matplotlib-devel Mailing List for matplotlib

John Hunter wrote:
>>>>>>"Fernando" == Fernando Perez <Fer...@co...> writes:
> 
> 
>     Fernando> Finally, is this really a close bug?
> 
>     Fernando> In [20]: fig=plot(range(10))
> 
>     Fernando> In [21]: close(fig) ERROR: Unrecognized argument type to
>     Fernando> close
> 
> No, its a Fernando bug :-)
> 
> plot returns a list of Line2D instances.  Perhaps you mean
> 
>     fig = figure()
>     plot(range(10))
>     close(fig)

No, it's a John bug :)  I also had tried that, and this is what I get with TkAgg:

In [4]: fig=figure()

In [5]: plot(range(10))
Out[5]: [<matplotlib.lines.Line2D instance at 0x4110494c>]

In [6]: close(fig)
---------------------------------------------------------------------------
exceptions.AttributeError                            Traceback (most recent 
call last)

/home/fperez/code/python/pylab/<console>

/usr/lib/python2.3/site-packages/matplotlib/pylab.py in close(*args)
     611         elif isinstance(arg, Figure):
     612             for manager in _pylab_helpers.Gcf.get_all_fig_managers():
--> 613                 if manager.figure==arg:
     614                     _pylab_helpers.Gcf.destroy(manager.num)
     615         else:

AttributeError: FigureManagerTkAgg instance has no attribute 'figure'

Which is why I thought it might be the other way around.  So this may be a 
backend-specifig bug.

But still a bug :)

Cheers,

f

>>>>> "Fernando" == Fernando Perez <Fer...@co...> writes:

    Fernando> Finally, is this really a close bug?

    Fernando> In [20]: fig=plot(range(10))

    Fernando> In [21]: close(fig) ERROR: Unrecognized argument type to
    Fernando> close

No, its a Fernando bug :-)

plot returns a list of Line2D instances.  Perhaps you mean

    fig = figure()
    plot(range(10))
    close(fig)

It's OK, you can stop hitting yourself on the head now.  Actually, the
error message would have been more helpful if it reported the type,
which it will do in the next release.

JDH

John Hunter wrote:

>And your figure num patch is already in....

Atop the docstring:

     figure(num = 1, figsize=(8, 6), dpi=80, facecolor='w', edgecolor='k')

should read

     figure(num = None, figsize=(8, 6), dpi=80, facecolor='w', edgecolor='k')

since that is the real new default.

Cheers,

f

John Hunter wrote:
>>>>>>"Fernando" == Fernando Perez <Fer...@co...> writes:
> 
> 
>     Fernando> You have to carefully wire reload() calls into the
>     Fernando> proper backends.  It's doable, but doing it generically
>     Fernando> and with all the complex mpl backend machinery would
>     Fernando> likely take a bit of effort.
> 
> I have something in CVS that appears to work.  You can interactively
> switch backends in the pylab interface.  The caveat is that you lose
> all current figures when doing the switch (close('all') is called).
> With some work I could probably patch the current figure manager to
> work with multiple simultaneous backends but have no real interest in
> doing this now.  But it could serve as a basis for an ipython patch
> that allowed you to run as ps, eg something like the following
> 
> 
> def runps(fname):
> 
>     curr = pylab.rcParams['backend']
>     pylab.switch_backend('PS')
>     reload(pylab)
>     run(fname)
>     pylab.switch_backend(curr)
>     reload(pylab)
>        
> 
> or modify "run" to take a kwarg for the backend.

Modifying run is defitely easy.  How would you like to have this done?

run -backend=BACKEND foo.py

?

I can't use '-d' because that's already used by %run for something else.  Or 
we can have a different run altogether

runb BACKEND foo.py

which would be specific to backend switching, modeled on your runps() above.

Please note that I'll only add this if you really see it as an issue, I 
brought it up mostly for discussion, because I'm just getting my bearings 
around mpl.  If you feel it's best to leave things as they are, I'll go along.

