readTsgDataAstrolabe.m

function [error] = readTsgDataAstrolabe( hMainFig, filename )
% readTsgDataAstrolabe( hMainFig, filename )
% Function to read TSG data from Astrolabe ship.
%
% Input
% -----
% hMainFig ........... Handle to the main user interface
% filename ........... Data filename
%
% Output
% ------
% error .............. 1: OK - -1 : an error occured
%

% Get the data from the application GUI
% -------------------------------------
tsg = getappdata( hMainFig, 'tsg_data');

% Get the fieldnames of tsg structure
% -----------------------------------
tsgNames     = fieldnames(tsg);
nbFieldNames = length( tsgNames );

% Get NO_CONTROL, GOOD, PROBABLY_BAD codes
% ----------------------------------------
%NO_CONTROL   = int8(tsg.qc.hash.NO_CONTROL.code);
GOOD         = int8(tsg.qc.hash.GOOD.code);
PROBABLY_BAD = int8(tsg.qc.hash.PROBABLY_BAD.code);
BAD          = int8(tsg.qc.hash.BAD.code);

% Display read file info on console
% ---------------------------------
fprintf('\nREAD_ASCII_FILE\n'); tic;

% Open the file
% -------------
fid = fopen( filename, 'rt' );

% Check file
% -----------
if fid == -1
  msg_error = ['TSG file : Open file error : ' filename];
  warndlg( msg_error, 'ASCII error dialog');
  sprintf('...cannot locate %s\n', filename);
  error = -1;
  return;
end

% Display more info about read file on console
% --------------------------------------------
fprintf('...reading %s : ', filename);

% Read the header till the header line has been read
% --------------------------------------------------
OK = 0;
while ~OK

  % Read every line
  % ---------------
  line = fgetl( fid );
  c = textscan( line, '%s');

  switch char( c{1}(1) )

    case '%HEADER'

      % Read the header then quit the while loop
      % ----------------------------------------
      header = c{1}(2:end);
      nHeader = length( header );
      OK = 1;

    otherwise

      % Get the parameter Name (Delete '%')
      % ----------------------------------
      Para = char( strtok(c{1}(1), '%') );

      % Read the parameter value
      % ------------------------
      ind = strmatch( Para, tsgNames);
      if ~isempty( ind )
        
        % patch added for composed name
        % -----------------------------
        a = c{1}(2:end)';
        str=[];
        for i=a
          str = sprintf('%s %s', str, char(i));
        end
        
        % copy to tsg struct & remove leading and trailing white space
        % ------------------------------------------------------------
        tsg.(Para) = strtrim(str);
      end

  end
end

% Build the format depending on the header parameters
% 1 - Decimate the HEADER - The 5th first parameters are always
%     %HEADER YEAR MNTH DAYX hh mm ss
% 2 - The 4 Date and time parametes are read in %d
% -------------------------------------------------------------
format = '%d %d %d %d';
for i = 5 : nHeader
  format = [format ' %f'];
end

% Read the data in a cell
% -----------------------
cellData = textscan( fid, format );

% Convert cell to a structure
% ---------------------------
s = cell2struct(cellData, header, 2);

clear cellData

% Date (y m d h m s) in the first 4 elements in data
% --------------------------------------------------
% ddmmyy = char(s.(char(header(1)))) ;
% dd = str2num(ddmmyy(:,1:2));
% mm = str2num(ddmmyy(:,3:4));
ddmmyy = double(s.(char(header(1)))) ;
nn = length(ddmmyy);
dd = repmat(NaN, [nn 1]);
mm = repmat(NaN, [nn 1]);
yy = repmat(NaN, [nn 1]);
for it = 1:nn
    ddmmyy_str = sprintf('%06d', ddmmyy(it));
    dd(it) = str2num(ddmmyy_str(:,1:2)); %#ok<ST2NM>
    mm(it) = str2num(ddmmyy_str(:,3:4)); %#ok<ST2NM>
    yy(it) = 2000 + str2num(ddmmyy_str(:,5:6)); %#ok<ST2NM>
end

% Warning: for post-2000 files only!
% ----------------------------------
%yy = 2000 + str2num(ddmmyy(:,5:6));

hh = double( s.(char(header(2))) );
mi = double( s.(char(header(3))) );
ss = double( s.(char(header(4))) );

tsg.report.tsgfile = filename;
tsg.DAYD = datenum(yy, mm, dd, hh, mi, ss);
tsg.DATE = datestr( tsg.DAYD, 'yyyymmddHHMMSS' );

nHeader = length( header );
for i = 5 : nHeader

  % QC should be converted in int8
  % ----------------------------------
  if ~isempty( strfind(char(header(i)), '_QC'))
    tsg.(char(header(i))) = int8(s.(char(header(i))));
  else
    tsg.(char(header(i))) = s.(char(header(i)));
  end

end

% Fill TSG attributes
% -------------------
tsg.PLATFORM_NAME     = 'astrolabe';
tsg.SHIP_CALL_SIGN    = 'FHZI';
tsg.PROJECT_NAME      = 'SURVOSTRAL';
tsg.PI_NAME           = 'Rosemary Morrow';
tsg.DATA_ACQUISITION  = 'IPEV';
tsg.PROCESSING_CENTRE = 'SURVOSTRAL';
tsg.PROCESSING_STATES = '2C+';
tsg.SAMPLING_PERIOD   = '60';

% Missing value to be replaced by NaNs
% ------------------------------------
miss = -90;

% Fill TSG variables
% by default, SSPS before correction flagged PROBABLY_BAD 
% SSPS_ADJUSTED and SSTP flagged GOOD
% -------------------------------------------------------

if ~isempty(tsg.SSTP)
    tsg.SSTP(tsg.SSTP < miss) = NaN;
    tsg.SSTP_QC = castByteQC( GOOD, tsg.DAYD );
    tsg.SSTP_QC(isnan(tsg.SSTP)) = BAD;
end

tsg.SSPS_QC = castByteQC(PROBABLY_BAD, tsg.DAYD);
tsg.SSPS_ADJUSTED_QC = castByteQC(GOOD, tsg.DAYD);
tsg.SSPS(tsg.SSPS < miss) = NaN;
tsg.SSJT(tsg.SSJT < miss) = NaN;
tsg.SSPS_ADJUSTED(tsg.SSPS_ADJUSTED < miss) = NaN;
tsg.SSPS_QC(isnan(tsg.SSPS)) = BAD;
tsg.SSPS_ADJUSTED_QC(isnan(tsg.SSPS)) = BAD;

% populate tsg.file structure
% ---------------------------
[tsg.file.pathstr, tsg.file.name, tsg.file.ext] = ...
  fileparts(filename);

% Perform somme automatic tests
% -----------------------------
automaticQC( hMainFig );

tsg.file.type = 'ASCII';

% Save the data in the application GUI
% ------------------------------------
setappdata( hMainFig, 'tsg_data', tsg );

% Close the file
% --------------
fclose( fid );

% Display time to read file on console
% ------------------------------------
t = toc; fprintf('...done (%6.2f sec).\n\n',t);

% Everything OK
% -------------
error = 1;

end