Can I save a PSD spectrum in an mne .fif file?

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  • MNE version: e.g. 1.3.1
  • operating system: e.g. Windows 10

I am trying to save some epochs as a psd spectrum in a .fif file, so that my colleague can just load them into their computations. I can create the object and save it just fine, but when I try to load it, it gives me the error: ‘[filename] does not start with a file id tag’.

Here is my code:


# make epochs
epochs = mne.Epochs(raw, events=myevents, event_id=events_dict, tmin=ep_start, tmax=ep_end, baseline=(None,None), reject= None) 

# Compute PSD
PSD_epochs = epochs['ML'].compute_psd(method='multitaper', fmin=frqs[0], fmax=frqs[1], picks=sensors[i_sens] ) 

# save psd epochs
fname=PATHOUT+'PSD_MLpochs/' + SUBS[i_sub] + '_'+ CONDS[i_con] + sens[i_sens] + 'ML_psd_epo.fif'
PSD_epochs.save(fname, overwrite=True)

# load to check
loadpochs = mne.read_epochs(fname, preload=True)

Will I need to simply save the extracted data as a numpy array, or is there a way to save the object as it is?

Thanks for reading!

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This saves an HDF5 file, so you shouldn’t use the .fif extension.

You can read the spectrum object back via:

spectrum = mne.time_frequency.read_spectrum(fname)

Best wishes,
Richard

cc @drammock, I wonder if providing an “unsuitable” filename extension during saving should raise an error or a warning.

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as @richard says, EpochsSpectrum.save() does not save in .fif format, it saves in HDF5 format. If your colleague uses MNE-Python, Richard’s suggestion will work fine: they can use mne.time_frequency.read_spectrum(). If your colleague uses MATLAB it should also be possible to read HDF5 files using h5read()

an error seems too strict, but PR welcome to add a warning.

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Thanks! This works perfectly

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