List of usage examples for org.jfree.data.xy XYSeries getItemCount
@Override public int getItemCount()
From source file:org.fhcrc.cpl.viewer.gui.MRMDialog.java
private int indexOfMaxY(XYSeries s) { double _maxy = -10000000000.0; int retVal = -1; for (int i = 0; i < s.getItemCount(); i++) { XYDataItem xydi = s.getDataItem(i); if (_maxy < xydi.getY().doubleValue()) { _maxy = xydi.getY().doubleValue(); retVal = i;//from w w w. ja v a2 s . c om } } return retVal; }
From source file:org.fhcrc.cpl.viewer.gui.MRMDialog.java
protected void createChartInPanelDaughterTasksOnly(XYPlot xyp) { XYSeries coloredDataset = transitionOnPlot.getCurrentDaughter().getGraphData(); Paint daughterColor = Utils.paleColor((Color) transitionOnPlot.getCurrentDaughter().getGraphColor()); ArrayList<XYLineAnnotation> coloredDaughters = new ArrayList<XYLineAnnotation>(); //Trace calculated elution curves over data spikes if (transitionOnPlot.getElutionCurves() != null && !transitionOnPlot.getElutionCurves().isEmpty()) { MRMDaughter curDaughter = transitionOnPlot.getCurrentDaughter(); ElutionCurveStrategy ecs = transitionOnPlot.getElutionCurves().get(curDaughter); //Is current daughter rejected? Boolean accepted = (Boolean) ((PeaksTableModel) peaksTable.getModel()).data[curDaughter .getElutionDataTableRow()][peaksData.Accept.colno]; if (accepted == null || !accepted) { xyp.setBackgroundPaint(new Color(255, 230, 230)); }// ww w . j a v a2s . c o m List<ElutionCurve> ecl = ecs.getDaughterCurves(); if (ecl != null) { for (ElutionCurve e : ecl) { List<Line2D.Double> ll2dd = e.getSegments(); for (Line2D.Double l2dd : ll2dd) { xyp.addAnnotation(Utils.line2Annotation(l2dd, new BasicStroke(2.0f), ecs.isBestDaughterCurve(e) ? Color.BLACK : Color.LIGHT_GRAY)); } } } } // If there is a valid "current" daughter draw the spikes in the daughter's color // as annotations (sensu JFree) if (coloredDataset != null) { int nOfPoints = coloredDataset.getItemCount(); for (int i = 0; i < (nOfPoints - 1); i++) { XYDataItem p1 = coloredDataset.getDataItem(i); XYDataItem p2 = coloredDataset.getDataItem(i + 1); coloredDaughters.add(new XYLineAnnotation(p1.getX().doubleValue(), p1.getY().doubleValue(), p2.getX().doubleValue(), p2.getY().doubleValue(), new BasicStroke(1.5f), transitionOnPlot.getCurrentDaughter().getGraphColor()) // new XYLineAnnotation(p1.getX().doubleValue(),p1.getY().doubleValue(),p2.getX().doubleValue(),p2.getY().doubleValue(),new BasicStroke(1.5f),daughterColor) ); } } if (_traceAllFragments) { for (MRMDaughter d : transitionOnPlot.getDaughters().values()) { if (d == transitionOnPlot.getCurrentDaughter()) continue; XYSeries curXYSeries = d.getContinDaughterData(); if (curXYSeries == null || curXYSeries.getItemCount() == 0) continue; if (d.getBestElutionCurve() == null) continue; int nOfPoints = curXYSeries.getItemCount(); for (int i = 0; i < (nOfPoints - 1); i++) { XYDataItem p1 = curXYSeries.getDataItem(i); XYDataItem p2 = curXYSeries.getDataItem(i + 1); coloredDaughters.add( // new XYLineAnnotation(p1.getX().doubleValue(),p1.getY().doubleValue(),p2.getX().doubleValue(),p2.getY().doubleValue(),new BasicStroke(1f),Utils.paleColor((Color)d.getGraphColor())) new XYLineAnnotation(p1.getX().doubleValue(), p1.getY().doubleValue(), p2.getX().doubleValue(), p2.getY().doubleValue(), new BasicStroke(1f), d.getGraphColor())); } } } if (coloredDaughters != null) { for (XYLineAnnotation xyla : coloredDaughters) { xyp.addAnnotation(xyla); } } coloredDaughters.clear(); //Display L or H label in upper left hand corner Range xRange = xyp.getDomainAxis().getRange(); Range yRange = xyp.getRangeAxis().getRange(); XYTextAnnotation lab = new XYTextAnnotation( (String) ((PeaksTableModel) peaksTable.getModel()).data[transitionOnPlot.getCurrentDaughter() .getElutionDataTableRow()][peaksData.Label.colno], xRange.getUpperBound() - (0.05 * xRange.getLength()), yRange.getUpperBound() - (0.05 * yRange.getLength())); lab.setFont(lab.getFont().deriveFont(Font.BOLD, 40.0F)); xyp.addAnnotation(lab); XYTextAnnotation midMarker = new XYTextAnnotation("\u25BC", ((MRMTransition) transitionOnPlot).getCalcXatMaxYAllDaughters(), ((MRMTransition) transitionOnPlot).getCalcMaxYAllDaughters()); midMarker.setPaint(Color.RED); midMarker.setFont(midMarker.getFont().deriveFont(Font.BOLD, 20F)); XYTextAnnotation midMarkerOutline = new XYTextAnnotation("\u25BC", ((MRMTransition) transitionOnPlot).getCalcXatMaxYAllDaughters(), ((MRMTransition) transitionOnPlot).getCalcMaxYAllDaughters()); midMarkerOutline.setPaint(Color.BLACK); midMarkerOutline.setFont(midMarker.getFont().deriveFont(Font.BOLD, 23F)); xyp.addAnnotation(midMarkerOutline); xyp.addAnnotation(midMarker); }
From source file:edu.ucla.stat.SOCR.chart.util.MixtureEMExperiment.java
private void pointSegmenting() { segmentedPoints = new XYSeriesCollection(); XYSeries mainGroup = new XYSeries(""); // mainGroup saves the points not included in any kernel XYSeries[] otherGroups = new XYSeries[num_kernels]; int num_pts = DB.nPoints(); double[][] kernel_x = new double[num_pts][num_kernels]; double[][] kernel_y = new double[num_pts][num_kernels]; int[] num_pts_in_kernel = new int[num_kernels]; for (int i = 0; i < DB.nPoints(); i++) // For each point find the 2-nd level Gaussian {/*from w w w . ja v a 2 s . c om*/ boolean found = false; double x_value = DB.xVal(i); double y_value = DB.yVal(i); for (int k = 1; k <= num_kernels; k++) // for each kernel { if (CGMix.getKernel(k) instanceof CurvedGaussian && ((CurvedGaussian) (CGMix.getKernel(k))).getPolygon().contains(x_value, y_value)) // point inside the 2nd polygon Ellipse // "CGMix") { // System.out.println("Inside::pointSegmenting()"); // System.out.println("found one point in "+k); // k is index of kernel+1 if (otherGroups[k - 1] == null) otherGroups[k - 1] = new XYSeries(""); otherGroups[k - 1].add(x_value, y_value); found = true; kernel_x[num_pts_in_kernel[k - 1]][k - 1] = (x_value); kernel_y[num_pts_in_kernel[k - 1]][k - 1] = (y_value); num_pts_in_kernel[k - 1]++; k = num_kernels; // exit inner // loop } } if (!found) { mainGroup.add(x_value, y_value); } } num_group = 0; color_groups = new Paint[num_kernels]; int results_rowCount = 0; String[][] results = new String[num_kernels * 6 + num_pts + 2][2]; Paint[] row_color = new Paint[num_kernels * 6 + num_pts + 2]; for (int i = 0; i < num_kernels; i++) { if (otherGroups[i] != null) { color_groups[num_group] = color_kernels[i]; segmentedPoints.addSeries(otherGroups[i]); num_group++; results[results_rowCount][0] = "Kernel:" + num_group; results[results_rowCount][1] = color_kernels[i].toString(); row_color[results_rowCount] = color_kernels[i]; results_rowCount++; results[results_rowCount][0] = "mX = " + CGMix.getkmx(i + 1); ; results[results_rowCount][1] = "mY = " + CGMix.getkmy(i + 1); ; row_color[results_rowCount] = color_kernels[i]; results_rowCount++; results[results_rowCount][0] = "sXX = " + CGMix.getksx(i + 1); ; results[results_rowCount][1] = "sXY = " + CGMix.getksxy(i + 1); ; row_color[results_rowCount] = color_kernels[i]; results_rowCount++; results[results_rowCount][0] = "sYX = " + CGMix.getksxy(i + 1); ; results[results_rowCount][1] = "sYY = " + CGMix.getksy(i + 1); row_color[results_rowCount] = color_kernels[i]; results_rowCount++; results[results_rowCount][0] = "weight = " + CGMix.getWeight(i + 1); results[results_rowCount][1] = "likelihood = " + CGMix.likelihood(); row_color[results_rowCount] = color_kernels[i]; results_rowCount++; results[results_rowCount][0] = "Points"; results[results_rowCount][1] = "Count = " + num_pts_in_kernel[i]; row_color[results_rowCount] = color_kernels[i]; for (int j = 0; j < num_pts_in_kernel[i]; j++) { results_rowCount++; results[results_rowCount][0] = Double.toString(kernel_x[j][i]); results[results_rowCount][1] = Double.toString(kernel_y[j][i]); row_color[results_rowCount] = color_kernels[i]; } results_rowCount++; } } results[results_rowCount][0] = "The rest"; results[results_rowCount][1] = color_mainGroup.toString(); row_color[results_rowCount] = color_mainGroup; results_rowCount++; results[results_rowCount][0] = "Points"; results[results_rowCount][1] = "Count = " + Integer.toString(mainGroup.getItemCount()); row_color[results_rowCount] = color_mainGroup; results_rowCount++; for (int i = 0; i < mainGroup.getItemCount(); i++) { results[results_rowCount][0] = mainGroup.getX(i).toString(); results[results_rowCount][1] = mainGroup.getY(i).toString(); row_color[results_rowCount] = color_mainGroup; results_rowCount++; } String[] resultsHeading = new String[2]; resultsHeading[0] = "Kernel"; resultsHeading[1] = "Resutls"; tempResultsTable = new JTable(results, resultsHeading); resetRTableRows(tempResultsTable.getRowCount()); for (int i = 0; i < tempResultsTable.getRowCount(); i++) for (int j = 0; j < tempResultsTable.getColumnCount(); j++) { resultsTable.setValueAt(tempResultsTable.getValueAt(i, j), i, j); } resultsTable.setColor(row_color, num_kernels * 6 + num_pts); num_group++; segmentedPoints.addSeries(mainGroup); }
From source file:org.lmn.fc.frameworks.starbase.plugins.observatory.ui.tabs.charts.ChartHelper.java
/*********************************************************************************************** * Create a new Chart to show only those channels which are selected. * This must work even if the ChannelSelector is NULL. * * @param chartui//from w ww .j a v a 2 s. c o m * @param dao * @param datasettype * @param primarydataset * @param secondarydatasets * @param updatetype * @param isrefreshable * @param isclickrefresh * @param displaylimit * @param domainstartpoint * @param domainendpoint * @param channelselector * @param debug * * @return JFreeChart */ private static JFreeChart createChartForSelection(final ChartUIComponentPlugin chartui, final ObservatoryInstrumentDAOInterface dao, final DatasetType datasettype, final XYDataset primarydataset, final List<XYDataset> secondarydatasets, final DataUpdateType updatetype, final boolean isrefreshable, final boolean isclickrefresh, final int displaylimit, final int domainstartpoint, final int domainendpoint, final ChannelSelectorUIComponentInterface channelselector, final boolean debug) { final String SOURCE = "ChartHelper.createChartForSelection() "; final JFreeChart jFreeChart; LOGGER.debug(debug, SOURCE); if ((datasettype != null) && (primarydataset != null) && (secondarydatasets != null) && (updatetype != null)) { final XYDataset xyNewPrimaryDataset; final List<XYDataset> listNewSecondaryDatasets; final List<XYDataset> listParentSecondaryDatasetForSeries; final Iterator iterOriginalSecondaryDatasets; final Calendar calObservatory; // Create a list of NewSecondaryDatasets for display // Add an appropriate *empty* new dataset for every one existing in the secondary set // and record the parent new Dataset for each Series in each original Dataset // So much complexity just to handle the very few cases of secondary datasets... listNewSecondaryDatasets = new ArrayList<XYDataset>(10); listParentSecondaryDatasetForSeries = new ArrayList<XYDataset>(10); iterOriginalSecondaryDatasets = secondarydatasets.iterator(); // Either find the Current Observatory calendar, or provide a default calObservatory = ObservatoryInstrumentHelper.getCurrentObservatoryCalendar(REGISTRY.getFramework(), dao, debug); while (iterOriginalSecondaryDatasets.hasNext()) { final XYDataset xyDatasetOriginal; xyDatasetOriginal = (XYDataset) iterOriginalSecondaryDatasets.next(); if ((xyDatasetOriginal != null) && (xyDatasetOriginal.getSeriesCount() > 0)) { final XYDataset xyDatasetNew; // Create an empty Dataset to correspond with the original if (datasettype.getName().equals(DatasetType.XY.getName())) { xyDatasetNew = new