% LISST100Xasc2nc convert LISST.EXE processed ascii output to netCDF EPIC
%
% function lisst = LISST100Xasc2nc(LISSTroot, ncroot, metadata)
% LISSTroot = root file name for the LISST.EXE output
%       will seek the processed .asc files
%       does not work on settling experiment files
% ncroot = root file name for converted netCDF data
%       processed data will go to an .nc file as a time series
% the .asc file columns are
%         1:32 Volume concentration (in ul/l) for size class 1 through 32
%         33 Laser transmission Sensor
%         34 Battery voltage in calibrated units
%         35 External Auxiliary input 1 in calibrated units
%         36 Laser Reference sensor in calibrated units
%         37 Pressure in calibrated units
%         38 Temperature in calibrated units of degrees C
%         39 (Day*100 + Hour) at which data taken
%         40 (Minutes*100 + Seconds) at which data taken
%         41 Computed % Optical transmission over path
%         42 Computed Beam-C in units of 1/m
% there must be a deployment start date!!
% metadata.deployment_start = gatt.Deployment_date; % the in water time
% metadata.deployment_end = gatt.Recovery_date; % the out of water time
% metadata.lon = gatt.longitude; % decimal degrees, West = negative
% metadata.lat = gatt.latitude; % decimal degrees, South = negative
% metadata.WATER_DEPTH = gatt.WATER_DEPTH; % m (DO NOT OMIT!)
% % LISST specific information
% metadata.serial = '1172'; % serial number of the LISST
% metadata.type = 'C'; % LISST type (indicating size range)
% metadata.zscFile = '1172bench29nov07gmt1602.asc'; %best background scatter file
% metadata.factoryFile = 'factory_zsc_1172.asc'; % best background scatter file
% metadata.ringFile = 'ringarea_1172.asc'; % best background scatter file
% % these are [slope, offset] 
% metadata.cal.laserpower = [0.00081556 0]; % raw count to mW
% metadata.cal.battery = [0.01 0]; % raw count to volts
% metadata.cal.external = [0 0]; % none for LISST-ST
% metadata.cal.laserreference = [0.00076741 0]; %raw count to mW
% metadata.cal.pressure = [0.01 -10]; %raw count to meters
% metadata.cal.temperature = [0.01 0]; % raw count to deg C
% metadata.cal.volumeconversion = 45733; %in instrumentdata.txt
% % this height will be tagged to all variables
% metadata.inst_height = 0.31; % m pressure port height, about the same as the optics
% metadata.STtopopening_height = 0; % m
% metadata.STnsettlingsamples = 0; % a settling experiment
% metadata.MOORING = '8482';
% 
% metadata.metafile = mfilename('fullpath');
% metadata.metafile_date = datestr(now);
% metadata.metafile_version = '0.0';
% metadata.metafile_author = 'MM';
% 
% metadata.DATA_ORIGIN = gatt.DATA_ORIGIN; % with collaborator's data, could be USC, etc.
% metadata.EXPERIMENT = gatt.EXPERIMENT; 
% metadata.PROJECT = gatt.PROJECT; % might also use OFA funding agency, such as MWRA, EPA, WCMG
% metadata.DESCRIPTION = gatt.DESCRIPTION;
% metadata.SciPi = gatt.SciPi;
% metadata.Conventions = gatt.Conventions; 
% metadata.DATA_CMNT = '';  % your metadata
% metadata.longitude = gatt.longitude; % negative degrees in western hemisphere
% metadata.lonUnits = 'degrees_east';
% metadata.latitude = gatt.latitude; % always positive degrees in northern
% metadata.latUnits = 'degrees_north';
% 
% metadata.dataFile = LISSTroot;
% 
% metadata.goodsamples = [681 20528]; % use [1 Inf] for all data
%
% lisst = a structure of the data 
%            tm: [1x378 double]
%            tj: [1x378 double]
%       volconc: [378x32 double]
%     laserxmit: [1x378 double]
%          batt: [1x378 double]
%          aux1: [1x378 double]
%      laserref: [1x378 double]
%         press: [1x378 double]
%          temp: [1x378 double]
%        ptrans: [1x378 double]
%         beamc: [1x378 double]
%         sizes: [1x32 double]
%      procFile: source file name
%       zscData: background scatter data
%
% Settling experiments will be treated as simple time series.

