numpy-discussion — Discussion list for all users of Numerical Python

Re: [Numpy-discussion] f.p. powers and masked arrays

[Michael F. <mp...@be...>]

On Saturday 24 June 2006 13:12, Pierre GM wrote:
> I haven't really time to double-check/create a patch, tough. Meanwhile,
> Michael, you could just modify your numpy/core/ma.py accordingly.

Hi Pierre,

Thank you for the fix.  I checked it out and and numpy now behaves correctly 
for 0**1. in masked arrays.  Attached are the diffs for numpy (scipy.org SVN) 
and numarray (sf.net CVS).

Mike

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Re: [Numpy-discussion] (no subject)

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　かまいませんので気軽にメールを送って頂けると嬉しいです。
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　まずゎ会ってみないとはじまらなぃょね？！
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Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Sasha <nd...@ma...>]

On 6/24/06, Eric Firing <ef...@ha...> wrote:
> Out of curiosity, is there a simple explanation as to why "and" cannot
> be overridden but operators like "&" can?  Is it a fundamental
> distinction between operators and keywords?
>

There is no fundamental reason. In fact overloadable boolean operators
were proposed for python: <http://www.python.org/dev/peps/pep-0335>

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Fernando P. <fpe...@gm...>]

On 5/30/06, Travis Oliphant <oli...@ie...> wrote:

> 4) Please provide any suggestions for improving NumPy.

Well, if I can beg for one thing, it would be fixing dot():

http://projects.scipy.org/scipy/numpy/ticket/156

This bug is currently stalling us pretty badly, since dot() is at the
core of everything we do.  While the codebase I alluded to in my
previous message is fine, a project that sits on top of it is blocked
from moving on due to this particular problem.

If it's a problem on our side, I'll gladly correct it, but it does
seem like a bug to me (esp. with Stefan's test of r2651 which passes).

If there's any extra info that you need from me, by all means let me
know an I'll be happy to provide it.  If you have a feel for where the
problem may be but don't have time to fix it right now, I can look
into it myself, if you can point me in the right direction.

Cheers,

f

Re: [Numpy-discussion] Any Numeric or numarray users on this list?

[Fernando P. <fpe...@gm...>]

On 5/30/06, Travis Oliphant <oli...@ie...> wrote:
>
> Please help the developers by responding to a few questions.

Sorry for not replying before, I wanted a more complete picture before
answering.

> 1) Have you transitioned or started to transition to NumPy (i.e. import
> numpy)?

The day this email came in, I had just started to look into porting
our major research code.  I actually did the work 2 weeks ago, and it
went remarkably well.  It took a single (marathon) day, about 14 hours
of solid work, to go through the old codebase and convert it.  This
project had a mix of legacy Fortran wrapped via f2py, hand-written C
extensions using Numeric, a fair bit of weave.inline() and pure
python.  It uses matplotlib, PyX and Mayavi for various visualization
tasks.

There are some 40k loc in the Fortran sources (2/3 of that
auto-generated in python from Mathematica computations), and about 13k
loc in the C and python sources.

This codebase is heavily unit-tested, which was critical for the port.
 For this kind of effort, unittests make an enormous difference, as
they guide you directly to all the problematic spots.  Without
unittests, this kind of port would have been a nightmare, and I would
have never known whether things were actually finished or not.

Most of my changes had to do with explicit uses of 'typecode=' which
became dtype, and uses of .flat, which used to return a normal array
and is now an iterator.

I haven't benchmarked things right away, because I expect the
numpy-based code to take quite a hit.  In this code, I've heavily
abused arrays for very trivial 2 and 3-element arithmetic operations,
but that means that I create literally millions of extremely small
arrays.  Even with Numeric, this overhead was already measurable, and
I imagine it will get worse with numpy.  But since this was silly
anyway, and I need to use these little arrays as dictionary keys,
instead of doing lots of tuple(array()) all the time, I'm using David
Cooke's Vector as a template for a hand-written mini-array class that
will do exactly what I need with as little overhead as possible.

If for any reason you do want to see actual benchmarks, I can try to
run some with the codebases immediately before and after the
Numeric->numpy change and report back.

