Mailman 3 December 2008 - SciPy-Dev

Ticket #803 test_pbdv failed
by Xavier Gnata Dec. 16, 2008

Dec. 16, 2008

Hi, Any idea to try to debug that issue (the only one I have with the current svn scipy)? My fortran residual knowledge is now so poor that I cannot really debug this issue. What I would first like to do is to run a small fortran routine calling the pbdv procedure from cephes to see what I get (but with my poor fortran knowledge it will take time :( ) My second point is the following: If my understanding of pbdv is supposed to do, (0.0, 1.0) is the correct answer : http://mathworld.wolfram.com/ParabolicCylinderFunction.html I must be missing something here. Xavier

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openopt has to move out from scikits
by Dmitrey Dec. 16, 2008

Dec. 16, 2008

Hi all, openopt v. 0.21 has been released. However, old svn location is no longer valid (my chiefs have forced me to move my code into other location). All details here http://openopt.blogspot.com/2008/12/openopt-release-021.html Regards, Dmitrey.

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Re: [SciPy-dev] FFT docstrings (was: Scipy Tutorial (and updating it))
by jh＠physics.ucf.edu Dec. 15, 2008

Dec. 15, 2008

Tom Grydeland <tom.grydeland(a)gmail.com> wrote: > I've gone on to rfft, irfft, fftn and irfftn, and I am struggling a > bit with these, especially with the description of the length/shape > argument. I know perfectly well what they should tell the reader, but > I am not 100% convinced the current prose actually tells it clearly. Thanks for your work, Tom! I think the text so far is fine. I tweaked some of the pages a little. There's room and need for a bit more, since FFTs are among the most used and abused methods out there. Recall that our audience is one level below likely users. There's need for a short intro to the whole concept on the module page (I added one), which each routine page should refer to (but I haven't put those references in). Also, the current routine examples satisfy a mathematician but do not give insight into what the FT actually *does*, i.e., extract the periodic content of a signal. Also, an example should show the most basic use, i.e., taking the modulus and the arctan of the inputs to get the amplitude and phase of the contributing sinusoids. Too many people take the real part of an FFT and think they've got the amplitude. If you did a sine wave of amplitude 2 in 8 points, you could show in a simple example how to pull that out of the fft. For the complex case, point out that you have to fold (or double) the first half of the output, etc., since the negative frequencies get half the signal for real inputs. Then refer to rfft. Note that many users will not at first understand why (or even that) we have rfft, since most packages do not provide it, which is why it is worth some explanation. Doing all this consistently across the many routines would be very valuable. The rfft vs. fft explanation might best belong on the module page, since there are several routines for each. Then the routines themselves can have relatively spare pages. The formulae themselves might best go on the module page, for the same reason. Thanks again for your contributions. Send me your postal address and your T-shirt size by private email and we'll send you one right away! --jh--

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Writing Matlab 5 cells containing structures with long field names
by Lee Kamentsky Dec. 15, 2008

