Mailman 3 November 2007 - SciPy-User

lil_matrix
by Giovanni Samaey 04 Dec '07

04 Dec '07

Hello all, I have a basic question concerning lil_matrix slice assignments. The following code does not behave as intended : import scipy.sparse as S A = S.lil_matrix((5,5)) A.setdiag(ones(5)) B = S.lil_matrix((6,6)) B[:5,:5]=A B.getnnz() This returns 0 instead of the expected 5. Am I using the code incorrectly ? Giovanni

2 1

Error in scipy.test(10) even after compiling successfully- Mac OS X 10.4.11 Apple GCC 4.0.1
by Joshua Lippai 04 Dec '07

04 Dec '07

Hello all, After building scipy, I ran the scipy tests and got this error in check_integer: ====================================================================== ERROR: check_integer (scipy.io.tests.test_array_import.TestReadArray) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/io/tests/test_array_import.py", line 55, in check_integer from scipy import stats File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/stats/stats.py", line 191, in <module> import scipy.special as special File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/__init__.py", line 8, in <module> from basic import * File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/basic.py", line 8, in <module> from _cephes import * ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so, 2): Symbol not found: __gfortran_pow_r8_i4 Referenced from: /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/special/_cephes.so Expected in: dynamic lookup It would appear it's not finding a symbol for gfrotran in one of the files, and this in turn makes it impossible to import _cephes. How would I go about remedying this?

2 3

Re: [SciPy-user] surface plotting
by Joe Harrington 03 Dec '07

03 Dec '07

Well, I was hoping for a lighter solution, but I gave it a one-hour try. It didn't help that when I did the link to the user docs was broken (it's fixed now). I got so far as installing mayavi2 and trying to figure it out without the doc, but ran out of time and wasn't able to figure out surface plotting my existing numpy array. This was for use in a class and I decided that if I couldn't figure out how to do it in an hour I probably couldn't expect the students to do it at all. It would be good to have a cookbook recipe about how to do surface plotting of a 2D numpy array in mayavi2. When will mayavi2 be available as a deb file? This looks like software that everyone should be able to get in the easiest fashion possible. Thanks, --jh--

