From nwagner at mecha.uni-stuttgart.de Tue Dec 2 04:54:29 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Tue, 02 Dec 2003 10:54:29 +0100 Subject: [SciPy-user] Solving linear matrix equations with scipy Message-ID: <3FCC6155.CDF44B8D@mecha.uni-stuttgart.de> Hi all, Are there any efforts to add solvers for linear matrix equations to scipy ? Nils References http://www.win.tue.nl/niconet/ http://www.math.tu-berlin.de/~benner/Publicat/pub/SimaBenner_ECC03.pdf From loredo at astro.cornell.edu Tue Dec 2 16:51:12 2003 From: loredo at astro.cornell.edu (Tom Loredo) Date: Tue, 2 Dec 2003 16:51:12 -0500 (EST) Subject: [SciPy-user] more OSX build problems Message-ID: <200312022151.hB2LpCt17695@laplace.astro.cornell.edu> Chris wrote: > The only one you will have to install explicitly is f2py; ATLAS, LAPACK > and fftw are available when you install the developer tools. Is this only true for Panther? What's the situation (re: libraries) with Jaguar? -Tom From camartin at snet.net Tue Dec 2 16:55:44 2003 From: camartin at snet.net (camartin at snet.net) Date: Tue, 02 Dec 2003 16:55:44 -0500 Subject: [SciPy-user] re: gplt fails Message-ID: <3FCD0A60.8090708@snet.net> "Hetal Patel" wrote: Whenever I try to plot complex data using either plt or gplt from any pyhton shell(Python,PythonWin,IDLE,PyCrust). windows reports that pythonw has crashed. I know that it's a bit unfair to ask the plot routines to plot complex data but I would expect an error, not python to crash. I'm running the latest SciPy release on Windows XP. Example code below crashes. You probably want to plot the modulus of the complex number. It's interesting that if you use plt.plot(b) it gives you an error message that the array is complex then plots the modulus of b for you! Nice error trapping. gplt failes as you say. Cliff >>>>>from scipy import * >> >> >>>>>>a = arange(1,10,0.2) >>>>>>b = a + 2.j >>>>>>b >>> >>> array([ 1. +2.j, 1.2+2.j, 1.4+2.j, 1.6+2.j, 1.8+2.j, 2. +2.j, 2.2+2.j, 2.4+2.j, 2.6+2.j, 2.8+2.j, 3. +2.j, 3.2+2.j, 3.4+2.j, 3.6+2.j, 3.8+2.j, 4. +2.j, 4.2+2.j, 4.4+2.j, 4.6+2.j, 4.8+2.j, 5. +2.j, 5.2+2.j, 5.4+2.j, 5.6+2.j, 5.8+2.j, 6. +2.j, 6.2+2.j, 6.4+2.j, 6.6+2.j, 6.8+2.j, 7. +2.j, 7.2+2.j, 7.4+2.j, 7.6+2.j, 7.8+2.j, 8. +2.j, 8.2+2.j, 8.4+2.j, 8.6+2.j, 8.8+2.j, 9. +2.j, 9.2+2.j, 9.4+2.j, 9.6+2.j, 9.8+2.j]) >>>>>>gplt.plot(b) >>> >>> At this point python\pythonw crashes with the following error "python.exe has encountered a problem and needs to close. We are sorry for the inconvenience." If anyone can help me resolve this then I would greatly appreciate it. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris at fonnesbeck.org Tue Dec 2 17:11:12 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Tue, 2 Dec 2003 17:11:12 -0500 Subject: [SciPy-user] more OSX build problems In-Reply-To: <200312022151.hB2LpCt17695@laplace.astro.cornell.edu> References: <200312022151.hB2LpCt17695@laplace.astro.cornell.edu> Message-ID: <70B45726-2514-11D8-B6EF-000A956FDAC0@fonnesbeck.org> If you get the latest developer tools, they should be included: http://developer.apple.com/documentation/ReleaseNotes/MacOSX/vecLib.html On Dec 2, 2003, at 4:51 PM, Tom Loredo wrote: > > Chris wrote: > >> The only one you will have to install explicitly is f2py; ATLAS, >> LAPACK >> and fftw are available when you install the developer tools. > > Is this only true for Panther? What's the situation (re: libraries) > with Jaguar? > > -Tom > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia "Reports that say something hasn't happened are always interesting to me, because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns -- the ones we don't know we don't know." -- Donald Rumsfeld, US Secretary of War -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1189 bytes Desc: not available URL: From joe at enthought.com Wed Dec 3 17:36:45 2003 From: joe at enthought.com (Joe Cooper) Date: Wed, 03 Dec 2003 16:36:45 -0600 Subject: [SciPy-user] Reboot and Zope Upgrade on SciPy.org Message-ID: <3FCE6593.8030804@enthought.com> Hi all, There will be a short (possibly longer than short, if all doesn't go well) service outage in a couple of hours on scipy.org (sometime between 6 and 7PM CST). All scipy.org/scipy.net services will be unavailable during this time. This includes mailing lists, the website, CVS, etc. I will be performing routine maintenence, a kernel upgrade, and a Zope upgrade. I expect the outage to last about five to ten minutes, though Zope has historically thwarted my attempts to achieve a quick and painless upgrade. Nothing should change significantly on the server, as the Zope upgrade is minor (2.6.1 to 2.6.2). There are plans afoot to bring SciPy.org into the modern age with a migration to Plone instead of the older CMF that we're currently using. The planners (mainly me) are adragging their afeet, however, so there's no telling when the switch will be pulled. If you have useful content (or merely content you are fond of) on the site that uses DTML, it would be in all of our interests for you to consider converting it to using ZPT or structured text. DTML is apparently deprecated in Plone, and there also seems to be some other content type issues that we'll be fighting with one day in the not too distant future. Let me know if you have anything there, and I'll see if I can assist with getting it ready for the migration to Plone. Holler if this service outage will cause significant pain for anyone. Thanks! From joe at enthought.com Wed Dec 3 19:53:38 2003 From: joe at enthought.com (Joe Cooper) Date: Wed, 03 Dec 2003 18:53:38 -0600 Subject: [SciPy-user] SciPy.org is back up Message-ID: <3FCE85A8.6060409@enthought.com> Hi all, The upgrades seem to have gone smoothly, and the website, lists, mail, CVS, etc. should all be available again on scipy.org. If you run into any problems, let me know. Thanks! From hoel at gl-group.com Thu Dec 4 06:46:36 2003 From: hoel at gl-group.com (=?iso-8859-15?Q?Berthold_H=F6llmann?=) Date: Thu, 04 Dec 2003 12:46:36 +0100 Subject: [SciPy-user] Problem with scipy_distutils Message-ID: Hello, I'm trying build a FORTRAN module using scipy_distutils. Due to some hidden dynamic libraries I'm trying to use the "runtime_library_dirs" in the extension definition. But with the "ifc" for Linux I get warnigs: ifc: Command line warning: ignoring unknown option '-R/usr/local/fitools/linux/lib' ifc does not know the "-R" switch, but requires "-Xlinker -rpath -Xlinker ". I thougt, after looking into the code, adding a method def runtime_library_dir_option(self, dir): return "-Xlinker -rpath -Xlinker " + dir should do the trick, but unfortunately it does not. I still get the "-R" in the link command. What can be done about this? Kind regards Berthold H?llmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel at gl-group.com Internet: http://www.gl-group.com **************************************************** Please notice: We would like to inform you that the e-mail address of Germanischer Lloyd as well as our internet address had been changed to gl-group.com with effect from 1st March 2003. This means that the previous address shortmark at germanlloyd.org will be replaced by shortmark at gl-group.com. From now on the GL homepage can be accessed at the address 'http://www.gl-group.com'. The old addresses remain