Mailman 3 October 2001 - SciPy-Dev

RPMs and source distribution
by Travis Oliphant 24 Dec '01

24 Dec '01

I've been playing for hours and finally have it so that python setup.py sdist python setup.by bdist_rpm work as expected. I have distributions and RPM's that I need to put somewhere. Thanks, -Travis

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plotting enhancements and copyright
by Jochen Küpper 01 Nov '01

01 Nov '01

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Cc'ed to the scipy lists. Should also make it into the archive. This message is to inform the users and developers od SciPy what's going on in politics. The plot_window class (an earlier version of which I send to this lists) or respective changes to plot_canvas and some further changes to scipy.plt won't get included in scipy 'cause of politcal issues. This is sad as it provided a first implementation of zooming and an *useful* interface to use scipy.plt as wxWindow in other applications. See below for more. Because this is new for most people I cite a little more. Eric, eric> 4) Do you feel strongly about the inclusion of the copyright? For clarification: This is refering to a line at the top of the respective source file: "#Copyright (C) 2001 Jochen Küpper" >> Yes. The code is copyrighted by me anyway, so why not tell everybody? eric> Ok. Unfortunately, I am not interested in encumbering the eric> existing code with another copyright for a single or even eric> multiple additional features. This sort of thing is almost eric> never done because it can lead to major hassles in the future eric> trying to work with the 20 people who have added feature patches eric> and bug fixes to a file over its lifetime. What problems are you thinking of here? Changing the license? What else? eric> So I guess the best thing to do then if for you to derive a new eric> plot_canvas class and add/override the methods you need to and eric> place it in a new module. That's what I did to begin with. eric> You can then copyright this module. Yeah. I guess I just put it into jkext, so I can everything the way I like it, not restricted by scipy rules. (I do not want to argue about these rules. I think there have to be rules and the ones that are there are appropriate for the project from my point of view.) The module is GPL'ed. eric> I guess you need to include the Enthought/BSD copyright also if eric> any or my original code is in the modules and you plan on eric> distributing it separately. Yes. eric> As for how it is handled in SciPy, I'm not sure. We can include eric> your module, but the zoom capability is also likely to be folded eric> back into the original class once someone has the time to sit eric> down and work on the graphics code (with someone having to redo eric> your work). It isn't hard, as I showed. I actually spent more time to fit it into scipy than writing the stuff in the first place:( And this while I was learning wxPython. eric> I guess we'll need to add a policy that copyrights for patches eric> and bug fixes will need to be assigned to the original code eric> author or copyright holder. Contributors will be acknowledged in eric> the THANKS file. This is the standard practice in OS projects eric> so I didn't feel the need to make it explicit, but I will now to eric> prevent future confusion on the issue. New modules can retain eric> the authors copyright, as long as it is BSD compliant (or eric> whatever we eventually end up with). I think you are confusing things here. "Copyright" and "license" are two distinct features. Any code I write I do have a copyright on, no matter what the license is. I can give up my copyright i.e. by transfering it to someone else, but unless I explicitely do that I'll own the copyright. The license is whole different story. (I am ok with the BSD style licens, esp. since I see that there is (good) reasoning behind it.) Many people never write the FSF-papers. So far I am one of them. (Not that they would seriously need mine.) For now I am not going to transfer my copyright on BSD licensed code to a company, sorry. I wish SciPy good luck! Bye, Jochen - -- Einigkeit und Recht und Freiheit http://www.Jochen-Kuepper.de Liberté, Égalité, Fraternité GnuPG key: 44BCCD8E Sex, drugs and rock-n-roll -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6-cygwin-fcn-1 (Cygwin) Comment: Processed by Mailcrypt and GnuPG <http://www.gnupg.org/> iD8DBQE74HPBiJ/aUUS8zY4RAkg8AJ9/samJAatCoGs8HtHZiyFYGa2LQQCfT0OY aFLQzbp5IzVZZKaUGovzZFA= =4r2z -----END PGP SIGNATURE-----

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ml archives
by Jochen Küpper 30 Oct '01

30 Oct '01

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Eric, Travis, is it possible to obtain the articles in the ml archive in raw text? Or, how is one supposed to get a patch out of the archives into a raw text file? Am I overseeing something? (I tried copy/pasting from the web-page and the source, but this always includes the html encodings of special chars.) Greetings, Jochen - -- University of North Carolina phone: +1-919-962-4403 Department of Chemistry phone: +1-919-962-1579 Venable Hall CB#3290 (Kenan C148) fax: +1-919-843-6041 Chapel Hill, NC 27599, USA GnuPG key: 44BCCD8E -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6-cygwin-fcn-1 (Cygwin) Comment: Processed by Mailcrypt and GnuPG <http://www.gnupg.org/> iD8DBQE73b2yiJ/aUUS8zY4RApbzAJ4oJUuYbJyGHEWK+wa8aH3xNfbERACgsAVq APmSY9qqW5xPVLVJdd56px0= =bWRg -----END PGP SIGNATURE-----

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Broken link in www.scipy.org
by Roy Bryant 29 Oct '01

