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ft_databrowser.m
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ft_databrowser.m
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function [cfg] = ft_databrowser(cfg, data)
% FT_DATABROWSER can be used for visual inspection of data. Artifacts that
% were detected by artifact functions (see FT_ARTIFACT_xxx functions where
% xxx is the type of artifact) are marked. Additionally data pieces can be
% marked and unmarked as artifact by manual selection. The output cfg
% contains the updated specification of the artifacts. When visually selection
% data, a right-click will bring up a context-menu containing functions to be
% executed on the selected data. You can use your own function using cfg.selfun
% and cfg.selcfg. You can use multiple functions by giving the names/cfgs as a
% cell-array.
%
% In butterfly mode, you can use the "identify" button to reveal the name
% of a channel. Please be aware that it searches only vertically. This
% means that it will return the channel with the amplitude closest to the
% point you have clicked at the specific time point. This might be
% counterintuitive at first.
%
% Use as
% cfg = ft_databrowser(cfg)
% where the configuration structure contains the reference to the dataset
% on your hard disk (see below), or use as
% cfg = ft_databrowser(cfg, data)
% where the input data is a structure as obtained from FT_PREPROCESSING or
% from FT_COMPONENTANALYSIS.
%
% If you want to browse data that is on disk, you have to specify
% cfg.dataset = string with the filename
% Instead of specifying the dataset, you can also explicitely specify the
% name of the file containing the header information and the name of the
% file containing the data, using
% cfg.datafile = string with the filename
% cfg.headerfile = string with the filename
%
% The following configuration options are supported:
% cfg.ylim = vertical scaling, can be 'maxmin', 'maxabs' or [ymin ymax] (default = 'maxabs')
% cfg.zlim = color scaling to apply to component topographies, 'minmax', 'maxabs' (default = 'maxmin')
% cfg.blocksize = duration in seconds for cutting the data up
% cfg.trl = structure that defines the data segments of interest, only applicable for trial-based data
% cfg.continuous = 'yes' or 'no' whether the data should be interpreted as continuous or trial-based
% cfg.channel = cell-array with channel labels, see FT_CHANNELSELECTION
% cfg.plotlabels = 'yes' (default), 'no', 'some'; whether
% to plot channel labels in vertical viewmode ('some' plots one in every ten
% labels; useful when plotting a large number of channels at a time)
% cfg.ploteventlabels = 'type=value', 'colorvalue' (default = 'type=value');
% cfg.viewmode = string, 'butterfly', 'vertical', 'component' for visualizing components e.g. from an ICA (default is 'butterfly')
% cfg.artfctdef.xxx.artifact = Nx2 matrix with artifact segments see FT_ARTIFACT_xxx functions
% cfg.selectfeature = string, name of feature to be selected/added (default = 'visual')
% cfg.selectmode = 'markartifact', 'markpeakevent', 'marktroughevent' (default = 'markartifact')
% cfg.colorgroups = 'sequential' 'allblack' 'labelcharx' (x = xth character in label), 'chantype' or
% vector with length(data/hdr.label) defining groups (default = 'sequential')
% cfg.channelcolormap = COLORMAP (default = customized lines map with 15 colors)
% cfg.selfun = string, name of function which is evaluated using the right-click context menu
% The selected data and cfg.selcfg are passed on to this function.
% cfg.selcfg = configuration options for function in cfg.selfun
% cfg.eegscale = number, scaling to apply to the EEG channels prior to display
% cfg.eogscale = number, scaling to apply to the EOG channels prior to display
% cfg.ecgscale = number, scaling to apply to the ECG channels prior to display
% cfg.emgscale = number, scaling to apply to the EMG channels prior to display
% cfg.megscale = number, scaling to apply to the MEG channels prior to display
% cfg.gradscale = number, scaling to apply to the MEG gradiometer channels prior to display (in addition to the cfg.megscale factor)
% cfg.magscale = number, scaling to apply to the MEG magnetometer channels prior to display (in addition to the cfg.megscale factor)
% cfg.mychanscale = number, scaling to apply to the channels specified in cfg.mychan
% cfg.mychan = Nx1 cell-array with selection of channels
% cfg.chanscale = Nx1 vector with scaling factors, one per channel specified in cfg.channel
% cfg.compscale = string, 'global' or 'local', defines whether the colormap for the topographic scaling is
% applied per topography or on all visualized components (default 'global')
% cfg.renderer = string, 'opengl', 'zbuffer', 'painters',
% see MATLAB Figure Properties. If the
% databrowser crashes, set to 'painters'.
%
% The scaling to the EEG, EOG, ECG, EMG and MEG channels is optional and
% can be used to bring the absolute numbers of the different channel types
% in the same range (e.g. fT and uV). The channel types are determined from
% the input data using FT_CHANNELSELECTION.
%
% You can specify preprocessing options that are to be applied to the data prior
% to display. Most options from FT_PREPROCESSING are supported. They should be
% specified in the sub-structure cfg.preproc like these examples
% cfg.preproc.lpfilter = 'no' or 'yes' lowpass filter (default = 'no')
% cfg.preproc.lpfreq = lowpass frequency in Hz
% cfg.preproc.demean = 'no' or 'yes', whether to apply baseline correction (default = 'no')
% cfg.preproc.detrend = 'no' or 'yes', remove linear trend from the data (done per trial) (default = 'no')
% cfg.preproc.baselinewindow = [begin end] in seconds, the default is the complete trial (default = 'all')
%
% In case of component viewmode, a layout is required. If no layout is specified, an attempt is
% made to construct one from the sensor definition that is present in the data or specified in
% the configuration.
