Java tutorial
package com.brainflow.application.toplevel; import com.brainflow.application.*; import com.brainflow.application.dnd.BrainCanvasTransferHandler; import com.brainflow.application.actions.*; import com.brainflow.application.presentation.*; import com.brainflow.application.services.ImageViewMousePointerEvent; import com.brainflow.colormap.ColorTable; import com.brainflow.colormap.IColorMap; import com.brainflow.colormap.LinearColorMap2; import com.brainflow.core.*; import com.brainflow.core.layer.AbstractLayer; import com.brainflow.core.layer.ImageLayer; import com.brainflow.core.layer.ImageLayer3D; import com.brainflow.core.layer.ImageLayerProperties; import com.brainflow.image.anatomy.AnatomicalPoint3D; import com.brainflow.image.anatomy.Anatomy; import com.brainflow.image.anatomy.Anatomy3D; import com.brainflow.image.data.IImageData; import com.brainflow.image.io.IImageDataSource; import com.brainflow.utils.Range; import com.jgoodies.forms.layout.CellConstraints; import com.jgoodies.forms.layout.FormLayout; import com.jidesoft.docking.DefaultDockingManager; import com.jidesoft.docking.DockContext; import com.jidesoft.docking.DockableFrame; import com.jidesoft.document.DocumentComponent; import com.jidesoft.document.DocumentPane; import com.jidesoft.plaf.LookAndFeelFactory; import com.jidesoft.plaf.UIDefaultsLookup; import com.jidesoft.plaf.basic.ThemePainter; import com.jidesoft.status.LabelStatusBarItem; import com.jidesoft.status.StatusBar; import com.jidesoft.swing.JideBoxLayout; import com.jidesoft.swing.JideTabbedPane; import com.jidesoft.dialog.JideOptionPane; import com.jidesoft.action.CommandBar; import com.jidesoft.action.CommandMenuBar; import com.pietschy.command.CommandContainer; import com.pietschy.command.GuiCommands; import com.pietschy.command.configuration.ParseException; import com.pietschy.command.group.CommandGroup; import com.pietschy.command.group.ExpansionPointBuilder; import com.pietschy.command.toggle.ToggleCommand; import com.pietschy.command.toggle.ToggleGroup; import com.sun.java.swing.plaf.windows.WindowsLookAndFeel; import org.apache.commons.vfs.FileObject; import org.apache.commons.vfs.FileSystemException; import org.apache.commons.vfs.VFS; import org.bushe.swing.event.EventBus; import org.bushe.swing.event.EventSubscriber; import javax.swing.*; import java.awt.*; import java.awt.event.KeyEvent; import java.awt.event.AWTEventListener; import java.awt.event.ActionListener; import java.awt.event.ActionEvent; import java.io.IOException; import java.io.PrintWriter; import java.io.StringWriter; import java.text.NumberFormat; import java.util.HashMap; import java.util.Map; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Callable; import java.util.concurrent.FutureTask; import java.util.logging.Level; import java.util.logging.LogManager; import java.util.logging.Logger; /** * Created by IntelliJ IDEA. * User: Owner * Date: Nov 24, 2004 * Time: 9:00:59 AM * To change this template use File | Settings | File Templates. */ public class Brainflow { static { com.jidesoft.utils.Lm.verifyLicense("UIN", "BrainFlow", "S5XiLlHH0VReaWDo84sDmzPxpMJvjP3"); } private final static Logger log = Logger.getLogger(Brainflow.class.getCanonicalName()); private BrainFrame brainFrame = null; private RecentPathMenu pathMenu = new RecentPathMenu(); private DocumentPane documentPane = new DocumentPane(); private ImageFileExplorer loadingDock = null; private StatusBar statusBar; private SelectedViewStatus viewStatus; private CommandContainer commandContainer; private ExecutorService threadService = Executors.newCachedThreadPool(); protected Brainflow() { // Exists only to thwart instantiation. } public static Brainflow getInstance() { return (Brainflow) SingletonRegistry.REGISTRY.getInstance("com.brainflow.application.toplevel.Brainflow"); } public static void main(String[] args) { final Brainflow bflow = getInstance(); SwingUtilities.invokeLater(new Runnable() { public void run() { try { log.info("Launching Brainflow ..."); bflow.launch(); } catch (Throwable e) { Logger.getAnonymousLogger().severe("Error Launching Brainflow, exiting"); e.printStackTrace(); System.exit(-1); } } }); } public JFrame getApplicationFrame() { return brainFrame; } private void splashMessage(String message) { Graphics2D g = SplashScreen.getSplashScreen().createGraphics(); //g.setComposite(AlphaComposite.Clear); //g.fillRect(20,430,100,460); //g.setPaintMode(); g.setColor(Color.WHITE); g.setFont(new Font("helvetica", Font.PLAIN, 16)); g.drawString(message, 20, 430); SplashScreen.getSplashScreen().update(); } private void reportTime(long startTime, String message) { long curTime = System.currentTimeMillis(); long duration = curTime - startTime; log.info(message + " : " + duration); } public void launch() throws Throwable { try { String osname = System.getProperty("os.name"); if (osname.toUpperCase().contains("WINDOWS")) { UIManager.setLookAndFeel(new WindowsLookAndFeel()); //UIManager.setLookAndFeel(new com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel()); //LookAndFeelFactory.NimbusInitializer init = new LookAndFeelFactory.NimbusInitializer(); //init.initialize(UIManager.getDefaults()); //UIManager.getDefaults(). LookAndFeelFactory.installJideExtension(); //LookAndFeelFactory.installJideExtension(LookAndFeelFactory.OFFICE2003_STYLE); } else if (osname.toUpperCase().contains("LINUX")) { UIManager.setLookAndFeel("com.sun.java.swing.plaf.gtk.GTKLookAndFeel"); LookAndFeelFactory.installJideExtension(LookAndFeelFactory.XERTO_STYLE); } else { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); LookAndFeelFactory.installJideExtension(); } } catch (UnsupportedLookAndFeelException e) { log.severe("could not load look and feel"); } //final SplashScreen splash = SplashScreen.getSplashScreen(); //JFrame.setDefaultLookAndFeelDecorated(true); long startTime = System.currentTimeMillis(); brainFrame = new BrainFrame(); statusBar = new StatusBar(); reportTime(startTime, "created brainframe"); brainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); log.info("initializing DisplayManager ..."); DisplayManager.getInstance().createCanvas(); log.info("initializing resources ..."); FutureTask<Boolean> initResources = new FutureTask<Boolean>(new Callable<Boolean>() { public Boolean call() throws Exception { return initializeResources(); } }); threadService.execute(initResources); log.info("loading commands ..."); FutureTask<Boolean> loadCommandsTask = new FutureTask<Boolean>(new Callable<Boolean>() { public Boolean call() throws Exception { return loadCommands(); } }); threadService.execute(loadCommandsTask); log.info("initializing IO ..."); FutureTask<Boolean> initIOTask = new FutureTask<Boolean>(new Callable<Boolean>() { public Boolean call() throws Exception { return initImageIO(); } }); threadService.execute(initIOTask); log.info("initializing status bar ..."); initializeStatusBar(); reportTime(startTime, "initialized status bar"); log.info("initializing work space ..."); initializeWorkspace(); reportTime(startTime, "initialized work space"); loadCommandsTask.get(); reportTime(startTime, "loaded commands"); log.info("binding container ..."); bindContainer(); reportTime(startTime, "bound container"); log.info("initializing tool bar ..."); initializeToolBar(); reportTime(startTime, "initialized tool bar"); log.info("initializing menu ..."); initializeMenu(); reportTime(startTime, "initialized menu"); initIOTask.get(); reportTime(startTime, "initialized IO"); initResources.get(); reportTime(startTime, "initialized resources"); initExceptionHandler(); } private boolean loadCommands() { try { GuiCommands.load("resources/commands/ImageViewCommands"); GuiCommands.load("resources/commands/BrainFlowCommands"); } catch (ParseException e) { log.severe(e.getMessage()); throw new RuntimeException(e); } return true; } public CommandContainer getCommandContainer() { return commandContainer; } private void bindContainer() { commandContainer = new CommandContainer(); commandContainer.bind(brainFrame); CommandGroup imageViewGroup = new