Re: [Matplotlib-users] Errorbars not drawn correctly in logarithmic scales

2012-03-09 Thread Wolfgang Draxinger
On Thu, 8 Mar 2012 19:47:05 -0600
Benjamin Root  wrote:

> Which version of matplotlib are you using?  Also, are you setting the
> log scale before (preferred) or after (won't work) the call to hist()?

Version is matplotlib-1.1.0, installed through standard Gentoo ebuild.
And the scale parameters are set before all the drawing calls.


Wolfgang

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Re: [Matplotlib-users] backend with edition capabilities

2012-03-09 Thread François Beaubert

Le 05/03/2012 21:37, Federico Ariza a écrit :

Hi

As I thought, this is a tricky subject.

So far I just opened a github account and added the three files that I 
am using.

https://github.com/fariza/MPL-Experimental-Backend
I have tested this on linux, I do not know if it works on windows.

I know glade is not the right way to do it if I want this to be taken 
serously.
So far the only thing I want is to experiment and see what subset of 
actions are needed by most people.


The code is ugly but if this is something that more people find 
useful, I will do something about that, if not I will keep it to 
myself and my personal use.


Thanks
Federico


P.S. The group expander is because I have personal need of line group 
management

P.S.2. The toolbar will be modified to be unified among all the figures
P.S.3. The figures are arranged in a notebook because I hate having 
multiple open windows from the same source.
P.S.4. I am thinking on adding a "shell" with all the figure and line 
instances ready to be modified by hand.


On Wed, Feb 29, 2012 at 5:02 PM, Federico Ariza 
mailto:ariza.feder...@gmail.com>> wrote:


Dear all

I am a long time matplotlib user  (under linux) but new to the
list (second post).

On of the things that bothers me the most is the inability of the
standard backend to change simple things (line color, labels, etc...).

I resorted to create a simple FrankeinBackend (based on the GtkAgg)
I guess I am not the only one missing this kind of features or
experimenting with similar ideas.

Some points comes to my mind:
Is there any special place where we can share and discuss this?
Is it better if I just open a googlecode place for my code.?
This is a recurring question and I have no idea what I am talking
about
This is already done I am reinventing the wheel

Thanks
Federico

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Hi,

Great project and addition to matplotlib ! Something that was missing 
for me ... thanks !
I've tried to use your backend with editions capabilities but i'm stick 
with this erro:


python test.py
Traceback (most recent call last):
  File "test.py", line 4, in 
import matplotlib.pyplot as plt
  File "/usr/lib/pymodules/python2.7/matplotlib/pyplot.py", line 95, in 


new_figure_manager, draw_if_interactive, show = pylab_setup()
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/__init__.py", 
line 25, in pylab_setup

globals(),locals(),[backend_name])
  File 
"/home/beaubert/Téléchargements/fariza-MPL-Experimental-Backend-aa7ce4a/experimentalbackend.py", 
line 34, in 

settings.props.gtk_button_images = True
AttributeError: 'gobject.GProps' object has no attribute 'gtk_button_images'

I'm on Kubuntu 11.10.
Thank's

Cheers
Francois
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[Matplotlib-users] Clearing 3D plots plotted in figure canvas

2012-03-09 Thread Sourabh Bajaj
I am creating a PyQT based tool. that has a Figure canvas embedded in it.

I want to update the plot on some event. I can draw the plot perfectly.
But how do I clear the plot without removing the mouse movement 
capabilities.

axes.cla, fixes the axis movement as well.


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[Matplotlib-users] Stack Plot

2012-03-09 Thread Trillian

Hello All, 

How do I control a width and length of a boxes in a stack plot? Currently
with the code I have, I can only control the separation or the white-space
between the two plots. I would like the top plot to be larger in length and
narrow in width while the bottom plot to have the same width as the top but
the length to be much shorter than the top. Please see figure. 

http://old.nabble.com/file/p33468632/RVs.png RVs.png 


#!/usr/bin/env python

import asciitable
data = asciitable.read('RVs.dat')
# To use the variables in asciitable use col1, col2, etc..

from pylab import *

f = figure()
subplots_adjust(hspace=1)

ax1 = subplot(211)
ax1.plot(data.col6,data.col5, 'ko')
ylabel('RV using GJ406')
title('RV comparison')

ax2 = subplot(212, sharex=ax1)
ax2.plot(data.col6,data.col5-data.col6,'ko' )
xlabel('RV (km/s)')
ylabel('Residuals (km/s)')
# The line below takes away the x-axis values from top plot. 
xticklabels = ax1.get_xticklabels()+ax2.get_xticklabels()
setp(xticklabels, visible=True)
savefig('RVs.png')

Thanks, 

Trillian


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Re: [Matplotlib-users] Has nxutils been removed from mpl?

