[Mne_analysis] [merge/add/replace events & save - not?]
Virginie van Wassenhove
virginie.van.wassenhove at gmail.com
Wed Aug 1 08:04:23 EDT 2018
External Email - Use Caution
OK but that solution does not work for this analysis and/or not practical
because I only need these triggers to crop data (unless I can pass an
events file in a raw or sss appended data?)
+ I want to illustrate that this is not intuitive for the end user.
- it was pointed out I had code error with overlapping variable names
(evts, tmpevts) but when this solved, that does not change anything .
- if I do this (case 5)
tmpevts = mne.merge_events(evts, [1],
runs_info['evts_list'][r-1][0],replace_events=True)
tmpevts = mne.merge_events(tmpevts, [2],
runs_info['evts_list'][r-1][1],replace_events=True)
print(tmpevts)
[[ 63196 0 102]
[363197 0 202]]
I get what I want (with no real need to preserve prior triggers) but it is
still does not get saved
blah = mne.find_events(tmp, stim_channel=stim_channel, output='onset',
min_duration=0.001, uint_cast=True,
initial_event=True)
2 events found
Event IDs: [1 2]
On Wed, Aug 1, 2018 at 1:44 PM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:
> External Email - Use Caution
>
> hi Virginie,
>
> as you have a single stim channel you cannot have 2 events with different
> values
> at the same instant. So what you wish is not possible like this.
>
> What you can do however is to store the events you want in a distinct file.
>
> You can use:
>
> https://martinos.org/mne/stable/generated/mne.write_events.html
>
> Note that you can pass events to raw.plot to see when are the events you
> used.
> It's a good sanity check that they are correct.
>
> HTH
> Ale
>
>
> On Wed, Aug 1, 2018 at 1:38 PM Virginie van Wassenhove
> <virginie.van.wassenhove at gmail.com> wrote:
> >
> > External Email - Use Caution
> >
> > Here are simplified steps + 4 cases used to try and explain what I would
> think as inconsistencies from the user's viewpoint:
> >
> > #__________________________
> > #load raw, maxfilter, find events
> > #__________________________
> > raw = mne.io.Raw(fname, allow_maxshield=True, preload=True)
> > sss = maxwell_filter(raw, calibration=cal_path, cross_talk=ct_path,
> > verbose=False, destination=refrun_path,
> > bad_condition='warning')
> > #find events
> > evts = mne.find_events(sss, stim_channel=stim_channel, output='onset',
> > min_duration=0.001, uint_cast=True,
> initial_event=True)
> > print(evts)
> > 2 events found
> > Event IDs: [1 2]
> > [[ 63196 0 1]
> > [363197 0 2]]
> >
> > _________________________________________________________
> > (1) Case 1: does "merge" (or here, add) events but does not save
> > _________________________________________________________
> > #add events
> > evts = mne.merge_events(evts, [1],
> runs_info['evts_list'][r-1][0],replace_events=False)
> > evts = mne.merge_events(evts, [2],
> runs_info['evts_list'][r-1][1],replace_events=False)
> >
> > print(evts)
> > [[ 63196 0 1]
> > [ 63196 0 102]
> > [363197 0 2]
> > [363197 0 202]]
> >
> > sss.resample(returnResampFreq(), npad="auto", events=evts)
> > sss.save(sss_fname, overwrite=True, verbose=False)
> > del raw, evts, sss
> >
> > # reload and check after saving
> > tmp = mne.io.Raw(sss_fname, preload=True)
> > evts = mne.find_events(tmp, stim_channel=stim_channel, output='onset',
> > min_duration=0.001,
> > uint_cast=True, initial_event=True)
> > print(evts)
> > 2 events found
> > Event IDs: [1 2]
> > [[15799 0 1]
> > [90799 0 2]]
> >
> > __________________________________________________
> > (2) Case 2: does "merge" (or here, add) events but does not save
> > [same as Case 1 w/o resampling] => resampling not an issue just to check
> > _________________________________________________________
> > evts = mne.merge_events(evts, [1],
> runs_info['evts_list'][r-1][0],replace_events=False)
> > evts = mne.merge_events(evts, [2],
> runs_info['evts_list'][r-1][1],replace_events=False)
> > print(evts)
> > [[ 63196 0 1]
> > [ 63196 0 102]
> > [363197 0 2]
> > [363197 0 202]]
> > sss.save(sss_fname, overwrite=True, verbose=False)
> >
> > # reload and check after saving
> > tmp = mne.io.Raw(sss_fname, preload=True)
> > evts = mne.find_events(tmp, stim_channel=stim_channel, output='onset',
> > min_duration=0.001,
> > uint_cast=True, initial_event=True)
