From sigidagi at hotmail.com  Tue Jul  1 06:19:10 2003
From: sigidagi at hotmail.com (Sigis Dagilis)
Date: Tue, 01 Jul 2003 10:19:10 +0000
Subject: [SciPy-user] scipy.plt and py2exe problem
Message-ID: <Law14-F5VOmurpgPBg500047c92@hotmail.com>

Hi,

I build an application with wxPython (GUI) and use scipy.plt module to plot 
a data. The application works OK - "python myfile.py". The problem appears 
when I tryed to compile script to exe file using py2exe:

The following modules were not found:
  Image
  line_endings
  scipy_base.transpose
  curses
  utilsc
  scipy_base.sqrt
  scipy_base.imag
  scipy_base.product
  scipy_base.diag
  scipy.fftpack.ifft2
  scipy_base.shape
  scipy_base.polydiv
  reportlab.pdfbase.pdfmetrics
  scipy_base.roots
  scipy_base.expand_dims
  scipy_base.polyder
  scipy_base.nan
  scipy_base.atleast_2d
  scipy_base.sort
  controls2c
  sizersc
  scipy_base.where
  scipy_base.array
  scipy_base.reshape
  scipy_base.poly1d
  f2py2e
  scipy_base.amin
  scipy_base.isscalar
  scipy_base.eye
  scipy.fftpack.fft2
  scipy_base.around
  scipy_base.poly
  scipy_base.polyint
  scipy_base.NewAxis
....
...

Can enyone help me to solve this problem?

_________________________________________________________________
F? MSN Hotmail p? mobilen http://www.msn.dk/mobile



From "oliphant." at ee.byu.edu  Tue Jul  1 19:43:51 2003
From: "oliphant." at ee.byu.edu (Travis Oliphant)
Date: Tue, 01 Jul 2003 17:43:51 -0600
Subject: [SciPy-user] read_array
References: <3F00E5A3.40005@snet.net>
Message-ID: <3F021CB7.8080907@ee.byu.edu>


Cliff Martin wrote:
> I'm trying to read a large ASCII file (each line has a carraige return) 
> with elements separated by spaces(it can be variable due to large number 
> differences). My code is below and the error message from the code 
> follows. By the way the size of the array is 223 by 221.  This read 
> works quite well with a smaller file.  What is the problem?
> 
> A = scipy.io.read_array('c:/transfer/av56tst1.int')
> Traceback (most recent call last):
>  File "<interactive input>", line 1, in ?
>  File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 
> 369, in read_array
>    outarr[k][row] = vals[k]
> ValueError: matrices are not aligned for copy
> 

This looks like one of the lines is not the same as the others (or is 
not being interpreted as the same).  Are you sure each line has the same 
number of elements?  Are there lines with text on them?

If you send a copy of your file I can tell you specifically what's wrong.

-Travis O.



From guest at guest.com  Wed Jul  2 00:15:18 2003
From: guest at guest.com (guest)
Date: Wed, 2 Jul 2003 12:15:18 +0800
Subject: [SciPy-user] The Uncertainty Principle Is Untenable
Message-ID: <20030702053650.A2F373EB0C@www.scipy.com>

please reply to hdgbyi at public.guangzhou.gd.cn
thank you.
 

THE UNCERTAINTY PRINCIPLE IS UNTENABLE

By re-analysing Heisenberg's Gamma-Ray Microscope experiment and the ideal experiment from which the uncertainty principle is derived, it is actually found that the uncertainty principle can not be obtained from them. It is therefore found to be untenable. 

Key words: 
uncertainty principle; Heisenberg's Gamma-Ray Microscope Experiment; ideal experiment 

Ideal Experiment 1

                 Heisenberg's Gamma-Ray Microscope Experiment


A free electron sits directly beneath the center of the microscope's lens (please see AIP page http://www.aip.org/history/heisenberg/p08b.htm or diagram below) . The circular lens forms a cone of angle 2A from the electron. The electron is then illuminated from the left by gamma rays--high energy light which has the shortest wavelength. These yield the highest resolution, for according to a principle of wave optics, the microscope can resolve (that is, "see" or distinguish) objects to a size of dx, which is related to and to the wavelength L of the gamma ray, by the expression: 

dx = L/(2sinA) (1) 

However, in quantum mechanics, where a light wave can act like a particle, a gamma ray striking an electron gives it a kick. At the moment the light is diffracted by the electron into the microscope lens, the electron is thrust to the right. To be observed by the microscope, the gamma ray must be scattered into any angle within the cone of angle 2A. In quantum mechanics, the gamma ray carries momentum as if it were a particle. The total momentum p is related to the wavelength by the formula, 

p = h / L, where h is Planck's constant. (2) 

In the extreme case of diffraction of the gamma ray to the right edge of the lens, the total momentum would be the sum of the electron's momentum P'x in the x direction and the gamma ray's momentum in the x direction: 

P' x + (h sinA) / L', where L' is the wavelength of the deflected gamma ray. 

In the other extreme, the observed gamma ray recoils backward, just hitting the left edge of the lens. In this case, the total momentum in the x direction is: 

P''x - (h sinA) / L''. 

The final x momentum in each case must equal the initial x momentum, since momentum is conserved. Therefore, the final x momenta are equal to each other: 

P'x + (h sinA) / L' = P''x - (h sinA) / L'' (3) 

If A is small, then the wavelengths are approximately the same, 

L' ~ L" ~ L. So we have 

P''x - P'x = dPx ~ 2h sinA / L (4) 

Since dx = L/(2 sinA), we obtain a reciprocal relationship between the minimum uncertainty in the measured position, dx, of the electron along the x axis and the uncertainty in its momentum, dPx, in the x direction: 

dPx ~ h / dx or dPx dx ~ h. (5) 

For more than minimum uncertainty, the "greater than" sign may added. 

Except for the factor of 4pi and an equal sign, this is Heisenberg's uncertainty relation for the simultaneous measurement of the position and momentum of an object. 

Re-analysis

To be seen by the microscope, the gamma ray must be scattered into any angle within the cone of angle 2A. 

The microscope can resolve (that is, "see" or distinguish) objects to a size of dx, which is related to and to the wavelength L of the gamma ray, by the expression: 

dx = L/(2sinA) (1) 

This is the resolving limit of the microscope and it is the uncertain quantity of the object's position. 

The microscope can not see the object whose size is smaller than its resolving limit, dx. Therefore, to be seen by the microscope, the size of the electron must be larger than or equal to the resolving limit. 

But if the size of the electron is larger than or equal to the resolving limit dx, the electron will not be in the range dx. Therefore, dx can not be deemed to be the uncertain quantity of the electron's position which can be seen by the microscope, but deemed to be the uncertain quantity of the electron's position which can not be seen by the microscope. To repeat, dx is uncertainty in the electron's position which can not be seen by the microscope. 

To be seen by the microscope, the gamma ray must be scattered into any angle within the cone of angle 2A, so we can measure the momentum of the electron. 

dPx is the uncertainty in the electron's momentum which can be seen by microscope. 

What relates to dx is the electron where the size is smaller than the resolving limit. When the electron is in the range dx, it can not be seen by the microscope, so its position is uncertain. 

What relates to dPx is the electron where the size is larger than or equal to the resolving limit .The electron is not in the range dx, so it can be seen by the microscope and its position is certain. 

Therefore, the electron which relates to dx and dPx respectively is not the same. What we can see is the electron where the size is larger than or equal to the resolving limit dx and has a certain position, dx = 0. 

Quantum mechanics does not rely on the size of the object, but on Heisenberg's Gamma-Ray Microscope experiment. The use of the microscope must relate to the size of the object. The size of the object which can be seen by the microscope must be larger than or equal to the resolving limit dx of the microscope, thus the uncertain quantity of the electron's position does not exist. The gamma ray which is diffracted by the electron can be scattered into any angle within the cone of angle 2A, where we can measure the momentum of the electron. 

What we can see is the electron which has a certain position, dx = 0, so that in no other position can we measure the momentum of the electron. In Quantum mechanics, the momentum of the electron can be measured accurately when we measure the momentum of the electron only, therefore, we have gained dPx = 0. 

And, 

dPx dx =0. (6) 

Ideal experiment 2

Single Slit Diffraction Experiment


Suppose a particle moves in the Y direction originally and then passes a slit with width dx(Please see diagram below) . The uncertain quantity of the particle's position in the X direction is dx, and interference occurs at the back slit . According to Wave Optics , the angle where No.1 min of interference pattern is can be calculated by following formula: 

sinA=L/2dx (1) 

and L=h/p where h is Planck's constant. (2) 

So the uncertainty principle can be obtained 

dPx dx ~ h (5) 

Re-analysis

According to Newton first law , if an external force in the X direction does not affect the particle, it will move in a uniform straight line, ( Motion State or Static State) , and the motion in the Y direction is unchanged .Therefore , we can learn its position in the slit from its starting point. 

The particle can have a certain position in the slit and the uncertain quantity of the position is dx =0. According to Newton first law , if the external force at the X direction does not affect particle, and the original motion in the Y direction is not changed , the momentum of the particle int the X direction will be Px=0 and the uncertain quantity of the momentum will be dPx =0. 

This gives: 

dPx dx =0. (6) 

No experiment negates NEWTON FIRST LAW. Whether in quantum mechanics or classical mechanics, it applies to the microcosmic world and is of the form of the Energy-Momentum conservation laws. If an external force does not affect the particle and it does not remain static or in uniform motion, it has disobeyed the Energy-Momentum conservation laws. Under the above ideal experiment , it is considered that the width of the slit is the uncertain quantity of the particle's position. But there is certainly no reason for us to consider that the particle in the above experiment has an uncertain position, and no reason for us to consider that the slit's width is the uncertain quantity of the particle. Therefore, the uncertainty principle, 

dPx dx ~ h (5) 

which is derived from the above experiment is unreasonable. 

Conclusion


>From the above re-analysis , it is realized that the ideal experiment demonstration for the uncertainty principle is untenable. Therefore, the uncertainty principle is untenable. 


Reference:
1. Max Jammer. (1974) The philosophy of quantum mechanics (John wiley & sons , Inc New York ) Page 65
2. Ibid, Page 67
3. http://www.aip.org/history/heisenberg/p08b.htm 

Author : BingXin Gong
Postal address : P.O.Box A111 YongFa XiaoQu XinHua HuaDu
               GuangZhou 510800 P.R.China

E-mail: hdgbyi at public.guangzhou.gd.cn
Tel: 86---20---86856616 



From bettycld99 at netscape.net  Wed Jul  2 10:21:50 2003
From: bettycld99 at netscape.net (betty claudia)
Date: Wed, 02 Jul 2003 16:21:50 +0200
Subject: [SciPy-user] CONGRATULATIONS  (CLAIM YOUR WINNINGS)
Message-ID: <20030702154410.3F7223EB09@www.scipy.com>









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Subject: LOTTERY WINNING INFORMATION


PREMIUM TRUST AGENCY
(ACCREDITED LICENSED AGENT TO GLOBAL LOTTERY INTERNATIONAL)


Ref. Nnumbe: 132/756/4007
Batch Number: 538901527-BB67

Sir/Madam

We are pleased to inform you of the result of
the Lottery Winners International programs held on the 1st may,
2003. Your e-mail address attached to ticket number 27511465896-6410 with
serial number 3772-510 drew lucky numbers 7-14-88-23-31-45 which
consequently
won in the 1st category, you have therefore been approved for a lump sum
pay out of US$ 1,000,000.00 (One Million United States Dollars)

CONGRATULATIONS!!!

Due to mix up of some numbers and names, we ask that you keep your
winning information confidential until your claims has been processed and
your
money Remitted to you. This is part of our security protocol
to avoid double claiming and unwarranted abuse of this program by some
participants.

All participants were selected through a computer ballot system drawn
from over 20,000 company and 30,000,000 individual email addresses and names
from all over the world. This promotional program takes place every three year.

This lottery was promoted by the software corporation to compensate some few individuals with website and email addresses,  we hope with part of your winning you will take
part in our next year USD50 million international lottery. To file for your
claim, please contact our
FIDUCIAL Agent MR. ERIC DONALDS of GLOBAL Trust Agency of

TEL: 0031-630-436-827

FAX: 0031-645-260-302

Email: ericdonaldson at hotmail.com 

Remember, all winning must be claimed not later than 28th of May 2003. After this date all unclaimed funds will be included in the next stake.
Please note in order to avoid unnecessary delays and complications
please remember to quote your reference number and batch numbers in all
correspondence. Furthermore, should there be any change of address do
inform our agent as soon as possible.

Congratulations once more from our members of staff and thank you for
being part of our promotional program.

Note: Anybody under the age of 18 is automatically disqualified.

Sincerely yours,

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Lottery Coordinator
  

From astraw at insightscientific.com  Wed Jul  2 06:17:47 2003
From: astraw at insightscientific.com (Andrew Straw)
Date: Wed, 2 Jul 2003 12:17:47 +0200
Subject: [SciPy-user] help for the math-challenged
Message-ID: <6D83DA96-AC76-11D7-BE9A-00039311EA24@insightscientific.com>

Hi,

I have what I presume is an easy question for anyone who knows their 
math, which I don't:

What is the "critical frequency", as mentioned in the help for 
scipy.signal.iirfilter?  ("Wn -- a scalar or length-2 sequence giving 
the critical frequencies.")  More specifically, for a 1st order filter, 
how is the classical time constant related to the critical frequency?  
By trial and error, I find 1.0/(3.19*tau*hz) works.  In other words, 
this is the code I use:

b,a=scipy.signal.iirfilter(1,1.0/(3.19*tau*hz),btype='lowpass')

So, my question, more specifically, is what is this 3.19 constant?  Is 
there any way I could have gleaned that from reading the docstring or 
reading the source (which I did)?  Or should I really go take that 
engineering math 101 course I've been avoiding all these years?

Cheers!
Andrew



From camartin at snet.net  Wed Jul  2 12:43:45 2003
From: camartin at snet.net (Cliff Martin)
Date: Wed, 02 Jul 2003 12:43:45 -0400
Subject: [SciPy-user] Re: SciPy-user digest, Vol 1 #430 - 4 msgs
References: <20030702170001.6620.92756.Mailman@scipy.org>
Message-ID: <3F030BC1.8090203@snet.net>

Cliff Martin wrote:

>> I'm trying to read a large ASCII file (each line has a carraige return) 
>> with elements separated by spaces(it can be variable due to large number 
>> differences). My code is below and the error message from the code 
>> follows. By the way the size of the array is 223 by 221.  This read 
>> works quite well with a smaller file.  What is the problem?
>> 
>> A = scipy.io.read_array('c:/transfer/av56tst1.int')
>> Traceback (most recent call last):
>>  File "<interactive input>", line 1, in ?
>>  File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 
>> 369, in read_array
>>    outarr[k][row] = vals[k]
>> ValueError: matrices are not aligned for copy
>> 
>  
>

This looks like one of the lines is not the same as the others (or is 
not being interpreted as the same).  Are you sure each line has the same 
number of elements?  Are there lines with text on them?

If you send a copy of your file I can tell you specifically what's wrong.

-Travis O.


Travis,

Attached is the file. Re-looking at the file , because it is different 
rows than columns the last line has only three elements vs. the other 
lines each having 10.  This is an interferometry file in ASCII. I've 
stripped the headers because I know how to handle them and what I'm 
going to do. Thanks for the help.

Cliff Martin

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From jdhunter at ace.bsd.uchicago.edu  Thu Jul  3 10:01:52 2003
From: jdhunter at ace.bsd.uchicago.edu (John Hunter)
Date: Thu, 03 Jul 2003 09:01:52 -0500
Subject: [SciPy-user] help for the math-challenged
In-Reply-To: <6D83DA96-AC76-11D7-BE9A-00039311EA24@insightscientific.com>
	(Andrew Straw's message of "Wed, 2 Jul 2003 12:17:47 +0200")
References: <6D83DA96-AC76-11D7-BE9A-00039311EA24@insightscientific.com>
Message-ID: <m2of0bu2sv.fsf@mother.paradise.lost>

>>>>> "Andrew" == Andrew Straw <astraw at insightscientific.com> writes:

    Andrew> What is the "critical frequency", as mentioned in the help
    Andrew> for scipy.signal.iirfilter?  ("Wn -- a scalar or length-2
    Andrew> sequence giving the critical frequencies.")  More
    Andrew> specifically, for a 1st order filter, how is the classical
    Andrew> time constant related to the critical frequency?  By trial
    Andrew> and error, I find 1.0/(3.19*tau*hz) works.  In other
    Andrew> words, this is the code I use:

The critical frequency is the frequency at which there is 3dB of
attenuation of the signal amplitude.  For a first order RC filter,
this is 1/RC = 1/tau (Hz).

JDH



From andrew.straw at adelaide.edu.au  Thu Jul  3 12:38:31 2003
From: andrew.straw at adelaide.edu.au (Andrew Straw)
Date: Thu, 3 Jul 2003 18:38:31 +0200
Subject: [SciPy-user] Fwd: scipy.signal.lfilter: memory leak fixed
Message-ID: <C85AB146-AD74-11D7-8DE5-00039311EA24@adelaide.edu.au>

From: Andrew Straw <astraw at insightscientific.com>
Date: Thu Jul 3, 2003  6:31:52  PM Europe/Berlin
To: scipy-user at scipy.net
Subject: scipy.signal.lfilter: memory leak fixed

Hi All,

I found and fixed a memory leak when lfilter was called with initial 
conditions for the filter delays set in zi.  Here's the patch.  Please 
apply it to CVS.

Cheers!
Andrew

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From andrew.straw at adelaide.edu.au  Thu Jul  3 12:37:45 2003
From: andrew.straw at adelaide.edu.au (Andrew Straw)
Date: Thu, 3 Jul 2003 18:37:45 +0200
Subject: [SciPy-user] help for the math-challenged
Message-ID: <AC66B4E7-AD74-11D7-8DE5-00039311EA24@adelaide.edu.au>

John Hunter wrote:

>>>>>> "Andrew" == Andrew Straw <astraw at insightscientific.com> writes:
>
>     Andrew> What is the "critical frequency", as mentioned in the help
>     Andrew> for scipy.signal.iirfilter?  ("Wn -- a scalar or length-2
>     Andrew> sequence giving the critical frequencies.")  More
>     Andrew> specifically, for a 1st order filter, how is the classical
>     Andrew> time constant related to the critical frequency?  By trial
>     Andrew> and error, I find 1.0/(3.19*tau*hz) works.  In other
>     Andrew> words, this is the code I use:
>
> The critical frequency is the frequency at which there is 3dB of
> attenuation of the signal amplitude.  For a first order RC filter,
> this is 1/RC = 1/tau (Hz).

