matplotlib-users Mailing List for matplotlib

I don't think that Matplotlib has such a plot, but I would also be
interested in using such a plot - for presenting hierarchical
clustering results.

Michael

On 8/31/06, R. Padraic Springuel <R.S...@um...> wrote:
> Can Matplotlib create dendrograms?  As best I can tell, there isn't a
> plotting function for doing so directly, but maybe one could make one by
> combining a series of commands.  Has anyone done this?  Does anyone know
> if it is possible, or if there is another package that would do the job
> if it isn't?
> --
>
> R. Padraic Springuel
> Teaching Assistant
> Department of Physics and Astronomy
> University of Maine
> Bennett 309
> Office Hours: By Appointment only during the Summer
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Aug 31, 2006, at 2:56 PM, John Hunter wrote:

>>>>>> "Michael" == Michael Fitzgerald <mp...@be...> writes:
>
>     Michael> Is there a way to force some sort of pseudo-draw event,
>     Michael> such that the sizing is done and the ticks are created
>     Michael> from the protoTick, but the draw isn't actually performed
>     Michael> by the backend?  That way one could set the visibility
>     Michael> property rather than wrap the Formatter.
>
> Try fig.canvas.draw() and see if that helps.
>
> If not, we'll come up with something else...

I placed that command before the ax.get_xticklabels(), and no dice.

Thanks for looking into this,
Mike

Jim,

The problem is that the new quiver--the one for which Jeff quoted a 
docstring extract--appeared after 0.87.3.  I hope you can update to 
0.87.4 or to svn.  I gather there will be another release within a week 
or two, also, to support the latest numpy.

Eric

James Boyle wrote:
> when I call quiver in the Basemap toolkit, the scale keyword has the  
> effect of eliminating all vectors, no matter what value I assign  
> (except None).
> I am using matplotlib 0.87.3 -  Basemap 0.9
> In any case the exact effect of the scale parameter is obscure - how  
> does is scale? units/inch, units/gridbox ???
> 
> Thanks for any help.
> --Jim
> 
> 
> the calls I use are below:
> mercMap =  
> Basemap(llcrnrlon=120.,llcrnrlat=-20,urcrnrlon=200.,urcrnrlat=20.,\
>              resolution='c',area_thresh=10000.,projection='merc',\
>              lon_0=160.,lat_ts=0.)
> istride = 3
> mercMap.quiver(x[::istride,::istride],y[::istride,::istride],uERA[:: 
> istride,::istride],vERA[::istride,::istride],scale=None)
> 
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

>>>>> "Michael" == Michael Fitzgerald <mp...@be...> writes:

    Michael> Is there a way to force some sort of pseudo-draw event,
    Michael> such that the sizing is done and the ticks are created
    Michael> from the protoTick, but the draw isn't actually performed
    Michael> by the backend?  That way one could set the visibility
    Michael> property rather than wrap the Formatter.

Try fig.canvas.draw() and see if that helps.

If not, we'll come up with something else...

JDH

James Boyle wrote:
> when I call quiver in the Basemap toolkit, the scale keyword has the  
> effect of eliminating all vectors, no matter what value I assign  
> (except None).
> I am using matplotlib 0.87.3 -  Basemap 0.9
> In any case the exact effect of the scale parameter is obscure - how  
> does is scale? units/inch, units/gridbox ???
>
> Thanks for any help.
> --Jim
>
>
> the calls I use are below:
> mercMap =  
> Basemap(llcrnrlon=120.,llcrnrlat=-20,urcrnrlon=200.,urcrnrlat=20.,\
>              resolution='c',area_thresh=10000.,projection='merc',\
>              lon_0=160.,lat_ts=0.)
> istride = 3
> mercMap.quiver(x[::istride,::istride],y[::istride,::istride],uERA[:: 
> istride,::istride],vERA[::istride,::istride],scale=None)
>
>
>   
Jim:  Basemap passes the scale keyword directly to matplotlib quiver.   
 From the docstrings in quiver.py:

 * scale = None | float
            data units per arrow unit, e.g. m/s per plot width;
            a smaller scale parameter makes the arrow longer.
            If None, a simple autoscaling algorithm is used, based
            on the average vector length and the number of vectors.

I just tried changing the projection to 'merc' in the quiver_demo.py 
example, and it looked OK with the default (scale=None).

