Java tutorial
/* * To change this license header, choose License Headers in Project Properties. * To change this template file, choose Tools | Templates * and open the template in the editor. */ package be.ugent.maf.cellmissy.gui.controller.analysis.singlecell; import be.ugent.maf.cellmissy.entity.PlateCondition; import be.ugent.maf.cellmissy.entity.Track; import be.ugent.maf.cellmissy.entity.Well; import be.ugent.maf.cellmissy.entity.result.singlecell.SingleCellConditionDataHolder; import be.ugent.maf.cellmissy.entity.result.singlecell.TrackDataHolder; import be.ugent.maf.cellmissy.gui.experiment.analysis.singlecell.PlotOptionsPanel; import be.ugent.maf.cellmissy.gui.experiment.analysis.singlecell.PlotSettingsMenuBar; import be.ugent.maf.cellmissy.gui.experiment.analysis.singlecell.PlotSettingsRendererGiver; import be.ugent.maf.cellmissy.gui.view.renderer.jfreechart.TrackXYLineAndShapeRenderer; import be.ugent.maf.cellmissy.utils.GuiUtils; import be.ugent.maf.cellmissy.utils.JFreeChartUtils; import java.awt.BorderLayout; import java.awt.GridBagConstraints; import java.awt.event.ActionEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.ArrayList; import java.util.Enumeration; import java.util.List; import javax.swing.AbstractButton; import javax.swing.ButtonGroup; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.plot.PlotOrientation; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Controller; /** * This class takes care of rendering a global view showing cell trajectories * for all wells of a condition. * * @author Paola */ @Controller("globalViewConditionController") public class GlobalViewConditionController { private static final org.apache.log4j.Logger LOG = org.apache.log4j.Logger .getLogger(GlobalViewConditionController.class); // model private List<List<TrackDataHolder>> trackDataHoldersList; private List<XYSeriesCollection> xYSeriesCollections; // view private PlotSettingsMenuBar plotSettingsMenuBar; private List<ChartPanel> coordinatesChartPanels; private PlotOptionsPanel plotOptionsPanel; // parent controller @Autowired private TrackCoordinatesController trackCoordinatesController; // child controllers // services private GridBagConstraints gridBagConstraints; /** * Initialize controller */ public void init() { coordinatesChartPanels = new ArrayList<>(); trackDataHoldersList = new ArrayList<>(); xYSeriesCollections = new ArrayList<>(); gridBagConstraints = GuiUtils.getDefaultGridBagConstraints(); // init views initPlotSettingsMenuBar(); initPlotOptionsPanel(); } /** * Pass the view to the parent controller. * * @param plateCondition */ public void renderConditionGlobalView(PlateCondition plateCondition) { resetPlotLogic(); generateTrackDataHolders(plateCondition); generateDataForPlots(true); setChartsWithCollections(Integer.parseInt((String) plotOptionsPanel.getnColsComboBox().getSelectedItem())); } /** * Private methods and classes. */ /** * This will reset the plot logic. */ private void resetPlotLogic() { coordinatesChartPanels.stream().forEach((chartPanel) -> { trackCoordinatesController.getTrackCoordinatesPanel().getGlobalViewConditionParentPanel() .remove(chartPanel); }); trackCoordinatesController.getTrackCoordinatesPanel().getGlobalViewConditionParentPanel().revalidate(); trackCoordinatesController.getTrackCoordinatesPanel().getGlobalViewConditionParentPanel().repaint(); if (!xYSeriesCollections.isEmpty()) { xYSeriesCollections.clear(); } if (!coordinatesChartPanels.isEmpty()) { coordinatesChartPanels.clear(); } if (!trackDataHoldersList.isEmpty()) { trackDataHoldersList.clear(); } } /** * Action Listener for MenuItems */ private class ItemActionListener implements ItemListener { @Override public void