matplotlib-users Mailing List for matplotlib

The following boxplot raises a warning:

>>> boxplot([1], whis=float('inf'))
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/axes.py:5487:
RuntimeWarning: invalid value encountered in double_scalars
  hi_val = q3 + whis*iq

I think that it would be nice if it did not, so that users know that things
are fine, in this case. :)
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On 10/18/2011 06:19 AM, RuiDC wrote:
>
> As of 1.1.0, FigureCanvasQTAgg.draw() now no longer calls
> FigureCanvasAgg.draw(), and as a result I am getting problems with code that
> used to update positions/size of legend and labels during on_draw.
>
> 1. Is there a new way to get the canvas to draw? or is this a bug?

I would say it is a bug that has been lurking undetected for 9 months.

https://github.com/matplotlib/matplotlib/pull/539

I think this pull request fixes it.

Eric

>
> The "what's new in 1.1.0" page,
> http://matplotlib.sourceforge.net/users/whats_new.html refers to:
> "An rcParam entry, “backend.qt4”, has been added to allow users to select
> PyQt4, PyQt4v2, or PySide."
>
> 2. I cannot see any reference to PyQt4v2 in the code, and any attempt to set
> the rcParam to use it results in a param validation error, is this a mistake
> in the web page or omission in the code?
>
> Thanks in advance
> RuiDC

Hi All,

I would like to ask how I can invoke the interactive option in a gtk 
GUI. Basically, I have something like this

         self.figure = Figure(figsize=(8,6), dpi=72)
         self.axis = self.figure.add_subplot(111)
         self.axis.plot(x,y)

which works, except that I have to explicitly call something like this

     def refresh_plot(self):
         self.canvas.draw_idle()
         while gtk.events_pending():
             gtk.main_iteration()

My question is, whether it is possible to set interactive(True) or ion() 
in such a case, so that the plot would be displayed immediately. If that 
is not the case, is it possible to figure out whether a graph has 
changed since some point in time? If that is an option, then I could 
just check for the state of the figure, and if necessary, call the 
refresh_plot function.

Thanks,
v923z

On 10/18/2011 06:19 AM, RuiDC wrote:
>
> As of 1.1.0, FigureCanvasQTAgg.draw() now no longer calls
> FigureCanvasAgg.draw(), and as a result I am getting problems with code that
> used to update positions/size of legend and labels during on_draw.
>
> 1. Is there a new way to get the canvas to draw? or is this a bug?

The problem is that all drawing is now deferred until a paintEvent 
occurs.  draw() is using the update() method to queue the request for a 
paintEvent, where all actual drawing is done, consistent with what I 
understand to be the recommended mode of operation for QT, but maybe not 
with the way mpl operates; it has the effect of making draw() work like 
draw_idle().

It looks like what I should do is move the call to FigureCanvasAgg.draw 
back into the FigureCanvasQTAgg.draw method.  I'll give it a try.

Eric

>
> The "what's new in 1.1.0" page,
> http://matplotlib.sourceforge.net/users/whats_new.html refers to:
> "An rcParam entry, “backend.qt4”, has been added to allow users to select
> PyQt4, PyQt4v2, or PySide."
>
> 2. I cannot see any reference to PyQt4v2 in the code, and any attempt to set
> the rcParam to use it results in a param validation error, is this a mistake
> in the web page or omission in the code?
>
> Thanks in advance
> RuiDC

On Tue, Oct 18, 2011 at 11:19 AM, RuiDC <ru...@ya...> wrote:

>
>
> The "what's new in 1.1.0" page,
> http://matplotlib.sourceforge.net/users/whats_new.html refers to:
> "An rcParam entry, “backend.qt4”, has been added to allow users to select
> PyQt4, PyQt4v2, or PySide."
>
> 2. I cannot see any reference to PyQt4v2 in the code, and any attempt to
> set
> the rcParam to use it results in a param validation error, is this a
> mistake
> in the web page or omission in the code?
>
>
RuiDC,

I think that might have been a little unclear.  You should only need to
select 'PyQt4' or 'PySide'.  If PyQt4 is selected, then (I think) the v2 is
automatically tested for internally.

Ben Root

As of 1.1.0, FigureCanvasQTAgg.draw() now no longer calls
FigureCanvasAgg.draw(), and as a result I am getting problems with code that
used to update positions/size of legend and labels during on_draw.

1. Is there a new way to get the canvas to draw? or is this a bug?

The "what's new in 1.1.0" page,
http://matplotlib.sourceforge.net/users/whats_new.html refers to:
"An rcParam entry, “backend.qt4”, has been added to allow users to select
PyQt4, PyQt4v2, or PySide."

2. I cannot see any reference to PyQt4v2 in the code, and any attempt to set
the rcParam to use it results in a param validation error, is this a mistake
in the web page or omission in the code?

