inflor.core.plots.DensityPlot.java Source code

Introduction

Here is the source code for inflor.core.plots.DensityPlot.java

Source

/*
 * ------------------------------------------------------------------------
 *  Copyright 2016 by Aaron Hart
 *  Email: Aaron.Hart@gmail.com
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License, Version 3, as
 *  published by the Free Software Foundation.
 *
 *  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>.
 * ---------------------------------------------------------------------
 *
 * Created on December 14, 2016 by Aaron Hart
 */
package inflor.core.plots;

import java.util.BitSet;
import java.util.Optional;

import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.LookupPaintScale;
import org.jfree.chart.renderer.xy.XYBlockRenderer;
import org.jfree.data.xy.DefaultXYZDataset;
import org.jfree.ui.RectangleAnchor;

import com.google.common.primitives.Doubles;

import inflor.core.data.FCSDimension;
import inflor.core.data.FCSFrame;
import inflor.core.data.Histogram2D;
import inflor.core.transforms.AbstractTransform;
import inflor.core.transforms.TransformSet;
import inflor.core.utils.FCSUtilities;
import inflor.core.utils.PlotUtils;

public class DensityPlot extends AbstractFCChart {

    private ColorSchemes colorScheme = ChartingDefaults.DEFAULT_COLOR_SCHEME;
    private XYPlot plot;
    private Histogram2D histogram;

    public DensityPlot(ChartSpec spec, String priorUUID) {
        super(priorUUID, spec);
        this.spec = spec;
    }

    public DensityPlot(ChartSpec spec) {
        this(spec, null);
    }

    @Override
    public JFreeChart createChart(FCSFrame data, TransformSet transforms) {
        Optional<FCSDimension> domainDimension = FCSUtilities.findCompatibleDimension(data,
                spec.getDomainAxisName());
        Optional<FCSDimension> rangeDimension = FCSUtilities.findCompatibleDimension(data, spec.getRangeAxisName());
        if (domainDimension.isPresent() && rangeDimension.isPresent()) {
            AbstractTransform domainTransform = transforms.get(domainDimension.get().getShortName());
            double[] domainData = domainTransform.transform(domainDimension.get().getData());
            double domainMin = domainTransform.getMinTranformedValue();
            double domainMax = domainTransform.getMaxTransformedValue();

            AbstractTransform rangeTransform = transforms.get(rangeDimension.get().getShortName());
            double[] rangeData = rangeTransform.transform(rangeDimension.get().getData());
            double rangeMin = rangeTransform.getMinTranformedValue();
            double rangeMax = rangeTransform.getMaxTransformedValue();
            histogram = new Histogram2D(domainData, domainMin, domainMax, rangeData, rangeMin, rangeMax);

            DefaultXYZDataset plotData = new DefaultXYZDataset();

            BitSet nonEmptyMask = histogram.getNonEmptyBins();
            double[] x = FCSUtilities.filterColumn(nonEmptyMask, histogram.getXBins());
            double[] y = FCSUtilities.filterColumn(nonEmptyMask, histogram.getYBins());
            double[] z = FCSUtilities.filterColumn(nonEmptyMask, histogram.getZValues());
            plotData.addSeries(data.toString(), new double[][] { x, y, z });

            XYBlockRenderer renderer = updateRenderer(histogram);

            plot = new XYPlot();
            // Create the plot
            plot.setDataset(plotData);
            plot.setDomainAxis(PlotUtils.createAxis(domainDimension.get().getDisplayName(), domainTransform));
            plot.setRangeAxis(PlotUtils.createAxis(rangeDimension.get().getDisplayName(), rangeTransform));
            plot.setRenderer(renderer);
            // Add to panel.
            JFreeChart chart = new JFreeChart(plot);
            chart.removeLegend();
            return chart;
        } else {
            return null;
        }
    }

    private XYBlockRenderer updateRenderer(Histogram2D histogram) {
        BitSet nonEmptyMask = histogram.getNonEmptyBins();
        double[] z = FCSUtilities.filterColumn(nonEmptyMask, histogram.getZValues());
        LookupPaintScale paintScale = PlotUtils.createPaintScale(Doubles.max(z), colorScheme);

        // Renderer configuration
        XYBlockRenderer renderer = new XYBlockRenderer();
        renderer.setBlockWidth(histogram.getXBinWidth());
        renderer.setBlockHeight(histogram.getYBinWidth());
        renderer.setBlockAnchor(RectangleAnchor.BOTTOM_LEFT);
        renderer.setSeriesVisible(0, true);
        renderer.setPaintScale(paintScale);
        return renderer;
    }

    public void updateColorScheme(ColorSchemes newScheme) {
        this.colorScheme = newScheme;
        plot.setRenderer(updateRenderer(histogram));
    }
}