org.rhwlab.ace3d.VolumeIntensityPlot.java Source code

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Here is the source code for org.rhwlab.ace3d.VolumeIntensityPlot.java

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package org.rhwlab.ace3d;

import java.util.Set;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javax.swing.JPanel;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartMouseEvent;
import org.jfree.chart.ChartMouseListener;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.entity.ChartEntity;
import org.jfree.chart.entity.XYItemEntity;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYDotRenderer;
import org.jfree.data.xy.XYDataItem;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;
import org.rhwlab.dispim.ImagedEmbryo;
import org.rhwlab.dispim.nucleus.BHCNucleusData;
import org.rhwlab.dispim.nucleus.Nucleus;
import org.rhwlab.dispim.nucleus.SelectedNucleus;

/**
 *
 * @author gevirl
 */
public class VolumeIntensityPlot extends JPanel implements ChangeListener {
    public VolumeIntensityPlot(ImagedEmbryo emb) {
        this.embryo = emb;
        collect = new XYSeriesCollection();
        series = new XYSeries("Nuclei");
        collect.addSeries(series);
        chart = ChartFactory.createScatterPlot("", "Volume", "AvgIntensity", collect, PlotOrientation.VERTICAL,
                false, true, true);
        XYPlot plot = (XYPlot) chart.getPlot();
        plot.setDomainCrosshairVisible(true);
        plot.setRangeCrosshairVisible(true);
        XYDotRenderer renderer = new XYDotRenderer();
        renderer.setDotHeight(4);
        renderer.setDotWidth(4);
        //        plot.setRenderer(renderer);
        ChartPanel panel = new ChartPanel(chart);
        panel.addChartMouseListener(new ChartMouseListener() {
            @Override
            public void chartMouseClicked(ChartMouseEvent event) {
                ChartEntity entity = event.getEntity();
                if (entity instanceof XYItemEntity) {
                    XYItemEntity xyEntity = (XYItemEntity) entity;
                    NucleusPlotDataItem item = (NucleusPlotDataItem) series.getDataItem(xyEntity.getItem());
                    embryo.setSelectedNucleus(item.nuc);
                }
            }

            @Override
            public void chartMouseMoved(ChartMouseEvent event) {

            }
        });
        this.add(panel);
        embryo.getNucleusFile().addSelectionOberver(this);
    }

    public void setNuclei(Set<Nucleus> nucs) {
        series.clear();
        for (Nucleus nuc : nucs) {
            BHCNucleusData bhcNuc = (BHCNucleusData) nuc.getNucleusData();
            NucleusPlotDataItem item = new NucleusPlotDataItem(bhcNuc.getVolume(), bhcNuc.getAverageIntensity(),
                    nuc);
            series.add(item);
        }
    }

    @Override
    public void changed(ObservableValue observable, Object oldValue, Object newValue) {
        SelectedNucleus selNuc = (SelectedNucleus) observable;
        Nucleus nuc = selNuc.getSelected();
        if (nuc == null) {
            return;
        }
        //       if ((nuc.getTime() != time  && this.isVisible()) || time==-1){
        time = nuc.getTime();
        setNuclei(embryo.getNuclei(time));
        chart.setTitle(String.format("Time: %d , Nuclei: %d", time, series.getItemCount()));
        //        }
    }

    public class NucleusPlotDataItem extends XYDataItem {
        public NucleusPlotDataItem(double x, double y, Nucleus nuc) {
            super(x, y);
            this.nuc = nuc;
        }

        public Nucleus nuc;
    }

    ImagedEmbryo embryo;
    XYSeriesCollection collect;
    JFreeChart chart;
    XYSeries series;
    int time = -1;
}