valid for a transitional period. **************************************************** This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc. From pearu at scipy.org Thu Dec 4 07:59:15 2003 From: pearu at scipy.org (Pearu Peterson) Date: Thu, 4 Dec 2003 06:59:15 -0600 (CST) Subject: [SciPy-user] Problem with scipy_distutils In-Reply-To: Message-ID: On Thu, 4 Dec 2003, [iso-8859-15] Berthold H?llmann wrote: > Hello, > > I'm trying build a FORTRAN module using scipy_distutils. Due to some > hidden dynamic libraries I'm trying to use the "runtime_library_dirs" > in the extension definition. But with the "ifc" for Linux I get > warnigs: > > ifc: Command line warning: ignoring unknown option '-R/usr/local/fitools/linux/lib' > > ifc does not know the "-R" switch, but requires "-Xlinker -rpath -Xlinker ". > > I thougt, after looking into the code, adding a method > > def runtime_library_dir_option(self, dir): > return "-Xlinker -rpath -Xlinker " + dir > > should do the trick, but unfortunately it does not. I still get the > "-R" in the link command. What can be done about this? I remember that this issue has been come up earlier but I don't exactly recall the solution. What Python, ifc versions are you using? This "-R" switch comes from runtime_library_dir_option method of distutils/unixccompiler.py, see the comment in this file, sending a fix to Python people might be a good idea. Pearu From chris at fonnesbeck.org Thu Dec 4 11:33:47 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Thu, 4 Dec 2003 11:33:47 -0500 Subject: [SciPy-user] g95 for OSX Message-ID: Just to let folks know, there is a binary of the g95 FORTRAN compiler for OSX available on the HPC site (http://hpc.sourceforge..net). Not sure if it will work with f2py, but I will give it a try this afternoon. C. -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia From hoel at gl-group.com Thu Dec 4 11:44:46 2003 From: hoel at gl-group.com (=?iso-8859-15?Q?Berthold_H=F6llmann?=) Date: Thu, 04 Dec 2003 17:44:46 +0100 Subject: [SciPy-user] Re: Problem with scipy_distutils In-Reply-To: (Pearu Peterson's message of "Thu, 4 Dec 2003 06:59:15 -0600 (CST)") References:

Message-ID: Pearu Peterson writes: > On Thu, 4 Dec 2003, [iso-8859-15] Berthold H?llmann wrote: > >> Hello, >> >> I'm trying build a FORTRAN module using scipy_distutils. Due to some >> hidden dynamic libraries I'm trying to use the "runtime_library_dirs" >> in the extension definition. > > Hmm, while reading ifc_issues.txt I wonder if your environment is > set up properly for ifc. Does LD_LIBRARY_PATH contain a path > /compiler70/ia32/lib? Have you sourced ifcvars.sh script > to your environment? My environment is set up properly. The problem are not the ifc runtime libraries but 3rd party or self compiled dynamic libraries spread over lots of directories. I would prefer to refer to them using the "-R" linker option to allow other people running my programs without fiddeling with the "LD_LIBRARY_PATH". I'm not shure if "get_linker_so" is the correct for the fix. In the process of building the linker flags the method "runtime_library_dir_option" gets called in "distutils/ccompiler.py". For some reason I can't overload "runtime_library_dir_option", but I think overloading this method in "intel_ia32_fortran_compiler" would be the correct way. Kind regards Berthold H?llmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel at gl-group.com Internet: http://www.gl-group.com **************************************************** Please notice: We would like to inform you that the e-mail address of Germanischer Lloyd as well as our internet address had been changed to gl-group.com with effect from 1st March 2003. This means that the previous address shortmark at germanlloyd.org will be replaced by shortmark at gl-group.com. From now on the GL homepage can be accessed at the address 'http://www.gl-group.com'. The old addresses remain valid for a transitional period. **************************************************** This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc. From pajer at iname.com Fri Dec 5 21:54:25 2003 From: pajer at iname.com (Gary Pajer) Date: Fri, 5 Dec 2003 21:54:25 -0500 Subject: [SciPy-user] Building on Windows? References: <200312022151.hB2LpCt17695@laplace.astro.cornell.edu> <70B45726-2514-11D8-B6EF-000A956FDAC0@fonnesbeck.org> Message-ID: <001901c3bba4$42d4aa50$01fd5644@playroom> I've been trying to build cvs scipy on WinXP. No other reason than to be up to date, so I may punt this activity. It's not compiling. There are hints and instructions on the web site, and included with cvs. Are these instructions up to date? I think I've settled all the dependencies (never sure). I'm using the Enthought edition of python, which includes Mingc. I'm guessing that that compiler should work, otherwise why would it be included? The error is: error: Python was built with version 6 of Visual Studio, and extensions need to be built with the same version of the compiler, but it isn't installed. If it takes recompiling python, I think I'll pass. On the other hand, maybe I'm missing something relatively simple. I've built scipy on linux without much difficulty. Is building scipy on WinXP just a royal pain, or can it be done with reasonable effort? -gary From astraw at insightscientific.com Fri Dec 5 23:28:28 2003 From: astraw at insightscientific.com (Andrew Straw) Date: Sat, 6 Dec 2003 14:58:28 +1030 Subject: [SciPy-user] Building on Windows? In-Reply-To: <001901c3bba4$42d4aa50$01fd5644@playroom> Message-ID: Sorry, I can't answer most of your questions, but I have built Python extensions many times with mingw and used them successfully with PythonLab's Python 2.2.x for win32 (which was compiled with MSVC 6). Gary Pajer wrote: > I've been trying to build cvs scipy on WinXP. No other reason than to > be up > to date, so I may punt this activity. > > It's not compiling. There are hints and instructions on the web site, > and > included with cvs. Are these instructions up to date? > > I think I've settled all the dependencies (never sure). I'm using the > Enthought edition of python, which includes Mingc. I'm guessing that > that > compiler should work, otherwise why would it be included? > > The error is: > error: Python was built with version 6 of Visual Studio, and > extensions > need to be built with the same version of the compiler, but it isn't > installed. > > If it takes recompiling python, I think I'll pass. On the other hand, > maybe I'm missing something relatively simple. > > I've built scipy on linux without much difficulty. Is building scipy > on > WinXP just a royal pain, or can it be done with reasonable effort? > > -gary -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 155 bytes Desc: not available URL: From travis at enthought.com Sat Dec 6 09:31:17 2003 From: travis at enthought.com (Travis N. Vaught) Date: Sat, 6 Dec 2003 08:31:17 -0600 Subject: [SciPy-user] Building on Windows? In-Reply-To: <001901c3bba4$42d4aa50$01fd5644@playroom> Message-ID: <077c01c3bc05$a7e580c0$9701a8c0@tvlaptop> Gary, I think you can use: python setup.py build --compiler=mingw32 and it should work for the build. > -----Original Message----- > From: scipy-user-bounces at scipy.net [mailto:scipy-user-bounces at scipy.net] > On Behalf Of Gary Pajer > Sent: Friday, December 05, 2003 8:54 PM > To: SciPy Users List > Subject: [SciPy-user] Building on Windows? > > I've been trying to build cvs scipy on WinXP. No other reason than to be > up > to date, so I may punt this activity. > > It's not compiling. There are hints and instructions on the web site, and > included with cvs. Are these instructions up to date? > > I think I've settled all the dependencies (never sure). I'm using the > Enthought edition of python, which includes Mingc. I'm guessing that that > compiler should work, otherwise why would it be included? > > The error is: > error: Python was built with version 6 of Visual Studio, and extensions > need to be built with the same version of the compiler, but it isn't > installed. > > If it takes recompiling python, I think I'll pass. On the other hand, > maybe I'm missing something relatively simple. > > I've built scipy on linux without much difficulty. Is building scipy on > WinXP just a royal pain, or can it be done with reasonable effort? > > -gary > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user From simon.duane at npl.co.uk Mon Dec 8 10:08:23 2003 From: simon.duane at npl.co.uk (Simon Duane) Date: Mon, 8 Dec 2003 15:08:23 -0000 Subject: [SciPy-user] Scipy for Python 2.3? Message-ID: <8B3E03343914D411A51000062938C79607437B81@golf.npl.co.uk> I run Python 2.3.2 (with Numeric, wxPython and assorted other packages) on Win2k and would like to install SciPy. However, I find that the SciPy installer demands python 2.2 (though I think I read somewhere the assertion that it is compatible with 2.3). Is there any plan to make a windows binary package of SciPy that will install on top of Python 2.3? I would hesitate before switching to Enthought's Python 2.x for Windows (which has SciPy, but lots more that I have no immediate need for), feeling more comfortable with the one I download from python.org. Thanks Simon ------------------------------------------------------------------- This e-mail and any attachments may contain confidential and/or privileged material; it is for the intended addressee(s) only. If you are not a named addressee, you must not use, retain or disclose such information. 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No: 2937881 Registered Office: Teddington, Middlesex, United Kingdom TW11 0LW. ------------------------------------------------------------------- From chris at fonnesbeck.org Mon Dec 8 10:44:32 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Mon, 8 Dec 2003 10:44:32 -0500 Subject: [SciPy-user] Build errors in supermatrix.h Message-ID: <6A9D800C-2995-11D8-BC31-000A956FDAC0@fonnesbeck.org> After updating from CVS, building gives the following errors on OSX that I have not seen before: In file included from Lib/sparse/SuperLU2.0/SRC/zsp_defs.h:23, from Lib/sparse/_zsuperlumodule.c:26: Lib/sparse/SuperLU2.0/SRC/supermatrix.h:19: error: parse error before numeric constant In file included from Lib/sparse/_zsuperlumodule.c:27: Lib/sparse/SuperLU2.0/SRC/util.h:95: warning: function declaration isn't a prototype Lib/sparse/SuperLU2.0/SRC/util.h:101: warning: function declaration isn't a prototype Lib/sparse/_zsuperlumodule.c: In function `NRFormat_from_spMatrix': Lib/sparse/_zsuperlumodule.c:46: warning: implicit declaration of function `zCreate_CompRow_Matrix' Lib/sparse/_zsuperlumodule.c: In function `Py_zgssv': Lib/sparse/_zsuperlumodule.c:164: warning: implicit declaration of function `superlu_delete_allkeys' Lib/sparse/_zsuperlumodule.c: At top level: Lib/sparse/_zsuperlumodule.c:191: warning: function declaration isn't a prototype Lib/sparse/_zsuperlumodule.c: In function `init_zsuperlu': Lib/sparse/_zsuperlumodule.c:192: warning: unused variable `d' error: command 'gcc' failed with exit status 1 Any ideas on a workaround? -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia From pearu at scipy.org Mon Dec 8 16:04:59 2003 From: pearu at scipy.org (Pearu Peterson) Date: Mon, 8 Dec 2003 15:04:59 -0600 (CST) Subject: [SciPy-user] Build errors in supermatrix.h In-Reply-To: <6A9D800C-2995-11D8-BC31-000A956FDAC0@fonnesbeck.org> Message-ID: On Mon, 8 Dec 2003, Christopher Fonnesbeck wrote: > After updating from CVS, building gives the following errors on OSX > that I have not seen before: Has Lib/sparse/_zsuperlumodule.c compiled without errors before you updated from CVS? There has been no changes in CVS that would concern this file. > In file included from Lib/sparse/SuperLU2.0/SRC/zsp_defs.h:23, > from Lib/sparse/_zsuperlumodule.c:26: > Lib/sparse/SuperLU2.0/SRC/supermatrix.h:19: error: parse error before > numeric constant > In file included from Lib/sparse/_zsuperlumodule.c:27: > Lib/sparse/SuperLU2.0/SRC/util.h:95: warning: function declaration > isn't a prototype > Lib/sparse/SuperLU2.0/SRC/util.h:101: warning: function declaration > isn't a prototype > Lib/sparse/_zsuperlumodule.c: In function `NRFormat_from_spMatrix': > Lib/sparse/_zsuperlumodule.c:46: warning: implicit declaration of > function `zCreate_CompRow_Matrix' > Lib/sparse/_zsuperlumodule.c: In function `Py_zgssv': > Lib/sparse/_zsuperlumodule.c:164: warning: implicit declaration of > function `superlu_delete_allkeys' > Lib/sparse/_zsuperlumodule.c: At top level: > Lib/sparse/_zsuperlumodule.c:191: warning: function declaration isn't a > prototype > Lib/sparse/_zsuperlumodule.c: In function `init_zsuperlu': > Lib/sparse/_zsuperlumodule.c:192: warning: unused variable `d' > error: command 'gcc' failed with exit status 1 > > Any ideas on a workaround? Try compiling this particular file manually and find out why compiler fails here. Or if you don't need scipy.sparse module then disable it by adding 'sparse' to the ignore_packages list in setup.py file. Pearu From chris at fonnesbeck.org Tue Dec 9 12:16:09 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Tue, 9 Dec 2003 12:16:09 -0500 Subject: [SciPy-user] continuing trouble outputting gplt plots to file Message-ID: <61E401DA-2A6B-11D8-8230-000A956FDAC0@fonnesbeck.org> I have recompiled scipy from CVS on OSX, but still have no luck outputting plots made with gplt. I have gnuplot installed, and the plots look great, but when I try and save them as png files using either gplt.png or gplt.output, nothing happens. Moreover, there are no errors given that would help debug this problem. I would appreciate any guidance anyone has to offer, as that my main use of scipy. Can I output to other formats, like pdf or eps? Thanks, C. -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia From chris at fonnesbeck.org Tue Dec 9 13:47:00 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Tue, 9 Dec 2003 13:47:00 -0500 Subject: [SciPy-user] f2py error during scipy build on Linux Message-ID: <12B421BB-2A78-11D8-8230-000A956FDAC0@fonnesbeck.org> I get the following when building on RedHat Linux: building 'scipy.xxx.spam' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -lcc _dynamic -fPIC -I/usr/lib/python2.3/site-packages/f2py2e/src -I/usr/include/pyth on2.3 -c /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c -o build/te mp.linux-i686-2.3/usr/lib/python2.3/site-packages/f2py2e/src/ fortranobject.o /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c: In function `array_ from_pyobj': /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c:591: parse error bef