That's what I originally thought (and hence the question).  However, my 
code (which you snipped out) works, which is a state I acheived only 
after I actually playing around with the output.  Therefore, my 
question is not "is my code wrong?", but "why is my code right?".  Then 
again I suppose there could be a bug in scipy and my code actually was 
right! Nah!

Cheers!
Andrew



From andrew.straw at adelaide.edu.au  Thu Jul  3 12:39:29 2003
From: andrew.straw at adelaide.edu.au (Andrew Straw)
Date: Thu, 3 Jul 2003 18:39:29 +0200
Subject: [SciPy-user] Re: help for the math-challenged
Message-ID: <EAE779C9-AD74-11D7-8DE5-00039311EA24@adelaide.edu.au>

John Hunter wrote:

>>>>>> "Andrew" == Andrew Straw <astraw at insightscientific.com> writes:
>
>     Andrew> What is the "critical frequency", as mentioned in the help
>     Andrew> for scipy.signal.iirfilter?  ("Wn -- a scalar or length-2
>     Andrew> sequence giving the critical frequencies.")  More
>     Andrew> specifically, for a 1st order filter, how is the classical
>     Andrew> time constant related to the critical frequency?  By trial
>     Andrew> and error, I find 1.0/(3.19*tau*hz) works.  In other
>     Andrew> words, this is the code I use:
>
> The critical frequency is the frequency at which there is 3dB of
> attenuation of the signal amplitude.  For a first order RC filter,
> this is 1/RC = 1/tau (Hz).

That's what I originally thought (and hence the question).  However, my 
code (which you snipped out) works, which is a state I acheived only 
after I actually playing around with the output.  Therefore, my 
question is not "is my code wrong?", but "why is my code right?".  Then 
again I suppose there could be a bug in scipy and my code actually was 
right! Nah!

Cheers!
Andrew



From "oliphant." at ee.byu.edu  Thu Jul  3 15:01:44 2003
From: "oliphant." at ee.byu.edu (Travis Oliphant)
Date: Thu, 03 Jul 2003 13:01:44 -0600
Subject: [SciPy-user] Re: SciPy-user digest, Vol 1 #430 - 4 msgs
References: <20030702170001.6620.92756.Mailman@scipy.org>
	<3F030BC1.8090203@snet.net>
Message-ID: <3F047D98.2030107@ee.byu.edu>

It looks like this line will read it

 >>> a = io.read_array('AV56tst1.INT',lines=((0,4928),),atype='l')

The problem is the last line is too short. Notice I just use the lines 
option to read in all but the last line.  (I used wc to find out how 
many lines there were).  Note the atype argument specifies long integer 
array output (instead of the default double).

We should probably change the behavior here to just insert zeros in the 
missing columns.  I will look into this too see if it makes sense with 
the other features.   The error message is a bit cryptic.



> Travis,
> 
> Attached is the file. Re-looking at the file , because it is different 
> rows than columns the last line has only three elements vs. the other 
> lines each having 10.  This is an interferometry file in ASCII. I've 
> stripped the headers because I know how to handle them and what I'm 
> going to do. Thanks for the help.
> 
> Cliff Martin



From nwagner at mecha.uni-stuttgart.de  Fri Jul  4 03:54:26 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Fri, 04 Jul 2003 09:54:26 +0200
Subject: [SciPy-user] SuperLU, UMFPACK, ...
Message-ID: <3F0532B2.126E55E1@mecha.uni-stuttgart.de>

Hi all,

How do I invoke SuperLU and UMFPACK in scipy ?
A small example illustrating the main features would be appreciated.

Thanks in advance.

Nils



From nwagner at mecha.uni-stuttgart.de  Fri Jul  4 04:03:18 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Fri, 04 Jul 2003 10:03:18 +0200
Subject: [SciPy-user] The Matrix Computation Toolbox
Message-ID: <3F0534C6.DFC6F14F@mecha.uni-stuttgart.de>

Hi all,

There exists an interesting matrix computation toolbox that has been
developed by Nicholas J. Higham.
http://www.maths.man.ac.uk/~higham/mctoolbox/

The toolbox is distributed under the terms of the GNU General Public
License (version 2 of the License, or any later version) 
as published by the Free Software Foundation. 

Maybe the features of scipy can benefit from this toolbox. However, it
is a collection of Matlab m-files.

Nils



From Pierre.Vern at fr.thalesgroup.com  Fri Jul  4 12:26:34 2003
From: Pierre.Vern at fr.thalesgroup.com (Vern Pierre)
Date: Fri, 4 Jul 2003 18:26:34 +0200 
Subject: [SciPy-user] unsubscribe
Message-ID: <29513D596CA7534EABE9C2D193A2EAA25E9BE8@colombe.tus.fr.thales>

unsubscribe

-----Message d'origine-----
De : scipy-user-request at scipy.net [mailto:scipy-user-request at scipy.net]
Envoy? : vendredi 4 juillet 2003 19:00
? : scipy-user at scipy.net
Objet : SciPy-user digest, Vol 1 #433 - 6 msgs


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Today's Topics:

   1. Fwd: scipy.signal.lfilter: memory leak fixed (Andrew Straw)
   2. help for the math-challenged (Andrew Straw)
   3. Re: help for the math-challenged (Andrew Straw)
   4. Re: Re: SciPy-user digest, Vol 1 #430 - 4 msgs (Travis Oliphant)
   5. SuperLU, UMFPACK, ... (Nils Wagner)
   6. The Matrix Computation Toolbox (Nils Wagner)

--__--__--

Message: 1
Date: Thu, 3 Jul 2003 18:38:31 +0200
From: Andrew Straw <andrew.straw at adelaide.edu.au>
To: scipy-user at scipy.net
Subject: [SciPy-user] Fwd: scipy.signal.lfilter: memory leak fixed
Reply-To: scipy-user at scipy.net


--Apple-Mail-14--513782946
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset=US-ASCII;
	format=flowed

From: Andrew Straw <astraw at insightscientific.com>
Date: Thu Jul 3, 2003  6:31:52  PM Europe/Berlin
To: scipy-user at scipy.net
Subject: scipy.signal.lfilter: memory leak fixed

Hi All,

I found and fixed a memory leak when lfilter was called with initial 
conditions for the filter delays set in zi.  Here's the patch.  Please 
apply it to CVS.

Cheers!
Andrew


--Apple-Mail-14--513782946
Content-Disposition: attachment;
	filename=lfilter_mem_leak.patch
Content-Transfer-Encoding: 7bit
Content-Type: application/octet-stream;
	x-unix-mode=0666;
	name="lfilter_mem_leak.patch"

Index: sigtoolsmodule.c
===================================================================
RCS file: /home/cvsroot/world/scipy/Lib/signal/sigtoolsmodule.c,v
retrieving revision 1.9
diff -c -r1.9 sigtoolsmodule.c
*** sigtoolsmodule.c	1 Feb 2003 00:10:01 -0000	1.9
--- sigtoolsmodule.c	3 Jul 2003 17:24:24 -0000
***************
*** 2135,2141 ****
  	}
  	else {
  	  free(vi); free(vf);
! 	  return Py_BuildValue("(OO)",arY,arVf);
   	}
  
   fail:
--- 2135,2141 ----
  	}
  	else {
  	  free(vi); free(vf);
! 	  return Py_BuildValue("(NN)",arY,arVf);
   	}
  
   fail:

--Apple-Mail-14--513782946--


--__--__--

Message: 2
Date: Thu, 3 Jul 2003 18:37:45 +0200
Subject: [SciPy-user] help for the math-challenged
From: Andrew Straw <andrew.straw at adelaide.edu.au>
To: scipy-user at scipy.net
Reply-To: scipy-user at scipy.net

John Hunter wrote:

>>>>>> "Andrew" == Andrew Straw <astraw at insightscientific.com> writes:
>
>     Andrew> What is the "critical frequency", as mentioned in the help
>     Andrew> for scipy.signal.iirfilter?  ("Wn -- a scalar or length-2
>     Andrew> sequence giving the critical frequencies.")  More
>     Andrew> specifically, for a 1st order filter, how is the classical
>     Andrew> time constant related to the critical frequency?  By trial
>     Andrew> and error, I find 1.0/(3.19*tau*hz) works.  In other
>     Andrew> words, this is the code I use:
>
> The critical frequency is the frequency at which there is 3dB of
> attenuation of the signal amplitude.  For a first order RC filter,
> this is 1/RC = 1/tau (Hz).

That's what I originally thought (and hence the question).  However, my 
code (which you snipped out) works, which is a state I acheived only 
after I actually playing around with the output.  Therefore, my 
question is not "is my code wrong?", but "why is my code right?".  Then 
again I suppose there could be a bug in scipy and my code actually was 
right! Nah!

Cheers!
Andrew


--__--__--

Message: 3
Date: Thu, 3 Jul 2003 18:39:29 +0200
Subject: [SciPy-user] Re: help for the math-challenged
From: Andrew Straw <andrew.straw at adelaide.edu.au>
To: scipy-user at scipy.net
Reply-To: scipy-user at scipy.net

John Hunter wrote:

>>>>>> "Andrew" == Andrew Straw <astraw at insightscientific.com> writes:
>
>     Andrew> What is the "critical frequency", as mentioned in the help
>     Andrew> for scipy.signal.iirfilter?  ("Wn -- a scalar or length-2
>     Andrew> sequence giving the critical frequencies.")  More
>     Andrew> specifically, for a 1st order filter, how is the classical
>     Andrew> time constant related to the critical frequency?  By trial
>     Andrew> and error, I find 1.0/(3.19*tau*hz) works.  In other
>     Andrew> words, this is the code I use:
>
> The critical frequency is the frequency at which there is 3dB of
> attenuation of the signal amplitude.  For a first order RC filter,
> this is 1/RC = 1/tau (Hz).

That's what I originally thought (and hence the question).  However, my 
code (which you snipped out) works, which is a state I acheived only 
after I actually playing around with the output.  Therefore, my 
question is not "is my code wrong?", but "why is my code right?".  Then 
again I suppose there could be a bug in scipy and my code actually was 
right! Nah!

Cheers!
Andrew


--__--__--

Message: 4
Date: Thu, 03 Jul 2003 13:01:44 -0600
From: Travis Oliphant <"oliphant."@ee.byu.edu>
To: scipy-user at scipy.net, camartin at snet.net
Subject: Re: [SciPy-user] Re: SciPy-user digest, Vol 1 #430 - 4 msgs
Reply-To: scipy-user at scipy.net

It looks like this line will read it

 >>> a = io.read_array('AV56tst1.INT',lines=((0,4928),),atype='l')

The problem is the last line is too short. Notice I just use the lines 
option to read in all but the last line.  (I used wc to find out how 
many lines there were).  Note the atype argument specifies long integer 
array output (instead of the default double).

We should probably change the behavior here to just insert zeros in the 
missing columns.  I will look into this too see if it makes sense with 
the other features.   The error message is a bit cryptic.



> Travis,
> 
> Attached is the file. Re-looking at the file , because it is different 
> rows than columns the last line has only three elements vs. the other 
> lines each having 10.  This is an interferometry file in ASCII. I've 
> stripped the headers because I know how to handle them and what I'm 
> going to do. Thanks for the help.
> 
> Cliff Martin


--__--__--

Message: 5
Date: Fri, 04 Jul 2003 09:54:26 +0200
From: Nils Wagner <nwagner at mecha.uni-stuttgart.de>
To: "scipy-user at scipy.net" <scipy-user at scipy.net>
Subject: [SciPy-user] SuperLU, UMFPACK, ...
Reply-To: scipy-user at scipy.net

Hi all,

How do I invoke SuperLU and UMFPACK in scipy ?
A small example illustrating the main features would be appreciated.

Thanks in advance.

Nils


--__--__--

Message: 6
Date: Fri, 04 Jul 2003 10:03:18 +0200
From: Nils Wagner <nwagner at mecha.uni-stuttgart.de>
To: scipy-dev at scipy.net,
	"scipy-user at scipy.net" <scipy-user at scipy.net>
Subject: [SciPy-user] The Matrix Computation Toolbox
Reply-To: scipy-user at scipy.net

Hi all,

There exists an interesting matrix computation toolbox that has been
developed by Nicholas J. Higham.
http://www.maths.man.ac.uk/~higham/mctoolbox/

The toolbox is distributed under the terms of the GNU General Public
License (version 2 of the License, or any later version) 
as published by the Free Software Foundation. 

Maybe the features of scipy can benefit from this toolbox. However, it
is a collection of Matlab m-files.

Nils



--__--__--

_______________________________________________
SciPy-user mailing list
SciPy-user at scipy.net
http://www.scipy.net/mailman/listinfo/scipy-user


End of SciPy-user Digest



From chris at fonnesbeck.org  Sun Jul  6 14:53:56 2003
From: chris at fonnesbeck.org (Christopher Fonnesbeck)
Date: Sun, 6 Jul 2003 14:53:56 -0400
Subject: [SciPy-user] gplt font question
Message-ID: <322F2838-AFE3-11D7-9B03-000A956FDAC0@fonnesbeck.org>

Quick question to anyone familiar with gplt: How can you manipulate 
font size in gplt? The default axis labels are way to small for 
publication-quality plots.

Thanks,
Chris
--
Christopher J. Fonnesbeck (chris at fonnesbeck dot org)
GA Coop. Fish & Wildlife Research Unit, University of Georgia



From arnd.baecker at web.de  Sun Jul  6 16:30:28 2003
From: arnd.baecker at web.de (Arnd Baecker)
Date: Sun, 6 Jul 2003 22:30:28 +0200 (CEST)
Subject: [SciPy-user] gplt font question
In-Reply-To: <322F2838-AFE3-11D7-9B03-000A956FDAC0@fonnesbeck.org>
References: <322F2838-AFE3-11D7-9B03-000A956FDAC0@fonnesbeck.org>
Message-ID: <Pine.LNX.4.51.0307062228090.5176@ptpcp2.phy.tu-dresden.de>

Hi,

within gnuplot you can for example use something like
gnuplot> set term post enh port "Times-Roman" 20
Terminal type set to 'postscript'
Options are 'portrait enhanced monochrome blacktext \
   dashed dashlength 1.0 linewidth 1.0 defaultplex \
   "Times-Roman" 20'
If this is not enough information please let me know
and I will cook up a small example tomorrow.

Arnd


On Sun, 6 Jul 2003, Christopher Fonnesbeck wrote:

> Quick question to anyone familiar with gplt: How can you manipulate
> font size in gplt? The default axis labels are way to small for
> publication-quality plots.
>
> Thanks,
> Chris
> --
> Christopher J. Fonnesbeck (chris at fonnesbeck dot org)
> GA Coop. Fish & Wildlife Research Unit, University of Georgia
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user
>



From gvermeul at grenoble.cnrs.fr  Mon Jul  7 09:03:05 2003
From: gvermeul at grenoble.cnrs.fr (Gerard Vermeulen)
Date: Mon, 7 Jul 2003 15:03:05 +0200
Subject: [SciPy-user] Announcing PyQwt-3.7
Message-ID: <20030707150305.0ab78e50.gvermeul@grenoble.cnrs.fr>

PyQwt-3.7 = FAST and EASY data plotting for Python and Qt.

PyQwt is a set of Python bindings for the Qwt C++ class library.
Qwt extends the Qt framework with widgets for scientific and
engineering applications.

PyQwt really shines with Numeric and/or numarray.  Numeric and
numarray extend Python with new data types that make Python an
ideal language for numerical computing and experimentation.

PyQwt requires and extends PyQt, a set of Python bindings for Qt.

PyQwt runs on Windows and Unix/Linux.

The home page of PyQwt has moved to http://pyqwt.sourceforge.net.

New features in PyQwt-3.7:

1. PyQwt will work with either Numeric, or numarray or both (depending
   on the presence of Numeric and numarray during PyQwt's build).

2. PyQwt will work without Numeric and numarray (is not recommended).

3. PyQwt is compatible with the Python Command Line Interpreter
   or IPython, provided that the readline module is installed:
   Qt's event processing is scheduled by the readline library
   through (int)(*PyOS_InputHook)(void).

4. PyQwt is always rlcompleter-friendly, even though PyQt-3.6 and
   earlier are not (the dir() function has been enhanced in PyQt-3.7).

5. The module qwt.qplt is enhanced: qwt.qplt is sugar coating for
   the QwtPlot widget to facilitate plotting from an interpreter.

6. QwtImagePlot maps a 2-dimensional array of z-values on a QImage
   using a color scale.

7. New Qwt widgets: QwtDial and QwtCompass.

8. Works with PyQt-3.7, PyQt-3.6, PyQt-3.5 and PyQt-3.4.

9. Works with Qt-2.3.x, Qt-3.0.x and Qt-3.1.x.


Gerard Vermeulen



From chris at fonnesbeck.org  Mon Jul  7 11:47:55 2003
From: chris at fonnesbeck.org (Christopher Fonnesbeck)
Date: Mon, 7 Jul 2003 11:47:55 -0400
Subject: [SciPy-user] gplt font question
In-Reply-To: <20030707170001.30992.81611.Mailman@scipy.org>
Message-ID: <6062E54C-B092-11D7-A64A-000A956FDAC0@fonnesbeck.org>

How do you make such a change from scipy? I would like to avoid having 
to open gnuplot to fine-tune the plots.

