matplotlib-users Mailing List for matplotlib (Page 3)

On Jul 19, 2013, at 4:49 PM, Benjamin Root <ben...@ou...> wrote:

> What does "print matplotlib.get_backend()" say?

'MacOSX'

What does "print matplotlib.get_backend()" say?

I just installed matplotlib on a new MacBook Pro

ActivePython 2.7.2.5 (ActiveState Software Inc.) based on
Python 2.7.2 (default, Jun 24 2011, 12:20:15) 
[GCC 4.2.1 (Apple Inc. build 5664)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'1.7.1'
>>> import matplotlib
>>> matplotlib.__version__
'1.2.1'
>>> matplotlib.matplotlib_fname()
'/Users/tgrav/.matplotlib/matplotlibrc'
>>> 

That works fine. However, when I try to do

import matplotlib.pyplot as plt

it tries to open X11, which I have not installed and would like to 
try to avoid. The matplotlibrc file has

backend     : MacOSX 

Anyone know why it is still trying to open X11 and how I can avoid that?

Le Mer 17 juillet 2013 14:56, Michael Droettboom a écrit :
> Can you please provide a completely standalone example?  The following
> code has undefined variables etc.

Here it is, I'm afraid this testcase intent is less clear than what I
pasted previously (I replaced variables with precomputed values)

As shown in the attached png, the bottom tick labels (month names) are
missing. It worked in matplotlib ≤ 1.2.0

-- 
Nicolas Mailhot

Le Jeu 18 juillet 2013 14:12, Nicolas Mailhot a écrit :
> Le Mer 17 juillet 2013 15:04, Michael Droettboom a écrit :
>> This patch doesn't make a whole lot of sense to me.  get_name should
>> work just fine if self._family is None, and indeed it does in my own
>> testing:
>>
>> ```
>> from matplotlib import font_manager
>>
>> f = font_manager.FontProperties(None)
>> print f._family
>> print f.get_family()
>> print f.get_name()
>> ```
>>
>> So I'd much prefer to get to the bottom of the root cause of this
>> problem than patch it unnecessarily in this way.  Any idea what that is?
>
> I haven't the faintest idea. The function seems to be called with a "None"
> font, and then it crashes. As it's executed under a Linux system it uses
> the fontconfig backend with cairo. The call only occurs when matplotlib is
> fed more data than can be isolated in an simple example
>
> Attaching the only patches Fedora/Red Hat applied before the build :
>
> Patch0:         %{name}-noagg.patch
> Patch1:         %{name}-tk.patch
> # http://sourceforge.net/mailarchive/message.php?msg_id=30202451
> # https://github.com/matplotlib/matplotlib/pull/1666
> # https://bugzilla.redhat.com/show_bug.cgi?id=896182
> Patch2:         %{name}-fontconfig.patch
>
> […]
>
> # Remove bundled libraries
> rm -r agg24 lib/matplotlib/pyparsing_py?.py
>
> # Remove references to bundled libraries
> %patch0 -p1 -b .noagg
> sed -i -e s/matplotlib\.pyparsing_py./pyparsing/g lib/matplotlib/*.py
>
> # Correct tcl/tk detection
> %patch1 -p1 -b .tk
> sed -i -e 's|@@libdir@@|%{_libdir}|' setupext.py
>
> # Use fontconfig by default
> %patch2 -p1 -b .fontconfig

BTW if you have some code to add to the crashing function to identify
what's wrong, I can reproduce the crash at will (though the processing
before crash time is rather long)

Regards,

-- 
Nicolas Mailhot

@Eric: thanks, i see the point

@Jody: thanks for the trick, I'll first try Eric's approach

2013/7/18 Eric Firing <ef...@ha...>:
> On 2013/07/17 11:25 PM, Gregorio Bastardo wrote:
>> Thanks Mike, it's hard to spot, but still better than nothing. Anyway,
>> could it be the default behaviour of plotting masked arrays (single
>> pixel for an isolated element)?
>
> Gregorio,
>
> I don't think this would be a good idea.  It adds quite a bit of
> complexity for a special case--and inevitably, the next request from
> someone would be to have the option of using any marker for the isolated
> points.  The concept of "single pixel" gets slippery across backends and
> output devices.
>
> A better solution would be a simple function to identify such isolated
> points, for use when needed, to plot such points however you choose,
> typically with a separate call to "plot" specifying a marker.  This way,
> the extra complexity is called explicitly when needed, not carried along
> by every call to "plot".
>
> Eric
>
>>
>> 2013/7/17 Michael Droettboom <md...@st...>:
>>> You could use a single pixel for a marker (','), I guess.  But as you
>>> say, you need at least two points for a line segment.
>>>
>>> Mike
>>>
>>> On 07/17/2013 10:45 AM, Gregorio Bastardo wrote:
>>>> Hi,
>>>>
>>>> The following example demonstrates the problem, value 5 could not be
>>>> seen w/o marker:
>>>>
>>>> data = np.arange(10)
>>>> mask = [0,0,0,1,1,0,1,0,0,0]
>>>> x = np.ma.masked_array(data, mask)
>>>> plot(x)
>>>> plot(x, '+')
>>>>
>>>> In my datasets, isolated unmasked values are rare, but placing a
>>>> marker to spot them makes the whole graph cluttered. I do realize that
>>>> at least 2 valid points are needed for a line segment, but still, is
>>>> there any way to visualize these isolated unmasked values w/o a
>>>> marker?
>>>>
>>>> Thanks,
>>>> Gregorio
>
>
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Hi Brendan, Justin,
Thanks for your reply. I agree then that a .stop() method is needed. This is not very difficult; I'll try and implement it over the weekend.
Best,
-Michiel.