% 8/12/08 brain dead, beam-c and % trans was swapped.
% 7/22/08 More metadata stuff
% 5/4/06 Add EPIC compliance details
% Written by Marinna Martini 2/18/06

     
function lisst = LISST100Xasc2nc(LISSTroot, ncroot, metadata)

% get the current SVN version- the value is automatically obtained in svn
% is the file's svn.keywords which is set to "Revision"
rev_info = 'SVN $Revision$';
disp(sprintf('%s %s running',mfilename,rev_info))

lisst = [];
metadata.settling = 0;
ndatacols = 42;

disp(sprintf('%s now running %s',mfilename,datestr(now,0)))

if ~exist('metadata','var'), 
    disp('Metadata is required for processing')
    eval(['help ',mfilename])
end
if ~exist('LISSTroot','var'),
    LISSTroot = '';
end
[pathname, fname] = fileparts(LISSTroot);
procFile = fullfile(pathname,[fname,'.asc']);
% get the data file
if fname(1) == 'S',
    disp('This is a settling experiment')
    metadata.settling = 1;
    if ~isfield(metadata,'nsettlingsamples')
        buf = inputdlg('Enter the number of samples per settling experiment: ',...
            'Required information',1,{'82'});
        if isempty(buf), return, end
        metadata.nsettlingsamples = str2double(buf{1});
    end
else
    metadata.nsettlingsamples = 0;
end
if ~exist(procFile,'file'),
    FilterSpec(1,:) = {'*.asc','*.asc processed LISST data file'};  
    [fname, pathname] = uigetfile(FilterSpec, 'Pick a LISST data file');
    if isequal(fname,0) || isequal(pathname,0)
        disp('User pressed cancel')
        return
    end
    procFile = fullfile(pathname, fname);
end
disp(['User selected processed data file ', procFile])
% metadata.zscFile = background scatter file chosen by user based on field conditions
if ~isfield(metadata, 'zscFile') 
    FilterSpec(1,:) = {'*.asc','*.asc LISST background scatter file'};  
    [fname, pathname] = uigetfile(FilterSpec, 'Pick a LISST background scatter file');
    metadata.zscFile = fullfile(pathname, fname);
end
metadata.zscData = load(metadata.zscFile);
if isempty(metadata.zscData)
    disp('No background scatter file data available, aborting')
    return
end

% metadata.factoryFile = factory background scatter file
if ~isfield(metadata, 'factoryFile') 
    FilterSpec(1,:) = {'*.asc','*.asc LISST factory background scatter file'};  
    [fname, pathname] = uigetfile(FilterSpec, 'Pick a LISST factory background scatter file');
    metadata.factoryFile = fullfile(pathname, fname);
end
metadata.factoryData = load(metadata.factoryFile);
if isempty(metadata.factoryData)
    disp('No factory background scatter file data available, aborting')
    return
end
% metadata.ringFile = ring area calibration file
if ~isfield(metadata, 'ringFile') 
    FilterSpec(1,:) = {'*.asc','*.asc LISST ring file'};  
    [fname, pathname] = uigetfile(FilterSpec, 'Pick a LISST ring file');
    metadata.ringFile = fullfile(pathname, fname);
end
metadata.ringData = load(metadata.ringFile);
if isempty(metadata.ringData)
    disp('No ring file data available, aborting')
    return
end
% figure out the time
if ~isfield(metadata,'deployment_start'),
    % guess from the data file time stamp
    junk = dir(rawFile);
    dvec = datevec(datenum(junk.date));
    disp(sprintf('Deployment year %d taken from data file time stamp',dvec(1)))
    disp(sprintf('Deployment month %d taken from data file time stamp',dvec(2)))
else
    % take it from the in water time
    dvec = datevec(datenum(metadata.deployment_start));
    disp(sprintf('Deployment year %d taken from in water time',dvec(1)))
    disp(sprintf('Deployment month %d taken from in water time',dvec(2)))
end
if isfield(metadata,'goodsamples'),
    goodsamples = metadata.goodsamples;
    if goodsamples(1) < 1, goodsamples(1) = 1; end
    %if goodsamples(2) > nsamples, goodsamples(2) = nsamples; end
    %data = data(goodsamples(1):goodsamples(2),:);
end
if isfield(metadata, 'type'),
    metadata.type = lower(metadata.type);
else
    metadata.type = {'A','B','C','F'};
    [n,v] = listdlg('PromptString','Select type of instrument:',...
        'SelectionMode','single','ListString',metadata.type);
    if ~v,
        disp('LISST type is required information')
        return
    end
    metadata.type = lower(metadata.type{n});
end
disp(sprintf('The LISST type is %s',metadata.type))
if ~isfield(metadata, 'serial'),
    metadata.serial = '';
    disp('No serial number provided')
end

