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Michael Reimpell | 1 Oct 2004 13:24
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www.scipy.org

on: http://www.scipy.org/documentation/buildscipy.txt
link: http://www.scipy.org/documentation/numarraydiscuss
link: http://www.scipy.org/development/atlasbinaries/

Anyway, does someone provide a fedora apt repository for SciPy and its 
dependencies?
Michael
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Nick Arnett | 1 Oct 2004 16:38

Fixes to svd?

In trying to use linalg.svd, I found that I had to make a couple of 
changes to decomp.py to get things to work... and I'm wondering if they 
were correct.  This is my first stab at using Scipy.

The first problem I hit was that Python didn't recognize the call to 
diag (part = diag(s)) in diagsvd.  Looking around for where that seemed 
to live, I decided to add matrix_base to the scipy_base imports:

from scipy_base import asarray_chkfinite, asarray, matrix_base

... and then changed the first line of diagsvd to:

part = matrix_base.diag(s)

That seems to work.

Just below, also in diagsvd, Python didn't recognize "zeros", which I'm 
assuming it should be getting from Numeric... and although I'm certain 
that Scipy is supposed to use Numeric, I couldn't see where it was being 
imported in decomp, so I added:

from Numeric import zeros

Now things seem to be working and the matrix produced by diagsvd looks 
reasonable, though I haven't yet done any of the really big matrices 
I'll be processing.

Any feedback on whether or not this was the appropriate way to fix things?

Nick
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Janet Swisher | 1 Oct 2004 16:45

www.scipy.org

Thanks for catching these.

> -----Original Message-----
> From:  Michael Reimpell
> 
> on: http://www.scipy.org/documentation/buildscipy.txt

> link: http://www.scipy.org/documentation/numarraydiscuss
Fixed to: http://www.scipy.org/documentation/numarraydiscuss.html

> link: http://www.scipy.org/development/atlasbinaries/
Fixed to: http://www.scipy.org/download/atlasbinaries/

-------------------------
Janet Swisher
Senior Technical Writer
Enthought, Inc.
1-512-536-1057
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Joe Cooper | 2 Oct 2004 23:04

www.scipy.org

Michael Reimpell wrote:

> Anyway, does someone provide a fedora apt repository for SciPy and its 
> dependencies?

I've setup a yum repository, but it's still a bit iffy in spots (though 
it does work, and can be uninstalled cleanly if it doesn't work for you 
and you want to get rid of it).

http://www.enthought.com/python/fedora/1/RPMS/

I expect it to get better soon.  I've had a few offers from the 
community to assist with maintenance of the packages...so we'll see how 
things move with some more hands fixing packaging problems.
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Stuart Murdock | 4 Oct 2004 13:23
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Matrix square root

Hi

I am trying to calculate the matrix square root (lets say B) of a Matrix 
(A) which is an array.

A = array([[1,2],[3,4]])

such that

A = matrixmultiply(B,B)

are there any functions in SciPy to do that ?

Thanks

Stuart

--

-- 

Stuart Murdock Ph.D,
Research Fellow,
Dept. of Chemistry / E-Science,
University of Southampton,
Highfield, Southampton,
SO17 1BJ, United Kingdom

http://www.biosimgrid.org
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Nils Wagner | 4 Oct 2004 13:35
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Re: Matrix square root

Stuart Murdock wrote:

> Hi
>
> I am trying to calculate the matrix square root (lets say B) of a 
> Matrix (A) which is an array.
>
> A = array([[1,2],[3,4]])
>
> such that
>
> A = matrixmultiply(B,B)
>
> are there any functions in SciPy to do that ?
>
> Thanks
>
> Stuart
>
AFAIK there is no direct support for sqrtm but you may use funm.

 >>> a = array(([1,2],[3,4]))
 >>> b = linalg.funm(a,sqrt)
 >>> b
array([[ 0.55368857+0.46439416j,  0.80696073-0.21242648j],
       [ 1.21044109-0.31863972j,  1.76412966+0.14575444j]])
 >>> dot(b,b)-a
array([[  2.22044605e-16 -3.19839641e-17j,   0.00000000e+00 
-2.83518868e-17j],
       [  4.44089210e-16 -1.06821019e-16j,   0.00000000e+00
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Nils Wagner | 4 Oct 2004 13:44
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Re: Matrix square root

Nils Wagner wrote:

> Stuart Murdock wrote:
>
>> Hi
>>
>> I am trying to calculate the matrix square root (lets say B) of a 
>> Matrix (A) which is an array.
>>
>> A = array([[1,2],[3,4]])
>>
>> such that
>>
>> A = matrixmultiply(B,B)
>>
>> are there any functions in SciPy to do that ?
>>
>> Thanks
>>
>> Stuart
>>
> AFAIK there is no direct support for sqrtm but you may use funm.

BTW, some algorithms for sqrtm can be found at

http://www.ma.man.ac.uk/~higham/pap-mf.html

This might be a starting point for an implementation of sqrtm in scipy.

Any comments ?
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Pearu Peterson | 4 Oct 2004 14:31
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Re: Matrix square root


On Mon, 4 Oct 2004, Nils Wagner wrote:

> AFAIK there is no direct support for sqrtm but you may use funm.

I just discovered that there might be a bug in funm. I have added
a test to scipy.linalg.test_matfuncs that demonstrates the bug.
So, be aware to check the results of funm(..,sqrt).

Pearu
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Nils Wagner | 4 Oct 2004 14:33
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Re: Matrix square root

Pearu Peterson wrote:

>
>
> On Mon, 4 Oct 2004, Nils Wagner wrote:
>
>> AFAIK there is no direct support for sqrtm but you may use funm.
>
>
> I just discovered that there might be a bug in funm. I have added
> a test to scipy.linalg.test_matfuncs that demonstrates the bug.
> So, be aware to check the results of funm(..,sqrt).
>
That might give a reason to implement sqrtm seperately.
What is your opinion ?

Nils

> Pearu
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user <at> scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user
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Michael Reimpell | 4 Oct 2004 16:08
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RPM building trouble

There are some troubles building rpm packages:

With the scipy CVS (2004-10-03) version,
"python setup.py bdist_rpm --fix-python"
fails, because the file "scipy_base/_compiled_base.c" contains
two includes (e.g. _scipy_mapping.c), that do not handle the path correctly 
(therefore _scipy_mapping.c is not found).

With the SciPy_complete-0.3.tar.gz version,
"python setup.py bdist_rpm --fix-python"
fails, because SciPy_complete-0.3/scipy_core/setup.py is missing.

Also, in order to build a rpm package from scipy CVS, the scipy_distutils rpm 
has to be installed, but this package confilcts with the scipy rpm itself, 
afterwards.

Also, recent versions of f2py fail completely building rpms with
"python setup.py bdits_rpm --fix-python", because of path problems in setup.py 
(complains about missing 'src'-directory). This is a known issue at least 
since F2PY-2.39.235_1693.

After installing scipy I stumbled across the following issues:

Following the plotting tutorial on
"http://www.scipy.org/documentation/plottutorial.html",
I had to use gui_thread.start(use_main=1) instead of gui_thread.start(). Also
plt.title('some text') fails with:
"Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.3/site-packages/scipy/plt/interface.py", line 144, in
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Gmane