List of usage examples for org.jfree.chart.axis NumberAxis setRange
public void setRange(double lower, double upper)
From source file:it.eng.spagobi.engines.chart.bo.charttypes.scattercharts.MarkerScatter.java
public JFreeChart createChart(DatasetMap datasets) { DefaultXYDataset dataset = (DefaultXYDataset) datasets.getDatasets().get("1"); JFreeChart chart = ChartFactory.createScatterPlot(name, yLabel, xLabel, dataset, PlotOrientation.HORIZONTAL, false, true, false);//ww w. j a va 2s. c o m TextTitle title = setStyleTitle(name, styleTitle); chart.setTitle(title); chart.setBackgroundPaint(Color.white); if (subName != null && !subName.equals("")) { TextTitle subTitle = setStyleTitle(subName, styleSubTitle); chart.addSubtitle(subTitle); } XYPlot plot = (XYPlot) chart.getPlot(); plot.setForegroundAlpha(0.65f); XYItemRenderer renderer = plot.getRenderer(); //defines colors int seriesN = dataset.getSeriesCount(); if ((colorMap != null && colorMap.size() > 0) || (defaultColor != null && !defaultColor.equals(""))) { for (int i = 0; i < seriesN; i++) { String serieName = (String) dataset.getSeriesKey(i); Color color = new Color(Integer.decode(defaultColor).intValue()); if (colorMap != null && colorMap.size() > 0) color = (Color) colorMap.get(serieName); if (color != null) renderer.setSeriesPaint(i, color); } } // add un interval marker for the Y axis... if (yMarkerStartInt != null && yMarkerEndInt != null && !yMarkerStartInt.equals("") && !yMarkerEndInt.equals("")) { Marker intMarkerY = new IntervalMarker(Double.parseDouble(yMarkerStartInt), Double.parseDouble(yMarkerEndInt)); intMarkerY.setLabelOffsetType(LengthAdjustmentType.EXPAND); intMarkerY.setPaint( new Color(Integer.decode((yMarkerIntColor.equals("")) ? "0" : yMarkerIntColor).intValue())); //intMarkerY.setLabel(yMarkerLabel); intMarkerY.setLabelAnchor(RectangleAnchor.BOTTOM_RIGHT); intMarkerY.setLabelTextAnchor(TextAnchor.TOP_RIGHT); plot.addDomainMarker(intMarkerY, Layer.BACKGROUND); } // add un interval marker for the X axis... if (xMarkerStartInt != null && xMarkerEndInt != null && !xMarkerStartInt.equals("") && !xMarkerEndInt.equals("")) { Marker intMarkerX = new IntervalMarker(Double.parseDouble(xMarkerStartInt), Double.parseDouble(xMarkerEndInt)); intMarkerX.setLabelOffsetType(LengthAdjustmentType.EXPAND); intMarkerX.setPaint( new Color(Integer.decode((xMarkerIntColor.equals("")) ? "0" : xMarkerIntColor).intValue())); //intMarkerX.setLabel(xMarkerLabel); intMarkerX.setLabelAnchor(RectangleAnchor.BOTTOM_RIGHT); intMarkerX.setLabelTextAnchor(TextAnchor.TOP_RIGHT); plot.addRangeMarker(intMarkerX, Layer.BACKGROUND); } // add a labelled marker for the Y axis... if (yMarkerValue != null && !yMarkerValue.equals("")) { Marker markerY = new ValueMarker(Double.parseDouble(yMarkerValue)); markerY.setLabelOffsetType(LengthAdjustmentType.EXPAND); if (!yMarkerColor.equals("")) markerY.setPaint(new Color(Integer.decode(yMarkerColor).intValue())); markerY.setLabel(yMarkerLabel); markerY.setLabelFont(new Font("Arial", Font.BOLD, 11)); markerY.setLabelAnchor(RectangleAnchor.TOP_RIGHT); markerY.setLabelTextAnchor(TextAnchor.TOP_RIGHT); plot.addDomainMarker(markerY, Layer.BACKGROUND); } // add a labelled marker for the X axis... if (xMarkerValue != null && !xMarkerValue.equals("")) { Marker markerX = new ValueMarker(Double.parseDouble(xMarkerValue)); markerX.setLabelOffsetType(LengthAdjustmentType.EXPAND); if (!xMarkerColor.equals("")) markerX.setPaint(new Color(Integer.decode(xMarkerColor).intValue())); markerX.setLabel(xMarkerLabel); markerX.setLabelAnchor(RectangleAnchor.BOTTOM_RIGHT); markerX.setLabelTextAnchor(TextAnchor.TOP_RIGHT); plot.addRangeMarker(markerX, Layer.BACKGROUND); } if (xRangeLow != null && !xRangeLow.equals("") && xRangeHigh != null && !xRangeHigh.equals("")) { if (Double.valueOf(xRangeLow).doubleValue() > xMin) xRangeLow = String.valueOf(xMin); if (Double.valueOf(xRangeHigh).doubleValue() < xMax) xRangeHigh = String.valueOf(xMax); ValueAxis rangeAxis = plot.getRangeAxis(); //rangeAxis.setRange(Double.parseDouble(xRangeLow), Double.parseDouble(xRangeHigh)); rangeAxis.setRangeWithMargins(Double.parseDouble(xRangeLow), Double.parseDouble(xRangeHigh)); } else { NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setAutoRange(true); rangeAxis.setRange(xMin, xMax); } if (yRangeLow != null && !yRangeLow.equals("") && yRangeHigh != null && !yRangeHigh.equals("")) { if (Double.valueOf(yRangeLow).doubleValue() > yMin) yRangeLow = String.valueOf(yMin); if (Double.valueOf(yRangeHigh).doubleValue() < yMax) yRangeHigh = String.valueOf(yMax); NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis(); //domainAxis.setRange(Double.parseDouble(yRangeLow), Double.parseDouble(yRangeHigh)); domainAxis.setRangeWithMargins(Double.parseDouble(yRangeLow), Double.parseDouble(yRangeHigh)); domainAxis.setAutoRangeIncludesZero(false); } else { NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis(); domainAxis.setAutoRange(true); domainAxis.setRange(yMin, yMax); domainAxis.setAutoRangeIncludesZero(false); } //add annotations if requested if (viewAnnotations != null && viewAnnotations.equalsIgnoreCase("true")) { if (annotationMap == null || annotationMap.size() == 0) logger.error("Annotations on the chart are requested but the annotationMap is null!"); else { int cont = 1; for (Iterator iterator = annotationMap.keySet().iterator(); iterator.hasNext();) { String text = (String) iterator.next(); String pos = (String) annotationMap.get(text); double x = Double.parseDouble(pos.substring(0, pos.indexOf("__"))); double y = Double.parseDouble(pos.substring(pos.indexOf("__") + 2)); //default up position XYTextAnnotation annotation = new XYTextAnnotation(text, y - 1, x + ((text.length() > 20) ? text.length() / 3 + 1 : text.length() / 2 + 1)); if (cont % 2 != 0) //dx annotation = new XYTextAnnotation(text, y, x + ((text.length() > 20) ? text.length() / 3 + 1 : text.length() / 2 + 1)); else //sx //annotation = new XYTextAnnotation(text, y, x-((text.length()%2==0)?text.length():text.length()-1)); annotation = new XYTextAnnotation(text, y, x - (text.length() - 1)); annotation.setFont(new Font("SansSerif", Font.PLAIN, 11)); //annotation.setRotationAngle(Math.PI / 4.0); annotation.setRotationAngle(0.0); // horizontal plot.addAnnotation(annotation); cont++; } renderer.setShape(new Ellipse2D.Double(-3, -5, 8, 8)); } } else if (viewAnnotations != null && viewAnnotations.equalsIgnoreCase("false")) { renderer.setShape(new Ellipse2D.Double(-3, -5, 8, 8)); } if (legend == true) { drawLegend(chart); } return chart; }
From source file:edu.fullerton.timeseriesapp.TimeSeriesApp.java
