package gdsc.smlm.filters;
import gdsc.core.ij.Utils;
import java.util.Arrays;
import java.util.List;
/*-----------------------------------------------------------------------------
* GDSC SMLM Software
*
* Copyright (C) 2015 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.
*---------------------------------------------------------------------------*/
/**
* Identifies candidate spots (local maxima) in an image. The image is smoothed with a circular mean filter.
*/
public class CircularMeanDataProcessor extends DataProcessor
{
private final double radius;
private CircularMeanFilter filter;
/**
* Constructor
*
* @param border
* The border to ignore for maxima
* @param smooth
* The distance into neighbouring pixels to extend
*/
public CircularMeanDataProcessor(int border, double smooth)
{
super(border);
this.radius = getSigma(smooth);
filter = new CircularMeanFilter();
}
/**
* Get the radius for the desired smoothing distance.
*
* @return the radius for the desired smoothing distance.
*/
public static double getSigma(double smooth)
{
if (smooth < 0)
return 0;
return smooth;
}
/**
* @param data
* @param width
* @param height
* @return
*/
@Override
public float[] process(float[] data, int width, int height)
{
float[] smoothData = data;
if (radius > 0)
{
// Smoothing destructively modifies the data so create a copy
smoothData = Arrays.copyOf(data, width * height);
if (CircularMeanFilter.getBorder(radius) <= getBorder())
filter.convolveInternal(smoothData, width, height, radius);
else
filter.convolve(smoothData, width, height, radius);
}
return smoothData;
}
/**
* @return the smoothing radius
*/
public double getRadius()
{
return radius;
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#clone()
*/
public CircularMeanDataProcessor clone()
{
CircularMeanDataProcessor f = (CircularMeanDataProcessor) super.clone();
// Ensure the object is duplicated and not passed by reference.
f.filter = filter.clone();
return f;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.filters.DataProcessor#getName()
*/
@Override
public String getName()
{
return "Circular Mean";
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.filters.DataProcessor#getParameters()
*/
@Override
public List<String> getParameters()
{
List<String> list = super.getParameters();
list.add("radius = " + Utils.rounded(radius));
return list;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.filters.DataProcessor#getSpread()
*/
@Override
public double getSpread()
{
return CircularMeanFilter.getPixelRadius(radius) * 2;
}
}