% make sure this is a time series experiment, not a settling experiment
fid = fopen(procFile,'r');
buf = fgetl(fid);
[data, count] = sscanf(buf, '%f', ndatacols);
if count < ndatacols,
   disp(sprintf('detected %d columns of data where %d were expected',...
       count, ndatacols))
   disp(sprintf('%s only reads output from LISST.EXE for the LISST 100X',...
       mfilename))
   return
end
fclose(fid);

disp('defining netCDF')
[pathname] = fileparts(procFile);
ncFile = fullfile(pathname,[ncroot,'.nc']);
nc = netcdf(ncFile,'clobber');
definenc(nc, metadata)
fid = fopen(procFile,'r');

% we are reading line by line so that large time series will not overwhelm
% computer memory.  But it does take longer than load()
% TODO try to estimate number of samples by files size 
% and preallocate for speed
tic;
count = ndatacols;
ncidx = 0;
dataidx = 0;
while count == ndatacols,
    dataidx = dataidx + 1;
    [data,count] = fscanf(fid, '%f', ndatacols);
    if count < 42, break; end
    data = data';
    if isempty(data), break; end
      
    nzeros = length(find(data == 0));
    if metadata.settling && (nzeros == count), 
        % this is a header, do nothing
        disp(sprintf('skipping record %d as settling experiment header',dataidx))
    elseif dataidx >= goodsamples(1),       
        ncidx = ncidx + 1;

        rec(ncidx) = dataidx;
        % compute the time stamps
        % yearday includes the first day, so dayone is decremented by one
        dayone = datenum([dvec(1),1,1,0,0,0])-1;
        % the first index of yearday is Jan 1 of the given year
        yearday = floor(data(1,39)./100);
        yday(ncidx) = yearday; % save for finding year rollover later
        hour =  rem(data(1,39),100);
        min = floor(data(1,40)./100);
        sec =  rem(data(1,40),100);
        tm(ncidx) = dayone+yearday+hour./24+min./(24*60)+sec./(24*3600);
        tj(ncidx) = julian(datevec(tm(ncidx)));
        %clear yearday hour min sec dayone
        % parse the other data
        volconc(ncidx,:) = data(:,1:32);
        laserxmit(ncidx) = data(:,33);
        batt(ncidx) = data(:,34);
        aux1(ncidx) = data(:,35);
        laserref(ncidx) = data(:,36);
        press(ncidx) = data(:,37);
        temp(ncidx) = data(:,38);
        ptrans(ncidx) = data(:,41);
        beamc(ncidx) = data(:,42);
        
        % attempt to fix temperature rollover
        % hmm... this created a mess... maybe fixed in new firmware?
        %         if temp(ncidx) < 377,
        %             temp(ncidx) = (temp(ncidx) + 655.36)./100;
        %         end
        
