gdsc.smlm.ij.plugins.ImageBackground.java Source code

Introduction

Here is the source code for gdsc.smlm.ij.plugins.ImageBackground.java

Source

package gdsc.smlm.ij.plugins;

/*----------------------------------------------------------------------------- 
 * 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.ij.utils.Utils;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.plugin.ZProjector;
import ij.plugin.filter.GaussianBlur;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;

import org.apache.commons.math3.util.FastMath;

/**
 * Produces a background intensity image and a mask from a sample image.
 * <p>
 * The input image should be representative of the super-resolution imaging conditions and so will produce suitable
 * input for the Create Data plugin to create realistic images.
 */
public class ImageBackground implements PlugInFilter {
    private final static String TITLE = "Image Background";

    private static float bias = 500;
    private static double sigma = 2;

    private int flags = DOES_16 | DOES_8G | DOES_32 | NO_CHANGES;
    private ImagePlus imp;

    /*
     * (non-Javadoc)
     * 
     * @see ij.plugin.filter.PlugInFilter#setup(java.lang.String, ij.ImagePlus)
     */
    public int setup(String arg, ImagePlus imp) {
        if (imp == null) {
            IJ.noImage();
            return DONE;
        }

        this.imp = imp;

        return showDialog();
    }

    private int showDialog() {
        GenericDialog gd = new GenericDialog(TITLE);
        gd.addHelp(About.HELP_URL);

        gd.addMessage("Creates a background and mask image from a sample input stack\nusing a median projection");

        gd.addNumericField("Bias", bias, 0);
        gd.addSlider("Blur", 0, 20, sigma);

        gd.showDialog();

        if (gd.wasCanceled())
            return DONE;

        bias = (float) gd.getNextNumber();
        sigma = gd.getNextNumber();

        // Check arguments
        try {
            Parameters.isPositive("Bias", bias);
        } catch (IllegalArgumentException e) {
            IJ.error(TITLE, e.getMessage());
            return DONE;
        }

        return flags;
    }

    /*
     * (non-Javadoc)
     * 
     * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
     */
    public void run(ImageProcessor ip) {
        ImageProcessor median = getProjection();
        //Utils.display("Median", median);

        ImageProcessor background = applyBlur(median);
        subtractBias(background);

        Utils.display("Background", background);

        // Q. Is there a better way to do the thresholding for foreground pixels. 
        // Ideally we want to outline cell shapes. 
        ImageProcessor mask = median.convertToByte(true);
        mask.autoThreshold();

        Utils.display("Mask", mask);
    }

    private ImageProcessor getProjection() {
        // Get median intensity projection
        ZProjector p = new ZProjector(imp);
        p.setMethod(ZProjector.MEDIAN_METHOD);
        p.doProjection();
        ImageProcessor median = p.getProjection().getProcessor();
        return median;
    }

    private ImageProcessor applyBlur(ImageProcessor median) {
        ImageProcessor blur = median;
        if (sigma > 0) {
            blur = median.duplicate();
            GaussianBlur gb = new GaussianBlur();
            gb.blurGaussian(blur, sigma, sigma, 0.0002);
        }
        return blur;
    }

    private void subtractBias(ImageProcessor background) {
        float[] data = (float[]) background.getPixels();
        for (int i = 0; i < data.length; i++)
            data[i] = (float) FastMath.max(0f, data[i] - bias);
        background.resetMinAndMax();
    }
}