[Mne_analysis] BrainVision files
Teon Brooks
teon.brooks at gmail.com
Tue Jan 5 16:30:31 EST 2016
Hi Boris,
If I understand this correctly, you're saying that you want to preserve the
string information?
In MNE, the default is to have events represented as int and these are
later referred to by strings in a dict. The event_id that is mentioned in
the raw reader would be the same one you could use in your epochs
constructor. This will allow you refer to the events as strings again.
Since the underlying data representation are numpy.array of floats, this is
the best approach to maintain max cross-talk to other packages.
If I missed the mark, could you share an example file with me, and try
expressing again what you want the reader to do.
HTH,
On Tue, Jan 5, 2016 at 16:24 Boris BURLE <boris.burle at univ-amu.fr> wrote:
> Hi Jona,
>
> Thanks for looking at it.
>
> On 05/01/2016 22:13, Jona Sassenhagen wrote:
> > Teon has recently added extended BV support:
> > https://github.com/mne-tools/mne-python/pull/2634/files
> >
> > Now with the most up-to-date version,
> >
> > event_id :dict | None
> > Theid of the event to consider. If None (default),
> > only stimulus events are added to the stimulus channel. Ifdict,
> > the keys will be mapped to trigger values on the stimulus
> channel
> > in addition to the stimulus events. Keys are case-sensitive.
> > Example: {'SyncStatus':1;'Pulse Artifact':3}.
> >
> >
> > Does that help?
> >
>
> Not really, since this still assumes that the trigger values are
> integers, and we translate those integers into strings (or whatever).
> But if the triggers are already strings, then the code fails.
>
> A workaround could be to check whether "trigger" is an int, and if not,
> return keep the description (mdesc) of the event. Code around line 206
> would read:
>
> if mtype.lower().startswith('response'):
> if response_trig_shift is not None:
> if isinstance(trigger, int):
> trigger += response_trig_shift
> else:
> trigger = mdesc
>
>
> This small modification helps reading files with marker descriptions
> such as "Resp_Left" for example. But I'm not sure whether that would
> introduce other issues elsewhere...
>
> hope this helps...
> B.
>
> >
> >> On 5 Jan 2016, at 22:10, Alexandre Gramfort
> >> <alexandre.gramfort at telecom-paristech.fr
> >> <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> >>
> >> Jona and Teon. Any thought on this?
> >>
> >> thanks
> >> Alex
> >>
> >> On Tue, Jan 5, 2016 at 5:56 PM, Boris BURLE <boris.burle at univ-amu.fr
> >> <mailto:boris.burle at univ-amu.fr>> wrote:
> >>
> >> Hi again,
> >>
> >> Trying to find the issue, I realized that my installed version of
> mne
> >> was pretty old (0.8.6), and that this issue has already been fixed
> (at
> >> least it is in the dev version...). I apologize for that...
> >>
> >> But I found another issue:
> >>
> >> If I read correctly, it looks like line 201 of _read_vmrk_events
> >> assumes
> >> that response triggers name must contain an integer, probably
> >> considering that the names are "Rxxx", with "xxx" being integers.
> >> However, this is not a requirement of the file format and,
> especially
> >> after some preprocessing, the triggers names may have been changed
> to
> >> pure text (for example 'LeftResp'). In this case, the code does
> >> not seem
> >> to work, since 'trigger' is None, and line 206 issues an error:
> >>
> >> trigger += response_trig_shift
> >> TypeError: unsupported operand type(s) for +=: 'NoneType' and 'int'
> >>
> >> Am I reading the code correctly?
> >>
> >> Thanks in advance,
> >> B.
> >>
> >>
> >>
> >>
> >>
> >> On 05/01/2016 13:32, Alexandre Gramfort wrote:
> >> > hi Boris,
> >> >
> >> > our test data are in:
> >> >
> >> >
> >>
> https://github.com/mne-tools/mne-python/tree/master/mne/io/brainvision/tests/data
> >> >
> >> > don't hesitate to share a file so we can patch the reader to fix
> >> the issue.
