Re: [Numpy-discussion] Matrices for testing

2006-10-26 Thread Nils Wagner
Bill Baxter wrote:
>
> On 10/26/06, *jeremito* <[EMAIL PROTECTED]
> > wrote:
>
>
> Hmmm.  I guess I'll have to find another way to get some
> "standard/well-known" matrices to work with.  Thanks for your help.
>
>
> Well if all you want is some matrices, there's nothing stopping you
> from grabbing the matrices in the LAPACK distribution and using them
> yourself.  Robert's just saying they won't be included in Numpy.
>
> There's also the matrix market, whcih has a large number of
> (sparse-only?) example matrices.
> http://math.nist.gov/MatrixMarket/index.html
>  
> --bb
> 
>
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You might be also interested in the Matrix Computation Toolbox which is
a collection of MATLAB M-files containing functions for constructing
test matrices ...
http://www.ma.man.ac.uk/~higham/mctoolbox/

and
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/*gallery*.html

BTW, you can easily import matrices given in the MatrixMarket format in
scipy. See* io.mmread *

mmread(source)
Reads the contents of a Matrix Market file 'filename' into a matrix.

Inputs:

  source- Matrix Market filename (extensions .mtx, .mtz.gz)
  or open file object.

Outputs:

  a - sparse or full matrix

Nils


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Re: [Numpy-discussion] eigh: eigenvalue order

2006-10-24 Thread Nils Wagner
On Tue, 24 Oct 2006 11:16:19 -0700
  "Keith Goodman" <[EMAIL PROTECTED]> wrote:
> Is there any guarantee on the order of eigenvalues (and 
>eigenvectors)
> returned by numpy.linalg.eigh?
> 
> If I want to make sure the eigenvalues are in ascending 
>order of
> magnitude should I sort them myself?
> 
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AFAIK eigh is based on dsyevd.f
http://www.netlib.org/lapack/double/dsyevd.f. (real 
symmetric)
http://www.netlib.org/lapack/complex16/zheevd.f (complex 
Hermitian).
If INFO = 0, the eigenvalues are given in ascending order.

Please correct me if I get it wrong.

Nils

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Re: [Numpy-discussion] Please test the SVN branch

2006-10-11 Thread Nils Wagner
Travis Oliphant wrote:
> I made some fixes to the "asbuffer" code which let me feel better about 
> exposing it in NumPy (where it is now named int_asbuffer).
>
> This code takes a Python integer and a size and returns a buffer object 
> that points to that memory.  A little test is performed by trying to 
> read (and possibly write if a writeable buffer is requested) to the 
> first and last elements of the buffer.  Any segfault is trapped and used 
> to raise a Python error indicating you can't use that area of memory. 
>
> It doesn't guarantee you won't shoot yourself, but it does make it more 
> difficult to segfault Python.  Previously a simple int_asbuffer(3423423, 
> 5) would have segfaulted (unless by chance you the memory area 3423423 
> happens to be owned by Python).
>
> I have not tested the code on other platforms to make sure it works as 
> expected, so please try and compiled it.
>
> -Travis
>
>
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Numpy version 1.0.dev3315
Scipy version 0.5.2.dev2254

Works fine here. All tests passed !
x86_64 x86_64 x86_64 GNU/Linux

Nils


 


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Re: [Numpy-discussion] select part of array using two conditions

2006-10-11 Thread Nils Wagner
Mark Bakker wrote:
> Hello -
>
> I want to select part of an array using two conditions.
> I know how to do it with one condition (and it works great), but when
> I use two conditions I get an error message?
> This is probably easy, but I cannot figure it out.
> Thanks for any help, Mark
>
> >>> a = arange(10)
> >>> a
> array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
> >>> a[ a>2 ]
> array([3, 4, 5, 6, 7, 8, 9])
> >>> a[ a>2 and a<8 ]
> Traceback (most recent call last):
>   File "", line 1, in ?
> a[ a>2 and a<8 ]
> ValueError: The truth value of an array with more than one element is
> ambiguous. Use a.any() or a.all()
>
> 
>
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a[ (a>2) & (a<8) ]

Nils
 

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Re: [Numpy-discussion] feasability study to migrate from numarray to numpy

