% scriptexample - example file for running the ADCP toolbox in automated mode



%%% START USGS BOILERPLATE -------------% These programs are intened for us in adjusting metadata terms in 
% netCDF files from the USGS CMGP Oceanographic time-series data 
% archive
%
% Program written Matlab 7.6.0.342 (R2008a)
% Program ran on Linux PC with RHEL4 and on Windows XP PC.
%
% "Although this program has been used by the USGS, no warranty, 
% expressed or implied, is made by the USGS or the United States 
% Government as to the accuracy and functioning of the program 
% and related program material nor shall the fact of distribution 
% constitute any such warranty, and no responsibility is assumed 
% by the USGS in connection therewith."
%%% END USGS BOILERPLATE --------------

clear % a good idea 
 
% --------- set up the information needed by the programs
%
% this is what should be used if using a single source of global attributes
% 9/15/07 etm
% modified to use the universal metadata file : 7751glatt.txt
% change the line below to fit your system path for the location of m_cmg
mfRoot='C:\home\ellyn\mtl\';
   gatt=read_globalatts('globatt_805.txt');
 
% assign the rootName based on the Mooring #, then plug in values from
% the global attributes.  UNIX users : check CASE of files carefully!
rootName=[num2str(gatt.MOORING) ];
rootName=[rootName '1'];   % ADCP is usually the top thing, but it could be
                           % second or third- change this value accordingly
%% the basics
settings.numRawFile = 1; % number of raw binary ADCP files (*.000 or *.PD0), max = 2
settings.rawdata1 = [rootName 'WH000.000']; % raw file #1
settings.rawdata2 = ''; % raw file #2, if numrawfile=2, must have a name
settings.rawcdf = [rootName 'wh.cdf']; % output file name for the raw data in netCDF format
settings.theFilledFile = [rootName 'whF.cdf']; % the name of the fill file
settings.theMaskFile = [rootName 'wh.msk']; % the name of the mask file
settings.theNewADCPFile = [rootName 'whM.cdf']; % the name of the new file with the mask applied
settings.trimFile = [rootName 'whT.cdf']; % the name of the file trimmed by time out of water and by bin
settings.deployed_orientation = 'UP'; % or DOWN, to check against what is set in the ADCP
%% conversion from RDI binary to raw netCDF
settings.rdi2cdf.run = 1; % force runadcp to run rdi2cdf 
settings.rdi2cdf.Mooring_number = gatt.MOORING; % mooring number (USGS) or other identifier
settings.rdi2cdf.platform_type = gatt.platform_type;
settings.rdi2cdf.Deployment_date = gatt.Deployment_date; % the in water time
settings.rdi2cdf.Recovery_date = gatt.Recovery_date; % the out of water time
settings.rdi2cdf.water_depth = gatt.WATER_DEPTH; % m (DO NOT OMIT!)
settings.rdi2cdf.water_depth_source = 'Mooring Log';
%  the user needs to edit the ones below
settings.rdi2cdf.ADCP_serial_number = 185; 
settings.rdi2cdf.transducer_offset = 3.34; % ADCP transducer offset from the sea bed
settings.rdi2cdf.pred_accuracy = 0.35; % from TRDI PLAN in cm/s
settings.rdi2cdf.slow_by = -45; % clock drift
settings.rdi2cdf.long = gatt.longitude; % negative degrees in western hemisphere
settings.rdi2cdf.latit = gatt.latitude; % always positive degrees in northern
settings.rdi2cdf.burst_sampling = 'No'; % if TB and TC were used
%settings.rdi2cdf.TB_command = '01:00:00.00'; % use the actual setting
%settings.rdi2cdf.TC_command = 1024; % use the actual setting
settings.rdi2cdf.AZ_applied = 'Yes'; % was pressure zeroed before deployment
%%  now look for missing ensembles (restarts)
settings.fixens.run = 1; % force runadcp to run fixens (future implementation)
%% now trim the profiles
% there are several methods one can use to trim bins to the surface
% see trimbins.m documentation for more information
%methods: 'RDI Surface Program' | 'User Input' | 'Pressure Sensor' | 'USGS Surface Program'
%  use pressure sensor, if available!
settings.trimbins.method = 'Pressure Sensor'; %'USGS Surface Program'; 
% percent of water column to make sure is preserved when trimming (1 = 100%)
settings.trimbins.percentwc = 1.12; % to capture full range of tide
settings.trimbins.ADCP_offset = settings.rdi2cdf.transducer_offset; % leave this alone
% these control the MATLAB surface detect algorithm findsurface.m
settings.trimbins.findsurface.cdfFile = settings.rawcdf; % leave this alone
settings.trimbins.findsurface.S = 32; % local salinity assumption
% if you know the approximate range of the surface, you can avoid a 
% dialog box by entering that information here
settings.trimbins.findsurface.trimrange = []; % range to clip surface data
%% set up adcp2ep, the final rotation to earth, conversion to EPIC conventions
settings.adcp2ep.epDataFile = [rootName 'wh.nc']; % final output file name
settings.adcp2ep.origin = gatt.DATA_ORIGIN; % with collaborator's data, could be USC, etc.
settings.adcp2ep.experiment = gatt.EXPERIMENT; 
settings.adcp2ep.descript = gatt.DESCRIPTION; 
settings.adcp2ep.SciPi = gatt.SciPi;
settings.adcp2ep.conventions = gatt.Conventions; 
settings.adcp2ep.project = gatt.PROJECT; % might also use OFA funding agency, such as MWRA, EPA, WCMG
settings.adcp2ep.cmnt = '';  % your metadata
settings.adcp2ep.water_mass = ' '; % an EPIC requirement
settings.adcp2ep.magnetic_variation_at_site = gatt.magnetic_variation;
% your data will be rotated byt his value!
settings.adcp2ep.magnetic_variation_applied = settings.adcp2ep.magnetic_variation_at_site;
% the dialog file for your ADCP, there is one in the Demo directory.
% the toolbox use the instrument elevation and azimuth specific to each ADCP
% which can vary slightly as the manufacturing process does not line up the
% transducers exactly, and RDI has a correction for this.
% if you want to use the default matrix, use 'default' for the file name
settings.adcp2ep.dlgFile = 'wh185.dlg'; % generated by the ADCP using the PS3 command
settings.adcp2ep.ADCPtype = 'WH'; % WH for workhorse or BB for broadband


