Hi All, I've attached a patch which addresses two small issues. The first is a bug in patches.py. When doing 3d scatter plots xs, ys = zip(*self.xy) (line 480) crashes, as the right hand side expands to 3 values. The other is a speedup, normalising an entire array at once, rather than element by element, speeding up the attached script by a factor of 6x (and upgrading my actual application from 'too slow' to 'quite reasonable' :-) Cheers, Tim
On 4/9/07, Tim Leslie <tim...@gm...> wrote: > > The other is a speedup, normalising an entire array at once, rather > than element by element, speeding up the attached script by a factor > of 6x (and upgrading my actual application from 'too slow' to 'quite > reasonable' :-) Thanks Tim, I just committed this. I see that my sinister plan of releasing the 3d stuff w/o support in hopes of reeling in contributers is starting to work.... <laughs maniacally>
On 4/10/07, John Hunter <jd...@gm...> wrote: > On 4/9/07, Tim Leslie <tim...@gm...> wrote: > > > > > The other is a speedup, normalising an entire array at once, rather > > than element by element, speeding up the attached script by a factor > > of 6x (and upgrading my actual application from 'too slow' to 'quite > > reasonable' :-) > > Thanks Tim, I just committed this. I see that my sinister plan of > releasing the 3d stuff w/o support in hopes of reeling in contributers > is starting to work.... Well I've got a bit of work to do which involves 3D stuff in the coming week or so, so if I run up against anything else I'll keep the patches coming. Thanks for the quick commit. Cheers, Tim > > <laughs maniacally> >
On 4/10/07, John Hunter <jd...@gm...> wrote: > On 4/9/07, Tim Leslie <tim...@gm...> wrote: > > > > > The other is a speedup, normalising an entire array at once, rather > > than element by element, speeding up the attached script by a factor > > of 6x (and upgrading my actual application from 'too slow' to 'quite > > reasonable' :-) > > Thanks Tim, I just committed this. I see that my sinister plan of > releasing the 3d stuff w/o support in hopes of reeling in contributers > is starting to work.... > > <laughs maniacally> Here's another patch. This one cleans up the line2d_seg_dist function and also speeds it up by a factor of ~2. Cheers, Tim >
On 4/10/07, Tim Leslie <tim...@gm...> wrote: > Here's another patch. This one cleans up the line2d_seg_dist function > and also speeds it up by a factor of ~2 Excellent, thanks. Committed. JDH
It appears matplotlib does not have a dendrogram plot. I may be interested in developing one, if I can get a sense for what it would take. Could someone suggest some code I could look at as a model for developing a new plot? Thanks, --Tim
Timothy <te...@xm...> writes: > It appears matplotlib does not have a dendrogram plot. I may be > interested in developing one, if I can get a sense for what it would > take. Could someone suggest some code I could look at as a model for > developing a new plot? In the file axes.py, search for the comment "Specialized plotting" and look at the functions after that. The first function is "bar", which looks quite complicated, but perhaps "stem" would be a good starting point. -- Jouni K. Seppänen http://www.iki.fi/jks
I've spent some time on this problem and have a 44 line solution for
generating dendrogram line segments and root ending locations, i.e. x
and y values. The format for cluster information is a nested tuple like
this:
cluster=(4.5,(3.0,'c',(1.0,'a','b')),(2.0,'e',(1.5,'f','g')))
where the FP numbers are distance information and the strings are the
names of the items being clustered. The code can also handle cluster
data without distance information, by assuming a fixed distance of 1.0:
cluster=(('c',('a','b')),('e',('f','g')))
The output is a list of root location and value tuples: (x,y,item) and a
list of dendrogram line segment tuples: (x1,y1,x2,y2). I've purposely
avoided recursion back into the function by using list stacks because
I'm always a little leery of how much space is available on the
[virtual] machine stack. Note that this code has not been extensively
tested. One limitation on this dendrogram code is that only pairs of
objects may be clustered together at a time. Obviously a lot of work
would need to be done to apply these data to a Matplotlib plot, but I
don't know how to do it. The output could also be used to generate
images in SVG, Postscript, mechanical plotters, or any other vector
oriented graphical system.
Anyway, FWIW, my code is listed, below. I'm sure it can be improved
upon. In hopes of someone doing something useful for others with it, I
hereby release it under the Matplotlib license, while retaining the
copyright for my own additional use. Please let me know if there is a
better way to submit the code.
--Tim
import sys
def dendrogram(ctree,hasDistances='yes',yincr=1.0):
stype=type("")
tstack=[ctree[:]] ## make a copy
nstack=[] ## node stack
baselist=[]
linelist=[]
y=0.0
while len(tstack)>0:
tob=tstack.pop()
if hasDistances=='yes':
dist=tob[0]
tob=tob[1:]
elif hasDistances=='ignore':
dist=1.0
tob=tob[1:]
elif hasDistances=='no':
dist=1.0
else:
raise Exception("unknown value '%s' for named argument
'hasDistances'" % self.hasDistances)
obflag=False
for ob in tob:
if type(ob)==stype:
baselist.append( (0.0,y,ob) )
nstack.append( (0.0,y,dist) )
y+=yincr
else:
tstack.append(ob)
obflag=True
if obflag: nstack.append((dist,))
while len(nstack)>1 and len(nstack[-1])>1 and len(nstack[-2])>1:
x1,y1,d1=nstack.pop()
x2,y2,d2=nstack.pop()
if d1>d2: d=d1
else: d=d2
if x1>x2: xnew=x1+d
else: xnew=x2+d
ynew=(y1+y2)/2.0
linelist.append((x1,y1,xnew,y1))
linelist.append((x2,y2,xnew,y2))
linelist.append((xnew,y1,xnew,y2))
if len(nstack)>0 and len(nstack[-1])<=1:
dist=nstack.pop()[0]
nstack.append( (xnew,ynew,dist) )
return baselist,linelist
if __name__=="__main__":
baselist,linelist=dendrogram(
(4.5,(3.0,'c',(1.0,'a','b')),(2.0,'e',(1.5,'f','g'))) )
print baselist
print
print linelist
Jouni K. Seppänen wrote:
> Timothy <te...@xm...> writes:
>
>
>> It appears matplotlib does not have a dendrogram plot. I may be
>> interested in developing one, if I can get a sense for what it would
>> take. Could someone suggest some code I could look at as a model for
>> developing a new plot?
>>
>
> In the file axes.py, search for the comment "Specialized plotting" and
> look at the functions after that. The first function is "bar", which
> looks quite complicated, but perhaps "stem" would be a good starting
> point.
>
>
Timothy wrote: > Please let me know if there is a > better way to submit the code. > Hi Timothy, If you make it into a complete example that plots something, send it as an attachment to the list (so their are no line-break issues), I will commit it into the examples directory. From there, we can figure out where the key dendrogram() function should live, but at least your work will get in the repository as soon as possible. -Andrew