2006-09-19 Thread Nils Wagner
mg wrote:
> I forget a last question,
>
> We currently advise a High Performance Platform for our customers 
> (Opteron cluster) where our applications are linked with GOTO blas library.
>
> I found in the Numpy distribution the file site.cfg, used to specify the 
> BLAS to used at the link time. (It could be an interesting feature for 
> us.) I noted some configuration variables have names depending on the 
> name of the chosen BLAS library. So, my question is: is GOTO is 
> supported or is it easy for us to add it? I wonder too if the string 
> "[atlas]" written in site.cfg is used or not ?
>
> thanks,
> Mathieu.
>   
There is a ticket concerning your inquiry.

http://projects.scipy.org/scipy/numpy/ticket/73

Nils

> Travis Oliphant wrote:
>   
>> mg wrote:
>>   
>> 
>>> Hi all,
>>>
>>> I am doing a feseability study to migrate our Python based FEM 
>>> applications from Numarray to Numpy.
>>>
>>> First, I tried to install Numpy from Python-2.4 on linux-x86, 
>>> linux-86-64bit. So, all work fine. Great! Moreover, I change easily the 
>>> BLAS linked libraries. I tried with ATLAS and GOTO. Great again!
>>>
>>> Second, I try to do the same think on windows-x86 without success. So my 
>>> first question is: is Numpy-1.0b5 has been tested and is supported on 
>>> Windows?
>>>   
>>> 
>>>   
>> Yes, it should work.  Builds for windows were provided.   But, perhaps 
>> there are configuration issues for your system that we are not handling 
>> correctly.
>>
>>   
>> 
>>> Third, I tried to install Numpy from Python-2.5, which is our standard 
>>> Python, on linux-x86... and the compilation stopped during the 
>>> compilation of core/src/multiarraymodule.c. So my second question is: is 
>>> there a workaround or is the porting to Python2.5 is yet schedule?
>>>   
>>> 
>>>   
>> There was a problem with Python 2.5 and NumPy 1.0 that is fixed in SVN.  
>> Look for NumPy 1.0rc1 to come out soon.
>>   
>> 
>>> My third question is: is the tool to migrate the numarray based Python 
>>> scripts (numpy.numarray.alter_code1) work fine? (I suppose yes...)
>>>   
>>> 
>>>   
>> It needs more testing.  It would be great if you could help us find and 
>> fix bugs in it.   I don't have a lot of numarray code to test.
>>   
>> 
>>> We have created a lot of bindings in order to pilote our generic-C++ 
>>> framework with Python scripts. So, about the Numpy API, is it widely 
>>> different than the Numarray API? (We will order the Numpy Guide too.)
>>>   
>>> 
>>>   
>> It is more similar to the Numeric C-API.  However, the numarray C-API is 
>> completely supported by including numpy/libnumarray.h so you should be 
>> able to convert your C code very easily.   Any problems encountered 
>> should be noted and we'll get them fixed.
>>   
>> 
>>> To not duplicate large numerical memory arrays, Numarray allows to 
>>> aliasing the memory of some bindings with arrays from Numarray, and we 
>>> have used this feature intensively. So, I wonder if it is currently 
>>> supported (or even scheduled)?
>>> 
>>>   
>> I'm pretty sure the answer is yes (because the Numarray C-API is 
>> supported), though I'm not exactly sure what you mean.  Do you mean that 
>> you have memory created in the C/C++ framework and then you have an 
>> array use that memory for it's data area?  If that is what you mean, 
>> then the answer is definitely yes.
>>
>>
>> -Travis
>>
>>
>>
>> -
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Re: [Numpy-discussion] NumPy 1.0 release-candidate 1.0 this weekend

2006-09-13 Thread Nils Wagner
Travis Oliphant wrote:
> I'd like to make the first release-candidate of NumPy 1.0 this weekend.
>
> Any additions wanting to make the first official release candidate 
> should be checked in by then.
>
> -Travis
>
>
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Is it possible to circumvent the error messages if one uses Python2.4 ?

ImportError: ctypes is not available.

