Mailman 3 December 2005 - SciPy-User

Warnings about incompatibilities ahead
by Travis Oliphant 02 Dec '05

02 Dec '05

This is a warning regarding changes to the C-API of scipy core I'm going to check in (hopefully by the end of the day). 1) PyArray_Typecode structure is going away --- I always hated it. All C-API interfaces that use it will instead take a pointer to PyArray_Descr *. If the C-API actually used the funny fortran member of the structure, a new argument called fortran will be placed in the calling sequence. 2) The itemsize member on the array is going back into the PyArray_Descr where it belongs. Note that PyArray_ITEMSIZE(self) will not be affected its just that 3) There will be a new attribute .descr that returns the PyArray_Descr object (it's now a real object). 4) New C-API calls will be added. These changes are being made to facilitated nested records, but I think they are good changes anyway and now is better than later. I'm the one who has to pay the biggest price by fixing all the code in scipy core to get rid of PyArray_Typecode, references to self->itemsize and to allow for dynamic PyArray_Descr * objects. I noticed people are starting to use the C-API, so this is a warning not to 1) use PyArray_Typecode and 2) use direct access to the itemsize member of an array. Thanks, -Travis

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how to get matplotlib working with new scipy?
by Sven Schreiber 02 Dec '05

02 Dec '05

Dear experienced scipy users, I apologize if this is not the best/correct list to ask, but I joined only recently and so here goes: I'd like to try matplotlib, and I have the new scipy (core & rest) installed on win32. After installation, the command "from pylab import *" fails with the message "ImportError: No module named Numeric". That's not too surprising, but I'm unsure about the best strategy to pursue. Is matplotlib supposed to work with new scipy (alone, without extra numeric or numarray)? If so, how do I have to set it up? If numeric or numarray is still needed, is there any danger of "double definitions" of arrays etc., such that scripts could get confused or, worse, produce wrong results? (In theory I guess everything should be fine, but I'd be glad to hear what's the actual status quo with respect to known bugs and such.) Thanks much for your help, Sven

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[Scipy installation] No admin account
by José María 02 Dec '05

02 Dec '05

My name is José María and this is my first post here. I have started this week learning both: python and scipy. I had no problem to install Scipy at windows and linux in my computer. I would like to use Scipy at work where we use windows 2000. The installation software tells me than i can't install Scipy because I don't have enough privilegies. There exist any alternative to install Scipy without an administrative account? Best regards from Spain (sorry my english, please), José María

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Re: [SciPy-user] [SciPy-dev] PyArray_New problem
by Travis Oliphant 02 Dec '05

02 Dec '05

Robert Cimrman wrote: >Could someone tell me what I am doing wrong? I would like to use a >function like the snippet below to create an array. > >PyArrayObject *helper_newCArrayObject_i32( int32 len, int32 *array ) { > intp plen[1]; > PyArrayObject *obj = 0; > > plen[0] = len; > printf( "11111 %d\n", PyArray_INT32 ); >/* obj = (PyArrayObject *) PyArray_SimpleNew( 1, plen, PyArray_INT32 ); */ > > obj = (PyArrayObject *) PyArray_New( &PyArray_Type, 1, plen, >PyArray_INT32, NULL, NULL, 0, CARRAY_FLAGS, NULL ); >.... > > First of all, don't pass in CARRAY_FLAGS when the data argument to PyArray_New is NULL. A non-zero flags entry tells the subroutine to create a FORTRAN strides array if no data is passed. Remember: DATA flags are only to describe already available memory. If you create the memory in PyArray_New, then the only thing to decide is FORTRAN or C- contiguous. So, in this routine, you are creating a Fortran array. Perhaps this is causing problems later. Also, you are not showing us the rest of the code. Your traceback is showing PyArray_ValidType being called which is not shown anywere... -Travis

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Version 0.3.2 or 0.4.3?
by Dave Kuhlman 02 Dec '05

02 Dec '05

At www.scipy.org I find SciPy_complete-0.3.2.tar.gz. At http://sourceforge.net/projects/scipy/, I find scipy-0.4.3.tar.gz. Are these two separate projects? They seem very different. Could someone tell me where I can find a description of the difference between these two and a guide on how I determine which I should be using. I'm sure this question must have been raised before, but I did some searching at www.scipy.org and in the FAQ and in the mail-list archives and could not find anything helpful. Thanks in advance for help. Dave -- Dave Kuhlman http://www.rexx.com/~dkuhlman

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AstroAsciiData: first release!
by Martin Kuemmel 02 Dec '05