________________________________
 From: Brendan Barnwell <bre...@br...>
To: mat...@li... 
Sent: Friday, July 19, 2013 3:54 AM
Subject: Re: [Matplotlib-users] timer objects in macosx backend
 

On 2013-07-18 06:56, Justin Lazear wrote:> Hi Michiel,
>
> On my system, deleting the timer has no effect and the timer continues
> to send events. The __del__ method seems to call the same unimplemented
> _timer_stop method. Regardless, something else has a reference to the
> timer (MPL event loop maybe?) and __del__ is not being called once the
> timer has been started. It's not clear to me what should be 
stopping the
> timer in that case.
>
> Does del t stop the timer on your system? If so, could we hunt down 
what
> is happening after you delete the name t that is causing the timer 
to stop?
>
> I would personally prefer an explicit .stop() method, since I would
> prefer not to rely on the garbage collector's behavior being consistent
> (hard to make sure nothing else is holding a reference to timer) when
> there is a very well-defined function that does what I want.

    Relying on "del t" can't be the right solution, since like you note, 
it only deletes the name, not the object.  If you create multiple 
references to a timer and only del some of them, e.g.:

t = fig.canvas.new_timer()
x = t
del t

Then the object's __del__ will definitely not be called yet.  It makes 
sense to have a way to stop the timer directly, regardless of how many 
names are pointing to it.

-- 
Brendan Barnwell
"Do not follow where the path may lead.  Go, instead, where there is 
no path, and leave a trail."
    --author unknown

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On 2013-07-18 06:56, Justin Lazear wrote:> Hi Michiel,
 >
 > On my system, deleting the timer has no effect and the timer continues
 > to send events. The __del__ method seems to call the same unimplemented
 > _timer_stop method. Regardless, something else has a reference to the
 > timer (MPL event loop maybe?) and __del__ is not being called once the
 > timer has been started. It's not clear to me what should be 
stopping the
 > timer in that case.
 >
 > Does del t stop the timer on your system? If so, could we hunt down 
what
 > is happening after you delete the name t that is causing the timer 
to stop?
 >
 > I would personally prefer an explicit .stop() method, since I would
 > prefer not to rely on the garbage collector's behavior being consistent
 > (hard to make sure nothing else is holding a reference to timer) when
 > there is a very well-defined function that does what I want.

	Relying on "del t" can't be the right solution, since like you note, 
it only deletes the name, not the object.  If you create multiple 
references to a timer and only del some of them, e.g.:

t = fig.canvas.new_timer()
x = t
del t

Then the object's __del__ will definitely not be called yet.  It makes 
sense to have a way to stop the timer directly, regardless of how many 
names are pointing to it.

-- 
Brendan Barnwell
"Do not follow where the path may lead.  Go, instead, where there is 
no path, and leave a trail."
    --author unknown

Or make a stairstep, if each time has a finite duration.   like the following (though I am sure there are some inelegant code in there. 

data = np.arange(10)
mask = [0,0,0,1,1,0,1,0,0,0]
x = np.ma.masked_array(data, mask)
t = arange(-0.5,shape(x)[0]-0.5,1.)

xx=ma.zeros((2,10))
xx[0,:]=x
xx[1,:]=x
tt=0.*xx
tt[0,:]=t
tt[1,:]=t+0.9999999
tt=reshape(tt,(20),order='F')
xx=reshape(xx,(20),order='F')
plot(tt,xx)

On Jul 17, 2013, at  7:45 AM, Gregorio Bastardo <gre...@gm...> wrote:

> Hi,
> 
> The following example demonstrates the problem, value 5 could not be
> seen w/o marker:
> 
> data = np.arange(10)
> mask = [0,0,0,1,1,0,1,0,0,0]
> x = np.ma.masked_array(data, mask)
> plot(x)
> plot(x, '+')
> 
> In my datasets, isolated unmasked values are rare, but placing a
> marker to spot them makes the whole graph cluttered. I do realize that
> at least 2 valid points are needed for a line segment, but still, is
> there any way to visualize these isolated unmasked values w/o a
> marker?
> 
> Thanks,
> Gregorio
> 
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
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--
Jody Klymak    
http://web.uvic.ca/~jklymak/

On 2013/07/17 11:25 PM, Gregorio Bastardo wrote:
> Thanks Mike, it's hard to spot, but still better than nothing. Anyway,
> could it be the default behaviour of plotting masked arrays (single
> pixel for an isolated element)?

