List of usage examples for org.jfree.data.xy XYSeriesCollection addSeries
public void addSeries(XYSeries series)
From source file:org.jfree.chart.demo.SparklineDemo1.java
public static void main(String args[]) { XYSeries xyseries = new XYSeries("Series 1"); xyseries.add(1.0D, 1.0D);/*from ww w .j a va2s . c o m*/ xyseries.add(2D, 3D); xyseries.add(3D, 2D); xyseries.add(4D, 4D); XYSeriesCollection xyseriescollection = new XYSeriesCollection(); xyseriescollection.addSeries(xyseries); JFreeChart jfreechart = ChartFactory.createXYLineChart(null, "X", "Y", xyseriescollection, PlotOrientation.VERTICAL, false, false, false); XYPlot xyplot = (XYPlot) jfreechart.getPlot(); xyplot.setInsets(RectangleInsets.ZERO_INSETS); xyplot.setDomainGridlinesVisible(false); xyplot.setRangeGridlinesVisible(false); xyplot.setOutlinePaint(null); xyplot.getDomainAxis().setVisible(false); xyplot.getRangeAxis().setVisible(false); try { ChartUtilities.saveChartAsPNG(new File("Sparky.png"), jfreechart, 100, 20); } catch (IOException ioexception) { ioexception.printStackTrace(); } }
From source file:org.jfree.chart.demo.SecondDemo.java
public static void main(String args[]) { XYSeries xyseries = new XYSeries("Advisory Range"); xyseries.add(new Integer(1200), new Integer(1)); xyseries.add(new Integer(1500), new Integer(1)); XYSeries xyseries1 = new XYSeries("Normal Range"); xyseries1.add(new Integer(2000), new Integer(4)); xyseries1.add(new Integer(2300), new Integer(4)); XYSeries xyseries2 = new XYSeries("Recommended"); xyseries2.add(new Integer(2100), new Integer(2)); XYSeries xyseries3 = new XYSeries("Current"); xyseries3.add(new Integer(2400), new Integer(3)); XYSeriesCollection xyseriescollection = new XYSeriesCollection(); xyseriescollection.addSeries(xyseries); xyseriescollection.addSeries(xyseries1); xyseriescollection.addSeries(xyseries2); xyseriescollection.addSeries(xyseries3); JFreeChart jfreechart = ChartFactory.createXYLineChart("My Chart", "Calories", "Y", xyseriescollection, PlotOrientation.VERTICAL, true, true, false); StandardXYItemRenderer standardxyitemrenderer = new StandardXYItemRenderer(3, null); XYPlot xyplot = (XYPlot) jfreechart.getPlot(); xyplot.setRenderer(standardxyitemrenderer); ValueAxis valueaxis = xyplot.getRangeAxis(); valueaxis.setTickLabelsVisible(false); valueaxis.setRange(0.0D, 5D);/*from w w w .ja v a 2s . c o m*/ ChartFrame chartframe = new ChartFrame("Test", jfreechart); chartframe.pack(); chartframe.setVisible(true); }
From source file:Trabalho_1.java
/** * @param args the command line arguments *///from w ww. j ava 2s . c om public static void main(String[] args) { // TODO code application logic here Ambiente n = new Ambiente(51, 51); n.inicializa(100, 30); XYSeries series = new XYSeries("Lobos"); XYSeries series1 = new XYSeries("Ovelhas"); XYSeries series2 = new XYSeries("Vegetacao"); for (int i = 0; i < 5000; i++) { n.iteracao(i); series.add(i, n.getLobos()); series1.add(i, n.getOvelhas()); series2.add(i, n.getVegetacao()); } // Add the series to your data set XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(series); dataset.addSeries(series1); dataset.addSeries(series2); XYSeriesCollection dataset2 = new XYSeriesCollection(); dataset2.addSeries(series); dataset2.addSeries(series1); // Generate the graph JFreeChart chart = ChartFactory.createXYLineChart("Lobos, Ovelhas e Vegetacao", "Iteracoes", "Numero de Animais", dataset, PlotOrientation.VERTICAL, // Plot Orientation true, // Show Legend true, // Use tooltips false // Configure chart to generate