Mailman 3 November 2007 - SciPy-User

Specifying fortran compiler
by Adam Mercer 18 Nov '07

18 Nov '07

Hi I'm trying to build SciPy on Mac OS 10.5 using gfortran from MacPorts gcc-4.2.2, which gets installed as gfortran-mp-4.2. When I build I get the following error: Command output: customize IbmFCompiler customize GnuFCompiler Could not locate executable g77 Could not locate executable f77 customize Gnu95FCompiler Could not locate executable gfortran Could not locate executable f95 customize G95FCompiler customize GnuFCompiler Could not locate executable g77 Could not locate executable f77 customize Gnu95FCompiler Could not locate executable gfortran Could not locate executable f95 customize NAGFCompiler customize NAGFCompiler using build_clib building 'dfftpack' library compiling Fortran sources Fortran f77 compiler: f95 -fixed -O4 -target=native Fortran f90 compiler: f95 -O4 -target=native Fortran fix compiler: f95 -fixed -O4 -target=native creating build/temp.macosx-10.3-i386-2.5 creating build/temp.macosx-10.3-i386-2.5/scipy creating build/temp.macosx-10.3-i386-2.5/scipy/fftpack creating build/temp.macosx-10.3-i386-2.5/scipy/fftpack/dfftpack compile options: '-c' f95:f77: scipy/fftpack/dfftpack/dcosqb.f sh: f95: command not found sh: f95: command not found error: Command "f95 -fixed -O4 -target=native -c -c scipy/fftpack/dfftpack/dcosqb.f -o build/temp.macosx-10.3-i386-2.5/scipy/fftpack/dfftpack/dcosqb.o" failed with exit status 127 >From this error it looks like SciPy is trying to use f95 as the fortran compiler executable, not gfortran-mp-4.2. Is there a way that I can specify which fortran compiler to use? Cheers Adam

3 10

2D arrays in weave.inline
by Alan Jackson 17 Nov '07

17 Nov '07

This is probably an astonishingly simple question, but I've been struggling for some time with it. I am trying to work with weave for the first time, and it is becoming clear that I don't understand how 2D arrays get passed. The example below illustrates the problem I'm having... the 2D indexing doesn't seem to be working right at all. BTW the link to the weave documentation is a dead link. Is there any documentation beyond a couple of short examples? Every promising google link turns up dead. #!/usr/bin/env python from numpy import array, zeros, abs, ones, arange, ravel, nan, empty, isnan, histogram, hstack, multiply, log, shape, triu import scipy.weave as weave from scipy.weave import converters def Matrix(width, minval, maxval, exponent, type="HorseSaddle"): halfSqrt2 = 0.707106781185 sin45 = halfSqrt2 cos45 = halfSqrt2 Matrix = zeros((width, width), dtype=float) for j in range(0,width): jScaled = j / (halfSqrt2 * (width-1)) jTranslated = jScaled - halfSqrt2 jsin45 = jTranslated * sin45 jcos45 = jsin45 for i in range(j,width): iScaled = i / (halfSqrt2 * (width-1)); iTranslated = iScaled - halfSqrt2; iRotated = iTranslated * cos45 + jsin45; jRotated = - iTranslated * sin45 + jcos45; iRotated = abs(iRotated); jRotated = abs(jRotated); Matrix[i, j] = round(maxval * iRotated**exponent + \ minval * jRotated**exponent, 2) Matrix[j,i] = Matrix[i,j] return Matrix ################################################################################ # algorithm - WEAVE version ################################################################################ def Fast(s1, s2, wt1, wt2, M): seq1 = s1[0] seq2 = s2[0] t1 = s1[1] t2 = s2[1] code = ''' for (unsigned int idx2 = 0; idx2 < 10; ++idx2) { printf("\\n"); for (unsigned int idx1 = 0; idx1 < 10; ++idx1) { printf("%6f ", M[idx1, idx2]); }// for whole s1 }// for whole s2 printf("\\n"); ''' weave.inline(code, ["seq1", "seq2", "t1", "t2", "M" ]) ################################################################################ # test section ################################################################################ if __name__ == '__main__' : attr1 = array([1,2,2,3,2,4,3,5,4,3,3, 3,4,6,1,0,2,4,2,5,2,3]) attr2 = array([1,2,2,3,2,5,3,5,4,3,2,6, 3,4,6,1,0,1,4,2,5,2,3]) t = arange(1, len(attr1)+1, dtype=float) wt1 = ones(len(attr1), dtype=float) t2 = arange(1, len(attr2)+1, dtype=float) wt2 = ones(len(attr2), dtype=float) seq1 = [attr1, t] seq2 = [attr2, t2] M = Matrix(7,-10,10,2.) print M s1s2, s2s1 = Fast(seq1, seq2, wt1, wt2, M ) -- ----------------------------------------------------------------------- | Alan K. Jackson | To see a World in a Grain of Sand | | alan(a)ajackson.org | And a Heaven in a Wild Flower, | | www.ajackson.org | Hold Infinity in the palm of your hand | | Houston, Texas | And Eternity in an hour. - Blake | -----------------------------------------------------------------------