ore `int' /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c:597: `is_cont' undec lared (first use in this function) /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c:597: (Each undeclare d identifier is reported only once /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c:597: for each functi on it appears in.) error: command 'gcc' failed with exit status 1 Not sure why this should be. -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia From pearu at scipy.org Tue Dec 9 16:18:10 2003 From: pearu at scipy.org (Pearu Peterson) Date: Tue, 9 Dec 2003 15:18:10 -0600 (CST) Subject: [SciPy-user] f2py error during scipy build on Linux In-Reply-To: <12B421BB-2A78-11D8-8230-000A956FDAC0@fonnesbeck.org> Message-ID: On Tue, 9 Dec 2003, Christopher Fonnesbeck wrote: > I get the following when building on RedHat Linux: > > /usr/lib/python2.3/site-packages/f2py2e/src/fortranobject.c:591: parse > error before `int' This should be now fixed in f2py CVS. Thanks for reporting it. Pearu From Boris.Breidenbach at mf.mpg.de Wed Dec 10 08:15:07 2003 From: Boris.Breidenbach at mf.mpg.de (Boris Breidenbach) Date: Wed, 10 Dec 2003 14:15:07 +0100 Subject: [SciPy-user] Problem with plt.plot() Message-ID: <20031210141507.A30831@lfluids11.mpi-stuttgart.mpg.de> Hello! I am new to scipy. I tried the example given in the plotting tutorial (http://www.scipy.org/site_content/tutorials/plot_tutorial, section "Starting plt"). First, I imported gui_thread. But I did not get any message of the kind "". But I did not get any error message either. Then I did: >>> from scipy import plt and >>> plt.plot((1,2,3)) After that I get a message like but no window appears. Any idea why? On ending python, a window seems to pop up, just for a split second. It is not displayed long enough to recognize any content. Did anyone experience similar problems? Any suggestions what might be wrong? Cheers, Boris From pearu at scipy.org Wed Dec 10 08:56:46 2003 From: pearu at scipy.org (Pearu Peterson) Date: Wed, 10 Dec 2003 07:56:46 -0600 (CST) Subject: [SciPy-user] Problem with plt.plot() In-Reply-To: <20031210141507.A30831@lfluids11.mpi-stuttgart.mpg.de> Message-ID: On Wed, 10 Dec 2003, Boris Breidenbach wrote: > Hello! > > I am new to scipy. I tried the example given in the plotting tutorial (http://www.scipy.org/site_content/tutorials/plot_tutorial, section "Starting plt"). > First, I imported gui_thread. But I did not get any message of the kind "". But I did not get any error message either. > Then I did: > >>> from scipy import plt > and > >>> plt.plot((1,2,3)) > After that I get a message like > > but no window appears. Any idea why? > On ending python, a window seems to pop up, just for a split second. It is not displayed long enough to recognize any content. > > Did anyone experience similar problems? Any suggestions what might be wrong? Try: >>> from gui_thread import wxPython_thread >>> wxPython_thread() >>> from scipy import plt >>> plt.plot((1,2,3)) The plotting tutorial needs to be updated... Pearu From Boris.Breidenbach at mf.mpg.de Wed Dec 10 09:22:35 2003 From: Boris.Breidenbach at mf.mpg.de (Boris Breidenbach) Date: Wed, 10 Dec 2003 15:22:35 +0100 Subject: [SciPy-user] Problem with plt.plot() In-Reply-To: References: <20031210141507.A30831@lfluids11.mpi-stuttgart.mpg.de> Message-ID: <20031210152235.A31573@lfluids11.mpi-stuttgart.mpg.de> Thanks. It works. I found another way to make it work. After importing gui_thread one can invoke >>> gui_thread.start() which produces an output similar to the one mentioned in the tutorial : Thereafter plt.plot() works fine. Boris On Wed, Dec 10, 2003 at 07:56:46AM -0600, Pearu Peterson wrote: > Try: > > >>> from gui_thread import wxPython_thread > >>> wxPython_thread() > >>> from scipy import plt > >>> plt.plot((1,2,3)) > > The plotting tutorial needs to be updated... > > Pearu > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user From travis at enthought.com Wed Dec 10 09:51:07 2003 From: travis at enthought.com (Travis N. Vaught) Date: Wed, 10 Dec 2003 08:51:07 -0600 Subject: [SciPy-user] Problem with plt.plot() In-Reply-To: Message-ID: <0c2401c3bf2d$0b14ec60$9701a8c0@tvlaptop> > -----Original Message----- > From: scipy-user-bounces at scipy.net [mailto:scipy-user-bounces at scipy.net] > On Behalf Of Pearu Peterson > Sent: Wednesday, December 10, 2003 7:57 AM > To: SciPy Users List > Subject: Re: [SciPy-user] Problem with plt.plot() > > > Try: > > >>> from gui_thread import wxPython_thread > >>> wxPython_thread() > >>> from scipy import plt > >>> plt.plot((1,2,3)) > > The plotting tutorial needs to be updated... > > Pearu > I was just about to update the tutorial and noticed that the wxPython_thread import doesn't work with Python 2.3 for Windows - Enthought Edition build 1028 (the current download from http://www.enthought.com/python ): C:\>python Enthought Edition build 1028 Python 2.3 (#46, Aug 11 2003, 09:34:05) [MSC v.1200 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> from gui_thread import wxPython_thread Traceback (most recent call last): File "", line 1, in ? File ".\site-packages\gui_thread\wxPython_thread.py", line 17, in ? ImportError: cannot import name ParallelExec I'm going to test with a more recent build (not yet released) shortly, but I wanted to point this out. > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user From simon.duane at npl.co.uk Wed Dec 10 11:05:21 2003 From: simon.duane at npl.co.uk (Simon Duane) Date: Wed, 10 Dec 2003 16:05:21 -0000 Subject: [SciPy-user] Problem with plt.plot() Message-ID: <8B3E03343914D411A51000062938C79607437B9E@golf.npl.co.uk> Any chance of releasing a build of scipy that will install over standard Python 2.3, as opposed to the Enthought edition? Cheers Simon > -----Original Message----- > From: Travis N. Vaught [mailto:travis at enthought.com] > Sent: 10 December 2003 14:51 > To: 'SciPy Users List' > Subject: RE: [SciPy-user] Problem with plt.plot() > > > > > > -----Original Message----- > > From: scipy-user-bounces at scipy.net > [mailto:scipy-user-bounces at scipy.net] > > On Behalf Of Pearu Peterson > > Sent: Wednesday, December 10, 2003 7:57 AM > > To: SciPy Users List > > Subject: Re: [SciPy-user] Problem with plt.plot() > > > > > > > Try: > > > > >>> from gui_thread import wxPython_thread > > >>> wxPython_thread() > > >>> from scipy import plt > > >>> plt.plot((1,2,3)) > > > > The plotting tutorial needs to be updated... > > > > Pearu > > > > > I was just about to update the tutorial and noticed that the > wxPython_thread import doesn't work with Python 2.3 for Windows - > Enthought Edition build 1028 (the current download from > http://www.enthought.com/python ): > > C:\>python > Enthought Edition build 1028 > Python 2.3 (#46, Aug 11 2003, 09:34:05) [MSC v.1200 32 bit (Intel)] on > win32 > Type "help", "copyright", "credits" or "license" for more information. > >>> from gui_thread import wxPython_thread > Traceback (most recent call last): > File "", line 1, in ? > File ".