[Patch] Topological output and minor changes

[exhuma]

Converted from SourceForge issue 1535137, submitted by ajaksu2

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

[exhuma]

Submitted by ajaksu2

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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.

[exhuma]

Submitted by exhuma

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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

[exhuma]

Submitted by exhuma

Logged In: YES user_id=560690

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