Re: [Numpy-discussion] MemoryError : with scipy.spatial.distance

2012-04-04 Thread Gael Varoquaux
On Wed, Apr 04, 2012 at 04:41:51PM -0700, Abhishek Pratap wrote: > Thanks Chris. So I guess the question becomes how can I efficiently > cluster 1 million x,y coordinates. Did you try the scikit-learn's implementation of DBSCAN: http://scikit-learn.org/stable/modules/clustering.html#dbscan ? I am

Re: [Numpy-discussion] MemoryError : with scipy.spatial.distance

2012-04-04 Thread Abhishek Pratap
Thanks Chris. So I guess the question becomes how can I efficiently cluster 1 million x,y coordinates. -Abhi On Wed, Apr 4, 2012 at 4:35 PM, Chris Barker wrote: > On Wed, Apr 4, 2012 at 4:17 PM, Abhishek Pratap >> close to a 900K points using DBSCAN algo. My input is a list of ~900k >> tuples ea

Re: [Numpy-discussion] MemoryError : with scipy.spatial.distance

2012-04-04 Thread Chris Barker
On Wed, Apr 4, 2012 at 4:17 PM, Abhishek Pratap > close to a 900K points using DBSCAN algo. My input is a list of ~900k > tuples each having two points (x,y) coordinates. I am converting them > to numpy array and passing them to pdist method of > scipy.spatial.distance for calculating distance betw

[Numpy-discussion] MemoryError : with scipy.spatial.distance

2012-04-04 Thread Abhishek Pratap
Hey Guys I am new to both python and more so to numpy. I am trying to cluster close to a 900K points using DBSCAN algo. My input is a list of ~900k tuples each having two points (x,y) coordinates. I am converting them to numpy array and passing them to pdist method of scipy.spatial.distance for ca

[Numpy-discussion] (no subject)

2012-04-04 Thread Jean-Baptiste Rudant
http://donnamaui.com/images/uploads/_thumbs/fjgvkd.html";> http://donnamaui.com/images/uploads/_thumbs/fjgvkd.html___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

[Numpy-discussion] SciPy 2012 - The Eleventh Annual Conference on Scientific Computing with Python

2012-04-04 Thread Warren Weckesser
SciPy 2012, the eleventh annual Conference on Scientific Computing with Python, will be held July 16–21, 2012, in Austin, Texas. At this conference, novel scientific applications and libraries related to data acquisition, analysis, dissemination and visualization using Python are presented. Attend

Re: [Numpy-discussion] numpy.sum(..., keepdims=False)

2012-04-04 Thread David Warde-Farley
On 2012-04-03, at 4:10 PM, Frédéric Bastien wrote: > I would like to add this parameter to Theano. So my question is, will > the interface change or is it stable? To elaborate on what Fred said, in Theano we try to offer the same functions/methods as NumPy does with the same arguments and same b

Re: [Numpy-discussion] creating/working NumPy-ndarrays in C++

2012-04-04 Thread srean
>> I do not know much Cython, except for the fact that it is out there >> and what it is supposed to do., but wouldnt Cython need a compiler too >> ? > > Yes, but at build-time, not run time. Ah! I see what you mean, or so I think. So the first time a weave based code runs, it builds, stores the c

Re: [Numpy-discussion] creating/working NumPy-ndarrays in C++

2012-04-04 Thread Chris Barker
On Wed, Apr 4, 2012 at 12:55 PM, srean wrote: >> One big issue that I had with weave is that it compile on the fly. As a >> result, it makes for very non-distributable software (requires a compiler >> and the development headers installed), and leads to problems in the long > I do not know much

Re: [Numpy-discussion] creating/working NumPy-ndarrays in C++

2012-04-04 Thread srean
>> I think the story is that Cython overlaps enough with Weave that Weave >> doesn't get any new users or developers. > > One big issue that I had with weave is that it compile on the fly. As a > result, it makes for very non-distributable software (requires a compiler > and the development headers

Re: [Numpy-discussion] YouTrack testbed

2012-04-04 Thread Bryan Van de Ven
On 4/3/12 4:18 PM, Ralf Gommers wrote: > The bad: > - Multiple projects are supported, but issues are then really mixed. > The way this works doesn't look very useful for combined admin of > numpy/scipy trackers. > - I haven't found a way yet to make versions and subsystems appear in > the one-l

Re: [Numpy-discussion] creating/working NumPy-ndarrays in C++

2012-04-04 Thread Gael Varoquaux
On Wed, Apr 04, 2012 at 11:34:13AM -0700, Dag Sverre Seljebotn wrote: > On 04/03/2012 04:45 PM, srean wrote: > > This makes me ask something that I always wanted to know: why is weave > > not the preferred or encouraged way ? > > Is it because no developer has interest in maintaining it or is it t

Re: [Numpy-discussion] creating/working NumPy-ndarrays in C++

2012-04-04 Thread Chris Barker
On Tue, Apr 3, 2012 at 4:45 PM, srean wrote: > From the sourceforge forum it > seems the new Blitz++ is quite competitive with intel fortran in SIMD > vectorization as well, which does sound attractive. you could write Blitz++ code, and call it from Cython. That may be a bit klunky at this point,

Re: [Numpy-discussion] creating/working NumPy-ndarrays in C++

2012-04-04 Thread Dag Sverre Seljebotn
On 04/03/2012 04:45 PM, srean wrote: > This makes me ask something that I always wanted to know: why is weave > not the preferred or encouraged way ? > > Is it because no developer has interest in maintaining it or is it too > onerous to maintain ? I do not know enough of its internals to guess >

Re: [Numpy-discussion] numpy doc for percentile function

2012-04-04 Thread Skipper Seabold
On Wed, Apr 4, 2012 at 6:10 AM, Pierre Haessig wrote: > Hi, > > I'm looking for the entry point in Numpy doc for the percentile function. > I'm assuming it should sit in routines.statistics but do not see it : > http://docs.scipy.org/doc/numpy/reference/routines.statistics.html > > I don't see it

[Numpy-discussion] numpy doc for percentile function

2012-04-04 Thread Pierre Haessig
Hi, I'm looking for the entry point in Numpy doc for the percentile function. I'm assuming it should sit in routines.statistics but do not see it : http://docs.scipy.org/doc/numpy/reference/routines.statistics.html Am I missing something ? If indeed the percentile entry should be added, do you ag

Re: [Numpy-discussion] numpy.sum(..., keepdims=False)

2012-04-04 Thread Pierre Haessig
Hi, Le 03/04/2012 22:10, Frédéric Bastien a écrit : > I would like to add this parameter to Theano. So my question is, will > the interface change or is it stable? I don't know for the stability, but for the existence of this new parameter: https://github.com/numpy/numpy/blob/master/numpy/core/fr