[SciPy-User] inverting pdist.

Éric Depagne edepagne@aip...
Thu Apr 19 02:07:38 CDT 2012


Le jeudi 19 avril 2012 06:52:49, srean a écrit :
Hi.

Sorry for my unclear explanation. My choice of wording for the subject of my 
email was very poor, sorry for that.

I have the coordinates of a,b,c and d from the start.

What I needed (see the end of my message) was a way to find what are the two 
points for which their distance (given by pdist) is the largest.
So in my cases, I have a, b, c and d, their coordinates, and pdist gives me 
the values ab, ac,ad bc, bd and cd. I can then extract the largest value (thus 
the longest distance). Then I want to find to which pair it corresponds.

> I lost you on your description about the index of the largest
> distance. If what you are looking for is that given all pairwise
> distance ab, ac, ad, bc, bd, cd to find the coordinates of a,b,c and
> d, then the problem you are looking for is multidimensional scaling
> (MDS). You will get lots of hits if you search for it. In general it
> does not have a unique solution. On the other hand if you had all
> pairs of dot products (or similarities) you can obtain the coordinates
> by an eigen decomposition of the pairwise dot product matrix.
I've kept googling since, and I've found that Ben Root did exactly what I need 
here:

http://old.nabble.com/unravel_index-for-pdist--p32151477.html

Cheers, 
Éric.
> 
> On Mon, Apr 16, 2012 at 9:55 AM, Éric Depagne <eric@depagne.org> wrote:
> > Hi.
> > 
> > I'm using scipy.spatial.distance.pdist.
> > 
> > I was wondering if it was possible to invert the result to get the
> > elements of the input matrix that produced a given result.
> > Let me explain a little.
> > 
> > Say  we have a,b, c and d. The possible distances are ab, ac, ad,  bc, bd
> > and cd. pdist will give the values for those 6 distances. Say the
> > largest is at index 5. How can I get from the pdist result array that it
> > is the bd distance?
> > 
> > 
> > And if it is not, is there another way of doing so? My data are such that
> > I have close to 100k distances to compute.
> > 
> > Thanks.
> > Éric.
> > 
> > Un clavier azerty en vaut deux
> > ----------------------------------------------------------
> > Éric Depagne                            eric@depagne.org
> > _______________________________________________
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> 
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-- 
Un clavier azerty en vaut deux
----------------------------------------------------------
Éric Depagne                            edepagne@aip.de
Leibniz-Institut für Astrophysik Potsdam
An der Sternwarte 16
14482 Potsdam
Germany
----------------------------------------------------------


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