[Matplotlib-users] Memory leak involving matplotlib in webapplication

2011-10-13 Thread Viktor Forsman
Hi,

I have problems with a memory leak in a webapplication involving matplotlib.
Basically, I have a function which usies the OO way of generating the graph,
printing it to a StringIO object and returning that. I've posted a question
with the details on stackoverflow (
http://stackoverflow.com/questions/7740832/need-help-identifying-a-memory-leak-involving-matplotlib-and-flask).
Any ideas are highly appreciated.
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[Matplotlib-users] Matplotlib 1.1.0 and PySide

2011-10-13 Thread Durrieu Jean-Louis
Dear all, matplotlib users and devs,

I have been trying the latest announced version of Matplotlib (1.1.0). The new 
feature that attracted me is the PySide support. 

However, I tried to install it under Ubuntu 11.04, but I needed pyqt4 installed 
in order to install it from source. Is there a way to install it with only 
pyside installed? 

Once installed, I could uninstall pyqt4, and run my python scripts, with 
replacing pyqt4 by pyside. However, I am not sure what the ETS environment 
variable is (yes, it s related to the enthought tool suite, but what if I do 
not want it - for now), and I had to set the QT_API variable on the command 
line call to python: setting it as a normal environment variable does not 
work. So, to be able to use only pyside, I need to do:

QT_API=pyside python myscript.py

Is that the right way to do so? Is there any way of setting the QT_API more 
definitely, and not having to change the call to python?

So far, my program (I really have only one at the moment) seems to work well, 
using QtCore, QtGui and phonon, except for phonon, where it seems that 
seeking in a file does not really work under Ubuntu... if anyone has an idea 
(I know, not the right mailing list, but just in case).

At last, probably a question that will solve all the above ones: when is the 
new Matplotlib version going to be included in EPD? That's, by the way, mainly 
the reason why I consider using PySide instead of PyQt4. 

Thanks for reading!

Cheers,

Jean-Louis
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Re: [Matplotlib-users] Memory leak involving matplotlib in webapplication

2011-10-13 Thread John Hunter
On Thu, Oct 13, 2011 at 12:42 AM, Viktor Forsman
viktor.fors...@gmail.com wrote:
 Hi,

 I have problems with a memory leak in a webapplication involving matplotlib.
 Basically, I have a function which usies the OO way of generating the graph,
 printing it to a StringIO object and returning that. I've posted a question
 with the details on stackoverflow
 (http://stackoverflow.com/questions/7740832/need-help-identifying-a-memory-leak-involving-matplotlib-and-flask).
 Any ideas are highly appreciated.

What version of matplotlib and numpy are you using?  Does it help to do:

import gc
gc.collect()

after a call to plot total or plot month?

Also, you appear to be adding data to plot_values and storing this
on every call.  Are you sure the leak is in mpl and not here?
JDH

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[Matplotlib-users] X Error since upgrade to 1.1.0

2011-10-13 Thread Neal Becker
Using interactively (via emacs/ipython), on closing a plot window I see:

 X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x5802e1b



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Re: [Matplotlib-users] X Error since upgrade to 1.1.0

2011-10-13 Thread John Hunter
On Thu, Oct 13, 2011 at 8:03 AM, Neal Becker ndbeck...@gmail.com wrote:
 Using interactively (via emacs/ipython), on closing a plot window I see:

  X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x5802e1b

Could you give us some more information.

What operating system?

Which matplotlib backend and GUI version?

What version of ipython?

What, exactly do you do to reproduce the problem?

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Re: [Matplotlib-users] X Error since upgrade to 1.1.0

2011-10-13 Thread Neal Becker
linux fedora 15 x86_64

backend : Qt4Agg

Now it's gone away, after killing the *Python* buffer and restarting the python 
process.  If it comes back I'll try to get more info.