2012-03-09 Thread Dharhas Pothina


As someone who has never contributed to matplotlib before, are there any 
instructions on how to contribute to writing tests. We have some data and 
scripts we could probably convert to tests for the nxutils points in poly 
functions. Should I just do i pull the branch nxutilsbackwards branch and make 
a pull request after adding tests on github?  

- dharhas

>>> Michael Droettboom  3/8/2012 5:51 PM >>>
There is a proposed solution to all of this here:

https://github.com/matplotlib/matplotlib/pull/746

Please test -- I don't have any nxutils-using code myself, and matplotlib 
itself has none.  We should probably convert some of the nxutils code in the 
wild into some unit tests.

Mike

On 03/08/2012 12:37 PM, Benjamin Root wrote: 





On Thu, Mar 8, 2012 at 11:16 AM, Benjamin Root  wrote:






On Thu, Mar 8, 2012 at 10:47 AM, John Hunter  wrote:






On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root  wrote:




+1 as well.  I just took another look at the Path object and I see no such 
function.  The lack of this function is a problem for me as well in my existing 
apps.  In order to deprecate nxutils, this functionality needs to be added to 
Path.  Otherwise, nxutils *must* be reinstated before the next release.

 



Michael has already agreed to make a nxutils compatibility layer that would 
have the same interface as the old nxutils.  So we are talking about 
performance, not core functionality. 



We should remember that Michael did the lion's share of the work on  porting 
mpl to python 3 (https://github.com/matplotlib/matplotlib/pull/565/commits).  
He elected not to port all of the C++ if he could replace some of the 
functionality with the core.  So those who rely on bare metal speed the you are 
getting in nxutils should step up to either : 



1) help with the port of nxutils to python 3 



2) help with exposing methods in _path.cpp that are almost as fast or faster 



3) live with slower speeds in the compatibility layer he has agreed to write 



4) ask (nicely) for someone to help you 



I prefer option 2 because this is fairly easy and avoids code redundancy.  It 
would take just a few lines of extra code to do this with the python sequence 
protocol as inputs and python lists as return values.  It would take a bit more 
to support numpy arrays as input and output, and we should get input from 
Michael about the desirability of making _path.cpp depend on numpy.  I don't 
see the harm, but I'd like to verify. 



In my opinion, a slower implementation in a nxutils.py compatibility module is 
not a release stopper, even if it is undesirable.   



JDH 
 


Don't get me wrong.  If help is needed, I can certainly provide it since it is 
my itch.  I am just a little exasperated with how this issue has been handled 
up to now.  The shim is a very good idea and it should have been done back when 
the py3k merge happened.  I didn't press the issue then because I was traveling 
and didn't have time to examine the issue closely, and having _nxutils.so still 
in my build hide the problem from me (my own fault).

As for shim implementation, I would be willing to accept a slightly slower 
function now (with the promise of improvements later), but if the 
implementation is too much slower, then effort will need to be made to get it 
up to acceptable levels.  I know of several users **cough**my future 
employer**cough** who uses functionality such as this, and they would not be 
happy if their products are dragged down by such a bottleneck.

Probably about time I dug more into CXX wrapped stuff...

Ben Root
 



Looking over the code, it looks like we could generalize point_in_path_impl() 
into points_in_path_impl().  The current code iterates through the path 
vertices to test a single point.  Putting this action inside a loop (for each 
point that we want to test) would mean that this iterator has to be processed 
each time, which I suspect would kill performance when the number of vertices 
is far greater than the number of test points.

Tinkering

Ben Root




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Re: [Matplotlib-users] Clearing 3D plots plotted in figure canvas

2012-03-09 Thread Benjamin Root
On Thu, Mar 8, 2012 at 4:02 PM, Sourabh Bajaj wrote:

> I am creating a PyQT based tool. that has a Figure canvas embedded in it.
>
> I want to update the plot on some event. I can draw the plot perfectly.
> But how do I clear the plot without removing the mouse movement
> capabilities.
>
> axes.cla, fixes the axis movement as well.
>
>
>
Just took a look at the cla() method in mplot3d and it seems that the
original author of the module put in a call to disable all user interaction
when ax.cla() is called.  I find this to be very odd and undesirable.  I
suspect that it was needed when the module was originally done, but I don't
think that is the case anymore.

Unless someone can tell me the reason for disabling mouse interaction for
mplot3d axes, I will submit a bug fix.

