package gdsc.smlm.filters;
import gdsc.core.ij.Utils;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.math3.util.FastMath;
/*-----------------------------------------------------------------------------
* 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 an average box filter.
*/
public class BlockAverageDataProcessor extends DataProcessor
{
private final double smooth;
private AverageFilter filter = new AverageFilter();
/**
* Constructor
*
* @param border
* The border to ignore for maxima
* @param smooth
* The smoothing width to apply to the data
*/
public BlockAverageDataProcessor(int border, double smooth)
{
super(border);
this.smooth = convert(smooth);
}
/**
* Convert the smoothing parameter to the value which is used for the AverageFilter.
* We only use int smoothing. Values below zero are set to zero.
*
* @see AverageFilter
*
* @param smooth
* @return The adjusted value
*/
public static double convert(double smooth)
{
if (smooth < 0)
return 0;
return (int) smooth;
}
/**
* @param data
* @param width
* @param height
* @return
*/
@Override
public float[] process(float[] data, int width, int height)
{
float[] smoothData = data;
if (smooth > 0)
{
// Smoothing destructively modifies the data so create a copy
smoothData = Arrays.copyOf(data, width * height);
// Check upper limits are safe
final int tmpSmooth = FastMath.min((int) smooth, FastMath.min(width, height) / 2);
if (tmpSmooth <= getBorder())
{
filter.rollingBlockAverageInternal(smoothData, width, height, tmpSmooth);
}
else
{
filter.rollingBlockAverage(smoothData, width, height, tmpSmooth);
}
}
return smoothData;
}
/**
* @return the smoothing width
*/
public double getSmooth()
{
return smooth;
}
/*
* (non-Javadoc)
*
* @see java.lang.Object#clone()
*/
public BlockAverageDataProcessor clone()
{
BlockAverageDataProcessor f = (BlockAverageDataProcessor) 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 "Block Average";
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.filters.DataProcessor#getParameters()
*/
@Override
public List<String> getParameters()
{
List<String> list = super.getParameters();
list.add("smooth = " + Utils.rounded(smooth));
return list;
}
/*
* (non-Javadoc)
*
* @see gdsc.smlm.filters.DataProcessor#getSpread()
*/
@Override
public double getSpread()
{
return 2 * smooth + 1;
}
}