XYSeriesCollection(); listNewSecondaryDatasets.add(xyDatasetNew); } else if (datasettype.getName().equals(DatasetType.TIMESTAMPED.getName())) { xyDatasetNew = new TimeSeriesCollection(calObservatory.getTimeZone()); listNewSecondaryDatasets.add(xyDatasetNew); } else { xyDatasetNew = new XYSeriesCollection(); listNewSecondaryDatasets.add(xyDatasetNew); } // Record the *same* parent Dataset for each Series in each original Secondary Dataset // This creates a List in channel order, but with references to Datasets not Series for (int i = 0; i < xyDatasetOriginal.getSeriesCount(); i++) { listParentSecondaryDatasetForSeries.add(xyDatasetNew); } } } LOGGER.debug(debug, SOURCE + "Check the DatasetType"); // Confirm the DatasetType if ((datasettype.getName().equals(DatasetType.XY.getName())) && (primarydataset instanceof XYSeriesCollection)) { final XYSeriesCollection collectionPrimary; // Prepare a new XYSeriesCollection for display xyNewPrimaryDataset = new XYSeriesCollection(); // There should be a collection of <channelcount> XYSeries in the Primary Dataset // but there may also be some in the Secondary Datasets collectionPrimary = (XYSeriesCollection) primarydataset; if ((collectionPrimary.getSeriesCount() > 0) && (collectionPrimary.getSeries() != null)) { final int intChannelCount; if (channelselector != null) { channelselector.debugSelector(debug, SOURCE); if ((channelselector.getChannelSelectionModes() != null) && (channelselector.showChannels())) { intChannelCount = channelselector.getChannelSelectionModes().size(); LOGGER.debug(debug, SOURCE + "[channelcount.channelselector=" + intChannelCount + "]"); } else if (dao != null) { intChannelCount = dao.getRawDataChannelCount(); LOGGER.debug(debug, SOURCE + "[channelcount.dao.raw=" + intChannelCount + "] (has channelselector?)"); } else { intChannelCount = collectionPrimary.getSeriesCount(); LOGGER.debug(debug, SOURCE + "[channelcount.primary.series=" + intChannelCount + "]"); } } else if (dao != null) { intChannelCount = dao.getRawDataChannelCount(); LOGGER.debug(debug, SOURCE + "[channelcount.dao.raw" + intChannelCount + "] (no channelselector)"); } else { // This should never happen! intChannelCount = collectionPrimary.getSeriesCount(); LOGGER.debug(debug, SOURCE + "[channelcount.primary.series" + intChannelCount + "] (last resort)"); } LOGGER.debug(debug, SOURCE + DatasetType.XY.getName() + " [domain.start.point=" + domainstartpoint + "] [domain.end.point=" + domainendpoint + "] [channelcount.inferred=" + intChannelCount + "]"); // Find which channels to use this time round for (int intChannelIndex = 0; intChannelIndex < intChannelCount; intChannelIndex++) { final ChannelSelectionMode selectionMode; // Use the ChannelSelectionMode if we can if ((channelselector != null) && (channelselector.getChannelSelectionModes() != null) && (channelselector.showChannels())) { selectionMode = channelselector.getChannelSelectionModes().get(intChannelIndex); } else { // If there is no ChannelSelector then we can safely assume the Channel is ON selectionMode = ChannelSelectionMode.X1; } if (!ChannelSelectionMode.OFF.equals(selectionMode)) { final XYSeries seriesOriginalData; seriesOriginalData = (XYSeries) getSeriesForIndex(datasettype, primarydataset, secondarydatasets, intChannelIndex, debug); if (seriesOriginalData != null) { final XYSeries seriesChangedData; final List listOriginalDataItems; int intStartIndex; int intEndIndex; listOriginalDataItems = seriesOriginalData.getItems(); // Prepare a new Series for the changed data, with the same Key seriesChangedData = new XYSeries(seriesOriginalData.getKey()); // Map the slider values to data indexes intStartIndex = transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainstartpoint, DatasetDomainUIComponentInterface.INDEX_LEFT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.XY, calObservatory, seriesOriginalData, debug); intEndIndex = transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainendpoint, DatasetDomainUIComponentInterface.INDEX_RIGHT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.XY, calObservatory, seriesOriginalData, debug); if ((intStartIndex == -1) || (intEndIndex == -1)) { // If either index is returned as -1, then there's nothing to do... // ...so stop the for() loop intStartIndex = 0; intEndIndex = 0; } else if (intEndIndex <= intStartIndex) { intEndIndex = intStartIndex + 1; } LOGGER.debug(debug, SOURCE + "before copy of selected series subset [channel=" + intChannelIndex + "] [index.start=" + intStartIndex + "] [index.end=" + intEndIndex + "] [show.ticks=" + ((intEndIndex - intStartIndex) <= 25) + "]"); // Copy over only the selected range from the Slider for (int intDataIndex = intStartIndex; ((intDataIndex < intEndIndex) && (listOriginalDataItems.size() > 0)); intDataIndex++) { final XYDataItem dataOriginalItem; final XYDataItem dataChangedItem; dataOriginalItem = (XYDataItem) listOriginalDataItems.get(intDataIndex); if (!ChannelSelectionMode.X1.equals(selectionMode)) { // Change each value of the series according to the multiplier dataChangedItem = new XYDataItem(dataOriginalItem.getX(), dataOriginalItem.getY().doubleValue() * selectionMode.getMultiplier()); } else { // Just use the whole series unaltered for gain of X1 dataChangedItem = new XYDataItem(dataOriginalItem.getX(), dataOriginalItem.getY()); } seriesChangedData.add(dataChangedItem); } // Place the changed series in the correct collection // to correspond with the original // Did we collect any data for this Series? // If not, place a dummy point at the origin of the *visible* chart if (seriesChangedData.getItemCount() == 0) { // TODO seriesChangedData.add(new XYDataItem(0, 0)); } if (intChannelIndex < collectionPrimary.getSeriesCount()) { // Simply add the changed Primary series to the PrimaryDataset collection ((XYSeriesCollection) xyNewPrimaryDataset).addSeries(seriesChangedData); } else { // It must be a secondary dataset // Add the changed Secondary series to the parent SecondaryDataset // given by the *secondary* channel index addSecondarySeries(datasettype, listParentSecondaryDatasetForSeries, seriesChangedData, intChannelIndex - collectionPrimary.getSeriesCount()); } } else { LOGGER.warn(SOURCE + "OriginalData XYSeries unexpectedly NULL"); } } } // Dump the (partial) contents of each Series in the composite XYdataset dumpXYDataset(debug, calObservatory, xyNewPrimaryDataset, 4, SOURCE + "XYSeriesCollection --> createCustomisedChart() xyNewPrimaryDataset"); jFreeChart = chartui.createCustomisedChart(datasettype, xyNewPrimaryDataset, listNewSecondaryDatasets, updatetype, displaylimit, channelselector, debug); } else { LOGGER.error(SOURCE + " The XYSeriesCollection does not have any XYSeries"); jFreeChart = null; } } else if ((datasettype.getName().equals(DatasetType.TIMESTAMPED.getName())) && (primarydataset instanceof TimeSeriesCollection)) { final TimeSeriesCollection collectionPrimary; // Prepare a new TimeSeriesCollection for display xyNewPrimaryDataset = new TimeSeriesCollection(calObservatory.getTimeZone()); // There should be a collection of <channelcount> TimeSeries in the Primary Dataset // but there may also be some in the Secondary Datasets collectionPrimary = (TimeSeriesCollection) primarydataset; if ((collectionPrimary.getSeriesCount() > 0) && (collectionPrimary.getSeries() != null)) { final int intChannelCount; if (channelselector != null) { channelselector.debugSelector(debug, SOURCE); if ((channelselector.getChannelSelectionModes() != null) && (channelselector.showChannels())) { intChannelCount = channelselector.getChannelSelectionModes().size(); LOGGER.debug(debug, SOURCE + "[channelcount.channelselector=" + intChannelCount + "]"); } else if (dao != null) { intChannelCount = dao.getRawDataChannelCount(); LOGGER.debug(debug, SOURCE + "[channelcount.dao.raw=" + intChannelCount + "] (has channelselector)"); } else { intChannelCount = collectionPrimary.getSeriesCount(); LOGGER.debug(debug, SOURCE + "[channelcount.primary.series=" + intChannelCount + "]"); } } else if (dao != null) { intChannelCount = dao.getRawDataChannelCount(); LOGGER.debug(debug, SOURCE + "[channelcount.dao.raw=" + intChannelCount + "] (no channelselector)"); } else { // This should never happen! intChannelCount = collectionPrimary.getSeriesCount(); LOGGER.debug(debug, SOURCE + "[channelcount.primary.series=" + intChannelCount + "] (last resort)"); } LOGGER.debug(debug, SOURCE + DatasetType.TIMESTAMPED.getName() + " [domain.startpoint=" + domainstartpoint + "] [domain.endpoint=" + domainendpoint + "] [domain.lowerbound=" + (long) collectionPrimary.getDomainLowerBound(true) + "] [domain.upperbound=" + (long) collectionPrimary.getDomainUpperBound(true) + "] [channelcount.inferred=" + intChannelCount + "]"); // Find which channels to use this time round for (int intChannelIndex = 0; intChannelIndex < intChannelCount; intChannelIndex++) { final ChannelSelectionMode selectionMode; // Use the ChannelSelectionMode if we can if ((channelselector != null) && (channelselector.getChannelSelectionModes() != null) && (channelselector.showChannels())) { selectionMode = channelselector.getChannelSelectionModes().get(intChannelIndex); } else { // If there is no ChannelSelector then we can safely assume the Channel is ON selectionMode = ChannelSelectionMode.X1; } if (!ChannelSelectionMode.OFF.equals(selectionMode)) { final TimeSeries seriesOriginalData; seriesOriginalData = (TimeSeries) getSeriesForIndex(datasettype, primarydataset, secondarydatasets, intChannelIndex, debug); if (seriesOriginalData != null) { final TimeSeries seriesChangedData; final List listOriginalDataItems; int intStartIndex; int intEndIndex; listOriginalDataItems = seriesOriginalData.getItems(); // Prepare a new Series for the changed data, with the same Key seriesChangedData = new TimeSeries(seriesOriginalData.getKey().toString(), seriesOriginalData.getTimePeriodClass()); // Map the slider values to data indexes intStartIndex = transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainstartpoint, DatasetDomainUIComponentInterface.INDEX_LEFT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.TIMESTAMPED, calObservatory, seriesOriginalData, debug); intEndIndex = transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainendpoint, DatasetDomainUIComponentInterface.INDEX_RIGHT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.TIMESTAMPED, calObservatory, seriesOriginalData, debug); if ((intStartIndex == -1) || (intEndIndex == -1)) { // If either index is returned as -1, then there's nothing to do... // ...so stop the for() loop intStartIndex = 0; intEndIndex = 0; } else if (intEndIndex <= intStartIndex) { intEndIndex = intStartIndex + 1; } LOGGER.debug(debug, SOURCE + "before copy of selected series subset [channel=" + intChannelIndex + "] [index.start=" + intStartIndex + "] [index.end=" + intEndIndex + "] [item.count=" + listOriginalDataItems.size() + "]"); // Copy over only the selected range from the Slider for (int intDataIndex = intStartIndex; ((intDataIndex < intEndIndex) && (intDataIndex < listOriginalDataItems.size())); intDataIndex++) { final TimeSeriesDataItem dataOriginalItem; final TimeSeriesDataItem dataChangedItem; dataOriginalItem = (TimeSeriesDataItem) listOriginalDataItems.get(intDataIndex); if (!ChannelSelectionMode.X1.equals(selectionMode)) { // Change each value of the series according to the multiplier dataChangedItem = new TimeSeriesDataItem(dataOriginalItem.getPeriod(), dataOriginalItem.getValue().doubleValue() * selectionMode.getMultiplier()); } else { // Just use the whole series unaltered for gain of X1 dataChangedItem = new TimeSeriesDataItem(dataOriginalItem.getPeriod(), dataOriginalItem.getValue().doubleValue()); } seriesChangedData.add(dataChangedItem); } // Did