Index (BigDataViewer Core 10.6.11 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Z
All Classes All Packages

A

abort() - Method in class bdv.tools.bookmarks.BookmarksEditor
abort() - Method in class bdv.tools.transformation.ManualTransformationEditor: End the ongoing manual transformation and discard the incremental transformation.
AbstractAnimator - Class in bdv.viewer.animate: Mother abstract class for animators that can animate the current view in a ViewerFrame instance.
AbstractAnimator(long) - Constructor for class bdv.viewer.animate.AbstractAnimator: Create new animator with the given duration.
AbstractCachedViewerSetupImgLoader<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>,A extends net.imglib2.img.basictypeaccess.volatiles.VolatileAccess & net.imglib2.img.basictypeaccess.DataAccess> - Class in bdv: Abstract ViewerSetupImgLoader with a VolatileGlobalCellCache.
AbstractCachedViewerSetupImgLoader(int, long[][], int[][], double[][], T, V, CacheArrayLoader<A>, VolatileGlobalCellCache) - Constructor for class bdv.AbstractCachedViewerSetupImgLoader
AbstractKeymapManager<T extends AbstractKeymapManager<T>> - Class in bdv.ui.keymap: Manages a collection of Keymap.
AbstractKeymapManager() - Constructor for class bdv.ui.keymap.AbstractKeymapManager
AbstractLegacyViewerImgLoader<T,V extends net.imglib2.Volatile<T>> - Class in bdv.spimdata.legacy
AbstractLegacyViewerImgLoader(T, V) - Constructor for class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
AbstractSource<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
AbstractSource(Supplier<T>, String) - Constructor for class bdv.util.AbstractSource
AbstractSource(T, String) - Constructor for class bdv.util.AbstractSource
AbstractSource(T, String, boolean) - Constructor for class bdv.util.AbstractSource
AbstractSource(T, String, VoxelDimensions) - Constructor for class bdv.util.AbstractSource
AbstractSource(T, String, VoxelDimensions, boolean) - Constructor for class bdv.util.AbstractSource
AbstractSpimSource<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv
AbstractSpimSource(AbstractSpimData<?>, int, String) - Constructor for class bdv.AbstractSpimSource
AbstractStyle<S extends AbstractStyle<S>> - Class in bdv.ui.settings.style
AbstractStyle(String) - Constructor for class bdv.ui.settings.style.AbstractStyle
AbstractStyleManager<M extends AbstractStyleManager<M,S>,S extends Style<S>> - Class in bdv.ui.settings.style
AbstractStyleManager() - Constructor for class bdv.ui.settings.style.AbstractStyleManager
AbstractTransformAnimator - Class in bdv.viewer.animate: Mother abstract class for animators that animate the current view in a ViewerFrame instance by modifying the viewer transform.
AbstractTransformAnimator(long) - Constructor for class bdv.viewer.animate.AbstractTransformAnimator: Create new animator with the given duration.
AbstractTransformedBoxModel - Class in bdv.tools.boundingbox: A transformed box that can be modified and notifies listeners about changes.
AbstractTransformedBoxModel(AffineTransform3D) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxModel
AbstractTransformedBoxModel.IntervalChangedListener - Interface in bdv.tools.boundingbox
AbstractTransformedBoxSelectionDialog<R> - Class in bdv.tools.boundingbox
AbstractTransformedBoxSelectionDialog(Window, String) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog
AbstractTransformedBoxSelectionDialog.OkCancelPanel - Class in bdv.tools.boundingbox: A panel containing OK and Cancel buttons, and callback lists for both.
AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel - Class in bdv.tools.boundingbox: A panel that contains sliders to adjust timepoint, timepoint range, or nothing.
AbstractViewerPanel - Class in bdv.viewer: Abstract base class for ViewerPanel.
AbstractViewerPanel(LayoutManager) - Constructor for class bdv.viewer.AbstractViewerPanel
AbstractViewerPanel(LayoutManager, boolean) - Constructor for class bdv.viewer.AbstractViewerPanel
AbstractViewerPanel.AlignPlane - Enum in bdv.viewer: The planes which can be aligned with the viewer coordinate system: XY, ZY, and XZ plane.
AbstractViewerPanel.MouseCoordinateListener - Class in bdv.viewer
AbstractViewerSetupImgLoader<T,V extends net.imglib2.Volatile<T>> - Class in bdv
AbstractViewerSetupImgLoader(T, V) - Constructor for class bdv.AbstractViewerSetupImgLoader
Access() - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
Access(BoxRealRandomAccessible.Access) - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
accessible - Variable in class bdv.util.RealRandomAccessibleSource
accumulate(Cursor<? extends A>[], B) - Method in class bdv.viewer.render.AccumulateProjector
ACCUMULATE_PROJECTOR_CHANGED - bdv.viewer.ViewerStateChange
AccumulateProjector<A,B> - Class in bdv.viewer.render
AccumulateProjector(List<VolatileProjector>, List<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval) - Constructor for class bdv.viewer.render.AccumulateProjector
AccumulateProjector(List<VolatileProjector>, List<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjector: Deprecated.
Use AccumulateProjector(List, List, RandomAccessibleInterval). The numThreads and executorService arguments are ignored.
AccumulateProjectorARGB - Class in bdv.viewer.render
AccumulateProjectorARGB() - Constructor for class bdv.viewer.render.AccumulateProjectorARGB
AccumulateProjectorARGB.Factory - Class in bdv.viewer.render
accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.util.BdvOptions: Set the factory for creating AccumulateProjector.
accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.viewer.ViewerOptions: Set the factory for creating AccumulateProjector.
AccumulateProjectorFactory<A> - Interface in bdv.viewer.render
actionPerformed(ActionEvent) - Method in class bdv.tools.ToggleDialogAction
activeSourcesDialog - Variable in class bdv.BigDataViewer
add(int, E) - Method in class bdv.util.WrappedList
add(E) - Method in class bdv.util.WrappedList
add(String) - Method in class bdv.viewer.animate.MessageOverlayAnimator
addAll(int, Collection<? extends E>) - Method in class bdv.util.WrappedList
addAll(Collection<? extends E>) - Method in class bdv.util.WrappedList
addCacheControl(CacheControl) - Method in class bdv.cache.CacheControl.CacheControls
addCacheControl(CacheControl, int) - Method in class bdv.cache.CacheControl.CacheControls
addCard(Object, String, JComponent, boolean) - Method in class bdv.ui.CardPanel
addCard(Object, String, JComponent, boolean, Insets) - Method in class bdv.ui.CardPanel: Add a new JComponent to the card panel.
addCard(String, JComponent, boolean) - Method in class bdv.ui.CardPanel
addCard(String, JComponent, boolean, Insets) - Method in class bdv.ui.CardPanel: Add a new JComponent to the card panel.
addGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Add group to the state.
addGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Add group to the state.
addGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState: Add group to the state (optional operation).
addGroup(SourceGroup) - Method in class bdv.viewer.state.ViewerState: Deprecated.
addGroup(SourceGroup) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
addGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.BasicViewerState: Add all groups in collection to the state.
addGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.SynchronizedViewerState: Add all groups in collection to the state.
addGroups(Collection<? extends SourceGroup>) - Method in interface bdv.viewer.ViewerState: Add all groups in collection to the state (optional operation).
addHandler(Object) - Method in interface bdv.viewer.InteractiveDisplay: Add new event handler.
addHandler(Object) - Method in class bdv.viewer.InteractiveDisplayCanvas: Add new event handler.
addInterpolationModeListener(InterpolationModeListener) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use interpolationModeListeners().add( listener ).
addLafComponent(Component) - Method in class bdv.ui.appearance.AppearanceManager: Add components here that should be notified via SwingUtilities.updateComponentTreeUI() when the Look-And-Feel is changed.
addOverlayAnimator(OverlayAnimator) - Method in class bdv.viewer.AbstractViewerPanel: Add a new OverlayAnimator to the list of animators.
addOverlayAnimator(OverlayAnimator) - Method in class bdv.viewer.ViewerPanel: Add a new OverlayAnimator to the list of animators.
addOverlayRenderer(OverlayRenderer) - Method in class bdv.viewer.InteractiveDisplayCanvas: Deprecated.
Use overlays().add(renderer) instead
addPage(SettingsPage) - Method in class bdv.tools.PreferencesDialog
addPage(SettingsPage) - Method in class bdv.ui.settings.SettingsPanel
addRenderTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use renderTransformListeners().add( listener ).
addRenderTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use renderTransformListeners().add( index, listener ).
addSetup(ConverterSetup) - Method in class bdv.tools.brightness.MinMaxGroup: Add a ConverterSetup which will have its display range updated to the interval (BoundedIntervalDouble.getMinBoundedValue(), BoundedIntervalDouble.getMaxBoundedValue()).
addSetup(ConverterSetup) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.

Add the setup in a new group.
addSource(int) - Method in class bdv.viewer.state.SourceGroup: Deprecated.
addSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Add source to the state.
addSource(SourceAndConverter<?>) - Method in class bdv.viewer.state.ViewerState: Deprecated.
addSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Add source to the state.
addSource(SourceAndConverter<?>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
addSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Add source to the state (optional operation).
addSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.BasicViewerState: Add all sources in collection to the state.
addSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.SynchronizedViewerState: Add all sources in collection to the state.
addSources(Collection<? extends SourceAndConverter<?>>) - Method in interface bdv.viewer.ViewerState: Add all sources in collection to the state (optional operation).
addSources(Collection<SourceAndConverter<?>>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.BasicViewerState: Add all sources in collection to group.
addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Add all sources in collection to group.
addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in interface bdv.viewer.ViewerState: Add all sources in collection to group (optional operation).
addSourceToGroup(int, int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.BasicViewerState: Add source to group.
addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Add source to group.
addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in interface bdv.viewer.ViewerState: Add source to group (optional operation).
addTimePointListener(TimePointListener) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use timePointListeners().add( listener ).
addTimePointListener(TimePointListener, int) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use timePointListeners().add( index, listener ).
addTo() - Method in class bdv.util.BdvOptions.Values
addTo(Bdv) - Method in class bdv.util.BdvOptions: When showing content using one of the BdvFunctions methods, this option can be given to specify that the content should be added to an existing window.
addToViewer() - Method in class bdv.tools.boundingbox.TransformedBoxOverlaySource
addTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use transformListeners().add( listener ).
addTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use transformListeners().add( index, listener ).
addTreeModelListener(TreeModelListener) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel: Adds a listener for the TreeModelEvent posted after the tree changes.
addUpdateListener(VisibilityAndGrouping.UpdateListener) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
addVisibilityChangeListener(PlaceHolderOverlayInfo.VisibilityChangeListener) - Method in class bdv.util.PlaceHolderOverlayInfo: Deprecated.
Use visibilityChangeListeners().add(listener) instead.
Affine3DHelpers - Class in bdv.util: Helpers to extract parts (rotation, scale, etc) from AffineTransform3D.
Affine3DHelpers() - Constructor for class bdv.util.Affine3DHelpers
AffineTransform3DJsonSerializer - Class in bdv.img.remote
AffineTransform3DJsonSerializer() - Constructor for class bdv.img.remote.AffineTransform3DJsonSerializer
afterEachPlane(boolean) - Method in interface bdv.export.ExportScalePyramid.AfterEachPlane: Called after a "plane of blocks" is written.
align(AbstractViewerPanel.AlignPlane) - Method in class bdv.viewer.AbstractViewerPanel: Align the XY, ZY, or XZ plane of the local coordinate system of the currently active source with the viewer coordinate system.
ALIGN_PLANE - Static variable in class bdv.viewer.NavigationActions: Deprecated.
ALIGN_XY_PLANE - Static variable in class bdv.viewer.NavigationActions
ALIGN_XY_PLANE_KEYS - Static variable in class bdv.viewer.NavigationActions
ALIGN_XZ_PLANE - Static variable in class bdv.viewer.NavigationActions
ALIGN_XZ_PLANE_KEYS - Static variable in class bdv.viewer.NavigationActions
ALIGN_ZY_PLANE - Static variable in class bdv.viewer.NavigationActions
ALIGN_ZY_PLANE_KEYS - Static variable in class bdv.viewer.NavigationActions
alignPlaneAction(ViewerPanel, AbstractViewerPanel.AlignPlane, String...) - Method in class bdv.viewer.NavigationActions: Deprecated.
alignPlanes(ViewerPanel) - Method in class bdv.viewer.NavigationActions: Deprecated.
AlphaWeightedAccumulateProjectorARGB - Class in bdv.viewer.render
AlphaWeightedAccumulateProjectorARGB() - Constructor for class bdv.viewer.render.AlphaWeightedAccumulateProjectorARGB
AlphaWeightedAccumulateProjectorARGB.Factory - Class in bdv.viewer.render
appearance() - Method in class bdv.ui.appearance.AppearanceManager
Appearance - Class in bdv.ui.appearance: Appearance settings.
Appearance() - Constructor for class bdv.ui.appearance.Appearance
Appearance.UpdateListener - Interface in bdv.ui.appearance
appearanceChanged() - Method in interface bdv.ui.appearance.Appearance.UpdateListener
AppearanceIO - Class in bdv.ui.appearance: De/serialize Appearance to/from YAML file
AppearanceIO() - Constructor for class bdv.ui.appearance.AppearanceIO
appearanceManager(AppearanceManager) - Method in class bdv.util.BdvOptions: Set the AppearanceManager to share appearance settings with other BigDataViewer windows.
appearanceManager(AppearanceManager) - Method in class bdv.viewer.ViewerOptions: Set the AppearanceManager to share appearance settings with other BigDataViewer windows.
AppearanceManager - Class in bdv.ui.appearance: Manages the Appearance (save/load config file, propagate changes to Prefs and LookAndFeel).
AppearanceManager() - Constructor for class bdv.ui.appearance.AppearanceManager
AppearanceManager(String) - Constructor for class bdv.ui.appearance.AppearanceManager
AppearanceSettingsPage - Class in bdv.ui.appearance: Preferences page for changing Appearance.
AppearanceSettingsPage(AppearanceManager) - Constructor for class bdv.ui.appearance.AppearanceSettingsPage
AppearanceSettingsPage(String, AppearanceManager) - Constructor for class bdv.ui.appearance.AppearanceSettingsPage
apply() - Method in class bdv.tools.transformation.ManualTransformationEditor: End the ongoing manual transformation and fix the incremental transformation.
apply() - Method in class bdv.ui.appearance.AppearanceSettingsPage
apply() - Method in class bdv.ui.settings.SelectAndEditProfileSettingsPage
apply() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager
apply() - Method in interface bdv.ui.settings.SettingsPage: Called by the SettingsPanel if user presses "OK" or "Apply".
apply() - Method in class bdv.ui.settings.SimpleSettingsPage
apply() - Method in class bdv.ui.settings.style.StyleProfileManager
apply(Interpolation) - Method in class bdv.util.DefaultInterpolators
ARGB_COLOR_MODEL - Static variable in class bdv.util.AWTUtils
ArrayData(int[], int, int, int, int, int) - Constructor for class bdv.viewer.render.ProjectorUtils.ArrayData
asMask() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result: Returns the transformed box as an imglib2 roi.
assignNewAttributeIds(AbstractSpimData<?>, Map<String, Set<Integer>>) - Static method in class bdv.spimdata.tools.ChangeAttributeId: For the specified spimData data set, re-assign attribute id's that are already in use.
assignNewViewSetupIds(AbstractSpimData<?>, Set<Integer>) - Static method in class bdv.spimdata.tools.ChangeViewSetupId: For the specified spimData data set, re-assign setup id's that are already in use.
asVolatile() - Method in class bdv.viewer.SourceAndConverter
asVolatile() - Method in class bdv.viewer.state.SourceState: Deprecated.
asVolatile(SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
asVolatile(SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
asVolatile(Supplier<V>, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
asVolatile(Supplier<V>, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
asVolatile(V, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
asVolatile(V, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
ATTRIBUTES_CACHE - Static variable in class bdv.export.n5.meta.AttributesCaching
AttributesCaching - Class in bdv.export.n5.meta
AttributesCaching() - Constructor for class bdv.export.n5.meta.AttributesCaching
AVG - bdv.viewer.BlendMode
AWTUtils - Class in bdv.util: Static helper methods for setting up GraphicsConfiguration and BufferedImages.
AWTUtils() - Constructor for class bdv.util.AWTUtils
axisOrder() - Method in class bdv.util.BdvOptions.Values
axisOrder(AxisOrder) - Method in class bdv.util.BdvOptions: Specified when adding a stack.
AxisOrder - Enum in bdv.util

B

backingCache - Variable in class bdv.img.cache.VolatileGlobalCellCache
baseUrl - Variable in class bdv.img.remote.RemoteImageLoader
BasicViewerState - Class in bdv.viewer: Maintains the BigDataViewer state and implements ViewerState to expose query and modification methods.
BasicViewerState() - Constructor for class bdv.viewer.BasicViewerState: Create an empty state without any sources or groups.
BasicViewerState(ViewerState) - Constructor for class bdv.viewer.BasicViewerState: Create a copy of the given ViewerState (except for (@link #changeListeners()}, which are not copied).
bdv - package bdv
Bdv - Interface in bdv.util: Something that has a BdvHandle.
bdv.cache - package bdv.cache
bdv.export - package bdv.export
bdv.export.n5 - package bdv.export.n5
bdv.export.n5.meta - package bdv.export.n5.meta
bdv.img - package bdv.img
bdv.img.cache - package bdv.img.cache
bdv.img.catmaid - package bdv.img.catmaid
bdv.img.hdf5 - package bdv.img.hdf5
bdv.img.imaris - package bdv.img.imaris
bdv.img.n5 - package bdv.img.n5
bdv.img.openconnectome - package bdv.img.openconnectome
bdv.img.remote - package bdv.img.remote
bdv.spimdata - package bdv.spimdata
bdv.spimdata.legacy - package bdv.spimdata.legacy
bdv.spimdata.tools - package bdv.spimdata.tools
bdv.tools - package bdv.tools
bdv.tools.bookmarks - package bdv.tools.bookmarks
bdv.tools.boundingbox - package bdv.tools.boundingbox
bdv.tools.brightness - package bdv.tools.brightness
bdv.tools.crop - package bdv.tools.crop
bdv.tools.transformation - package bdv.tools.transformation
bdv.ui - package bdv.ui
bdv.ui.appearance - package bdv.ui.appearance
bdv.ui.convertersetupeditor - package bdv.ui.convertersetupeditor
bdv.ui.keymap - package bdv.ui.keymap: Manage user key mappings, with IO and descriptions.
bdv.ui.rangeslider - package bdv.ui.rangeslider
bdv.ui.settings - package bdv.ui.settings: Classes to build UIs that store and manage user settings in an app.
bdv.ui.settings.style - package bdv.ui.settings.style: Classes to manage a collection of styles.
bdv.ui.sourcegrouptree - package bdv.ui.sourcegrouptree
bdv.ui.sourcetable - package bdv.ui.sourcetable
bdv.ui.splitpanel - package bdv.ui.splitpanel
bdv.ui.viewermodepanel - package bdv.ui.viewermodepanel
bdv.util - package bdv.util
bdv.util.volatiles - package bdv.util.volatiles
bdv.viewer - package bdv.viewer
bdv.viewer.animate - package bdv.viewer.animate
bdv.viewer.overlay - package bdv.viewer.overlay
bdv.viewer.render - package bdv.viewer.render
bdv.viewer.render.awt - package bdv.viewer.render.awt
bdv.viewer.state - package bdv.viewer.state
BdvDefaultCards - Class in bdv.ui: Default cards added to the card panel.
BdvDefaultCards() - Constructor for class bdv.ui.BdvDefaultCards
BdvFunctions - Class in bdv.util: all show methods return a Bdv which can be used to add more stuff to the same window
BdvFunctions() - Constructor for class bdv.util.BdvFunctions
BdvHandle - Class in bdv.util: Represents a BigDataViewer frame or panel and can be used to get to the bdv internals.
BdvHandle(BdvOptions) - Constructor for class bdv.util.BdvHandle
BdvHandleFrame - Class in bdv.util
BdvHandlePanel - Class in bdv.util
BdvHandlePanel(Frame, BdvOptions) - Constructor for class bdv.util.BdvHandlePanel
BdvN5Format - Class in bdv.img.n5
BdvN5Format() - Constructor for class bdv.img.n5.BdvN5Format
bdvOptions - Variable in class bdv.util.BdvHandle
BdvOptions - Class in bdv.util: Optional parameters for BdvFunctions.
BdvOptions() - Constructor for class bdv.util.BdvOptions
BdvOptions.Values - Class in bdv.util: Read-only BdvOptions values.
BdvOverlay - Class in bdv.util: An overlay that can be shown with BdvFunctions.showOverlay(BdvOverlay, String, BdvOptions): This method will add a dummy Source and ConverterSetup to the BigDataViewer such that the visibility, display range, and color for the overlay can be adjusted by the user, like for a normal Source.
BdvOverlay() - Constructor for class bdv.util.BdvOverlay
BdvOverlaySource<O extends OverlayRenderer> - Class in bdv.util
BdvOverlaySource(BdvHandle, int, PlaceHolderConverterSetup, SourceAndConverter<Void>, PlaceHolderOverlayInfo, O) - Constructor for class bdv.util.BdvOverlaySource
BdvPointsSource - Class in bdv.util
BdvPointsSource(BdvHandle, int, PlaceHolderConverterSetup, SourceAndConverter<Void>, PlaceHolderOverlayInfo, PointsOverlay) - Constructor for class bdv.util.BdvPointsSource
BdvSource - Class in bdv.util
BdvSource(BdvHandle, int) - Constructor for class bdv.util.BdvSource
bdvSources - Variable in class bdv.util.BdvHandle
BdvStackSource<T> - Class in bdv.util
BdvStackSource(BdvHandle, int, T, List<ConverterSetup>, List<SourceAndConverter<T>>) - Constructor for class bdv.util.BdvStackSource
BdvVirtualChannelSource - Class in bdv.util
BdvVirtualChannelSource(BdvHandle, int, PlaceHolderConverterSetup, SourceAndConverter<ARGBType>, PlaceHolderOverlayInfo, VirtualChannels.ChannelSourceCoordinator) - Constructor for class bdv.util.BdvVirtualChannelSource
BigDataViewer - Class in bdv
BigDataViewer(ArrayList<ConverterSetup>, ArrayList<SourceAndConverter<?>>, AbstractSpimData<?>, int, CacheControl, String, ProgressWriter, ViewerOptions) - Constructor for class bdv.BigDataViewer: Deprecated.
BigDataViewer(List<ConverterSetup>, List<SourceAndConverter<?>>, AbstractSpimData<?>, int, CacheControl, String, ProgressWriter, ViewerOptions) - Constructor for class bdv.BigDataViewer
BIGDATAVIEWER - Static variable in interface bdv.KeyConfigContexts: The action or behaviour applies to the BDV views.
BIGDATAVIEWER - Static variable in interface bdv.KeyConfigScopes
BigDataViewerActions - Class in bdv
BigDataViewerActions(KeyStrokeAdder.Factory) - Constructor for class bdv.BigDataViewerActions: Deprecated.
BigDataViewerActions.Descriptions - Class in bdv
BlendMode - Enum in bdv.viewer: Blending modes.
blendModeChanged(BlendMode) - Method in interface bdv.viewer.BlendModeSwitcher.BlendModeChangeListener
BlendModeSwitcher - Class in bdv.viewer
BlendModeSwitcher(ViewerState) - Constructor for class bdv.viewer.BlendModeSwitcher
BlendModeSwitcher.BlendModeChangeListener - Interface in bdv.viewer: BlendModeChangeListeners are notified about blend mode changes.
bookmarkEditor - Variable in class bdv.BigDataViewer
bookmarks - Variable in class bdv.BigDataViewer
bookmarks(BookmarksEditor) - Method in class bdv.BigDataViewerActions: Deprecated.
bookmarks(Actions, BookmarksEditor) - Static method in class bdv.BigDataViewerActions
Bookmarks - Class in bdv.tools.bookmarks
Bookmarks() - Constructor for class bdv.tools.bookmarks.Bookmarks
BookmarksEditor - Class in bdv.tools.bookmarks
BookmarksEditor(AbstractViewerPanel, InputActionBindings, Bookmarks) - Constructor for class bdv.tools.bookmarks.BookmarksEditor
BookmarkTextOverlayAnimator - Class in bdv.tools.bookmarks: Draw one line of text in the center or bottom right of the display.
BookmarkTextOverlayAnimator(AbstractViewerPanel) - Constructor for class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
BookmarkTextOverlayAnimator(AbstractViewerPanel, Font) - Constructor for class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
BOTTOM_RIGHT - bdv.viewer.animate.TextOverlayAnimator.TextPosition
BoundedInterval - Class in bdv.util: A interval consisting of BoundedValue minimum and maximum that can span any interval in a given range.
BoundedInterval(int, int, int, int, int) - Constructor for class bdv.util.BoundedInterval
BoundedIntervalDouble - Class in bdv.util: A interval consisting of BoundedValueDouble minimum and maximum that can span any interval in a given range.
BoundedIntervalDouble(double, double, double, double, double) - Constructor for class bdv.util.BoundedIntervalDouble
BoundedRange - Class in bdv.util: A bounded range with minBound <= min <= max <= maxBound.
BoundedRange(double, double, double, double) - Constructor for class bdv.util.BoundedRange
BoundedValue - Class in bdv.util: A int variable that can take any value in a given range.
BoundedValue(int, int, int) - Constructor for class bdv.util.BoundedValue
BoundedValue.UpdateListener - Interface in bdv.util
BoundedValueDouble - Class in bdv.util: A double variable that can take any value in a given range.
BoundedValueDouble(double, double, double) - Constructor for class bdv.util.BoundedValueDouble
BoundedValueDouble.UpdateListener - Interface in bdv.util
BoundingBoxDialog - Class in bdv.tools.boundingbox: Deprecated.
Use TransformedBoxSelectionDialog instead.
BoundingBoxDialog(Frame, String, ViewerPanel, SetupAssignments, int, Interval, Interval) - Constructor for class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
BoundingBoxDialog(Frame, String, ViewerPanel, SetupAssignments, int, Interval, Interval, boolean, boolean) - Constructor for class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
BoundingBoxUtil - Class in bdv.tools.boundingbox
BoundingBoxUtil() - Constructor for class bdv.tools.boundingbox.BoundingBoxUtil
Bounds - Class in bdv.util: A range with minBound <= maxBound.
Bounds(double, double) - Constructor for class bdv.util.Bounds
box - Variable in class bdv.viewer.overlay.MultiBoxOverlayRenderer: Navigation wire-frame cube.
box() - Method in class bdv.tools.boundingbox.TransformedBoxModel
boxConverterSetup - Variable in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
boxDisplayMode() - Method in class bdv.tools.boundingbox.TransformedBoxEditor
boxDisplayMode() - Method in class bdv.tools.boundingbox.TransformedBoxOverlay: Get/set BoxDisplayMode, which specifies whether to show 3D wireframe box (FULL), or only intersection with viewer plane (SECTION).
BoxDisplayModePanel - Class in bdv.tools.boundingbox: Panel with radio-buttons to switch between TransformedBoxOverlay.BoxDisplayModes.
BoxDisplayModePanel(ListenableVar<TransformedBoxOverlay.BoxDisplayMode, ChangeListener>) - Constructor for class bdv.tools.boundingbox.BoxDisplayModePanel
boxEditor - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
boxEditor - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
boxInterval - Variable in class bdv.viewer.overlay.MultiBoxOverlayRenderer: Screen interval in which to display navigation wire-frame cube.
boxOverlay - Variable in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
boxRealRandomAccessible - Variable in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
BoxRealRandomAccessible<T extends net.imglib2.type.Type<T>> - Class in bdv.tools.boundingbox
BoxRealRandomAccessible(RealInterval, T, T) - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible
BoxRealRandomAccessible.Access - Class in bdv.tools.boundingbox
BoxSelectionOptions - Class in bdv.tools.boundingbox: Optional parameters for TransformedBoxSelectionDialog and TransformedRealBoxSelectionDialog.
BoxSelectionOptions() - Constructor for class bdv.tools.boundingbox.BoxSelectionOptions
BoxSelectionOptions.TimepointSelection - Enum in bdv.tools.boundingbox
BoxSelectionOptions.Values - Class in bdv.tools.boundingbox: Read-only BoxSelectionOptions values.
boxSelectionPanel - Variable in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
boxSelectionPanel - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
boxSelectionPanel - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
BoxSelectionPanel - Class in bdv.tools.boundingbox: A JPanel containing X,Y,Z,... min/max sliders for adjusting a Interval
BoxSelectionPanel(BoxSelectionPanel.Box, Interval) - Constructor for class bdv.tools.boundingbox.BoxSelectionPanel
BoxSelectionPanel.Box - Interface in bdv.tools.boundingbox: Provides current interval and receives interval changes.
boxSourceAndConverter - Variable in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
boxSources - Variable in class bdv.viewer.overlay.MultiBoxOverlayRenderer
BRIGHTNESS_SETTINGS - Static variable in class bdv.BigDataViewerActions
BRIGHTNESS_SETTINGS_KEYS - Static variable in class bdv.BigDataViewerActions
brightnessDialog - Variable in class bdv.BigDataViewer
BrightnessDialog - Class in bdv.tools.brightness: Deprecated.
BrightnessDialog(Frame, SetupAssignments) - Constructor for class bdv.tools.brightness.BrightnessDialog: Deprecated.
BrightnessDialog.ColorsPanel - Class in bdv.tools.brightness: Deprecated.
BrightnessDialog.MinMaxPanel - Class in bdv.tools.brightness: Deprecated.

