function ncMicrocat(filename, ncFilename)
% ncMicrocat - Convert a concatenated oasis microcat file to netcdf
%
% This assumes the file is in the usual Oasis format. The file will have the 
% following columns: dayOfYear temp(C) conductivity ctdTime
%
% Use as: ncMicrocat(filename, ncFilename)
%
% Inputs: filename = name of the microcat data file to read
%         ncFilename = the name of the netcdf file to create

% Brian Schlining
% 16 May 2000

%===========
% Open File
%===========
if ~nargin | isempty(filename)
   [infile inpath] = uigetfile('*.*','Select microcat data file',0,0);
   if infile == 0
      return                            % Return if CANCEL is selected
   end
   filename = [inpath infile];
   if nargin < 2 | isempty(ncFilename)
      [p f ext] = fileparts(filename);
      ncFilename = [p f '.nc'];
   end
   
end

fid = fopen(filename, 'rt');

if fid <= 0 
   error(['Unable to open ' filename])
else
   outfile = netcdf(ncFilename, 'clobber');
   if isempty(outfile)
      fclose(fid);
      error(['Unable to create ' ncFilename]);
   end
   
end



n     = 0;
R     = 4.2914;
depth = 1;

[Year Month Day]     = datevec(now);
dateS                = sprintf('%02i/%02i/%04i', Month, Day, Year);

outfile.conventions  = 'MBARI/timeSeries/mooring/microcat';
outfile.creationDate = dateS;
outfile.lastModified = dateS;
mooring              = input('Enter mooring ID (All CAPS): ');
%mooring = 'EP1';

fprintf(1,'Creating netcdf schema')
outfile.mooring      = mooring;
outfile.description  = 'Moored microcat CTD data from the Equatorial Pacific';

switch lower(mooring)
case 'ep1'
   outfile.longitude = '150W';
   outfile.latitude  = '0';
   lon = -150;
   lat = 0;
case 'ep2'
   outfile.longitude = '170W';
   outfile.latitude  = '2S';
   lon = -170;
   lat = -2;
end

outfile.waterDepth             = '4000m';
outfile.keywords               = 'salinity, temperature, microcat';
outfile.instumentType          = 'Serial microcat';

outfile('latitude')            = 1;                     % Dimension
outfile{'latitude'}            = ncdouble('latitude');  % Specify Co-ordinate variable dimensions
outfile{'latitude'}.long_name  = 'Latitude';
outfile{'latitude'}.units      = 'degrees_north (+N/-S)';
outfile{'latitude'}(:)         = lat;

outfile('longitude')           = 1;                     % Dimension
outfile{'longitude'}           = ncdouble('longitude'); % Specify Co-ordinate variable dimensions
outfile{'longitude'}.long_name = 'Longitude';
outfile{'longitude'}.units     = 'degrees_east (+E/-W)';
outfile{'longitude'}(:)        = lon;

outfile('depth')               = 1;                     % Dimension
outfile{'depth'}               = ncdouble('depth'); % Specify Co-ordinate variable dimensions
outfile{'depth'}.long_name     = 'Depth';
outfile{'depth'}.units         = 'meters';
outfile{'depth'}.positive      = 'down';
outfile{'depth'}(:)            = 1.5;

outfile('time')                = 0;                     % Define Unlimited dimension
outfile{'time'}                = ncdouble('time');
outfile{'time'}.long_name      = 'time GMT';
outfile{'time'}.units          = 'seconds since 1970-01-01 00:00:00';

outfile{'temp'}                = ncfloat('time','latitude','longitude','depth');
outfile{'temp'}.long_name      = 'Temperature';
outfile{'temp'}.units          = 'Celsius';
outfile{'temp'}.symbol         = 'T';
outfile{'temp'}.FillValue_     = -999;
outfile{'temp'}.missing_value  = -999;

outfile{'sal'}                = ncfloat('time','latitude','longitude','depth');
outfile{'sal'}.long_name      = 'Salinity';
outfile{'sal'}.units          = 'psu';
outfile{'sal'}.symbol         = 'S';
outfile{'sal'}.FillValue_     = -999;
outfile{'sal'}.missing_value  = -999;

fprintf(1,'...completed\n')

fprintf(1,'Reading microcat data.')
dayOfYear = ones(50000,1)*-999;
year = dayOfYear;
temp = dayOfYear;
C    = dayOfYear;
dateS = cell(50000,1);

while ~feof(fid)
   s = fgetl(fid);
   n = n + 1;
   buf = sscanf(s, '%f %f, %f');
   %dayOfYear(n) = buf(1);
   temp(n) = buf(2);
   C(n)    = buf(3);
   mdy     = stringtokenizer(s, 3, ',');
   buf     = stringtokenizer(s, 4, ',');
   if isempty(buf)
      s
      return
   end
   
   hms     = stringtokenizer(buf, 1);
   dateS{n}  = [mdy ' ' hms];
   %dayOfYear(n) = sscanf(stringtokenizer(s, 1), '%f');
   %year(n)      = sscanf(stringtokenizer(s, 6), '%f');
   %buf       = stringtokenizer(s, 1, ',');
   %temp(n)   = sscanf(stringtokenizer(buf, 2), '%f');
   %C(n)      = sscanf(stringtokenizer(s, 2, ','), '%f');
   if ~rem(n,1000)
      fprintf(1,'.')
   end
   
end
fclose(fid);

fprintf(1,'completed\n')

fprintf(1,'Processing data.')
%time = jul2date(dayOfYear, year);
dateS = char(dateS(1:n));
sdn  = datenum(dateS);
utc  = sdn2utc(sdn);
temp = temp(1:n);
sal  = salin_(C(1:n)./R, temp, depth);
outfile{'time'}(1:length(utc)) = utc;
%for i = 1:length(sdn)
%   outfile{'time'}(i) = utc(i);
%   if ~rem(i, 1000)
%      fprintf(1, '.');
%   end
%   
%end

outfile{'temp'}(:) = temp;
outfile{'sal'}(:)  = sal;

fprintf(1,'...completed\n')

ncquit(outfile);