CommandGroup("image-view-menu"); imageViewGroup.bind(brainFrame); } private void initializeLogging() { } private void initializeMenu() { log.info("initializing Menu"); GoToVoxelCommand gotoVoxelCommand = new GoToVoxelCommand(); gotoVoxelCommand.bind(getApplicationFrame()); gotoVoxelCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CommandGroup fileMenuGroup = new CommandGroup("file-menu"); fileMenuGroup.bind(getApplicationFrame()); CommandGroup viewMenuGroup = new CommandGroup("view-menu"); viewMenuGroup.bind(getApplicationFrame()); CommandGroup gotoMenuGroup = new CommandGroup("goto-menu"); gotoMenuGroup.bind(getApplicationFrame()); CommandBar menuBar = new CommandMenuBar(); menuBar.setStretch(true); menuBar.setPaintBackground(false); //JMenuBar menuBar = new JMenuBar(); menuBar.add(fileMenuGroup.createMenuItem()); menuBar.add(viewMenuGroup.createMenuItem()); menuBar.add(gotoMenuGroup.createMenuItem()); brainFrame.setJMenuBar(menuBar); MountFileSystemCommand mountFileSystemCommand = new MountFileSystemCommand(); mountFileSystemCommand.bind(getApplicationFrame()); ExitApplicationCommand exitCommand = new ExitApplicationCommand(); exitCommand.bind(getApplicationFrame()); ExpansionPointBuilder builder = fileMenuGroup.getExpansionPointBuilder(); builder.add(pathMenu.getCommandGroup()); builder.applyChanges(); brainFrame.getJMenuBar().add(DockWindowManager.getInstance().getDockMenu()); } private void initializeStatusBar() { viewStatus = new SelectedViewStatus(); log.info("initialzing status bar"); statusBar.setAutoAddSeparator(false); statusBar.add(viewStatus.getComponent(), JideBoxLayout.FIX); statusBar.add(new com.jidesoft.status.StatusBarSeparator(), JideBoxLayout.FIX); LabelStatusBarItem crossLabel = new LabelStatusBarItem(); crossLabel.setText("Cross: "); statusBar.add(crossLabel, JideBoxLayout.FIX); CursorCoordinates cursorCoordinates = new CursorCoordinates(); CrosshairCoordinates crosshairCoordinates = new CrosshairCoordinates(); statusBar.add(crosshairCoordinates.getXaxisLabel(), JideBoxLayout.FIX); statusBar.add(crosshairCoordinates.getYaxisLabel(), JideBoxLayout.FIX); statusBar.add(crosshairCoordinates.getZaxisLabel(), JideBoxLayout.FIX); statusBar.addSeparator(); LabelStatusBarItem cursorLabel = new LabelStatusBarItem(); cursorLabel.setText("Cursor: "); statusBar.add(cursorLabel, JideBoxLayout.FIX); statusBar.add(cursorCoordinates.getXaxisLabel(), JideBoxLayout.FIX); statusBar.add(cursorCoordinates.getYaxisLabel(), JideBoxLayout.FIX); statusBar.add(cursorCoordinates.getZaxisLabel(), JideBoxLayout.FIX); statusBar.addSeparator(); statusBar.add(new ValueStatusItem(), JideBoxLayout.FIX); statusBar.add(new LabelStatusBarItem(), JideBoxLayout.VARY); //statusBar.add(new com.jidesoft.status.ProgressStatusBarItem(), JideBoxLayout.FIX); //statusBar.add(new com.jidesoft.status.MemoryStatusBarItem()); brainFrame.getContentPane().add(statusBar, "South"); } private void initializeToolBar() { CommandGroup mainToolbarGroup = new CommandGroup("main-toolbar"); mainToolbarGroup.bind(getApplicationFrame()); ToggleGroup interpToggleGroup = new ToggleGroup("toggle-interp-group"); interpToggleGroup.bind(getApplicationFrame()); OpenImageCommand openImageCommand = new OpenImageCommand(); openImageCommand.bind(getApplicationFrame()); SnapshotCommand snapshotCommand = new SnapshotCommand(); snapshotCommand.bind(getApplicationFrame()); CreateAxialViewCommand axialCommand = new CreateAxialViewCommand(); axialCommand.bind(getApplicationFrame()); axialCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CreateSagittalViewCommand sagittalCommand = new CreateSagittalViewCommand(); sagittalCommand.bind(getApplicationFrame()); sagittalCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CreateCoronalViewCommand coronalCommand = new CreateCoronalViewCommand(); coronalCommand.bind(getApplicationFrame()); coronalCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CreateVerticalOrthogonalCommand vertCommand = new