Nils

 


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Re: [Numpy-discussion] diagflat

2006-09-03 Thread Nils Wagner
On Sun, 3 Sep 2006 12:20:09 -0600
  "Charles R Harris" <[EMAIL PROTECTED]> wrote:
> Travis has introduced the function diagflat for creating 
>diagonal arrays. It
> flattens whatever array is supplied and returns its 
>values as the diagonal
> of a 2-D array or matrix. As the function is currently 
>undocumented I
> thought now might be a good time to discuss other 
>possible choices for the
> name. Here is a quick list that comes to mind
> 
> diagflat (current name)
> asdiagonal
> todiagonal
> asdiag
> todiag
> ...
> 
> Chuck

+1 for todiag

Nils

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Re: [Numpy-discussion] bug with numpy.linalg.eig for complex output

2006-08-18 Thread Nils Wagner
Bill Baxter wrote:
> If you do this:
> >>>  numpy.linalg.eig(numpy.random.rand(3,3))
>
> You'll (almost always) get a wrong answer back from numpy.  Something
> like:
>
> (array([ 1.72167898, -0.07251007, -0.07251007]),
>  array([[ 0.47908847,  0.72095163,  0.72095163],
>[ 0.56659142, -0.46403504, -0.46403504],
>[ 0.67040914,  0.01361572,  0.01361572]]))
>
> The return value should be complex (unless rand() just happens to
> return something symmetric).
>
> It really needs to either throw an exception, or preferably for this
> function, just go ahead and return something complex, like the
> numpy.dft functions do.
> On the other hand it, would be nice to stick with plain doubles if the
> output isn't complex, but I'd rather get the right output all the time
> than get the minimal type that will handle the output.
>
> This is with beta 1.
>
> Incidentally, I tried logging into the Trac here:
> http://projects.scipy.org/scipy/scipy
> to file a bug, but it wouldn't let me in under the account I've been
> using for a while now.  Is the login system broken?  Were passwords
> reset or something?
>
>
> --bb
>
> 
>
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AFAIK this problem is fixed.

http://projects.scipy.org/scipy/numpy/ticket/215

I have no problem wrt the Trac system.

Nils


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Re: [Numpy-discussion] some work on arpack

2006-08-16 Thread Nils Wagner
On Wed, 16 Aug 2006 08:08:16 -0700
  "David Grant" <[EMAIL PROTECTED]> wrote:
> On 8/16/06, Nils Wagner <[EMAIL PROTECTED]> 
>wrote:
>>
>> Keith Goodman wrote:
>> > On 8/15/06, David Grant <[EMAIL PROTECTED]> wrote:
>> >
>> >
>> >> My idea is (if I have time) to write an eigs-like 
>>function in python
>> >> that will only perform a subset of what Matlab's eigs 
>>does for. It
>> >> will, for example, compute a certain number of 
>>eigenvalues and
>> >> eigenvectors for a real, sparse, symmetric matrix 
>>(the case I'm
>> >> interested in)
>> >>
>> >
>> >
>> AFAIK, pysparse (in the sandbox) includes a module that 
>>implements a
>> Jacobi-Davidson
>> eigenvalue solver for the symmetric, generalised matrix 
>>eigenvalue
>> problem (JDSYM).
>> Did someone test pysparse ?
>>
>> I did try pysparse a few years ago (I think right before 
>>sparse stuff came
> into scipy). I think there is probably an old post 
>asking the list about
> sparse stuff and I think Travis had just written it and 
>told me about it...
> can't remember. Can JDSYM just return the k lowest 
>eigenvalues/eigenvectors?
> 
> -- 
> David Grant
> http://www.davidgrant.ca

Yes. See
  http://people.web.psi.ch/geus/pyfemax/pysparse_examples.html

for details.

Nils

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Re: [Numpy-discussion] some work on arpack

2006-08-16 Thread Nils Wagner
Nils Wagner wrote:
> Keith Goodman wrote:
>   
>> On 8/15/06, David Grant <[EMAIL PROTECTED]> wrote:
>>
>>   
>> 
>>> My idea is (if I have time) to write an eigs-like function in python
>>> that will only perform a subset of what Matlab's eigs does for. It
>>> will, for example, compute a certain number of eigenvalues and
>>> eigenvectors for a real, sparse, symmetric matrix (the case I'm
>>> interested in)
>>> 
>>>   
>>   
>> 
> AFAIK, pysparse (in the sandbox) includes a module that implements a
> Jacobi-Davidson
> eigenvalue solver for the symmetric, generalised matrix eigenvalue
> problem (JDSYM).
> Did someone test pysparse ?
>
> Nils
>
>   
>> Will it also work for a real, dense, symmetric matrix? That's the case
>> I'm interested in. But even if it doesn't, your work is great news for
>> numpy.
>>
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>
>
>  
>
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Ok it's not ready...