% cfg.layout = filename of the layout, see FT_PREPARE_LAYOUT
% cfg.elec = structure with electrode positions, see FT_DATATYPE_SENS
% cfg.grad = structure with gradiometer definition, see FT_DATATYPE_SENS
% cfg.elecfile = name of file containing the electrode positions, see FT_READ_SENS
% cfg.gradfile = name of file containing the gradiometer definition, see FT_READ_SENS
%
% The "artifact" field in the output cfg is a Nx2 matrix comparable to the
% "trl" matrix of FT_DEFINETRIAL. The first column of which specifying the
% beginsamples of an artifact period, the second column contains the
% endsamples of the artifactperiods.
%
% Note for debugging: in case the databrowser crashes, use delete(gcf) to kill
% the figure.
%
% See also FT_PREPROCESSING, FT_REJECTARTIFACT, FT_ARTIFACT_EOG,
% FT_ARTIFACT_MUSCLE, FT_ARTIFACT_JUMP, FT_ARTIFACT_MANUAL,
% FT_ARTIFACT_THRESHOLD, FT_ARTIFACT_CLIP, FT_ARTIFACT_ECG,
% FT_COMPONENTANALYSIS
% Copyright (C) 2009-2013, Robert Oostenveld, Ingrid Nieuwenhuis
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip
% 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/>.
%
% $Id$
% FIXME these should be removed or documented
% cfg.preproc
% cfg.channelcolormap
% cfg.colorgroups
revision = '$Id$';
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble provenance
ft_preamble trackconfig
ft_preamble debug
% the abort variable is set to true or false in ft_preamble_init
if abort
return
end
hasdata = (nargin>1);
hascomp = hasdata && ft_datatype(data, 'comp');
% for backward compatibility
cfg = ft_checkconfig(cfg, 'unused', {'comps', 'inputfile', 'outputfile'});
cfg = ft_checkconfig(cfg, 'renamed', {'zscale', 'ylim'});
cfg = ft_checkconfig(cfg, 'renamedval', {'ylim', 'auto', 'maxabs'});
cfg = ft_checkconfig(cfg, 'renamedval', {'selectmode', 'mark', 'markartifact'});
% ensure that the preproc specific options are located in the cfg.preproc substructure
cfg = ft_checkconfig(cfg, 'createsubcfg', {'preproc'});
% set the defaults
if ~isfield(cfg, 'ylim'), cfg.ylim = 'maxabs'; end
if ~isfield(cfg, 'artfctdef'), cfg.artfctdef = struct; end
if ~isfield(cfg, 'selectfeature'), cfg.selectfeature = 'visual'; end % string or cell-array
if ~isfield(cfg, 'selectmode'), cfg.selectmode = 'markartifact'; end
if ~isfield(cfg, 'blocksize'), cfg.blocksize = []; end % now used for both continuous and non-continuous data, defaulting done below
if ~isfield(cfg, 'preproc'), cfg.preproc = []; end % see preproc for options
if ~isfield(cfg, 'selfun'), cfg.selfun = []; end % default functions: 'simpleFFT', 'multiplotER', 'topoplotER', 'topoplotVAR', 'movieplotER'
if ~isfield(cfg, 'selcfg'), cfg.selcfg = []; end % defaulting done below, requires layouts/etc to be processed
if ~isfield(cfg, 'colorgroups'), cfg.colorgroups = 'sequential'; end
if ~isfield(cfg, 'channelcolormap'), cfg.channelcolormap = [0.75 0 0;0 0 1;0 1 0;0.44 0.19 0.63;0 0.13 0.38;0.5 0.5 0.5;1 0.75 0;1 0 0;0.89 0.42 0.04;0.85 0.59 0.58;0.57 0.82 0.31;0 0.69 0.94;1 0 0.4;0 0.69 0.31;0 0.44 0.75]; end
if ~isfield(cfg, 'eegscale'), cfg.eegscale = []; end
if ~isfield(cfg, 'eogscale'), cfg.eogscale = []; end
if ~isfield(cfg, 'ecgscale'), cfg.ecgscale = []; end
if ~isfield(cfg, 'emgscale'), cfg.emgscale = []; end
if ~isfield(cfg, 'megscale'), cfg.megscale = []; end
if ~isfield(cfg, 'magscale'), cfg.magscale = []; end
if ~isfield(cfg, 'gradscale'), cfg.gradscale = []; end
if ~isfield(cfg, 'chanscale'), cfg.chanscale = []; end
if ~isfield(cfg, 'mychanscale'), cfg.mychanscale = []; end
if ~isfield(cfg, 'layout'), cfg.layout = []; end
if ~isfield(cfg, 'plotlabels'), cfg.plotlabels = 'yes'; end
if ~isfield(cfg, 'event'), cfg.event = []; end % this only exists for backward compatibility and should not be documented
if ~isfield(cfg, 'continuous'), cfg.continuous = []; end % the default is set further down in the code, conditional on the input data
if ~isfield(cfg, 'ploteventlabels'), cfg.ploteventlabels = 'type=value'; end
if ~isfield(cfg, 'precision'), cfg.precision = 'double'; end
cfg.zlim = ft_getopt(cfg, 'zlim', 'maxmin');
cfg.compscale = ft_getopt(cfg, 'compscale', 'global');
cfg.renderer = ft_getopt(cfg, 'renderer', []);
if ~isfield(cfg, 'viewmode')
% butterfly, vertical, component
if hascomp
cfg.viewmode = 'component';
else
cfg.viewmode = 'butterfly';
end
end
if ~isempty(cfg.chanscale)
if ~isfield(cfg, 'channel')
warning('ignoring cfg.chanscale; this should only be used when an explicit channel selection is being made');
