[Numpy-discussion] matplotlib is breaking numpy

Mathew Yeates mat.yeates@gmail....
Thu Nov 19 13:20:40 CST 2009


yes, a GTK app from the python shell. And not using the toolbar.
I'll see if I can extract out a sample of code that demonstrates the problem
I'm having.

Thx
Mathew

On Thu, Nov 19, 2009 at 10:56 AM, John Hunter <jdh2358@gmail.com> wrote:

>
>
>
>
> On Nov 19, 2009, at 12:53 PM, Mathew Yeates <mat.yeates@gmail.com> wrote:
>
> I am running my gtk app from python. I am deleting the canvas and running
> gc.collect(). I still seem to have a reference to my memmapped data.
>
> Any other hints?
>
>
> Gtk app from the standard python shell?
>
> Are you using the mpl toolbar?  It keeps a ref to the canvas. If you can
> create a small freestanding example, that would help
>
>
>
>
> -Mathew
>
> On Thu, Nov 19, 2009 at 10:42 AM, John Hunter < <jdh2358@gmail.com>
> jdh2358@gmail.com> wrote:
>
>>
>>
>>
>>
>> On Nov 19, 2009, at 12:35 PM, Mathew Yeates < <mat.yeates@gmail.com>
>> mat.yeates@gmail.com> wrote:
>>
>> Yeah, I tried that.
>>
>> Here's what I'm doing. I have an application which displays different
>> dataset which a user selects from a drop down list. I want to overwrite the
>> existing plot with a new one. I've tried deleting just about everything get
>> matplotlib to let go of my data!
>>
>>
>>
>> What is everything?  Are you using pyplot or are you embedding mpl in a
>> GUI?  If the latter, are you deleting the FigureCanvas?  You will also need
>> to call gc.collect after deleting the mpl objects because we use a lot of
>> circular references. Pyplot close does this automatically, but this does not
>> apply to embedding.
>>
>> How are you running you app?  From the shell or IPython?
>>
>>
>>
>>
>> Mathew
>>
>> On Thu, Nov 19, 2009 at 10:30 AM, John Hunter < <jdh2358@gmail.com><jdh2358@gmail.com>
>> jdh2358@gmail.com> wrote:
>>
>>>
>>>
>>>
>>>
>>> On Nov 19, 2009, at 11:57 AM, Robert Kern < <robert.kern@gmail.com><robert.kern@gmail.com>
>>> robert.kern@gmail.com> wrote:
>>>
>>> > On Thu, Nov 19, 2009 at 11:52, Mathew Yeates < <mat.yeates@gmail.com><mat.yeates@gmail.com>
>>> mat.yeates@gmail.com>
>>> > wrote:
>>> >> There is definitely something wrong with matplotlib/numpy. Consider
>>> >> the
>>> >> following
>>> >>> from numpy import *
>>> >>> mydata=memmap('map.dat',dtype=float64,mode='w+',shape=56566500)
>>> >>> del mydata
>>> >>
>>> >> I can now remove the file map.dat with (from the command line) $rm
>>> >> map.dat
>>> >>
>>> >> However
>>> >> If I plot  mydata before the line
>>> >>> del mydata
>>> >>
>>> >>
>>> >> I can't get rid of the file until I exit python!!
>>> >> Does matplotlib keep a reference to the data?
>>> >
>>> > Almost certainly.
>>> >
>>> >> How can I remove this
>>> >> reference?
>>> >
>>> > Probably by deleting the plot objects that were created and close all
>>> > matplotlib windows referencing the data. If you are using IPython, you
>>> > should know that many of the returned objects are kept in Out, so you
>>> > will need to clear that. There might be some more places internal to
>>> > matplotlib, I don't know.
>>> >
>>>
>>> Closing the figure window containg the data *should* be enough. In
>>> pylab/pyplot, this also triggers a call to gc.collect.
>>>
>>>
>>>
>>>
>>> > With some care, you can use gc.get_referrers() to find the objects
>>> > that are holding direct references to your memmap.
>>> >
>>> > --
>>> > Robert Kern
>>> >
>>> > "I have come to believe that the whole world is an enigma, a harmless
>>> > enigma that is made terrible by our own mad attempt to interpret it as
>>> > though it had an underlying truth."
>>> >  -- Umberto Eco
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