% doNORTEKoptic - translate optic sensor voltage from nortek profiler
% (whether AWAC or Aquadopp) to scientific units
% function [optic = doAWACoptic(extmeta, extvolts)
% borrowed from dohydraoptic to convert the external voltages of a
% extmeta is the structure of metadata for a Hydra external optical sensor
%
% for TRANS
% extmeta.serial = 'TRANS290'; % OBS### | TRANS### | XXX####
% extmeta.height = 0; % m
% extmeta.cals.pre = [0 0]; % for trans: [air blocked]
% extmeta.cals.post = [0 0]; % for trans: [air blocked]
% extmeta.cals.focallen = 25; % folcal length of the trans, 0.5 | 0.25 | 1 m
% extmeta.cals.M = 0; % for trans
% extmeta.cals.B = 0; % for trans
% optic returns the attenuation suitable for:
%  55:ATTN:ATTENUATION             :attn:m-1:f7.5:added for r2d2 ctd data
%
% extmeta for OBS
% extmeta.serial = 'OBS1711'; % OBS### | TRANS### | XXX####
% extmeta.height = 0.23; % m
% if coef is present, dohydraoptic will apply them to OBS data
% extmeta.coef = [0 1 0]; % or [] coefficients to a quadratic calibration eqation
% extmeta.units = 'kg/m-3';
% extmeta.equation = 'Conc [kg/m-3] = coef(1)+coef(2)*V+coef(3)*V@2';
% optic returns nephylometer output, simply the volts it received
%  56:NEP:BACKSCATTER INTENSITY    :nephylometer:v:f10.6: added for Dave Pashinski
%
% If neither of these, then optic = extvolts 

% 29 Mar 2005
% -- add OBS calibration handling
% 27 Jan 2009 
%   translated for AWAC, and include OBS3+
% Written by Marinna Martini for the U.S. Geological Survey 
% Coastal & Marine Program Woods Hole Field Center, Woods Hole, MA
% http://woodshole.er.usgs.gov/ Please report bugs to mmartini@usgs.gov
function optic = doNORTEKoptic(extmeta, extvolts)

% for transmissometers
if ~isempty(findstr('TRANS',extmeta.sensor_type)),
    % bail myself out....
    if isfield(extmeta.cals,'focallen'),
        extmeta.cals.path_length = extmeta.cals.focallen;
        %disp('Warning: path length attribute will be called focallen')
    end
    % first make sure the required fields are there
    if ~isfield(extmeta.cals,'pre') || ~isfield(extmeta.cals,'post') || ...
            ~isfield(extmeta.cals,'path_length'),
        disp('dohydraoptic: Incorrect metadata for the transmissometer')
        disp(extmeta.cals)
        optic = [];
        return
    end
    if extmeta.cals.pre(1) >= extmeta.cals.post(1),
        Vair = extmeta.cals.pre(1);
    else Vair = extmeta.cals.post(1);
    end
    len = extmeta.cals.path_length;
    optic = -(1/len) .* log(extvolts./(.95*Vair));
elseif ~isempty(strmatch('OBS',extmeta.sensor_type,'exact')),
    if isfield(extmeta.cals,'SEDcoef') && ~isempty(extmeta.cals.SEDcoef),
        % user has supplied coefficients
        optic = extmeta.cals.SEDcoef(1).*ones(size(extvolts));
        for n = 2:length(extmeta.cals.SEDcoef),
            optic = optic + extmeta.cals.SEDcoef(n).*(extvolts.^(n-1));
        end 
    else
        % No coefficients, no conversion
        %disp('dohydraoptic: No coefficients supplied for the OBS')
        optic = [];
    end
%for OBS3+ on the AWAC
elseif ~isempty(strmatch('OBS3+',extmeta.sensor_type,'exact')),
    if isfield(extmeta.cals,'NTUcoef') && ~isempty(extmeta.cals.NTUcoef),
        % user has supplied coefficients for NTU's
        optic1 = extmeta.cals.NTUcoef(1);%.*ones(size(extvolts));
        for n = 2:length(extmeta.cals.NTUcoef),
            optic1 = optic1 + extmeta.cals.NTUcoef(n).*(extvolts.^(n-1));
        end 
        optic = optic1;
        if isfield(extmeta.cals,'SEDcoef') && ~isempty(extmeta.cals.SEDcoef),
           % user has supplied coefficients for sediment concentration
           optic2 = extmeta.cals.SEDcoef(1).*ones(size(extvolts));
           for n = 2:length(extmeta.cals.SEDcoef),
               optic2 = optic2 + extmeta.cals.SEDcoef(n).*(extvolts.^(n-1));
           end 
           optic = [optic1 optic2];
        end
    else
        % No coefficients, no conversion
        %disp('dohydraoptic: No coefficients supplied for the OBS')
        optic = [extvolts];
    end
else
    optic = extvolts;
end