> >> >
> >> > Best,
> >> > Alex
> >> >
> >> > On Tue, Jan 5, 2016 at 10:17 AM, Boris BURLE
> >> <boris.burle at univ-amu.fr <mailto:boris.burle at univ-amu.fr>> wrote:
> >> >> Dear colleagues,
> >> >>
> >> >> I'm just starting to use MNE-python, and I face a problem opening
> >> >> BrainVisionAnalyer files. When calling the
> >> >> "mne.io.read_raw_brainvision", I get the following error (full
> >> traceback
> >> >> at the end):
> >> >>
> >> >> --> 462 params, settings = settings.split('[Comment]')
> >> >> 463 cfg = configparser.ConfigParser()
> >> >> 464 if hasattr(cfg, 'read_file'): # newer API
> >> >>
> >> >> ValueError: need more than 1 value to unpack
> >> >>
> >> >> It appears that 'read_raw_brainvision' is searching for a
> "section"
> >> >> untitled "Comment" in the header (vhdr) file. I have been using
> >> >> BrainVision files quite a lot (actually, I would like to get
> >> rid of it
> >> >> by using mne-python...), and I never encountered such a
> >> "Comment" field
> >> >> in my vhdr files. However, I always worked with data
> >> **exported** from
> >> >> BrainVision, not acquired with it. So I guess the "Comment"
> >> field the
> >> >> parser is searching might come from the files created by
> >> >> BrainVisionRecorder. But since I do not have any such file, I
> >> cannot check.
> >> >>
> >> >> I do have python code that, I believe, open all variants of files
> >> >> **exported** from BrainVisionAnalyser (be they ASCII or binary,
> >> 16, 32
> >> >> ... bits etc...). The code outputs a dictionary for the header
> >> (vhdr)
> >> >> file, a numpy.array for the data, and a list of events for the
> >> >> markers/events/triggers. Although I guess it should also open
> files
> >> >> created by BrainVisionRecorder, I cannot be sure.
> >> >>
> >> >> So, if someone could provide me with a small file that is
> currently
> >> >> openable by "mne.io.read_raw_brainvision", I would be happy to
> >> check
> >> >> whether my code also open it. And, if you find it useful, I
> >> would be
> >> >> more than happy to share the code and adapt it to mne-python
> >> (with a bit
> >> >> of help from you, probably ...)
> >> >>
> >> >> All the best,
> >> >> B.
> >> >>
> >> >> full traceback:
> >> >> In [4]: mne.io.read_raw_brainvision('COUBA_EMG_PC_CompLeft.vhdr')
> >> >> Extracting eeg Parameters from COUBA_EMG_PC_CompLeft.vhdr...
> >> >>
> >>
> ---------------------------------------------------------------------------
> >> >> ValueError Traceback (most
> >> recent call last)
> >> >> <ipython-input-4-b9123e703050> in <module>()
> >> >> ----> 1 mne.io.read_raw_brainvision('COUBA_EMG_PC_CompLeft.vhdr')
> >> >>
> >> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc
> in
> >> >> read_raw_brainvision(vhdr_fname, elp_fname, elp_names, preload,
> >> >> reference, eog, ch_names, verbose)
> >> >> 681 """
> >> >> 682 raw = RawBrainVision(vhdr_fname, elp_fname,
> >> elp_names, preload,
> >> >> --> 683 reference, eog, ch_names,
> verbose)
> >> >> 684 return raw
> >> >>
> >> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc
> in
> >> >> __init__(self, vhdr_fname, elp_fname, elp_names, preload,
> >> reference,
> >> >> eog, ch_names, verbose)
> >> >>
> >> >> /usr/lib/python2.7/dist-packages/mne/utils.pyc in
> verbose(function,
> >> >> *args, **kwargs)
> >> >> 549 return ret
> >> >> 550 else:
> >> >> --> 551 ret = function(*args, **kwargs)
> >> >> 552 return ret
> >> >> 553
> >> >>
> >> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc
> in
> >> >> __init__(self, vhdr_fname, elp_fname, elp_names, preload,
> >> reference,
> >> >> eog, ch_names, verbose)
> >> >> 82 self.info <http://self.info/>, self._eeg_info, events
> =
> >> >> _get_eeg_info(vhdr_fname,
> >> >> 83
> >> >> elp_fname, elp_names,
> >> >> ---> 84
> >> >> reference, eog)
> >> >> 85 self.set_brainvision_events(events)
> >> >> 86 logger.info <http://logger.info/>('Creating Raw.info
> >> <http://raw.info> structure...')
> >> >>
> >> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc
> in
> >> >> _get_eeg_info(vhdr_fname, elp_fname, elp_names, reference, eog)
> >> >> 460 settings = f.read()
> >> >> 461
> >> >> --> 462 params, settings = settings.split('[Comment]')
> >> >> 463 cfg = configparser.ConfigParser()
> >> >> 464 if hasattr(cfg, 'read_file'): # newer API
> >> >>
> >> >> ValueError: need more than 1 value to unpack
> >> >>
> >> >> In [5]:
> >> >> _______________________________________________
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> >> >>
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--
teon
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