Thanks in advance
RuiDC
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As far as I know, the 'arrow' function is not recommended. The 'annotate'
function has a lot more features. Here's your code with the annotate
function:

import pylab
from scipy import optimize
import numpy
x1=numpy.arange(-4000,1000,0.1)
x2=numpy.arange(-1000,4000,0.1)
y1=100*numpy.square(x1+1500)
y2=100*numpy.square(x2-1500)-0.1e9
pylab.figure()
pylab.plot(x1,y1,x2,y2)
pylab.grid(True)
pylab.annotate('',(-3000,0),(-3000,-100000000),
        arrowprops=dict(arrowstyle='<->'))
pylab.xlim(-5000,5000)
pylab.ylim(-2e8,7e8)
pylab.show()

Hope that helps a little.

Ryan

On Mon, Oct 17, 2011 at 12:02 PM, Piter_ <x....@gm...> wrote:

> Hi all
> I want to draw an two headed arrow between two points.
> But I get a line. What I am doing wrong? I actually try to plot an
> image similar to this one:
>
> http://upload.wikimedia.org/wikipedia/commons/a/a3/Parameters_of_the_Marcus_Equation.JPG
> may be I can use an annotate function for this.
> Thanks for help.
> Petro.
> ########
> import pylab
> from scipy import optimize
> import numpy
> x1=numpy.arange(-4000,1000,0.1)
> x2=numpy.arange(-1000,4000,0.1)
> y1=100*numpy.square(x1+1500)
> y2=100*numpy.square(x2-1500)-0.1e9
> pylab.figure()
> pylab.plot(x1,y1,x2,y2)
> pylab.grid("True")
> pylab.arrow(-3000,0,0,-100000000,width=1)
> pylab.xlim(-5000,5000)
> pylab.ylim(-2e8,7e8)
> pylab.show()
> ###########x
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Thank you for the tip. I actually had played around with 
matplotlib.rcdefaults() before, but that didn't work. I tried now the 
using exactly the clear_state function you suggested. Since it still 
didn't work, I finally found out that I had a very similar problem with 
another module from which I determine axes, figure size and other 
things. So, thank you very much, that helped me a lot and now things 
work the way I want!

On Die 18 Okt 2011 04:45:27 CEST, John Hunter wrote:
> On Mon, Oct 17, 2011 at 2:57 PM, tinux <hof...@gm...> wrote:
>>
>> I have around 100 python files, that each create one figure using matplotlib.
>> Since I want to use all CPU cores, I basically did "for filename in files:
>> execfile(filename)" using a python script. However, this does not produce
>> the same output as running each file separately (for instance axes, figure
>> size are sometime wrong).
>> I _think_ I narrowed it down to this: In all files I need to do
>> "matplotlib.rcParams(update)". I guess that this influences the matplotlib
>> rc parameters and thus somehow values from some figures are used for others.
>>
>> So, my question is, how can I do something like
>> "matplotlib.rcParams(update)" so that it does not influence other scripts
>> that are run in parallel using 'execfile'? Or, how do I set rc parameters
>> for one specific script?
>>
>> BTW, I tried 'pp' and 'multiprocessing', same problem with both.
>
> The problem is that the rc params are module level in matplotlib so in
> a persistent process like ipython if one script modifies the rc
> params, subsequent files executed in the same process will be
> affected.  You can restore the rc params to their default state by
> doing before each call to execfile
>
>     import matplotlib
>     matplotlib.rc_file_defaults()
>
>
> We face the same issue in the "plot_directive" which we use when
> building the matplotlib documentation.  We define a function
> "clear_state" in
>
>   https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/sphinxext/plot_directive.py#L484
>
> which closes all open figures, restore the rc defaults, and the
> updates the defaults to an rc dictionary of the parameters we want for
> each run.

two lines:

ax.set_xlim(min(ax.get_xlim()+ax.get_ylim()),max(ax.get_xlim()+ax.get_ylim()))
ax.set_ylim(ax.get_xlim())

chao

2011/10/18 Chao YUE <cha...@gm...>

> Dear all,
>
> I am making a 1:1 ratio plot to compare data.
> I can write a small part of code to detect which range of the x or y axis
> is bigger and then adjust the axis of shorter range to have the same range
> with the longer one.
> and use set_aspect('equal') method to have the same tick interval on both
> axises.
> but is there an automatic method to do this job?
>
> Thanks,
>
> Chao
>
> --
>
> ***********************************************************************************
> Chao YUE
> Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
> UMR 1572 CEA-CNRS-UVSQ
> Batiment 712 - Pe 119
> 91191 GIF Sur YVETTE Cedex
> Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
>
> ************************************************************************************
>
>


-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

Dear all,

I am making a 1:1 ratio plot to compare data.
I can write a small part of code to detect which range of the x or y axis is
bigger and then adjust the axis of shorter range to have the same range with
the longer one.
and use set_aspect('equal') method to have the same tick interval on both
axises.
but is there an automatic method to do this job?

