[Mne_analysis] Saving data from mne.Epochs

[Eric Larson]

Hey Vincent,

Yes, you should be able to save epochs with 'epochs.save()'. Could you
double-check that "mne.__version__" is at '0.6.git'? That's the development
version, and it should have support for the '.save()' method. (I think the
most recent release version 0.5 also had it, incidentally.)

Eric



On Tue, Feb 12, 2013 at 1:17 PM, Vincent Rupp <rupp.vincent at gmail.com>wrote:

> Hello all,
>
> I am trying to epoch resting MEG data into 4 second events, remove EOG
> artifacts, and save as a new file including only the good epochs. I've
> upgraded to the latest nightly yesterday and attempted running this script,
> but it fails to save with this error message: *
>
> AttributeError: 'Epochs' object has no attribute 'save'*
>
> Doesn't mne.epochs return an object which should be able to save as a fif
> file?
>
> Here is my full script in case it helps to look at:
>
> *data_path = '/home/vrupp/data/restMEG/'
> subj = raw_input('Subject ID:')
> raw_fname = data_path + subj + '/' + subj + '_rest_raw_sss.fif'
> event_id, tmin, tmax = 1, 0.0, 4.0
>
> # Setup for reading the raw data
> raw = fiff.Raw(raw_fname)
>
> # Epoch data into 4s intervals
> events = mne.make_fixed_length_events(raw, 1, start=0, stop=None,
>         duration=4.)
>
> # Set up pick list: (MEG-bad channels)
> exclude = raw.info['bads']
> picks = fiff.pick_types(raw.info, meg=True, eeg=False, stim=True,
> eog=True,
>         exclude=exclude)
>
> # Read epochs and remove bad epochs
> epochs_outfile = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
>         picks=picks, baseline=(None, 0), preload=True,
>         reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
>
> # Save output file
> epochs_outfile.save(data_path + subj + '/' + subj + '_rest_raw_epoch.fif')
> *
>
> Thanks very much for any help.
>
>
> Best wishes,
>
> Vincent Rupp
>
>
> On Mon, Dec 17, 2012 at 4:10 PM, Denis-Alexander Engemann <
> d.engemann at fz-juelich.de> wrote:
>
>>  Hi Vincent,
>>
>>  the code you posted constructs an epochs object from which you get the
>> data by calling .get_data().
>> The returned value however is not an epochs object anymore but a regular
>> numpy array.
>> For saving your epochs say:
>>
>>  myepochs.save('subj_rest_raw_epoch.fif')
>>
>>  However make sure your mne-python version already supports this quite
>> recent method.
>> In IPython try myepochs. <TAB> and see whether 'save'  is being provided.
>> In case you don't use the current development master, there will be an
>> official new relase before christmas.
>>
>>  I hope this helps.
>>
>>  Denis
>>
>>
>>
>>
>>
>> On Tue, Dec 18, 2012 at 12:22 AM, Vincent <cloud.ctl at gmail.com> wrote:
>>
>>>  Greetings,
>>>
>>>  When running a script which contains the following line:
>>>
>>> <<<
>>> # Read epochs
>>> myepochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
>>>         picks=picks, baseline=(None, 0), preload=True,
>>>         reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
>>> outfile = myepochs.get_data()
>>>
>>> outfile.save('subj_rest_raw_epoch.fif')
>>>  >>>
>>>
>>>  *I receive this error message:
>>>
>>> *<<<
>>> Traceback (most recent call last):
>>>   File "resting_V3.py", line 55, in <module>
>>>     outfile.save('subj_rest_raw_epoch.fif')
>>> AttributeError: 'numpy.ndarray' object has no attribute 'save'
>>> >>>
>>>
>>>   *Alternatively, I could forgo running epochs.get_data and just save
>>> directly (epochs.save(...))*,
>>>
>>> but I run into the same error except it specifies "Epochs" instead of
>>> "numpy.ndarray" as the object with no 'save' attribute.
>>>
>>>  Is this error occurring because of a problem with my script, or might
>>> I have something wrong with my installation of mne-python?
>>>
>>>  Thank you in advance.
>>>
>>>  ::vincent
>>>
>>>
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