Mailman 3 February 2005 - SciPy-Dev

Error in savemat
by Larsson Omberg 27 Feb '05

27 Feb '05

Hi: I have been using savemat in mio.py to save numerical arrays but ran into problem of saving text arrays. The issue seems to be that the 'c' typecode is not included in the storage dictionary. According to the level 4 mat file format it should be represented by a P=5. I have included a diff of the edited file. I also include a sample python script that crashes the original code. Could this be included in the scipy code? /larsson *** mio.py 2005-02-27 20:17:38.000000000 -0600 --- /SciPy_complete-0.3.2/build/lib.linux-i686-2.3/scipy/io/mio.py 2003-12-13 07:44:50.000000000 -0600 *************** *** 787,793 **** This saves the arrayobjects in the given dictionary to a matlab Version 4 style .mat file. """ ! storage = {'D':0,'d':0,'F':1,'f':1,'l':2,'i':2,'s':3,'b':5,'c':5,} if filename[-4:] != ".mat": filename = filename + ".mat" fid = fopen(filename,'wb') --- 787,793 ---- This saves the arrayobjects in the given dictionary to a matlab Version 4 style .mat file. """ ! storage = {'D':0,'d':0,'F':1,'f':1,'l':2,'i':2,'s':3,'b':5} if filename[-4:] != ".mat": filename = filename + ".mat" fid = fopen(filename,'wb') from scipy import * from scipy.io import savemat dict={} dict['names'] = array(['hello', 'there', 'ha']) savemat('test', dict)

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Delivery by mail
by Eric 26 Feb '05

26 Feb '05

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Bug in matfuncs.py
by Nils Wagner 25 Feb '05

25 Feb '05

I am reporting a bug in matfuncs.py Python 2.3.3 (#1, Feb 5 2005, 16:22:10) [GCC 3.3.3 (SuSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy import * numerix Numeric 23.7 >>> a = zeros((2,2),Float) >>> linalg.expm(a) Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/scipy/linalg/matfuncs.py", line 32, in expm e = int(floor(val)) OverflowError: cannot convert float infinity to long >>> linalg.expm2(a) array([[ 1., 0.], [ 0., 1.]]) >>> linalg.expm3(a) array([[ 1., 0.], [ 0., 1.]]) The matrix exponential is defined via it's series expansion exp(x) = 1 + x+ x^2/2! + x^3/3! + \dots + x^n/n! So exp(zeros((m,m),Float) is the identity of order m. Nils

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SciPy.org and Enthought.com scheduled downtime today at ~12 CST
by Joe Cooper 24 Feb '05

24 Feb '05

Hi all, Both SciPy.org and Enthought.com and all of the services that they host will be taken offline today at around noon CST. We are moving upstairs today and taking the servers with us. SBC willing, the servers will be out of service for no more than an hour or so. Anyway, if you're planning a check-in for lunchtime today, hold off a while, or get it in before then. ;-) Thanks!

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Pade approximants
by Nils Wagner 23 Feb '05

23 Feb '05

Hi all, Has someone written a wrapper for the FORTRAN subroutine pade which is available through http://lib-www.lanl.gov/numerical/bookfpdf/f5-12.pdf It would be nice to have a function called pade in scipy :-) . Any comments or suggestions ? Nils

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A faster version of cosm
by Nils Wagner 23 Feb '05

23 Feb '05

Hi all, Please find attached a small program illustrating the computation of the matrix cosine cosm(a). It's faster than the current implementation. Details can be found in a recent report http://www.maths.man.ac.uk/~nareports/narep461.pdf Any comments or suggestions ? Nils

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Registration is accepted
by Eric 22 Feb '05

22 Feb '05

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gen_pydocs.py problem
by Joe Cooper 22 Feb '05

22 Feb '05

Hi all, I'm updating the .chm for the next Enthon release, and would like to try getting the SciPy API docs in, as well. I see that the gen_pydocs.py script in util ought to do it for me, but I just get an empty directory when I run it. The box where I'm running it is Fedora Core 3, with Python 2.3.4 and SciPy built from a two or three week old snapshot. There is no error, just this: [joe@localhost util]$ python gen_pydocs.py numerix Numeric 23.3 Anyone have any clues for me? I don't necessarily have to have this script working, if there is a downloadable tarball of the generated docs somewhere that I'm not seeing. Thanks!

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Efficient algorithms for the matrix cosine and sine
by Nils Wagner 21 Feb '05

21 Feb '05

Hi all, This paper might be of interest http://www.ma.man.ac.uk/~hargreaves/narep461.pdf Nils The current implementation uses a Pade approximant (7,7) of the matrix exponential. def cosm(A): """matrix cosine. """ A = asarray(A) if A.typecode() not in ['F','D']: return toreal(0.5*(expm(1j*A) + expm(-1j*A))) else: return 0.5*(expm(1j*A) + expm(-1j*A)) def sinm(A): """matrix sine. """ A = asarray(A) if A.typecode() not in ['F','D']: return toreal(-0.5j*(expm(1j*A) - expm(-1j*A))) else: return -0.5j*(expm(1j*A) - expm(-1j*A)) def expm(A,q=7): """Compute the matrix exponential using Pade approximation of order q. """ ...

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Possibly bug in Sparse.py
by Nils Wagner 17 Feb '05

17 Feb '05

Hi all, I am going to solve large-scale linear systems of equations. The test matrices can be found at http://www.imtek.uni-freiburg.de/simulation/benchmark/?li=30&nr=38886 File "meerbergen.py", line 34, in ? y, info = linalg.bicgstab(omega[i]*B-A,v) File "/usr/lib/python2.3/site-packages/scipy/sparse/Sparse.py", line 441, in __sub__ c,rowc,ptrc,ierr = func(data1,self.rowind,self.indptr,-data2,other.rowind,other.indptr) File "/usr/lib/python2.3/site-packages/scipy/sparse/Sparse.py", line 210, in __getattr__ raise AttributeError, attr + " not found." AttributeError: rowind not found. >>> A <22692x22692 sparse matrix of type 'D' with 1482390 stored elements (space for 1482390) in COOrdinate format> >>> B <22692x22692 sparse matrix of type 'd' with 1481988 stored elements (space for 1481988) in COOrdinate format> >>> omega[i] (0.049939772810258624+0.0024533837163709009j) >>> Any suggestion would be appreciated. Thanks in advance Nils P.S. Is there any progress in supporting sparse eigensolvers (e.g. ARPACK) in scipy ?

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