Ben Root
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Re: [Matplotlib-users] Errorbars not drawn correctly in logarithmic scales

2012-03-09 Thread Benjamin Root
On Fri, Mar 9, 2012 at 3:29 AM, Wolfgang Draxinger <
wdraxinger.maill...@draxit.de> wrote:

> On Thu, 8 Mar 2012 19:47:05 -0600
> Benjamin Root  wrote:
>
> > Which version of matplotlib are you using?  Also, are you setting the
> > log scale before (preferred) or after (won't work) the call to hist()?
>
> Version is matplotlib-1.1.0, installed through standard Gentoo ebuild.
> And the scale parameters are set before all the drawing calls.
>
>
> Wolfgang
>
>
Wolfgang,

Can I have the data you used to produce these errorbars so I can test this
bug?

Ben Root
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[Matplotlib-users] x and y labels that span multiple axes

2012-03-09 Thread Jonathan Slavin
Hi all,

I'm plotting a set of subplots (2 x 3) and I'd like to label the x and y
axes with one title each (i.e. spanning the axes) since the units of all
the x axes and y axes are the same.  I know that I can use fig.text to
do it, though that would require some fiddling on my part to get the
placement right.  Is there an easier way?

Jon
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Re: [Matplotlib-users] Errorbars not drawn correctly in logarithmic scales

2012-03-09 Thread Wolfgang Draxinger
On Fri, 9 Mar 2012 11:19:15 -0600
Benjamin Root  wrote:
 
> Can I have the data you used to produce these errorbars so I can test
> this bug?

Here's the data

#  Fluence -sigma Signal...  -sigma   area
  1127  48.32  9.114  10.31 0.1318
 1.127e+04  482.9  35.96  16.15 0.4994
 1.127e+05   4829  231.2  101.1  2.568
 1.127e+06  4.829e+04   4631   1689  12.22

And here's the ploting tool source code (also used for generating the
linked PDF).

#!/usr/bin/env python2
# -*- coding: utf-8 -*-
# vim: filetype python

import sys, os, argparse

import math, numpy, scipy, scipy.optimize

import matplotlib, matplotlib.cm
import matplotlib.pyplot as pyplot
import pylab

def expmodel(p, x):
return p[0] + numpy.exp(p[1]*x)*p[2]

def experror(p, x, y):
return y - expmodel(p, x)

def linmodel(p, x):
return p[0] + p[1]*x

def linerror(p, x, y):
return y - linmodel(p, x)

if __name__ == '__main__':
optparse = argparse.ArgumentParser(description='plot raddark dat files 
with errorbars and linear or exponential model regression plots', 
prog=sys.argv[0])
optparse.add_argument('--xlabel', type=str, default='Particle Count')
optparse.add_argument('--ylabel', type=str, default='Signal')
optparse.add_argument('--title', type=str, default='')
optparse.add_argument('--outlier', '-O', action='append', type=str)
optfitgrp = optparse.add_mutually_exclusive_group()
optfitgrp.add_argument('--exp', '-e', action='store_true')
optfitgrp.add_argument('--lin', '-l', action='store_true')
optparse.add_argument('--log', action='store_true')
optparse.add_argument('files', type=str, nargs='+')

options = optparse.parse_args(sys.argv[1:])

data = [ numpy.loadtxt(filename) for filename in options.files ]

if options.outlier:
outlier = [ numpy.loadtxt(filename) for filename in 
options.outlier ]

ax = pyplot.subplot(1,1,1)
if options.log:
ax.loglog()

ax.set_title(options.title)
ax.set_xlabel(options.xlabel)
ax.set_ylabel(options.ylabel)
ax.grid(True, 'both')

for f,d in zip(options.files, data):
ax.errorbar(d[..., 0], d[..., 2], d[..., 3], d[..., 1], 
fmt='o', label=f)

if options.outlier:
for f,d in zip(options.outlier, outlier):
ax.errorbar(d[..., 0], d[..., 2], d[..., 3], d[..., 1], 
fmt='+', label=f)

if options.exp or options.lin:
data_xs = numpy.concatenate( [ d[..., 0] for d in data ] )
data_ys = numpy.concatenate( [ d[..., 2] for d in data ] )
if options.outlier:
x_max = numpy.nanmax( numpy.concatenate((data_xs, 
numpy.concatenate([ o[..., 0] for o in outlier ]))) )
x_min = numpy.nanmin( numpy.concatenate((data_xs, 
numpy.concatenate([ o[..., 0] for o in outlier ]))) )
else:
x_max = numpy.nanmax(data_xs)
x_min = numpy.nanmin(data_xs)
x_ptp = x_max - x_min
xs = numpy.arange(x_min - 0.05*x_ptp, x_max + 0.05*x_ptp, 
x_ptp/1.)

