Mailman 3 May 2003 - SciPy-User

unable to import scipy package
by Vernon May 14, 2003

May 14, 2003

Hi all. I just installed the scipy package 0.2.0 for win32. I am using activestate python 2.2.2 and have installed numeric 21 and numarray 0.4 The scipy installer completed its installation sucessfully. However when I type >>> from scipy import * I get the following errors noted below. Does anyone know what I am doing wrong. Thank you very much for your help. Traceback (most recent call last): File "Text3.py", line 1, in ? from scipy import * File "C:\Python22\Lib\site-packages\scipy\__init__.py", line 29, in ? from scipy_base import * File "C:\Python22\Lib\site-packages\scipy_base\__init__.py", line 124, in ? import limits File "C:\Python22\Lib\site-packages\scipy_base\limits.py", line 41, in ? float_epsilon = epsilon(Numeric.Float32) File "C:\Python22\Lib\site-packages\scipy_base\limits.py", line 26, in epsilon x = x * cast(.5) ArithmeticError: Integer overflow in multiply. __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com

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Syntax for assigning to a complex matrix via weave?
by Fernando Perez May 14, 2003

May 14, 2003

Hi all, I'm trying to speed up via weave some code which uses complex matrices, and I can't seem to find the right form. I tried reading the blitz sources, but that didn't get me very far. Here's a simple example which should get me going for my 'real' problem, if someone can show me how to make this work: ########################################################################### from Numeric import * from weave import * def complex_test(): a = zeros((4,4),Complex) a[0,0] = 1+2j a[1,1] = 2+3.5j print 'Before\n',a code = \ """ std::cout << a(1,1) << std::endl; a(2,2).real = 3.0; // THIS DOESN'T WORK a(2,2).imag = 4.5; // THIS DOESN'T WORK """ inline(code,['a'],type_converters = converters.blitz) print 'After\n',a complex_test() ########################################################################### Along these lines, I'm also curious as to the possiblity of doing complex arithmetic and calling functions on the entries of a Numeric complex array. Are there proper complex exp, sin, etc. functions accessible from within weave? And is a(1,1)/a(2,2) properly executed as complex division if 'a' is complex? Thanks for any help, f.

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ANN: matplotlib-0.2 matlab style plotting for python
by John Hunter May 14, 2003

May 14, 2003

Announcing Matplotlib 0.2 matplotlib is a pure python plotting library designed to bring publication quality plotting to python with a syntax familiar to matlab users. Although the goal of publication quality is not yet attained, the library does produce high quality 2D plots. All of the plotting commands can be accessed either via a functional interface familiar to matlab users or an object oriented interface familiar to python users. http://matplotlib.sourceforge.net matplotlib requires python2.2, Numeric-22+ and pygtk-1.99.16, and should run anywhere those packages are available. It has been tested under linux and win32. The following matlab compatible plotting commands are provided: axes, axis, bar, close, errorbar, figure, gca, gcf, get, hist, plot, scatter, set, subplot, text, title, xlabel, ylabel What's new in 0.2 Font handling - Major improvements in font and text handling. matplotlib 0.1 drew all text in the same, non-configurable font. In 0.2, font name, size, weight, and angle, color, rotation, and more are easily configurable. See the text tutorial on the website Multiple figures -- Multiple figures supported with the figure command. See the Working with multiple figures and axes in the tutorial Interactive shell -- Interactive use from the python shell if you have pygtk compiled with threads. See Using matplotlib interactively. Saving figures- Ability to save figures in arbitrary resolution PNG or TIFF with a bug fix that caused saved figures to be corrupted by anything blocking the figure window. A GUI widget has been added to the figure toolbar to save figures and a new comand savefig has been added. Navigation - A new and hopefully improved navigation toolbar has been added that doesn't require a wheel mouse, but still works with one. See the Navigation tutorial. More examples and screenshots - New examples and screenshot illustrating the new text functionality, the new plot types, and new commands. See the examples subdirectory in the src distribution. Patches - A Patch class added for drawing patches (rectangles, polygons, circles). This supports three new plotting commands scatter, hist and bar, with more to come. New commands - New plotting commands bar, close, errorbar, figure, hist, text, scatter, savefig, ylabel. Matplotlib on sourceforge - matplotlib homepage moved to sourceforge with a (hopefully) more useful homepage. Documentation - Much better documentation and a tutorial. Refactoring - Substantial rewrite of class library. All text now handled by the AxisText class in text.py. Axis handling refactored into a dedicated class Axis defined in figure.py.