gcc: Lib/sandbox/pysparse/src/spmatrixmodule.c
In file included from Lib/sandbox/pysparse/src/spmatrixmodule.c:17:
Lib/sandbox/pysparse/src/ll_mat.c: In function ‘LLMat_matvec_transp’:
Lib/sandbox/pysparse/src/ll_mat.c:760: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
Lib/sandbox/pysparse/src/ll_mat.c:760: error: (Each undeclared
identifier is reported only once
Lib/sandbox/pysparse/src/ll_mat.c:760: error: for each function it
appears in.)
Lib/sandbox/pysparse/src/ll_mat.c: In function ‘LLMat_matvec’:
Lib/sandbox/pysparse/src/ll_mat.c:797: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
In file included from Lib/sandbox/pysparse/src/spmatrixmodule.c:18:
Lib/sandbox/pysparse/src/csr_mat.c: In function ‘CSRMat_matvec_transp’:
Lib/sandbox/pysparse/src/csr_mat.c:119: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
Lib/sandbox/pysparse/src/csr_mat.c: In function ‘CSRMat_matvec’:
Lib/sandbox/pysparse/src/csr_mat.c:146: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
In file included from Lib/sandbox/pysparse/src/spmatrixmodule.c:19:
Lib/sandbox/pysparse/src/sss_mat.c: In function ‘SSSMat_matvec’:
Lib/sandbox/pysparse/src/sss_mat.c:83: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
In file included from Lib/sandbox/pysparse/src/spmatrixmodule.c:17:
Lib/sandbox/pysparse/src/ll_mat.c: In function ‘LLMat_matvec_transp’:
Lib/sandbox/pysparse/src/ll_mat.c:760: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
Lib/sandbox/pysparse/src/ll_mat.c:760: error: (Each undeclared
identifier is reported only once
Lib/sandbox/pysparse/src/ll_mat.c:760: error: for each function it
appears in.)
Lib/sandbox/pysparse/src/ll_mat.c: In function ‘LLMat_matvec’:
Lib/sandbox/pysparse/src/ll_mat.c:797: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
In file included from Lib/sandbox/pysparse/src/spmatrixmodule.c:18:
Lib/sandbox/pysparse/src/csr_mat.c: In function ‘CSRMat_matvec_transp’:
Lib/sandbox/pysparse/src/csr_mat.c:119: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
Lib/sandbox/pysparse/src/csr_mat.c: In function ‘CSRMat_matvec’:
Lib/sandbox/pysparse/src/csr_mat.c:146: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
In file included from Lib/sandbox/pysparse/src/spmatrixmodule.c:19:
Lib/sandbox/pysparse/src/sss_mat.c: In function ‘SSSMat_matvec’:
Lib/sandbox/pysparse/src/sss_mat.c:83: error: ‘CONTIGUOUS’ undeclared
(first use in this function)
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC
-ILib/sandbox/pysparse/include/
-I/usr/l

Re: [Numpy-discussion] some work on arpack

2006-08-16 Thread Nils Wagner
Keith Goodman wrote:
> On 8/15/06, David Grant <[EMAIL PROTECTED]> wrote:
>
>   
>> My idea is (if I have time) to write an eigs-like function in python
>> that will only perform a subset of what Matlab's eigs does for. It
>> will, for example, compute a certain number of eigenvalues and
>> eigenvectors for a real, sparse, symmetric matrix (the case I'm
>> interested in)
>> 
>
>   
AFAIK, pysparse (in the sandbox) includes a module that implements a
Jacobi-Davidson
eigenvalue solver for the symmetric, generalised matrix eigenvalue
problem (JDSYM).
Did someone test pysparse ?