public ArrayList<Integer> makePlot(ArrayList<ChanDataBuffer> dbufs, boolean compact) throws WebUtilException { int imageId;// ww w . ja v a 2s . co m try { PluginSupport psupport = new PluginSupport(); String gtitle = psupport.getTitle(dbufs, compact); String xAxisLabel = ""; XYSeriesCollection xyds = new XYSeriesCollection(); TimeSeriesCollection mtds = new TimeSeriesCollection(); compact = dbufs.size() > 2 ? false : compact; for (ChanDataBuffer dbuf : dbufs) { int npts = dbuf.getDataLength(); int sum = 1; if (npts > 2000) { sum = npts / 2000; } String legend = psupport.getLegend(dbuf, compact); if (timeAxis.equalsIgnoreCase("utc")) { TimeSeries ts = psupport.getTimeSeries(dbuf, legend, sum); xAxisLabel = "Time (UTC)"; mtds.addSeries(ts); } else { boolean isDt = timeAxis.equalsIgnoreCase("dt"); XYSeries xys = psupport.addXySeries(dbuf, legend, isDt, sum); xAxisLabel = psupport.getxAxisLabel(); xyds.addSeries(xys); } } Double minx, miny, maxx, maxy; Double[] rng = new Double[4]; if (timeAxis.equalsIgnoreCase("utc")) { PluginSupport.getRangeLimits(mtds, rng); } else { int skip = 0; PluginSupport.getRangeLimits(xyds, rng, skip); } minx = rng[0]; miny = rng[1]; maxx = rng[2]; maxy = rng[3]; int exp; if (timeAxis.equalsIgnoreCase("utc")) { exp = PluginSupport.scaleRange(mtds, miny, maxy); } else { exp = PluginSupport.scaleRange(xyds, miny, maxy); } ChartPanel cpnl; DefaultXYDataset ds = new DefaultXYDataset(); JFreeChart chart; if (timeAxis.equalsIgnoreCase("utc")) { chart = ChartFactory.createTimeSeriesChart(gtitle, "Time (UTC)", "Counts", ds, true, true, false); } else { chart = ChartFactory.createXYLineChart(gtitle, xAxisLabel, "Counts", ds, PlotOrientation.VERTICAL, true, false, false); } chart.setBackgroundPaint(Color.WHITE); chart.setAntiAlias(true); XYPlot plot = (XYPlot) chart.getPlot(); plot.setBackgroundPaint(Color.white); plot.setRangeGridlinePaint(Color.LIGHT_GRAY); plot.setDomainGridlinePaint(Color.LIGHT_GRAY); NumberAxis rangeAxis = new NumberAxis("Counts"); ScaledAxisNumberFormat sanf = new ScaledAxisNumberFormat(); sanf.setExp(exp); NumberTickUnit tickUnit; double plotRange; if (maxy != 0 && Math.abs(maxy - miny) < Math.abs(maxy) * 1e-30) { // this garbage is to get jFreeChart to always put labels on the Y axis double dt = Math.abs(miny) / 10; double scaledMin = (miny - dt) * Math.pow(10., exp); double scaledMax = (maxy + dt) * Math.pow(10., exp); rangeAxis.setRange(scaledMin, scaledMax); plotRange = scaledMax - scaledMin; rangeAxis.setAutoRange(false); } else { sanf.setMinMax(miny, maxy); plotRange = maxy - miny; rangeAxis.setAutoRange(true); } tickUnit = rangeAxis.getTickUnit(); double tickSize = tickUnit.getSize(); int nticks = (int) ((plotRange) / tickSize); if (nticks > yTicks) { double newTickSize = plotRange / yTicks; rangeAxis.setTickUnit(new NumberTickUnit(newTickSize)); } rangeAxis.setNumberFormatOverride(sanf); rangeAxis.setAutoRangeIncludesZero(false); plot.setRangeAxis(rangeAxis); if (timeAxis.equalsIgnoreCase("utc")) { plot.setDataset(0, mtds); } else { plot.setDataset(0, xyds); } // Set the line thickness XYLineAndShapeRenderer r = (XYLineAndShapeRenderer) plot.getRenderer(); BasicStroke str = new BasicStroke(lineThickness); int n = plot.getSeriesCount(); for (int i = 0; i < n; i++) { r.setSeriesStroke(i, str); } if (compact) { chart.removeLegend(); } cpnl = new ChartPanel(chart); if (outFilename.isEmpty()) { imageId = psupport.saveImageAsPNG(cpnl); } else { imageId = 0; psupport.saveImageAsPdfFile(chart, outFilename); } } catch (SQLException | NoSuchAlgorithmException | IOException ex) { throw new WebUtilException(ex); } ArrayList<Integer> ret = new ArrayList<>(); ret.add(imageId); return ret; }
From source file:diet.gridr.g5k.gui.GanttChart.java
/** * Method creating the chart//from w ww . j a va2 s .com * * @param dataset dataset containing the data for the chart * @return a chart */ private JFreeChart createChart(XYZDataset dataset) { DateAxis xAxis = new DateAxis("Date"); xAxis.setLowerMargin(0.0); xAxis.setUpperMargin(0.0); xAxis.setDateFormatOverride(new SimpleDateFormat(durationsFormatterArray[this.visualizationDuration])); xAxis.setRange(Calendar.getInstance().getTime(), new Date(System.currentTimeMillis() + HistoryUtil.durationsTimesArray[visualizationDuration] - HistoryUtil.blockWidthsArray[visualizationDuration])); NumberAxis yAxis = new NumberAxis("Nodes"); yAxis.setAutoRangeIncludesZero(false); yAxis.setInverted(true); yAxis.setLowerMargin(0.0); yAxis.setUpperMargin(0.0); yAxis.setRange(1, numberOfNodes); yAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); XYBlockRenderer renderer = new XYBlockRenderer(); LookupPaintScale paintScale = new LookupPaintScale(); for (int i = 0; i < jobsList.get(visualizationDuration).size(); i++) { // String jobId = jobsList.get(visualizationDuration).get(i).getId().substring(0,jobsList.get(visualizationDuration).get(i).getId().indexOf(".")); String jobId = jobsList.get(visualizationDuration).get(i).getParameterValue(GridJob.KEY_GRID_JOB_ID); int seed = Integer.parseInt(jobId); Random rng = new Random(seed); Color tempColor = Color.red; int red = tempColor.getRed(); int green = tempColor.getGreen(); int blue = tempColor.getBlue(); int redRNG = rng.nextInt(255); int greenRNG = rng.nextInt(255); int blueRNG = rng.nextInt(255); if (red == redRNG && green == greenRNG && blue == blueRNG) { tempColor = new Color(rng.nextInt(255), rng.nextInt(255), rng.nextInt(255)); } else { tempColor = new Color(redRNG, greenRNG, blueRNG); } if (seed == 0) tempColor = Color.red; paintScale.add(new Double(i), tempColor); } renderer.setBlockWidth(HistoryUtil.blockWidthsArray[visualizationDuration]); renderer.setBlockAnchor(RectangleAnchor.TOP_LEFT); renderer.setPaintScale(paintScale); XYPlot plot = new XYPlot(dataset, xAxis, yAxis, renderer); plot.setOrientation(PlotOrientation.VERTICAL); plot.setBackgroundPaint(Color.white); plot.setDomainGridlinePaint(Color.black); plot.setRangeGridlinePaint(Color.black); JFreeChart chart = new JFreeChart("Gantt Chart activity for cluster " + siteName, plot); chart.removeLegend(); chart.setBackgroundPaint(Color.white); LoggingManager.log(Level.CONFIG, LoggingManager.RESOURCESTOOL, this.getClass().getName(), "createChart", "Chart created"); return chart; }
From source file:hudson.graph.jfreechart.Utils.java