URLs? ); try { ChartUtilities.saveChartAsJPEG(new File("Grafico.jpg"), chart, 640, 480); } catch (IOException e) { System.err.println("Problem occurred creating chart."); } // Generate the graph JFreeChart chart2 = ChartFactory.createXYLineChart("Lobos e ovelhas", "Iteracoes", "Numero de Animais", dataset2, PlotOrientation.VERTICAL, // Plot Orientation true, // Show Legend true, // Use tooltips false // Configure chart to generate URLs? ); try { ChartUtilities.saveChartAsJPEG(new File("Grafico2.jpg"), chart2, 640, 480); } catch (IOException e) { System.err.println("Problem occurred creating chart."); } }
From source file:org.jfree.chart.demo.Second.java
/** * Starting point for the demo./*from w w w. j ava2s . c om*/ * * @param args ignored. */ public static void main(final String[] args) { // create some data... final XYSeries series1 = new XYSeries("Advisory Range"); series1.add(new Integer(1200), new Integer(1)); series1.add(new Integer(1500), new Integer(1)); final XYSeries series2 = new XYSeries("Normal Range"); series2.add(new Integer(2000), new Integer(4)); series2.add(new Integer(2300), new Integer(4)); final XYSeries series3 = new XYSeries("Recommended"); series3.add(new Integer(2100), new Integer(2)); final XYSeries series4 = new XYSeries("Current"); series4.add(new Integer(2400), new Integer(3)); final XYSeriesCollection data = new XYSeriesCollection(); data.addSeries(series1); data.addSeries(series2); data.addSeries(series3); data.addSeries(series4); // create a chart... final JFreeChart chart = ChartFactory.createXYLineChart("My Chart", "Calories", "Y", data, PlotOrientation.VERTICAL, true, true, false); // **************************************************************************** // * JFREECHART DEVELOPER GUIDE * // * The JFreeChart Developer Guide, written by David Gilbert, is available * // * to purchase from Object Refinery Limited: * // * * // * http://www.object-refinery.com/jfreechart/guide.html * // * * // * Sales are used to provide funding for the JFreeChart project - please * // * support us so that we can continue developing free software. * // **************************************************************************** final XYItemRenderer renderer = new StandardXYItemRenderer(StandardXYItemRenderer.SHAPES_AND_LINES, null); final XYPlot plot = (XYPlot) chart.getPlot(); plot.setRenderer(renderer); final ValueAxis axis = plot.getRangeAxis(); axis.setTickLabelsVisible(false); axis.setRange(0.0, 5.0); // create and display a frame... final ChartFrame frame = new ChartFrame("Test", chart); frame.pack(); frame.setVisible(true); }
From source file:pl.dpbz.poid.zadanie3.Main.java
public static void main(String args[]) throws UnsupportedAudioFileException, IOException { //Zassanie pliku File f = new File("ExampleSounds/artificial/easy/100Hz.wav"); Integer[] ints = WaveToSamplesConverter.convertWaveToIntSamples(f); double samplingFrequency = WaveToSamplesConverter.getSamplingFrequency(f); //Zwyky sound, ktry nie potrzebuje zespolonych elementw Sound s = new Sound(ints, samplingFrequency); //Obliczenie czstotliwoci przy pomocy fazwki PhaseSpaceMultiDimensional pS = new PhaseSpaceMultiDimensional(s); pS.setupPhaseSpace();//from w w w . j a v a2 s. co m pS.computeFrequency(); System.out.println("Phase space " + pS.getFrequency()); //Zespolony dwik, ktry jest bardziej zoony ComplexSound cs = new ComplexSound(ints, samplingFrequency, 15); //To oblicza fouriera cs.setupElementsOfComplexSound(); //Tutaj obliczanie czstotliwoci przy pomocy fouriera CombFiltering