% writeeeg - Generating CNT/EDF/BDF/GDF-files using BIOSIG toolbox. Note
% that the CNT file format is not fully functional. See also the
% writecnt.m Matlab function (there is no fully working
% Neuroscan writing function to our knowledge).
%
% writeeeg( filename, data, srate, 'key', 'val')
%
% Inputs:
% filename - [string] filename
% data - [float] continuous or epoched data (channels x times x
% epochs)
% srate - [float] sampling rate in Hz
%
% Optional keys:
% 'TYPE' - ['GDF'|'EDF'|'BDF'|'CFWB'|'CNT'] file format for writing
% default is 'EDF'.
% 'EVENT' - event structure (BIOSIG or EEGLAB format)
% 'Label' - cell array of channel labels. Warning, this input is
% case sensitive.
% 'SPR' - [integer] sample per block, default is 1000
%
% Other optional keys:
% 'Patient.id' - [string] person identification, max 80 char
% 'Patient.Sex' - [0|1|2] 0: undefined (default), 1: male, 2: female
% 'Patient.Birthday' - Default [1951 05 13 0 0 0];
% 'Patient.Name' - [string] default 'anonymous' for privacy protection
% 'Patient.Handedness' - [0|1|2|3] 0: unknown (default), 1:left, 2:right,
% 3: equal
% 'Patient.Weight' - [integer] default 0, undefined
% 'Patient.Height' - [integer] default 0, undefined
% 'Patient.Impairment.Heart' - [integer] 0: unknown 1: NO 2: YES 3: pacemaker
% 'Patient.Impairment.Visual' - [integer] 0: unknown 1: NO 2: YES
% 3: corrected (with visual aid)
% 'Patient.Smoking' - [integer] 0: unknown 1: NO 2: YES
% 'Patient.AlcoholAbuse' - [integer] 0: unknown 1: NO 2: YES
% 'Patient.DrugAbuse' - [integer] 0: unknown 1: NO 2: YES
%
% 'Manufacturer.Name - [string] default is 'BioSig/EEGLAB'
% 'Manufacturer.Model - [string] default is 'writeeeg.m'
% 'Manufacturer.Version - [string] default is current version in CVS repository
% 'Manufacturer.SerialNumber - [string] default is '00000000'
%
% 'T0' - recording time [YYYY MM DD hh mm ss.ccc]
% 'RID' - [string] StudyID/Investigation, default is empty
% 'REC.Hospital - [string] default is empty
% 'REC.Technician - [string] default is empty
% 'REC.Equipment - [string] default is empty
% 'REC.IPaddr - [integer array] IP address of recording system. Default is
% [127,0,0,1]
%
% Author: Arnaud Delorme, SCCN, UCSD/CERCO, 2009
% Based on BIOSIG, sopen and swrite
% Copyright (C) 22 March 2002 Arnaud Delorme, Salk Institute, arno@salk.edu
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.
function HDR = writeeeg(filename, x, srate, varargin)
% decode structures
HDR = [];
for i=1:2:length( varargin )
str = varargin{i};
val = varargin{i+1};
ind = strfind(str, '.');
if length(ind) == 2
HDR = setfield(HDR, varargin{i}(1:ind(1)-1), {1}, varargin{i}(ind(1)+1:ind(2)-1), ...
