Mailman 3 December 2002 - SciPy-User

Using the mouse in gplt ?
by Yann Le Du Jan. 22, 2003

Jan. 22, 2003

Hello, I have gnuplot installed, that I use outside of SciPy with the mouse enabled (I can click inside the gnuplot frame and do things like zoom, rotate, etc). But when I use it through SciPy, the mouse is not enabled. Does anyone know how to enable the mouse in gplt plot windows ? Yann

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Help:Why Can not import scipy?
by loo yee Dec. 30, 2002

Dec. 30, 2002

I installed Python 2.2,Numeric 22.0, Numarray 0.4, wyPython 2.3.4.2u and my OS is WinXP, scipy version is 0.2.0_alpha_152.4463 But when I import scipy in PythonWin 2.2.1,there is an error >>> import gui_thread >>> <wxPython imported> >>> from scipy import * Traceback (most recent call last): File "<interactive input>", line 1, in ? File "C:\PYTHON22\Lib\site-packages\scipy\__init__.py", line 49, in ? import special, io, linalg, stats, fftpack File "C:\PYTHON22\Lib\site-packages\scipy\stats\__init__.py", line 195, in ? from stats import * File "C:\PYTHON22\Lib\site-packages\scipy\stats\stats.py", line 1500, in ? import distributions File "C:\PYTHON22\Lib\site-packages\scipy\stats\distributions.py", line 18, in ? from scipy_base import atleast_1d, polyval, angle, ceil, insert, extract, \ ImportError: cannot import name insert >>> and when i import scipy in IDLE,there is another error: >>> import gui_thread >>> from scipy import * Traceback (most recent call last): File "<pyshell#1>", line 1, in ? from scipy import * File "C:\PYTHON22\Lib\site-packages\scipy\__init__.py", line 49, in ? import special, io, linalg, stats, fftpack File "C:\PYTHON22\Lib\site-packages\scipy\linalg\__init__.py", line 42, in ? from basic import * File "C:\PYTHON22\Lib\site-packages\scipy\linalg\basic.py", line 11, in ? from lapack import get_lapack_funcs File "C:\PYTHON22\Lib\site-packages\scipy\linalg\lapack.py", line 9, in ? from scipy_distutils.misc_util import PostponedException ImportError: cannot import name PostponedException >>> What can i do? Regards, LuYi

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warning: compilation failed. Executing as python code
by Joseph O'Ruanaidh Dec. 23, 2002

Dec. 23, 2002

warning: compilation failed. Executing as python code I am getting this message when running scipy.test_all() under Redhat 7.1. Has this anyhing to do with the crappy compiler? gcc version 2.96 20000731 (Red Hat Linux 7.1 2.96-85) Joe 2nd run(Numeric,compiled,speed up): 1.3802, 18.1977, 0.0758 ...................................................................................... ---------------------------------------------------------------------- Ran 188 tests in 691.652s OK >>> P.S. results:

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Re: [SciPy-user] Sparse Compilation Issues (again)
by Costas Malamas Dec. 19, 2002

Dec. 19, 2002

>Ahh. You want something else then. Sparse is not a sparse array, it is >only a sparse matrix. Sparse matrices have been well studied and there >are many good storage mechanisms and algorithms using them. > >Sparse arrays, on the other hand are usually just implemented as >dictionaries. I know of no sparse array implementation for any >array-oriented environment. You could make your own without too much >difficulty, supporting just the operations you care about. > >Which operations do you want to do on these "sparse arrays"? > Well, pretty much everything NumPy supplies --array arithmetic and inner products at least. I am looking for a quick way to a prototype, a cleaner solution will have to wait. I did find a pure-python implementation of just what you described: dict-based sparse array, but I doubt that a python dictionary could handle 1e9 members in a reasonable amount of time. I took a look at NumPy's arrayobject.c; as I said, my C is rusty but it looks simple enough to create a default-value array that "looks" like a NumPy array... Thanks again, Costas _________________________________________________________________ Tired of spam? Get advanced junk mail protection with MSN 8. http://join.msn.com/?page=features/junkmail

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Re: [SciPy-user] Sparse Compilation Issues (again)
by Costas Malamas Dec. 19, 2002

