Mailman 3 November 2008 - NumPy-Discussion

ANN: numpy.i - added managed deallocation to ARGOUTVIEW_ARRAY1 (ARGOUTVIEWM_ARRAY1)
by Egor Zindy Jan. 8, 2009

Jan. 8, 2009

Dear List, after I tried to write a simple ARGOUTVIEW_ARRAY1 example (see http://code.google.com/p/ezwidgets/wiki/NumpySWIGMinGW#A_simple_ARGOUTVIEW_… ), I started wondering about memory deallocation. Turns out a few clever people already did all the thinking (see http://blog.enthought.com/?p=62 ) and a few more clever people use this in a swig file (see http://niftilib.sourceforge.net/pynifti, file nifticlib.i). All this concentrated knowledge helped me implement a single ARGOUTVIEWM_ARRAY1 fragment in numpy.i to do some testing (see attached numpy.i). How to use it? In yourfile.i, the %init function has a few lines added to it: %init %{ import_array(); /* initialize the new Python type for memory deallocation */ _MyDeallocType.tp_new = PyType_GenericNew; if (PyType_Ready(&_MyDeallocType) < 0) return; %} ... and that's it! then just use ARGOUTVIEWM_ARRAY1 instead of ARGOUTVIEW_ARRAY1 and python does the deallocation for you when the python array is destroyed (see the examples attached). Everything compiles, but it would be nice to get rid of the warnings... ezalloc_wrap.c:2763: warning: initialization from incompatible pointer type ezalloc_wrap.c: In function `_wrap_alloc_managed': ezalloc_wrap.c:2844: warning: assignment from incompatible pointer type writing build\temp.win32-2.5\Release\_ezalloc.def Compilation: python setup_alloc.py build Testing: The attached test_alloc.py does 2048 allocations of 1MB each for managed and unmanaged arrays. Output on my XP laptop with 1GB RAM as follows: ARGOUTVIEWM_ARRAY1 (managed arrays) - 2048 allocations (1048576 bytes each) Done! ARGOUTVIEW_ARRAY1 (unmanaged, leaking) - 2048 allocations (1048576 bytes each) Step 482 failed TODO: Find a better name for the methods (not sure I like ARGOUTVIEWM_ARRAY), then do the missing fragments (2D arrays), clear the warnings and verify the method for a possible inclusion in the official numpy.i file. Thank you for reading! Regards, Egor

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Old-style classes in tests
by Tom Wright Jan. 6, 2009

Jan. 6, 2009

I am currently working on the Ironclad project porting numpy to Ironpython. It would be quite useful for me if HermitianTestCase in test_linalg.py was a new style-class instead of an old-style class - since Ironpython has a bug where dir operations do not work for classes inheriting from both old- and new- style classes and I'd very much prefer not to patch my version of numpy. In general, it would be useful if whenever this multiple inheritence pattern is used new-style classes are used rather than old style classes. This would require the following classes to change: test_numerictypes - create_values, read_values_plain, read_values_nested test_print - create_zeros, create_values, assign_values, byteorder_values test_io - Roundtriptest test_linalg - LinalgTestCase, HermitianTestCase Would people be ameniable to these change? Thank you very much for your help, Tom Wright

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Re: [Numpy-discussion] Missing numpy.i
by Nicolas ROUX Dec. 19, 2008

Dec. 19, 2008

Hello, Under windows, using the latest numpy 1.20 and Swig release, I can't find anymore the numpy.i file. I used to find it in numpy/doc/ in the release 1.04. I tried to look some info the web without any success. Thanks for you help, Cheers, Nicolas.

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access ndarray in C++
by Thomas Hrabe Dec. 10, 2008

Dec. 10, 2008

Hi all! I am currently developing a python module in C/C++ which is supposed to access nd arrays as defined by the following command in python a = numpy.array([1,1,1]) I want to access the array the following way and use the nd array data for further processing in C. mymod.doSthg(a) The example code on http://numpy.sourceforge.net/numdoc/HTML/numdoc.htm#pgfId-36721 (!PyArg_ParseTuple(args, "O!",&PyArray_Type, &array)) does not work for nd arrays. I always get TypeError: argument 1 must be array, not numpy.ndarray I assume the error is the constant provided as the third parameter, saying that the imput is of PyArray_Type and no nd array. So here are my questions: 1. is there any good tutorial / example code for acessing nd arrays in C? 2. what is the difference between both (arrays and nd arrays? - I am new to python and heard there were different approaches to arrays and that nd arrays work better for multi dimensional applications. Is this right?) 3. which one of both will be used in the future? Thank you in advance for your help, Thomas

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ANNOUNCE: EPD with Py2.5 version 4.0.30002 RC2 available for testing
by Travis E. Oliphant Dec. 5, 2008

