function varargout=jv_genea_120119(varargin)
%Reading GENEActive (http://www.geneactiv.co.uk/) binary files
%   Returning int16/int8 data structure
%   .x .y .z        uncalibrated acceleration values, when reading watch
%   .light          x is up, y is right, z toward wrist
%   .marker
%
%   .time           contains Matlab datenum points, -693960 for Excel 
%                   date/time
%
%   .time           only once in 300 datapoint block
%   .temperature
%   .battery
%
%   Versions:
%       120119 calibrate returns single precision values and also time
%           field
%       120117 corrected number of pages, calibration, close file, light
%           marker.
%       120116 first version, tested with model 1.1m firmware 1.30
%
%   Examples:
%       genea=@jv_genea_120117;
%       data=genea('tst.bin');      %read all blocks
%       data=genea('tst.bin',1);     
%       data=genea('tst.bin',0:data.pages-1)     
%       data=genea('tst.bin',1200); %read every 1200th block
%       data=genea('tst.bin',0:99); %read first 100 blocks
%       data=genea('tst.bin',0);    %read only first block
%
%       xyz=genea(data);            %calibrate
%       xyz=genea(data,100);        %calibrate, every 100th sample
%
%       plot(xyz.time,xyz.x);
%       datetick('keeplimits');
%       xlim([xyz.t(1)+12/24 xyz.t(1)+24/24]);
%       datetick('keeplimits');
%
%   References
%       Based on geneactiv_instruction_manual_v1.1.pdf

%       jussi.virkkala@ttl.fi @neuroupdate.com

%%main part
file=varargin{1};
if nargin<2,
    index=1;
else
    index=varargin{2};
end
if isstruct(file),
    data=calibrate(file,index);
else
    data=read(file,index);
end
varargout{1}=data;

%%Calibrate
%2012-01-19 Returning single precision, also time
function xyz=calibrate(g,index);
    if length(index)==1,
        index=1:index:length(g.x);
    end
%2012-01-18 single    
%2012-01-17 corrected )*100    
    xyz.x=(single(g.x(index))*100-g.x_offset)/g.x_gain;
    xyz.y=(single(g.y(index))*100-g.y_offset)/g.y_gain;
    xyz.z=(single(g.z(index))*100-g.z_offset)/g.z_gain;
    xyz.light=(single(g.light(index))*g.lux)/g.volts;
    xyz.time=(index-1)'/24/3600/g.rate+g.time(1);
%%Reading data
function g=read(file,index);
f=fopen(file,'r');
e=~feof(f);