5 12

Problems compiling Scipy with Cygwin
by Boris von Loesch 17 Nov '07

17 Nov '07

Hello, I tried to compile scipy with cygwin, but the building ended in an error. I use the latest Atlas 3.8.0, and numpy 1.0.4 compiled without problems using python.exe setup.py config --compiler=mingw32 build --compiler=mingw32 bdist_wininst If I build scipy the following error occur: ... building 'scipy.integrate.vode' extension compiling C sources C compiler: gcc -mno-cygwin -O2 -Wall -Wstrict-prototypes compile options: '-DATLAS_INFO="\"?.?.?\"" -Ic:\cygwin\usr\include -Ibuild\src.w in32-2.5 -Ic:\programme\python2.5\lib\site-packages\numpy\core\include -Ic:\prog ramme\python2.5\include -Ic:\programme\python2.5\PC -c' C:\cygwin\bin\g77.exe -g -Wall -mno-cygwin -g -Wall -mno-cygwin -shared build\te mp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o build\temp .win32-2.5\Release\build\src.win32-2.5\fortranobject.o -Lc:\cygwin\usr\lib -Lc:\ programme\python2.5\libs -Lc:\programme\python2.5\PCBuild -Lbuild\temp.win32-2.5 -lodepack -llinpack_lite -lmach -lf77blas -lcblas -latlas -lpython25 -lg2c -o b uild\lib.win32-2.5\scipy\integrate\vode.pyd build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0x367): undefined reference to `__impure_ptr' build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0x462): undefined reference to `__impure_ptr' build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0x585): undefined reference to `__impure_ptr' build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0x9b1): undefined reference to `__impure_ptr' build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0xb23): undefined reference to `__impure_ptr' build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0xb79): more undefined references to `__impure_ptr' follow build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0x18f4): undefined reference to `_setjmp' build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemodule.o:vo demodule.c:(.text+0x1ac5): undefined reference to `_setjmp' collect2: ld returned 1 exit status error: Command "C:\cygwin\bin\g77.exe -g -Wall -mno-cygwin -g -Wall -mno-cygwin -shared build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\integrate\vodemod ule.o build\temp.win32-2.5\Release\build\src.win32-2.5\fortranobject.o -Lc:\cygw in\usr\lib -Lc:\programme\python2.5\libs -Lc:\programme\python2.5\PCBuild -Lbuil d\temp.win32-2.5 -lodepack -llinpack_lite -lmach -lf77blas -lcblas -latlas -lpyt hon25 -lg2c -o build\lib.win32-2.5\scipy\integrate\vode.pyd" failed with exit st atus 1 I also tried to build scipy with "-fno-second-underscore" enabled via F77FLAGS, but that doesn't change anything. Does anybody know how to fix this? Best Regards, Boris