-Jeff


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

On Aug 31, 2006, at 4:36 AM, John Hunter wrote:
> So: how do you solve your problem, of making the first tick invisible?
> What I do when I need to solve this problem, which comes up a lot with
> multiple axes where ticks can overlap, is the following
>
> from matplotlib.ticker import ScalarFormatter
>
> class MyFormatter(ScalarFormatter):
>     def __call__(self, x, pos=None):
>         if pos==0: return ''
>         else: return ScalarFormatter(self, x, pos)
>
> ax.xaxis.set_major_formatter(MyFormatter())
>
> I often want to do this for the last tick as well, but there is
> currently no convenient way to do this, as the tick locator produces
> the tick location list and the tick formatter doesn't know how many of
> them there are.  I've been considering modifying the tick locator code
> to pass -1 for the pos for the last tick to solve just this use case.
> If others need this or think it desirable, just give me a nudge and
> I'll do it.

Hi John,

Hmm.... I have 3 use cases where I want to isolate individual tick  
labels and make them invisible:

1) the first tick (0; for stacked plots)
2) the last tick (-1; for stacked plots)
3) every other tick for the last few ticks (e.g. -2, -4, -6; for a  
log-scale axis with large tick labels, which can overlap on one end)

Is there a way to force some sort of pseudo-draw event, such that the  
sizing is done and the ticks are created from the protoTick, but the  
draw isn't actually performed by the backend?  That way one could set  
the visibility property rather than wrap the Formatter.

Thanks,
Mike

when I call quiver in the Basemap toolkit, the scale keyword has the  
effect of eliminating all vectors, no matter what value I assign  
(except None).
I am using matplotlib 0.87.3 -  Basemap 0.9
In any case the exact effect of the scale parameter is obscure - how  
does is scale? units/inch, units/gridbox ???

Thanks for any help.
--Jim


the calls I use are below:
mercMap =  
Basemap(llcrnrlon=120.,llcrnrlat=-20,urcrnrlon=200.,urcrnrlat=20.,\
             resolution='c',area_thresh=10000.,projection='merc',\
             lon_0=160.,lat_ts=0.)
istride = 3
mercMap.quiver(x[::istride,::istride],y[::istride,::istride],uERA[:: 
istride,::istride],vERA[::istride,::istride],scale=None)

Hi Eric,

This shows what I'm talking about:

--------------------
from pylab import *

delta = 0.025
x = arange(-3.0, 3.0, delta)
y = arange(-2.0, 2.0, delta)
X, Y = meshgrid(x, y)
Z1 = bivariate_normal(X, Y, 1.0, 1.0, 0.0, 0.0)
Z2 = bivariate_normal(X, Y, 1.5, 0.5, 1, 1)
# difference of Gaussians
Z = 10.0 * (Z2 - Z1)

contourf(X, Y, sin(Y)*cos(X),
         alpha=0.2)
hot()
contour(X, Y, Z, 6,
        linewidths=4,
        colors=('r', 'green', 'blue', (1,1,0), '#afeeee', '0.5'),
        alpha=0.4)
show()

-------------------

On Thursday 31 August 2006 13:50, Eric Firing wrote:
> Scott,
>
> Please send a minimal example that I can use as a test case.  This
> sounds vaguely familiar.
>
> Thanks.
>
> Eric
>
> Scott Ransom wrote:
> > Hi All,
> >
> > I'm using matplotlib (with agg backends) from recent svn:
> >
> > In [63]: matplotlib.__version__
> > Out[63]: '0.87.4'
> >
> > and I can't seem to get contour() or contourf() to utilize the
> > alpha keyword.  No matter what value I set, alpha=1.0 on the
> > output.  Alpha in general works fine, as the scatter_demo2.py
> > example gives very nicely alpha-channeled output.
> >
> > Any ideas?  Thanks a bunch,
> >
> > Scott

-- 
Scott M. Ransom            Address:  NRAO
Phone:  (434) 296-0320               520 Edgemont Rd.
email:  sr...@nr...             Charlottesville, VA 22903 USA
GPG Fingerprint: 06A9 9553 78BE 16DB 407B  FFCA 9BFA B6FF FFD3 2989

Samuel,

Trying to manipulate variables with leading underscores is 
discouraged--that is the meaning of the leading underscores.