cf = new CombFiltering(cs, samplingFrequency); cf.computeFrequency(); cf.drawComplexSound(); System.out.println("Comb Filtering " + cf.getFrequency()); //Przy sekwencjach nie ma majstrowania przy ustawieniach, uytkownik // zmiennie moe podawa tylko liczb prbek, reszt jak czstotliwo prbkowania // i audio format pobiera si z otwieranego pliku //Test sekwencji na fazie File file = new File("ExampleSounds/seq/DWK_violin.wav"); Integer[] seqInte = WaveToSamplesConverter.convertWaveToIntSamples(file); System.out.println("Samples overview " + seqInte.length); double seqSamplingFrequency = WaveToSamplesConverter.getSamplingFrequency(file); int samplesPerPart = 3000; SamplesToWaveConverter conv = new PhaseSpaceSampleConverter(seqSamplingFrequency, samplesPerPart, WaveToSamplesConverter.getAudioFormat(file)); conv.setupFrequenciesFromSamples(seqInte); System.out.println("Zapisuj"); conv.saveGeneratedSamples("XDPhase.wav"); //Test sekwencji na grzebieniu SamplesToWaveConverter conv2 = new CombFilteringSampleConverter(seqSamplingFrequency, samplesPerPart, WaveToSamplesConverter.getAudioFormat(file)); conv2.setupFrequenciesFromSamples(seqInte); System.out.println("Zapisuj"); conv2.saveGeneratedSamples("XDComb.wav"); //Rysowanie wykresu sygnau dwikowego final XYSeries dist = new XYSeries("P0"); int index = 0; for (Integer i : ints) { dist.add(index / samplingFrequency, i); index++; } final XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(dist); JFreeChart chart = ChartFactory.createXYLineChart(f.getName(), "index", "Distance", dataset, PlotOrientation.VERTICAL, true, true, false); XYPlot xyPlot = (XYPlot) chart.getPlot(); xyPlot.setDomainCrosshairVisible(true); xyPlot.setRangeCrosshairVisible(true); XYItemRenderer renderer = xyPlot.getRenderer(); renderer.setSeriesPaint(0, Color.blue); NumberAxis domain = (NumberAxis) xyPlot.getRangeAxis(); domain.setRange(-32768, 32768); ChartDrawer.drawChart(chart); System.out.println("FINISHED"); }
From source file:interpolation.Polyfit.java
public static void main(String[] args) { final ArrayList<Pair<Integer, Double>> mts = loadsimple( new File("/Users/varunkapoor/Documents/Ines_Fourier/Cell39.txt")); final ArrayList<Pair<Integer, Double>> mtspoly = new ArrayList<Pair<Integer, Double>>(); double[] x = new double[mts.size()]; double[] y = new double[mts.size()]; int i = 0;// w w w . j a v a2 s . com for (Pair<Integer, Double> point : mts) { x[i] = point.getA(); y[i] = point.getB(); i++; } int degree = 20; Polyfit regression = new Polyfit(x, y, degree); for (double t = x[0]; t <= x[x.length - 1]; ++t) { double poly = regression.predict(t); mtspoly.add(new ValuePair<Integer, Double>((int) t, poly)); } XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(Tracking.drawPoints(mtspoly, new double[] { 1, 1, 1 }, "Function fit")); dataset.addSeries(Tracking.drawPoints(mts, new double[] { 1, 1, 1 }, "Original Data")); JFreeChart chart = Tracking.makeChart(dataset); Tracking.display(chart, new Dimension(500, 400)); Tracking.setColor(chart, i, new Color(255, 0, 0)); Tracking.setStroke(chart, i, 0.5f); for (int j = degree; j >= 0; --j) System.out.println(regression.GetCoefficients(j) + " *x power " + j); }
From source file:visualize.Visualize.java
