package gdsc.smlm.results.filter;
import com.thoughtworks.xstream.annotations.XStreamAsAttribute;
import com.thoughtworks.xstream.annotations.XStreamOmitField;
/*-----------------------------------------------------------------------------
* 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;
/**
* Filter results using a precision threshold
*/
public class PrecisionFilter extends DirectFilter implements IMultiFilter
{
public static final double DEFAULT_INCREMENT = 1;
public static final double DEFAULT_RANGE = 10;
public static final double UPPER_LIMIT = 70;
@XStreamAsAttribute
final double precision;
@XStreamOmitField
double variance;
@XStreamOmitField
double nmPerPixel = 100;
@XStreamOmitField
boolean emCCD = true;
@XStreamOmitField
double gain = 1;
public PrecisionFilter(double precision)
{
this.precision = Math.max(0, precision);
}
@Override
public void setup(MemoryPeakResults peakResults)
{
variance = Filter.getDUpperSquaredLimit(precision);
nmPerPixel = peakResults.getNmPerPixel();
gain = peakResults.getGain();
emCCD = peakResults.isEMCCD();
}
@Override
public boolean accept(PeakResult peak)
{
final double s = nmPerPixel * peak.getSD();
final double N = peak.getSignal();
// Use the background noise to estimate precision
return PeakResult.getVariance(nmPerPixel, s, N / gain, peak.getNoise() / gain, emCCD) <= variance;
}
@Override
public int validate(final PreprocessedPeakResult peak)
{
if (peak.getLocationVariance() > variance)
return V_LOCATION_VARIANCE;
return 0;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#getDescription()
*/
@Override
public String getDescription()
{
return "Filter results using an upper precision 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 precision;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#getParameterIncrement(int)
*/
@Override
public double getParameterIncrement(int index)
{
checkIndex(index);
return PrecisionFilter.DEFAULT_INCREMENT;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#getParameterType(int)
*/
@Override
public ParameterType getParameterType(int index)
{
checkIndex(index);
return ParameterType.PRECISION;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#adjustParameter(int, double)
*/
@Override
public Filter adjustParameter(int index, double delta)
{
checkIndex(index);
return new PrecisionFilter(updateParameter(precision, delta, DEFAULT_RANGE));
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#create(double[])
*/
@Override
public Filter create(double... parameters)
{
return new PrecisionFilter(parameters[0]);
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#weakestParameters(double[])
*/
@Override
public void weakestParameters(double[] parameters)
{
setMax(parameters, 0, precision);
}
/*
* (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 0;
}
public double getShift()
{
return 0;
}
public double getEShift()
{
return 0;
}
public double getPrecision()
{
return precision;
}
public boolean isPrecisionUsesLocalBackground()
{
return false;
}
}