\site-packages\gui_thread\wxPython_thread.py", line 17, in ? > ImportError: cannot import name ParallelExec > > I'm going to test with a more recent build (not yet released) shortly, > but I wanted to point this out. > > > _______________________________________________ > > SciPy-user mailing list > > SciPy-user at scipy.net > > http://www.scipy.net/mailman/listinfo/scipy-user > > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > ------------------------------------------------------------------- This e-mail and any attachments may contain confidential and/or privileged material; it is for the intended addressee(s) only. If you are not a named addressee, you must not use, retain or disclose such information. NPL Management Ltd cannot guarantee that the e-mail or any attachments are free from viruses. NPL Management Ltd. Registered in England and Wales. No: 2937881 Registered Office: Teddington, Middlesex, United Kingdom TW11 0LW. ------------------------------------------------------------------- From gpajer at rider.edu Wed Dec 10 13:39:30 2003 From: gpajer at rider.edu (Gary Pajer) Date: Wed, 10 Dec 2003 13:39:30 -0500 Subject: [SciPy-user] Problem with plt.plot() In-Reply-To: <0c2401c3bf2d$0b14ec60$9701a8c0@tvlaptop> Message-ID: <30F39208-2B40-11D8-AD72-000393A41AAE@rider.edu> > I was just about to update the tutorial and noticed that the > wxPython_thread import doesn't work with Python 2.3 for Windows - > Enthought Edition build 1028 (the current download from > http://www.enthought.com/python ): > Does the Enthought Edition get updated? If it does, maybe you can indicate this by naming the file enthought_python-2.3-1028.exe, or give some other indication. Since I saw nothing, I've been assuming that it's been static for a while. -gary From chris at fonnesbeck.org Wed Dec 10 17:39:58 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Wed, 10 Dec 2003 17:39:58 -0500 Subject: [SciPy-user] zero-size graphic files from gplt.output Message-ID: I think I finally have gplt.output (mostly) working on OSX; the lone problem that remains is that often the resultant file will be of zero size. Here is the code: from scipy.gplt import * def plot_time_series(data,name,xlab='Time',ylab='State',suffix=''): 'Plot (mutiple) time series' plot(data) print 'Plotting',name grid('off') xtitle(xlab) ytitle(ylab) output("%s%s.png" % (name,suffix),'png') close() Any hints? C. -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia From travis at enthought.com Thu Dec 11 15:09:44 2003 From: travis at enthought.com (Travis N. Vaught) Date: Thu, 11 Dec 2003 14:09:44 -0600 Subject: [SciPy-user] Problem with plt.plot() In-Reply-To: <8B3E03343914D411A51000062938C79607437B9E@golf.npl.co.uk> Message-ID: <0de701c3c022$bc427980$9701a8c0@tvlaptop> There is a very good chance of that, but I'm afraid it will happen after the New Year at the earliest. If anyone has a 2.3.x windows build with the installer created with: python setup.py bdist_wininst please send it along and I'll post it to the site. Travis > -----Original Message----- > From: scipy-user-bounces at scipy.net [mailto:scipy-user-bounces at scipy.net] > On Behalf Of Simon Duane > Sent: Wednesday, December 10, 2003 10:05 AM > To: 'SciPy Users List' > Subject: RE: [SciPy-user] Problem with plt.plot() > > Any chance of releasing a build of scipy that will install over standard > Python 2.3, as opposed to the Enthought edition? > > Cheers > Simon > > > -----Original Message----- > > From: Travis N. Vaught [mailto:travis at enthought.com] > > Sent: 10 December 2003 14:51 > > To: 'SciPy Users List' > > Subject: RE: [SciPy-user] Problem with plt.plot() > > > > > > > > > > > -----Original Message----- > > > From: scipy-user-bounces at scipy.net > > [mailto:scipy-user-bounces at scipy.net] > > > On Behalf Of Pearu Peterson > > > Sent: Wednesday, December 10, 2003 7:57 AM > > > To: SciPy Users List > > > Subject: Re: [SciPy-user] Problem with plt.plot() > > > > > > > > > > > Try: > > > > > > >>> from gui_thread import wxPython_thread > > > >>> wxPython_thread() > > > >>> from scipy import plt > > > >>> plt.plot((1,2,3)) > > > > > > The plotting tutorial needs to be updated... > > > > > > Pearu > > > > > > > > > I was just about to update the tutorial and noticed that the > > wxPython_thread import doesn't work with Python 2.3 for Windows - > > Enthought Edition build 1028 (the current download from > > http://www.enthought.com/python ): > > > > C:\>python > > Enthought Edition build 1028 > > Python 2.3 (#46, Aug 11 2003, 09:34:05) [MSC v.1200 32 bit (Intel)] on > > win32 > > Type "help", "copyright", "credits" or "license" for more information. > > >>> from gui_thread import wxPython_thread > > Traceback (most recent call last): > > File "", line 1, in ? > > File ".\site-packages\gui_thread\wxPython_thread.py", line 17, in ? > > ImportError: cannot import name ParallelExec > > > > I'm going to test with a more recent build (not yet released) shortly, > > but I wanted to point this out. > > > > > _______________________________________________ > > > SciPy-user mailing list > > > SciPy-user at scipy.net > > > http://www.scipy.net/mailman/listinfo/scipy-user > > > > > > _______________________________________________ > > SciPy-user mailing list > > SciPy-user at scipy.net > > http://www.scipy.net/mailman/listinfo/scipy-user > > > > ------------------------------------------------------------------- > This e-mail and any attachments may contain confidential and/or > privileged material; it is for the intended addressee(s) only. > If you are not a named addressee, you must not use, retain or > disclose such information. > > NPL Management Ltd cannot guarantee that the e-mail or any > attachments are free from viruses. > > NPL Management Ltd. Registered in England and Wales. No: 2937881 > Registered Office: Teddington, Middlesex, United Kingdom TW11 0LW. > ------------------------------------------------------------------- > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user From travis at enthought.com Thu Dec 11 15:16:36 2003 From: travis at enthought.com (Travis N. Vaught) Date: Thu, 11 Dec 2003 14:16:36 -0600 Subject: [SciPy-user] Problem with plt.plot() In-Reply-To: <30F39208-2B40-11D8-AD72-000393A41AAE@rider.edu> Message-ID: <0de901c3c023$af162bc0$9701a8c0@tvlaptop> > -----Original Message----- > From: scipy-user-bounces at scipy.net [mailto:scipy-user-bounces at scipy.net] > On Behalf Of Gary Pajer > Sent: Wednesday, December 10, 2003 12:40 PM > To: SciPy Users List > Subject: Re: [SciPy-user] Problem with plt.plot() > > > I was just about to update the tutorial and noticed that the > > wxPython_thread import doesn't work with Python 2.3 for Windows - > > Enthought Edition build 1028 (the current download from > > http://www.enthought.com/python ): > > > > Does the Enthought Edition get updated? > If it does, maybe you can indicate this by naming the file > enthought_python-2.3-1028.exe, or give some other indication. > Since I saw nothing, I've been assuming that it's been static for a > while. > You are correct that it has been static for a while. 