Mailman 3 December 2003 - SciPy-Dev

band matrices in scipy
by Arnd Baecker 05 Jan '04

05 Jan '04

Hi, I am in the progress of wrapping the Lapack dsbev.f routine (for band-matrices). Thanks to the amazing f2py I got pretty far (actually in addition the good docs and Fernandos notes helped a lot!). Once this is finished I would be happy to see this included in scipy ;-). But before this could happen I have a couple of questions (sorry, the text below is long, but I wanted to be explicit ;-): - Is the following way of calling dsbev from python alright, (eg., I omitted ldab on the python side.) Would that parameter be useful to someone so that it is better to expose it (the full details of my few pyf lines are at the end of this mail)? In [7]: MODULENAME.dsbev? Type: fortran String Form: <fortran object at 0x4028ebf0> Namespace: Interactive Docstring: dsbev - Function signature: w,z,info = dsbev(ab,[compute_v,lower]) Required arguments: ab : input rank-2 array('d') with bounds (ldab,*) Optional arguments: compute_v := 1 input int lower := 0 input int Return objects: w : rank-1 array('d') with bounds (n) z : rank-2 array('d') with bounds (ldz,ldz) info : int - How can one supply better doc-strings to this routine? I.e., help(MODULENAME.dsbev) just gives "Help on fortran: <fortran object>" and scipy.info gives the same as ? from Ipython. I would like to add a more detailed description and an example. Is this somehow possible to do from within the .pyf wrapper? (I know that this is a pure f2py question, so maybe I should ask this question as well on the f2py mailing list...) - And one more technical aspect (before I forget about it): Is the wrapping done such that for _large_ matrices no unnecessary copies of arrays are made? - One thing which puzzled me a bit (presumably it is alright) concerns the return object z which contains the eigenvectors if compute_v=1. For compute_v=0 I changed ldz in the wrapper such that it is of length 1 (it is never referenced by dsbev.f). So if someone is just interested in eigenvalues and not eigenvectors a dummy variable for z has to be given. Is this alright (for a more "low" level routine like this)? In principle one could write a wrapper a la scipy.linalg.eig for the band matrices, but for my purposes I don't mind about the (sometimes needed) dummy variable. - Is the following correct? To get this into scipy.linalg.flapack the lines from MODULENAME.pyf have to be added to generic_flapack.pyf and <tchar=s,d> and <type_in_c>* and <type_in> have to be added at the corresponding place. And that's all? - Unittests: I think it would be good to have a few unit-tests for these routines. Presently I just created a sample 10x10 band matrix (see below), converted this to upper band storage and compared the eigenvalues/eigenvectors of scipy.linalg.eig with those of dsbev. In principle one should do this for both upper and lower triangle storage and for single and double. Would something like that be a reasonable unit-test for inclusion in scipy or is there some better approach (better test-matrices etc.)? - Further routines I am thinking of wrapping in this context a) for symmetric band matrices: dsbevd, dsbevx b) for Hermitian band matrices: zhbev, zhbevd, zhbevx and their single precision partners. Any opinions? Many thanks, Arnd ############################# And here the full example plus test: MODULENAME.pyf: # ------ snip here ------------------- ! -*- f90 -*- python module MODULENAME ! in interface ! in :MODULENAME !subroutine dsbev(ab,compute_v,lower) ! in :MODULENAME:dsbev.f subroutine dsbev(ab,compute_v,lower,n,ldab,kd,w,z,ldz,work,info) ! in :MODULENAME:dsbev.f callstatement (*f2py_func)((compute_v?"V":"N"),(lower?"L":"U"),&n,&kd,ab,&ldab,w,z,&ldz,work,&info) callprotoargument char*,char*,int*,int*,double*,int*,double*,double*,int*,double*,int* double precision dimension(ldab,*) :: ab integer optional,intent(in):: compute_v = 1 check(compute_v==1||compute_v==0) compute_v integer optional,intent(in),check(lower==0||lower==1) :: lower = 0 ! FIXME: does one really need the ldab as optional argument ? !integer optional,check(shape(ab,0)==ldab),depend(ab) :: ldab=shape(ab,0) integer intent(hide),depend(ab) :: ldab=shape(ab,0) integer intent(hide),depend(ab) :: n=shape(ab,1) integer intent(hide),depend(ab) :: kd=shape(ab,0)-1 double precision dimension(n),intent(out),depend(n) :: w double precision dimension(ldz,ldz),intent(out),depend(ldz) :: z ! For compute_v=1 z is used and contains the eigenvectors integer intent(hide),depend(n) :: ldz=compute_v?n:1 double precision dimension(ldz,ldz),depend(ldz) :: z double precision dimension(MAX(1,3*n-1)),intent(hide),depend(n) :: work integer intent(out)::info end subroutine dsbev end interface end python module MODULENAME ! This file was auto-generated with f2py (version:2.37.233-1545). ! See http://cens.ioc.ee/projects/f2py2e/ ! and then modified ... # ------ snip here ------------------- Then (dsbev.f from lapack is needed for this) f2py --debug-capi -c MODULENAME.pyf dsbev.f -llapack and a small test is ########### snip here ########### import MODULENAME from Numeric import * from scipy import diag,linalg N=10 fullmat=diag(-1.0*ones(N-1),-1)+diag(-1.0*ones(N-1),1)+diag(1.0*ones(N)) KD=2 # number of diagonals above the diagonal LDAB=KD+1 mat=zeros( (LDAB,N),typecode=Float) for i in arange(LDAB): # Transform to band matrix mat[LDAB-i-1,i:N]=diag(fullmat,i) w,evec,info=MODULENAME.dsbev(mat) w_lin,evec_lin=linalg.eig(fullmat) print sort(w)-sort(w_lin.real) print evec[:,0] print evec_lin[:,0] ########### snip here ###########

