mt.DisplayHistogram.java Source code

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Here is the source code for mt.DisplayHistogram.java

Source

/*-
 * #%L
 * Microtubule tracker.
 * %%
 * Copyright (C) 2017 MTrack developers.
 * %%
 * 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.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/gpl-3.0.html>.
 * #L%
 */
package mt;

import java.awt.Color;
import java.util.ArrayList;
import java.util.List;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.StandardXYBarPainter;
import org.jfree.chart.renderer.xy.XYBarRenderer;
import org.jfree.data.xy.IntervalXYDataset;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;

import net.imglib2.util.ValuePair;

public class DisplayHistogram {

    protected static double min;
    protected static double max;

    public static List<ValuePair<Double, Integer>> binData(final List<Double> data, final double min,
            final double max, final int numBins) {
        // avoid the one value that is exactly 100%
        final double size = max - min + 0.000001;

        // bin and count the entries
        final int[] bins = new int[numBins];

        for (final double v : data)
            ++bins[(int) Math.floor(((v - min) / size) * numBins)];

        // make the list of bins
        final ArrayList<ValuePair<Double, Integer>> hist = new ArrayList<ValuePair<Double, Integer>>();

        final double binSize = size / numBins;
        for (int bin = 0; bin < numBins; ++bin)
            hist.add(new ValuePair<Double, Integer>(min + binSize / 2 + binSize * bin, bins[bin]));

        return hist;
    }

    public static double getMin() {
        return min;
    }

    public static double getMax() {
        return max;
    }

    public static ValuePair<Double, Double> getMinMax(final List<Double> data) {
        // compute min/max/size
        double min = data.get(0);
        double max = data.get(0);

        for (final double v : data) {
            min = Math.min(min, v);
            max = Math.max(max, v);
        }

        return new ValuePair<Double, Double>(min, max);
    }

    public static IntervalXYDataset createDataset(final List<Double> values, final int numBins,
            final String title) {
        final XYSeries series = new XYSeries(title);

        final ValuePair<Double, Double> minmax = getMinMax(values);
        min = minmax.getA();
        max = minmax.getB();

        final List<ValuePair<Double, Integer>> hist = binData(values, min, max, numBins);

        for (final ValuePair<Double, Integer> pair : hist)
            series.add(pair.getA(), pair.getB());

        final XYSeriesCollection dataset = new XYSeriesCollection(series);
        dataset.setAutoWidth(true);

        return dataset;
    }

    public static JFreeChart makehistXChart(final List<Double> Xdataset, final int numBins) {
        return makehistXChart(Xdataset, "MT Lifetime Distribution", "px", "Count", numBins);
    }

    public static JFreeChart makehistXChart(final List<Double> Xdataset, final String title, final String x,
            final String y, final int numBins) {

        final IntervalXYDataset SigmaXdataset = createDataset(Xdataset, numBins, title);

        final JFreeChart sigmaXchart = createChart(SigmaXdataset, title, x);

        return sigmaXchart;
    }

    protected static JFreeChart createChart(final IntervalXYDataset dataset, final String title,
            final String units) {
        final JFreeChart chart = ChartFactory.createXYBarChart(title, "Lifetime [" + units + "]", false, "Count",
                dataset, PlotOrientation.VERTICAL, false, // legend
                false, false);

        NumberAxis range = (NumberAxis) chart.getXYPlot().getDomainAxis();
        range.setRange(getMin(), getMax());

        XYPlot plot = chart.getXYPlot();
        XYBarRenderer renderer = (XYBarRenderer) plot.getRenderer();

        renderer.setSeriesPaint(0, Color.red);
        renderer.setDrawBarOutline(true);
        renderer.setSeriesOutlinePaint(0, Color.black);
        renderer.setBarPainter(new StandardXYBarPainter());

        return chart;
    }

}