1028 could have been the first public release or possibly a minor follow-up. We use more recent builds here internally, and will take your advice on the naming of the download when we post one publicly. Thanks, Travis From pearu at cens.ioc.ee Thu Dec 11 04:11:18 2003 From: pearu at cens.ioc.ee (Pearu Peterson) Date: Thu, 11 Dec 2003 11:11:18 +0200 (EET) Subject: [SciPy-user] zero-size graphic files from gplt.output In-Reply-To: Message-ID: On Wed, 10 Dec 2003, Christopher Fonnesbeck wrote: > I think I finally have gplt.output (mostly) working on OSX; the lone > problem that remains is that often the resultant file will be of zero > size. Here is the code: > > from scipy.gplt import * > def plot_time_series(data,name,xlab='Time',ylab='State',suffix=''): > 'Plot (mutiple) time series' > > plot(data) > print 'Plotting',name > grid('off') > xtitle(xlab) > ytitle(ylab) > output("%s%s.png" % (name,suffix),'png') > close() > > Any hints? Why don't you trace the cause of this problem yourself? Under linux (and probably also under win32) there is no problem saving files from gplt. So, the issue is probably related to your platform. Look at the code of gplt and see where something may go wrong.. ie do the usual debugging.. Pearu From jdhunter at ace.bsd.uchicago.edu Mon Dec 15 10:54:01 2003 From: jdhunter at ace.bsd.uchicago.edu (John Hunter) Date: Mon, 15 Dec 2003 09:54:01 -0600 Subject: [SciPy-user] ANN: matplotlib-0.40 python plots with matlab syntax Message-ID: matplotlib is a pure python 2D plotting library with a matlab syntax which produces publication quality figures using in a variety of hardcopy formats (PNG, JPG, TIFF, PS) and interactive GUI environments (WX, GTK) across platforms. matplotlib can be used in python scripts, interactively from the python shell (ala matlab or mathematica), in web application servers generating dynamic charts, or embedded in GTK or WX applications. http://matplotlib.sourceforge.net What's new WX python backend Jeremy O'Donoghue has done an amazing job implementing the backend for wxpython, with all the features such as interactive navigation that are supported in the GTk backend. matplotlib should not be available with a GUI anywhere wxpython, Numeric and python work, including linux and friends, win32, and Mac OS X. See http://matplotlib.sourceforge.net/matplotlib.backends.backend_wx.html for a summary of known issues. Pseudo color plots The pcolor command generates pseudo color plots. See http://matplotlib.sourceforge.net/screenshots.html#pcolor_demo and http://matplotlib.sourceforge.net/screenshots.html#mri_with_eeg for screenshots and example code New time-series plotting functions * psd - plots the power spectral density of a time series * csd - plots the cross spectral density of two time series * cohere - plots the coherence See the examples dir in the src distro: psd_demo.py and csd_demo.py Substantially improved layout The transform architecture was refactored, allowing much more precise layout. Lines, patches, text, etc... can now be placed and scaled in arbitrary units, relative axes units, or physical size. Applicaiton programmers who want to create lines, patches and text directly using the API should read the transform module docs for more info. See the text help for an example of how to specify text locations in axes coords (0,0 is lower left and 1,1 is upper right) Expanded legend capabilities The legend class is improved, with a more sophisticated layout engine and the ability to accept lines and rectangle patches as an optional first argument to specify which lines/patches make up the legend. There are also additional legend placement locations, like 'upper center'. See http://matplotlib.sourceforge.net/screenshots.html#legend_demo Expanded errorbar capabilities Gary Ruben contributed some code to support x and y errorbars, either symmetrix or asymettric, in one enhanced function 'errorbar'. See the errorbar_demo.py for examples of all the wild and wonderful errorbar styles. Bar charts can now also display errorbars; see http://matplotlib.sourceforge.net/screenshots.html#barchart_demo Figure size and DPI controllable from matlab interface The figure command now takes optional args figsize and dpi to set the figure size and DPI in the matlab interface. This change involved some changes in the way default sizes and resolutions were handled among the various backends, with the effect that figures generated by existing scripts may appear different, eg, in the relative size of text to the figure elements. The advantage is that the current implementation does a better job of computing true sizes with increased fidelity between backends. Apologies for any inconveniences! API changes There have been some minor changes to the API for those using matplotlib embedded in GTK applications. * If you instantiate an Axes of Subplot intace, the first arg to __init__ must be the figure that contains it. * If you instantiate any artists, eg, Line2D, Rectangle, or AxisTextGTk, you must initialize them with their dpi, bbox, and transforms. See the help for the transforms modules and the examples logo.py and mri_with_eeg.py, where the objects are explicity created using the new API. * The only change to the matlab interface is in the signature of the errorbar func, which breaks matlab compatibility for the enhanced ability to do x and y errorbars. * See matplotlib.axes.py for a complete list of API changes John Hunter From mike_sorich at hotmail.com Tue Dec 16 00:30:35 2003 From: mike_sorich at hotmail.com (Michael Sorich) Date: Tue, 16 Dec 2003 16:00:35 +1030 Subject: [SciPy-user] optimization with bounded parameter values Message-ID: <1099A28095159443B2FF2655C96BB20A040346CB@exstaffe.levels.unisa.edu.au> Hi All, I am trying to solve a nonlinear regression problem with 4 inputs and 8 parameters. I have used the leastsq function, however, the parameter values returned are not realistic and thus I would like to constrain the parameters to be within certain bounds. Is it possible to do this in scipy? If not, I would welcome suggestions of other free code (preferably in python) or software that can. Thanks for your time, Michael Sorich From jdhunter at ace.bsd.uchicago.edu Tue Dec 16 06:55:34 2003 From: jdhunter at ace.bsd.uchicago.edu (John Hunter) Date: Tue, 16 Dec 2003 05:55:34 -0600 Subject: [SciPy-user] optimization with bounded parameter values In-Reply-To: <1099A28095159443B2FF2655C96BB20A040346CB@exstaffe.levels.unisa.edu.au> ("Michael Sorich"'s message of "Tue, 16 Dec 2003 16:00:35 +1030") References: <1099A28095159443B2FF2655C96BB20A040346CB@exstaffe.levels.unisa.edu.au> Message-ID: >>>>> "Michael" == Michael Sorich writes: Michael> Hi All, I am trying to solve a nonlinear regression Michael> problem with 4 inputs and 8 parameters. I have used the Michael> leastsq function, however, the parameter values returned Michael> are not realistic and thus I would like to constrain the Michael> parameters to be within certain bounds. Is it possible to Michael> do this in scipy? If not, I would welcome suggestions of Michael> other free code (preferably in python) or software that Michael> can. qoca looks nice for a bounded optimizer; you can do linear arithmetic constraints, and there is a python interface http://www.csse.monash.edu.au/projects/qoca/ Last time I tried to build it, several months ago, I ran into some problems with an out-of-date prerequisite ch2xx and got side tracked and so haven't succeeded in building and testing it. If you use debian, however, there is a package. Let me know if you succeed. John Hunter From nwagner at mecha.uni-stuttgart.de Tue Dec 16 10:18:18 2003 From: nwagner at mecha.uni-stuttgart.de (Nils Wagner) Date: Tue, 16 Dec 2003 16:18:18 +0100 Subject: [SciPy-user] Test for singular matrices Message-ID: <3FDF223A.92D6BA84@mecha.uni-stuttgart.de> Dear experts, The RQI begins with a fixed square, complex matrix A, an initial estimated eigenvalue \mu_0, and an initial estimated eigenvector x_0, then the algorithm iterates the following steps (a) Solve the system (A-\mu_n I) y = x_n (b) let x_{n+1} be the unit vector in the direction of y (c) \mu_{n+1} = x_{n+1}^H A x_{n+1} I denotes the identity matrix x0 = ones(n) mu0 = rand(1)+rand(1)*1j y = linalg.solve(A-mu0*identity(n),x0) x1 = y/linalg.norm(y) mu1 = dot(conjugate(x1),dot(A,x1)) x0 = x1 mu0 = mu1 The iteration should halt when the system to be solved is singular, up to numerical tolerance. How can I realize this condition in scipy ? Thanks in advance. Nils From pajer at iname.com Tue Dec 16 17:26:50 2003 From: pajer at iname.com (Gary Pajer) Date: Tue, 16 Dec 2003 17:26:50 -0500 Subject: [SciPy-user] Looking for function that returns indicies acc'd to condition References: <3FDF223A.92D6BA84@mecha.uni-stuttgart.de> Message-ID: <00aa01c3c423$b3b2ba00$01fd5644@playroom> This function must exist in Numeric or scipy, but I can't find it. Given an array, return an array (or list) of indicies corresponding to elements that satisfy a condition. I.e., a = array((1,2,3,4,5)) find_index(a>3) returns [3,4] tia, gary From mike_sorich at hotmail.com Tue Dec 16 18:11:32 2003 From: mike_sorich at hotmail.com (Michael Sorich) Date: Wed, 17 Dec 2003 09:41:32 +1030 Subject: [SciPy-user] Looking for function that returns indicies acc'd to condition In-Reply-To: <00aa01c3c423$b3b2ba00$01fd5644@playroom> Message-ID: <1099A28095159443B2FF2655C96BB20A040346CC@exstaffe.levels.unisa.edu.au> Hi Gary, I think nonzero is what you are looking for: >>> from Numeric import * >>> a = array((1,2,3,4,5)) >>> print nonzero(a>3) [3 4] >>> As per numpy manual "nonzero() returns an array containing the indices of the elements in a that are nonzero. These indices only make sense for 1d arrays, so the function refuses to act on anything else." Cheers, Michael Sorich -----Original Message----- From: scipy-user-bounces at scipy.net [mailto:scipy-user-bounces at scipy.net] On Behalf Of Gary Pajer Sent: Wednesday, 17 December 2003 8:57 AM To: SciPy Users List Subject: [SciPy-user] Looking for function that returns indicies acc'd to condition This function must exist in Numeric or scipy, but I can't find it. Given an array, return an array (or list) of indicies corresponding to elements that satisfy a condition. I.e., a = array((1,2,3,4,5)) find_index(a>3) returns [3,4] tia, gary _______________________________________________ SciPy-user mailing list SciPy-user at scipy.net http://www.scipy.net/mailman/listinfo/scipy-user From radnix at hotmail.com Tue Dec 16 20:30:47 2003 From: radnix at hotmail.com (Carlos) Date: Tue, 16 Dec 2003 19:30:47 -0600 Subject: [SciPy-user] SciPy install Message-ID: Hi, I'm really interrested in SciPy and tried to install it but it refuses to install with Python ver. 2.3. Do I need to revert back to Python ver 2.2 or is there a new release of SciPy that allows install for Python 2.3? Any work arounds? Thanks ahead. _____________________________ Bill Boykin Software Engineer SoftScience _____________________________ "Only those who will risk going too far can possibly find out how far one can go." --T.S. Eliot -------------- next part -------------- An HTML attachment was scrubbed... URL: From james.analytis at physics.ox.ac.uk Wed Dec 17 16:01:41 2003 From: james.analytis at physics.ox.ac.uk (James Analytis) Date: Wed, 17 Dec 2003 21:01:41 +0000 Subject: [SciPy-user] Looking for function that returns indicies acc'd to condition In-Reply-To: <1099A28095159443B2FF2655C96BB20A040346CC@exstaffe.levels.unisa.edu.au> References: <1099A28095159443B2FF2655C96BB20A040346CC@exstaffe.levels.unisa.edu.au> Message-ID: <200312172101.41945.james.analytis@physics.ox.ac.uk> Hey, Maybe you could also find a similar solution for >1-dimensional arrays by taking advantage of python lists. This one for 2-d arrays >>> a array([[1, 2, 3], [3, 2, 1], [3, 1, 4]]) >>> index=[] >>> for i in range(len(a)): ... for j in range(len(a[:,])): ... if a[i,j]>=3: ... index.append([i,j]) ... else: ... pass ... >>> print index [[0, 2], [1, 0], [2, 0], [2, 2]] You would need as many for loops as there are dimensions. This may prove to be too slow for you. James On Tuesday 16 Dec 2003 11:11 pm, Michael Sorich wrote: > Hi Gary, > > I think nonzero is what you are looking for: > >>> from Numeric import * > >>> a = array((1,2,3,4,5)) > >>> print nonzero(a>3) > > [3 4] > > > As per numpy manual "nonzero() returns an array containing the indices > of the elements in a that are nonzero. These indices only make > sense for 1d arrays, so the function refuses to act on anything else." > > Cheers, > > Michael Sorich > > > -----Original Message----- > From: scipy-user-bounces at scipy.net [mailto:scipy-user-bounces at scipy.net] > On Behalf Of Gary Pajer > Sent: Wednesday, 17 December 2003 8:57 AM > To: SciPy Users List > Subject: [SciPy-user] Looking for function that returns indicies acc'd > to condition > > This function must exist in Numeric or scipy, but I can't find it. > > Given an array, return an array (or list) of indicies corresponding to > elements that satisfy a condition. > > I.e., > a = array((1,2,3,4,5)) > find_index(a>3) > > returns [3,4] > > tia, > gary > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user -- James Analytis Department of Physics Clarendon Laboratory, Parks Rd. Oxford, OX1 3PU MB: +447876 453 171 WK: +441865 272 221 From pearu at scipy.org Wed Dec 17 16:12:04 2003 From: pearu at scipy.org (Pearu Peterson) Date: Wed, 17 Dec 2003 15:12:04 -0600 (CST) Subject: [SciPy-user] SciPy install In-Reply-To: Message-ID: On Tue, 16 Dec 2003, Carlos wrote: > Hi, I'm really interrested in SciPy and tried to install it but it > refuses to install with Python ver. 2.3. Do I need to revert back to > Python ver 2.2 or is there a new release of SciPy that allows install > for Python 2.3? Any work arounds? Thanks ahead. Get Scipy from CVS and it will install with Python 2.3 fine. And don't forget reading INSTALL.txt for prerequisites. Pearu From pajer at iname.com Wed Dec 17 16:45:29 2003 From: pajer at iname.com (Gary Pajer) Date: Wed, 17 Dec 2003 16:45:29 -0500 Subject: [SciPy-user] Looking for function that returns indicies acc'd tocondition References: <1099A28095159443B2FF2655C96BB20A040346CC@exstaffe.levels.unisa.edu.au> <200312172101.41945.james.analytis@physics.ox.ac.uk> Message-ID: <005c01c3c4e7$172499f0$01fd5644@playroom> > Hey, > Maybe you could also find a similar solution for >1-dimensional arrays by > taking advantage of python lists. This one for 2-d arrays Thanks. nonzero() works fine for my application. Thanks to M.S. for finding it in the manual for me. -g From chris at fonnesbeck.org Mon Dec 22 12:08:25 2003 From: chris at fonnesbeck.org (Christopher Fonnesbeck) Date: Mon, 22 Dec 2003 11:08:25 -0600 Subject: [SciPy-user] more OSX build problems In-Reply-To: References:

