Re: [Numpy-discussion] searchsorted() and memory cache

On Thu, May 8, 2008 at 11:06 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > > On Thu, May 8, 2008 at 10:30 PM, Charles R Harris < > [EMAIL PROTECTED]> wrote: > >> >> >> On Thu, May 8, 2008 at 9:55 PM, Robert Kern <[EMAIL PROTECTED]> >> wrote: >> >>> On Thu, May 8, 2008 at 10:51 PM, Andrew Str

Re: [Numpy-discussion] searchsorted() and memory cache

On Thu, May 8, 2008 at 10:30 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > > On Thu, May 8, 2008 at 9:55 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > >> On Thu, May 8, 2008 at 10:51 PM, Andrew Straw <[EMAIL PROTECTED]> >> wrote: >> > I've got a big element array (25 million int64s) that sear

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 11:31 PM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/5/8 Robert Kern <[EMAIL PROTECTED]>: >> On Thu, May 8, 2008 at 10:39 PM, Anne Archibald >> <[EMAIL PROTECTED]> wrote: >>> 2008/5/8 Robert Kern <[EMAIL PROTECTED]>: If anyone knows enough to explicitly reques

Re: [Numpy-discussion] Why are ufunc docstrings useless?

2008/5/8 Robert Kern <[EMAIL PROTECTED]>: > On Thu, May 8, 2008 at 10:39 PM, Anne Archibald > <[EMAIL PROTECTED]> wrote: >> 2008/5/8 Robert Kern <[EMAIL PROTECTED]>: >>> >>> If anyone knows enough to explicitly request a docstring from >>> __call__, they already know what it does. >> >> How exactly

Re: [Numpy-discussion] searchsorted() and memory cache

On Thu, May 8, 2008 at 9:55 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Thu, May 8, 2008 at 10:51 PM, Andrew Straw <[EMAIL PROTECTED]> wrote: > > I've got a big element array (25 million int64s) that searchsorted() > > takes a long time to grind through. After a bit of digging in the > > liter

Re: [Numpy-discussion] searchsorted() and memory cache

On Thu, May 8, 2008 at 10:51 PM, Andrew Straw <[EMAIL PROTECTED]> wrote: > I've got a big element array (25 million int64s) that searchsorted() > takes a long time to grind through. After a bit of digging in the > literature and the numpy source code, I believe that searchsorted() is > implementing

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 10:39 PM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/5/8 Robert Kern <[EMAIL PROTECTED]>: >> On Thu, May 8, 2008 at 9:52 PM, Anne Archibald >> <[EMAIL PROTECTED]> wrote: >> >>> Thanks! Done add, reduce, outer, and reduceat. What about __call__? >> >> If anyone knows eno

[Numpy-discussion] searchsorted() and memory cache

I've got a big element array (25 million int64s) that searchsorted() takes a long time to grind through. After a bit of digging in the literature and the numpy source code, I believe that searchsorted() is implementing a classic binary search, which is pretty bad in terms of cache misses. There are

Re: [Numpy-discussion] Why are ufunc docstrings useless?

2008/5/8 Robert Kern <[EMAIL PROTECTED]>: > On Thu, May 8, 2008 at 9:52 PM, Anne Archibald > <[EMAIL PROTECTED]> wrote: > >> Thanks! Done add, reduce, outer, and reduceat. What about __call__? > > If anyone knows enough to explicitly request a docstring from > __call__, they already know what it do

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 9:12 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > > On Thu, May 8, 2008 at 9:07 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > >> On Thu, May 8, 2008 at 9:52 PM, Anne Archibald >> <[EMAIL PROTECTED]> wrote: >> >> > Thanks! Done add, reduce, outer, and reduceat. What abo

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 10:12 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > It's easier/better to do this in numpy/add_newdocs.py. For example: > > In [14]: from numpy.lib import add_newdoc as add > > In [15]: add('numpy.core','ufunc',('reduce','hello world')) > > In [16]: ufunc.reduce.__doc__