Gregorio,

I don't think this would be a good idea.  It adds quite a bit of 
complexity for a special case--and inevitably, the next request from 
someone would be to have the option of using any marker for the isolated 
points.  The concept of "single pixel" gets slippery across backends and 
output devices.

A better solution would be a simple function to identify such isolated 
points, for use when needed, to plot such points however you choose, 
typically with a separate call to "plot" specifying a marker.  This way, 
the extra complexity is called explicitly when needed, not carried along 
by every call to "plot".

Eric

>
> 2013/7/17 Michael Droettboom <md...@st...>:
>> You could use a single pixel for a marker (','), I guess.  But as you
>> say, you need at least two points for a line segment.
>>
>> Mike
>>
>> On 07/17/2013 10:45 AM, Gregorio Bastardo wrote:
>>> Hi,
>>>
>>> The following example demonstrates the problem, value 5 could not be
>>> seen w/o marker:
>>>
>>> data = np.arange(10)
>>> mask = [0,0,0,1,1,0,1,0,0,0]
>>> x = np.ma.masked_array(data, mask)
>>> plot(x)
>>> plot(x, '+')
>>>
>>> In my datasets, isolated unmasked values are rare, but placing a
>>> marker to spot them makes the whole graph cluttered. I do realize that
>>> at least 2 valid points are needed for a line segment, but still, is
>>> there any way to visualize these isolated unmasked values w/o a
>>> marker?
>>>
>>> Thanks,
>>> Gregorio

Apologies: I didn't realize the link to the raw results only exists for 
users with edit permissions.  The public URL for the raw results is:

https://docs.google.com/spreadsheet/ccc?key=0AjrPjlTMRTwTdHpQS25pcTZIRWdqX0pNckNSU01sMHc&usp=sharing

Mike

On 07/18/2013 09:42 AM, Michael Droettboom wrote:
> We have had 508 responses to the matplotlib user survey.  Quite a nice 
> turnout!
>
> You can view the results here:
>
> https://docs.google.com/spreadsheet/viewanalytics?key=0AjrPjlTMRTwTdHpQS25pcTZIRWdqX0pNckNSU01sMHc&gridId=0#chart
>
> and from there, you can access the complete raw results.
>
> I will be doing more analysis of the results over the coming days and 
> weeks, including dedup'ing some of the responses and converting some 
> of the free-form responses into github issues etc.  Volunteers to help 
> with this are of course welcome!
>
> Cheers,
> Mike

Hi Michiel,

On my system, deleting the timer has no effect and the timer continues 
to send events. The __del__ method seems to call the same unimplemented 
_timer_stop method. Regardless, something else has a reference to the 
timer (MPL event loop maybe?) and __del__ is not being called once the 
timer has been started. It's not clear to me what should be stopping the 
timer in that case.

Does del t stop the timer on your system? If so, could we hunt down what 
is happening after you delete the name t that is causing the timer to stop?

I would personally prefer an explicit .stop() method, since I would 
prefer not to rely on the garbage collector's behavior being consistent 
(hard to make sure nothing else is holding a reference to timer) when 
there is a very well-defined function that does what I want.

Thanks,
Justin

On 7/18/13 12:54 AM, Michiel de Hoon wrote:
> Hi Justin,
>
> The .stop() method was indeed never implemented for Timer objects in 
> the MacOSX backend.
> I am not sure if a .stop() method is really needed, because deleting 
> the timer has the same effect as stopping the timer.
> Is there some reason you prefer
> >>> t.stop()
> instead of
> >>> del t
> ?
>
> Best,
> -Michiel
>
>
> ------------------------------------------------------------------------
> *From:* Justin Lazear <jl...@gm...>
> *To:* Mat...@li...
> *Sent:* Thursday, July 18, 2013 12:13 AM
> *Subject:* [Matplotlib-users] timer objects in macosx backend
>
> Hi all,
>
> I'm using a timer object to interact with the MPL event loop on my OS 
> X laptop. However, it seems to be missing a few key methods that are 
> making using it a little difficult. In particular, I can't find a way 
> to stop the timer from sending events:
>
>         $ ipython --pylab
>
>     In [1]: def fun():
>        ...:     for i in range(5):
>        ...:         print "We're having fun!"; yield
>        ...:     for i in range(5):
>        ...:         print "Too much fun..."; yield
>        ...:     while True:
>        ...:         print "Stop the fun! No more!"; yield
>
>     In [2]: f = fun().next
>
>     In [3]: fig = plt.figure()
>
>     In [4]: t = fig.canvas.new_timer()
>
>     In [5]: t.add_callback(f)
>
>     In [6]: t.start()
>
>     In [7]: t.stop()
>
>     In [8]: del t  # It's all over now...
>
>
> It looks like the stop method may never have been implemented:
>
>     In [3]: t.stop??
>     Type:       instancemethod
>     String Form:<bound method TimerMac.stop of Timer object
>     0x106ba33b0 wrapping CFRunLoopTimerRef 0x0>
>     File:
>     /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py
>     Definition: t.stop(self)
>     Source:
>         def stop(self):
>             '''
>             Stop the timer.
>             '''
>             self._timer_stop()
>
>     In [4]: t._timer_stop??
>     Type:       instancemethod
>     String Form:<bound method TimerMac._timer_stop of Timer object
>     0x106ba33b0 wrapping CFRunLoopTimerRef 0x0>
>     File:
>     /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py
>     Definition: t._timer_stop(self)
>     Source:
>         def _timer_stop(self):
>             pass
>
>
> I'm able to remove the callback function from the timer's callback 
> list, but I suspect that won't stop the events from being triggered. 
> But I'd really prefer to completely stop the timer events, since in my 
> application I may end up going through many timers.
>
> Is this the expected behavior? Is there an easy fix I'm overlooking?
>
> Version info:
>
>     In [3]: sys.version
>     Out[3]: '2.7.3 (default, Feb 19 2013, 18:00:31) \n[GCC 4.2.1
>     Compatible Apple LLVM 4.2 (clang-425.0.24)]'
>
>     In [4]: mpl.__version__
>     Out[4]: '1.2.0'
>
>
> Thanks,
> Justin
>
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
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> Mat...@li... 
> <mailto:Mat...@li...>
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

