Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Stéfan van der Walt
Hi Dag

On Tue, Apr 1, 2008 at 12:52 AM, Dag Sverre Seljebotn
[EMAIL PROTECTED] wrote:
  I am going to apply for a Google Summer of Code project about Developing
   Cython towards better NumPy integration (Cython: http://cython.org).
   Anyone interested in how this is done can have a look at the links below,
   any feedback is welcome.
  

  The application I am going to submit (to Python Foundation):
   http://wiki.cython.org/DagSverreSeljebotn/soc

  I now have time to actively discuss and improve it so any feedback from
  the NumPy community is greatly appreciated.

Sorry for only responding now; I was traveling back from Europe.

The project your propose has important implications for NumPy.
Currently, much of the core is implemented in C and very few people
have in-depth knowledge of its inner workings.  We therefore have
fewer eyes on that code than we'd like.  Furthermore, there are only
two ways of extending the core: 1) use Python callbacks, which are
slow or 2) learn the C API and deal with reference counting -- too
much to ask from a scientist who simply wishes to implement a fast
algorithm.

There are also some other projects, like scipy.ndimage, that could do
with a fair bit of refactoring, and this task would be so much easier
if Cython could generate the C-level ndarray code; we have precious
little developer resources available as it is, and would rather spend
it on solving problems than on arranging low-level API calls.

Having the following implemented would already be a vast improvement
on the current situation:

 - Array indexing
   x[1,2]
   x[1:2,3:4]
   x[1,...]
   x[1,:]

 - Assignment
   x[1,2] = 3
   x[1,...] = 1
   ...

 - Calling array methods:
   y = x.sum()

Doing this would be easier with Travis Oliphant's numpy developer's
reference at hand, and, if I recall the page on scipy.org (which is
currently down) correctly, he would provide it to you free of charge
on request.

I am very excited about your proposal, and I really hope it takes off.
 Let us know if there is anything we can do to help.

Best of luck,
Stéfan
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Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Stéfan van der Walt
Hi Dag

On Tue, Apr 1, 2008 at 12:52 AM, Dag Sverre Seljebotn
[EMAIL PROTECTED] wrote:
  I am going to apply for a Google Summer of Code project about Developing
   Cython towards better NumPy integration (Cython: http://cython.org).
   Anyone interested in how this is done can have a look at the links below,
   any feedback is welcome.
  

  The application I am going to submit (to Python Foundation):
   http://wiki.cython.org/DagSverreSeljebotn/soc

  I now have time to actively discuss and improve it so any feedback from
  the NumPy community is greatly appreciated. See especially:


  http://wiki.cython.org/enhancements/numpy

One more comment about the constructor described on the page above.
It would be good if we could have the same syntax as the current
numpy.ndarray, and then simply call through to the underlying C
constructor.  We'd also need zeros, empty, ones_like and some other
select functions.  The goal is to remain as faithful as possible to
the original API, so that there is hardly a distinction between Python
and Cython.

Cheers
Stéfan
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Re: [Numpy-discussion] Applying PIL patch

2008-04-01 Thread izak marais
Thank you for the reply. I in fact did not have the latest PIL binary. It works 
beautifully now. Luckily I won't be needing RGBA support soon.

Izak

- Original Message 
From: Stéfan van der Walt [EMAIL PROTECTED]
To: Discussion of Numerical Python numpy-discussion@scipy.org
Sent: Monday, March 31, 2008 11:45:52 PM
Subject: Re: [Numpy-discussion] Applying PIL patch

Unfortunately, RGBA images cannot be read this way.  A patch that
fixes the issue was posted here:

http://www.mail-archive.com/[EMAIL PROTECTED]/msg01482.html

No response from the Image SIG guys.

Regards
Stéfan

On Mon, Mar 31, 2008 at 6:29 PM, Christopher Barker
[EMAIL PROTECTED] wrote:
 izak marais wrote:
   Sorry for the beginner question. I want to apply the PIL-numpy patch
   from http://www.scipy.org/Cookbook/PIL?highlight=%28PIL%29 . I have the
   latest windows binaries of numpy, scipy and PIL installed.

  Then you have the patch already-- it was added to the latest PIL.

  http://effbot.org/zone/pil-changes-116.htm

  -Chris
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Re: [Numpy-discussion] Applying PIL patch

2008-04-01 Thread izak marais
Stéfan wrote:Unfortunately, RGBA images cannot be read this way.  

