build_xyl_trackdat.m

function [ trackdat_xyl ] =  build_xyl_trackdat ( tracks_input, px_spacing, Nframes )
% Create a data structure with a more streamlined reference for the
% positions, luminations, and changes in position of the various tracks.

Num_comp_tracks = length( tracks_input);

% Loop through each independent track (of length T frames) and figure
% out how many sub-tracks need to be considered for each case:
for ti = 1:Num_comp_tracks

    Nsubtracks(ti)  =  size( tracks_input(ti).tracksCoordAmpCG, 1);

    % get the offset from which this composite track starts and finishes.
    comptrack_birth     = min( tracks_input(ti).seqOfEvents(:,1) );

    comptrack_death_lag = Nframes - max( tracks_input(ti).seqOfEvents(:,1) );
    % the number of frames that should be appended to the end of this comptrack to make it to the end of the movie.

    for sti = 1:Nsubtracks( ti )
       % Within each sub-track, extract the position and change values
       % segment in which the particle could not be located on either side
       % of the window

       % get birth and death time points for each subtrack _within_ the composite window
       obituary = tracks_input(ti).seqOfEvents( tracks_input(ti).seqOfEvents(:,3)==sti, 1 );

       xdat_compwindow = px_spacing * tracks_input(ti).tracksCoordAmpCG(sti,1:8:end);
       ydat_compwindow = px_spacing * tracks_input(ti).tracksCoordAmpCG(sti,2:8:end);
       % the above sets the raw *COORDINATES* in units of micrometers. All
       % diffs are carried out accordingly.

       Adat_compwindow = tracks_input(ti).tracksCoordAmpCG(sti,4:8:end);

       trackdat_xyl(ti).xpos(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), xdat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
       trackdat_xyl(ti).ypos(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), ydat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
       trackdat_xyl(ti).Lamp(sti,:) = [ repmat(NaN,[1 , (comptrack_birth-1)]), Adat_compwindow, repmat(NaN,[1 , comptrack_death_lag]) ];
       
    end % terminate forloop through subtracks

    % Sanity check: is this track data the right dimensions:
    if(  ~all(  size( trackdat_xyl(ti).xpos ) == [ Nsubtracks(ti), Nframes] ) ||  ~all(  size( trackdat_xyl(ti).ypos ) == [ Nsubtracks(ti), Nframes] ) )
       disp("FATAL ERROR: unexpected dimension in trackdat_xyl.")
       return
    end

    trackdat_xyl(ti).dx  = diff ( trackdat_xyl(ti).xpos, 1, 2 );
    trackdat_xyl(ti).dy  = diff ( trackdat_xyl(ti).ypos, 1, 2 );

    if(  ~all (  size( trackdat_xyl(ti).Lamp ) ==  [ Nsubtracks(ti), Nframes] ) )
        disp("FATAL ERROR: unexpected dimension in trackdat_xyl.Lamp.")
        return
    end

end % terminate forloop through comptracks


end