function ocr3000ToNetCDF (deployment,configfile)
%function ssds_netcdf_multwavelengths_test (netCDF_path, fileroot, mooring, rad_name, files, suffixes)
%script for producing netcdf files that are compatible with Mike McCann's
%ssds framework.  Creates a single netcdf file for all 5 ocr3000s on M0- 9
%selected wavelengths for each.
%
%
% Created by Seth M. Bushinsky(sethb@mbari.org) December 2006


%%BASE_DIR = regexprep(pwd, 'cimt', '');       % Assume user is in their cimt dir
BASE_DIR = '/u/ssdsadmin/dev/DPforSSDS/';

% Add dods and netcdf to path if necessary
if(isempty (strfind(path, 'netcdf_toolbox'))),

    % loaddap should be in the default matlab path (/usr/local/DODS_ml/bin)
    % The old unsupported toolbox
    addpath([BASE_DIR 'mexcdf/snctools']);
    addpath([BASE_DIR 'mexcdf/netcdf_toolbox/netcdf']);
    addpath([BASE_DIR 'mexcdf/netcdf_toolbox/netcdf/nctype']);
    addpath([BASE_DIR 'mexcdf/netcdf_toolbox/netcdf/ncutility']);

    % mexnc for x86_a64 - Important: add this last so that it's first
    addpath([BASE_DIR 'mexnc']);

end

% set up some useful constants

rad_name = 'ocr3000';
%basePath     = pwd;
prop         = readProperties(configfile);
mooring.name = getProperty(prop, 'mooring');
radiometer_names = getProperty(prop, [mooring.name '.radiometers']);
suffixes    = {'_mean', '_median'};
%suffixTitles    = {'Mean', 'Median'};
netCDF_path = MBARI_path(getProperty(prop, 'netCDF_path'));
netCDF_path = [netCDF_path '/' deployment];

delim = ',';
coms = strfind(radiometer_names,delim);
first = 1;
for v = 1:length(coms)+1,
    if v == length(coms)+1,
        radiometers{v} = radiometer_names(first:end);
        radiometers{v} = radiometers{v}(find(~isspace(radiometers{v})));
    else
        radiometers{v} = radiometer_names(first:coms(v)-1);
        first = coms(v)+1;
        radiometers{v} = radiometers{v}(find(~isspace(radiometers{v})));
    end
end

disp('writing netcdf files for ssds');
wavelengths= [410 440 490 510 550 610 650 670 700];

%creates a new file
ssds_nc_filename = [netCDF_path '/ssds_netcdf/test/'  mooring.name ...
    '_' rad_name '_ssds.nc'];
disp(['Opening file for writing: ' ssds_nc_filename]);
ssds_nc_file = netcdf(ssds_nc_filename, 'clobber');

%Initialize dimensions
ssds_nc_file('latitude') = 1;
ssds_nc_file('longitude') = 1;

%Initialize variables, copies lat and lon from original netcdf

ssds_nc_file{'latitude'} = ncdouble('latitude');
ssds_nc_file{'latitude'}.units = 'degrees North';

ssds_nc_file{'longitude'} = ncdouble('longitude');
ssds_nc_file{'longitude'}.units = 'degrees East';

warning off all %matching to specific wavelength(int32) generates error message

for rad =1:length(radiometers),
    for suf = 1:length(suffixes),
        fileroot = [char(radiometers(rad)) char(suffixes(suf))];
        %opens and reads the netcdf file being used for plotting
        nc_filename = ([netCDF_path '/' fileroot '.nc']);
        fid = fopen(nc_filename);

        if(fid == -1)
            close;
            nc_filename = [netCDF_path '/' mooring.name '_ocr_' fileroot '.nc'];
            fid = fopen(nc_filename);
            if (fid == -1)
                close;
                return
            end
        end

        fclose(fid);
        %opens the netcdf file according to the radiometer name and suffix
        nc_file = netcdf(nc_filename);

        ssds_nc_file{'latitude'}(:) = nc_file{'latitude'}(:);
        ssds_nc_file{'longitude'}(:) = nc_file{'longitude'}(:);

        %finds the variable with multiple dimensions - contains the
        %radiometer data
        for vars = length(ncnames(var(nc_file))) : -1 : 1,
            var_dims = length(dim(nc_file{vars}));
            if(var_dims > 1)
                var_name = char(ncnames(nc_file{vars}));
                break;
            end
        end

        %new_times is the record of instrument times that are not already
        %written to the ssds_netcdf file
        new_times = nc_file{'time'}(1:end);

        %gets all of the wavelengths into spectra
        spectra = squeeze(nc_file{var_name}(1:end,:));
        if isempty(spectra),
            break,
        end

        %searches the time record, removes any time stamps that do not
        %increase.  Does this until there are no negative or 0 increases-
        %makes the time series monotonic
        y = diff([0;new_times]);
        w = find(y>=0);
        mono_time = new_times(w);
        mono_spectra = spectra(w,:);

        neg = 1;
        while (isempty(neg)==0),
            q = diff([0;mono_time]);
            w = find(q>0);
            neg = find(q<=0);
            mono_time = mono_time(w);
            mono_spectra = mono_spectra(w,:);
        end

        ssds_nc_file(['time_' fileroot]) = length(mono_time);
        ssds_nc_file(['depth_' fileroot]) = 1;

        ssds_nc_file{['time_' fileroot]} = ncdouble(['time_' fileroot]);
        ssds_nc_file{['time_' fileroot]}.units = 'seconds since 1970-01-01 00:00:00';
        ssds_nc_file{['time_' fileroot]}.long_name = 'time GMT';
        ssds_nc_file{['time_' fileroot]}(:) = mono_time;

