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 com.thoughtworks.xstream.annotations.XStreamAsAttribute;
import com.thoughtworks.xstream.annotations.XStreamOmitField;
/**
* Filter results using a signal threshold
*/
public class SignalFilter extends DirectFilter implements IMultiFilter
{
public static final double DEFAULT_INCREMENT = 5;
public static final double DEFAULT_RANGE = 30;
@XStreamAsAttribute
final double signal;
@XStreamOmitField
float signalThreshold;
public SignalFilter(double signal)
{
this.signal = Math.max(0, signal);
}
@Override
public void setup(MemoryPeakResults peakResults)
{
// Set the signal limit using the gain
signalThreshold = (float) (signal * peakResults.getGain());
}
@Override
public boolean accept(PeakResult peak)
{
return peak.getSignal() >= signalThreshold;
}
@Override
public int validate(final PreprocessedPeakResult peak)
{
if (peak.getPhotons() < signal)
return V_PHOTONS;
return 0;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#getDescription()
*/
@Override
public String getDescription()
{
return "Filter results using a lower signal threshold. The threshold is applied in photons (i.e. the signal is divided by the calibrated gain).";
}
/*
* (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 signal;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#getParameterIncrement(int)
*/
@Override
public double getParameterIncrement(int index)
{
checkIndex(index);
return SignalFilter.DEFAULT_INCREMENT;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#getParameterType(int)
*/
@Override
public ParameterType getParameterType(int index)
{
checkIndex(index);
return ParameterType.SIGNAL;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#adjustParameter(int, double)
*/
@Override
public Filter adjustParameter(int index, double delta)
{
checkIndex(index);
return new SignalFilter(updateParameter(signal, delta, DEFAULT_RANGE));
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#create(double[])
*/
@Override
public Filter create(double... parameters)
{
return new SignalFilter(parameters[0]);
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.results.filter.Filter#weakestParameters(double[])
*/
@Override
public void weakestParameters(double[] parameters)
{
setMin(parameters, 0, signal);
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.ga.Chromosome#mutationStepRange()
*/
public double[] mutationStepRange()
{
return new double[] { DEFAULT_RANGE };
}
public double getSignal()
{
return signal;
}
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 0;
}
public boolean isPrecisionUsesLocalBackground()
{
return false;
}
}