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[ANN] imv.py: 3D plots with MayaVi: Important bug fix.
by Prabhu Ramachandran May 13, 2003

May 13, 2003

Hi, This is to announce a newer version of imv.py that fixes a few important and pretty bad bugs. ChangeLog: May 7, 2003: Added support to use surf on an existing MayaVi window. May 8, 2003: Fixed bad bugs in sampler function. The broadcasting was wrong, the return value needed to be transposed and the y array also needed broadcasting in case the function did not depend on x. Thanks to Prof. Ramakrishna for bringing this to my attention. Essentially, surf based plots would have their X and Y's swapped since the array was not being transposed before being displayed. For symmetric functions this would not be an issue at all. There was also a problem when different sized x and y arrays were given. Finally the new version can create a plot on an existing window. I'm sorry that these errors crept up but I was not using the module enough to catch the error and the error was brought to my notice just this week. imv.py is available here: http://www.aero.iitm.ernet.in/~prabhu/software/mayavi.html here: http://www.ae.iitm.ac.in/~prabhu/software/mayavi.html or here: http://av.stanford.edu/~prabhu/software/mayavi.html About imv.py: imv.py is a module that lets you sample surfaces and arrays from the Python interpreter via convenient one line functions. It requires MayaVi (version 1.2) to be installed and running as a Python module i.e. the binary installs will not be able to use this. cheers, prabhu p.s. Sorry about the cross posting!

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by james＠hello.com May 13, 2003

May 13, 2003

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[numarray issue] nonzero? Comments on new name solicited
by Perry Greenfield May 13, 2003

May 13, 2003

[In the next week or so I am going to be raising some issues regarding the next numarray release, 0.6. By the way, we keep the version number less than 1.0 because we still hold out the possiblity of changing some interface issues (generally it has been in the direction of making numarray more compatible with Numeric). The following raises one of these interface issues. numarray has a more general approach to the nonzero function than does Numeric. It is able to return multiple index arrays for multidimensional arrays (where as nonzero only works for 1-d arrays). In the interest of giving a more generic interface for the function, numarray always returns the index array(s) as part of a tuple, even if the argument to nonzero is 1-D and there is only one resulting index array. However, this is a problem for Numeric old code that uses nonzero and expects an array instead of a tuple. The sensible thing to do is to retain compatibilty with the Numeric nonzero (and likewise only support 1-d arrays). So we need a new name for our new nonzero function. To tell you the truth, I always felt that nonzero was a terrible name anyway and much preferred the name that IDL used for that function, namely "where". Alas, "where" is already used for another purpose in Numeric. But to illustrate, which is clearer? x[nonzero(x > 0.)] = 0. or x[where(x > 0.)] = 0 So, we considered some other alternatives, in particular nz wheretrue but our favorite is: "at". For example: x[at(x > 0.)] = 0. This has the benefit of being short and having a fairly clear meaning. Short is important since it will keep expressions of arrays using index arrays short and more readable. True, this is more likely to conflict with existing user variable or function names, but if one is simply trying to use existing files, then there is no problem since they won't need the "at" function since its functionality was not previously available. Any objections to using "at"? Any better suggestions. Of course, these changes will break existing numarray code that use the nonzero function. Perry Greenfield

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by xxx May 12, 2003

May 12, 2003

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PyTables 0.5.1
by Francesc Alted May 12, 2003

May 12, 2003

PyTables 0.5.1 -------------- This is a maintenance release of PyTables. Due to a problem with an specific optimization in PyTables 0.5, it does not work with numarray 0.4 (although it works just fine with numarray 0.5). Thanks to Marc Gehling for reporting that. Todd Miller has already warned me that this optimization was not safe, so I am *disabling* it in 0.5.1. The consequence is that the 20% of improvement during reading tables has almost evaporated to a rather small 4%, but that's life!. If you already have installed PyTables 0.5, I strongly suggest you to upgrade to 0.5.1, even if you are already using numarray 0.5. I will try to further investigate the problem, and, if a good solution is found, I will enable again the optimization in a future release. Another new thing you can find in 0.5.1 is that the use of "UInt64" data types has been removed (it has been replaced by the "Int64" type) of the tutorial chapters in User's Manual. I've done that because the numarray Windows version does not support such a type (due to MSVC compiler limitations). Now, the tutorial section should run fine in all the supported platforms (even Windows). My apologies for being a sinner and trying to optimize too soon ;-) Web site -------- Go to the PyTables web site for more details: http://pytables.sourceforge.net/ Share your experience --------------------- Let me know of any bugs, suggestions, gripes, kudos, etc. you may have. Have fun! -- Francesc Alted

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Negative entries in matrices get lost by using io.read_array
by Nils Wagner May 12, 2003

May 12, 2003

Hi all, I have a problem with io:read_array Negative entries in matrices get lost by using io.read_array. This is llustrated by means of a short test program ioread.py. Any idea ? Nils 1.0 2.0 3.0 -1.0 2.0 2.0 3.0 0.0 3.0 4.0 4.0 1.0 4.0 5.0 6.0 7.0 from scipy import * file = open("test.mat") a = io.read_array(file) print a

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by xxx May 11, 2003

May 11, 2003

1 0