6 8

weave and compiler install help
by Michael ODonnell 03 Dec '07

03 Dec '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). 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 gcc-4.1.2-mingw-setup.exe cygwin: 3.2.25 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 This file is created and automatically opens in python: import os import sys sys.path.insert(0,'C:\\Python24\\lib\\site-packages\\numpy\\distutils') from exec_command import exec_command del sys.path[0] cmd = ['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\\scipy\\weave\\blitz', '-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_e6928d48a5ee12fb55c3b29ed6bf49ef4.cpp', '-o', 'c:\\docume~1\\michael\\locals~1\\temp\\Michael\\python24_intermediate\\compiler_921933e1c4e3c013306c4ed6f4c15144\\Release\\docume~1\\michael\\locals~1\\temp\\michael\\python24_compiled\\sc_e6928d48a5ee12fb55c3b29ed6bf49ef4.o'] os.environ = {'TMP': 'C:\\WINDOWS\\TEMP', 'COMPUTERNAME': 'ALDER', 'USERDOMAIN': 'ALDER', 'ARCHOME': 'C:\\arcgis\\arcexe9x', 'COMMONPROGRAMFILES': 'C:\\Program Files\\Common Files', 'PROCESSOR_IDENTIFIER': 'x86 Family 6 Model 13 Stepping 8, GenuineIntel', 'PROGRAMFILES': 'C:\\Program Files', 'PROCESSOR_REVISION': '0d08', 'PATH': 'c:\\mingw\\bin;C:\\Program Files\\Common Files\\Roxio Shared\\DLLShared;C:\\arcgis\\arcexe9x\\bin;C:\\Program Files\\FWTools1.2.2\\pymod;C:\\Program Files\\R\\R-2.5.1\\bin;C:\\Documents and Settings\\Michael\\My Documents\\mod_web\\ems_web\\web-content\\mapserver-4.8.1bin;C:\\cygwin\\bin;C:\\program files\\imagemagick-6.3.6-q16;C:\\Python24;C:\\Program Files\\gs\\gs8.51\\lib;C:\\Program Files\\gnuplot\\bin;C:\\ModisTools\\MRT\\bin;C:\\ModisTools\\LDOPE\\LDOPE_Win_bin\\ANCILLARY;C:\\Documents and Settings\\Michael\\My Documents\\my_home\\py_scripting\\src\\tools;C:\\Program Files\\HEG\\HEG_Win\\bin;C:\\Perl\\site\\bin;C:\\Perl\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\Program Files\\Microsoft SQL Server\\80\\Tools\\Binn\\;C:\\Program Files\\MySQL\\MySQL Server 5.0\\bin;C:\\Program Files\\QuickTime\\QTSystem;C:\\WINDOWS\\system32\\config\\systemprofile\\Local Settings\\Temp;C:\\ModisTools\\MRT\\bin; C:\\ModisTools\\LDOPE\\LDOPE_Win_bin\\ANCILLARY;C:\\Program Files\\R\\R-2.5.1\\bin;;c:\\Program Files\\HEG\\HEG_Win\\bin;c:\\Program Files\\HEG\\HEG_Win\\bin;c:\\Program Files\\HEG\\HEG_Win\\bin', 'SYSTEMROOT': 'C:\\WINDOWS', 'ATHOME': 'C:\\arcgis\\arcexe9x\\arctools', 'SCRIPTING': 'C:\\Documents and Settings\\Michael\\My Documents\\my_home\\py_scripting', 'ARCHOME_USER': 'C:\\arcgis\\arcexe9x', 'TEMP': 'C:\\DOCUME~1\\Michael\\LOCALS~1\\Temp', 'PROCESSOR_ARCHITECTURE': 'x86', 'ANCPATH': 'C:\\ModisTools\\LDOPE\\LDOPE_Win_bin\\ANCILLARY', 'ALLUSERSPROFILE': 'C:\\Documents and Settings\\All Users', 'SESSIONNAME': 'Console', 'ARCINFOFONTSIZE': '8', 'HOMEPATH': '\\Documents and Settings\\Michael', 'USERNAME': 'Michael', 'LOGONSERVER': '\\\\ALDER', 'COMSPEC': 'C:\\WINDOWS\\system32\\cmd.exe', 'QTJAVA': 'C:\\Program Files\\Java\\jre1.6.0_01\\lib\\ext\\QTJava.zip', 'PYTHONPATH': 'C:\\Program Files\\ArcGIS\\bin;C:\\Python24\\Lib\\site-packages\\gdal;C:\\Program Files\\R\\R-2.5.1\\bin;C:\\Documents and Settings\\Michael\\My Documents\\my_home\\py_scripting\\src\\tools;C:\\Documents and Settings\\Michael\\My Documents\\my_home\\py_scripting\\lib;C:\\WINDOWS\\system32\\config\\systemprofile\\Local Settings\\Temp;C:\\cygwin\\bin;C:\\mingw\\bin;c:\\mingw\\bin;C:\\Program Files\\Common Files\\Roxio Shared\\DLLShared;C:\\arcgis\\arcexe9x\\bin;C:\\Program Files\\FWTools1.2.2\\pymod;C:\\Program Files\\R\\R-2.5.1\\bin;C:\\Documents and Settings\\Michael\\My Documents\\mod_web\\ems_web\\web-content\\mapserver-4.8.1bin;C:\\cygwin\\bin;C:\\program files\\imagemagick-6.3.6-q16;C:\\Python24;C:\\Program Files\\gs\\gs8.51\\lib;C:\\Program Files\\gnuplot\\bin;C:\\ModisTools\\MRT\\bin;C:\\ModisTools\\LDOPE\\LDOPE_Win_bin\\ANCILLARY;C:\\Documents and Settings\\Michael\\My Documents\\my_home\\py_scripting\\src\\tools;C:\\Program Files\\HEG\\HEG_Win\\bin;C:\\Perl\\site\\bin;C:\\Perl\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\Program Files\\Microsoft SQL Server\\80\\Tools\\Binn\\;C:\\Program Files\\MySQL\\MySQL Server 5.0\\bin;C:\\Program Files\\QuickTime\\QTSystem;%USERPROFILE%\\Local Settings\\Temp;', 'CLASSPATH': '.;C:\\Program Files\\Java\\jre1.6.0_01\\lib\\ext\\QTJava.zip', 'PLAT': 'win32', 'PYTHONSRC': 'C:\\Python24', 'PGSHOME': 'c:\\Program Files\\HEG\\HEG_Win\\TOOLKIT_MTD', 'PATHEXT': '.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.py;.pdf', 'CLIENTNAME': 'Console', 'FP_NO_HOST_CHECK': 'NO', 'WINDIR': 'C:\\WINDOWS', 'APPDATA': 'C:\\Documents and Settings\\Michael\\Application Data', 'HOMEDRIVE': 'C:', 'ARCINFOFONTNAME': 'Courier New', 'SYSTEMDRIVE': 'C:', 'NUMBER_OF_PROCESSORS': '1', 'ARCGISHOME': 'C:\\Program Files\\ArcGIS\\', 'MRTBINDIR': 'c:\\Program Files\\HEG\\HEG_Win\\bin', 'PROCESSOR_LEVEL': '6', 'MRTDATADIR': 'C:\\ModisTools\\MRT\\data', 'OS': 'Windows_NT', '__COMPAT_LAYER': 'EnableNXShowUI ', 'USERPROFILE': 'C:\\Documents and Settings\\Michael'} s,o = exec_command(cmd, _with_python=0, **{}) f=open('c:\\docume~1\\michael\\locals~1\\temp\\tmp0gk0g_',"w") f.write(str(s)) f.close() f=open('c:\\docume~1\\michael\\locals~1\\temp\\tmpadrrdg',"w") f.write(o) f.close() ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