We have had 508 responses to the matplotlib user survey.  Quite a nice 
turnout!

You can view the results here:

https://docs.google.com/spreadsheet/viewanalytics?key=0AjrPjlTMRTwTdHpQS25pcTZIRWdqX0pNckNSU01sMHc&gridId=0#chart

and from there, you can access the complete raw results.

I will be doing more analysis of the results over the coming days and 
weeks, including dedup'ing some of the responses and converting some of 
the free-form responses into github issues etc.  Volunteers to help with 
this are of course welcome!

Cheers,
Mike

Jeffrey,

Sorry if the documentation is a bit vague on the _axinfo front.  It was
intentionally done that way to keep the number of people dependent upon
that kludge down.  It was created as an improvement upon the previous
hard-coded constants that completely prevented anybody from making any
customizations at all.

The spacing of tick labels for an axis can be modified like so:

ax.xaxis._axinfo['ticklabel']['space_factor'] = 0.7   # This is the default
value. Make it less to bring it closer to the axis

and for the axis label:

ax.xaxis._axinfo['label']['space_factor'] = 1.6  # Again, this is the
default value. Make it larger to move it away from the axis

I hope that helps!
Ben Root



On Thu, Jul 18, 2013 at 3:18 AM, Jeffrey Spencer <jef...@gm...>wrote:

> I have a problem with labels overlapping the tickmark labels. No matter
> changing the fontsize or plot_size or other things. I can't find something
> that works properly. I found somethwhere setting linespacing should work
> but this seems to do nothing in my case.
>
> Any good suggestions or updates on this??
>
> I'm using 1.2.x matplotlib version. I put a plot here showing how the
> label overlaps but I know this has been a problem in the past.
>
> Also, I couldn't figure out how to get access to the _axinfo like stated
> in the documentation for a possible fix. Where is this located?? How do I
> acess or modify it as a temporary fix??
>
>
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
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>
>

Le Mer 17 juillet 2013 15:04, Michael Droettboom a écrit :
> This patch doesn't make a whole lot of sense to me.  get_name should
> work just fine if self._family is None, and indeed it does in my own
> testing:
>
> ```
> from matplotlib import font_manager
>
> f = font_manager.FontProperties(None)
> print f._family
> print f.get_family()
> print f.get_name()
> ```
>
> So I'd much prefer to get to the bottom of the root cause of this
> problem than patch it unnecessarily in this way.  Any idea what that is?

I haven't the faintest idea. The function seems to be called with a "None"
font, and then it crashes. As it's executed under a Linux system it uses
the fontconfig backend with cairo. The call only occurs when matplotlib is
fed more data than can be isolated in an simple example

Attaching the only patches Fedora/Red Hat applied before the build :

Patch0:         %{name}-noagg.patch
Patch1:         %{name}-tk.patch
# http://sourceforge.net/mailarchive/message.php?msg_id=30202451
# https://github.com/matplotlib/matplotlib/pull/1666
# https://bugzilla.redhat.com/show_bug.cgi?id=896182
Patch2:         %{name}-fontconfig.patch

[…]

# Remove bundled libraries
rm -r agg24 lib/matplotlib/pyparsing_py?.py

# Remove references to bundled libraries
%patch0 -p1 -b .noagg
sed -i -e s/matplotlib\.pyparsing_py./pyparsing/g lib/matplotlib/*.py

# Correct tcl/tk detection
%patch1 -p1 -b .tk
sed -i -e 's|@@libdir@@|%{_libdir}|' setupext.py

# Use fontconfig by default
%patch2 -p1 -b .fontconfig

Regards,

-- 
Nicolas Mailhot

Thanks Mike, it's hard to spot, but still better than nothing. Anyway,
could it be the default behaviour of plotting masked arrays (single
pixel for an isolated element)?