        nc{'rec'}(ncidx,1,1,1) = rec(ncidx);
        nc{'time'}(ncidx,1,1,1) = floor(tj(ncidx));
        nc{'time2'}(ncidx,1,1,1) = (tj(ncidx) - floor(tj(ncidx))).*(3600*24*1000);
        nc{'vconc'}(ncidx,:) = volconc(ncidx,:);
        nc{'ltrans'}(ncidx,1,1,1) = laserxmit(ncidx);
        nc{'batt'}(ncidx,1,1,1) = batt(ncidx);
        nc{'lref'}(ncidx,1,1,1) = laserref(ncidx);
        nc{'P_1'}(ncidx,1,1,1) = press(ncidx);
        nc{'T_20'}(ncidx,1,1,1) = temp(ncidx);
        nc{'ATTN_55'}(ncidx,1,1,1) = beamc(ncidx);
        nc{'ptrans'}(ncidx,1,1,1) = ptrans(ncidx);
    end
    if dataidx > goodsamples(2), break; end
    
    if exist('tm','var'),
        if ncidx == 1,
            disp(sprintf('First date stamp is %s',datestr(datenum(gregorian(tj(1)))))); end
        if ncidx<50 && ~rem(ncidx,10),
            disp(sprintf('Finished sample #%d %s %4.2f min elapsed',ncidx,datestr(tm(ncidx)),toc./60)), end
        if ncidx>50 && ~rem(ncidx,100),
            disp(sprintf('Finished sample #%d %s %4.2f min elapsed',ncidx,datestr(tm(ncidx)),toc./60)), end
    end
end
metadata.nsamples = ncidx;

% must correct time if there was a year rollover
if (yday(1) > 1), % we didn't start at the beginning of a year
    yendidx = find(yday == 365,1,'last');
    if ~isempty(yendidx), % a new year started during our experiment
        disp(sprintf('Found a year rollover at index %d, correcting for it',yendidx))
        tj(yendidx+1:end) = tj(yendidx+1:end)+365;
%        tg = gregorian(tj);
%         TODO fix this leap year code
%         if (any(~mod(tg(:,1),4)) && any(mod(tg(:,1),100))) || any(~mod(tg(:,1),400)),
%             then leap
% this next line bombs for starts after feb!
%             mar1idx = find(tg(:,2) > 2 ,1,'first');
%             if ~isempty(mar1idx)
%                 disp(sprintf('Found a leap year Mar 1 at index %d, correcting for it',mar1idx))
%                 tj(mar1idx-1:end) = tj(mar1idx-1:end)+1;
%             end
%         end
        nc{'time'}(:,1,1,1) = floor(tj);
    end
end

disp(sprintf('%d samples stored to nc file',ncidx))

fclose(fid);

% finish up the EPIC attributes
nc.history = ncchar(sprintf('Converted by %s %s;\n',mfilename,rev_info));
nc.DELTA_T = gmean(diff(tj)).*(24*3600);
nc.start_time = ncchar(datestr(datenum(gregorian(tj(1)))));
nc.stop_time = ncchar(datestr(datenum(gregorian(tj(end)))));
nc.original_data_file = ncchar(LISSTroot);

add_minmaxvalues(nc);
add_fillvalues(nc,1E35);
add_vardesc(nc);
% add depth attributes to variables
% uses the height of the pressure port or whatever is given by inst_height
add_depth_atts(nc)

close(nc);


lisst.tm = tm;
lisst.tj = tj;
lisst.volconc = volconc;
lisst.laserxmit = laserxmit;
lisst.batt = batt;
lisst.aux1 = aux1;
lisst.laserref = laserref;
lisst.press = press;
lisst.temp = temp;
lisst.ptrans = ptrans;
lisst.beamc = beamc;
lisst.sizes = sizeclass(metadata.type);
lisst.procFile = procFile;
if metadata.type == 'a' || metadata.type == 'f',
    lisst.sizeunits = 'ring number';
else
    lisst.sizeunits = 'microns';
end

return

function definenc(nc, metadata)