02 Dec '05

Dear all, this email is the announcement of the first release of the Python module AstroAsciiData. With this module it is possible to: * read ASCII tables; * access its elements for reading and writing; * save the ASCII table back to a file; * delete/add rows and columns; * convert columns to numarrays. To get a first impression on what this module does and how it works, please check the example below. More information, and of course the software itself and the manual, is available on the project webpages at: http://www.stecf.org/software/astroasciidata/ The software was developed as a contribution to the AstroLib project. Any kind of feedback can be posted on the AstroAsciiData wiki at http://www.scipy.org/wikis/topical_software/AstroAsciiData or sent by email to AstroAsciiData(a)stecf.org Please check on the webpage if the module could be useful for your work and give it a try! Cheers, Martin Kuemmel Jonas Haase ----------------------------------------------------------------------------- Example ======= What follows is an example of how the AstroAsciiData module might be used. With this example also some of the basic functionality of the module is explained. More example can be found in Section 3 of the User Manual. * Imagine you would like to work with the file "webexa.txt": # # Some objects on the sky # J02994.34+62.4844 189.2207323 62.2357983 231.9 521.8 26.87 0.1 J09234.54+62.9485 189.1408929 62.2376331 720.4 962.1 24.97 0.1 J09267.65+62.8293 189.1409453 62.1696844 927.1 327.9 25.30 0.1 J09738.55+62.4327 188.9014716 62.2037839 223.7 192.5 25.95 0.1 * To load this ASCII table, go into Python, load the AstroAsciiData module and read in the table with: >>> import asciidata >>> demo = asciidata.open('webexa.txt') >>> print demo # # Some objects on the sky # J02994.34+62.4844 189.2207323 62.2357983 231.9 521.8 26.87 0.1 J09234.54+62.9485 189.1408929 62.2376331 720.4 962.1 24.97 0.1 J09267.65+62.8293 189.1409453 62.1696844 927.1 327.9 25.30 0.1 J09738.55+62.4327 188.9014716 62.2037839 223.7 192.5 25.95 0.1 The print command at the end was just to confirm the correct reading of the file. * Let's assume that column4 and 5 contain object coordinates. You would like to compute and store the distance to the distances to the image center at (x,y)=(500.0,500.0): >>> import math >>> xcen=500.0 >>> ycen=500.0 >>> for index in range(demo.nrows): ... demo['distance'][index] = math.sqrt((demo[3][index]-xcen)**2+(demo[4][inde x]-ycen)**2) ... >>> print demo # # Some objects on the sky # J02994.34+62.4844 189.2207323 62.2357983 231.9 521.8 26.87 0.1 2.689849e+02 J09234.54+62.9485 189.1408929 62.2376331 720.4 962.1 24.97 0.1 5.119693e+02 J09267.65+62.8293 189.1409453 62.1696844 927.1 327.9 25.30 0.1 4.604702e+02 J09738.55+62.4327 188.9014716 62.2037839 223.7 192.5 25.95 0.1 4.133980e+02 As the print command reveals, there is now a new column with the computed values. * Now you would like to save the result: >>> demo.flush() >>> work>more webexa.txt # # Some objects on the sky # J02994.34+62.4844 189.2207323 62.2357983 231.9 521.8 26.87 0.1 2.689849e+02 J09234.54+62.9485 189.1408929 62.2376331 720.4 962.1 24.97 0.1 5.119693e+02 J09267.65+62.8293 189.1409453 62.1696844 927.1 327.9 25.30 0.1 4.604702e+02 J09738.55+62.4327 188.9014716 62.2037839 223.7 192.5 25.95 0.1 4.133980e+02 The new column was saved back to the file!

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fortran compilers, f2py and scipy core.
by George Nurser 02 Dec '05

02 Dec '05

This may be a stupid question, but ... I want to use f2py together with scipy core, and new scipy, on an Opteron. I am used to writing my fortran programs with ifort 9.0. Does this mean that I have to compile scipy, scipy core with ifort, or can a scipy core compiled with gcc coexist with fortran routines, compiled on ifort 9.0, linked into f2py? Problem is there don't seem to be options set for 64-bit emt ifort in scipy/distutils/fcompiler/ --George Nurser.

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strange scipy.f2py error
by Chris Fonnesbeck 01 Dec '05

01 Dec '05

For some reason, the fcompiler object gets set to "None" when building on a 10.3 machine. Using today's svn build of scipy_core and the IBM XLF compiler: compiling Fortran sources Traceback (most recent call last): File "setup.py", line 17, in ? ext_modules = [flib] File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/distutils/core.py", line 91, in setup return old_setup(**new_attr) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/core.py", line 149, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/dist.py", line 946, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/distutils/command/build_ext.py", line 107, in run self.build_extensions() File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/command/build_ext.py", line 405, in build_extensions self.build_extension(ext) File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/distutils/command/build_ext.py", line 246, in build_extension f_objects += self.fcompiler.compile(f_sources, AttributeError: 'NoneType' object has no attribute 'compile' -- Chris Fonnesbeck Atlanta, GA

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