public static void main(String[] args) throws NotEnoughDataPointsException, IllDefinedDataPointsException { XYSeries seriesQ = new XYSeries("quadratic"); XYSeries seriesL = new XYSeries("linear"); XYSeries seriesI = new XYSeries("intepolated"); final ArrayList<Point> pointsQ = new ArrayList<Point>(); for (double x = -5.0; x <= 5.0; x = x + 0.5) pointsQ.add(new Point(new double[] { x, 2.0 * x * x * x - 10 * x * x })); final LinearFunction fl = new LinearFunction(); final HigherOrderPolynomialFunction fq = new HigherOrderPolynomialFunction(3); final InterpolatedPolynomial<LinearFunction, HigherOrderPolynomialFunction> fi = new InterpolatedPolynomial<LinearFunction, HigherOrderPolynomialFunction>( new LinearFunction(), fq.copy(), 0.5); fl.fitFunction(pointsQ);// w w w . j a va 2 s. co m fq.fitFunction(pointsQ); fi.fitFunction(pointsQ); System.out.println(fl); System.out.println(fq); System.out.println(fi.interpolatedFunction); for (double x = -5.0; x <= 5.0; x = x + 0.5) { seriesQ.add(x, fq.predict(x)); seriesL.add(x, fl.predict(x)); seriesI.add(x, fi.predict(x)); } XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(seriesQ); dataset.addSeries(seriesL); dataset.addSeries(seriesI); JFreeChart chart = ChartFactory.createXYLineChart("XY Chart", "x-axis", "y-axis", dataset, PlotOrientation.VERTICAL, true, true, false); final XYPlot plot = chart.getXYPlot(); final XYItemRenderer renderer = plot.getRenderer(); renderer.setSeriesPaint(0, new Color(0, 0, 255)); renderer.setSeriesStroke(0, new BasicStroke(0.5f)); renderer.setSeriesPaint(1, new Color(255, 0, 0)); renderer.setSeriesStroke(1, new BasicStroke(0.5f)); renderer.setSeriesPaint(2, new Color(0, 200, 40)); renderer.setSeriesStroke(2, new BasicStroke(1.5f)); //chart.getXYPlot().setRenderer(new XYSplineRenderer(100)); JPanel panel = new JPanel(); ChartPanel chartPanel = new ChartPanel(chart); panel.add(chartPanel); JFrame frame = new JFrame(); frame.setContentPane(panel); frame.validate(); Dimension d = new Dimension(800, 500); frame.setSize(d); frame.setVisible(true); try { Thread.sleep(3000); } catch (InterruptedException e) { e.printStackTrace(); } System.out.println("starting"); for (int lambda = 0; lambda <= 100; ++lambda) { fi.setLambda(lambda / 100.0); fi.fitFunction(pointsQ); System.out.println(fi.interpolatedFunction); dataset.getSeries(2).clear(); for (double x = -5.0; x <= 5.0; x = x + 0.5) seriesI.add(x, fi.predict(x)); try { Thread.sleep(100); } catch (InterruptedException e) { e.printStackTrace(); } // makeScreenshot( lambda ); } }
From source file:Graph_with_jframe_and_arduino.java
public static void main(String[] args) { // create and configure the window JFrame window = new JFrame(); window.setTitle("Sensor Graph GUI"); window.setSize(600, 400);// w w w . j av a 2 s . co m window.setLayout(new BorderLayout()); window.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); // create a drop-down box and connect button, then place them at the top of the window JComboBox<String> portList_combobox = new JComboBox<String>(); Dimension d = new Dimension(300, 100); portList_combobox.setSize(d); JButton connectButton = new JButton("Connect"); JPanel topPanel = new JPanel(); topPanel.add(portList_combobox); topPanel.add(connectButton); window.add(topPanel, BorderLayout.NORTH); //pause button JButton Pause_btn = new JButton("Start"); // populate the drop-down box SerialPort[] portNames; portNames = SerialPort.getCommPorts(); //check for new port available Thread thread_port = new Thread() { @Override public void run() { while (true) { SerialPort[] sp = SerialPort.getCommPorts(); if (sp.length > 0) { for (SerialPort sp_name : sp) { int l = portList_combobox.getItemCount(), i; for (i = 0; i < l; i++) { //check port name already exist or not if (sp_name.getSystemPortName().equalsIgnoreCase(portList_combobox.getItemAt(i))) { break; } } if (i == l) { portList_combobox.addItem(sp_name.getSystemPortName()); } } } else { portList_combobox.removeAllItems(); } portList_combobox.repaint(); } } }; thread_port.start(); for (SerialPort sp_name : portNames) portList_combobox.addItem(sp_name.getSystemPortName()); //for(int i = 0; i < portNames.length; i++) // portList.addItem(portNames[i].getSystemPortName()); // create the line graph XYSeries series = new XYSeries("line 1"); XYSeries series2 = new XYSeries("line 2"); XYSeries series3 = new XYSeries("line 3"); XYSeries series4 = new XYSeries("line 4"); for (int i = 0; i < 100; i++) { series.add(x, 0); series2.add(x, 0); series3.add(x, 0); series4.add(x, 10); x++; } XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(series); dataset.addSeries(series2); XYSeriesCollection dataset2 = new XYSeriesCollection(); dataset2.addSeries(series3); dataset2.addSeries(series4); //create jfree chart JFreeChart chart = ChartFactory.createXYLineChart("Sensor Readings", "Time (seconds)", "Arduino Reading", dataset); JFreeChart chart2 = ChartFactory.createXYLineChart("Sensor Readings", "Time (seconds)", "Arduino Reading 2", dataset2); //color render for chart 1 XYLineAndShapeRenderer r1 = new XYLineAndShapeRenderer(); r1.setSeriesPaint(0, Color.RED); r1.setSeriesPaint(1, Color.GREEN); r1.setSeriesShapesVisible(0, false); r1.setSeriesShapesVisible(1, false); XYPlot plot = chart.getXYPlot(); plot.setRenderer(0, r1); plot.setRenderer(1, r1); plot.setBackgroundPaint(Color.WHITE); plot.setDomainGridlinePaint(Color.DARK_GRAY); plot.setRangeGridlinePaint(Color.blue); //color render for chart 2 XYLineAndShapeRenderer r2 = new XYLineAndShapeRenderer(); r2.setSeriesPaint(0, Color.BLUE); r2.setSeriesPaint(1, Color.ORANGE); r2.setSeriesShapesVisible(0, false); r2.setSeriesShapesVisible(1, false); XYPlot plot2 = chart2.getXYPlot(); plot2.setRenderer(0, r2); plot2.setRenderer(1, r2); ChartPanel cp = new ChartPanel(chart); ChartPanel cp2 = new ChartPanel(chart2); //multiple graph container JPanel graph_container = new JPanel(); graph_container.setLayout(new BoxLayout(graph_container, BoxLayout.X_AXIS)); graph_container.add(cp); graph_container.add(cp2); //add chart panel in main window window.add(graph_container, BorderLayout.CENTER); //window.add(cp2, BorderLayout.WEST); window.add(Pause_btn, BorderLayout.AFTER_LAST_LINE); Pause_btn.setEnabled(false); //pause btn action Pause_btn.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (Pause_btn.getText().equalsIgnoreCase("Pause")) { if (chosenPort.isOpen()) { try { Output.write(0); } catch (IOException ex) { Logger.getLogger(Graph_with_jframe_and_arduino.class.getName()).log(Level.SEVERE, null, ex); } } Pause_btn.setText("Start"); } else { if (chosenPort.isOpen()) { try { Output.write(1); } catch (IOException ex) { Logger.getLogger(Graph_with_jframe_and_arduino.class.getName()).log(Level.SEVERE, null, ex); } } Pause_btn.setText("Pause"); } throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates. } }); // configure the connect button and use another thread to listen for data connectButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent arg0) { if (connectButton.getText().equals("Connect")) { // attempt to connect to the serial port chosenPort = SerialPort.getCommPort(portList_combobox.getSelectedItem().toString()); chosenPort.setComPortTimeouts(SerialPort.TIMEOUT_SCANNER, 0, 0); if (chosenPort.openPort()) { Output = chosenPort.getOutputStream(); connectButton.setText("Disconnect"); Pause_btn.setEnabled(true); portList_combobox.setEnabled(false); } // create