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 9:07 PM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Thu, May 8, 2008 at 9:52 PM, Anne Archibald > <[EMAIL PROTECTED]> wrote: > > > Thanks! Done add, reduce, outer, and reduceat. What about __call__? > > If anyone knows enough to explicitly request a docstring from > __call_

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 9:52 PM, Anne Archibald <[EMAIL PROTECTED]> wrote: > Thanks! Done add, reduce, outer, and reduceat. What about __call__? If anyone knows enough to explicitly request a docstring from __call__, they already know what it does. -- Robert Kern "I have come to believe that th

Re: [Numpy-discussion] Why are ufunc docstrings useless?

2008/5/8 Robert Kern <[EMAIL PROTECTED]>: > On Thu, May 8, 2008 at 5:28 PM, Anne Archibald > <[EMAIL PROTECTED]> wrote: >> Hi, >> >> I frequently use functions like np.add.reduce and np.add.outer, but >> their docstrings are totally uninformative. Would it be possible to >> provide proper docstring

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 2:37 PM, Warren Focke <[EMAIL PROTECTED]> wrote: > > > On Thu, 8 May 2008, Charles R Harris wrote: > > > On Thu, May 8, 2008 at 11:46 AM, Anne Archibald < > [EMAIL PROTECTED]> > > wrote: > > > >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > >>> > >>> On Thu, May 8, 2008

Re: [Numpy-discussion] Status Report for NumPy 1.1.0

On Thu, May 8, 2008 at 6:38 PM, Charles Doutriaux <[EMAIL PROTECTED]> wrote: > I don't think it is reasonable to say the trunk is in good shape when > the power function does not work... > > Just my thoughts... > Is that ticket #301? What are you suggesting it do? Chuck _

Re: [Numpy-discussion] Status Report for NumPy 1.1.0

I don't think it is reasonable to say the trunk is in good shape when the power function does not work... Just my thoughts... C. Charles R Harris wrote: > Hi Jarrod, > > On Tue, May 6, 2008 at 2:40 AM, Jarrod Millman <[EMAIL PROTECTED] > > wrote: > > Hey, > >

Re: [Numpy-discussion] online (1-shot) calculation of variance (complex)

On Thu, May 8, 2008 at 6:05 PM, Neal Becker <[EMAIL PROTECTED]> wrote: > Robert Kern wrote: > >> On Thu, May 8, 2008 at 5:45 PM, Neal Becker <[EMAIL PROTECTED]> wrote: >>> I saw some links on 1-pass recursive calculation of mean/variance. When >>> I tried the algorithms, it did not seem to give co

Re: [Numpy-discussion] online (1-shot) calculation of variance (complex)

Robert Kern wrote: > On Thu, May 8, 2008 at 5:45 PM, Neal Becker <[EMAIL PROTECTED]> wrote: >> I saw some links on 1-pass recursive calculation of mean/variance. When >> I tried the algorithms, it did not seem to give correct results for >> complex >> values. Anyone know how to correctly impleme

Re: [Numpy-discussion] online (1-shot) calculation of variance (complex)

Robert Kern wrote: > On Thu, May 8, 2008 at 5:45 PM, Neal Becker <[EMAIL PROTECTED]> wrote: >> I saw some links on 1-pass recursive calculation of mean/variance. When >> I tried the algorithms, it did not seem to give correct results for >> complex >> values. Anyone know how to correctly impleme

Re: [Numpy-discussion] online (1-shot) calculation of variance (complex)

On Thu, May 8, 2008 at 5:45 PM, Neal Becker <[EMAIL PROTECTED]> wrote: > I saw some links on 1-pass recursive calculation of mean/variance. When I > tried the algorithms, it did not seem to give correct results for complex > values. Anyone know how to correctly implement this? Well, exactly what

[Numpy-discussion] online (1-shot) calculation of variance (complex)

I saw some links on 1-pass recursive calculation of mean/variance. When I tried the algorithms, it did not seem to give correct results for complex values. Anyone know how to correctly implement this? ___ Numpy-discussion mailing list Numpy-discussion@

Re: [Numpy-discussion] Why are ufunc docstrings useless?