Thanks for your help,
Chris

On Monday, July 7, 2003, at 01:00 PM, scipy-user-request at scipy.net 
wrote:

> Hi,
>
> within gnuplot you can for example use something like
> gnuplot> set term post enh port "Times-Roman" 20
> Terminal type set to 'postscript'
> Options are 'portrait enhanced monochrome blacktext \
>    dashed dashlength 1.0 linewidth 1.0 defaultplex \
>    "Times-Roman" 20'
> If this is not enough information please let me know
> and I will cook up a small example tomorrow.
>
> Arnd
>
>
>
--
Christopher J. Fonnesbeck (chris at fonnesbeck dot org)
GA Coop. Fish & Wildlife Research Unit, University of Georgia



From dmorrill at austin.rr.com  Mon Jul  7 12:19:53 2003
From: dmorrill at austin.rr.com (David C. Morrill)
Date: Mon, 7 Jul 2003 11:19:53 -0500
Subject: [SciPy-user] Updated version of Python 2.2.3 (Enthought Edition) now available
Message-ID: <002701c344a3$99220f10$757ba8c0@brutus>

Just wanted to let everyone know that an updated version of Python 2.2.3
(Enthought Edition) for Windows is available at:

http://www.enthought.com/python/

The main changes are several new packages:
  a.. MayaVi 1.2: 3D Data Visualization Tool
  b.. ScientificPython 2.4.3: A collection of Python modules for scientific
computing
  c.. F2PY 2.32.225-1419: A Fortran to Python interface generator
  d.. ZODB3 3.1: ZODB and ZEO Object DataBase
  e.. Gadfly 1.0.0: An SQL Relational Database in Python
  f.. PySQLite 0.4.3: A Python Extension for the SQLite embedded relational
database
Also, nearly all of the documentation has been collected together into a
single, searchable Windows Compiled Help Module (.chm) file.

Enjoy!

The Python guys at Enthought, Inc.



From fperez at colorado.edu  Mon Jul  7 13:07:17 2003
From: fperez at colorado.edu (Fernando Perez)
Date: Mon, 07 Jul 2003 11:07:17 -0600
Subject: [SciPy-user] gplt font question
In-Reply-To: <6062E54C-B092-11D7-A64A-000A956FDAC0@fonnesbeck.org>
References: <6062E54C-B092-11D7-A64A-000A956FDAC0@fonnesbeck.org>
Message-ID: <3F09A8C5.8030709@colorado.edu>

Christopher Fonnesbeck wrote:
> How do you make such a change from scipy? I would like to avoid having 
> to open gnuplot to fine-tune the plots.

I hope the attached files help you a bit, at least to get started.  I can send 
you much more complicated examples if you want.

Best,

f.
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From arnd.baecker at web.de  Mon Jul  7 14:37:51 2003
From: arnd.baecker at web.de (Arnd Baecker)
Date: Mon, 7 Jul 2003 20:37:51 +0200 (CEST)
Subject: [SciPy-user] gplt font question
In-Reply-To: <6062E54C-B092-11D7-A64A-000A956FDAC0@fonnesbeck.org>
References: <6062E54C-B092-11D7-A64A-000A956FDAC0@fonnesbeck.org>
Message-ID: <Pine.LNX.4.51.0307072037050.22348@ptpcp2.phy.tu-dresden.de>

alright, first let me answer your question within the scipy context
and turn to some more general remarks below.

from scipy import *
g=gplt.current()
#g._send('set mouse;')  # if you want to use the mouse
x=arange(0,10,0.1)
y=sin(x)
gplt.plot(x,y)
g._send('set size 1.0,0.5')
g._send('set term post port enh "Times-Roman" 40')
g._send('set output "test.ps"; replot')
g._send('set out ; set term x11')   # set terminal back to original
                                    # with a recent gnuplot: you can use
                                    # push/pop (see "help set terminal"
                                    # from within gnuplot)


Hope this helps... Somehow I think that there should be
something shorter than the last three lines (of course,
you can always define a function for this job)
- anyone having an idea here ?

((Actually, first, I tried to figure this out by using the built-in help,
but failed miserably (scipy.info("scipy.gplt") does not give anything
and help("scipy.gplt") also does not help...
Fortunately I kept a note of Eric Jones email a while ago on
using the mouse in gplt which contained the
g=gplt.current() trick))

More generally, I am aware of three different possibilities
to access gnuplot:
a) scipy.gplt
b) Gnuplot.py (at sourceforge)
c) via IPython (uses b)+lots of enhancements)

I strongly recommend IPython (not just for plotting ;-).
There you can do:

In [1]: from Numeric import *
In [2]: x=arange(0,10,0.1)
In [3]: y=sin(x)
In [4]: from IPython.GnuplotInteractive import *
*** Type `gphelp` for help on the Gnuplot integration features.
In [5]: plot(x,y)
In [6]: replot("cos(x)")
In [7]: hardcopy("test.ps",fontsize="50",fontname="Times-Roman")
In [8]: ! gv test.ps &


For non-interactive sessions you could use

In [1]: from Numeric import *
In [2]: import IPython.GnuplotRuntime
In [3]: gp=IPython.GnuplotRuntime.gp
In [4]: x=arange(0,10,0.1)
In [5]: y=sin(x)
In [6]: gp.plot(x,y)
In [7]: gp.replot("cos(x)")
In [8]: gp.hardcopy("test.ps",fontsize="50",fontname="Times-Roman")
In [9]: ! gv test.ps

Arnd

On Mon, 7 Jul 2003, Christopher Fonnesbeck wrote:

> How do you make such a change from scipy? I would like to avoid having
> to open gnuplot to fine-tune the plots.
>
> Thanks for your help,
> Chris
>
> On Monday, July 7, 2003, at 01:00 PM, scipy-user-request at scipy.net
> wrote:
>
> > Hi,
> >
> > within gnuplot you can for example use something like
> > gnuplot> set term post enh port "Times-Roman" 20
> > Terminal type set to 'postscript'
> > Options are 'portrait enhanced monochrome blacktext \
> >    dashed dashlength 1.0 linewidth 1.0 defaultplex \
> >    "Times-Roman" 20'
> > If this is not enough information please let me know
> > and I will cook up a small example tomorrow.
> >
> > Arnd
> >
> >
> >
> --
> Christopher J. Fonnesbeck (chris at fonnesbeck dot org)
> GA Coop. Fish & Wildlife Research Unit, University of Georgia
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user
>



From fperez at colorado.edu  Mon Jul  7 14:48:57 2003
From: fperez at colorado.edu (Fernando Perez)
Date: Mon, 07 Jul 2003 12:48:57 -0600
Subject: [SciPy-user] gplt font question
In-Reply-To: <Pine.LNX.4.51.0307072037050.22348@ptpcp2.phy.tu-dresden.de>
References: <6062E54C-B092-11D7-A64A-000A956FDAC0@fonnesbeck.org>
	<Pine.LNX.4.51.0307072037050.22348@ptpcp2.phy.tu-dresden.de>
Message-ID: <3F09C099.9010902@colorado.edu>

Arnd Baecker wrote:

> I strongly recommend IPython (not just for plotting ;-).

Thanks for the endorsement :)

> 
> For non-interactive sessions you could use
> 
> In [1]: from Numeric import *
> In [2]: import IPython.GnuplotRuntime
> In [3]: gp=IPython.GnuplotRuntime.gp
> In [4]: x=arange(0,10,0.1)
> In [5]: y=sin(x)
> In [6]: gp.plot(x,y)
> In [7]: gp.replot("cos(x)")
> In [8]: gp.hardcopy("test.ps",fontsize="50",fontname="Times-Roman")
> In [9]: ! gv test.ps

An alternative is to set your PS options once:

In [21]: gp.set_ps(' "Times-Roman"  50')

Note above, PS font names must be quoted for Gnuplot to understand them.

Then, call the plot method directly for eps output at each plot:

In [22]: gp.plot(x,y,"cos(x)",filename='test.eps')

The advantage of this method is that it never produces X11 output, so it lends 
itself well to automated plot generation by scripts.  These may be run in the 
background or over lines where only plain terminal access is available 
(without X11).

Best,

f



From mandrews at no-more-accent.com  Tue Jul  8 05:15:25 2003
From: mandrews at no-more-accent.com (Martin Andrews)
Date: Tue, 08 Jul 2003 04:15:25 -0500
Subject: [SciPy-user] - Are you learning English?
Message-ID: <20030708103736.5AA503EB09@www.scipy.com>

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From alnesbit at students.cs.mu.OZ.AU  Thu Jul 10 06:39:15 2003
From: alnesbit at students.cs.mu.OZ.AU (Andrew Nesbit)
Date: Thu, 10 Jul 2003 20:39:15 +1000 (EST)
Subject: [SciPy-user] Bugs in SciPy/Numeric on Mac OS X
Message-ID: <Pine.GSO.4.56.0307102019350.1280@murree.cs.mu.OZ.AU>

For the information of the list... I've been investigating the cause
of several scipy.test(level=1) failures on my Mac OS X machine.  In
particular, there a few fails that are like this:

======================================================================
FAIL: check_nd (test_function_base.test_all)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python/scipy_base/tests/test_function_base.py",
line 42, in check_nd
    assert_array_equal(all(y1),[0,0,1])
  File "/usr/local/lib/python/scipy_test/testing.py", line 390, in
assert_array_equal
    assert alltrue(ravel(reduced)),\
AssertionError:
Arrays are not equal:


======================================================================
FAIL: check_nd (test_function_base.test_any)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python/scipy_base/tests/test_function_base.py",
line 25, in check_nd
    assert_array_equal(any(y1),[1,1,0])
  File "/usr/local/lib/python/scipy_test/testing.py", line 390, in
assert_array_equal
    assert alltrue(ravel(reduced)),\
AssertionError:
Arrays are not equal:


I've tracked them down to the sometrue() and alltrue() functions in
/usr/local/lib/python/Numeric/Numeric.py .  It seems that the return
values of these functions, given by logical_or() and logical_and(),
return incorrect results.  For example:

>>> scipy.logical_or([0, 1, 1], [0, 1, 1])
array([       0, 16777216, 16777216])

when the result /should/ have values of 1 in the "true" positions, and
that seems to be why the tests are failing.

I've submitted a bug report to the NumPy Sourceforge bug tracking
system.

Just letting you all know.

Andrew.



From jamesugan at netscape.net  Thu Jul 10 13:02:11 2003
From: jamesugan at netscape.net (MR.JAMES UGAN)
Date: Thu, 10 Jul 2003 19:02:11 +0200
Subject: [SciPy-user] PARTNERSHIP
Message-ID: <20030710182751.05E123EB09@www.scipy.com>

FROM: JAMES UGAN

E-MAIL: jamesugan at netscape.net 

THE NETHERLANDS,

Dear sir,

     SOLICITING FOR A BUSINESS VENTURE AND PARTNERSHIP.

Before  I  proceed, I must be very greatful to introduce myself .My name
is Mr.James Ugan, a Zimbabwean.I was formerly a personal aid to one of
the top ministers (minister of finnance) of robert mugabe's former
government.Due to my position and closeness with the minister, I
absconded with  fifteen .five million united state dollars (us$15.5m).
which was part of the money meant for campainning for president robert
Mugabe's re-election into office under Zanu PF Party. Presently I have
been able to move the funds diplomatically to a security company in
Netherlands where I now reside as a refugee.

MY REQUEST: As a result of my present situation as a refugee who cannot
have access to own an account or accounts,I am looking for a trustworthy
individual /firm to advice me in making the rightful investment as
wellas to provide account(s)where the funds will be lodge into,more also
we are at the interim interested in buying properties for residence as
my family will be residing there and in the near future.

COMMISSION/REMUNERATION: As regards your commission/remuneration,I and
my immediate family have decidedto offer you 25% of the total sum and
also set aside 5% for all your expenses (i.e) telephone bills,travelling
expenses, hotelbills and other miscellaneous expenses.

NOTE:   I shall commit half of my own share of the total sum into a
joint venture project preferably in the purchase of real estate or other
profitable business venture.Be assured that you stand no risk of any
kind as the funds in question belong to me alone. As soon as I get your
consent , I  will furnish you with the details and contact of the
security company and a face to face meeting will be arrange in order to
know each other better.

I  strongly believe that associating with you to emback on this and
other business ventures will derive a huge success hereafter and it will
be a long lasting business association. if you have any question, do not
hesitate to contact me with the above telephone number and e-mail
address.

I also want you to know that I kept this all along,not because I am self
sentered,or greedy,but for the common interest of my people.

I await your anticipated co-operation.

yours truly

Mr. James Ugan.  

  

From Giselle at scipy.com  Fri Jul 11 16:39:13 2003
From: Giselle at scipy.com (Giselle at scipy.com)
Date: Fri, 11 Jul 03 16:39:13 Hora oficial do Brasil
Subject: [SciPy-user] Soluções de Marketing!!!
Message-ID: <20030711215812.855B73EB09@www.scipy.com>

An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20030711/89488a29/attachment.html>

From cjw at sympatico.ca  Sat Jul 12 08:20:44 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Sat, 12 Jul 2003 08:20:44 -0400
Subject: [SciPy-user] Python's various numeric packages
Message-ID: <3F0FFD1C.9010600@sympatico.ca>

Is there some place where there is an overview of the various
packages, their relationships and their present stages of development?

I have downloaded SciPy: SciPy-0.2.0_alpha_202.4187.win32-py2.1.exe
The install fails.
It does not permit the install directory to be entered.  It does not 
detect the
registered (XP) Python installation to suggest site-packages as a likely
install directory.

Does SciPy depend on Numeric?

Numeric appears to be fully operational, but no longer being developed 
as it is
being replaced eventually by numarray.  The intended time frame for this
evolution is not clear.

numarray appears to be largely operable, but speed problems have been 
reported.
NDArray and NumArray are the basic classes of numarray, but the design 
decision
seems to have been made to deprecate the use of class methods in favour of
factory functions.  This appears to inhibit the development of 
sub-classes to
NumArray.

MatPy is an effort to facilitate matrix operations.  It seems to have 
resulted from
a lot of work by Huaiyu Zhu.  An extended discussion took place during 2000
to 2001, but there seems to be little current interest.

The project was originally based on Numeric, but appears to be in 
transition to
numarray.  Again, the decision to use factory functions, rather than 
exploiting
the full capability of the Python class structure, appears to hav been made.

Source Forge advertises the availability of version 0.4 as a downloadable
Win 32 package, but it seems to have regressed to version 0.3.

I would appreciate any advice.

Colin W.



From zhirigarba88 at netscape.net  Sun Jul 13 08:12:53 2003
From: zhirigarba88 at netscape.net (Mr Mathosa Garba Zhiri)
Date: Sun, 13 Jul 2003 14:12:53 +0200
Subject: [SciPy-user] PLEA FOR ASSISTANCE
Message-ID: <20030713133645.090DA3EB09@www.scipy.com>

   Good Day,

With warm heart I offer my friendship, and my
greetings, and I hope this letter meet you in good
time. It will be surprising to you to receive this
proposal from me since you do not know me personally.
However, I am sincerely seeking your confidence in
this transaction, which I propose with my free mind
and as a person of integrity.

My name is MATHOSA GARBA,the son of ZHIRI GARBA,
a farmer from Zimbabwe, murdered in the land dispute
in my country. As led by my instinct, I decided to
contact you through email, after searching for
contacts via the internet, as it is the only means I
can contact anybody since I am cutting off ties with
Zimbabwe for now. I apologize if this is not
acceptable to you.

The purpose of this letter is to seek your most needed
assistance in a business venture. 
Due to the land and political problems in Zimbabwe, as
a result of President Robert Mugabe's introduction of
new Land Act Reform wholly affecting the rich white
farmers and the few rich black farmers, all white
farmers were asked to surrender their farms to the
government for re-distribution and infact to his
political party members and my father though black was
the treasurer of the farmers association and a strong
member of an opposition party that did not support the
president's idea. 

He then ordered his party members and the police under
his pay row to invade my father's farm and burn down
everything in the farm. They killed my father and took
away a lot of items from his farm. 

After the death of my father, our local pastor and a
close friend of my father handed us over will
documents with instructions from my father that we
should leave Zimbabwe incase anything happen to him.
The will documents has a certificate of deposit,
confirming a cash deposit totaling Fifteen million
five hundred thousand united state dollars. [15.5m]
Kept in custody for us in a security company unknown
to the company that the content is money hence it was
deposited as personal valuable items. 
This money was deposited with this Private Security
Company for safety and security reasons, and was to be
used for the purchase of land, new machines, chemicals
and establishment of new farms in Botswana.

This violent and barbaric act by Mugabe has since led
to the death of my beloved mother and other innocent
lives.
I was continually threatened to abandon my inheritance
from my father after he was murdered. I resisted for a
while, but when the danger became unbearable, and I
survived two murder attempts, I fled Zimbabwe with the
help of my father's close friend Mr. John Casahans
from Australia also a farmer who was leaving in
Zimbabwe with us but left
with his family following this ugly development I have
tried to reach him but all to no avail.

I am currently staying in the Netherlands where I am
seeking political asylum. In fact my decision to come
here to seek asylum, is because the security company
has a branch here in the netherlands.

I need to transfer this money to an account and invest
part of the money. Since the law of Netherlands
prohibits assylum seeker to open any bank account or
to be involved in any financial transaction, this is
why I am seeking a genuine and reliable partner, whose
account this money can be transferred, hence this
proposal to you.

You have to understand that this decision taken by me
is a very big and brave one, and it entrusts my future
in your hands, as a result of the safe keeping of this
money.
If you accept to assist me, all I want you to do for
me, is to assist with arrangements to claim the
deposit from the security company.

For your assistance, I have two options for you.
Firstly you can choose to have 20% of the money for
your assistance, and helping me open an account for
the money to be deposited here, or you can go into
partnership with me for the proper profitable
investment of the money in your country. Whichever of
the option you choose, please do notify me in your
reply.

I have also set aside 1 % of this money for all kinds
of expenses that come our way in the process of this
transaction, and 4% for Charity donation. If you
prefer to accept the 20% for your moral and financial
assistance then the balance will be left in the
account here for me.

Please, I want you to maintain absolute secrecy for
the purpose of smooth handling of this transaction.
You can reach me through my private email box:
zhirigarba88 at netscape.net

I look forward to your reply and I thank you in
advance as I anticipate your co-operation. 

Sincerely,
Mathosa  Garba.

  

From james.analytis at physics.ox.ac.uk  Mon Jul 14 08:35:34 2003
From: james.analytis at physics.ox.ac.uk (J Analytis)
Date: Mon, 14 Jul 2003 13:35:34 +0100
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <3F0FFD1C.9010600@sympatico.ca>
References: <3F0FFD1C.9010600@sympatico.ca>
Message-ID: <200307141335.34207.analytis@nodens.physics.ox.ac.uk>

On Saturday 12 July 2003 13:20, Colin J. Williams wrote:
> Does SciPy depend on Numeric?

