insight-CVS-VC2005-WrapITK-ExternalProjects\PyBuffer\_Bu fferConversionPython.dir\Release\BuildLog.htm" 1>_BufferConversionPython - 16 error(s), 0 warning(s) 2>------ Build started: Project: ALL_BUILD, Configuration: Release Win32 ------ 2>"Build all projects" 2>Build log was saved at "file://c:\packages\Insight-CVS-VC2005-WrapITK-ExternalProjects\PyBuffer\ALL _BUILD.dir\Release\BuildLog.htm" 2>ALL_BUILD - 0 error(s), 0 warning(s) ========== Build: 1 succeeded, 1 failed, 2 up-to-date, 0 skipped ==========

1 0

getting numPy happening for sciPy
by Tim Mortimer 27 Jul '07

27 Jul '07

Hello There, I'm pretty new to Python, picking it up recently in order to begin to experiment with Csound / Python interconnectivity (generating scores, GUI elements, using Vpython to model mechanical "systems"... that sort of thing...) Have so far written about 500 lines of Python code (over the last few weeks) to do various housekeeping of of my Csound .sco's & beginning to play with some Python / Csound score generative stuff. Sowhen it comes to Python i'm a novice, but with some grasp of the basics. Anyway, I wanted to "beef up" my python arsenal with some of the SciPY stuff - initially a wider & more solid range of random number generators, histograms & statistical packages etc. So it is with some regret that i see at present that it is not possible to build SciPy on top of the standard "out the box" NumPy installation? I am not an experienced programmer, so the idea of building NumPy from the "bleeding edge" repository is beyond my capability, as there appears to be no specific instructions for how to do this (that don't assume you have some degree of experience at what your doing anyway.. ) So I guess my question is 1) can i get an idiots guide to what's required to get the current NumPy installation happening in order to host SciPy on top of it? 2) if 1) involves a whole lot of faffing about & acquiring a whole heap of new skill set (that only really has limited long term relevance to me, & isn't likely to stick in my head very long anyway) - how long do I have to wait before i can just run a new NumPy installer, followed by a SciPy installer, & get the full kit & kaboodle happening? Regrettably, I'm on Win XP. Thanks for any help or advice. Can't imaging i'll be having too much of a contribution to this community, but will be interested to see what sort of topics float through the NumPY world.... with thanks Tim - Adelaide, Australia.

9 14

C-extension -- how do I accept a vector of both type double and type int?
by Geoffrey Zhu 26 Jul '07

26 Jul '07

Hi Everyone, I finally build a C extension. The one problem I found is that it is too picky about the input. For example, it accepts array([1.0,2.0,3.0]) with no problem, but when I pass in array([1,2,3]), since the dtype of the array is now int, my extension does not like it. How do I handle this situation? Is there any way to access any data type that can be converted into a double? Thanks, cg

2 7

Change to get_printoptions?
by Zachary Pincus 26 Jul '07

26 Jul '07

Hello all, I just recently updated to the SVN version of numpy to test my code against it, and found that a small change made to numpy.get_printoptions (it now returns a dictionary instead of a list) breaks my code. Here's the changeset: http://projects.scipy.org/scipy/numpy/changeset/3877 I'm not really looking forward to needing to detect numpy versions just so I can do the right thing with get_printoptions, but I do agree that the new version of the function is more sensible. My question is if there's any particular policy about backwards- incompatible python api changes, or if I need to be aware of their possibility at every point release. (Either is fine -- I'm happy for numpy to be better at the cost of incompatibility, but I'd like to know if changes like these are the rule or exception.) Also, in terms of compatibility checking, has anyone written a little function to check if numpy is within a particular version range? Specifically, one that handles numpy's built from SVN as well as from release tarballs. Thanks, Zach Pincus Program in Biomedical Informatics and Department of Biochemistry Stanford University School of Medicine

2 1

How do I get numpy.distutils.core setup to properly handle an optimize=1 in setup.cfg when doing bdist_rpm?
by Stanley A. Klein 26 Jul '07