2013/7/17 Michael Droettboom <md...@st...>:
> You could use a single pixel for a marker (','), I guess.  But as you
> say, you need at least two points for a line segment.
>
> Mike
>
> On 07/17/2013 10:45 AM, Gregorio Bastardo wrote:
>> Hi,
>>
>> The following example demonstrates the problem, value 5 could not be
>> seen w/o marker:
>>
>> data = np.arange(10)
>> mask = [0,0,0,1,1,0,1,0,0,0]
>> x = np.ma.masked_array(data, mask)
>> plot(x)
>> plot(x, '+')
>>
>> In my datasets, isolated unmasked values are rare, but placing a
>> marker to spot them makes the whole graph cluttered. I do realize that
>> at least 2 valid points are needed for a line segment, but still, is
>> there any way to visualize these isolated unmasked values w/o a
>> marker?
>>
>> Thanks,
>> Gregorio
>>
>> ------------------------------------------------------------------------------
>> See everything from the browser to the database with AppDynamics
>> Get end-to-end visibility with application monitoring from AppDynamics
>> Isolate bottlenecks and diagnose root cause in seconds.
>> Start your free trial of AppDynamics Pro today!
>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
> ------------------------------------------------------------------------------
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> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

I have a problem with labels overlapping the tickmark labels. No matter
changing the fontsize or plot_size or other things. I can't find something
that works properly. I found somethwhere setting linespacing should work
but this seems to do nothing in my case.

Any good suggestions or updates on this??

I'm using 1.2.x matplotlib version. I put a plot here showing how the label
overlaps but I know this has been a problem in the past.

Also, I couldn't figure out how to get access to the _axinfo like stated in
the documentation for a possible fix. Where is this located?? How do I
acess or modify it as a temporary fix??

Hi Justin,

The .stop() method was indeed never implemented for Timer objects in the MacOSX backend.
I am not sure if a .stop() method is really needed, because deleting the timer has the same effect as stopping the timer.
Is there some reason you prefer
>>> t.stop()
instead of
>>> del t
?

Best,
-Michiel




________________________________
 From: Justin Lazear <jl...@gm...>
To: Mat...@li... 
Sent: Thursday, July 18, 2013 12:13 AM
Subject: [Matplotlib-users] timer objects in macosx backend
 


Hi all,

I'm using a timer object to interact with the MPL event loop on my
    OS X laptop. However, it seems to be missing a few key methods that
    are making using it a little difficult. In particular, I can't find
    a way to stop the timer from sending events:

        $ ipython --pylab

In [1]: def fun():
>   ...:     for i in range(5):
>   ...:         print "We're having fun!"; yield
>   ...:     for i in range(5):
>   ...:         print "Too much fun..."; yield
>   ...:     while True:
>   ...:         print "Stop the fun! No more!"; yield
>
>In [2]: f = fun().next
>
>In [3]: fig = plt.figure()
>
>In [4]: t = fig.canvas.new_timer()
>
>In [5]: t.add_callback(f)
>
>In [6]: t.start()
>
>In [7]: t.stop()
>
>In [8]: del t  # It's all over now...
>
It looks like the stop method may never have been implemented:


In [3]: t.stop??
>Type:       instancemethod
>String Form:<bound method TimerMac.stop of Timer object
      0x106ba33b0 wrapping CFRunLoopTimerRef 0x0>
>File:      
      /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py
>Definition: t.stop(self)
>Source:
>    def stop(self):
>        '''
>        Stop the timer.
>        '''
>        self._timer_stop()
>
>In [4]: t._timer_stop??
>Type:       instancemethod
>String Form:<bound method TimerMac._timer_stop of Timer object
      0x106ba33b0 wrapping CFRunLoopTimerRef 0x0>
>File:      
      /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py
>Definition: t._timer_stop(self)
>Source:
>    def _timer_stop(self):
>        pass
>
I'm able to remove the callback function from the timer's callback
    list, but I suspect that won't stop the events from being triggered.
    But I'd really prefer to completely stop the timer events, since in
    my application I may end up going through many timers. 

Is this the expected behavior? Is there an easy fix I'm overlooking?