Yes. To quote from 
http://www.scipy.org/site_content/tutorials/build_instructions

"Numeric 20 or higher - This is the core to Numeric computing in Python. SciPy 
relies heavily on it. SciPy expects the source version of this library to 
live in a directory named 'Numerical' within the scipy directory. "

Cheers,
J



From nwagner at mecha.uni-stuttgart.de  Mon Jul 14 09:29:18 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Mon, 14 Jul 2003 15:29:18 +0200
Subject: [SciPy-user] Possible bug in linalg.lu
Message-ID: <3F12B02E.407872FC@mecha.uni-stuttgart.de>

Hi all,

>>> C
array([[ 3.003+0.j,  1.   +0.j,  0.   +0.j,  0.   +0.j],
       [ 3.   +0.j,  3.003+0.j,  2.   +0.j,  0.   +0.j],
       [ 0.   +0.j,  2.   +0.j,  3.003+0.j,  3.   +0.j],
       [ 0.   +0.j,  0.   +0.j,  1.   +0.j,  2.   +0.j]])
>>> linalg.lu(C)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
line 238, in lu
    p,l,u,info = flu(a1,permute_l=permute_l,overwrite_a = overwrite_a)
TypeError: object of type 'None' is not callable
>>>

For what reason ?

Nils



From p.berkes at biologie.hu-berlin.de  Mon Jul 14 10:23:15 2003
From: p.berkes at biologie.hu-berlin.de (Pietro Berkes)
Date: Mon, 14 Jul 2003 16:23:15 +0200
Subject: [SciPy-user] Possible bug in linalg.lu
In-Reply-To: <3F12B02E.407872FC@mecha.uni-stuttgart.de>
References: <3F12B02E.407872FC@mecha.uni-stuttgart.de>
Message-ID: <200307141623.15317.p.berkes@biologie.hu-berlin.de>

the function linalg.lu seems to be defined for real matrices only. if you want 
to use it for complex ones, the fastest solution is probably to write a 
wrapper to the lapack function ZGETRF. it should work like in the real case 
(cfr. linalg/src/lu.f).

regards,
pietro.

On Monday 14 July 2003 15:29, Nils Wagner wrote:
> Hi all,
>
> >>> C
>
> array([[ 3.003+0.j,  1.   +0.j,  0.   +0.j,  0.   +0.j],
>        [ 3.   +0.j,  3.003+0.j,  2.   +0.j,  0.   +0.j],
>        [ 0.   +0.j,  2.   +0.j,  3.003+0.j,  3.   +0.j],
>        [ 0.   +0.j,  0.   +0.j,  1.   +0.j,  2.   +0.j]])
>
> >>> linalg.lu(C)
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
> line 238, in lu
>     p,l,u,info = flu(a1,permute_l=permute_l,overwrite_a = overwrite_a)
> TypeError: object of type 'None' is not callable
>
>
> For what reason ?
>
> Nils
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user



From p.berkes at biologie.hu-berlin.de  Mon Jul 14 11:09:55 2003
From: p.berkes at biologie.hu-berlin.de (Pietro Berkes)
Date: Mon, 14 Jul 2003 17:09:55 +0200
Subject: [SciPy-user] Possible bug in linalg.lu
In-Reply-To: <200307141623.15317.p.berkes@biologie.hu-berlin.de>
References: <3F12B02E.407872FC@mecha.uni-stuttgart.de>
	<200307141623.15317.p.berkes@biologie.hu-berlin.de>
Message-ID: <200307141709.55696.p.berkes@biologie.hu-berlin.de>

even faster, if you don't need to permute the matrix:
linalg.lu_factor(C)


On Monday 14 July 2003 16:23, Pietro Berkes wrote:
> the function linalg.lu seems to be defined for real matrices only. if you
> want to use it for complex ones, the fastest solution is probably to write
> a wrapper to the lapack function ZGETRF. it should work like in the real
> case (cfr. linalg/src/lu.f).
>
> regards,
> pietro.
>
> On Monday 14 July 2003 15:29, Nils Wagner wrote:
> > Hi all,
> >
> > >>> C
> >
> > array([[ 3.003+0.j,  1.   +0.j,  0.   +0.j,  0.   +0.j],
> >        [ 3.   +0.j,  3.003+0.j,  2.   +0.j,  0.   +0.j],
> >        [ 0.   +0.j,  2.   +0.j,  3.003+0.j,  3.   +0.j],
> >        [ 0.   +0.j,  0.   +0.j,  1.   +0.j,  2.   +0.j]])
> >
> > >>> linalg.lu(C)
> >
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
> > line 238, in lu
> >     p,l,u,info = flu(a1,permute_l=permute_l,overwrite_a = overwrite_a)
> > TypeError: object of type 'None' is not callable
> >
> >
> > For what reason ?
> >
> > Nils
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.net
> > http://www.scipy.net/mailman/listinfo/scipy-user
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user



From nwagner at mecha.uni-stuttgart.de  Mon Jul 14 11:26:16 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Mon, 14 Jul 2003 17:26:16 +0200
Subject: [SciPy-user] Possible bug in linalg.lu
References: <3F12B02E.407872FC@mecha.uni-stuttgart.de>
	<200307141709.55696.p.berkes@biologie.hu-berlin.de>
Message-ID: <3F12CB98.A444537B@mecha.uni-stuttgart.de>

Pietro Berkes schrieb:
> 
> even faster, if you don't need to permute the matrix:
> linalg.lu_factor(C)


BTW, how can I check the sign of \det(C)= \pm \det(U) ?

P,L,U,info = linalg.lu(C)

detA = \pm prod(diag(U))

Nils

Remarks:

\pm denotes plus minus...


\det(A) = \det(P) \det(L) \det(U) = \det(P) \det(U)


> 
> On Monday 14 July 2003 16:23, Pietro Berkes wrote:
> > the function linalg.lu seems to be defined for real matrices only. if you
> > want to use it for complex ones, the fastest solution is probably to write
> > a wrapper to the lapack function ZGETRF. it should work like in the real
> > case (cfr. linalg/src/lu.f).
> >
> > regards,
> > pietro.
> >
> > On Monday 14 July 2003 15:29, Nils Wagner wrote:
> > > Hi all,
> > >
> > > >>> C
> > >
> > > array([[ 3.003+0.j,  1.   +0.j,  0.   +0.j,  0.   +0.j],
> > >        [ 3.   +0.j,  3.003+0.j,  2.   +0.j,  0.   +0.j],
> > >        [ 0.   +0.j,  2.   +0.j,  3.003+0.j,  3.   +0.j],
> > >        [ 0.   +0.j,  0.   +0.j,  1.   +0.j,  2.   +0.j]])
> > >
> > > >>> linalg.lu(C)
> > >
> > > Traceback (most recent call last):
> > >   File "<stdin>", line 1, in ?
> > >   File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
> > > line 238, in lu
> > >     p,l,u,info = flu(a1,permute_l=permute_l,overwrite_a = overwrite_a)
> > > TypeError: object of type 'None' is not callable
> > >
> > >
> > > For what reason ?
> > >
> > > Nils
> > >
> > > _______________________________________________
> > > SciPy-user mailing list
> > > SciPy-user at scipy.net
> > > http://www.scipy.net/mailman/listinfo/scipy-user
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.net
> > http://www.scipy.net/mailman/listinfo/scipy-user
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user



From haase at msg.ucsf.edu  Mon Jul 14 13:41:09 2003
From: haase at msg.ucsf.edu (Sebastian Haase)
Date: Mon, 14 Jul 2003 10:41:09 -0700
Subject: [SciPy-user] Python's various numeric packages
References: <3F0FFD1C.9010600@sympatico.ca>
Message-ID: <013801c34a2f$1c09d2b0$421ee6a9@rodan>

Hi Colin,
thanks for asking these questions. I also thing the situation isn't very
clear.

For what I know the latest version on numarray (0.5) is supposed to have
fixed lot's of speed problems; that is: for small arrays, since for arrays
larger than about 10000 it (reportedly) always was faster.

My specific question is: WHY does SciPy claim (for a long time !) that it
can work with both Numeric and with numarry. But instructions or even
further comments on that are nowhere to be found ????

My impression is that currently Numeric is still supported if not further
developed (as python's main numeric library)  and the numarray is  still
being hold back - even though it shouldn't, ... <wink> [ some kind of
Roadmap would be nice ]

For the data-structures of numarray:  NDArray was used (until) 0.3.6 but is
nowhere to be found since 0.4.  The reason is a political one:  They what to
make it as close to Numeric as possible to simplify (encourage) the
transition [[ the doc says (said) that there is now one main structure,
called PyArrayObject, and so it a"first class citizen" - just like it is in
Numeric --- what is a "first class citizen" anyway?? ]]

Hope this thread continues  (and then get's copy&pasted to
www.python.org/cgi-bin/moinmoin/NumArray -- once they have space again ;-)

Cheers,
Sebastian Haase


> Is there some place where there is an overview of the various
> packages, their relationships and their present stages of development?
>
> I have downloaded SciPy: SciPy-0.2.0_alpha_202.4187.win32-py2.1.exe
> The install fails.
> It does not permit the install directory to be entered.  It does not
> detect the
> registered (XP) Python installation to suggest site-packages as a likely
> install directory.
>
> Does SciPy depend on Numeric?
>
> Numeric appears to be fully operational, but no longer being developed
> as it is
> being replaced eventually by numarray.  The intended time frame for this
> evolution is not clear.
>
> numarray appears to be largely operable, but speed problems have been
> reported.
> NDArray and NumArray are the basic classes of numarray, but the design
> decision
> seems to have been made to deprecate the use of class methods in favour of
> factory functions.  This appears to inhibit the development of
> sub-classes to
> NumArray.
>
> MatPy is an effort to facilitate matrix operations.  It seems to have
> resulted from
> a lot of work by Huaiyu Zhu.  An extended discussion took place during
2000
> to 2001, but there seems to be little current interest.
>
> The project was originally based on Numeric, but appears to be in
> transition to
> numarray.  Again, the decision to use factory functions, rather than
> exploiting
> the full capability of the Python class structure, appears to hav been
made.
>
> Source Forge advertises the availability of version 0.4 as a downloadable
> Win 32 package, but it seems to have regressed to version 0.3.
>
> I would appreciate any advice.
>
> Colin W.
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user
>



From j_r_fonseca at yahoo.co.uk  Mon Jul 14 18:57:37 2003
From: j_r_fonseca at yahoo.co.uk (=?iso-8859-15?Q?Jos=E9?= Fonseca)
Date: Mon, 14 Jul 2003 23:57:37 +0100
Subject: [SciPy-user] Debian packages of scipy and f2py
Message-ID: <20030714225737.GB1869@prometeu>

I've make Debian packages of scipy and f2py. They are available from my
apt-get repository at:

  http://jrfonseca.dyndns.org/debian/

I referred to Joe Reinhardt's packages http://people.debian.org/~jmr/
but have done these packages from scratch. These come for all python
versions in debian unstable (2.1, 2.2 and 2.3).

I've run the standard tests successfully but I'd appreciate that
problems with these packages to be reported to me [privately] as I'd
like to have these on Debian proper at some time.

One tricky issue I'd like to address with the scipy and f2py maintainers
is the the scipy_distutils. Both scipy and f2py attempt to install to
/usr/lib/python*/site-packages/scipy_distutils and at least on Debian
this is not admissible so the packages conflict with each other and are
mutually exclusive. This is particularly even more annoying for me,
since for building scipy f2py is needed, so I need to install and
uninstall them as a maniac. Is there any solution that allow both these
packages to happily co-exist in a tree without overlapping?


Enjoy,

Jos? Fonseca


PS: Please CC'me on any reply as I'm not subscribed to all these lists.



From alnesbit at students.cs.mu.OZ.AU  Mon Jul 14 22:43:11 2003
From: alnesbit at students.cs.mu.OZ.AU (Andrew Nesbit)
Date: Tue, 15 Jul 2003 12:43:11 +1000 (EST)
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <013801c34a2f$1c09d2b0$421ee6a9@rodan>
References: <3F0FFD1C.9010600@sympatico.ca>
	<013801c34a2f$1c09d2b0$421ee6a9@rodan>
Message-ID: <Pine.GSO.4.56.0307151239310.25942@murree.cs.mu.OZ.AU>

> My specific question is: WHY does SciPy claim (for a long time !) that it
> can work with both Numeric and with numarry. But instructions or even
> further comments on that are nowhere to be found ????

I have had problems with Numeric... in particular, a bug that I found
and reported, but seeing as Numeric is no longer being developed, I'm
not holding my breath as to when it's going to be fixed.  I had a look
at fixing it myself, but the code is extremely hairy, and I'm totally
lost in it.

Which leads me to the following extension of your question: has
anybody here had experience in using Numarray with SciPy?

Andrew.



From eric at enthought.com  Tue Jul 15 02:18:59 2003
From: eric at enthought.com (eric jones)
Date: Mon, 14 Jul 2003 22:18:59 -0800
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <3F0FFD1C.9010600@sympatico.ca>
Message-ID: <000501c34a98$fa82daf0$957ba8c0@ericlaptop>

Hey Colin,

> Is there some place where there is an overview of the various
> packages, their relationships and their present stages of development?

Numeric is the only required prerequisite.  wxPython for plotting and a
C++ compiler for weave are helpful but not required.

> 
> I have downloaded SciPy: SciPy-0.2.0_alpha_202.4187.win32-py2.1.exe
> The install fails. It does not permit the install directory to be
entered.  > It does not detect the registered (XP) Python installation
to suggest site-
> packages as a likely install directory.

I am not sure why it doesn't work on your machine.  I just installed the
2.2 version of the same file, and it found my Python2.2 installation and
installed fine.  

Are others having problem with the 2.1 file?

The easiest way to get a windows installation is to use the full python
installation found here:

http://www.enthought.com/python/

> Does SciPy depend on Numeric?

Yes.  I believe that 20.3 or beyond should work.  Most people are
probably using 22 or 23 currently.

> Numeric appears to be fully operational, but no longer being developed
> as it is being replaced eventually by numarray.  The intended time
frame for 
> this evolution is not clear.

Numarray will be the successor to Numeric.  I talked with Perry
Greenfield from STSci at OSCON last week.  STSci is developing numarray.
He said that pretty much the only things left before numarray is a
"feature complete" replacement for Numeric are PyObject array support
and Paul Dubois Masked Array (MA) classes.  He wants a full replacement
before releasing 1.0.  I'll let him pronounce the official release
dates, but it is not so far off.

Numarray and Numeric will co-exist for a long while.  Numarray is new
and therefore less well tested.  It also has slower performance for
small arrays by about a factor of 3, but is faster for large arrays.
There are also many packages that rely on Numeric out in the wild, and
the transition will be slow.  

At some point, SciPy will cut over to using Numarray.  STSci folks are
working on getting the major portions of the port to work.  The process
and time for doing this hasn't been decided.  If it is easy to support
both Numeric and numarray, we will.  If it isn't, we'll have to think
hard about when and how to do the transition.

> 
> numarray appears to be largely operable, but speed problems have been
> reported. NDArray and NumArray are the basic classes of numarray, but
the 
> design decision seems to have been made to deprecate the use of class 
> methods in favour of factory functions.  This appears to inhibit the 
> development of sub-classes to NumArray.

Not sure what this is about because I haven't followed it that closely,
but I will say that sub-classing arrays isn't all that it is cracked up
to be in practice.  One of the nicest things about arrays is there array
arithmetic. They allow you to write mathematic formula-like code for
numerical operations.  When you sub-class an array, say with an Image
class, all mathematic operations work, but they return arrays instead of
images -- not so nice.  You end up having to do a lot of work to get the
behavior you want from the sub-classing.  I'm not saying it isn't
occasionally useful, it just isn't as nice as it first sounds...

> MatPy is an effort to facilitate matrix operations.  It seems to have
> resulted from a lot of work by Huaiyu Zhu.  An extended discussion
took 
> place during 2000 to 2001, but there seems to be little current
interest.

Don't know much about this.

> The project was originally based on Numeric, but appears to be in
> transition to
> numarray.  Again, the decision to use factory functions, rather than
> exploiting
> the full capability of the Python class structure, appears to hav been
made.
> 
> Source Forge advertises the availability of version 0.4 as a
downloadable
> Win 32 package, but it seems to have regressed to version 0.3.
> 
> I would appreciate any advice.
> 
> Colin W.
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user




From eric at enthought.com  Tue Jul 15 02:23:23 2003
From: eric at enthought.com (eric jones)
Date: Mon, 14 Jul 2003 22:23:23 -0800
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <Pine.GSO.4.56.0307151239310.25942@murree.cs.mu.OZ.AU>
Message-ID: <000701c34a99$9b55d090$957ba8c0@ericlaptop>

Hey Andrew,

> > My specific question is: WHY does SciPy claim (for a long time !)
that it
> > can work with both Numeric and with numarry. But instructions or
even
> > further comments on that are nowhere to be found ????
> 
> I have had problems with Numeric... in particular, a bug that I found
> and reported, but seeing as Numeric is no longer being developed, I'm
> not holding my breath as to when it's going to be fixed.  

Bugs are periodically fixed by Travis Oliphant, but he is pretty much
the only one pitching in on this now.  

> I had a look at fixing it myself, but the code is extremely hairy, and
I'm 
> totally lost in it.

Hence, numarray. :-)


> Which leads me to the following extension of your question: has
> anybody here had experience in using Numarray with SciPy?

Not I.  It isn't ported yet.

eric




From eric at enthought.com  Tue Jul 15 02:29:55 2003
From: eric at enthought.com (eric jones)
Date: Mon, 14 Jul 2003 22:29:55 -0800
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <013801c34a2f$1c09d2b0$421ee6a9@rodan>
Message-ID: <000801c34a9a$84b1f520$957ba8c0@ericlaptop>

> Hi Colin,
> thanks for asking these questions. I also thing the situation isn't
very
> clear.
> 
> For what I know the latest version on numarray (0.5) is supposed to
have
> fixed lot's of speed problems; that is: for small arrays, since for
arrays
> larger than about 10000 it (reportedly) always was faster.

It is much better now than it was even a few months ago -- Perry
presented results at OSCON last week.  It is still slower, but not
cripplingly so as it was before.

> My specific question is: WHY does SciPy claim (for a long time !) that
it
> can work with both Numeric and with numarry. But instructions or even
> further comments on that are nowhere to be found ????

I wasn't aware of this claim, so I apologize if I made it. <wink...>
Where is this information posted?