>     Fernando> But for now, I'd rather see the tk close bug fixed and
>     Fernando> the figure() improvements I referred to in my other mail
>     Fernando> ;)
> 
> Well, the tk close bug should be a non-issue with CVS matplotlib.
> Just make sure you use the rc param (which is the default in CVS)
> 
> tk.pythoninspect  : False    # tk sets PYTHONINSEPCT

Sorry, but no.  I just updated CVS (and I did get my new patch, so it seems to 
be pretty up to date), set this variable in my .matplolibrc, and I still get this:


In [1]: run tkbug.py
*** I'm about to close figure 1, this will crash VTK!!! ***

Generic Warning: In 
/usr/local/installers/src/vtk/VTK/Rendering/vtkTkRenderWidget.cxx, line 633
A TkRenderWidget is being destroyed before it associated vtkRenderWindow is 
destroyed. This is very bad and usually due to the order in which objects are 
being destroyed. Always destroy the vtkRenderWindow before destroying the user 
interface components.

So the Tk window destruction bug remains...  Let me know if you make updates, 
I'll gladly test.  Or if you have TkAgg/Mayavi, this is again  the simple test 
case for reference:

planck[pylab]> cat tkbug.py
# This script crashes vtk, when run in an ipython -pylab session, with TkAgg
# as the default backend.

# The key is that the pylab.plot() call is made BEFORE the imv.surf call.  If
# I call imv.surf() first, it works fine.  Something in matplotlib is
# destroying windows it shouldn't.

from matplotlib import pylab
from mayavi.tools import imv

x= y = pylab.arange(256)
z= pylab.rand(256,256)

pylab.plot(range(10))
pylab.show()

imv.surf(x,y,z)

print "*** I'm about to close figure 1, this will crash VTK!!! *** \n"
pylab.close(1)
########################## EOF


> And your figure num patch is already in....

I saw that, great.  Many thanks, I really like it better this way.

Best,

f

>>>>> "Fernando" == Fernando Perez <Fer...@co...> writes:

    Fernando> You have to carefully wire reload() calls into the
    Fernando> proper backends.  It's doable, but doing it generically
    Fernando> and with all the complex mpl backend machinery would
    Fernando> likely take a bit of effort.

I have something in CVS that appears to work.  You can interactively
switch backends in the pylab interface.  The caveat is that you lose
all current figures when doing the switch (close('all') is called).
With some work I could probably patch the current figure manager to
work with multiple simultaneous backends but have no real interest in
doing this now.  But it could serve as a basis for an ipython patch
that allowed you to run as ps, eg something like the following


def runps(fname):

    curr = pylab.rcParams['backend']
    pylab.switch_backend('PS')
    reload(pylab)
    run(fname)
    pylab.switch_backend(curr)
    reload(pylab)
       

or modify "run" to take a kwarg for the backend.

    Fernando> But for now, I'd rather see the tk close bug fixed and
    Fernando> the figure() improvements I referred to in my other mail
    Fernando> ;)

Well, the tk close bug should be a non-issue with CVS matplotlib.
Just make sure you use the rc param (which is the default in CVS)

tk.pythoninspect  : False    # tk sets PYTHONINSEPCT


And your figure num patch is already in....

JDH

John Hunter wrote:
>>>>>>"Fernando" == Fernando Perez <Fer...@co...> writes:
> 
> 
>     Fernando> Hi all, I have a question: in interactive (ipython
>     Fernando> -pylab) mode, a call to savefig('foo.eps') (either via
>     Fernando> %run or straight at the prompt) still pops up a GUI plot
>     Fernando> window.  If I run the same script from a system command
>     Fernando> line, the eps is made, but no GUI opens (what I consider
>     Fernando> the correct behavior).
> 
>     Fernando> Is this something that should be fixed in ipython or in
>     Fernando> matplotlib?
> 
> For the sake of clarity, let's consider the canonical script
> 
>     import matplotlib
>     matplotlib.use('PS')
>     from pylab import *
>     plot([1,2,3])
>     savefig('test.ps')
>     show()
> 
> When run from the shell, it does what you want -- makes a PS with no
> popup.  It fails in  ipython (pops up a window) because you have
> already selected a backend and all pylab commands are directed to that
> backend.
> 
> How to fix it?
> 
>  * ipython invokes an external python process to run each script.  Of
>    course you pay a performance hit here, and this would likely change
>    the meaning of the way run is meant to work (eg, are local ipython
>    shell vars available in a "run" script.

