function output_array = ecobb_calibrate(input_array,p,prop)
% ecobb_calibrate - Provide calibrated output data for the BB2F.
%
% Use as: output_array = ecobb_calibrate(input_array)
%
% Inputs: input_array = Array of raw counts data.
%
% Output: output_array = an array of raw and calibrated data elements.
%
% Example:
%   output_array = ecobb_calibrate(input_array)
% Where Col(1)=datenum,  Col(2)=reference, Col(3)=signal, and Col(4)=thermistor. 

% MC Harlan  21 Nov 2003
% rpm 27 May 2004 Modified to read cal from file.

% Read the calibration constants from cal file
disp(['Calibrations for device ', p.dev, ', ECOBB ', p.serial])
ANGLE=str2num(getProperty(prop,'calibration.ANGLE'));
WAVELEN=str2num(getProperty(prop,'calibration.WAVELEN'));
DARK_CNTS=str2num(getProperty(prop,'calibration.DARK_CNTS'));
CAL_SW=str2num(getProperty(prop,'calibration.CAL_SW'));
SCALE_FACTOR=str2num(getProperty(prop,'calibration.SCALE_FACTOR'));
X=str2num(getProperty(prop,'calibration.X'));
SAL=str2num(getProperty(prop,'calibration.SAL'));

[rows,cols] = size(input_array); % returns the size of matrix X in separate variables.
%t=zeros(rows,3); 
%fprintf(1,'rows=%d  cols=%d\n', rows, cols);
%output_array = [input_array,t];clear t;save i:\bog\matlab\ecobb.mat;
output_array = input_array;
% Calculations are from the WetLabs Scattering Meter ECO-BB User's Guide,
% see \\tornado\diatom\CIMT\documentation\ECO
% Volume scattering of water (Morel, 1974)
Bw = (1.38 * (WAVELEN/500) ^ -4.32) * ((1 + (0.3 * SAL)/37)*10 ^ -4) * (1 + (cos(117))^2) * ((1 - 0.09) / (1 + 0.09));

for row = 1:rows
  raw_cnts = input_array(row, 8);  % RANGE = 0 to 4120 counts
  B_117_700 = (raw_cnts - DARK_CNTS) * SCALE_FACTOR; % volume scatter coefficients, units are m-1 sr-1t
  Bp = B_117_700 - Bw;  % Particle beta, scattering of particles.
  b_bp = 2 * pi * X * Bp; %Particulate backscattering coefficients (m-1)
  b_sw = 0.0029308 * (WAVELEN/500) ^ -4.24; % total scattering of seawater
  t_bbs = b_bp + (b_sw / 2.0); %Total backscattering coefficients bb(l) units m-1
  output_array(row, cols+1) = t_bbs; 
  output_array(row, cols+2) = B_117_700; 
  output_array(row, cols+3) = Bp; 
end
% assign variable names for output file
sdn=output_array(:,1); % serial date number timestamp
ecobbraw=output_array(:,8); % averaged raw backscatter counts
siam_date=output_array(:,4); % SIAM style timestamp
ecobbtempraw=output_array(:,5); % averaged raw thermistor counts
otime=output_array(:,6); % OASIS style timestamp
ecobbrefraw=output_array(:,7); % averaged raw reference light counts
ecobbcal=output_array(:,9); %calibrated backscatter
ecobbvol=output_array(:,10); %volume scattering coefficients
ecobbpart=output_array(:,11); % volume scattering of particulates only
jday=date2jul(sdn);
year=datestr(sdn,10);
date_time=datestr(sdn,0);
hours=datestr(sdn,15);
hour=(str2num(hours(:,1))*10)+str2num(hours(:,2));
min=(str2num(hours(:,4))*10)+str2num(hours(:,5));
jtime=jday+((hour/24) + ((min/60)/24));
pacific_date = sdn-(7/24);
output_array(:, cols+4) = pacific_date;
% write to output file
if strcmp(p.otype,'plot')
    outfile=[p.ddir,'/ecobb_calibrated.csv'];t='w';
else
    outfile=[p.ddir,'/ecobb.csv'];t='at+';
end %if strcmp(p.otype,'plot')
fid=fopen(outfile,t);
if t=='w'
fprintf(fid,'%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s\n','%date_time','sdn','siam_date','year','jday','otime','ecobbcal','ecobbvol','ecobbpart','ecobbraw','ecotempraw','ecorefraw','pacific_time' );
end
[row col]=size(output_array);
for J=1: row
    fprintf(fid,'%s,%f,%f,%s,%i,%f,%f,%f,%f,%f,%f,%f,%f\n',date_time(J,:),sdn(J,:),siam_date(J,:),num2str(year(J,:)),jday(J,:),otime(J,:),ecobbcal(J,:),ecobbvol(J,:),ecobbpart(J,:),ecobbraw(J,:),ecobbtempraw(J,:) ,ecobbrefraw(J,:),pacific_date(J,:));
end
fclose(fid);
% Write to log file
fid=fopen([p.ldir,'/',p.log],'at+');
fprintf(fid,'%s\n',['  4. ECOBB_CALIBRATE: ',p.ecotype,' angle=', num2str(ANGLE), ' wavelen=',num2str(WAVELEN), ' dark_cnts=',num2str(DARK_CNTS)]);
fprintf(fid,'%s\n',['     cal_sw=',num2str(CAL_SW), ' scale_factor=',num2str(SCALE_FACTOR), ' x=',num2str(X), ' sal=',num2str(SAL) ]);
fprintf(fid,'%s\n',['     Rows processed: ',num2str(rows), ' columns processed: ', num2str(cols) ]);
fprintf(fid,'%s\n',['     Calibrated data file: ',outfile]);
fclose(fid);

return;