{1}, varargin{i}(ind(2)+1:end), val);
elseif length(ind) == 1
HDR = setfield(HDR, varargin{i}(1:ind-1), {1}, varargin{i}(ind+1:end), val);
else
HDR = setfield(HDR, varargin{i}, varargin{i+1});
end
end
HDR.FileName = filename;
HDR.FLAG.UCAL = 0; % see also https://sccn.ucsd.edu/bugzilla/show_bug.cgi?id=1020
% select file format
if ~isfield(HDR, 'EVENT'), HDR.EVENT = []; end
if ~isfield(HDR, 'TYPE'), HDR.TYPE ='GDF'; end
if ~isfield(HDR, 'Patient'), HDR.Patient = []; end
if ~isfield(HDR.Patient, 'ID'), HDR.Patient.ID = 'P0000'; end
if ~isfield(HDR.Patient, 'Sex'), HDR.Patient.Sex = 0; end
if ~isfield(HDR.Patient, 'Name'), HDR.Patient.Name = 'Anonymous'; end
if ~isfield(HDR.Patient, 'Handedness'), HDR.Patient.Handedness = 0; end;% unknown, 1:left, 2:right, 3: equal
% description of recording device
if ~isfield(HDR,'Manufacturer'), HDR.Manufacturer = []; end
if ~isfield(HDR.Manufacturer, 'Name'), HDR.Manufacturer.Name = 'BioSig/EEGLAB'; end
if ~isfield(HDR.Manufacturer, 'Model'), HDR.Manufacturer.Model = 'writeeeg.m'; end
if ~isfield(HDR.Manufacturer, 'Version'), HDR.Manufacturer.Version = '$Revision'; end
if ~isfield(HDR.Manufacturer, 'SerialNumber'), HDR.Manufacturer.SerialNumber = '00000000'; end
% recording identification, max 80 char.
if ~isfield(HDR,'RID'), HDR.RID = ''; end; %StudyID/Investigation [consecutive number];
if ~isfield(HDR,'REC'), HDR.REC = []; end
if ~isfield(HDR.REC, 'Hospital'), HDR.REC.Hospital = ''; end;
if ~isfield(HDR.REC, 'Technician'), HDR.REC.Technician = ''; end
if ~isfield(HDR.REC, 'Equipment'), HDR.REC.Equipment = ''; end
if ~isfield(HDR.REC, 'IPaddr'), HDR.REC.IPaddr = [127,0,0,1]; end; % IP address of recording system
if ~isfield(HDR.Patient, 'Weight'), HDR.Patient.Weight = 0; end; % undefined
if ~isfield(HDR.Patient, 'Height'), HDR.Patient.Height = 0; end; % undefined
if ~isfield(HDR.Patient, 'Birthday'), HDR.Patient.Birthday = [1951, 5, 13, 0, 0, 0]; end; % undefined
if ~isfield(HDR.Patient, 'Impairment'), HDR.Patient.Impairment = []; end;
if ~isfield(HDR.Patient.Impairment, 'Heart'), HDR.Patient.Impairment.Heart = 0; end; % 0: unknown 1: NO 2: YES 3: pacemaker
if ~isfield(HDR.Patient.Impairment, 'Visual'), HDR.Patient.Impairment.Visual = 0; end; % 0: unknown 1: NO 2: YES 3: corrected (with visual aid)
if ~isfield(HDR.Patient,'Smoking'), HDR.Patient.Smoking = 0; end; % 0: unknown 1: NO 2: YES
if ~isfield(HDR.Patient,'AlcoholAbuse'), HDR.Patient.AlcoholAbuse = 0; end; % 0: unknown 1: NO 2: YES
if ~isfield(HDR.Patient,'DrugAbuse'), HDR.Patient.DrugAbuse = 0; end; % 0: unknown 1: NO 2: YES
% recording time [YYYY MM DD hh mm ss.ccc]
if ~isfield(HDR,'T0'), HDR.T0 = clock; end
if ~isfield(HDR,'SPR'), HDR.SPR = size(x,2); end
if isfield(HDR,'label'), HDR.Label = HDR.label; HDR = rmfield(HDR, 'label'); end
if HDR.SPR > 1000, HDR.SPR = round(srate); end
% channel identification, max 80 char. per channel
if ~isfield(HDR,'Label')
for i = 1:size(x,1)
chans{i} = sprintf('Chan %d', i);
end
HDR.Label = chans;
end
if iscell(HDR.Label), HDR.Label = char(HDR.Label{:}); end