On Thu, May 8, 2008 at 5:28 PM, Anne Archibald <[EMAIL PROTECTED]> wrote: > Hi, > > I frequently use functions like np.add.reduce and np.add.outer, but > their docstrings are totally uninformative. Would it be possible to > provide proper docstrings for these ufunc methods? They need not be > speci

[Numpy-discussion] Why are ufunc docstrings useless?

Hi, I frequently use functions like np.add.reduce and np.add.outer, but their docstrings are totally uninformative. Would it be possible to provide proper docstrings for these ufunc methods? They need not be specific to np.add; just an explanation of what arguments to give (for example) reduce() (

Re: [Numpy-discussion] Log Arrays

On Thu, 8 May 2008, Charles R Harris wrote: > On Thu, May 8, 2008 at 11:46 AM, Anne Archibald <[EMAIL PROTECTED]> > wrote: > >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: >>> >>> On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> >> wrote: When you're running an optim

Re: [Numpy-discussion] Log Arrays

2008/5/8 T J <[EMAIL PROTECTED]>: > On 5/8/08, Anne Archibald <[EMAIL PROTECTED]> wrote: > > Is "logarray" really the way to handle it, though? it seems like you > > could probably get away with providing a logsum ufunc that did the > > right thing. I mean, what operations does one want to do on

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 11:46 AM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > > > On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> > wrote: > > > > > > When you're running an optimizer over a PDF, you will be stuck in the > > > regi

Re: [Numpy-discussion] Log Arrays

On 5/8/08, Anne Archibald <[EMAIL PROTECTED]> wrote: > Is "logarray" really the way to handle it, though? it seems like you > could probably get away with providing a logsum ufunc that did the > right thing. I mean, what operations does one want to do on logarrays? > > add -> logsum > subtract -> ?

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 2:12 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > On Thu, May 8, 2008 at 11:46 AM, Anne Archibald <[EMAIL PROTECTED]> > wrote: >> >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: >> > >> > On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> >> > wrote: >>

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 11:46 AM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > > > On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> > wrote: > > > > > > When you're running an optimizer over a PDF, you will be stuck in the > > > regi

Re: [Numpy-discussion] Changes to matrix class broke scipy

On Thu, May 8, 2008 at 12:25 PM, Stéfan van der Walt <[EMAIL PROTECTED]> wrote: > Developers, take note: > > http://thread.gmane.org/gmane.comp.python.scientific.user/16297 > ___ > Yep, not unexpected. I suppose the real question is whether is should ha

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 12:39 PM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > > > David, what you are using is a log(log(x)) representation internally. > IEEE > > is *not* linear, it is logarithmic. > > As Robert Kern says, yes, this is exactly wha

Re: [Numpy-discussion] Log Arrays

2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > David, what you are using is a log(log(x)) representation internally. IEEE > is *not* linear, it is logarithmic. As Robert Kern says, yes, this is exactly what the OP and all the rest of us want. But it's a strange thing to say that IEEE is logar

[Numpy-discussion] Changes to matrix class broke scipy

Developers, take note: http://thread.gmane.org/gmane.comp.python.scientific.user/16297 ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 11:31 AM, Warren Focke <[EMAIL PROTECTED]> wrote: > > > On Thu, 8 May 2008, Charles R Harris wrote: > > > On Thu, May 8, 2008 at 10:11 AM, Anne Archibald < > [EMAIL PROTECTED]> > > wrote: > > > >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > >>> > >>> What realistic prob

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 12:53 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > On Thu, May 8, 2008 at 11:18 AM, David Cournapeau <[EMAIL PROTECTED]> > wrote: >> >> On Fri, May 9, 2008 at 2:06 AM, Nadav Horesh <[EMAIL PROTECTED]> >> wrote: >> > Is the 80 bits float (float96 on IA32, float128 on AM