Anyway, numarray support will come as the STSci people have time to work
on the port.  F2py support apparently exists now, which is a huge step.
Perry mentioned that the special function library is one of the harder
things remaining with all of its ufunc support.  After that, it will
just be working through the issues that come up.  Generally though, the
API, both Python and C level, for Numeric and Numarray are fairly
compatible.

> 
> My impression is that currently Numeric is still supported if not
further
> developed (as python's main numeric library)  and the numarray is
still
> being hold back - even though it shouldn't, ... <wink> [ some kind of
> Roadmap would be nice ]

The numarray folks are doing periodic releases and CVS is available to
anyone wishing to tinker with it.

eric




From cjw at sympatico.ca  Tue Jul 15 16:21:30 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Tue, 15 Jul 2003 16:21:30 -0400
Subject: [SciPy-user] Re: SciPy-user digest, Vol 1 #445 - 6 msgs
In-Reply-To: <20030715170001.15241.42787.Mailman@scipy.org>
References: <20030715170001.15241.42787.Mailman@scipy.org>
Message-ID: <3F14624A.5090204@sympatico.ca>

An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20030715/c29da6c3/attachment.html>

From cjw at sympatico.ca  Tue Jul 15 16:59:10 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Tue, 15 Jul 2003 16:59:10 -0400
Subject: [SciPy-user] Matrix Arithmetic
In-Reply-To: <20030715170001.15241.42787.Mailman@scipy.org>
References: <20030715170001.15241.42787.Mailman@scipy.org>
Message-ID: <3F146B1E.1000607@sympatico.ca>

An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20030715/d908be9a/attachment.html>

From perry at stsci.edu  Tue Jul 15 19:37:59 2003
From: perry at stsci.edu (Perry Greenfield)
Date: Tue, 15 Jul 2003 19:37:59 -0400
Subject: [SciPy-user] Matrix Arithmetic
In-Reply-To: <NEBBIJKBMLDBLNCEEFOCCEMBDAAA.perry@stsci.edu>
Message-ID: <NEBBIJKBMLDBLNCEEFOCOEMBDAAA.perry@stsci.edu>

I haven't had much time to respond to these comments and queries,
but I'll do my best.

> Behalf Of Colin J. Williams
> From: "eric jones" <eric at enthought.com>
> [snip]
>
>>> numarray appears to be largely operable, but speed problems have been
>>> reported. NDArray and NumArray are the basic classes of numarray, but
>>>
>>> the
>>>
>>> design decision seems to have been made to deprecate the use of class
>>> methods in favour of factory functions.  This appears to inhibit the
>>> development of sub-classes to NumArray.
>
I'm not sure what this comment refers to. If it is important, can you
be more explicit about the inhibition regarding subclasses?
>
>> Not sure what this is about because I haven't followed it that closely,
>> but I will say that sub-classing arrays isn't all that it is cracked up
>> to be in practice.  One of the nicest things about arrays is there array
>> arithmetic. They allow you to write mathematic formula-like code for
>> numerical operations.  When you sub-class an array, say with an Image
>> class, all mathematic operations work, but they return arrays instead of
>> images -- not so nice.  You end up having to do a lot of work to get the
>> behavior you want from the sub-classing.  I'm not saying it isn't
>> occasionally useful, it just isn't as nice as it first sounds...
>
My 2 cents on subclassing: It isn't useless, but it is rarely trivial.
Eric is right that most subclassing involves overriding all the operators
and that will generally involve some work. On the other hand, subclassing is
generally far more preferable to writing your own stuff from scratch (I'm
guessing anyway). But on the third hand, outside of the customizations
referred
to below, I haven't seen a good practical example of subclassing numeric
arrays
yet so I can't comment on how useful it is yet (not to say we won't
eventually
come up with some).

> I have been looking at the sub-classing of NumArray to provide matrix
> arithmetic, along
> the lines of  Huaiyu Zhu, but not quite as ambitious.
>
> So that A + B, A * B, A  /  B all make sense, where A and B are matrices.
>
> Similarly A.T delivers the transpose of A or B.I delivers the
> inverse of B.
>
> Does anyone have any thoughts?
>
> Colin W.
>
Yes, I do. Doing this would be (relatively) easy. But it would be
wrong (IMHO). If you do this, you will break interoperability with
other numarray modules and packages. There will be lots of code that
will assume that * means element-by-element multiplication, not matrix
multiplication. So by doing this you in effect will be fracturing the
numeric community. If the judgement is that there is very little shared
code (e.g., FFT, signal processing, linear algebra, etc.) between the
two, little harm would be done. I tend to think that isn't the case.
Now one has to wrap these modules to work with the matrix arrays, or
if there are matrix modules available, then they have to be wrapped to
work with numarray.

I'd rather see one of the proposals to allow extending operator syntax to
allow defining new Python operators so that matrix multiplication and
the small number of other matrix operations can be accomodated rather
than making incompatible types of arrays/matrices. I believe Guido will
accomodate this should enough of the community make a case for it.

>
>>> MatPy is an effort to facilitate matrix operations.  It seems to have
>>> resulted from a lot of work by Huaiyu Zhu.  An extended discussion
>>>
>>> took
>>>
>>> place during 2000 to 2001, but there seems to be little current
>>>
>>> interest.
>
>> Don't know much about this.
>
>
> The project was originally based on Numeric, but appears to be in
> transition to
> numarray.  Again, the decision to use factory functions, rather than
> exploiting
> the full capability of the Python class structure, appears to hav been
>
> made.
>
Again, not sure what this refers to. Also, I'm not aware of any work that
that Huaiyu is doing with regard to this or numarray recently.

> Source Forge advertises the availability of version 0.4 as a
>
> downloadable
>
> Win 32 package, but it seems to have regressed to version 0.3.
>
numarray? The latest version should be 0.5 (and 0.6 will be released
very shortly).


Perry Greenfield




From perry at stsci.edu  Tue Jul 15 19:45:52 2003
From: perry at stsci.edu (Perry Greenfield)
Date: Tue, 15 Jul 2003 19:45:52 -0400
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <000501c34a98$fa82daf0$957ba8c0@ericlaptop>
Message-ID: <NEBBIJKBMLDBLNCEEFOCGEMCDAAA.perry@stsci.edu>


> -----Original Message-----
> From: scipy-user-admin at scipy.net [mailto:scipy-user-admin at scipy.net]On
> Behalf Of eric jones
> Sent: Tuesday, July 15, 2003 2:19 AM
> To: scipy-user at scipy.net
> Subject: RE: [SciPy-user] Python's various numeric packages
>
> > Numeric appears to be fully operational, but no longer being developed
> > as it is being replaced eventually by numarray.  The intended time
> frame for
> > this evolution is not clear.
>
> Numarray will be the successor to Numeric.  I talked with Perry
> Greenfield from STSci at OSCON last week.  STSci is developing numarray.
> He said that pretty much the only things left before numarray is a
> "feature complete" replacement for Numeric are PyObject array support
> and Paul Dubois Masked Array (MA) classes.  He wants a full replacement
> before releasing 1.0.  I'll let him pronounce the official release
> dates, but it is not so far off.
>
No dates fixed in stone, but here is the basic plan

0.6 to be released this week, this reorganizes numarray as a package

0.7 (few weeks?) Will include PyObject support

0.8 (2 months?) Will include MA support. At this point we hope to replicate
all Numeric functionality (other than the planned changes).

v1.0 will come out when 0.8 has been tested by users for a little while
(with
perhaps a 0.9 if many changes and fixes are needed)

> Numarray and Numeric will co-exist for a long while.  Numarray is new
> and therefore less well tested.  It also has slower performance for
> small arrays by about a factor of 3, but is faster for large arrays.
> There are also many packages that rely on Numeric out in the wild, and
> the transition will be slow.
>
There may be some rough corners where performance of numarray needs
optimization
that haven't yet been handled (e.g. printing? slicing?)

> At some point, SciPy will cut over to using Numarray.  STSci folks are
> working on getting the major portions of the port to work.  The process
> and time for doing this hasn't been decided.  If it is easy to support
> both Numeric and numarray, we will.  If it isn't, we'll have to think
> hard about when and how to do the transition.
>
yep

Perry Greenfield




From perry at stsci.edu  Tue Jul 15 19:48:47 2003
From: perry at stsci.edu (Perry Greenfield)
Date: Tue, 15 Jul 2003 19:48:47 -0400
Subject: [SciPy-user] Python's various numeric packages
In-Reply-To: <000801c34a9a$84b1f520$957ba8c0@ericlaptop>
Message-ID: <NEBBIJKBMLDBLNCEEFOCMEMCDAAA.perry@stsci.edu>


> -----Original Message-----
> From: scipy-user-admin at scipy.net [mailto:scipy-user-admin at scipy.net]On
> Behalf Of eric jones
> Sent: Tuesday, July 15, 2003 2:30 AM
> To: scipy-user at scipy.net
> Subject: RE: [SciPy-user] Python's various numeric packages
> 
> 
> 
> > My specific question is: WHY does SciPy claim (for a long time !) that
> it
> > can work with both Numeric and with numarry. But instructions or even
> > further comments on that are nowhere to be found ????
> 
> I wasn't aware of this claim, so I apologize if I made it. <wink...>
> Where is this information posted?
>
I wasn't aware of this claim either. There is a module in kiva that 
implies this (num_compat if I recall correctly), but I wasn't aware
of any explicit claim to this effect.
 
> Anyway, numarray support will come as the STSci people have time to work
> on the port.  F2py support apparently exists now, which is a huge step.
> Perry mentioned that the special function library is one of the harder
> things remaining with all of its ufunc support.  After that, it will
> just be working through the issues that come up.  Generally though, the
> API, both Python and C level, for Numeric and Numarray are fairly
> compatible.
>
We will start working on this when we get to v0.8.
> 



From pajer at iname.com  Tue Jul 15 21:58:03 2003
From: pajer at iname.com (Gary Pajer)
Date: Tue, 15 Jul 2003 21:58:03 -0400
Subject: [SciPy-user] MacNewbie needs MacHelp
References: <000501c34a98$fa82daf0$957ba8c0@ericlaptop>
Message-ID: <008201c34b3d$b170bdf0$c0135544@playroom>

I have a perfectly functional system on WinXP, and a serviceable one on
Linux.  So of course my new employer is Mac centric.  I have no religious
attachement to anything, but I am all thumbs on the Mac. Never touched one.
it's  OS X, 10.1

I have the fink version of python running, and the fink version of Numeric.
and X11.  Idle runs.  Numeric works.

How the heck do I get scipy up?  I started with the fink version because I
want to use the visual package, which claims to work only with the fink
python.

There's a fink package called scipy-2002xxxxx in the unstable area.  As an
example of my expertise with Mac, I can't figure out how to copy the .info
file from the "unstable" directory to the "local" directory (as directed by
some instructions somewhere).

Any help?

Once I get this nailed down, I'll start looking for a mouse with three
buttons ...

-gary



From cjw at sympatico.ca  Wed Jul 16 06:55:40 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Wed, 16 Jul 2003 06:55:40 -0400
Subject: [SciPy-user] Enthought package of various Python related stuff
Message-ID: <3F152F2C.6020209@sympatico.ca>

I have downloaded this, it is massive - 62MB.

It includes BTrees and freetype, which are not referenced in the included
documentation, also massive - 29MB.

Colin W.



From nwagner at mecha.uni-stuttgart.de  Wed Jul 16 07:54:32 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Wed, 16 Jul 2003 13:54:32 +0200
Subject: [SciPy-user] Detecting clusters in an array
Message-ID: <3F153CF8.FF9705@mecha.uni-stuttgart.de>

Hi all,

Let us assume that we have a one-dimensional array, let's say A, of
complex and/or real numbers.
Now, I am interested in the detection of clusters.
Each cluster, if any, consists of the elements of A, which lie inside a
circle with fixed radius epsilon)
How can I solve this problem most efficiently in scipy.

A small example would be appreciated.

Thanks in advance

                      Nils

nc, nec, cl = cluster(A, epsilon)

Output

nc : total number of clusters
nec[i] : number of elements of cluster i
cl[0:sum(nec)] : elements of all clusters



From eric at enthought.com  Wed Jul 16 11:46:02 2003
From: eric at enthought.com (eric jones)
Date: Wed, 16 Jul 2003 10:46:02 -0500
Subject: [SciPy-user] Enthought package of various Python related stuff
In-Reply-To: <3F152F2C.6020209@sympatico.ca>
Message-ID: <008601c34bb1$5f45f260$8901a8c0@ERICDESKTOP>

> I have downloaded this, it is massive - 62MB.

It includes a lot of tools.

> It includes BTrees and freetype, which are not referenced in the
included
> documentation, also massive - 29MB.

Those are components used by other mentioned libraries.  Freetype is
part of Chaco/Kiva.  You could use it on its own, but I'm not sure what
for. I'm not sure what BTrees is used in, but I'm betting it is part of
SQLite (most likely), GadFly or ZODB.

eric




From jdhunter at ace.bsd.uchicago.edu  Wed Jul 16 16:56:11 2003
From: jdhunter at ace.bsd.uchicago.edu (John Hunter)
Date: Wed, 16 Jul 2003 15:56:11 -0500
Subject: [SciPy-user] finding djbfft
Message-ID: <m2ptkaqjh0.fsf@mother.paradise.lost>

I am trying to build scipy SciPy-0.2.0_alpha_200.4161 with djbfft on a
linux box.  I have built djbfft, ran install and instcheck.  This
created /usr/local/djbfft/lib/ which contains djbfft.a.  When I build
scipy with

 > python setup.py build

I get

  djbfft_info:
    NOT AVAILABLE

    DJBFFT (http://cr.yp.to/djbfft.html) libraries not found.
    Directories to search for the libraries can be specified in the
    scipy_distutils/site.cfg file (section [djbfft]) or by setting
    the DJBFFT environment variable.

I have tried setting 

  setenv DJBFFT /usr/local/djbfft/lib

and
 
  setenv DJBFFT /usr/local/djbfft

as well as placing djbfft.a in /usr/lib and when that failed, renaming
it to libdjbfft.a.  To no avail. 

I find no site.cfg file in the scipy src tree to modify.

How do I build scipy with djbfft?

Thanks,
John Hunter



From cjw at sympatico.ca  Wed Jul 16 21:00:23 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Wed, 16 Jul 2003 21:00:23 -0400
Subject: [SciPy-user] Using NumArray to facilitate Matrix arithmetic
Message-ID: <3F15F527.4070404@sympatico.ca>

-------- Original Message --------

[Perry Greenfield]

I haven't had much time to respond to these comments and queries,
but I'll do my best.

[Colin W.
>>> NDArray and NumArray are the basic classes of numarray, but
>>> the design decision seems to have been made to deprecate the use 
>>> of class methods in favour of factory functions.  This appears 
>>> to inhibit the development of sub-classes to NumArray.
>

[Perry Greenfield]

 I'm not sure what this comment refers to. If it is important, can you
be more explicit about the inhibition regarding subclasses?

[Colin W.]

I feel that it could be important and will try to put together an
illustrative example over the next week or so.  There are a number
of functions in the package which might, with benefit, be replaced
with methods of NumArray.  Such methods could then be inherited by
any sub-classes.  In the case of a possible Matrix class, there are
some functions/methods which my be represented, in a more user
friendly way by class properties.

For example, in matrix algebra, one typically represents transpose
with a superscript T or an inverse with a superscript -1.

Using properties, we could use A.T or B.I to represent the transpose
or the inverse of matrices A and B respectively.

These are not new ideas. Huaiyu Zhu started implementing them in 
his MatPy project.

[Eric Jones]
 >> Not sure what this is about because I haven't followed it that closely,
>> but I will say that sub-classing arrays isn't all that it is cracked up
>> to be in practice.  One of the nicest things about arrays is there array
>> arithmetic. They allow you to write mathematic formula-like code for
>> numerical operations.  When you sub-class an array, say with an Image
>> class, all mathematic operations work, but they return arrays instead of
>> images -- not so nice.  You end up having to do a lot of work to get the
>> behavior you want from the sub-classing.  I'm not saying it isn't
>> occasionally useful, it just isn't as nice as it first sounds...
>

[Colin W.]
This notion of being able to write mathematics like code is at the
root of this.

Suppose that A is a Matrix and B is an array, then

A + B ==> a matrix, with coercion, is not that much different from 
          array operations.

A * B ==> a matrix is similar but the multiplication implies the 
          operation of linear algebra, rather than a simple element 
          by element multiplication.

If we wished to find the common norm for A, it is a little simpler 
to write A.Norm than to write A.Norm(), using a method or Norm(A),
for a function.

[Perry Greenfield]
 My 2 cents on subclassing: It isn't useless, but it is rarely trivial.
Eric is right that most subclassing involves overriding all the operators
and that will generally involve some work. On the other hand, subclassing is
generally far more preferable to writing your own stuff from scratch (I'm
guessing anyway). But on the third hand, outside of the customizations
referred to below, I haven't seen a good practical example of subclassing 
numeric arrays yet so I can't comment on how useful it is yet (not to 
say we won't eventually come up with some).

[Colin W.]
Let's look at each of these:
  Overriding:  Yes, that's a chore, but a boiler plate could be 
               prepared for the class and then be used by each
               sub-class builder.
  Less work:   The sub-class constructor is largely riding on
               the back of the class builder.  Labour saving is
               one of the potential benefits of the object
               oriented approach.
  An example:  Since Huaiyu Zhu was working largely with Numeric,
               he could not sub-class.  The latest version of
               Matrix.py that I've seen is of 26-Aug-01.
               I'll put a simple illustrative example together.

[Colin W.]
> I have been looking at the sub-classing of NumArray to provide 
> matrix arithmetic, along the lines of  Huaiyu Zhu, but not quite 
> as ambitious.
>
> So that A + B, A * B, A  /  B all make sense, where A and B are matrices.
>
> Similarly A.T delivers the transpose of A or B.I delivers the
> inverse of B.
>
> Does anyone have any thoughts?
>

[Perry Greenfield]
Yes, I do. Doing this would be (relatively) easy. But it would be
wrong (IMHO). If you do this, you will break interoperability with
other numarray modules and packages. There will be lots of code that
will assume that * means element-by-element multiplication, not matrix
multiplication. So by doing this you in effect will be fracturing the
numeric community. If the judgement is that there is very little shared
code (e.g., FFT, signal processing, linear algebra, etc.) between the
two, little harm would be done. I tend to think that isn't the case.
Now one has to wrap these modules to work with the matrix arrays, or
if there are matrix modules available, then they have to be wrapped to
work with numarray.

