matplotlib-users Mailing List for matplotlib

On Fri, Nov 14, 2008 at 5:20 PM, Gael Varoquaux
<gae...@no...> wrote:
> On Fri, Nov 14, 2008 at 11:12:14AM -0800, Benjamin J. Racine wrote:
>>    I use pause in matlab to cycle through an interactive do-loop and view a
>>    bunch of plots in interactively...
>
>>    Don't bother reproducing it here, but I am just wondering if this is
>>    possible in ipython/matplotlib
>
> pylab.waitforbuttonpress will do what you want.
>
> Gaël
>


waitforbuttonpress immediately returns for any keyboard or mouse event
(from the gui canvas).
If you want to examine the plot (pan, zoom, etc) with mouse, a quick
solution would be to use a loop

while not waitforbuttonpress():
    pass

The loop stops only for a key press.
Also, take a look at ginput().

-JJ

On Fri, Nov 14, 2008 at 11:12:14AM -0800, Benjamin J. Racine wrote:
>    I use pause in matlab to cycle through an interactive do-loop and view a
>    bunch of plots in interactively...

>    Don't bother reproducing it here, but I am just wondering if this is
>    possible in ipython/matplotlib

pylab.waitforbuttonpress will do what you want.

Gaël

I've had the same problem.  You can write a pause function using the
python input() function but it hangs the GIL and as a result your
window becomes unresponsive.  If anyone knows a GIL friendly way to
pause i would also be very interested.


On Fri, Nov 14, 2008 at 1:12 PM, Benjamin J. Racine
<bjr...@gl...> wrote:
> I use pause in matlab to cycle through an interactive do-loop and view a
> bunch of plots in interactively...
>
> Don't bother reproducing it here, but I am just wondering if this is
> possible in ipython/matplotlib
>
> Many thanks,
>
> Ben Racine
> _______________________________________________
> IPython-user mailing list
> IPy...@sc...
> http://lists.ipython.scipy.org/mailman/listinfo/ipython-user
>
>

I'm not at the bottom of this yet, but thought I'd share my progress so 
far -->

It is leaking actual Python references (meaning len(gc.get_objects()) is 
increasing).  So it's not a malloc/free pair.

Seems to be Gtk-specific.  (Both GtkAgg and Gtk).  Other backends are 
unaffected (Qt4 has some sort of leak of a much smaller magnitude).

The proper way to destroy pygtk objects appears to be a little bit of a 
black art.  What's there now was pretty much arrived at by 
experimentation and seems very brittle.

I know at one point it was working better than it is now.  My next step 
will be to try to revert to a state where the leak wasn't so bad.  Given 
the architecture of pygtk, I'm not sure it's possible to not leak at all 
when creating/destroying windows like this, but we should at least be 
able to reduce the leakage.

If your use case is just generating a bunch of images in batch, I'd 
recommend using the Agg backend, rather than Gtk.  That doesn't leak for 
me.  If you really need to be opening and closing this many windows in 
succession, then we still don't have a good solution.

Mike

Michael Droettboom wrote:
> Ok.  Thanks, I'll look into it.  Just wanted to rule out that this 
> wasn't the known Gtk memory leak with old versions of Gtk before 
> devoting time to it.
>
> Cheers,
> Mike
>
> Eric Firing wrote:
>   
>> Michael Droettboom wrote:
>>     
>>> Can you provide more information about the platform and backend that 
>>> you are using?
>>>       
>> Mike,
>>
>> I was able to reproduce this with my ubuntu 8.10, gtkagg backend.  I 
>> ran  the code via cut and paste with the stock python interpreter, not 
>> ipython.  I did not measure the memory use carefully, but used the 
>> system monitor to observe memory for that process climbing, maybe 500k 
>> per cycle.
>>
>> Our usual memleak tester shows no problem, however.
>>
>> Eric
>>
>>     
>>> D2Hitman wrote:
>>>       
>>>> I am getting a memory leak when i am using the pylab.close() 
>>>> function. I am
>>>> running matplotlib-0.98.3. It happens in a very simple script such as:
>>>>
>>>> #!/usr/bin/python
>>>> import time
>>>> import pylab
>>>>
>>>> while True:
>>>>     time.sleep(1)
>>>>     print 'calling pylab'
>>>>     pylab.box()
>>>>     pylab.close()
>>>>
>>>> Every close seems to store megabytes in physical memory. Any idea 
>>>> why this
>>>> happens?
>>>>
>>>> Cheers.
>>>>
>>>>
>>>>   
>>>>         
>
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

I use pause in matlab to cycle through an interactive do-loop and view a bunch of plots in interactively...