> 2) Will you transition within the next 6 months? (if you answered No to #1)

That's it: by now we've moved all of our code and it doesn't really
work with Numeric anymore, so we're committed :)


Again, many thanks for the major improvements that numpy brings!

Cheers,

f

[Numpy-discussion] basearray

[Karol L. <kar...@kn...>]

Dear all,

 Some of you might be aware that a project has been granted to me for this 
year's Google's Summer of Code, which aims at preparing a base 
multidimensional array type for Python. While I had a late start at it, I 
would like to go through with the project.

 The focus is on preparing a minimal type, that basically only defines how 
memory is alllocated for the array, and which can be used by other, more 
sophisticated types. Later during the project, the type may be enhanced, 
depending on how using it in practice (also part of the project) works out.

 Wiki page about the project: http://scipy.org/BaseArray
 SVN repository: http://svn.scipy.org/svn/PEP/

 In order to make this a potential success, I definately need feedback from 
all you out there interested in pushing such a base type towards Python core. 
So any comments and opinions are welcome! I will keep you informed on my 
progress and ask about things that may need concensus (although I'm not sure 
which lists will be the most interested in this). Please note that I am still 
in the phase of completing the minimal type, so the svn repository does not 
contain a working example, yet.

Regards,
Karol Langner

-- 
written by Karol Langner
nie cze 25 19:18:45 CEST 2006

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Alan G I. <ai...@am...>]

On Sat, 24 Jun 2006, Eric Firing apparently wrote: 
> I suspect that many other people will trip over the lack 
> of && in the same way that I have, and will similarly 
> consider it an irritant that we work around because we 
> have to, not because it is good. 

I agree with this.

In addition, turning to & when && is wanted
will likely cause occasional stumbles over operator 
precedence.  (At least I've been bitten that way.)

But I do not see this changing unless Python grants
the ability to define new operators, in which case
I'm sure the wish lists will come out ...

Cheers,
Alan Isaac

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Eric F. <ef...@ha...>]

Robert Kern wrote:
> Eric Firing wrote:
> 
>>That makes sense, and implies that the real solution would be the 
>>introduction of operators && and || into Python, or a facility that 
>>would allow extensions to add operators.  I guess it would be a matter 
>>of having hooks into the parser.  I have no idea whether either of these 
>>is a reasonable goal--but it certainly would be a big plus for Numpy.
> 
> 
> I don't really see how. We already have the & and | operators. The only 
> difference between them and the && and || operators would be that the latter 
> would automatically coerce to boolean arrays. But you can do that explicitly, now.
> 
>    a.astype(bool) | b.astype(bool)
> 

Another difference pointed out in the Wiki is precedence, which requires 
one to be more careful about parentheses when using the bitwise 
operators.  This arises because although the bitwise operators 
effectively do the right thing, given boolean arguments, there really is 
a difference between & and &&--that is why C, for example, has both. 
Using & when one means && is a hack that obscures the meaning of the 
code, and using logical_and is clear but cluttered--a significant step 
away from the goal of having code be clear, concise and readable.

I suspect that many other people will trip over the lack of && in the 
same way that I have, and will similarly consider it an irritant that we 
work around because we have to, not because it is good.

> Of course, it's highly likely that you are applying & and | to arrays that are 
> already boolean. Consequently, I don't see a real need for more operators.
> 
> But if you'd like to play around with the grammar:
> 
>    http://www.fiber-space.de/EasyExtend/doc/EE.html
> 

Interesting, thanks--but I will back off now.

Eric

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Robert K. <rob...@gm...>]

Eric Firing wrote:
> That makes sense, and implies that the real solution would be the 
> introduction of operators && and || into Python, or a facility that 
> would allow extensions to add operators.  I guess it would be a matter 
> of having hooks into the parser.  I have no idea whether either of these 
> is a reasonable goal--but it certainly would be a big plus for Numpy.

I don't really see how. We already have the & and | operators. The only 
difference between them and the && and || operators would be that the latter 
would automatically coerce to boolean arrays. But you can do that explicitly, now.

   a.astype(bool) | b.astype(bool)

Of course, it's highly likely that you are applying & and | to arrays that are 
already boolean. Consequently, I don't see a real need for more operators.