Nils

> Will it also work for a real, dense, symmetric matrix? That's the case
> I'm interested in. But even if it doesn't, your work is great news for
> numpy.
>
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Re: [Numpy-discussion] test fails

2006-08-15 Thread Nils Wagner
Steve Schmerler wrote:
> The test in
>
> In [2]: numpy.__version__
> Out[2]: '1.0b2.dev3007'
>
> fails:
>
>
> [...]
> check_1D_array (numpy.lib.tests.test_shape_base.test_vstack) ... ok
> check_2D_array (numpy.lib.tests.test_shape_base.test_vstack) ... ok
> check_2D_array2 (numpy.lib.tests.test_shape_base.test_vstack) ... ok
>
> ==
> ERROR: check_ascii (numpy.core.tests.test_multiarray.test_fromstring)
> --
> Traceback (most recent call last):
>File 
> "/usr/local/lib/python2.3/site-packages/numpy/core/tests/test_multiarray.py", 
> line 120, in check_ascii
>  a = fromstring('1 , 2 , 3 , 4',sep=',')
> ValueError: don't know how to read character strings for given array type
>
> --
> Ran 476 tests in 1.291s
>
> FAILED (errors=1)
>
>
>   
I cannot reproduce it here

Numpy version 1.0b3.dev3025

python
/usr/lib64/python2.4/site-packages/numpy/core/tests/test_multiarray.py
  Found 153 tests for numpy.core.multiarray
  Found 0 tests for __main__
.
--
Ran 153 tests in 0.047s

OK


Nils


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Re: [Numpy-discussion] Regarding Matrices

2006-08-14 Thread Nils Wagner
On Mon, 14 Aug 2006 21:58:50 +0200
  Sven Schreiber <[EMAIL PROTECTED]> wrote:
> Hi,
> 
> Satya Upadhya schrieb:
> 
> from Numeric import *
> 
> Well this list is about the numpy package, but anyway...
> 
>> the power function is giving a resultant matrix in which 
>>each element of
>> matrix B is raised to the power of 0 so as to make it 1. 
>>But, taken as a
>> whole i.e. matrix B to the power of 0 should have given 
>>the identity
>> matrix.
> 
> afaik, in numpy terms if you are dealing with a numpy 
>array, such
> functions are elementwise by design.
> In contrast, if you have a numpy matrix (a special 
>subclass of the array
> class) --constructed e.g. as mat(eye(3))-- then power is 
>redefined to be
> the matrix power; at least that's the rule for the ** 
>operator, not 100%
> sure if for the explicit power() function as well, but I 
>suppose so.
> 
>>  
>> Also, what is the procedure for taking the log of an 
>>entire matrix
>> (log(A) where A is a matrix takes the log of every 
>>individual element in
>> A, but thats not the same as taking the log of the 
>>entire matrix)
> 
> I don't understand what you want, how do you take the 
>log of a matrix
> mathematically?
> 
> -Sven
> 
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Help on function logm in module scipy.linalg.matfuncs:

logm(A, disp=1)
 Matrix logarithm, inverse of expm.

Nils

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Re: [Numpy-discussion] svn install failure on amd64

2006-07-31 Thread Nils Wagner
Angus McMorland wrote:
> Hi people who know what's going on,
>
> I'm getting an install failure with the latest numpy from svn (revision
> 2940). This is on an amd64 machine running python 2.4.4c0.
>
> The build halts at: 
>
> compile options: '-Ibuild/src.linux-x86_64-2.4/numpy/core/src
> -Inumpy/core/include -Ibuild/src.linux-x86_64-2.4/numpy/core
> -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c'
> gcc: numpy/core/src/multiarraymodule.c
> In file included from numpy/core/src/arrayobject.c:508,
>  from numpy/core/src/multiarraymodule.c:64:
> numpy/core/src/arraytypes.inc.src: In function 'set_typeinfo':
> numpy/core/src/arraytypes.inc.src:2139: error: 'PyIntpArrType_Type'
> undeclared (first use in this function)
> numpy/core/src/arraytypes.inc.src:2139: error: (Each undeclared
> identifier is reported only once
> numpy/core/src/arraytypes.inc.src:2139: error: for each function it
> appears in.)
> In file included from numpy/core/src/arrayobject.c:508,
>  from numpy/core/src/multiarraymodule.c:64:
> numpy/core/src/arraytypes.inc.src: In function 'set_typeinfo':
> numpy/core/src/arraytypes.inc.src:2139: error: 'PyIntpArrType_Type'
> undeclared (first use in this function)
> numpy/core/src/arraytypes.inc.src:2139: error: (Each undeclared
> identifier is reported only once
> numpy/core/src/arraytypes.inc.src:2139: error: for each function it
> appears in.)
> error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
> -Wstrict-prototypes -fPIC -Ibuild/src.linux-x86_64-2.4/numpy/core/src
> -Inumpy/core/include -Ibuild/src.linux-x86_64-2.4/numpy/core
> -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.4 -c
> numpy/core/src/multiarraymodule.c -o
> build/temp.linux-x86_64-2.4/numpy/core/src/multiarraymodule.o" failed
> with exit status 1
>
> Am I missing something or might this be a bug?
>
> Cheers,
>
> Angus.
>   


I can build numpy on a 32-bit machine but it fails on a 64-bit machine.
Travis, please can you have a look at this issue.

