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

[Numpy-discussion] Numpy-discussion--Bachelor's Diploma, Master's, or PhD - No Classes Necessary

[Noemi L. <de...@ma...>]

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[Numpy-discussion] question/request with Numeric compress and putmask

[Vineet J. <vi...@es...>]

I'm using the Numeric arrays for financial data elements. I'm interfacing
with an external c library which does not support invalid elements. To get
around this I maintain a separate mask array in my python class which
denotes which elements are valid. I then use the compress function with the
mask array to get an array with valid elements which I pass to the c
function.

I was then going to use the putmask to assign the returned values to their
corresponding place in the original array. This obviously (after reading the
documentation) is not going to work.

Example:

financial_data 	= [10, 11, 22, 33, INVALID, INVALID, 44, 55]
full_return_value = INVALID+zeros(lenfinancial_data)

my_mask 		= [1, 1, 1, 1, 0, 0, 1, 1]
compressed_data	= compress(financiali_data, my_mask)
			  [10, 11, 22, 33, 44, 55]

return_value 	= some_c_function(compressed_data)

Now the problem I have is copying the values in return_value to their
original place in the financial_data. I was happily going to use putmask
till about an hour back when I found out that this is not going to work.

What I would like to do is:

putmask(full_return_value, my_mask, return_value)

where return_value is treated like a list so that every 1 that is found in
my_mask the next element in return_value is used. Is their anything that
matches this?

I've looked at Masked Array. I don't like the fact that it return copies of
data and not references. I'm also unsure on how to pass it to c functions
(since it is a pure python package).

Any suggestions? and thanks for any help.

Re: [Numpy-discussion] numarray-0.8.1

[RayS <ra...@bl...>]

At 08:32 PM 1/30/04 -0600, Austin Luminais wrote:
>As for why it doesn't work with Installer, I'm not sure.  At least part of 
>the problem is that it is hardcoded to load LICENSE.TXT in __init__.py in 
>a way that is incompatible with Installer.
>I tried removing the loading of LICENSE.TXT (which I realize is a 
>questionable thing to do; I was just trying to get it working), but it 
>doesn't work after that either.

I saw this thread before:
http://aspn.activestate.com/ASPN/Mail/Message/numpy-discussion/1967514
seems the solution though I haven't had to try it.
I prefer McMillan to py2exe for it's smaller exe-s.

Ray 

[Numpy-discussion] array resizing?

[Daniel H. <dh...@fa...>]

Is it possible for a C function to take an array from Python and resize
it for returned results?

[Numpy-discussion] numarray-0.8.1

[Austin L. <au...@ma...>]

Hello, is there any place I can download a Windows installer for numarray 
0.8.1?  I upgraded to 0.8.2 a while back, but it does not work with 
McMillan's Installer.  0.8.1 worked fine, but I neglected to keep a copy of it.

As for why it doesn't work with Installer, I'm not sure.  At least part of 
the problem is that it is hardcoded to load LICENSE.TXT in __init__.py in a 
way that is incompatible with Installer.
I tried removing the loading of LICENSE.TXT (which I realize is a 
questionable thing to do; I was just trying to get it working), but it 
doesn't work after that either.

[Numpy-discussion] shape, size

[Daniel H. <dh...@se...>]

apoligies if this is a duplicate...

How do you write nb = na[:,:4] in a C extension module?

Thanks, Daniel Holth

Re: [Numpy-discussion] shape, size

[Todd M. <jm...@st...>]

On Thu, 2004-01-29 at 23:12, Daniel Holth wrote:
> In python, if na is a numarray:
> 
> >>> na
> array([[0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0],
>        [1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1]])
> 
> I can type
> 
> >>> nb = na[:,:4]
> >>> nb
> array([[0, 1, 0, 1],
>        [1, 0, 1, 0]])
> 
> >>> nb[0][0]=17
> 
> >>> na
> array([[17,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0],
>        [ 1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1]])
> 
> nb and na share data.
> 
> How do you write nb = na[:,:4] in a C extension module?

Here's the quick and dirty way:

nb = (PyArrayObject *) PyObject_CallMethod(na, "view", NULL);
if (na->dimensions[1] >= 4)
	nb->dimensions[1] = 4;

Todd
> 
> Thanks,
> 
> Daniel Holth
> 
> 
> 
> -------------------------------------------------------
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-- 
Todd Miller 			
Space Telescope Science Institute
3700 San Martin Drive
Baltimore MD, 21030
(410) 338 - 4576

[Numpy-discussion] shape, size

[Daniel H. <dh...@fa...>]

In python, if na is a numarray:

>>> na
array([[0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0],
       [1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1]])

I can type

>>> nb = na[:,:4]
>>> nb
array([[0, 1, 0, 1],
       [1, 0, 1, 0]])

>>> nb[0][0]=17

>>> na
array([[17,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0],
       [ 1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1,  0,  1]])

nb and na share data.