A panel containing min/max SliderPanels, view setup check-boxes and advanced settings.
BrightnessDialog.MinMaxPanels - Class in bdv.tools.brightness: Deprecated.
BufferedImageOverlayRenderer - Class in bdv.viewer.render.awt: OverlayRenderer drawing a BufferedImage, scaled to fill the canvas.
BufferedImageOverlayRenderer() - Constructor for class bdv.viewer.render.awt.BufferedImageOverlayRenderer
BufferedImageRenderResult - Class in bdv.viewer.render.awt
BufferedImageRenderResult() - Constructor for class bdv.viewer.render.awt.BufferedImageRenderResult
builtinStyles - Variable in class bdv.ui.settings.style.AbstractStyleManager
buttons - Variable in class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog

C

cache - Variable in class bdv.AbstractCachedViewerSetupImgLoader
cache - Variable in class bdv.img.remote.RemoteImageLoader
CacheArrayLoader<A extends net.imglib2.img.basictypeaccess.DataAccess> - Interface in bdv.img.cache: Provider of volatile Cell data.
CacheControl - Interface in bdv.cache: This is the part of the VolatileGlobalCellCache interface that is exposed to the renderer directly (that is, not via images).
CacheControl.CacheControls - Class in bdv.cache: CacheControl backed by a set of CacheControls.
CacheControl.Dummy - Class in bdv.cache: CacheControl that does nothing.
cacheControls - Variable in class bdv.util.BdvHandle
CacheControls() - Constructor for class bdv.cache.CacheControl.CacheControls
cancel() - Method in class bdv.ui.appearance.AppearanceSettingsPage
cancel() - Method in class bdv.ui.settings.SelectAndEditProfileSettingsPage
cancel() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager
cancel() - Method in interface bdv.ui.settings.SettingsPage: Called by the SettingsPanel if user presses "Cancel".
cancel() - Method in class bdv.ui.settings.SettingsPanel
cancel() - Method in class bdv.ui.settings.SimpleSettingsPage
cancel() - Method in class bdv.ui.settings.SingleSettingsPanel
cancel() - Method in class bdv.ui.settings.style.StyleProfileManager
cancel() - Method in class bdv.viewer.render.AccumulateProjector
cancel() - Method in class bdv.viewer.render.EmptyProjector
cancel() - Method in class bdv.viewer.render.SimpleVolatileProjector
cancel() - Method in interface bdv.viewer.render.VolatileProjector: Abort VolatileProjector.map() if it is currently running.
canImport(TransferHandler.TransferSupport) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree.SourceGroupTreeTransferHandler
CardPanel - Class in bdv.ui: CardPanel handles components in named Cards which can be expanded or collapsed.
CardPanel() - Constructor for class bdv.ui.CardPanel: Empty card panel.
cards - Variable in class bdv.util.BdvHandle
castToDoubles(int[]) - Static method in class bdv.img.hdf5.Util
castToDoubles(int[][]) - Static method in class bdv.img.hdf5.Util
castToInts(double[]) - Static method in class bdv.img.hdf5.Util
castToInts(double[][]) - Static method in class bdv.img.hdf5.Util
CatmaidImageLoader - Class in bdv.img.catmaid
CatmaidImageLoader(long, long, long, double, int, String, int, int) - Constructor for class bdv.img.catmaid.CatmaidImageLoader
CatmaidImageLoader(long, long, long, double, int, String, int, int, boolean) - Constructor for class bdv.img.catmaid.CatmaidImageLoader
CatmaidImageLoader(long, long, long, double, int, String, int, int, int, int) - Constructor for class bdv.img.catmaid.CatmaidImageLoader
CatmaidImageLoader(long, long, long, double, int, String, int, int, int, int, boolean) - Constructor for class bdv.img.catmaid.CatmaidImageLoader
CatmaidImageLoader(long, long, long, double, String, int, int, int[][]) - Constructor for class bdv.img.catmaid.CatmaidImageLoader
CatmaidImageLoader(long, long, long, double, String, int, int, int[][], boolean) - Constructor for class bdv.img.catmaid.CatmaidImageLoader
CatmaidVolatileIntArrayLoader - Class in bdv.img.catmaid
CatmaidVolatileIntArrayLoader(String, int, int, int[]) - Constructor for class bdv.img.catmaid.CatmaidVolatileIntArrayLoader: Create a CacheArrayLoader for a CATMAID source.
cellDimensions - Variable in class bdv.AbstractCachedViewerSetupImgLoader
cellsDimensions - Variable in class bdv.img.remote.RemoteImageLoader
CENTER - bdv.viewer.animate.TextOverlayAnimator.TextPosition
changeAttributeId(AbstractSpimData<?>, String, int, int) - Static method in class bdv.spimdata.tools.ChangeAttributeId: TODO
ChangeAttributeId - Class in bdv.spimdata.tools
ChangeAttributeId() - Constructor for class bdv.spimdata.tools.ChangeAttributeId
changeListeners() - Method in class bdv.viewer.BasicViewerState: ViewerStateChangeListeners can be added/removed here.
changeListeners() - Method in class bdv.viewer.BlendModeSwitcher
changeListeners() - Method in class bdv.viewer.SynchronizedViewerState
changeListeners() - Method in interface bdv.viewer.ViewerState: ViewerStateChangeListeners can be added/removed here, and will be notified about changes to this ViewerState.
changeViewSetupId(AbstractSpimData<?>, int, int) - Static method in class bdv.spimdata.tools.ChangeViewSetupId: TODO
ChangeViewSetupId - Class in bdv.spimdata.tools
ChangeViewSetupId() - Constructor for class bdv.spimdata.tools.ChangeViewSetupId
channelDimension() - Method in enum bdv.util.AxisOrder
ChannelSources<T> - Interface in bdv.util: Channels of an image as a collection of sources.
clear() - Method in class bdv.cache.CacheControl.CacheControls
clear() - Method in class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
clear() - Method in class bdv.util.WrappedList
clearCache() - Method in class bdv.img.cache.VolatileGlobalCellCache: Remove all references to loaded data.
clearGroups() - Method in class bdv.viewer.BasicViewerState: Remove all groups from the state.
clearGroups() - Method in class bdv.viewer.SynchronizedViewerState: Remove all groups from the state.
clearGroups() - Method in interface bdv.viewer.ViewerState: Remove all groups from the state (optional operation).
clearSources() - Method in class bdv.viewer.BasicViewerState: Remove all sources from the state.
clearSources() - Method in class bdv.viewer.SynchronizedViewerState: Remove all sources from the state.
clearSources() - Method in interface bdv.viewer.ViewerState: Remove all sources from the state (optional operation).
close() - Method in class bdv.img.hdf5.Hdf5ImageLoader: Clear the cache.
close() - Method in class bdv.img.n5.N5ImageLoader: Clear the cache.
close() - Method in interface bdv.util.Bdv
close() - Method in class bdv.util.BdvHandle
close() - Method in class bdv.util.BdvHandleFrame
close() - Method in class bdv.util.BdvHandlePanel
CLOSE_DIALOG - Static variable in class bdv.tools.CloseWindowActions
CLOSE_DIALOG_KEYS - Static variable in class bdv.tools.CloseWindowActions
CLOSE_WINDOW - Static variable in class bdv.tools.CloseWindowActions
CLOSE_WINDOW_KEYS - Static variable in class bdv.tools.CloseWindowActions
CloseWindowActions - Class in bdv.tools
CloseWindowActions() - Constructor for class bdv.tools.CloseWindowActions
CloseWindowActions.Descriptions - Class in bdv.tools
coerceAffineDimension - Variable in enum bdv.viewer.AbstractViewerPanel.AlignPlane: Axis index.
COLLAPSE_CARDS - Static variable in class bdv.BigDataViewerActions
COLLAPSE_CARDS_KEYS - Static variable in class bdv.BigDataViewerActions
collapseCardPanel() - Method in class bdv.BigDataViewer
collapseCardPanel() - Method in class bdv.util.BdvHandlePanel
COLOR_COLUMN - Static variable in class bdv.ui.sourcetable.SourceTableModel
ColorIcon - Class in bdv.tools.brightness: Adapted from http://stackoverflow.com/a/3072979/230513
ColorIcon(Color) - Constructor for class bdv.tools.brightness.ColorIcon
ColorIcon(Color, int, int, boolean) - Constructor for class bdv.tools.brightness.ColorIcon
ColorIcon(Color, int, int, int, int) - Constructor for class bdv.tools.brightness.ColorIcon
ColorIcon(Color, int, int, int, int, boolean) - Constructor for class bdv.tools.brightness.ColorIcon
ColorIcon(Color, int, int, int, int, boolean, Color) - Constructor for class bdv.tools.brightness.ColorIcon
ColorsPanel(SetupAssignments) - Constructor for class bdv.tools.brightness.BrightnessDialog.ColorsPanel: Deprecated.
compare(MipmapOrdering.Level, MipmapOrdering.Level) - Method in class bdv.viewer.render.MipmapOrdering.PrefetchOrderComparator
compare(MipmapOrdering.Level, MipmapOrdering.Level) - Method in class bdv.viewer.render.MipmapOrdering.RenderOrderComparator
compareTo(ViewLevelId) - Method in class bdv.img.hdf5.ViewLevelId: Order by ascending timepoint id, then setup id, then level.
composed - Variable in class bdv.tools.transformation.TransformedSource: temporary. concatenation of TransformedSource.sourceTransform and the transform obtained from the decorated source.
configDir - Static variable in class bdv.BigDataViewer
ConstantRandomAccess() - Constructor for class bdv.util.ConstantRandomAccessible.ConstantRandomAccess
ConstantRandomAccessible<T> - Class in bdv.util: A RandomAccessible that has a given constant value everywhere.
ConstantRandomAccessible(T, int) - Constructor for class bdv.util.ConstantRandomAccessible
ConstantRandomAccessible.ConstantRandomAccess - Class in bdv.util
contains(Object) - Method in class bdv.util.WrappedList
contains(ViewId) - Method in class bdv.img.hdf5.Partition: Does this partition contain the given view (timepoint-setup pair)?
containsAll(Collection<?>) - Method in class bdv.util.WrappedList
containsGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Check whether the state contains the group.
containsGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Check whether the state contains the group.
containsGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState: Check whether the state contains the group.
containsSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Check whether the state contains the source.
containsSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Check whether the state contains the source.
containsSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Check whether the state contains the source.
content - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
content - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
converter - Variable in class bdv.viewer.SourceAndConverter: converts SourceAndConverter.spimSource type T to ARGBType for display
ConverterSetup - Interface in bdv.tools.brightness: Modify the range and color of the converter for a source.
ConverterSetup.SetupChangeListener - Interface in bdv.tools.brightness: ConverterSetup.SetupChangeListeners are notified about changes to a ConverterSetup.
ConverterSetupBounds - Class in bdv.viewer: Map from ConverterSetup to Bounds on the range bounds to put on the range slider.
ConverterSetupEditPanel - Class in bdv.ui.convertersetupeditor: A JPanel containing a ColorPanel and a BoundedRangePanel.
ConverterSetupEditPanel() - Constructor for class bdv.ui.convertersetupeditor.ConverterSetupEditPanel
ConverterSetupEditPanel(SourceGroupTree, ConverterSetups) - Constructor for class bdv.ui.convertersetupeditor.ConverterSetupEditPanel
ConverterSetupEditPanel(SourceTable, ConverterSetups) - Constructor for class bdv.ui.convertersetupeditor.ConverterSetupEditPanel
ConverterSetups - Class in bdv.viewer: Provides a mapping between ConverterSetups and sources.
ConverterSetups(ViewerState) - Constructor for class bdv.viewer.ConverterSetups
convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
copy() - Method in class bdv.img.cache.VolatileCachedCellImg
copy() - Method in class bdv.img.cache.VolatileCachedCellImg.VolatileCachedCells
copy() - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
copy() - Method in class bdv.ui.keymap.Keymap
copy() - Method in interface bdv.ui.settings.style.Style
copy() - Method in class bdv.util.ConstantRandomAccessible.ConstantRandomAccess
copy() - Method in class bdv.viewer.state.SourceGroup: Deprecated.
copy() - Method in class bdv.viewer.state.ViewerState: Deprecated.
copy(ViewerState) - Method in class bdv.viewer.state.SourceState: Deprecated.
copy(String) - Method in class bdv.ui.keymap.Keymap: Returns a new style instance, copied from this style.
copy(String) - Method in interface bdv.ui.settings.style.Style: Returns a new style instance, copied from this style.
corner(RealInterval, int) - Static method in class bdv.tools.boundingbox.IntervalCorners
corner(RealInterval, int, double[]) - Static method in class bdv.tools.boundingbox.IntervalCorners
corners(RealInterval) - Static method in class bdv.tools.boundingbox.IntervalCorners
create(TransformState) - Method in interface bdv.TransformEventHandlerFactory: Create a new TransformEventHandler.
create(SourceAndConverter<T>, ViewerState) - Static method in class bdv.viewer.state.SourceState: Deprecated.

Create a SourceState from a SourceAndConverter.
createAccumulateProjector(ArrayList<VolatileProjector>, ArrayList<Source<?>>, ArrayList<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval<A>, int, ExecutorService) - Method in interface bdv.viewer.render.AccumulateProjectorFactory: Deprecated.
Use AccumulateProjectorFactory.createProjector(List, List, List, RandomAccessibleInterval, int, ExecutorService) instead. The new variant of the method is named "createProjector" instead of "createAccumulateProjector" because it has the same erasure. The default implementation of "createProjector" is forwarded to the (deprecated) "createAccumulateProjector", so existing AccumulateProjectorFactory implementations should keep working.
createCacheArrayLoader(N5Reader, String) - Static method in class bdv.img.n5.N5ImageLoader
createCellsDimensions() - Method in class bdv.img.remote.RemoteImageLoaderMetaData: Create an map from ViewLevelId (timepoint, setup, level) to int[].
createContent() - Method in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
createContent() - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog: Adds TransformedBoxSelectionDialog.boxSelectionPanel etc to TransformedBoxSelectionDialog.content.
createContent() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog: Adds TransformedRealBoxSelectionDialog.boxSelectionPanel etc to TransformedRealBoxSelectionDialog.content.
createConverterSetup(SourceAndConverter<?>, int) - Static method in class bdv.BigDataViewer: Create a ConverterSetup for the given SourceAndConverter.
createConverterToARGB(T) - Static method in class bdv.BigDataViewer: Create standard converter from the given type to ARGB: For RealTypes a RealARGBColorConverter is returned. For ARGBTypes a ScaledARGBConverter.ARGB is returned. For VolatileARGBTypes a ScaledARGBConverter.VolatileARGB is returned.
createDataset(int, long[], int[]) - Method in interface bdv.export.ExportScalePyramid.DatasetIO: Create a dataset for the image of the given resolution level.
createImg(CellGrid, int, int, int, CacheHints, CacheArrayLoader<A>, T) - Method in class bdv.img.cache.VolatileGlobalCellCache: Create a VolatileCachedCellImg backed by this VolatileGlobalCellCache, using the provided CacheArrayLoader to load data.
createImg(CellGrid, int, int, int, CacheHints, SimpleCacheArrayLoader<A>, T) - Method in class bdv.img.cache.VolatileGlobalCellCache: Create a VolatileCachedCellImg backed by this VolatileGlobalCellCache, using the provided SimpleCacheArrayLoader to load data.
createInvalid(Long) - Method in class bdv.img.cache.CreateInvalidVolatileCell
CreateInvalidVolatileCell<A> - Class in bdv.img.cache: A CreateInvalid that produces empty cells of VolatileArrayDataAccess type A, with the correct dimensions, etc.
CreateInvalidVolatileCell(CellGrid, Fraction, EmptyArrayCreator<A>) - Constructor for class bdv.img.cache.CreateInvalidVolatileCell
createN5PropertiesInstance() - Method in class bdv.img.n5.N5ImageLoader: Create a new N5Properties (provides metadata and resolves dataset paths).
createPrimitiveArray() - Method in class bdv.img.n5.DataTypeProperties
createProjector(List<VolatileProjector>, List<SourceAndConverter<?>>, List<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval<A>, int, ExecutorService) - Method in interface bdv.viewer.render.AccumulateProjectorFactory
createProjector(List<VolatileProjector>, List<SourceAndConverter<?>>, List<? extends RandomAccessible<? extends ARGBType>>, RandomAccessibleInterval<ARGBType>, int, ExecutorService) - Method in class bdv.viewer.render.AccumulateProjectorARGB.Factory
createProjector(List<VolatileProjector>, List<SourceAndConverter<?>>, List<? extends RandomAccessible<? extends ARGBType>>, RandomAccessibleInterval<ARGBType>, int, ExecutorService) - Method in class bdv.viewer.render.AlphaWeightedAccumulateProjectorARGB.Factory
createRegistrationsFromXml(Element) - Static method in class bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy
createRenderResult() - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer
createRenderResult() - Method in interface bdv.viewer.render.RenderTarget: Returns a new RenderResult.
createResult(boolean) - Method in class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog
createResult(boolean) - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
createResult(boolean) - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
createViewDescription(int, int) - Method in class bdv.spimdata.SequenceDescriptionMinimal
createVolatileArrayAccess() - Method in class bdv.img.n5.DataTypeProperties
crop(AffineTransform3D, RealInterval, Source<T>, int) - Static method in class bdv.tools.crop.CropImgLoader: Crop a region from a Source.
CROP - Static variable in class bdv.BigDataViewerActions
CROP_KEYS - Static variable in class bdv.BigDataViewerActions
cropDialog - Variable in class bdv.BigDataViewer
CropDialog - Class in bdv.tools.crop
CropDialog(Frame, ViewerPanel, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.tools.crop.CropDialog
cropGlobal(int, int, File, File) - Method in class bdv.tools.crop.CropDialog
CropImgLoader - Class in bdv.tools.crop: This ImgLoader provides views and transformations into a cropped region of a data-set (provided by list of Sources).
CropImgLoader(ArrayList<Source<?>>, AffineTransform3D, RealInterval, Map<Integer, Integer>, Map<Integer, Integer>) - Constructor for class bdv.tools.crop.CropImgLoader
CropImgLoader.SetupImgLoader<T> - Class in bdv.tools.crop
cube_dimension - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
CURRENT_GROUP_CHANGED - bdv.viewer.ViewerStateChange
CURRENT_GROUP_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
CURRENT_SOURCE_CHANGED - bdv.viewer.ViewerStateChange
CURRENT_SOURCE_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
CURRENT_TIMEPOINT_CHANGED - bdv.viewer.ViewerStateChange
currentLookAndFeelInfo() - Static method in class bdv.ui.appearance.Appearance
currentTimePointIndex - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource4D
currentTimePointIndex - Variable in class bdv.util.RandomAccessibleIntervalSource4D
currentTimePointIndex - Variable in class bdv.util.RandomAccessibleSource4D
CUSTOM - bdv.viewer.BlendMode