/** * Adjusts the Y-axis so that abnormally large value won't spoil the whole chart * by making everything look virtually 0. * * <p>// w w w . j a v a2s . c o m * The algorithm is based on <a href="http://en.wikipedia.org/wiki/Chebyshev%27s_inequality">Chebyshev's inequality</a>, * which states that given any number sequence, nore more than 1/(N^2) values are more than N x stddev away * from the average. * * <p> * So the algorithm is to set Y-axis range so that we can see all data points that are within N x stddev * of the average. Most of the time, Cebyshev's inequality is very conservative, so it shouldn't do * much harm. * * <p> * When the algorithm does kick in, however, we can kick out at most 1 in N^2 data points. * (So for example if N=3 then we can "fix" the graph as long as we only have less than 1/(3*3)=11.111...% bad data. * * <p> * Also see issue #1246. */ public static void adjustChebyshev(CategoryDataset dataset, NumberAxis yAxis) { // first compute E(X) and Var(X) double sum = 0, sum2 = 0; final int nColumns = dataset.getColumnCount(); final int nRows = dataset.getRowCount(); for (int i = 0; i < nRows; i++) { Comparable rowKey = dataset.getRowKey(i); for (int j = 0; j < nColumns; j++) { Comparable columnKey = dataset.getColumnKey(j); double n = dataset.getValue(rowKey, columnKey).doubleValue(); sum += n; sum2 += n * n; } } double average = sum / (nColumns * nRows); double stddev = Math.sqrt(sum2 / (nColumns * nRows) - average * average); double rangeMin = average - stddev * CHEBYSHEV_N; double rangeMax = average + stddev * CHEBYSHEV_N; // now see if there are any data points that fall outside (rangeMin,rangeMax) boolean found = false; double min = 0, max = 0; for (int i = 0; i < nRows; i++) { Comparable rowKey = dataset.getRowKey(i); for (int j = 0; j < nColumns; j++) { Comparable columnKey = dataset.getColumnKey(j); double n = dataset.getValue(rowKey, columnKey).doubleValue(); if (n < rangeMin || rangeMax < n) { found = true; continue; // ignore this value } min = Math.min(min, n); max = Math.max(max, n); } } if (!found) return; // no adjustment was necessary // some values fell outside the range, so adjust the Y-axis // if we are ever to extend this method to handle negative value ranges correctly, // the code after this needs modifications min = Math.min(0, min); // always include 0 in the graph max += yAxis.getUpperMargin() * (max - min); yAxis.setRange(min, max); }
From source file:edu.fullerton.viewerplugin.TsPlot.java
@Override public ArrayList<Integer> makePlot(ArrayList<ChanDataBuffer> dbufs, boolean compact) throws WebUtilException { int imageId;/*from w w w . j a v a 2 s. c o m*/ try { if (parameterMap.containsKey("ts_newplt")) { imageId = makeAddPlotFiles(dbufs, compact); } else { String gtitle = getTitle(dbufs, compact); XYSeriesCollection xyds = new XYSeriesCollection(); TimeSeriesCollection mtds = new TimeSeriesCollection(); compact = dbufs.size() > 2 ? false : compact; for (ChanDataBuffer dbuf : dbufs) { if (timeAxis.equalsIgnoreCase("utc")) { addTimeSeries(dbuf, compact, mtds); } else { addXySeries(dbuf, compact, xyds); } } Double minx, miny, maxx, maxy; Double[] rng = new Double[4]; if (timeAxis.equalsIgnoreCase("utc")) { PluginSupport.getRangeLimits(mtds, rng); } else { PluginSupport.getRangeLimits(xyds, rng, 0); } minx = rng[0]; miny = rng[1]; maxx = rng[2]; maxy = rng[3]; int exp; if (timeAxis.equalsIgnoreCase("utc")) { exp = PluginSupport.scaleRange(mtds, miny, maxy); } else { exp = PluginSupport.scaleRange(xyds, miny, maxy); } ChartPanel cpnl; DefaultXYDataset ds = new DefaultXYDataset(); JFreeChart chart; if (timeAxis.equalsIgnoreCase("utc")) { chart = ChartFactory.createTimeSeriesChart(gtitle, "Time (UTC)", "Amplitude (Counts)", ds, true, true, false); } else { chart = ChartFactory.createXYLineChart(gtitle, xAxisLabel, "Amplitude (Counts)", ds, PlotOrientation.VERTICAL, true, false, false); } XYPlot plot = (XYPlot) chart.getPlot(); NumberAxis rangeAxis = new NumberAxis("Amplitude (Counts)"); ScaledAxisNumberFormat sanf = new ScaledAxisNumberFormat(); sanf.setExp(exp); if (maxy != 0 && Math.abs(maxy - miny) <= Math.abs(maxy) * 1e-25) { // this garbage is to get jFreeChart to put labels on the Y axis double dt = Math.abs(miny) / 10; double scaledMin = (miny - dt) * Math.pow(10., exp); double scaledMax = (maxy + dt) * Math.pow(10., exp); rangeAxis.setRange(scaledMin, scaledMax); NumberTickUnit unit = new NumberTickUnit((scaledMax - scaledMin) / 10.); rangeAxis.setTickUnit(unit); rangeAxis.setAutoRange(false); } // else // { // sanf.setMinMax(miny, maxy); // rangeAxis.setRange(miny, maxy); // NumberTickUnit unit = new NumberTickUnit((maxy - miny)/6.); // rangeAxis.setTickUnit(unit); // rangeAxis.setAutoRange(false); // } rangeAxis.setNumberFormatOverride(sanf); rangeAxis.setAutoRangeIncludesZero(false); plot.setRangeAxis(rangeAxis); if (timeAxis.equalsIgnoreCase("utc")) { plot.setDataset(0, mtds); } else { plot.setDataset(0, xyds); } // Set the line thickness XYLineAndShapeRenderer r = (XYLineAndShapeRenderer) plot.getRenderer(); BasicStroke str = new BasicStroke(lineThickness); int n = plot.getSeriesCount(); for (int i = 0; i < n; i++) { r.setSeriesStroke(i, str); } plot.setBackgroundPaint(Color.WHITE); // add plot.setDomainGridlinesVisible(true); plot.setDomainGridlinePaint(Color.BLACK); plot.setRangeGridlinesVisible(true); plot.setRangeGridlinePaint(Color.BLACK); r.setBaseFillPaint(Color.WHITE); if (compact) { chart.removeLegend(); } chart.setBackgroundPaint(Color.WHITE); cpnl = new ChartPanel(chart); imageId = saveImageAsPNG(cpnl); } } catch (LdvTableException | NoSuchAlgorithmException | SQLException | IOException ex) { throw new WebUtilException("Making time series plot: ", ex); } ArrayList<Integer> ret = new ArrayList<Integer>(); ret.add(imageId); return ret; }
From source file:org.matsim.integration.weekly.fundamentaldiagram.CreateAutomatedFDTest.java
