package tracking;

import util.Cell;
import util.GenericDataLoader;
import java.io.IOException;
import java.util.List;

/**
 * Simple-minded tracking.
 * Locates the nearest cell in the next frame and if it hasn't already been
 * assigned into a trajectory, add it to the current cell.
 * Simply presented as a demonstration and not intended for actual use.
 * This plugin is very slow when used with large cell populations.
 *
 * Compile with, e.g.
 * javac -cp /Users/mike/java/libraries/ij.jar:/Users/mike/java/libraries/LineageTracker_1.0.2.jar SimpleNearest.java

 * 
 * @author Mike Downey
 * @version 16 Feb 2011
 */
public class SimpleNearest extends AbstractTracker{

    @Override
    public List<Cell> run() throws IOException {
        // Load in the segmented cell data
        cellsToTrack = GenericDataLoader.loadData(expLoader);

        int storeOld = TrackedCell.maximumCellSeparation;
        TrackedCell.maximumCellSeparation=50;

        for(Cell c : cellsToTrack){
            int f = c.getFrame();
            if(f<expLoader.getFrames()){
                Cell nearest = TrackedCell.findNearestCell(f+1, c.getX(), c.getY(), cellsToTrack);
                if(nearest!=null && nearest.getPreviousCell()==null)
                    c.setNextCell(nearest);
            }
        }

        TrackedCell.maximumCellSeparation = storeOld;
        return cellsToTrack;
    }

    @Override
    // Method does not use tracking parameters so return null.
    public TrackingParameters getTrackingParameters() {
        return null;
    }

    @Override
    public String getName() {
        return "Simple Nearest Cell";
    }


}