Not good.  If users want this, they can always just call !python foo.py and be 
done.  The whole point of %run is to benefit from enhanced tracebacks, debug 
hooks, variable access, etc.  Doing that across processes is basically impossible.

>  * provide better support for backend switching in matplotlib.  Eg,
>    allowing you at any time to call matplotlib.use.  Currently, this
>    only works before the import of pylab.  It may be possible to write
>    a pylab.use that simply rebinds the 4 backend functions:
>    new_figure_manager, error_msg, draw_if_interactive, show.  At the
>    end of a "run", you could simply do a
>    matplotlib.pylab.use(defaultBackend) to rebind.  run could be
>    enhanced to support backend switching
> 
>      run somescript.py -dPS
> 
>    much like one can do from the shell.
> 
>   You know more about python module reloading than I do.  How does one
>   force a module to reload, eg if I wanted to set the rc 'backend'
>   param and then do, eg
> 
>  
>     rcParams['backend'] = 'PS'
>     from backends import new_figure_manager, error_msg, draw_if_interactive, show
> 
> 
>   to get new symbols?

You have to carefully wire reload() calls into the proper backends.  It's 
doable, but doing it generically and with all the complex mpl backend 
machinery would likely take a bit of effort.

> There may be another way, but those two come to mind.  I'll mull it
> over.

It's not a big deal anyway, just something to think about.  My concern is that 
if I run from ipython (for testing/debugging) some big script which is wired 
to dump hundreds of EPS figures to a plots directory (yes, I do stuff like 
that with Gnuplot), my screen is going to be instantly flooded with hundreds 
of windows.


But for now, I'd rather see the tk close bug fixed and the figure() 
improvements I referred to in my other mail ;)

Cheers,

f

John Hunter wrote:
>>>>>>"Fernando" == Fernando Perez <Fer...@co...> writes:
> 
>     Fernando> planck[pylab]> cat tkbug.py from matplotlib import pylab
> 
>     Fernando> pylab.plot(range(10)) pylab.show()
> 
>     Fernando> # Now I try to run this with plain python, no ipython in
>     Fernando> sight:
> 
> This is the result of adding
> 
>     if rcParams['tk.pythoninspect']:
>         os.environ['PYTHONINSPECT'] = '1'
> 
> to tkagg.  Comment out the pythoninspect line (or set the rc param
> accordingly) and see if makes a difference.  The pythoninspect thing
> appears to be required to make idle work in interactive mode, though
> it was introduced for other reasons I won't go into now.

OK, to summarize things with respect to this bug.  Indeed, commenting out the 
pythoninspect line solves the spurious prompt problem.  But it does nothing to 
the close('all') bug.  I managed to find a small test case to replicate the bug:

planck[pylab]> pylab

In [1]: cat tkbug.py
# This script crashes vtk, when run in an ipython -pylab session, with TkAgg
# as the default backend.

# The key is that the pylab.plot() call is made BEFORE the imv.surf call.  If
# I call imv.surf() first, it works fine.  Something in matplotlib is
# destroying windows it shouldn't.

from matplotlib import pylab
from mayavi.tools import imv

x = y = pylab.arange(256)
z = pylab.rand(256,256)

pylab.plot(range(10))
pylab.show()

imv.surf(x,y,z)

print "*** I'm about to close figure 1, this will crash VTK!!! *** \n"
pylab.close(1)
########################## EOF

In [2]: run tkbug
*** I'm about to close figure 1, this will crash VTK!!! ***

Generic Warning: In 
/usr/local/installers/src/vtk/VTK/Rendering/vtkTkRenderWidget.cxx, line 633
A TkRenderWidget is being destroyed before it associated vtkRenderWindow is 
destroyed. This is very bad and usually due to the order in which objects are 
being destroyed. Always destroy the vtkRenderWindow before destroying the user 
interface components.


Somehow, it seems that the Tk figure manager is messing with windows it 
shouldn't touch.

On a related note, I've been playing with some things in matplotlib which 
require looping through figure lists, making new figures with guaranteed new 
numbers, etc.  I'd like to propose a change.