John Hunter wrote:

 On Thu, Oct 13, 2011 at 8:03 AM, Neal Becker
 ndbeck...@gmail.com wrote:
 Using interactively (via emacs/ipython), on closing a plot window I see:

 X Error: BadWindow (invalid Window parameter) 3
 Major opcode: 20 (X_GetProperty)
 Resource id:  0x5802e1b
 
 Could you give us some more information.
 
 What operating system?
 
 Which matplotlib backend and GUI version?
 
 What version of ipython?
 
 What, exactly do you do to reproduce the problem?
 
 --
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 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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Re: [Matplotlib-users] X Error since upgrade to 1.1.0

2011-10-13 Thread Benjamin Root
On Thursday, October 13, 2011, Neal Becker ndbeck...@gmail.com wrote:
 Using interactively (via emacs/ipython), on closing a plot window I see:

  X Error: BadWindow (invalid Window parameter) 3
  Major opcode: 20 (X_GetProperty)
  Resource id:  0x5802e1b



Which backend/platform?

Ben Root
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Re: [Matplotlib-users] plotting two (x) axes for the same figure

2011-10-13 Thread Gökhan Sever
Hi,

Not directly answering your questions but the code below produces what you
are trying to achieve:

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid.parasite_axes import SubplotHost

plt.close('all')
fig1 = plt.figure(figsize=(11, 8.5))
ax1 = SubplotHost(fig1, 111)
fig1.add_subplot(ax1)

## define data
x = np.arange(1,11)
y = np.random.random(len(x))

# First X-axis
ax1.plot(x, y)
xmin, xmax = ax1.xaxis.get_view_interval()
ax1.xaxis.set_label_text(First X-axis)
ax1.yaxis.set_label_text(Sample data)

# Second X-axis
parx = ax1.twiny()
offset = 0, -60
new_axisline = parx.get_grid_helper().new_fixed_axis
parx.axis[bottom] = new_axisline(loc=bottom, axes=parx, offset=offset)
parx.axis[bottom].label.set_text(Second X-axis)
line1, = parx.plot((1./x), np.ones(len(x)))
line1.set_visible(0)
parx.set_xlim(xmin=xmax,xmax=xmin)
parx.axis[top].set_visible(False)

ax1.grid(1)
plt.tight_layout()
plt.show()


A few notes:

1-) axes is plural for axis. I always get confused with these words. Tricky
English :)

2-) This code uses the older AxisGrid toolkit functions, and not super
efficient since it makes an empty plot call with a different x-units.
However, using the same ideas and with some dedication you can create
multi-axes like the one shown here -
http://imageshack.us/photo/my-images/820/plot1r.png/

I had tried the newer AxisGrid approach as JJ suggested but I failed making
the plot look pretty. Plus sometimes using the AffineTransforms are not very
practical.

3-) I said empty plot call but it is actually where you convert your unit.
(np.ones call is another dummy call since the line is made invisible after
its call) To me it is more explicit than converting units via transforms. In
this example I just assume x as wavelength and convert it to wavenumber with
1/x. You need to adjust that call according to your unit conversion as well
as adjusting the limits of your newly scaled unit.

As usual JJ can give a more elegant solution for your question, but
sometimes practicality beats purity and you engineer your own solution.

On Wed, Oct 12, 2011 at 11:36 PM, List Comprehension 
listcomprehens...@gmail.com wrote:


 Hello, I am interested in plotting two (x) axes for the same figure (one of
 is just showing linearly transformed values of the other); one of them
 offset from the plot if possible. For instance, I have the following code:

 import numpy as np
 import matplotlib.pyplot as plt
 import mpl_toolkits.axisartist as AA

 ## define data
 x = np.array(range(11))
 xlab = x*2
 y = np.random.random(len(x))

 fig = plt.figure()
 ## first axes which is only for drawing the axis
 axsecond = AA.Subplot(fig, 1,1,1)
 fig.add_subplot(axsecond)
 axsecond.set_xlim([min(xlab),max(xlab)])
 axsecond.set_xticks(np.linspace(min(xlab),max(xlab),5))
 axsecond.axis[bottom, top, left, right].set_visible(False)
 axsecond.axis[newx] = axsecond.new_floating_axis(nth_coord=0, value=1)
 axsecond.axis[newx].set_axis_direction(top)
 axsecond.set_clip_on(False)
 axsecond.axis[newx].toggle(all=True)
 axsecond.axis[newx].set_visible(True)
 plt.draw()
 ## the main set of axes containing the data
 axmain = fig.add_subplot(1,1,1)
 plt.plot(x,y)


 In this example I wonder

 1) How to turn off the top axis of axmain so the ticks from axsecond are
 visible? Something like axmain[top].set_visible(False) (which does not
 work of course).

