Handle EGI MFF files with multiple epochs

mne.io.read_raw_egi does not properly process MFF files with multiple epochs. In the worst case, the function returns, but the events are misaligned with respect to the data. In the best case, the function raises an exception as events are created beyond the end of the recording as below. The event start times need to be adjusted to account for any time gaps between the epochs.

 data = mne.io.read_raw_egi('test.mff')
Reading EGI MFF Header from test.mff...
    Reading events ...
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-2-b23e6b31e949> in <module>()
----> 1 data = mne.io.read_raw_egi('test.mff')

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/egi.py in read_raw_egi(input_fname, montage, eog, misc, include, exclude, preload, channel_naming, verbose)

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/utils.py in verbose(function, *args, **kwargs)
    727         with use_log_level(verbose_level):
    728             return function(*args, **kwargs)
--> 729     return function(*args, **kwargs)
    730 
    731 

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/egi.py in read_raw_egi(input_fname, montage, eog, misc, include, exclude, preload, channel_naming, verbose)
    164     if input_fname.endswith('.mff'):
    165         return _read_raw_egi_mff(input_fname, montage, eog, misc, include,
--> 166                                  exclude, preload, channel_naming, verbose)
    167     return RawEGI(input_fname, montage, eog, misc, include, exclude, preload,
    168                   channel_naming, verbose)

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/egimff.py in _read_raw_egi_mff(input_fname, montage, eog, misc, include, exclude, preload, channel_naming, verbose)

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/utils.py in verbose(function, *args, **kwargs)
    727         with use_log_level(verbose_level):
    728             return function(*args, **kwargs)
--> 729     return function(*args, **kwargs)
    730 
    731 

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/egimff.py in _read_raw_egi_mff(input_fname, montage, eog, misc, include, exclude, preload, channel_naming, verbose)
    258     """
    259     return RawMff(input_fname, montage, eog, misc, include, exclude,
--> 260                   preload, channel_naming, verbose)
    261 
    262 

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/egimff.py in __init__(self, input_fname, montage, eog, misc, include, exclude, preload, channel_naming, verbose)

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/utils.py in verbose(function, *args, **kwargs)
    727         with use_log_level(verbose_level):
    728             return function(*args, **kwargs)
--> 729     return function(*args, **kwargs)
    730 
    731 

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/egimff.py in __init__(self, input_fname, montage, eog, misc, include, exclude, preload, channel_naming, verbose)
    278 
    279         logger.info('    Reading events ...')
--> 280         egi_events, egi_info = _read_events(input_fname, egi_info)
    281         gains = _get_gains(op.join(input_fname, egi_info['info_fname']))
    282         if egi_info['value_range'] != 0 and egi_info['bits'] != 0:

/Users/roh17004/anaconda3/lib/python3.6/site-packages/mne/io/egi/events.py in _read_events(input_fname, info)
     30     for n, event in enumerate(event_codes):
     31         for i in mff_events[event]:
---> 32             events[n][i] = n + 1
     33     return events, info
     34 

IndexError: index 413166 is out of bounds for axis 0 with size 413096

[rhancockn]

@larsoner Yes, I have a first pass at a fix, but it fails some preload=False test cases. I will take another look at getting this integrated and passing.

[larsoner]

Ahh right forgot about that, thanks @rhancockn . That should be good enough for at least developing a solution for people to test in the meantime.