But if you'd like to play around with the grammar:

   http://www.fiber-space.de/EasyExtend/doc/EE.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

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Eric F. <ef...@ha...>]

Robert Kern wrote:
> Eric Firing wrote:
> 
>>Robert Kern wrote:
>>
>>>Eric Firing wrote:
>>>
>>>
>>>>It seems that the logical operators || and &&, corresponding to 
>>>>logical_or and logical_and are missing; one can do
>>>>
>>>>z = logical_and(x,y)
>>>>
>>>>but not
>>>>
>>>>z = x && y
>>>>
>>>>Is there an inherent reason, or is this a bug?
>>>
>>>Python does not have a && operator. It has an "and" keyword, but that cannot be 
>>>overridden. If you know x and y to be boolean arrays, & and | work fine.
>>
>>Out of curiosity, is there a simple explanation as to why "and" cannot 
>>be overridden but operators like "&" can?  Is it a fundamental 
>>distinction between operators and keywords?
> 
> 
> Sort of. "and" and "or" short-circuit, that is they stop evaluating as soon as 
> the right value to return is unambiguous.
> 
> In [1]: def f():
>     ...:     print "Shouldn't be here."
>     ...:
>     ...:
> 
> In [2]: False and f()
> Out[2]: False
> 
> In [3]: True or f()
> Out[3]: True
> 
> Consequently, they must yield True and False only.

That makes sense, and implies that the real solution would be the 
introduction of operators && and || into Python, or a facility that 
would allow extensions to add operators.  I guess it would be a matter 
of having hooks into the parser.  I have no idea whether either of these 
is a reasonable goal--but it certainly would be a big plus for Numpy.

Eric

Re: [Numpy-discussion] How do I seed the radom number generator?

[Robert K. <rob...@gm...>]

Keith Goodman wrote:

> Using the same seed sometimes gives different results:
> 
> from numpy import random
> def rtest():
>   rs = random.RandomState([11,21,699,1])
>   a = rs.rand(100,1)
>   b = rs.randn(100,1)
>   return sum(a + b)
> 
>>> mytest.rtest()
> array([ 41.11776129])
> 
>>> mytest.rtest()
> array([ 40.16631018])

Fixed in SVN. Thank you.

http://projects.scipy.org/scipy/numpy/ticket/155

-- 
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

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Robert K. <rob...@gm...>]

Eric Firing wrote:
> Robert Kern wrote:
>> Eric Firing wrote:
>>
>>> It seems that the logical operators || and &&, corresponding to 
>>> logical_or and logical_and are missing; one can do
>>>
>>> z = logical_and(x,y)
>>>
>>> but not
>>>
>>> z = x && y
>>>
>>> Is there an inherent reason, or is this a bug?
>>
>> Python does not have a && operator. It has an "and" keyword, but that cannot be 
>> overridden. If you know x and y to be boolean arrays, & and | work fine.
> 
> Out of curiosity, is there a simple explanation as to why "and" cannot 
> be overridden but operators like "&" can?  Is it a fundamental 
> distinction between operators and keywords?

Sort of. "and" and "or" short-circuit, that is they stop evaluating as soon as 
the right value to return is unambiguous.

In [1]: def f():
    ...:     print "Shouldn't be here."
    ...:
    ...:

In [2]: False and f()
Out[2]: False

In [3]: True or f()
Out[3]: True

Consequently, they must yield True and False only.

> In any case, it sounds like we are indeed stuck with an unfortunate wart 
> on numpy, unless some changes in Python can be made.  Maybe for 
> Python3000...
> 
> The NumPy for Matlab users wiki is misleading in this area; I will try 
> to fix it.

Thank you.

-- 
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

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Eric F. <ef...@ha...>]

Robert Kern wrote:
> Eric Firing wrote:
> 
>>It seems that the logical operators || and &&, corresponding to 
>>logical_or and logical_and are missing; one can do
>>
>>z = logical_and(x,y)
>>
>>but not
>>
>>z = x && y
>>
>>Is there an inherent reason, or is this a bug?
> 
> 
> Python does not have a && operator. It has an "and" keyword, but that cannot be 
> overridden. If you know x and y to be boolean arrays, & and | work fine.