[Colin W.]
I agree that interoperability with other numarray modules 
and packages is essential and doubt that very much would 
need to be changed in NumArray to facilitate inheritance.

For some, the idea of element by element operations takes 
a little getting use to.  For multi-dimensional arrays, it
is the only way to go.  For two dimensional array, there
could well be a choice, which the user makes by choosing
to work with a NumArray class or a Matrix class.  The
latter is based on an extensive literature which has grown
over that last 50 and more years.

It would seem to be mutually beneficial to have these 
classes from the same root.

[Perry Greenfield]
I'd rather see one of the proposals to allow extending operator syntax to
allow defining new Python operators so that matrix multiplication and
the small number of other matrix operations can be accomodated rather
than making incompatible types of arrays/matrices. I believe Guido will
accomodate this should enough of the community make a case for it.

[Colin W]
It would be nice if there were more functional characters 
available on the keyboard.  However, groupings of characters 
to achieve operations on particular data types would 
complicate Python and would not likely appeal to our
BDFL.

The idea of operator overloading is already well established
for Python.

[Colin W]
>>> MatPy is an effort to facilitate matrix operations.  It 
>>> seems to have resulted from a lot of work by Huaiyu Zhu.  
>>>
>>> An extended discussion took place during 2000 to 2001, 
>>> but there seems to be little current interest.

[Eric Jones]
>>>
>>> Don't know much about this.


[Colin W]
>>> The project was originally based on Numeric, but appears 
>>> to be in transition to numarray.  Again, the decision 
>>> to use factory functions, rather than exploiting the 
>>> full capability of the Python class structure, appears 
>>> to have been made.
>

[Perry Greenfield]
Again, not sure what this refers to. Also, I'm not aware of 
any work that that Huaiyu is doing with regard to this or 
numarray recently.

[Colin W.]
> Source Forge advertises the availability of version 0.4 
> as a downloadable Win 32 package, but it seems to have 
> regressed to version 0.3.
>

[Perry Greenfield]
numarray? The latest version should be 0.5 (and 0.6 will be released
very shortly).

[Colin W.]
No, my comments here were with regard to MatPy.
Please see: http://matpy.sourceforge.net/
The last change appears to be about August 2001.
   




From nwagner at mecha.uni-stuttgart.de  Thu Jul 17 11:46:42 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Thu, 17 Jul 2003 17:46:42 +0200
Subject: [SciPy-user] linalg.lu_factor
Message-ID: <3F16C4E2.EE284952@mecha.uni-stuttgart.de>

Hi all,

How can I use linalg.lu_factor to compute the determinant of a matrix A
?
Of course I know, that I can use linalg.det(A) directly.

detA = linalg.det(A)

d,piv = linalg.lu_factor(A)

Afaik

prod(diag(d)) is the determinant except the sign. Am I missing something
?
How do I find the sign of det(A)

Nils



From chris at fonnesbeck.org  Thu Jul 17 15:06:24 2003
From: chris at fonnesbeck.org (Christopher Fonnesbeck)
Date: Thu, 17 Jul 2003 15:06:24 -0400
Subject: [SciPy-user] using scipy.stats.distributions
Message-ID: <C2CB982E-B889-11D7-B9D1-000A956FDAC0@fonnesbeck.org>

Is there a tutorial or some examples on how to use the distributions in 
scipy.stats? I am putting together some Markov chain Monte Carlo code, 
and need to use several different distributions, but cannot get the 
hang of distribution classes (e.g. setting parameters, generating 
values).

Thanks,
chris
--
Christopher J. Fonnesbeck (chris at fonnesbeck dot org)
GA Coop. Fish & Wildlife Research Unit, University of Georgia



From TravisOliphant at netscape.net  Fri Jul 18 01:19:20 2003
From: TravisOliphant at netscape.net (Travis Oliphant)
Date: Thu, 17 Jul 2003 23:19:20 -0600
Subject: [SciPy-user] Matrix Arithmetic
References: <20030715170001.15241.42787.Mailman@scipy.org>
	<3F146B1E.1000607@sympatico.ca>
Message-ID: <3F178358.406@netscape.net>

Numeric has a very nice matrix object called Matrix.  This is why Zhu's 
MatPy has received little attention from SciPy.

I'm not sure if Numarray has this Matrix object or not, but I think it 
should.


Travis O.





From cjw at sympatico.ca  Fri Jul 18 09:53:57 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Fri, 18 Jul 2003 09:53:57 -0400
Subject: [SciPy-user] Matrix Arithmetic
In-Reply-To: <3F178358.406@netscape.net>
References: <20030715170001.15241.42787.Mailman@scipy.org>
	<3F146B1E.1000607@sympatico.ca> <3F178358.406@netscape.net>
Message-ID: <3F17FBF5.9060909@sympatico.ca>

Travis Oliphant wrote:

> Numeric has a very nice matrix object called Matrix.  This is why 
> Zhu's MatPy has received little attention from SciPy.
>
> I'm not sure if Numarray has this Matrix object or not, but I think it 
> should.
>
>
> Travis O.

Many thanks, I hadn't spotted this.  It is just what I had in mind for 
my example. 
I will abandon my endeavours with the example.

There is a bit more to Matrix.py than the Numpy.pdf let's on.

    Matrix.py
    The Matrix.py python module defines a class Matrix which is a
    subclass of UserArray. The only differences
    between Matrix instances and UserArray instances is that the *
    operator on Matrix performs a
    matrix multiplication, as opposed to element-wise multiplication,
    and that the power operator ** is disallowed
    for Matrix instances.

numarray appears to rely on array functions to perform matrix 
functions.  There is
no equivalent of Matrix.py in Numeric.

A rewrite for numarray might use the class property to provide for 
transpose, inverse etc.

Similarly, Matrix might become a sub-class of NumArray.

I would be glad to help with the transfer of Matrix to numarray.  Please 
let be know.

Colin W.





From soneh at metri.re.kr  Sat Jul 19 00:22:29 2003
From: soneh at metri.re.kr (=?ks_c_5601-1987?B?vNXAusfP?=)
Date: Sat, 19 Jul 2003 13:22:29 +0900
Subject: [SciPy-user] K-MEANS ALGORITHM(ASKING)
Message-ID: <000801c34dad$5e26ade0$6c0310ac@LocalHost>

Hi
I Have stuck up with a project based on clustering using K-Means algorithm
Please help me find the relevent C code for theK-Means algorithm
Regards
-------------- next part --------------
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From philippe.dalet at voila.fr  Tue Jul 22 13:38:17 2003
From: philippe.dalet at voila.fr (=?utf-8?Q?philippe.dalet@voila.fr?=)
Date: Tue, 22 Jul 2003 19:38:17 +0200
Subject: [SciPy-user] =?iso-8859-1?Q?chaco?=
Message-ID: <HIFSZT$2A8A4E87166C1E97AA6D7FFDF73EF099@voila.fr>

under win2k and py22 and wxPythonWIN32-2.4.1.2-Py22.exe

I've downloaded the last update of sciPy (SciPy-0.2.0_alpha_202.4187.win32-py2.2.exe) 
and I could not execute chaco wx_plt_demo.py
If I setup the version of chaco (installer) It runs. 
If I run a simple demo I have a system memory bug.

before all was running.

Do You know this bug ?

Thanks a lot

DALET philippe
Laboratoire STS ?lectronique
Lyp champollion
avenue pezet
46100 FIGEAC

FRANCE
------------------------------------------

Faites un voeu et puis Voila ! www.voila.fr 




From helen.kemp at tesco.net  Wed Jul 23 03:34:21 2003
From: helen.kemp at tesco.net (Helen Kemp)
Date: Wed, 23 Jul 2003 08:34:21 +0100
Subject: [SciPy-user] chaco
References: <HIFSZT$2A8A4E87166C1E97AA6D7FFDF73EF099@voila.fr>
Message-ID: <004001c350ec$d60b13e0$18ec89d9@pc>

Sorry,
I think this e-mail was sent to me by mistake.
Helen
----- Original Message ----- 
From: <philippe.dalet at voila.fr>
To: <scipy-user at scipy.net>
Sent: Tuesday, July 22, 2003 6:38 PM
Subject: [SciPy-user] chaco


under win2k and py22 and wxPythonWIN32-2.4.1.2-Py22.exe

I've downloaded the last update of sciPy
(SciPy-0.2.0_alpha_202.4187.win32-py2.2.exe)
and I could not execute chaco wx_plt_demo.py
If I setup the version of chaco (installer) It runs.
If I run a simple demo I have a system memory bug.

before all was running.

Do You know this bug ?

Thanks a lot

DALET philippe
Laboratoire STS ?lectronique
Lyp champollion
avenue pezet
46100 FIGEAC

FRANCE
------------------------------------------

Faites un voeu et puis Voila ! www.voila.fr


_______________________________________________
SciPy-user mailing list
SciPy-user at scipy.net
http://www.scipy.net/mailman/listinfo/scipy-user




From nwagner at mecha.uni-stuttgart.de  Wed Jul 23 08:37:37 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Wed, 23 Jul 2003 14:37:37 +0200
Subject: [SciPy-user] xplt.plot
Message-ID: <3F1E8191.ADB364A8@mecha.uni-stuttgart.de>

Hi all,

How can I plot two curves on two different graphs with xplt ?
A small example would be appreciated.

Thanks in advance,

                    Nils



From arnd.baecker at web.de  Wed Jul 23 09:30:40 2003
From: arnd.baecker at web.de (Arnd Baecker)
Date: Wed, 23 Jul 2003 15:30:40 +0200 (CEST)
Subject: [SciPy-user] xplt.plot
In-Reply-To: <3F1E8191.ADB364A8@mecha.uni-stuttgart.de>
References: <3F1E8191.ADB364A8@mecha.uni-stuttgart.de>
Message-ID: <Pine.LNX.4.51.0307231528300.26441@ptpcp2.phy.tu-dresden.de>

Hi Nils,

do you mean something like this?

###########
from scipy import *
from scipy.xplt import *

x=arange(0.0,2.0*pi,0.01)
y1=sin(x)
y2=cos(x)

window(0)
plot(x,y1)
title ("sin")     # yes, the title has to be after the plot !
window(1)
plot(x,y2)
title ("cos")
############

Notice that only up to 7 windows can be opened
(moreover scipy.xplt has its rough edges ... ;-),
for example I never understood, why the title has to
be given after the plot ...)

Arnd



On Wed, 23 Jul 2003, Nils Wagner wrote:

> Hi all,
>
> How can I plot two curves on two different graphs with xplt ?
> A small example would be appreciated.
>
> Thanks in advance,
>
>                     Nils
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user
>



From nwagner at mecha.uni-stuttgart.de  Wed Jul 23 09:36:55 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Wed, 23 Jul 2003 15:36:55 +0200
Subject: [SciPy-user] xplt.plot
References: <3F1E8191.ADB364A8@mecha.uni-stuttgart.de>
	<Pine.LNX.4.51.0307231528300.26441@ptpcp2.phy.tu-dresden.de>
Message-ID: <3F1E8F76.2120BE03@mecha.uni-stuttgart.de>

Arnd Baecker schrieb:
> 
> Hi Nils,
> 
> do you mean something like this?

Yes, and how about labels ?

Nils

> 
> ###########
> from scipy import *
> from scipy.xplt import *
> 
> x=arange(0.0,2.0*pi,0.01)
> y1=sin(x)
> y2=cos(x)
> 
> window(0)
> plot(x,y1)
> title ("sin")     # yes, the title has to be after the plot !
> window(1)
> plot(x,y2)
> title ("cos")
> ############
> 
> Notice that only up to 7 windows can be opened
> (moreover scipy.xplt has its rough edges ... ;-),
> for example I never understood, why the title has to
> be given after the plot ...)
> 
> Arnd
> 
> On Wed, 23 Jul 2003, Nils Wagner wrote:
> 
> > Hi all,
> >
> > How can I plot two curves on two different graphs with xplt ?
> > A small example would be appreciated.
> >
> > Thanks in advance,
> >
> >                     Nils
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.net
> > http://www.scipy.net/mailman/listinfo/scipy-user
> >
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user



From arnd.baecker at web.de  Wed Jul 23 09:48:24 2003
From: arnd.baecker at web.de (Arnd Baecker)
Date: Wed, 23 Jul 2003 15:48:24 +0200 (CEST)
Subject: [SciPy-user] xplt.plot
In-Reply-To: <3F1E8F76.2120BE03@mecha.uni-stuttgart.de>
References: <3F1E8191.ADB364A8@mecha.uni-stuttgart.de>
 <Pine.LNX.4.51.0307231528300.26441@ptpcp2.phy.tu-dresden.de>
 <3F1E8F76.2120BE03@mecha.uni-stuttgart.de>
Message-ID: <Pine.LNX.4.51.0307231541210.26441@ptpcp2.phy.tu-dresden.de>


On Wed, 23 Jul 2003, Nils Wagner wrote:

> Arnd Baecker schrieb:
> >
> > Hi Nils,
> >
> > do you mean something like this?
>
> Yes, and how about labels ?

In general you can try (* remark below!)

  help("scipy.xplt")

which guides you to
  help("scipy.xplt.xlabel")

So in the example you just have to add
  xlabel("xlabel text")
  ylabel("ylabel text")


Remark concerning help("scipy.xplt"):
If you start with a clean python interactive session,
the first call to
  help("scipy.xplt")
will just give
"""
Help on instance of _ModuleLoader in scipy:

scipy.xplt = <module 'scipy.xplt' from
'/home/python/PYTHON/l...site-packages/sc
ipy/xplt/__init__.py' [imported]>
"""

Only a second call gives the expected help
(scipy.__version__: '0.2.0_alpha_200.4160')
Personally I find this pretty annoying, and
also problematic for new-comers..
Maybe this is due to the "delayed import" stuff ?
(does any of the scipy experts have a clue on this ?)

Arnd




From TravisOliphant at netscape.net  Wed Jul 23 11:20:14 2003
From: TravisOliphant at netscape.net (Travis Oliphant)
Date: Wed, 23 Jul 2003 09:20:14 -0600
Subject: [SciPy-user] xplt.plot
References: <3F1E8191.ADB364A8@mecha.uni-stuttgart.de>
Message-ID: <3F1EA7AE.1040103@netscape.net>

from scipy import xplt

xplt.subplot(2,1)
xplt.plsys(1)
xplt.plot(x1,y1,x2,y2)
xplt.plsys(2)
xplt.plot(x1,y1,x2,y2)



Nils Wagner wrote:
> Hi all,
> 
> How can I plot two curves on two different graphs with xplt ?
> A small example would be appreciated.
> 
> Thanks in advance,
> 
>                     Nils
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user


-- 
Your favorite stores, helpful shopping tools and great gift ideas.
Experience the convenience of buying online with Shop at Netscape!
http://shopnow.netscape.com/



From eric at enthought.com  Wed Jul 23 17:30:20 2003
From: eric at enthought.com (eric jones)
Date: Wed, 23 Jul 2003 16:30:20 -0500
Subject: [SciPy-user] K-MEANS ALGORITHM(ASKING)
In-Reply-To: <000801c34dad$5e26ade0$6c0310ac@LocalHost>
Message-ID: <00ba01c35161$a1082910$8901a8c0@ERICDESKTOP>

The following link has the C++ code for the vq algorithm.

 

http://www.scipy.org/site_content/remap?rmurl=http%3A//scipy.net/cgi-bin
/viewcvsx.cgi/scipy/Lib/cluster/src/vq.h%3Frev%3D1.2%26content-type%3Dte
xt/vnd.viewcvs-markup

 

The kmeans algorithm was written in pure python and lives here.

 

http://www.scipy.org/site_content/remap?rmurl=http%3A//scipy.net/cgi-bin
/viewcvsx.cgi/scipy/Lib/cluster/vq.py%3Frev%3D1.16%26content-type%3Dtext
/vnd.viewcvs-markup

 

If you get the SciPy source code, look in the scipy/Lib/cluster
directory.

 

see ya,

eric

----------------------------------------------
eric jones                    515 Congress Ave
www.enthought.com             Suite 1614
512 536-1057                  Austin, Tx 78701

-----Original Message-----
From: scipy-user-admin at scipy.net [mailto:scipy-user-admin at scipy.net] On
Behalf Of ??????
Sent: Friday, July 18, 2003 10:22 PM
To: SciPy-user at scipy.net
Subject: [SciPy-user] K-MEANS ALGORITHM(ASKING)

 

Hi
I Have stuck up with a project based on clustering using K-Means
algorithm
Please help me find the relevent C code for theK-Means algorithm
Regards

-------------- next part --------------
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From Paul_Kunz at SLAC.Stanford.EDU  Thu Jul 24 20:39:08 2003
From: Paul_Kunz at SLAC.Stanford.EDU (Paul F. Kunz)
Date: Thu, 24 Jul 2003 17:39:08 -0700
Subject: [SciPy-user] How to submit a paper
Message-ID: <200307250039.h6P0d8Q06783@libra3.slac.stanford.edu>

I'm interested in submitting a paper to SciPy '03.   How to I do that?
This list seems to be the only contact point to thw workshop.



From travis at enthought.com  Thu Jul 24 21:40:41 2003
From: travis at enthought.com (Travis N. Vaught)
Date: Thu, 24 Jul 2003 20:40:41 -0500
Subject: [SciPy-user] How to submit a paper
In-Reply-To: <200307250039.h6P0d8Q06783@libra3.slac.stanford.edu>
Message-ID: <000e01c3524d$c66bf870$0200a8c0@tvlaptop>

Hey Paul,

Please contact Eric Jones at eric at enthought.com regarding presentations.
Look for a formal announcement in a few minutes.

Travis

> -----Original Message-----
> From: scipy-user-admin at scipy.net [mailto:scipy-user-admin at scipy.net]
On
> Behalf Of Paul F. Kunz
> Sent: Thursday, July 24, 2003 6:39 PM
> To: scipy-user at scipy.org
> Subject: [SciPy-user] How to submit a paper
> 
> I'm interested in submitting a paper to SciPy '03.   How to I do that?
> This list seems to be the only contact point to thw workshop.
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.net
> http://www.scipy.net/mailman/listinfo/scipy-user




From travis at enthought.com  Thu Jul 24 21:53:20 2003
From: travis at enthought.com (Travis N. Vaught)
Date: Thu, 24 Jul 2003 20:53:20 -0500
Subject: [SciPy-user] [ANN] SciPy 03 Workshop - Scientific Computing with Python
Message-ID: <001401c3524f$8d372000$0200a8c0@tvlaptop>

------------------
SciPy '03 Workshop
------------------

The SciPy '03 Workshop on Scientific Computing with Python is being held
at Cal Tech again this year.  Online registration is now available.
After last year's success, we expect another great turnout with
compelling presentations/tutorials.