Don't bother reproducing it here, but I am just wondering if this is possible in ipython/matplotlib

Many thanks,

Ben Racine

openSUSE 11.0 (x86_64) KDE 3.5.9 "release 49.1" with GTKAgg backend


Michael Droettboom-3 wrote:
> 
> Can you provide more information about the platform and backend that you 
> are using?
> 
> D2Hitman wrote:
>> I am getting a memory leak when i am using the pylab.close() function. I
>> am
>> running matplotlib-0.98.3. It happens in a very simple script such as:
>>
>> #!/usr/bin/python
>> import time
>> import pylab
>>
>> while True:
>>     time.sleep(1)
>>     print 'calling pylab'
>>     pylab.box()
>>     pylab.close()
>>
>> Every close seems to store megabytes in physical memory. Any idea why
>> this
>> happens?
>>
>> Cheers.
>>
>>
>>   
> 
> -- 
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
> 
> 
> -------------------------------------------------------------------------
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Ok.  Thanks, I'll look into it.  Just wanted to rule out that this 
wasn't the known Gtk memory leak with old versions of Gtk before 
devoting time to it.

Cheers,
Mike

Eric Firing wrote:
> Michael Droettboom wrote:
>> Can you provide more information about the platform and backend that 
>> you are using?
>
> Mike,
>
> I was able to reproduce this with my ubuntu 8.10, gtkagg backend.  I 
> ran  the code via cut and paste with the stock python interpreter, not 
> ipython.  I did not measure the memory use carefully, but used the 
> system monitor to observe memory for that process climbing, maybe 500k 
> per cycle.
>
> Our usual memleak tester shows no problem, however.
>
> Eric
>
>>
>> D2Hitman wrote:
>>> I am getting a memory leak when i am using the pylab.close() 
>>> function. I am
>>> running matplotlib-0.98.3. It happens in a very simple script such as:
>>>
>>> #!/usr/bin/python
>>> import time
>>> import pylab
>>>
>>> while True:
>>>     time.sleep(1)
>>>     print 'calling pylab'
>>>     pylab.box()
>>>     pylab.close()
>>>
>>> Every close seems to store megabytes in physical memory. Any idea 
>>> why this
>>> happens?
>>>
>>> Cheers.
>>>
>>>
>>>   
>>
>

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Michael Droettboom wrote:
> Can you provide more information about the platform and backend that you 
> are using?

Mike,

I was able to reproduce this with my ubuntu 8.10, gtkagg backend.  I ran 
  the code via cut and paste with the stock python interpreter, not 
ipython.  I did not measure the memory use carefully, but used the 
system monitor to observe memory for that process climbing, maybe 500k 
per cycle.

Our usual memleak tester shows no problem, however.

Eric

> 
> D2Hitman wrote:
>> I am getting a memory leak when i am using the pylab.close() function. I am
>> running matplotlib-0.98.3. It happens in a very simple script such as:
>>
>> #!/usr/bin/python
>> import time
>> import pylab
>>
>> while True:
>>     time.sleep(1)
>>     print 'calling pylab'
>>     pylab.box()
>>     pylab.close()
>>
>> Every close seems to store megabytes in physical memory. Any idea why this
>> happens?
>>
>> Cheers.
>>
>>
>>   
> 

>> Hi all,
>>
>> I'm having problems with axis labels for large integers (1471674   
>> is  represented as 1000 +1.479e6) .... I really need to see the  
>> number as  a conventional integer. I have the feeling that it  
>> should be possible  with ticker. FormatStrFormatter but I have not  
>> been able to work out  how. Any advice would be greatly appreciated.
>>
> Assuming 'ax' is your current set of axes (obtained from gca() or a  
> call to subplot(), for example)...
>  from matplotlib import ticker
>  ...
>
>  ax.xaxis.set_major_formatter(ticker.FormatStrFormatter("%d"))
>  ax.yaxis.set_major_formatter(ticker.FormatStrFormatter("%d"))
>> While I'm asking stupid questions, I'd also like to know how to  
>> let  the absolute dimensions of a subplot (with a barh()  
>> horizontal bar  chart) adjust themselves according to the number  
>> of bars added  (keeping the height of the bars strictly constant  
>> rather than the bar  height adjusting according to the number of  
>> data points).
>>

Fantastic .... I knew this should be easy


>>
> There's no direct way to do this, but by setting the figure size  
> based on the number of bars, you should be able to fake it.  You  
> can set the overall figure size either when you create the figure:
>
>  figure(figsize=(4,3))
>
> or after the fact (which doesn't really work with interactive GUIs  
> -- that is, it won't resize the window) --
>
>  gcf().set_size_inches((4, 3))
>
> The unit is in inches -- the dpi of the figure can also be set in a  
> similar way.
>

Hmm, the thing is that I'm using a barh() subplot underneath a series  
of bar() subplots. The bar() subplots always have the same y axes,  
but the number of items in the barh() subplot varies (I use the barh 
() to illustrate features along a stretch of genomic DNA which also  
has quantitative values attached to it in the bar() plots above). I  
need to make a series of figures in this way wherein the bar()  
subplots always have the same dimension, but only the "height" of the  
barh() subplot varies (with the number of instances to plot) while  
the Y axes ALL need to remain the same.