a new thread that listens for incoming text and populates the graph Thread thread = new Thread() { @Override public void run() { Scanner scanner = new Scanner(chosenPort.getInputStream()); while (scanner.hasNextLine()) { try { String line = scanner.nextLine(); int number = Integer.parseInt(line); series.add(x, number); series2.add(x, number / 2); series3.add(x, number / 1.5); series4.add(x, number / 5); if (x > 100) { series.remove(0); series2.remove(0); series3.remove(0); series4.remove(0); } x++; window.repaint(); } catch (Exception e) { } } scanner.close(); } }; thread.start(); } else { // disconnect from the serial port chosenPort.closePort(); portList_combobox.setEnabled(true); Pause_btn.setEnabled(false); connectButton.setText("Connect"); } } }); // show the window window.setVisible(true); }
From source file:mzmatch.ipeak.align.CowCoda.java
@SuppressWarnings("unchecked") public static void main(String args[]) { final String lbl_mcq = "mcq"; try {/*from ww w . java2 s. c om*/ Tool.init(); // parse the commandline options final Options options = new Options(); CmdLineParser cmdline = new CmdLineParser(options); // check whether we need to show the help cmdline.parse(args); if (options.help) { Tool.printHeader(System.out, application, version); cmdline.printUsage(System.out, ""); return; } if (options.verbose) { Tool.printHeader(System.out, application, version); cmdline.printOptions(); } // check the command-line parameters int filetype = JFreeChartTools.PDF; { if (options.ppm == -1) { System.err.println("[ERROR]: the ppm-value needs to be set."); System.exit(0); } if (options.order == -1) { System.err.println("[ERROR]: the order for the polynomial fit needs to be set."); System.exit(0); } if (options.maxrt == -1) { System.err.println("[ERROR]: the maximum retention time shift is not set."); System.exit(0); } if (options.image != null) { String extension = options.image.substring(options.image.lastIndexOf('.') + 1); if (extension.toLowerCase().equals("png")) filetype = JFreeChartTools.PNG; else if (extension.toLowerCase().equals("pdf")) filetype = JFreeChartTools.PDF; else { System.err.println( "[ERROR]: file extension of the image file needs to be either PDF or PNG."); System.exit(0); } } // if the output directories do not exist, create them if (options.output != null) Tool.createFilePath(options.output, true); if (options.image != null) Tool.createFilePath(options.image, true); if (options.selection != null) Tool.createFilePath(options.selection, true); } // load the data if (options.verbose) System.out.println("Loading the data"); double maxrt = 0; Vector<ParseResult> data = new Vector<ParseResult>(); Vector<IPeakSet<IPeak>> matchdata = new Vector<IPeakSet<IPeak>>(); for (String file : options.input) { System.out.println("- " + new File(file).getName()); // load the mass chromatogram data ParseResult result = PeakMLParser.parse(new FileInputStream(file), true); data.add(result); // select the best mass chromatograms Vector<IPeak> selection = new Vector<IPeak>(); for (IPeak peak : (IPeakSet<IPeak>) result.measurement) { maxrt = Math.max(maxrt, maxRT(peak)); double mcq = codaDW(peak); peak.addAnnotation(lbl_mcq, Double.toString(mcq), Annotation.ValueType.DOUBLE); if (mcq >= options.codadw) selection.add(peak); } // keep track of the selected mass chromatograms int id = options.input.indexOf(file); IPeakSet<IPeak> peakset = new IPeakSet<IPeak>(selection); peakset.setMeasurementID(id); for (IPeak mc : peakset) mc.setMeasurementID(id); matchdata.add(peakset); } // match the selection together if (options.verbose) System.out.println("Matching the data"); Vector<IPeakSet<IPeak>> matches = IPeak.match((Vector) matchdata, options.ppm, new IPeak.MatchCompare<IPeak>() { public double distance(IPeak peak1, IPeak peak2) { double diff = Math.abs(peak1.getRetentionTime() - peak2.getRetentionTime()); if (diff > options.maxrt) return -1; Signal signal1 = new Signal(peak1.getSignal()); signal1.normalize(); Signal signal2 = new Signal(peak2.getSignal()); signal2.normalize(); double offset = bestOffSet(peak1, peak2, options.maxrt); for (int i = 0; i < signal2.getSize(); ++i) signal2.getX()[i] += offset; double correlation = signal2 .pearsonsCorrelation(signal1)[Statistical.PEARSON_CORRELATION]; if (correlation < 0.5) return -1; // the match-function optimizes toward 0 (it's a distance) return 1 - correlation; } }); // filter out all incomplete sets Vector<IPeakSet<IPeak>> valids = new Vector<IPeakSet<IPeak>>(); for (IPeakSet<IPeak> set : matches) { if (set.size() < options.input.size()) continue; valids.add((IPeakSet) set); } // calculate the alignment factors if (options.verbose) System.out.println("Calculating the alignment factors"); double medians[] = new double[valids.size() + 2]; DataFrame.Double dataframe = new DataFrame.Double(valids.size() + 2, options.input.size()); medians[0] = 0; medians[medians.length - 1] = maxrt; for (int i = 0; i < options.input.size(); ++i) { dataframe.set(0, i, 0.1); dataframe.set(dataframe.getNrRows() - 1, i, 0); } for (int matchid = 0; matchid < valids.size(); ++matchid) { IPeakSet<IPeak> match = valids.get(matchid); // find the most central double offsets[][] = new double[match.size()][match.size()]; for (int i = 0; i < match.size(); ++i) for (int j = i + 1; j < match.size(); ++j) { offsets[i][j] = bestOffSet(match.get(i), match.get(j), options.maxrt); offsets[j][i] = -offsets[i][j]; } int besti = 0; double bestabssum = Double.MAX_VALUE; for (int i = 0; i < match.size(); ++i) { double abssum = 0; for (int j = 0; j < match.size(); ++j) abssum += Math.abs(offsets[i][j]); if (abssum < bestabssum) { besti = i; bestabssum = abssum; } } for (int i = 0; i < match.size(); ++i) dataframe.set(matchid + 1, match.get(i).getMeasurementID(), (i == besti ? 0 : offsets[i][besti])); medians[matchid + 1] = match.get(besti).getRetentionTime(); dataframe.setRowName(matchid, Double.toString(match.get(besti).getRetentionTime())); } double minmedian = Statistical.min(medians); double maxmedian = Statistical.max(medians); // calculate for each profile the correction function PolynomialFunction functions[] = new PolynomialFunction[valids.size()]; for (int i = 0; i < options.input.size(); ++i) functions[i] = PolynomialFunction.fit(options.order, medians, dataframe.getCol(i)); // make a nice plot out of the whole thing if (options.verbose) System.out.println("Writing results"); if (options.image != null) { org.jfree.data.xy.XYSeriesCollection dataset = new org.jfree.data.xy.XYSeriesCollection(); JFreeChart linechart = ChartFactory.createXYLineChart(null, "Retention Time (seconds)", "offset", dataset, PlotOrientation.VERTICAL, true, // legend false, // tooltips false // urls ); // setup the colorkey Colormap colormap = new Colormap(Colormap.EXCEL); // get the structure behind the graph XYPlot plot = (XYPlot) linechart.getPlot(); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); // setup the plot area