Apparently it does not work with 16bit greyscale tif images either. 
For anyone else stumbling upon this thread, there is a work-about to get the 
data into a numpy array.

i = Image.open('16bitGreyscaleImage.tif')
a = numpy.array(i.getdata())# a 1d numpy array
a = a.reshape(i.size)  #2d numpy array

Perhaps there is a better way of doing it (?), but this works for me. 


Izak




  

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Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Dag Sverre Seljebotn




Dag Sverre Seljebotn wrote:

  
  
  
  

   http://wiki.cython.org/enhancements/numpy



One more comment about the constructor described on the page above.

  

I read this a different way now, if what you meant is the parameters to
ndarray in 
cdef c_numpy.ndarray(c_numpy.float, 2) x
then my answer is that the paranthezis is not part of a constructor, it
is part of the type of the variable (which is not a Python concept at
all). This is perhaps clearer here:

import numpy

def negative_grayscale_image(numpy.ndarray(numpy.uint8, 2) img):
  cdef int i, j
  for i in range(arr.shape[0]):
for j in range(arr.shape[1]):
  img[i, j] = 255 - img[i, j]

-- 
Dag Sverre



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Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Dag Sverre Seljebotn






  

 http://wiki.cython.org/enhancements/numpy

  
  
One more comment about the constructor described on the page above.
It would be good if we could have the same syntax as the current
numpy.ndarray, and then simply call through to the underlying C
constructor.  We'd also need zeros, empty, ones_like and some other
select functions.  The goal is to remain as faithful as possible to
the original API, so that there is hardly a distinction between Python
and Cython.
  

This will be automatic from how Cython operates :-) And that is, I
think, what makes all of this great. Objects are Python objects all the
time and by default retain all Python implementation, and we only
override this implementation when the behaviour is retained.

I'll walk through this code line by line:
cdef c_numpy.ndarray(c_numpy.float, 2) x
x = exp(4 + numpy.zeros([10, 10], dtype=numpy.float))
y = x + 3
print x[1, 3]
print y[3, 5]


#1: This is only a variable type declaration and constructs nothing.

#2: Operating on Python objects as normal (there is nothing "special"
about numpy.zeros from the perspective of Cython, it returns a Python
object like all other Python functions), and the resulting object is
then assigned to the typed x variable; which is no different from
assigning it to an untyped variable except that a run-time type-check
assertion is inserted (is the Python object an ndarray object with the
right dimensions and data type).

#3: (x + 3) will treat x as a Python object once again, so y will be an
untyped variable referencing an ndarray like normal Python.

#4: This is where it gets interesting. Because x is typed so that
Cython knows the C structure of the Python objects, it translates this
directly to a lookup in the buffer, using stride information, so that
it ends up as saying something like *(x-data + x-strides[0] * 1
+ x-strides[1] * 3) directly in C (though hopefully we can in time
cache strides lookups outside for loops etc, see the gcc discussion on
the page).

#5: Here the data is instead accessed through the ndarray's Python
__getitem__, which is much slower: A tuple is constructed, 3 and 5 put
into the tuple, the tuple passed to ndarray.__getitem__ (or similar for
extension types...) and so on.

Question: How does strides fit in this? I've been thinking that strides
could merely fall back to the Python access method because it is
somewhat of a high-level operation; is there any significant gains in
skipping the Python access layer? (However this question is not
important for the design and either approach will fit in, so it is not
a big concern for me now.)

-- 
Dag Sverre



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Re: [Numpy-discussion] planet.scipy.org

2008-04-01 Thread Matthieu Brucher
Hi,

The planet is no longer accessible. Anyone has the same issue ?

Matthieu

2008/1/1, Jarrod Millman [EMAIL PROTECTED]:

 Hey,

 I just wanted to announce that we now have a NumPy/SciPy blog
 aggregator thanks to Gaël Varoquaux:  http://planet.scipy.org/

 Feel free to contact me if you have a blog that you would like included.

 Thanks,

 --
 Jarrod Millman
 Computational Infrastructure for Research Labs
 10 Giannini Hall, UC Berkeley
 phone: 510.643.4014
 http://cirl.berkeley.edu/
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[Numpy-discussion] server down

2008-04-01 Thread Christopher Hanley
Hi,

I cannot access the numpy, scipy, or astropy repositories at scipy.org. 
  The servers appear to be down.