In file included from numpy/core/src/arrayobject.c:508,
from numpy/core/src/multiarraymodule.c:64:
numpy/core/src/arraytypes.inc.src: In function ‘set_typeinfo’:
numpy/core/src/arraytypes.inc.src:2139: error: ‘PyIntpArrType_Type’
undeclared (first use in this function)
numpy/core/src/arraytypes.inc.src:2139: error: (Each undeclared
identifier is reported only once
numpy/core/src/arraytypes.inc.src:2139: error: for each function it
appears in.)
In file included from numpy/core/src/arrayobject.c:508,
from numpy/core/src/multiarraymodule.c:64:
numpy/core/src/arraytypes.inc.src: In function ‘set_typeinfo’:
numpy/core/src/arraytypes.inc.src:2139: error: ‘PyIntpArrType_Type’
undeclared (first use in this function)
numpy/core/src/arraytypes.inc.src:2139: error: (Each undeclared
identifier is reported only once
numpy/core/src/arraytypes.inc.src:2139: error: for each function it
appears in.)
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC
-Ibuild/src.linux-x86_64-2.4/numpy/core/src -Inumpy/core/include
-Ibuild/src.linux-x86_64-2.4/numpy/core -Inumpy/core/src
-Inumpy/core/include -I/usr/include/python2.4 -c
numpy/core/src/multiarraymodule.c -o
build/temp.linux-x86_64-2.4/numpy/core/src/multiarraymodule.o" failed
with exit status 1

Nils


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Re: [Numpy-discussion] [Fwd: Re: A few comments (MDP conversion)]

2006-07-14 Thread Nils Wagner
Pietro Berkes wrote:
> On Thu, 13 Jul 2006, Nils Wagner wrote:
>
>   
>> It seems to be line 281 instead of 269. I am using latest svn.
>> BTW, in linalg.py in
>>
>> def pinv:
>>
>> there is another Complex with capital C.
>> 
>
> Well, the problem is not really the capital 'C', but rather the lack of 
> quotation marks...
>
>
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 >>> p = linalg.pinv(a)
Traceback (most recent call last):
  File "", line 1, in ?
  File "/usr/lib64/python2.4/site-packages/numpy/linalg/linalg.py", line 
426, in pinv
if issubclass(a.dtype.dtype, complexfloating):
AttributeError: 'numpy.dtype' object has no attribute 'dtype'

Nils



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[Numpy-discussion] [Fwd: Re: A few comments (MDP conversion)]

2006-07-13 Thread Nils Wagner


--- Begin Message ---

Pietro Berkes wrote:

Dear numpys,

a couple of weeks ago Tiziano and I completed the conversion of our data
processing library MDP to numpy. We collected a few ideas and
questions:

- we found the convertcode.py module quite useful to perform a first,
  low-level conversion. We had some problem when 'typecode' was
  used as a keyword argument because the parser only converts
  'typecode=' to 'dtype=' and skips the cases where there is an
  additional space character before the equal sign ('typecode =').
  Other names that might be easily converted are 'ArrayType' and
  'NewAxis'.

- some functions changed the columns/rows conventions ('cov', for
  example). It would be really helpful to explicitly write this in the
  list of necessary changes in the documentation.  It could be nice
  to have the file 'convertcode.py' to print a warning every time one 
  of this functions is used in the code.


- the linalg functions svd, eig, inv, pinv, diag, and possibly
  others perform an upcast, e.g. from 'f' to 'd'. This is apparently
  because the litelapack module only wraps double precision routines.
  Wouldn't it be more consistent to cast the results back to the
  numerical type of the input? Otherwise, the user always has to take
  care of the casting, which makes the use of single precision
  arrays quite cumbersome.