How do you write nb = na[:,:4] in a C extension module?

Thanks,

Daniel Holth

Re: [Numpy-discussion] Writing arrays to files.

[Andrea R. <ari...@pi...>]

On 27 Jan 2004, at 19:31, John Hunter wrote:

> If your array is not monstrously large, and you can do it all in
> memory, do

1-dim arrays with 1000 elements and  2-dim arrays with (1000 x 1000) 
elements have to be considered "monstrously large"?

Cheers,
	Andrea.

---
Andrea Riciputi

"Science is like sex: sometimes something useful comes out,
   but that is not the reason we are doing it" -- (Richard Feynman)

Re: [Numpy-discussion] atan2

[Niall D. <ni...@la...>]

On Wed, 2004-01-28 at 17:39, John Hunter wrote:
> >>>>> "Niall" == Niall Dalton <ni...@la...> writes:
> 
>     Niall> I do need to use atan2

>  Numeric.arctan2
> 
> If you run into a similar problem in the future, you may want to try
> 
> >>> import Numeric
> >>> dir(Numeric)
> 
> Hope this helps,

It does indeed, thanks! I blame the first snowfall we just had minutes
ago for the oversight - its my story and I'm sticking to it ;-)

Thanks,
niall


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Re: [Numpy-discussion] atan2

[John H. <jdh...@ac...>]

>>>>> "Niall" == Niall Dalton <ni...@la...> writes:

    Niall> Hello, I'm using Numeric 23.1, and finding it very useful!
    Niall> I do need to use atan2, and a browse of the manual suggests
    Niall> its not available as a binary ufunc.

 Numeric.arctan2

If you run into a similar problem in the future, you may want to try

>>> import Numeric
>>> dir(Numeric)

Hope this helps,
JDH

[Numpy-discussion] atan2

[Niall D. <ni...@la...>]

Hello,

I'm using Numeric 23.1, and finding it very useful! I do need to use
atan2, and a browse of the manual suggests its not available as a binary
ufunc.

I'm happy to add it myself if I'm correct - I'm guessing it should be
simple to based on the code of one of the existing functions. Is Numeric
still accepting patches, or should I consider switching to Numarray?

Regards,
Niall


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Re: [Numpy-discussion] Writing arrays to files.

[John H. <jdh...@ac...>]

>>>>> "Andrea" == Andrea Riciputi <ari...@pi...> writes:

    Andrea> On 27 Jan 2004, at 19:31, John Hunter wrote:
    >> If your array is not monstrously large, and you can do it all
    >> in memory, do

    Andrea> 1-dim arrays with 1000 elements and 2-dim arrays with
    Andrea> (1000 x 1000) elements have to be considered "monstrously
    Andrea> large"?

You should have no trouble with either the 1D or 2D approaches I
posted with arrays this size.

Even though 1000x1000 is a lot of elements, the 2D approach does the
string operations row by row, so only 1000 will be converted at a
time, which will be trivial for all but the clunkiest machines.

JDH

Re: [Numpy-discussion] Writing arrays to files.

[John H. <jdh...@ac...>]

>>>>> "Andrea" == Andrea Riciputi <ari...@pi...> writes:

    Andrea> Hi, I need a little help here. I need to write some
    Andrea> Numeric arrays (coming from some simulations) to ASCII
    Andrea> files. I'm sure it's a well known topic and I'd be happy
    Andrea> not to have to reinvent the wheel. I've both 1-dim and
    Andrea> 2-dim arrays and I'd like to get something like this:

    Andrea> - 1-dim array ASCII file:

    Andrea> 0.1 0.2 0.3 etc...

If your array is not monstrously large, and you can do it all in
memory, do

  fh = file('somefile.dat', 'w')
  s = ' '.join([str(val) for val in a])
  fh.write(s)

where a is your 1D array

    Andrea> - 2-dim array ASCII file:

    Andrea> 0.1 0.2 0.3 0.4 0.5 0.6 etc....

    Andrea> How can I get them?

Same idea

  fh = file('somefile.dat', 'w')
  for row in a:
      s = ' '.join([str(val) for val in row])
      fh.write('%s\n' % s)

where a is your 2D array

The scipy module also has support for reading and writing ASCII files.

Note if you are concerned about efficiency and are willing to use
binary files, use the fromstring and tostring methods.

JDH

[Numpy-discussion] Writing arrays to files.