Thanks,

Chao

-- 
***********************************************************************************
Chao YUE
Laboratoire des Sciences du Climat et de l'Environnement (LSCE-IPSL)
UMR 1572 CEA-CNRS-UVSQ
Batiment 712 - Pe 119
91191 GIF Sur YVETTE Cedex
Tel: (33) 01 69 08 29 02; Fax:01.69.08.77.16
************************************************************************************

On Mon, Oct 17, 2011 at 10:42 PM, pratik <pra...@gm...> wrote:

> Is there a function that can draw an ellipsoid like matlab's ellipsoid
> function?
> relevant:
>
> http://stackoverflow.com/questions/2153768/draw-ellipse-and-ellipsoid-in-matlab
>
> Thanks,
>
>
from matplotlib.patches import Ellipse
import matplotlib.pyplot as plt

x = 0.5
y = 0.5
a = 4
b = 1
theta = 45.0
ell = Ellipse((x, y), a, b, theta)

ax = plt.gca()
ax.add_artist(ell)
plt.show()

There are some additional kwargs to the Ellipse constructor that allows you
to control color and such.

I hope that helps!
Ben Root

Is there a function that can draw an ellipsoid like matlab's ellipsoid
function?
relevant:
http://stackoverflow.com/questions/2153768/draw-ellipse-and-ellipsoid-in-matlab

Thanks,

On Mon, Oct 17, 2011 at 2:57 PM, tinux <hof...@gm...> wrote:
>
> I have around 100 python files, that each create one figure using matplotlib.
> Since I want to use all CPU cores, I basically did "for filename in files:
> execfile(filename)" using a python script. However, this does not produce
> the same output as running each file separately (for instance axes, figure
> size are sometime wrong).
> I _think_ I narrowed it down to this: In all files I need to do
> "matplotlib.rcParams(update)". I guess that this influences the matplotlib
> rc parameters and thus somehow values from some figures are used for others.
>
> So, my question is, how can I do something like
> "matplotlib.rcParams(update)" so that it does not influence other scripts
> that are run in parallel using 'execfile'? Or, how do I set rc parameters
> for one specific script?
>
> BTW, I tried 'pp' and 'multiprocessing', same problem with both.

The problem is that the rc params are module level in matplotlib so in
a persistent process like ipython if one script modifies the rc
params, subsequent files executed in the same process will be
affected.  You can restore the rc params to their default state by
doing before each call to execfile

    import matplotlib
    matplotlib.rc_file_defaults()


We face the same issue in the "plot_directive" which we use when
building the matplotlib documentation.  We define a function
"clear_state" in

  https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/sphinxext/plot_directive.py#L484

which closes all open figures, restore the rc defaults, and the
updates the defaults to an rc dictionary of the parameters we want for
each run.

On Mon, Oct 17, 2011 at 6:58 PM, Floyd John
<Joh...@en...> wrote:
> Hello,
>
> I have read your instruction for bug reporting but this is fairly simple.
>
> There is a call to self.get_cpp_triangulation() which exists but there is also a call to self._get_cpp_triangulation at line 174 to obtain the neighbours.
>
> Easy to fix.

Thanks for the report.  Even easy issues are best reported on the
issue tracker so they will be less likely to fall between the cracks,
we can tag them and assign developers to them, etc.

I've opened https://github.com/matplotlib/matplotlib/issues/535

JDH

Somehow, Figure.legend flattens the given handle list and this is the
cause of the problem.

https://github.com/matplotlib/matplotlib/blob/master/lib/matplotlib/figure.py#L994

Does anyone know why this is necessary?
I just filed a pull request to remove this.

https://github.com/matplotlib/matplotlib/pull/534/files

Meanwhile, you may do

from matplotlib.legend import Legend
l = Legend(fig, h, l, loc='lower right')
fig.legends.append(l)

This should be equivalent to fig.legend(h,l,loc='lower right').

Or, if you don't need axes legend, you may do

legend(h,l,loc='lower right', bbox_to_anchor=[0,0,1,1],
       bbox_transform=fig.transFigure)

Regards,

-JJ

On Tue, Oct 18, 2011 at 6:59 AM, Sterling Smith <sm...@fu...> wrote:
> Let me first say that I appreciate the work that the developers have put into matplotlib.  You're doing a great job.
>
> I have filed a bug report at
>
> https://github.com/matplotlib/matplotlib/issues/533
>
> wherein I post the following
>
> Consider:
>
> from pylab import *
> x = arange(0,1,.01)
> y = x**2
> fig = figure(2)
> ax = fig.add_subplot(111)
> errorbar(x,y,yerr=x/10.,label='$x^2$')
> errorbar(x,y**3,yerr=x/10.,label='$x^6$')
> legend(loc='upper center')
> h,l = ax.get_legend_handles_labels()
> fig.legend(h,l,loc='lower right')
>
>
> I am getting the right legend for the axes based legend, but the figure based legend seems to be using the different parts of the errorbar for subsequent handles, instead of using them as a group.  From what I can tell, this has appeared since the upgrade to version 1.1.0.
>
> I am running on Linux, python 2.7, gtkAgg backend.
>
> Thanks,
> Sterling
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Hello,

I have read your instruction for bug reporting but this is fairly simple.

There is a call to self.get_cpp_triangulation() which exists but there is also a call to self._get_cpp_triangulation at line 174 to obtain the neighbours. 

Easy to fix. 

Regards
John
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