It is a two day workshop held September 11-12 in Pasadena, CA.

More information may be found at:
http://www.scipy.org/site_content/scipy03 

Online registration is available at: https://www.enthought.com/scipy03 

Please register early.  Last minute registrants will have to suffer the
indignity of a handwritten name tag.

It currently looks like breakfast (bagels, etc.), lunch and supper will
be provided Thursday, and breakfast and lunch will be provided Friday.

Discussion about the workshop may be directed to the SciPy-user mailing
list (http://www.scipy.org/site_content/MailList) to which you may post
messages at scipy-user at scipy.org.


Presenters:

If you would like to present at the workshop, there are two formats:

- Lightning Talks:
Short (5-15 minute) presentations of a particular scientific problem
solved with Python.

- Presentations:
Traditional presentation format ~45 minute talks.

If you would like to present, contact Eric Jones at eric at enthought.com. 

For any other questions, please feel free to call or email Travis
Vaught: travis at enthought.com, (512)536-1057.  You can call the same
number to register via phone (Business Hours CST).

Links:

SciPy.org community site:
http://www.scipy.org

Workshop Home:
http://www.scipy.org/site_content/scipy03

Summary of last year's workshop:
http://www.scipy.org/site_content/scipy02/scipy02summary.htm





From nwagner at mecha.uni-stuttgart.de  Fri Jul 25 07:30:26 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Fri, 25 Jul 2003 13:30:26 +0200
Subject: [SciPy-user] TypeError: object has read-only attributes
Message-ID: <3F2114D2.25E9A838@mecha.uni-stuttgart.de>

Hi all,

I would like to change an entry of a complex array.

>>> t
array([ 0.30993965+0.21102825j,  0.40232318+0.48098591j,
             0.30927754+0.3310895j ,  0.36197345+0.36041015j])
>>> t[0]
(0.30993964566340926+0.21102825078044135j)
>>> t[0].real
0.30993964566340926
>>> t[0].real=0
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
TypeError: object has read-only attributes

>>> t[0]=1
>>> t[0]
(1+0j)
>>>

What's the trouble ?

Nils



From cjw at sympatico.ca  Fri Jul 25 14:15:39 2003
From: cjw at sympatico.ca (Colin J. Williams)
Date: Fri, 25 Jul 2003 14:15:39 -0400
Subject: [SciPy-user] TypeError: object has read-only attributes
In-Reply-To: <3F2114D2.25E9A838@mecha.uni-stuttgart.de>
References: <3F2114D2.25E9A838@mecha.uni-stuttgart.de>
Message-ID: <3F2173CB.6000504@sympatico.ca>

Nils Wagner wrote:

>Hi all,
>
>I would like to change an entry of a complex array.
>
>  
>
>>>>t
>>>>        
>>>>
>array([ 0.30993965+0.21102825j,  0.40232318+0.48098591j,
>             0.30927754+0.3310895j ,  0.36197345+0.36041015j])
>  
>
>>>>t[0]
>>>>        
>>>>
>(0.30993964566340926+0.21102825078044135j)
>  
>
>>>>t[0].real
>>>>        
>>>>
>0.30993964566340926
>  
>
>>>>t[0].real=0
>>>>        
>>>>
>Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>TypeError: object has read-only attributes
>
>  
>
>>>>t[0]=1
>>>>t[0]
>>>>        
>>>>
>(1+0j)
>  
>
>
>What's the trouble ?
>
>Nils
>
>_______________________________________________
>SciPy-user mailing list
>SciPy-user at scipy.net
>http://www.scipy.net/mailman/listinfo/scipy-user
>
>  
>
Nils,

You probably need something like:

a= t[0].imag
t[0]= complex(0, a)

Colin W.



From nwagner at mecha.uni-stuttgart.de  Mon Jul 28 06:27:07 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Mon, 28 Jul 2003 12:27:07 +0200
Subject: [SciPy-user] Use and abuse of floating point operations
Message-ID: <3F24FA7B.72ACE975@mecha.uni-stuttgart.de>

Hi all,

I would like to compare two different algorithms with respect 
to their performance. What is a suitable measure for that task 
and what is obsolete ?

Any suggestion ?


Nils



From nwagner at mecha.uni-stuttgart.de  Mon Jul 28 09:36:51 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Mon, 28 Jul 2003 15:36:51 +0200
Subject: [SciPy-user] Removing rows and columns of a matrix
Message-ID: <3F2526F3.70F9B095@mecha.uni-stuttgart.de>

Hi all,

 How can I delete a column/row from a matrix.

In Matlab:

>> a=rand(4,4)

a =

    0.9501    0.8913    0.8214    0.9218
    0.2311    0.7621    0.4447    0.7382
    0.6068    0.4565    0.6154    0.1763
    0.4860    0.0185    0.7919    0.4057

use

>> a(:,2)=[]

a =

    0.9501    0.8214    0.9218
    0.2311    0.4447    0.7382
    0.6068    0.6154    0.1763
    0.4860    0.7919    0.4057

>> a(2,:)=[]

a =

    0.9501    0.8214    0.9218
    0.6068    0.6154    0.1763
    0.4860    0.7919    0.4057

>> 

Is there something similar in scipy, numpy or numarray ?

Any suggestion ?

Nils



From nwagner at mecha.uni-stuttgart.de  Mon Jul 28 10:26:41 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Mon, 28 Jul 2003 16:26:41 +0200
Subject: [SciPy-user] Re: [Numpy-discussion] Removing rows and columns of a matrix
References: <3F2526F3.70F9B095@mecha.uni-stuttgart.de>
	<200307281609.18652.hinsen@cnrs-orleans.fr>
Message-ID: <3F2532A1.1DD9418E@mecha.uni-stuttgart.de>

Konrad Hinsen schrieb:
> 
> >  How can I delete a column/row from a matrix.
> 
> As an in-place operation, not at all. To get a copy of an array with some
> columns/rows removed, use Numeric.take.
> 
The in-place operation of matlab is a nice feature. Is it thinkable to
have this
in scipy or numarray at a later date ?

Nils

> Konrad.
> --
> -------------------------------------------------------------------------------
> Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
> Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
> Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
> 45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
> France                                   | Nederlands/Francais
> -------------------------------------------------------------------------------
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
> _______________________________________________
> Numpy-discussion mailing list
> Numpy-discussion at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion



From perry at stsci.edu  Mon Jul 28 10:34:16 2003
From: perry at stsci.edu (Perry Greenfield)
Date: Mon, 28 Jul 2003 10:34:16 -0400
Subject: [SciPy-user] RE: [Numpy-discussion] Removing rows and columns of a matrix
In-Reply-To: <3F2532A1.1DD9418E@mecha.uni-stuttgart.de>
Message-ID: <CEELJPECNGEGKFNDLHFFKEBLCAAA.perry@stsci.edu>

> 
> Konrad Hinsen schrieb:
> > 
> > >  How can I delete a column/row from a matrix.
> > 
> > As an in-place operation, not at all. To get a copy of an array 
> with some
> > columns/rows removed, use Numeric.take.
> > 
> The in-place operation of matlab is a nice feature. Is it thinkable to
> have this
> in scipy or numarray at a later date ?
> 
> Nils
> 
Speaking for numarray, no, not really. But I wonder what is
really done for matlab. Either they have a more complex representation
of arrays, or all they really are doing is making a new copy of
the array and giving you the impression it is being done in place.
After all you are changing the size and structure of the array.

Perry



From nwagner at mecha.uni-stuttgart.de  Mon Jul 28 11:19:30 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Mon, 28 Jul 2003 17:19:30 +0200
Subject: [SciPy-user] Re: [Numpy-discussion] Removing rows and columns of a matrix
References: <3F2526F3.70F9B095@mecha.uni-stuttgart.de>
	<200307281609.18652.hinsen@cnrs-orleans.fr>
	<3F2532A1.1DD9418E@mecha.uni-stuttgart.de>
	<200307281640.34643.hinsen@cnrs-orleans.fr>
Message-ID: <3F253F02.F953C6D6@mecha.uni-stuttgart.de>

Konrad Hinsen schrieb:
> 
> On Monday 28 July 2003 16:26, Nils Wagner wrote:
> > Konrad Hinsen schrieb:
> > > >  How can I delete a column/row from a matrix.
> > >
> > > As an in-place operation, not at all. To get a copy of an array with some
> > > columns/rows removed, use Numeric.take.
> >
> > The in-place operation of matlab is a nice feature. Is it thinkable to
> > have this
> > in scipy or numarray at a later date ?
> 
> I'd say that the obvious way to implement it is as
> 
>   del a[2:3,:]
> 
> That can certainly be done, but someone has to do it.
> 
> Personally, I am not convinced that it is very useful. The consequences of an
> in-place change can be disastrous when many references point to that array.
> But then, we have other in-place operations which sometimes are handy, so my
> usefulness estimation may be wrong.
> 
> Konrad.

In my opinion, this operation is quite useful. For example a finite
element model
where we have to impose several homogeneous boundary conditions. This
can be done 
by deleting columns and associated rows.

Nils

In any case I am interested in a reliable workaround for this feature.

A small example would be appreciated.
Thanks in advance.



> --
> -------------------------------------------------------------------------------
> Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
> Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
> Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
> 45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
> France                                   | Nederlands/Francais
> -------------------------------------------------------------------------------
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
> _______________________________________________
> Numpy-discussion mailing list
> Numpy-discussion at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/numpy-discussion



From nwagner at mecha.uni-stuttgart.de  Tue Jul 29 09:32:42 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Tue, 29 Jul 2003 15:32:42 +0200
Subject: [SciPy-user] xplt.hold
Message-ID: <3F267779.F560C85D@mecha.uni-stuttgart.de>

Hi all,

Is it possible to use

xplt.hold('on') for window(1)

and

xplot.hold('off') for window(2) ?

A small example would be appreciated.

Nils



From nwagner at mecha.uni-stuttgart.de  Tue Jul 29 10:21:45 2003
From: nwagner at mecha.uni-stuttgart.de (Nils Wagner)
Date: Tue, 29 Jul 2003 16:21:45 +0200
Subject: [SciPy-user] generalized eigenvalue problem with singular matrices a,b
Message-ID: <3F2682F9.ABF061DD@mecha.uni-stuttgart.de>

Hi all,

Attention should be paid to the output of linalg.eig when both matrices
are singular.
Please find attached a small example.

Any comment ?

Nils

from scipy import *
a = diag(arange(0,10))
b = identity(10)
b[0,0] = b[0,0]-1
#
# Uncomment
#w,vr = linalg.eig(a,b)
#print w
w = linalg.eigvals(a,b)
print w


Traceback (most recent call last):
  File "singular.py", line 7, in ?
    w,vr = linalg.eig(a,b)
  File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
line 108, in eig
    return _geneig(a1,b,left,right,overwrite_a,overwrite_b)
  File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
line 68, in _geneig
    vr = _make_complex_eigvecs(w, vr, t)
  File "/usr/local/lib/python2.1/site-packages/scipy/linalg/decomp.py",
line 29, in _make_complex_eigvecs
    vnew.real = scipy_base.take(vin,ind[::2],1)
ValueError: matrices are not aligned for copy



From perry at stsci.edu  Tue Jul 29 14:23:53 2003
From: perry at stsci.edu (Perry Greenfield)
Date: Tue, 29 Jul 2003 14:23:53 -0400
Subject: [SciPy-user] RE: [Numpy-discussion] Removing rows and columns of a matrix
Message-ID: <CEELJPECNGEGKFNDLHFFIECDCAAA.perry@stsci.edu>

Nils Wagner writes:
> 
> In any case I am interested in a reliable workaround for this feature.
> 
> A small example would be appreciated.
> Thanks in advance.
> 
Numarray (and Numeric to a certain extent) currently is
centered around what rows or columns you want rather than
those you don't. Writing a reasonably efficient function
to do this in a more convenient way is not hard. Here is
an example for numarray (not tested, nor does it have
any error checking to ensure the input array has sufficient
dimensions or that the index is within the array bounds):

def remove(arr, index, dim=0):
    """Remove subarray at index and dimension specified"""
    # make selected dimension the first one
    swparr = swapaxes(arr, 0, dim)
    indices = range(swparr.shape[0])
    del indices[index]
    newarray = swparr[indices]
    # reorder axes as they originally appeared.
    return swapaxes(newarray, 0, dim)	

Then you can say

x = remove(x, 5)

to remove the 6th row or

x = remove(x, 4, dim=1)

to remove the 5th column.
(depending on what you call rows or columns; in the examples
I'm taking an image-oriented view rather than a matrix-oriented
view)

Perry



From wagner.nils at vdi.de  Tue Jul 29 15:03:16 2003
From: wagner.nils at vdi.de (Nils Wagner)
Date: Tue, 29 Jul 2003 21:03:16 +0200
Subject: [SciPy-user] RE: [Numpy-discussion] Removing rows and columns of
	a matrix
In-Reply-To: <CEELJPECNGEGKFNDLHFFIECDCAAA.perry@stsci.edu>
Message-ID: <20030729203315.C44B63EB0C@www.scipy.com>

-------------------  
Nils Wagner writes:  
>   
> In any case I am interested in a reliable  
workaround for this feature.  
>   
> A small example would be appreciated.  
> Thanks in advance.  
>   
Numarray (and Numeric to a certain extent) currently  
is  
centered around what rows or columns you want rather  
than  
those you don't. Writing a reasonably efficient  
function  
to do this in a more convenient way is not hard. Here  
is  
an example for numarray (not tested, nor does it have  
any error checking to ensure the input array has  
sufficient  
dimensions or that the index is within the array  
bounds):  
  
def remove(arr, index, dim=0):  
    """Remove subarray at index and dimension  
specified"""  
    # make selected dimension the first one  
    swparr = swapaxes(arr, 0, dim)  
    indices = range(swparr.shape[0])  
    del indices[index]  
    newarray = swparr[indices]  
    # reorder axes as they originally appeared.  
    return swapaxes(newarray, 0, dim)	  
  
Then you can say  
  
x = remove(x, 5)  
  
to remove the 6th row or  
  
x = remove(x, 4, dim=1)  
  
to remove the 5th column.  
(depending on what you call rows or columns; in the  
examples  
I'm taking an image-oriented view rather than a  
matrix-oriented  
view)  
  
Perry  
  
  
Perry, 
 
Thank you for your reply. Unfortunately, I am not 
familiar with numarray. 
 
This is the output of my test program. 
 
from scipy import * 
from RandomArray import * 
from numarray import * 
 
def remove(arr, index, dim=0): 
    """Remove subarray at index and dimension specified""" 
    # make selected dimension the first one 
    swparr = swapaxes(arr, 0, dim) 
    indices = range(swparr.shape[0]) 
    del indices[index] 
    newarray = swparr[indices] 
    # reorder axes as they originally appeared. 
    return swapaxes(newarray, 0, dim) 
 
#Then you can say 
 
a = rand(5,5) 
print a 
a = remove(a, 2) 
print a 
 
#to remove the 3th row or 
#to remove the 3th column 
 
a = remove(a, 2, dim=1) 
print a 
 
[[ 0.87329948  0.81829292  0.72929943  0.13012239  0.49291104] 
 [ 0.58665377  0.78030288  0.85906255  0.11409029  0.77719343] 
 [ 0.01325159  0.03389675  0.25417367  0.51117259  0.61979091] 
 [ 0.32406124  0.24500449  0.06147733  0.04323368  0.64497042] 
 [ 0.10133368  0.25028452  0.33645368  0.34395722  0.34052679]] 
Traceback (most recent call last): 
  File "nils.py", line 19, in ? 
    a = remove(a, 2) 
  File "nils.py", line 8, in remove 
    swparr = swapaxes(arr, 0, dim) 
  File "/usr/lib/python2.2/site-packages/numarray/generic.py", line 
855, in swapaxes 
    v = _nc.inputarray(array).view() 
  File "/usr/lib/python2.2/site-packages/numarray/numarraycore.py", 
line 310, in inputarray 
    return array(seq, type=type, typecode=typecode, copy=0) 
  File "/usr/lib/python2.2/site-packages/numarray/numarraycore.py", 
line 303, in array 
    raise ValueError("Unknown input type") 
ValueError: Unknown input type 
 
Any idea ? 
 
Nils 
 
 
_______________________________________________  
SciPy-user mailing list  
SciPy-user at scipy.net  
http://www.scipy.net/mailman/listinfo/scipy-user  
  



From wagner.nils at vdi.de  Tue Jul 29 15:03:16 2003
From: wagner.nils at vdi.de (Nils Wagner)
Date: Tue, 29 Jul 2003 21:03:16 +0200
Subject: [SciPy-user] RE: [Numpy-discussion] Removing rows and columns of
	a matrix
In-Reply-To: <CEELJPECNGEGKFNDLHFFIECDCAAA.perry@stsci.edu>
Message-ID: <20030729203315.BA6743EB09@www.scipy.com>

-------------------  
Nils Wagner writes:  
>   
> In any case I am interested in a reliable  
workaround for this feature.  
>   
> A small example would be appreciated.  
> Thanks in advance.  
>   
Numarray (and Numeric to a certain extent) currently  
is  
centered around what rows or columns you want rather  
than  
those you don't. Writing a reasonably efficient  
function  
to do this in a more convenient way is not hard. Here  
is  
an example for numarray (not tested, nor does it have  
any error checking to ensure the input array has  
sufficient  
dimensions or that the index is within the array  
bounds):  
  
def remove(arr, index, dim=0):  
    """Remove subarray at index and dimension  
specified"""  
    # make selected dimension the first one  
    swparr = swapaxes(arr, 0, dim)  
    indices = range(swparr.shape[0])  
    del indices[index]  
    newarray = swparr[indices]  
    # reorder axes as they originally appeared.  
    return swapaxes(newarray, 0, dim)	  
  
Then you can say  
  
x = remove(x, 5)  
  
to remove the 6th row or  
  
x = remove(x, 4, dim=1)  
  
to remove the 5th column.  
(depending on what you call rows or columns; in the  
examples  
I'm taking an image-oriented view rather than a  
matrix-oriented  
view)  
  
Perry  
  
  
Perry, 
 
Thank you for your reply. Unfortunately, I am not 
familiar with numarray. 
 