[Andrea R. <ari...@pi...>]

Hi,
I need a little help here. I need to write some Numeric arrays (coming 
from some simulations) to ASCII files. I'm sure it's a well known topic 
and I'd be happy not to have to reinvent the wheel. I've both 1-dim and 
2-dim arrays and I'd like to get something like this:

- 1-dim array ASCII file:

0.1 0.2 0.3 etc...

- 2-dim array ASCII file:

0.1 0.2 0.3
0.4 0.5 0.6
etc....

How can I get them?

Thanks in advance,
	Andrea.

---
Andrea Riciputi

"Science is like sex: sometimes something useful comes out,
   but that is not the reason we are doing it" -- (Richard Feynman)

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[Numpy-discussion] Status

[<is...@ce...>]

The message contains Unicode characters and has been sent as a binary attachment.

Re: [Numpy-discussion] cygwin problems?

[Michiel J. L. de H. <md...@im...>]

Patch 732520 for Numeric fixes both problems. The problem is caused by some 
lapack routines being inadvertently compiled with optimization; see the patch 
description for a full explanation. Note that the same error may occur on 
platforms other than Cygwin, and also with other linear algebra functions.

--Michiel, U Tokyo.

Paul F. Dubois wrote:

> A user (see below) has complained that svd and other functions hang on 
> cygwin, with numarray and Numeric. Anyone know anything about this?
> 
> Hi Paul
> 
> I tried the svd of numarray, version 0.6.2,  I did not download the 
> newest version of
> numarray,  and still the same problem happen, it hanged on my cygwin box.
> 
> I've also, noticed that calculating the eigenvalues of a square matrix 
> with Numeric also
> hang the python 2.3  I wonder if the problem is related....
> 
> Let me know, if you have some idea of what to do next.
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
> 
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon

Re: [Numpy-discussion] summing "sparse" 2D arrays? Results...

[Ray S. <ra...@bl...>]

I just realized...
where() belongs to Numeric, so I need
sum([Numeric.where(a < 255, a, 0) for a in y])
duh.

I did just compare Numeric vs. Masked arrays:
===========================================================
# test.py
from MA import masked_array, sum
from RandomArray import *
import time

seed()
y = randint(240,256, (480,640,16))
start = time.time()

x=masked_array(y, y>=255)
maskTime = time.time() - start
sum_1 = sum(x,axis=2)
maskedTime = time.time() - start
print sum_1.shape
print sum_1
print "mask make time: " + str(maskTime)
print "time using MA: " + str(maskedTime) + "\n"

z = Numeric.reshape(y, (16, 480, 640))
newStart = time.time()
sum_2 = sum([Numeric.where(a < 255, a, 2) for a in z])
numTime = time.time() - newStart
print sum_2.shape
print sum_2
print "time using Numeric: " + str(numTime) + "\n"
======================================================

Result:
C:\projects\Astro>python test.py
(480, 640)
array (480,640) , type = O, has 307200 elements
mask make time: 1.07899999619
time using MA: 3.39100003242

(480, 640)
array (480,640) , type = l, has 307200 elements
time using Numeric: 2.39099979401

So, MA's sum() is slightly faster, but the penalty for making a mask first 
is large.

Now I have to figure out why I had to reshape the array for the second 
computation.

Thanks,
Ray












At 09:17 AM 1/26/2004 +0100, you wrote:
>On 26.01.2004, at 07:14, RJS wrote:
>
>>The problem: I have a "stack" of 8,  640 x 480 integer image arrays from 
>>a FITS cube concatenated into a 3D array, and I want to sum each pixel 
>>such that the result ignores clipped values (255+); i.e., if two images 
>>have clipped pixels at (x,y) the result along z will be the sum of the other 6.
>Memory doesn't seem critical for such small arrays, so you can just do
>
>sum([where(a < 255, a, 0) for a in images])

Hello Konrad,

I just tried:

from MA import masked_array, sum
from RandomArray import *
seed()
y = randint(240,256, (480,640,2))
print sum([where(a < 255, a, 0) for a in y])

and it errors:
Traceback (most recent call last):
   File "test.py", line 21, in ?
     print sum([where(a < 255, a, 0) for a in y])
NameError: name 'where' is not defined

Could you enlighten me further?
I have not found a good resource for compound Numeric statements yet.

Thank you,

Ray

[Numpy-discussion] cygwin problems?

[Paul F. D. <du...@ll...>]

A user (see below) has complained that svd and other functions hang on 
cygwin, with numarray and Numeric. Anyone know anything about this?

Hi Paul

I tried the svd of numarray, version 0.6.2,  I did not download the 
newest version of
numarray,  and still the same problem happen, it hanged on my cygwin box.