D

data() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
DATA_TYPE_KEY - Static variable in class bdv.img.n5.BdvN5Format
dataset - Variable in class bdv.img.openconnectome.OpenConnectomeProject
dataset - Variable in class bdv.img.openconnectome.OpenConnectomeTokenInfo
dataType() - Method in class bdv.img.n5.DataTypeProperties
DataTypeProperties<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>,P,A extends net.imglib2.img.basictypeaccess.DataAccess> - Class in bdv.img.n5: Types and creators for N5 DataType.
dataurl - Variable in class bdv.img.openconnectome.OpenConnectomeProject
dbname - Variable in class bdv.img.openconnectome.OpenConnectomeProject
DebugTilingOverlay - Class in bdv.viewer.render: Overlay to show how the display is tiled for rendering.
DebugTilingOverlay(MultiResolutionRenderer) - Constructor for class bdv.viewer.render.DebugTilingOverlay
DebugTilingOverlay.Tiles - Class in bdv.viewer.render
decide(RandomAccessibleInterval<?>, int[], int, int[], int[]) - Method in class bdv.export.ExportScalePyramid.DefaultLoopbackHeuristic
decide(RandomAccessibleInterval<?>, int[], int, int[], int[]) - Method in interface bdv.export.ExportScalePyramid.LoopbackHeuristic
DEFAULT - bdv.util.AxisOrder
DEFAULT_SOURCEGROUPS_CARD - Static variable in class bdv.ui.BdvDefaultCards
DEFAULT_SOURCES_CARD - Static variable in class bdv.ui.BdvDefaultCards
DEFAULT_VIEWERMODES_CARD - Static variable in class bdv.ui.BdvDefaultCards
DefaultEmptyArrayCreator<A extends net.imglib2.img.basictypeaccess.volatiles.VolatileArrayDataAccess<A>> - Class in bdv.img.cache: EmptyArrayCreator implementation for standard access types.
DefaultEmptyArrayCreator(A) - Constructor for class bdv.img.cache.DefaultEmptyArrayCreator
DefaultInterpolators<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
DefaultInterpolators() - Constructor for class bdv.util.DefaultInterpolators
DefaultLoopbackHeuristic() - Constructor for class bdv.export.ExportScalePyramid.DefaultLoopbackHeuristic
DefaultMipmapOrdering - Class in bdv.viewer.render: The standard mipmap ordering strategy for local hdf5 data.
DefaultMipmapOrdering(Source<?>) - Constructor for class bdv.viewer.render.DefaultMipmapOrdering
DefaultMipmapOrdering(Source<?>, boolean, LoadingStrategy, boolean, LoadingStrategy, boolean) - Constructor for class bdv.viewer.render.DefaultMipmapOrdering
DefaultN5Properties - Class in bdv.img.n5
DefaultN5Properties() - Constructor for class bdv.img.n5.DefaultN5Properties
DelayedPackDialog - Class in bdv.tools: A JDialog that delays pack() calls until the dialog is made visible.
DelayedPackDialog(Frame, String, boolean) - Constructor for class bdv.tools.DelayedPackDialog
delete(StyleProfile<S>) - Method in class bdv.ui.settings.style.StyleProfileManager
delete(T) - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager
description - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
Descriptions() - Constructor for class bdv.BigDataViewerActions.Descriptions
Descriptions() - Constructor for class bdv.tools.CloseWindowActions.Descriptions
Descriptions() - Constructor for class bdv.TransformEventHandler2D.Descriptions
Descriptions() - Constructor for class bdv.TransformEventHandler3D.Descriptions
Descriptions() - Constructor for class bdv.viewer.NavigationActions.Descriptions
deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class bdv.img.remote.AffineTransform3DJsonSerializer
dialog - Variable in class bdv.tools.ToggleDialogAction
dialog(BrightnessDialog) - Method in class bdv.BigDataViewerActions: Deprecated.
dialog(CropDialog) - Method in class bdv.BigDataViewerActions: Deprecated.
dialog(HelpDialog) - Method in class bdv.BigDataViewerActions: Deprecated.
dialog(RecordMaxProjectionDialog) - Method in class bdv.BigDataViewerActions: Deprecated.
dialog(RecordMovieDialog) - Method in class bdv.BigDataViewerActions: Deprecated.
dialog(VisibilityAndGroupingDialog) - Method in class bdv.BigDataViewerActions: Deprecated.
dialog(Actions, BrightnessDialog) - Static method in class bdv.BigDataViewerActions: Deprecated.
dialog(Actions, CropDialog) - Static method in class bdv.BigDataViewerActions
dialog(Actions, HelpDialog) - Static method in class bdv.BigDataViewerActions
dialog(Actions, RecordMaxProjectionDialog) - Static method in class bdv.BigDataViewerActions
dialog(Actions, RecordMovieDialog) - Static method in class bdv.BigDataViewerActions
dialog(Actions, VisibilityAndGroupingDialog) - Static method in class bdv.BigDataViewerActions: Deprecated.
dimensions - Variable in class bdv.AbstractCachedViewerSetupImgLoader
dimsAndExistence - Variable in class bdv.img.remote.RemoteImageLoaderMetaData: Maps ViewLevelId (timepoint, setup, level) to DimsAndExistence.
DimsAndExistence - Class in bdv.img.hdf5: The dimensions of an image and a flag indicating whether that image exists (can be loaded)
DimsAndExistence(long[], int[], boolean) - Constructor for class bdv.img.hdf5.DimsAndExistence
discoverCommandDescriptions() - Method in class bdv.ui.keymap.KeymapManager: Discover all CommandDescriptionProviders with scope KeyConfigScopes.BIGDATAVIEWER, build CommandDescriptions, and set it.
DISPLAY_MODE_CHANGED - bdv.viewer.ViewerStateChange
DISPLAY_MODE_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
DisplayMode - Enum in bdv.viewer
displayModeFromXml(Element) - Method in class bdv.viewer.state.XmlIoViewerState
displayModeToXml(DisplayMode) - Method in class bdv.viewer.state.XmlIoViewerState
DisplaySettingsPanel - Class in bdv.ui.viewermodepanel: This panel adds buttons to toggle fused, grouped, and interpolation mode.
DisplaySettingsPanel(ViewerState) - Constructor for class bdv.ui.viewermodepanel.DisplaySettingsPanel
DisplaySettingsPanel(ViewerState, boolean) - Constructor for class bdv.ui.viewermodepanel.DisplaySettingsPanel
displayToGlobalCoordinates(double[]) - Method in class bdv.viewer.ViewerPanel: Set gPos to the display coordinates at gPos transformed into the global coordinate system.
displayToGlobalCoordinates(double, double, RealPositionable) - Method in class bdv.viewer.ViewerPanel: Set gPos to the display coordinates (x,y,0)^T transformed into the global coordinate system.
displayToGlobalCoordinates(P) - Method in class bdv.viewer.ViewerPanel: Set gPos to the display coordinates at gPos transformed into the global coordinate system.
doBoundingBoxCulling() - Method in class bdv.tools.transformation.TransformedSource
doBoundingBoxCulling() - Method in class bdv.util.AbstractSource
doBoundingBoxCulling() - Method in class bdv.util.RealRandomAccessibleSource
doBoundingBoxCulling() - Method in interface bdv.viewer.Source: Whether this source participates in bounding box culling.
doBoundingBoxIntersectionCheck - Variable in class bdv.util.RealRandomAccessibleSource
done() - Method in class bdv.tools.bookmarks.BookmarksEditor
DONT_MODIFY_LOOK_AND_FEEL - Static variable in class bdv.ui.appearance.Appearance
DOWNSAMPLING_FACTORS_KEY - Static variable in class bdv.img.n5.BdvN5Format
DRAG_ROTATE - Static variable in class bdv.TransformEventHandler2D
DRAG_ROTATE - Static variable in class bdv.TransformEventHandler3D
DRAG_ROTATE_FAST - Static variable in class bdv.TransformEventHandler3D
DRAG_ROTATE_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
DRAG_ROTATE_KEYS - Static variable in class bdv.TransformEventHandler2D
DRAG_ROTATE_KEYS - Static variable in class bdv.TransformEventHandler3D
DRAG_ROTATE_SLOW - Static variable in class bdv.TransformEventHandler3D
DRAG_ROTATE_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
DRAG_TRANSLATE - Static variable in class bdv.TransformEventHandler2D
DRAG_TRANSLATE - Static variable in class bdv.TransformEventHandler3D
DRAG_TRANSLATE_KEYS - Static variable in class bdv.TransformEventHandler2D
DRAG_TRANSLATE_KEYS - Static variable in class bdv.TransformEventHandler3D
draw(Graphics2D) - Method in class bdv.util.BdvOverlay
draw(Graphics2D) - Method in class bdv.util.PointsOverlay
drawOverlays(Graphics) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
drawOverlays(Graphics) - Method in class bdv.tools.RecordMaxProjectionDialog
drawOverlays(Graphics) - Method in class bdv.tools.RecordMovieDialog
drawOverlays(Graphics) - Method in class bdv.util.BdvOverlay
drawOverlays(Graphics) - Method in interface bdv.viewer.OverlayRenderer: Render overlays.
drawOverlays(Graphics) - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer
drawOverlays(Graphics) - Method in class bdv.viewer.render.DebugTilingOverlay
drawOverlays(Graphics) - Method in class bdv.viewer.ViewerPanel
drawString(Graphics, UIUtils.TextPosition, int, String) - Static method in class bdv.ui.UIUtils
Dummy() - Constructor for class bdv.cache.CacheControl.Dummy
duplicate(StyleProfile<S>) - Method in class bdv.ui.settings.style.StyleProfileManager
duplicate(S) - Method in class bdv.ui.settings.style.AbstractStyleManager: Returns a copy of the specified style, making sure that the copy receives a name not already present in this manager's list of styles.
duplicate(S) - Method in interface bdv.ui.settings.style.StyleManager
duplicate(T) - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager: Duplicate profile with a new derived name and add it to user profiles list.
duration - Variable in class bdv.viewer.animate.MessageOverlayAnimator

E

EmptyArrayCreator<A> - Interface in bdv.img.cache: Produce empty, invalid VolatileAccess to be used as placeholder invalid cell data.
EmptyProjector<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.viewer.render
EmptyProjector(RandomAccessibleInterval<T>) - Constructor for class bdv.viewer.render.EmptyProjector
ensureNumPriorities(int) - Method in class bdv.img.cache.VolatileGlobalCellCache: Make sure that the fetch queue has at least numPriorities priority levels.
equals(Object) - Method in class bdv.img.cache.VolatileGlobalCellCache.Key
equals(Object) - Method in class bdv.img.hdf5.ViewLevelId: Two ViewLevelId are equal if they have the same timepoint, setup, and level. ids.
equals(Object) - Method in class bdv.ui.settings.style.StyleProfile
equals(Object) - Method in class bdv.util.BoundedRange
equals(Object) - Method in class bdv.util.Bounds
equals(Object) - Method in class bdv.util.WrappedList
equals(Object) - Method in class bdv.viewer.state.SourceGroup: Deprecated.
equals(AffineTransform3D, AffineTransform3D) - Static method in class bdv.util.Affine3DHelpers: Compare two transforms for equality.
err() - Method in interface bdv.export.ProgressWriter
err() - Method in class bdv.export.ProgressWriterConsole
err() - Method in class bdv.export.ProgressWriterNull
err() - Method in class bdv.export.SubTaskProgressWriter
estimateSourceRange(Source<?>, int, double, double) - Static method in class bdv.tools.InitializeViewerState
Event(int, VisibilityAndGrouping) - Constructor for class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
exceptions - Variable in class bdv.img.openconnectome.OpenConnectomeProject
exists() - Method in class bdv.img.hdf5.DimsAndExistence
existsImageData(ViewLevelId) - Method in class bdv.img.hdf5.Hdf5ImageLoader: Checks whether the given image data is present in the hdf5.
existsImageData(ViewLevelId) - Method in class bdv.img.remote.RemoteImageLoader: Checks whether the given image data is present on the server.
EXPAND_CARDS - Static variable in class bdv.BigDataViewerActions
EXPAND_CARDS_KEYS - Static variable in class bdv.BigDataViewerActions
expandAndFocusCardPanel() - Method in class bdv.BigDataViewer
expandAndFocusCardPanel() - Method in class bdv.util.BdvHandlePanel
ExportMipmapInfo - Class in bdv.export
ExportMipmapInfo(int[][], int[][]) - Constructor for class bdv.export.ExportMipmapInfo
ExportScalePyramid - Class in bdv.export: Write an image to a chunked mipmap representation.
ExportScalePyramid() - Constructor for class bdv.export.ExportScalePyramid
ExportScalePyramid.AfterEachPlane - Interface in bdv.export: Callback that is called after each "plane of blocks" is written, giving the opportunity to clear caches, etc.
ExportScalePyramid.DatasetIO<D,T extends net.imglib2.type.NativeType<T>> - Interface in bdv.export: Writing and reading back data for each resolution level.
ExportScalePyramid.DefaultLoopbackHeuristic - Class in bdv.export: Simple heuristic: use loopback image loader if saving 8 times or more on number of pixel access with respect to the original image.
ExportScalePyramid.LoopbackHeuristic - Interface in bdv.export: A heuristic to decide for a given resolution level whether the source pixels should be taken from the original image or read from a previously written resolution level in the output dataset.
extendAndInterpolateMasked(RandomAccessibleInterval<M>, Interpolation) - Static method in class bdv.viewer.MaskUtils: Zero-extend (value and mask are set to zero) and interpolate a RandomAccessibleInterval<Masked<NumericType>>.
extractApproximateRotationAffine(AffineTransform3D, double[], int) - Static method in class bdv.util.Affine3DHelpers: Extract a rotation from a general AffineTransform3D.
extractRotation(AffineTransform3D, double[]) - Static method in class bdv.util.Affine3DHelpers: Extract the rotation part of a similarity transform stored in a AffineTransform3D.
extractRotationAnisotropic(AffineTransform3D, double[]) - Static method in class bdv.util.Affine3DHelpers: Extract the rotation from an AffineTransform3D comprising anisotropic scaling, rotation, and translation.
extractScale(AffineTransform3D, int) - Static method in class bdv.util.Affine3DHelpers: Get the scale factor along the X, Y, or Z axis.

F

factory - Static variable in class bdv.viewer.render.AccumulateProjectorARGB
factory - Static variable in class bdv.viewer.render.AlphaWeightedAccumulateProjectorARGB
factory() - Method in class bdv.img.cache.VolatileCachedCellImg
factory() - Method in class bdv.img.cache.VolatileCachedCellImg.VolatileCachedCells
Factory() - Constructor for class bdv.viewer.render.AccumulateProjectorARGB.Factory
Factory() - Constructor for class bdv.viewer.render.AlphaWeightedAccumulateProjectorARGB.Factory
fadeIn(String, long) - Method in class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
fadeInTime - Variable in class bdv.viewer.animate.MessageOverlayAnimator
fadeInTime - Variable in class bdv.viewer.animate.TextOverlayAnimator
fadeOut(String, long) - Method in class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
fadeOutTime - Variable in class bdv.viewer.animate.MessageOverlayAnimator
fadeOutTime - Variable in class bdv.viewer.animate.TextOverlayAnimator
fetchCells(AffineTransform3D, int[], long[], Dimensions, Interpolation, RandomAccess<?>) - Static method in class bdv.viewer.render.Prefetcher: Access cells that will be needed for rendering to the screen.
fetchTokenInfo(String, String) - Static method in class bdv.img.openconnectome.OpenConnectomeImageLoader: Fetch information for a token from an OpenConnectome volume cutout service, e.g.
fetchTokenList(String) - Static method in class bdv.img.openconnectome.OpenConnectomeImageLoader: Fetch the list of public tokens from an OpenConnectome volume cutout service, e.g.
fileChooser - Variable in class bdv.BigDataViewer
fillIntersection(boolean) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
finalize() - Method in class bdv.img.imaris.HDF5AccessHack
fixedTransform - Variable in class bdv.tools.transformation.TransformedSource: Fixed part of the extra transformation.
flavor - Static variable in class bdv.ui.SourcesTransferable
flush() - Method in interface bdv.export.ExportScalePyramid.DatasetIO: Blocks until all pending data was written to dataset.
font - Variable in class bdv.viewer.animate.MessageOverlayAnimator
font - Variable in class bdv.viewer.animate.TextOverlayAnimator
forStyle(M, M, SelectAndEditProfileSettingsPage.ProfileEditPanel<StyleProfile<S>>, String) - Static method in class bdv.ui.settings.SelectAndEditProfileSettingsPage
frameTitle(String) - Method in class bdv.util.BdvOptions: Set the title of the BigDataViewer window.
from(Consumer<AffineTransform3D>, Consumer<AffineTransform3D>) - Static method in interface bdv.TransformState
fromPrefs() - Method in class bdv.ui.appearance.AppearanceManager: Deprecated.
Prefs will be replaced eventually by directly using Appearance in BDV
fromXml(Element) - Method in class bdv.tools.transformation.XmlIoTransformedSources
fromXml(Element, File) - Static method in class bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy
fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.catmaid.XmlIoCatmaidImageLoader
fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.hdf5.XmlIoHdf5ImageLoader
fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.imaris.XmlIoImarisImageLoader
fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.n5.XmlIoN5ImageLoader
fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.openconnectome.XmlIoOpenConnectomeImageLoader
fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.remote.XmlIoRemoteImageLoader
fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class bdv.img.n5.XmlIoN5ImageLoader
fromXmlAffine(Element) - Method in class bdv.tools.transformation.XmlIoTransformedSources
FULL - bdv.tools.boundingbox.TransformedBoxOverlay.BoxDisplayMode
FUSED - bdv.viewer.DisplayMode
FUSEDGROUP - bdv.viewer.DisplayMode