% data from read_globalatts
if isfield(metadata,'DATA_ORIGIN'), nc.DATA_ORIGIN = ncchar(metadata.DATA_ORIGIN); end
if isfield(metadata,'EXPERIMENT'), nc.EXPERIMENT = ncchar(metadata.EXPERIMENT); end
if isfield(metadata,'PROJECT'), nc.PROJECT = ncchar(metadata.PROJECT); end
if isfield(metadata,'DESCRIPTION'), nc.DESCRIPTION = ncchar(metadata.DESCRIPTION); end
if isfield(metadata,'SciPi'), nc.SciPi = ncchar(metadata.SciPi); end
if isfield(metadata,'Conventions'), nc.Conventions = ncchar(metadata.Conventions); end
if isfield(metadata,'DATA_CMNT'), nc.DATA_CMNT = ncchar(metadata.DATA_CMNT); end
if isfield(metadata,'latitude'), nc.latitude = metadata.latitude;
else nc.latitude = ncfloat(999); end
if isfield(metadata,'latUnits'), nc.latUnits = metadata.latUnits; end
if isfield(metadata,'longitude'), nc.longitude = ncfloat(metadata.longitude);
else nc.longitude = ncfloat(999); end
if isfield(metadata,'lonUnits'), nc.lonUnits = metadata.lonUnits; end
if isfield(metadata,'Deployment_date'), nc.Deployment_date = ncfloat(metadata.Deployment_date);
else nc.Deployment_date = ncfloat(999); end
if isfield(metadata,'Recovery_date'), nc.Recovery_date = ncfloat(metadata.Recovery_date);
else nc.Recovery_date = ncfloat(999); end

if isfield(metadata,'DATA_SUBTYPE'), nc.DATA_SUBTYPE = ncchar(metadata.DATA_SUBTYPE); end
if isfield(metadata,'MOORING'), nc.MOORING = ncchar(metadata.MOORING); end
if isfield(metadata,'WATER_DEPTH'), nc.WATER_DEPTH = ncfloat(metadata.WATER_DEPTH); end

nc.CREATION_DATE = ncchar(datestr(now));
nc.DATA_TYPE = ncchar('TIME');
cdf.COORD_SYSTEM = ncchar('GEOGRAPHICAL');
nc.WATER_MASS = ncchar('?');
nc.COMPOSITE = nclong(0); % for flagging patched together data sets
nc.POS_CONST = nclong(0);
nc.DEPTH_CONST = nclong(1); % depth will change
nc.FILL_FLAG = nclong(1);
nc.VAR_FILL = ncfloat(1e35);
nc.water_depth = ncfloat(metadata.WATER_DEPTH);
nc.INST_TYPE = ncchar('Sequoia LISST100X');
nc.inst_height = ncfloat(metadata.inst_height);
nc.inst_depth = ncfloat(metadata.WATER_DEPTH-metadata.inst_height);
if metadata.settling, 
    nc.STnsettlingsamples = metadata.STnsettlingsamples;
    nc.STtopopening_height = metadata.STtopopening_height;
end
nc.ringFile = ncchar(metadata.ringFile);
nc.ringData = ncdouble(metadata.ringData);
nc.factoryFile = ncchar(metadata.factoryFile);
nc.factoryData = ncdouble(metadata.factoryData);
nc.zscFile = ncchar(metadata.zscFile);
nc.zscData = ncdouble(metadata.zscData);
nc.cal_laserpower = metadata.cal.laserpower; % raw count to mW
nc.cal_battery = metadata.cal.battery; % raw count to volts
nc.cal_external = metadata.cal.external; % none for LISST-ST
nc.cal_laserreference = metadata.cal.laserreference; %raw count to mW
nc.cal_pressure = metadata.cal.pressure; %raw count to meters
nc.cal_temperature = metadata.cal.temperature; % raw count to deg C
nc.cal_volumeconversion = metadata.cal.volumeconversion; %in instrumentdata.txt

%% Dimensions:
 
nc('time') = 0;
nc('depth') = 1;
nc('lat') = 1;
nc('lon') = 1;
nc('size') = 32;