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 11:18 AM, David Cournapeau <[EMAIL PROTECTED]> wrote: > On Fri, May 9, 2008 at 2:06 AM, Nadav Horesh <[EMAIL PROTECTED]> > wrote: > > Is the 80 bits float (float96 on IA32, float128 on AMD64) isn't enough? > It has a 64 bits mantissa and can represent numbers up to nearly 1E

Re: [Numpy-discussion] Log Arrays

2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> wrote: > > > > When you're running an optimizer over a PDF, you will be stuck in the > > region of exp(-1000) for a substantial amount of time before you get > > to the peak. If you d

Re: [Numpy-discussion] Log Arrays

On Thu, 8 May 2008, Charles R Harris wrote: > On Thu, May 8, 2008 at 10:11 AM, Anne Archibald <[EMAIL PROTECTED]> > wrote: > >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: >>> >>> What realistic probability is in the range exp(-1000) ? >> >> Well, I ran into it while doing a maximum-likelihoo

Re: [Numpy-discussion] Log Arrays

On Fri, May 9, 2008 at 2:06 AM, Nadav Horesh <[EMAIL PROTECTED]> wrote: > Is the 80 bits float (float96 on IA32, float128 on AMD64) isn't enough? It > has a 64 bits mantissa and can represent numbers up to nearly 1E(+-)5000. It only make the problem happen later, I think. If you have a GMM with m

Re: [Numpy-discussion] Log Arrays

On Fri, May 9, 2008 at 1:54 AM, Charles R Harris <[EMAIL PROTECTED]> wrote: > Yes, and Gaussians are a delusion beyond a few sigma. One of my pet peeves. > If you have more than 8 standard deviations, then something is fundamentally > wrong in the concept and formulation. If you have a mixture of

Re: [Numpy-discussion] Log Arrays

Is the 80 bits float (float96 on IA32, float128 on AMD64) isn't enough? It has a 64 bits mantissa and can represent numbers up to nearly 1E(+-)5000. Nadav. -הודעה מקורית- מאת: [EMAIL PROTECTED] בשם Charles R Harris נשלח: ה 08-מאי-08 19:25 אל: Discussion of Numerical Python נושא: Re: [

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 12:02 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> wrote: >> >> On Thu, May 8, 2008 at 11:25 AM, Charles R Harris >> <[EMAIL PROTECTED]> wrote: >> > >> > On Thu, May 8, 2008 at 10:11 AM, Anne Archibald >>

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 10:56 AM, Robert Kern <[EMAIL PROTECTED]> wrote: > On Thu, May 8, 2008 at 11:25 AM, Charles R Harris > <[EMAIL PROTECTED]> wrote: > > > > On Thu, May 8, 2008 at 10:11 AM, Anne Archibald < > [EMAIL PROTECTED]> > > wrote: > >> > >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 10:52 AM, David Cournapeau <[EMAIL PROTECTED]> wrote: > On Fri, May 9, 2008 at 1:25 AM, Charles R Harris > <[EMAIL PROTECTED]> wrote: > > > > > > > But to expand on David's computation... If the numbers are stored without > > using logs, i.e., as the exponentials, then the s

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 11:25 AM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > On Thu, May 8, 2008 at 10:11 AM, Anne Archibald <[EMAIL PROTECTED]> > wrote: >> >> 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: >> > >> > What realistic probability is in the range exp(-1000) ? >> >> Well, I ran into

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 10:42 AM, David Cournapeau <[EMAIL PROTECTED]> wrote: > On Fri, May 9, 2008 at 1:04 AM, Charles R Harris > <[EMAIL PROTECTED]> wrote: > > > < 1e-308 ? > > Yes, all the time. I mean, if it was not, why people would bother with > long double and co ? Why denormal would exist

Re: [Numpy-discussion] Log Arrays

On Fri, May 9, 2008 at 1:25 AM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > > But to expand on David's computation... If the numbers are stored without > using logs, i.e., as the exponentials, then the sum is of the form: > > x_1*2**y_1 + ... + x_i*2**y_i You missed the part on parametric mod