G

get() - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
get() - Method in interface bdv.TransformState: Get the current transform.
get() - Method in class bdv.util.ConstantRandomAccessible.ConstantRandomAccess
get(double) - Method in class bdv.viewer.animate.AbstractTransformAnimator: Returns an AffineTransform3D for the specified completion factor.
get(double) - Method in class bdv.viewer.animate.RotationAnimator
get(double) - Method in class bdv.viewer.animate.SimilarityTransformAnimator
get(double) - Method in class bdv.viewer.animate.TranslationAnimator
get(int) - Method in class bdv.util.WrappedList
get(long) - Method in class bdv.img.cache.VolatileCachedCellImg.VolatileCachedCells
get(long, CacheHints) - Method in interface bdv.img.cache.VolatileCachedCellImg.Get
get(Interpolation) - Method in class bdv.util.DefaultInterpolators
get(String) - Method in class bdv.tools.bookmarks.Bookmarks
get(CellGrid, Fraction, PrimitiveType, boolean) - Static method in class bdv.img.cache.CreateInvalidVolatileCell
get(CellGrid, T, boolean) - Static method in class bdv.img.cache.CreateInvalidVolatileCell
get(AffineTransform3D) - Method in interface bdv.TransformState: Get the current transform.
get(PrimitiveType, boolean) - Static method in class bdv.img.cache.DefaultEmptyArrayCreator
get(PrimitiveType, boolean) - Static method in interface bdv.img.cache.EmptyArrayCreator
getAccumulateProjectorFactory() - Method in class bdv.viewer.BasicViewerState
getAccumulateProjectorFactory() - Method in class bdv.viewer.SynchronizedViewerState
getAccumulateProjectorFactory() - Method in class bdv.viewer.ViewerOptions.Values
getAccumulateProjectorFactory() - Method in interface bdv.viewer.ViewerState: Get the current AccumulateProjectorFactory.
getActiveGroups() - Method in class bdv.viewer.BasicViewerState: Get the set of active groups.
getActiveGroups() - Method in class bdv.viewer.SynchronizedViewerState: Get the set of active groups.
getActiveGroups() - Method in interface bdv.viewer.ViewerState: Get the set of active groups.
getActiveSources() - Method in class bdv.viewer.BasicViewerState: Get the set of active sources.
getActiveSources() - Method in class bdv.viewer.SynchronizedViewerState: Get the set of active sources.
getActiveSources() - Method in interface bdv.viewer.ViewerState: Get the set of active sources.
getAppearanceManager() - Method in class bdv.BigDataViewer
getAppearanceManager() - Method in class bdv.util.BdvHandle
getAppearanceManager() - Method in class bdv.util.BdvHandleFrame
getAppearanceManager() - Method in class bdv.util.BdvHandlePanel
getAppearanceManager() - Method in class bdv.util.BdvOptions.Values
getAppearanceManager() - Method in class bdv.viewer.ViewerFrame
getAppearanceManager() - Method in class bdv.viewer.ViewerOptions.Values
getARGBArrayData(RandomAccessible<?>) - Static method in class bdv.viewer.render.ProjectorUtils
getARGBArrayImgData(RandomAccessible<?>) - Static method in class bdv.viewer.render.ProjectorUtils: Extracts the underlying int[] array in case img is a standard ArrayImg<ARGBType>.
getArrayString(int[][]) - Static method in class bdv.export.ProposeMipmaps: Format in[][] array, such as resolutions or chunksizes definition, as a String (to be used in export dialog textfields).
getAxisOrder(AxisOrder, EuclideanSpace, boolean) - Static method in enum bdv.util.AxisOrder
getBdvHandle() - Method in interface bdv.util.Bdv
getBdvHandle() - Method in class bdv.util.BdvHandle
getBdvHandle() - Method in class bdv.util.BdvSource
getBestMipMapLevel(AffineTransform3D, int) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the mipmap level that best matches the given screen scale for the given source.
getBestMipMapLevel(AffineTransform3D, Source<?>) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the mipmap level that best matches the given screen scale for the given source.
getBestMipMapLevel(AffineTransform3D, Source<?>, int) - Static method in class bdv.util.MipmapTransforms: Get the mipmap level that best matches the given screen scale for the given source.
getBigDataViewer() - Method in class bdv.util.BdvHandleFrame
getBlockSize() - Method in class bdv.img.hdf5.DimsAndExistence
getBoundingBox(List) - Static method in class bdv.util.IntervalBoundingBox: get bounding box of a list of points.
getBounds() - Method in class bdv.util.BoundedRange
getBounds() - Method in class bdv.viewer.ConverterSetups
getBounds(ConverterSetup) - Method in class bdv.viewer.ConverterSetupBounds
getBoxToViewerTransform(AffineTransform3D) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay: Get the transformation from the local coordinate frame of the TransformedBox to viewer coordinates.
getBufferedImage() - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
getBufferedImage(ARGBScreenImage) - Static method in class bdv.util.AWTUtils: Get a BufferedImage for the given ARGBScreenImage.
getBufferedImage(ARGBScreenImage, boolean) - Static method in class bdv.util.AWTUtils: Get a BufferedImage for the given ARGBScreenImage.
getBuiltinStyles() - Method in class bdv.ui.settings.style.AbstractStyleManager
getBuiltinStyles() - Method in interface bdv.ui.settings.style.StyleManager
getBytesPerElement() - Method in interface bdv.img.cache.CacheArrayLoader: How many bytes does one element (voxel) occupy?
getBytesPerElement() - Method in class bdv.img.catmaid.CatmaidVolatileIntArrayLoader
getBytesPerElement() - Method in class bdv.img.imaris.ImarisVolatileByteArrayLoader
getBytesPerElement() - Method in class bdv.img.imaris.ImarisVolatileFloatArrayLoader
getBytesPerElement() - Method in class bdv.img.imaris.ImarisVolatileShortArrayLoader
getBytesPerElement() - Method in class bdv.img.openconnectome.OpenConnectomeVolatileArrayLoader
getBytesPerElement() - Method in class bdv.img.remote.RemoteVolatileShortArrayLoader
getCache() - Method in class bdv.img.cache.VolatileCachedCellImg
getCache() - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
getCacheControl() - Method in class bdv.img.catmaid.CatmaidImageLoader
getCacheControl() - Method in class bdv.img.hdf5.Hdf5ImageLoader
getCacheControl() - Method in class bdv.img.imaris.ImarisImageLoader
getCacheControl() - Method in class bdv.img.n5.N5ImageLoader
getCacheControl() - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
getCacheControl() - Method in class bdv.img.remote.RemoteImageLoader
getCacheControl() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper
getCacheControl() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper
getCacheControl() - Method in class bdv.spimdata.WrapBasicImgLoader
getCacheControl() - Method in interface bdv.util.ChannelSources: Get handle for controlling cache behaviour.
getCacheControl() - Method in class bdv.util.volatiles.VolatileViewData: Get the CacheControl for the CachedCellImg(s) at the bottom of the view cascade.
getCacheControl() - Method in interface bdv.ViewerImgLoader
getCacheControls() - Method in class bdv.util.BdvHandle
getCardPanel() - Method in class bdv.util.BdvHandle
getCardPanel() - Method in class bdv.viewer.ViewerFrame
getCellsPath(int, int, int) - Static method in class bdv.img.hdf5.Util
getCellsPath(ViewLevelId) - Static method in class bdv.img.hdf5.Util
getCellsPath(ViewId, int) - Static method in class bdv.img.hdf5.Util
getChild(Object, int) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
getChildCount(Object) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
getColor() - Method in interface bdv.tools.brightness.ConverterSetup: Get the color for this converter.
getColor() - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
getColor() - Method in class bdv.util.PlaceHolderConverterSetup
getColor() - Method in class bdv.util.PlaceHolderOverlayInfo: Get the color for this converter.
getColumnClass(int) - Method in class bdv.ui.sourcetable.SourceTableModel
getColumnCount() - Method in class bdv.ui.sourcetable.SourceTableModel
getColumnName(int) - Method in class bdv.ui.sourcetable.SourceTableModel
getCommandDescriptions() - Method in class bdv.ui.keymap.KeymapManager
getCommandDescriptions(CommandDescriptions) - Method in class bdv.BigDataViewerActions.Descriptions
getCommandDescriptions(CommandDescriptions) - Method in class bdv.tools.CloseWindowActions.Descriptions
getCommandDescriptions(CommandDescriptions) - Method in class bdv.TransformEventHandler2D.Descriptions
getCommandDescriptions(CommandDescriptions) - Method in class bdv.TransformEventHandler3D.Descriptions
getCommandDescriptions(CommandDescriptions) - Method in class bdv.viewer.NavigationActions.Descriptions
getComponent() - Method in class bdv.ui.CardPanel
getConfig() - Method in class bdv.ui.keymap.Keymap
getConverter() - Method in class bdv.viewer.SourceAndConverter: Get the Converter (converts source type T to ARGBType for display).
getConverterSetup(SourceAndConverter<?>) - Method in class bdv.viewer.ConverterSetups
getConverterSetup(SourceAndConverter<?>) - Method in interface bdv.viewer.SourceToConverterSetupBimap
getConverterSetups() - Method in class bdv.BigDataViewer
getConverterSetups() - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.
getConverterSetups() - Method in class bdv.util.BdvHandle
getConverterSetups() - Method in class bdv.util.BdvStackSource
getConverterSetups() - Method in class bdv.viewer.AbstractViewerPanel: Get the ConverterSetups which manages the mapping between ConverterSetups and sources.
getConverterSetups() - Method in class bdv.viewer.ViewerFrame
getConverterSetups() - Method in class bdv.viewer.ViewerPanel
getConverterSetups(List<? extends SourceAndConverter<?>>) - Method in interface bdv.viewer.SourceToConverterSetupBimap: Returns list of all non-null ConverterSetups associated to sources.
getCornerHighlighter() - Method in class bdv.tools.boundingbox.TransformedBoxOverlay: Returns a MouseMotionListener that can be installed into a bdv (see ViewerPanel.getDisplay().addHandler(...)).
getCorners(RealInterval) - Static method in class bdv.util.IntervalBoundingBox: get "corners" of an interval as a list of points.
getCroppedTransform(ViewId) - Method in class bdv.tools.crop.CropImgLoader
getCurrent(long) - Method in class bdv.viewer.animate.AbstractTransformAnimator: Returns an AffineTransform3D that can be used to set the viewpoint of a ViewerFrame instance, for the time specified.
getCurrentGroup() - Method in class bdv.viewer.BasicViewerState: Get the current group.
getCurrentGroup() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the index of the current group.
getCurrentGroup() - Method in class bdv.viewer.SynchronizedViewerState: Get the current group.
getCurrentGroup() - Method in interface bdv.viewer.ViewerState: Get the current group.
getCurrentGroup() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
getCurrentMode() - Method in class bdv.viewer.BlendModeSwitcher
getCurrentSource() - Method in class bdv.viewer.BasicViewerState: Get the current source.
getCurrentSource() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the index of the current source.
getCurrentSource() - Method in class bdv.viewer.SynchronizedViewerState: Get the current source.
getCurrentSource() - Method in interface bdv.viewer.ViewerState: Get the current source.
getCurrentSource() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
getCurrentTimepoint() - Method in class bdv.viewer.BasicViewerState
getCurrentTimepoint() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the timepoint index that is currently displayed.
getCurrentTimepoint() - Method in class bdv.viewer.SynchronizedViewerState
getCurrentTimepoint() - Method in interface bdv.viewer.ViewerState: Get the current timepoint.
getCurrentTransform2D(AffineTransform2D) - Method in class bdv.util.BdvOverlay: Can be used by derived classes in the BdvOverlay.draw(Graphics2D) method to get the current transform from 2D source coordinates to screen coordinates.
getCurrentTransform3D(AffineTransform3D) - Method in class bdv.util.BdvOverlay: Can be used by derived classes in the BdvOverlay.draw(Graphics2D) method to get the current transform from 3D source coordinates to 3D screen coordinates (where Z coordinate is distance from the slice shown on the screen).
getCurrentValue() - Method in class bdv.util.BoundedValue
getCurrentValue() - Method in class bdv.util.BoundedValueDouble
getDatasetPath(N5Reader, int, int, int) - Method in class bdv.img.n5.DefaultN5Properties
getDatasetPath(N5Reader, int, int, int) - Method in interface bdv.img.n5.N5Properties
getDataType(N5Reader, int) - Method in class bdv.img.n5.DefaultN5Properties
getDataType(N5Reader, int) - Method in interface bdv.img.n5.N5Properties
getDefaultCacheHints() - Method in class bdv.img.cache.VolatileCachedCellImg
getDefaultProperties() - Static method in class bdv.util.Prefs
getDimensions() - Method in class bdv.img.hdf5.DimsAndExistence
getDimensions(N5Reader, int, int, int) - Method in class bdv.img.n5.DefaultN5Properties
getDimensions(N5Reader, int, int, int) - Method in interface bdv.img.n5.N5Properties
getDimsAndExistence(ViewLevelId) - Method in class bdv.img.hdf5.Hdf5ImageLoader
getDimsAndExistence(ViewLevelId) - Method in class bdv.img.imaris.HDF5AccessHack
getDimsAndExistence(ViewLevelId) - Method in interface bdv.img.imaris.IHDF5Access
getDimsAndExistence(ViewLevelId) - Method in class bdv.img.remote.RemoteImageLoader
getDisplay() - Method in class bdv.viewer.AbstractViewerPanel: Get the viewer canvas.
getDisplay() - Method in class bdv.viewer.ViewerPanel: Get the viewer canvas.
getDisplayComponent() - Method in class bdv.viewer.AbstractViewerPanel: Get the AWT Component of the viewer canvas.
getDisplayComponent() - Method in class bdv.viewer.ViewerPanel: Get the AWT Component of the viewer canvas.
getDisplayMode() - Method in class bdv.viewer.BasicViewerState
getDisplayMode() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the current DisplayMode.
getDisplayMode() - Method in class bdv.viewer.SynchronizedViewerState
getDisplayMode() - Method in interface bdv.viewer.ViewerState: Get the current DisplayMode.
getDisplayMode() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
getDisplayRangeMax() - Method in interface bdv.tools.brightness.ConverterSetup: Get the (smallest) source value that is mapped to the maximum of the target range.
getDisplayRangeMax() - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
getDisplayRangeMax() - Method in class bdv.util.PlaceHolderConverterSetup
getDisplayRangeMax() - Method in class bdv.util.PlaceHolderOverlayInfo: Get the (smallest) source value that is mapped to the maximum of the target range.
getDisplayRangeMin() - Method in interface bdv.tools.brightness.ConverterSetup: Get the (largest) source value that is mapped to the minimum of the target range.
getDisplayRangeMin() - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
getDisplayRangeMin() - Method in class bdv.util.PlaceHolderConverterSetup
getDisplayRangeMin() - Method in class bdv.util.PlaceHolderOverlayInfo: Get the (largest) source value that is mapped to the minimum of the target range.
getEmptyArray(long) - Method in class bdv.img.cache.DefaultEmptyArrayCreator
getEmptyArray(long) - Method in interface bdv.img.cache.EmptyArrayCreator
getEmptyArrayCreator() - Method in interface bdv.img.cache.CacheArrayLoader: Implementing classes must override this if A is not a standard VolatileArrayDataAccess type.
getEmptyArrayCreator() - Method in interface bdv.img.cache.SimpleCacheArrayLoader: Implementing classes must override this if A is not a standard VolatileArrayDataAccess type.
getExportResolutions() - Method in class bdv.export.ExportMipmapInfo
getFillIntersection() - Method in class bdv.tools.boundingbox.TransformedBoxEditor: Only meaningful if BoxSourceType == NONE
getFillIntersection() - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
getFixedTransform(AffineTransform3D) - Method in class bdv.tools.transformation.TransformedSource: Get the fixed part of the extra transformation.
getFloatImage(int, boolean, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getFont(String) - Static method in class bdv.ui.UIUtils
getForwardSelectedKeymap() - Method in class bdv.ui.keymap.AbstractKeymapManager: Returns a final Keymap instance that always has the same properties as the selected keymap.
getFrameTitle() - Method in class bdv.util.BdvOptions.Values
getFullRangeMax() - Method in class bdv.tools.brightness.MinMaxGroup
getFullRangeMin() - Method in class bdv.tools.brightness.MinMaxGroup
getGlobalMouseCoordinates(RealPositionable) - Method in class bdv.viewer.AbstractViewerPanel: Set gPos to the current mouse coordinates transformed into the global coordinate system.
getGroupName(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Get the name of a group.
getGroupName(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Get the name of a group.
getGroupName(SourceGroup) - Method in interface bdv.viewer.ViewerState: Get the name of a group.
getGroupPath(int, int, int) - Static method in class bdv.img.hdf5.Util
getGroupPath(ViewLevelId) - Static method in class bdv.img.hdf5.Util
getGroupPath(ViewId, int) - Static method in class bdv.img.hdf5.Util
getGroups() - Method in class bdv.viewer.BasicViewerState: Get the list of groups.
getGroups() - Method in class bdv.viewer.SynchronizedViewerState: Get the list of groups.
getGroups() - Method in interface bdv.viewer.ViewerState: Get the list of groups.
getHandle() - Method in class bdv.viewer.state.SourceState: Deprecated.