- we found a bug in the 'eig' function in the case the solution
  is complex: in (linalg.py, line 269) 'Complex' should be 'w.dtype'

  

Did you file a ticket ?
http://projects.scipy.org/scipy/numpy

It seems to be line 281 instead of 269. I am using latest svn.
BTW, in linalg.py in

def pinv:

there is another Complex with capital C.

Nils

We wondered whether it would be possible to obtain SVN write access in 
orderto be able to fix this kind of issues by ourselves in the future.  
We could also contribute docstrings for some of the functions.


In general, we found the conversion to numpy quite straightforward
and would like to thank you all for the great work!

Cheers,
Pietro Berkes and Tiziano Zito
http://mdp-toolkit.sourceforge.net/


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--- End Message ---

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[Numpy-discussion] Number of digits

2006-07-10 Thread Nils Wagner
Hi all,

how can I increase the number of digits in the output of str(.) ?

>>> lam**2
493.48022005446808
>>> str(lam**2)
'493.480220054'

'493.4802200544680' would be fine.

Nils




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[Numpy-discussion] Converting a list

2006-07-10 Thread Nils Wagner
Hi all,

I have a list consisting of arrays of different size

data =  [array([-1.+0.j, -1.+0.j, -1.6667+0.j]),
array([-2.+0.j, -2.-0.6667j, -2.-1.j]),
array([-2.-2.j, -1.-2.j, -0.6667-2.j]), array([
0.-2.j,  0.-1.6667j,  0.-1.j]), array([ 
6.12323400e-17-1.j,  -2.58819045e-01-0.96592583j,
-5.e-01-0.8660254j ,  -7.07106781e-01-0.70710678j,
-8.66025404e-01-0.5j   ,  -9.65925826e-01-0.25881905j])]

type(data) =  

shape(data) results in

shape(data) =
Traceback (most recent call last):
  File "sinai.py", line 107, in ?
p = polygon(P)
  File "sinai.py", line 67, in polygon
print 'shape(data) = ',shape(data)
  File "/usr/lib64/python2.4/site-packages/numpy/core/fromnumeric.py",
line 258, in shape
result = asarray(a).shape
  File "/usr/lib64/python2.4/site-packages/numpy/core/numeric.py", line
119, in asarray
return array(a, dtype, copy=False, order=order)
TypeError: a float is required

Is this a bug ?

Nils



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[Numpy-discussion] numpy.linalg.pinv has no docstring

2006-06-27 Thread Nils Wagner
Hi Travis,

Just now I saw that you have fixed the failing test.
You have used pinv (pseudo inverse).
Please can you add a docstring to numpy.linalg.pinv.

Thanks in advance.

Nils

In [4]: numpy.linalg.pinv?
Type:   function
Base Class: 
String Form:
Namespace:  Interactive
File:   /usr/lib64/python2.4/site-packages/numpy/linalg/linalg.py
Definition: numpy.linalg.pinv(a, rcond=1e-10)
Docstring:


 


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[Numpy-discussion] ImportError: cannot import name inverse_fft

2006-06-12 Thread Nils Wagner
matplotlib data path /usr/lib64/python2.4/site-packages/matplotlib/mpl-data
$HOME=/home/nwagner
loaded rc file /home/nwagner/matplotlibrc
matplotlib version 0.87.3
verbose.level helpful
interactive is False
platform is linux2
numerix numpy 0.9.9.2603
Traceback (most recent call last):
  File "cascade.py", line 3, in ?
from pylab import plot, show, xlim, ylim, subplot, xlabel, ylabel,
title, legend,savefig,clf,scatter
  File "/usr/lib64/python2.4/site-packages/pylab.py", line 1, in ?
from matplotlib.pylab import *
  File "/usr/lib64/python2.4/site-packages/matplotlib/pylab.py", line
198, in ?
import mlab  #so I can override hist, psd, etc...
  File "/usr/lib64/python2.4/site-packages/matplotlib/mlab.py", line 74,
in ?
from numerix.fft import fft, inverse_fft
ImportError: cannot import name inverse_fft



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[Numpy-discussion] numpy.test(1,10) results in a segfault

2006-05-31 Thread Nils Wagner
test_wrap (numpy.core.tests.test_umath.test_special_methods) ... ok
check_types (numpy.core.tests.test_scalarmath.test_types)*** glibc
detected *** free()   : invalid pointer:
0xb7ab74a0 ***