2 1

1D Correlation on 3D array
by Ryan May 30 Nov '07

30 Nov '07

Hi, I was curious if anyone has a fast non-looping way to calculate 1D correlations on a N-dim array (my case is specifically 3). What i have right now is rather slow: import numpy as N from scipy.signal import correlate ts_data = N.ones((360,1201,17), dtype=N.complex64) for index in N.ndindex(ts_data.shape[:-1]): x = ts_data[index] R = correlate(x, x.conj()) I've looked at just passing in the whole array, but that seems to want to do full N-dim correlation. Thanks, Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

1 0

Re: [SciPy-user] surface plotting
by Joe Harrington 30 Nov '07

30 Nov '07

> For the purposes of your class, I find that a simple imshow or pcolor > of 2D data with a color map is usually good enough to visualize a 2D > array. Surf doesn't really add much unless you are interactively > panning and zooming, when the movement generates extra 3D visual cues. Mostly we use a combination of imshow and ds9 in astronomy. There is a *lot* of zooming and panning, and real-time, interactive colormap and scaling manipulations, and zooming the cursor around and watching what values go under the cursor. If there's a way to do any of those in matplotlib it would be good to know how, but I didn't see it in the manual. The numdisplay interface to ds9 is pretty good, but not perfect, as it interpolates the image before sending it to ds9, which is a throwback to an interface defined in the days of yore. But, the particular application for which surface really stands out is looking at the relative brightnesses of stars. Yeah, you can get an idea of it with a colormap, but green is not three times red, and even shades of gray are hard to divide by eye. Differing heights are easy to do by eye. Within that category, the one thing I simply can't do well with an image display is look at bad pixels. To find these, and find if you've killed them all, you really need to do an edge-on look at a surface plot. With images that are several k by several k, a single pixel just gets swallowed up in an image display. Its spike does not get swallowed up. Also, a good 2D display will examine the histogram and scale to, say 98% of the histogram so that spurious spikes in the data with values of 10**12 don't make it impossible to see the stars. For this particular application, surface really is the only good way I've found. As I said in an earlier post, the matplotlib surface looks fine, except that it is too slow. I'm not sure if that's because the other methods I've used are in compiled code or if there is some better algorithm. But, I've been using surface plots for ~20 years, and the computers back then were slower than current ones by more than the difference between compiled and python code, I think. The IRAF package is open-source and has such an algorithm, though it's in a bowdlerized version of FORTRAN. --jh--

1 0

enthough python: installing sandbox packages
by lorenzo bolla 30 Nov '07

30 Nov '07

Hi all, is there a simple way to install sandbox packages (e.g. arpack) in a Enthough python using tools like easy_install.exe or enstaller.exe? Thanks in advance, L.

