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Merge pull request #111 from fahrenfort/bugfixes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| function adam_epoch(cfg) | ||
| % Reads in CONTINUOUS (!) EEGLAB data, epochs and writes out as EPOCHED (!) EEGLAB file. | ||
| % No pre-processing is applied other than mean removal from every trial after epoching. | ||
| % The output of this function can serve as input for ADAM_MVPA_FIRSTLEVEL. | ||
| % | ||
| % cfg.datadir = string specifiying the directory where the input files are | ||
| % located; | ||
| % cfg.outputdir = string specifying the directory where the results should be | ||
| % saved. Choose an informative name. | ||
| % cfg.filenames = N by 1 cell array containing N strings, in which each string | ||
| % contains the base of a filename (e.g. cfg.filenames = | ||
| % {'subject1', 'subject2'};). Do not add a file extension to the | ||
| % file name, ADAM will automatically look for EEGLAB .set files. | ||
| % cfg.start_epoch = in seconds (relative to target events) | ||
| % cfg.end_epoch = in seconds (relative to target events) | ||
| % cfg.event_codes = numeric array or comma separated list containing the relevant event | ||
| % values for the experiment. | ||
| % | ||
| % Part of the ADAM toolbox, J.J.Fahrenfort, UvA/VU 2019 | ||
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| v2struct(cfg); | ||
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| % do some checking | ||
| if ~exist('datadir','var') | ||
| error('You need to specify in cfg.datadir where the data are located'); | ||
| end | ||
| if ~exist('outputdir','var') | ||
| error('You need to specify in cfg.outputdir where the results should be stored'); | ||
| end | ||
| if ~exist('filenames','var') | ||
| error('You need to specify a cell array in cfg.filenames containing the filenames containing the data of each subject'); | ||
| end | ||
| if ~exist('event_codes','var') | ||
| error('You need to specify in cfg.event_codes which event values you want to epoch on'); | ||
| end | ||
| if ~exist('start_epoch','var') | ||
| error('You need to specify in cfg.start_epoch defining the onset time of your epoch (in seconds)'); | ||
| end | ||
| if ~exist('end_epoch','var') | ||
| error('You need to specify in cfg.end_epoch defining the offset time of your epoch (in seconds)'); | ||
| end | ||
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| % some further input checking | ||
| if isempty(outputdir) | ||
| outputdir = filepath; | ||
| else | ||
| if ~exist(outputdir,'dir') | ||
| mkdir(outputdir); | ||
| end | ||
| end | ||
| if ischar(start_epoch); | ||
| start_epoch = string2double(start_epoch); | ||
| end | ||
| if ischar(end_epoch) | ||
| end_epoch = string2double(end_epoch); | ||
| end | ||
| if ~iscell(filenames) && (~isempty(strfind(filenames,'*')) || ~isempty(strfind(filenames,'?'))) | ||
| if ~strcmp(filenames(end-3:end),'.set') | ||
| filenames = [filenames '.set']; | ||
| end | ||
| filenames = dir([filepath filesep filenames]); | ||
| filenames = {filenames(:).name}; | ||
| end | ||
| if ~iscell(filenames) | ||
| filenames = regexp(filenames, ',', 'split'); | ||
| end | ||
| % conditions can either be defined as a string of comma separated values, | ||
| % or a cell array of numbers or strings, and is converted to a ell array of | ||
| % strings to be fed into pop_epoch | ||
| if ischar(event_codes) | ||
| conditions = regexp(event_codes, ',', 'split'); | ||
| end | ||
| if isnumeric(event_codes) | ||
| conditions = num2cell(event_codes); | ||
| end | ||
| % go | ||
| for filename = filenames | ||
| [~,fname,~] = fileparts(filename{1}); | ||
| % load and filter | ||
| EEG = pop_loadset('filename',[fname '.set'],'filepath',datadir); | ||
| % epoch data | ||
| if ~isempty(conditions) | ||
| EEG = pop_epoch(EEG, conditions, [start_epoch end_epoch], 'newname', ['epoched_ ' fname], 'epochinfo', 'yes'); | ||
| end | ||
| % remove mean of every trial | ||
| EEG = pop_rmbase( EEG,[]); | ||
| % save data | ||
| pop_saveset(EEG, 'filename',[fname '.set'],'filepath',outputdir); | ||
| end | ||
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