itemStateChanged(ItemEvent e) { int length = GuiUtils.getAvailableColors().length; // iterate through the charts plotted and set the renderer for each of them for (int i = 0; i < coordinatesChartPanels.size(); i++) { ChartPanel coordinatesChartPanel = coordinatesChartPanels.get(i); JFreeChart chart = coordinatesChartPanel.getChart(); XYSeriesCollection xYSeriesCollection = (XYSeriesCollection) chart.getXYPlot().getDataset(); List<Integer> endPoints = getEndPoints(xYSeriesCollection); PlotSettingsRendererGiver plotSettingsRendererGiver = new PlotSettingsRendererGiver(-1, plotSettingsMenuBar, endPoints); TrackXYLineAndShapeRenderer renderer = plotSettingsRendererGiver.getRenderer(e); renderer.setChosenColor(GuiUtils.getAvailableColors()[i % length]); chart.getXYPlot().setRenderer(renderer); } } } /** * For the color menu item, a Color Chooser has to be shown for the user to * select the color to use. */ private class ColorItemActionListener implements ItemListener { @Override public void itemStateChanged(ItemEvent e) { int selectedTrackIndex = -1; int length = GuiUtils.getAvailableColors().length; // iterate through the charts plotted and set the renderer for each of them for (int i = 0; i < coordinatesChartPanels.size(); i++) { ChartPanel coordinatesChartPanel = coordinatesChartPanels.get(i); JFreeChart chart = coordinatesChartPanel.getChart(); XYSeriesCollection xYSeriesCollection = (XYSeriesCollection) chart.getXYPlot().getDataset(); List<Integer> endPoints = getEndPoints(xYSeriesCollection); PlotSettingsRendererGiver plotSettingsRendererGiver = new PlotSettingsRendererGiver( selectedTrackIndex, plotSettingsMenuBar, endPoints); TrackXYLineAndShapeRenderer renderer = plotSettingsRendererGiver.getRenderer(e); renderer.setChosenColor(GuiUtils.getAvailableColors()[i % length]); coordinatesChartPanel.getChart().getXYPlot().setRenderer(renderer); } } } /** * Initialize plot settings menu bar */ private void initPlotSettingsMenuBar() { // create new object plotSettingsMenuBar = new PlotSettingsMenuBar(); /** * Add item listeners to the menu items */ ItemActionListener itemActionListener = new ItemActionListener(); plotSettingsMenuBar.getPlotLinesCheckBoxMenuItem().addItemListener(itemActionListener); plotSettingsMenuBar.getPlotPointsCheckBoxMenuItem().addItemListener(itemActionListener); plotSettingsMenuBar.getShowEndPointsCheckBoxMenuItem().addItemListener(itemActionListener); for (Enumeration<AbstractButton> buttons = plotSettingsMenuBar.getLinesButtonGroup().getElements(); buttons .hasMoreElements();) { AbstractButton button = buttons.nextElement(); button.addItemListener(itemActionListener); } plotSettingsMenuBar.getUseCellMissyColors().addItemListener(new ColorItemActionListener()); } /** * Initialize plot options panel. */ private void initPlotOptionsPanel() { // make new view plotOptionsPanel = new PlotOptionsPanel(); // add radiobuttons to a button group ButtonGroup scaleAxesButtonGroup = new ButtonGroup(); scaleAxesButtonGroup.add(plotOptionsPanel.getDoNotScaleAxesRadioButton()); scaleAxesButtonGroup.add(plotOptionsPanel.getScaleAxesRadioButton()); plotOptionsPanel.getDoNotScaleAxesRadioButton().setSelected(true); // another button group for the shifted/unshifted coordinates ButtonGroup shiftedCoordinatesButtonGroup = new ButtonGroup(); shiftedCoordinatesButtonGroup.add(plotOptionsPanel.getShiftedCoordinatesRadioButton()); shiftedCoordinatesButtonGroup.add(plotOptionsPanel.getUnshiftedCoordinatesRadioButton()); plotOptionsPanel.getUnshiftedCoordinatesRadioButton().setSelected(true); /** * Action listeners */ // do not scale axes plotOptionsPanel.getDoNotScaleAxesRadioButton().addActionListener((ActionEvent e) -> { int nCols = Integer.parseInt((String) plotOptionsPanel.getnColsComboBox().getSelectedItem()); boolean useRawData = plotOptionsPanel.getUnshiftedCoordinatesRadioButton().isSelected(); resetPlotLogic(); generateTrackDataHolders(trackCoordinatesController.getCurrentCondition()); generateDataForPlots(useRawData); // use the data to set the charts setChartsWithCollections(nCols); }); // scale axes to the experiment range plotOptionsPanel.getScaleAxesRadioButton().addActionListener((ActionEvent e) -> { boolean useRawData = plotOptionsPanel.getUnshiftedCoordinatesRadioButton().isSelected(); coordinatesChartPanels.stream().forEach((chartPanel) -> { trackCoordinatesController.scaleAxesToExperiment(chartPanel.getChart(), useRawData); }); }); // shift the all coordinates to the origin plotOptionsPanel.getShiftedCoordinatesRadioButton().addActionListener((ActionEvent e) -> { int nCols = Integer.parseInt((String) plotOptionsPanel.getnColsComboBox().getSelectedItem()); resetPlotLogic(); generateTrackDataHolders(trackCoordinatesController.getCurrentCondition()); generateDataForPlots(false); // use the data to set the charts setChartsWithCollections(nCols); }); // replot the unshifted coordinates plotOptionsPanel.getUnshiftedCoordinatesRadioButton().addActionListener((ActionEvent e) -> { int nCols = Integer.parseInt((String) plotOptionsPanel.getnColsComboBox().getSelectedItem()); resetPlotLogic(); generateTrackDataHolders(trackCoordinatesController.getCurrentCondition()); generateDataForPlots(true); // use the data to set the charts setChartsWithCollections(nCols); }); // replot with a different number of columns plotOptionsPanel.getnColsComboBox().addActionListener((ActionEvent e) -> { int nCols = Integer.parseInt((String) plotOptionsPanel.getnColsComboBox().getSelectedItem()); boolean useRawData = plotOptionsPanel.getUnshiftedCoordinatesRadioButton().isSelected(); resetPlotLogic(); generateTrackDataHolders(trackCoordinatesController.getCurrentCondition()); generateDataForPlots(useRawData); // use the data to set the charts setChartsWithCollections(nCols); }); plotOptionsPanel.getPlotSettingsPanel().add(plotSettingsMenuBar, BorderLayout.CENTER); // add view to parent component trackCoordinatesController.getTrackCoordinatesPanel().getOptionsConditionParentPanel().add(plotOptionsPanel, gridBagConstraints); } /** * Generate all the track data holders for a given condition. * * @param plateCondition */ private void generateTrackDataHolders(PlateCondition plateCondition) { SingleCellConditionDataHolder conditionDataHolder = trackCoordinatesController .getConditionDataHolder(plateCondition); conditionDataHolder.getSingleCellWellDataHolders().stream().forEach((singleCellWellDataHolder) -> { trackDataHoldersList.add(singleCellWellDataHolder.getTrackDataHolders()); }); } /** * @param useRawData * @return */ private void generateDataForPlots(boolean useRawData) { trackDataHoldersList.stream().map((trackDataHolders) -> { XYSeriesCollection xYSeriesCollection = new XYSeriesCollection(); // this is not the best way to fix this multiple locations issue, but for the moment fair enough !! int counter = 0; for (TrackDataHolder trackDataHolder : trackDataHolders) { // the matrix to use is either the raw coordinates matrix or the shifted matrix Double[][] coordinatesMatrix; if (useRawData) { coordinatesMatrix = trackDataHolder.getStepCentricDataHolder().getCoordinatesMatrix(); } else { coordinatesMatrix = trackDataHolder.getStepCentricDataHolder().getShiftedCoordinatesMatrix(); } XYSeries xySeries = JFreeChartUtils.generateXYSeries(coordinatesMatrix); Track track = trackDataHolder.getTrack(); int trackNumber = track.getTrackNumber(); Well well = track.getWellHasImagingType().getWell(); String