CreateVerticalOrthogonalCommand(); vertCommand.bind(getApplicationFrame()); vertCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CreateHorizontalOrthogonalCommand horizCommand = new CreateHorizontalOrthogonalCommand(); horizCommand.bind(getApplicationFrame()); horizCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CreateTriangularOrthogonalCommand triCommand = new CreateTriangularOrthogonalCommand(); triCommand.bind(getApplicationFrame()); triCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); CommandGroup orthoGroup = new CommandGroup("ortho-view-group"); orthoGroup.bind(getApplicationFrame()); final NextSliceCommand nextSliceCommand = new NextSliceCommand(); nextSliceCommand.bind(getApplicationFrame()); nextSliceCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); final PreviousSliceCommand previousSliceCommand = new PreviousSliceCommand(); previousSliceCommand.bind(getApplicationFrame()); previousSliceCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); Toolkit.getDefaultToolkit().addAWTEventListener(new AWTEventListener() { public void eventDispatched(AWTEvent event) { if (event.getID() == KeyEvent.KEY_PRESSED) { KeyEvent ke = (KeyEvent) event; if (ke.getKeyCode() == KeyEvent.VK_LEFT) { previousSliceCommand.execute(); } else if (ke.getKeyCode() == KeyEvent.VK_RIGHT) { nextSliceCommand.execute(); } } } }, AWTEvent.KEY_EVENT_MASK); PageBackSliceCommand pageBackSliceCommand = new PageBackSliceCommand(); pageBackSliceCommand.bind(getApplicationFrame()); pageBackSliceCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); PageForwardSliceCommand pageForwardSliceCommand = new PageForwardSliceCommand(); pageForwardSliceCommand.bind(getApplicationFrame()); pageForwardSliceCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); IncreaseContrastCommand increaseContrastCommand = new IncreaseContrastCommand(); increaseContrastCommand.bind(getApplicationFrame()); increaseContrastCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); DecreaseContrastCommand decreaseContrastCommand = new DecreaseContrastCommand(); decreaseContrastCommand.bind(getApplicationFrame()); decreaseContrastCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); ToggleCommand nearest = new NearestInterpolationToggleCommand(); nearest.bind(getApplicationFrame()); decreaseContrastCommand.installShortCut(documentPane, JComponent.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT); ToggleCommand linear = new LinearInterpolationToggleCommand(); linear.bind(getApplicationFrame()); ToggleCommand cubic = new CubicInterpolationToggleCommand(); cubic.bind(getApplicationFrame()); ToggleCommand toggleAxisLabelCommand = new ToggleAxisLabelCommand(); toggleAxisLabelCommand.bind(getApplicationFrame()); JToolBar mainToolbar = mainToolbarGroup.createToolBar(); //ActionCommand increaseContrastCommand = new IncreaseContrastCommand(); //increaseContrastCommand.bind(brainFrame); //mainToolbar.add(increaseContrastCommand.getActionAdapter()); //ActionCommand decreaseContrastCommand = new DecreaseContrastCommand(); //decreaseContrastCommand.bind(brainFrame); //mainToolbar.add(decreaseContrastCommand.getActionAdapter()); brainFrame.getContentPane().add(mainToolbar, BorderLayout.NORTH); //InputMap map = documentPane.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); //for (KeyStroke ks : map.keys()) { // System.out.println("key : " + ks); //} } private void initializeWorkspace() throws Exception { log.info("initializing workspace"); brainFrame.getDockingManager().getWorkspace().setLayout(new BorderLayout()); brainFrame.getDockingManager().getWorkspace().add(documentPane, "Center"); JComponent canvas = DisplayManager.getInstance().getSelectedCanvas().getComponent(); canvas.setRequestFocusEnabled(true); canvas.setBorder(BorderFactory.createEmptyBorder(1, 1, 1, 1)); documentPane.setTabPlacement(DocumentPane.BOTTOM); documentPane.openDocument(new DocumentComponent(new JScrollPane(canvas), "Canvas-1")); documentPane.setActiveDocument("Canvas-1"); log.info("initializing loading dock"); initLoadingDock(); log.info("initializing project