[redcedar:~/dev/scipy] chanley% svn update
svn: PROPFIND request failed on '/svn/scipy/trunk'
svn: PROPFIND of '/svn/scipy/trunk': could not connect to server 
(http://svn.scipy.org)


Thanks,
Chris

-- 
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Systems Software Engineer
Space Telescope Science Institute
3700 San Martin Drive
Baltimore MD, 21218
(410) 338-4338
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Re: [Numpy-discussion] planet.scipy.org

2008-04-01 Thread Gael Varoquaux
On Tue, Apr 01, 2008 at 02:29:13PM +0200, Matthieu Brucher wrote:
The planet is no longer accessible. Anyone has the same issue ?

Yes, the scipy.org server is down. I think we need to wait for the US to
wake up to take care of this.

Ga�l
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Re: [Numpy-discussion] planet.scipy.org

2008-04-01 Thread Travis Vaught
Fixed now...many apologies for the outage.

Travis


On Apr 1, 2008, at 8:19 AM, Gael Varoquaux wrote:
 On Tue, Apr 01, 2008 at 02:29:13PM +0200, Matthieu Brucher wrote:
   The planet is no longer accessible. Anyone has the same issue ?

 Yes, the scipy.org server is down. I think we need to wait for the  
 US to
 wake up to take care of this.

 Gaël
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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Charles Doutriaux
Hi Pierre,

Im ccing Bob on this, he's the main developper for cdms2 package. At 
this point I think Travis original suggestion was the best. We should 
leave it like it was for 1.0.5 There's a lot of changes to do in order 
to get the backward compatibility going. And I feel it should wait until 
1.1. I don't feel comfortable doing all these changes and releasing our 
software like this. It's a major change and it needs to be tested for a 
while.  OUr users are massively hammering the MA and rely on it so much. 
Although I do see the usefulness of the new ma and at term I believe it 
has major merits to be used instead of oldnumeric.ma.

Your thoughts?

C.

Pierre GM wrote:
 Charles,

   
 Any idea where that comes from ?
 

 No, not really. Seems that TransientVariable(*args) doesn't work. I guess 
 it's 
 because it has inherited a __call__method, and tries to use that method 
 instead of the __new__. Try to call TransientVariable.__new__ instead of just 
 TransientVariable in l505 of avariables.py, and see how it goes. You may want 
 to rethink what subSlice does as well. Instead of calling the class 
 constructor, you can also just create a view of your array and update the 
 attributes accordingly.

 Once again, a stripped-down version of the class and its parents would be 
 useful.

   
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[Numpy-discussion] confusion in eigenlib code

2008-04-01 Thread gordon
hi
i came across some code for eigenface construction from some
images ,using the old Numeric .
http://www.owlnet.rice.edu/~elec301/Projects99/faces/code.html
In the eigenlib.py
http://www.owlnet.rice.edu/~elec301/Projects99/faces/code/eigenlib.py
i  converted the calls to Numeric functions to their numpy equivalents
(to linalg.eigh() and numpy.dot())and ran the code.In this eigenlib.py
i am confused by some parts where they derrive eigenvectors and sort
them

evalues, evectors = LinearAlgebra.eigenvectors(L)
# sort them by eigenvalue and keep the top M_prime
evs = map(None, evalues, evectors)
evs.sort()
evs.reverse()
evs = evs[0:M_prime]

# write those into the directory
v = map(lambda x: x[1], evs)
self.u = []
for k in range(M_prime):
print(' ' + str(k+1))
self.u.append(Numeric.matrixmultiply(v[k], self.Phi))
#self.vector_to_image(self.u[-1], '%s/eig%03d.gif' % (dir, k))

(Here self.Psi is the average face from a collection of face images
and  self.Phi is obtained by substracting Psi from original image
data ...mean centering i guess)

what i can't understand in the above code is that when evs[0:M_prime]
is taken it takes the rows from evectors.Is not the correct way to
take a column of evectors as an eigenvector? If someone can make this
clear please do
thanks
gordon
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Amit Itagi
On Mon, Mar 31, 2008 at 11:06 PM, Robert Kern [EMAIL PROTECTED] wrote:

 On Mon, Mar 31, 2008 at 4:17 PM, Amit Itagi [EMAIL PROTECTED] wrote:
  Hi,
 
  I am having problems with numpy installation.
 