1 0

Re: [SciPy-user] Instruction in math and science
by David Joyner 17 Nov '07

17 Nov '07

David: I'd like to suggest Sage, http://www.sagemath.org/ which comes with python 2.5 and scipy http://www.sagemath.org/packages/standard/ and is available in binary for macs and windows http://www.sagemath.org/download.html I've been using it for teaching DEs http://sage.math.washington.edu/home/wdj/teaching/index.html http://cadigweb.ew.usna.edu/%7Ewdj/teach/sm212/ - David Joyner ---- Original message ---- >Date: Fri, 16 Nov 2007 23:38:49 -0800 >From: David Arnold <dwarnold45(a)suddenlink.net> >Subject: [SciPy-user] Instruction in math and science >To: scipy-user(a)scipy.org > >All, > >We are considering using Python and some of its libraries to aid >instruction in mathematics and science at our college. I've read much >of the documentation and installation directions for python and some >of its libraries, such as matplotlib, numpy, and scipy. > >I am aware that there are binary installations for the Mac at: > >http://www.pythonmac.org/packages/ > >But no binary for scipy at this site for the 2.5x version of python. > >I am also aware of the enthought distribution for windows and the >installer at: > >http://code.enthought.com/downloads/enthon-python2.4-1.0.0.exe > >I am looking for advice from experienced educators who have advised >their students on installation on Mac and Windows. These students at >our school are unlikely to have the expertise to unzip, configure, >compile, etc., and need a "one-click" solution to install the >software needed. > >Can anyone share their experience with their students and/or give >advice? > >Thanks. > >David Arnold >College of the Redwoods >http://online.redwoods.edu/instruct/darnold/ >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.org >http://projects.scipy.org/mailman/listinfo/scipy-user

1 0

Instruction in math and science
by David Arnold 17 Nov '07

17 Nov '07

All, We are considering using Python and some of its libraries to aid instruction in mathematics and science at our college. I've read much of the documentation and installation directions for python and some of its libraries, such as matplotlib, numpy, and scipy. I am aware that there are binary installations for the Mac at: http://www.pythonmac.org/packages/ But no binary for scipy at this site for the 2.5x version of python. I am also aware of the enthought distribution for windows and the installer at: http://code.enthought.com/downloads/enthon-python2.4-1.0.0.exe I am looking for advice from experienced educators who have advised their students on installation on Mac and Windows. These students at our school are unlikely to have the expertise to unzip, configure, compile, etc., and need a "one-click" solution to install the software needed. Can anyone share their experience with their students and/or give advice? Thanks. David Arnold College of the Redwoods http://online.redwoods.edu/instruct/darnold/

1 0

adaptive simulated annealing (ASA)
by Georg Holzmann 16 Nov '07

16 Nov '07

Hallo! Is there already a python implementation of the adaptive simulated annealing optimization algorithm (maybe a wrapper to the following C library: http://www.ingber.com/ASA-README.html) ? I did quite some google search and did not find something - so any hint is very much appreciated ! Thanks, LG Georg

4 3

Biblioteca_algortimos _geneticos
by Yennifer Santiago 16 Nov '07

16 Nov '07

Hola.. Quisiera saber como se llama la biblioteca de clases de Algoritmos Geneticos dentro del paquete scipy-0.6.0 que se descarga de internet. Necesito ver los metodos para operar con Algoritmos Geneticos con que cuenta esta biblioteca, alli veo varias carpetas pero ninguna referente a Algoritmos Geneticos. Gracias Yennifer Santiago

