/
ft_trialfun_general.m
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ft_trialfun_general.m
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function [trl, event] = ft_trialfun_general(cfg)
% FT_TRIALFUN_GENERAL reads events from the dataset using FT_READ_EVENT and
% constructs a trial definition. This function should in general not be called
% directly, it will be called by FT_DEFINETRIAL.
%
% Use this function by calling
% [cfg] = ft_definetrial(cfg)
% where the configuration structure should contain
% cfg.dataset = string with the filename
% cfg.trialdef = structure with the details of trial definition, see below
% cfg.trialfun = 'ft_trialfun_general'
%
% The cfg.trialdef structure can contain the following specifications
% cfg.trialdef.eventtype = string, or cell-array with strings
% cfg.trialdef.eventvalue = number, string, or list with numbers or strings
% cfg.trialdef.prestim = number, latency in seconds (optional)
% cfg.trialdef.poststim = number, latency in seconds (optional)
%
% You can specify these options that are passed to FT_READ_EVENT for trigger detection
% cfg.trialdef.detectflank = string, can be 'up', 'updiff', 'down', 'downdiff', 'both', 'any', 'biton', 'bitoff'
% cfg.trialdef.trigshift = integer, number of samples to shift from flank to detect trigger value
% cfg.trialdef.chanindx = list with channel numbers for the trigger detection, specify -1 in case you don't want to detect triggers
% cfg.trialdef.threshold = threshold for analog trigger channels
% cfg.trialdef.tolerance = tolerance in samples when merging analogue trigger channels, only for Neuromag
%
% If you want to read all data from a continuous file in segments, you can specify
% cfg.trialdef.length = duration of the segments in seconds (can be Inf)
% cfg.trialdef.ntrials = number of trials (optional, can be 1)
% cfg.trialdef.overlap = single number (between 0 and 1 (exclusive)) specifying the fraction of overlap between snippets (0 = no overlap)
%
% See also FT_DEFINETRIAL, FT_TRIALFUN_GUI, FT_TRIALFUN_SHOW
% Copyright (C) 2005-2023, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% most defaults are in trialdef
cfg.trialdef = ft_getopt(cfg, 'trialdef', struct());
% check if the input cfg is valid for this function
cfg.trialdef = ft_checkconfig(cfg.trialdef, 'renamed', {'triallength', 'length'});
cfg.trialdef = ft_checkconfig(cfg.trialdef, 'renamedval', {'ntrials', inf, []});
% set the defaults
cfg.trialdef.eventtype = ft_getopt(cfg.trialdef, 'eventtype');
cfg.trialdef.eventvalue = ft_getopt(cfg.trialdef, 'eventvalue');
cfg.trialdef.prestim = ft_getopt(cfg.trialdef, 'prestim');
cfg.trialdef.poststim = ft_getopt(cfg.trialdef, 'poststim');
% these options are similar to those in FT_REDEFINETRIALS
cfg.trialdef.length = ft_getopt(cfg.trialdef, 'length');
cfg.trialdef.overlap = ft_getopt(cfg.trialdef, 'overlap', 0); % between 0 and 1
cfg.trialdef.ntrials = ft_getopt(cfg.trialdef, 'ntrials');
% construct the low-level options as key-value pairs, these are passed to FT_READ_HEADER and FT_READ_DATA
headeropt = {};
headeropt = ft_setopt(headeropt, 'headerformat', ft_getopt(cfg, 'headerformat')); % is passed to low-level function, empty implies autodetection
headeropt = ft_setopt(headeropt, 'readbids', ft_getopt(cfg, 'readbids')); % is passed to low-level function
headeropt = ft_setopt(headeropt, 'coordsys', ft_getopt(cfg, 'coordsys', 'head')); % is passed to low-level function
headeropt = ft_setopt(headeropt, 'coilaccuracy', ft_getopt(cfg, 'coilaccuracy')); % is passed to low-level function
headeropt = ft_setopt(headeropt, 'checkmaxfilter', ft_getopt(cfg, 'checkmaxfilter')); % this allows to read non-maxfiltered neuromag data recorded with internal active shielding
headeropt = ft_setopt(headeropt, 'chantype', ft_getopt(cfg, 'chantype', {})); % 2017.10.10 AB required for NeuroOmega files
% construct the low-level options as key-value pairs, these are passed to FT_READ_EVENT
eventopt = {};
eventopt = ft_setopt(eventopt, 'headerformat', ft_getopt(cfg, 'headerformat')); % is passed to low-level function, empty implies autodetection
eventopt = ft_setopt(eventopt, 'dataformat', ft_getopt(cfg, 'dataformat')); % is passed to low-level function, empty implies autodetection
eventopt = ft_setopt(eventopt, 'eventformat', ft_getopt(cfg, 'eventformat')); % is passed to low-level function, empty implies autodetection
eventopt = ft_setopt(eventopt, 'readbids', ft_getopt(cfg, 'readbids'));
eventopt = ft_setopt(eventopt, 'detectflank', ft_getopt(cfg.trialdef, 'detectflank'));
eventopt = ft_setopt(eventopt, 'trigshift', ft_getopt(cfg.trialdef, 'trigshift'));
eventopt = ft_setopt(eventopt, 'chanindx', ft_getopt(cfg.trialdef, 'chanindx'));
eventopt = ft_setopt(eventopt, 'threshold', ft_getopt(cfg.trialdef, 'threshold'));
eventopt = ft_setopt(eventopt, 'tolerance', ft_getopt(cfg.trialdef, 'tolerance'));
eventopt = ft_setopt(eventopt, 'combinebinary', ft_getopt(cfg.trialdef, 'combinebinary'));
eventopt = ft_setopt(eventopt, 'checkmaxfilter', ft_getopt(cfg, 'checkmaxfilter')); % this allows to read non-maxfiltered neuromag data recorded with internal active shielding
