Back to the main page.
Bug 1305 - preproc requires the deprecated offset as input
| Status | CLOSED FIXED |
| Reported | 2012-02-01 14:38:00 +0100 |
| Modified | 2013-01-17 10:44:31 +0100 |
| Product: | FieldTrip |
| Component: | preproc |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P3 minor |
| Assigned to: | Roemer van der Meij |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Roemer van der Meij - 2012-02-01 14:38:56 +0100
Roemer van der Meij - 2012-02-01 14:47:04 +0100
Fixed for clip, zvalue was already fixed some time ago by someone else.
Boris Reuderink - 2012-02-06 15:57:04 +0100
Roemer, I looked through you commits from this period, but I can't find it. Could you look up you change?
Roemer van der Meij - 2012-02-06 17:11:58 +0100
Woops! Wrong bug. I was wondering why I had to close another twice bug twice last wednessday, I appears I accidentally replied and closed this bug. I'll reopen and remove my last comments. (I did nothing to preproc)
Jan-Mathijs Schoffelen - 2012-02-08 13:32:36 +0100
Roemer, could you look into this?
Roemer van der Meij - 2012-02-10 13:57:46 +0100
From the looks of it, offset is a irrelevant field in prerpoc. It is only used to create a time-axis, is a piece of cake to replace it with the non-deprecated time-axis. (i.e. no computation is being done with it). There are not that many dependencies on preproc: (see below) However, what I am more worried about, is external dependencies... The preproc module is being used by SPM right? Can I edit all the below functions and replace offset with time without breaking anything outside of fieldtrip? grep 'preproc(' *.m */*.m */*/*.m */*/*/*.m */*/*/*/*.m ft_artifact_clip.m: datflt = preproc(dat, label, hdr.Fs, artfctdef, trl(trlop,3)); ft_artifact_ecg.m: ecg{j} = preproc(ecg{j}, artfctdef.channel, hdr.Fs, artfctdef, [], fltpadding, fltpadding); ft_artifact_threshold.m: dat = preproc(dat, channel, hdr.Fs, artfctdef, cfg.trl(trlop,3)); ft_artifact_zvalue.m: dat = preproc(dat, cfg.artfctdef.zvalue.channel, hdr.Fs, cfg.artfctdef.zvalue, [], fltpadding, fltpadding); ft_artifact_zvalue.m: dat{trlop} = preproc(dat{trlop}, cfg.artfctdef.zvalue.channel, hdr.Fs, cfg.artfctdef.zvalue, [], fltpadding, fltpadding); ft_artifact_zvalue.m: dat = preproc(dat, cfg.artfctdef.zvalue.channel, hdr.Fs, cfg.artfctdef.zvalue, [], fltpadding, fltpadding); ft_artifact_zvalue.m:% dat{trlop} = preproc(dat{trlop}, cfg.artfctdef.zvalue.channel(sgnlop), hdr.Fs, cfg.artfctdef.zvalue, [], fltpadding, fltpadding); ft_artifact_zvalue.m:%data = preproc(data, '', hdr.Fs, artcfg, [], artcfg.fltpadding, artcfg.fltpadding); ft_connectivitysimulation.m: mixsignal = preproc(mixsignal, label, cfg.fsample, cfg, -fltpad, fltpad, fltpad); ft_connectivitysimulation.m: newtmp = preproc(newtmp, label, cfg.fsample, cfg, -fltpad, fltpad, fltpad); ft_databrowser.m:[dat, lab, tim] = preproc(dat, opt.hdr.label(chanindx), opt.fsample, cfg.preproc, offset); ft_preprocessing.m: [dataout.trial{i}, dataout.label, dataout.time{i}, cfg] = preproc(data.trial{i}(rawindx,:), data.label(rawindx), data.fsample, cfg, time2offset(data.time{i},data.fsample)); ft_preprocessing.m: [cutdat{i}, label, time{i}, cfg] = preproc(dat, hdr.label(rawindx), hdr.Fs, cfg, cfg.trl(i,3), begpadding, endpadding); ft_spikedetection.m: dat = preproc(org, hdr.label(i), hdr.Fs, cfg.preproc); ft_spikedownsample.m: dat = preproc(org, label, hdr.Fs, cfg.preproc); ft_volumesegment.m: p = spm_preproc(Va, px); ft_volumesegment.m: p = spm_preproc(Va); compat/ft_artifact_manual.m: [dataY{i}, dumlab, dumtime, dumcfg] = preproc(dataY{i}', cfg.artfctdef.manual.channel, hdr.Fs, cfg.artfctdef.manual, cfg.trl(i,3)-begpadding, 0, 0); compat/ft_databrowser_old.m:[dat, lab, tim] = preproc(dat, opt.hdr.label(chanindx), opt.fsample, opt.cfg.preproc, offset); private/artifact_viewer.m:% data = preproc(data, channel, hdr.Fs, artfctdef, [], fltpadding, fltpadding); private/preproc.m:function [dat, label, time, cfg] = preproc(dat, label, fsample, cfg, offset, begpadding, endpadding) private/preproc.m:% [dat, label, time, cfg] = preproc(dat, label, fsample, cfg, offset, begpadding, endpadding) private/preproc.m: [dat ] = preproc(dat, label, fsample, tmpcfg, offset, begpadding, endpadding); private/preproc.m: [dat, label ] = preproc(dat, label, fsample, tmpcfg, offset, begpadding, endpadding); private/preproc.m: [dat, label, time ] = preproc(dat, label, fsample, tmpcfg, offset, begpadding, endpadding); private/preproc.m: [dat, label, time, tmpcfg] = preproc(dat, label, fsample, tmpcfg, offset, begpadding, endpadding); private/rejectvisual_channel.m: [data.trial{i}, label, time, cfg.preproc] = preproc(data.trial{i}, data.label, fsample, cfg.preproc, offset(i)); private/rejectvisual_summary.m: [dat] = preproc(info.data.trial{i}, info.data.label, info.fsample, info.cfg.preproc, info.offset(i)); private/rejectvisual_summary.m: [dat, label, time, info.cfg.preproc] = preproc(info.data.trial{i}, info.data.label, info.fsample, info.cfg.preproc, info.offset(i)); private/rejectvisual_trial.m: [data.trial{i}, label, time, cfg.preproc] = preproc(data.trial{i}, data.label, fsample, cfg.preproc, offset(i)); external/spm8/spm_preproc.m:function results = spm_preproc(varargin) external/spm8/spm_preproc.m:% FORMAT results = spm_preproc(V,opts) realtime/example/ft_realtime_downsample.m: % dat = preproc(data.trial{1}, data.label, data.fsample, cfg);
Roemer van der Meij - 2012-02-10 14:52:37 +0100
(I added Robert as CC)
Arjen Stolk - 2012-02-15 13:24:23 +0100
(In reply to comment #6) also remove fsample, and replace it with timeaxis
Roemer van der Meij - 2012-02-29 17:16:55 +0100
changed to input to preproc to be dat, label, time, cfg, optional, and removed the fsample and offset as input. Preproc itself has not been adjusted thoroughly inside, but all code to mak e it work is in place. After this, preproc itself can be cleaned up. --This line, and those below, will be ignored-- M ft_artifact_threshold.m M ft_connectivitysimulation.m M ft_preprocessing.m M ft_spikedetection.m M ft_spikedownsample.m M ft_databrowser.m M ft_artifact_ecg.m M private/preproc.m M private/rejectvisual_summary.m M private/rejectvisual_channel.m M private/rejectvisual_trial.m M ft_artifact_clip.m M compat/ft_databrowser_old.m M compat/ft_artifact_manual.m M ft_artifact_zvalue.m Next step, is adjusting and cleaning up preproc on the inside. (keeping bug open)
Roemer van der Meij - 2012-03-02 15:17:44 +0100
Preproc has been cleaned up, there were only a few lines that were no longer necessary. Switch is now complete, and if now preproccesing bugs pop up during the next few days the bug can be closed.