cfg.chanscale = [];
elseif numel(cfg.channel) ~= numel(cfg.chanscale)
error('cfg.chanscale should have the same number of elements as cfg.channel');
end
% make sure chanscale is a column vector, not a row vector
if size(cfg.chanscale,2) > size(cfg.chanscale,1)
cfg.chanscale = cfg.chanscale';
end
end
if ~isempty(cfg.mychanscale) && ~isfield(cfg, 'mychan')
warning('ignoring cfg.mychanscale; no channels specified in cfg.mychan');
cfg.mychanscale = [];
end
if ~isfield(cfg, 'channel'),
if hascomp
if size(data.topo,2)>9
cfg.channel = 1:10;
else
cfg.channel = 1:size(data.topo,2);
end
else
cfg.channel = 'all';
end
end
if strcmp(cfg.viewmode, 'component')
% read or create the layout that will be used for the topoplots
if ~isempty(cfg.layout)
tmpcfg = [];
tmpcfg.layout = cfg.layout;
cfg.layout = ft_prepare_layout(tmpcfg);
else
warning('No layout specified - will try to construct one using sensor positions');
tmpcfg = [];
try, tmpcfg.elec = cfg.elec; end
try, tmpcfg.grad = cfg.grad; end
try, tmpcfg.elecfile = cfg.elecfile; end
try, tmpcfg.gradfile = cfg.gradfile; end
if hasdata
cfg.layout = ft_prepare_layout(tmpcfg, data);
else
cfg.layout = ft_prepare_layout(tmpcfg);
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% set the defaults and do some preparation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if hasdata
% save whether data came from a timelock structure
istimelock = strcmp(ft_datatype(data), 'timelock');
% check if the input data is valid for this function
data = ft_checkdata(data, 'datatype', {'raw+comp', 'raw'}, 'feedback', 'yes', 'hassampleinfo', 'yes');
% fetch the header from the data structure in memory
hdr = ft_fetch_header(data);
if isfield(data, 'cfg') && ~isempty(ft_findcfg(data.cfg, 'origfs'))
% don't use the events in case the data has been resampled
warning('the data has been resampled, not showing the events');
event = [];
elseif isfield(data, 'cfg') && isfield(data.cfg, 'event')
% use the event structure from the data as per bug #2501
event = data.cfg.event;
elseif ~isempty(cfg.event)
% use the events that the user passed in the configuration
event = cfg.event;
else
% fetch the events from the data structure in memory
%event = ft_fetch_event(data);
event = [];
end
cfg.channel = ft_channelselection(cfg.channel, hdr.label);
chansel = match_str(data.label, cfg.channel);
Nchans = length(chansel);
if isempty(cfg.continuous)
if numel(data.trial) == 1 && ~istimelock
cfg.continuous = 'yes';
else
cfg.continuous = 'no';
end
else
if strcmp(cfg.continuous, 'yes') && (numel(data.trial) > 1)
warning('interpreting trial-based data as continous, time-axis is no longer appropriate. t(0) now corresponds to the first sample of the first trial, and t(end) to the last sample of the last trial')
end
end
% this is how the input data is segmented
trlorg = zeros(numel(data.trial), 3);
trlorg(:, [1 2]) = data.sampleinfo;
% recreate offset vector (databrowser depends on this for visualisation)
for ntrl = 1:numel(data.trial)
trlorg(ntrl,3) = time2offset(data.time{ntrl}, data.fsample);
end
Ntrials = size(trlorg, 1);
else
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');
cfg = ft_checkconfig(cfg, 'required', {'headerfile', 'datafile'});
cfg = ft_checkconfig(cfg, 'renamed', {'datatype', 'continuous'});
cfg = ft_checkconfig(cfg, 'renamedval', {'continuous', 'continuous', 'yes'});
% read the header from file
hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat);
if isempty(cfg.continuous)
if hdr.nTrials==1
cfg.continuous = 'yes';
else
cfg.continuous = 'no';
end
end
if ~isempty(cfg.event)
% use the events that the user passed in the configuration
event = cfg.event;
else
% read the events from file
event = ft_read_event(cfg.dataset);
end
cfg.channel = ft_channelselection(cfg.channel, hdr.label);
chansel = match_str(hdr.label, cfg.channel);
Nchans = length(chansel);
if strcmp(cfg.continuous, 'yes')
Ntrials = 1;
else
Ntrials = hdr.nTrials;
end
% FIXME in case of continuous=yes the trl should be [1 hdr.nSamples*nTrials 0]
% and a scrollbar should be used
% construct trl-matrix for data from file on disk
trlorg = zeros(Ntrials,3);
if strcmp(cfg.continuous, 'yes')
trlorg(1, [1 2]) = [1 hdr.nSamples*hdr.nTrials];
else
for k = 1:Ntrials
trlorg(k, [1 2]) = [1 hdr.nSamples] + [hdr.nSamples hdr.nSamples] .* (k-1);
end
end
end % if hasdata
if strcmp(cfg.continuous, 'no') && isempty(cfg.blocksize)
