% This script makes a .mat-file for each EDF xbt file in a given
% directory, as well as a summary .mat-file describing the bulk
% properties related to each XBT profile. Comments, which include
% information on what is produced, are embedded within this script

% data directory can be relative or absolute, but the directory
% must be writeable (Original data are not altered -- the EDF files
% can be read only)
data_dir = '../newxbt/';

% run a perl script that separates the data from the header -- making
% files ending with EDF_dat and EDF_hdr -- and extracts info from the
% header that is of interest (year, month, day, hour. minute, second,
% longitude, latitude) into a file with the extension EDF_info
eval(['!perl remove_header.pl ', data_dir]);

% now use the info from the perl output to make a .mat-file for each
% XBT cast. Each cast has a Matlab structure array with the same
% name as the file, within that structure array are the following
% elements:
%         year
%         month
%         day
%         hour
%         minute
%         second
%         longitude (in decimal degrees, negative longitudes are
%                    degrees West)
%         latitude (in decimal degrees, negative values are degrees
%                   north)
%         depth (vector of depths where XBT recordings are made,
%                NaN if empty)
%         temperature (vector of temperature recordings, NaN if
%                      empty)
%         c_s (vector of sound speeds, NaN if empty)
%         date (date in Matlab's "datenum" format)
%         datestr (date in a string format)
% The vectors depth, temperature, and c_s should all be the same length
%
% In addition, a mat-file called "summary" is made. It contains a
% structured array called "summary" with the following elements
%         longitude (a vector of longitudes)
%         latitude (a vector of latitude)
%         date (a vector of dates in Matlab's "datenum" format
%         maxdepth (a vector of maximum depths)
%         fname (name of .mat-file containing data)
%         ncasts (number of casts)
%         datadir (data directory, whatever was used above)
% Other than "ncasts", and "datadir", all elemens will have a
% length of "ncasts".


d = dir([data_dir, '*.EDF']);

for i = 1:length(d)
  varname = getfilename(d(i).name);
  info = load([data_dir, d(i).name , '_info']);
  eval([varname, '.year = info(1);']);
  eval([varname, '.month = info(2);']);
  eval([varname, '.day = info(3);']);
  eval([varname, '.hour = info(4);']);
  eval([varname, '.minute = info(5);']);
  eval([varname, '.second = info(6);']);
  eval([varname, '.longitude = info(7);']);
  eval([varname, '.latitude = info(8);']);
  eval([varname, '.date = datenum(info(1:6)'');']);
  eval([varname, '.datestr = datestr(datenum(info(1:6)''));']);
  
  summary.lon(i) = info(7);
  summary.lat(i) = info(8);
  summary.date(i) = datenum(info(1:6)');

  clear info
  data = load([data_dir, d(i).name, '_dat']);
  
  if(isempty(data))
    eval([varname, '.depth = NaN;']);
    eval([varname, '.temperature = NaN;']);
    eval([varname, '.c_s = NaN;']);
    summary.maxdepth(i) = NaN;
  else
    eval([varname, '.depth = data(:,1);']);
    eval([varname, '.temperature = data(:,2);']);
    eval([varname, '.c_s = data(:,3);']); % note that speed of sound
                                       % assumes a salinity of
				       % 33.50 ppt
    summary.maxdepth(i) = max(data(:,1));
  end
  
  summary.datadir = data_dir;
  summary.fname{i} = varname;
  
  eval(['save ', data_dir, varname, ' ', varname]);
  eval(['clear ', varname]);
    
end

summary.ncasts = i;

eval(['save ', data_dir, 'summary summary']);

% remove files made by the perl script
eval(['!rm ', data_dir, '*hdr']);
eval(['!rm ', data_dir, '*dat']);
eval(['!rm ', data_dir, '*info']);