[Mne_analysis] How to save figures in a loop without displaying them?

Sun Aug 17 16:13:39 EDT 2014

Hi Maria,

that's a bit unexpected. Maybe it depends on the matplotlib version.
Have you tried adding plt.ioff() to turn off interactive mode?

-D

On Sun, Aug 17, 2014 at 10:11 PM, Maria Hakonen <maria.hakonen at gmail.com>
wrote:

> I have imported matplotlib.use('Agg') before matplotlib.pyplot as plt and
> also tried import it after matplotlib.pyplot but the result is the same.
>
> -Maria
>
>
> 2014-08-17 22:35 GMT+03:00 Denis-Alexander Engemann <
> denis.engemann at gmail.com>:
>
> Hi Maria,
>>
>>
>> On Sun, Aug 17, 2014 at 9:18 PM, Maria Hakonen <maria.hakonen at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I tried to activate Agg by adding matplotlib.use('Agg') in my code.
>>> Before it I have imported:
>>>
>>>
>> matplotlib.use('Agg') must be importet before
>>
>>
>>> import numpy as np
>>> import mne
>>> from mne.io import Raw
>>> import os
>>> from mne.preprocessing import ICA, create_eog_epochs
>>> import matplotlib
>>>
>>
>> the line below
>>
>>
>>>  import matplotlib.pyplot as plt
>>>
>>>
>> can you confirm this is the case?
>>
>>
>>>  I also added plt.close('all') at the end of the code.
>>> I started python without --pylab qt flag (i.e. typing ipython).
>>>
>>> However, I think that Agg is not activated because the script still
>>> plots the figures and waits until the figure is closed.
>>>
>>> -Maria
>>>
>>>
>>> 2014-08-17 19:32 GMT+03:00 Denis-Alexander Engemann <
>>> denis.engemann at gmail.com>:
>>>
>>> Maria, does this happen for all plots that you try not to show? Might be
>>>> a bug in that particular function.
>>>>
>>>> Btw. what did you mean when you said the script is running very long
>>>> time?
>>>> You mean it hangs (because it's waiting for you to close the figures)?
>>>> Have you been able to activate the 'Agg' silent backend using the lines
>>>> I suggested?
>>>>
>>>> -Denis
>>>>
>>>> On Sun, Aug 17, 2014 at 6:27 PM, Maria Hakonen <maria.hakonen at gmail.com
>>>> > wrote:
>>>>
>>>>> I have set the show parameter false as follows:
>>>>>  ica.plot_sources(epochs_bp,eog_inds,show=False)
>>>>>
>>>>> However, the figures are still shown. I wonder what could be wrong
>>>>> there?
>>>>>
>>>>> -Maria
>>>>>
>>>>>
>>>>>
>>>>> 2014-08-17 16:26 GMT+03:00 Alexandre Gramfort <
>>>>> alexandre.gramfort at telecom-paristech.fr>:
>>>>>
>>>>> hi Maria,
>>>>>>
>>>>>> > Thanks for the answer.
>>>>>> > However, the script seems to run very long time if ipython is
>>>>>> started
>>>>>> > without --pylab qt flag. I wonder if there is any other ways to
>>>>>> save the
>>>>>> > figures in the loop without displaying them?
>>>>>>
>>>>>> most viz functions have a show parameter that is true by default. Set
>>>>>> it
>>>>>> to false to avoid showing the figures.
>>>>>>
>>>>>> HTH
>>>>>> Alex
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