29 Oct '01

There appears to be a problem on this page of your site. On page http://www.scipy.org/site_content/tutorials/build_instructions when you click on "the fftw home", the link to http://www.scipy.org/site_content/tutorials/www.fftw.org gives the error: Not found. Suggestion: You may have forgotten the "http:" As recommended by the Robot Guidelines, this email is to explain our robot's activities and to let you know about one of the broken links we encountered. LinkWalker does not store or publish the content of your pages, but rather uses the link information to update our map of the World Wide Web. Are these reports helpful? I'd love some feedback. If you prefer not to receive these occasional error notices please let me know. Roy Bryant ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Roy Bryant, roybryant(a)seventwentyfour.com President SEVENtwentyfour Inc. ("Always watching the Web") http://www.seventwentyfour.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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plot_window, zooming, and such
by Jochen Küpper 28 Oct '01

28 Oct '01

Eric, here comes the next... zooming is there I put a class plot_window in plt/wxplt.py that corresponds to the PlotCanvas I send to the list before. Moreover I added zooming to the plot_canvas class. Seems to work, but I haven't tested it too much in interactive mode. Besides that I added the __type_hack__ stuff to figure() and cleaned up wxplt.py a bit, esp. changed method names according to the guidelines. One problem I run into (worked around here) is the interrelation between interface and wxplt: I cannot call autoscale() from plot_canvas methods, as validate_active seems to lead to a race condition in that case:( A demo application using plot_window can be found in jkext (on my homepage). Once that is a little further down the stream I'll make a standalone distro, but for testing that should be good enough. Almost all functionality is in scipy anyway. Greetings, Jochen -- Einigkeit und Recht und Freiheit http://www.Jochen-Kuepper.de Liberté, Égalité, Fraternité GnuPG key: 44BCCD8E Sex, drugs and rock-n-roll

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PlotCanvas
by Jochen Küpper 27 Oct '01

27 Oct '01

All, I have created a very q+d-hacked PlotCanvas based on scipy.plt. In case anybody is interested, the bare class file is attached. Feel free to add this to scipy.plt if you see it fit. It requires one patch to scipy.plt itself to access _active from the outside (q+d, as I said!): Index: plt/interface.py =================================================================== RCS file: /home/cvsroot/world/scipy/plt/interface.py,v retrieving revision 1.10 diff -u -r1.10 interface.py --- plt/interface.py 2001/10/12 20:07:08 1.10 +++ plt/interface.py 2001/10/24 15:05:19 @@ -498,3 +498,7 @@ else: p.SetSize(s1) + +def setActive(active): + global _active + _active = active You can also download the code including a small application from my homepage -> homemade software page; it's part of jkext. See files gui/plot.py, gui/kplot.py and scripts/plot. I am planning to add some more functionality and then release this as a small sample app. Greetings, Jochen -- University of North Carolina phone: +1-919-962-4403 Department of Chemistry phone: +1-919-962-1579 Venable Hall CB#3290 (Kenan C148) fax: +1-919-843-6041 Chapel Hill, NC 27599, USA GnuPG key: 44BCCD8E

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Reading in arrays.
by Travis Oliphant 26 Oct '01

26 Oct '01

As eric pointed out reading arrays of ASCII data is actually quite easy (and fairly sophisticated). It is available thanks to the support of Agilent who has given some money for the development of SciPy. Reading ascii data can be as simple as a = io.read_array('test.dat') # you can pass a string object already. to read in space-separated data as an array of doubles. Eric, Why on earth would you reach for Excel now that you have it this easy? (Except for maybe getting better graphics on windows --- if you have an X-server you can already do quite a bit). I'm not sure I agree with Eric that this is "buried" way to deep. io.read_array does not seem very deep to me. There are many options which can make the reading in easier. >>> help(io.read_array) read_array(fileobject, separator=None, columns=None, comment='#', lines=None, atype='d', linesep='\n', rowsize=10000, missing=0) Return an array represented ascii_formatted data in |fileobject|. Inputs: fileobject -- An open file object or a string for a valid filename. separator -- a string or a tuple of strings to indicate the column separators. If the length of the string tuple is less than the total number of columns, then the last separator is assumed to be the separator for the rest of the columns. columns -- a tuple of integers and range-tuples which describe the columns to read from the file. A negative entry in the last column specifies the negative skip value to the end. Example: columns=(1, 4, (5, 9), (11, 15, 3), 17, -2) will read [1,4,5,6,7,8,11,14,17,18,20,22,...] lines -- a tuple with the same structure as columns which indicates the lines to read. comment -- the comment character (line will be ignored even if it is specified by the lines tuple) linesep -- separator between rows. missing -- value to insert in array when conversion to number fails. atype -- the typecode of the output array. rowsize -- the allocation row size (array grows by this amount as data is read in). Adding wizards to make this more "interactive" may be useful especially for beginners. But, the functionality is there. -Travis

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SciPy versus Matlab, Excel, and other tools
by Kevin Altis 26 Oct '01

