Mailman 3 April 2005 - SciPy-User

Re: problems with glplt and new scipy install
by Alimamy Bangura April 24, 2005

April 24, 2005

Hi, Thanks for your speedy response. I actually meant gplt rather than glplot in my previous message... The following for example doesn't work, but no error message pops up. >>> import scipy >>> from scipy import gplt >>> x=arange(0,10,0.1) >>> y=sin(x) >>> gplt.plot(x,y) thanks again, Ali > > Message: 7 > Date: Sat, 23 Apr 2005 19:26:47 -0700 > From: Robert Kern <rkern(a)ucsd.edu> > Subject: Re: [SciPy-user] problems with glplt and > new scipy install > To: SciPy Users List <scipy-user(a)scipy.net> > Message-ID: <426B03E7.9050805(a)ucsd.edu> > Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > > Alimamy Bangura wrote: > > Hi, > > > > I have just spent a long time getting a version of > > scipy installed on my powerbook G4 . I am a > newbie to > > python and the whole unix thing so I have found > the > > whole ordeal rather difficult, but interesting! > > > > All seemed lost until I found the package by Peter > > Maxwell at: > > > > > http://cbis.anu.edu.au/misc/SciPy_complete-0.3.2.mpkg.zip > > > > I should really have looked at this list first > before > > trying to build from the source... > > > > It all seems to work great except plotting with > glplt. > > The program I have been testing with I know works > on > > other machines, but doesn't work when I use it on > > mine. > > > > I can import scipy and the scipy.test() seems to > work > > fine. I have reinstalled the newest version of > xfree86 > > from fink, after deleting all previous > incarnations, > > but it just doesn't open the window when it is > > supposed to, no error message is popped up either. > > Whose gnuplot are you using? IIRC, Fink's gnuplot > doesn't use X. Use > Fink to install AquaTerm. > > I do recommend using matplotlib instead. > > -- > Robert Kern > rkern(a)ucsd.edu > > "In the fields of hell where the grass grows high > Are the graves of dreams allowed to die." > -- Richard Harter > > > > ------------------------------ > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > > End of SciPy-user Digest, Vol 20, Issue 12 > ****************************************** > Send instant messages to your online friends http://uk.messenger.yahoo.com

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problems with glplt and new scipy install
by Alimamy Bangura April 23, 2005

April 23, 2005

Hi, I have just spent a long time getting a version of scipy installed on my powerbook G4 . I am a newbie to python and the whole unix thing so I have found the whole ordeal rather difficult, but interesting! All seemed lost until I found the package by Peter Maxwell at: http://cbis.anu.edu.au/misc/SciPy_complete-0.3.2.mpkg.zip I should really have looked at this list first before trying to build from the source... It all seems to work great except plotting with glplt. The program I have been testing with I know works on other machines, but doesn't work when I use it on mine. I can import scipy and the scipy.test() seems to work fine. I have reinstalled the newest version of xfree86 from fink, after deleting all previous incarnations, but it just doesn't open the window when it is supposed to, no error message is popped up either. Any clues? thanks, Ali Send instant messages to your online friends http://uk.messenger.yahoo.com

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mmwrite and sparse matrices. It works?
by Stas Fomin April 23, 2005

April 23, 2005

Hello! I am newbie in SciPy. (Just installed Numeric-23.5.win32-py2.3.exe and SciPy_complete-0.3.2.win32-py2.3-num23.5.exe) http://oliphant.ee.byu.edu:81/scipy/io/mmwrite declares that "mmwrite Writes the sparse or dense matrix A to a Matrix Market formatted file". I try small piece of code: Python 2.3.2 (#49, Nov 13 2003, 10:34:54) [MSC v.1200 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy import *; >>> A = sparse.dok_matrix() >>> A[1,3] = 4 >>> print A (1, 3) 4 >>> fn=open('file.mtx','w') >>> io.mmio.mmwrite(fn,A) Traceback (most recent call last): File "<stdin>", line 1, in ? File "C:\Python\Lib\site-packages\scipy\io\mmio.py", line 266, in mmwrite if typecode in 'fF': TypeError: 'in <string>' requires string as left operand Also, I failed to "mmwrite" csc_matrices... Does "mmio" package work with matrices from "sparse"? If so, please, provide small example. Sincerely, Stas Fomin.

