% -- 
% Jeff Sevadjian
% Research Technician
% Monterey Bay Aquarium Research Institute
% 7700 Sandholdt Rd
% Moss Landing, CA 95039, USA
% ph: +1 831-775-1888

% Parses CTD.txt capture file from Sea-Term (internally-logged data).
% Extra data here, not logged by cntl due to failed charging system
%  (3 solar panels busted out by end of depl).
% QC's [T, S] in a manner consisent w/ 'OA2_201505_convQC_datalog.m'.
% SBE-logged data [T, S] are slightly different, presumably due to OASIS AtoD?

%define buoy, deployment, data directory
 buoy = 'OA2';
 dep = '201505';
 mydir = ['//atlas.shore.mbari.org/OA_Moorings/deployment_data/' ...
   buoy '/' dep '/'];
 myfile = 'CTD';

%read-in SBE internally-logged data
 data = [];
 time = [];
 fid = fopen([mydir 'raw/ctd/' myfile '.txt']);
 while ~feof(fid)
   fline = fgetl(fid);
   f = strfind(fline,',');
   if length(f)==5 & length(fline)==60
     s = str2num(fline(1:f(4)-1));
     if length(s)==4
       data = [data; s];
       time = [time; fline(f(4)+2:end)];
     end
   end
 end
 fclose(fid);
 clear fid ans fline f s;

%form to matrix
 CTD = [datenum(time), data(:,[1,4])]; %I looked at press, don't need anymore
 clear data time;

%save raw .mat file
 save([mydir 'raw/CTD/' myfile '.mat'],'CTD'); 

%load un-QC'd CTD data from cntl
 load([mydir 'raw/cntl/DATALOG.mat']);
 clear AANDERAA_O2 AIRMAR_PB200 EXT_ANALOG* PCO2 SPECIAL*;

 figure; hold on;
 plot(MICROCAT(:,1),MICROCAT(:,5),'r.-');
 plot(CTD(:,1),CTD(:,3),'b.');

 figure; hold on;
 plot(MICROCAT(:,1),MICROCAT(:,2),'r.-');
 plot(CTD(:,1),CTD(:,2),'b.');

%tBeg, tEnd
 tBeg = datenum([2015 5 13 20 36 0]); %slightly diff, one extra data pt
 tEnd = datenum([2016 9 27 16  4 0]);

%QC
 f = find(CTD(:,1)<tBeg | CTD(:,1)>tEnd);
 CTD(f,:) = [];
 clear f;

 %QC salinity
  %pump failed
   f = find( CTD(:,1) > datenum([2016 3 6 2 6 0]) );
   CTD(f,3) = NaN;
   clear f;
  %variance filter
   win = 100; %window
   nst = 5; %number of stdev's above median
   sm = slidingmed(CTD(:,3), win);
   ss = slidingstdev(CTD(:,3), win);
   fs = find(abs(CTD(:,3) - sm) > nst*ss);
   CTD(fs,3) = NaN;
   clear win nst sm ss fs;
  %manual outliers
   f = find( CTD(:,1) > datenum([2015 9 30 16 6 0]) & ...
     CTD(:,1) < datenum([2015 10 16 4 5 0]) ); %prolonged dip in S; T vs S out-of-whack
   CTD(f,3) = NaN;
   clear f;

%save
 save([mydir 'QC/' myfile '_QC.mat'],'CTD');