I'd like figure() to allow calling wit None as the num argument.  If num is 
None, it would produce a guaranteed new figure window, with a number equal to 
the currently highest + 1.  This would make it easy, amongst other things, to 
write code which displays arrays with a proper aspect ratio by wrapping 
imshow() or figimage().  I can currently make such a guaranteed new number by 
using the following as a patch to pylab.py:


     if num==0:
         error_msg('Figure number can not be 0.\n' + \
                   'Hey, give me a break, this is matlab(TM) compatability')

     # NEW CODE
     if num is None:
         allnums = [f.num for f in _pylab_helpers.Gcf.get_all_fig_managers()]
         if allnums:
             num = max(allnums) + 1
         else:
             num = 1
     # /NEW CODE

I also think the default value for num should be None instead of 1.  This 
would allow you to make the following simple, clean use for building new plots:

planck[~]> pylab

In [1]: plot(range(10))
Out[1]: [<matplotlib.lines.Line2D instance at 0x412ccd8c>]

In [2]: figure()
Out[2]: <matplotlib.figure.Figure instance at 0x412ccd2c>

In [3]: plot(range(20))
Out[3]: [<matplotlib.lines.Line2D instance at 0x410d320c>]

In [4]: figure()
Out[4]: <matplotlib.figure.Figure instance at 0x410d32ac>

In [5]: plot(range(30))
Out[5]: [<matplotlib.lines.Line2D instance at 0x4115b02c>]


without never having to worry about manually managing figure number lists 
(unless you explicitly want to, which you still can).


Finally, is this really a close bug?

In [20]: fig=plot(range(10))

In [21]: close(fig)
ERROR: Unrecognized argument type to close

It sounds to me from reading the docstring like this should work, but maybe I 
just misunderstood things...

Regards,

f

>>>>> "Fernando" == Fernando Perez <Fer...@co...> writes:

    Fernando> Hi all, I have a question: in interactive (ipython
    Fernando> -pylab) mode, a call to savefig('foo.eps') (either via
    Fernando> %run or straight at the prompt) still pops up a GUI plot
    Fernando> window.  If I run the same script from a system command
    Fernando> line, the eps is made, but no GUI opens (what I consider
    Fernando> the correct behavior).

    Fernando> Is this something that should be fixed in ipython or in
    Fernando> matplotlib?

For the sake of clarity, let's consider the canonical script

    import matplotlib
    matplotlib.use('PS')
    from pylab import *
    plot([1,2,3])
    savefig('test.ps')
    show()

When run from the shell, it does what you want -- makes a PS with no
popup.  It fails in  ipython (pops up a window) because you have
already selected a backend and all pylab commands are directed to that
backend.

How to fix it?

 * ipython invokes an external python process to run each script.  Of
   course you pay a performance hit here, and this would likely change
   the meaning of the way run is meant to work (eg, are local ipython
   shell vars available in a "run" script.

 * provide better support for backend switching in matplotlib.  Eg,
   allowing you at any time to call matplotlib.use.  Currently, this
   only works before the import of pylab.  It may be possible to write
   a pylab.use that simply rebinds the 4 backend functions:
   new_figure_manager, error_msg, draw_if_interactive, show.  At the
   end of a "run", you could simply do a
   matplotlib.pylab.use(defaultBackend) to rebind.  run could be
   enhanced to support backend switching

     run somescript.py -dPS

   much like one can do from the shell.

  You know more about python module reloading than I do.  How does one
  force a module to reload, eg if I wanted to set the rc 'backend'
  param and then do, eg

 
    rcParams['backend'] = 'PS'
    from backends import new_figure_manager, error_msg, draw_if_interactive, show


  to get new symbols?

There may be another way, but those two come to mind.  I'll mull it
over.

    Fernando> ps. Yes, John, I've finally started to use matplotlib
    Fernando> for my own work.  Brace yourself, I'm compiling a pretty
    Fernando> hefty list of things to do.  I hope you don't plan on
    Fernando> sleeping much in the coming months ;)

Well, I knew it was coming....  Stress tests are usually a good
thing.  Plus, I'm sure you can't do anything to interrupt my sleep
that my 3 kids haven't already mastered!

JDH

Hi all,

I have a question:  in interactive (ipython -pylab) mode, a call to 
savefig('foo.eps') (either via %run or straight at the prompt) still pops up a 
GUI plot window.  If I run the same script from a system command line, the eps 
is made, but no GUI opens (what I consider the correct behavior).