Program received signal SIGABRT, Aborted.
[Switching to Thread 16384 (LWP 14948)]
0xb7ca51f1 in kill () from /lib/i686/libc.so.6
(gdb) bt
#0  0xb7ca51f1 in kill () from /lib/i686/libc.so.6
#1  0xb7e90401 in pthread_kill () from /lib/i686/libpthread.so.0
#2  0xb7e9044b in raise () from /lib/i686/libpthread.so.0
#3  0xb7ca4f84 in raise () from /lib/i686/libc.so.6
#4  0xb7ca6498 in abort () from /lib/i686/libc.so.6
#5  0xb7cd8cf6 in __libc_message () from /lib/i686/libc.so.6
#6  0xb7cde367 in malloc_printerr () from /lib/i686/libc.so.6
#7  0xb7cdfacf in free () from /lib/i686/libc.so.6
#8  0xb7ae3fc5 in gentype_dealloc (v=0x0) at scalartypes.inc.src:281
#9  0xb7f57bed in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#10 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#11 0xb7f58cc5 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#12 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#13 0xb7f1113a in function_call () from /usr/lib/libpython2.4.so.1.0
#14 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#15 0xb7f02edb in instancemethod_call () from /usr/lib/libpython2.4.so.1.0
#16 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
---Type  to continue, or q  to quit---
#17 0xb7f58097 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#18 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#19 0xb7f1113a in function_call () from /usr/lib/libpython2.4.so.1.0
#20 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#21 0xb7f02edb in instancemethod_call () from /usr/lib/libpython2.4.so.1.0
#22 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#23 0xb7f34c2c in slot_tp_call () from /usr/lib/libpython2.4.so.1.0
#24 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#25 0xb7f58097 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#26 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#27 0xb7f1113a in function_call () from /usr/lib/libpython2.4.so.1.0
#28 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#29 0xb7f02edb in instancemethod_call () from /usr/lib/libpython2.4.so.1.0
#30 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#31 0xb7f34c2c in slot_tp_call () from /usr/lib/libpython2.4.so.1.0
#32 0xb7ef9c37 in PyObject_Call () from /usr/lib/libpython2.4.so.1.0
#33 0xb7f58097 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
---Type  to continue, or q  to quit---
#34 0xb7f5a663 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#35 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#36 0xb7f58cc5 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#37 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#38 0xb7f58cc5 in PyEval_EvalFrame () from /usr/lib/libpython2.4.so.1.0
#39 0xb7f5ad21 in PyEval_EvalCodeEx () from /usr/lib/libpython2.4.so.1.0
#40 0xb7f5aff5 in PyEval_EvalCode () from /usr/lib/libpython2.4.so.1.0
#41 0xb7f75778 in run_node () from /usr/lib/libpython2.4.so.1.0
#42 0xb7f77228 in PyRun_InteractiveOneFlags () from
/usr/lib/libpython2.4.so.1.0
#43 0xb7f77396 in PyRun_InteractiveLoopFlags () from
/usr/lib/libpython2.4.so.1.0
#44 0xb7f774a7 in PyRun_AnyFileExFlags () from /usr/lib/libpython2.4.so.1.0
#45 0xb7f7d66a in Py_Main () from /usr/lib/libpython2.4.so.1.0
#46 0x0804871a in main (argc=0, argv=0x0) at ccpython.cc:10

Can someone reproduce the segfault ?

Linux amanda 2.6.11.4-21.12-default #1 Wed May 10 09:38:20 UTC 2006 i686
athlon i386 GNU/Linux
>>> numpy.__version__
'0.9.9.2553'



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[Numpy-discussion] test_scalarmath.py", line 63

2006-05-31 Thread Nils Wagner
>>> numpy.__version__
'0.9.9.2553'


 numpy.test(1,10) results in
==
FAIL: check_types (numpy.core.tests.test_scalarmath.test_types)
--
Traceback (most recent call last):
  File
"/usr/lib64/python2.4/site-packages/numpy/core/tests/test_scalarmath.py",
line 63, in check_types
assert val.dtype.num == typeconv[k,l] and \
AssertionError: error with (0,7)

--
Ran 368 tests in 0.479s

FAILED (failures=1)

Nils



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