This is the output of my test program. 
 
from scipy import * 
from RandomArray import * 
from numarray import * 
 
def remove(arr, index, dim=0): 
    """Remove subarray at index and dimension specified""" 
    # make selected dimension the first one 
    swparr = swapaxes(arr, 0, dim) 
    indices = range(swparr.shape[0]) 
    del indices[index] 
    newarray = swparr[indices] 
    # reorder axes as they originally appeared. 
    return swapaxes(newarray, 0, dim) 
 
#Then you can say 
 
a = rand(5,5) 
print a 
a = remove(a, 2) 
print a 
 
#to remove the 3th row or 
#to remove the 3th column 
 
a = remove(a, 2, dim=1) 
print a 
 
[[ 0.87329948  0.81829292  0.72929943  0.13012239  0.49291104] 
 [ 0.58665377  0.78030288  0.85906255  0.11409029  0.77719343] 
 [ 0.01325159  0.03389675  0.25417367  0.51117259  0.61979091] 
 [ 0.32406124  0.24500449  0.06147733  0.04323368  0.64497042] 
 [ 0.10133368  0.25028452  0.33645368  0.34395722  0.34052679]] 
Traceback (most recent call last): 
  File "nils.py", line 19, in ? 
    a = remove(a, 2) 
  File "nils.py", line 8, in remove 
    swparr = swapaxes(arr, 0, dim) 
  File "/usr/lib/python2.2/site-packages/numarray/generic.py", line 
855, in swapaxes 
    v = _nc.inputarray(array).view() 
  File "/usr/lib/python2.2/site-packages/numarray/numarraycore.py", 
line 310, in inputarray 
    return array(seq, type=type, typecode=typecode, copy=0) 
  File "/usr/lib/python2.2/site-packages/numarray/numarraycore.py", 
line 303, in array 
    raise ValueError("Unknown input type") 
ValueError: Unknown input type 
 
Any idea ? 
 
Nils 
 
 
_______________________________________________  
SciPy-user mailing list  
SciPy-user at scipy.net  
http://www.scipy.net/mailman/listinfo/scipy-user  
  



From perry at stsci.edu  Tue Jul 29 15:23:54 2003
From: perry at stsci.edu (Perry Greenfield)
Date: Tue, 29 Jul 2003 15:23:54 -0400
Subject: [SciPy-user] RE: [Numpy-discussion] Removing rows and columns of
	a matrix
In-Reply-To: <E19hZlL-0002jw-00@sc8-sf-list1.sourceforge.net>
Message-ID: <CEELJPECNGEGKFNDLHFFEECECAAA.perry@stsci.edu>

 
> from scipy import * 
> from RandomArray import * 
> from numarray import * 
>  
I believe the problem is in this part. You are getting some
functions (like rand) which return a numeric array which
some numarray functions don't recognize (we will be fixing
this soon, they should accept any Python sequence that fits
the basic requirements). For the moment you will need to 
generate a numarray array for that function to work. In 
the latest release you would do the imports as follows
(for version 0.6 and later)

from numarray.numeric import *
from numarray.random_array import *

a = random((5,5))

and so forth

Perry



From daishi at egcrc.net  Tue Jul 29 22:23:18 2003
From: daishi at egcrc.net (daishi at egcrc.net)
Date: Tue, 29 Jul 2003 19:23:18 -0700
Subject: [SciPy-user] gui_thread
Message-ID: <3F272C16.3040606@egcrc.net>

I'm having some problems following the tutorial found here:
	http://www.scipy.org/site_content/tutorials/plot_tutorial
In particular, when in the Python interpreter I do
	>>> import gui_thread
nothing seems to happen - I simply get an interpreter prompt.
I took a look at
	gui_thread/__init__.py,
and it appears that there are only import statements -
is there something that I'm missing?

I noticed that in a previous version of __init__.py there
was a call to main.start(), so I tried re-inserting that
into the file, but this simply hangs the interpreter.
(The interpreter must be killed from another terminal).

What is somewhat odd is that if I leave the code as is
(i.e., without the explicit call to main.start()), and do:
	>>> import gui_thread
	>>> gui_thread.main.start()
Things seem to work as advertised. I.e.,
	<Importing wxPython...  done.>
	>>> from scipy import plt
	>>> plt.plot(range(3))
	<scipy.plt.wxplt.plot_frame instance; proxy of C++ wxFrame instance at _8664858_wxFrame_p>
	>>>
shows an appropriate window.

Is there a reason why calling main.start() from the interpreter
behaves differently then when called from within the __init__.py?
(I realize the contexts are different, but having looked at what
main.start() does, it's not clear to me why that would matter).

On a separate note, trying to use Chaco results in the following:
 >>> from chaco import wxplt
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File "/usr/local/lib/python2.2/site-packages/chaco/wxplt.py", line 19, in ?
     from wxplot        import *
   File "/usr/local/lib/python2.2/site-packages/chaco/wxplot.py", line 17, in ?
     from wxplot_window import PlotWindow, PlotTraitSheet
   File "/usr/local/lib/python2.2/site-packages/chaco/wxplot_window.py", line 25, in ?
     from wxplot_trait_sheet import TraitPanel, TraitSheet, trait_sheet_handler
   File "/usr/local/lib/python2.2/site-packages/chaco/wxplot_trait_sheet.py", line 18, in ?
     from traits.wxtrait_sheet import *
   File "/usr/local/lib/python2.2/site-packages/traits/__init__.py", line 20, in ?
     from traits          import HasTraits, HasDynamicTraits, Trait, Disallow, \
   File "/usr/local/lib/python2.2/site-packages/traits/traits.py", line 100, in ?
     from trait_delegates import TraitDelegate
   File "/usr/local/lib/python2.2/site-packages/traits/trait_delegates.py", line 38, in ?
     class TraitDelegate:
   File "/usr/local/lib/python2.2/site-packages/traits/trait_delegates.py", line 40, in TraitDelegate
     def __init__ ( self, delegate = None, mutate_or_prefix = False ):
NameError: name 'False' is not defined
 >>>

Does one need Python 2.3 to use Chaco? (I know that wxPython uses
'True' and 'False' without requiring 2.3 - I believe it's dynamically
bound when one does 'import wx'?)

Thanks in advance for any insight,
d



Some system info follows:
------
os.name='posix'
------
sys.platform='linux2'
------
sys.version:
2.2 (#1, Feb 26 2002, 15:49:15)
[GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-81)]
------
sys.prefix:
/usr/local
------
Found Numeric version '21.3' in /usr/local/lib/python2.2/site-packages/Numeric/Numeric.pyc
------
Found f2py2e version '2.35.229-1492' in /usr/local/lib/python2.2/site-packages/f2py2e/f2py2e.pyc
------
Found scipy_distutils version '0.2.0_alpha_3.288' in '/usr/local/lib/python2.2/site-packages/scipy_distutils/__init__.pyc'
Importing scipy_distutils.command.build_flib ... ok
------
atlas_info:
   FOUND:
     libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
     library_dirs = ['/usr/local/lib']

blas_info:
   FOUND:
     libraries = ['blas']
     library_dirs = ['/usr/lib']

blas_src_info:
   NOT AVAILABLE

dfftw_info:
   NOT AVAILABLE

dfftw_threads_info:
   NOT AVAILABLE

djbfft_info:
   NOT AVAILABLE

fftw_info:
   FOUND:
     libraries = ['rfftw', 'fftw']
     library_dirs = ['/usr/local/lib']
     define_macros = [('SCIPY_FFTW_H', None)]
     include_dirs = ['/usr/local/include']

fftw_threads_info:
   NOT AVAILABLE

lapack_info:
   FOUND:
     libraries = ['lapack']
     library_dirs = ['/usr/local/lib']

lapack_src_info:
   NOT AVAILABLE

sfftw_info:
   NOT AVAILABLE

sfftw_threads_info:
   NOT AVAILABLE

x11_info:
   FOUND:
     libraries = ['X11']
     library_dirs = ['/usr/X11R6/lib']
     include_dirs = ['/usr/X11R6/include']
------
Gnu
  version='0.5.26'
  F77='g77'
  F77FLAGS=' -Wall -fno-second-underscore  -fPIC '
  F77OPT=' -O3 -funroll-loops  -march=i686  -malign-double -fomit-frame-pointer '
  LIBS='-lg2c'



From pajer at iname.com  Tue Jul 29 23:53:27 2003
From: pajer at iname.com (Gary Pajer)
Date: Tue, 29 Jul 2003 23:53:27 -0400
Subject: [SciPy-user] more on gui_thread;  plus chaco.tkplt
References: <3F272C16.3040606@egcrc.net>
Message-ID: <004301c3564e$2445d520$c0135544@playroom>

daishi at egcrc.net  reported problems with gui_thread under linux.  I have
been having the same problem in XP.  The only way I can use chaco.wxplt is
to run it from PyCrust.

Also, I cannot run anything from chaco.tkplt at all.  The begining of the
error stream is reproduced below.  About twice this amount of additional
errors follows after.

I had been having other problems with my XP installation, so I thought that
something was screwed up in my system.  (supported by a lack of similar
reports here) .  I was about to reformat my hard drive when I decided to do
a completely fresh python installation on an NT machine that never had
python on it.  I get *exactly* the same results.

No difference between Numeric 22.0 and Numeric 23.0

Perhaps there's something I should have installed ?????  I'm perplexed that
I've seen no mention of these problems, yet I have it on two different
machines with two different OSs.

off topic, but maybe related:  I frequently get a windows error concerning
an unreadable memory location when I close a Tkinter app.  Idle and Idlefork
always give this error when closing.  On both XP and NT.

I'm happy to provide whatever info you want ... just tell me what you need.
I have posted this problem on the chaco list but I've gotten no responses.

Any takers?
Gary

>>> from chaco import tkplt
>>> tkplt.plot((1,2,3))
Traceback (most recent call last):
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_window.py", line 227, in
_min_size
    dx, dy = canvas._min_size()
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_canvas.py", line 619, in
_min_size
    title_info = self._title_info()
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_canvas.py", line 596, in
_title_info
    return TitleInfo( self._titles )
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_info.py", line 67, in
__init__
    self.add_titles( titles )
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_info.py", line 76, in
add_titles
    self.min_size( title_item )
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_info.py", line 94, in
min_size
    dx, dy = title._min_size()
  File "C:\PYTHON22\Lib\site-packages\chaco\plot_frame.py", line 515, in
_min_size
    ( min_dx,  min_dy,
  File "C:\PYTHON22\Lib\site-packages\kiva\basecore2d.py", line 1266, in
get_full_text_extent
    return self.device_get_full_text_extent(textstring)
  File "C:\PYTHON22\Lib\site-packages\kiva\basecore2d.py", line 1274, in
device_get_full_text_extent
    ft_engine.select_font( f.name, f.size, f.style, f.encoding )   ###
TEMPORARY ###
AttributeError: Font instance has no attribute 'name'



From msajec at tqs.com  Wed Jul 30 15:09:25 2003
From: msajec at tqs.com (Sajec, Mike TQO)
Date: Wed, 30 Jul 2003 12:09:25 -0700
Subject: [SciPy-user] Please help : wxplt line-plot to box-plot?
Message-ID: <2E5FEA6E71B22B46BBD13D126F719209026C27FD@STARBURST.tqs.com>

Hello,

Can anyone give an example (or fill in below) how to change a value's
plot-type from line to bar without manually editing through chaco?

I'd like to create a histogram generating function based on wxplt.plot .  

Thanks in advance,
Mike

###################################
from scipy import *
from chaco import wxplt as plt
import RandomArray as ra

#data for testing...
data = ra.normal(0,3,100)

mu = mean(data)
sigma = std(data)

mhist = stats.histogram(data)
xhist = mhist[1]
yhist = mhist[0]

fig1 = plt.plot(xhist,yhist)

## CHANGE FROM LINE PLOT TO BAR PLOT????? ##
# fig1.canvas.???



From falted at openlc.org  Thu Jul 31 18:54:21 2003
From: falted at openlc.org (Francesc Alted)
Date: Fri, 1 Aug 2003 00:54:21 +0200
Subject: [SciPy-user] ANN: PyTables 0.7
Message-ID: <200308010054.21757.falted@openlc.org>

Announcing PyTables 0.7
-----------------------

PyTables is a hierarchical database package designed to efficently
manage very large amounts of data. PyTables is built on top of the
HDF5 library and the numarray package and features an object-oriented
interface that, combined with C-code generated from Pyrex sources,
makes it a fast, yet extremely easy to use tool for interactively save
and retrieve large amounts of data.
 
Release 0.7 is the third public beta release. The version 0.6 was
internal and will never be released.

On this release you will find:
       - new AttributeSet class 
       - 25% I/O speed improvement 
       - fully multidimensional table cells support
       - new column descriptors
       - row deletion in tables is finally here
       - much more!

More in detail:

What's new
-----------

- A new AttributeSet class has been added. This will allow the
  addition and deletion of generic attributes (any scalar type plus
  any Python object supported by Pickle) as easy as this:

  table.attrs.date = "2003/07/28 10:32"     # Attach a string to table
  group._v_attrs.tempShift = 1.2            # Attach a float to group
  array.attrs.detectorList = [1,2,3,4]      # Attach a list to array
  del array.attrs.detectorList        # Detach detectorList attr from array

- PyTables now has support for fully multidimensional table cells. This
  has been made possible in part by implementation of multidimensional
  cells in numarray.records.RecArray object. Thanks to numarray crew,
  and especially to Jin-chung Hsu, for willingly accepting to do
  that, and also for including some cache improvements in RecArray.

- New column descriptors added: IntCol, Int8Col, UInt8Col, Int16Col,
  UInt16Col, Int32Col, UInt32Col, Int64Col, UInt64Col, FloatCol,
  Float32Col, Float64Col and StringCol. I think they are more explicit
  and easy-to-use than the now deprecated (but still supported)
  Col() descriptor. All the examples and user's manual has been
  accordingly updated.

- The new Table.removeRows(start, stop) function allows you to remove 
  rows from tables. This feature was requested a long time ago. There 
  are still limitations, however: you cannot delete rows in extremely 
  large Tables (as the remaining rows after the stop parameter 
  are stored in memory). Nor is the performance optimized.  These issues 
  will hopefully be addressed in future releases.

- Added iterators to File, Group and Table (they now support the special
  __iter__() method). They make the object much more user-friendly,
  especially in interactive mode. See documentation for usage examples.

- Added a __getitem__() method to Table that works more or less like
  read(), but with extended slices support.

- As a consequence of rewriting table iterators in C (with the help of
  Pyrex, of course) the table read performance has been improved
  between 20% and 30%. Data selections in PyTables are now starting to
  beat powerful relational databases like SQLite, even compared to
  in-core selects (!). I think there is still room for another 20% or
  30% speed improvement, so stay tuned.

- A checksum is now added automatically when using LZO (not with UCL
  where I'm having some difficulties implementing that
  capability). The Adler32 algorithm has been chosen because of its
  speed. With that, the compressing/decompressing speed has dropped 1%
  or 2%, which is hardly noticeable. I think this addition will allow
  the cautious user to be a bit more confident about this excellent
  compressor. Code has been added to be able to read files created
  without this checksum (so you can be confident that you will be able
  to read your existing files compressed with LZO and UCL).

- Recursion has been removed from PyTables. Before, this made the
  maximum depth tree to be less than the Python recursion limit (which
  depends on implementation, but is around 900, at least in
  Linux). Now, the limit has been set (somewhat arbitrarily) at
  2048. Thanks to John Nielsen for implementing the new iterative
  method!.

- A new rootUEP parameter to openFile() has been added. You can now 
  define the root from which you want to start to build the object tree. 
  Thanks to John Nielsen for the suggestion and a first implementation.

- A small bug fixed when dealing with non-native PyTables files that
  prevented the use of the "classname" filter during a listNodes()
  call. Thanks to Jeff Robbins for reporting that.

- Some (non-serious) bugs were discovered and fixed.

- Updated documentation to explain all these new bells and whistles. It 
  is also available on the web:
  http://pytables.sourceforge.net/html-doc/usersguide-html.html

- Added more unit tests (more than 350 now!)

- PyTables 0.7 *needs* numarray 0.6 or higher and HDF-1.6.0 or higher
  to compile and work. It has been tested with Python 2.2 and 2.3 and
  should work fine on both versions.

What is a table?
----------------

A table is defined as a collection of records whose values are stored
in fixed-length fields. All records have the same structure and all
values in each field have the same data type.  The terms
"fixed-length" and "strict data types" seems to be quite a strange
requirement for an language like Python, that supports dynamic data
types, but they serve a useful function if the goal is to save very
large quantities of data (such as is generated by many scientific
applications, for example) in an efficient manner that reduces demand
on CPU time and I/O resources.

What is HDF5?
-------------

For those people who know nothing about HDF5, it is is a general
purpose library and file format for storing scientific data made at
NCSA. HDF5 can store two primary objects: datasets and groups. A
dataset is essentially a multidimensional array of data elements, and
a group is a structure for organizing objects in an HDF5 file. Using
these two basic constructs, one can create and store almost any kind of
scientific data structure, such as images, arrays of vectors, and
structured and unstructured grids. You can also mix and match them in
HDF5 files according to your needs.

Platforms
---------

I'm using Linux as the main development platform, but PyTables should
be easy to compile/install on other UNIX machines. This package has
also passed all the tests on a UltraSparc platform with Solaris 7 and
Solaris 8. It also compiles and passes all the tests on a SGI
Origin2000 with MIPS R12000 processors and running IRIX 6.5.

Regarding Windows platforms, PyTables has been tested with Windows
2000 and Windows XP, but it should also work with other flavors.

An example?
-----------

For online code examples, have a look at

http://pytables.sourceforge.net/tut/tutorial1-1.html

and 

http://pytables.sourceforge.net/tut/tutorial1-2.html

Web site
--------

Go to the PyTables web site for more details:

http://pytables.sourceforge.net/

Share your experience
---------------------

Let me know of any bugs, suggestions, gripes, kudos, etc. you may
have.

Have fun!

-- Francesc Alted
falted at openlc.org