private void scatterPlot(Map<Double, Map<String, Tuple<Double, Double>>> inputData, String outFile) { String mode1 = travelModes[0]; XYSeries carFlow = new XYSeries(mode1 + " flow"); XYSeries carSpeed = new XYSeries(mode1 + " speed"); XYSeries bikeFlow = null;/*from www . j a va 2 s . c o m*/ XYSeries bikeSpeed = null; if (travelModes.length == 2) { bikeFlow = new XYSeries(travelModes[1] + " flow"); bikeSpeed = new XYSeries(travelModes[1] + " speed"); } for (double d : inputData.keySet()) { carFlow.add(d, inputData.get(d).get(mode1).getFirst()); carSpeed.add(d, inputData.get(d).get(mode1).getSecond()); if (travelModes.length == 2) { bikeFlow.add(d, inputData.get(d).get(travelModes[1]).getFirst()); bikeSpeed.add(d, inputData.get(d).get(travelModes[1]).getSecond()); } } // flow vs density XYSeriesCollection flowDataset = new XYSeriesCollection(); flowDataset.addSeries(carFlow); NumberAxis flowAxis = new NumberAxis("Flow (PCU/h)"); flowAxis.setRange(0.0, 1700.0); XYPlot plot1 = new XYPlot(flowDataset, null, flowAxis, new XYLineAndShapeRenderer(false, true)); plot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT); // speed vs density XYSeriesCollection speedDataset = new XYSeriesCollection(); speedDataset.addSeries(carSpeed); if (travelModes.length == 2) { flowDataset.addSeries(bikeFlow); speedDataset.addSeries(bikeSpeed); } NumberAxis speedAxis = new NumberAxis("Speed (m/s)"); speedAxis.setRange(0.0, 17.0); XYPlot plot2 = new XYPlot(speedDataset, null, speedAxis, new XYLineAndShapeRenderer(false, true)); plot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT); NumberAxis densityAxis = new NumberAxis("Overall density (PCU/km)"); densityAxis.setRange(0.0, 140.00); CombinedDomainXYPlot plot = new CombinedDomainXYPlot(densityAxis); plot.setGap(10.); plot.add(plot1); plot.add(plot2); plot.setOrientation(PlotOrientation.VERTICAL); JFreeChart chart = new JFreeChart("Fundamental diagrams", JFreeChart.DEFAULT_TITLE_FONT, plot, true); try { ChartUtilities.saveChartAsPNG(new File(outFile), chart, 800, 600); } catch (IOException e) { throw new RuntimeException("Data is not plotted. Reason " + e); } }
From source file:gov.nih.nci.caintegrator.ui.graphing.chart.plot.ClinicalPlot.java
private void createChart() { //String xLabel = factor1.toString(); String xLabel = factor1AxisLabel; //String yLabel = factor2.toString(); String yLabel = factor2AxisLabel; clinicalChart = ChartFactory.createScatterPlot("Clinical Plot", xLabel, yLabel, null, PlotOrientation.VERTICAL, true, true, false); XYPlot plot = (XYPlot) clinicalChart.getPlot(); buildLegend();//from w w w . j ava 2s. co m plot.setNoDataMessage(null); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); renderer.setToolTipGenerator(new StandardXYToolTipGenerator()); renderer.setUseOutlinePaint(true); plot.setRangeCrosshairVisible(false); plot.setDomainCrosshairVisible(false); NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis(); NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); //should determine axis range using datapoints. domainAxis.setAutoRangeIncludesZero(false); //get domain and range of the axis. DataRange domainAxisLimits = getDataRange(dataPoints, factor1, true); DataRange rangeAxisLimits = getDataRange(dataPoints, factor2, true); //domainAxis.setRange(domainAxisLimits.getMinRange(), domainAxisLimits.getMaxRange()); //rangeAxis.setRange(rangeAxisLimits.getMinRange(), rangeAxisLimits.getMaxRange()); double domainMax = Math.max(100.0, domainAxisLimits.getMaxRange()) + 5.0; double rangeMax = Math.max(100.0, rangeAxisLimits.getMaxRange()) + 5.0; domainAxis.setRange(0.0, domainMax); rangeAxis.setRange(0.0, rangeMax); System.out.println("domainAxis=" + domainAxis.getLabel()); System.out.println("rangeAxis=" + rangeAxis.getLabel()); createGlyphsAndAddToPlot(plot); }
From source file:MSUmpire.DIA.TargetMatchScoring.java
public void MixtureModeling() throws IOException { if (libTargetMatches.isEmpty()) { return;//from w ww . j a v a2 s . co m } int IDNo = 0; int decoyNo = 0; int modelNo = 0; double IDmean = 0d; double Decoymean = 0d; for (UmpireSpecLibMatch match : libIDMatches) { if (match.BestHit != null) { IDNo++; IDmean += match.BestHit.UmpireScore; } } decoyNo = decoyModelingList.size(); for (PeakGroupScore peakGroupScore : decoyModelingList) { Decoymean += peakGroupScore.UmpireScore; } for (UmpireSpecLibMatch match : libTargetMatches) { //modelNo+= match.TargetHits.size(); if (match.BestMS1Hit != null) { modelNo++; } if (match.BestMS2Hit != null) { modelNo++; } } Decoymean /= decoyNo; IDmean /= IDNo; PVector[] points = new PVector[modelNo]; PVector[] centroids = new PVector[2]; int idx = 0; for (UmpireSpecLibMatch match : libTargetMatches) { if (match.BestMS1Hit != null) { points[idx] = new PVector(1); points[idx].array[0] = match.BestMS1Hit.UmpireScore; idx++; } if (match.BestMS2Hit != null) { points[idx] = new PVector(1); points[idx].array[0] = match.BestMS2Hit.UmpireScore; idx++; } // for(PeakGroupScore peakGroupScore : match.TargetHits){ // points[idx] = new PVector(1); // points[idx].array[0] = match.BestMS2Hit.UmpireScore; // idx++; // } } MixtureModel mmc; centroids[0] = new PVector(1); centroids[0].array[0] = Decoymean; centroids[1] = new PVector(1); centroids[1].array[0] = IDmean; Vector<PVector>[] clusters = KMeans.run(points, 2, centroids); MixtureModel mm = ExpectationMaximization1D.initialize(clusters); mmc = ExpectationMaximization1D.run(points, mm); DecimalFormat df = new DecimalFormat("#.####"); Logger.getRootLogger() .debug("----------------------------------------------------------------------------------------"); Logger.getRootLogger().debug("No. of modeling points=" + modelNo); Logger.getRootLogger().debug("ID hits mean=" + df.format(IDmean)); Logger.getRootLogger().debug("Decoy hits mean=" + df.format(Decoymean)); //System.out.print("T-test: p-value=" + df.format(model.ttest.pValue).toString() + "\n"); Logger.getRootLogger() .debug("Incorrect hits model mean=" + df.format(((PVector) mmc.param[0]).array[0]) + " variance=" + df.format(((PVector) mmc.param[0]).array[1]) + " weight=" + df.format(mmc.weight[0])); Logger.getRootLogger() .debug("Correct hits model mean=" + df.format(((PVector) mmc.param[1]).array[0]) + " variance=" + df.format(((PVector) mmc.param[1]).array[1]) + " weight=" + df.format(mmc.weight[1])); if (((PVector) mmc.param[0]).array[0] > ((PVector) mmc.param[1]).array[0]) { return; } float max = (float) (((PVector) mmc.param[1]).array[0] + 4 * Math.sqrt(((PVector) mmc.param[1]).array[1])); float min = (float) (((PVector) mmc.param[0]).array[0] - 4 * Math.sqrt(((PVector) mmc.param[0]).array[1])); IDNo = 0; decoyNo = 0; modelNo = 0; for (PeakGroupScore peakGroupScore : decoyModelingList) { if (peakGroupScore.UmpireScore > min && peakGroupScore.UmpireScore < max) { decoyNo++; } } for (UmpireSpecLibMatch match : libIDMatches) { if (match.BestHit != null && match.BestHit.UmpireScore > min && match.BestHit.UmpireScore < max) { IDNo++; } } for (UmpireSpecLibMatch match : libTargetMatches) { //targetNo += match.TargetHits.size(); //decoyNo += match.DecoyHits.size(); if (match.BestMS1Hit != null && match.BestMS1Hit.UmpireScore > min && match.BestMS1Hit.UmpireScore < max) { modelNo++; } if (match.BestMS2Hit != null && match.BestMS2Hit.UmpireScore > min && match.BestMS2Hit.UmpireScore < max) { modelNo++; } //modelNo += match.TargetHits.size(); } double[] IDObs = new double[IDNo]; double[] DecoyObs = new double[decoyNo]; double[] ModelObs = new double[modelNo]; idx = 0; int didx = 0; int midx = 0; for (UmpireSpecLibMatch match : libIDMatches) { if (match.BestHit != null && match.BestHit.UmpireScore > min && match.BestHit.UmpireScore < max) { IDObs[idx++] = match.BestHit.UmpireScore; } } for (PeakGroupScore peakGroupScore : decoyModelingList) { if (peakGroupScore.UmpireScore > min && peakGroupScore.UmpireScore < max) { DecoyObs[didx++] = peakGroupScore.UmpireScore; } } for (UmpireSpecLibMatch match : libTargetMatches) { // for(PeakGroupScore peak : match.TargetHits){ // ModelObs[midx++]=peak.UmpireScore; // } if (match.BestMS1Hit != null && match.BestMS1Hit.UmpireScore > min && match.BestMS1Hit.UmpireScore < max) { ModelObs[midx++] = match.BestMS1Hit.UmpireScore; } if (match.BestMS2Hit != null && match.BestMS2Hit.UmpireScore > min && match.BestMS2Hit.UmpireScore < max) { ModelObs[midx++] = match.BestMS2Hit.UmpireScore; } } String pngfile = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatchModel.png"; XYSeries model1 = new XYSeries("Incorrect matches"); XYSeries model2 = new XYSeries("Correct matches"); XYSeries model3 = new XYSeries("All target hits"); String modelfile = FilenameUtils.getFullPath(pngfile) + "/" + FilenameUtils.getBaseName(pngfile) + "_ModelPoints.txt"; FileWriter writer = new FileWriter(modelfile); writer.write("UScore\tModel\tCorrect\tDecoy\n"); int NoPoints = 1000; double[] model_kde_x = new double[NoPoints]; float intv = (max - min) / NoPoints; PVector point = new PVector(2); for (int i = 0; i < NoPoints; i++) { point.array[0] = max - i * intv; model_kde_x[i] = point.array[0]; point.array[1] = mmc.EF.density(point, mmc.param[0]) * mmc.weight[0]; model1.add(point.array[0], point.array[1]); point.array[1] = mmc.EF.density(point, mmc.param[1]) * mmc.weight[1]; model2.add(point.array[0], point.array[1]); } KernelDensityEstimator kde = new KernelDensityEstimator(); kde.SetData(ModelObs); double[] model_kde_y = kde.Density(model_kde_x); for (int i = 0; i < NoPoints; i++) { if (model_kde_x[i] > min && model_kde_x[i] < max) { point.array[0] = max - i * intv; model_kde_x[i] = point.array[0]; model3.add(model_kde_x[i], model_kde_y[i]); writer.write(point.array[0] + "\t" + mmc.EF.density(point, mmc.param[0]) * mmc.weight[0] + "\t" + mmc.EF.density(point, mmc.param[1]) * mmc.weight[1] + "\t" + model_kde_y[i] + "\n"); } } writer.close(); MixtureModelProb = new float[NoPoints + 1][3]; float positiveaccu = 0f; float negativeaccu = 0f; MixtureModelProb[0][0] = (float) model2.getMaxX() + Float.MIN_VALUE; MixtureModelProb[0][1] = 1f; MixtureModelProb[0][2] = 1f; for (int i = 1; i < NoPoints + 1; i++) { float positiveNumber = model2.getY(NoPoints - i).floatValue(); float negativeNumber = model1.getY(NoPoints - i).floatValue(); MixtureModelProb[i][0] = model2.getX(NoPoints - i).floatValue(); positiveaccu += positiveNumber; negativeaccu += negativeNumber; MixtureModelProb[i][2] = positiveNumber / (negativeNumber + positiveNumber); MixtureModelProb[i][1] = positiveaccu / (negativeaccu + positiveaccu); } XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(model1); dataset.addSeries(model2); dataset.addSeries(model3); HistogramDataset histogramDataset = new HistogramDataset(); histogramDataset.setType(HistogramType.SCALE_AREA_TO_1); histogramDataset.addSeries("ID hits", IDObs, 100); histogramDataset.addSeries("Decoy hits", DecoyObs, 100); //histogramDataset.addSeries("Model hits", ModelObs, 100); JFreeChart chart = ChartFactory.createHistogram(FilenameUtils.getBaseName(pngfile), "Score", "Hits", histogramDataset, PlotOrientation.VERTICAL, true, false, false); XYPlot plot = chart.getXYPlot(); NumberAxis domain = (NumberAxis) plot.getDomainAxis(); domain.setRange(min, max); plot.setBackgroundPaint(Color.white); plot.setDomainGridlinePaint(Color.white); plot.setRangeGridlinePaint(Color.white); plot.setForegroundAlpha(0.8f); chart.setBackgroundPaint(Color.white); XYLineAndShapeRenderer render = new XYLineAndShapeRenderer(); // render.setSeriesPaint(0, Color.DARK_GRAY); // render.setSeriesPaint(1, Color.DARK_GRAY); // render.setSeriesPaint(2, Color.GREEN); // render.setSeriesShape(0, new Ellipse2D.Double(0, 0, 2, 2)); // render.setSeriesShape(1, new Ellipse2D.Double(0, 0, 2, 2)); // render.setSeriesShape(2, new Ellipse2D.Double(0, 0, 2.5f, 2.5f)); // render.setSeriesStroke(1, new BasicStroke(1.0f)); // render.setSeriesStroke(0, new BasicStroke(1.0f)); // render.setSeriesStroke(2, new BasicStroke(2.0f)); plot.setDataset(1, dataset); plot.setRenderer(1, render); plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); try { ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600); } catch (IOException e) { } }
From source file:lu.lippmann.cdb.ext.hydviga.ui.GapFillingFrame.java
private GapFillingCase refresh(final Algo algo, final int[] indexesOfUsedSeries, final boolean hideOthers, final boolean showError, final boolean zoom, final boolean showEnvelope, final boolean multAxis) throws Exception { if (!inBatchMode) this.centerPanel.removeAll(); int[] arr = new int[] { attr.index(), dateIdx }; for (final int iii : indexesOfUsedSeries) { arr = ArraysUtil.concat(arr, new int[] { dataSet.attribute(this.attrNames.get(iii)).index() }); }//www. ja va 2s. c o m Instances filteredDs = WekaDataProcessingUtil.buildFilteredByAttributesDataSet(dataSet, arr); //System.out.println(filteredDs.toSummaryString()); Attribute original = null; Instances filteredDsWithOriginal = null; if (this.isGapSimulated) { original = new Attribute("original"); filteredDsWithOriginal = new Instances(filteredDs); filteredDsWithOriginal.insertAttributeAt(original, filteredDsWithOriginal.numAttributes() - 1); final Attribute origAttr = filteredDsWithOriginal.attribute(original.name()); for (int ii = position - 1; ii < position + gapsize + 1; ii++) { filteredDsWithOriginal.instance(ii).setValue(origAttr, this.originalDataBeforeGapSimulation[ii]); } } filteredDs = WekaDataProcessingUtil.buildFilteredDataSet(filteredDs, 0, filteredDs.numAttributes() - 1, Math.max(0, this.position - this.valuesBeforeAndAfter), Math.min(this.position + this.gapsize + this.valuesBeforeAndAfter, filteredDs.numInstances() - 1)); this.gapFiller = GapFillerFactory.getGapFiller(algo); final Instances completedds = this.gapFiller.fillGaps(filteredDs); final Instances diff = WekaTimeSeriesUtil.buildDiff(filteredDs, completedds); final int valuesToCheckForError = this.valuesBeforeAndAfter / 4; double maeByEnlargingGap = Double.NaN; double maeByAddingAGapBefore = Double.NaN; double maeByAddingAGapAfter = Double.NaN; double maeByComparingWithOriginal = Double.NaN; double rmseByEnlargingGap = Double.NaN; double rmseByAddingAGapBefore = Double.NaN; double rmseByAddingAGapAfter = Double.NaN; double rmseByComparingWithOriginal = Double.NaN; double rsrByEnlargingGap = Double.NaN; double rsrByAddingAGapBefore = Double.NaN; double rsrByAddingAGapAfter = Double.NaN; double rsrByComparingWithOriginal = Double.NaN; double pbiasByEnlargingGap = Double.NaN; double pbiasByAddingAGapBefore = Double.NaN; double pbiasByAddingAGapAfter = Double.NaN; double pbiasByComparingWithOriginal = Double.NaN; double nsByEnlargingGap = Double.NaN; double nsByAddingAGapBefore = Double.NaN; double nsByAddingAGapAfter = Double.NaN; double nsByComparingWithOriginal = Double.NaN; double indexOfAgreementByEnlargingGap = Double.NaN; double indexOfAgreementByAddingAGapBefore = Double.NaN; double indexOfAgreementByAddingAGapAfter = Double.NaN; double indexOfAgreementByComparingWithOriginal = Double.NaN; if (this.isGapSimulated) { //System.out.println(attr.index()+" begin="+(this.position)+" end="+(this.position+this.gapsize)); final Instances correctedDataSet = buildCorrectedDataset(diff); final double[] cad = correctedDataSet.attributeToDoubleArray(attr.index()); maeByComparingWithOriginal = MathsUtil.mae(this.originalDataBeforeGapSimulation, cad, this.position, this.position + this.gapsize); rmseByComparingWithOriginal = MathsUtil.rmse(this.originalDataBeforeGapSimulation, cad, this.position, this.position + this.gapsize); rsrByComparingWithOriginal = MathsUtil.rsr(this.originalDataBeforeGapSimulation, cad, this.position, this.position + this.gapsize); pbiasByComparingWithOriginal = MathsUtil.pbias(this.originalDataBeforeGapSimulation, cad, this.position, this.position + this.gapsize); nsByComparingWithOriginal = MathsUtil.nashSutcliffe(this.originalDataBeforeGapSimulation, cad, this.position, this.position + this.gapsize); indexOfAgreementByComparingWithOriginal = MathsUtil.indexOfAgreement( this.originalDataBeforeGapSimulation, cad, this.position, this.position + this.gapsize); } else { maeByEnlargingGap = this.gapFiller.evaluateMAEByEnlargingGap(filteredDs, valuesToCheckForError); maeByAddingAGapBefore = this.gapFiller.evaluateMAEByAddingAGapBefore(filteredDs, valuesToCheckForError); maeByAddingAGapAfter = this.gapFiller.evaluateMAEByAddingAGapAfter(filteredDs, valuesToCheckForError); rmseByEnlargingGap = this.gapFiller.evaluateRMSEByEnlargingGap(filteredDs, valuesToCheckForError); rmseByAddingAGapBefore = this.gapFiller.evaluateRMSEByAddingAGapBefore(filteredDs, valuesToCheckForError); rmseByAddingAGapAfter = this.gapFiller.evaluateRMSEByAddingAGapAfter(filteredDs, valuesToCheckForError); nsByEnlargingGap = this.gapFiller.evaluateNSByEnlargingGap(filteredDs, valuesToCheckForError); nsByAddingAGapBefore = this.gapFiller.evaluateNSByAddingAGapBefore(filteredDs, valuesToCheckForError); nsByAddingAGapAfter = this.gapFiller.evaluateNSByAddingAGapAfter(filteredDs, valuesToCheckForError); } if (hideOthers) { if (this.isGapSimulated) { filteredDs = WekaDataProcessingUtil.buildFilteredByAttributesDataSet(filteredDsWithOriginal, new int[] { 0, 1, filteredDsWithOriginal.attribute(original.name()).index() }); filteredDs = WekaDataProcessingUtil.buildFilteredDataSet(filteredDs, 0, filteredDs.numAttributes() - 1, Math.max(0, this.position - this.valuesBeforeAndAfter), Math.min(this.position + this.gapsize + this.valuesBeforeAndAfter, filteredDs.numInstances() - 1)); } else { filteredDs = WekaDataProcessingUtil.buildFilteredByAttributesDataSet(filteredDs, new int[] { 0, 1 }); } } final Instances decomposition = WekaTimeSeriesUtil.buildMergedDataSet(filteredDs, diff); final Attribute diffAttribute = decomposition.attribute(attr.name() + "_diff"); final List<XYAnnotation> aaa = new ArrayList<XYAnnotation>(); if (showError) { showError(this.isGapSimulated ? maeByComparingWithOriginal : maeByEnlargingGap, decomposition, diffAttribute, aaa); } if (showEnvelope) { final MainViewLoadingFrame loadingFrame = new MainViewLoadingFrame(); loadingFrame.setVisible(true); loadingFrame.pack(); loadingFrame.repaint(); showEnvelope(arr, aaa); loadingFrame.setVisible(false); } if (!inBatchMode) { final ChartPanel cp; /*if (showError) { cp=TimeSeriesChartUtil.buildChartPanelForAllAttributesInterval(decomposition,WekaDataStatsUtil.getFirstDateAttributeIdx(decomposition),mae,diffAttribute.index()); } else {*/ cp = TimeSeriesChartUtil.buildChartPanelForAllAttributes(decomposition, multAxis, WekaDataStatsUtil.getFirstDateAttributeIdx(decomposition), null, aaa); /*}*/ final Marker gapBeginMarker = new ValueMarker( dataSet.instance(Math.max(0, position - 1)).value(dateIdx)); gapBeginMarker.setPaint(Color.RED); gapBeginMarker.setLabel("Gap begin"); gapBeginMarker.setLabelAnchor(RectangleAnchor.TOP_LEFT); gapBeginMarker.setLabelTextAnchor(TextAnchor.TOP_RIGHT); cp.getChart().getXYPlot().addDomainMarker(gapBeginMarker); final Marker gapEndMarker = new ValueMarker( dataSet.instance(Math.min(dataSet.numInstances() - 1, position + gapsize)).value(dateIdx)); gapEndMarker.setPaint(Color.RED); gapEndMarker.setLabel("Gap end"); gapEndMarker.setLabelAnchor(RectangleAnchor.TOP_RIGHT); gapEndMarker.setLabelTextAnchor(TextAnchor.TOP_LEFT); cp.getChart().getXYPlot().addDomainMarker(gapEndMarker); if (!zoom) { final NumberAxis na = (NumberAxis) (cp.getChart().getXYPlot().getRangeAxis()); na.setRange(0, WekaDataStatsUtil.getMaxValue(dataSet, attrNames)); } String errorInfo; if (!this.isGapSimulated) { errorInfo = "By enlarging the gap:\t MAE=" + FormatterUtil.DECIMAL_FORMAT_4.format(maeByEnlargingGap) + "\t RMSE=" + FormatterUtil.DECIMAL_FORMAT_4.format(rmseByEnlargingGap) + "\t NASH-SUTCLIFFE=" + FormatterUtil.DECIMAL_FORMAT_4.format(nsByEnlargingGap) + "\nBy adding a gap before:\t MAE=" + FormatterUtil.DECIMAL_FORMAT_4.format(maeByAddingAGapBefore) + "\t RMSE=" + FormatterUtil.DECIMAL_FORMAT_4.format(rmseByAddingAGapBefore) + "\t NASH-SUTCLIFFE=" + FormatterUtil.DECIMAL_FORMAT_4.format(nsByAddingAGapBefore) + "\nBy adding a gap after:\t MAE=" + FormatterUtil.DECIMAL_FORMAT_4.format(maeByAddingAGapAfter) + "\t RMSE=" + FormatterUtil.DECIMAL_FORMAT_4.format(rmseByAddingAGapAfter) + "\t NASH-SUTCLIFFE=" + FormatterUtil.DECIMAL_FORMAT_4.format(nsByAddingAGapAfter); } else { errorInfo = "MAE: " + FormatterUtil.DECIMAL_FORMAT_4.format(maeByComparingWithOriginal); errorInfo += "\n"; errorInfo += "RMSE: " + FormatterUtil.DECIMAL_FORMAT_4.format(rmseByComparingWithOriginal); errorInfo += "\n"; errorInfo += "RSR: " + FormatterUtil.DECIMAL_FORMAT_4.format(rsrByComparingWithOriginal); errorInfo += "\n"; errorInfo += "PBIAS: " + FormatterUtil.DECIMAL_FORMAT_4.format(pbiasByComparingWithOriginal); errorInfo += "\n"; errorInfo += "NASH-SUTCLIFFE: " + FormatterUtil.DECIMAL_FORMAT_4.format(nsByComparingWithOriginal); errorInfo += "\n"; errorInfo += "INDEX OF AGREEMENT: " + FormatterUtil.DECIMAL_FORMAT_4.format(indexOfAgreementByComparingWithOriginal); } cp.setBorder(new TitledBorder("")); final JTextArea errorTextArea = new JTextArea(errorInfo); errorTextArea.setBorder(new TitledBorder("")); this.centerPanel.add(errorTextArea, BorderLayout.NORTH); this.centerPanel.add(cp, BorderLayout.CENTER); final JXPanel cmdPanel = new JXPanel(); final JXButton okButton = new JXButton("Ok"); okButton.addActionListener(new ActionListener() { @Override public void actionPerformed(final ActionEvent e) { final Instances correctedDataSet = buildCorrectedDataset(diff); final DataChange change = new DataChange(correctedDataSet, TabView.DataChangeTypeEnum.Update); atv.pushDataChange(change); setVisible(false); } }); cmdPanel.add(okButton); final JXButton cancelButton = new JXButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(final ActionEvent e) { setVisible(false); } }); cmdPanel.add(cancelButton); this.centerPanel.add(cmdPanel, BorderLayout.SOUTH); this.centerPanel.updateUI(); getContentPane().repaint(); } final double globalMAE = (this.isGapSimulated) ? maeByComparingWithOriginal : ((maeByEnlargingGap + maeByAddingAGapBefore + maeByAddingAGapAfter) / 3); final double globalRMSE = (this.isGapSimulated) ? rmseByComparingWithOriginal : ((rmseByEnlargingGap + rmseByAddingAGapBefore + rmseByAddingAGapAfter) / 3); final double globalRSR = (this.isGapSimulated) ? rsrByComparingWithOriginal : ((rsrByEnlargingGap + rsrByAddingAGapBefore + rsrByAddingAGapAfter) / 3); final double globalPBIAS = (this.isGapSimulated) ? pbiasByComparingWithOriginal : ((pbiasByEnlargingGap + pbiasByAddingAGapBefore + pbiasByAddingAGapAfter) / 3); final double globalNS = (this.isGapSimulated) ? nsByComparingWithOriginal : ((nsByEnlargingGap + nsByAddingAGapBefore + nsByAddingAGapAfter) / 3); final double globalIndexOfAgreement = (this.isGapSimulated) ? indexOfAgreementByComparingWithOriginal : ((indexOfAgreementByEnlargingGap + indexOfAgreementByAddingAGapBefore + indexOfAgreementByAddingAGapAfter) / 3); // usage logs for stats final long firstTimestamp = (long) dataSet.instance(position).value(dateIdx); final boolean isDuringRising; if (nearest == null) isDuringRising = GapsUtil.isDuringRising(dataSet, position, gapsize, new int[] { dateIdx, attr.index() }); else isDuringRising = GapsUtil.isDuringRising(dataSet, position, gapsize, new int[] { dateIdx, attr.index(), dataSet.attribute(nearest).index() }); return new GapFillingCase(DateUtil.getSeason(firstTimestamp), DateUtil.getYear(firstTimestamp), algo, gapsize, position, attr, gcp.getCoordinates(attr.name())[0], gcp.getCoordinates(attr.name())[1], gcp.findDownstreamStation(attr.name()) != null, gcp.findUpstreamStation(attr.name()) != null, globalMAE, globalRMSE, globalRSR, globalPBIAS, globalNS, globalIndexOfAgreement, ArraysUtil.contains(indexesOfUsedSeries, attrNames.indexOf(mostSimilar)), ArraysUtil.contains(indexesOfUsedSeries, attrNames.indexOf(nearest)), ArraysUtil.contains(indexesOfUsedSeries, attrNames.indexOf(downstream)), ArraysUtil.contains(indexesOfUsedSeries, attrNames.indexOf(upstream)), isDuringRising, GapsUtil.measureHighMiddleLowInterval(dataSet, attr.index(), position - 1)); }
From source file:org.openmrs.web.servlet.ShowGraphServlet.java
/** * The main method for this class. It will create a JFreeChart object to be written to the * response.// w ww . j av a2s . com * * @param request the current request will all the parameters needed * @return JFreeChart object to be rendered * @should set value axis label to given units * @should set value axis label to concept numeric units if given units is null */ protected JFreeChart getChart(HttpServletRequest request) { // All available GET parameters String patientId = request.getParameter("patientId"); // required String conceptId1 = request.getParameter("conceptId"); // required String conceptId2 = request.getParameter("conceptId2"); String chartTitle = request.getParameter("chartTitle"); String units = request.getParameter("units"); String minRangeString = request.getParameter("minRange"); String maxRangeString = request.getParameter("maxRange"); String hideDate = request.getParameter("hideDate"); Patient patient = Context.getPatientService().getPatient(Integer.parseInt(patientId)); // Set date range to passed values, otherwise set a default date range to the last 12 months Calendar cal = Calendar.getInstance(); Date fromDate = getFromDate(request.getParameter("fromDate")); Date toDate = getToDate(request.getParameter("toDate")); // Swap if fromDate is after toDate if (fromDate.getTime() > toDate.getTime()) { Long temp = fromDate.getTime(); fromDate.setTime(toDate.getTime()); toDate.setTime(temp); } // Graph parameters Double minRange = null; Double maxRange = null; Double normalLow = null; Double normalHigh = null; Double criticalLow = null; Double criticalHigh = null; String timeAxisTitle = null; String rangeAxisTitle = null; boolean userSpecifiedMaxRange = false; boolean userSpecifiedMinRange = false; // Fetching obs List<Obs> observations1 = new ArrayList<Obs>(); List<Obs> observations2 = new ArrayList<Obs>(); Concept concept1 = null, concept2 = null; if (conceptId1 != null) { concept1 = Context.getConceptService().getConcept(Integer.parseInt(conceptId1)); } if (conceptId2 != null) { concept2 = Context.getConceptService().getConcept(Integer.parseInt(conceptId2)); } if (concept1 != null) { observations1 = Context.getObsService().getObservationsByPersonAndConcept(patient, concept1); chartTitle = concept1.getName().getName(); rangeAxisTitle = ((ConceptNumeric) concept1).getUnits(); minRange = ((ConceptNumeric) concept1).getLowAbsolute(); maxRange = ((ConceptNumeric) concept1).getHiAbsolute(); normalLow = ((ConceptNumeric) concept1).getLowNormal(); normalHigh = ((ConceptNumeric) concept1).getHiNormal(); criticalLow = ((ConceptNumeric) concept1).getLowCritical(); criticalHigh = ((ConceptNumeric) concept1).getHiCritical(); // Only get observations2 if both concepts share the same units; update chart title and ranges if (concept2 != null) { String concept2Units = ((ConceptNumeric) concept2).getUnits(); if (concept2Units != null && concept2Units.equals(rangeAxisTitle)) { observations2 = Context.getObsService().getObservationsByPersonAndConcept(patient, concept2); chartTitle += " + " + concept2.getName().getName(); if (((ConceptNumeric) concept2).getHiAbsolute() != null && ((ConceptNumeric) concept2).getHiAbsolute() > maxRange) { maxRange = ((ConceptNumeric) concept2).getHiAbsolute(); } if (((ConceptNumeric) concept2).getLowAbsolute() != null && ((ConceptNumeric) concept2).getLowAbsolute() < minRange) { minRange = ((ConceptNumeric) concept2).getLowAbsolute(); } } else { log.warn("Units for concept id: " + conceptId2 + " don't match units for concept id: " + conceptId1 + ". Only displaying " + conceptId1); concept2 = null; // nullify concept2 so that the legend isn't shown later } } } else { chartTitle = "Concept " + conceptId1 + " not found"; rangeAxisTitle = "Value"; } // Overwrite with user-specified values, otherwise use default values if (units != null && units.length() > 0) { rangeAxisTitle = units; } if (minRangeString != null) { minRange = Double.parseDouble(minRangeString); userSpecifiedMinRange = true; } if (maxRangeString != null) { maxRange = Double.parseDouble(maxRangeString); userSpecifiedMaxRange = true; } if (chartTitle == null) { chartTitle = ""; } if (rangeAxisTitle == null) { rangeAxisTitle = ""; } if (minRange == null) { minRange = 0.0; } if (maxRange == null) { maxRange = 200.0; } // Create data set TimeSeriesCollection dataset = new TimeSeriesCollection(); TimeSeries series1, series2; // Interval-dependent units Class<? extends RegularTimePeriod> timeScale = null; if (toDate.getTime() - fromDate.getTime() <= 86400000) { // Interval <= 1 day: minutely timeScale = Minute.class; timeAxisTitle = "Time"; } else if (toDate.getTime() - fromDate.getTime() <= 259200000) { // Interval <= 3 days: hourly timeScale = Hour.class; timeAxisTitle = "Time"; } else { timeScale = Day.class; timeAxisTitle = "Date"; } if (concept1 == null) { series1 = new TimeSeries("NULL", Hour.class); } else { series1 = new TimeSeries(concept1.getName().getName(), timeScale); } if (concept2 == null) { series2 = new TimeSeries("NULL", Hour.class); } else { series2 = new TimeSeries(concept2.getName().getName(), timeScale); } // Add data points for concept1 for (Obs obs : observations1) { if (obs.getValueNumeric() != null && obs.getObsDatetime().getTime() >= fromDate.getTime() && obs.getObsDatetime().getTime() < toDate.getTime()) { cal.setTime(obs.getObsDatetime()); if (timeScale == Minute.class) { Minute min = new Minute(cal.get(Calendar.MINUTE), cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series1.addOrUpdate(min, obs.getValueNumeric()); } else if (timeScale == Hour.class) { Hour hour = new Hour(cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series1.addOrUpdate(hour, obs.getValueNumeric()); } else { Day day = new Day(cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series1.addOrUpdate(day, obs.getValueNumeric()); } } } // Add data points for concept2 for (Obs obs : observations2) { if (obs.getValueNumeric() != null && obs.getObsDatetime().getTime() >= fromDate.getTime() && obs.getObsDatetime().getTime() < toDate.getTime()) { cal.setTime(obs.getObsDatetime()); if (timeScale == Minute.class) { Minute min = new Minute(cal.get(Calendar.MINUTE), cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series2.addOrUpdate(min, obs.getValueNumeric()); } else if (timeScale == Hour.class) { Hour hour = new Hour(cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series2.addOrUpdate(hour, obs.getValueNumeric()); } else { Day day = new Day(cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series2.addOrUpdate(day, obs.getValueNumeric()); } } } // Add series to dataset dataset.addSeries(series1); if (!series2.isEmpty()) { dataset.addSeries(series2); } // As of JFreeChart 1.0.11 the default background color is dark grey instead of white. // This line restores the original white background. ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme()); JFreeChart chart = null; // Show legend only if more than one series if (concept2 == null) { chart = ChartFactory.createTimeSeriesChart(chartTitle, timeAxisTitle, rangeAxisTitle, dataset, false, false, false); } else { chart = ChartFactory.createTimeSeriesChart(chartTitle, timeAxisTitle, rangeAxisTitle, dataset, true, false, false); } // Customize title font Font font = new Font("Arial", Font.BOLD, 12); TextTitle title = chart.getTitle(); title.setFont(font); chart.setTitle(title); // Add subtitle, unless 'hideDate' has been passed if (hideDate == null) { TextTitle subtitle = new TextTitle(fromDate.toString() + " - " + toDate.toString()); subtitle.setFont(font); chart.addSubtitle(subtitle); } XYPlot plot = (XYPlot) chart.getPlot(); plot.setNoDataMessage("No Data Available"); // Add abnormal/critical range background color (only for single-concept graphs) if (concept2 == null) { IntervalMarker abnormalLow, abnormalHigh, critical; if (normalHigh != null) { abnormalHigh = new IntervalMarker(normalHigh, maxRange, COLOR_ABNORMAL); plot.addRangeMarker(abnormalHigh); } if (normalLow != null) { abnormalLow = new IntervalMarker(minRange, normalLow, COLOR_ABNORMAL); plot.addRangeMarker(abnormalLow); } if (criticalHigh != null) { critical = new IntervalMarker(criticalHigh, maxRange, COLOR_CRITICAL); plot.addRangeMarker(critical); } if (criticalLow != null) { critical = new IntervalMarker(minRange, criticalLow, COLOR_CRITICAL); plot.addRangeMarker(critical); } // there is data outside of the absolute lower limits for this concept (or of what the user specified as minrange) if (plot.getRangeAxis().getLowerBound() < minRange) { IntervalMarker error = new IntervalMarker(plot.getRangeAxis().getLowerBound(), minRange, COLOR_ERROR); plot.addRangeMarker(error); } if (plot.getRangeAxis().getUpperBound() > maxRange) { IntervalMarker error = new IntervalMarker(maxRange, plot.getRangeAxis().getUpperBound(), COLOR_ERROR); plot.addRangeMarker(error); } } // Visuals XYItemRenderer r = plot.getRenderer(); if (r instanceof XYLineAndShapeRenderer) { XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r; renderer.setBaseShapesFilled(true); renderer.setBaseShapesVisible(true); } // Customize the plot (range and domain axes) // Modify x-axis (datetime) DateAxis timeAxis = (DateAxis) plot.getDomainAxis(); if (timeScale == Day.class) { timeAxis.setDateFormatOverride(new SimpleDateFormat("dd-MMM-yyyy")); } timeAxis.setRange(fromDate, toDate); // Set y-axis range (values) NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); if (userSpecifiedMinRange) { minRange = (rangeAxis.getLowerBound() < minRange) ? rangeAxis.getLowerBound() : minRange; } if (userSpecifiedMaxRange) { // otherwise we just use default range maxRange = (rangeAxis.getUpperBound() > maxRange) ? rangeAxis.getUpperBound() : maxRange; } rangeAxis.setRange(minRange, maxRange); return chart; }