key; key = "track " + trackNumber + ", well " + well; // we check here if the collection already contains this key int seriesIndex = xYSeriesCollection.getSeriesIndex(key); if (seriesIndex == -1) { key = "track " + trackNumber + ", well " + well; } else { // should be able to get the number of the series already present !! key = "track " + trackNumber + ", well " + well + ", " + (counter + 1); counter++; } xySeries.setKey(key); xYSeriesCollection.addSeries(xySeries); } return xYSeriesCollection; }).forEach((xYSeriesCollection) -> { xYSeriesCollections.add(xYSeriesCollection); }); } /** * Set all the charts with the generated XYSeriesCollections. * * @param nCols */ private void setChartsWithCollections(int nCols) { // plot logic boolean plotLines = plotSettingsMenuBar.getPlotLinesCheckBoxMenuItem().isSelected(); boolean plotPoints = plotSettingsMenuBar.getPlotPointsCheckBoxMenuItem().isSelected(); boolean showEndPoints = plotSettingsMenuBar.getShowEndPointsCheckBoxMenuItem().isSelected(); Float lineWidth = plotSettingsMenuBar.getSelectedLineWidth(); boolean useCellMissyColor = plotSettingsMenuBar.getUseCellMissyColors().isSelected(); int nPlots = xYSeriesCollections.size(); int length = GuiUtils.getAvailableColors().length; for (int i = 0; i < nPlots; i++) { XYSeriesCollection collection = xYSeriesCollections.get(i); int numberTracks = collection.getSeries().size(); SingleCellConditionDataHolder conditionDataHolder = trackCoordinatesController .getConditionDataHolder(trackCoordinatesController.getCurrentCondition()); String title = numberTracks + " tracks" + " - " + conditionDataHolder.getSingleCellWellDataHolders().get(i).getWell(); // create a chart for each plate condition JFreeChart coordinatesChart = ChartFactory.createXYLineChart(title, "x (m)", "y (m)", collection, PlotOrientation.VERTICAL, false, true, false); // and a new chart panel as well ChartPanel coordinatesChartPanel = new ChartPanel(null); coordinatesChartPanel.setOpaque(false); // compute the constraints GridBagConstraints tempBagConstraints = GuiUtils.getTempBagConstraints(nPlots, i, nCols); trackCoordinatesController.getTrackCoordinatesPanel().getGlobalViewConditionParentPanel() .add(coordinatesChartPanel, tempBagConstraints); // see if exes need to be scaled if (plotOptionsPanel.getScaleAxesRadioButton().isSelected()) { trackCoordinatesController.scaleAxesToExperiment(coordinatesChart, plotOptionsPanel.getUnshiftedCoordinatesRadioButton().isSelected()); } JFreeChartUtils.setupTrackChart(coordinatesChart); TrackXYLineAndShapeRenderer trackXYLineAndShapeRenderer = new TrackXYLineAndShapeRenderer(plotLines, plotPoints, showEndPoints, getEndPoints(collection), -1, lineWidth, useCellMissyColor); trackXYLineAndShapeRenderer.setChosenColor(GuiUtils.getAvailableColors()[i % length]); coordinatesChart.getXYPlot().setRenderer(trackXYLineAndShapeRenderer); coordinatesChartPanel.setChart(coordinatesChart); // add the chart panels to the list coordinatesChartPanels.add(coordinatesChartPanel); trackCoordinatesController.getTrackCoordinatesPanel().getGlobalViewConditionParentPanel().revalidate(); trackCoordinatesController.getTrackCoordinatesPanel().getGlobalViewConditionParentPanel().repaint(); } } /** * Iterate through the current track data holders and get the endpoints of * the correspondent tracks. * * @return: a List of Integers, each Integer being the endpoint for a track. */ private List<Integer> getEndPoints(XYSeriesCollection xYSeriesCollection) { List<Integer> endPoints = new ArrayList<>(); for (int i = 0; i < xYSeriesCollection.getSeries().size(); i++) { endPoints.add(xYSeriesCollection.getSeries(i).getItemCount()); } return endPoints; } }