function output_array = calibrate_ecofl2(input_array,p,prop)
% m1_ecofl_calibrate - Provide calibrated output data for the Fluorometer.
%
% Use as: output_array = m1_ecofl_calibrate(input_array)
%
% Inputs: input_array = Array of raw counts data and configuration
% directory as a string.
%
% Output: output_array = an array of raw and calibrated data elements.
%
% Example:
%   output_array = m1_ecofl_calibrate(input_array,'//tornado/diatom/cimt/configuration/ECO/ecofl.properties')
%
% Where Col(1)=datenum,  Col(2)=OASIS time, Col(3)=reference, Col(4)=signal, and Col(5)=thermistor.
% MC Harlan
% 21 Nov 2003
% Updated for the CIMT Mooring.  Add the temperature correction
% re: new device FLNTUS a combination scattering meter with fluorometer and
% backscatter
% Where Col(1)=datenum,  Col(2)=OASIS time, Col(3)=fl_reference, Col(4)=fl_signal, col(5)=bb_ref col(6)=bb_signal and Col(7)=thermistor.

% These calculations are from the WetLabs Calibration sheet.  rpm
% The averaged ECOFL raw data counts are in column 2, thermistor counts are in column 5
% Read the calibration constants from cal file
disp(['Calibrations for ECOFL device ', p.dev, ', serial number ', p.serial])
SCALE_FACTOR=str2num(getProperty(prop,'calibration.SCALE_FACTOR'));
CWO=str2num(getProperty(prop,'calibration.CWO'));
%SCALE_FACTOR = 0.0079; % from calibration sheet
[rows,cols] = size(input_array) % returns the size of matrix X in separate variables.
fprintf(1,'ecofl calibrate: rows=%d  cols=%d\n', rows, cols);
output_array = input_array;

% chlorophyll calculation
for row = 1:rows
   % alrighty let's calculate the temperature correction
   temp_correction = input_array(row,2)/(0.2805 * (input_array(row,5)/547.645)/0.7204);
   % and now the chlorophyll calc
   output_array(row, cols+1) = (input_array(row,2) - CWO) * SCALE_FACTOR; %ecofl_cal
   output_array(row, cols+2) = (temp_correction - CWO) * SCALE_FACTOR; %ecofl_cal_corr
   output_array(row, cols+3) = temp_correction;
end

% assign variables and calculate interim values
siam_date=output_array(:,4); % SIAM style timestamp
otime=output_array(:,6); % OASIS style timestamp
ecoflcal=output_array(:,9); %calibrated fluorescence
ecoflraw=output_array(:,2); % averaged raw fluorescence counts
ecoflcaltemp=output_array(:,10); %temperature corrected calibrated fluorescence
ecofltemp=output_array(:,11); % temperature corrected value
ecofltempraw=output_array(:,5); % averaged raw thermistor counts
ecoflrefraw=output_array(:,7); % averaged raw reference light counts
sdn=output_array(:,1); % serial date number timestamp
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 results to output file
if strcmp(p.otype,'plot')
    outfile=[p.ddir,'/ecofl_calibrated.csv']; t='w';
else
    outfile=[p.ddir,'/ecofl.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','ecoflcal','ecoflcaltemp','ecoflraw','ecotempcorr','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,:),ecoflcal(J,:),ecoflcaltemp(J,:),ecoflraw(J,:),ecofltemp(J,:),ecofltempraw(J,:) ,ecoflrefraw(J,:),pacific_date(J,:));
end
fclose(fid);
% Write to log file
fid=fopen([p.ldir,'/',p.log],'at+');
fprintf(fid,'%s\n',['  4. ECOFL_CALIBRATE: scale_factor=',num2str(SCALE_FACTOR), ' CWO=',num2str(CWO)]);
fprintf(fid,'%s\n',['     Rows processed: ',num2str(rows), ' columns processed: ', num2str(cols) ]);
fprintf(fid,'%s\n',['     Calibrated data file: ',outfile]);
fclose(fid);

return;