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Bug 2673 - ft_rejectvisual plots all channels
| Status | CLOSED FIXED |
| Reported | 2014-08-12 13:10:00 +0200 |
| Modified | 2018-11-22 16:51:26 +0100 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P5 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: | http://bugzilla.fcdonders.nl/show_bug.cgi?id=2625http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3459 |
- 2014-08-12 13:10:25 +0200
Hi guys, ft_rejectvisual (in latest FT-version used at DCCN: '/home/common/matlab/fieldtrip'), plots all channels instead of only the MEG channels. This is happening despite the following cfg I'm using: cfg = []; cfg.layout = 'CTF275.lay'; cfg.channel = 'MEG'; data_rejvis = ft_rejectvisual(cfg,data_denoise); Best, Erik te Woerd
Diego Lozano Soldevilla - 2014-08-12 13:40:26 +0200
(In reply to e.tewoerd from comment #0) Fixed Transmitting file data . Committed revision 9772.
Nir Ofir - 2018-09-13 10:38:08 +0200
Created attachment 871 Example data structure
Nir Ofir - 2018-09-13 10:41:50 +0200
Hi, I tried using cfg to select trials and/or channels with ft_rejectvisual, but the function disregards it. The trial selection seems to have no effect, while selecting channels means that subplot are still creadted but have no traces in them. I'm using the latest FT from the FTP (2018/09/12). I attached example data, and here are the lines I used to call ft_rejectvisual: cfg = []; cfg.trials = 1; cfg.channel = 1; cfg.method = 'trial'; cfg.preproc.detrend = 'yes'; ft_rejectvisual(cfg, dat) Thanks, Nir Ofir
Jan-Mathijs Schoffelen - 2018-11-05 13:32:42 +0100
If you want this to work, how would you suggest it to be fixed? I think that what is missing from the function is a call to ft_selectdata (which is typically used early in a fieldtrip function to select channels and trials). Just look in ft_timelockanalysis or ft_freqnalysis to get inspired. Please file a pull request with a suggested fix to ft_rejectvisual on the FT repository on github. Also, note that the people who are working on improvements of the code, don't do this because their boss wants them to do it, it's on a voluntary basis, so that means that filing something as a bug does not automatically mean that it will be fixed for you.
Jan-Mathijs Schoffelen - 2018-11-05 13:34:15 +0100
*** Bug 3459 has been marked as a duplicate of this bug. ***
Diego Lozano Soldevilla - 2018-11-06 09:27:10 +0100
(In reply to Jan-Mathijs Schoffelen from comment #4) I added selectdata early in ft_rejectvisual https://github.com/fieldtrip/fieldtrip/pull/868 Let me know what do you think
Jan-Mathijs Schoffelen - 2018-11-06 09:32:29 +0100
Good stuff Diego! Thanks for doing Nir's work :).
Diego Lozano Soldevilla - 2018-11-06 09:51:24 +0100
(In reply to Jan-Mathijs Schoffelen from comment #7) my pleasure!
Nir Ofir - 2018-11-12 16:26:46 +0100
(In reply to Diego Lozano Soldevilla from comment #8) Thanks for doing my work :) Next time I would do it myself. Anyway, the previous correction doesn't work as intended: the functions called by ft_rejectvisual (rejectvisual_trial, rejectvisual_channel and rejectvisual_summary) do their own sort of data selection (which I'll elaborate in a second). The outcome is that if I were to use cfg.trials starting not at 1 (say 10:20), the function would crash after the interactive part, because it will look for the non-existing trials 10:20. This happens because the specific functions (trial, channel and summary) are built such that instead of only showing the chosen trials, they mark them as BAD, and then allow the user to revert that decision, like this: (this is the beginning of rejectvisual_trial, rejectvisual_channel and rejectvisual_summary) ntrl = length(data.trial); if isequal(cfg.trials, 'all') % support specification like 'all' cfg.trials = 1:ntrl; end trlsel = false(1,ntrl); trlsel(cfg.trials) = true; If I use cfg.trials=10:20, the last line of the snippet is going to ADD new elements to trlsel instead of just changing their values. This trlsel ends up as used in line 406 in ft_rejectvisual: data = ft_selectdata(tmpcfg, data); This call of ft_selectdata attempts selecting trials that were removed from data at lines 207-211 in the correction of ft_rejectvisual. Because of the way ft_rejectvisual was written, I suggest the following: 1. Revert the correction for now. 2. Give me a week or two to push a new correction that will not cause this issue and will not be so "patchy" (having data selection twice in the function). I would like to hear your thoughts now, and sorry for wasting your time. Best, Nir
Diego Lozano Soldevilla - 2018-11-12 16:55:59 +0100
Hi Nir, Thank your for your work and sorry for introducing my NO-FIX. Your proposal sounds good to me. I failed to see that rejectvisual_trial, rejectvisual_channel and rejectvisual_summary do their own sort of data selection: my bad