Get the SourceAndConverter that this SourceState represents.
getHdf5File() - Method in class bdv.img.hdf5.Hdf5ImageLoader
getHdf5ImageLoader(AbstractSequenceDescription<?, ?, ?>) - Static method in class bdv.spimdata.tools.MergePartitionList: Get the Hdf5ImageLoader of a AbstractSequenceDescription, or throw an exception if the sequence doesn't have an Hdf5ImageLoader.
getHdf5PerSetupExportMipmapInfos(AbstractSequenceDescription<?, ?, ?>) - Static method in class bdv.spimdata.tools.MergePartitionList: Return map from setup id to ExportMipmapInfo for the Hdf5ImageLoader of the specified AbstractSequenceDescription.
getHeight() - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer
getHeight() - Method in interface bdv.viewer.render.RenderTarget: Get the current canvas height.
getHeight() - Method in class bdv.viewer.ViewerOptions.Values
getHighlightedCornerIndex() - Method in class bdv.tools.boundingbox.TransformedBoxOverlay: Get the index of the highlighted corner (if any).
getIconHeight() - Method in class bdv.tools.brightness.ColorIcon
getIconWidth() - Method in class bdv.tools.brightness.ColorIcon
getImage(int) - Method in interface bdv.export.ExportScalePyramid.DatasetIO: Opens a dataset that was already written as a RaπdomAccessibleInterval.
getImage(int, int, ImgLoaderHint...) - Method in class bdv.AbstractCachedViewerSetupImgLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.img.catmaid.CatmaidImageLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.img.imaris.ImarisImageLoader.SetupImgLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.img.remote.RemoteImageLoader.SetupImgLoader
getImage(int, int, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getImage(int, int, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getImage(int, ImgLoaderHint...) - Method in class bdv.AbstractViewerSetupImgLoader
getImage(int, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getImage(int, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getImage(int, ImgLoaderHint...) - Method in class bdv.tools.crop.CropImgLoader.SetupImgLoader
getImage(ViewId) - Method in class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
getImage(ViewId, int) - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
getImageSize(int) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getImageSize(int, int) - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getImageSize(int, int) - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
getImageType() - Method in class bdv.AbstractViewerSetupImgLoader
getImageType() - Method in class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
getImageType() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getImageType() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getImageType() - Method in class bdv.tools.crop.CropImgLoader.SetupImgLoader
getImg() - Method in class bdv.util.volatiles.VolatileViewData: Get the wrapped RandomAccessible.
getImsFile() - Method in class bdv.img.imaris.ImarisImageLoader
getIncrementalTransform(AffineTransform3D) - Method in class bdv.tools.transformation.TransformedSource: Get the incremental part of the extra transformation.
getIndexOfChild(Object, Object) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
getInitialMaxTimepoint() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getInitialMinTimepoint() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getInputTriggerConfig() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getInputTriggerConfig() - Method in class bdv.util.BdvOptions.Values
getInputTriggerConfig() - Method in class bdv.viewer.AbstractViewerPanel
getInputTriggerConfig() - Method in class bdv.viewer.ViewerOptions.Values
getInputTriggerConfig() - Method in class bdv.viewer.ViewerPanel
getInputTriggerConfig(ViewerOptions) - Static method in class bdv.BigDataViewer: Deprecated.
This method is no longer used internally. InputTriggerConfigs are now managed through KeymapManager.
getInstance() - Static method in class bdv.util.Prefs
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.AbstractSpimSource
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.tools.transformation.TransformedSource
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.util.AbstractSource
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.util.PlaceHolderSource
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleSource
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleSource4D
getInterpolatedMaskedSource(int, int, Interpolation) - Method in class bdv.util.RealRandomAccessibleSource
getInterpolatedMaskedSource(int, int, Interpolation) - Method in interface bdv.viewer.Source: Get a Masked version of the 3D stack at timepoint index t, extended to infinity and interpolated.
getInterpolatedMaskedSource(int, int, Interpolation, ThreadGroup) - Method in class bdv.AbstractSpimSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.AbstractSpimSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.tools.transformation.TransformedSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.AbstractSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.PlaceHolderSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleIntervalSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleIntervalSource4D
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleSource
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.RandomAccessibleSource4D
getInterpolatedSource(int, int, Interpolation) - Method in class bdv.util.RealRandomAccessibleSource
getInterpolatedSource(int, int, Interpolation) - Method in interface bdv.viewer.Source: Get the 3D stack at timepoint index t, extended to infinity and interpolated.
getInterpolatedSource(int, int, Interpolation, ThreadGroup) - Method in class bdv.AbstractSpimSource
getInterpolation() - Method in class bdv.viewer.BasicViewerState
getInterpolation() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the interpolation method.
getInterpolation() - Method in class bdv.viewer.SynchronizedViewerState
getInterpolation() - Method in interface bdv.viewer.ViewerState: Get the interpolation method.
getInterval() - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible
getInterval() - Method in interface bdv.tools.boundingbox.BoxSelectionPanel.Box
getInterval() - Method in interface bdv.tools.boundingbox.RealBoxSelectionPanel.RealBox
getInterval() - Method in interface bdv.tools.boundingbox.TransformedBox
getInterval() - Method in class bdv.tools.boundingbox.TransformedBoxModel
getInterval() - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog.Result: Returns the selected interval.
getInterval() - Method in class bdv.tools.boundingbox.TransformedRealBoxModel
getInterval() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result: Returns the selected interval.
getInterval(int, int) - Method in class bdv.util.RealRandomAccessibleIntervalSource
getInterval(int, int) - Method in class bdv.util.RealRandomAccessibleSource: Return the interval which should be used to bound the wrapped (unbounded) RealRandomAccessible for RealRandomAccessibleSource.getSource(int, int).
getJPanel() - Method in class bdv.ui.appearance.AppearanceSettingsPage
getJPanel() - Method in class bdv.ui.settings.SelectAndEditProfileSettingsPage
getJPanel() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileEditPanel
getJPanel() - Method in interface bdv.ui.settings.SettingsPage
getJPanel() - Method in class bdv.ui.settings.SimpleSettingsPage
getKeybindings() - Method in class bdv.util.BdvHandle
getKeybindings() - Method in class bdv.util.BdvHandleFrame
getKeybindings() - Method in class bdv.util.BdvHandlePanel
getKeybindings() - Method in class bdv.viewer.ViewerFrame
getKeymapManager() - Method in class bdv.BigDataViewer
getKeymapManager() - Method in class bdv.util.BdvHandle
getKeymapManager() - Method in class bdv.util.BdvHandleFrame
getKeymapManager() - Method in class bdv.util.BdvHandlePanel
getKeymapManager() - Method in class bdv.util.BdvOptions.Values
getKeymapManager() - Method in class bdv.viewer.ViewerFrame
getKeymapManager() - Method in class bdv.viewer.ViewerOptions.Values
getKeyPressedManager() - Method in class bdv.viewer.ViewerOptions.Values
getLastFrameRenderNanoTime() - Method in class bdv.viewer.render.AccumulateProjector
getLastFrameRenderNanoTime() - Method in class bdv.viewer.render.EmptyProjector
getLastFrameRenderNanoTime() - Method in class bdv.viewer.render.SimpleVolatileProjector
getLastFrameRenderNanoTime() - Method in interface bdv.viewer.render.VolatileProjector: How many nano-seconds did the last VolatileProjector.map() take.
getLevel() - Method in class bdv.img.hdf5.ViewLevelId
getLevelCellDimensions() - Method in class bdv.img.openconnectome.OpenConnectomeTokenInfo
getLevelDimensions(String) - Method in class bdv.img.openconnectome.OpenConnectomeTokenInfo
getLevels() - Method in class bdv.viewer.render.MipmapOrdering.MipmapHints
getLevelScales(String) - Method in class bdv.img.openconnectome.OpenConnectomeTokenInfo
getLevelTransforms(String) - Method in class bdv.img.openconnectome.OpenConnectomeTokenInfo
getManualTransformEditor() - Method in class bdv.BigDataViewer
getManualTransformEditor() - Method in class bdv.util.BdvHandle
getManualTransformEditor() - Method in class bdv.util.BdvHandleFrame
getManualTransformEditor() - Method in class bdv.util.BdvHandlePanel
getMaskedSource(int, int) - Method in class bdv.AbstractSpimSource
getMaskedSource(int, int) - Method in class bdv.tools.transformation.TransformedSource
getMaskedSource(int, int) - Method in class bdv.util.AbstractSource
getMaskedSource(int, int) - Method in class bdv.util.PlaceHolderSource
getMaskedSource(int, int) - Method in class bdv.util.RandomAccessibleSource
getMaskedSource(int, int) - Method in class bdv.util.RandomAccessibleSource4D
getMaskedSource(int, int) - Method in class bdv.util.RealRandomAccessibleSource
getMaskedSource(int, int) - Method in interface bdv.viewer.Source: Get a Masked version of the 3D stack at timepoint index t.
getMaskedSource(int, int, ThreadGroup) - Method in class bdv.AbstractSpimSource
getMax() - Method in class bdv.util.BoundedRange
getMaxBound() - Method in class bdv.util.BoundedRange
getMaxBound() - Method in class bdv.util.Bounds
getMaxBoundedValue() - Method in class bdv.util.BoundedInterval: Get the current maximum of the interval.
getMaxBoundedValue() - Method in class bdv.util.BoundedIntervalDouble: Get the current maximum of the interval.
getMaxLevel() - Method in class bdv.img.MipmapInfo: Get the maximum mipmap level.
getMaxTimepoint() - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog.Result
getMaxTimepoint() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result
getMergedHdf5PartitionList(AbstractSequenceDescription<?, ?, ?>, AbstractSequenceDescription<?, ?, ?>) - Static method in class bdv.spimdata.tools.MergePartitionList
getMin() - Method in class bdv.util.BoundedRange
getMinBound() - Method in class bdv.util.BoundedRange
getMinBound() - Method in class bdv.util.Bounds
getMinBoundedValue() - Method in class bdv.util.BoundedInterval: Get the current minimum of the interval.
getMinBoundedValue() - Method in class bdv.util.BoundedIntervalDouble: Get the current minimum of the interval.
getMinMaxGroup(ConverterSetup) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.
getMinMaxGroups() - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.
getMinTimepoint() - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog.Result
getMinTimepoint() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result
getMipmapHints(AffineTransform3D, int, int) - Method in class bdv.tools.transformation.TransformedSource
getMipmapHints(AffineTransform3D, int, int) - Method in class bdv.viewer.render.DefaultMipmapOrdering
getMipmapHints(AffineTransform3D, int, int) - Method in interface bdv.viewer.render.MipmapOrdering: Evaluate mipmap levels such that they can be ordered for rendering and/or prefetching.
getMipmapHints(AffineTransform3D, int, int) - Method in class bdv.VolatileSpimSource
getMipmapInfo() - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getMipmapInfo(int) - Method in class bdv.img.remote.RemoteImageLoader
getMipmapLevel() - Method in class bdv.viewer.render.MipmapOrdering.Level
getMipmapResolutions() - Method in class bdv.AbstractCachedViewerSetupImgLoader
getMipmapResolutions() - Method in class bdv.img.catmaid.CatmaidImageLoader
getMipmapResolutions() - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getMipmapResolutions() - Method in class bdv.img.imaris.ImarisImageLoader.SetupImgLoader
getMipmapResolutions() - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
getMipmapResolutions() - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
getMipmapResolutions() - Method in class bdv.img.remote.RemoteImageLoader.SetupImgLoader
getMipmapResolutions() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getMipmapResolutions() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getMipmapResolutions(int) - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
getMipmapResolutions(N5Reader, int) - Method in class bdv.img.n5.DefaultN5Properties
getMipmapResolutions(N5Reader, int) - Method in interface bdv.img.n5.N5Properties
getMipmapTransformDefault(double[]) - Static method in class bdv.util.MipmapTransforms: Compute the transformation (scale and shift) that maps from coordinates in a down-scaled image to coordinates in the original image.
getMipmapTransforms() - Method in class bdv.AbstractCachedViewerSetupImgLoader
getMipmapTransforms() - Method in class bdv.img.catmaid.CatmaidImageLoader
getMipmapTransforms() - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getMipmapTransforms() - Method in class bdv.img.imaris.ImarisImageLoader.SetupImgLoader
getMipmapTransforms() - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
getMipmapTransforms() - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
getMipmapTransforms() - Method in class bdv.img.remote.RemoteImageLoader.SetupImgLoader
getMipmapTransforms() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getMipmapTransforms() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getMipmapTransforms(int) - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
getMissingDataImage(ViewLevelId, T) - Method in class bdv.img.remote.RemoteImageLoader: For images that are missing in the hdf5, a constant image is created.
getModel() - Method in class bdv.ui.sourcetable.SourceTable
getMouseCoordinates(Positionable) - Method in class bdv.viewer.AbstractViewerPanel: Set p to the current mouse coordinates wrt to the display component.
getMouseCoordinates(Positionable) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
getMsgOverlay() - Method in class bdv.viewer.ViewerOptions.Values
getN5File() - Method in class bdv.img.n5.N5ImageLoader
getN5URI() - Method in class bdv.img.n5.N5ImageLoader
getName() - Method in class bdv.AbstractSpimSource
getName() - Method in class bdv.tools.transformation.TransformedSource
getName() - Method in class bdv.ui.keymap.Keymap: Returns the name of this Keymap.
getName() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.Profile
getName() - Method in class bdv.ui.settings.style.AbstractStyle
getName() - Method in interface bdv.ui.settings.style.Style
getName() - Method in class bdv.ui.settings.style.StyleProfile
getName() - Method in class bdv.util.AbstractSource
getName() - Method in class bdv.util.PlaceHolderSource
getName() - Method in class bdv.util.RealRandomAccessibleSource
getName() - Method in enum bdv.viewer.BlendMode
getName() - Method in enum bdv.viewer.DisplayMode
getName() - Method in enum bdv.viewer.Interpolation
getName() - Method in interface bdv.viewer.Source: Get the name of the source.
getName() - Method in class bdv.viewer.state.SourceGroup: Deprecated.
getNumLevels() - Method in class bdv.img.MipmapInfo: Get the number of mipmap levels (MipmapInfo.getMaxLevel() + 1).
getNumMipmapLevels() - Method in class bdv.AbstractSpimSource
getNumMipmapLevels() - Method in class bdv.tools.transformation.TransformedSource
getNumMipmapLevels() - Method in class bdv.util.AbstractSource
getNumMipmapLevels() - Method in class bdv.util.PlaceHolderSource
getNumMipmapLevels() - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
getNumMipmapLevels() - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
getNumMipmapLevels() - Method in class bdv.util.RealRandomAccessibleSource
getNumMipmapLevels() - Method in class bdv.util.VolatileSource
getNumMipmapLevels() - Method in interface bdv.viewer.Source
getNumRenderingThreads() - Method in class bdv.viewer.ViewerOptions.Values
getNumScales(long, long, long, long) - Static method in class bdv.img.catmaid.CatmaidImageLoader
getNumSourceGroups() - Method in class bdv.viewer.ViewerOptions.Values
getNumTimepoints() - Method in class bdv.util.BdvSource
getNumTimepoints() - Method in class bdv.viewer.BasicViewerState
getNumTimepoints() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the number of timepoints.
getNumTimepoints() - Method in class bdv.viewer.SynchronizedViewerState
getNumTimepoints() - Method in interface bdv.viewer.ViewerState: Get the number of timepoints.
getOffsets(String) - Method in class bdv.img.openconnectome.OpenConnectomeTokenInfo
getOptionValues() - Method in class bdv.viewer.ViewerPanel
getOverlay() - Method in class bdv.util.BdvOverlaySource
getPartitions() - Method in class bdv.img.hdf5.Hdf5ImageLoader
getPartitions(AbstractSequenceDescription<?, ?, ?>) - Static method in class bdv.spimdata.tools.MergePartitionList: Get the Partition list for the Hdf5ImageLoader of the specified AbstractSequenceDescription.
getPath() - Method in class bdv.img.hdf5.Partition: Get the path to the hdf5 file for this partition.
getPathForLocation(int, int) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
getPathName(int) - Static method in class bdv.img.n5.BdvN5Format
getPathName(int, int) - Static method in class bdv.img.n5.BdvN5Format
getPathName(int, int, int) - Static method in class bdv.img.n5.BdvN5Format
getPathTo(SourceGroupTreeModel.GroupModel) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
getPathTo(SourceGroup) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
getPixelSourceSize(AffineTransform3D, Source<?>, int, int) - Static method in class bdv.util.MipmapTransforms: Compute the size of the backprojected screen pixel in the Source space.
getPlaceHolderOverlayInfo() - Method in class bdv.util.BdvVirtualChannelSource
getPrefetchCacheHints() - Method in class bdv.viewer.render.MipmapOrdering.Level
getPrefetchOrder() - Method in class bdv.viewer.render.MipmapOrdering.Level
getProfiles() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager
getProfiles() - Method in class bdv.ui.settings.style.StyleProfileManager
getRangeMax() - Method in class bdv.util.BoundedInterval: Get the current maximum of the allowed range.
getRangeMax() - Method in class bdv.util.BoundedIntervalDouble: Get the current maximum of the allowed range.
getRangeMax() - Method in class bdv.util.BoundedValue
getRangeMax() - Method in class bdv.util.BoundedValueDouble
getRangeMaxTimepoint() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getRangeMin() - Method in class bdv.util.BoundedInterval: Get the current minimum of the allowed range.
getRangeMin() - Method in class bdv.util.BoundedIntervalDouble: Get the current minimum of the allowed range.
getRangeMin() - Method in class bdv.util.BoundedValue
getRangeMin() - Method in class bdv.util.BoundedValueDouble
getRangeMinTimepoint() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getRenderCacheHints() - Method in class bdv.viewer.render.MipmapOrdering.Level
getRenderOrder() - Method in class bdv.viewer.render.MipmapOrdering.Level
getResolutions() - Method in class bdv.img.MipmapInfo: Get the subsampling factors, indexed by mipmap level and dimension.
getResolutionsPath(int) - Static method in class bdv.img.hdf5.Util
getResult() - Method in class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog: Makes the dialog visible and waits for the user to close the dialog, click ok, or cancel.
getReusableRenderResult() - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer
getReusableRenderResult() - Method in interface bdv.viewer.render.RenderTarget: Returns a RenderResult for rendering to.
getRoot() - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
getRowCount() - Method in class bdv.ui.sourcetable.SourceTableModel
getScaleFactor() - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
getScaleFactor() - Method in interface bdv.viewer.render.RenderResult: Get the scale factor from target coordinates to screen resolution.
getScreenScales() - Method in class bdv.viewer.ViewerOptions.Values
getSelectedConverterSetups() - Method in class bdv.ui.sourcetable.SourceTable
getSelectedProfile() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager
getSelectedProfile() - Method in class bdv.ui.settings.style.StyleProfileManager
getSelectedSources() - Method in class bdv.ui.sourcegrouptree.SourceGroupTree: Get list of sources in selected groups.
getSelectedSources() - Method in class bdv.ui.sourcetable.SourceTable
getSelectedStyle() - Method in class bdv.ui.settings.style.AbstractStyleManager
getSelectedStyle() - Method in interface bdv.ui.settings.style.StyleManager
getSetupAssignments() - Method in class bdv.BigDataViewer: Deprecated.
Instead getViewer().state() returns the ViewerState that can be modified directly.
getSetupAssignments() - Method in class bdv.util.BdvHandle: Deprecated.
getSetupId() - Method in class bdv.AbstractSpimSource
getSetupId() - Method in interface bdv.tools.brightness.ConverterSetup: Get the id of the BasicViewSetup this converter acts on.
getSetupId() - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
getSetupId() - Method in class bdv.util.PlaceHolderConverterSetup
getSetupIdSequenceToPartition() - Method in class bdv.img.hdf5.Partition: Get a map from setup ids of the full sequence to setup ids of this partition.
getSetupImgLoader(int) - Method in class bdv.img.catmaid.CatmaidImageLoader
getSetupImgLoader(int) - Method in class bdv.img.hdf5.Hdf5ImageLoader
getSetupImgLoader(int) - Method in class bdv.img.imaris.ImarisImageLoader
getSetupImgLoader(int) - Method in class bdv.img.n5.N5ImageLoader
getSetupImgLoader(int) - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
getSetupImgLoader(int) - Method in class bdv.img.remote.RemoteImageLoader
getSetupImgLoader(int) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper
getSetupImgLoader(int) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper
getSetupImgLoader(int) - Method in class bdv.spimdata.WrapBasicImgLoader
getSetupImgLoader(int) - Method in class bdv.tools.crop.CropImgLoader
getSetupImgLoader(int) - Method in interface bdv.ViewerImgLoader
getSetupPath(int) - Static method in class bdv.img.hdf5.Util
getShowTiles() - Method in class bdv.viewer.render.DebugTilingOverlay
getSource(int, int) - Method in class bdv.AbstractSpimSource
getSource(int, int) - Method in class bdv.tools.transformation.TransformedSource
getSource(int, int) - Method in class bdv.util.PlaceHolderSource
getSource(int, int) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
getSource(int, int) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
getSource(int, int) - Method in class bdv.util.RandomAccessibleIntervalSource
getSource(int, int) - Method in class bdv.util.RandomAccessibleIntervalSource4D
getSource(int, int) - Method in class bdv.util.RandomAccessibleSource
getSource(int, int) - Method in class bdv.util.RandomAccessibleSource4D
getSource(int, int) - Method in class bdv.util.RealRandomAccessibleSource
getSource(int, int) - Method in class bdv.util.VolatileSource
getSource(int, int) - Method in interface bdv.viewer.Source: Get the 3D stack at timepoint index t.
getSource(int, int, ThreadGroup) - Method in class bdv.AbstractSpimSource
getSource(ConverterSetup) - Method in class bdv.viewer.ConverterSetups
getSource(ConverterSetup) - Method in interface bdv.viewer.SourceToConverterSetupBimap
getSourceGroups() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Returns a list of all source groups.
getSourceGroups() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
getSourceIds() - Method in class bdv.viewer.state.SourceGroup: Deprecated.
getSourceInfoOverlayRenderer() - Method in class bdv.viewer.ViewerPanel
getSourceInterval() - Method in class bdv.viewer.overlay.IntervalAndTransform
getSourceInterval() - Method in interface bdv.viewer.overlay.MultiBoxOverlay.IntervalAndTransform: Get interval of the source (stack) in source-local coordinates.
getSources() - Method in class bdv.ui.SourcesTransferable.SourceList
getSources() - Method in class bdv.util.BdvStackSource
getSources() - Method in interface bdv.util.ChannelSources: Get the list of sources, one for each channel.
getSources() - Method in class bdv.viewer.BasicViewerState: Get the list of sources.
getSources() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Returns a list of all sources.
getSources() - Method in class bdv.viewer.SynchronizedViewerState: Get the list of sources.
getSources() - Method in interface bdv.viewer.ViewerState: Get the list of sources.
getSources() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
getSourcesBoundingBox(ViewerState) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil: Deprecated.
getSourcesBoundingBox(ViewerState, int, int) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil: Deprecated.
getSourcesBoundingBox(ViewerState) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
getSourcesBoundingBox(ViewerState, int, int) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
getSourcesBoundingBox(Collection<? extends Source<?>>, int, int) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
getSourcesBoundingBoxReal(ViewerState) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil: Deprecated.
getSourcesBoundingBoxReal(ViewerState, int, int) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil: Deprecated.
getSourcesBoundingBoxReal(ViewerState) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
getSourcesBoundingBoxReal(ViewerState, int, int) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
getSourcesBoundingBoxReal(Collection<? extends Source<?>>, int, int) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
getSourcesInGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Get the set sources in group.
getSourcesInGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Get the set sources in group.
getSourcesInGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState: Get the set sources in group.
getSourceToViewer() - Method in class bdv.viewer.overlay.IntervalAndTransform
getSourceToViewer() - Method in interface bdv.viewer.overlay.MultiBoxOverlay.IntervalAndTransform: Current transformation from source to viewer.
getSourceTransform() - Method in class bdv.util.BdvOptions.Values
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.AbstractSpimSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.tools.transformation.TransformedSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.PlaceHolderSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RandomAccessibleIntervalSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RandomAccessibleIntervalSource4D
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RandomAccessibleSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RandomAccessibleSource4D
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RealRandomAccessibleIntervalSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.RealRandomAccessibleSource
getSourceTransform(int, int, AffineTransform3D) - Method in class bdv.util.VolatileSource
getSourceTransform(int, int, AffineTransform3D) - Method in interface bdv.viewer.Source: Get the transform from the source at the given timepoint index and mipmap level into the global coordinate system.
getSpimSource() - Method in class bdv.viewer.SourceAndConverter: Get the Source (provides image data for all timepoints of one angle).
getSplitPanel() - Method in class bdv.util.BdvHandle
getSplitPanel() - Method in class bdv.viewer.ViewerFrame
getState() - Method in class bdv.viewer.state.ViewerState: Deprecated.
getState() - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use ViewerPanel.state() instead. Get a copy of the current ViewerState.
getState() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
getStyle() - Method in class bdv.ui.settings.style.StyleProfile
getSubdivisions() - Method in class bdv.img.MipmapInfo: Get the subdivision block sizes, indexed by mipmap level and dimension.
getSubdivisionsPath(int) - Static method in class bdv.img.hdf5.Util
getSuitableGraphicsConfiguration(ColorModel) - Static method in class bdv.util.AWTUtils: Get a GraphicsConfiguration from the default screen GraphicsDevice that matches the transparency of the given colorModel.
getTagName() - Method in class bdv.tools.transformation.XmlIoTransformedSources
getTagName() - Method in class bdv.viewer.state.XmlIoViewerState
getTargetImage() - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
getTargetImage() - Method in interface bdv.viewer.render.RenderResult: Get the image to render to.
getTargetRenderNanos() - Method in class bdv.viewer.ViewerOptions.Values
getTimePointId() - Method in class bdv.img.hdf5.ViewLevelId
getTimepointIdSequenceToPartition() - Method in class bdv.img.hdf5.Partition: Get a map from timepoint ids of the full sequence to timepoint ids of this partition.
getTimePointIndex() - Method in class bdv.util.PlaceHolderOverlayInfo
getTimepointSelection() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getTitle() - Method in class bdv.tools.boundingbox.BoxSelectionOptions.Values
getTransferData(DataFlavor) - Method in class bdv.ui.SourcesTransferable
getTransferDataFlavors() - Method in class bdv.ui.SourcesTransferable
getTransform(AffineTransform3D) - Method in class bdv.tools.boundingbox.AbstractTransformedBoxModel
getTransform(AffineTransform3D) - Method in interface bdv.tools.boundingbox.TransformedBox
getTransform(AffineTransform3D) - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog.Result: Stores the box transform into t.
getTransform(AffineTransform3D) - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result: Stores the box transform into t.
getTransformBehaviours() - Method in class bdv.viewer.ViewerFrame: Get Behaviours hook where TransformEventHandler behaviours are installed.
getTransformEventHandler() - Method in class bdv.viewer.ViewerPanel
getTransformEventHandlerFactory() - Method in class bdv.viewer.ViewerOptions.Values
getTransforms() - Method in class bdv.img.MipmapInfo: Get the transformation from coordinates of the subsampled image of a mipmap level to coordinates of the full resolution image.
getTransforms() - Method in class bdv.tools.transformation.ManualSourceTransforms
getTreePath() - Method in class bdv.ui.appearance.AppearanceSettingsPage
getTreePath() - Method in class bdv.ui.settings.SelectAndEditProfileSettingsPage
getTreePath() - Method in interface bdv.ui.settings.SettingsPage: Get the path of this page in the settings tree.
getTreePath() - Method in class bdv.ui.settings.SimpleSettingsPage
getTriggerbindings() - Method in class bdv.util.BdvHandle
getTriggerbindings() - Method in class bdv.util.BdvHandleFrame
getTriggerbindings() - Method in class bdv.util.BdvHandlePanel
getTriggerbindings() - Method in class bdv.viewer.ViewerFrame
getType() - Method in class bdv.SpimSource
getType() - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible
getType() - Method in class bdv.tools.transformation.TransformedSource
getType() - Method in class bdv.util.AbstractSource
getType() - Method in interface bdv.util.ChannelSources: Get (an instance of) the pixel type.
getType() - Method in class bdv.util.ConstantRandomAccessible
getType() - Method in class bdv.util.PlaceHolderSource
getType() - Method in class bdv.util.RealRandomAccessibleSource
getType() - Method in class bdv.util.volatiles.VolatileRandomAccessibleIntervalView
getType() - Method in class bdv.util.volatiles.VolatileRandomAccessibleView
getType() - Method in class bdv.util.volatiles.VolatileViewData: Get the pixel type of the original image.
getType() - Method in interface bdv.viewer.Source: Get an instance of the pixel type.
getType() - Method in class bdv.VolatileSpimSource
getUIBoolean(String, boolean) - Static method in class bdv.ui.UIUtils: Get boolean property with the specified key from the swing UIManager.
getUIScaleFactor(Object) - Static method in class bdv.ui.UIUtils: Get an approximate UI scaling factor.
getUnusedSetupId(BigDataViewer) - Static method in class bdv.util.BdvFunctions: Deprecated.
Ok to use for now, but shouldn't be required in the future.
getUnusedSetupId(SetupAssignments) - Static method in class bdv.tools.brightness.SetupAssignments: Deprecated.

Get a setup id that is not used in the specified setupAssignments.
getUnusedSetupId(SetupAssignments) - Static method in class bdv.util.BdvFunctions: Deprecated.
Ok to use for now, but shouldn't be required in the future.
getUpperValue() - Method in class bdv.ui.rangeslider.RangeSlider: Returns the upper value in the range.
getUserStyles() - Method in class bdv.ui.settings.style.AbstractStyleManager
getUserStyles() - Method in interface bdv.ui.settings.style.StyleManager
getValue() - Method in class bdv.ui.rangeslider.RangeSlider: Returns the lower value in the range.
getValueAt(int) - Method in class bdv.ui.sourcetable.SourceTableModel
getValueAt(int, int) - Method in class bdv.ui.sourcetable.SourceTableModel
getViewer() - Method in class bdv.BigDataViewer
getViewerFrame() - Method in class bdv.BigDataViewer
getViewerOptions() - Method in class bdv.util.BdvOptions.Values
getViewerPanel() - Method in class bdv.util.BdvHandle
getViewerPanel() - Method in class bdv.viewer.ViewerFrame
getViewerTransform() - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
getViewerTransform() - Method in interface bdv.viewer.render.RenderResult: Get the viewer transform used to render image.
getViewerTransform() - Method in interface bdv.viewer.ViewerState: Get the viewer transform.
getViewerTransform(AffineTransform3D) - Method in class bdv.util.PlaceHolderOverlayInfo
getViewerTransform(AffineTransform3D) - Method in class bdv.viewer.BasicViewerState
getViewerTransform(AffineTransform3D) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Get the viewer transform.
getViewerTransform(AffineTransform3D) - Method in class bdv.viewer.SynchronizedViewerState
getViewerTransform(AffineTransform3D) - Method in interface bdv.viewer.ViewerState: Get the viewer transform.
getViewSetupId() - Method in class bdv.img.hdf5.ViewLevelId
getVisibilityAndGrouping() - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly Returns the VisibilityAndGrouping that can be used to modify visibility and currentness of sources and groups, as well as grouping of sources, and display mode.
getVisibleAndPresentSources() - Method in class bdv.viewer.BasicViewerState: Get the set of visible sources that also provide image data for the current timepoint.
getVisibleAndPresentSources() - Method in class bdv.viewer.SynchronizedViewerState: Get the set of visible sources that also provide image data for the current timepoint.
getVisibleAndPresentSources() - Method in interface bdv.viewer.ViewerState: Get the set of visible sources that also provide image data for the current timepoint.
getVisibleSourceIndices() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Returns a list of the indices of all currently visible sources.
getVisibleSources() - Method in class bdv.viewer.BasicViewerState: Get the set of visible sources.
getVisibleSources() - Method in class bdv.viewer.SynchronizedViewerState: Get the set of visible sources.
getVisibleSources() - Method in interface bdv.viewer.ViewerState: Get the set of visible sources.
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.AbstractCachedViewerSetupImgLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.img.catmaid.CatmaidImageLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.img.imaris.ImarisImageLoader.SetupImgLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.img.remote.RemoteImageLoader.SetupImgLoader
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getVolatileImage(int, int, ImgLoaderHint...) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getVolatileImage(int, int, ImgLoaderHint...) - Method in interface bdv.ViewerSetupImgLoader
getVolatileImage(ViewId, int) - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
getVolatileImageType() - Method in class bdv.AbstractViewerSetupImgLoader
getVolatileImageType() - Method in class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
getVolatileImageType() - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
getVolatileImageType() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getVolatileImageType() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
getVolatileImageType() - Method in interface bdv.ViewerSetupImgLoader
getVolatileType() - Method in class bdv.util.volatiles.VolatileViewData: Get the pixel type of the wrapped RandomAccessible.
getVolatileTypeForType(T) - Static method in class bdv.util.volatiles.VolatileTypeMatcher
getVolatileViewData() - Method in class bdv.util.volatiles.VolatileRandomAccessibleIntervalView
getVolatileViewData() - Method in class bdv.util.volatiles.VolatileRandomAccessibleView
getVolatileViewData() - Method in interface bdv.util.volatiles.VolatileView
getVoxelDimensions() - Method in class bdv.AbstractSpimSource
getVoxelDimensions() - Method in class bdv.tools.transformation.TransformedSource
getVoxelDimensions() - Method in class bdv.util.AbstractSource
getVoxelDimensions() - Method in class bdv.util.PlaceHolderSource
getVoxelDimensions() - Method in class bdv.util.RealRandomAccessibleSource
getVoxelDimensions() - Method in class bdv.util.VolatileSource
getVoxelDimensions() - Method in interface bdv.viewer.Source: Get voxel size and unit for this source.
getVoxelScreenSize(AffineTransform3D, Source<?>, int, int) - Static method in class bdv.util.MipmapTransforms: Compute the projected voxel size at the given screen transform and mipmap level of a Source.
getVoxelSize(int) - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
getVoxelSize(int) - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
getVoxelSize(int) - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
getWidth() - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer
getWidth() - Method in interface bdv.viewer.render.RenderTarget: Get the current canvas width.
getWidth() - Method in class bdv.viewer.ViewerOptions.Values
getWrappedSource() - Method in class bdv.tools.transformation.TransformedSource
getWrappedState() - Method in class bdv.viewer.SynchronizedViewerState: Returns the wrapped ViewerState.
getX() - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
getY() - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
GO_TO_BOOKMARK - Static variable in class bdv.BigDataViewerActions
GO_TO_BOOKMARK_KEYS - Static variable in class bdv.BigDataViewerActions
GO_TO_BOOKMARK_ROTATION - Static variable in class bdv.BigDataViewerActions
GO_TO_BOOKMARK_ROTATION_KEYS - Static variable in class bdv.BigDataViewerActions
GROUP - bdv.viewer.DisplayMode
GROUP_ACTIVITY_CHANGED - bdv.viewer.ViewerStateChange
GROUP_ACTIVITY_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
GROUP_NAME_CHANGED - bdv.viewer.ViewerStateChange
GROUP_NAME_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
GroupingPanel(ViewerState, BooleanSupplier) - Constructor for class bdv.tools.VisibilityAndGroupingDialog.GroupingPanel: Deprecated.
groupName - Variable in class bdv.viewer.overlay.SourceInfoOverlayRenderer
groupOrder() - Method in class bdv.viewer.BasicViewerState: Returns a Comparator that compares groups according to the order in which they occur in the groups list.
groupOrder() - Method in class bdv.viewer.SynchronizedViewerState: Returns a Comparator that compares groups according to the order in which they occur in the groups list.
groupOrder() - Method in interface bdv.viewer.ViewerState: Returns a Comparator that compares groups according to the order in which they occur in the groups list.