% specify the default file formats
cfg.eventformat = ft_getopt(cfg, 'eventformat');
cfg.headerformat = ft_getopt(cfg, 'headerformat');
cfg.dataformat = ft_getopt(cfg, 'dataformat');
cfg.representation = ft_getopt(cfg, 'representation');
% get the header, this is among others for the sampling frequency
if isfield(cfg, 'hdr')
ft_info('using the header from the configuration structure\n');
hdr = cfg.hdr;
else
% read the header, contains the sampling frequency
ft_info('reading the header from ''%s''\n', cfg.headerfile);
hdr = ft_read_header(cfg.headerfile, headeropt{:});
end
% get the events
if isfield(cfg, 'event')
ft_info('using the events from the configuration structure\n');
event = cfg.event;
else
ft_info('reading the events from ''%s''\n', cfg.headerfile);
event = ft_read_event(cfg.headerfile, eventopt{:});
end
if ~isempty(cfg.trialdef.length) && ~isinf(cfg.trialdef.length)
% make as many trials as possible with the specified length and offset
begsample = 1;
endsample = round(hdr.nSamples*hdr.nTrials);
offset = 0;
nsmp = round(cfg.trialdef.length*hdr.Fs);
nshift = round((1-cfg.trialdef.overlap)*nsmp);
alltrl = (begsample:nshift:(endsample+1-nsmp))';
alltrl(:,2) = alltrl(:,1) + nsmp - 1;
alltrl(:,3) = alltrl(:,1) + offset - alltrl(1,1);
% trim to the requested number of trials
if ~isempty(cfg.trialdef.ntrials)
trl = alltrl(1:cfg.trialdef.ntrials,:);
else
trl = alltrl;
end
return
elseif isscalar(cfg.trialdef.ntrials) || isequal(cfg.trialdef.length, inf)
% construct a single trial
if isscalar(cfg.trialdef.ntrials) && cfg.trialdef.ntrials~=1
ft_error('this is only supported for a single trial');
end
begsample = 1;
endsample = round(hdr.nSamples*hdr.nTrials);
offset = 0;
trl = [begsample endsample offset];
return
else
% select events on basis of event types and values
sel = true(1, length(event)); % this should be a row vector
% select all events of the specified type
if isfield(cfg.trialdef, 'eventtype') && ~isempty(cfg.trialdef.eventtype)
for i=1:numel(event)
sel(i) = sel(i) && ismatch(event(i).type, cfg.trialdef.eventtype);
end
elseif isempty(cfg.trialdef.eventtype)
% search for trial events
for i=1:numel(event)
sel(i) = sel(i) && ismatch(event(i).type, 'trial');
end
end
% select all events with the specified value
if isfield(cfg.trialdef, 'eventvalue') && ~isempty(cfg.trialdef.eventvalue)
for i=1:numel(event)
sel(i) = sel(i) && ismatch(event(i).value, cfg.trialdef.eventvalue);
end
end
% convert from boolean vector into a list of indices
sel = find(sel);
% start with an empty list
trl = [];
for i=sel
% catch empty fields in the event table and interpret them meaningfully
if isempty(event(i).offset)
% time axis has no offset relative to the event
event(i).offset = 0;
end
if isempty(event(i).duration)
% the event does not specify a duration
event(i).duration = 0;
end
% determine where the trial starts with respect to the event
if isempty(cfg.trialdef.prestim)
trloff = event(i).offset;
trlbeg = event(i).sample;
else
% override the offset of the event
trloff = round(-cfg.trialdef.prestim*hdr.Fs);
% also shift the begin sample with the specified amount
trlbeg = event(i).sample + trloff;
end
% determine the number of samples that has to be read (excluding the begin sample)
if isempty(cfg.trialdef.poststim)
trldur = max(event(i).duration - 1, 0);
else
% this will not work if prestim was not defined, the code will then crash
trldur = round((cfg.trialdef.poststim+cfg.trialdef.prestim)*hdr.Fs) - 1;
end
trlend = trlbeg + trldur;
if isnumeric(event(i).value) && ~isempty(event(i).value)
trlval = event(i).value;
elseif ischar(event(i).value) && ~isempty(regexp(event(i).value, '^[SR]+[\s]*+[0-9]{1,3}$'))
% This looks like Brainvision event markers. For backward compatibility, convert
% the strings into the numerals following the 'S' or 'R', unless the user has specified
% the cfg.representation to be a table
if ~isequal(cfg.representation, 'table')
ft_warning('Brainvision markers are converted to numeric representation, if you want tabular output please specify cfg.representation=''table''');
trlval = str2double(event(i).value(2:end));
else
trlval = event(i).value;
end
elseif ischar(event(i).value) && ~isequal(cfg.representation, 'numeric')
trlval = event(i).value;
else
% the following depends on cfg.representation
if isequal(cfg.representation, 'numeric') || isempty(cfg.representation)
trlval = nan;
else
trlval = event(i).value;
end
end
% add the trial only if all samples are in the dataset
if trlbeg>0 && trlend<=hdr.nSamples*hdr.nTrials
if isnumeric(trlval)
% create a numeric array
thistrl = [trlbeg trlend trloff trlval];
else
thistrl = cell2table({trlbeg trlend trloff trlval});
end
trl = cat(1, trl, thistrl);
end
end
if ~isempty(trl) && ~istable(trl) && all(isnan(trl(:,4)))
% the values are not informative, remove them
trl = trl(:,1:3);
elseif ~isempty(trl) && istable(trl)
% add names to the columns of the table
trl.Properties.VariableNames = {'begsample', 'endsample', 'offset', 'eventvalue'};
end
end