Re: [Numpy-discussion] Log Arrays

On Fri, May 9, 2008 at 1:04 AM, Charles R Harris <[EMAIL PROTECTED]> wrote: > < 1e-308 ? Yes, all the time. I mean, if it was not, why people would bother with long double and co ? Why denormal would exist ? I don't consider the comparison with the number of particules to be really relevant here

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 10:11 AM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > > > What realistic probability is in the range exp(-1000) ? > > Well, I ran into it while doing a maximum-likelihood fit - my early > guesses had exceedingly low probabil

Re: [Numpy-discussion] Log Arrays

2008/5/8 Charles R Harris <[EMAIL PROTECTED]>: > > What realistic probability is in the range exp(-1000) ? Well, I ran into it while doing a maximum-likelihood fit - my early guesses had exceedingly low probabilities, but I needed to know which way the probabilities were increasing. Anne

Re: [Numpy-discussion] Log Arrays

2008/5/8 David Cournapeau <[EMAIL PROTECTED]>: > On Thu, May 8, 2008 at 10:20 PM, Charles R Harris > <[EMAIL PROTECTED]> wrote: > > > > > > Floating point numbers are essentially logs to base 2, i.e., integer > > exponent and mantissa between 1 and 2. What does using the log buy you? > > Prec

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 9:20 AM, David Cournapeau <[EMAIL PROTECTED]> wrote: > On Thu, May 8, 2008 at 10:20 PM, Charles R Harris > <[EMAIL PROTECTED]> wrote: > > > > > > Floating point numbers are essentially logs to base 2, i.e., integer > > exponent and mantissa between 1 and 2. What does using t

[Numpy-discussion] Test

This is a test to see if the list is working for me. -teo ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 10:20 PM, Charles R Harris <[EMAIL PROTECTED]> wrote: > > > Floating point numbers are essentially logs to base 2, i.e., integer > exponent and mantissa between 1 and 2. What does using the log buy you? Precision, of course. I am not sure I understand the notation base = 2,

[Numpy-discussion] Problems with Trac

There seem to be several problems with the Trac system. 1) Submitting/modifying tickets yields 500 internal server error, even though the changes are made. This leads to duplicate tickets. 2) Mail isn't sent to the numpy-ticket mailing list. 3) It still always takes two tries to log in. Chu

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 1:26 AM, T J <[EMAIL PROTECTED]> wrote: > Hi, > > For precision reasons, I almost always need to work with arrays whose > elements are log values. My thought was that it would be really neat > to have a 'logarray' class implemented in C or as a subclass of the > standard ar

Re: [Numpy-discussion] First steps with f2py and first problems...

On Thu, May 8, 2008 2:06 pm, LB wrote: > Hi, > > I've tried to follow the example given at : > http://www.scipy.org/Cookbook/Theoretical_Ecology/Hastings_and_Powell > but I've got errors when compiling the fortran file : > > 12:53 loic:~ % f2py -c -m hastings hastings.f90 --fcompiler=gnu95 ...

[Numpy-discussion] First steps with f2py and first problems...

Hi, I've tried to follow the example given at : http://www.scipy.org/Cookbook/Theoretical_Ecology/Hastings_and_Powell but I've got errors when compiling the fortran file : -errors -- 12:53 loic:~ % f2py -c -m hast

Re: [Numpy-discussion] Log Arrays

On Thu, May 8, 2008 at 12:26 AM, T J <[EMAIL PROTECTED]> wrote: > > >>> x = array([-2,-2,-3], base=2) > >>> y = array([-1,-2,-inf], base=2) > >>> z = x + y > >>> z > array([-0.415037499279, -1.0, -3]) > >>> z = x * y > >>> z > array([-3, -4, -inf]) > >>> z[:2].sum() > -2.41503749928 > Wh

[Numpy-discussion] Log Arrays

Hi, For precision reasons, I almost always need to work with arrays whose elements are log values. My thought was that it would be really neat to have a 'logarray' class implemented in C or as a subclass of the standard array class. Here is a sample of how I'd like to work with these objects: >