% This is an example metadata run script for a Nortek Aquadopp.
% Reqired NetCDF attributes are noted and must not be removed.
% Users may remove any non-required attributes or add any
% additional attributes they choose
%
% K.Rosenberger, 1/4/07, version 1.0, modified from Charlene Sullivan's metaRDI
%get the global attributes - need the metadata toolbox
% gatt=read_globalattsKJR('/Projects/Tijuana/MooringLogs/gatts_TJR08C1T.txt');
metadata=read_globalattsKJR('/Projects/Tijuana/MooringLogs/gatts_TJR08C1T.txt');
%if there was a significant clock error enter it here
metadata.ClockError = 96;
metadata.INST_TYPE = 'Nortek Aquadopp';                                            % type of instrument and instrument manufacturer
metadata.xducer_offset_from_bottom = 1.05;                                      % height of transducer heads off the bottom
metadata.Orientation = 'DOWN';                                             % 'UP' or 'DOWN' use this to identify orientation of profiler
metadata.DATA_CMNT = 'Downward looking Aquadopp Profiler with OBS3+ T8334';% your metadata about this instrument
% provide an instument number, the order of instruments on the mooring
instnum = '5';
% metadata.MOORING = gatt.MOORING;                                         % mooring identifier number
% metadata.longitude = str2num(gatt.longitude);                            % (required) instrument longitude, negative is West   
% metadata.latitude = str2num(gatt.latitude);                              % (required) instrument latitude, positive is North   
% metadata.WATER_DEPTH = str2num(gatt.WATER_DEPTH);                        % water depth in meters
% metadata.WATER_DEPTH_NOTE = gatt.WATER_DEPTH_NOTE;                       % source of water depth information            
% metadata.PROGRAM = gatt.PROGRAM;                                         % program name       
% metadata.PROJECT = gatt.PROJECT;                                         % project name       
% metadata.EXPERIMENT = gatt.EXPERIMENT;                                   % experiment name         
% metadata.Region = gatt.Region;                                           % place name of general area, e.g., Southern CA Bight       
% metadata.DESCRIPTION = gatt.DESCRIPTION;                                 % descriptive info about site and platform    
% metadata.magnetic_variation = str2num(gatt.MagneticVariation);           % degrees between magnetic and true north at data location 
% metadata.SciPi = gatt.SciPi;                                             % principal investigator(s)
% metadata.Site = gatt.Site;                                               % Site name - goog to have in the metadata for plotting
% metadata.MooringType = gatt.MooringType;                                 % type of mooring platform; tripod, surface, subsurface, TRBM, etc
% metadata.CruiseID = gatt.CruiseID;                                       % for WRCMG, the InfoBank Deployment Cruise ID
% metadata.Deployment_date = '26-Aug-2008 19:50:00';                       % This needs to be actual deployment date and time on the Bottom
% metadata.Recovery_date = '27-Aug-2008 17:48:00';                         % This needs to be actual recovery date and time on the Bottom

%use this to crop the bad data using the water level data. Currently water
%level is the only option, but might add backscatter later. Leave empty or
%comment out if not desired
metadata.crop_method = 'Water Level Data';    

                                                                                        
%these attributes are part of the EPIC standard and don't change from
%deployment to deployment, so keep them for the next deployment
metadata.DATA_SUBTYPE = 'MOORED';
metadata.DATA_ORIGIN = 'USGS WRCMG Sed Trans Group';
metadata.COORD_SYSTEM = 'GEOGRAPHIC';
metadata.Conventions = 'PMEL/EPIC';
metadata.WATER_MASS = '?';                                                                  % water mass flag used for EPIC contouring programs   
metadata.POS_CONST = 0;                                                                     % consistent position flag (=1 not consistent)       
metadata.DEPTH_CONST = 0;                                                                   % consistent depth flag (=1 not consistent)     
metadata.DRIFTER = 0;                                                                       % drifter flag (=1 if drifter)      
metadata.COMPOSITE = 0;                                                                     % number of pieces in composite series  


%use these attributes if you have external sensors, otherwise comment them
%out
metadata.AnalogInput1.sensor_type = 'OBS3+';
metadata.AnalogInput1.manufacturer = 'D+A Instruments';
metadata.AnalogInput1.serial_number = 'T8334';
metadata.AnalogInput1.sensor_height = 0.6;                                      %in meters
metadata.AnalogInput1.range = 250;                                            %in NTU's - get from calibration certificate
metadata.AnalogInput1.cals.NTUcoef = [0.0375 47.305 0.4819];                     %[x^0 x^1 x^2] - get from calibration certificate
metadata.AnalogInput2.sensor_type = 'OBS3+';            
metadata.AnalogInput2.manufacturer = 'D+A Instruments';
metadata.AnalogInput2.serial_number = 'T8334';
metadata.AnalogInput2.sensor_height = 0.6;                                      %in meters
metadata.AnalogInput2.range = 1000;                                           %in NTU's - get from calibration certificate
metadata.AnalogInput2.cals.NTUcoef = [-0.1587 177.2471 19.0];                      %[x^0 x^1 x^2] - get from calibration certificate
%for a regular OBS3
% metadata.AnalogInput1.sensor_type = 'OBS3';
% metadata.AnalogInput1.manufacturer = 'D+A Instruments';
% metadata.AnalogInput1.serial_number = 1244;
% metadata.AnalogInput1.sensor_height = 0.6;                                 %in meters
% metadata.AnalogInput1.gain = 'medium';                                     %Gain setting

% if you have done a tank calibration - leave empty if not
%from calibration certificate
metadata.AnalogInput1.cals.SEDcoef = [0.2 30 3.5];                       %[x^0 x^1 x^2]                                  
metadata.AnalogInput1.cals.SEDcoefUnits = 'g/L';                        % or whatever your units are                                  
metadata.AnalogInput2.cals.SEDcoef = [0.2 30 3.5];                       %[x^0 x^1 x^2] 
metadata.AnalogInput2.cals.SEDcoefUnits = 'g/L';                        % or whatever your units are                                  

%use this if you need to correct the time, for instance if the instrument
%was not set in GMT - a positive value adds time, thus moving it forward 
%(e.g., for Hawaii, use 10 hours to correct to GMT).
%Leave blank if not necessary - use hours
metadata.TimeCorrection = [];
% version of the metafile
metadata.metadatafile_name = 'metadatadata.txt';                                                    % name of metadatafile
metadata.metadatafile_author = 'Kurt Rosenberger, USGS MP';                                     % author of the metadatafile
metadata.metadatafile_version = '2.0';                                                          % version of the metadatafile

% Get this from the planning stage - use if there is no .log file
% metadata.AQDHorVelocityPrecision = '1.2cm/s';                                               % Predicted precision of velocity measurements


%now run the scripts
prfFile = 'OBStst01';cdfFile = [metadata.MOORING instnum 'aqd'];
if 1
    aqdprf2cdf(prfFile,cdfFile,metadata);
end


%convert raw data to netcdf
CDFFile = [cdfFile '-raw'];outFile = cdfFile;
if 1
    aqdprf2nc(CDFFile,outFile,metadata)
end