        ssds_nc_file{['depth_' fileroot]} = ncfloat (['depth_' fileroot]);
        ssds_nc_file{['depth_' fileroot]}.units = 'meters';
        ssds_nc_file{['depth_' fileroot]}(:) = nc_file{'depth'}(:);

        if size(spectra)==[1 1],
            ssds_nc_file{fileroot} = ncfloat(['time_' fileroot], ['depth_' fileroot],'latitude', 'longitude');
            ssds_nc_file{fileroot}.units = nc_file{var_name}.units(:);
            ssds_nc_file{fileroot} = [var_name char(suffixes(suf)) '_' wavelength_name]
            ssds_nc_file{fileroot} = spectra;
        else
            
            for lambda = 1:length(wavelengths),
                wavelength_name = num2str(wavelengths(lambda));
                %finds the wavelength index that matches 'lambda'.  selects that
                %wavelength out of spectra.
                wave_index = find(int32(nc_file{'wavelength'}(:))==wavelengths(lambda));
                spectra_wave = mono_spectra(:,wave_index);
                if isempty(spectra_wave),
                    break,
                else
                    %writes the new data and times to the ssds_nc_file
                    ssds_nc_file{[fileroot '_' wavelength_name]} = ncfloat(['time_' fileroot], ['depth_' fileroot],'latitude', 'longitude');
                    ssds_nc_file{[fileroot '_' wavelength_name]}.units = nc_file{var_name}.units(:);
                    ssds_nc_file{[fileroot '_' wavelength_name]}.long_name = [var_name char(suffixes(suf)) '_' wavelength_name];
                    ssds_nc_file{[fileroot '_' wavelength_name]}(:) = spectra_wave;
                end
            end
        end
    
        
        close(nc_file);
    end
end

derived_vars = {'chl_490_Kd_0_10_mean'; 'Kd_0_10_mean'};

for rad =1:length(derived_vars),
    fileroot = char(derived_vars(rad));
    %opens and reads the netcdf file being used for plotting
    nc_filename = ([netCDF_path '/' fileroot '.nc']);
    fid = fopen(nc_filename);

    if(fid == -1)
        close;
        nc_filename = [netCDF_path '/' mooring.name '_ocr_' fileroot '.nc'];
        fid = fopen(nc_filename);
        if (fid == -1)
            close;
            return
        end
    end

    fclose(fid);
    %opens the netcdf file according to the radiometer name and suffix
    nc_file = netcdf(nc_filename);

    %finds the variable with multiple dimensions - contains the
    %radiometer data
    for vars = length(ncnames(var(nc_file))) : -1 : 1,
        var_dims = length(dim(nc_file{vars}));
        if(var_dims > 1)
            var_name = char(ncnames(nc_file{vars}));
            break;
        end
    end

    %new_times is the record of instrument times that are not already
    %written to the ssds_netcdf file
    new_times = nc_file{'time'}(1:end);

    %gets all of the wavelengths into spectra
    spectra = squeeze(nc_file{var_name}(1:end,:));
    if isempty(spectra),
        break,
    end

    %searches the time record, removes any time stamps that do not
    %increase.  Does this until there are no negative or 0 increases-
    %makes the time series monotonic
    y = diff([0;new_times]);
    w = find(y>=0);
    mono_time = new_times(w);
    mono_spectra = spectra(w,:);

    neg = 1;
    while (isempty(neg)==0),
        q = diff([0;mono_time]);
        w = find(q>0);
        neg = find(q<=0);
        mono_time = mono_time(w);
        mono_spectra = mono_spectra(w,:);
    end

    ssds_nc_file(['time_' fileroot]) = length(mono_time);
    ssds_nc_file(['depth_' fileroot]) = 1;

    ssds_nc_file{['time_' fileroot]} = ncdouble(['time_' fileroot]);
    ssds_nc_file{['time_' fileroot]}.units = 'seconds since 1970-01-01 00:00:00';
    ssds_nc_file{['time_' fileroot]}.long_name = 'time GMT';
    ssds_nc_file{['time_' fileroot]}(:) = mono_time;

    ssds_nc_file{['depth_' fileroot]} = ncfloat (['depth_' fileroot]);
    ssds_nc_file{['depth_' fileroot]}.units = 'meters';
    ssds_nc_file{['depth_' fileroot]}(:) = nc_file{'depth'}(:);

    if 
    wavelength_name = '490';
    %finds the wavelength index that matches 'lambda'.  selects that
    %wavelength out of spectra.
    wave_index = find(int32(nc_file{'wavelength'}(:))==wavelengths(lambda));
    spectra_wave = mono_spectra(:,wave_index);
    if isempty(spectra_wave),
        break,
    else
        %writes the new data and times to the ssds_nc_file
        ssds_nc_file{[fileroot '_' wavelength_name]} = ncfloat(['time_' fileroot], ['depth_' fileroot],'latitude', 'longitude');
        ssds_nc_file{[fileroot '_' wavelength_name]}.units = 'W m-2';
        ssds_nc_file{[fileroot '_' wavelength_name]}.long_name = [var_name char(suffixes(suf)) '_' wavelength_name];
        ssds_nc_file{[fileroot '_' wavelength_name]}(:) = spectra_wave;
    end




    close(nc_file);

end
close(ssds_nc_file);

disp('ocr3000ToNetCDF() done.');

return;