Java tutorial
/* The contents of this file are subject to the Mozilla Public License Version 1.1 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.mozilla.org/MPL/ Software distributed under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License. The Original Code is "DefaultPlotter.java". Description: "Default Plotter implementation" The Initial Developer of the Original Code is Bryan Tripp & Centre for Theoretical Neuroscience, University of Waterloo. Copyright (C) 2006-2008. All Rights Reserved. Alternatively, the contents of this file may be used under the terms of the GNU Public License license (the GPL License), in which case the provisions of GPL License are applicable instead of those above. If you wish to allow use of your version of this file only under the terms of the GPL License and not to allow others to use your version of this file under the MPL, indicate your decision by deleting the provisions above and replace them with the notice and other provisions required by the GPL License. If you do not delete the provisions above, a recipient may use your version of this file under either the MPL or the GPL License. */ /* * Created on 15-Jun-2006 */ package ca.nengo.plot.impl; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; import java.util.List; import javax.swing.JFrame; import javax.swing.JPanel; import org.jfree.chart.ChartColor; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.LegendItem; import org.jfree.chart.LegendItemCollection; import org.jfree.chart.axis.AxisLocation; import org.jfree.chart.axis.NumberAxis; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.renderer.xy.XYItemRenderer; import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import org.jfree.util.ShapeUtilities; import ca.nengo.math.Function; import ca.nengo.model.Noise; import ca.nengo.model.Origin; import ca.nengo.model.RealOutput; import ca.nengo.model.SimulationException; import ca.nengo.model.SimulationMode; import ca.nengo.model.StructuralException; import ca.nengo.model.nef.NEFEnsemble; import ca.nengo.model.nef.NEFNode; import ca.nengo.model.nef.impl.DecodedOrigin; import ca.nengo.model.nef.impl.NEFEnsembleImpl; import ca.nengo.model.neuron.Neuron; import ca.nengo.model.neuron.impl.SpikingNeuron; import ca.nengo.plot.Plotter; import ca.nengo.util.MU; import ca.nengo.util.SpikePattern; import ca.nengo.util.TimeSeries; import ca.nengo.util.TimeSeries1D; /** * Default Plotter implementation. * * @author Bryan Tripp */ public class DefaultPlotter extends Plotter { private static Color[] ourColors = { ChartColor.BLACK, ChartColor.LIGHT_GRAY, ChartColor.DARK_BLUE, ChartColor.BLUE, ChartColor.LIGHT_CYAN, ChartColor.LIGHT_GREEN, ChartColor.YELLOW, ChartColor.ORANGE, ChartColor.LIGHT_RED }; /** * @see ca.nengo.plot.Plotter#doPlot(ca.nengo.util.TimeSeries, java.lang.String) */ public void doPlot(TimeSeries series, String title) { XYSeriesCollection dataset = getDataset(series); JFreeChart chart = ChartFactory.createXYLineChart(title, "Time (s)", "", dataset, PlotOrientation.VERTICAL, (series.getDimension() < 10), false, false); showChart(chart, "Time Series Plot"); } /** * @see ca.nengo.plot.Plotter#doPlot(ca.nengo.util.TimeSeries, ca.nengo.util.TimeSeries, java.lang.String) */ public void doPlot(TimeSeries ideal, TimeSeries actual, String title) { XYSeriesCollection idealDataset = getDataset(ideal); XYSeriesCollection actualDataset = getDataset(actual); JFreeChart chart = ChartFactory.createXYLineChart(title, "Time (s)", "", idealDataset, PlotOrientation.VERTICAL, false, false, false); XYPlot plot = (XYPlot) chart.getPlot(); plot.setDataset(1, actualDataset); XYLineAndShapeRenderer idealRenderer = new XYLineAndShapeRenderer(true, false); idealRenderer.setDrawSeriesLineAsPath(true); idealRenderer.setStroke(new BasicStroke(1f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL, 10f, new float[] { 10f, 10f }, 