cfg.blocksize = (trlorg(1,2) - trlorg(1,1)+1) ./ hdr.Fs;
elseif strcmp(cfg.continuous, 'yes') && isempty(cfg.blocksize)
cfg.blocksize = 1;
end
% FIXME make a check for the consistency of cfg.continous, cfg.blocksize, cfg.trl and the data header
if Nchans == 0
error('no channels to display');
end
if Ntrials == 0
error('no trials to display');
end
if ischar(cfg.selectfeature)
% ensure that it is a cell array
cfg.selectfeature = {cfg.selectfeature};
end
if ~isempty(cfg.selectfeature)
for i=1:length(cfg.selectfeature)
if ~isfield(cfg.artfctdef, cfg.selectfeature{i})
cfg.artfctdef.(cfg.selectfeature{i}) = [];
cfg.artfctdef.(cfg.selectfeature{i}).artifact = zeros(0,2);
end
end
end
% determine the vertical scaling
if ischar(cfg.ylim)
if hasdata
% the first trial is used to determine the vertical scaling
dat = data.trial{1}(chansel,:);
else
% one second of data is read from file to determine the vertical scaling
dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', 1, 'endsample', round(hdr.Fs), 'chanindx', chansel, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat, 'headerformat', cfg.headerformat);
end % if hasdata
% convert the data to another numeric precision, i.e. double, single or int32
if ~isempty(cfg.precision)
dat = cast(dat, cfg.precision);
end
minval = min(dat(:));
maxval = max(dat(:));
switch cfg.ylim
case 'maxabs'
maxabs = max(abs([minval maxval]));
scalefac = 10^(fix(log10(maxabs)));
maxabs = (round(maxabs / scalefac * 100) / 100) * scalefac;
cfg.ylim = [-maxabs maxabs];
case 'maxmin'
cfg.ylim = [minval maxval];
otherwise
error('unsupported value for cfg.ylim');
end % switch ylim
% zoom in a bit when viemode is vertical
if strcmp(cfg.viewmode, 'vertical')
cfg.ylim = cfg.ylim/10;
end
else
if (numel(cfg.ylim) ~= 2) || ~isnumeric(cfg.ylim)
error('cfg.ylim needs to be a 1x2 vector [ymin ymax], describing the upper and lower limits')
end
end
% determine coloring of channels
if hasdata
labels_all = data.label;
else
labels_all= hdr.label;
end
if size(cfg.channelcolormap,2) ~= 3
error('cfg.channelcolormap is not valid, size should be Nx3')
end
if isnumeric(cfg.colorgroups)
% groups defined by user
if length(labels_all) ~= length(cfg.colorgroups)
error('length(cfg.colorgroups) should be length(data/hdr.label)')
end
R = cfg.channelcolormap(:,1);
G = cfg.channelcolormap(:,2);
B = cfg.channelcolormap(:,3);
chancolors = [R(cfg.colorgroups(:)) G(cfg.colorgroups(:)) B(cfg.colorgroups(:))];
elseif strcmp(cfg.colorgroups, 'allblack')
chancolors = zeros(length(labels_all),3);
elseif strcmp(cfg.colorgroups, 'chantype')
type = ft_chantype(labels_all);
[tmp1 tmp2 cfg.colorgroups] = unique(type);
fprintf('%3d colorgroups were identified\n',length(tmp1))
R = cfg.channelcolormap(:,1);
G = cfg.channelcolormap(:,2);
B = cfg.channelcolormap(:,3);
chancolors = [R(cfg.colorgroups(:)) G(cfg.colorgroups(:)) B(cfg.colorgroups(:))];
elseif strcmp(cfg.colorgroups(1:9), 'labelchar')
% groups determined by xth letter of label
labelchar_num = str2double(cfg.colorgroups(10));
vec_letters = num2str(zeros(length(labels_all),1));
for iChan = 1:length(labels_all)
vec_letters(iChan) = labels_all{iChan}(labelchar_num);
end
[tmp1 tmp2 cfg.colorgroups] = unique(vec_letters);
fprintf('%3d colorgroups were identified\n',length(tmp1))
R = cfg.channelcolormap(:,1);
G = cfg.channelcolormap(:,2);
B = cfg.channelcolormap(:,3);
chancolors = [R(cfg.colorgroups(:)) G(cfg.colorgroups(:)) B(cfg.colorgroups(:))];
elseif strcmp(cfg.colorgroups, 'sequential')
% no grouping
chancolors = lines(length(labels_all));
else
error('do not understand cfg.colorgroups')
end
% collect the artifacts that have been detected from cfg.artfctdef.xxx.artifact
artlabel = fieldnames(cfg.artfctdef);
sel = zeros(size(artlabel));
artifact = cell(size(artlabel));
for i=1:length(artlabel)
sel(i) = isfield(cfg.artfctdef.(artlabel{i}), 'artifact');
if sel(i)
artifact{i} = cfg.artfctdef.(artlabel{i}).artifact;
fprintf('detected %3d %s artifacts\n', size(artifact{i}, 1), artlabel{i});
end
end
% get the subset of the artfctdef fields that seem to contain artifacts
artifact = artifact(sel==1);
artlabel = artlabel(sel==1);
if length(artlabel) > 9
error('only up to 9 artifacts groups supported')
end
% make artdata representing all artifacts in a "raw data" format
datendsample = max(trlorg(:,2));
artdata = [];
artdata.trial{1} = convert_event(artifact, 'boolvec', 'endsample', datendsample); % every artifact is a "channel"
