Mailman 3 May 2008 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani 14 Mar '22

14 Mar '22

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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3D plotting
by Robert Cimrman 10 Sep '09

10 Sep '09

Hi, I need to do some simple 3D plots, so I tried the two Cookbook recipes (xplt, mplot3d) and failed: * xplt: does not work when using a custom installation directory such as python setup.py install --root=/home/share/software apparently the gistdata directory path is wrong: gist.error: failed to create drawing -- Gist work.gs style sheet missing * mplot3d: does not work with my version of matplotlib (0.80). I have made the changes mentioned in the Cookbook to no avail. (Axes.__init__() args apparently changed, as well as some other matplotlib object attributes) Any ideas? mplot3d looks great, I would really like to use it! thanks, r.

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assign to diagonal values?
by Carlos Scheidegger 07 Jul '09

07 Jul '09

Say I have a matrix m whose diagonal values I want to replace with the contents of vector new_diagonal. Right now, I'm using m -= diag(m) m += diag(new_diagonal) but that seems pretty wasteful (especially if diag() creates new arrays, which I suspect it does). Is there a standard (or any efficient) way to assign the diagonal values directly without an explicit for loop? Googling for "site:www.scipy.org assign diagonal" only returned results for sparse matrices, which is not the case here - these are plain numpy arrays. Thanks in advance, -carlos

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Is numpy's argsort lying about its numpy.int32 types?
by Rob Clewley 15 May '09

15 May '09

Hi, I'm having a problem comparing some types when using numpy's argsort. I'm using numpy 1.0.2. I can reproduce it simply: Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] << snip >> In [1]: from numpy import argsort, sort, int32, array In [2]: x=array([1,3,2]) In [3]: aa=argsort(x) In [4]: as=sort(x) In [5]: type(aa[0]) Out[5]: <type 'numpy.int32'> In [6]: type(as[0]) Out[6]: <type 'numpy.int32'> In [7]: int32 Out[7]: <type 'numpy.int32'> In [8]: type(as[0])==int32 Out[8]: True In [9]: type(aa[0])==int32 Out[9]: False Any of the three indices in aa give me the same problem. Can someone explain if I should be doing this a different way, and if this is a bug?! Thanks, Rob

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ANN: NumPy 1.1.0
by Jarrod Millman 30 Jun '08

30 Jun '08

I'm pleased to announce the release of NumPy 1.1.0. NumPy is the fundamental package needed for scientific computing with Python. It contains: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * basic linear algebra functions * basic Fourier transforms * sophisticated random number capabilities * tools for integrating Fortran code. Besides it's obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide-variety of databases. This is the first minor release since the 1.0 release in October 2006. There are a few major changes, which introduce some minor API breakage. In addition this release includes tremendous improvements in terms of bug-fixing, testing, and documentation. For information, please see the release notes: http://sourceforge.net/project/shownotes.php?release_id=602575&group_id=1369 Thank you to everybody who contributed to this release. Enjoy, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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The IO library and image file formats -- compare with with PIL
by Sebastian Haase 16 Jun '08

16 Jun '08

Hi, Could someone here please summarize the plans for the io library !? I saw that there are parts of it going into numpy already. And more stuff is already in SciPy -- IIRC. What is the status / plans regrading image formats like TIFF. Are you guys planning to duplicate the efforts of the Python Imaging Library ( PIL ) ? Or can you just copy-paste some of the code ? The reason I'm asking now, is that I just submitted a patch to PIL that adds writing capabilities for MultiPage TIFF files. I did not get any response on the PIL list, and I'm actually still not clear on their handling of free vs. commercial. The commercial PIL license sounds like you have to pay $2000 to get access to svn, i.e. the current development version of PIL. Anyone here who could comment on this ? Thanks, Sebastian Haase

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ANN: NumPy/SciPy Documentation Marathon 2008
by Joe Harrington 11 Jun '08