if options.exp:
p = scipy.optimize.leastsq(experror, 
[numpy.nanmin(data_ys), 1e-6/x_ptp, 1./numpy.ptp(data_ys)], args=(data_xs, 
data_ys))
ys = expmodel(p[0], xs)
if options.lin:
p = scipy.optimize.leastsq(linerror, 
[numpy.nanmin(data_ys), 1./x_ptp, 1./numpy.ptp(data_ys)], args=(data_xs, 
data_ys))
ys = linmodel(p[0], xs)

ax.plot(xs, ys, label="fit")

ax.legend(loc='upper left')

pyplot.show()

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Re: [Matplotlib-users] Stack Plot

2012-03-09 Thread Benjamin Root
On Thu, Mar 8, 2012 at 5:05 PM, Trillian  wrote:

>
> Hello All,
>
> How do I control a width and length of a boxes in a stack plot? Currently
> with the code I have, I can only control the separation or the white-space
> between the two plots. I would like the top plot to be larger in length and
> narrow in width while the bottom plot to have the same width as the top but
> the length to be much shorter than the top. Please see figure.
>
> http://old.nabble.com/file/p33468632/RVs.png RVs.png
>
>
> #!/usr/bin/env python
>
> import asciitable
> data = asciitable.read('RVs.dat')
> # To use the variables in asciitable use col1, col2, etc..
>
> from pylab import *
>
> f = figure()
> subplots_adjust(hspace=1)
>
> ax1 = subplot(211)
> ax1.plot(data.col6,data.col5, 'ko')
> ylabel('RV using GJ406')
> title('RV comparison')
>
> ax2 = subplot(212, sharex=ax1)
> ax2.plot(data.col6,data.col5-data.col6,'ko' )
> xlabel('RV (km/s)')
> ylabel('Residuals (km/s)')
> # The line below takes away the x-axis values from top plot.
> xticklabels = ax1.get_xticklabels()+ax2.get_xticklabels()
> setp(xticklabels, visible=True)
> savefig('RVs.png')
>
> Thanks,
>
> Trillian
>
>
Perhaps GridSpec is what you need:

http://matplotlib.sourceforge.net/users/gridspec.html

Cheers!
Ben Root
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Re: [Matplotlib-users] x and y labels that span multiple axes

2012-03-09 Thread Jeffrey Blackburne

On Mar 9, 2012, at 1:05 PM, Jonathan Slavin wrote:

> Hi all,
>
> I'm plotting a set of subplots (2 x 3) and I'd like to label the x  
> and y
> axes with one title each (i.e. spanning the axes) since the units  
> of all
> the x axes and y axes are the same.  I know that I can use fig.text to
> do it, though that would require some fiddling on my part to get the
> placement right.  Is there an easier way?
>
> Jon

Hi Jon,

The way I do this is to create a "master" axis that overlaps the  
others with dimensions equal to the outer border of all the other  
axes. Then I just use this axis for the labels:
masterAxis.set_xlabel("ick")
masterAxis.set_ylabel("blech")

You also have to turn off ticks and tick labels for this axis:
masterAxis.xaxis.set_major_formatter(mpl.ticker.NullFormatter())
masterAxis.yaxis.set_major_formatter(mpl.ticker.NullFormatter())

Since it doesn't know about tick labels, it may not position the axis  
labels far enough away from the axis line, so you can adjust the  
spacing:
masterAxis.xaxis.labelpad += 6
masterAxis.yaxis.labelpad += 4

It's still a little fiddly, but less fiddly than using fig.text. I  
bet this could be significantly improved, e.g. with Axes_Grid, but I  
don't know how to do that.

Cheers,
Jeff



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Re: [Matplotlib-users] Stack Plot

2012-03-09 Thread Trillian

Perfect! That is what I was looking for! 

Thanks a lot! 