Dec. 15, 2008

Hi all, Unfortunately, the patch that Vebjorn made on my behalf earlier this week (checked in as 5237 I believe) had a bug. I failed to change calls to instantiate Mat5WriterGetter to pass the long_field_names flag. This makes the code fail when a cell contains a structure that has long field names because the cell code does not create a Mat5WriterGetter with the long_field_names flag set. Enclosed is a diff of scipy/io/matlab/mio5.py against revision 5240 that fixes the problem and a diff of scipy/io/matlab/tests/test_mio.py that contains regression tests that demonstrate the problem. In addition, test_mio.py contains a regression test that demonstrates the bug that Ray submitted yesterday on my behalf. Thanks for your timely action over the last week. --Lee Index: io/matlab/mio5.py =================================================================== --- io/matlab/mio5.py (revision 5240) +++ io/matlab/mio5.py (working copy) @@ -789,7 +789,7 @@ self.write_header(mclass=mxCELL_CLASS) # loop over data, column major A = np.atleast_2d(self.arr).flatten('F') - MWG = Mat5WriterGetter(self.file_stream, self.unicode_strings) + MWG = Mat5WriterGetter(self.file_stream, self.unicode_strings, self.long_field_names) for el in A: MW = MWG.matrix_writer_factory(el, '') MW.write() @@ -801,7 +801,7 @@ self.write_header(mclass=mxFUNCTION_CLASS) # loop over data, column major A = np.atleast_2d(self.arr).flatten('F') - MWG = Mat5WriterGetter(self.file_stream, self.unicode_strings) + MWG = Mat5WriterGetter(self.file_stream, self.unicode_strings,self.long_field_names) for el in A: MW = MWG.matrix_writer_factory(el, '') MW.write() @@ -827,7 +827,8 @@ mdtype=miINT8) A = np.atleast_2d(self.arr).flatten('F') MWG = Mat5WriterGetter(self.file_stream, - self.unicode_strings) + self.unicode_strings, + self.long_field_names) for el in A: for f in fieldnames: MW = MWG.matrix_writer_factory(el[f], '') Index: io/matlab/tests/test_mio.py =================================================================== --- io/matlab/tests/test_mio.py (revision 5240) +++ io/matlab/tests/test_mio.py (working copy) @@ -370,3 +370,36 @@ st1 = np.zeros((1,1), dtype=[(fldname, object)]) assert_raises(ValueError, savemat, StringIO(), {'longstruct': st1}, format='5',long_field_names=True) + +def test_long_field_names_in_struct(): + # Regression test - long_field_names was erased if you passed a struct + # within a struct + # + lim = 63 + fldname = 'a' * lim + cell = np.ndarray((1,2),dtype=object) + st1 = np.zeros((1,1), dtype=[(fldname, object)]) + cell[0,0]=st1 + cell[0,1]=st1 + mat_stream = StringIO() + savemat(StringIO(), {'longstruct': cell}, format='5',long_field_names=True) + # + # Check to make sure it fails with long field names off + # + assert_raises(ValueError, savemat, StringIO(), + {'longstruct': cell}, format='5', long_field_names=False) + +def test_cell_with_one_thing_in_it(): + # Regression test - make a cell array that's 1 x 2 and put two strings in it. + # It works. Make a cell array that's 1 x 1 and put a string + # in it. It should work but didn't. + cells = np.ndarray((1,2),dtype=object) + cells[0,0]='Hello' + cells[0,1]='World' + mat_stream = StringIO() + savemat(StringIO(), {'x': cells}, format='5') + + cells = np.ndarray((1,1),dtype=object) + cells[0,0]='Hello, world' + mat_stream = StringIO() + savemat(StringIO(), {'x': cells}, format='5')

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Re: [SciPy-dev] Scipy Tutorial (and updating it)
by Elston, Gareth R Dec. 15, 2008

