[Mne_analysis] Saving data from mne.Epochs

[Vincent Rupp]

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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