linechart.setBackgroundPaint(java.awt.Color.WHITE); linechart.setBorderVisible(false); linechart.setAntiAlias(true); plot.setBackgroundPaint(java.awt.Color.WHITE); plot.setDomainGridlinesVisible(true); plot.setRangeGridlinesVisible(true); // create the datasets for (int i = 0; i < options.input.size(); ++i) { org.jfree.data.xy.XYSeries series = new org.jfree.data.xy.XYSeries(dataframe.getColName(i)); org.jfree.data.xy.XYSeries function = new org.jfree.data.xy.XYSeries( dataframe.getColName(i) + "-function"); dataset.addSeries(series); dataset.addSeries(function); renderer.setSeriesPaint(dataset.getSeriesCount() - 1, new java.awt.Color(colormap.getColor(i))); renderer.setSeriesPaint(dataset.getSeriesCount() - 2, new java.awt.Color(colormap.getColor(i))); renderer.setSeriesLinesVisible(dataset.getSeriesCount() - 2, false); renderer.setSeriesShapesVisible(dataset.getSeriesCount() - 2, true); // add the data-points for (int j = 0; j < valids.size(); ++j) series.add(medians[j], dataframe.get(j, i)); for (double x = minmedian; x < maxmedian; ++x) function.add(x, functions[i].getY(x)); } dataset.removeAllSeries(); for (int i = 0; i < options.input.size(); ++i) { Function function = functions[i]; org.jfree.data.xy.XYSeries series = new org.jfree.data.xy.XYSeries(dataframe.getColName(i)); dataset.addSeries(series); renderer.setSeriesPaint(i, new java.awt.Color(colormap.getColor(i))); renderer.setSeriesLinesVisible(i, false); renderer.setSeriesShapesVisible(i, true); // add the data-points for (int j = 0; j < valids.size(); ++j) series.add(medians[j], dataframe.get(j, i) - function.getY(medians[j])); } JFreeChartTools.writeAs(filetype, new FileOutputStream(options.image), linechart, 800, 500); } // save the selected if (options.selection != null) { Header header = new Header(); // set the number of peaks to be stored header.setNrPeaks(valids.size()); // create a set for the measurements SetInfo set = new SetInfo("", SetInfo.SET); header.addSetInfo(set); // create the measurement infos for (int i = 0; i < options.input.size(); ++i) { String file = options.input.get(i); // create the measurement info MeasurementInfo measurement = new MeasurementInfo(i, data.get(i).header.getMeasurementInfo(0)); measurement.addFileInfo(new FileInfo(file, file)); header.addMeasurementInfo(measurement); // add the file to the set set.addChild(new SetInfo(file, SetInfo.SET, i)); } // write the data PeakMLWriter.write(header, (Vector) valids, null, new GZIPOutputStream(new FileOutputStream(options.selection)), null); } // correct the values with the found function and save them for (int i = 0; i < options.input.size(); ++i) { Function function = functions[i]; ParseResult result = data.get(i); IPeakSet<MassChromatogram<Peak>> peakset = (IPeakSet<MassChromatogram<Peak>>) result.measurement; for (IPeak peak : peakset) align(peak, function); File filename = new File(options.input.get(i)); String name = filename.getName(); PeakMLWriter.write(result.header, (Vector) peakset.getPeaks(), null, new GZIPOutputStream(new FileOutputStream(options.output + "/" + name)), null); } } catch (Exception e) { Tool.unexpectedError(e, application); } }
From source file:org.jfree.chart.demo.GridBandDemo1.java
public static JPanel createDemoPanel() { XYSeries xyseries = new XYSeries("Random Data"); for (int i = 0; i < 100; i++) xyseries.add(Math.random() + 1.0D, Math.random() + 1.0D); XYSeriesCollection xyseriescollection = new XYSeriesCollection(); xyseriescollection.addSeries(xyseries); JFreeChart jfreechart = createChart(xyseriescollection); ChartPanel chartpanel = new ChartPanel(jfreechart); return chartpanel; }