while e,
    r=fgetl(f);
    if r==-1,r='';end %last one -1
    e=~feof(f);
    i=findstr([r ':'],':');
    switch(r(1:i(1)-1)),
        case 'Device Identity',
            g.device_identity=r;
            for i=2:6,g.device_identity=str2mat(g.device_identity,fgetl(f));end
        case 'Device Capabilities',
            g.device_capabilities=r;
            for i=2:10,g.device_capabilities=str2mat(g.device_capabilities,fgetl(f));end
        case 'Configuration Info',
            g.configuration=r;
            for i=2:5,g.configuration=str2mat(g.configuration,fgetl(f));end
        case 'Trial Info',
            g.trial=r;
            for i=2:11,g.trial=str2mat(g.trial,fgetl(f));end
        case 'Subject Info',
            g.subject_info=r;
            for i=2:9,
                r=fgetl(f);
                if i==2,g.location=r(22:end);end
                if i==3,g.subject=r(14:end);end                   
                g.subject_info=str2mat(g.subject_info,r);
            end            
        case 'Calibration Data',
            %x gain:25576            
            r=fgetl(f);g.x_gain=eval(r(8:end));
            %x offset:694
            r=fgetl(f);g.x_offset=eval(r(10:end));
            %y gain:25813
            r=fgetl(f);g.y_gain=eval(r(8:end));
            %y offset:-407
            r=fgetl(f);g.y_offset=eval(r(10:end));
            %z gain:25421
            r=fgetl(f);g.z_gain=eval(r(8:end));
            %z offset:-2102
            r=fgetl(f);g.z_offset=eval(r(10:end));
            %Volts:300
            r=fgetl(f);g.volts=eval(r(7:end));
            %Lux:800
            r=fgetl(f);g.lux=eval(r(5:end));
        case 'Memory Status',
            %Number of pages:
            r=fgetl(f);
            np=eval(r(17:length(r)));
            g.pages=np;
            if length(index)==1,
                if index,
%2012-01-17 (np-1)                    
                    index=0:index:(np-1);
                end
            end
            g.x=zeros(length(index)*300,1,'int16');
            g.y=g.x;
            g.z=g.x;
            g.light=g.x;
            g.marker=zeros(length(index)*300,1,'uint8');
            g.battery=zeros(length(index),1);
            g.time=g.battery;
            g.temperature=g.time;
            g.serial='';
            g.rate=0;            
            cp=0;
            cpd=-1;
        case 'Recorded Data',
            %skip data blocks
            while cp<index(1),               
                fgetl(f);fgetl(f);fgetl(f);fgetl(f);fgetl(f);fgetl(f);fgetl(f);fgetl(f);fgetl(f);fgetl(f);                
                cp=cp+1;
            end
            %Device Unique Serial Code:011648
            r=fgetl(f);
            if isempty(g.serial),
                g.serial=r(27:end);
            else
                if ~strcmp(g.serial,r(27:end)),error('Serial changed between pages');end
            end
            %Sequence Number:0
            r=fgetl(f);
            if cp~=eval(r(17:end)),error('Sequence number error');end
            cp=cp+1;
            %Page Time:2012-01-13 11:05:00:500
            r=fgetl(f);
            g.time(cp)=datenum(datevec(r(11:end-4),'yyyy-mm-dd HH:MM:SS'))+eval(r(end-2:end))/1000/3600/24;            
            if cp>cpd,disp(['...' r]);cpd=cpd+1200;end
            %Unassigned:
            r=fgetl(f);
            %Temperature:30.1
            r=fgetl(f);
            g.temperature(cp)=eval(r(13:end));
            %Battery voltage:4.2090
            r=fgetl(f);
            g.battery(cp)=eval(r(17:end));
            %Device Status:Recording
            fgetl(f);
            %Measurement Frequency:100.0         
            r=fgetl(f);                
            g.rate=eval(r(23:end));
            %300 measurements*6*2
            hex=fgetl(f);
            cpi=[cp*300-299:cp*300];
            dec=hex2dec(reshape(hex,2,1800)');
            mat=reshape(dec,6,300)';
            %x, 12 bit
            x=bitshift(mat(:,1),4)+bitshift(mat(:,2),-4);
            g.x(cpi)=bitand(x,2047)-bitand(x,2048);
            %y, 12 bit
            y=bitshift(mat(:,2),8)+mat(:,3);
            g.y(cpi)=bitand(y,2047)-bitand(y,2048);
            %z, 12 bit
            z=bitshift(mat(:,4),4)+bitshift(mat(:,5),-4);
            g.z(cpi)=bitand(z,2047)-bitand(z,2048);
            %light 0-1024
%2012-01-17 (cpi)
            g.light(cpi)=bitshift(bitand(mat(:,5),15),2)+bitshift(mat(:,6),-2);
            if find(g.light(cpi)<0);errordlg('Light level should non negative');end
            %marker button
%2012-01-17 (cpi)
            g.marker(cpi)=bitand(mat(:,6),3);
            if find(g.marker(cpi)==1),errodlg('Last reserved bit should be zero');end
            index=index(2:end);
            if isempty(index),
                e=0;
            end            
    end
end
%2012-01-17 closing file
fclose(f);

%end