Bulk_load.m

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%This file is part of TEAP.
%
%TEAP 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.
%
%TEAP 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 TEAP.  If not, see <http://www.gnu.org/licenses/>.
% 
%> @file Bulk_load.m
%> @brief Loads a bdf file, into a TEAP bulk signal, containing EEG, ECG,
%> GSR, etc.
%> @param file_name: this variable includes the full path; 
%> it can be any file supported by biogs sload/sopn
% 
%> @retval BulkSig a TEAP bulk signal vector
 
function [BulkSig] = Bulk_load(file_name)
%Copyright Mohammad Soleymani, 2014
 
if(nargin ~= 1)
    error('Usage: BulkSig = Bulk_load(phys_data)');
end
 
if (~exist(file_name, 'file'))
    error('Usage: the input file does not exist');
end
% if it is a mat file; it is assumed to be an EEGLAB file
if strcmp(file_name(end-2:end),'mat')
    S = load(file_name);
    vars = fieldnames(S);
    phys_data = S.(vars{1});
else %otherwise load the file
    phys_data = pop_biosig(file_name);
end
 
%initialize signals to load
config_file;
 
%initialize EEG electrode labels
signals = {};
electrode_labels = struct;
config_file;
 
%Number of epochs:
nEpochs = length(phys_data.epoch);
 
 
%foreach epoch
if nEpochs>0
    for iEpoch = [1:nEpochs]
        Bulk = Bulk_new_empty();
        for signal = signals
            eval(['Bulk = add' signal{1} '(Bulk, iEpoch, electrode_labels.' signal{1} ');']);
        end
        BulkSig(iEpoch) = Bulk;
        clear Bulk;
    end
else
    Bulk = Bulk_new_empty();
    for signal = signals
        eval(['Bulk = add' signal{1} '(Bulk, 0, electrode_labels.' signal{1} ');']);
    end
    BulkSig(1) = Bulk;
    clear Bulk;
    
end
 
%EEG
    function BulkSig = addEEG(BulkSig, iEpoch,correspondance)
        numel = length(correspondance);
        datlen = length(phys_data.data(1, :, 1));
        data = zeros(numel, datlen);
        
        for i = [1:numel]
            chaname = strtrim(correspondance{i});
            chan = findMyChannel(chaname);
            %       disp(['Will do ' chaname ' - ' num2str(chan)]);
            if(chan == 0)
                warning(['The EEG channel ' correspondance{i} ' does not '...
                    'exist. Aborting EEG']);
                return;
            end
            if iEpoch ==0
                data(i,:) = squeeze(phys_data.data(chan, :));
            else
                data(i, :) = squeeze(phys_data.data(chan, :, iEpoch));
            end
        end
        
        EEGSig = EEG_aqn_variable(correspondance, data, phys_data.srate);
        BulkSig = Bulk_add_signal(BulkSig, EEG__get_signame(), EEGSig);
    end
 
%GSR
    function BulkSig = addGSR(BulkSig, iEpoch,correspondance)
        GSRChannel = findMyChannel(correspondance{1});
        if(GSRChannel == 0)
            return;
        end
        if iEpoch ==0
            data = phys_data.data(GSRChannel, :);
        else
            data = phys_data.data(GSRChannel, :, iEpoch);
        end
        
        GSRSig = GSR_aqn_variable(squeeze(data), phys_data.srate);
        BulkSig = Bulk_add_signal(BulkSig, GSR__get_signame(), GSRSig);
    end
 
%Temp/HST
    function BulkSig = addHST(BulkSig, iEpoch,correspondance)
        HSTChannel = findMyChannel(correspondance{1});
        if(HSTChannel == 0)
            return;
        end
        if iEpoch ==0
            data = phys_data.data(HSTChannel, :);
        else
            data = phys_data.data(HSTChannel, :, iEpoch);
        end
        
        HSTSig = HST_aqn_variable(squeeze(data), phys_data.srate);
        BulkSig = Bulk_add_signal(BulkSig, HST__get_signame(), HSTSig);
    end
 
%Respiration
    function BulkSig = addRES(BulkSig, iEpoch,correspondance)
        RESChannel = findMyChannel(correspondance{1});
        if(RESChannel == 0)
            return;
        end
        if iEpoch ==0
            data = phys_data.data(RESChannel, :);
        else
            data = phys_data.data(RESChannel, :, iEpoch);
        end
        
        RESSig = RES_aqn_variable(squeeze(data), phys_data.srate);
        BulkSig = Bulk_add_signal(BulkSig, RES__get_signame(), RESSig);
    end
 
%BVT/Plet
    function BulkSig = addBVP(BulkSig, iEpoch,correspondance)
        BVPChannel = findMyChannel(correspondance{1});
        if(BVPChannel == 0)
            return;
        end
        if iEpoch ==0
            data = phys_data.data(BVPChannel, :);
        else
            data = phys_data.data(BVPChannel, :, iEpoch);
        end
        
        BVPSig = BVP_aqn_variable(squeeze(data), phys_data.srate);
        BulkSig = Bulk_add_signal(BulkSig, BVP__get_signame(), BVPSig);
    end
 
%EMG
    function BulkSig = addEMG(BulkSig, iEpoch,correspondance)
        for i = 1:length(correspondance)
            EMGChannel(i) = findMyChannel(correspondance{i});
        end
        if any(EMGChannel == 0)
            return;
        end
        if iEpoch ==0
            data = phys_data.data(EMGChannel, :);
        else
            data = phys_data.data(EMGChannel, :, iEpoch);
        end
        temp = squeeze(zeros(size(data,1)/2,size(data,2),size(data,3)));
        if mod(size(data,1),2)==0
            for j = 1:size(data,1)/2
                temp(j,:,:) = data(j*2-1,:,:) - data(j*2,:,:); %subtracting two leads
            end
            data = temp;
        else
            error('Usage: You need two leads!');
        end
            EMGSig = EMG_aqn_variable(squeeze(data), phys_data.srate);
            BulkSig = Bulk_add_signal(BulkSig, EMG__get_signame(), EMGSig);
    end
 
%ECG
    function BulkSig = addECG(BulkSig, iEpoch,correspondance)
        for i = 1:length(correspondance)
            ECGChannel(i) = findMyChannel(correspondance{i});
        end
        if any(ECGChannel == 0)
            return;
        end
        if iEpoch ==0
            data = phys_data.data(ECGChannel, :);
        else
            data = phys_data.data(ECGChannel, :, iEpoch);
            data = squeeze(data);
        end
        if size(data,1)==2
            data = data(1,:,:) - data(2,:,:); %subtracting two leads
        elseif size(data,1)>2
            error('Usage: We dont support more than two leads at the moment!');
        else
            error('Usage: You need two leads at least!');
        end
        
        ECGSig = ECG_aqn_variable(data, phys_data.srate);
        BulkSig = Bulk_add_signal(BulkSig, ECG__get_signame(), ECGSig);
    end
 
%Find my channel
    function iChannel = findMyChannel(chanName)
        for iChannel = [1:length(phys_data.chanlocs)]
            %       disp(['Will compare ' chanName ' and ' phys_data.chanlocs(iChannel).labels]);
            if(strcmp(chanName, phys_data.chanlocs(iChannel).labels) == 1)
                return;
            end
        end
        iChannel = 0;
        warning(['Could not find channel ' chanName ', it will not be included in the bulk. Please correct the configuration file (config_file.m) accordingly'])
    end
 
 
end