Version info:


In [3]: sys.version
>Out[3]: '2.7.3 (default, Feb 19 2013, 18:00:31) \n[GCC 4.2.1
      Compatible Apple LLVM 4.2 (clang-425.0.24)]'
>
>In [4]: mpl.__version__
>Out[4]: '1.2.0'
>
Thanks,
Justin

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I am able to import matplotlib.pyplt under python 3.3.2 from www.python.org in OS X 10.6.8.  matplotlib 1.2.1, libfreetype and libpng were built from source using gcc 4.2.1 from Xcode 3.2.6.
Are you using python from macports or from www.python.org?  You might try using python from the installer at www.python.org and building libfreetype and libpng from source.  I did a simple

./configure
make
sudo make install

in the libfreetype and libpng source directories.  You can download the latest source from

http://sourceforge.net/projects/libpng/files/libpng16/1.6.2/
http://sourceforge.net/projects/freetype/files/freetype2/2.5.0/

hth,
Scott

On Jul 8, 2013, at 12:17 PM, p.maxted <p.m...@ke...> wrote:

> Trying to install matplotlib-1.2.1 from source, i.e.,
> 
> [macpflm:~/matplotlib-1.2.1] pflm% python3 setup.py install
> 
> Everything seems to run ok, but I cannot import macplotlib:
> 
> [macpflm:~] pflm% python3
> Python 3.3.1 (v3.3.1:d9893d13c628, Apr  6 2013, 11:07:11) 
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib.pyplot
> Python(16295) malloc: *** error for object 0x101c86820: pointer being freed
> was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort
> 
> 
> I tried updating libpng and freetype using macports and re-building, it did
> not solve the problem.
> 
> There are some warnings printed during the build, e.g., 
> 
> ld: warning: in /opt/local/lib/libfreetype.dylib, file was built for
> unsupported file format which is not the architecture being linked (i386)
> ld: warning: in /opt/local/lib/libz.dylib, file was built for unsupported
> file format which is not the architecture being linked (i386)
> ld: warning: in
> /Developer/SDKs/MacOSX10.6.sdk/usr/local/lib/libstdc++.dylib, file was built
> for unsupported file format which is not the architecture being linked
> (i386)
> 
> ..and..
> 
> /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2:
> warning: #warning "Using deprecated NumPy API, disable it by #defining
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
> 
> (both warning several times).
> 
> Some details from the start of the screen output during the build.
> basedirlist is: ['/usr/local/', '/usr', '/usr/X11', '/opt/local']
> ============================================================================
> BUILDING MATPLOTLIB
>            matplotlib: 1.2.1
>                python: 3.3.1 (v3.3.1:d9893d13c628, Apr  6 2013, 11:07:11)
>                        [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
>              platform: darwin
> 
> REQUIRED DEPENDENCIES
>                 numpy: 1.7.0
>             freetype2: 16.2.10
> 
> OPTIONAL BACKEND DEPENDENCIES
>                libpng: 1.5.16
>               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: no
>                PySide: no
>                 Cairo: no
> 
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
>              dateutil: matplotlib will provide
>                  pytz: matplotlib will provide
>                   six: matplotlib will provide
> 
> OPTIONAL USETEX DEPENDENCIES
>                dvipng: 1.5
>           ghostscript: 6.01
>                 latex: 3.141592
> 
> [Edit setup.cfg to suppress the above messages]
> ============================================================================
> 
> Help!
> 
> 
> --
> View this message in context: http://matplotlib.1069221.n5.nabble.com/Install-problems-OSX-10-6-8-Python-3-3-1-tp41430.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.

You could use a single pixel for a marker (','), I guess.  But as you 
say, you need at least two points for a line segment.

Mike

On 07/17/2013 10:45 AM, Gregorio Bastardo wrote:
> Hi,
>
> The following example demonstrates the problem, value 5 could not be
> seen w/o marker:
>
> data = np.arange(10)
> mask = [0,0,0,1,1,0,1,0,0,0]
> x = np.ma.masked_array(data, mask)
> plot(x)
> plot(x, '+')
>
> In my datasets, isolated unmasked values are rare, but placing a
> marker to spot them makes the whole graph cluttered. I do realize that
> at least 2 valid points are needed for a line segment, but still, is
> there any way to visualize these isolated unmasked values w/o a
> marker?
>
> Thanks,
> Gregorio
>
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Hi all,

I'm using a timer object to interact with the MPL event loop on my OS X 
laptop. However, it seems to be missing a few key methods that are 
making using it a little difficult. In particular, I can't find a way to 
stop the timer from sending events:

         $ ipython --pylab

    In [1]: def fun():
        ...:     for i in range(5):
        ...:         print "We're having fun!"; yield
        ...:     for i in range(5):
        ...:         print "Too much fun..."; yield
        ...:     while True:
        ...:         print "Stop the fun! No more!"; yield

    In [2]: f = fun().next

    In [3]: fig = plt.figure()

    In [4]: t = fig.canvas.new_timer()

    In [5]: t.add_callback(f)

    In [6]: t.start()

    In [7]: t.stop()

    In [8]: del t  # It's all over now...


It looks like the stop method may never have been implemented:

    In [3]: t.stop??
    Type:       instancemethod
    String Form:<bound method TimerMac.stop of Timer object 0x106ba33b0
    wrapping CFRunLoopTimerRef 0x0>
    File: /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py
    Definition: t.stop(self)
    Source:
         def stop(self):
             '''
             Stop the timer.
             '''
             self._timer_stop()

    In [4]: t._timer_stop??
    Type:       instancemethod
    String Form:<bound method TimerMac._timer_stop of Timer object
    0x106ba33b0 wrapping CFRunLoopTimerRef 0x0>
    File: /usr/local/lib/python2.7/site-packages/matplotlib/backend_bases.py
    Definition: t._timer_stop(self)
    Source:
         def _timer_stop(self):
             pass


I'm able to remove the callback function from the timer's callback list, 
but I suspect that won't stop the events from being triggered. But I'd 
really prefer to completely stop the timer events, since in my 
application I may end up going through many timers.