3 2

inline.weave compile error
by Michael ODonnell 16 Nov '07

16 Nov '07

I am trying to compile some inline c++ code inside python using weave. I always get a similar problem where the compiled file cannot be found (See below output). I am not sure if the problem is with the compiler or something else. I am a new user of scipy and a novice with python so I would appreciate any direction someone can give me because I have not been able to figure out a work around. Thank you, Michael +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I have the following related applications installed: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Python: 2.4.1 (I am using an older version because this is what ESRI GIS application supports) Scipy: scipy-0.6.0.win32-py2.4.exe MinGW: MinGW-5.1.3.exe OS: Windows XP SP2 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ When I test the installation of Weave I get the following output: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> weave.test() Found 1 tests for scipy.weave.ast_tools Found 2 tests for scipy.weave.blitz_tools Found 9 tests for scipy.weave.build_tools Found 0 tests for scipy.weave.c_spec Found 26 tests for scipy.weave.catalog building extensions here: c:\docume~1\michael\locals~1\temp\Michael\python24_compiled\m3 Found 1 tests for scipy.weave.ext_tools Found 0 tests for scipy.weave.inline_tools Found 74 tests for scipy.weave.size_check Found 16 tests for scipy.weave.slice_handler Found 3 tests for scipy.weave.standard_array_spec Found 0 tests for __main__ ...warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations .....warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ............................removing 'c:\docume~1\michael\locals~1\temp\tmpdqudhmcat_test' (and everything under it) error removing c:\docume~1\michael\locals~1\temp\tmpdqudhmcat_test: c:\docume~1\michael\locals~1\temp\tmpdqudhmcat_test\win3224compiled_catalog: Permission denied error removing c:\docume~1\michael\locals~1\temp\tmpdqudhmcat_test: c:\docume~1\michael\locals~1\temp\tmpdqudhmcat_test: Directory not empty .removing 'c:\docume~1\michael\locals~1\temp\tmpw144aycat_test' (and everything under it) ............................................................................................... ---------------------------------------------------------------------- Ran 132 tests in 2.625s OK <unittest.TextTestRunner object at 0x020D6F70> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ When I try to test the following script or any other script I get the following message: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ def prod(m, v): #C++ version nrows, ncolumns = m.shape res = numpy.zeros((nrows, ncolumns), float) code = r""" for (int i=0; i<nrows; i++) { for (int j=0; j<ncolumns; j++) { res(i) += m(i,j)*v(j); } } """ #err = weave.inline(code,['nrows', 'ncolumns', 'res', 'm', 'v'], type_converters=converters.blitz, compiler='mingw32', verbose=2) err = weave.inline(code,['nrows', 'ncolumns', 'res', 'm', 'v'], verbose=2) <weave: compiling> running build_ext running build_src building extension "sc_045cfaf40ef1a0738b1066aaa886a55d7" sources customize Mingw32CCompiler customize Mingw32CCompiler using build_ext customize Mingw32CCompiler customize Mingw32CCompiler using build_ext building 'sc_045cfaf40ef1a0738b1066aaa886a55d7' extension compiling C++ sources C compiler: g++ -mno-cygwin -O2 -Wall compile options: '-IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include -IC:\Python24\PC -c' g++ -mno-cygwin -O2 -Wall -IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include -IC:\Python24\PC -c c:\docume~1\michael\locals~1\temp\Michael\python24_compiled\sc_045cfaf40ef1a0738b1066aaa886a55d7.cpp -o c:\docume~1\michael\locals~1\temp\Michael\python24_intermediate\compiler_c8350d870e6c54e8f29dd7094c2bfb45\Release\docume~1\michael\locals~1\temp\michael\python24_compiled\sc_045cfaf40ef1a0738b1066aaa886a55d7.o Traceback (most recent call last): File "C:\Python24\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py", line 310, in RunScript exec codeObject in __main__.__dict__ File "C:\Documents and Settings\Michael\Application Data\ESRI\ArcToolbox\scripts\test_weave.py", line 179, in ? main() File "C:\Documents and Settings\Michael\Application Data\ESRI\ArcToolbox\scripts\test_weave.py", line 170, in main prod(m, v) File "C:\Documents and Settings\Michael\Application Data\ESRI\ArcToolbox\scripts\test_weave.py", line 44, in prod err = weave.inline(code,['nrows', 'ncolumns', 'res', 'm', 'v'], verbose=2) File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 338, in inline auto_downcast = auto_downcast, File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 447, in compile_function verbose=verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py", line 365, in compile verbose = verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py", line 269, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "C:\Python24\lib\site-packages\numpy\distutils\core.py", line 173, in setup return old_setup(**new_attr) File "C:\Python24\lib\distutils\core.py", line 159, in setup raise SystemExit, error CompileError: error: c:\docume~1\michael\locals~1\temp\tmp2dwbkp: No such file or directory ____________________________________________________________________________________ Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ

1 0

Scipy-AlgoritmosGeneticos
by Yennifer Santiago 16 Nov '07

16 Nov '07

Hola, Por favor necesito información sobre el uso de Scipy, especificamente para aplicaciones con Algoritmos Genéticos. Si tienen o conocen alguna dirección donde pueda encontrar algun tutorial sobre esto. Gracias Yennifer Santiago

4 3

KDE question
by Zachary Pincus 15 Nov '07

15 Nov '07

Hello all, I'm using scipy.stats.gaussian_kde to estimate the a probability density based on some scattered 2D samples. What I would like to do eventually is plot a line that surrounds (say) 90% of the probability density. Clearly this line corresponds to some contour of the density function (which I can extract out easily enough from KDE density estimates on a grid), but I'm not sure how to figure out what exact contour value it is that I want. Given the KDE density estimates on a grid, I could empirically figure out which value is closest, but I was wondering if there's a simpler closed-form solution... (And apologies if it's somehow obvious; I'm feeling a bit foggy-headed about this.) Best, Zach

6 16