I've also, noticed that calculating the eigenvalues of a square matrix 
with Numeric also
hang the python 2.3  I wonder if the problem is related....

Let me know, if you have some idea of what to do next.

[Numpy-discussion] Searchable online documentation of Numeric Python

[F. <j_r...@ya...>]

I've made this mainly for myself, but in case anybody here finds it
useful, here is the online documentation of Numeric Python with
TOC/index/search navigation:

  http://mefriss1.swan.ac.uk/htmlhelp/php/index.php?book_id=49

There's also Python documention there if you fancy it.

NOTE: The URL may go dead eventually, but until I'll arrange a way to
have this documentation elsewhere, so it won't worry about that.

I hope you enjoy it.

Jose Fonseca

Re: [Numpy-discussion] Status of Numeric

[Chris B. <Chr...@no...>]

I remember that thread clearly, as I think making it easy to write new 
Ufuncs (and others) that perform at C speed could make a real difference 
to how effective SciPy ultimately is. I say SciPy, because I believe a 
large collection of special purpose optimized functions probably doesn't 
belong in in Numarray itself.

Francesc Alted wrote:

> So, it seems that he don't liked the idea to implement "templates" in Pyrex.

Yes, I remember that answer, and was disappointed, though the logic of 
not-re-implkimenting C++ templates is pretty obvious. Which brings up 
the obvious question: why not use C++ templates themselves? which is 
what Blitz does. This points ot weave.blitz at the obvious way to write 
optimized special purpose functions for SciPy. Does weave.Blitz work 
with Numarray yet?

Clearly it's time for me to check it out more...

> Yeah, I'm quite convinced that a mix between Pyrex and the existing solution
> in numarray for dealing with templates could be worth the effort.  At least,
> some analysis could be done on that aspect.

allowing Pyrex to use templates would be great.. but how would that be 
better than weave.blitz? Or maybe Pyrex could use blitz.

I'm kind of over my head here, but I hope something comes of this.

-Chris


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Chr...@no...

Re: [Numpy-discussion] simple Numarray question

[Todd M. <jm...@st...>]

On Mon, 2004-01-26 at 11:38, Nancy Keuss wrote:
> Hi,
> 
> What do I have to include in my Python file for Python to recognize Numarray
> functions? For instance, in a file called hello.py I try:
> 
> a = arange(10)
> print a[1:5]
> 
> and I get the error:
> 
> Traceback (most recent call last):
>   File "C:\Python23\hello.py", line 3, in ?
>     a = arange(10)
> NameError: name 'arange' is not defined
> 
There are a number of ways to import numarray (or any Python module),
but the way I recommend is this:

import numarray

a = numarray.arange(10)
print a[1:5]

If you're writing quick scripts that you're not worried about
maintaining, do this:

from numarray import *

a = arange(10)
print a[1:5]

If writing "numarray." is too tedious, but you still care about
maintenance, try something like this:

import numarray as _n

a  = _n.arange(10)
print a[1:5]


Todd

> Thank you,
> Nancy
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
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> _______________________________________________
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> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
-- 
Todd Miller <jm...@st...>

Re: [Numpy-discussion] simple Numarray question

[Jon S. <js...@wm...>]

Read point 6 of the Python Tutorial.

Read chapter 2 (Installing NumPy) of Numeric Python manual.

Hope this helps.


Jon Saenz.				| Tfno: +34 946012445
Depto. Fisica Aplicada II               | Fax:  +34 944648500
Facultad de Ciencias.   \\ Universidad del Pais Vasco \\
Apdo. 644   \\ 48080 - Bilbao  \\ SPAIN

On Mon, 26 Jan 2004, Nancy Keuss wrote:

> Hi,
>
> What do I have to include in my Python file for Python to recognize Numarray
> functions? For instance, in a file called hello.py I try:
>
> a = arange(10)
> print a[1:5]
>
> and I get the error:
>
> Traceback (most recent call last):
>   File "C:\Python23\hello.py", line 3, in ?
>     a = arange(10)
> NameError: name 'arange' is not defined
>
> Thank you,
> Nancy
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> Numpy-discussion mailing list
> Num...@li...
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion
>

[Numpy-discussion] simple Numarray question

[Nancy K. <na...@MI...>]

Hi,

What do I have to include in my Python file for Python to recognize Numarray
functions? For instance, in a file called hello.py I try:

a = arange(10)
print a[1:5]

and I get the error:

Traceback (most recent call last):
  File "C:\Python23\hello.py", line 3, in ?
    a = arange(10)
NameError: name 'arange' is not defined

Thank you,
Nancy