26 Oct '01

I asked a number of friends involved in science on a daily basis what tools they use day to day and for publication. The top answer for doing analysis and graphs seems to be Excel and presentations are done in PowerPoint which are then projected rather than printed and then publications are done in PDF format. One person was using Calcusyn for statistical analysis. Matlab seemed to be the most popular tool after Excel. Excel can be manipulated via COM (and possibly AppleEvents) so it can be scripted from Python, but then that would be a Windows and Mac solution. Is the big issue here something that will run under Unix? I'm assuming that the costs of Excel and Matlab are prohibitive for some people. Matlab in particular looks pretty expensive for an individual. Can Matlab be scripted from Python? Of course, Excel doesn't have most of the libraries that SciPy has, so my investigations may have been too focused on the visualization aspect. Again, I'm not a scientific computing user, so I'm just trying to better understand the SciPy goals, so I can understand how SciPy relates to PythonCard. Thanks, ka --- Kevin Altis altis(a)semi-retired.com

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reading ascii files into arrays
by eric jones 25 Oct '01

25 Oct '01

> Hi Eric ! > > I have decided to use python & scipy for data evaluation/presentation for > the future. Excellent. Glad to hear it. > One thing that I did not find in scipy (maybe I did not look > carefully enough) are commands for simple reading-in of ascii data from data files > with simple contents like: > > 1 2 > 2 4 > 3 9 > 4 7 > 5 9 > 6 1 > > Nothing more than 2 simple blank-seperated vectors in two columns. I have > tried it in pure python with the readline command an splitting the lines into > the blank-sepatated elements, but I think it is not very elegant since it > takes too many commands to do so. > Reading in of data from an external file is such a very fundamental think in > science that there should be a simple solution (imagine handling big data > sets). > > Do you see a possibility to make it easier ? I agree this is important. Travis Oliphant's scipy.io package has a module called array_import that I think will do what you want. It was adapted from some of Konrad Hinsen's work. file: test.dat 1 2 2 4 >>> from scipy import * >>> import scipy.io.array_import >>> help(scipy.io.array_import.read_array) read_array(fileobject, separator=None, columns=None, comment='#', lines=None, atype='d', linesep='\n', rowsize=10000, missing=0) Return an array containing the data from file |fileobject|. >>> q = scipy.io.array_import.read_array('c:\\test.dat') >>> q array([[ 1., 2.], [ 2., 4.]]) While this is available, I think it is buried way to deep in scipy. We need to pull the functionality up a level or two. As you say, this is a very common need and it should be made easily accessible. I also think it should be augmented to read from a string instead of just from a file -- although I guess this would need another name. The code for read_array is at the bottom of this file: http://scipy.net/cgi-bin/viewcvs.cgi/scipy/io/array_import.py?rev=1.5&conten t-type=text/vnd.viewcvs-markup Also: There has been a short discussion about the merits of MS Excel (which counts me as a user) on the scipy-dev list, and this is one of the things it does extremely well. It has an import capability that lets you split data in a fixed format or character delimited way. Whenever I need a quick and dirty plot of data in a file, I always reach for Excel to do this. It'd be nice to have something similar to Excel's import wizard available to those who like that sort of thing. For now, read_array will work quite nicely. see ya, eric

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wxplt
by Jochen Küpper 24 Oct '01

24 Oct '01

Patch against current cvs, cleaning up wildcard handling a bit and fixing a typo. Index: plt/wxplt.py =================================================================== RCS file: /home/cvsroot/world/scipy/plt/wxplt.py,v retrieving revision 1.7 diff -u -r1.7 wxplt.py --- plt/wxplt.py 2001/08/09 20:46:07 1.7 +++ plt/wxplt.py 2001/10/24 05:25:03 @@ -564,14 +564,13 @@ def OnFileSaveAs(self, event): import os - dlg = wx.wxFileDialog(self, "Save As", ".", "", "*.*", wx.wxSAVE) wildcard = "PNG files (*.png)|*.png|" \ "BMP files (*.bmp)|*.bmp|" \ "JPEG files (*.jpg)|*.jpg|" \ "PCX files (*.pcx)|*.pcx|" \ - "TIFF files (*.tif)|*.tif" - dlg.SetWildcard(wildcard) - dlg.SetWildcard(wildcard) + "TIFF files (*.tif)|*.tif|" \ + "All Files |*|" + dlg = wx.wxFileDialog(self, "Save As", ".", "", wildcard, wx.wxSAVE) if dlg.ShowModal() == wx.wxID_OK: f = dlg.GetPath() dummy, ftype = os.path.splitext(f) @@ -581,13 +580,14 @@ self.client.save(dlg.GetPath(),ftype) else: msg = "Extension is currently used to determine file type." \ - "'%s' is not a vaild extension." \ + "'%s' is not a valid extension." \ "You may use one of the following extensions. %s" \ % (ftype,image_type_map.keys()) d = wx.wxMessageDialog(self,msg,style=wx.wxOK) d.ShowModal() d.Destroy() - dlg.Destroy() + dlg.Destroy() + def OnFileExit(self, event): self.Close() Greetings, Jochen -- Einigkeit und Recht und Freiheit http://www.Jochen-Kuepper.de Liberté, Égalité, Fraternité GnuPG key: 44BCCD8E Sex, drugs and rock-n-roll

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