Dec. 15, 2008

>On Sat, Dec 13, 2008 at 4:27 PM, Gael Varoquaux ><gael.varoquaux(a)normalesup.org> wrote: >> On Sat, Dec 13, 2008 at 09:26:45PM +0000, Pauli Virtanen wrote: >>> Sat, 13 Dec 2008 22:21:43 +0100, Gael Varoquaux wrote: >> >>> > On Sat, Dec 13, 2008 at 09:18:23PM +0000, Pauli Virtanen wrote: >>> >> Thu, 04 Dec 2008 10:44:13 -0500, josef.pktd wrote: [clip] >>> >> > I haven't tried yet to generate my own numpy, scipy docs, since they >>> >> > are makefile based, and I didn't want to spend the time to figure out >>> >> > how to use the build scripts on windows, but a windows helpfile is on >>> >> > my wish/todo list, since sphinx makes it very easy to do. >> >>> >> Windows help files (CHM) are now available at docs.scipy.org. >> >>> > Pauli, you are impressive! >> >>> Well, Sphinx supports it out of the box, so one just needs to install >>> MS's HTML help workshop. >> >> I know. But you really get things done. >> >> Ga?l >> _______________________________________________ >> Scipy-dev mailing list >> Scipy-dev(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/scipy-dev >> > > In both numpy and scipy chm files I get: > The page cannot be displayed > The page you are looking for is currently unavailable. The Web site > might be experiencing technical difficulties, or you may need to > adjust your browser settings. > > contents,search, index work correctly, but the page content is not found. > > I decompiled and recompiled in with the html help workshop and it > looks pretty good. Search and Index are very fast and helpful. > > Thank you from a Windows user. > > Josef I am able to see all the help pages in the .chm after clicking on the "Unblock" button in the "Properties" dialogue box. See also http://support.microsoft.com/kb/902225/ Thanks again from another Windows user. Gareth. ------------------------------------------------------------- IMPORTANT NOTICE. This E-Mail and any files transmitted with it, are confidential and may be privileged and are for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of distribution, copying or use of this communication or the information in it, is strictly prohibited and may be unlawful. If you have received this E-Mail in error please return it to the sender. We should be grateful if you would also copy the communication to postmaster(a)doosanbabcock.com the delete the E-Mail and destroy any copies of it. It is your responsibility to scan any attachments for viruses. For further information, visit us at WWW.DOOSANBABCOCK.COM

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Hankel transform
by Tom Grydeland Dec. 15, 2008

Dec. 15, 2008

Hi developers, When I recently needed a Hankel transform I was unable to find one in Scipy. I found one in MATLAB though[1], written by Prof. Brian Borchers at New Mexico Tech. The code is based on a previous FORTRAN implementation by W. L. Anderson [2], and the MATLAB code is not marked with any copyright statements. Hankel transforms of the first and second order can be computed through digital filtering. I have rewritten the code in Python/numpy, complete with tests and acknowledgements of the origins, and my employer has agreed that I can donate the code to Scipy. I believe this should be of interest. Hankel transforms arise often in acoustics and other systems with cylinder symmetry. If you want it, I would like a suggestion where it belongs (with other integral transforms, probably) and how I should shape the tests to make them suitable for inclusion. The tests I currently have use Hankel transforms of five different functions with known analytical transforms and compares the transformed values to the numerically evaluated analytical expressions. Currently plots are generated, but for automated testing I suppose something else would be better. Pointing me at an example is sufficient. [1] http://infohost.nmt.edu/~borchers/hankel.html [2] Anderson, W. L., 1979, Computer Program Numerical Integration of Related Hankel Transforms of Orders 0 and 1 by Adaptive Digital Filtering. Geophysics, 44(7):1287-1305. Best regards, -- Tom Grydeland <Tom.Grydeland(a)(discoverpetroleum.com|gmail.com)>

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Re: [SciPy-dev] FFT docstrings (was: Scipy Tutorial (and updating it))
by jh＠physics.ucf.edu Dec. 15, 2008

Dec. 15, 2008

On Fri, Dec 12, 2008 at 03:19:05PM -0500, jh(a)physics.ucf.edu wrote: > Also, the current routine examples satisfy a mathematician but do not > give insight into what the FT actually *does*, i.e., extract the > periodic content of a signal. Gael responded: > Yes, I was thinking similarly. This is exactly why I brought up the > question about plotting. We avoid plots when possible, of course, but I think that if ever there were a case for a line plot in numpy, it would be fft. The constraints are that we want a plot in the docs but can't have one in the most basic doc reader, help(). A compromise might be to put it in the package docstring and not the routine docstrings. We might also include the full filename of the plot, so someone working in text could view the plot separately. Looking ahead, would it be possible to get Python to use a module's help() method if it exists? Then we could replace help() with a full-functioning reader that defaults to the current help() behavior but could be configured by a state variable to run a browser for the PDF or HTML docs. I assume this would require a PEP and providing some code. --jh--

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Re: [SciPy-dev] Scipy Tutorial (and updating it)
by jh＠physics.ucf.edu Dec. 15, 2008

