bdv.viewer.ViewerOptions Java Examples

private static ViewerAndTransforms create(
		final GlobalTransformManager manager,
		final CacheControl cacheControl,
		final ViewerOptions optional,
		final ViewerAxis axis,
		final Function<Source<?>, Interpolation> interpolation)
{
	final AffineTransform3D globalToViewer = ViewerAxis.globalToViewer(axis);
	LOG.debug("Generating viewer, axis={}, globalToViewer={}", axis, globalToViewer);
	final ViewerPanelFX viewer = new ViewerPanelFX(
			1,
			cacheControl,
			optional,
			interpolation
	);
	final AffineTransformWithListeners displayTransform        = new AffineTransformWithListeners();
	final AffineTransformWithListeners globalToViewerTransform = new AffineTransformWithListeners(globalToViewer);

	return new ViewerAndTransforms(viewer, manager, displayTransform, globalToViewerTransform);
}
 

public ViewerPanelFX(
		final List<SourceAndConverter<?>> sources,
		final int numTimePoints,
		final CacheControl cacheControl,
		final Function<Source<?>, Interpolation> interpolation)
{
	this(sources, numTimePoints, cacheControl, ViewerOptions.options(), interpolation);
}
 

/**
 *
 * @param manager manages the transform from world coordinates to shared viewer space and is shared by all {@link ViewerPanelFX viewers}.
 * @param cacheControl shared between all {@link ViewerPanelFX viewers}
 * @param optional Options for {@link ViewerPanelFX}
 * @param bottomRight bottom right child
 * @param interpolation {@link Interpolation interpolation} lookup for every {@link Source}
 */
public OrthogonalViews(
		final GlobalTransformManager manager,
		final CacheControl cacheControl,
		final ViewerOptions optional,
		final BR bottomRight,
		final Function<Source<?>, Interpolation> interpolation)
{
	this.manager = manager;
	this.topLeft = create(this.manager, cacheControl, optional, ViewerAxis.Z, interpolation);
	this.topRight = create(this.manager, cacheControl, optional, ViewerAxis.X, interpolation);
	this.bottomLeft = create(this.manager, cacheControl, optional, ViewerAxis.Y, interpolation);
	this.grid = new ResizableGridPane2x2<>(topLeft.viewer, topRight.viewer, bottomLeft.viewer, bottomRight);
	this.queue = cacheControl;
}
 

/**
 *
 * delegates to {@link #PainteraBaseView(int, ViewerOptions, KeyAndMouseConfig) {@code PainteraBaseView(numFetcherThreads, ViewerOptions.options())}}
 */
public PainteraBaseView(
		final int numFetcherThreads,
		final KeyAndMouseConfig keyAndMouseBindings)
{
	this(numFetcherThreads, ViewerOptions.options(), keyAndMouseBindings);
}
 

/**
 *
 * @param numFetcherThreads number of threads used for {@link net.imglib2.cache.queue.FetcherThreads}
 * @param viewerOptions options passed down to {@link OrthogonalViews viewers}
 */
public PainteraBaseView(
		final int numFetcherThreads,
		final ViewerOptions viewerOptions,
		final KeyAndMouseConfig keyAndMouseBindings)
{
	super();
	this.sharedQueue = new SharedQueue(numFetcherThreads, 50);
	this.keyAndMouseBindings = keyAndMouseBindings;
	this.viewerOptions = viewerOptions
			.accumulateProjectorFactory(new CompositeProjectorPreMultiply.CompositeProjectorFactory(sourceInfo
					.composites()))
			// .accumulateProjectorFactory( new
			// ClearingCompositeProjector.ClearingCompositeProjectorFactory<>(
			// sourceInfo.composites(), new ARGBType() ) )
			.numRenderingThreads(Math.min(3, Math.max(1, Runtime.getRuntime().availableProcessors() / 3)));
	this.views = new OrthogonalViews<>(
			manager,
			this.sharedQueue,
			this.viewerOptions,
			viewer3D,
			s -> Optional.ofNullable(sourceInfo.getState(s)).map(SourceState::interpolationProperty).map(ObjectProperty::get).orElse(Interpolation.NLINEAR));
	this.allowedActionsProperty = new SimpleObjectProperty<>(DEFAULT_ALLOWED_ACTIONS);
	this.vsacUpdate = change -> views.setAllSources(visibleSourcesAndConverters);
	visibleSourcesAndConverters.addListener(vsacUpdate);
	LOG.debug("Meshes group={}", viewer3D.meshesGroup());
}
 

public static void main( String[] args )
{
	new ImageJ();
	SpimData spimData = twoAngles();
	