Trillian


Benjamin Root-2 wrote:
> 
> On Thu, Mar 8, 2012 at 5:05 PM, Trillian  wrote:
> 
>>
>> Hello All,
>>
>> How do I control a width and length of a boxes in a stack plot? Currently
>> with the code I have, I can only control the separation or the
>> white-space
>> between the two plots. I would like the top plot to be larger in length
>> and
>> narrow in width while the bottom plot to have the same width as the top
>> but
>> the length to be much shorter than the top. Please see figure.
>>
>> http://old.nabble.com/file/p33468632/RVs.png RVs.png
>>
>>
>> #!/usr/bin/env python
>>
>> import asciitable
>> data = asciitable.read('RVs.dat')
>> # To use the variables in asciitable use col1, col2, etc..
>>
>> from pylab import *
>>
>> f = figure()
>> subplots_adjust(hspace=1)
>>
>> ax1 = subplot(211)
>> ax1.plot(data.col6,data.col5, 'ko')
>> ylabel('RV using GJ406')
>> title('RV comparison')
>>
>> ax2 = subplot(212, sharex=ax1)
>> ax2.plot(data.col6,data.col5-data.col6,'ko' )
>> xlabel('RV (km/s)')
>> ylabel('Residuals (km/s)')
>> # The line below takes away the x-axis values from top plot.
>> xticklabels = ax1.get_xticklabels()+ax2.get_xticklabels()
>> setp(xticklabels, visible=True)
>> savefig('RVs.png')
>>
>> Thanks,
>>
>> Trillian
>>
>>
> Perhaps GridSpec is what you need:
> 
> http://matplotlib.sourceforge.net/users/gridspec.html
> 
> Cheers!
> Ben Root
> 
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Re: [Matplotlib-users] Error when saving as PDF using $\alpha$ and 'text.usetex':True

2012-03-09 Thread Alejandro Weinstein
On Thu, Mar 8, 2012 at 12:45 PM, Jouni K. Seppänen  wrote:
> Alejandro Weinstein  writes:
>
>> TypeError: unicode argument expected, got 'str'
>> I am using MPL verion 1.2.x (built from commit 396a6446).
>
> That reminds me of a problem fixed in commit 680edf7, so could you
> either try cherry-picking that commit or updating to a later revision?
> Your test case doesn't produce an error on a recent-ish master.

You're right. Just updated to the last version and the problem is gone.

Thanks!

Alejandro.

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Re: [Matplotlib-users] Centering Text with axes_divider

2012-03-09 Thread Patrick Marsh
Hi, All,

Here's an update to the problem I submitted last night.

I was able to utilize anchored text to work for centering a title, which is
ultimately what I'm wanting to do now. (Although, I'd still like to know
the proper way to get the axes bounds when using axes_divider).  The new
problem lies how to horizontally align the text inside the anchored box.
When the horizontal alignment is "left", the text lines up in the anchored
box. However, as the updated example below shows, then you use "center" or
"right", the text is now positioned outside the anchored box.  Is this a
bug in how the text is aligned? If so, how might I go about tracking it
down?


https://gist.github.com/2004869 (rev: b984ca)


Cheers,
Patrick
---
Patrick Marsh
Ph.D. Student / Liaison to the HWT
School of Meteorology / University of Oklahoma
Cooperative Institute for Mesoscale Meteorological Studies
National Severe Storms Laboratory
http://www.patricktmarsh.com



On Fri, Mar 9, 2012 at 12:12 AM, Patrick Marsh wrote:

> Greetings,
>
> Let me begin by saying that I've fallen in love with ImageGrid. I love the
> control it gives me in setting up plots, and I really like the control it
> offers for setting up a colorbar. Unfortunately, like all relationships,
> ImageGrid and I have hit a rough patch.
>
> I like to manually place titles and other boxes of texts on plots that I
> make using ImageGrid. However, to center things I have to know what the
> axes bounds are so I can do the centering calculations. Unfortunately, when
> using ImageGrid, or axes_divider, I have yet to find a way to get the axes
> bounds that are actually used to do the plotting. When I try to use
>
> ax.get_position().bounds
>
> I get the pre-adjusted bounds, even if I use plt.draw() before requesting
> the axes_positions. This means the only way I can center the text is by
> guessing what the final axes bounds will be.  Is there any way of getting
> the final bounds? It appears anchored text is able to do it, but I haven't
> been able to...
>
>
> Here's a self-contained example script that demonstrates the problem.  I
> don't use ImageGrid, instead using axes_divider, however this is the same
> problem that AxesGrid has. (I'm guessing this is because ImageGrid
> ultimately does what I did here behind the scenes.)
>
> https://gist.github.com/2004869
>
>
> Thanks for any help!
>
>
> Patrick
> ---
> Patrick Marsh
> Ph.D. Student / Liaison to the HWT
> School of Meteorology / University of Oklahoma
> Cooperative Institute for Mesoscale Meteorological Studies
> National Severe Storms Laboratory
> http://www.patricktmarsh.com
>
>
>
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