% check_fan_alignment - Script to look at fan angles and mult. sweeps
which_experiment = 'mvco05'
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';
end
      %settings.img_nums = 250;
settings.sweep = 1;
settings.dxy = 0.02;
plottype = 'check_sweep';

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);

% set up how many images to process
n=length(ncr{'time'});
qa = zeros(n,5);
qn = zeros(n,5);
qm = zeros(n,5);
qf = zeros(n,5);
c = zeros(n,5);
for i=1:n,
   ik = i;

   jt= ncr{'time'}(ik)+ncr{'time2'}(ik)./86400000;
   fprintf(1,'Processing %s\n',datestr(gregorian(jt),'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'}(ik,:,2:nscans-1);
   prange = ncr{'profile_range'}(ik,2:nscans-1);
   headpos = ncr{'head_pos'}(ik,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,:);
   %%

         ib = 10;
         is = 5;
         ir=80; ia=(600:800);
   for j=1:5,
      %is = input('offset? ')
      s1s = 1+ib;
      s1e = nangles/2-ib; %2321-ib;
      s2s = nangles/2+1+ib+is; % 2322+ib+is;
      s2e = nangles-ib+is; % 4642-ib+is;
      s1 = imagedata(:,s1s:s1e);
      s2 = fliplr(imagedata(:,s2s:s2e));
      s3 = s1-s2;
      C = cov(s1,s2); c(i,j)=C(1,2)./sqrt(C(1,1)*C(2,2));
      qa(i,j)=sqrt(mean(mean(s3.^2)));
      qn(i,j)=sqrt(mean(mean(s3(75:125,:).^2)));
      qm(i,j)=sqrt(mean(mean(s3(225:275).^2)));
      qf(i,j)=sqrt(mean(mean(s3(350:400,:).^2)));
      is = is+1;
   end
   if(make_plots),
      figure(1)
      clf
      subplot(121)
      imagesc((s3))
      title(num2str(is))
      subplot(122)
      plot(s1(ir,ia),'b')
      hold on
      plot(s2(ir,ia),'-r')
      plot(s3(ir,ia),'-k')
      hold off
      shg
      figure(4)
      clf
      imagesc(log10(0.5*(s1+s2)));
      figure(2)
      clf
      imagesc(log10(s1))
      figure(3)
      clf
      imagesc(log10(s2))
      for m=1:50,
         fno = 2+mod(m,2);
         figure(fno)
         pause(.2)
      end
      pause
      is = is+1;
   end

end