3 3

Linear filter
by Claes Hagström 28 Dec '03

28 Dec '03

Hi! About a year ago I noted that the linear filter (signal.lfilter) had a bug when filtering 3D matrices: http://www.scipy.net/pipermail/scipy-user/2002-March/000201.html Working in Unix I made a fix in the sigtoolsmodule.c RawFilter code: while (num_loops--) { filt(ptrb, ptra, ptrX, ptrY, ptrVf, filt_size, len, stride_X, stride_Y); incr = increment(loop_index, ndims, max_index); /* Returns number of N-D indices incremented. */ k = ndims - incr; if (num_loops > 0) { /* Adjust index array and move pointers to right place for next iteration */ if ( k==0 && ndims==2 ) { ptrX -= loop_strides_X[1]*(max_index[1]-1); /* Stride information */ ptrY -= loop_strides_Y[1]*(max_index[1]-1); /* 20020304 */ } ptrX += loop_strides_X[k]; /* Stride information */ ptrY += loop_strides_Y[k]; which I think fixes the problem for the 3D case I now increasingly work in windows, so I wonder if you would consider fixing the problem I haven't been able to compile the fix and make it work in windows yet. Claes Hagström -- Using M2, Opera's revolutionary e-mail client: http://www.opera.com/m2/

1 0

More OSX fun
by Robert Kern 26 Dec '03

26 Dec '03

I have managed to compile scipy on Mac OS X using unstable Fink's Python, ATLAS, and FFTW. I fixed the problem that prevented Chris Fonnesbeck from compiling, but as there are no unittests, I'm not sure it totally works. The fix is a bit of a hack, but it compiles. Turns out some of the enum names in supermatrix.h are #defined constants in some header. My grep-fu hasn't yet revealed where they are from, yet, but I can conditionally #undef them. I also fixed a problem in fastumath by porting in some changes from Numeric 23.1's umath's logical_* functions to address the same problem. Unfortunately, porting in similar changes from the equal, less, greater, etc. functions breaks things. I'll look into that some more when I can steal some more time. Below are the last two failures from the tests. They are errors in numerical accuracy only. ====================================================================== FAIL: check_bei_zeros (scipy.special.basic.test_basic.test_bei_zeros) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 580, in check_bei_zeros -7.940178689168587]),11) File "/sw/lib/python2.3/site-packages/scipy_test/testing.py", line 635, in assert_array_almost_equal assert cond,\ AssertionError: Arrays are not almost equal (mismatch 20.0%): Array 1: [-2.294439682614 -4.073155089072 -5.512395729664 -6.78129444599 -7.940178689185] Array 2: [-2.294439682614 -4.073155089072 -5.512395729664 -6.78129444599 -7.940178689169] ====================================================================== FAIL: check_nrdtrimn (scipy.special.basic.test_basic.test_cephes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 344, in check_nrdtrimn assert_equal(cephes.nrdtrimn(0.5,1,1),1.0) File "/sw/lib/python2.3/site-packages/scipy_test/testing.py", line 546, in assert_equal assert desired == actual, msg AssertionError: Items are not equal: DESIRED: 1.0 ACTUAL: 0.99999999999999989 ---------------------------------------------------------------------- Ran 1028 tests in 9.264s FAILED (failures=2) -- Robert Kern rkern(a)ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter

1 0

An attempt to get Weave working on OSX
by Aza Raskin 26 Dec '03

26 Dec '03

I am attempting to get weave to work on OSX— and Linux too (RH 9)— however I am not able to get even the simplest weave.inline calls to work. On my OSX, box I have Python 2.3 and gcc 3.1 with a working version of wxPython 2.4.1.2. On my Linux box, I have Python 2.3.3 and gcc 3.2.2 with wxPython 2.4.2.4. Both give this error (although this particular message is from my OSX box): >>> import weave >>> weave.inline('1+1') In file included from /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/cxxsupport.cxx:6: /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1143: no class template named `random_access_iterator' in `std' /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1279: no class template named `random_access_iterator' in `std' /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1409: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1410: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1411: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1412: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1413: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: ` typename Py::SeqBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1414: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1416: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1417: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1418: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1419: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1420: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: ` typename Py::SeqBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:1421: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: ` typename Py::MapBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: ` typename Py::MapBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2348: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: ` typename Py::MapBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: ` typename Py::MapBase<T>::iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2349: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: ` typename Py::MapBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: ` typename Py::MapBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2350: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: ` typename Py::MapBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: implicit typename is deprecated, please see the documentation for details /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: ` typename Py::MapBase<T>::const_iterator' is implicitly a typename /Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/CXX/Objects.hxx:2351: warning: implicit typename is deprecated, please see the documentation for details Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/inline_tools.py", line 327, in inline auto_downcast = auto_downcast, File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/inline_tools.py", line 426, in compile_function verbose=verbose, **kw) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/ext_tools.py", line 349, in compile verbose = verbose, **kw) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/build_tools.py", line 194, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/ distutils/core.py", line 166, in setup raise SystemExit, "error: " + str(msg) weave.build_tools.CompileError: error: command 'gcc' failed with exit status 1 What am I doing wrong? -- Aza Raskin

2 1

FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson)
by Nils Wagner 16 Dec '03

16 Dec '03

====================================================================== FAIL: check_normal (scipy.stats.morestats.test_morestats.test_anderson) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy/stats/tests/test_morestats.py", line 49, in check_normal assert(scipy.all(A < crit[-2:])) AssertionError ---------------------------------------------------------------------- Ran 1028 tests in 3.709s FAILED (failures=1) <unittest.TextTestRunner object at 0x43954e0c> >>> scipy.__version__ '0.2.1_251.4492' >>>

2 1

AttributeError:intel_itanium_fortran_compiler instance has no attribute 'version'
by Nils Wagner 14 Dec '03