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SUSe 64 bit
by Jarmila Bohmanova April 22, 2005

April 22, 2005

Does anybody has an experience with SciPy on SUSe 9.1 64 bit? When I try to import scipy it gives me: File "<stdin>", line 1, in ? File "/usr/lib64/python2.3/site-packages/PIL/__init__.py", line 11, in ? File "/usr/lib64/python2.3/site-packages/scipy_base/__init__.py", line 16, in ? import fastumath # no need to use scipy_base.fastumath ImportError: /usr/lib64/python2.3/site-packages/scipy_base/fastumath.so: cannot open shared object file: No such file or directory I also tried to recompile setup_scipy_base.py 'python setup_scipy_base.py install' But I got another error message: package init file '/usr/lib64/python2.3/site-packages/scipy_base/tests/__init__.py' not found (or not a regular file) package init file '/usr/lib64/python2.3/site-packages/scipy_base/tests/__init__.py' not found (or not a regular file) running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'scipy_base.display_test' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -DHAVE_LARGEFILE_SUPPORT -O2 -fmessage-length=0 -Wall -fPIC' compile options: '-DHAVE_X11 -I/usr/X11R6/include -I/usr/include/python2.3 -c' gcc: /usr/lib64/python2.3/site-packages/scipy_base/src/display_test.c /usr/lib64/python2.3/site-packages/scipy_base/src/display_test.c:65: warning: initialization from incompatible pointer type gcc -pthread -shared build/temp.linux-x86_64-2.3/usr/lib64/python2.3/site-packages/scipy_base/src /display_test.o -L/usr/X11R6/lib -lX11 -o build/lib.linux-x86_64-2.3/scipy_base/display_test.so /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: cannot find -lX11 collect2: ld returned 1 exit status /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin /ld: cannot find -lX11 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.3/usr/lib64/python2.3/site-packages/scipy_base/src /display_test.o -L/usr/X11R6/lib -lX11 -o build/lib.linux-x86_64-2.3/scipy_base/display_test.so" failed with exit status 1 Jarmila.

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Interpolation
by Tim Gray April 21, 2005

April 21, 2005

Hi, I've got a question for everyone. I'm trying to some code from IDL that uses the interpolate function. Basically I've got a big 2d array of data with time as one index and radius on the other index. Each value in the array is "data". I basically need to interpolate this data to other radii. Here's what IDL's interpolate does (to 2d arrays). It takes an array such as: x =[[ 0, 1, 2, 3,] [ 4, 5, 6, 7,] [ 8, 9,10,11,] [12,13,14,15,]] and given two vectors which define the desired indices to interpolate the data to, it spits out a new array. So for an input of: interpolate(x,[.5,1.5,2.5],[.5,1.5,2.5]), you get a 3x3 array of: [[ 2.5, 3, 4.5] [ 6.5, 7.5, 8.5] [10.5, 11.5, 12.5]] I'm sure something like this is in Scipy already, I'm just having problems finding it. Any suggestions? Tim

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Re[2]: ANN: Veusz 0.5 - a scientific plotting package
by Joe Harrington April 20, 2005

April 20, 2005

Nicely said, Bob. I'll add/reiterate this simple test: Say that the "other" package were available from two (or more) independent sources with different licenses but the same API. Internally, those packages could be entirely different. Your SOURCE code is not a derived work if you could have chosen to develop under either package without it changing your code. It is not even a derived work if this is hypothetically possible (e.g., there is currently only one Qt, but there could be another with the same API someday). Your source code *is* a derived work if this is not true, as for example if you had actually taken some Qt code and used it, even modified, in yours. In that case, the second implementation of Qt would not have had the same code in it, and your code would have looked different because the text you appropriated would have looked different in the other package. The complete running/runnable object code, of course, is a derived work, even if it is a binary in memory, produced at runtime by an interpreter. If you #include something in a C program, the .o and even post-preprocessor data would also be derived works. --jh--

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unhandled exception ind leastsq
by Christian Kristukat April 20, 2005

April 20, 2005

Hi, a couple of weeks ago there was some discussion about calculating the covariance from the result of lmdif/lmder and eventually some code was added to the leastsq() function. I propose that an exception handler for the following error should be added which occurs when the data has very little noise:: File "/usr/lib/python2.3/site-packages/scipy/optimize/minpack.py", line 255, in leastsq cov_x = sl.inv(dot(transpose(R),R)) File "/usr/lib/python2.3/site-packages/scipy/linalg/basic.py", line 216, in inv if info>0: raise LinAlgError, "singular matrix" scipy.linalg.basic.LinAlgError: singular matrix Anyway, as we finally have the covariance matrix, could explain to me how I get a e.g. 95% confidence interval? Regards, Christian

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ANN: Veusz 0.5 - a scientific plotting package
by Jeremy Sanders April 20, 2005