  1) These is an atlas 3.8.0 library installed somewhere in the search
 path.
  However, the installation gives errors with that installation. Is there
 a
  way to tell the installer to install the default (possibly slower) blas,
  instead of using the one in the path ?

 Create a site.cfg file with the appropriate section; copy and modify
 the site.cfg.example file.


*I figured how to specify a particular installation of the libraries. I want
to do the opposite. How do I specify the following in site.cfg - Don't
search for the library. Assume that it is absent and use the default slower
library ?*
 *
*



  2) Also, my main Python directory is called Python-2.5.2. When I try to
  configure with the installprefix, it changes Python-2.5.2 to
  python-2.5.2 and creates a new directory. How can I make the installer
 not
  convert the upper-case P to a lower-case ?

 Can you give more information like the platform you are on, the full
 path to this directory, the exact commands that you executed, and the
 results of these commands?


*I am installing this on a CENTOS linux platform (64 bit AMD opteron). The
path to my python directory is /home/amit/packages/Python-2.5.2 . If I
temporarily make the atlas library unavailable (by renaming the directory to
some name that is not in the path), I can perform the build. Now in the
installation stage, I use
python setup.py
and then choose the option 2/home/amit/packages/Python-2.5.2. In the
proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2.
Incidentally, it also creates this new directory during install.
*
*Thanks Robert.

Rgds,
Amit*




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 I have come to believe that the whole world is an enigma, a harmless
 enigma that is made terrible by our own mad attempt to interpret it as
 though it had an underlying truth.
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Re: [Numpy-discussion] linalg.eigh() newbie doubt

2008-04-01 Thread Matthieu Brucher

 but the notation evectors[:3] will give me an ndarray of shape(3,6)
 Am i missing something here?


Yes : evectors[:3] selects the first three lines, evectors[:,3] selects the
fourth column.

Matthieu
-- 
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Website : http://matthieu-brucher.developpez.com/
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Re: [Numpy-discussion] linalg.eigh() newbie doubt

2008-04-01 Thread gordon



 Yes : evectors[:3] selects the first three lines, evectors[:,3] selects the
 fourth column.


arggg!!
my mistake!
sorry Lorenzo
thanks Matthieu

gordon
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Re: [Numpy-discussion] linalg.eigh() newbie doubt

2008-04-01 Thread gordon


   The normalized eigenvector corresponding to the eigenvalue w[i]
 is  the column v[:,i].
  so, yes, the eigvec coresponding to the eigval w[i] is v[:,i].

Lorenzo
sorry i don't understand
from the above sample(unordered)
if i select the the 4th eigenvalue i get 1.7
evals[3]=1.7

i believe the corresponding eigenvector should be the 4th column in
evectors?
[6.
7.
5.
4.
4.
4.]

but the notation evectors[:3] will give me an ndarray of shape(3,6)
Am i missing something here?
thanks
gordon
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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Travis E. Oliphant
Charles Doutriaux wrote:
 Hi Pierre,

 Im ccing Bob on this, he's the main developper for cdms2 package.
I've uploaded the original ma.py file back into oldnumeric so that 
oldnumeric.ma should continue to work as before.  Can you verify this?

Thanks,

-Travis O.


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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Pierre GM
All,
Because numpy.ma.MaskedArray objects are now derived from classical ndarrays, 
the subclassing rules should be followed. As we observed yesterday with 
Charles, the adaptation is not as straightforward as we hoped.

If you have time constraints, the easiest would indeed be to revert to the 
previous implementation of MaskedArray (viz, as an object, where the 
initialization is performed with a __init__ function). Now, I'm not sure how 
well it's gonna interface with numpy.ma, we need to try.

In the long run however, I think you should try to switch to regular ndarrays 
and ndarray subclasses. I do agree it's more of a long-term process, but I'd 
be happy to help (you and I are working more or less on the same field 
anyway, I needed some tools to handle my environmental/climatic time series)

Let me try to cook something up. In the meantime, please keep me posted.
P.


On Tuesday 01 April 2008 11:07:41 Charles Doutriaux wrote:
 Hi Pierre,

 Im ccing Bob on this, he's the main developper for cdms2 package. At
 this point I think Travis original suggestion was the best. We should
 leave it like it was for 1.0.5 There's a lot of changes to do in order
 to get the backward compatibility going. And I feel it should wait until
 1.1. I don't feel comfortable doing all these changes and releasing our
 software like this. It's a major change and it needs to be tested for a
 while.  OUr users are massively hammering the MA and rely on it so much.
 Although I do see the usefulness of the new ma and at term I believe it
 has major merits to be used instead of oldnumeric.ma.