 2) If I wanted to include an offset (below the main axis), I feel like
 something like the following should work but doesn't:

 ax.axis[newx] = ax.new_floating_axis(nth_coord=0, value=-0.2) ## outside
 of (0,1)
 ax.axis[newx].set_axis_direction(bottom)
 ax.set_clip_on(False)

 Thanks in advance!




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Re: [Matplotlib-users] Memory leak involving matplotlib in webapplication

2011-10-13 Thread Viktor Forsman
I use matplotlib 1.1 and numpy 1.5.0

gc.collect() after the function call solved the problem! Thanks alot!

Den torsdagen den 13:e oktober 2011 skrev John Hunterjdh2...@gmail.com:
 On Thu, Oct 13, 2011 at 12:42 AM, Viktor Forsman
 viktor.fors...@gmail.com wrote:
 Hi,

 I have problems with a memory leak in a webapplication involving
matplotlib.
 Basically, I have a function which usies the OO way of generating the
graph,
 printing it to a StringIO object and returning that. I've posted a
question
 with the details on stackoverflow
 (
http://stackoverflow.com/questions/7740832/need-help-identifying-a-memory-leak-involving-matplotlib-and-flask
).
 Any ideas are highly appreciated.

 What version of matplotlib and numpy are you using?  Does it help to do:

import gc
gc.collect()

 after a call to plot total or plot month?

 Also, you appear to be adding data to plot_values and storing this
 on every call.  Are you sure the leak is in mpl and not here?
 JDH

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Re: [Matplotlib-users] Matplotlib 1.1.0 and PySide

2011-10-13 Thread Fernando Perez
Hi Jean-Louis,

On Thu, Oct 13, 2011 at 1:47 AM, Durrieu Jean-Louis
jean-louis.durr...@epfl.ch wrote:

 Is that the right way to do so? Is there any way of setting the QT_API more 
 definitely, and not having to change the call to python?


Yes, in your $HOME/.bashrc file that your shell loads at startup time,
you can write

export QT_API=pyside

And this will ensure that you always have this variable set as part of
your 'environment'.  The concept of 'environment' is a unix-specific
idea of a set of variables and other parameters visible to any
program; you can actually read and write the enviroment in python by
importing 'os' and using the os.environ variable:

$ export SOMEVAR=Hello matplotlib
$ ipython --no-banner

In [1]: import os

In [2]: os.environ['SOMEVAR']
Out[2]: 'Hello matplotlib'

Cheers,

f

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Re: [Matplotlib-users] Matplotlib 1.1.0 and PySide

2011-10-13 Thread Eric Firing
On 10/12/2011 10:47 PM, Durrieu Jean-Louis wrote:
 Dear all, matplotlib users and devs,

 I have been trying the latest announced version of Matplotlib
 (1.1.0). The new feature that attracted me is the PySide support.

 However, I tried to install it under Ubuntu 11.04, but I needed pyqt4
 installed in order to install it from source. Is there a way to
 install it with only pyside installed?

There is no compiled qt4 code, so installation should not require 
pyqt4--and I don't think it does.  What led to your conclusion that you 
needed it to install from source?

In any case, I opened
https://github.com/matplotlib/matplotlib/issues/521 for this.