Dec. 19, 2002

Nope, straight checkout from CVS. I had the same thought as you, so I checked it out twice with the same results. I also looked for SuperLU itself, but the only version I found out there was 2.0 which (surprise) doesnt compile with sparse (I think it's bundled with 1.2?)... Another question that's been bugging me now that I've been staring at sparse's source code... it looks to me like it's just a sparse matrix equation solver. I will need to instantiate very large "cubes", say 1e3x1e3x1e4, with low population densities (max around 20%, typically 5-10%). This 1e10 cube doesn't even allocate in Numpy/Scipy (smaller cubes actually crash my Win2K laptop), so I was _hoping_ that scipy.sparse would implement a "default value" array: i.e. the operation: x = zeros([1e3,1e3,1e3]) would be instantaneous as x would be an empty "shell" with 0 as it's default value. However, I don't see a capability like that in scipy.sparse's source code though. Am I missing it? is there anything like this for SciPy/NumPy? Thanks for all your help, Costas >From: Travis Oliphant <oliphant.travis(a)ieee.org> >Reply-To: scipy-user(a)scipy.net >To: scipy-user(a)scipy.net >Subject: Re: [SciPy-user] Sparse Compilation Issues (again) >Date: 19 Dec 2002 08:14:10 -0700 > >On Thu, 2002-12-19 at 01:48, Costas Malamas wrote: > > > > I've been trying to compile sparse on win32 to no avail. I tried both > > mingw32 with pre-built ATLAS and LAPACK and Cygwin, both with the Scipy >CVS. > > Both setups work OK (well, cluster also fails on Cygwin, but I took it > > out), and they crash more-or-less with the same error ("parse error >before > > numeric constant", below). Extensive Googling shows that this means a > > numeric constant is already used somewhere else, but I got no solution >to > > work around it... > > > > Ideas? > > > > Thanks, > > > > Costas > > > > > > gcc -shared -Wl,--enable-auto-image-base > > build/temp.cygwin-1.3.17-i686-2.2/convo > > lve.o build/temp.cygwin-1.3.17-i686-2.2/fortranobject.o > > build/temp.cygwin-1.3.17 > > -i686-2.2/convolvemodule.o -Lbuild/temp.cygwin-1.3.17-i686-2.2 > > -L/usr/lib/python > > 2.2/config -Lbuild/temp.cygwin-1.3.17-i686-2.2 -ldfftpack -lpython2.2 > > -lc_misc - > > lcephes -lrootfind -lsuperlu -lmyblas -lg2c -o > > build/lib.cygwin-1.3.17-i686-2.2/ > > scipy/fftpack/convolve.dll > > building 'scipy.sparse._zsuperlu' extension > > gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -DUSE_DL_IMPORT > > -I/usr/include/pyt > > hon2.2 -c /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c -o > > build/temp. > > cygwin-1.3.17-i686-2.2/_zsuperlumodule.o > > In file included from > > /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/zsp_defs > > .h:23, > > from > > /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c:26 > > : > > /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/supermatrix.h:19: >parse > > error > > before numeric constant > > /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/supermatrix.h:21: >parse > > error > > before numeric constant > > >Are you sure you have the correct CVS files? This is odd for there to >be a parse error in SuperLU. Did you modify this file somehow or not >get a complete checkout. > >You could erase this file and check it out again. You might try that >for that whole SuperLU directory. > >Good luck, > >-Travis > > >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.net >http://www.scipy.net/mailman/listinfo/scipy-user _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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Sparse Compilation Issues (again)
by Costas Malamas Dec. 19, 2002