 Your thoughts?
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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Charles Doutriaux
Hi Travis,

I get this:

import numpy, numpy.oldnumeric.ma as MA, numpy.oldnumeric as 
Numeric, PropertiedClasses
  File 
/lgm/cdat/latest/lib/python2.5/site-packages/numpy/oldnumeric/ma.py, 
line 2204, in module
array.mean = _m(average)
NameError: name 'average' is not defined

C.

Travis E. Oliphant wrote:
 Charles Doutriaux wrote:
   
 Hi Pierre,

 Im ccing Bob on this, he's the main developper for cdms2 package.
 
 I've uploaded the original ma.py file back into oldnumeric so that 
 oldnumeric.ma should continue to work as before.  Can you verify this?

 Thanks,

 -Travis O.


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[Numpy-discussion] output arguments for dot(), tensordot()

2008-04-01 Thread Andreas Klöckner
Hi all,

is there a particular reason why dot() and tensordot() don't have output 
arguments?

Andreas


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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread David Cournapeau
On Tue, Apr 1, 2008 at 8:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:

 I figured how to specify a particular installation of the libraries. I want
 to do the opposite. How do I specify the following in site.cfg - Don't
 search for the library. Assume that it is absent and use the default slower
 library ?

If you want to avoid compiling with say ATLAS, you can do something like

ATLAS=None python setup.py build

Disabling one specific version of one library is more difficult, though.

cheers,

David
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Robert Kern
On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:
 I am installing this on a CENTOS linux platform (64 bit AMD opteron). The
 path to my python directory is /home/amit/packages/Python-2.5.2 . If I
 temporarily make the atlas library unavailable (by renaming the directory to
 some name that is not in the path), I can perform the build. Now in the
 installation stage, I use
  python setup.py
 and then choose the option 2/home/amit/packages/Python-2.5.2. In the
 proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2.
 Incidentally, it also creates this new directory during install.

Looking at the code, I can confirm that the menu system is simply
buggy and the cause of your problem. Do not use it.

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth.
 -- Umberto Eco
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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Travis E. Oliphant
Charles Doutriaux wrote:
 Hi Travis,

 I get this:

 import numpy, numpy.oldnumeric.ma as MA, numpy.oldnumeric as 
 Numeric, PropertiedClasses
   File 
 /lgm/cdat/latest/lib/python2.5/site-packages/numpy/oldnumeric/ma.py, 
 line 2204, in module
 array.mean = _m(average)
 NameError: name 'average' is not defined
   
Thanks,

Can you try again?

Best regards,

-Travis

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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Robert Kern
On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:

 On Mon, Mar 31, 2008 at 11:06 PM, Robert Kern [EMAIL PROTECTED] wrote:
 
  On Mon, Mar 31, 2008 at 4:17 PM, Amit Itagi [EMAIL PROTECTED] wrote:
   Hi,
  
   I am having problems with numpy installation.
  
   1) These is an atlas 3.8.0 library installed somewhere in the search
 path.
   However, the installation gives errors with that installation. Is there
 a
   way to tell the installer to install the default (possibly slower) blas,
   instead of using the one in the path ?
 
  Create a site.cfg file with the appropriate section; copy and modify
  the site.cfg.example file.

 I figured how to specify a particular installation of the libraries. I want
 to do the opposite. How do I specify the following in site.cfg - Don't
 search for the library. Assume that it is absent and use the default slower
 library ?

There's nothing default about it. You should use the [lapack_opt]
section to specify whichever BLAS and LAPACK libraries you like, even
if they are not optimized.

   2) Also, my main Python directory is called Python-2.5.2. When I try to
   configure with the installprefix, it changes Python-2.5.2 to
   python-2.5.2 and creates a new directory. How can I make the installer
 not
   convert the upper-case P to a lower-case ?
 
  Can you give more information like the platform you are on, the full
  path to this directory, the exact commands that you executed, and the
  results of these commands?

 I am installing this on a CENTOS linux platform (64 bit AMD opteron). The
 path to my python directory is /home/amit/packages/Python-2.5.2 . If I
 temporarily make the atlas library unavailable (by renaming the directory to
 some name that is not in the path), I can perform the build. Now in the
 installation stage, I use
  python setup.py
 and then choose the option 2/home/amit/packages/Python-2.5.2. In the
 proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2.
 Incidentally, it also creates this new directory during install.

