% fan_correlation - Correlate fan images over time
which_experiment = 'mvco07'
% which_experiment = 'pasta1'
make_plots = 1;
switch which_experiment
   case 'mvco07'
      settings.fname = 'D:\crs\data\MVCO2007\8369fan_raw.cdf';
   case 'mvco05'
      settings.fname = 'D:\crs\data\Ripple_data\8044fan_raw.cdf';
   case 'pasta1'
      settings.fname = 'D:\crs\data\Ripple_data\701fan_raw.cdf';
   case 'pasta2'
      settings.fname = 'D:\crs\data\Ripple_data\711Gfan_raw.cdf';
   case 'pasta3'
      settings.fname = 'D:\crs\data\Ripple_data\711Hfan_raw.cdf';
end

rev_info= 'SVN $Revision: 982 $';

% Check for raw sonar netcdf file
if(exist(settings.fname,'file')~=2),
   error('Cannot find sonar file %s\n',settings.fname);
end

% open existing cdf file of raw fan data
ncr=netcdf(settings.fname);
jt= ncr{'time'}(:)+ncr{'time2'}(:)./86400000;
% set up how many images to process
n=length(jt);
c = zeros(n,1);
cs = zeros(n,1);

% first image
tmp = size(ncr{'raw_image'});
ntimes=tmp(1); NPoints=tmp(2); nscans=tmp(3);
% trim the redundant first and last ping
imagedata = ncr{'raw_image'}(1,:,2:nscans-1);
[npoints,nangles] = size(imagedata);
% prange = ncr{'profile_range'}(1,2:nscans-1);
% headpos = ncr{'head_pos'}(1,2:nscans-1); %recorded
% headangle=ncr{'headangle'}(2:nscans-1); % calculated

% trim range to real area of data
nearfieldcutoff = 52;
farfieldcutoff = NPoints;
imagedata = imagedata(nearfieldcutoff:farfieldcutoff,:);
switch which_experiment
   case 'mvco07' % two scans
      ib = 10;
      % correct offset between CW and CCW sweeps
      is = 8;
      s1s = 1+ib;
      s1e = 2321-ib;
      s2s = 2322+ib+is;
      s2e = 4642-ib+is;
      s1 = imagedata(:,s1s:s1e);
      s2 = fliplr(imagedata(:,s2s:s2e));
      % average CW and CCW sweeps
      s = 0.5*(s1+s2);
      % calculate correlation among CW and CCW sweeps
      Cs = cov(s1,s2); cs(1)=Cs(1,2)./sqrt(Cs(1,1)*Cs(2,2));
   otherwise
      ib = 2;
      s = imagedata(1+ib:nangles-ib);
end
s_old=s;

for i=1:n,
   fprintf(1,'Processing %s\n',datestr(gregorian(jt(i)),'HHMM dd-mmm-yy'));
   tmp = size(ncr{'raw_image'});
   ntimes=tmp(1); NPoints=tmp(2); nscans=tmp(3);

   % trim the redundant first and last ping
   imagedata = ncr{'raw_image'}(i,:,2:nscans-1);
%    prange = ncr{'profile_range'}(i,2:nscans-1);
%    headpos = ncr{'head_pos'}(i,2:nscans-1); %recorded
%    headangle=ncr{'headangle'}(2:nscans-1); % calculated
   [npoints,nangles] = size(imagedata);  % necessary to

   % trim range to real area of data
   nearfieldcutoff = 52;
   farfieldcutoff = NPoints;
   imagedata = imagedata(nearfieldcutoff:farfieldcutoff,:);
   switch which_experiment
      case 'mvco07' % two scans
         ib = 10;
         is = 8;
         s1s = 1+ib;
         s1e = 2321-ib;
         s2s = 2322+ib+is;
         s2e = 4642-ib+is;
         s1 = imagedata(:,s1s:s1e);
         s2 = fliplr(imagedata(:,s2s:s2e));
         s = 0.5*(s1+s2);
         Cs = cov(s1,s2); cs(i,1)=Cs(1,2)./sqrt(Cs(1,1)*Cs(2,2));
      otherwise
         ib = 2;
         s = imagedata(1+ib:nangles-ib);
   end
   C = cov(s,s_old); c(i,1)=real(C(1,2)./sqrt(C(1,1)*C(2,2)));
   s_old = s;
end