clear
% ------------- Step I where is the data
LISSTroot = 'L3370000.asc';
LISSTdat = 'L3370000.DAT';
ncroot = '8482lisst'; % the name for the output files

% --------- set up the information needed by the programs
%
% this is what should be used if using a single source of global attributes
% modified to use the universal metadata file : globatt_805.txt
% change the line below to fit your system path for the location of m_cmg
% comment out this line and enter the metadata below by hand if you do not
% have the metadata toolbox.
gatt=read_globalatts('..\global_atts848.txt');

% ------------- Step II what is the metadata?
%
% 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';

% if the following fields are missing, UNKOWN will be used
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

% these programs take a long time to run, so keep a diary
diary(sprintf('run%s',datestr(now,30)))

if 0,
    % convert the raw data in the .log file to netCDF
    lisstraw = LISST100Xlog2cdf(LISSTroot, ncroot, metadata);
end
if 0,
    % convert the raw data in the .asc file into netCDF
    lisst = LISST100Xasc2nc(LISSTroot, ncroot, metadata);
end

if 0,
    % do it from the binary using Sequoia code, results in a .mat file
    dvec = datevec(metadata.deployment_start);
    settings.expYear = dvec(1);
    settings.LISSTtype = metadata.type;
    settings.LISSTserial = str2double(metadata.serial);
    settings.volconv = metadata.cal.volumeconversion;
    settings.pscale = metadata.cal.pressure(1);
    settings.poffset = metadata.cal.pressure(2);
    settings.raux = 2.5/4095;

    [lisstmat, settings] = do100X(LISSTdat, metadata.zscFile, metadata.ringFile, ...
        settings, metadata.goodsamples, 0);

    save(ncroot,'lisstmat', 'metadata', 'settings');
    
end

diary off