Can you just do a python setup.py install instead of going through
the menu system? The menu system may be bitrotten.

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth.
 -- Umberto Eco
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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Charles Doutriaux
Hi Travis,
Ok we're almost there, in my test suite i get:
maresult = numpy.core.ma.take(ta, indices, axis=axis)
AttributeError: 'module' object has no attribute 'ma'
data = numpy.core.ma.take(ax[:], indices)
AttributeError: 'module' object has no attribute 'ma'

I don't know if it was automatically put there by the converter or if we 
put it by hand.

If it's the first one, you might want to correct this, otherwise don't 
worry it's easy enough to fix (i think ?)

C.

Travis E. Oliphant wrote:
 Charles Doutriaux wrote:
   
 Hi Travis,

 I get this:

 import numpy, numpy.oldnumeric.ma as MA, numpy.oldnumeric as 
 Numeric, PropertiedClasses
   File 
 /lgm/cdat/latest/lib/python2.5/site-packages/numpy/oldnumeric/ma.py, 
 line 2204, in module
 array.mean = _m(average)
 NameError: name 'average' is not defined
   
 
 Thanks,

 Can you try again?

 Best regards,

 -Travis

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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Amit Itagi
On Tue, Apr 1, 2008 at 12:43 PM, David Cournapeau [EMAIL PROTECTED]
wrote:

 On Tue, Apr 1, 2008 at 8:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:
 
  I figured how to specify a particular installation of the libraries. I
 want
  to do the opposite. How do I specify the following in site.cfg - Don't
  search for the library. Assume that it is absent and use the default
 slower
  library ?

 If you want to avoid compiling with say ATLAS, you can do something like

 ATLAS=None python setup.py build


*The shell does not understand this command. Is this the correct syntax ?

Thanks

Rgds,
Amit

*




 Disabling one specific version of one library is more difficult, though.

 cheers,

 David
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Amit Itagi
On Tue, Apr 1, 2008 at 12:43 PM, David Cournapeau [EMAIL PROTECTED]
wrote:

 On Tue, Apr 1, 2008 at 8:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:
 
  I figured how to specify a particular installation of the libraries. I
 want
  to do the opposite. How do I specify the following in site.cfg - Don't
  search for the library. Assume that it is absent and use the default
 slower
  library ?

 If you want to avoid compiling with say ATLAS, you can do something like

 ATLAS=None python setup.py build



*Ok, this part works. I am using tcsh. So I had to do
setenv ATLAS None.

Rgds,
Amit
*



 Disabling one specific version of one library is more difficult, though.

 cheers,

 David
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Robert Kern
On Tue, Apr 1, 2008 at 1:31 PM, Amit Itagi [EMAIL PROTECTED] wrote:

 On Tue, Apr 1, 2008 at 1:21 PM, Robert Kern [EMAIL PROTECTED] wrote:
 
  On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:
   I am installing this on a CENTOS linux platform (64 bit AMD opteron).
 The
   path to my python directory is /home/amit/packages/Python-2.5.2 . If I
   temporarily make the atlas library unavailable (by renaming the
 directory to
   some name that is not in the path), I can perform the build. Now in the
   installation stage, I use
python setup.py
   and then choose the option 2/home/amit/packages/Python-2.5.2. In the
   proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2.
   Incidentally, it also creates this new directory during install.
 
  Looking at the code, I can confirm that the menu system is simply
  buggy and the cause of your problem. Do not use it.
 

 Robert,

 Could you kindly suggest an alternate way of getting it right ?

Just like every other Python package:

  $ python setup.py build
  ...
  $ sudo python setup.py install --prefix=/home/amit/packages/Python-2.5.2

http://docs.python.org/inst/inst.html

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth.
 -- Umberto Eco
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Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Stéfan van der Walt
Hi Dag

On Tue, Apr 1, 2008 at 11:06 AM, Dag Sverre Seljebotn
[EMAIL PROTECTED] wrote:
 One more comment about the constructor described on the page above.
 It would be good if we could have the same syntax as the current
 numpy.ndarray, and then simply call through to the underlying C
 constructor. We'd also need zeros, empty, ones_like and some other
 select functions. The goal is to remain as faithful as possible to
 the original API, so that there is hardly a distinction between Python
 and Cython.