Changing the shared status of axes involves changes in additional 
variables.  This could be encapsulated in a single method.  It might be 
very easy, or complexities and gotchas might turn up. How important is 
it?  What is the problem with setting the shared status when you make 
the axes, as in your first example?

Eric

Samuel GARCIA wrote:
> Hi all,
> is there a possibility to change the sharex and sharey after creating a 
> axes ?
> 
> For example this perfectitly work :
> 
> import pylab
> fig = pylab.figure()
> ax1 = fig.add_subplot(121)
> ax2 = fig.add_subplot(122, sharex=ax1)
> ax1.plot(rand(5))
> ax2.plot(rand(5))
> pylab.show()
> 
> But when I try naively to change _sharex and _masterx  after creating 
> the axes it doesn't work :
> 
> 
> import pylab
> fig = pylab.figure()
> ax1 = fig.add_subplot(121)
> ax2 = fig.add_subplot(122)
> ax1.plot(rand(5))
> ax2.plot(rand(5))
> ax2._sharex = ax1
> ax1._masterx = True
> pylab.show()
> 
> What 's the solution ?
> thank you
> 
> Samuel
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
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> Get stuff done quickly with pre-integrated technology to make your job easier
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> 
> 
> ------------------------------------------------------------------------
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
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Scott,

Please send a minimal example that I can use as a test case.  This 
sounds vaguely familiar.

Thanks.

Eric

Scott Ransom wrote:
> Hi All,
> 
> I'm using matplotlib (with agg backends) from recent svn:
> 
> In [63]: matplotlib.__version__
> Out[63]: '0.87.4'
> 
> and I can't seem to get contour() or contourf() to utilize the
> alpha keyword.  No matter what value I set, alpha=1.0 on the
> output.  Alpha in general works fine, as the scatter_demo2.py
> example gives very nicely alpha-channeled output.
> 
> Any ideas?  Thanks a bunch,
> 
> Scott
> 

Perhaps NetworkX <https://networkx.lanl.gov/> will do what you want, 
depending on how much control you need over the node placement. There 
are a few more suggestions for general graph plotting solutions here:
<https://networkx.lanl.gov/wiki/Drawing>.
hth
Gary R.

R. Padraic Springuel wrote:
> Can Matplotlib create dendrograms?  As best I can tell, there isn't a 
> plotting function for doing so directly, but maybe one could make one by 
> combining a series of commands.  Has anyone done this?  Does anyone know 
> if it is possible, or if there is another package that would do the job 
> if it isn't?

>>>>> "Michael" == Michael Fitzgerald <mp...@be...> writes:

    Michael> Hi all,

    Michael> I'm still having trouble figuring out what's going on
    Michael> with tick labels.  I can't figure out why
    Michael> Axes.get_{x,y}ticklabels() is returning a list of length
    Michael> unity when I expect to have the list of all labels.

    Michael> If I run the code below (test.py), I expect a list of 9 x
    Michael> tick labels.  If I run the code once ('run test' in
    Michael> ipython), then it gives me a list of 1 tick label.  If I
    Michael> close the interactive window it generates and run it
    Michael> again, it again returns 1 tick label.  However, if I
    Michael> leave the window open and re-run the test, it gives the
    Michael> right answer.

    Michael> Can anyone else reproduce this?  Is there something I'm
    Michael> missing?  I'm using svn rev 2730 of matplotlib, and I
    Michael> think this is new behavior in the last couple months.

It's a feature, not a bug :-)

Here is what is happening.  matplotlib allocates a different number of
ticks depending on the zoom level, and the axis seeds itself with a
single tick called the "protoTick".  If you zoom to the right and new
ticks need to be created, the properties from the protoTick are copied
to the newly created ticks. 99% of the time, this is what you want.
If you have large bold tick labels, and zoom to the right, you want
the new ticks that appear to be large and bold.  So this explains why
you see a single tick before the window is drawn (the protoTick), a
list of ticks after the window is drawn, and why the properties of the
first tick (the "visible" property in this case) are transferred to
the other ticks.

