Pretty simple. I don't do any transformations. It is a euclidean distance
matrix between n vectors in my data space, so I use it for lookup of minima
and I recalculate portions of it during the processing of my algorithm.
It is the single largest limitation of my code, both in terms of
clustering yes, hierarchical no.
On Wed, Jun 11, 2008 at 4:55 PM, Charles R Harris [EMAIL PROTECTED]
wrote:
On Wed, Jun 11, 2008 at 9:33 AM, Simon Palmer [EMAIL PROTECTED]
wrote:
Pretty simple. I don't do any transformations. It is a euclidean
distance matrix between n vectors in my
You could do something like this, where MyDIstanceFunc is written with weave
and some intelligent caching. This only computes the upper diagonal
elements in a sparse matrix:
self.NumDatapoints = len(self.DataPoints)
self.Distances = sparse.lil_matrix((self.NumDatapoints,self.NumDatapoints))
for
Charles R Harris wrote:
On Wed, Jun 11, 2008 at 9:33 AM, Simon Palmer [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED] wrote:
Pretty simple. I don't do any transformations. It is a euclidean
distance matrix between n vectors in my data space, so I use it
for lookup of minima and I
On Wed, Jun 11, 2008 at 9:47 AM, Simon Palmer [EMAIL PROTECTED] wrote:
clustering yes, hierarchical no.
I think scipy-cluster [1] only stores the upper triangle of the
distance matrix.
[1] http://code.google.com/p/scipy-cluster/
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2008/6/10 Simon Palmer [EMAIL PROTECTED]:
Hi I have a problem which involves the creation of a large square matrix
which is zero across its diagonal and symmetrical about the diagonal i.e.
m[i,j] = m[j,i] and m[i,i] = 0. So, in fact, it is a large triangular
matrix. I was wondering whether
Actually that is very close to what I currently do, which is why I want to
throw it away.
The factor of two memory hit is not really the problem, it is the scaling
O(N^2) which is the limitation
I suspect I may end up using the 1-d array plus arithmetic as it is at least
efficient for retrieval.
The factor of two memory hit is not really the problem, it is the scaling
O(N^2) which is the limitation
Have you thought about using kd-trees or similar structures? If you
are only concerned about the minimum distances between two points,
that is the ideal data structure. It would reduce
On Wed, Jun 11, 2008 at 15:14, Simon Palmer [EMAIL PROTECTED] wrote:
Actually that is very close to what I currently do, which is why I want to
throw it away.
The factor of two memory hit is not really the problem, it is the scaling
O(N^2) which is the limitation
I suspect I may end up
Could this also be added as a comment in the module docstring for
test modules? It seems that anyone hacking on test code would be most
likely to see it there...?
Barry
On Tue, Jun 10, 2008 at 2:57 AM, Stéfan van der Walt [EMAIL PROTECTED] wrote:
2008/6/10 Alan McIntyre [EMAIL PROTECTED]:
Is
On Tue, Jun 10, 2008 at 04:57, Stéfan van der Walt [EMAIL PROTECTED] wrote:
2008/6/10 Alan McIntyre [EMAIL PROTECTED]:
Is the stuff Robert pointed out on a wiki page somewhere? It would be
nice to have a Welcome noob NumPy developer, here's how to do
NumPy-specific development things, page.
On Sun, Jun 8, 2008 at 3:54 AM, Anne Archibald
[EMAIL PROTECTED] wrote:
2008/6/7 Robert Kern [EMAIL PROTECTED]:
On Sat, Jun 7, 2008 at 14:37, Ondrej Certik [EMAIL PROTECTED] wrote:
Hi,
what is the current plan with array and matrix with regard of calculating
sin(A)
? I.e. elementwise vs
On Wed, Jun 11, 2008 at 6:09 PM, Robert Kern [EMAIL PROTECTED] wrote:
On Tue, Jun 10, 2008 at 04:57, Stéfan van der Walt [EMAIL PROTECTED] wrote:
2008/6/10 Alan McIntyre [EMAIL PROTECTED]:
Is the stuff Robert pointed out on a wiki page somewhere? It would be
nice to have a Welcome noob NumPy
2008/6/12 Robert Kern [EMAIL PROTECTED]:
On Tue, Jun 10, 2008 at 04:57, Stéfan van der Walt [EMAIL PROTECTED] wrote:
2008/6/10 Alan McIntyre [EMAIL PROTECTED]:
Is the stuff Robert pointed out on a wiki page somewhere? It would be
nice to have a Welcome noob NumPy developer, here's how to do
On Wed, Jun 11, 2008 at 19:51, Stéfan van der Walt [EMAIL PROTECTED] wrote:
2008/6/12 Robert Kern [EMAIL PROTECTED]:
On Tue, Jun 10, 2008 at 04:57, Stéfan van der Walt [EMAIL PROTECTED] wrote:
2008/6/10 Alan McIntyre [EMAIL PROTECTED]:
Is the stuff Robert pointed out on a wiki page somewhere?
Hi,
Short story: it would make my life simpler to have two mandatory
scons scripts per package instead of only one. Long story: for some
reasons linked to scons' notion of build directory, having two scons
scripts files per package (instead of one) would simplify quite a bit
some parts of
On Wed, Jun 11, 2008 at 23:35, David Cournapeau
[EMAIL PROTECTED] wrote:
Hi,
Short story: it would make my life simpler to have two mandatory
scons scripts per package instead of only one. Long story: for some
reasons linked to scons' notion of build directory, having two scons
scripts
Robert Kern wrote:
Can you give me a longer story? What are the three lines? Why are they
necessary in a separate, boilerplate file?
Sure: scons builds everything from the sources in the source directory,
and build everything in the build directory. By default, both
directories are the same
On Thu, Jun 12, 2008 at 00:08, David Cournapeau
[EMAIL PROTECTED] wrote:
Robert Kern wrote:
Can you give me a longer story? What are the three lines? Why are they
necessary in a separate, boilerplate file?
Sure: scons builds everything from the sources in the source directory,
and build
Robert Kern wrote:
Works for me.
Do you mean having two files/packages is ok ?
cheers,
David
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On Thu, Jun 12, 2008 at 00:28, David Cournapeau
[EMAIL PROTECTED] wrote:
Robert Kern wrote:
Works for me.
Do you mean having two files/packages is ok ?
Yes. You had me at The recommended way to do it in scons
--
Robert Kern
I have come to believe that the whole world is an enigma, a
Hi,
Just to mention that building numpy and scipy with numscons will be
broken for a few hours, the time to change some organizations.
Sorry for the trouble,
David
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