11 Jun '08

NUMPY/SCIPY DOCUMENTATION MARATHON 2008 As we all know, the state of the numpy and scipy reference documentation (aka the docstrings) is best described as "incomplete". Most functions have docstrings shorter than 5 lines, whereas our competitors IDL and Matlab usually have a concise and well-written page or two per function. The (wonderful) categorized list of functions is very new and isn't included in the package yet. There isn't even a "Getting Started"-type of document you can hand a new user so they can dive right in. Documentation tools are limited to plain-text paginators, while our competition enjoys HTML-based documents with formulae, images, search capability, and cross linking. Tales of woe abound. A university class switched to Numpy and got hopelessly bogged down because students couldn't find out how to call the functions. A developer looked something up while giving a presentation and the words "Blah, Blah, Blah" stared down at the audience in response. To head off another pedagogical meltdown, the University of Central Florida has hired Stefan van der Walt full time to coordinate a community documentation effort to write reference documentation and tools. The project starts now and continues through the summer. The goals: 1. Produce complete docstrings for all numpy functions and as much of scipy as possible, 2. Produce an 8-15 page Getting Started tutorial that is not discipline-specific, 3. Write reference sections on topics in numpy, such as slicing and the use principles of the modules, 4. Complete a first edition, in both PDF and HTML, of a NumPy Reference Manual, and 5. Check everything into the sources by 1 August 2008 so that the Packaging Team can cut a release and have it available in time for Fall 2008 classes. Even Stefan could not document the hundreds of functions that need it by himself, and in any case such a large contribution requires community review. To make it easy for everyone to contribute, Pauli Virtanen and Emmanuelle Guillart have provided a wiki system for editing reference documentation. The idea was developed by Fernando Perez, Stefan, and Gael Varoquaux. We encourage community members to write, review, and proofread reference pages on this wiki. Stefan will check updates into the sources roughly weekly. Near the end of the project, we will put these wiki pages through a vetting process and then check them into the sources a final time for a release hopefully to occur in early August. Meanwhile, Perry Greenfield has taken the lead on on task 3, writing reference docs for things that currently don't have docstrings, such as basic concepts like slicing. We have proposed two small extensions to the current docstring format, for images (to be used sparingly) and indexing. These appear in updated versions of the doc standard, which are linked from the wiki frontpage. Please take a look and comment on these if you like. All docstrings will remain readable in plain text, but we are now generating a full reference guide in PDF and HTML (you guessed it, linked from the wiki). These are searchable formats. There are several ways you can help: 1. Write some docstrings on the wiki! Many people can do this, many more than can write code for the package itself. However, you must know numpy, the function group, and the function you are writing well. You should be familiar with the concept of a reference page and write in that concise style. We'll do tutorial docs in another project at a later date. See the instructions on the wiki for guidelines and format. 2. Review others' docstrings and leave comments on their wiki pages. 3. Proofread docstrings. Make sure they are correct, complete, and concise. Fix grammar. 4. Write examples ("doctests"). Even if you are not a top-notch English writer, you can help by producing a code snippet of a few lines that demonstrates a function. It is fine for them to go into the docstring templates before the actual text. 5. Write a new help function that optionally produces ASCII or points the user's PDF or HTML reader to the right page (either local or global). 6. If you are in a position to hire someone, such as a knowledgeable student or short-term consultant, hire them to work on the tasks above for the summer. We can provide supervision to them or guidance to you if you like. The home for this project is here: http://scipy.org/Developer_Zone/DocMarathon2008 This is not a sprint. It is a marathon, and this time we are going to finish. We hope you will join us! --jh-- and Stefan and Perry and Pauli and Emmanuelle...and you! Joe Harrington Stefan van der Walt Perry Greenfield Pauli Virtanen Emmanuelle Guillart ...and you!

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[ Python(x,y) ] New release : 1.2.3
by Pierre Raybaut 30 May '08

30 May '08

Hi all, Python(x,y) 1.2.3 is now available on http://www.pythonxy.com. Hopefully, updates should now be released at a lower rate. This update is recommended for Python(x,y) 1.2.x users, as a bug showed up with the new PyQt release: zoom/pan mode in embedded matplotlib (0.91.2) widgets is very slow. So PyQt 4.3.3 is back on Python(x,y), as well as the associated Qt Eclipse integration plugin and Qt help files (Eclipse help browser). Anyway PyQt 4.4.2 new features were of no particular interest for purely scientific use. Please see other changes below. Changes history 05 -30 -2008 - Version 1.2.3 : * Corrected: o PyQt 4.4.2 --> PyQt 4.3.3 (performance bug in new version for embedded matplotlib widgets) o Qt Eclipse Integration 1.4.0 --> 1.0.1 (see above) o Windows installer bug: Documentation directory customization was not taken into account * Added: o Windows installer: Python(x,y) may be partially (i.e. without wxPython and Enthought Tool Suite) installed without any administrative privilege Regards, Pierre Raybaut

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Tutorials at Scipy 2008
by Fernando Perez 30 May '08

30 May '08

Hi all, Travis Oliphant and myself have signed up to coordinate the tutorials sessions at this year's SciPy conference. Our tentative plan is described here: http://scipy.org/SciPy2008/Tutorials but it basically consists of holding in parallel: 1. A 2-day hands-on tutorial for beginners. 2. A set of 2 or 4 hour sessions on special topics. We need input from people on: - Do you like this idea? - If yes for #1, any suggestions/wishes? Eric Jones, Travis O and myself have all taught similar things and could potentially do it again, but none of us is trying to impose it. If someone else wants to do it, by all means mention it. The job could be split across multiple people once an agenda is organized. - For #2, please go to the wiki and fill in ideas for topics and/or presenters. We'll need a list of viable topics with actual presenters before we start narrowing down the schedule into something more concrete. Feel free to either discuss things here or to just put topics on the wiki. I find wikis to be a poor place for conversation but excellent for summarizing items. I'll try to update the wiki with ideas that arise here, but feel free to directly edit the wiki if you just want to suggest a specific topic or brief piece of info, do NOT feel like you have to vet anything on list. Cheers, Travis and Fernando.

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Re: [SciPy-user] [ Python(x, y) ] New release : 1.2.1 - Critical bug fix
by Pierre Raybaut 30 May '08

30 May '08

scipy-user-request(a)scipy.org a écrit : >> Python(x,y) 1.2.1 is now available on http://www.pythonxy.com. >> >> It is highly recommended to update if you have installed the previous >> release: a critical bug in Eclipse installation is now fixed. >> Besides, it is quite a small update patch (<1Mb) so it's definitely >> worth it. >> > > Congratulation for your work. I tried to download the sources, and could > not find a link on the website ? > > thanks, > > David > Thanks. Actually, sources were available at the beginning of the project, but then priority was given to releases and patches. Furthermore, I'm working on it at home where I'm currently struggling to upload new releases due to bandwidth limitations. Right now for example, I have been uploading (or more exactly trying to upload) the new release for 3 hours... That can be very discouraging sometimes. This being said, I will update the sources again shortly (but these are not really "sources", the real sources are distributed by the developers of included packages: this is just a redistribution, like a zip archive containing all these binary packages). Regards, Pierre

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