Dec. 19, 2002

I've been trying to compile sparse on win32 to no avail. I tried both mingw32 with pre-built ATLAS and LAPACK and Cygwin, both with the Scipy CVS. Both setups work OK (well, cluster also fails on Cygwin, but I took it out), and they crash more-or-less with the same error ("parse error before numeric constant", below). Extensive Googling shows that this means a numeric constant is already used somewhere else, but I got no solution to work around it... Ideas? Thanks, Costas gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.3.17-i686-2.2/convo lve.o build/temp.cygwin-1.3.17-i686-2.2/fortranobject.o build/temp.cygwin-1.3.17 -i686-2.2/convolvemodule.o -Lbuild/temp.cygwin-1.3.17-i686-2.2 -L/usr/lib/python 2.2/config -Lbuild/temp.cygwin-1.3.17-i686-2.2 -ldfftpack -lpython2.2 -lc_misc - lcephes -lrootfind -lsuperlu -lmyblas -lg2c -o build/lib.cygwin-1.3.17-i686-2.2/ scipy/fftpack/convolve.dll building 'scipy.sparse._zsuperlu' extension gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -DUSE_DL_IMPORT -I/usr/include/pyt hon2.2 -c /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c -o build/temp. cygwin-1.3.17-i686-2.2/_zsuperlumodule.o In file included from /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/zsp_defs .h:23, from /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c:26 : /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/supermatrix.h:19: parse error before numeric constant /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/supermatrix.h:21: parse error before numeric constant In file included from /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c:27 : /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/util.h:95: warning: function d eclaration isn't a prototype /d/Projects/scipy/scipy_cygwin/sparse/SuperLU/SRC/util.h:101: warning: function declaration isn't a prototype /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c: In function `NRFormat_f rom_spMatrix': /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c:46: warning: implicit de claration of function `zCreate_CompRow_Matrix' /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c: In function `Py_zgssv': /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c:163: warning: implicit d eclaration of function `superlu_delete_allkeys' /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c: At top level: /d/Projects/scipy/scipy_cygwin/sparse/_zsuperlumodule.c:190: warning: function d eclaration isn't a prototype error: command 'gcc' failed with exit status 1 _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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wxWindow_GetClientSizeTuple problem using plt.plot
by David Humphrey Dec. 19, 2002

Dec. 19, 2002

Yesterday, I installed SciPy-0.2.0_alpha_144.4350_src.tar.gz wxPython 2.3.3.1 for Python 2.2 wxWindows 2.2.9 Numeric 22.0 I've had Python 2.2.1 from www.python.org installed for several weeks. On a Windows NT 4.0 SP6a machine. I spent some time getting used to SciPy as I have some prior experience with each of the other packages. At the moment, I'm interested in plt.plot(). While I've been able to get a few simple 2-D plots to work, I'm having a proble with the following code residing in the file test2.py: import gui_thread from Numeric import * from scipy import plt from scipy import * binz = array([-162., -126., -90., -54., -18., 18., 54., 90., 126., 162.],Float) countz = array([ 9006, 1621, 26248, 2912, 7096, 8537, 1533, 22517, 1224, 6563],Float) plt.plot(binz,countz) When I execute this script, I get the following results: $ python test2.py <wxPython imported> >>> Traceback (most recent call last): File "D:\Utils\Python22\Lib\site-packages\scipy\plt\wxplt.py", line 143, in on_paint self.draw(wx.wxPaintDC(self)) File "D:\Utils\Python22\Lib\site-packages\scipy\plt\wxplt.py", line 411, in draw t1 = time.clock();self.reset_size(dc);t2 = time.clock() File "D:\Utils\Python22\Lib\site-packages\scipy\plt\wxplt.py", line 357, in reset_size new_size = self.GetClientSizeTuple() File "d:\Utils\Python22\lib\site-packages\wxPython\windows.py", line 194, in GetClientSizeTuple val = apply(windowsc.wxWindow_GetClientSizeTuple,(self,) + _args, _kwargs) AttributeError: 'NoneType' object has no attribute 'wxWindow_GetClientSizeTuple' 17:52:44: Debug: c:\projects\wx\src\msw\app.cpp(439): 'UnregisterClass(canvas)' failed with error 0x00000584 (class still has open windows.). Exception exceptions.TypeError: "'NoneType' object is not callable" in <bound method wxPaintDC.__del__ of <C wxPaintDC instance at _274db50_wxPaintDC_p>> ignored Can anyone tell me what I'm doing wrong? Regards, David Humphrey Director, Technical Services Bell Geospace, Inc

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Undefined symbol problems (flapack/min and clapack/clapack_sgetri)
by Fernando Perez Dec. 17, 2002