0f)); plot.setRenderer(plot.indexOf(idealDataset), idealRenderer); XYLineAndShapeRenderer actualRenderer = new XYLineAndShapeRenderer(true, false); actualRenderer.setDrawSeriesLineAsPath(true); //idealRenderer.setStroke(new BasicStroke(1f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL, 10f, new float[]{10f, 10f}, 0f)); plot.setRenderer(plot.indexOf(actualDataset), actualRenderer); showChart(chart, "Time Series Plot"); } /** * @see ca.nengo.plot.Plotter#doPlot(java.util.List, java.util.List, java.lang.String) */ public void doPlot(List<TimeSeries> series, List<SpikePattern> patterns, String title) { JFreeChart chart = ChartFactory.createXYLineChart(title, "Time (s)", "", null, PlotOrientation.VERTICAL, true, false, false); XYPlot plot = (XYPlot) chart.getPlot(); //we will change the legend to show one item per series/pattern (rather than dimension/neuron) LegendItemCollection revisedItems = new LegendItemCollection(); int legendItemIndex = 0; int i = 0; for (; series != null && i < series.size(); i++) { plot.setDataset(i, getDataset(series.get(i))); XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(true, false); renderer.setDrawSeriesLineAsPath(true); renderer.setPaint(getColor(i)); plot.setRenderer(i, renderer); String seriesName = series.get(i).getName(); if (seriesName == null) seriesName = "Time Series " + i; revisedItems.add(getCopy(plot.getLegendItems().get(legendItemIndex), seriesName)); legendItemIndex += series.get(i).getDimension(); } for (int j = 0; patterns != null && j < patterns.size(); j++) { int index = i + j; plot.setDataset(index, getDataset(patterns.get(j))); XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(true, false); configSpikeRenderer(renderer); renderer.setPaint(getColor(j)); plot.setRenderer(index, renderer); revisedItems.add(getCopy(plot.getLegendItems().get(legendItemIndex), "Spike Pattern " + j)); legendItemIndex += patterns.get(j).getNumNeurons(); } plot.setFixedLegendItems(revisedItems); showChart(chart, title); } private static LegendItem getCopy(LegendItem original, String newLabel) { return new LegendItem(newLabel, null, //description null, //tooltip text null, //URL original.isShapeVisible(), original.getShape(), original.isShapeFilled(), original.getFillPaint(), original.isShapeOutlineVisible(), original.getOutlinePaint(), original.getOutlineStroke(), original.isLineVisible(), original.getLine(), original.getLineStroke(), original.getLinePaint()); } private XYSeriesCollection getDataset(TimeSeries series) { XYSeriesCollection dataset = new XYSeriesCollection(); float[] times = series.getTimes(); if (times.length > 0) { if (series instanceof TimeSeries1D) { XYSeries xy = new XYSeries(series.getLabels()[0]); float[] values = ((TimeSeries1D) series).getValues1D(); for (int i = 0; i < values.length; i++) { xy.add(times[i], values[i]); } dataset.addSeries(xy); } else { float[][] values = series.getValues(); for (int j = 0; j < values[0].length; j++) { XYSeries xy = new XYSeries(series.getLabels()[j]); for (int i = 0; i < values.length; i++) { xy.add(times[i], values[i][j]); } dataset.addSeries(xy); } } } return dataset; } /** * @see ca.nengo.plot.Plotter#doPlot(ca.nengo.model.nef.NEFEnsemble, java.lang.String) */ public void doPlot(NEFEnsemble ensemble, String name) { try { Origin o = ensemble.getOrigin(name); if (!