So: how do you solve your problem, of making the first tick invisible?
What I do when I need to solve this problem, which comes up a lot with
multiple axes where ticks can overlap, is the following

from matplotlib.ticker import ScalarFormatter

class MyFormatter(ScalarFormatter):
    def __call__(self, x, pos=None):
        if pos==0: return ''
        else: return ScalarFormatter(self, x, pos)

ax.xaxis.set_major_formatter(MyFormatter())

I often want to do this for the last tick as well, but there is
currently no convenient way to do this, as the tick locator produces
the tick location list and the tick formatter doesn't know how many of
them there are.  I've been considering modifying the tick locator code
to pass -1 for the pos for the last tick to solve just this use case.
If others need this or think it desirable, just give me a nudge and
I'll do it.

Details about the tick locators and formatter can be found at
http://matplotlib.sourceforge.net/matplotlib.ticker.html and there are
a number of examples

  ~/mpl/examples> grep -l Formatter *.py
  custom_ticker1.py
  dashtick.py
  date_demo1.py
  date_demo2.py
  date_demo_rrule.py
  finance_demo.py
  major_minor_demo1.py
  major_minor_demo2.py
  newscalarformatter_demo.py
  shared_axis_demo.py

Hope this helps,
JDH

Hi all,

Sorry to trouble you with this (likely) trivial issue, but I  
installed matplotlib 0.87.4_r2587 using the .mpkg included with SciPy  
SuperPack for Intel, and I'm unable to import pylab from the iPython  
command line. When I try I get the error message "no module named  
matplotlib.pylab." I checked and the matplotlib sub-directory is  
there under my /Library/Frameworks/Python.framework/Versions/2.4/lib/ 
python2.4/site-packages directory. In iPython a help(); modules shows  
pylab but importing doesn't work. I'm new to this framework business  
that seems to be favored by Apple, so I'm not really familiar with  
how Python is setup in OS X. Any tips are much appreciated.

Thanks,
Aaron

Hi all,

I'm still having trouble figuring out what's going on with tick  
labels.  I can't figure out why Axes.get_{x,y}ticklabels() is  
returning a list of length unity when I expect to have the list of  
all labels.

If I run the code below (test.py), I expect a list of 9 x tick  
labels.  If I run the code once ('run test' in ipython), then it  
gives me a list of 1 tick label.  If I close the interactive window  
it generates and run it again, it again returns 1 tick label.   
However, if I leave the window open and re-run the test, it gives the  
right answer.

Can anyone else reproduce this?  Is there something I'm missing?  I'm  
using svn rev 2730 of matplotlib, and I think this is new behavior in  
the last couple months.

Can Matplotlib create dendrograms?  As best I can tell, there isn't a 
plotting function for doing so directly, but maybe one could make one by 
combining a series of commands.  Has anyone done this?  Does anyone know 
if it is possible, or if there is another package that would do the job 
if it isn't?
-- 

R. Padraic Springuel
Teaching Assistant
Department of Physics and Astronomy
University of Maine
Bennett 309
Office Hours: By Appointment only during the Summer

http://euclid.uits.iupui.edu/files/

For the record, these will probably be pulled after the next release.

On 8/30/06, Adriaan Hough <adr...@gm...> wrote:
> hi
>
> i'm looking for a recent binary build for windows that'll work with
> numpy-1.0b4 (maybe compatible with 1.0b3?). the links in the previous
> message don't seem to work anymore. would someone take pity on a
> win-python newbie?
>
>
> regards
>
> adriaan peens-hough
>
>
>
> >From: Charlie Moad <cwmoad@gm...>
> >                Snapshot build for use with numpy-1.0b3
> >               2006-08-23 06:11
> >Here is a snapshot of svn this morning for those wanting to work with
> > the numpy beta.  Both builds are for python2.4 and windows.
> >
> > exe: http://tinyurl.com/gf299
> > egg: http://tinyurl.com/fbjmg
> >
> > -Charlie
> >
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

hi

i'm looking for a recent binary build for windows that'll work with
numpy-1.0b4 (maybe compatible with 1.0b3?). the links in the previous
message don't seem to work anymore. would someone take pity on a
win-python newbie?


regards

adriaan peens-hough



>From: Charlie Moad <cwmoad@gm...>
>		 Snapshot build for use with numpy-1.0b3
> 		2006-08-23 06:11 	     	 		 			
>Here is a snapshot of svn this morning for those wanting to work with
> the numpy beta.  Both builds are for python2.4 and windows.
>
> exe: http://tinyurl.com/gf299
> egg: http://tinyurl.com/fbjmg
>
> -Charlie
>

Hi all,
is there a possibility to change the sharex and sharey after creating a
axes ?