  This will be automatic from how Cython operates :-) And that is, I think,
 what makes all of this great. Objects are Python objects all the time and by
 default retain all Python implementation, and we only override this
 implementation when the behaviour is retained.

  I'll walk through this code line by line:
  cdef c_numpy.ndarray(c_numpy.float, 2) x
 x = exp(4 + numpy.zeros([10, 10], dtype=numpy.float))
 y = x + 3
 print x[1, 3]
 print y[3, 5]

Thanks for this example;  I didn't notice that you were making a type
declaration, so my original comment was not valid.

  #3: (x + 3) will treat x as a Python object once again, so y will be an
 untyped variable referencing an ndarray like normal Python.

I can foresee certain situations under which we can predict the type
of the result of operations like this one.  Would it be possible to
then handle 'y' as an ndarray as well, instead of reverting to Python
object calls?

Regards
Stéfan
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Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Dag Sverre Seljebotn

 I can foresee certain situations under which we can predict the type
 of the result of operations like this one.  Would it be possible to
 then handle 'y' as an ndarray as well, instead of reverting to Python
 object calls?
   
Indeed - plans are underway to add automatic type inference to Cython. 
It is all about developer resources etc. (the preliminaries can be done 
in another GSoC project that we hope to get accepted).

When/if that happens, a lot of typing will not be necesarry, including 
this case. This will be an automatic consequence of Cython compiler 
development and not something that would need to be specifically for the 
case of NumPy (well, one declares would some more operator and function 
type signatures for NumPy, and then it would work).

Basically one would then only need to declare the type of arguments to 
the function, while local variables would be inferred automatically. 
(Getting around this is impossible, though we might add a different 
syntax for type declaration (using decorators) so that the same code can 
also be run using the Python interpreter.)

Perhaps in a year or so, if the current GSoCs are accepted :-) no 
promises though.

-- 
Dag Sverre

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Re: [Numpy-discussion] Project for Cython integration with NumPy

2008-04-01 Thread Gael Varoquaux
On Tue, Apr 01, 2008 at 10:48:30PM +0200, Dag Sverre Seljebotn wrote:
 though we might add a different syntax for type declaration (using
 decorators) so that the same code can also be run using the Python
 interpreter.)

That would be very neat. I can see how you can get around dynamical
typing in a very nice way using this. As the pypy projects says, giving a
dynamically-typed language to people does not necessarily means they type
dynamically-typed code.

I must say I like the idea a lot, you are really pushing the concept all
the way.

Gaël
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Amit Itagi
Robert,

I followed the recommended steps. Now I have numpy and 
numpy-1.0.4-py2.5.egg-info in
Python-2.5.2/lib/python2.5/site-packages. However, I am not able to import
numpy at the python prompt. Do I have to set pythonpath or something ?

Thanks

Rgds,
Amit

On Tue, Apr 1, 2008 at 2:44 PM, Robert Kern [EMAIL PROTECTED] wrote:

 On Tue, Apr 1, 2008 at 1:31 PM, Amit Itagi [EMAIL PROTECTED] wrote:
 
  On Tue, Apr 1, 2008 at 1:21 PM, Robert Kern [EMAIL PROTECTED]
 wrote:
  
   On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote:
I am installing this on a CENTOS linux platform (64 bit AMD
 opteron).
  The
path to my python directory is /home/amit/packages/Python-2.5.2 . If
 I
temporarily make the atlas library unavailable (by renaming the
  directory to
some name that is not in the path), I can perform the build. Now in
 the
installation stage, I use
 python setup.py
and then choose the option 2/home/amit/packages/Python-2.5.2. In the
proposed sys.argv the path is shown as /home/amit/packages/python-
 2.5.2.
Incidentally, it also creates this new directory during install.
  
   Looking at the code, I can confirm that the menu system is simply
   buggy and the cause of your problem. Do not use it.
  
 
  Robert,
 
  Could you kindly suggest an alternate way of getting it right ?