we collect any data for this Series? // If not, place a dummy point at the origin of the *visible* chart if (seriesChangedData.getItemCount() == 0) { seriesChangedData.add(createDummyTimeSeriesDataItemAtOrigin(collectionPrimary, seriesOriginalData, domainstartpoint, debug)); } // Place the changed series in the correct collection // to correspond with the original if (intChannelIndex < collectionPrimary.getSeriesCount()) { // Simply add the changed Primary series to the PrimaryDataset collection ((TimeSeriesCollection) xyNewPrimaryDataset).addSeries(seriesChangedData); } else { // It must be a secondary dataset // Add the changed Secondary series to the parent SecondaryDataset // given by the *secondary* channel index addSecondarySeries(datasettype, listParentSecondaryDatasetForSeries, seriesChangedData, intChannelIndex - collectionPrimary.getSeriesCount()); } } else { LOGGER.warn(SOURCE + "OriginalData TimeSeries unexpectedly NULL"); } } } // Dump the (partial) contents of each Series in the composite XYdataset dumpXYDataset(debug, calObservatory, xyNewPrimaryDataset, 4, SOURCE + "TimeSeriesCollection --> createCustomisedChart() xyNewPrimaryDataset"); jFreeChart = chartui.createCustomisedChart(datasettype, xyNewPrimaryDataset, listNewSecondaryDatasets, updatetype, displaylimit, channelselector, debug); } else { LOGGER.error(SOURCE + " The TimeSeriesCollection does not have any TimeSeries"); jFreeChart = null; } } else { LOGGER.error(SOURCE + " The Dataset is of an invalid type"); jFreeChart = null; } } else { LOGGER.debug(debug, SOURCE + " Unable to change the Chart - invalid parameters"); jFreeChart = null; } return (jFreeChart); }
From source file:org.lmn.fc.frameworks.starbase.plugins.observatory.ui.tabs.charts.ChartUIComponent.java
/*********************************************************************************************** * Update the existing Chart referenced by the DAO, by applying the specified datasets, * using all existing channel selections and range selections. * This implementation ASSUMES a ChannelSelector is present. * * @param dao/* w w w. java 2 s .c o m*/ * @param datasettype * @param primarydataset * @param secondarydatasets * @param displaylimit * @param domainstartpoint * @param domainendpoint * @param channelselector * @param debug */ public void updateChartForSelection(final ObservatoryInstrumentDAOInterface dao, final DatasetType datasettype, final XYDataset primarydataset, final List<XYDataset> secondarydatasets, final int displaylimit, final int domainstartpoint, final int domainendpoint, final ChannelSelectorUIComponentInterface channelselector, final boolean debug) { final String SOURCE = "ChartUIComponent.updateChartForSelection() "; if ((dao != null) && (dao.getChartUI() != null) && (dao.getChartUI().getChartPanel() != null) && (dao.getChartUI().getChartPanel().getChart() != null) && (dao.getChartUI().getChartPanel().getChart().getXYPlot() != null) && (datasettype != null) && (primarydataset != null) && (secondarydatasets != null) && (channelselector != null)) { final XYDataset xyNewPrimaryDataset; final List<XYDataset> listNewSecondaryDatasets; final List<XYDataset> listParentSecondaryDatasetForSeries; final Iterator iterOriginalSecondaryDatasets; final Calendar calObservatory; // Either find the Current Observatory calendar, or provide a default calObservatory = ObservatoryInstrumentHelper.getCurrentObservatoryCalendar(REGISTRY.getFramework(), dao, debug); // Create a list of NewSecondaryDatasets for display // Add an appropriate *empty* new dataset for every one existing in the secondary set // and record the parent new Dataset for each Series in each original Dataset // So much complexity just to handle the very few cases of secondary datasets... listNewSecondaryDatasets = new ArrayList<XYDataset>(10); listParentSecondaryDatasetForSeries = new ArrayList<XYDataset>(10); iterOriginalSecondaryDatasets = secondarydatasets.iterator(); while (iterOriginalSecondaryDatasets.hasNext()) { final XYDataset xyDatasetOriginal; xyDatasetOriginal = (XYDataset) iterOriginalSecondaryDatasets.next(); if ((xyDatasetOriginal != null) && (xyDatasetOriginal.getSeriesCount() > 0)) { final XYDataset xyDatasetNew; // Create an empty Dataset to correspond with the original if (datasettype.getName().equals(DatasetType.XY.getName())) { xyDatasetNew = new XYSeriesCollection(); listNewSecondaryDatasets.add(xyDatasetNew); } else if (datasettype.getName().equals(DatasetType.TIMESTAMPED.getName())) { xyDatasetNew = new TimeSeriesCollection(calObservatory.getTimeZone()); listNewSecondaryDatasets.add(xyDatasetNew); } else { xyDatasetNew = new XYSeriesCollection(); listNewSecondaryDatasets.add(xyDatasetNew); } // Record the *same* parent Dataset for each Series in each original Secondary Dataset // This creates a List in channel order, but with references to Datasets not Series for (int i = 0; i < xyDatasetOriginal.getSeriesCount(); i++) { listParentSecondaryDatasetForSeries.add(xyDatasetNew); } } } // Confirm the DatasetType if ((datasettype.getName().equals(DatasetType.XY.getName())) && (primarydataset instanceof XYSeriesCollection)) { final XYSeriesCollection collectionPrimary; // Prepare a new XYSeriesCollection for display xyNewPrimaryDataset = new XYSeriesCollection(); // There should be a collection of <channelcount> XYSeries in the Primary Dataset // but there may also be some in the Secondary Datasets collectionPrimary = (XYSeriesCollection) primarydataset; // ToDo Make this work for ChannelSelector NULL, get channel count from primary and secondaries? Set mode to X1? if ((collectionPrimary.getSeriesCount() > 0) && (collectionPrimary.getSeries() != null) && (channelselector.getChannelSelectionModes() != null)) { LOGGER.debug(debug, SOURCE + "XY domainstartpoint=" + domainstartpoint + " domainendpoint=" + domainendpoint); ChartHelper.dumpXYDataset(debug, calObservatory, collectionPrimary, 4, SOURCE + "XYSeriesCollection --> Original Dataset"); // Find which channels and data range to use this time round for (int intChannelIndex = 0; intChannelIndex < channelselector.getChannelSelectionModes() .size(); intChannelIndex++) { final ChannelSelectionMode selectionMode; selectionMode = channelselector.getChannelSelectionModes().get(intChannelIndex); if (!ChannelSelectionMode.OFF.equals(selectionMode)) { final XYSeries seriesOriginalData; // We needed to know about the secondary datasets in order to get the correct index seriesOriginalData = (XYSeries) ChartHelper.getSeriesForIndex(datasettype, primarydataset, secondarydatasets, intChannelIndex, debug); if (seriesOriginalData != null) { final XYSeries seriesChangedData; final List listOriginalDataItems; int intStartIndex; int intEndIndex; listOriginalDataItems = seriesOriginalData.getItems(); // Prepare a new Series for the changed data, with the same Key seriesChangedData = new XYSeries(seriesOriginalData.getKey()); if (listOriginalDataItems.size() > 0) { // Map the slider values to data indexes intStartIndex = ChartHelper.transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainstartpoint, DatasetDomainUIComponentInterface.INDEX_LEFT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.XY, calObservatory, seriesOriginalData, debug); intEndIndex = ChartHelper.transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainendpoint, DatasetDomainUIComponentInterface.INDEX_RIGHT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.XY, calObservatory, seriesOriginalData, debug); if ((intStartIndex == -1) || (intEndIndex == -1)) { // If either index is returned as -1, then there's nothing to do... // ...so stop the for() loop intStartIndex = 0; intEndIndex = 0; } else if (intEndIndex <= intStartIndex) { intEndIndex = intStartIndex + 1; } LOGGER.debug(debug, SOURCE + "before copy of selected series subset [channel=" + intChannelIndex + "] [index.start=" + intStartIndex + "] [index.end=" + intEndIndex + "]"); // Copy over only the selected range from the Slider for (int intDataIndex = intStartIndex; intDataIndex < intEndIndex; intDataIndex++) { final XYDataItem dataOriginalItem; final XYDataItem dataChangedItem; dataOriginalItem = (XYDataItem) listOriginalDataItems.get(intDataIndex); if (!ChannelSelectionMode.X1.equals(selectionMode)) { // Change each value of the series according to the multiplier dataChangedItem = new XYDataItem(dataOriginalItem.getX(), dataOriginalItem.getY().doubleValue() * selectionMode.getMultiplier()); } else { // Just use the whole series unaltered for gain of X1 dataChangedItem = new XYDataItem(dataOriginalItem.getX(), dataOriginalItem.getY()); } seriesChangedData.add(dataChangedItem); } // Did we collect any data for this Series? // If not, place a dummy point at the origin of the *visible* chart if (seriesChangedData.getItemCount() == 0) { // TODO ChartHelper.createDummyXYSeriesDataItemAtOrigin() seriesChangedData.add(new XYDataItem(0, 0)); } // Place the changed series in the correct collection // to correspond with the original if (intChannelIndex < collectionPrimary.getSeriesCount()) { // Simply add the changed Primary series to the PrimaryDataset collection ((XYSeriesCollection) xyNewPrimaryDataset).addSeries(seriesChangedData); } else { // It must be a secondary dataset // Add the changed Secondary series to the parent SecondaryDataset // given by the *secondary* channel index ChartHelper.addSecondarySeries(datasettype, listParentSecondaryDatasetForSeries, seriesChangedData, intChannelIndex - collectionPrimary.getSeriesCount()); } } else { LOGGER.warn(SOURCE + "OriginalData XYSeries unexpectedly NULL"); } } else { // There are no data! Do nothing... LOGGER.warn(SOURCE + "There are no data, so do nothing"); } } } LOGGER.debug(debug, SOURCE + "Update the data shown on existing Chart"); // The outputs are xyNewPrimaryDataset and listNewSecondaryDatasets // This Chart does not use secondary datasets (yet) // Dump the (partial) contents of each Series in the new XYdataset ChartHelper.dumpXYDataset(debug, calObservatory, xyNewPrimaryDataset, 4, SOURCE + "XYSeriesCollection --> setDataset"); dao.getChartUI().getChartPanel().getChart().getXYPlot().setDataset(INDEX_DATA, xyNewPrimaryDataset); } else { LOGGER.error(SOURCE + " The XYSeriesCollection does not have any XYSeries"); } } else if ((datasettype.getName().equals(DatasetType.TIMESTAMPED.getName())) && (primarydataset instanceof TimeSeriesCollection)) { final TimeSeriesCollection collectionPrimary; LOGGER.debug(debug, SOURCE + "TIMESTAMPED domainstartpoint=" + domainstartpoint + " domainendpoint=" + domainendpoint); // Prepare a new TimeSeriesCollection for display xyNewPrimaryDataset = new TimeSeriesCollection(calObservatory.getTimeZone()); // There should be a collection of <channelcount> TimeSeries in the Primary Dataset // but there may also be some in the Secondary Datasets collectionPrimary = (TimeSeriesCollection) primarydataset; if ((collectionPrimary.getSeriesCount() > 0) && (collectionPrimary.getSeries() != null) && (channelselector.getChannelSelectionModes() != null)) { ChartHelper.dumpXYDataset(debug, calObservatory, collectionPrimary, 4, SOURCE + "TimeSeriesCollection PrimaryDataset --> Original Dataset"); // Find which channels and data range to use this time round for (int intChannelIndex = 0; intChannelIndex < channelselector.getChannelSelectionModes() .size(); intChannelIndex++) { final ChannelSelectionMode selectionMode; selectionMode = channelselector.getChannelSelectionModes().get(intChannelIndex); if (!ChannelSelectionMode.OFF.equals(selectionMode)) { final TimeSeries seriesOriginalData; // We needed to know about the secondary datasets in order to get the correct index seriesOriginalData = (TimeSeries) ChartHelper.getSeriesForIndex(datasettype, primarydataset, secondarydatasets, intChannelIndex, debug); if (seriesOriginalData != null) { final List listOriginalDataItems; final TimeSeries seriesChangedData; listOriginalDataItems = seriesOriginalData.getItems(); // Prepare a new Series for the changed data, with the same Key seriesChangedData = new TimeSeries(seriesOriginalData.getKey().toString(), seriesOriginalData.getTimePeriodClass()); if (listOriginalDataItems.size() > 0) { int intStartIndex; int intEndIndex; // Map the slider values to data indexes intStartIndex = ChartHelper.transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainstartpoint, DatasetDomainUIComponentInterface.INDEX_LEFT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.TIMESTAMPED, calObservatory, seriesOriginalData, debug); intEndIndex = ChartHelper.transformDomainSliderValueToSeriesIndex( ChartUIComponentPlugin.DOMAIN_SLIDER_MINIMUM, ChartUIComponentPlugin.DOMAIN_SLIDER_MAXIMUM, domainendpoint, DatasetDomainUIComponentInterface.INDEX_RIGHT, collectionPrimary.getDomainLowerBound(true), collectionPrimary.getDomainUpperBound(true), DatasetType.TIMESTAMPED, calObservatory, seriesOriginalData, debug); if ((intStartIndex == -1) || (intEndIndex == -1)) { // If either index is returned as -1, then there's nothing to do... // ...so stop the for() loop LOGGER.debug(debug, SOURCE + "Set EndIndex = StartIndex = 0"); intStartIndex = 0; intEndIndex = 0; } else if (intEndIndex <= intStartIndex) { LOGGER.debug(debug, SOURCE + "Correcting EndIndex less than StartIndex"); intEndIndex = intStartIndex + 1; } LOGGER.debug(debug, SOURCE + "before copy of selected series subset [channel=" + intChannelIndex + "] [start_index=" + intStartIndex + "] [end_index=" + intEndIndex + "]"); // Copy over only the selected range from the Slider for (int intDataIndex = intStartIndex; intDataIndex < intEndIndex; intDataIndex++) { final TimeSeriesDataItem dataOriginalItem; final TimeSeriesDataItem dataChangedItem; dataOriginalItem = (TimeSeriesDataItem) listOriginalDataItems .get(intDataIndex); if (!ChannelSelectionMode.X1.equals(selectionMode)) { // Change each value of the series according to the multiplier dataChangedItem = new TimeSeriesDataItem(dataOriginalItem.getPeriod(), dataOriginalItem.getValue().doubleValue() * selectionMode.getMultiplier()); } else { // Just use the whole series unaltered for gain of X1 dataChangedItem = new TimeSeriesDataItem(dataOriginalItem.getPeriod(), dataOriginalItem.getValue().doubleValue()); } seriesChangedData.add(dataChangedItem); } // Did we collect any data for this Series? // If not, place a dummy point at the origin of the *visible* chart if (seriesChangedData.getItemCount() == 0) { seriesChangedData.add(ChartHelper.createDummyTimeSeriesDataItemAtOrigin( collectionPrimary, seriesOriginalData, domainstartpoint, debug)); } // Place the changed series in the correct collection // to correspond with the original if (intChannelIndex < collectionPrimary.getSeriesCount()) { // Simply add the changed Primary series to the PrimaryDataset collection ((TimeSeriesCollection) xyNewPrimaryDataset).addSeries(seriesChangedData); } else { // It must be a secondary dataset // Add the changed Secondary series to the parent SecondaryDataset // given by the *secondary* channel index ChartHelper.addSecondarySeries(datasettype, listParentSecondaryDatasetForSeries, seriesChangedData, intChannelIndex - collectionPrimary.getSeriesCount()); } } else { // There are no data! Do nothing... LOGGER.warn(SOURCE + "There are no data, so do nothing [channel.index=" + intChannelIndex + "]"); } } else { LOGGER.warn(SOURCE + "OriginalData TimeSeries unexpectedly NULL [channel.index=" + intChannelIndex + "]"); } } else { LOGGER.debug(debug, SOURCE + "Channel is OFF [channel.index=" + intChannelIndex + "]"); } } LOGGER.debug(debug, SOURCE + "Update the data shown on existing Chart"); // The outputs are xyNewPrimaryDataset and listNewSecondaryDatasets // This Chart superclass does not use secondary datasets (yet) // Dump the (partial) contents of each Series in the new XYdataset ChartHelper.dumpXYDataset(debug, calObservatory, xyNewPrimaryDataset, 4, SOURCE + "TimeSeriesCollection NewPrimaryDataset --> setDataset"); dao.getChartUI().getChartPanel().getChart().getXYPlot().setDataset(INDEX_DATA, xyNewPrimaryDataset); } else { LOGGER.error(SOURCE + " The TimeSeriesCollection does not have any TimeSeries"); } } else { LOGGER.error(SOURCE + " The Dataset is of an invalid type"); } } else { LOGGER.debug(debug, SOURCE + " Unable to change the Chart - invalid parameters"); } }
From source file:org.micromanager.asidispim.fit.Fitter.java
/** * Utility to facilitate fitting data plotted in JFreeChart * Provide data in JFReeChart format (XYSeries), and retrieve univariate * function parameters that best fit (using least squares) the data. All data * points will be weighted equally./* www. j a va 2s . c o m*/ * * TODO: investigate whether weighting (possibly automatic weighting) can * improve accuracy * * @param data xy series in JFReeChart format * @param type one of the Fitter.FunctionType predefined functions * @param guess initial guess for the fit. The number and meaning of these parameters depends on the FunctionType. Implemented: Gaussian: 0: Normalization, 1: Mean 2: Sigma * @return array with parameters, whose meaning depends on the FunctionType. * Use the function getXYSeries to retrieve the XYDataset predicted * by this fit */ public static double[] fit(XYSeries data, FunctionType type, double[] guess) { if (type == FunctionType.NoFit) { return null; } // create the commons math data object from the JFreeChart data object final WeightedObservedPoints obs = new WeightedObservedPoints(); for (int i = 0; i < data.getItemCount(); i++) { obs.add(1.0, data.getX(i).doubleValue(), data.getY(i).doubleValue()); } double[] result = null; switch (type) { case Pol1: final PolynomialCurveFitter fitter1 = PolynomialCurveFitter.create(1); result = fitter1.fit(obs.toList()); break; case Pol2: final PolynomialCurveFitter fitter2 = PolynomialCurveFitter.create(2); result = fitter2.fit(obs.toList()); break; case Pol3: final PolynomialCurveFitter fitter3 = PolynomialCurveFitter.create(3); result = fitter3.fit(obs.toList()); break; case Gaussian: final GaussianWithOffsetCurveFitter gf = GaussianWithOffsetCurveFitter.create(); if (guess != null) { gf.withStartPoint(guess); } result = gf.fit(obs.toList()); default: break; } return result; }