	// crashes for version 2.0.0
	// with version 2.2.0-SNAPSHOT it crashes when calling the brightness dialog, silently
	// doesn't rotate afterwards
	BigDataViewer.open( spimData, "Test 32bit", null, new ViewerOptions() );
}
 

public ViewSetupExplorerPanel( final ViewSetupExplorer< AS, X > explorer, final AS data, final String xml, final X io )
	{
		this.explorer = explorer;
		this.listeners = new ArrayList< SelectedViewDescriptionListener< AS > >();
		this.data = data;
		this.xml = xml.replace( "\\", "/" ).replace( "//", "/" ).replace( "/./", "/" );
		this.io = io;
		this.isMac = System.getProperty( "os.name" ).toLowerCase().contains( "mac" );
		this.selectedRows = new HashSet< BasicViewDescription< ? extends BasicViewSetup > >();
		this.firstSelectedVD = null;

		initComponent();

		if ( Hdf5ImageLoader.class.isInstance( data.getSequenceDescription().getImgLoader() ) )
		{
			final BDVPopup bdvpopup = bdvPopup();
			
			if ( bdvpopup != null )
			{
				bdvpopup.bdv = BigDataViewer.open( getSpimData(), xml(), IOFunctions.getProgressWriter(), ViewerOptions.options() );

//				if ( !bdv.tryLoadSettings( panel.xml() ) ) TODO: this should work, but currently tryLoadSettings is protected. fix that.
					InitializeViewerState.initBrightness( 0.001, 0.999, bdvpopup.bdv.getViewer(), bdvpopup.bdv.getSetupAssignments() );

				// do not rotate BDV view by default
				BDVPopup.initTransform( bdvpopup.bdv.getViewer() );

				setFusedModeSimple( bdvpopup.bdv, data );
			}
		}
	}
 

/**
 *
 * Will create {@link ViewerPanelFX} and populate with {@code sources}.
 *
 * @param sources
 * 		the {@link SourceAndConverter sources} to display.
 * @param numTimepoints
 * 		number of available timepoints.
 * @param cacheControl
 * 		to control IO budgeting and fetcher queue.
 * @param optional
 * 		optional parameters. See {@link ViewerOptions#options()}.
 * @param interpolation
 *      Get interpolation method for each data source.
 */
public ViewerPanelFX(
		final List<SourceAndConverter<?>> sources,
		final int numTimepoints,
		final CacheControl cacheControl,
		final ViewerOptions optional,
		final Function<Source<?>, Interpolation> interpolation)
{
	super();
	super.getChildren().setAll(canvasPane, overlayPane);
	this.renderingExecutorService = Executors.newFixedThreadPool(optional.values.getNumRenderingThreads(), new RenderThreadFactory());
	options = optional.values;

	threadGroup = new ThreadGroup(this.toString());
	viewerTransform = new AffineTransform3D();

	transformListeners = new CopyOnWriteArrayList<>();

	mouseTracker.installInto(this);

	this.renderUnit = new RenderUnit(
		threadGroup,
		this::getState,
		interpolation,
		options.getAccumulateProjectorFactory(),
		cacheControl,
		options.getTargetRenderNanos(),
		options.getNumRenderingThreads(),
		renderingExecutorService
	);

	setRenderedImageListener();
	this.widthProperty().addListener((obs, oldv, newv) -> this.renderUnit.setDimensions((long)getWidth(), (long)getHeight()));
	this.heightProperty().addListener((obs, oldv, newv) -> this.renderUnit.setDimensions((long)getWidth(), (long)getHeight()));
	setWidth(options.getWidth());
	setHeight(options.getHeight());