artdata.time{1} = offset2time(0, hdr.Fs, datendsample);
artdata.label = artlabel;
artdata.fsample = hdr.Fs;
artdata.cfg.trl = [1 datendsample 0];
% determine amount of unique event types (for cfg.ploteventlabels)
if ~isempty(event) && isstruct(event)
eventtypes = unique({event.type});
else
eventtypes = [];
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% set up default functions to be available in the right-click menu
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% cfg.selfun - labels that are presented in rightclick menu, and is appended using ft_getuserfun(..., 'browse') later on to create a function handle
% cfg.selcfg - cfgs for functions to be executed
defselfun = [];
defselcfg = [];
% simplefft
defselfun{1} = 'simpleFFT';
tmpcfg = [];
tmpcfg.chancolors = chancolors;
defselcfg{1} = tmpcfg;
% multiplotER
defselfun{2} = 'multiplotER';
tmpcfg = [];
tmpcfg.layout = cfg.layout;
defselcfg{2} = tmpcfg;
% topoplotER
defselfun{3} = 'topoplotER';
tmpcfg = [];
tmpcfg.layout = cfg.layout;
defselcfg{3} = tmpcfg;
% topoplotVAR
defselfun{4} = 'topoplotVAR';
tmpcfg = [];
tmpcfg.layout = cfg.layout;
defselcfg{4} = tmpcfg;
% movieplotER
defselfun{5} = 'movieplotER';
tmpcfg = [];
tmpcfg.layout = cfg.layout;
tmpcfg.interactive = 'yes';
defselcfg{5} = tmpcfg;
% add defselfuns to user-specified defselfuns
if ~iscell(cfg.selfun) && ~isempty(cfg.selfun)
cfg.selfun = {cfg.selfun};
cfg.selfun = [cfg.selfun defselfun];
% do the same for the cfgs
cfg.selcfg = {cfg.selcfg}; % assume the cfg isnt a cell
cfg.selcfg = [cfg.selcfg defselcfg];
else
cfg.selfun = defselfun;
cfg.selcfg = defselcfg;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% set up the data structures used in the GUI
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% opt represents the global data/settings, it should contain
% - the original data, epoched or continuous
% - the artifacts represented as continuous data
% - the redraw_cb settings
% - the preproc settings
% - the select_range_cb settings (also used in keyboard_cb)
% these elements are stored inside the figure so that the callback routines can modify them
opt = [];
if hasdata
opt.orgdata = data;
else
opt.orgdata = []; % this means that it will look in cfg.dataset
end
if strcmp(cfg.continuous, 'yes')
opt.trialviewtype = 'segment';
else
opt.trialviewtype = 'trial';
end
opt.artdata = artdata;
opt.hdr = hdr;
opt.event = event;
opt.trlop = 1; % the active trial being displayed
opt.ftsel = find(strcmp(artlabel,cfg.selectfeature)); % current artifact/feature being selected
opt.trlorg = trlorg;
opt.fsample = hdr.Fs;
opt.artcolors = [0.9686 0.7608 0.7686; 0.7529 0.7098 0.9647; 0.7373 0.9725 0.6824;0.8118 0.8118 0.8118; 0.9725 0.6745 0.4784; 0.9765 0.9176 0.5686; 0.6863 1 1; 1 0.6863 1; 0 1 0.6000];
opt.chancolors = chancolors;
opt.cleanup = false; % this is needed for a corrent handling if the figure is closed (either in the corner or by "q")
opt.chanindx = []; % this is used to check whether the component topographies need to be redrawn
opt.eventtypes = eventtypes;
opt.eventtypescolors = [0 0 0; 1 0 0; 0 0 1; 0 1 0; 1 0 1; 0.5 0.5 0.5; 0 1 1; 1 1 0];
opt.eventtypecolorlabels = {'black', 'red', 'blue', 'green', 'cyan', 'grey', 'light blue', 'yellow'};
opt.nanpaddata = []; % this is used to allow horizontal scaling to be constant (when looking at last segment continous data, or when looking at segmented/zoomed-out non-continous data)
opt.trllock = []; % this is used when zooming into trial based data
% save original layout when viewmode = component
if strcmp(cfg.viewmode, 'component')
opt.layorg = cfg.layout;
end
% determine labelling of channels
if strcmp(cfg.plotlabels, 'yes')
opt.plotLabelFlag = 1;
elseif strcmp(cfg.plotlabels, 'some')
opt.plotLabelFlag = 2;
else
opt.plotLabelFlag = 0;
end
h = figure;
setappdata(h, 'opt', opt);
setappdata(h, 'cfg', cfg);
if ~isempty(cfg.renderer)
set(h, 'renderer', cfg.renderer);
end
% enable custom data cursor text
dcm = datacursormode(h);
set(dcm, 'updatefcn', @datacursortext);
% set the figure window title
funcname = mfilename();
if nargin < 2
if isfield(cfg, 'dataset')
dataname = cfg.dataset;
elseif isfield(cfg, 'datafile')
dataname = cfg.datafile;
else
dataname = [];
end
else
dataname = inputname(2);
end
set(gcf, 'Name', sprintf('%d: %s: %s', double(gcf), funcname, join_str(', ',dataname)));
set(gcf, 'NumberTitle', 'off');
% set zoom option to on
