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


%%% START USGS BOILERPLATE -------------%
% Use of this program is described in:
%
% Acoustic Doppler Current Profiler Data Processing System Manual 
% Jessica M. Côté, Frances A. Hotchkiss, Marinna Martini, Charles R. Denham
% Revisions by: Andrée L. Ramsey, Stephen Ruane
% U.S. Geological Survey Open File Report 00-458 
% Check for later versions of this Open-File, it is a living document.
%
% Program written in Matlab v7.1.0 SP3
% Program updated in Matlab 7.2.0.232 (R2006a)
% Program ran on PC with Windows XP Professional OS.
%
% "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
%
%% there are two ways to input metadata for the experiment and site.
% capitalized items are required by EPIC conventions

% using read_globalatts from the USGS meta_tools toolbox
% filename must contain a list of Global attributes 
gatt=read_globalatts('..\global_atts.txt');  % provides values to insert below
% syntax and capitalization counts!
% the following are required!
settings.MOORING = gatt.MOORING; %four digit NNNL, NNN mooring + L logger
settings.Deployment_date = gatt.Deployment_date; % the in water time
settings.Recovery_date = gatt.Recovery_date; % the out of water time
settings.longitude = gatt.longitude; % decimal degrees, West = negative
settings.latitude = gatt.latitude; % decimal degrees, South = negative
settings.magnetic_variation = gatt.magnetic_variation; % degrees west is negative
settings.WATER_DEPTH = gatt.WATER_DEPTH; % m (DO NOT OMIT!)
settings.WATER_DEPTH_NOTE = gatt.WATER_DEPTH_NOTE;
% if the following fields are missing, UNKOWN will be used
settings.DATA_ORIGIN = gatt.DATA_ORIGIN; % with collaborator's data, could be USC, etc.
settings.EXPERIMENT = gatt.EXPERIMENT; 
settings.DESCRIPTION = gatt.DESCRIPTION; 
settings.PROJECT = gatt.PROJECT; % might also use OFA funding agency, such as MWRA, EPA, WCMG
settings.Data_Cmnt = gatt.Data_Cmnt;
settings.SciPi = gatt.SciPi;
settings.DATA_ORIGIN = gatt.DATA_ORIGIN;

% or - input it all by hand
% settings.MOORING = 9991; %four digit NNNL, NNN mooring + L logger
% settings.Deployment_date = '09-feb-05 17:00:00'; % the in water time
% settings.Recovery_date = '18-may-2005 13:02 '; % the out of water time
% settings.longitude = -70.7809; % decimal degrees, West = negative
% settings.latitude = 42.3786; % decimal degrees, South = negative
% settings.magnetic_variation = -15.5; % degrees west is negative
% settings.WATER_DEPTH = 32; % m (DO NOT OMIT!)
% settings.WATER_DEPTH_NOTE = 'taken from ship depth sounder on deployment';
% % if the following fields are missing, UNKOWN will be used
% settings.DATA_ORIGIN = 'USGS'; % with collaborator's data, could be USC, etc.
% settings.EXPERIMENT = '2007-2008 PV BBL Experiment'; 
% settings.DESCRIPTION = 'Currents, temp profiles, bottom stress, SSC, sed. traps, and PCB samplers'; 
% settings.PROJECT = 'USGS/EPA Palos Verdes'; % might also use OFA funding agency, such as MWRA, EPA, WCMG
% settings.Data_Cmnt = 'geoprobe tripod at site B3';
% settings.SciPi = 'C. Sherwood, M. Noble, J. Xu, K. Rosenberger';
% settings.DATA_ORIGIN = 'USGS WHSC and PSC Sed. Trans. Groups';

%% ABSS information
settings.ABSSmodel = 'Aquascat1000'; 
% it is recommended that a test run be done on a small subset of .aqa files
% in a separate directory, then run both operations on the entire data set
settings.input_directory = 'D:\PalosVerdes\8445ABSS\testfiles'; % where the .aqa files are
%settings.input_directory = 'D:\PalosVerdes\8445ABSS\datafiles'; % where the .aqa files are
settings.output_directory = 'D:\PalosVerdes\8445ABSS'; % where the .cdf file will go
settings.outFileRoot = '8427abss';
settings.metaFileName = [settings.outFileRoot 'Meta.mat'];
settings.sensor_height = [0.99 0.99 0.99]; % height of each probe

%% --------------------- run the programs
%
% turn each step "on" and "off" by setting "if 0" to "if 1"
% steps must be run in sequence

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

if 0, % translate to .mat using the Aquatec toolbox and get 
    % metadata directly from the raw binary files
    settings = aqa2mat(settings, 1);
end

if 0,
    settings = aqamat2cdfbychan(settings);
end

if 0, % trimming average *and* burst
    bins2keep = {[9 156]; [4 156]; [2 163]};
    for ixducer = 1:3,
        oldDataFile = sprintf('%s%ds.cdf',settings.outFileRoot,ixducer);
        trimFile =  sprintf('%s%dsT.cdf',settings.outFileRoot,ixducer);
        trimprofile(oldDataFile, bins2keep{ixducer}, trimFile);
        d = dir(sprintf('%s%d_*b.cdf',settings.outFileRoot,ixducer));
        for ifile = 1:length(d),
            [thePath theName theExt] = fileparts(d(ifile).name);
            trimFile = fullfile(thePath, [theName 'T' theExt]);
            trimprofile(d(ifile).name, bins2keep{ixducer}, trimFile);
        end
    end
end

diary off