if ~isempty(HDR.EVENT)
if ~isfield(HDR.EVENT, 'TYP')
EVENT = [];
EVENT.CHN = zeros(length(HDR.EVENT),1);
EVENT.TYP = zeros(length(HDR.EVENT),1);
EVENT.POS = zeros(length(HDR.EVENT),1);
EVENT.DUR = ones( length(HDR.EVENT),1);
EVENT.VAL = zeros(length(HDR.EVENT),1)*NaN;
if isfield(HDR.EVENT, 'type')
for index = 1:length(HDR.EVENT)
HDR.EVENT(index).type = num2str(HDR.EVENT(index).type);
end
alltypes = unique_bc( { HDR.EVENT.type } );
end
for i = 1:length(HDR.EVENT)
if isfield(HDR.EVENT, 'type')
ind = str2num(HDR.EVENT(i).type);
if isempty(ind)
ind = strmatch(HDR.EVENT(i).type, alltypes, 'exact');
end
EVENT.TYP(i) = ind;
end
if isfield(HDR.EVENT, 'latency')
EVENT.POS(i) = HDR.EVENT(i).latency;
end
if isfield(HDR.EVENT, 'duration')
EVENT.DUR(i) = HDR.EVENT(i).duration;
end
end
HDR.EVENT = EVENT;
HDR.EVENT.SampleRate = srate;
end
end
% reformat data
HDR.NRec = size(x,3);
x = double(x);
x = reshape(x, [size(x,1) size(x,2)*size(x,3) ]);
% recreate event channel
if isempty(HDR.EVENT)
HDR.EVENT.POS = [];
HDR.EVENT.TYP = [];
HDR.EVENT.POS = [];
HDR.EVENT.DUR = [];
HDR.EVENT.VAL = [];
HDR.EVENT.CHN = [];
elseif ~strcmpi(HDR.TYPE, 'GDF') % GDF can save events
disp('Recreating event channel');
x(end+1,:) = 0;
x(end,round(HDR.EVENT.POS')) = HDR.EVENT.TYP';
HDR.Label = char(HDR.Label, 'Status');
HDR.EVENT.POS = [];
end
% number of channels
HDR.NS = size(x,1);
% fix for BDF precision see https://sccn.ucsd.edu/bugzilla/show_bug.cgi?id=1020
% However, likely BIOSIG takes care of that now because there is no
% difference when the code below is added
if strcmpi(HDR.TYPE, 'BDF')
% BDF uses 24 bit signed integers
HDR.DigMax = repmat(2^23-1,1,HDR.NS);
HDR.DigMin = repmat(-2^23,1,HDR.NS);
end
if ~isfield(HDR,'Transducer')
HDR.Transducer = cell(1,HDR.NS);
HDR.Transducer(:) = { '' };
end
if ~isfield(HDR,'PhysDim')
HDR.PhysDim = cell(1,HDR.NS);
HDR.PhysDim(:) = { 'uV' };
end
% from https://github.com/INCF/p3-validator/blob/a0365b4d3a1ca21ac3c18d3fd1b8f1e63f35eeb8/trunk/lib/eeglab9_0_4_5s/external/biosig-partial/t200_FileAccess/physicalunits.m#L225
if ~isfield(HDR,'PhysDimCode')
HDR.PhysDimCode = zeros(1,HDR.NS);
HDR.PhysDimCode(:) = 4256 + 19;
end
% Duration of one block in seconds
HDR.SampleRate = srate;
HDR.Dur = HDR.SPR/HDR.SampleRate;
% define datatypes and scaling factors
absMax = max(abs(x(:)));
HDR.PhysMax = repmat(absMax, [size(x,1),1]);
HDR.PhysMin = -HDR.PhysMax;
fprintf('Unifying channel resolution, clipping at +-%d uV \n', absMax)
if strcmp(HDR.TYPE, 'GDF')
HDR.GDFTYP = 16*ones(1,HDR.NS); % float32
HDR.DigMax = ones(HDR.NS,1)*100; % FIXME: What are the correct values for float32?
HDR.DigMin = zeros(HDR.NS,1);
else
HDR.GDFTYP = 3*ones(1,HDR.NS); % int16
HDR.DigMin = repmat(-2^15, size(HDR.PhysMin));
HDR.DigMax = repmat(2^15-1, size(HDR.PhysMax));
end
HDR.Filter.Lowpass = zeros(1,HDR.NS)*NaN;
HDR.Filter.Highpass = zeros(1,HDR.NS)*NaN;
HDR.Filter.Notch = zeros(1,HDR.NS)*NaN;
HDR.VERSION = 2.11;
HDR = sopen(HDR,'w');
HDR = swrite(HDR, x');
HDR = sclose(HDR);
Datasets
Models
