gdsc.smlm.filters.MedianDataProcessor.java Source code

Introduction

Here is the source code for gdsc.smlm.filters.MedianDataProcessor.java

Source

package gdsc.smlm.filters;

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 median box filter.
 */
public class MedianDataProcessor extends DataProcessor {
    private final int smooth;
    private MedianFilter filter = new MedianFilter();

    /**
     * Constructor
     * 
     * @param border
     *            The border to ignore for maxima
     * @param smooth
     *            The smoothing width to apply to the data
     */
    public MedianDataProcessor(int border, double smooth) {
        super(border);
        this.smooth = convert(smooth);
    }

    /**
     * Convert the smoothing parameter to the value which is used for the MedianFilter.
     * We only use int smoothing. Values below zero are set to zero.
     * 
     * @see MedianFilter
     * 
     * @param smooth
     * @return The adjusted value
     */
    public static int 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);

            // JUnit speed tests show that the rolling median is faster on windows of n<=3
            if (tmpSmooth <= 3) {
                if (tmpSmooth <= getBorder()) {
                    filter.rollingMedianInternal(smoothData, width, height, tmpSmooth);
                } else {
                    filter.rollingMedian(smoothData, width, height, tmpSmooth);
                }
            } else {
                if (tmpSmooth <= getBorder()) {
                    filter.blockMedianInternal(smoothData, width, height, tmpSmooth);
                } else {
                    filter.blockMedian(smoothData, width, height, tmpSmooth);
                }
            }
        }
        return smoothData;
    }

    /**
     * @return the smoothing width
     */
    public int getSmooth() {
        return smooth;
    }

    /*
     * (non-Javadoc)
     * 
     * @see java.lang.Object#clone()
     */
    public Object clone() {
        MedianDataProcessor f = (MedianDataProcessor) super.clone();
        // Ensure the object is duplicated and not passed by reference.
        f.filter = (MedianFilter) filter.clone();
        return f;
    }

    /*
     * (non-Javadoc)
     * 
     * @see gdsc.smlm.filters.DataProcessor#getName()
     */
    @Override
    public String getName() {
        return "Median";
    }

    /*
     * (non-Javadoc)
     * 
     * @see gdsc.smlm.filters.DataProcessor#getParameters()
     */
    @Override
    public List<String> getParameters() {
        List<String> list = super.getParameters();
        list.add("smooth = " + smooth);
        return list;
    }

    /*
     * (non-Javadoc)
     * 
     * @see gdsc.smlm.filters.DataProcessor#getSpread()
     */
    @Override
    public double getSpread() {
        return 2 * smooth + 1;
    }
}