 Just like every other Python package:

  $ python setup.py build
  ...
  $ sudo python setup.py install --prefix=/home/amit/packages/Python-2.5.2

 http://docs.python.org/inst/inst.html

 --
 Robert Kern

 I have come to believe that the whole world is an enigma, a harmless
 enigma that is made terrible by our own mad attempt to interpret it as
 though it had an underlying truth.
  -- Umberto Eco
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Robert Kern
On Tue, Apr 1, 2008 at 4:03 PM, Amit Itagi [EMAIL PROTECTED] wrote:
 Robert,

 I followed the recommended steps. Now I have numpy and
 numpy-1.0.4-py2.5.egg-info in
 Python-2.5.2/lib/python2.5/site-packages. However, I am not able to import
 numpy at the python prompt. Do I have to set pythonpath or something ?

Possibly. Exactly what is in this .../Python-2.5.2/ directory? Is the
python executable .../Python-2.5.2/bin/python?

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth.
 -- Umberto Eco
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Re: [Numpy-discussion] Numpy installation

2008-04-01 Thread Robert Kern
On Tue, Apr 1, 2008 at 4:21 PM, Amit Itagi [EMAIL PROTECTED] wrote:
 This directory is just the Python source distribution (post configure and
 make). I don't have root permissions to our cluster and the default python
 distribution is an older one. Hence, I have my custom Python distribution in
 this /Python-2.5.2/ directory. The binary is /Python-2.5.2/python .

Okay, don't do that. You will have to actually install Python to
another location. For example, make a directory ~/python2.5/. Now go
to the Python source directory; it would probably be best to start
with a clean one. Configure Python using ~/python2.5 as the prefix:

  $ ./configure --prefix=~/python2.5

Now make and make install. Add ~/python2.5/bin to your $PATH,
preferably before /usr/bin or wherever the old python executable is.
Build and install numpy using the ~/python2.5/bin/python binary. You
should not need to set the --prefix.

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth.
 -- Umberto Eco
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Re: [Numpy-discussion] missing function in numpy.ma?

2008-04-01 Thread Travis E. Oliphant
Charles Doutriaux wrote:
 Hi Travis,
 Ok we're almost there, in my test suite i get:
 maresult = numpy.core.ma.take(ta, indices, axis=axis)
 AttributeError: 'module' object has no attribute 'ma'
 data = numpy.core.ma.take(ax[:], indices)
 AttributeError: 'module' object has no attribute 'ma'
   

I think the problem here is that numpy.core.ma is no longer the correct 
place.This should be

numpy.oldnumeric.ma.take  because numpy.oldnumeric.ma is the correct 
location.

In my mind you shouldn't really have been using numpy.core.ma, but 
instead numpy.ma because whether things are in core or lib could change 
;-) 

-Travis

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Re: [Numpy-discussion] output arguments for dot(), tensordot()

2008-04-01 Thread Robert Kern
On Tue, Apr 1, 2008 at 11:56 AM, Andreas Klöckner
[EMAIL PROTECTED] wrote:
 Hi all,

  is there a particular reason why dot() and tensordot() don't have output
  arguments?

No technical reason. It just hasn't been done. If you were to
implement it, we would be happy to accept it.

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth.
 -- Umberto Eco
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[Numpy-discussion] newbie doubt about dot()

2008-04-01 Thread harryos
i am slightly confused by this maths

i need to calculate
wk=uk o (L-Psi)
where
uk=a vector of size (1 X N^2)
o =scalar product
l,Psi=vectors of (N^2 X 1)

i have an ndarray U of shape(M X N^2)where uk is one of the rows , and
L of shape (M X N^2) where l.transpose() is one of the rows,
If i were to apply the above formula how can i find the matrix where
wk is an element.? I know i have to use dot() but the rest i am
finding a bit confusing
can someone please help?
harryos
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Re: [Numpy-discussion] newbie doubt about dot()

2008-04-01 Thread Alan G Isaac
On Tue, 1 Apr 2008, harryos apparently wrote:
 i need to calculate 
 wk=uk o (L-Psi)
 where 
 uk=a vector of size (1 X N^2)
 o =scalar product 
 l,Psi=vectors of (N^2 X 1)
 i have an ndarray U of shape(M X N^2)where uk is one of the rows , and 
 L of shape (M X N^2) where l.transpose() is one of the rows, 


Your explanation is not fully clear to me,
but perhaps the following will help.

#dummy values
rows = 2
cols = 3*3
U = numpy.ones((rows,cols)) + [[0],[1]]
L = numpy.random.random((rows,cols)) - 0.5
Psi = numpy.ones((cols,1))

#computation
numpy.dot(U,L.transpose() - Psi)

hth,
Alan Isaac



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