From source file:org.micromanager.asidispim.fit.Fitter.java
/** * Given a JFreeChart dataset and a commons math function, return a JFreeChart * dataset in which the original x values are now accompanied by the y values * predicted by the function/* w w w.j ava2s . co m*/ * * @param data input JFreeChart data set * @param type one of the Fitter.FunctionType predefined functions * @param parms parameters describing the function. These need to match the * selected function or an IllegalArgumentEception will be thrown * * @return JFreeChart dataset with original x values and fitted y values. */ public static XYSeries getFittedSeries(XYSeries data, FunctionType type, double[] parms) { XYSeries result = new XYSeries(data.getItemCount() * 10); double minRange = data.getMinX(); double maxRange = data.getMaxX(); double xStep = (maxRange - minRange) / (data.getItemCount() * 10); switch (type) { case NoFit: try { result = data.createCopy(0, data.getItemCount() - 1); result.setKey(data.getItemCount() * 10); } catch (CloneNotSupportedException ex) { return null; } break; case Pol1: case Pol2: case Pol3: checkParms(type, parms); PolynomialFunction polFunction = new PolynomialFunction(parms); for (int i = 0; i < data.getItemCount() * 10; i++) { double x = minRange + i * xStep; double y = polFunction.value(x); result.add(x, y); } break; case Gaussian: checkParms(type, parms); Gaussian.Parametric gf = new Gaussian.Parametric(); for (int i = 0; i < data.getItemCount() * 10; i++) { double x = minRange + i * xStep; double[] gparms = new double[3]; System.arraycopy(parms, 0, gparms, 0, 3); double y = gf.value(x, gparms) + parms[3]; result.add(x, y); } break; } return result; }
From source file:org.micromanager.asidispim.fit.Fitter.java
/** * Finds the x value corresponding to the maximum function value within the * range of the provided data set.//from w w w . j a v a2s .c om * * @param type one of the Fitter.FunctionType predefined functions * @param parms parameters describing the function. These need to match the * selected function or an IllegalArgumentEception will be thrown * @param data JFreeChart series, used to bracket the range in which the * maximum will be found * * @return x value corresponding to the maximum function value */ public static double getXofMaxY(XYSeries data, FunctionType type, double[] parms) { double xAtMax = 0.0; double minX = data.getMinX(); double maxX = data.getMaxX(); switch (type) { case NoFit: // find the position in data with the highest y value double highestScore = data.getY(0).doubleValue(); int highestIndex = 0; for (int i = 1; i < data.getItemCount(); i++) { double newVal = data.getY(i).doubleValue(); if (newVal > highestScore) { highestScore = newVal; highestIndex = i; } } return data.getX(highestIndex).doubleValue(); case Pol1: case Pol2: case Pol3: checkParms(type, parms); PolynomialFunction derivativePolFunction = (new PolynomialFunction(parms)).polynomialDerivative(); final double relativeAccuracy = 1.0e-12; final double absoluteAccuracy = 1.0e-8; final int maxOrder = 5; UnivariateSolver solver = new BracketingNthOrderBrentSolver(relativeAccuracy, absoluteAccuracy, maxOrder); xAtMax = solver.solve(100, derivativePolFunction, minX, maxX); break; case Gaussian: // for a Gaussian we can take the mean and be sure it is the maximum // note that this may be outside our range of X values, but // this will be caught by our sanity checks below xAtMax = parms[1]; } // sanity checks if (xAtMax > maxX) xAtMax = maxX; if (xAtMax < minX) xAtMax = minX; return xAtMax; }
From source file:org.micromanager.asidispim.fit.Fitter.java
/** * Find the index in the data series with an x value closest to the given * searchValue//from w w w.j a va 2 s .co m * * @param data data in XYSeries format * @param searchValue x value that we try to get close to * @return index into data with x value closest to searhValue */ public static int getIndex(XYSeries data, double searchValue) { int index = 0; double diff = dataDiff(data.getX(0), searchValue); for (int i = 1; i < data.getItemCount(); i++) { double newVal = dataDiff(data.getX(i), searchValue); if (newVal < diff) { diff = newVal; index = i; } } return index; }
From source file:org.micromanager.asidispim.fit.Fitter.java
/** * Calculates a measure for the goodness of fit as defined here: * http://en.wikipedia.org/wiki/Coefficient_of_determination * R^2 = 1 - (SSres/SStot)//from w w w.j a v a 2 s. c o m * where * SSres = SUM(i) (yi - fi)^2 * end * SStot = SUM(i) (yi - yavg)^2 * * @param data input data (raw data that were fitted * @param type function type used for fitting * @param parms function parameters derived in the fit * @return */ public static double getRSquare(XYSeries data, FunctionType type, double[] parms) { // calculate SStot double yAvg = getYAvg(data); double ssTot = 0.0; for (int i = 0; i < data.getItemCount(); i++) { double y = data.getY(i).doubleValue(); ssTot += (y - yAvg) * (y - yAvg); } // calculate SSres double ssRes = 0.0; for (int i = 0; i < data.getItemCount(); i++) { double y = data.getY(i).doubleValue(); double f = getFunctionValue(data.getX(i).doubleValue(), type, parms); ssRes += (y - f) * (y - f); } return 1.0 - (ssRes / ssTot); }