H

hasChannels() - Method in enum bdv.util.AxisOrder
hasFused() - Method in enum bdv.viewer.DisplayMode
hasGrouping() - Method in enum bdv.viewer.DisplayMode
hashCode() - Method in class bdv.img.cache.VolatileGlobalCellCache.Key
hashCode() - Method in class bdv.img.hdf5.ViewLevelId
hashCode() - Method in class bdv.ui.settings.style.StyleProfile
hashCode() - Method in class bdv.util.BoundedRange
hashCode() - Method in class bdv.util.Bounds
hashCode() - Method in class bdv.util.WrappedList
hashCode() - Method in class bdv.viewer.state.SourceGroup: Deprecated.
hasPlaceHolderSources - Variable in class bdv.util.BdvHandle
hasPreferredSize() - Method in class bdv.util.BdvOptions.Values
hasTimepoints() - Method in enum bdv.util.AxisOrder
hasZ() - Method in enum bdv.util.AxisOrder
HDF5AccessHack - Class in bdv.img.imaris
HDF5AccessHack(IHDF5Reader) - Constructor for class bdv.img.imaris.HDF5AccessHack
Hdf5ImageLoader - Class in bdv.img.hdf5
Hdf5ImageLoader(File, IHDF5Reader, ArrayList<Partition>, AbstractSequenceDescription<?, ?, ?>, boolean) - Constructor for class bdv.img.hdf5.Hdf5ImageLoader
Hdf5ImageLoader(File, ArrayList<Partition>, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.img.hdf5.Hdf5ImageLoader
Hdf5ImageLoader(File, ArrayList<Partition>, AbstractSequenceDescription<?, ?, ?>, boolean) - Constructor for class bdv.img.hdf5.Hdf5ImageLoader
Hdf5ImageLoader.SetupImgLoader<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>> - Class in bdv.img.hdf5
height() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
height(int) - Method in class bdv.viewer.ViewerOptions: Set height of ViewerPanel canvas.
helpDialog - Variable in class bdv.BigDataViewer
HelpDialog - Class in bdv.tools
HelpDialog(Frame) - Constructor for class bdv.tools.HelpDialog: Instantiates and displays a JFrame that lists the help file for the SPIM viewer UI.
HelpDialog(Frame, URL) - Constructor for class bdv.tools.HelpDialog
highlight(int) - Method in class bdv.viewer.overlay.MultiBoxOverlay
highlight(int) - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer
highlightedCornerChanged() - Method in interface bdv.tools.boundingbox.TransformedBoxOverlay.HighlightedCornerListener
host - Variable in class bdv.img.openconnectome.OpenConnectomeProject

I

id - Variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
id() - Method in enum bdv.viewer.DisplayMode
IHDF5Access - Interface in bdv.img.imaris
imagesize - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
Imaris - Class in bdv.img.imaris
Imaris() - Constructor for class bdv.img.imaris.Imaris
ImarisImageLoader<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>,A extends net.imglib2.img.basictypeaccess.volatiles.VolatileAccess & net.imglib2.img.basictypeaccess.DataAccess> - Class in bdv.img.imaris
ImarisImageLoader(File, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.img.imaris.ImarisImageLoader
ImarisImageLoader.SetupImgLoader - Class in bdv.img.imaris
ImarisVolatileByteArrayLoader - Class in bdv.img.imaris
ImarisVolatileByteArrayLoader(IHDF5Access) - Constructor for class bdv.img.imaris.ImarisVolatileByteArrayLoader
ImarisVolatileFloatArrayLoader - Class in bdv.img.imaris
ImarisVolatileFloatArrayLoader(IHDF5Access) - Constructor for class bdv.img.imaris.ImarisVolatileFloatArrayLoader
ImarisVolatileShortArrayLoader - Class in bdv.img.imaris
ImarisVolatileShortArrayLoader(IHDF5Access) - Constructor for class bdv.img.imaris.ImarisVolatileShortArrayLoader
importData(TransferHandler.TransferSupport) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree.SourceGroupTreeTransferHandler
incrementalTransform - Variable in class bdv.tools.transformation.TransformedSource: Incremental part of the extra transformation.
indexOf(Object) - Method in class bdv.ui.CardPanel: TODO
indexOf(Object) - Method in class bdv.util.WrappedList
info - Variable in class bdv.util.BdvOverlay
init(int, int) - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
init(int, int) - Method in interface bdv.viewer.render.RenderResult: Allocate storage such that RenderResult.getTargetImage() holds an image of width * height.
init(BookmarksEditor.Mode, String) - Method in class bdv.tools.bookmarks.BookmarksEditor
initBrightness(double, double, AbstractViewerPanel, SetupAssignments) - Static method in class bdv.tools.InitializeViewerState: Deprecated.
initBrightness(double, double, ViewerState, SetupAssignments) - Static method in class bdv.tools.InitializeViewerState: Deprecated.
initBrightness(double, double, ViewerFrame) - Static method in class bdv.tools.InitializeViewerState
initBrightness(double, double, ViewerState, SetupAssignments) - Static method in class bdv.tools.InitializeViewerState: Deprecated.
initBrightness(double, double, ViewerState, ConverterSetups) - Static method in class bdv.tools.InitializeViewerState
initGoToBookmark() - Method in class bdv.BigDataViewer
initGoToBookmark() - Method in class bdv.tools.bookmarks.BookmarksEditor
initGoToBookmarkRotation() - Method in class bdv.BigDataViewer
initGoToBookmarkRotation() - Method in class bdv.tools.bookmarks.BookmarksEditor
INITIAL_EMPTY_SIZE - Static variable in class bdv.img.cache.DefaultEmptyArrayCreator
InitializeViewerState - Class in bdv.tools
InitializeViewerState() - Constructor for class bdv.tools.InitializeViewerState
initialTimepoint(int) - Method in class bdv.tools.boundingbox.BoxSelectionOptions
initialTimepointRange(int, int) - Method in class bdv.tools.boundingbox.BoxSelectionOptions
initSetBookmark() - Method in class bdv.BigDataViewer
initSetBookmark() - Method in class bdv.tools.bookmarks.BookmarksEditor
initSetups(AbstractSpimData<?>, List<ConverterSetup>, List<SourceAndConverter<?>>) - Static method in class bdv.BigDataViewer
initTransform(int, int, boolean, ViewerState) - Static method in class bdv.tools.InitializeViewerState: Deprecated.
initTransform(int, int, boolean, ViewerState) - Static method in class bdv.tools.InitializeViewerState: Get a "good" initial viewer transform.
initTransform(AbstractViewerPanel) - Static method in class bdv.tools.InitializeViewerState: Set a "good" initial viewer transform.
injectCachedAttributes(CachedGsonKeyValueN5Reader) - Static method in class bdv.export.n5.meta.AttributesCaching
inputTriggerConfig(InputTriggerConfig) - Method in class bdv.util.BdvOptions: Set the InputTriggerConfig from which keyboard and mouse action mapping is loaded.
inputTriggerConfig(InputTriggerConfig) - Method in class bdv.viewer.ViewerOptions: Set the InputTriggerConfig from which keyboard and mouse action mapping is loaded.
install() - Method in class bdv.tools.boundingbox.TransformedBoxEditor
install(Actions, BigDataViewer) - Static method in class bdv.BigDataViewerActions: Create BigDataViewer actions and install them in the specified Actions.
install(Actions, AbstractViewerPanel, boolean) - Static method in class bdv.viewer.NavigationActions: Create navigation actions and install them in the specified Actions.
install(Actions, JDialog) - Static method in class bdv.tools.CloseWindowActions: Create a close dialog action and install it in the specified Actions.
install(Actions, JFrame) - Static method in class bdv.tools.CloseWindowActions: Create a close window action and install it in the specified Actions.
install(Behaviours) - Method in interface bdv.TransformEventHandler: Install transformation behaviours into the specified behaviours contrainer.
install(Behaviours) - Method in class bdv.TransformEventHandler2D
install(Behaviours) - Method in class bdv.TransformEventHandler3D
installActionBindings(InputActionBindings, BigDataViewer, KeyStrokeAdder.Factory) - Static method in class bdv.BigDataViewerActions: Deprecated.
installActionBindings(InputActionBindings, ViewerPanel, KeyStrokeAdder.Factory) - Static method in class bdv.viewer.NavigationActions: Deprecated.
installAlignPlaneAction(Actions, AbstractViewerPanel, AbstractViewerPanel.AlignPlane, String...) - Static method in class bdv.viewer.NavigationActions: Deprecated.
installAlignPlaneActions(Actions, AbstractViewerPanel, boolean) - Static method in class bdv.viewer.NavigationActions
installFlatLafInfos() - Static method in class bdv.ui.UIUtils
installModeActions(Actions, ViewerState) - Static method in class bdv.viewer.NavigationActions
installSourceActions(Actions, ViewerState) - Static method in class bdv.viewer.NavigationActions
installTimeActions(Actions, ViewerState) - Static method in class bdv.viewer.NavigationActions
instantiateN5Reader() - Method in class bdv.img.n5.N5ImageLoader: Create a new N5Reader.
InteractiveDisplay - Interface in bdv.viewer
InteractiveDisplayCanvas - Class in bdv.viewer
InteractiveDisplayCanvas(int, int) - Constructor for class bdv.viewer.InteractiveDisplayCanvas: Create a new InteractiveDisplayCanvas.
Interpolation - Enum in bdv.viewer: Interpolation methods.
INTERPOLATION_CHANGED - bdv.viewer.ViewerStateChange
interpolationModeChanged(Interpolation) - Method in interface bdv.viewer.InterpolationModeListener
interpolationModeFromXml(Element) - Method in class bdv.viewer.state.XmlIoViewerState
InterpolationModeListener - Interface in bdv.viewer
interpolationModeListeners() - Method in class bdv.viewer.ViewerPanel: Add/remove InterpolationModeListener to notify when the interpolation mode is changed..
interpolationModeToXml(Interpolation) - Method in class bdv.viewer.state.XmlIoViewerState
interpolators - Variable in class bdv.util.AbstractSource
interval - Variable in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
IntervalAndTransform - Class in bdv.viewer.overlay
IntervalAndTransform() - Constructor for class bdv.viewer.overlay.IntervalAndTransform
IntervalBoundingBox - Class in bdv.util
IntervalBoundingBox() - Constructor for class bdv.util.IntervalBoundingBox
intervalChanged() - Method in interface bdv.tools.boundingbox.AbstractTransformedBoxModel.IntervalChangedListener
intervalChangedListeners() - Method in class bdv.tools.boundingbox.AbstractTransformedBoxModel
IntervalCorners - Class in bdv.tools.boundingbox: Utilities for computing the corners of a RealInterval.
intResolutions - Variable in class bdv.export.ExportMipmapInfo
invokeAndWait(Runnable) - Static method in class bdv.util.InvokeOnEDT
InvokeOnEDT - Class in bdv.util
InvokeOnEDT() - Constructor for class bdv.util.InvokeOnEDT
IS_ACTIVE_COLUMN - Static variable in class bdv.ui.sourcetable.SourceTableModel
IS_CURRENT_COLUMN - Static variable in class bdv.ui.sourcetable.SourceTableModel
is2D() - Method in class bdv.util.BdvOptions: Set up the BigDataViewer for 2D navigation.
is2D() - Method in class bdv.util.BdvOptions.Values
is2D() - Method in class bdv.viewer.ViewerOptions.Values
is2D(boolean) - Method in class bdv.viewer.ViewerOptions: Set up the BigDataViewer for 2D navigation.
isActive - Variable in class bdv.viewer.state.SourceGroup: Deprecated.

Whether the group is active (visible in DisplayMode.FUSED mode).
isActive() - Method in class bdv.viewer.state.SourceGroup: Deprecated.

Is the group active (visible in fused mode)?
isActive() - Method in class bdv.viewer.state.SourceState: Deprecated.

Is the source is active (visible in fused mode)?
isBuiltin() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.Profile
isBuiltin() - Method in class bdv.ui.settings.style.StyleProfile
isCardExpanded(Object) - Method in class bdv.ui.CardPanel: Get expanded state of a card.
isCellEditable(int, int) - Method in class bdv.ui.sourcetable.SourceTableModel
isCollapsed() - Method in class bdv.ui.splitpanel.SplitPanel
isComplete() - Method in class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
isComplete() - Method in class bdv.viewer.animate.AbstractAnimator: Returns true if the animation is completed at the current time.
isComplete() - Method in class bdv.viewer.animate.MessageOverlayAnimator
isComplete() - Method in interface bdv.viewer.animate.OverlayAnimator: Returns true if the animation is complete and the animator can be removed.
isCurrent - Variable in class bdv.viewer.state.SourceGroup: Deprecated.

Whether the group is current (only group visible in DisplayMode.FUSED mode).
isCurrent() - Method in class bdv.util.BdvOverlaySource
isCurrent() - Method in class bdv.util.BdvSource
isCurrent() - Method in class bdv.util.BdvStackSource
isCurrent() - Method in class bdv.util.BdvVirtualChannelSource
isCurrent() - Method in class bdv.viewer.state.SourceGroup: Deprecated.

Is this group the current group?
isCurrent() - Method in class bdv.viewer.state.SourceState: Deprecated.

Is this source the current source?
isCurrentGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Returns true if group is the current group.
isCurrentGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Returns true if group is the current group.
isCurrentGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState: Returns true if group is the current group.
isCurrentSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Returns true if source is the current source.
isCurrentSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Returns true if source is the current source.
isCurrentSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Returns true if source is the current source.
isDark(String) - Static method in class bdv.ui.UIUtils: Tell if the LAF color specified for the provided key is darker than 50% gray.
isDataFlavorSupported(DataFlavor) - Method in class bdv.ui.SourcesTransferable
isEditable() - Method in class bdv.tools.boundingbox.TransformedBoxEditor
isEmpty() - Method in class bdv.util.WrappedList
isFusedEnabled() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
isGroupActive(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
isGroupActive(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Check whether the given group is active.
isGroupActive(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Check whether the given group is active.
isGroupActive(SourceGroup) - Method in interface bdv.viewer.ViewerState: Check whether the given group is active.
isGroupingEnabled() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
isHighlightInProgress() - Method in class bdv.viewer.overlay.MultiBoxOverlay
isHighlightInProgress() - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer
isLeaf(Object) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
isMouseInsidePanel() - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
isPathEditable(TreePath) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
isPlaceHolderSource() - Method in class bdv.util.BdvOverlaySource
isPlaceHolderSource() - Method in class bdv.util.BdvSource
isPlaceHolderSource() - Method in class bdv.util.BdvStackSource
isPlaceHolderSource() - Method in class bdv.util.BdvVirtualChannelSource
isPresent(int) - Method in class bdv.AbstractSpimSource
isPresent(int) - Method in class bdv.tools.transformation.TransformedSource
isPresent(int) - Method in class bdv.util.AbstractSource
isPresent(int) - Method in class bdv.util.PlaceHolderSource
isPresent(int) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource4D
isPresent(int) - Method in class bdv.util.RandomAccessibleIntervalSource4D
isPresent(int) - Method in class bdv.util.RandomAccessibleSource4D
isPresent(int) - Method in class bdv.util.RealRandomAccessibleSource
isPresent(int) - Method in interface bdv.viewer.Source: Is there a stack at timepoint index t?
isSingleSourceMode() - Method in class bdv.viewer.state.ViewerState: Deprecated.
replaced by ViewerState.getDisplayMode()
isSourceActive(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
isSourceActive(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Check whether the given source is active.
isSourceActive(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Check whether the given source is active.
isSourceActive(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Check whether the given source is active.
isSourceVisible(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.
isSourceVisible(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
isSourceVisible(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Check whether the given source is visible.
isSourceVisible(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Check whether the given source is visible.
isSourceVisible(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Check whether the given source is visible.
isSourceVisibleAndPresent(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Check whether the given source is both visible and provides image data for the current timepoint.
isSourceVisibleAndPresent(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Check whether the given source is both visible and provides image data for the current timepoint.
isSourceVisibleAndPresent(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Check whether the given source is both visible and provides image data for the current timepoint.
isUseVolatileIfAvailable() - Method in class bdv.viewer.ViewerOptions.Values
isValid() - Method in class bdv.tools.boundingbox.TransformedBoxSelectionDialog.Result: Returns true iff dialog was closed by clicking "OK".
isValid() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result: Returns true iff dialog was closed by clicking "OK".
isValid() - Method in class bdv.viewer.render.AccumulateProjector
isValid() - Method in class bdv.viewer.render.EmptyProjector
isValid() - Method in class bdv.viewer.render.SimpleVolatileProjector
isValid() - Method in interface bdv.viewer.render.VolatileProjector
isVisible - Variable in class bdv.viewer.overlay.IntervalAndTransform
isVisible() - Method in class bdv.util.PlaceHolderOverlayInfo
isVisible() - Method in class bdv.viewer.overlay.IntervalAndTransform
isVisible() - Method in interface bdv.viewer.overlay.MultiBoxOverlay.IntervalAndTransform
iterator() - Method in class bdv.util.WrappedList

J

join(BoundedRange) - Method in class bdv.util.BoundedRange
join(Bounds) - Method in class bdv.util.Bounds

K

Key(int, int, int, long) - Constructor for class bdv.img.cache.VolatileGlobalCellCache.Key: Create a Key for the specified cell.
KEY_BACKWARD_Z - Static variable in class bdv.TransformEventHandler3D
KEY_BACKWARD_Z_FAST - Static variable in class bdv.TransformEventHandler3D
KEY_BACKWARD_Z_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_BACKWARD_Z_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_BACKWARD_Z_SLOW - Static variable in class bdv.TransformEventHandler3D
KEY_BACKWARD_Z_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_FORWARD_Z - Static variable in class bdv.TransformEventHandler3D
KEY_FORWARD_Z_FAST - Static variable in class bdv.TransformEventHandler3D
KEY_FORWARD_Z_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_FORWARD_Z_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_FORWARD_Z_SLOW - Static variable in class bdv.TransformEventHandler3D
KEY_FORWARD_Z_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_IN - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_IN - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_IN_FAST - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_IN_FAST - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_IN_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_IN_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_IN_KEYS - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_IN_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_IN_SLOW - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_IN_SLOW - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_IN_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_IN_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_OUT - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_OUT - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_OUT_FAST - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_OUT_FAST - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_OUT_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_OUT_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_OUT_KEYS - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_OUT_KEYS - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_OUT_SLOW - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_OUT_SLOW - Static variable in class bdv.TransformEventHandler3D
KEY_ZOOM_OUT_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
KEY_ZOOM_OUT_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
KeyConfigContexts - Interface in bdv: Constants that specify to what context an action or a behaviour applies.
KeyConfigScopes - Interface in bdv: The CommandDescription scope used for actions and behaviours defined in BigDataViewer
Keymap - Class in bdv.ui.keymap
Keymap() - Constructor for class bdv.ui.keymap.Keymap
Keymap(String, InputTriggerConfig) - Constructor for class bdv.ui.keymap.Keymap
Keymap.UpdateListener - Interface in bdv.ui.keymap
keymapChanged() - Method in interface bdv.ui.keymap.Keymap.UpdateListener
keymapManager(KeymapManager) - Method in class bdv.util.BdvOptions: Set the KeymapManager to share keymap settings with other BigDataViewer windows.
keymapManager(KeymapManager) - Method in class bdv.viewer.ViewerOptions: Set the KeymapManager to share keymap settings with other BigDataViewer windows.
KeymapManager - Class in bdv.ui.keymap: Manages a collection of Keymap.
KeymapManager() - Constructor for class bdv.ui.keymap.KeymapManager
KeymapManager(String) - Constructor for class bdv.ui.keymap.KeymapManager
KeymapSettingsPage - Class in bdv.ui.keymap
KeymapSettingsPage(String, KeymapManager, CommandDescriptions) - Constructor for class bdv.ui.keymap.KeymapSettingsPage: Creates a new settings page for Keymaps.
KeymapSettingsPage(String, M, M, CommandDescriptions) - Constructor for class bdv.ui.keymap.KeymapSettingsPage: Creates a new settings page for Keymaps.
kill() - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer: DON'T USE THIS.
kill() - Method in class bdv.viewer.render.MultiResolutionRenderer: DON'T USE THIS.
kill() - Method in class bdv.viewer.state.ViewerState: Deprecated.

DON'T USE THIS.