Is this something that should be fixed in ipython or in matplotlib?

Cheers,

f.

ps. Yes, John, I've finally started to use matplotlib for my own work.  Brace 
yourself, I'm compiling a pretty hefty list of things to do.  I hope you don't 
plan on sleeping much in the coming months ;)

John Hunter wrote:
>>>>>>"Fernando" == Fernando Perez <Fer...@co...> writes:
> 
>     Fernando> planck[pylab]> cat tkbug.py from matplotlib import pylab
> 
>     Fernando> pylab.plot(range(10)) pylab.show()
> 
>     Fernando> # Now I try to run this with plain python, no ipython in
>     Fernando> sight:
> 
> This is the result of adding
> 
>     if rcParams['tk.pythoninspect']:
>         os.environ['PYTHONINSPECT'] = '1'
> 
> to tkagg.  Comment out the pythoninspect line (or set the rc param
> accordingly) and see if makes a difference.  The pythoninspect thing
> appears to be required to make idle work in interactive mode, though
> it was introduced for other reasons I won't go into now.

OK, my report from this afternoon was written in the office, where I have mpl 
0.71.  I'm now home, and my laptop runs 0.70.  Here, I don't see the problem 
at all.  I can't test here the big code where I saw the massive mayavi 
breakdown, because that was written by my officemate.  But at least I can 
confirm that 0.70, whose show() looks like:

def show():
     """
     Show all the figures and enter the gtk mainloop

     This should be the last line of your script
     """
     for manager in Gcf.get_all_fig_managers():
         manager.show()
     import matplotlib
     matplotlib.interactive(True)
     #os.environ['PYTHONINSPECT'] = '1'
     if show._needmain:
         Tk.mainloop()
         show._needmain = False


does not show the spurious prompt thingie (note the PYTHONINSPECT thingie is 
commented out).  I'll try to make this change to 0.71 and test the larger code 
with the mayavi problems, but it may be a few days before I can do that.

HTH,

f

>>>>> "Fernando" == Fernando Perez <Fer...@co...> writes:
    Fernando> planck[pylab]> cat tkbug.py from matplotlib import pylab

    Fernando> pylab.plot(range(10)) pylab.show()

    Fernando> # Now I try to run this with plain python, no ipython in
    Fernando> sight:

This is the result of adding

    if rcParams['tk.pythoninspect']:
        os.environ['PYTHONINSPECT'] = '1'

to tkagg.  Comment out the pythoninspect line (or set the rc param
accordingly) and see if makes a difference.  The pythoninspect thing
appears to be required to make idle work in interactive mode, though
it was introduced for other reasons I won't go into now.

The rc param is only in CVS -- you may just want to comment out the
whole bit and see if it helps.

Let me know...

JDH

John Hunter wrote:

> Just a guess,
> 
> The problem may be arising when the backend tries to quit when the
> total figure count reaches zero.  The relevant backend_tkagg section
> is
> 
>     def destroy(self, *args):
>         if Gcf.get_num_fig_managers()==0 and not matplotlib.is_interactive():
>             if self.window is not None:
>                 self.window.quit()
>         if self.window is not None:
>             #print 'calling window destroy'
>             self.window.destroy()
>         self.window = None
> 
> Try playing with this function and see if you can deduce where the
> problem is.

Sorry, but no luck.  I tried a few simple things and made no progress, and I 
really can't spend more time on this right now.  But I did find something 
bizarre.  Consider:

planck[pylab]> cat tkbug.py
from matplotlib import pylab

pylab.plot(range(10))
pylab.show()

#
Now I try to run this with plain python, no ipython in sight:

planck[pylab]> python tkbug.py
 >>>


The '>>>' prompt came in after I closed the plot window, and this is exactly 
the same thing I see with ipython: I get tossed into a naked python prompt, 
which is half-broken.  With ipython, you get all sorts of weird errors related 
to ipython having been torn down already.  With plain python, the only obvious 
sign of trouble is that readline is broken (^]]A instead of up-arrow, etc.)

So something fishy is going on there, but I really don't have time to track it 
down.  For now, I'll live with my hackish 'window sentinel' approach, ugly as 
it may be.

Cheers,

f