<06C06AB5-2372-11D8-9C3B-000A956FDAC0@fonnesbeck.org> Message-ID: <74208418-34A1-11D8-994B-000A956FDAC0@fonnesbeck.org> Make sure the following is in your CFLAGS environmental variable: -framework vecLib in fact, my CFLAGS looks like this: -faltivec -lcc_dynamic -framework vecLib Let me know if this does not help. C. On Dec 19, 2003, at 2:04 PM, John Hunter wrote: >>>>>> "Christopher" == Christopher Fonnesbeck >>>>>> writes: > > Christopher> The only one you will have to install explicitly is > Christopher> f2py; ATLAS, LAPACK and fftw are available when you > Christopher> install the developer tools. > > > Hi Christopher, > > I've been trying to build scipy on OSX. I am not clear on how the > ATLAS / LAPACK / BLAS thing is supposed to work. I have > /System/Library/Frameworks/vecLib.framework on my system, but do no > see liblapack or libatlas or libblas. If these libs are contained in > vecLib, as was suggested in your post, how do I make scipy aware of > them? > > I have spent a fair amount of time following the links at > http://developer.apple.com/documentation/ReleaseNotes/MacOSX/ > vecLib.html > but do not see anything to download that looks like it has > blas, lapack and atlas. > > Also, > miriam:/System/Library/Frameworks/vecLib.framework> du > 1280 ./Versions/A/Headers > 8 ./Versions/A/Resources/English.lproj > 24 ./Versions/A/Resources > 1928 ./Versions/A > 1936 ./Versions > 1960 . > > is too small to contain atlas, lapack and blas > > On my linux box, liblapack with ATLAS built in is 5MB + . > > Thanks for any help, > JDH > > -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia From pajer at iname.com Sun Dec 28 11:48:31 2003 From: pajer at iname.com (Gary Pajer) Date: Sun, 28 Dec 2003 11:48:31 -0500 Subject: [SciPy-user] Still trying to compile on WinXP References:

<06C06AB5-2372-11D8-9C3B-000A956FDAC0@fonnesbeck.org> <74208418-34A1-11D8-994B-000A956FDAC0@fonnesbeck.org> Message-ID: <000501c3cd62$6d5d3560$01fd5644@playroom> My pet project continues. Latest cvs. I don't get very far. with python setup.py build --compiler=mingw32 I get the following. Something's not being found, but I haven't been able to figure out what. TIA for any help, -gary ---------------------------------------------------------------------------- --------- SciPy Core Version 0.2.1_alpha_21.1020 running build running build_py package init file 'C:\Documents and Settings\Gary Pajer\My Documents\cvs\scipy\s cipy_core\scipy_base\tests\__init__.py' not found (or not a regular file) package init file 'C:\Documents and Settings\Gary Pajer\My Documents\cvs\scipy\s cipy_core\scipy_base\tests\__init__.py' not found (or not a regular file) running build_ext building 'scipy_base.fastumath' extension writing c:\documents and settings\gary pajer\my documents\cvs\scipy\scipy_core\s cipy_base\fastumath.def C:\PYTHON23\Enthought\MingW\bin\gcc.exe -mno-cygwin -shared -s "c:\documents and settings\gary pajer\my documents\cvs\scipy\scipy_core\scipy_base\fastumathmodul e.o" "c:\documents and settings\gary pajer\my documents\cvs\scipy\scipy_core\sci py_base\isnan.o" "c:\documents and settings\gary pajer\my documents\cvs\scipy\sc ipy_core\scipy_base\fastumath.def" -LC:\PYTHON23\libs -LC:\PYTHON23\PCBuild -lpy thon23 -o build\lib.win32-2.3\scipy_base\fastumath.pyd c:\documents and settings\gary pajer\my documents\cvs\scipy\scipy_core\scipy_bas e\fastumathmodule.o(.text+0x15b2):fastumathmodule.c: undefined reference to `_im p__PyExc_ValueError' [a dozen or so similar errors removed ...] error: command 'gcc' failed with exit status 1 Traceback (most recent call last): File "setup.py", line 127, in ? setup_package(ignore_packages) File "setup.py", line 77, in setup_package assert not s,'failed on scipy_core' AssertionError: failed on scipy_core ---------------------------------------------------------------------------- ------------- From josh at cs.byu.edu Mon Dec 29 16:23:18 2003 From: josh at cs.byu.edu (Joshua Menke) Date: Mon, 29 Dec 2003 14:23:18 -0700 Subject: [SciPy-user] gcc error Using weave.blitz() Message-ID: <3FF09B46.2030500@cs.byu.edu> I'm having problems getting weave.blitz() to work. I'm running RedHat 9 with gcc 3.2. I've gotten the latest scipy and weave from cvs. The error seems to manifest whenever I try to pass in a variable from Python to the inline code. For example this works fine: from weave import line code = 'printf("test\n"); inline(code) But this doesn't: a = 1 code = 'a=2' inline(code,['a']) It returns the following (not sure what the "file changed" thing is either): file changed /home/josh/.python22_compiled/sc_83a88ab12cf3296e031df84985733d331.cpp: In function `PyObject* compiled_func(PyObject*, PyObject*)': /home/josh/.python22_compiled/sc_83a88ab12cf3296e031df84985733d331.cpp:650: parse error before `}' token Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/weave/inline_tools.py", line 335, in inline auto_downcast = auto_downcast, File "/usr/lib/python2.2/site-packages/weave/inline_tools.py", line 439, in compile_function verbose=verbose, **kw) File "/usr/lib/python2.2/site-packages/weave/ext_tools.py", line 340, in compile verbose = verbose, **kw) File "/usr/lib/python2.2/site-packages/weave/build_tools.py", line 272, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/usr/lib/python2.2/site-packages/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/usr/lib/python2.2/distutils/core.py", line 157, in setup raise SystemExit, "error: " + str(msg) weave.build_tools.CompileError: error: command 'gcc' failed with exit status 1 Any help would be great. thanks, Josh -- Joshua Menke NNML Lab BYU CS Dept. josh at cs.byu.edu From josh at cs.byu.edu Mon Dec 29 16:34:25 2003 From: josh at cs.byu.edu (Joshua Menke) Date: Mon, 29 Dec 2003 14:34:25 -0700 Subject: [SciPy-user] More weave.blitz() questions In-Reply-To: <3FF09B46.2030500@cs.byu.edu> References: <3FF09B46.2030500@cs.byu.edu> Message-ID: <3FF09DE1.1030409@cs.byu.edu> So my first question had me using weave.inline instead of weave.blitz, though I get the same error using blitz. My next question deals with what happens when I use functions from Numeric like exp or matrixmultiply. I get errors like this: from weave import blitz from Numeric import matrixmultiply expr="c=matrixmultiply(a,b)" blitz(expr) Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.2/site-packages/weave/blitz_tools.py", line 45, in blitz if check_size and not size_check.check_expr(expr,local_dict,global_dict): File "/usr/lib/python2.2/site-packages/weave/size_check.py", line 52, in check_expr exec(expr,values) File "", line 1, in ? NameError: name 'matrixmultiply' is not defined As if it can't find matrixmultiply in the size_check.check_expr function. This seems odd since the first line in size_check.py is "from Numeric import *" Line 52 in check_expr is "exec(expr,values) Any ideas? thanks, Josh -- Joshua Menke NNML Lab BYU CS Dept. josh at cs.byu.edu From zunzun at zunzun.com Sat Dec 27 10:44:33 2003 From: zunzun at zunzun.com (James R. Phillips) Date: Sat, 27 Dec 2003 10:44:33 -500 Subject: [SciPy-user] weave and Differential Evolution ga code Message-ID: <3feda8e1a6ae16.34642054@mercury.sabren.com> I have used weave to inline my genetic algorithm code for Differential Evolution, and it is b-b-blazing fast. The DE home page is http://www.icsi.berkeley.edu/~storn/code.html which is chock full of source code. My native Python implementation crawls compared to any other language, but I do understand the algorithm now :) I'll put up the source code to my SciPy home page as soon as my membership stuff completes. James Phillips http://zunzun.com