2 1

problems installing scipy on windows with cygwin
by lorenzo bolla 30 Nov '07

30 Nov '07

I'm having problems installing scipy on my windows machine (Quad 2.3GHzIntel Pentium processors) using cygwin. Here is the error message: ------------------------- <many lines here> /cygdrive/c/Documents and Settings/bollalo001/My Documents/archive/scipy- 0.6.0/build/src.cygwin-1.5.24-i686-2.5/build/src.cygwin-1.5.24-i686-2.5/scipy/lib/blas/fblasmodule.c:474: undefined reference to `_csrot_' /cygdrive/c/Documents and Settings/bollalo001/My Documents/archive/scipy- 0.6.0/build/src.cygwin-1.5.24-i686-2.5/build/src.cygwin-1.5.24-i686-2.5/scipy/lib/blas/fblasmodule.c:487: undefined reference to `_zdrot_' collect2: ld returned 1 exit status error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.cygwin- 1.5.24-i686-2.5/build/src.cygwin-1.5.24-i686-2.5/build/src.cygwin- 1.5.24-i686-2.5/scipy/lib/blas/fblasmodule.o build/temp.cygwin- 1.5.24-i686-2.5/build/src.cygwin-1.5.24-i686-2.5/fortranobject.o build/temp.cygwin-1.5.24-i686-2.5/build/src.cygwin-1.5.24-i686-2.5/scipy/lib/blas/fblaswrap.o build/temp.cygwin-1.5.24-i686-2.5/build/src.cygwin-1.5.24-i686-2.5 /build/src.cygwin-1.5.24-i686-2.5/scipy/lib/blas/fblas-f2pywrappers.o-L/usr/lib -L/usr/lib/gcc/i686-pc-cygwin/3.4.4 -L/usr/lib/python2.5/config -Lbuild/temp.cygwin-1.5.24-i686-2.5 -lblas -lpython2.5 -lg2c -o build/lib.cygwin-1.5.24-i686-2.5/scipy/lib/blas/fblas.dll" failed with exit status 1 ------------------------- It seems like a LAPACK problem. I tried with both the cygwin provided blas/lapack and with the complete BLAS/LAPACK from netlib. what do you suggest? thank you! L.

1 0

spe file reader (Roper Scientific / Winview)
by Hazen Babcock 29 Nov '07

29 Nov '07

Hello, Does anyone know of a module for reading (and possibly writing) Roper Scientific / Winview .spe formatted files? thanks, -Hazen

2 1

Scipy in XP on VMWare Workstation
by William Purcell 29 Nov '07

29 Nov '07

I am trying to run scipy in XP on VMWare Workstation. The host OS is Ubuntu. When I attempt to start scipy I get the error: ____________________________________________________________________________ C:\Documents and Settings\Administrator>C:\Python25\python.exe C:\Python25\scrip ts\ipython -pylab -p scipy Traceback (most recent call last): File "C:\Python25\scripts\ipython", line 27, in <module> IPython.Shell.start().mainloop() File "C:\Python25\Lib\site-packages\IPython\Shell.py", line 1111, in start return shell(user_ns = user_ns) File "C:\Python25\Lib\site-packages\IPython\Shell.py", line 1008, in __init__ shell_class=MatplotlibShell) File "C:\Python25\Lib\site-packages\IPython\Shell.py", line 74, in __init__ debug=debug,shell_class=shell_class) File "C:\Python25\Lib\site-packages\IPython\ipmaker.py", line 95, in make_IPyt hon embedded=embedded,**kw) File "C:\Python25\Lib\site-packages\IPython\Shell.py", line 562, in __init__ user_ns,b2 = self._matplotlib_config(name,user_ns) File "C:\Python25\Lib\site-packages\IPython\Shell.py", line 463, in _matplotli b_config from matplotlib import backends File "C:\Python25\Lib\site-packages\matplotlib\backends\__init__.py", line 55, in <module> new_figure_manager, draw_if_interactive, show = pylab_setup() File "C:\Python25\Lib\site-packages\matplotlib\backends\__init__.py", line 24, in pylab_setup globals(),locals(),[backend_name]) File "C:\Python25\Lib\site-packages\matplotlib\backends\backend_tkagg.py", lin e 8, in <module> import tkagg # Paint image to Tk photo blitter extension File "C:\Python25\Lib\site-packages\matplotlib\backends\tkagg.py", line 1, in <module> import _tkagg ImportError: DLL load failed: The specified module could not be found. _____________________________________________________________________________________ Has anyone been successful in doing this or have any suggested fixes. Thanks, Bill

1 0