view"); initProjectView(); log.info("initializing image table view"); initLoadableImageTableView(); log.info("initializing control panel"); initControlPanel(); log.info("initializing event monitor"); initEventBusMonitor(); log.info("initializing log monitor"); initLogMonitor(); brainFrame.getDockingManager().beginLoadLayoutData(); brainFrame.getDockingManager().setInitSplitPriority(DefaultDockingManager.SPLIT_EAST_WEST_SOUTH_NORTH); brainFrame.getDockingManager().loadLayoutData(); brainFrame.toFront(); Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); brainFrame.setSize((int) screenSize.getWidth(), (int) screenSize.getHeight() - 50); brainFrame.setVisible(true); CanvasBar2 cbar = new CanvasBar2(); /// TODO add automatic updating of canvas to Canvas Bar via EventBus //cbar.setImageCanvas(canvas); //////////////////////////////////////////////////////////////////// canvas.add(cbar.getComponent(), BorderLayout.NORTH); } private void initLoadingDock() { try { loadingDock = new ImageFileExplorer(VFS.getManager() .resolveFile(DirectoryManager.getInstance().getCurrentLocalDirectory().getAbsolutePath())); BrainCanvasTransferHandler handler = new BrainCanvasTransferHandler(); loadingDock.getJTree().setDragEnabled(true); //loadingDock.setTransferHandler(handler); DisplayManager.getInstance().getSelectedCanvas().getComponent().setTransferHandler(handler); DirectoryManager.getInstance().addFileSystemEventListener(new FileSystemEventListener() { public void eventOccurred(FileSystemEvent event) { final FileObject fobj = event.getFileObject(); if (fobj != null) { SwingUtilities.invokeLater(new Runnable() { public void run() { loadingDock.addFileRoot(fobj); } }); } } }); SearchableImageFileExplorer explorer = new SearchableImageFileExplorer(loadingDock); DockableFrame dframe = DockWindowManager.getInstance().createDockableFrame("File Manager", "resources/icons/fldr_obj.gif", DockContext.STATE_FRAMEDOCKED, DockContext.DOCK_SIDE_WEST); //explorer.getComponent().setPreferredSize(new Dimension(400,200)); dframe.setPreferredSize(new Dimension(275, 200)); //JScrollPane jsp = new JScrollPane(explorer.getComponent()); //jsp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); dframe.getContentPane().add(explorer.getComponent()); brainFrame.getDockingManager().addFrame(dframe); } catch (FileSystemException e) { // this would be more or less fatal, no? log.log(Level.SEVERE, e.getMessage(), e); } } private void initProjectView() throws IOException { ProjectTreeView projectTreeView = new ProjectTreeView(ProjectManager.getInstance().getActiveProject()); DockableFrame dframe = DockWindowManager.getInstance().createDockableFrame("Project", "resources/icons/folder_page.png", DockContext.STATE_FRAMEDOCKED, DockContext.DOCK_SIDE_WEST, 1); dframe.getContentPane().add(new JScrollPane(projectTreeView.getComponent())); dframe.setPreferredSize(new Dimension(275, 200)); brainFrame.getDockingManager().addFrame(dframe); } private void initLoadableImageTableView() throws IOException { LoadableImageTableView loadView = new LoadableImageTableView(); DockableFrame dframe = DockWindowManager.getInstance().createDockableFrame("Loaded Images", "resources/icons/det_pane_hide.gif", DockContext.STATE_FRAMEDOCKED, DockContext.DOCK_SIDE_WEST, 1); dframe.getContentPane().add(new JScrollPane(loadView.getComponent())); dframe.setPreferredSize(new Dimension(275, 200)); brainFrame.getDockingManager().addFrame(dframe); } private void initLogMonitor() { DockableFrame dframe = DockWindowManager.getInstance().createDockableFrame("Log Monitor", "resources/icons/console_view.gif", DockContext.STATE_AUTOHIDE, DockContext.DOCK_SIDE_SOUTH, 1); LogMonitor monitor = new LogMonitor(); monitor.setLevel(Level.FINEST); LogManager.getLogManager().getLogger("").addHandler(monitor); dframe.getContentPane().add(new JScrollPane(monitor.getComponent())); dframe.setPreferredSize(new Dimension(800, 200)); brainFrame.getDockingManager().addFrame(dframe); } private void initEventBusMonitor() { DockableFrame dframe = DockWindowManager.getInstance().createDockableFrame("Event Monitor", "resources/icons/console_view.gif", DockContext.STATE_AUTOHIDE, DockContext.DOCK_SIDE_SOUTH, 1); dframe.getContentPane().add(new JScrollPane(new EventBusMonitor().getComponent())); dframe.setPreferredSize(new Dimension(800, 200)); brainFrame.getDockingManager().addFrame(dframe); } private void initControlPanel() { JideTabbedPane tabbedPane = new JideTabbedPane(); DockableFrame dframe = DockWindowManager.getInstance().createDockableFrame("Tool Box", "resources/icons/types.gif", DockContext.STATE_FRAMEDOCKED, DockContext.DOCK_SIDE_EAST); ColorAdjustmentControl colorAdjustmentControl = new ColorAdjustmentControl(); CoordinateControls coordinateControls = new CoordinateControls(); LayerInfoControl layerInfoControl = new LayerInfoControl(); //ColorMapTablePresenter tablePresenter = new ColorMapTablePresenter(); //MaskTablePresenter maskPresenter = new MaskTablePresenter(); tabbedPane.addTab("Adjustment", new JScrollPane(colorAdjustmentControl.getComponent())); tabbedPane.addTab("Layer Info", new JScrollPane(layerInfoControl.getComponent())); //tabbedPane.addTab("Color Table", tablePresenter.getComponent()); //tabbedPane.addTab("Mask Table", maskPresenter.getComponent()); tabbedPane.addTab("Coordinates", new JScrollPane(coordinateControls.getComponent())); dframe.getContentPane().add(tabbedPane); dframe.setPreferredSize(new Dimension(300, 500)); brainFrame.getDockingManager().addFrame(dframe); } private boolean initImageIO() { log.info("initializing imageio"); try { ImageIOManager.getInstance().initialize(); } catch (BrainflowException e) { log.severe("Could not initialize IO facilities, aborting"); throw new RuntimeException(e); } return true; } private boolean initializeResources() { log.info("initializing resources"); ResourceManager.getInstance().getColorMaps(); return true; } private void register(IImageDataSource limg) { DataSourceManager manager = DataSourceManager.getInstance(); boolean alreadyRegistered = manager.isRegistered(limg); if (alreadyRegistered) { StringBuffer sb = new StringBuffer(); sb.append("Image " + limg.getDataFile().getName().getBaseName()); sb.append(" has already been loaded, would you like to reload from disk?"); Integer ret = JOptionPane.showConfirmDialog(brainFrame, sb.toString(), "Image Already Loaded", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); log.info("return value is: " + ret); if (ret == JOptionPane.YES_OPTION) { limg.releaseData(); } } else { manager.register(limg); } } private IImageDataSource specialHandling(IImageDataSource dataSource) { if (dataSource.getFileFormat().equals("Analyze7.5")) { JPanel panel = new JPanel(); JLabel messageLabel = new JLabel("Please select correct image orientation from menu: "); java.util.List<Anatomy3D> choices = Anatomy3D.getInstanceList(); JComboBox choiceBox = new JComboBox(choices.toArray()); //todo hackery alert Anatomy anatomy = dataSource.getImageInfo().getAnatomy(); choiceBox.setSelectedItem(anatomy); FormLayout layout = new FormLayout("4dlu, l:p, p:g, 4dlu", "6dlu, p, 10dlu, p, 6dlu"); CellConstraints cc = new CellConstraints(); panel.setLayout(layout); panel.add(messageLabel, cc.xyw(2, 2, 2)); panel.add(choiceBox, cc.xyw(2, 4, 2)); JOptionPane.showMessageDialog(brainFrame, panel, "Analyze 7.5 image format ...", JOptionPane.WARNING_MESSAGE); Anatomy selectedAnatomy = (Anatomy) choiceBox.getSelectedItem(); if (selectedAnatomy != anatomy) { //todo hackery alert dataSource.getImageInfo().setAnatomy((Anatomy3D) selectedAnatomy); dataSource.releaseData(); } } return dataSource; } public void loadAndDisplay(final IImageDataSource dataSource) { final IImageDataSource checkedDataSource = specialHandling(dataSource); register(checkedDataSource); ImageProgressDialog id = DataSourceManager.getInstance().createProgressDialog(checkedDataSource, new ActionListener() { public void actionPerformed(ActionEvent e) { IImageDisplayModel displayModel = ProjectManager.getInstance() .addToActiveProject(dataSource); ImageView iview = ImageViewFactory.createAxialView(displayModel); DisplayManager.getInstance().getSelectedCanvas().addImageView(iview); } }); JDialog dialog = id.getDialog(); dialog.setVisible(true); id.execute(); } public void loadAndDisplay(final IImageDataSource dataSource, final ImageView view) { final IImageDataSource checkedDataSource = specialHandling(dataSource); register(checkedDataSource); ImageProgressDialog id = DataSourceManager.getInstance().createProgressDialog(checkedDataSource, new ActionListener() { public void actionPerformed(ActionEvent e) { IImageDisplayModel dset = view.getModel(); IImageData data = dataSource.getData(); //todo data range should be a property of ImageLayerProperties, not IColorMap ImageLayerProperties params = new ImageLayerProperties( new Range(data.minValue(), data.maxValue())); //todo check data caches min and max values params.colorMap.set(new LinearColorMap2(data.minValue(), data.maxValue(), ResourceManager.getInstance().getDefaultColorMap())); ImageLayer layer = new ImageLayer3D(dataSource, params); dset.addLayer(layer); } }); JDialog dialog = id.getDialog(); dialog.setVisible(true); id.execute(); } public ImageView getSelectedView() { return DisplayManager.getInstance().getSelectedCanvas().getSelectedView(); } public IBrainCanvas getSelectedCanvas() { return DisplayManager.getInstance().getSelectedCanvas(); } public IImageDataSource[] getSelectedLoadableImages() { IImageDataSource[] limg = loadingDock.requestLoadableImages(); return limg; } class ValueStatusItem extends LabelStatusBarItem implements EventSubscriber { private Map<Color, ImageIcon> colorMap = new HashMap<Color, ImageIcon>(); private NumberFormat format = NumberFormat.getNumberInstance(); public ValueStatusItem() { EventBus.subscribeExactly(ImageViewMousePointerEvent.class, this); setIcon(ColorTable.createImageIcon(Color.GRAY, 40, 15)); setText("Value :"); } public void onEvent(Object evt) { ImageViewMousePointerEvent event = (ImageViewMousePointerEvent) evt; //todo only publish events when cursorPos is over valid view ImageView view = event.getImageView(); if (view == null) { return; } if (view.getModel().getSelectedIndex() < 0) { // no layer selected return; } if (event.getLocation() == null) { // not clear why this should ever be the case. But it is. return; } AnatomicalPoint3D gpoint = event.getLocation(); AbstractLayer layer = view.getSelectedLayer(); double value = layer.getValue(gpoint); IColorMap cmap = layer.getImageLayerProperties().getColorMap(); Color c = null; try { c = cmap.getColor(value); } catch (Exception e) { e.printStackTrace(); } ImageIcon icon = colorMap.get(c); if (icon == null) { icon = ColorTable.createImageIcon(c, 40, 15); colorMap.put(c, icon); if (colorMap.size() > 256) { colorMap.clear(); } } setText("Value: " + format.format(value)); this.setIcon(icon); } } class SelectedViewStatus extends ImageViewPresenter { private LabelStatusBarItem anatomyLabel; public SelectedViewStatus() { anatomyLabel = new LabelStatusBarItem(); anatomyLabel.setText("Layer: None"); anatomyLabel.setMinimumSize(new Dimension(100, 0)); } public void allViewsDeselected() { anatomyLabel.setText("Layer: None"); anatomyLabel.setEnabled(false); } public void viewSelected(ImageView view) { int i = view.getSelectedLayerIndex(); if (i >= 0) { anatomyLabel.setText("Layer: " + view.getModel().getLayerName(i)); anatomyLabel.setEnabled(true); } else { anatomyLabel.setText("Layer: None Selected"); anatomyLabel.setEnabled(false); } } public JComponent getComponent() { return anatomyLabel; } } private void initExceptionHandler() { LookAndFeelFactory.UIDefaultsCustomizer uiDefaultsCustomizer = new LookAndFeelFactory.UIDefaultsCustomizer() { public void customize(UIDefaults defaults) { ThemePainter painter = (ThemePainter) UIDefaultsLookup.get("Theme.painter"); defaults.put("OptionPaneUI", "com.jidesoft.plaf.basic.BasicJideOptionPaneUI"); defaults.put("OptionPane.showBanner", Boolean.TRUE); // show banner or not. default is true //defaults.put("OptionPane.bannerIcon", JideIconsFactory.getImageIcon(JideIconsFactory.JIDE50)); defaults.put("OptionPane.bannerFontSize", 13); defaults.put("OptionPane.bannerFontStyle", Font.BOLD); defaults.put("OptionPane.bannerMaxCharsPerLine", 60); defaults.put("OptionPane.bannerForeground", painter != null ? painter.getOptionPaneBannerForeground() : null); // you should adjust this if banner background is not the default gradient paint defaults.put("OptionPane.bannerBorder", null); // use default border // set both bannerBackgroundDk and // set both bannerBackgroundLt to null if you don't want gradient defaults.put("OptionPane.bannerBackgroundDk", painter != null ? painter.getOptionPaneBannerDk() : null); defaults.put("OptionPane.bannerBackgroundLt", painter != null ? painter.getOptionPaneBannerLt() : null); defaults.put("OptionPane.bannerBackgroundDirection", Boolean.TRUE); // default is true // optionally, you can set a Paint object for BannerPanel. If so, the three UIDefaults related to banner background above will be ignored. defaults.put("OptionPane.bannerBackgroundPaint", null); defaults.put("OptionPane.buttonAreaBorder", BorderFactory.createEmptyBorder(6, 6, 6, 6)); defaults.put("OptionPane.buttonOrientation", SwingConstants.RIGHT); } }; uiDefaultsCustomizer.customize(UIManager.getDefaults()); Thread.setDefaultUncaughtExceptionHandler(new Thread.UncaughtExceptionHandler() { public void uncaughtException(Thread t, Throwable e) { e.printStackTrace(); JideOptionPane optionPane = new JideOptionPane( "Click \"Details\" button to see more information ... ", JOptionPane.ERROR_MESSAGE, JideOptionPane.CLOSE_OPTION); optionPane.setTitle("An " + e.getClass().getName() + " occurred in Brainflow : " + e.getMessage()); JTextArea textArea = new JTextArea(); StringWriter sw = new StringWriter(); PrintWriter out = new PrintWriter(sw); e.printStackTrace(out); // Add string to end of text area textArea.append(sw.toString()); textArea.setRows(10); optionPane.setDetails(new JScrollPane(textArea)); JDialog dialog = optionPane.createDialog(brainFrame, "Warning"); dialog.setResizable(true); dialog.pack(); dialog.setVisible(true); } }); } /*public static class NimbusInitializer implements LookAndFeelFactory.UIDefaultsInitializer { public void initialize(UIDefaults defaults) { Object marginBorder = new SwingLazyValue( "javax.swing.plaf.basic.BasicBorders$MarginBorder"); Object[] uiDefaults = { "textHighlight", new ColorUIResource(197, 218, 233), "controlText", new ColorUIResource(Color.BLACK), "activeCaptionText", new ColorUIResource(Color.BLACK), "MenuItem.acceleratorFont", new FontUIResource("Arial", Font.PLAIN, 12), "ComboBox.background", new ColorUIResource(Color.WHITE), "ComboBox.disabledForeground", new ColorUIResource(Color.DARK_GRAY), "ComboBox.disabledBackground", new ColorUIResource(Color.GRAY), "activeCaption", new ColorUIResource(197, 218, 233), "inactiveCaption", new ColorUIResource(Color.DARK_GRAY), "control", new ColorUIResource(220, 223, 228), "controlLtHighlight", new ColorUIResource(Color.WHITE), "controlHighlight", new ColorUIResource(Color.LIGHT_GRAY), "controlShadow", new ColorUIResource(133, 137, 144), "controlDkShadow", new ColorUIResource(Color.BLACK), "MenuItem.background", new ColorUIResource(237, 239, 242), "SplitPane.background", new ColorUIResource(220, 223, 228), "Tree.hash", new ColorUIResource(Color.GRAY), "TextField.foreground", new ColorUIResource(Color.BLACK), "TextField.inactiveForeground", new ColorUIResource(Color.BLACK), "TextField.selectionForeground", new ColorUIResource(Color.WHITE), "TextField.selectionBackground", new ColorUIResource(197, 218, 233), "Table.gridColor", new ColorUIResource(Color.BLACK), "TextField.background", new ColorUIResource(Color.WHITE), "Menu.border", marginBorder, "MenuItem.border", marginBorder, "CheckBoxMenuItem.border", marginBorder, "RadioButtonMenuItem.border", marginBorder, "Table.selectionBackground", new ColorUIResource(237, 239, 242), "Table.selectionForeground", new ColorUIResource(12, 239, 242) }; LookAndFeelFactory.putDefaults(defaults, uiDefaults); } } */ }