% zoom(h, 'on')
% set(zoom(h), 'actionPostCallback', @zoom_drawlabels_cb)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% set up the figure and callbacks
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
set(h, 'KeyPressFcn', @keyboard_cb);
set(h, 'WindowButtonDownFcn', {@ft_select_range, 'multiple', false, 'xrange', true, 'yrange', false, 'clear', true, 'contextmenu', cfg.selfun, 'callback', {@select_range_cb, h}, 'event', 'WindowButtonDownFcn'});
set(h, 'WindowButtonUpFcn', {@ft_select_range, 'multiple', false, 'xrange', true, 'yrange', false, 'clear', true, 'contextmenu', cfg.selfun, 'callback', {@select_range_cb, h}, 'event', 'WindowButtonUpFcn'});
set(h, 'WindowButtonMotionFcn', {@ft_select_range, 'multiple', false, 'xrange', true, 'yrange', false, 'clear', true, 'contextmenu', cfg.selfun, 'callback', {@select_range_cb, h}, 'event', 'WindowButtonMotionFcn'});
% make the user interface elements for the data view
uicontrol('tag', 'labels', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', opt.trialviewtype, 'userdata', 't')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'leftarrow')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'rightarrow')
if strcmp(cfg.viewmode, 'component')
uicontrol('tag', 'labels', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'component', 'userdata', 'c')
else
uicontrol('tag', 'labels', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'channel', 'userdata', 'c')
end
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'uparrow')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'downarrow')
uicontrol('tag', 'labels', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'horizontal', 'userdata', 'h')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '-', 'userdata', 'shift+leftarrow')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '+', 'userdata', 'shift+rightarrow')
uicontrol('tag', 'labels', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'vertical', 'userdata', 'v')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '-', 'userdata', 'shift+downarrow')
uicontrol('tag', 'buttons', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '+', 'userdata', 'shift+uparrow')
% legend artifacts/features
for iArt = 1:length(artlabel)
uicontrol('tag', 'artifactui', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', artlabel{iArt}, 'userdata', num2str(iArt), 'position', [0.91, 0.9 - ((iArt-1)*0.09), 0.08, 0.04], 'backgroundcolor', opt.artcolors(iArt,:))
uicontrol('tag', 'artifactui', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', ['shift+' num2str(iArt)], 'position', [0.91, 0.855 - ((iArt-1)*0.09), 0.03, 0.04], 'backgroundcolor', opt.artcolors(iArt,:))
uicontrol('tag', 'artifactui', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', ['control+' num2str(iArt)], 'position', [0.96, 0.855 - ((iArt-1)*0.09), 0.03, 0.04], 'backgroundcolor', opt.artcolors(iArt,:))
end
if true % strcmp(cfg.viewmode, 'butterfly')
% button to find label of nearest channel to datapoint
uicontrol('tag', 'artifactui', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'identify', 'userdata', 'i', 'position', [0.91, 0.1, 0.08, 0.05], 'backgroundcolor', [1 1 1])
end
% 'edit preproc'-button
uicontrol('tag', 'preproccfg', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'preproc cfg', 'position', [0.91, 0.55 - ((iArt-1)*0.09), 0.08, 0.04], 'callback', @preproc_cfg1_cb)
ft_uilayout(h, 'tag', 'labels', 'width', 0.10, 'height', 0.05);
ft_uilayout(h, 'tag', 'buttons', 'width', 0.05, 'height', 0.05);
ft_uilayout(h, 'tag', 'labels', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'buttons', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'artifactui', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'labels', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'buttons', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'viewui', 'BackgroundColor', [0.8 0.8 0.8], 'hpos', 'auto', 'vpos', 0);
definetrial_cb(h);
redraw_cb(h);
% %% Scrollbar
%
% % set initial scrollbar value
% dx = maxtime;
%
% % set scrollbar position
% fig_pos=get(gca, 'position');
% scroll_pos=[fig_pos(1) fig_pos(2) fig_pos(3) 0.02];
%
% % define callback
% S=['set(gca, ''xlim'',get(gcbo, ''value'')+[ ' num2str(mintime) ', ' num2str(maxtime) '])'];
%
% % Creating Uicontrol
% s=uicontrol('style', 'slider',...
% 'units', 'normalized', 'position',scroll_pos,...
% 'callback',S, 'min',0, 'max',0, ...