Out of curiosity, is there a simple explanation as to why "and" cannot 
be overridden but operators like "&" can?  Is it a fundamental 
distinction between operators and keywords?

In any case, it sounds like we are indeed stuck with an unfortunate wart 
on numpy, unless some changes in Python can be made.  Maybe for 
Python3000...

The NumPy for Matlab users wiki is misleading in this area; I will try 
to fix it.

Eric

Re: [Numpy-discussion] logical_and operator, &&, is missing?

[Robert K. <rob...@gm...>]

Eric Firing wrote:
> It seems that the logical operators || and &&, corresponding to 
> logical_or and logical_and are missing; one can do
> 
> z = logical_and(x,y)
> 
> but not
> 
> z = x && y
> 
> Is there an inherent reason, or is this a bug?

Python does not have a && operator. It has an "and" keyword, but that cannot be 
overridden. If you know x and y to be boolean arrays, & and | work fine.

> z = (x == y)
> 
> works, and a comment in umathmodule.c.src suggests that && and || should 
> also:
> 
> /**begin repeat
> 
> #kind=greater, greater_equal, less, less_equal, equal, not_equal, 
> logical_and, logical_or, bitwise_and, bitwise_or, bitwise_xor#
> #OP=>, >=, <, <=, ==, !=, &&, ||, &, |, ^#
> **/

Those operators are the C versions that will be put in the appropriate places in 
the generated code. That is not a comment for documentation.

-- 
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

Re: [Numpy-discussion] f.p. powers and masked arrays

[Pierre GM <pgm...@ma...>]

Michael,

> Is anyone else seeing this?  It should be easy to test.  If so, I
> think it's a bug.

Yeah, I see that as well.
In MA.power(a,b), a temporary mask is created, True for values a<=0.
(check L1577 of the sources, 
`md = make_mask(umath.less_equal (fa, 0), flag=1)`). The combination of this 
temp and the initial mask defines the final mask.

This condition could probably be relaxed to 
`md = make_mask(umath.less(fa, 0), flag=1)`
That way, the a=0 elements wouldn't be masked, and you'd get the proper 
result.

I haven't really time to double-check/create a patch, tough. Meanwhile, 
Michael, you could just modify your numpy/core/ma.py accordingly.

[Numpy-discussion] logical_and operator, &&, is missing?

[Eric F. <ef...@ha...>]

It seems that the logical operators || and &&, corresponding to 
logical_or and logical_and are missing; one can do

z = logical_and(x,y)

but not

z = x && y

Is there an inherent reason, or is this a bug?

z = (x == y)

works, and a comment in umathmodule.c.src suggests that && and || should 
also:

/**begin repeat

#kind=greater, greater_equal, less, less_equal, equal, not_equal, 
logical_and, logical_or, bitwise_and, bitwise_or, bitwise_xor#
#OP=>, >=, <, <=, ==, !=, &&, ||, &, |, ^#
**/

My version is '0.9.9.2584'.

Eric

[Numpy-discussion] =?GB2312?B?s7W85LncwO3Iy9SxsMvP7tDewbY8YWQ+?=

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Re: [Numpy-discussion] How do I seed the radom number generator?

[Keith G. <kwg...@gm...>]

On 6/22/06, Robert Kern <rob...@gm...> wrote:
> Keith Goodman wrote:
> > How do I seed rand and randn?
>
> If you can, please use the .rand() and .randn() methods on a RandomState object
> which you can initialize with whatever seed you like.
>
> In [1]: import numpy as np
> rs
> In [2]: rs = np.random.RandomState([12345678, 90123456, 78901234])
>
> In [3]: rs.rand(5)
> Out[3]: array([ 0.40355172,  0.27449337,  0.56989746,  0.34767024,  0.47185004])

Using the same seed sometimes gives different results:

from numpy import random
def rtest():
  rs = random.RandomState([11,21,699,1])
  a = rs.rand(100,1)
  b = rs.randn(100,1)
  return sum(a + b)

>> mytest.rtest()
array([ 41.11776129])

>> mytest.rtest()
array([ 40.16631018])

>> numpy.__version__
'0.9.7.2416'

I ran the test about 20 times before I got the 40.166 result.

