%% SETUP VARIABLES

% load the sonar
p = '\\storebox\Aquacoustic\Job Data\55562_Hydromax_Baltimore-County\Processed\Ready for Splitting\Mother''s Arms\47174 47175 47176 47178 47179 47180_001 CONCAT_dblchk.MAT'
a = load(p)

xsect = a.xsect
uconv = 0.3048
runlengths = [ 269 202 601 100 92] .*uconv
splits = zeros(1,numel(runlengths))
deltas = Inf(1,numel(runlengths))
thresh_2 = 1 %squared threshold for search function

%perform discrete integration of runlengths to find absolute payout of
%potential split locations
abspos = cumsum(runlengths)


%we're going to need to reset these cable lengths to 0 for the output files
%so we make an array for easily grabbing the offsets out of. it will have
%one extra value we dont need at the end that we can just ignore
offsets = [0 abspos]


%%FIND THE SPLITS

%find the split locations (looking for profile that most closely
%matches the absolute position)


for i = 1:numel(xsect.img)
    for j = 1:numel(runlengths)
        delta = xsect.img(i).cable - abspos(j);
        delta = delta*delta;
        if(delta<thresh_2)
            if(delta<deltas(j))
                splits(j) = i;
                deltas(j) = delta;
            end
        end
    end
end

%% build an array of indices for splitting

%start by padding the splits
splits_1 = splits+1
split_ind = reshape([splits;splits_1],1,[]) %this interleaves splits
                                            %and split_1

split_ind = [1 split_ind numel(xsect.img)]  %this adds a 1 and N entry
                                            %to split matrix

split_ind = reshape(split_ind',2,[])'



IN = xsect % we call the xsect var. "IN" now, the output var has to be called
           % "xsect" so it will still load in sonar express

%% DO THE SPLITTING
 for row = 1 : size(split_ind,1)
     xsect = struct;   %create the output structure

     % these are just some variables that need to be saved
     % with the file
     xsect.currentStation = 1;
     xsect.unit = IN.unit;
     xsect.renderOptions = IN.renderOptions;
     xsect.longVer = IN.longVer;

     %slice from the input
     xsect.img = IN.img( split_ind(row,1):split_ind(row,2));
     xsect.oper = IN.oper(split_ind(row,1):split_ind(row,2));

     %reset the payout (cable distance) so the segment starts
     %at 0
     for i=1:numel(xsect.img)
        %cable length is stored in 2 places in the output
        %structure
        xsect.img(i).cable = xsect.img(i).cable - offsets(row)
        xsect.oper(i).cable = xsect.oper(i).cable - offsets(row)
     end

    %finally, save the segment
     fprintf('Writing...\n');
     save(sprintf('%s.part%.0f.mat',p,row),...
        'xsect');
 end