April 20, 2005

Veusz 0.5 --------- Velvet Ember Under Sky Zenith ----------------------------- http://home.gna.org/veusz/ Veusz is Copyright (C) 2003-2005 Jeremy Sanders <jeremy(a)jeremysanders.net> Licenced under the GPL (version 2 or greater) Veusz is a scientific plotting package written in Python (currently 100% Python). It uses PyQt for display and user-interfaces, and numarray for handling the numeric data. Veusz is designed to produce publication-ready Postscript output. Veusz provides a GUI, command line and scripting interface (based on Python) to its plotting facilities. The plots are built using an object-based system to provide a consistent interface. Changes from 0.4: Installation: * distutils used to install the package. RPMS available. Plotting: * Different error bar styles (diamond, curve...) * "Matched" axes, with the same scale on each * Data can be linked from external files instead of embedded in document * Filled regions under/over functions or xy plots * Improved function clipping near edge of plot * Default values can be set for settings, which are remembered between sessions (e.g. blue points for xy3). * Rotated text labels * Improved fitting, giving results from chi2, etc.. UI: * Can move around widgets and delete them * Exception dump dialog to send bug reports * Improved import dialog help * Propagate settings between widgets * Window positions are saved between sessions Reading data: * Better error handling when reading data + Numerous bug fixes Features of package: * X-Y plots (with errorbars) * Stepped plots (for histograms) * Line plots * Function plots * Fitting functions to data * Stacked plots and arrays of plots * Plot keys * Plot labels * LaTeX-like formatting for text * EPS output * Simple data importing * Scripting interface * Save/Load plots To be done: * Contour plots * Images * UI improvements * Import filters (for qdp and other plotting packages, fits, csv) * Data manipulation * Python embedding interface (for embedding Veusz in other programs). [some of the external interface is complete] Requirements: Python (probably 2.3 or greater required) http://www.python.org/ Qt (free edition) http://www.trolltech.com/products/qt/ PyQt (SIP is required to be installed first) http://www.riverbankcomputing.co.uk/pyqt/ http://www.riverbankcomputing.co.uk/sip/ numarray http://www.stsci.edu/resources/software_hardware/numarray Microsoft Core Fonts (recommended) http://corefonts.sourceforge.net/ For documentation on using Veusz, see the "Documents" directory. The manual is in pdf, html and text format (generated from docbook). If you enjoy using Veusz, I would love to hear from you. Please join the mailing lists at https://gna.org/mail/?group=veusz to discuss new features or if you'd like to contribute code. The newest code can always be found in CVS. Cheers Jeremy

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Re[2]: ANN: Veusz 0.5 - a scientific plotting package
by Joe Harrington April 19, 2005

April 19, 2005

> Can I legally distribute sqw.py separately under the BSD (or > some GPL compatible license)? > So why should sqw.py be > > distributed as GPL code in the first place? > Some interpretations of copyright law (e.g. Larry Rosen's) say that no, > it doesn't have to. The FSF's, Trolltech's, and Riverbank's say > otherwise. If FSF et al. really say this, they're dreaming. Who says that the "Qt" library that it is going to be run with will be the one they know about? There are numerous clone products that provide API-compatible functionality under different licenses, and in fact this is the main business of the FSF. GNU really is Not Unix, in an IP sense, even though many of their program can be and frequently are compiled, linked, and run on UnixTM systems using native compilers and libraries. There is a distinction to be drawn between two types of "modified code". In the first instance, you take some source code from someone else and modify those actual lines of text. In the second, your subclass *asks the compiler, linker, or interpreter* to modify or extend something that the compiler defined due to instructions from elsewhere. The first case is certainly a derived work, and falls under the terms of the parent document. You used someone else's IP to make something new. GPL demands that you use GPL to license the derived work. As I understand it, the second is not a derived work *in its source form*, because you didn't start with or include substantial sections of prose or code someone else wrote. Rather, you wrote instructions for a compiler, possibly run by someone else, to do a modification to a construct it knew about. You do not know the user's license status with respect to Qt, or which Qt the user will choose. At compile or runtime, those terms may require that the *combination* of the parent library and your modification be licensed under terms of the parent library, so if you want people to be able to run your code you had better make your terms compatible with the terms you expect the user to have. However, there's no law against my writing a Qt clone under my own license and using that library with your code. In that case, it would certainly not be subject to the original Qt license terms, since I wouldn't be using Qt at all. Your instructions to the compiler would be applied to a different set of code from what you had originally envisioned. Any runnable program would now fall under both your and my terms, as opposed to yours and Qt's. My point here is that you can write any text you like, and as long as it does not include text someone else wrote, it's yours and you can distribute it under any terms you like in its source form. In this case, it's only when your IP gets combined with someone else's stuff to make a third product that a derived work exists. So, you could offer the user a choice of licenses. Those who did in fact use the GPL'd Qt might have to choose GPL, but others could chose from the full range of options. The latter category might include those who would replace the Qt calls with calls to another library, or those who would take pieces of the code and include them in their own packages. Like Robert, I like Rosen's book, and IANAL. --jh--

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job openings at Enthought
by eric jones April 19, 2005

April 19, 2005

Hey group, We have a number of scientific/python related jobs open. If you have any interest, please see: http://www.enthought.com/careers.htm thanks, eric

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