function  netcdf_pco2(mooringDirectory, ncFilename, mooring)
% NETCDF_PCO2 - create a netcdf file from pCO2 data
%
% Use as: netcdf_pco2(mooringDirectory, ncFilename, mooring)
%
% Inputs: mooringDirectory = Root directory of mooring directory tree
%            for example '\\tsunami.shore.mbari.org\oasis\m1'
%         ncFilename = Name of the netcdf file to be created. The file
%            created adheres to the COARDS and MBARI conventions
%         mooring = Id for the mooring. Example: 'M1'. This string is used to search
%            for properties in \\tsunami.shore.mbari.org\oasis\cfg\mooring.properties
%            file.

% Brian Schlining
% 20 Jul 2000

%===========
% Open File
%===========
outfile = netcdf(ncFilename, 'clobber'); % outfile is a netcdf object
if isempty(outfile)
   error(['Unable to create ' ncFilename]);
end

%
% Read the pco.data and pco.cal files
raw = readflatfile(fullfile(mooringDirectory, 'data', 'pco2.data'));
[buf i] = unique(raw(:,1));
raw = raw(i, :);
rawTime = raw(:,1);
rawData = raw(:,2);
clear raw

cal  = readflatfile(fullfile(mooringDirectory, 'data', 'pco2.cal'));
[buf i] = unique(cal(:,1));
cal = cal(i, :);
calTime = cal(:,1);
cal = cal(:,2);

% Create a column of corrected data and a column of interpolated cal data
% Interpolate cals to the same times as the data
calI = interp1(calTime, cal, rawTime);

% get corrected data
calData = rawData - calI;
calData(find(isnan(calData))) = -999;

%=================================================================
% Construct Netcdf schema for a single microcat on eqpac moorings
%=================================================================
[Year Month Day]     = datevec(now);
dateS                = sprintf('%02i/%02i/%04i', Month, Day, Year);

outfile.conventions  = 'MBARI/timeSeries/mooring/pco2';
outfile.creationDate = dateS;
outfile.lastModified = dateS;
if nargin < 3
   mooring              = upper(input('Enter mooring ID: ')); % Needed to specify mooring location
end


fprintf(1,'Creating netcdf schema')
outfile.mooring      = mooring;
outfile.description  = 'pCO2 data';

% Give location based on user input
%try 
%   prop = readProperties('g:\cfg\mooring.properties');
%catch
%   prop = readProperties('\\tsunami.shore.mbari.org\oasis\cfg\mooring.properties');
%end
prop = readProperties(fullfile([getOasisPath 'cfg'], 'mooring.properties'));
lon = str2num(getProperty(prop, [lower(mooring) '.longitude']));
if lon < 0
   lonS = [num2str(abs(lon)) 'W'];
else
   lonS = [num2str(lon) 'E'];
end
lat = str2num(getProperty(prop, [lower(mooring) '.latitude']));
if lat < 0
   latS = [num2str(abs(lat)) 'S'];
else
   latS = [num2str(lat) 'N'];
end

outfile.longitude = lonS;
outfile.latitude  = latS;
outfile.waterDepth             = getProperty(prop, [lower(mooring) '.waterdepth']);
outfile.keywords               = 'pCO2';
outfile.instumentType          = 'pCO2 Can';

outfile('latitude')            = 1;                     % Dimension
outfile{'latitude'}            = ncdouble('latitude');  % Specify Co-ordinate variable dimensions
outfile{'latitude'}.long_name  = 'Latitude';
outfile{'latitude'}.units      = 'degrees_north';
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';
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'}(:)            = 0;

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{'raw'}                = ncfloat('time','depth','longitude','latitude');
% outfile{'raw'}.long_name      = 'uncalibrated pCO2';
% outfile{'raw'}.units          = 'microatm';
% outfile{'raw'}.symbol         = 'pCO2u';
% outfile{'raw'}.FillValue_     = -999;
% outfile{'raw'}.missing_value  = -999;

outfile{'pco2'}                = ncfloat('time','depth','longitude','latitude');
outfile{'pco2'}.long_name      = 'calibrated pCO2';
outfile{'pco2'}.units          = 'microatm';
outfile{'pco2'}.symbol         = 'pCO2';
outfile{'pco2'}.FillValue_     = -999;
outfile{'pco2'}.missing_value  = -999;

outfile{'time'}(1:length(rawTime)) = rawTime./1000;
% outfile{'raw'}(:) = rawData;
outfile{'pco2'}(:)  = calData;
ncquit(outfile)