Dec. 17, 2002

Hi all, I'm trying to install the SciPy-0.2.0_alpha_144.4350_src.tar.gz to bring my scipy installation up to date. I successfully installed it but I'm getting two import errors: In [1]: import scipy.linalg.flapack --------------------------------------------------------------------------- ImportError Traceback (most recent call last) ? ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/flapack.so: undefined symbol: min In [2]: import scipy.linalg.clapack --------------------------------------------------------------------------- ImportError Traceback (most recent call last) ? ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgetri Any ideas? For the second problem, I read the instructions in INSTALL.txt and followed the suggested steps: Using ATLAS 3.2.1 ----------------- If import clapack fails with the following error ImportError: .../clapack.so : undefined symbol: clapack_sgetri then you most probably have ATLAS 3.2.1 but linalg module was built for newer versions of ATLAS. Fix: 1) Remove scipy/linalg/clapack.pyf 2) Rebuild/reinstall scipy. But this doesn't seem to fix anything (the clapack.pyf file is automatically recreated and the problem persists). I have ATLAS installed, this is the full output of system_info: root[scipy_distutils]# python system_info.py atlas_info: FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib/atlas'] include_dirs = ['/usr/local/include/atlas'] blas_info: NOT AVAILABLE blas_src_info: NOT AVAILABLE dfftw_info: NOT AVAILABLE dfftw_threads_info: NOT AVAILABLE djbfft_info: NOT AVAILABLE fftw_info: NOT AVAILABLE fftw_threads_info: NOT AVAILABLE lapack_info: NOT AVAILABLE lapack_src_info: NOT AVAILABLE sfftw_info: NOT AVAILABLE sfftw_threads_info: NOT AVAILABLE x11_info: FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] My system is a Mandrake 8.2 box. Any help would be greatly appreciated. Cheers, f.

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Re: [SciPy-user] Sparse Matrices (SciPy or elsewhere)?
by Costas Malamas Dec. 17, 2002

Dec. 17, 2002

Well, I need this to build a complicated prototype --I need Sparse to work, but not that well; if the prototype works, then things will change :-) I've tried two different approaches: 1) Tried to compile SciPy CVS on current Cygwin (gcc 3.2, python 2.2.1). I got ATLAS and LAPACK and all of SciPy compiling fine, but not sparse. I worked around the last error I posted on this list, but then I run into symbol issues and gave up. 2) I've now tried to compile SciPy CVS using gcc-mingw as specified on the website. I am running into the issue that my ATLAS and LAPACK are linked against another python (Cygwin's 2.2.1, whereas I am running 2.1 win32 on my box for another project). I downloaded pre-built ATLAS but I don't know if this will work, since it's probably built with another compiler (are there any ABI issues w/ ATLAS??; I am guessing not, but I'd like to be sure) If I go with (2), can I use pre-built ATLAS and LAPACK? Also, how did you compile sparse on Linux? with its makefile (which looks a bit out-of-date) or with setup_sparse.py? Thanks for all your help, Costas >From: Travis Oliphant <oliphant.travis(a)ieee.org> >To: Costas Malamas <costasm(a)hotmail.com> >Subject: Re: [SciPy-user] Sparse Matrices (SciPy or elsewhere)? >Date: 16 Dec 2002 22:32:50 -0700 > >On Mon, 2002-12-16 at 14:58, Costas Malamas wrote: > > Travis, > > > > I have tried my best to get scipy/sparse to compile. Can you point me >to > > which version is compiling for you? on what OS? How (makefile or > > setup_sparse.py)? > > > >I'm sorry I haven't been able to help you more. I would like to see >sparse work more reliably, but I have not had the time to make it >happen. > >I use Mandrake-9.0 (it worked on 8.2 too) which uses gcc 3.2 and >python2.2 > >When I saw "worked" I mean it compiled and loaded in python. There is >no doubt a few bugs. > >I just checked it again and it is compiling and loading for me. Can you >isolate your problem? Did you check the CVS version of SciPy out? > > >Good luck, > >-Travis _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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Accessing modules in packages
by Dave Bazell Dec. 17, 2002

Dec. 17, 2002

I am trying to use scipy.cluster.vq.kmeans. I have imported scipy: > import scipy and tried cluster.vq.kmeans(..) but I get an error "no module vq in cluster" or something like that. I have tried from scipy import * from scipy.cluster import * and from scipy.cluster.vq import * but none of these allow me to access cluster.vq.kmeans. If I copy the vq.py file to my working directory and do import vq then I can access it. What am I doing wrong? I am sure this is a simple thing to answer and displays my current (but decreasing) ignorance of python. Thanks, Dave Bazell

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