	// TODO why is this necessary?
	transformListeners.add(tf -> getDisplay().drawOverlays());

	this.state = new ViewerState(numTimepoints);
	state.addListener(obs -> requestRepaint());

	setAllSources(sources);
}
 

public void openBDV(File xmlFile) throws SpimDataException {
	options = ViewerOptions.options();
	viewer = BigDataViewer.open(xmlFile.getAbsolutePath(), xmlFile.getName(), new ProgressWriterIJ(), options);
}
 

public static BigDataViewer createBDV( final ExplorerWindow< ? , ? > panel , LinkOverlay lo)
{
	if ( AbstractImgLoader.class.isInstance( panel.getSpimData().getSequenceDescription().getImgLoader() ) )
	{
		if ( JOptionPane.showConfirmDialog( null,
				"Opening <SpimData> dataset that is not suited for interactive browsing.\n" +
				"Consider resaving as HDF5 for better performance.\n" +
				"Proceed anyways?",
				"Warning",
				JOptionPane.YES_NO_OPTION ) == JOptionPane.NO_OPTION )
			return null;
	}

	boolean allViews2D = true;
	@SuppressWarnings("unchecked")
	final Collection< BasicViewDescription< ? > > viewDescriptions =
		(Collection< BasicViewDescription< ? > >) panel.getSpimData().getSequenceDescription().getViewDescriptions().values();
	for (final BasicViewDescription< ? > vd : viewDescriptions)
		if (vd.isPresent() && vd.getViewSetup().hasSize() && vd.getViewSetup().getSize().dimension( 2 ) != 1)
		{
			allViews2D = false;
			break;
		}

	final ViewerOptions options = ViewerOptions.options().accumulateProjectorFactory( MaximumProjectorARGB.factory );
	if (allViews2D)
	{
		options.transformEventHandlerFactory(new BehaviourTransformEventHandlerPlanarFactory() );
	}

	BigDataViewer bdv = BigDataViewer.open( panel.getSpimData(), 
											"BigDataViewer", 
											null, 
											options );

	BDVPopup.initTransform( bdv.getViewer() );		
	// if ( !bdv.tryLoadSettings( panel.xml() ) ) TODO: this should
	// work, but currently tryLoadSettings is protected. fix that.
	BDVPopup.initBrightness( 0.001, 0.999, bdv.getViewer().getState(), bdv.getSetupAssignments() );

	FilteredAndGroupedExplorerPanel.setFusedModeSimple( bdv, panel.getSpimData() );

	minMaxGroupByChannels( bdv, panel.getSpimData() );
	colorByChannels( bdv, panel.getSpimData(), 0 );

	Set<Class<? extends Entity>> groupingFactors = new HashSet<>();
	groupingFactors.add( Channel.class );
	groupingFactors.add( Illumination.class );		
	groupSourcesByFactors( bdv, panel.getSpimData(), groupingFactors );

	FilteredAndGroupedExplorerPanel.updateBDV( bdv, panel.colorMode(), panel.getSpimData(), panel.firstSelectedVD(), ((GroupedRowWindow)panel).selectedRowsGroups());

	ScrollableBrightnessDialog.setAsBrightnessDialog( bdv );

	bdv.getViewer().addTransformListener( lo );
	bdv.getViewer().getDisplay().addOverlayRenderer( lo );
	
	bdv.getViewerFrame().setVisible( true );		
	bdv.getViewer().requestRepaint();

	return bdv;
	
}
 

public static BigDataViewer createBDV( final ViewSetupExplorerPanel< ?, ? > panel )
	{
		BasicImgLoader il = panel.getSpimData().getSequenceDescription().getImgLoader();
		if ( AbstractImgLoader.class.isInstance( il ) || StackImgLoader.class.isInstance( il ) )
		{
			if ( JOptionPane.showConfirmDialog( null,
					"Opening <SpimData> dataset that is not suited for interactive browsing.\n" +
					"Consider resaving as HDF5 for better performance.\n" +
					"Proceed anyways?",
					"Warning",
					JOptionPane.YES_NO_OPTION ) == JOptionPane.NO_OPTION )
				return null;
		}

		BigDataViewer bdv = BigDataViewer.open( panel.getSpimData(), panel.xml(), IOFunctions.getProgressWriter(), ViewerOptions.options() );
//		if ( !bdv.tryLoadSettings( panel.xml() ) ) TODO: this should work, but currently tryLoadSettings is protected. fix that.
			InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewer(), bdv.getSetupAssignments() );

		// do not rotate BDV view by default
		BDVPopup.initTransform( bdv.getViewer() );

		ViewSetupExplorerPanel.updateBDV( bdv, panel.colorMode(), panel.getSpimData(), panel.firstSelectedVD(), panel.selectedRows() );

