ANRFilter.java

package gdsc.smlm.results.filter;

import com.thoughtworks.xstream.annotations.XStreamAsAttribute;

/*----------------------------------------------------------------------------- 
 * 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.
 *---------------------------------------------------------------------------*/

import gdsc.smlm.results.PeakResult;
import gdsc.smlm.results.MemoryPeakResults;

/**
 * Filter results using an amplitude-to-noise ratio (ANR) threshold
 */
public class ANRFilter extends DirectFilter
{
	@XStreamAsAttribute
	final float anr;

	public ANRFilter(float anr)
	{
		this.anr = Math.max(0, anr);
	}

	@Override
	public void setup(MemoryPeakResults peakResults)
	{
	}

	@Override
	public boolean accept(PeakResult peak)
	{
		return getANR(peak) >= this.anr;
	}

	static float getANR(PeakResult peak)
	{
		return (peak.getNoise() > 0) ? peak.getAmplitude() / peak.getNoise() : Float.POSITIVE_INFINITY;
	}

	public int validate(final PreprocessedPeakResult peak)
	{
		if (getANR(peak) < this.anr)
			return V_AMPLITUDE | V_NOISE;
		return 0;
	}

	static float getANR(PreprocessedPeakResult peak)
	{
		return (peak.getNoise() > 0) ? peak.getAmplitude() / peak.getNoise() : Float.POSITIVE_INFINITY;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#getDescription()
	 */
	@Override
	public String getDescription()
	{
		return "Filter results using a lower ANR threshold.";
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#getNumberOfParameters()
	 */
	@Override
	public int getNumberOfParameters()
	{
		return 1;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#getParameterValueInternal(int)
	 */
	@Override
	protected double getParameterValueInternal(int index)
	{
		return anr;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#getParameterIncrement(int)
	 */
	@Override
	public double getParameterIncrement(int index)
	{
		checkIndex(index);
		return SNRFilter.DEFAULT_INCREMENT;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#getParameterType(int)
	 */
	@Override
	public ParameterType getParameterType(int index)
	{
		checkIndex(index);
		return ParameterType.ANR;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#adjustParameter(int, double)
	 */
	@Override
	public Filter adjustParameter(int index, double delta)
	{
		checkIndex(index);
		return new ANRFilter(updateParameter(anr, delta, SNRFilter.DEFAULT_RANGE));
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#create(double[])
	 */
	@Override
	public Filter create(double... parameters)
	{
		return new ANRFilter((float) parameters[0]);
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#weakestParameters(double[])
	 */
	@Override
	public void weakestParameters(double[] parameters)
	{
		setMin(parameters, 0, anr);
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.ga.Chromosome#mutationStepRange()
	 */
	public double[] mutationStepRange()
	{
		return new double[] { SNRFilter.DEFAULT_RANGE };
	}
}