Mailman 3 April 2004 - NumPy-Discussion

announcing a ds9 module and a question about indices
by Russell E Owen April 16, 2004

April 16, 2004

I wrote a simple module that allows one to display numarray arrays in ds9. It is available as part of the RO package (RO.DS9) <http://www.astro.washington.edu/owen/ROPython.html>, though it is presently self-contained. (I may well end up expanding it.) It sends a copy of the data, rather than trying to share a buffer. It uses the command-line XPA interface instead of trying to use the underlying C XPA API. I'm curious if anybody has gotten a python interface to the C XPA API working. It looks a bit messy, but popen2 messy in other ways (detecting errors without hanging on read, for example). I have what is probably a dumb question, but...if I load an array using PyFits and display it using ds9, I find that the array indices appear to be transposed relative to what I expect, i.e. numarray seems to use array[yind, xind]. Is this normal? Any hints on handling notation in code (I suspect there's not much I can do except document it)? -- Russell

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Delivery Bot (slrnbqbpqt.vf5.ramen@lackingtalent.com)
by numpy-discussion＠lists.sourceforge.net April 16, 2004

April 16, 2004

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Delivery Bot (slrnbqbpqt.vf5.ramen@lackingtalent.com)
by numpy-discussion＠lists.sourceforge.net April 16, 2004

April 16, 2004

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failure notice
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April 15, 2004

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take for character arrays?
by Faheem Mitha April 15, 2004

April 15, 2004

Hi, I'm trying to extract subarrays of a character array using take(), but getting mysterious errors, for example: ValueError: Invalid destination array: partial indices require contiguous non-byteswapped destination I am thinking that perhaps this operation is not supported for character arrays, and I should convert my character array to a numeric array instead (the strings are all of length 1). Advice, suggestions, enlightenment appreciated. Faheem.

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sa.ve on software?? this is for u orchard pterygium
by Audrey Shanice April 10, 2004

April 10, 2004

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Europython: Registration open - Talk submission deadline is Apr 15th
by Nicolas Chauvat April 10, 2004

April 10, 2004

Dear Scientific Pythonistas, I'm forwarding this update about the EuroPython conference. Please note that the talk submission deadline is April 15th but will probably be extended a bit. I suppose most of you will be interested in the Science Track at least. For previous years' program, please refer to : http://www.europython.org/2002/sessions/talks http://www.europython.org/2003/sessions/talks --------------------------------------------------------------------- Subject: [EuroPython] Europython Update: Registration open Europython Update ================= - Registration is now open. We apologise for the delay, but we have had some technical problems. - Due to this, we have decided to keep the submission of abstracts for the refereed track open for one more day. Last submission time is now on Sunday 11 April at 23.59 CET. - We have a limited number of beds available in very affordable accomodation near the conference venue. Book early before it runs out. - We are still receiving submissions for regular talks and tutorials. Closing date is 15 April. - There is now a wiki at the Europython website for sprint organising. Start planning! About the conference ==================== EuroPython 2004 will be held 7-9 June in Göteborg, Sweden. The EuroPython conference will have tracks for Science, Business, Education, Applications, Frameworks, Zope and the Python language itself. Lightning talks, Open Space and BOF sessions are also planned. There will be tutorials as well, both for newcomers to Python and Python users interested in special subjects. In the days before and after the conference, programming sprints will be arranged. Important dates =============== Refereed paper proposals: until 11 April. Submission of talks: 1 March - 15 April. Early Bird registration: 9 April - 1 May. Accomodation booking: 9 April - 1 May (or until space runs out) More information at http://www.europython.org. --------------------------------------------------------------------- Hope to see you there. -- Nicolas Chauvat logilab.fr - services en informatique avancée et gestion de connaissances

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Questions about C API
by Russell E Owen April 9, 2004

April 9, 2004

I'm trying to write a median function (surely one is there already, but if so I've not found it). The fastest technique seems to involve rearranging the data in place. So I'd like to offer two calls: - A version that rearranges the input array if no local copy needed to be made (e.g. the input data was already contiguous and of the expected type). I know how to write that one. - A safer, slower version that always makes a copy of the input data. I'm stuck on that. The high-level interface has flags for when to make a local copy, but none of them seems to mean "always make a local copy". Surely I am missing something there? I guess I could get the data, see if a local copy was made and if not, make a copy of my own, but that seems messy. Also, is there any simple sample code running around for handling arrays of any type (e.g. with C++ templates)? Right now I'm writing to a specific type (since it's easy and I know what type to expect for my application), but I'd rather make my code more general and numarray-like. I figured the numarray code itself would be a good example, but, well, I didn't understand the parts I looked at (maybe I'm clueless, maybe I didn't find the right bits to examine). -- Russell