% 'visible', 'off'); %'value', xmin
% set initial scrollbar value
% dx = maxtime;
%
% % set scrollbar position
% fig_pos=get(gca, 'position');
% scroll_pos=[fig_pos(1) fig_pos(2) fig_pos(3) 0.02];
%
% % define callback
% S=['set(gca, ''xlim'',get(gcbo, ''value'')+[ ' num2str(mintime) ', ' num2str(maxtime) '])'];
%
% % Creating Uicontrol
% s=uicontrol('style', 'slider',...
% 'units', 'normalized', 'position',scroll_pos,...
% 'callback',S, 'min',0, 'max',0, ...
% 'visible', 'off'); %'value', xmin
%initialize postion of plot
% set(gca, 'xlim', [xmin xmin+dx]);
if nargout
% wait until the user interface is closed, get the user data with the updated artifact details
set(h, 'CloseRequestFcn', @cleanup_cb);
while ishandle(h)
uiwait(h);
opt = getappdata(h, 'opt');
if opt.cleanup
delete(h);
end
end
% add the updated artifact definitions to the output cfg
for i=1:length(opt.artdata.label)
cfg.artfctdef.(opt.artdata.label{i}).artifact = convert_event(opt.artdata.trial{1}(i,:), 'artifact');
end
% add the updated preproc to the output
try
browsecfg = getappdata(h, 'cfg');
cfg.preproc = browsecfg.preproc;
end
% add the update event to the output cfg
cfg.event = opt.event;
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble trackconfig
ft_postamble provenance
ft_postamble previous data
end % if nargout
end % main function
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function cleanup_cb(h, eventdata)
opt = getappdata(h, 'opt');
opt.cleanup = true;
setappdata(h, 'opt', opt);
uiresume
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function definetrial_cb(h, eventdata)
opt = getappdata(h, 'opt');
cfg = getappdata(h, 'cfg');
if strcmp(cfg.continuous, 'no')
% when zooming in, lock the trial! one can only go to the next trial when horizontal scaling doesn't segment the data - from ft-meeting: this might be relaxed later on - roevdmei
if isempty(opt.trllock)
opt.trllock = opt.trlop;
end
locktrllen = ((opt.trlorg(opt.trllock,2)-opt.trlorg(opt.trllock,1)+1) ./ opt.fsample);
% if cfg.blocksize is close to the length of the locked trial, set it to that
if (abs(locktrllen-cfg.blocksize) / locktrllen) < 0.1
cfg.blocksize = locktrllen;
end
%%%%%%%%%
% trial is locked, change subdivision of trial
if cfg.blocksize < locktrllen
% lock the trial if it wasn't locked (and thus trlop refers to the actual trial)
if isempty(opt.trllock)
opt.trllock = trlop;
end
% save current position if already
if isfield(opt, 'trlvis')
thissegbeg = opt.trlvis(opt.trlop,1);
end
datbegsample = min(opt.trlorg(opt.trllock,1));
datendsample = max(opt.trlorg(opt.trllock,2));
smpperseg = round(opt.fsample * cfg.blocksize);
begsamples = datbegsample:smpperseg:datendsample;
endsamples = datbegsample+smpperseg-1:smpperseg:datendsample;
offset = (((1:numel(begsamples))-1)*smpperseg) + opt.trlorg(opt.trllock,3);
if numel(endsamples)<numel(begsamples)
endsamples(end+1) = datendsample;
end
trlvis = [];
trlvis(:,1) = begsamples';
trlvis(:,2) = endsamples';
trlvis(:,3) = offset;
% determine length of each trial, and determine the offset with the current requested zoom-level
trllen = (trlvis(:,2) - trlvis(:,1)+1);
sizediff = smpperseg - trllen;
opt.nanpaddata = sizediff;
if isfield(opt, 'trlvis')
% update the current trial counter and try to keep the current sample the same
opt.trlop = nearest(begsamples, thissegbeg);
end
% update trialviewtype
opt.trialviewtype = 'trialsegment';
% update button
set(findobj(get(h, 'children'), 'string', 'trial'), 'string', 'segment');
%%%%%%%%%
%%%%%%%%%
% trial is not locked, go to original trial division and zoom out
elseif cfg.blocksize >= locktrllen
trlvis = opt.trlorg;
% set current trlop to locked trial if it was locked before
if ~isempty(opt.trllock)
opt.trlop = opt.trllock;
end
smpperseg = round(opt.fsample * cfg.blocksize);
% determine length of each trial, and determine the offset with the current requested zoom-level
trllen = (trlvis(:,2) - trlvis(:,1)+1);
sizediff = smpperseg - trllen;
opt.nanpaddata = sizediff;
% update trialviewtype
opt.trialviewtype = 'trial';
% update button
set(findobj(get(h, 'children'), 'string', 'trialsegment'), 'string',opt.trialviewtype);
% release trial lock
opt.trllock = [];
%%%%%%%%%
end
% save trlvis
opt.trlvis = trlvis;
else
% construct a trial definition for visualisation
if isfield(opt, 'trlvis') % if present, remember where we were
thistrlbeg = opt.trlvis(opt.trlop,1);
end
% look at cfg.blocksize and make opt.trl accordingly
datbegsample = min(opt.trlorg(:,1));
datendsample = max(opt.trlorg(:,2));
smpperseg = round(opt.fsample * cfg.blocksize);
begsamples = datbegsample:smpperseg:datendsample;
endsamples = datbegsample+smpperseg-1:smpperseg:datendsample;
if numel(endsamples)<numel(begsamples)