Dec. 5, 2008

Hello, We've recently posted the beta1 build of EPD (the Enthought Python Distribution) with Python 2.5 version 4.1.30001 to the EPD website. You may download the beta from here: http://www.enthought.com/products/epdearlyaccess.php You can check out the release notes here: https://svn.enthought.com/epd/wiki/Python2.5.2/4.1.300/Beta1 Please help us test it out and provide feedback on the EPD Trac instance: https://svn.enthought.com/epd or via e-mail to epd-support(a)enthought.com. If everything goes well, we are planning a final release for December. About EPD --------- The Enthought Python Distribution (EPD) is a "kitchen-sink-included" distribution of the Python™ Programming Language, including over 60 additional tools and libraries. The EPD bundle includes NumPy, SciPy, IPython, 2D and 3D visualization, database adapters, GUI building libraries, and a lot of other tools right out of the box. http://www.enthought.com/products/epd.php It is currently available as a single-click installer for Windows XP (x86), Mac OS X (a universal binary for OS X 10.4 and above), and RedHat 3 and 4 (x86 and amd64). EPD is free for academic use. An annual subscription and installation support are available for individual commercial use. Enterprise subscriptions with support for particular deployment environments are also available for commercial purchase. Enthought Build Team

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in(np.nan) on python 2.6
by Pierre GM Dec. 4, 2008

Dec. 4, 2008

All, Sorry to bump my own post, and I was kinda threadjacking anyway: Some functions of numy.ma (eg, ma.max, ma.min...) accept explicit outputs that may not be MaskedArrays. When such an explicit output is not a MaskedArray, a value that should have been masked is transformed into np.nan. That worked great in 2.5, with np.nan automatically transformed to 0 when the explicit output had a int dtype. With Python 2.6, a ValueError is raised instead, as np.nan can no longer be casted to int. What should be the recommended behavior in this case ? Raise a ValueError or some other exception, to follow the new Python2.6 convention, or silently replace np.nan by some value acceptable by int dtype (0, or something else) ? Thanks for any suggestion, P.

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Compiler options for mingw?
by Zachary Pincus Dec. 4, 2008

Dec. 4, 2008

Hi all, I'm curious about how to control compiler options for mingw builds of numpy on windows... Specifically, I want to build binaries without SSE support, so that they can run on older hardware. Setting a CFLAGS variable on the command-line doesn't appear to do anything, but perhaps appearances are deceiving. Thanks for any suggestions -- I've googled fruitlessly for a while. Zach

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error importing a f2py compiled module.
by Fabrice Silva Nov. 30, 2008

Nov. 30, 2008

Dear all I've tried to run f2py on a fortran file which used to be usable from python some months ago. Following command lines are applied with success (no errors raised) : f2py -m modulename -h tmpo.pyf --overwrite-signature tmpo.f f2py -m modulename -c --f90exec=/usr/bin/f95 tmpo.f The output of these commands is available here: http://paste.debian.net/7307 When importing in Python with "import modulename", I have an ImportError: Traceback (most recent call last): File "Solveur.py", line 44, in <module> import modulename as Modele ImportError: modulename.so: failed to map segment from shared object: Operation not permitted How can that be fixed ? Any suggestion ? Thanks -- Fabrice Silva LMA UPR CNRS 7051 - équipe S2M

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2D phase unwrapping
by Nadav Horesh Nov. 29, 2008

Nov. 29, 2008

Is there a 2D phase unwrapping for python? I read a presentation by GERI (http://www.ljmu.ac.uk/GERI) that their code is implemented in scipy, but I could not find it. Nadav.

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numpy.loadtxt requires seek()?
by Ryan May Nov. 29, 2008

Nov. 29, 2008

Hi, Does anyone know why numpy.loadtxt(), in checking the validity of a filehandle, checks for the seek() method, which appears to have no bearing on whether an object will work? I'm trying to use loadtxt() directly with the file-like object returned by urllib2.urlopen(). If I change the check for 'seek' to one for 'readline', using the urlopen object works with a hitch. As far as I can tell, all the "filehandle" object needs to meet is: 1) Have a readline() method so that loadtxt can skip the first N lines and read the first line of data 2) Be compatible with itertools.chain() (should be any iterable) At a minimum, I'd ask to change the check for 'seek' to one for 'readline'. On a bit deeper thought, it would seem that loadtxt would work with any iterable that returns individual lines. I'd like then to change the calls to readline() to just getting the next object from the iterable (iter.next() ?) and change the check for a file-like object to just a check for an iterable. In fact, we could use the iter() builtin to convert whatever got passed. That would give automatically a next() method and would raise a TypeError if it's incompatible. Thoughts? I'm willing to write up the patch for either . Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

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