Dec. 15, 2008

Jarrod wrote: > I would also prefer changing the name from "Tutorial" to "User Guide". I disagree, for two reasons. First, we are badly diluting our doc effort and will fail to complete *any* documents to a user's satisfaction with this approach. We need to close the scipy doc wiki (maintainers can edit in SVN), pause on tutorials, and focus on the task at hand. First document the core software. Then document its general use. Of course, I can't force anyone to do this, but I hope you all will. Together, we are more than the sum of our parts. Separately, we cannot get this job done. Second, a (good) user manual takes a level of planning and commitment that has not gone into any of our documents so far. This tutorial document cannot grow into a good user manual, because documents *never* improve with organic growth. They must be planned and written with scope in mind from the outset. We should reserve the name "User Manual" for something we plan and execute to be good with that scope. To expand (only a little, I promise!) on the User Guide, it needs chapters on specific numpy topics, starting with the text in the new numpy.doc module, and it needs chapters on general topics like plotting, 3D visualization, handling datasets, scientific data formats, etc. Heavy-duty programming chapters belong in a separate document (NumPy Programmer's Guide?). Advanced tricks need to be limited in the User Guide or it will be far too long. It could go in its own guide, or might better go in a web cookbook. We are a grass-roots community, but good books are not, and have never been, written by a haphazard grass-roots effort, with everyone writing whatever they feel like writing. The best you can hope for is to scope and plan as a community, set goals for specific docs and sections of docs, form small groups of writers, parcel out pieces with specific goals to different groups, and then have a small editing team work with the chapter teams to unify the pieces. This is a standard process in academic publishing and it works well. Other than the small-team-does-it-all model, I'm not aware of any other successful authoring modes. Grass roots works on the doc wiki only because we've provided strict guidelines and process, and each page is done by just one or a few people. If we don't plan as a community and focus our efforts, the scattered docs will reflect the interests of the writers rather than the readers. The quality will be quite variable and key items will never be finished. Please everyone, new things are fun, but let's first finish what we've begun. Go write numpy docstrings. --jh--

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Re: [SciPy-dev] FFT docstrings (was: Scipy Tutorial (and updating it))
by jh＠physics.ucf.edu Dec. 14, 2008

Dec. 14, 2008

> Pauli says: > I'd think there are plenty of possibilities for plots in Numpy > documentation. For example, polyfit, etc. I'd also want to avoid putting > any file names to the docstrings, as the base directory for these is > ambiguous, and having a file name in the documentation is not really > helpful for the reader. Moreover, filenames may easily clash, eg. > plot-1.jpg, plot-2.jpg, etc. Well, we've had this discussion before, last spring when we discussed adding the "image" directive. Some felt strongly that any sort of image in the help() docs should be avoided since some people may be reading in a text-only mode or may not have matplotlib installed (e.g., OLPC users). We could have decided to write slightly different docs for help() and for the PDF/HTML version. Sadly, we do not control help(): whatever is in the docstring, directives and all, will be seen by the reader. But, we agreed on the principle of keeping the docstrings as the ultimate source of the reference docs, because a more removed source that produced the docstring would be even less likely to be kept updated by developers than docstrings, and we are very far behind on even the docstrings. So, putting a lot of images into our paper docs means putting them in our help() docs as well, and the more that are there the less happy text-only readers will be, particularly if the images/plots are critical to the text. Because matplotlib might not be available, we need to provide a copy of the image or plot. That requires a naming standard, and an obvious one would be the full name of the object followed by -plot1.png, -image1.png, etc. We need to identify a directory in the release to put these in (I think Stefan might have, already). Then the help() text gives the inclusion directive, the pathname for those using plain help(), and (usually) the commands to make it, set as an example. I will agree with those who say that help() text will be a little cluttered. But, given the constraints, we have the option not to serve OLPC users and maybe get removed from their release, to avoid images altogether, or to move to a higher-level source file that produces a cleaner help() text, and convince the developers to update that rather than ever touching the docstring. I prefer living with a little clutter, or mainly using the PDF or HTML versions, and I think that was also how others were leaning last spring. We need some regular input from some people who actually work in the OLPC environment, or others for whom PDF/HTML don't work for some reason, or who read only using help() for some reason other than religion. I'm defending their interests by applying theory rather than actually knowing what they care about and can/can't tolerate. > The help command can be overridden by replacing __builtin__.help, but I > don't think doing this kind of monkeypatching is the proper thing to do > on "import numpy". I do not advocate monkeypatching help()! That would have our help reading other packages() docstrings. Rather, I would feed back a help() that looks for packagename.help() and calls that if it exists, else just calls the current help(). We *could* monkeypatch that new help() temporarily, but I'd rather leave that to the user's discretion. --jh--

