FixedLifetimeImageModel.java

package gdsc.smlm.model;

/*----------------------------------------------------------------------------- 
 * GDSC SMLM Software
 * 
 * Copyright (C) 2013 Alex Herbert
 * Genome Damage and Stability Centre
 * University of Sussex, UK
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *---------------------------------------------------------------------------*/

/**
 * Contains a model for an image of fixed lifetime fluorophores. All fluorphores will have the same on time. The
 * activation time will be the incremented by the on-time plus the dark time between fluorophores.
 */
public class FixedLifetimeImageModel extends ImageModel
{
	private double next = 0;

	/**
	 * Construct a new image model
	 * 
	 * @param tOn
	 *            Fixed on-state time
	 * @param tOff
	 *            Dark time between successive fluorophores
	 */
	public FixedLifetimeImageModel(double tOn, double tOff)
	{
		super(tOn, tOff, 0, 0, 0);
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.model.ImageModel#createActivationTime(double[])
	 */
	@Override
	protected double createActivationTime(double[] xyz)
	{
		final double tAct = next + getRandom().getRandomGenerator().nextDouble();
		// Ensure at least tOff full dark frames between lifetimes:
		// Frames:    |      |      |      |
		//         ------|              
		//              end             |--------
		//                              start
		//                     tOff
		final int unit = (int) Math.ceil(tOff);
		final int endT = (int) Math.ceil((tAct + tOn) / unit);
		next = (endT + 1) * unit;
		return tAct;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.model.ImageModel#createFluorophore(int, double[])
	 */
	@Override
	protected FluorophoreSequenceModel createFluorophore(int id, double[] xyz, double tAct)
	{
		return new SimpleFluorophoreSequenceModel(id, xyz, tAct, tOn);
	}
}