Is this the expected behavior? Is there an easy fix I'm overlooking?

Version info:

    In [3]: sys.version
    Out[3]: '2.7.3 (default, Feb 19 2013, 18:00:31) \n[GCC 4.2.1
    Compatible Apple LLVM 4.2 (clang-425.0.24)]'

    In [4]: mpl.__version__
    Out[4]: '1.2.0'


Thanks,
Justin

Hi,

The following example demonstrates the problem, value 5 could not be
seen w/o marker:

data = np.arange(10)
mask = [0,0,0,1,1,0,1,0,0,0]
x = np.ma.masked_array(data, mask)
plot(x)
plot(x, '+')

In my datasets, isolated unmasked values are rare, but placing a
marker to spot them makes the whole graph cluttered. I do realize that
at least 2 valid points are needed for a line segment, but still, is
there any way to visualize these isolated unmasked values w/o a
marker?

Thanks,
Gregorio

I have a vague recollection of a similar problem faced by @dopplershift
when he was updating the animation module to pipe a stream to a
mencoder/ffmpeg process on certain Macs.  Maybe this is the same problem?


On Wed, Jul 17, 2013 at 9:18 AM, Michael Droettboom <md...@st...> wrote:

> To debug, it might be helpful to try
>
> ps -p PID -o rss,vsz
>
> (where PID is the process id of an interesting process)
>
> and see what happens.
>
> Mike
>
> On 07/17/2013 02:05 AM, Eric Firing wrote:
> > On 2013/07/16 5:50 PM, K.-Michael Aye wrote:
> >> Hi!
> >>
> >> I have just run an old code that I believe was working before on OSX.
> >> I am trying this with matplotlib 1.2.1 on an OSX EPD running Python
> 2.7.3
> > It works for me with OSX  Mountain Lion and mpl 1.2.1 compiled from
> > source.  I don't think this is fundamentally a problem with
> > cbook.report_memory.
> >
> > Eric
> >
> >>
> >> In [1]: from matplotlib.pylab import *
> >>
> >> In [2]: import matplotlib.cbook as cbook
> >>
> >> In [3]: data = ones((1500,1500,3))
> >>
> >> In [4]: imshow(data)
> >> Out[4]: <matplotlib.image.AxesImage at 0x109d343d0>
> >>
> >> In [5]: ax = gca()
> >>
> >> In [6]: print cbook.report_memory()
> >>
> ---------------------------------------------------------------------------
> >> IOError                                   Traceback (most recent call
> last)
> >> <ipython-input-6-88a73a5ab996> in <module>()
> >> ----> 1 print cbook.report_memory()
> >>
> >>
> /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cbook.py
> >> in report_memory(i)
> >>      1210     elif sys.platform.startswith('darwin'):
> >>      1211         a2 = Popen('ps -p %d -o rss,vsz' % pid, shell=True,
> >> -> 1212                    stdout=PIPE).stdout.readlines()
> >>      1213         mem = int(a2[1].split()[0])
> >>      1214     elif sys.platform.startswith('win'):
> >>
> >> IOError: [Errno 4] Interrupted system call
> >>
> >> First I thought, maybe this doesn't run in IPython for a reason, but
> >> trying it as a script also fails:
> >>
> >> (general_dev+)[maye@lunatic ~/Dropbox/src/pymars]$ python
> imshow_test.py
> >> Traceback (most recent call last):
> >>     File "imshow_test.py", line 7, in <module>
> >>       print cbook.report_memory()
> >>     File
> >>
> "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cbook.py",
> >> line 1212, in report_memory
> >>       stdout=PIPE).stdout.readlines()
> >> IOError: [Errno 4] Interrupted system call
> >>
> >>
> >> Is this cbook recipe maybe broken?
> >>
> >> Best,
> >> Michael
> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> See everything from the browser to the database with AppDynamics
> >> Get end-to-end visibility with application monitoring from AppDynamics
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> >>
> >
> >
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>
>
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To debug, it might be helpful to try

ps -p PID -o rss,vsz

(where PID is the process id of an interesting process)

and see what happens.

