ActivationEnergyImageModel.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 blinking fluorophores under pulsed activation illumination. Activation energy is
 * sampled from an exponential distribution. Fluorophores are created when the activation energy has been achieved under
 * the given illumination.
 * <p>
 * Based on the work of Coltharp et al (2012) Accurate Construction of photoactivated localization microscopy images for
 * quantitative measurements. PLOS One 7, Issue 12, pp 1-15
 */
public class ActivationEnergyImageModel extends ImageModel
{
	private double eAct;
	private SpatialIllumination illumination;

	/**
	 * Construct a new image model
	 * 
	 * @param eAct
	 *            Average energy for activation
	 * @param illumination
	 *            The illumination model
	 * @param tOn
	 *            Average on-state time
	 * @param tOff
	 *            Average off-state time for the first dark state
	 * @param tOff2
	 *            Average off-state time for the second dark state
	 * @param nBlinks
	 *            Average number of blinks int the first dark state (used for each burst between second dark states)
	 * @param nBlinks2
	 *            Average number of blinks into the second dark state
	 */
	public ActivationEnergyImageModel(double eAct, SpatialIllumination illumination, double tOn, double tOff,
			double tOff2, double nBlinks, double nBlinks2)
	{
		super(tOn, tOff, tOff2, nBlinks, nBlinks2);
		init(eAct, illumination);
	}

	private void init(double eAct, SpatialIllumination illumination)
	{
		checkParameter("eAct", eAct);
		if (illumination == null)
			throw new IllegalArgumentException("SpatialIllumination is null");
		this.eAct = eAct;
		this.illumination = illumination;
	}

	/**
	 * @return the average energy for activation
	 */
	public double getActivationEnergy()
	{
		return eAct;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.model.ImageModel#createActivationTime(double[])
	 */
	@Override
	protected double createActivationTime(double[] xyz)
	{
		return getActivationTime(xyz, frameLimit);
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.model.ImageModel#createFluorophore(int, double[], double)
	 */
	@Override
	protected FluorophoreSequenceModel createFluorophore(int id, double[] xyz, double tAct)
	{
		return new StandardFluorophoreSequenceModel(id, xyz, tAct, tOn, tOff, tOff2, nBlinks, nBlinks2,
				isUseGeometricDistribution(), getRandom());
	}

	private double getActivationTime(double[] xyz, int frames)
	{
		final double activation = getRandom().nextExponential(eAct);
		double e = 0;
		for (int t = 0; t < frames; t++)
		{
			// Q. Should the molecule be moving during the activation phase?
			final double[] photons = illumination.getPulsedPhotons(xyz, t + 1);

			e += photons[0]; // pulse energy
			if (e > activation)
				return t;

			e += photons[1]; // during energy
			if (e > activation)
			{
				// Interpolate
				return t + 1 - (e - activation) / photons[1];
			}
		}
		return frames; // default to the number of frames.
	}
}