 Once installed, I could uninstall pyqt4, and run my python scripts,
 with replacing pyqt4 by pyside. However, I am not sure what the ETS
 environment variable is (yes, it s related to the enthought tool
 suite, but what if I do not want it - for now), and I had to set the
 QT_API variable on the command line call to python: setting it as a
 normal environment variable does not work. So, to be able to use
 only pyside, I need to do:

 QT_API=pyside python myscript.py

 Is that the right way to do so? Is there any way of setting the
 QT_API more definitely, and not having to change the call to
 python?

This does not make sense to me.  Assuming you are using bash, put this 
in your .bashrc file:

export QT_API=pyside

Anything you execute in a terminal window opened after that change 
should find the new environment variable.

Eric


 So far, my program (I really have only one at the moment) seems to
 work well, using QtCore, QtGui and phonon, except for phonon, where
 it seems that seeking in a file does not really work under
 Ubuntu... if anyone has an idea (I know, not the right mailing list,
 but just in case).

 At last, probably a question that will solve all the above ones: when
 is the new Matplotlib version going to be included in EPD? That's, by
 the way, mainly the reason why I consider using PySide instead of
 PyQt4.

 Thanks for reading!

 Cheers,

 Jean-Louis

--
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Re: [Matplotlib-users] Matplotlib 1.1.0 and PySide

2011-10-13 Thread Durrieu Jean-Louis
Hi Eric, Fernando,

thanks for your answers!

On Oct 13, 2011, at 8:47 PM, Eric Firing wrote:

 On 10/12/2011 10:47 PM, Durrieu Jean-Louis wrote:
 
 There is no compiled qt4 code, so installation should not require 
 pyqt4--and I don't think it does.  What led to your conclusion that you 
 needed it to install from source?
 

It s just that when I type python setup.py build/--help/install, depending on 
whether pyqt4 is installed or not, the script detects that Qt is present or not 
(respectively), and pyside does not change that behaviour. I must admit I did 
not try to run my script even when Qt was not detected, maybe it works... But I 
guess there is a consequence to the detection of Qt at the build step?

Sorry for not providing the exact output of the build step, I m on another 
computer. On my mac, the section of interest is:
OPTIONAL BACKEND DEPENDENCIES
libpng: 1.5.2
   Tkinter: Tkinter: version not identified, Tk: 8.5, Tcl: 8.5
  Gtk+: no
* Building for Gtk+ requires pygtk; you must be able
* to import gtk in your build/install environment
   Mac OS X native: yes
Qt: no
   Qt4: Qt: 4.7.3, PyQt4: 4.8.5
 Cairo: no

Here, it detected my pyqt4. But when it s not there, even if pyside is 
installed, I get a Qt4: no instead... Do you mean that it's still going to 
work, even it was not detected there?

 This does not make sense to me.  Assuming you are using bash, put this 
 in your .bashrc file:
 
 export QT_API=pyside
 
 Anything you execute in a terminal window opened after that change 
 should find the new environment variable.
 

Oh, sorry for that! I must have been confused, I think I only typed 
QT_API=pyside at the prompt, so I guess without the export (doh!), that was 
useless... Since the doc (somewhere) talked about ETS environment variables, 
I thought there was something else to it. If not, then I ll have to learn my 
bash again :-)

Not a big issue, anyway!

Cheers! 

Jean-Louis
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Re: [Matplotlib-users] Matplotlib 1.1.0 and PySide

2011-10-13 Thread Eric Firing
On 10/13/2011 09:50 AM, Durrieu Jean-Louis wrote:
 Hi Eric, Fernando,

 thanks for your answers!

 On Oct 13, 2011, at 8:47 PM, Eric Firing wrote:

 On 10/12/2011 10:47 PM, Durrieu Jean-Louis wrote:

 There is no compiled qt4 code, so installation should not require
 pyqt4--and I don't think it does.  What led to your conclusion that
 you needed it to install from source?


 It s just that when I type python setup.py build/--help/install,
 depending on whether pyqt4 is installed or not, the script detects
 that Qt is present or not (respectively), and pyside does not change
 that behaviour. I must admit I did not try to run my script even when
 Qt was not detected, maybe it works... But I guess there is a
 consequence to the detection of Qt at the build step?

