Java tutorial
/* * This file is part of the GeMTC software for MTC model generation and * analysis. GeMTC is distributed from http://drugis.org/gemtc. * Copyright (C) 2009-2012 Gert van Valkenhoef. * * 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/>. */ package org.drugis.mtc.gui.results; import java.awt.Color; import javax.swing.JDialog; import javax.swing.JFrame; import javax.swing.JPanel; import javax.swing.JProgressBar; import javax.swing.JScrollPane; import org.drugis.common.gui.task.TaskProgressBar; import org.drugis.common.threading.SimpleSuspendableTask; import org.drugis.common.threading.ThreadHandler; import org.drugis.mtc.MCMCModel; import org.drugis.mtc.MCMCResults; import org.drugis.mtc.MCMCResultsEvent; import org.drugis.mtc.MCMCResultsListener; import org.drugis.mtc.MCMCSettings; import org.drugis.mtc.Parameter; import org.drugis.mtc.convergence.GelmanRubinConvergence; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; 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.XYLineAndShapeRenderer; import org.jfree.data.xy.XYDataset; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import com.jgoodies.forms.builder.PanelBuilder; import com.jgoodies.forms.layout.CellConstraints; import com.jgoodies.forms.layout.FormLayout; @SuppressWarnings("serial") public class ConvergencePlotsDialog extends JDialog { final static int DATA_SCALE = 200; private final XYSeries d_rHatSeries; private final XYSeries d_vHatSeries; private final XYSeries d_wSeries; private final SimpleSuspendableTask d_task; public ConvergencePlotsDialog(final JFrame main, final MCMCSettings settings, final MCMCModel mcmcModel, final Parameter p) { super(main, p + " convergence diagnostics", false); d_rHatSeries = new XYSeries("R-Hat"); d_vHatSeries = new XYSeries("sqrt(vHat)"); d_wSeries = new XYSeries("sqrt(W)"); d_task = createTask(mcmcModel.getResults(), settings, p); super.add(new JScrollPane(createPanel())); mcmcModel.getResults().addResultsListener(new MCMCResultsListener() { @Override public void resultsEvent(final MCMCResultsEvent event) { fillDataSets(); } }); if (mcmcModel.getResults().getNumberOfSamples() > 0) { fillDataSets(); } } private JPanel createPanel() { final FormLayout layout = new FormLayout("pref:grow:fill", "p, 3dlu, p, 3dlu, p"); final PanelBuilder builder = new PanelBuilder(layout); builder.setDefaultDialogBorder(); final CellConstraints cc = new CellConstraints(); final XYSeriesCollection datasetRhat = new XYSeriesCollection(); final XYSeriesCollection datasetVhatVsW = new XYSeriesCollection(); datasetRhat.addSeries(d_rHatSeries); datasetVhatVsW.addSeries(d_vHatSeries); datasetVhatVsW.addSeries(d_wSeries); final JFreeChart rHatChart = createRhatChart(datasetRhat); final JFreeChart vHatvsWChart = createVhatVsWChart(datasetVhatVsW); final ChartPanel chartPanelRhat = new ChartPanel(rHatChart); final ChartPanel chartPanelVhatVsW = new ChartPanel(vHatvsWChart); chartPanelRhat.setVisible(true); chartPanelVhatVsW.setVisible(true); final JProgressBar bar = new TaskProgressBar(d_task); builder.add(bar, cc.xy(1, 1)); builder.add(chartPanelRhat, cc.xy(1, 3)); builder.add(chartPanelVhatVsW, cc.xy(1, 5)); return builder.getPanel(); } private void fillDataSets() { ThreadHandler.getInstance().scheduleTask(d_task); } private SimpleSuspendableTask createTask(final MCMCResults results, final MCMCSettings settings, final Parameter p) { final Runnable r = new Runnable() { @Override public void run() { final int noResults = results.getNumberOfSamples(); final int resolution = noResults / DATA_SCALE; for (int i = resolution; i <= noResults; i += resolution) { final int iter = i * settings.getThinningInterval(); d_rHatSeries.add(iter, GelmanRubinConvergence.diagnose(results, p, i)); d_vHatSeries.add(iter, GelmanRubinConvergence.calculatePooledVariance(results, p, i)); d_wSeries.add(iter, GelmanRubinConvergence.calculateWithinChainVariance(results, p, i)); } } }; final SimpleSuspendableTask task = new SimpleSuspendableTask(r, "Computing results"); return task; } private JFreeChart createRhatChart(final XYDataset dataset) { final JFreeChart RhatChart = ChartFactory.createXYLineChart("Iterative PSRF Plot", "Iteration No.", "R-Hat(p)", dataset, PlotOrientation.VERTICAL, false, true, false); RhatChart.setBackgroundPaint(Color.white); final XYPlot RhatPlot = RhatChart.getXYPlot(); RhatPlot.setDomainGridlinePaint(Color.white); RhatPlot.setRangeGridlinePaint(Color.white); final NumberAxis rangeAxis = (NumberAxis) RhatPlot.getRangeAxis(); rangeAxis.setAutoRange(true); rangeAxis.setAutoRangeIncludesZero(false); return RhatChart; } private JFreeChart createVhatVsWChart(final XYDataset dataset) { final JFreeChart VhatVsWChart = ChartFactory.createXYLineChart("Plots of sqrt(vHat) and sqrt(W)", "Iteration No.", "Variance Estimates", dataset, PlotOrientation.VERTICAL, true, true, false); VhatVsWChart.setBackgroundPaint(Color.white); final XYPlot VhatVsWPlot = VhatVsWChart.getXYPlot(); VhatVsWPlot.setDomainGridlinePaint(Color.white); VhatVsWPlot.setRangeGridlinePaint(Color.white); final XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(); renderer.setSeriesPaint(0, Color.red); renderer.setSeriesPaint(1, Color.blue); renderer.setSeriesShapesVisible(0, false); renderer.setSeriesShapesVisible(1, false); VhatVsWPlot.setRenderer(renderer); return VhatVsWChart; } }