%% Variables and attributes:
%%   coordinate variables:
 
nc{'time'} = nclong('time') ;
nc{'time'}.FORTRAN_format = ncchar('F10.2');
nc{'time'}.units = ncchar('True Julian Day');
nc{'time'}.type = ncchar('EVEN');
nc{'time'}.epic_code = nclong(624);
 
nc{'time2'} = nclong('time') ;
nc{'time2'}.FORTRAN_format = ncchar('F10.2');
nc{'time2'}.units = ncchar('msec since 0:00 GMT');
nc{'time2'}.type = ncchar('EVEN');
nc{'time2'}.epic_code = nclong(624);
 
nc{'depth'} = ncfloat('depth') ;
nc{'depth'}.FORTRAN_format = ncchar('F10.2');
nc{'depth'}.units = ncchar('m');
nc{'depth'}.type = ncchar('EVEN');
nc{'depth'}.epic_code = nclong(3);
 
nc{'lat'} = ncfloat('lat') ;
nc{'lat'}.FORTRAN_format = ncchar('F10.2');
nc{'lat'}.units = ncchar('degrees_north');
nc{'lat'}.type = ncchar('EVEN');
nc{'lat'}.epic_code = nclong(500);
 
nc{'lon'} = ncfloat('lon') ;
nc{'lon'}.FORTRAN_format = ncchar('F10.2');
nc{'lon'}.units = ncchar('degrees_east');
nc{'lon'}.type = ncchar('EVEN');
nc{'lon'}.epic_code = nclong(502);

nc{'size'} = ncfloat('size') ;
ncobj = nc{'size'};
ncobj.FORTRAN_format = ncchar('F10.2');
ncobj(:) = sizeclass(metadata.type); 
if metadata.type == 'a' || metadata.type == 'f',
    ncobj.units = 'ring number';
else
    ncobj.units = 'microns';
end



%%    record variables:
nc{'rec'} = ncdouble('time', 'depth', 'lat', 'lon');
ncobj = nc{'rec'};
ncobj.long_name = ncchar('Record Number');
ncobj.units = ncchar('count');
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.valid_range = ncfloat([1 2^32]);

nc{'vconc'} = ncdouble('time', 'size', 'lat', 'lon');
ncobj = nc{'vconc'};
ncobj.long_name = ncchar('VOLUME CONCENTRATION (UL/L)        ');
ncobj.units = ncchar('ul/l');
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(metadata.serial);
ncobj.valid_range = ncfloat([0 10000]);

nc{'ltrans'} = ncfloat('time', 'depth','lat','lon');
ncobj = nc{'ltrans'};
ncobj.long_name = ncchar('LASER TRANSMISSION        ');
ncobj.units = ncchar('mW');
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(metadata.serial);
ncobj.valid_range = ncfloat([0 10000]);

nc{'batt'} = ncfloat('time', 'depth','lat','lon');
ncobj = nc{'batt'};
ncobj.long_name = ncchar('BATTERY VOLTAGE        ');
ncobj.units = ncchar('V');
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(metadata.serial);
ncobj.valid_range = ncfloat([0 10000]);

nc{'lref'} = ncfloat('time', 'depth','lat','lon');
ncobj = nc{'lref'};
ncobj.long_name = ncchar('LASER REFERENCE');
ncobj.units = ncchar('mW');
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(metadata.serial);
ncobj.valid_range = ncfloat([0 10000]);

nc{'ptrans'} = ncfloat('time', 'depth','lat','lon');
ncobj = nc{'ptrans'};
ncobj.long_name = ncchar('% OPTICAL TRANSMISSION');
ncobj.units = ncchar('%');
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(metadata.serial);
ncobj.valid_range = ncfloat([0 100]);

nc{'P_1'} = ncfloat('time', 'depth', 'lat', 'lon');
ncobj = nc{'P_1'};
ncobj.name = ncchar('P');
ncobj.long_name = ncchar('PRESSURE (DB)          ');
ncobj.generic_name = ncchar('depth');
ncobj.FORTRAN_format = ncchar('f10.1');
ncobj.units = ncchar('dbar');
ncobj.epic_code = nclong(1);
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(' ');
ncobj.valid_range = ncfloat([0 10000]);
ncobj.comment = ncchar('Absolute pressure reduced by 10.1325 to remove atmospheric pressure.');