 Sorry for not providing the exact output of the build step, I m on
 another computer. On my mac, the section of interest is: OPTIONAL
 BACKEND DEPENDENCIES libpng: 1.5.2 Tkinter: Tkinter: version not
 identified, Tk: 8.5, Tcl: 8.5 Gtk+: no * Building for Gtk+ requires
 pygtk; you must be able * to import gtk in your build/install
 environment Mac OS X native: yes Qt: no Qt4: Qt: 4.7.3, PyQt4: 4.8.5
 Cairo: no

 Here, it detected my pyqt4. But when it s not there, even if pyside
 is installed, I get a Qt4: no instead... Do you mean that it's
 still going to work, even it was not detected there?

Yes, it should work fine; as far as I know, nothing depends on the 
outcome of that auto-detection for qt4. The pyside support is always 
included in backend_qt4.py and backend_qt4agg.py, which are pure python, 
and are present regardless of whether pyqt4 itself is detected.

Eric


 This does not make sense to me.  Assuming you are using bash, put
 this in your .bashrc file:

 export QT_API=pyside

 Anything you execute in a terminal window opened after that change
 should find the new environment variable.


 Oh, sorry for that! I must have been confused, I think I only typed
 QT_API=pyside at the prompt, so I guess without the export
 (doh!), that was useless... Since the doc (somewhere) talked about
 ETS environment variables, I thought there was something else to
 it. If not, then I ll have to learn my bash again :-)

 Not a big issue, anyway!

 Cheers!

 Jean-Louis
 --


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 definitive record of customers, application performance, security
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 makes sense of it. Business sense. IT sense. Common sense.
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 mailing list Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


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Re: [Matplotlib-users] plot arrows for wind direction (degrees)

2011-10-13 Thread questions anon
Another quick question,
I noticed that the wind direction appeared back-to-front so I have added a
negative  to my equation as I am in the southern hemisphere. It now looks
correct but I wanted to check if this is the right way to do this? I saw
something called 'flip' for barb but nothing for quiver.
Thanks, see code below

   map = Basemap(projection='merc',llcrnrlat=-40,urcrnrlat=-33,

llcrnrlon=139.0,urcrnrlon=151.0,lat_ts=0,resolution='i')

x,y=map(*N.meshgrid(LON,LAT))
u=-1*N.sin(WDIR*N.pi/180)# added negative to account for
southern hemisphere
v=-1*N.cos(WDIR*N.pi/180)
map.quiver(x,y,u, v)



On Wed, Oct 5, 2011 at 3:20 PM, questions anon questions.a...@gmail.comwrote:

 thank you! of course!


 On Wed, Oct 5, 2011 at 3:08 PM, Eric Firing efir...@hawaii.edu wrote:

 On 10/04/2011 05:40 PM, questions anon wrote:
  Excellent, thank you. That works for both quiver and barb.
  In regards to the shape that has to do with the netcdf file, wind
  direction variable also has lat and lon. I ended up needing to slice so
  I could skip a few points otherwise there was too many arrows on the
 map.
  Below is the code that worked in case someone else needs help.

 Are you sure it worked correctly?  I don't think so.  See below.

  Thanks again
 
  from netCDF4 import Dataset
  import numpy as N
  import pylab as plt
  from numpy import ma as MA
  from mpl_toolkits.basemap import Basemap
  import os
 
  ncfile=Dataset('E:/temp_winddir/IDZ00026_VIC_ADFD_Wind_Dir_SFC.nc',
  'r+', 'NETCDF4')
  WDIR=ncfile.variables['Wind_Dir_SFC'][20,0::5,0::5]

 Don't you need to convert from degrees to radians?  sin and cos (used
 below) expect radians, not degrees.  You can use N.deg2rad(WDIR) to
 convert.