(o instanceof DecodedOrigin)) { throw new RuntimeException("Can't plot origin error: Origin must be a DecodedOrigin"); } DecodedOrigin origin = (DecodedOrigin) o; if (ensemble.getDimension() > 1) { doPlotMSE(ensemble, origin, name); return; } // float[][] encoders = ensemble.getEncoders(); float[] x = new float[101]; float[][] idealOutput = new float[x.length][]; float[][] actualOutput = new float[x.length][]; NEFNode[] nodes = (NEFNode[]) ensemble.getNodes(); SimulationMode mode = ensemble.getMode(); float radius = ensemble.getRadii()[0]; for (int i = 0; i < x.length; i++) { x[i] = -radius + (float) i * (2f * radius / (float) (x.length - 1)); ensemble.setMode(SimulationMode.CONSTANT_RATE); for (int j = 0; j < nodes.length; j++) { // ((NEFNode) nodes[j]).setRadialInput(x[i]*encoders[j][0]); ((NEFNode) nodes[j]).setRadialInput(getRadialInput(ensemble, j, x[i])); nodes[j].run(0f, 0f); } origin.run(null, 0f, 1f); actualOutput[i] = ((RealOutput) origin.getValues()).getValues(); ensemble.setMode(SimulationMode.DIRECT); float[] state = new float[ensemble.getDimension()]; state[0] = x[i]; origin.run(state, 0f, 1f); idealOutput[i] = ((RealOutput) origin.getValues()).getValues(); } ensemble.setMode(mode); //one plot per output dimension ... for (int i = 0; i < idealOutput[0].length; i++) { doPlot(x, idealOutput, actualOutput, i); } } catch (StructuralException e) { throw new RuntimeException("Can't plot origin error", e); } catch (SimulationException e) { e.printStackTrace(); throw new RuntimeException("Can't plot origin error", e); } } //plots MSE for each dimension of an Origin public void doPlotMSE(NEFEnsemble ensemble, DecodedOrigin origin, String name) { float[] error = new float[origin.getDimensions()]; float mseAvg; //MSE for all of the dimensions of the origin together JPanel panel = new JPanel(); JFrame frame = createFrame(); frame.setVisible(true); long time = System.currentTimeMillis() - 21; //plot MSE on continuously updating graph as more samples are used in the calculation for (int i = 1; i == 1 || frame.isVisible(); i++) { //will crash if runtime exceeds 4.1 years //synchronized(ensemble){ error = MU.sum(MU.prod(error, ((i - 1f) / i)), MU.prod(origin.getError(1), 1f / i)); //} mseAvg = MU.mean(error); if ((System.currentTimeMillis() - time) > 20l) { //frame limiter panel = getBarChart(error, "MSE per Dimension for Origin: " + origin.getName()); frame.getContentPane().removeAll(); frame.getContentPane().add(panel, BorderLayout.CENTER); frame.setTitle("Origin MSE Plot (Overall MSE=" + mseAvg + ")"); frame.validate(); time = System.currentTimeMillis(); } if (i == 1) { frame.pack(); frame.setVisible(true); } } } private static float getRadialInput(NEFEnsemble ensemble, int node, float radius) { //plot along preferred direction for multi-dimensional ensembles float radialInput = radius; //plot along positive axis for one-dimensional ensembles if (ensemble.getDimension() == 1) { if (ensemble instanceof NEFEnsembleImpl) { radialInput = ((NEFEnsembleImpl) ensemble).getRadialInput(new float[] { radius }, node); } else { radialInput = radius * ensemble.getEncoders()[node][0]; } } else if (ensemble instanceof NEFEnsembleImpl) { float[] state = new float[ensemble.getDimension()]; state[0] = radius; radialInput = ((NEFEnsembleImpl) ensemble).getRadialInput(state, node); } return radialInput; } //used by origin plot private void doPlot(float[] x, float[][] ideal, float[][] actual, int dim) { XYSeriesCollection dataset = new XYSeriesCollection(); XYSeries idealSeries = new XYSeries("Ideal"); for (int i = 0; i < x.length; i++) { idealSeries.add(x[i], ideal[i][dim]); } dataset.addSeries(idealSeries); XYSeries actualSeries = new XYSeries("Actual"); for (int i = 0; i < x.length; i++) { actualSeries.add(x[i], actual[i][dim]); } dataset.addSeries(actualSeries); JFreeChart chart = ChartFactory.createXYLineChart("Distortion", "X", "Estimate", dataset, PlotOrientation.VERTICAL, true, false, false); XYSeries errorSeries = new XYSeries("Error"); float[][] error = MU.difference(actual, ideal); for (int i = 0; i < x.length; i++) { // errorSeries.add(x[i], actual[i][dim] - ideal[i][dim]); errorSeries.add(x[i], error[i][dim]); } XYSeriesCollection errorDataset = new XYSeriesCollection(); errorDataset.addSeries(errorSeries); NumberAxis errorAxis = new NumberAxis("Error"); XYPlot plot = (XYPlot) chart.getPlot(); plot.setRangeAxis(1, errorAxis); plot.setRangeAxisLocation(AxisLocation.TOP_OR_RIGHT); plot.setDataset(1, errorDataset); plot.mapDatasetToRangeAxis(1, 