Mailman 3 August 2006 - NumPy-Discussion

astype char conversion
by Matthew Brett Aug. 9, 2006

Aug. 9, 2006

Hi, Sorry if this is silly question, but should this work to convert from int8 to character type? a = array([104, 105], dtype=N.int8) a.astype('|S1') I was a bit surprised by the output: array([1, 1], dtype='|S1') Thanks a lot, Matthew

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Moving docstrings from C to Python
by Stefan van der Walt Aug. 9, 2006

Aug. 9, 2006

Hi, Travis recently advertised the add_docstring and add_newdoc functions, which are used to add documentation to functions written in C. This brings the advantage that you don't have to recompile everytime you change a docstrings, and also that the docstrings are much simpler to format (no more "\n\" tokens all over the place). I took all the docstrings from numpy.core.src.multiarray and formatted them to be used with add_docstring. I have two questions: Would anyone mind if the change was made? If not, where should they go? (numpy/add_newdocs.py or numpy/core/something) Thanks for the feedback. Stéfan

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Examples of basic C API usage?
by Bill Baxter Aug. 9, 2006

Aug. 9, 2006

I see Pyrex and SWIG examples in numpy/doc but there doesn't seem to be an example of just a simple straightforward usage of the C-API. For instance make a few arrays by hand in C and then call numpy.multiply() on them. So far my attempts to call PyArray_SimpleNewFromData all result in segfaults. Anyone have such an example? --Bill

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how to reference Numerical Python in a scientific publication
by Sebastian Haase Aug. 9, 2006

Aug. 9, 2006

Hi, we are using numerical python as an integral part of a microscope development project over last few years. So far we have been using exclusively numarray but now I decided it's time to slowly but sure migrate to numpy. What is the proper way to reference these packages ? Thanks to everyone involved, Sebastian Haase UCSF

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numpy and matplotlib
by George Gumas Aug. 9, 2006

Aug. 9, 2006

I downloaded numpy 10000 and matplotlib and when running numpy i get the error message below from matplotlib._ns_cntr import * RuntimeError: module compiled against version 90709 of C-API but this version of numpy is 1000000 How do I go about chaning the version of rither numpy or matplotlib Thanks George

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NumPy, shared libraries and ctypes
by Albert Strasheim Aug. 9, 2006

Aug. 9, 2006

Hello all With the nice ctypes integration in NumPy, and with Python 2.5 which will include ctypes around the corner, a remote possibility exists that within the next year or two, I might not be the only person that wants to use NumPy with ctypes. This is probably going to mean that this someone is going to want to build a shared library for use with ctypes. This is all well and good if you're using a build tool that knows about shared libraries, but in case this person is stuck with distutils, here is what we might want to do. Following this thread from SciPy-dev: http://projects.scipy.org/pipermail/scipy-dev/2006-April/005708.html I came up with the following plan. As it happens, pretending your shared library is a Python extension mostly works. In your setup.py you can do something like this: config = Configuration(package_name,parent_package,top_path) config.add_extension('libsvm_', define_macros=[('LIBSVM_EXPORTS', None), ('LIBSVM_DLL', None)], sources=[join('libsvm-2.82', 'svm.cpp')], depends=[join('libsvm-2.82', 'svm.h')]) First caveat: on Windows, distutils forces the linker to look for an exported symbol called init<yourextensionname>. In your code you'll have to add an empty function like this: void initlibsvm_() {} This gets us a compiled Python extension, which also happens to be a shared library on every platform I know of, which is Linux and Windows. Counter-examples anyone?. Next caveat: on Windows, shared libraries aka DLLs, typically have a .dll extension. However, Python extensions have a .pyd extension. We have a utility function in NumPy called ctypes_load_library which handles finding and loading of shared libraries with ctypes. Currently, shared library extensions (.dll, .so, .dylib) are hardcoded in this function. I propose we modify this function to look something like this: def ctypes_load_library(libname, loader_path, distutils_hack=False): ... If distutils_hack is True, instead of the default mechanism (which is currently hardcoded extensions), ctypes_load_library should do: import distutils.config so_ext = distutils.sysconfig.get_config_var('SO') to figure out the extension it should use to load shared libraries. This should make it reasonably easy for people to build shared libraries with distutils and use them with NumPy and ctypes. Comments appreciated. Someone checking something along these lines into SVN appreciated more. A solution that doesn't make me want to cry appreciated most. Thanks for reading. Regards, Albert P.S. As it happens, the OOF2 guys have already created a SharedLibrary builder for distutils, but integrating this into numpy.distutils is probably non-trivial. http://www.ctcms.nist.gov/oof/oof2.html

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Re: [Numpy-discussion] (no subject)
by mike Aug. 8, 2006

Aug. 8, 2006

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numpy import problem
by Hanno Klemm Aug. 8, 2006

Aug. 8, 2006

Hello, finally after sorting out some homemade problems I managed to compile numpy-1.0b1. If I then start it from the directory where I compiled it, it works fine. However after I installed numpy with python setup.py install --prefix=/scratch/python2.4 I get the error message: Python 2.4.3 (#7, Aug 2 2006, 18:55:46) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-52)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/scratch/python2.4/lib/python2.4/site-packages/numpy/__init__.py", line 39, in ? import linalg File "/scratch/python2.4/lib/python2.4/site-packages/numpy/linalg/__init__.py", line 4, in ? from linalg import * File "/scratch/python2.4/lib/python2.4/site-packages/numpy/linalg/linalg.py", line 24, in ? from numpy.linalg import lapack_lite ImportError: /scratch/python2.4/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: atl_f77wrap_zgemv__ >>> I suppose I have to set a path somewhere to the directory where atlas is installed. How do I do this? Hanno -- Hanno Klemm klemm(a)phys.ethz.ch

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numpy and unittests
by Christian Meesters Aug. 7, 2006

Aug. 7, 2006

Hi, I used to work with some unittest scripts for a bigger project of mine. Now that I started the project again the tests don't work anymore, using numpy version '0.9.5.2100' . The errors I get look are like this: ERROR: _normalize() should return dataset scaled between 0 and 1 ---------------------------------------------------------------------- Traceback (most recent call last): File "testingSAXS.py", line 265, in testNormalization self.assertEqual(self.test1._normalize(minimum=0.0,maximum=1.0),self.test5) File "/usr/lib64/python2.4/unittest.py", line 332, in failUnlessEqual if not first == second: File "/home/cm/Documents/Informatics/Python/python_programming/biophysics/SAXS/lib/Data.py", line 174, in __eq__ if self.intensity == other.intensity: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() The 'self.intensity' objects are 1D-arrays containing integers <= 1E6. The unittest script looks like: if __name__=='__main__': from Data import * from Utils import * import unittest <snip> def test__eq__(self): """__eq__ should return True with identical array data""" self.assert_(self.test1 == self.test2) <snip> suite = unittest.TestSuite() suite.addTest(unittest.makeSuite(Test_SAXS_Sanity)) <snip> unittest.TextTestRunner(verbosity=1).run(suite) Any ideas what I have to change? (Possibly trivial, but I have no clue.) TIA Cheers Christian

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Histogram versus histogram2d
by Mikolai Fajer Aug. 7, 2006

Aug. 7, 2006

Hello, I have noticed some that the 1d histogram and 2d histogram. The histogram function bins everything between the elements of edges, and then includes everything greater than the last edge element in the last bin. The histrogram2d function only bins in the range specified by edges. Is there a reason these two functions do not operate in the same way? -- -Mikolai Fajer-

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