Re: [Numpy-discussion] matlab translation

[Mark T. <mtr...@gm...>]

A couple of months ago I started something similar but unfortunately it has
since stagnated.  Its located at pym.python-hosting.com.  With the exception
of a commit a few weeks ago I haven't touched it for 4 months.

That being said I havn't completly abandoned it and the basic foundation is
there, all that remains is most of the language rules.  I left it halfway
through implementing language precedence according to
http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_prog/f0-38155.html.


Mark.

On 6/24/06, Robert Kern <rob...@gm...> wrote:
>
> Vinicius Lobosco wrote:
> > Let's just let those who want to try to do that and give our support? I
> > would be happy if I could some parts of my old matlab programs
> > translated to Scipy.
>
> I do believe that, "Show me," is an *encouragement*. I am explicitly
> encouraging
> Mathew to work towards that end. Sheesh.
>
> --
> 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
>
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>

Re: [Numpy-discussion] flatiter and inequality comparison

[Alan G I. <ai...@am...>]

On Fri, 23 Jun 2006, Travis Oliphant apparently wrote: 
> option 2 does make sense (an array of resulting comparisions is returned).  
> Thus now: 
>  >> x=arange(3).flat 
>  >>> x>2 
> array([False, False, False], dtype=bool) 

Thanks!!
Alan

Re: [Numpy-discussion] matlab translation

[Robert K. <rob...@gm...>]

Vinicius Lobosco wrote:
> Let's just let those who want to try to do that and give our support? I 
> would be happy if I could some parts of my old matlab programs 
> translated to Scipy.

I do believe that, "Show me," is an *encouragement*. I am explicitly encouraging 
Mathew to work towards that end. Sheesh.

-- 
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

Re: [Numpy-discussion] matlab translation

[Vinicius L. <vin...@pa...>]

Let's just let those who want to try to do that and give our support? I
would be happy if I could some parts of my old matlab programs translated t=
o
Scipy.



On 6/24/06, Robert Kern <rob...@gm...> wrote:
>
> Keith Goodman wrote:
> >> I'm porting by hand. It does not seem easy to me. And even if it were
>
> Mathew Yeates wrote:
> > Ah. Do I detect a dare? Could start first by using Octaves matlab
> parser.
>
> Let's just say that anyone coming to this list saying something like, "It
> doesn't seem like it would be all THAT difficult to write," gets an
> automatic,
> "Show me," from me.
>
> --
> 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
>
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>



--=20
---------------------------------
Vinicius Lobosco, PhD
www.paperplat.com

+46   8 612 7803
+46 73 925 8476

Bj=F6rnn=E4sv=E4gen 21
SE-113 47 Stockholm, Sweden

[Numpy-discussion] Moving this mailing list to scipy.org

[Robert K. <rob...@gm...>]

Thanks to Sourceforge's new "feature" of ads on the bottom of all list emails, 
it has been suggested that we move this mailing list to scipy.org.

I've gotten some feedback from several of you already, all in favor of moving 
the mailing list from Sourceforge to scipy.org. However, I know there are plenty 
more of you out there. I wanted to move this topic up to the top level to make 
sure people see this.

If you care whether it moves or if it stays, please email me *offlist* stating 
your preference. If by Wednesday, June 28th, the response is still as positive 
as it has been, then we'll start moving the list.

Thank you.

-- 
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

Re: [Numpy-discussion] matlab translation

[Robert K. <rob...@gm...>]

Keith Goodman wrote:
>> I'm porting by hand. It does not seem easy to me. And even if it were

Mathew Yeates wrote:
> Ah. Do I detect a dare? Could start first by using Octaves matlab parser.

Let's just say that anyone coming to this list saying something like, "It 
doesn't seem like it would be all THAT difficult to write," gets an automatic, 
"Show me," from me.

-- 
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