initMetaData.m

function metaData = initMetaData(Header,GPS,seq,stat,dupl,HZ,instrumentType)

% Usage: metaData = initMetaData(Header,GPS,seq,stat,dupl,HZ,instrumentType)

if nargin < 5
    dupl = [];
end

if nargin < 6
    HZ = 1;
end

if nargin < 7
	instrumentType = 'NIMS';
end

NO_HEADER = 0;
if nargin > 0
    if isempty(Header)
        NO_HEADER = 1;
    end
else
    Header = '';
    NO_HEADER = 1;
end

try
    [runID,sensorID,siteName,Ex_wire,Ey_wire,GroundEinfo,nims_comments,H_comments,operator] = parseHeader(Header);
catch exception
    disp(['Header not processed due to ' exception.identifier ' error.']);
    disp('Do NOT edit the original DATA.BIN file to avoid introducing data gaps in the binary part.');
    disp('Instead, manually rename the file to *.nim, save the header in a *.hdr file and edit the header.');
    [runID,sensorID,siteName,Ex_wire,Ey_wire,GroundEinfo,nims_comments,H_comments,operator] = parseHeader;    
end

if nargin >= 4
    [lat, lon, elev, decl, decl_info, gain_char, error_flag, GPS_comments] = parseGPS(GPS);
else
    [lat, lon, elev, decl, decl_info, gain_char, error_flag, GPS_comments] = parseGPS;
end
    
% if gain_char is "Unknown" record gain change
if gain_char == 'U'
    GAIN_CHANGE = 1;
else
    GAIN_CHANGE = 0;
end

% error_flag non-zero if there were problems parsing the GPS string
if error_flag == 0
    NO_GPS = 0;
    GPS_ERROR = 0;
elseif error_flag <= 2
    NO_GPS = 1;
    GPS_ERROR = 1;
elseif error_flag > 2
    NO_GPS = 0;
    GPS_ERROR = 1;
end

% start date and time require special treatment: counting to the start
% of the time series from the so-called "GPS lock", using also the status
% byte string to find the lock, and the sequence string to find gaps
if nargin >= 4
    [start_time, error_flag, time_comments] = startTimeFromGPS(GPS, seq, stat);
elseif nargin >= 2
    [start_time, error_flag, time_comments] = startTimeFromGPS(GPS);
else
    [start_time, error_flag, time_comments] = startTimeFromGPS;
end
if error_flag
    disp(time_comments);
end
GPS_ERROR = GPS_ERROR || error_flag;

% The number of seconds could be different from the number of scans,
% when the missing data flags have been inserted. Here, nsec is the
% number of seconds, estimated using the sequence string, while nscan
% is the number of data records stored in the NIMS binary file (does
% not include any missing data).
% Edited by Anna Kelbert Nov 3, 2015: the reason for the -1 in the nsec
% calculation is to compute the correct end time.
% Note that for 8 Hz data, nscan is NOT the size of Data stream: it is 
% the number of data blocks in the NIMS binary file; each block has 
% 8 measurements (5 values each).
% This is different for ZEN data, where the number of scans corresponds
% to the length of the data stream. Do different things for NIMS and ZEN.
if nargin >= 4
    [gaps,gap_comments,gap_errors] = find_gaps(GPS,seq,stat);
    nscan = length(seq);
    if strcmp(instrumentType,'NIMS')
        if ~isempty(gaps.len)
            nsec = length(seq) + sum(gaps.len) - 1;
        else
            nsec = seq(end);
        end
    else
        if ~isempty(gaps.len)
            nsec = (length(seq) + sum(gaps.len) - 1)/HZ;
        else
            nsec = seq(end)/HZ;
        end
    end
else
    gaps = {};
    gaps.len = [];
    gaps.ind = [];
    gap_errors = '';
    nscan = 0;
    nsec = 0;
end

% now that we have the correct number of seconds, compute end time
sec2num = 1/(3600*24);
if isempty(start_time)
    startDate='yyyy-mm-dd';
    startTime='HH:MM:SS';
    endDate='yyyy-mm-dd';
    endTime='HH:MM:SS';
else
    startDate = datestr(datenum(start_time),29);
    startTime = datestr(datenum(start_time),13);
    endDate = datestr(datenum(start_time)+sec2num*nsec,29);
    endTime = datestr(datenum(start_time)+sec2num*nsec,13);
end

% leave the runID as it is; will only use it for processing
if ~isempty(runID)
    runID = char(runID);
end

% make sure the siteID is 5 char uppercase; run char is lowercase
siteID = runID; % default: unknown format
if (length(runID)==6) % e.g. ORG04a->ORG04
    siteID = upper(runID(1:5)); 
elseif (length(runID)==7) 
    if isstrprop(runID(4),'digit')
        if str2double(runID(4))==0 % e.g. ori006a->ORI06
            siteID = [upper(runID(1:3)) upper(runID(5:6))]; 
        else % e.g. pam486a->PA486
            siteID = [upper(runID(1:2)) upper(runID(4:6))]; 
        end
    end
end

id = strsplit(char(sensorID),';');
NIMS_ID = char(id(1));
if length(id) > 1 && length(NIMS_ID) >= 4
    Magn_ID = char(id(2));
    if length(Magn_ID)==2
        Magn_ID = [NIMS_ID(1:4) '-' Magn_ID];
    end
else
    Magn_ID = NIMS_ID;
end

metaData.siteName = siteName; 
metaData.siteID = siteID;
metaData.runID = runID;
metaData.InstrumentType = instrumentType;
metaData.InstrumentID = NIMS_ID;
metaData.Magnetometer = Magn_ID;
metaData.Ex_Electrodes = Ex_wire.electrodes;
metaData.Ex_wire_length = Ex_wire.length;
metaData.Ex_wire_azimuth = Ex_wire.azimuth;
metaData.Ey_Electrodes = Ey_wire.electrodes;
metaData.Ey_wire_length = Ey_wire.length;
metaData.Ey_wire_azimuth = Ey_wire.azimuth;
metaData.GroundEinfo = GroundEinfo;
metaData.HighPass = 'on';
metaData.mag_azimuth = [0. 90. 0.];
metaData.system_errors = [H_comments GPS_comments time_comments gap_errors];
metaData.errors = [H_comments GPS_comments time_comments gap_errors];
metaData.comments = '';
metaData.field_comments = nims_comments;
metaData.SiteInstalledBy = operator;
metaData.MetaDataCheckedBy = '';
metaData.lat = lat;
metaData.lon = lon;
metaData.elev = elev;
metaData.decl = decl;
metaData.decl_info = decl_info;
metaData.startDate = startDate;
metaData.startTime = startTime;
metaData.endDate = endDate;
metaData.endTime = endTime;
metaData.duplicates_deleted = length(dupl);
metaData.gain_char = gain_char;
metaData.gainApplied = 0;
metaData.dt = 1/HZ;
metaData.nsec = nsec;
metaData.nscan = nscan;
metaData.ngaps = length(gaps.ind);
metaData.gaps = gaps;
metaData.gapsFilled = 0;
metaData.scaling = [1 1 1 1 1];
metaData.nch = 5;
metaData.SystemResponse = NIMsysRsp(NIMS_ID,HZ);
metaData.NO_HEADER = NO_HEADER;
metaData.NO_GPS = NO_GPS;
metaData.GPS_ERROR = GPS_ERROR;
metaData.GAIN_CHANGE = GAIN_CHANGE;