%
%  Ed Hill
%  $Id: Commands.m,v 1.1 2004/06/18 19:31:06 edhill Exp $
%

%  Data from:
%    http://mqabi.gsfc.nasa.gov/cgi-bin/MQABI/subset/map_04_week_D1.sst.cgi

matlab -nojvm

  !./pre_process
  
  clear all
  files = [ ...
      '2002065'; '2002073'; '2002089'; '2002097'; '2002105'; ...
      '2002113'; ...
      '2002145'; '2002153'; '2002161'; '2002169'; '2002177'; ...
      '2002185'; '2002193'; '2002201'; '2002209'; '2002217'; ...
          ];
  lats = linspace(47.0, 29.0, 410);
  lons = linspace(-78.0, -54.0, 546);
  i = 1;
  nt = size(files,1);
  days = [1:nt];
  all = zeros(nt,length(lats),length(lons));
  for i = 1:size(files,1)
    
    var = load([ 'sst-' files(i,:) ]);
    vt = var;
    for j = 1:prod(size(vt))
      if vt(j) == -99
        vt(j) = NaN;
      end
    end
    all(i,:,:) = vt;
    days(i) = str2double(files(i,5:7));

    % surf(lons,lats,vt), view(2), shading interp
    % pause(1)

  end

  id = 'SST';
  units = 'deg C (weekly average)';

  nc = netcdf('modis_aqua_gulfstr.nc', 'clobber');
  nc.reference = 'Various MODIS-Aqua data sets of the Gulf Stream';
  nc.author = 'Ed Hill <eh3@mit.edu>';
  nc.date = 'Jun 16, 2004';
  
  nc('T') = nt;
  nc('Y') = length(lats);
  nc('X') = length(lons);
  nc{'T'}  = 'T';
  nc{'Y'}  = 'Y';
  nc{'X'}  = 'X';
  nc{ id } = { 'T', 'Y', 'X' };
  nc{'X'}.uniquename = 'X';
  nc{'X'}.long_name = 'longitude';
  nc{'X'}.gridtype = ncint(1);
  nc{'X'}.units = 'degree_east';
  nc{'Y'}.uniquename = 'Y';
  nc{'Y'}.long_name = 'latitude';
  nc{'Y'}.gridtype = ncint(0);
  nc{'Y'}.units = 'degree_north';
  nc{'T'}.uniquename = 'T';
  nc{'T'}.long_name = 'Time';
  nc{'T'}.gridtype = ncint(0);
  nc{'T'}.units = 'days since Jan 1, 2002';
  nc{ id }.units = units;
  nc{ id }.long_name = id;
  nc{ id }.missing_value = ncdouble(NaN);
  nc{ id }.FillValue_ = ncdouble(0.);
  nc{'Y'}(:) = lats;
  nc{'X'}(:) = lons;
  nc{'T'}(:) = days;
  nc{ id }(:) = permute(all,[ 1 2 3 ]);
  nc = close(nc);

  ! scp ./modis_aqua_gulfstr.nc channel.mit.edu:/home/edhill/INGRID_PEOPLE/EH3/modis-aqua