For example this perfectitly work :

import pylab
fig = pylab.figure()
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122, sharex=ax1)
ax1.plot(rand(5))
ax2.plot(rand(5))
pylab.show()

But when I try naively to change _sharex and _masterx  after creating
the axes it doesn't work :


import pylab
fig = pylab.figure()
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
ax1.plot(rand(5))
ax2.plot(rand(5))
ax2._sharex = ax1
ax1._masterx = True
pylab.show()

What 's the solution ?
thank you

Samuel

Thank you,
you are incredibly rapid to awnser a problem.

samuel

John Hunter wrote:
>>>>>> "Samuel" == Samuel GARCIA <sg...@ol...> writes:
>>>>>>             
>
>     Samuel> Hi all, there is a image.set_clim() but I can't find the
>     Samuel> image.get_clim()
>
>     Samuel> Any solution ?
>
> I just committed get_clim to SVN, but in the meantime, you can access
> with the image normalization instance, which is what clim is an
> interface to anyhow:
>
>
> In [5]: im = imshow(rand(10,10))
>
> In [6]: im.norm.vmin, im.norm.vmax
> Out[6]: (0.011246857233345509, 0.99705302715301514)
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

On Tue, 29 Aug 2006, John Hunter wrote:

> I think the PNG corruption happened in the cvs to svn migration. These
> files are from a short course that Fernando and I put together which was a
> general introduction to scientific computing in python, and so it is not
> just matplotlib.  We can probably provide you with a PDF.

John,

   That would be great. When I saw the integrated tutorial
(python->ipython->numpy->scipy->matplotlib) I knew it was the overview I
needed. That's why I tried to build it here.

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

>>>>> "Rich" == Rich Shepard <rsh...@ap...> writes:

    Rich>    Having just downloaded the latest code from svn trunk, I
    Rich> started to look at the courses/ directory and was delighted
    Rich> to see all the documentation in .lyx format. However, when I
    Rich> tried to export to pdflatex I discovered that all the .png
    Rich> images in figs/ have damaged headers.

    Rich>    They also do not display or convert.

I think the PNG corruption happened in the cvs to svn migration.
These files are from a short course that Fernando and I put together
which was a general introduction to scientific computing in python,
and so it is not just matplotlib.  We can probably provide you with a
PDF.

JDH

On 8/29/06, PGM <pgm...@gm...> wrote:
> Folks,
> I've just noticed that in order to get the size of a figure in inches, one can
> use:
> >>> fig.get_size_inches()
> However, the corresponding 'set' method is
> >>>fig.set_figsize_inches()
>
> Is this intentional ? Wouldn't it be better to keep the set/get methods
> consistent ?
>
> Thx for your insight

Agreed.  fig.set_figsize seems redundant, so I am changing it to
fig.set_size_inches.  The old one will still be present, but will
issue a deprecation warning.  I'll commit these changes soon.

- Charlie

   Having just downloaded the latest code from svn trunk, I started to look
at the courses/ directory and was delighted to see all the documentation in
.lyx format. However, when I tried to export to pdflatex I discovered that
all the .png images in figs/ have damaged headers.

   They also do not display or convert.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Folks,
I've just noticed that in order to get the size of a figure in inches, one can 
use:
>>> fig.get_size_inches()
However, the corresponding 'set' method is 
>>>fig.set_figsize_inches()

Is this intentional ? Wouldn't it be better to keep the set/get methods 
consistent ?

Thx for your insight
P.

this could be a very "large" solution depending on the size of your data
sets, but you could make a class for your data and then if you make a
change to the data just import it into your drawing code and then redraw
it.  this way if you have more than 1 set of data you are just creating
more than one instance of your data class.  but if you are using very
large sets of data this could maybe become very slow and ugly.

if you impliment your data class well enough you could make it so that you
have functions in the data class that "add the new stuff" that you need
to.  I'm currently working with a graph that has 6000+ plots of data I am
picking subplots from it and applying a cubic integration to it.  It runs
in a timely manner and i have no complaints.


>Hi,
>Does someone know of a convenient way to save a plotted figure in order to
>reloading it later, possible adding new stuffs to it ? Presently, i keep
>pickling my data and cut&pasting my drawing code, by hand. I'm interested if
>some of you would have better solutions.
>Thanks

>--
>Benjamin Thyreau
>CEA Orsay