#1 Topological output and minor changes

[ajaksu]

Hi Michel,

Pretty useful project you have here, I haven't read the
clustering algorithms yet but have used it (with
ecological similarity indexes among samples!).
Hierarchical clustering makes that a LOT more useful,
so thank you very much :)

This patch adds a topological output to
Cluster(.topology()) and a respective method to
BaseClusterMethod(.topo()). It also changes .data()
behavior to avoid the .data()[0] idiom.

Feeding the output of .topo() to
http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/139422
gives (e.g.):

9 -----+
|--+
8 -----+ |
|--
# --+ |
|--+ |
w --+ | |
|--+
e -----+

Regarding the .data() change:
* I think it'd be better to keep two different
datasets (.raw and .data?), because both states (flat
and clustered) are pretty different beasts.
* Perhaps having .data() "contents" stored as
.data would make things easier (in a "why call a method
with no parameters, that returns an object" way :)).
Making .data a property would keep current behavior and
require less ()s :)

I'm working on an advanced version of the topological
view and on a derivative of that printing recipe for my
own needs, but will forward them here when done.

Thanks again,
Daniel

[ajaksu]

Topology patch for cluster.py

[ajaksu]

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Duh, of course SF mangles the ASCII art.
Here's something I'm getting from very ugly, very poor code.
It's based on the recipe above, plus handling of tags
(levels) and a hack that lets Cluster.topology() know that I
want a label instead of each item's repr.

[ajaksu]

ASCII art for clusters.

[Michel Albert]

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Hi Daniel,

thanks for the input. It gives me the warm and fuzzy
feeling, that this project is indeed still in use ;)

Having topological output for the clusters is a brilliant
idea. I remember well, a couple of weeks ago. I was sitting
at the desk with several A4 pages taped together, and was
drawing the output of python-cluster for debugging. Hehe...
;)

Having this is very useful. I had a quick look through your
code, and it looks fine. I will merge it as soon as I get
the time.

Thanks a lot,

Michel

[Michel Albert]

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Bah, I accidentally updated an old revision with this
patch. Need to re-do the work :(