14 Dec '03

Traceback (most recent call last): File "setup.py", line 127, in ? setup_package(ignore_packages) File "setup.py", line 108, in setup_package url = "http://www.scipy.org", File "scipy_core/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/usr/local/lib/python2.3/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/local/lib/python2.3/distutils/dist.py", line 907, in run_commands self.run_command(cmd) File "/usr/local/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() File "/usr/local/lib/python2.3/distutils/command/build.py", line 107, in run self.run_command(cmd_name) File "/usr/local/lib/python2.3/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/local/lib/python2.3/distutils/dist.py", line 926, in run_command cmd_obj.ensure_finalized() File "/usr/local/lib/python2.3/distutils/cmd.py", line 117, in ensure_finalized self.finalize_options() File "scipy_core/scipy_distutils/command/build_flib.py", line 177, in finalize_options verbose = self.verbose) File "scipy_core/scipy_distutils/command/build_flib.py", line 1671, in find_fortran_compiler compiler = compiler_class(fc,f90c,verbose = verbose) File "scipy_core/scipy_distutils/command/build_flib.py", line 1260, in __init__ if not self.get_version(): File "scipy_core/scipy_distutils/command/build_flib.py", line 617, in get_version if self.version is not None: AttributeError: intel_itanium_fortran_compiler instance has no attribute 'version' nwagner@linux:~/cvs/scipy>

2 1

CVS build on windows -- ATLAS_INFO issues
by eric jones 14 Dec '03

14 Dec '03

Hey guys, I just tried building from CVS on windows and got the following error (perhaps line numbers are slightly off due to my hacking around on it): c:\mingw\bin\gcc.exe -O2 -w -Wstrict-prototypes -DATLAS_INFO="None" -Ic:\python2 3\include -Ic:\python23\PC -c Lib\linalg\atlas_version.c -o build\temp.win32-2.3 \Release\lib\linalg\atlas_version.o Lib/linalg/atlas_version.c: In function `initatlas_version': Lib/linalg/atlas_version.c:14: `None' undeclared (first use in this function) Lib/linalg/atlas_version.c:14: (Each undeclared identifier is reported only once Lib/linalg/atlas_version.c:14: for each function it appears in.) error: command 'gcc' failed with exit status 1 It appears that ATLAS_INFO is getting set to None instead of a correct value and this isn't acceptable to the printf statement in the .c code. I haven't built in a while, so perhaps something else is wrong? I am on windows XP, python 2.3, an older atlas (don't remember version), and using gcc 3.2. thanks, eric

2 1

Scipy cannot handle singular eigenvalue problems
by Nils Wagner 10 Dec '03

10 Dec '03

Hi all, Scipy cannot handle singular eigenvalue problems. Note, that both matrices are singular. from scipy import * A = array(([1.,-1.],[-1.,1.])) B = array(([1.0,0.0],[0.0,0.0])) w,vr = linalg.eig(A,B) print w print vr Traceback (most recent call last): File "sevp.py", line 4, in ? w,vr = linalg.eig(A,B) File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 109, in eig return _geneig(a1,b,left,right,overwrite_a,overwrite_b) File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 68, in _geneig vr = _make_complex_eigvecs(w, vr, t) File "/usr/lib/python2.3/site-packages/scipy/linalg/decomp.py", line 29, in _make_complex_eigvecs vnew.real = scipy_base.take(vin,ind[::2],1) ValueError: matrices are not aligned for copy Any suggestion ? The output of MATLAB is enclosed as well (out.ps) Nils

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Apparently bug in filter_design.py
by Joachim Saul 09 Dec '03

09 Dec '03

Hi there, while using a IIR filter designed using scipy.signal.iirfilter, an error occurs within lp2bp() and potentially in the other similar routines as well, where the line aprime[Dp-j] = val occurs. Since val can be complex, and aprime be e.g. of double type, an error may be (and im my situation is) issued: TypeError: can't convert complex to float; use abs(z) Which, in turn, doesn't quite make sense, at least *if* a real part of the values in aprime may be negative. A quick fix would be to modify lp2bp(): replace bprime = Num.zeros(Np+1,artype) aprime = Num.zeros(Dp+1,artype) by bprime = Num.zeros(Np+1, 'D') aprime = Num.zeros(Dp+1, 'D') and just before "return" add bprime = bprime.astype(artype) aprime = aprime.astype(artype) This would force aprime and bprime to be always double precision complex (which should never harm) and at the end cast to the originally wanted type. Since this is used in filter design only, the overhead though the conversion would be negligible. Any comments? Cheers, Joachim

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[SciPy-dev] [Fwd: [Math-atlas-devel] testing for stable: please help]
by Nils Wagner 08 Dec '03

08 Dec '03

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