> > print(evts)
> > 2 events found
> > Event IDs: [1 2]
> > [[ 63196 0 1]
> > [363197 0 2]]
> >
> > _______________________________________________________
> > (3) Case 3: does merge events but also add values and save
> > _________________________________________________________
> > same as (1) with add_events and no resampling of sss before saving
> > sss.add_events(evts,stim_channel)
> > sss.save(sss_fname, overwrite=True, verbose=False)
> >
> > # reload and check after saving
> > tmp = mne.io.Raw(sss_fname, preload=True)
> > evts = mne.find_events(tmp, stim_channel=stim_channel, output='onset',
> > min_duration=0.001, uint_cast=True,
> initial_event=True)
> > 2 events found
> > Event IDs: [103 204]
> > [[ 63196 0 103]
> > [363197 0 204]]
> >
> > _______________________________________________________
> > (4) Case 4: file in which there is no trigger to start with but I want
> to create some
> > _________________________________________________________
> > print(evts)
> > []
> >
> > #add evt on 50 consecutive samples (tried with 1 to 100, same outcome)
> > for si in range(0,50):
> > tmpevts += ([[sss.first_samp+si, 0, runs_info['evts_list'][r-1][0]]])
> > for si in range(0,50):
> > tmpevts += ([[sss.last_samp-si, 0, runs_info['evts_list'][r-1][1]]])
> >
> > sss.add_events(tmpevts,stim_channel)
> > sss.save(sss_fname, overwrite=True, verbose=False)
> >
> > # reload and check after saving
> > tmp = mne.io.Raw(sss_fname, preload=True)
> > evts = mne.find_events(tmp, stim_channel=stim_channel, output='onset',
> > min_duration=0.001, uint_cast=True,
> initial_event=True)
> > 2 events found
> > Event IDs: [101 201]
> > ____________________________________
> >
> > From these, I conclude that adding events with add_events may be saved
> when the initial event values are 0 and there are no triggers in the file.
> > If there are triggers at the sample I wish to transform w/o preserving
> existing triggers (value adding), it is saved.
> > If there are triggers at the sample I wish to transform while
> preserving existing triggers (duplicating sample and adding new values) it
> is not saved (*that's what I wish)
> > So the only option to save changes in events is to do a merge with
> replacement (aka adding value) but then I lose initial triggers.
> >
> >
> >
> > Virginie van Wassenhove
> >
> >
> >
> >
> >
> >
> > On Wed, Aug 1, 2018 at 11:54 AM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
> >>
> >> External Email - Use Caution
> >>
> >> hi Virginie,
> >>
> >> did you use:
> >>
> >>
> https://martinos.org/mne/dev/generated/mne.io.Raw.html#mne.io.Raw.add_events
> >>
> >> ?
> >>
> >> if you create events and add them with this method it should then be
> >> save to disk
> >> when writing the updated file. If it's not the case we have a bug.
> >>
> >> Alex
> >> On Wed, Aug 1, 2018 at 9:57 AM Virginie van Wassenhove
> >> <virginie.van.wassenhove at gmail.com> wrote:
> >> >
> >> > External Email - Use Caution
> >> >
> >> > Hi everyone,
> >> >
> >> > long story short, why saving a raw/sss file to which I either added
> or merged events do not actually preserve the new events? (longer story
> below)
> >> >
> >> > Thanks,
> >> > Virginie
> >> >
> >> >
> >> > Longer story:
> >> >
> >> > My goal: mark the initial/final few samples of raw data (not just
> with annotations but with my own new trigger) or replace existing triggers
> with new ones. This is so I can crop again preprocessed data (sss
> post-reject post-ICA raw) as I wish, after I concatenated runs to apply ICA.
> >> >
> >> > I tried:
> >> > - using merge/add operations (all going fine detecting the events I
> want to replace) but some events are systematically missing after I saved
> the file and reload it;
> >> > - tried to catch missing triggers again and redo the same operations
> before concatenation but the sss file is still not being saved with the
> added/replaced events
> >> >
> >> > What am I missing? Do you consider it no desirable to be able to
> rewrite a preprocessed sss file with new events?
> >> > Thanks.
> >> >
> >> >
> >> > Virginie van Wassenhove
> >> > https://brainthemind.com/
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Mne_analysis mailing list
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> >> >
> >> >
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