endsamples(end+1) = datendsample;
end
trlvis = [];
trlvis(:,1) = begsamples';
trlvis(:,2) = endsamples';
% compute the offset. In case if opt.trlorg has multiple trials, the first sample is t=0, otherwise use the offset in opt.trlorg
if size(opt.trlorg,1)==1
offset = begsamples - repmat(begsamples(1), [1 numel(begsamples)]); % offset for all segments compared to the first
offset = offset + opt.trlorg(1,3);
trlvis(:,3) = offset;
else
offset = begsamples - repmat(begsamples(1), [1 numel(begsamples)]);
trlvis(:,3) = offset;
end
if isfield(opt, 'trlvis')
% update the current trial counter and try to keep the current sample the same
% opt.trlop = nearest(round((begsamples+endsamples)/2), thissample);
opt.trlop = nearest(begsamples, thistrlbeg);
end
opt.trlvis = trlvis;
% NaN-padding when horizontal scaling is bigger than the data
% two possible situations, 1) zoomed out so far that all data is one segment, or 2) multiple segments but last segment is smaller than the rest
sizediff = smpperseg-(endsamples-begsamples+1);
opt.nanpaddata = sizediff;
end % if continuous
setappdata(h, 'opt', opt);
setappdata(h, 'cfg', cfg);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function help_cb(h, eventdata)
fprintf('------------------------------------------------------------------------------------\n')
fprintf('You can use the following keyboard buttons in the databrowser\n')
fprintf('1-9 : select artifact type 1-9\n');
fprintf('shift 1-9 : select previous artifact of type 1-9\n');
fprintf(' (does not work with numpad keys)\n');
fprintf('control 1-9 : select next artifact of type 1-9\n');
fprintf('alt 1-9 : select next artifact of type 1-9\n');
fprintf('arrow-left : previous trial\n');
fprintf('arrow-right : next trial\n');
fprintf('shift arrow-up : increase vertical scaling\n');
fprintf('shift arrow-down : decrease vertical scaling\n');
fprintf('shift arrow-left : increase horizontal scaling\n');
fprintf('shift arrow-down : decrease horizontal scaling\n');
fprintf('s : toggles between cfg.selectmode options\n');
fprintf('q : quit\n');
fprintf('------------------------------------------------------------------------------------\n')
fprintf('\n')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function select_range_cb(h, range, cmenulab) %range 1X4 in sec relative to current trial
opt = getappdata(h, 'opt');
cfg = getappdata(h, 'cfg');
% the range should be in the displayed box
range(1) = max(opt.hpos-opt.width/2, range(1));
range(2) = max(opt.hpos-opt.width/2, range(2));
range(1) = min(opt.hpos+opt.width/2, range(1));
range(2) = min(opt.hpos+opt.width/2, range(2));
range = (range-(opt.hpos-opt.width/2)) / opt.width; % left side of the box becomes 0, right side becomes 1
range = range * (opt.hlim(2) - opt.hlim(1)) + opt.hlim(1); % 0 becomes hlim(1), 1 becomes hlim(2)
begsample = opt.trlvis(opt.trlop,1);
endsample = opt.trlvis(opt.trlop,2);
offset = opt.trlvis(opt.trlop,3);
% determine the selection
begsel = round(range(1)*opt.fsample+begsample-offset-1);
endsel = round(range(2)*opt.fsample+begsample-offset);
% artifact selection is now always based on begsample/endsample/offset
% -roevdmei
% the selection should always be confined to the current trial
begsel = max(begsample, begsel);
endsel = min(endsample, endsel);
% mark or execute selfun
if isempty(cmenulab)
% the left button was clicked INSIDE a selected range, update the artifact definition or event
if strcmp(cfg.selectmode, 'markartifact')
% mark or unmark artifacts
artval = opt.artdata.trial{1}(opt.ftsel, begsel:endsel);
artval = any(artval,1);
if any(artval)
fprintf('there is overlap with the active artifact (%s), disabling this artifact\n',opt.artdata.label{opt.ftsel});
opt.artdata.trial{1}(opt.ftsel, begsel:endsel) = 0;
else
fprintf('there is no overlap with the active artifact (%s), marking this as a new artifact\n',opt.artdata.label{opt.ftsel});
opt.artdata.trial{1}(opt.ftsel, begsel:endsel) = 1;
end
% redraw only when marking (so the focus doesn't go back to the databrowser after calling selfuns
setappdata(h, 'opt', opt);
setappdata(h, 'cfg', cfg);
redraw_cb(h);
elseif strcmp(cfg.selectmode, 'markpeakevent') || strcmp(cfg.selectmode, 'marktroughevent')
%mark or unmark events, marking at peak/trough of window
if any(intersect(begsel:endsel, [opt.event.sample]))
fprintf('there is overlap with one or more event(s), disabling this/these event(s)\n');
ind_rem = intersect(begsel:endsel, [opt.event.sample]);
for iRemove = 1:length(ind_rem)
opt.event([opt.event.sample]==ind_rem(iRemove)) = [];
end
else
fprintf('there is no overlap with any event, adding an event to the peak/trough value\n');
% check if only 1 chan, other wise not clear max in which channel. %