Can I size the whole figure with the above and fix the dimensions of  
each of the subplots independently? If so I should be able to bodge it!

I'm pretty new to matplotlib and not really an expert programmer in  
any case. While I'm very pleased with the quality of the figures, I'm  
really struggling with ironing out a few maddening glitches.

Thanks again.

D




> Hope that at least helps,
> Mike
>> Many thanks
>>
>> David
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.Net email is sponsored by the Moblin Your Move Developer's  
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in  
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
> -- 
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>

Michael Droettboom wrote:
> or after the fact (which doesn't really work with interactive GUIs -- 
> that is, it won't resize the window) --
>   
>
I'll correct myself on this point.  According to the docs, the window 
will resize if forward=True for Gtk and Wx backends.

Cheers,
Mike

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

DAVID HORNER wrote:
> Hi all,
>
> I'm having problems with axis labels for large integers (1471674  is  
> represented as 1000 +1.479e6) .... I really need to see the number as  
> a conventional integer. I have the feeling that it should be possible  
> with ticker. FormatStrFormatter but I have not been able to work out  
> how. Any advice would be greatly appreciated.
>   
Assuming 'ax' is your current set of axes (obtained from gca() or a call 
to subplot(), for example)...
 
  from matplotlib import ticker
  ...

  ax.xaxis.set_major_formatter(ticker.FormatStrFormatter("%d"))
  ax.yaxis.set_major_formatter(ticker.FormatStrFormatter("%d"))
> While I'm asking stupid questions, I'd also like to know how to let  
> the absolute dimensions of a subplot (with a barh() horizontal bar  
> chart) adjust themselves according to the number of bars added  
> (keeping the height of the bars strictly constant rather than the bar  
> height adjusting according to the number of data points).
>   
There's no direct way to do this, but by setting the figure size based 
on the number of bars, you should be able to fake it.  You can set the 
overall figure size either when you create the figure:

  figure(figsize=(4,3))

or after the fact (which doesn't really work with interactive GUIs -- 
that is, it won't resize the window) --

  gcf().set_size_inches((4, 3))

The unit is in inches -- the dpi of the figure can also be set in a 
similar way.

Hope that at least helps,
Mike
> Many thanks
>
> David
>
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Can you provide more information about the platform and backend that you 
are using?

D2Hitman wrote:
> I am getting a memory leak when i am using the pylab.close() function. I am
> running matplotlib-0.98.3. It happens in a very simple script such as:
>
> #!/usr/bin/python
> import time
> import pylab
>
> while True:
>     time.sleep(1)
>     print 'calling pylab'
>     pylab.box()
>     pylab.close()
>
> Every close seems to store megabytes in physical memory. Any idea why this
> happens?
>
> Cheers.
>
>
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hi all,

I'm having problems with axis labels for large integers (1471674  is  
represented as 1000 +1.479e6) .... I really need to see the number as  
a conventional integer. I have the feeling that it should be possible  
with ticker. FormatStrFormatter but I have not been able to work out  
how. Any advice would be greatly appreciated.

While I'm asking stupid questions, I'd also like to know how to let  
the absolute dimensions of a subplot (with a barh() horizontal bar  
chart) adjust themselves according to the number of bars added  
(keeping the height of the bars strictly constant rather than the bar  
height adjusting according to the number of data points).

Many thanks

David

Hello, using matplotlib 0.98 with mpl_toolkit Basemap:

I'm trying to create a plot with a series of ellipses over a map. I've
followed the tutorial, and can create the same figure as shown here:
http://matplotlib.sourceforge.net/users/screenshots.html#ellipses

I can also create a series of ellipses over a map.

Now I am trying to label each circle using the following snippet:
for item in ells:
    #ells is now a tuple in the form: (Ellipse, (x,y)) and (x,y) is the same
as for the Ellipse
     e = item[0]
     xy = item[1]
     ax.add_artist(e)
     e.set_clip_box(ax.bbox)
     e.set_alpha(.7)
     pyplot.text(xy[0],xy[1],e.get_label())

however, for some reason it fails. Can someone provide some ideas on what I
am doing wrong? Also, is there more direct way to set the plots so that the
labels are drawn?

What is strange, is that it seems to work (at least debugging print
statements after the loop are printed)... and I can move the text function
out of the loop to label the 'last' ellipse...

As it is it fails when savefig() or show() are called. The error is:
TypeError: CXX : Error creating object of type N2Py3IntE

THoughts?

Thanks,
john

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