% --------------------- run the programs
%
% turn each step "on" by setting "if 1" and off by using "if 0" 
% steps must be run in sequence
settings.rdi2cdf.goodens = [1 500];  % use [1 inf] to process all

diary(sprintf('run%s',datestr(now, 30)))

% sometimes ADCPs don't know which way they were really facing.
% do rdi2cdf and fixorientation only for deployments that need orientation fixed:
% if 0, % run rdi2cdf separately to fix the orientation
%    rdi2cdf(settings.rawdata1,settings.rawcdf,[],[],...
%        settings.rdi2cdf); % user's provideing metadata
%    orientation = 'UP'; % 'UP' or 'DOWN'
%    fixorientation(settings.rawcdf,orientation);
%    % when rdi2cdf is run the second time via runadcp (below) 
%    % the file converted here will not be overwritten
% end

if 1, % translate to netcdf, mask for basic errors and trim the data
    % this encompasses doing a LOT of processing:
    %   rdi2cdf      Convert raw file to cdf.
    %   fixEns      Find and correct for missing ensembles
    %   runmas      applies mask from fixEns
    %   trimbin     WaterDepth computed & bins above the surface discarded
    runadcp(settings)
end

if 0, % apply a mask that tracks the surface - if you wish to
    [path, name, ext] = fileparts(settings.trimFile);
    theMaskFile = fullfile(path,[name, '.msk']);
    theNewADCPFile = fullfile(path,[name, 'P.cdf']);
    [theNewADCPFile, theMaskFile] = pressuremask (settings.trimFile,...
        theMaskFile,theNewADCPFile)
end

if 1, % rotate from beam to earth coordinates, translate raw netCDF to EPIC
    [path, name, ext] = fileparts(settings.trimFile);
    theNewADCPFile = fullfile(path,[name, 'P.cdf']);
    if exist(theNewADCPFile,'file'),
        settings.trimFile = theNewADCPFile;
        disp(['Using ',settings.trimFile,' for adcp2ep'])
    end
    adcp2ep(settings.trimFile, settings.adcp2ep.epDataFile, ...
        settings.adcp2ep.ADCPtype, settings.adcp2ep.dlgFile, settings.adcp2ep)
end

diary off