nc{'T_20'} = ncfloat('time', 'depth', 'lat', 'lon') ;
ncobj = nc{'T_20'};
ncobj.name = ncchar('T');
ncobj.long_name = ncchar('TEMPERATURE (C)          ');
ncobj.generic_name = ncchar('temp');
ncobj.FORTRAN_format = ncchar('f10.2');
ncobj.units = ncchar('C');
ncobj.epic_code = nclong(20);
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(' ');
ncobj.valid_range = ncfloat([-50 50]);
ncobj.comment = ncchar('IPTS-1968 Standard');

nc{'ATTN_55'} = ncfloat('time', 'depth', 'lat', 'lon') ;
ncobj = nc{'ATTN_55'};
ncobj.name = ncchar('ATTN');
ncobj.long_name = ncchar('ATTENUATION         ');
ncobj.generic_name = ncchar('attn');
ncobj.FORTRAN_format = ncchar('f7.5');
ncobj.units = ncchar('m-1');
ncobj.epic_code = nclong(55);
ncobj.sensor_depth = ncfloat(0);
ncobj.minimum = ncfloat(0);
ncobj.maximum = ncfloat(0);
ncobj.serial_number = ncchar(' ');
ncobj.valid_range = ncfloat([0 10000]);

%% calibration information
nc{'field_zscat'} = ncdouble('size');
ncobj = nc{'field_zscat'};
ncobj.long_name = ncchar('background scatter field readings');
ncobj.units = ncchar('counts');
ncobj.serial_number = ncchar(metadata.serial);
ncobj.calibration_file = ncchar(metadata.zscFile);
data = dir(metadata.zscFile);
ncobj.calibration_date = ncchar(data.date);
ncobj(:) = metadata.zscData(1:32);

nc{'factory_zscat'} = ncdouble('size');
ncobj = nc{'factory_zscat'};
ncobj.long_name = ncchar('background scatter factory readings');
ncobj.units = ncchar('counts');
ncobj.serial_number = ncchar(metadata.serial);
ncobj.calibration_file = ncchar(metadata.factoryFile);
data = dir(metadata.factoryFile);
ncobj.calibration_date = ncchar(data.date);
ncobj(:) = metadata.factoryData(1:32);

nc{'ring_data'} = ncdouble('size');
ncobj = nc{'ring_data'};
ncobj.long_name = ncchar('detector ring calibration');
ncobj.units = ncchar('counts');
ncobj.serial_number = ncchar(metadata.serial);
ncobj.calibration_file = ncchar(metadata.ringFile);
data = dir(metadata.ringFile);
ncobj.calibration_date = ncchar(data.date);
ncobj(:) = metadata.ringData;

return

function sc = sizeclass(type)
switch type,
    case 'a', sc = 1:32;
    case 'b', 
        sc = [1.36 1.60 1.89 2.23 2.63 3.11 3.67 4.33 ...
            5.11 6.03 7.11 8.39 9.90 11.7 13.8 16.3 ...
            19.2 22.7 26.7 31.6 37.2 44.0 51.9 61.2 ...
            72.2 85.2 101 119 140 165 195 230];
    case 'c',
        sc = [2.73 3.22 3.80 4.48 5.29 6.24 7.36 8.69 ...
            10.2 12.1 14.3 16.8 19.9 23.5 27.7 32.7 ...
            38.5 45.5 53.7 63.3 74.7 88.2 104 128 ...
            157 186 219 259 293 332 391 462];
        ncobj.units = 'microns';
    case 'f', sc = 1:32;
end
return

% add depth attributes to variables
% uses the height of the pressure port or whatever is given by inst_height
function add_depth_atts(cdf)
theVars = var(cdf);
for i = 1:length(theVars),
    if ~strcmp(ncnames(theVars{i}),'time') && ...
            ~strcmp(ncnames(theVars{i}),'time2') && ...
            ~strcmp(ncnames(theVars{i}),'lat') && ...
            ~strcmp(ncnames(theVars{i}),'lon') && ...
            ~strcmp(ncnames(theVars{i}),'rings'),
            theVars{i}.sensor_depth = ncfloat(cdf.WATER_DEPTH(:)-cdf.inst_height(:));
            theVars{i}.sensor_height = ncfloat(cdf.inst_height(:));
    end
end
return