  LAT=ncfile.variables['latitude'][0::5]
  LON=ncfile.variables['longitude'][0::5]
  TIME=ncfile.variables['time'][20]
  ncfile.close()
 
  map = Basemap(projection='merc',llcrnrlat=-40,urcrnrlat=-33,
 llcrnrlon=139.0,urcrnrlon=151.0,lat_ts=0,resolution='i')
  x,y=map(*N.meshgrid(LON,LAT))
  u=1*N.sin(WDIR)
  v=1*N.cos(WDIR)
  map.quiver(x,y,u, v)

 Assuming you do convert to radians the above will work for your mercator
 projection but it will not align the vectors correctly with respect to
 the parallels and meridians for other projections, so you should use
 map.rotate_vector as in the basemap quiver demo.

 Eric


 
  #  otherwise use the barb tool - map.barbs(x,y,u, v)
 
  plt.title('Wind Direction')
  plt.show()


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Re: [Matplotlib-users] plot arrows for wind direction (degrees)

2011-10-13 Thread Benjamin Root
On Thursday, October 13, 2011, questions anon questions.a...@gmail.com
wrote:
 Another quick question,
 I noticed that the wind direction appeared back-to-front so I have added a
negative  to my equation as I am in the southern hemisphere. It now looks
correct but I wanted to check if this is the right way to do this? I saw
something called 'flip' for barb but nothing for quiver.

It probably nothing to do with southern hemisphere but rather that it is
typical for wind data to be recorded and displayed as direction from,
instead of direction to.  If you think flip should be available for
quiver(), file a feature request.

Ben Root
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Re: [Matplotlib-users] plot arrows for wind direction (degrees)

2011-10-13 Thread Eric Firing
On 10/13/2011 12:22 PM, Benjamin Root wrote:


 On Thursday, October 13, 2011, questions anon questions.a...@gmail.com
 mailto:questions.a...@gmail.com wrote:
   Another quick question,
   I noticed that the wind direction appeared back-to-front so I have
 added a negative  to my equation as I am in the southern hemisphere. It
 now looks correct but I wanted to check if this is the right way to do
 this? I saw something called 'flip' for barb but nothing for quiver.

 It probably nothing to do with southern hemisphere but rather that it is
 typical for wind data to be recorded and displayed as direction from,
 instead of direction to.  If you think flip should be available for
 quiver(), file a feature request.

It looks to me like the barb flip is for something else entirely--it 
is a right-hand versus left-hand sort of flip.  This would be 
inappropriate for quiver, which makes symmetric arrows.  I would 
strongly oppose any proposal for a kwarg to reverse the direction of the 
arrows.

Eric



 Ben Root


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[Matplotlib-users] key_press_event weirdness

2011-10-13 Thread Jorge Scandaliaris
Hi,

I am experiencing something a bit strange with 'key_press_event': The event is
not detected unless I click with the mouse on the canvas (The grey area around
the axis). I verified this with my own code as well as with some unmodified
example (
http://matplotlib.sourceforge.net/examples/event_handling/keypress_demo.html?highlight=key_press_event
).
I built mpl from a recent revision (a few days old).

Does anyone else experience this? Is this the expected behavior? I believe it
was enough to have the figure window focused to get key events before, but I
haven't used this feature for some time.

Thanks,

Jorges


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Re: [Matplotlib-users] key_press_event weirdness

2011-10-13 Thread Benjamin Root
On Thu, Oct 13, 2011 at 9:52 PM, Jorge Scandaliaris
jorgesmbox...@yahoo.eswrote:

 Hi,

 I am experiencing something a bit strange with 'key_press_event': The event
 is
 not detected unless I click with the mouse on the canvas (The grey area
 around
 the axis). I verified this with my own code as well as with some unmodified
 example (

 http://matplotlib.sourceforge.net/examples/event_handling/keypress_demo.html?highlight=key_press_event
 ).
 I built mpl from a recent revision (a few days old).

 Does anyone else experience this? Is this the expected behavior? I believe
 it
 was enough to have the figure window focused to get key events before, but
 I
 haven't used this feature for some time.

 Thanks,

 Jorges


Which backend and platform are you using?

Ben Root
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