1); XYItemRenderer renderer = new XYLineAndShapeRenderer(true, false); plot.setRenderer(1, renderer); float[] err = MU.transpose(error)[dim]; float mse = MU.prod(err, err) / (float) err.length; showChart(chart, "Distortion Error Plot (MSE=" + mse + ")"); } /** * @see ca.nengo.plot.Plotter#doPlot(ca.nengo.model.nef.NEFEnsemble) */ public void doPlot(NEFEnsemble ensemble) { XYSeriesCollection dataset = new XYSeriesCollection(); synchronized (ensemble) { float[][] encoders = ensemble.getEncoders(); NEFNode[] nodes = (NEFNode[]) ensemble.getNodes(); float[] x = new float[101]; for (int i = 0; i < x.length; i++) { x[i] = -1f + (float) i * (2f / (float) (x.length - 1)); } SimulationMode mode = ensemble.getMode(); ensemble.setMode(SimulationMode.CONSTANT_RATE); float[][] rates = new float[nodes.length][]; for (int i = 0; i < nodes.length; i++) { //radius of encoded space in direction of this encoder float radius = MU.pnorm(MU.prodElementwise(encoders[i], ensemble.getRadii()), 2); XYSeries series = new XYSeries("Neuron " + i); rates[i] = new float[x.length]; for (int j = 0; j < x.length; j++) { float radialInput = (ensemble.getDimension() == 1) ? x[j] * encoders[i][0] : x[j]; // float radialInput = getRadialInput(ensemble, i, x[j]); ((NEFNode) nodes[i]).setRadialInput(radialInput); try { Noise noise = null; if (nodes[i] instanceof SpikingNeuron) { noise = ((SpikingNeuron) nodes[i]).getNoise(); ((SpikingNeuron) nodes[i]).setNoise(null); } nodes[i].run(0f, 0f); RealOutput output = (RealOutput) nodes[i].getOrigin(Neuron.AXON).getValues(); series.add(x[j] * radius, output.getValues()[0]); rates[i][j] = output.getValues()[0]; nodes[i].reset(false); if (noise != null) { ((SpikingNeuron) nodes[i]).setNoise(noise); } } catch (SimulationException e) { throw new RuntimeException("Can't plot activities: error running neurons", e); } catch (ClassCastException e) { throw new RuntimeException("Can't plot activities: neurons producing spike output", e); } catch (StructuralException e) { throw new RuntimeException("Can't plot activities: error running neurons", e); } } dataset.addSeries(series); } // MatlabExporter exporter = new MatlabExporter(); // exporter.add("x", new float[][]{x}); // exporter.add("rates", rates); // try { // exporter.write(new File("activities.mat")); // } catch (IOException e) { // e.printStackTrace(); // } ensemble.setMode(mode); } JFreeChart chart = ChartFactory.createXYLineChart("Activities", "X", "Firing Rate (spikes/s)", dataset, PlotOrientation.VERTICAL, false, false, false); showChart(chart, "Activities Plot"); } /** * @see ca.nengo.plot.Plotter#doPlot(ca.nengo.util.SpikePattern) */ public void doPlot(SpikePattern pattern) { XYSeriesCollection dataset = getDataset(pattern); JFreeChart chart = ChartFactory.createScatterPlot("Spike Raster", "Time (s)", "Neuron #", dataset, PlotOrientation.VERTICAL, false, false, false); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) chart.getXYPlot().getRenderer(); configSpikeRenderer(renderer); showChart(chart, "Spike Raster"); } private static XYSeriesCollection getDataset(SpikePattern pattern) { XYSeriesCollection dataset = new XYSeriesCollection(); for (int i = 0; i < pattern.getNumNeurons(); i++) { XYSeries series = new XYSeries("Neuron " + i); float[] spikes = pattern.getSpikeTimes(i); for (int j = 0; j < spikes.length; j++) { series.add(spikes[j], i); } dataset.addSeries(series); } return dataset; } private static void configSpikeRenderer(XYLineAndShapeRenderer renderer) { renderer.setShape(ShapeUtilities.createDiamond(1f)); renderer.setShapesVisible(true); renderer.setShapesFilled(true); renderer.setLinesVisible(false); renderer.setPaint(Color.BLACK); } /** * @see ca.nengo.plot.Plotter#doPlot(ca.nengo.math.Function, float, float, float, String) */ public void doPlot(Function function, float start, float