[Mne_analysis] Saving data from mne.Epochs

[Alexandre Gramfort]

hi Vincent,

I suspect you're not actually running the last released version. To check

>>> import mne
>>> print mne.__version__

you should see 0.5 or more.

HTH
Alex

On Tue, Feb 12, 2013 at 10:17 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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