26 Jul '07

I'm trying to do an rpm package of enthought kiva for a Fedora 5 system. Enthought kiva imports numpy.distutils.core setup, probably because it has a lot of mathematical functions to compile as part of the package. Doing bdist_rpm for Fedora requires using a setup.cfg that contains [install] optimize=1 because SE-Linux needs to know all the files involved, including the pyc and pyo files, and this is best done by having distutils/setuptools both create the pyc/pyo files and the rpm spec file. However, when I run the enthought kiva setup.py with the proper setup.cfg, I get an error ("unpackaged files") indicating that the numpy distutils did not properly process the setup.cfg file. How do I fix it? Thanks. Stan Klein

1 0

Possible bug -- importing numpy before f2py compiled module gives seg fault
by Kurt Smith 26 Jul '07

26 Jul '07

Hello - I've come up with the following test case to illustrate my problem: file empty.f: subroutine empty(arr, nx,ny ) implicit none integer, intent(in) :: nx,ny real, dimension(nx,ny), intent(out) :: arr print *, "in empty." arr = 1.0e0 end subroutine empty using the following to compile: f2py -c -m empty -lSystemStubs --opt=-O3 --fcompiler=ibm --f90exec=/ opt/ibmcmp/xlf/8.1/bin/xlf90 --f90flags=-O3 empty.f Builds empty.so just fine. Python 2.5.1 (r251:54869, Apr 18 2007, 22:08:04) [GCC 4.0.1 (Apple Computer, Inc. build 5367)] on darwin >>> from empty import empty as myempty >>> from numpy import * # for illustration purposes. >>> myempty(1,1) in empty. array([[ 1.]], dtype=float32) >>> But when I import numpy first, I get the following: Python 2.5.1 (r251:54869, Apr 18 2007, 22:08:04) [GCC 4.0.1 (Apple Computer, Inc. build 5367)] on darwin >>> from numpy import * >>> from empty import empty as myempty >>> myempty(1,1) Segmentation fault $ Platform: Mac OS X, 10.4.10, using ibm-xlfortran v. 8.1. $ f2py -v 2_3844

1 0

Downsampling a 2D array with min/max and nullvalues
by Ludwig M Brinckmann 26 Jul '07

26 Jul '07

Hi there, I have a 2D array of size, lets say 40000 * 512, which I need to downsample by a step of 4 in the y direction, and step 3 in the x direction, so I would get an array of 10000 * 170 (or 171, the edges do not matter much). But what I need to retain are the maxima and minima in every 4*3 window. I have a solution that works by first clipping off the edges of the array, so that its shape is divisible by 4*3, and then applying a two step process that will compute the min and max in strips --first in the x direction and then in the y-direction through reshaping and reduce (not super elegant, but it seems to work): def downsampleArray1D(data, step, nullValue): print 'downsampling %d' %step if data.shape[1] % step != 0: xlen = data.shape[1] - data.shape[1] % step data = data[...,:xlen] data1d = data.ravel() assert(data1d.shape[0] % step == 0) data1d.shape = (len(data1d)/step, step) maxdata = numpy.maximum.reduce(data1d,1) mindata = numpy.minimum.reduce(data1d,1) mindata.shape = ((data.shape[0],int(data.shape[1] / step))) maxdata.shape = ((data.shape[0],int(data.shape[1] / step))) return mindata, maxdata def downsampleArray2D(data, yStep, xStep, nullValue): # first adjust the data to the step size by ignoring edges if data.shape[0] % yStep != 0: ylen = data.shape[0] - data.shape[0] % yStep data = data[:ylen,...] if data.shape[1] % xStep != 0: xlen = data.shape[1] - data.shape[1] % xStep data = data[...,:xlen] minx, maxx = downsampleArray1D(data, xStep, nullValue) minxt = numpy.transpose(minx) minxt1, dummy = downsampleArray1D(minxt, yStep, nullValue) maxxt = numpy.transpose(maxx) dummy, maxxt1 = downsampleArray1D(maxxt, yStep, nullValue) minimum = numpy.transpose(minxt1) maximum = numpy.transpose(maxxt1) return minimum, maximum Now I need a solution that will ignore null values, i.e. that any value that is equivalent to e.g. -999 ignored in the min and max computation, but if all values in a 4*3 window are nullvalues, then min and max should be set to the null value. Any suggestions? Ludwig

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