WidthFilter.java

package gdsc.smlm.results.filter;

/*----------------------------------------------------------------------------- 
 * 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.MemoryPeakResults;
import gdsc.smlm.results.PeakResult;

import java.util.regex.Matcher;
import java.util.regex.Pattern;

import com.thoughtworks.xstream.annotations.XStreamAsAttribute;
import com.thoughtworks.xstream.annotations.XStreamOmitField;

/**
 * Filter results using an upper width factor
 */
public class WidthFilter extends DirectFilter implements IMultiFilter
{
	public static final double DEFAULT_INCREMENT = 0.05;
	public static final double DEFAULT_RANGE = 1;
	public static final double UPPER_LIMIT = 5;

	@XStreamAsAttribute
	final double width;
	@XStreamOmitField
	float upperSigmaThreshold;
	@XStreamOmitField
	boolean widthEnabled;

	public WidthFilter(double width)
	{
		this.width = Math.max(0, width);
	}

	@Override
	public void setup(MemoryPeakResults peakResults)
	{
		// Set the width limit
		upperSigmaThreshold = Float.POSITIVE_INFINITY;
		Pattern pattern = Pattern.compile("initialSD0>([\\d\\.]+)");
		Matcher match = pattern.matcher(peakResults.getConfiguration());
		if (match.find())
		{
			upperSigmaThreshold = Filter.getUpperLimit(Double.parseDouble(match.group(1)) * width);
		}
	}

	@Override
	public void setup()
	{
		setup(true);
	}

	@Override
	public void setup(int flags)
	{
		setup(!areSet(flags, DirectFilter.NO_WIDTH));
	}

	private void setup(final boolean widthEnabled)
	{
		this.widthEnabled = widthEnabled;
		if (widthEnabled)
		{
			upperSigmaThreshold = Filter.getUpperLimit(width);
		}
	}

	@Override
	public boolean accept(PeakResult peak)
	{
		return peak.getSD() <= upperSigmaThreshold;
	}

	@Override
	public int validate(final PreprocessedPeakResult peak)
	{
		if (widthEnabled)
		{
			if (peak.getXSDFactor() > upperSigmaThreshold)
				return V_X_SD_FACTOR;
		}
		return 0;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#getDescription()
	 */
	@Override
	public String getDescription()
	{
		return "Filter results using an upper width factor. (Width is relative to initial peak width.)";
	}

	/*
	 * (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 width;
	}

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

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

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

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

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#weakestParameters(double[])
	 */
	@Override
	public void weakestParameters(double[] parameters)
	{
		setMax(parameters, 0, width);
	}
	
	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.DirectFilter#lowerBoundOrientation(int)
	 */
	@Override
	public int lowerBoundOrientation(int index)
	{
		return 1;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.filter.Filter#upperLimit()
	 */
	@Override
	public double[] upperLimit()
	{
		return new double[] { UPPER_LIMIT };
	}

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

	public double getSignal()
	{
		return 0;
	}

	public double getSNR()
	{
		return 0;
	}

	public double getMinWidth()
	{
		return 0;
	}

	public double getMaxWidth()
	{
		return width;
	}

	public double getShift()
	{
		return 0;
	}

	public double getEShift()
	{
		return 0;
	}

	public double getPrecision()
	{
		return 0;
	}

	public boolean isPrecisionUsesLocalBackground()
	{
		return false;
	}
}