increment, float end, String title) { if (function.getDimension() > 2) { throw new IllegalArgumentException("Only 1-D and 2-D functions can be plotted with this method"); } XYSeriesCollection dataset = new XYSeriesCollection(); if (function.getDimension() == 1) { XYSeries series = new XYSeries("Function"); float x = start; while (x <= end) { float y = function.map(new float[] { x }); series.add(x, y); x += increment; } dataset.addSeries(series); } else if (function.getDimension() == 2) { float increment2 = increment * 10f; float x2 = start; while (x2 <= end) { XYSeries series = new XYSeries("" + x2); float x = start; while (x <= end) { float y = function.map(new float[] { x, x2 }); series.add(x, y); x += increment; } dataset.addSeries(series); x2 += increment2; } } JFreeChart chart = ChartFactory.createXYLineChart("Function", "Input", "Output", dataset, PlotOrientation.VERTICAL, false, false, false); showChart(chart, title); } /** * @see ca.nengo.plot.Plotter#doPlot(float[], String) */ public void doPlot(float[] vector, String title) { XYSeriesCollection dataset = new XYSeriesCollection(); XYSeries series = new XYSeries("Vector"); for (int i = 0; i < vector.length; i++) { series.add(i, vector[i]); } dataset.addSeries(series); JFreeChart chart = ChartFactory.createXYLineChart("Vector", "Index", "Value", dataset, PlotOrientation.VERTICAL, false, false, false); showChart(chart, title); } //creates a bar chart for origin MSE plots public ChartPanel getBarChart(float[] vector, String title) { XYSeriesCollection dataset = new XYSeriesCollection(); XYSeries series = new XYSeries("MSE Error Plot"); for (int i = 0; i < vector.length; i++) { series.add(i, vector[i]); } dataset.addSeries(series); JFreeChart chart = ChartFactory.createXYBarChart(title, "Origin Dimension", false, "Error", dataset, PlotOrientation.VERTICAL, false, false, false); chart.getXYPlot().getDomainAxis() .setStandardTickUnits(org.jfree.chart.axis.NumberAxis.createIntegerTickUnits()); return new ChartPanel(chart); } /** * @see ca.nengo.plot.Plotter#doPlot(float[], float[], java.lang.String) */ public void doPlot(float[] domain, float[] vector, String title) { if (domain.length < vector.length) { throw new IllegalArgumentException( "Not enough domain points (" + domain.length + "given; " + vector.length + "needed)"); } XYSeriesCollection dataset = new XYSeriesCollection(); XYSeries series = new XYSeries("Vector"); for (int i = 0; i < vector.length; i++) { series.add(domain[i], vector[i]); } dataset.addSeries(series); JFreeChart chart = ChartFactory.createXYLineChart("Vector", "Index", "Value", dataset, PlotOrientation.VERTICAL, false, false, false); showChart(chart, title); } /** * Accepts a matrix as the second argument, and plots each row of the matrix * separately as in doPlot(float[], float[], java.lang.String). */ public void doPlot(float[] domain, float[][] matrix, String title) { XYSeriesCollection dataset = new XYSeriesCollection(); for (int row = 0; row < matrix.length; row++) { if (domain.length < matrix[row].length) { throw new IllegalArgumentException( "Not enough domain points (" + domain.length + "given; " + matrix[row].length + "needed)"); } XYSeries series = new XYSeries("Vector" + row); for (int i = 0; i < matrix[row].length; i++) { series.add(domain[i], matrix[row][i]); } dataset.addSeries(series); } JFreeChart chart = ChartFactory.createXYLineChart("Matrix", "Index", "Value", dataset, PlotOrientation.VERTICAL, false, false, false); showChart(chart, title); } //shows a chart in a new window protected void showChart(JFreeChart chart, String title) { JPanel panel = new ChartPanel(chart); showPlot(panel, title); } /** * @param index Index of a chart dataset (eg 0 to 2 if there are 3 datasets in a chart) * @return A Color to use for rendering that dataset */ private static Color getColor(int index) { return ourColors[index % ourColors.length]; } }