cleanMetaData.m

function [metaData,res] = cleanMetaData(metaData)

% [metaData,res] = cleanMetaData(metaData)
%       
% Cleans and corrects metaData structure:
% 1. Converts strings to numbers.
% 2. Checks that no fields are empty.
% 3. Output true if there are no errors.
%
% Intended for use through checkHeaderGUI(metaData),
% but able to deal with arbitrarily incomplete metaData

fields = fieldnames(metaData);
errors = '';
res = 1;

for k=1:length(fields)
    value = metaData.(fields{k});
    switch fields{k}
        case {'NO_HEADER', 'NO_GPS', 'GPS_ERROR', 'GAIN_CHANGE', ...
                'gainApplied', 'gapsFilled'}
            if ischar(value)
                if strcmp(value,'[false]')
                    value = 0;
                elseif strcmp(value,'[true]')
                    value = 1;
                else
                    value = str2double(value);
                end
            elseif isnumeric(value)
                value = logical(value);
            elseif isnan(value)
                value = 0;
            end
        case {'nsec', 'nscan', 'nch', 'ngaps'}
            if ischar(value)
                value = str2double(value);
            end
        case 'lat'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value)
                errors = 'Please input latitude in degrees';
                res = 0;
            end
            if abs(value) > 90.
                errors = 'Invalid latitude';
                res = 0;
            end
        case 'lon'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value)
                errors = 'Please input longitude in degrees';
                res = 0;
            end
            if value > 180. % make sure longitudes are consistent
                value = value - 360.;
            end
        case 'elev'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value)
                errors = 'Please input elevation in meters';
                res = 0;
            end
        case 'decl'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value)
                errors = 'Please input magnetic declination';
                res = 0;
            end
        case 'decl_info'
            if isempty(value)
                value.igrf = [];
                value.igrf_conf = [];
                value.file_decl = metaData.decl;
            end
        case {'scaling', 'mag_azimuth'}
            if ischar(value)
                value = str2num(value); %#ok<ST2NM>
            end
        case 'gaps'
            if ~isnumeric(value.ind)
                value.ind = str2num(value.ind); %#ok<ST2NM>
            end
            if ~isnumeric(value.len)
                value.len = str2num(value.len); %#ok<ST2NM>
            end
            if ~isnumeric(value.err)
                value.err = str2num(value.err); %#ok<ST2NM>
            end
            if isfield(value,'spike')
                if ~isnumeric(value.spike)
                    value.spike = str2num(value.spike); %#ok<ST2NM>
                end
            end
        case 'Ex_wire_length'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value) || value <= 0
                errors = 'Please input correct Ex wire length';
                res = 0;
            end
        case 'Ex_wire_azimuth'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value)
                errors = 'Please input correct Ex wire azimuth';
                res = 0;
            end
        case 'Ey_wire_length'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value) || value <= 0
                errors = 'Please input correct Ey wire length';
                res = 0;
            end
        case 'Ey_wire_azimuth'
            if ischar(value)
                value = str2double(value);
            end
            if isempty(value) || isnan(value)
                errors = 'Please input correct Ey wire azimuth';
                res = 0;
            end
        case 'gain_char'
            if strcmp(value,'U') || isempty(value)
                errors = 'Gain char must be H(igh) or L(ow) or E(X) high or E(Y) high';
            end
        case 'siteName'
            if strfind(value,'Unknown')
                errors = 'Important: Please correct Site Name';
                res = 0;
            end
        case 'MetaDataCheckedBy'
            if isempty(value)
                errors = 'Please enter your full name in the Meta Data Checked By field';
                res = 0;
            end
        case 'runID' % don't change a valid runID
            if isempty(value) || strcmp(value,'data')
                errors = 'Important: Please correct Run ID';
                res = 0;
            end
        case 'siteID'
            value = upper(value);
        case 'InstrumentID'
            if strcmp(metaData.InstrumentType,'NIMS')
                rsp = NIMsysRsp(value);
                if isempty(rsp)
                    errors = 'Please correct system ID. Unknown NIMS.';
                    res = 0;
                else
                    metaData.SystemResponse = rsp;
                end
            end
        case 'dt'
            if ischar(value)
                value = str2double(value);
            end
        otherwise
            % do nothing at present
    end
    metaData.(fields{k}) = value;
    metaData.errors = errors;
end

% If the gaps structure has changed, update ngaps and nsec
metaData.ngaps = length(metaData.gaps.ind);
if strcmp(metaData.InstrumentType,'NIMS')
	metaData.nsec = metaData.nscan + sum(metaData.gaps.len) - 1;
else
	metaData.nsec = metaData.nscan*metaData.dt + sum(metaData.gaps.len) - 1;
end

% Declination model requires special treatment
if ~isfield(metaData,'decl_info')
    decl_info.igrf.version = 0;
    decl_info.igrf.toolbox = 'Declination obtained from the instrument GNSS NMEA sequence';
    decl_info.igrf_conf = [];
    decl_info.file_decl = metaData.decl;
    metaData.decl_info = decl_info;
end

% Time required special treatment
if ~isfield(metaData,'startDate') ...
        || ~isfield(metaData,'startTime') ...
        || ~isfield(metaData,'endDate') ...
        || ~isfield(metaData,'endTime')
    % assume that the subroutine is called for some unusual kind of
    % metaData
else
    if isempty(istime(metaData.startDate,metaData.startTime))
        metaData.errors = 'Please specify a valid start time before processing';
        res = 0;
    elseif isempty(istime(metaData.endDate,metaData.endTime))
        metaData.errors = 'Please specify a valid end time before processing';
        res = 0;
    elseif isfield(metaData,'nsec') && ~isempty(metaData.nsec)
        % check times for consistency
        tdiff = metaData.nsec/3600/24;
        [tstart] = istime(metaData.startDate,metaData.startTime);
        [ tend ] = istime(metaData.endDate,metaData.endTime);
        info = datenum(tend)-datenum(tstart)-tdiff;
		if strcmp(metaData.InstrumentType,'ZEN')
			tolerance = 600;
		else
			tolerance = 1;
		end
        if abs(info*3600*24)>tolerance
            info = datestr(datenum(tstart)+tdiff,31);
            metaData.errors = ['Times inconsistent: end time should be ' info];
            res = 0;
        end
    end
end