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problems with compiling and loading C++ extension
by Faheem Mitha April 7, 2004

April 7, 2004

Dear People, I have been having an odd problem with compiling and loading a simple C++ extension to python (as a .so file in Linux). Unfortunately, I'll need to include my files in here so I apologize in advance for the length of this message. You can download also the files below from http://www.stat.unc.edu/students/faheem/python/python.tar.gz in case that is more convenient. This needs blitz++ and python's distutils and numarray to compile. When I try to load arrmod.so into python I get In [1]: import arrmod --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /tmp/wc/corrmodel/ex/<console> ImportError: ./arrmod.so: undefined symbol: _Z11py_to_blitzIdLi2EEN5blitz5ArrayIT_XT0_EEEP13PyArrayObject If I move the py_to_blitz routine from conv.cc back into arrmod.cc, the error disappears, arrmod loads in python, and everything works correctly. I'm not sure what is going on here. Can someone enlighten me? At first I thought it might have to do with the need for C linkage, but I tried that, and it does not appear to be the case. I also got the following compilation warning, which I don't understand. I don't know if that is relevant. --------------------------------------------------------------------- gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.3 -c conv.cc -o /tmp/temp.linux-i686-2.3/conv.o -Wall /usr/include/python2.3/Numeric/arrayobject.h:286: warning: `void**PyArray_API' defined but not used --------------------------------------------------------------------- Thanks in advance for any enlightenment. Faheem. ********************************************************************** Makefile ********************************************************************** arrmod.so: arrmod.cc common.hh conv.cc python setup.py build --build-base=/tmp --build-lib=. # may not do the right thing for everyone clean: rm arrmod.so rm -r /tmp/temp.linux-i686-2.3 ********************************************************************** ********************************************************************** setup.py ********************************************************************** from distutils.core import setup, Extension module4 = Extension('arrmod', sources = ['arrmod.cc','conv.cc'],libraries=["blitz","m"], extra_compile_args = ['-Wall']) setup (name = 'arrmod', version = '1.0', description = 'This module performs different operations on arrays', ext_modules = [module4] ) ********************************************************************** ********************************************************************** common.hh ********************************************************************** #include "Python.h" #include "Numeric/arrayobject.h" #include <blitz/array.h> using namespace std; using namespace blitz; template<class T, int N> static Array<T,N> py_to_blitz(PyArrayObject* arr_obj); ********************************************************************** ********************************************************************** conv.cc ********************************************************************** #include "common.hh" // Convert a Numpy array to a blitz one, using the original's data (no // copy) template<class T, int N> static Array<T,N> py_to_blitz(PyArrayObject* arr_obj) { int T_size = sizeof(T); TinyVector<int,N> shape(0); TinyVector<int,N> strides(0); int *arr_dimensions = arr_obj->dimensions; int *arr_strides = arr_obj->strides; for (int i=0;i<N;++i) { shape[i] = arr_dimensions[i]; strides[i] = arr_strides[i]/T_size; } return Array<T,N>((T*) arr_obj->data,shape,strides,neverDeleteData); } ************************************************************************ ************************************************************************ arrmod.cc ************************************************************************ #include "common.hh" template<class T, int N> static Array<T,N> py_to_blitz(PyArrayObject* arr_obj); static PyObject * arrmod_elem(PyObject *self, PyObject *args); static PyMethodDef arrmod_methods[] = { {"elem", (PyCFunction)arrmod_elem, METH_VARARGS, "Returns the trace of a two-dimensional array.\n"}, {NULL, NULL, 0, NULL} }; PyMODINIT_FUNC initarrmod(void) { (void) Py_InitModule3("arrmod", arrmod_methods, "Returns the Trace of a two-dimensional array.\n"); import_array(); } static PyObject * arrmod_elem(PyObject *self, PyObject *args) { PyObject *input, *result; PyArrayObject *array; double el; int i, j; if (!PyArg_ParseTuple(args, "Oii", &input, &i, &j)) return NULL; array = (PyArrayObject *) PyArray_ContiguousFromObject(input, PyArray_DOUBLE, 2, 2); if (array == NULL) return NULL; Array<double,2> arr = py_to_blitz<double,2>(array); el = arr(i,j); result = Py_BuildValue("d",el); return result; } ********************************************************************************

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April 4, 2004

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