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error installing matplotlib-0.98.5
by Neal Becker Dec. 12, 2008

Dec. 12, 2008

sudo easy_install -U matplotlib Searching for matplotlib Reading http://pypi.python.org/simple/matplotlib/ Reading http://matplotlib.sourceforge.net Reading https://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278… Reading https://sourceforge.net/project/showfiles.php?group_id=80706&package_id=824… Reading http://sourceforge.net/project/showfiles.php?group_id=80706 Best match: matplotlib 0.98.5 Downloading http://downloads.sourceforge.net/matplotlib/matplotlib-0.98.5.tar.gz?modtim… Processing matplotlib-0.98.5.tar.gz Running matplotlib-0.98.5/setup.py -q bdist_egg --dist-dir /tmp/easy_install-CC1jw7/matplotlib-0.98.5/egg-dist-tmp-NSNvcC ============================================================================ BUILDING MATPLOTLIB matplotlib: 0.98.5 python: 2.5.2 (r252:60911, Sep 30 2008, 15:42:03) [GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] platform: linux2 REQUIRED DEPENDENCIES numpy: 1.2.0 freetype2: 9.18.3 OPTIONAL BACKEND DEPENDENCIES libpng: 1.2.33 Tkinter: Tkinter: 50704, Tk: 8.5, Tcl: 8.5 * Guessing the library and include directories for * Tcl and Tk because the tclConfig.sh and * tkConfig.sh could not be found and/or parsed. wxPython: 2.8.9.1 * WxAgg extension not required for wxPython >= 2.8 Gtk+: gtk+: 2.14.4, glib: 2.18.3, pygtk: 2.13.0, pygobject: 2.15.4 Mac OS X native: no Qt: Qt: 3.3.8, PyQt: 3.17.4 Qt4: Qt: 4.4.1, PyQt4: 4.4.3 Cairo: 1.4.12 OPTIONAL DATE/TIMEZONE DEPENDENCIES datetime: present, version unknown dateutil: 1.4 pytz: 2006p OPTIONAL USETEX DEPENDENCIES dvipng: 1.11 ghostscript: 8.63 latex: 3.141592 EXPERIMENTAL CONFIG PACKAGE DEPENDENCIES configobj: 4.5.2 enthought.traits: no [Edit setup.cfg to suppress the above messages] ============================================================================ error: lib/matplotlib/mpl-data/matplotlib.conf.template: No such file or directory Exception exceptions.OSError: (2, 'No such file or directory', 'src/image.cpp') in <bound method CleanUpFile.__del__ of <setupext.CleanUpFile instance at 0x7fc85b3c51b8>> ignored Exception exceptions.OSError: (2, 'No such file or directory', 'src/path.cpp') in <bound method CleanUpFile.__del__ of <setupext.CleanUpFile instance at 0x7fc85b3c4638>> ignored Exception exceptions.OSError: (2, 'No such file or directory', 'src/backend_gdk.c') in <bound method CleanUpFile.__del__ of <setupext.CleanUpFile instance at 0x7fc85978c7a0>> ignored Exception exceptions.OSError: (2, 'No such file or directory', 'src/backend_agg.cpp') in <bound method CleanUpFile.__del__ of <setupext.CleanUpFile instance at 0x7fc85b3c4fc8>> ignored

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