//		final ArrayList< InterestPointSource > interestPointSources = new ArrayList< InterestPointSource >();
//		interestPointSources.add( new InterestPointSource()
//		{
//			private final ArrayList< RealPoint > points;
//			{
//				points = new ArrayList< RealPoint >();
//				final Random rand = new Random();
//				for ( int i = 0; i < 1000; ++i )
//					points.add( new RealPoint( rand.nextDouble() * 1400, rand.nextDouble() * 800, rand.nextDouble() * 300 ) );
//			}
//
//			@Override
//			public final Collection< ? extends RealLocalizable > getLocalCoordinates( final int timepointIndex )
//			{
//				return points;
//			}
//
//			@Override
//			public void getLocalToGlobalTransform( final int timepointIndex, final AffineTransform3D transform )
//			{
//				transform.identity();
//			}
//		} );
//		final InterestPointOverlay interestPointOverlay = new InterestPointOverlay( bdv.getViewer(), interestPointSources );
//		bdv.getViewer().addRenderTransformListener( interestPointOverlay );
//		bdv.getViewer().getDisplay().addOverlayRenderer( interestPointOverlay );
//		bdv.getViewer().removeTransformListener( interestPointOverlay );
//		bdv.getViewer().getDisplay().removeOverlayRenderer( interestPointOverlay );

		return bdv;
	}
 

public static Pair< BigDataViewer, Boolean > getBDV( final AbstractSpimData< ? > spimData, final Collection< ViewId > viewIdsToProcess )
	{
		final BDVPopup popup = ViewSetupExplorerPanel.bdvPopup();
		BigDataViewer bdv;
		boolean bdvIsLocal = false;

		if ( popup == null || popup.panel == null )
		{
			// locally run instance
			if ( AbstractImgLoader.class.isInstance( spimData.getSequenceDescription().getImgLoader() ) )
			{
				if ( JOptionPane.showConfirmDialog( null,
						"Opening <SpimData> dataset that is not suited for interactive browsing.\n" +
						"Consider resaving as HDF5 for better performance.\n" +
						"Proceed anyways?",
						"Warning",
						JOptionPane.YES_NO_OPTION ) == JOptionPane.NO_OPTION )
					return null;
			}

			bdv = BigDataViewer.open( spimData, "BigDataViewer", IOFunctions.getProgressWriter(), ViewerOptions.options() );
			bdvIsLocal = true;

//			if ( !bdv.tryLoadSettings( panel.xml() ) ) TODO: this should work, but currently tryLoadSettings is protected. fix that.
				InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewer(), bdv.getSetupAssignments() );

			final List< BasicViewDescription< ? > > vds = new ArrayList< BasicViewDescription< ? > >();

			for ( final ViewId viewId : viewIdsToProcess )
				vds.add( spimData.getSequenceDescription().getViewDescriptions().get( viewId ) );

			ViewSetupExplorerPanel.updateBDV( bdv, true, spimData, null, vds );
		}
		else if ( popup.bdv == null )
		{
			// if BDV was closed by the user
			if ( popup.bdv != null && !popup.bdv.getViewerFrame().isVisible() )
				popup.bdv = null;

			try
			{
				bdv = popup.bdv = BDVPopup.createBDV( popup.panel );
			}
			catch (Exception e)
			{
				IOFunctions.println( "Could not run BigDataViewer: " + e );
				e.printStackTrace();
				bdv = popup.bdv = null;
			}
		}
		else
		{
			bdv = popup.bdv;
		}

		return new ValuePair< BigDataViewer, Boolean >( bdv, bdvIsLocal );
	}
 

/**
 * Will create {@link ViewerPanelFX} without any data sources and a single time point.
 *
 * @param cacheControl
 * 		to control IO budgeting and fetcher queue.
 * @param optional
 * 		optional parameters. See {@link ViewerOptions#options()}.
 * @param interpolation
 *      Get interpolation method for each data source.
 */
public ViewerPanelFX(
		final CacheControl cacheControl,
		final ViewerOptions optional,
		final Function<Source<?>, Interpolation> interpolation)
{
	this(1, cacheControl, optional, interpolation);
}
 

/**
 * Will create {@link ViewerPanelFX} without any data sources.
 *
 * @param numTimepoints
 * 		number of available timepoints.
 * @param cacheControl
 * 		to control IO budgeting and fetcher queue.
 * @param optional
 * 		optional parameters. See {@link ViewerOptions#options()}.
 * @param interpolation
 *      Get interpolation method for each data source.
 */
public ViewerPanelFX(
		final int numTimepoints,
		final CacheControl cacheControl,
		final ViewerOptions optional,
		final Function<Source<?>, Interpolation> interpolation)
{
	this(new ArrayList<>(), numTimepoints, cacheControl, optional, interpolation);
}