Mike

On 07/17/2013 02:05 AM, Eric Firing wrote:
> On 2013/07/16 5:50 PM, K.-Michael Aye wrote:
>> Hi!
>>
>> I have just run an old code that I believe was working before on OSX.
>> I am trying this with matplotlib 1.2.1 on an OSX EPD running Python 2.7.3
> It works for me with OSX  Mountain Lion and mpl 1.2.1 compiled from
> source.  I don't think this is fundamentally a problem with
> cbook.report_memory.
>
> Eric
>
>>
>> In [1]: from matplotlib.pylab import *
>>
>> In [2]: import matplotlib.cbook as cbook
>>
>> In [3]: data = ones((1500,1500,3))
>>
>> In [4]: imshow(data)
>> Out[4]: <matplotlib.image.AxesImage at 0x109d343d0>
>>
>> In [5]: ax = gca()
>>
>> In [6]: print cbook.report_memory()
>> ---------------------------------------------------------------------------
>> IOError                                   Traceback (most recent call last)
>> <ipython-input-6-88a73a5ab996> in <module>()
>> ----> 1 print cbook.report_memory()
>>
>> /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cbook.py
>> in report_memory(i)
>>      1210     elif sys.platform.startswith('darwin'):
>>      1211         a2 = Popen('ps -p %d -o rss,vsz' % pid, shell=True,
>> -> 1212                    stdout=PIPE).stdout.readlines()
>>      1213         mem = int(a2[1].split()[0])
>>      1214     elif sys.platform.startswith('win'):
>>
>> IOError: [Errno 4] Interrupted system call
>>
>> First I thought, maybe this doesn't run in IPython for a reason, but
>> trying it as a script also fails:
>>
>> (general_dev+)[maye@lunatic ~/Dropbox/src/pymars]$ python imshow_test.py
>> Traceback (most recent call last):
>>     File "imshow_test.py", line 7, in <module>
>>       print cbook.report_memory()
>>     File
>> "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/matplotlib/cbook.py",
>> line 1212, in report_memory
>>       stdout=PIPE).stdout.readlines()
>> IOError: [Errno 4] Interrupted system call
>>
>>
>> Is this cbook recipe maybe broken?
>>
>> Best,
>> Michael
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> See everything from the browser to the database with AppDynamics
>> Get end-to-end visibility with application monitoring from AppDynamics
>> Isolate bottlenecks and diagnose root cause in seconds.
>> Start your free trial of AppDynamics Pro today!
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>>
>
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Do any Mac experts have any ideas?

One thing that may help us is to fire this up in gdb and get a traceback.

1) Run "gdb python" (or "gdb python3").
2) At the gdb prompt, type "run"
3) At the Python prompt, type "import matplotlib.pyplot"
4) Python should crash, then type "bt" to get a backtrace
5) Post the *complete* backtrace to this list and maybe it will make the 
problem more obvious to us

Mike

On 07/08/2013 12:17 PM, p.maxted wrote:
> Trying to install matplotlib-1.2.1 from source, i.e.,
>
> [macpflm:~/matplotlib-1.2.1] pflm% python3 setup.py install
>
> Everything seems to run ok, but I cannot import macplotlib:
>
> [macpflm:~] pflm% python3
> Python 3.3.1 (v3.3.1:d9893d13c628, Apr  6 2013, 11:07:11)
> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib.pyplot
> Python(16295) malloc: *** error for object 0x101c86820: pointer being freed
> was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort
>
>
>   I tried updating libpng and freetype using macports and re-building, it did
> not solve the problem.
>
> There are some warnings printed during the build, e.g.,
>
> ld: warning: in /opt/local/lib/libfreetype.dylib, file was built for
> unsupported file format which is not the architecture being linked (i386)
> ld: warning: in /opt/local/lib/libz.dylib, file was built for unsupported
> file format which is not the architecture being linked (i386)
> ld: warning: in
> /Developer/SDKs/MacOSX10.6.sdk/usr/local/lib/libstdc++.dylib, file was built
> for unsupported file format which is not the architecture being linked
> (i386)
>
> ..and..
>
> /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2:
> warning: #warning "Using deprecated NumPy API, disable it by #defining
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
>
> (both warning several times).
>
> Some details from the start of the screen output during the build.
> basedirlist is: ['/usr/local/', '/usr', '/usr/X11', '/opt/local']
> ============================================================================
> BUILDING MATPLOTLIB
>              matplotlib: 1.2.1
>                  python: 3.3.1 (v3.3.1:d9893d13c628, Apr  6 2013, 11:07:11)
>                          [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
>                platform: darwin
>
> REQUIRED DEPENDENCIES
>                   numpy: 1.7.0
>               freetype2: 16.2.10
>
> OPTIONAL BACKEND DEPENDENCIES
>                  libpng: 1.5.16
>                 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: no
>                  PySide: no
>                   Cairo: no
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
>                dateutil: matplotlib will provide
>                    pytz: matplotlib will provide
>                     six: matplotlib will provide
>
> OPTIONAL USETEX DEPENDENCIES
>                  dvipng: 1.5
>             ghostscript: 6.01
>                   latex: 3.141592
>
> [Edit setup.cfg to suppress the above messages]
> ============================================================================
>
>   Help!
>
>
>
>
>
> --
> View this message in context: http://matplotlib.1069221.n5.nabble.com/Install-problems-OSX-10-6-8-Python-3-3-1-tp41430.html
> Sent from the matplotlib - users mailing list archive at Nabble.com.
>
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