L

LabeledOptionButton - Class in bdv.ui.viewermodepanel
LabeledOptionButton(Icon[], String[], String[]) - Constructor for class bdv.ui.viewermodepanel.LabeledOptionButton
lastIndexOf(Object) - Method in class bdv.util.WrappedList
legacyImgLoader - Variable in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper
legacyImgLoader - Variable in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper
LegacyViewerImgLoader<T,V extends net.imglib2.Volatile<T>> - Interface in bdv.spimdata.legacy
LegacyViewerImgLoaderExtWrapper<T,V extends net.imglib2.Volatile<T>,I extends LegacyViewerImgLoader<T,V> & mpicbg.spim.data.legacy.LegacyImgLoader<T>> - Class in bdv.spimdata.legacy
LegacyViewerImgLoaderExtWrapper(I) - Constructor for class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper
LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper - Class in bdv.spimdata.legacy
LegacyViewerImgLoaderWrapper<T,V extends net.imglib2.Volatile<T>,I extends LegacyViewerImgLoader<T,V>> - Class in bdv.spimdata.legacy
LegacyViewerImgLoaderWrapper(I) - Constructor for class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper
LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper - Class in bdv.spimdata.legacy
length - Static variable in enum bdv.viewer.DisplayMode
level - Variable in class bdv.img.hdf5.ViewLevelId
Level(int, int, int) - Constructor for class bdv.viewer.render.MipmapOrdering.Level
Level(int, int, int, CacheHints, CacheHints) - Constructor for class bdv.viewer.render.MipmapOrdering.Level
listeners() - Method in class bdv.viewer.ConverterSetups: All setupParametersChanged() events from ConverterSetup currently in the ViewerState are forwarded to these listeners.
listIterator() - Method in class bdv.util.WrappedList
listIterator(int) - Method in class bdv.util.WrappedList
load(String) - Static method in class bdv.ui.appearance.AppearanceIO
load(String, int) - Method in class bdv.spimdata.XmlIoSpimDataMinimal
load(String, SharedQueue) - Method in class bdv.spimdata.XmlIoSpimDataMinimal
LOAD_SETTINGS - Static variable in class bdv.BigDataViewerActions
LOAD_SETTINGS_KEYS - Static variable in class bdv.BigDataViewerActions
loadArray(int, int, int, int[], long[]) - Method in interface bdv.img.cache.CacheArrayLoader: Load cell data into memory.
loadArray(int, int, int, int[], long[]) - Method in class bdv.img.catmaid.CatmaidVolatileIntArrayLoader
loadArray(int, int, int, int[], long[]) - Method in class bdv.img.imaris.ImarisVolatileByteArrayLoader
loadArray(int, int, int, int[], long[]) - Method in class bdv.img.imaris.ImarisVolatileFloatArrayLoader
loadArray(int, int, int, int[], long[]) - Method in class bdv.img.imaris.ImarisVolatileShortArrayLoader
loadArray(int, int, int, int[], long[]) - Method in class bdv.img.openconnectome.OpenConnectomeVolatileArrayLoader
loadArray(int, int, int, int[], long[]) - Method in class bdv.img.remote.RemoteVolatileShortArrayLoader
loadArray(long[], int[]) - Method in interface bdv.img.cache.SimpleCacheArrayLoader: Load cell data into memory.
loadBuiltinStyles() - Method in class bdv.ui.keymap.KeymapManager
loadBuiltinStyles() - Method in class bdv.ui.settings.style.AbstractStyleManager
loader - Variable in class bdv.AbstractCachedViewerSetupImgLoader
loadProfile(T) - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileEditPanel
loadSettings() - Method in class bdv.BigDataViewer
loadSettings(String) - Method in class bdv.BigDataViewer
loadStyles() - Method in class bdv.ui.keymap.KeymapManager
loadStyles(File) - Method in class bdv.ui.keymap.AbstractKeymapManager
lookAndFeel() - Method in class bdv.ui.appearance.Appearance
lookAndFeelInfoForName(String) - Static method in class bdv.ui.appearance.Appearance

M

main(String[]) - Static method in class bdv.BigDataViewer
MANUAL_TRANSFORM - Static variable in class bdv.BigDataViewerActions
MANUAL_TRANSFORM_KEYS - Static variable in class bdv.BigDataViewerActions
ManualSourceTransforms - Class in bdv.tools.transformation
ManualSourceTransforms(List<AffineTransform3D>) - Constructor for class bdv.tools.transformation.ManualSourceTransforms
manualTransform(ManualTransformationEditor) - Method in class bdv.BigDataViewerActions: Deprecated.
manualTransform(Actions, ManualTransformationEditor) - Static method in class bdv.BigDataViewerActions
manualTransformActiveChanged(boolean) - Method in interface bdv.tools.transformation.ManualTransformActiveListener
ManualTransformActiveListener - Interface in bdv.tools.transformation
manualTransformActiveListeners() - Method in class bdv.tools.transformation.ManualTransformationEditor
manualTransformation - Variable in class bdv.BigDataViewer
ManualTransformation - Class in bdv.tools.transformation
ManualTransformation(AbstractViewerPanel) - Constructor for class bdv.tools.transformation.ManualTransformation
ManualTransformation(List<SourceAndConverter<?>>) - Constructor for class bdv.tools.transformation.ManualTransformation
manualTransformationEditor - Variable in class bdv.BigDataViewer
ManualTransformationEditor - Class in bdv.tools.transformation
ManualTransformationEditor(AbstractViewerPanel, InputActionBindings) - Constructor for class bdv.tools.transformation.ManualTransformationEditor
ManualTransformationEditor(Listeners<TransformListener<AffineTransform3D>>, ViewerState, Runnable, Consumer<String>, InputActionBindings) - Constructor for class bdv.tools.transformation.ManualTransformationEditor
map() - Method in interface bdv.viewer.render.VolatileProjector
map(boolean) - Method in class bdv.viewer.render.AccumulateProjector
map(boolean) - Method in class bdv.viewer.render.EmptyProjector
map(boolean) - Method in class bdv.viewer.render.SimpleVolatileProjector: Render the 2D target image by copying values from the source.
map(boolean) - Method in interface bdv.viewer.render.VolatileProjector: Render the target image.
MaskUtils - Class in bdv.viewer
MaskUtils() - Constructor for class bdv.viewer.MaskUtils
maxNumLevels - Variable in class bdv.img.remote.RemoteImageLoaderMetaData: The maximum number of mipmap levels occuring in all setups.
maxNumSetups - Variable in class bdv.img.remote.RemoteImageLoaderMetaData: The highest occurring setup id + 1.
maxNumTimepoints - Variable in class bdv.img.remote.RemoteImageLoaderMetaData: The highest occurring timepoint id + 1.
maxT - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource4D
memTypeId(DataType) - Static method in class bdv.img.hdf5.Util
merge(File, SpimDataMinimal...) - Static method in class bdv.spimdata.tools.MergeTools: Merge multiple non-overlapping SpimDataMinimal datasets.
merge(File, ArrayList<SpimDataMinimal>) - Static method in class bdv.spimdata.tools.MergeTools: Merge multiple non-overlapping SpimDataMinimal datasets.
MergeExample - Class in bdv.spimdata.tools
MergeExample() - Constructor for class bdv.spimdata.tools.MergeExample
mergeHdf5ViewsSetups(List<String>, List<ViewTransform>, String) - Static method in class bdv.spimdata.tools.MergeExample: Merge multiple HDF5 datasets, where each dataset contains the same timepoints but different views.
mergeHdf5ViewsTimepoints(List<String>, String) - Static method in class bdv.spimdata.tools.MergeExample: Append multiple HDF5 datasets, where each dataset contains the same setups but different timepoints.
MergePartitionList - Class in bdv.spimdata.tools
MergePartitionList() - Constructor for class bdv.spimdata.tools.MergePartitionList
MergeTools - Class in bdv.spimdata.tools
MergeTools() - Constructor for class bdv.spimdata.tools.MergeTools
MessageOverlayAnimator - Class in bdv.viewer.animate: Draw lines of text in the lower right corner of the display.
MessageOverlayAnimator(long) - Constructor for class bdv.viewer.animate.MessageOverlayAnimator
MessageOverlayAnimator(long, double, double) - Constructor for class bdv.viewer.animate.MessageOverlayAnimator
MessageOverlayAnimator(long, double, double, Font) - Constructor for class bdv.viewer.animate.MessageOverlayAnimator
MessageOverlayAnimator.TextAnimator - Class in bdv.viewer.animate
metadata - Variable in class bdv.img.remote.RemoteImageLoader
min - Variable in class bdv.export.SubTaskProgressWriter
minIntervalSize - Variable in class bdv.util.BoundedInterval: minimum interval size.
minIntervalSize - Variable in class bdv.util.BoundedIntervalDouble: minimum interval size.
MinMaxGroup - Class in bdv.tools.brightness: A double interval.
MinMaxGroup(double, double, double, double, double, double, double) - Constructor for class bdv.tools.brightness.MinMaxGroup
MinMaxGroup.UpdateListener - Interface in bdv.tools.brightness
MinMaxPanel(MinMaxGroup, SetupAssignments, BrightnessDialog.MinMaxPanels, boolean) - Constructor for class bdv.tools.brightness.BrightnessDialog.MinMaxPanel: Deprecated.
MinMaxPanels(SetupAssignments, JDialog, boolean) - Constructor for class bdv.tools.brightness.BrightnessDialog.MinMaxPanels: Deprecated.
minT - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource4D
MipmapHints(List<MipmapOrdering.Level>, boolean) - Constructor for class bdv.viewer.render.MipmapOrdering.MipmapHints
MipmapInfo - Class in bdv.img: Description of available mipmap levels for a BasicViewSetup.
MipmapInfo(double[][], AffineTransform3D[], int[][]) - Constructor for class bdv.img.MipmapInfo
MipmapOrdering - Interface in bdv.viewer.render
MipmapOrdering.Level - Class in bdv.viewer.render
MipmapOrdering.MipmapHints - Class in bdv.viewer.render
MipmapOrdering.PrefetchOrderComparator - Class in bdv.viewer.render
MipmapOrdering.RenderOrderComparator - Class in bdv.viewer.render
mipmapSources - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource
mipmapSources - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource4D
mipmapTransforms - Variable in class bdv.AbstractCachedViewerSetupImgLoader
mipmapTransforms - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource
mipmapTransforms - Variable in class bdv.util.RandomAccessibleIntervalMipmapSource4D
MipmapTransforms - Class in bdv.util
MipmapTransforms() - Constructor for class bdv.util.MipmapTransforms
mix(Color, Color, double) - Static method in class bdv.ui.UIUtils: Mix colors c1 and c2 by ratios c1Weight and (1-c1Weight), respectively.
model - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
model - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
ModePanel(ViewerState, BooleanSupplier) - Constructor for class bdv.tools.VisibilityAndGroupingDialog.ModePanel: Deprecated.
modes(ViewerPanel) - Method in class bdv.viewer.NavigationActions: Deprecated.
ModifiableInterval - Class in bdv.util
ModifiableInterval(int) - Constructor for class bdv.util.ModifiableInterval
ModifiableInterval(Interval) - Constructor for class bdv.util.ModifiableInterval
ModifiableRealInterval - Class in bdv.util
ModifiableRealInterval(int) - Constructor for class bdv.util.ModifiableRealInterval
ModifiableRealInterval(RealInterval) - Constructor for class bdv.util.ModifiableRealInterval
ModificationListener - Interface in bdv.ui.settings: A ModificationListener to a SettingsPage is notified, when any setting is changed.
modificationListeners() - Method in class bdv.ui.appearance.AppearanceSettingsPage
modificationListeners() - Method in class bdv.ui.settings.SelectAndEditProfileSettingsPage
modificationListeners() - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileEditPanel
modificationListeners() - Method in interface bdv.ui.settings.SettingsPage
modificationListeners() - Method in class bdv.ui.settings.SimpleSettingsPage
mouseClicked(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
MouseCoordinateListener() - Constructor for class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
mouseCoordinates - Variable in class bdv.viewer.AbstractViewerPanel: Keeps track of the current mouse coordinates, which are used to provide the current global position (see AbstractViewerPanel.getGlobalMouseCoordinates(RealPositionable)).
mouseDragged(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
mouseEntered(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
mouseExited(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
mouseMoved(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
mousePressed(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
mouseReleased(MouseEvent) - Method in class bdv.viewer.AbstractViewerPanel.MouseCoordinateListener
moveSetupToGroup(ConverterSetup, MinMaxGroup) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.

Add the specified setup to the specified group.
movieDialog - Variable in class bdv.BigDataViewer
movieMaxProjectDialog - Variable in class bdv.BigDataViewer
msgOverlay(MessageOverlayAnimator) - Method in class bdv.viewer.ViewerOptions
MultiBoxOverlay - Class in bdv.viewer.overlay: Paint an overlay showing multiple transformed boxes (interval + transform).
MultiBoxOverlay() - Constructor for class bdv.viewer.overlay.MultiBoxOverlay
MultiBoxOverlay.IntervalAndTransform - Interface in bdv.viewer.overlay
MultiBoxOverlayRenderer - Class in bdv.viewer.overlay: Render multibox overlay corresponding to a ViewerState into a Graphics2D.
MultiBoxOverlayRenderer() - Constructor for class bdv.viewer.overlay.MultiBoxOverlayRenderer
MultiBoxOverlayRenderer(int, int) - Constructor for class bdv.viewer.overlay.MultiBoxOverlayRenderer
MultiResolutionRenderer - Class in bdv.viewer.render: A renderer that uses a coarse-to-fine rendering scheme.
MultiResolutionRenderer(RenderTarget<?>, RequestRepaint, double[], long, int, ExecutorService, boolean, CacheControl) - Constructor for class bdv.viewer.render.MultiResolutionRenderer

N

n5DataType(T) - Static method in class bdv.img.n5.DataTypeProperties
N5ImageLoader - Class in bdv.img.n5
N5ImageLoader(File, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.img.n5.N5ImageLoader
N5ImageLoader(URI, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.img.n5.N5ImageLoader
N5ImageLoader(N5Reader, URI, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.img.n5.N5ImageLoader
N5ImageLoader.SetupImgLoader<T extends net.imglib2.type.NativeType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.NativeType<V>> - Class in bdv.img.n5
N5Properties - Interface in bdv.img.n5: Provides metadata and resolves dataset path names for (`setupId`, `timePointId` and multiresolution `level`) triples.
name - Variable in class bdv.tools.transformation.TransformedSource: optional new name. if null, the name of the original source will be used.
name - Variable in class bdv.util.AbstractSource
name - Variable in class bdv.util.RealRandomAccessibleSource
name - Variable in class bdv.viewer.state.SourceGroup: Deprecated.
NAME_COLUMN - Static variable in class bdv.ui.sourcetable.SourceTableModel
nameExists(String) - Method in class bdv.ui.settings.style.AbstractStyleManager
NavigationActions - Class in bdv.viewer
NavigationActions(KeyStrokeAdder.Factory) - Constructor for class bdv.viewer.NavigationActions: Deprecated.
NavigationActions.Descriptions - Class in bdv.viewer
NEARESTNEIGHBOR - bdv.viewer.Interpolation
neariso_imagesize - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
neariso_offset - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
neariso_voxelres - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
newThread(Runnable) - Method in class bdv.viewer.ViewerPanel.RenderThreadFactory
next() - Method in enum bdv.viewer.Interpolation
NEXT_TIMEPOINT - Static variable in class bdv.viewer.NavigationActions
NEXT_TIMEPOINT_KEYS - Static variable in class bdv.viewer.NavigationActions
nextTimePoint() - Method in class bdv.viewer.ViewerPanel: Show the next time-point.
nextTimePoint(ViewerState) - Static method in class bdv.viewer.NavigationActions
NLINEAR - bdv.viewer.Interpolation
NONE - bdv.tools.boundingbox.BoxSelectionOptions.TimepointSelection
NONE - bdv.tools.boundingbox.TransformedBoxEditor.BoxSourceType
normalizeVoxelSize(double[]) - Static method in class bdv.export.ProposeMipmaps: Adjust voxelSize such that the smallest dimension is 1.0
notifyIntervalChanged() - Method in class bdv.tools.boundingbox.AbstractTransformedBoxModel
notifyModified() - Method in class bdv.ui.settings.SimpleSettingsPage
NUM_GROUPS_CHANGED - bdv.viewer.ViewerStateChange
NUM_GROUPS_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
NUM_SOURCES_CHANGED - bdv.viewer.ViewerStateChange
NUM_SOURCES_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
NUM_TIMEPOINTS_CHANGED - bdv.viewer.ViewerStateChange
numChannels(Dimensions) - Method in enum bdv.util.AxisOrder
numCorners(RealInterval) - Static method in class bdv.tools.boundingbox.IntervalCorners
numDimensions() - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible
numDimensions() - Method in enum bdv.util.AxisOrder
numDimensions() - Method in class bdv.util.ConstantRandomAccessible
numDimensions() - Method in class bdv.util.volatiles.VolatileRandomAccessibleView
numGroups() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
numMipmapLevels() - Method in class bdv.AbstractCachedViewerSetupImgLoader
numMipmapLevels() - Method in class bdv.img.catmaid.CatmaidImageLoader
numMipmapLevels() - Method in class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
numMipmapLevels() - Method in class bdv.img.imaris.ImarisImageLoader.SetupImgLoader
numMipmapLevels() - Method in class bdv.img.n5.N5ImageLoader.SetupImgLoader
numMipmapLevels() - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader
numMipmapLevels() - Method in class bdv.img.remote.RemoteImageLoader.SetupImgLoader
numMipmapLevels() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
numMipmapLevels() - Method in class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
numMipmapLevels(int) - Method in interface bdv.spimdata.legacy.LegacyViewerImgLoader
numRenderingThreads(int) - Method in class bdv.util.BdvOptions: Set how many threads to use for rendering.
numRenderingThreads(int) - Method in class bdv.viewer.ViewerOptions: Set how many threads to use for rendering.
numSourceGroups() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Returns the number of source groups.
numSourceGroups(int) - Method in class bdv.util.BdvOptions: Set how many source groups there are initially.
numSourceGroups(int) - Method in class bdv.viewer.ViewerOptions: Set how many source groups there are initially.
numSources() - Method in class bdv.viewer.state.ViewerState: Deprecated.

Returns the number of sources.
numSources() - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
numTimepoints() - Method in interface bdv.util.ChannelSources: Get the number timepoints.
numTimepoints(Dimensions) - Method in enum bdv.util.AxisOrder

O

of(AccumulateProjectorFactory<ARGBType>) - Static method in enum bdv.viewer.BlendMode
of(DataType) - Static method in class bdv.img.n5.DataTypeProperties
offset - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
OkCancelPanel() - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog.OkCancelPanel
onApply(Runnable) - Method in class bdv.ui.settings.SimpleSettingsPage
onCancel(Runnable) - Method in class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog.OkCancelPanel
onCancel(Runnable) - Method in class bdv.ui.settings.SettingsPanel
onCancel(Runnable) - Method in class bdv.ui.settings.SimpleSettingsPage
onCancel(Runnable) - Method in class bdv.ui.settings.SingleSettingsPanel
onMouseMoved() - Method in class bdv.viewer.AbstractViewerPanel
onMouseMoved() - Method in class bdv.viewer.ViewerPanel
onOk(Runnable) - Method in class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog.OkCancelPanel
onOk(Runnable) - Method in class bdv.ui.settings.SettingsPanel
onOk(Runnable) - Method in class bdv.ui.settings.SingleSettingsPanel
open(String, String, ProgressWriter, ViewerOptions) - Static method in class bdv.BigDataViewer
open(ArrayList<ConverterSetup>, ArrayList<SourceAndConverter<?>>, int, CacheControl, String, ProgressWriter, ViewerOptions) - Static method in class bdv.BigDataViewer
open(AbstractSpimData<?>, String, ProgressWriter, ViewerOptions) - Static method in class bdv.BigDataViewer
OpenConnectomeDataset - Class in bdv.img.openconnectome: An openconnecto.me dataset as specified by example at http://openconnecto.me/ocp/ca/bock11/info/
OpenConnectomeDataset() - Constructor for class bdv.img.openconnectome.OpenConnectomeDataset
OpenConnectomeImageLoader - Class in bdv.img.openconnectome
OpenConnectomeImageLoader(String, String, String) - Constructor for class bdv.img.openconnectome.OpenConnectomeImageLoader
OpenConnectomeProject - Class in bdv.img.openconnectome: oenconnecto.me project as specified by example at
OpenConnectomeProject() - Constructor for class bdv.img.openconnectome.OpenConnectomeProject
OpenConnectomeTokenInfo - Class in bdv.img.openconnectome
OpenConnectomeTokenInfo() - Constructor for class bdv.img.openconnectome.OpenConnectomeTokenInfo
OpenConnectomeVolatileArrayLoader - Class in bdv.img.openconnectome
OpenConnectomeVolatileArrayLoader(String, String, String, long) - Constructor for class bdv.img.openconnectome.OpenConnectomeVolatileArrayLoader: Create a CacheArrayLoader for a source provided by the Open Connectome Volume Cutout Service.
openIms(String) - Static method in class bdv.img.imaris.Imaris
options - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
options - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
options() - Static method in class bdv.tools.boundingbox.BoxSelectionOptions: Create default BoxSelectionOptions.
options() - Static method in interface bdv.util.Bdv
options() - Static method in class bdv.util.BdvOptions: Create default BdvOptions.
options() - Static method in class bdv.viewer.ViewerOptions: Create default ViewerOptions.
optionsFromValues() - Method in class bdv.util.BdvOptions.Values
optionsFromValues() - Method in class bdv.viewer.ViewerOptions.Values
org.bigdataviewer.core - module org.bigdataviewer.core
origNumTimepoints - Variable in class bdv.util.BdvHandle
out() - Method in interface bdv.export.ProgressWriter
out() - Method in class bdv.export.ProgressWriterConsole
out() - Method in class bdv.export.ProgressWriterNull
out() - Method in class bdv.export.SubTaskProgressWriter
overlay - Variable in class bdv.util.BdvOverlaySource
OverlayAnimator - Interface in bdv.viewer.animate
OverlayRenderer - Interface in bdv.viewer: Draw something to a Graphics canvas and receive notifications about changes of the canvas size.
overlays() - Method in interface bdv.viewer.InteractiveDisplay: OverlayRenderers can be added/removed here.
overlays() - Method in class bdv.viewer.InteractiveDisplayCanvas: OverlayRenderers can be added/removed here.
ox() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
oy() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData

P

pack() - Method in class bdv.tools.DelayedPackDialog
paint() - Method in interface bdv.viewer.render.PainterThread.Paintable: This is called by the painter thread to repaint the display.
paint() - Method in class bdv.viewer.ViewerPanel
paint(ViewerState) - Method in class bdv.viewer.render.MultiResolutionRenderer: Render image at the requested screen scale.
paint(Graphics2D) - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer
paint(Graphics2D) - Method in class bdv.viewer.overlay.ScaleBarOverlayRenderer
paint(Graphics2D) - Method in class bdv.viewer.overlay.SourceInfoOverlayRenderer
paint(Graphics2D, long) - Method in class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
paint(Graphics2D, long) - Method in class bdv.viewer.animate.MessageOverlayAnimator
paint(Graphics2D, long) - Method in interface bdv.viewer.animate.OverlayAnimator
paint(Graphics2D, long) - Method in class bdv.viewer.animate.TextOverlayAnimator
paint(Graphics2D, List, Interval, Interval) - Method in class bdv.viewer.overlay.MultiBoxOverlay: This paints the box overlay with perspective and scale set such that it fits approximately into the specified screen area.
paintComponent(Graphics) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
paintComponent(Graphics) - Method in class bdv.ui.sourcetable.SourceTable
paintComponent(Graphics) - Method in class bdv.viewer.InteractiveDisplayCanvas
PainterThread - Class in bdv.viewer.render: Thread to repaint display.
PainterThread(PainterThread.Paintable) - Constructor for class bdv.viewer.render.PainterThread
PainterThread(ThreadGroup, PainterThread.Paintable) - Constructor for class bdv.viewer.render.PainterThread
PainterThread(ThreadGroup, String, PainterThread.Paintable) - Constructor for class bdv.viewer.render.PainterThread
PainterThread.Paintable - Interface in bdv.viewer.render
paintIcon(Component, Graphics, int, int) - Method in class bdv.tools.brightness.ColorIcon
panelNumber - Static variable in class bdv.viewer.ViewerPanel
Partition - Class in bdv.img.hdf5: Partition describes one partition file of a dataset that is split across multiple hdf5 files.
Partition(String, int[], int[], int[], int[]) - Constructor for class bdv.img.hdf5.Partition: Create a new Partition description.
Partition(String, Map<Integer, Integer>, Map<Integer, Integer>) - Constructor for class bdv.img.hdf5.Partition: Create a new Partition description.
patch(RenderResult, Interval, double, double) - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
patch(RenderResult, Interval, double, double) - Method in interface bdv.viewer.render.RenderResult: Fill in interval with data from patch, scaled by the relative scale between this RenderResult and patch, and shifted such that (0,0) of the patch is placed at (ox,oy) of this RenderResult
path - Variable in class bdv.img.hdf5.Partition
perSetupMipmapInfo - Variable in class bdv.img.remote.RemoteImageLoaderMetaData: Description of available mipmap levels for each BasicViewSetup.
perspectiveX(double[]) - Method in class bdv.viewer.overlay.RenderBoxHelper
perspectiveY(double[]) - Method in class bdv.viewer.overlay.RenderBoxHelper
PLACEHOLDER - bdv.tools.boundingbox.TransformedBoxEditor.BoxSourceType
PlaceHolderConverterSetup - Class in bdv.util
PlaceHolderConverterSetup(int, double, double, int) - Constructor for class bdv.util.PlaceHolderConverterSetup
PlaceHolderConverterSetup(int, double, double, ARGBType) - Constructor for class bdv.util.PlaceHolderConverterSetup
PlaceHolderOverlayInfo - Class in bdv.util
PlaceHolderOverlayInfo(ViewerPanel, SourceAndConverter<?>, ConverterSetup) - Constructor for class bdv.util.PlaceHolderOverlayInfo
PlaceHolderOverlayInfo.VisibilityChangeListener - Interface in bdv.util
PlaceHolderSource - Class in bdv.util: A dummy Source that represents a BdvOverlay.
PlaceHolderSource(String) - Constructor for class bdv.util.PlaceHolderSource
PointsOverlay - Class in bdv.util
PointsOverlay() - Constructor for class bdv.util.PointsOverlay
position - Variable in class bdv.viewer.animate.TextOverlayAnimator
PREFER_URI_FOR_LOCAL_FILES - Static variable in class bdv.img.n5.XmlIoN5ImageLoader
PREFERENCES_DIALOG - Static variable in class bdv.BigDataViewerActions
PREFERENCES_DIALOG_KEYS - Static variable in class bdv.BigDataViewerActions
preferencesDialog - Variable in class bdv.BigDataViewer
PreferencesDialog - Class in bdv.tools
PreferencesDialog(Frame, Keymap, String[]) - Constructor for class bdv.tools.PreferencesDialog
preferredSize(int, int) - Method in class bdv.util.BdvOptions: Set preferred size of ViewerPanel canvas.
prefetch(int) - Method in class bdv.img.n5.N5ImageLoader: Touch all metadata in advance in parallel so the N5-API caches them.
Prefetcher - Class in bdv.viewer.render
prefetchOrderComparator - Static variable in interface bdv.viewer.render.MipmapOrdering
PrefetchOrderComparator() - Constructor for class bdv.viewer.render.MipmapOrdering.PrefetchOrderComparator
Prefs - Class in bdv.util
Prefs.OverlayPosition - Enum in bdv.util
prepareCachedImage(int, int, int, LoadingStrategy, T) - Method in class bdv.img.catmaid.CatmaidImageLoader: Create a VolatileCachedCellImg backed by the cache.
prepareCachedImage(int, int, int, LoadingStrategy, T) - Method in class bdv.img.openconnectome.OpenConnectomeImageLoader: Create a VolatileCachedCellImg backed by the cache.
prepareCachedImage(int, int, LoadingStrategy, S) - Method in class bdv.AbstractCachedViewerSetupImgLoader
prepareCachedImage(ViewLevelId, LoadingStrategy, T) - Method in class bdv.img.imaris.ImarisImageLoader: (Almost) create a CellImg backed by the cache.
prepareCachedImage(ViewLevelId, LoadingStrategy, T) - Method in class bdv.img.remote.RemoteImageLoader: Create a VolatileCachedCellImg backed by the cache.
prepareCachedImage(String, int, int, int, CacheHints, T) - Method in class bdv.img.n5.N5ImageLoader: Create a CellImg backed by the cache.
prepareNextFrame() - Method in class bdv.cache.CacheControl.CacheControls
prepareNextFrame() - Method in class bdv.cache.CacheControl.Dummy
prepareNextFrame() - Method in interface bdv.cache.CacheControl: Prepare the cache for providing data for the "next frame".
prepareNextFrame() - Method in class bdv.cache.SharedQueue
prepareNextFrame() - Method in class bdv.img.cache.VolatileGlobalCellCache: Prepare the cache for providing data for the "next frame", by moving pending cell request to the prefetch queue (BlockingFetchQueues.clearToPrefetch()).
PREVIOUS_TIMEPOINT - Static variable in class bdv.viewer.NavigationActions
PREVIOUS_TIMEPOINT_KEYS - Static variable in class bdv.viewer.NavigationActions
previousTimePoint() - Method in class bdv.viewer.ViewerPanel: Show the previous time-point.
previousTimePoint(ViewerState) - Static method in class bdv.viewer.NavigationActions
printDefaultProperties() - Static method in class bdv.util.Prefs
printMipmapInfo() - Method in class bdv.img.hdf5.Hdf5ImageLoader
processMouseEvent(MouseEvent) - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
processMouseEvent(MouseEvent) - Method in class bdv.ui.sourcetable.SourceTable
processMouseMotionEvent(MouseEvent) - Method in class bdv.ui.sourcetable.SourceTable
progressWriter - Variable in class bdv.export.SubTaskProgressWriter
ProgressWriter - Interface in bdv.export
ProgressWriterConsole - Class in bdv.export
ProgressWriterConsole() - Constructor for class bdv.export.ProgressWriterConsole
ProgressWriterNull - Class in bdv.export
ProgressWriterNull() - Constructor for class bdv.export.ProgressWriterNull
project - Variable in class bdv.img.openconnectome.OpenConnectomeTokenInfo
project(double[]) - Method in class bdv.tools.boundingbox.RenderBoxHelper: Project a point.
project(double[], double[]) - Method in class bdv.tools.boundingbox.RenderBoxHelper: Project a point.
ProjectorUtils - Class in bdv.viewer.render
ProjectorUtils() - Constructor for class bdv.viewer.render.ProjectorUtils
ProjectorUtils.ArrayData - Class in bdv.viewer.render
projecttype - Variable in class bdv.img.openconnectome.OpenConnectomeProject
proposedSettingsFile - Variable in class bdv.BigDataViewer
proposeMipmaps(AbstractSequenceDescription<?, ?, ?>) - Static method in class bdv.export.ProposeMipmaps: Propose number of mipmap levels as well subsampling factors and chunk size for each level, for each setup of the given sequence.
proposeMipmaps(BasicViewSetup) - Static method in class bdv.export.ProposeMipmaps: Propose number of mipmap levels as well subsampling factors and chunk size for each level, based on the image and voxel size of the given setup.
proposeMipmaps(BasicViewSetup, int) - Static method in class bdv.export.ProposeMipmaps: Propose number of mipmap levels as well subsampling factors and chunk size for each level, based on the image and voxel size of the given setup.
ProposeMipmaps - Class in bdv.export: Propose number of mipmap levels, as well subsampling factors and chunk size for each level.
ProposeMipmaps() - Constructor for class bdv.export.ProposeMipmaps
put(SourceAndConverter<?>, ConverterSetup) - Method in class bdv.viewer.ConverterSetups
put(String, AffineTransform3D) - Method in class bdv.tools.bookmarks.Bookmarks

Q

qAlign - Variable in enum bdv.viewer.AbstractViewerPanel.AlignPlane: rotation from the xy-plane aligned coordinate system to this plane.

R

randomAccess() - Method in class bdv.util.ConstantRandomAccessible
randomAccess() - Method in class bdv.util.volatiles.VolatileRandomAccessibleIntervalView
randomAccess() - Method in class bdv.util.volatiles.VolatileRandomAccessibleView
randomAccess(Interval) - Method in class bdv.util.ConstantRandomAccessible
randomAccess(Interval) - Method in class bdv.util.volatiles.VolatileRandomAccessibleIntervalView
randomAccess(Interval) - Method in class bdv.util.volatiles.VolatileRandomAccessibleView
RandomAccessibleIntervalMipmapSource<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
RandomAccessibleIntervalMipmapSource(RandomAccessibleInterval<T>[], T, double[][], VoxelDimensions, String) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource
RandomAccessibleIntervalMipmapSource(RandomAccessibleInterval<T>[], T, double[][], VoxelDimensions, AffineTransform3D, String) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource
RandomAccessibleIntervalMipmapSource(RandomAccessibleInterval<T>[], T, double[][], VoxelDimensions, AffineTransform3D, String, boolean) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource
RandomAccessibleIntervalMipmapSource(RandomAccessibleInterval<T>[], T, AffineTransform3D[], VoxelDimensions, String, boolean) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource
RandomAccessibleIntervalMipmapSource4D<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
RandomAccessibleIntervalMipmapSource4D(RandomAccessibleInterval<T>[], T, double[][], VoxelDimensions, String) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource4D
RandomAccessibleIntervalMipmapSource4D(RandomAccessibleInterval<T>[], T, double[][], VoxelDimensions, AffineTransform3D, String) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource4D
RandomAccessibleIntervalMipmapSource4D(RandomAccessibleInterval<T>[], T, double[][], VoxelDimensions, AffineTransform3D, String, boolean) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource4D
RandomAccessibleIntervalMipmapSource4D(RandomAccessibleInterval<T>[], T, AffineTransform3D[], VoxelDimensions, String, boolean) - Constructor for class bdv.util.RandomAccessibleIntervalMipmapSource4D
RandomAccessibleIntervalSource<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
RandomAccessibleIntervalSource(RandomAccessibleInterval<T>, T, String) - Constructor for class bdv.util.RandomAccessibleIntervalSource
RandomAccessibleIntervalSource(RandomAccessibleInterval<T>, T, AffineTransform3D, String) - Constructor for class bdv.util.RandomAccessibleIntervalSource
RandomAccessibleIntervalSource(RandomAccessibleInterval<T>, T, AffineTransform3D, String, boolean) - Constructor for class bdv.util.RandomAccessibleIntervalSource
RandomAccessibleIntervalSource4D<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
RandomAccessibleIntervalSource4D(RandomAccessibleInterval<T>, T, String) - Constructor for class bdv.util.RandomAccessibleIntervalSource4D
RandomAccessibleIntervalSource4D(RandomAccessibleInterval<T>, T, AffineTransform3D, String) - Constructor for class bdv.util.RandomAccessibleIntervalSource4D
RandomAccessibleSource<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
RandomAccessibleSource(RandomAccessible<T>, Interval, T, String) - Constructor for class bdv.util.RandomAccessibleSource
RandomAccessibleSource(RandomAccessible<T>, Interval, T, AffineTransform3D, String) - Constructor for class bdv.util.RandomAccessibleSource
RandomAccessibleSource(RandomAccessible<T>, Interval, T, AffineTransform3D, String, boolean) - Constructor for class bdv.util.RandomAccessibleSource
RandomAccessibleSource4D<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv.util
RandomAccessibleSource4D(RandomAccessible<T>, Interval, T, String) - Constructor for class bdv.util.RandomAccessibleSource4D
RandomAccessibleSource4D(RandomAccessible<T>, Interval, T, AffineTransform3D, String) - Constructor for class bdv.util.RandomAccessibleSource4D
RandomAccessibleSource4D(RandomAccessible<T>, Interval, T, AffineTransform3D, String, boolean) - Constructor for class bdv.util.RandomAccessibleSource4D
RANGE - bdv.tools.boundingbox.BoxSelectionOptions.TimepointSelection
rangeChanged() - Method in interface bdv.tools.brightness.SliderPanelDouble.RangeListener
RangeSlider - Class in bdv.ui.rangeslider: An extension of JSlider to select a range of values using two thumb controls.
RangeSlider() - Constructor for class bdv.ui.rangeslider.RangeSlider: Constructs a RangeSlider with default minimum and maximum values of 0 and 100.
RangeSlider(int, int) - Constructor for class bdv.ui.rangeslider.RangeSlider: Constructs a RangeSlider with the specified default minimum and maximum values.
ratioComplete() - Method in class bdv.viewer.animate.AbstractAnimator: Returns the completion ratio.
readByteMDArrayBlockWithOffset(int, int, int, int[], long[]) - Method in class bdv.img.imaris.HDF5AccessHack
readByteMDArrayBlockWithOffset(int, int, int, int[], long[]) - Method in interface bdv.img.imaris.IHDF5Access
readByteMDArrayBlockWithOffset(int, int, int, int[], long[], byte[]) - Method in class bdv.img.imaris.HDF5AccessHack
readByteMDArrayBlockWithOffset(int, int, int, int[], long[], byte[]) - Method in interface bdv.img.imaris.IHDF5Access
readFloatMDArrayBlockWithOffset(int, int, int, int[], long[]) - Method in class bdv.img.imaris.HDF5AccessHack
readFloatMDArrayBlockWithOffset(int, int, int, int[], long[]) - Method in interface bdv.img.imaris.IHDF5Access
readFloatMDArrayBlockWithOffset(int, int, int, int[], long[], float[]) - Method in class bdv.img.imaris.HDF5AccessHack
readFloatMDArrayBlockWithOffset(int, int, int, int[], long[], float[]) - Method in interface bdv.img.imaris.IHDF5Access
readImarisAttributeString(String, String) - Method in class bdv.img.imaris.HDF5AccessHack
readImarisAttributeString(String, String) - Method in interface bdv.img.imaris.IHDF5Access
readImarisAttributeString(String, String, String) - Method in class bdv.img.imaris.HDF5AccessHack
readImarisAttributeString(String, String, String) - Method in interface bdv.img.imaris.IHDF5Access
readonly - Variable in class bdv.img.openconnectome.OpenConnectomeProject
readShortMDArrayBlockWithOffset(int, int, int, int[], long[]) - Method in class bdv.img.imaris.HDF5AccessHack
readShortMDArrayBlockWithOffset(int, int, int, int[], long[]) - Method in interface bdv.img.imaris.IHDF5Access
readShortMDArrayBlockWithOffset(int, int, int, int[], long[], short[]) - Method in class bdv.img.imaris.HDF5AccessHack
readShortMDArrayBlockWithOffset(int, int, int, int[], long[], short[]) - Method in interface bdv.img.imaris.IHDF5Access
RealARGBColorConverterSetup - Class in bdv.tools.brightness
RealARGBColorConverterSetup(int, List<ColorConverter>) - Constructor for class bdv.tools.brightness.RealARGBColorConverterSetup
RealARGBColorConverterSetup(int, ColorConverter...) - Constructor for class bdv.tools.brightness.RealARGBColorConverterSetup
RealBoxSelectionPanel - Class in bdv.tools.boundingbox: A JPanel containing X,Y,Z,... min/max sliders for adjusting a RealInterval
RealBoxSelectionPanel(RealBoxSelectionPanel.RealBox, RealInterval) - Constructor for class bdv.tools.boundingbox.RealBoxSelectionPanel
RealBoxSelectionPanel.RealBox - Interface in bdv.tools.boundingbox: Provides current interval and receives interval changes.
realRandomAccess() - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible
realRandomAccess(RealInterval) - Method in class bdv.tools.boundingbox.BoxRealRandomAccessible
RealRandomAccessibleIntervalSource<T extends net.imglib2.type.Type<T>> - Class in bdv.util
RealRandomAccessibleIntervalSource(RealRandomAccessible<T>, Interval, T, String) - Constructor for class bdv.util.RealRandomAccessibleIntervalSource
RealRandomAccessibleIntervalSource(RealRandomAccessible<T>, Interval, T, AffineTransform3D, String) - Constructor for class bdv.util.RealRandomAccessibleIntervalSource
RealRandomAccessibleIntervalSource(RealRandomAccessible<T>, Interval, T, AffineTransform3D, String, boolean) - Constructor for class bdv.util.RealRandomAccessibleIntervalSource
RealRandomAccessibleSource<T extends net.imglib2.type.Type<T>> - Class in bdv.util: A Source wrapping some RealRandomAccessible.
RealRandomAccessibleSource(RealRandomAccessible<T>, T, String) - Constructor for class bdv.util.RealRandomAccessibleSource
RealRandomAccessibleSource(RealRandomAccessible<T>, T, String, VoxelDimensions) - Constructor for class bdv.util.RealRandomAccessibleSource
RealRandomAccessibleSource(RealRandomAccessible<T>, T, String, VoxelDimensions, boolean) - Constructor for class bdv.util.RealRandomAccessibleSource
RECORD_MAX_PROJECTION_MOVIE - Static variable in class bdv.BigDataViewerActions
RECORD_MAX_PROJECTION_MOVIE_KEYS - Static variable in class bdv.BigDataViewerActions
RECORD_MOVIE - Static variable in class bdv.BigDataViewerActions
RECORD_MOVIE_KEYS - Static variable in class bdv.BigDataViewerActions
RecordMaxProjectionDialog - Class in bdv.tools
RecordMaxProjectionDialog(Frame, ViewerPanel, ProgressWriter) - Constructor for class bdv.tools.RecordMaxProjectionDialog
recordMovie(int, int, int, int, double, int, File) - Method in class bdv.tools.RecordMaxProjectionDialog
recordMovie(int, int, int, int, File) - Method in class bdv.tools.RecordMovieDialog
RecordMovieDialog - Class in bdv.tools
RecordMovieDialog(Frame, ViewerPanel, ProgressWriter) - Constructor for class bdv.tools.RecordMovieDialog
recreateContent() - Method in class bdv.tools.brightness.BrightnessDialog.ColorsPanel: Deprecated.
recreateContent() - Method in class bdv.tools.brightness.BrightnessDialog.MinMaxPanels: Deprecated.
reload() - Method in class bdv.AbstractSpimSource: Invalidate cached source transformations, triggering a reload from SpimData.
RemoteImageLoader - Class in bdv.img.remote
RemoteImageLoader(String) - Constructor for class bdv.img.remote.RemoteImageLoader
RemoteImageLoader(String, boolean) - Constructor for class bdv.img.remote.RemoteImageLoader
RemoteImageLoader.SetupImgLoader - Class in bdv.img.remote
RemoteImageLoaderMetaData - Class in bdv.img.remote
RemoteImageLoaderMetaData(Hdf5ImageLoader, AbstractSequenceDescription<?, ?, ?>) - Constructor for class bdv.img.remote.RemoteImageLoaderMetaData
RemoteVolatileShortArrayLoader - Class in bdv.img.remote
RemoteVolatileShortArrayLoader(RemoteImageLoader) - Constructor for class bdv.img.remote.RemoteVolatileShortArrayLoader
remove(int) - Method in class bdv.util.WrappedList
remove(Object) - Method in class bdv.util.WrappedList
remove(S) - Method in class bdv.ui.settings.style.AbstractStyleManager
remove(S) - Method in interface bdv.ui.settings.style.StyleManager
removeAll(Collection<?>) - Method in class bdv.util.WrappedList
removeAllSources() - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
removeCacheControl(CacheControl) - Method in class bdv.cache.CacheControl.CacheControls
removeCard(Object) - Method in class bdv.ui.CardPanel: Remove a card.
removeFromBdv() - Method in class bdv.util.BdvOverlaySource
removeFromBdv() - Method in class bdv.util.BdvSource
removeFromBdv() - Method in class bdv.util.BdvStackSource
removeFromBdv() - Method in class bdv.util.BdvVirtualChannelSource
removeFromViewer() - Method in class bdv.tools.boundingbox.TransformedBoxOverlaySource
removeGroup(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.
removeGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Remove group from the state.
removeGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Remove group from the state.
removeGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState: Remove group from the state (optional operation).
removeGroup(SourceGroup) - Method in class bdv.viewer.state.ViewerState: Deprecated.
removeGroup(SourceGroup) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
removeGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.BasicViewerState: Remove all groups in collection from the state.
removeGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.SynchronizedViewerState: Remove all groups in collection from the state.
removeGroups(Collection<? extends SourceGroup>) - Method in interface bdv.viewer.ViewerState: Remove all groups in collection from the state (optional operation).
removeHandler(Object) - Method in interface bdv.viewer.InteractiveDisplay: Remove an event handler.
removeHandler(Object) - Method in class bdv.viewer.InteractiveDisplayCanvas: Remove an event handler.
removeInterpolationModeListener(InterpolationModeListener) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use interpolationModeListeners().remove( listener ).
removeOverlayRenderer(OverlayRenderer) - Method in class bdv.viewer.InteractiveDisplayCanvas: Deprecated.
Use overlays().remove(renderer) instead
removePage(String) - Method in class bdv.tools.PreferencesDialog: Removes the settings page with the specified path.
removePage(String) - Method in class bdv.ui.settings.SettingsPanel: Removes the settings page with the specified path.
removeSetup(ConverterSetup) - Method in class bdv.tools.brightness.MinMaxGroup: Remove a ConverterSetup from this group.
removeSetup(ConverterSetup) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.
removeSetupFromGroup(ConverterSetup, MinMaxGroup) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.

Remove the specified setup from the specified group.
removeSource(int) - Method in class bdv.viewer.state.SourceGroup: Deprecated.
removeSource(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.
removeSource(Source<?>) - Method in class bdv.viewer.state.ViewerState: Deprecated.
removeSource(Source<?>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
removeSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Remove source from the state.
removeSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Remove source from the state.
removeSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Remove source from the state (optional operation).
removeSourceFromGroup(int, int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
removeSourceFromGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.BasicViewerState: Remove source from group.
removeSourceFromGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Remove source from group.
removeSourceFromGroup(SourceAndConverter<?>, SourceGroup) - Method in interface bdv.viewer.ViewerState: Remove source from group (optional operation).
removeSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.BasicViewerState: Remove all sources in collection from the state.
removeSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.SynchronizedViewerState: Remove all sources in collection from the state.
removeSources(Collection<? extends SourceAndConverter<?>>) - Method in interface bdv.viewer.ViewerState: Remove all sources in collection from the state (optional operation).
removeSources(Collection<Source<?>>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly
removeSourcesFromGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.BasicViewerState: Remove all sources in collection from group.
removeSourcesFromGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Remove all sources in collection from group.
removeSourcesFromGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in interface bdv.viewer.ViewerState: Remove all sources in collection from group (optional operation).
removeTimePointListener(TimePointListener) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use timePointListeners().remove( listener ).
removeTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Use transformListeners().remove( listener ) or renderTransformListeners().remove( listener ) (whichever the listener was added to).
removeTreeModelListener(TreeModelListener) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel: Removes a listener previously added with addTreeModelListener().
removeUpdateListener(VisibilityAndGrouping.UpdateListener) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
removeVisibilityChangeListener(PlaceHolderOverlayInfo.VisibilityChangeListener) - Method in class bdv.util.PlaceHolderOverlayInfo: Deprecated.
Use visibilityChangeListeners().remove(listener) instead.
removeWrapperIfPresent(AbstractSpimData<?>) - Static method in class bdv.spimdata.WrapBasicImgLoader
rename(StyleProfile<S>, String) - Method in class bdv.ui.settings.style.StyleProfileManager
rename(S, String) - Method in class bdv.ui.settings.style.AbstractStyleManager
rename(S, String) - Method in interface bdv.ui.settings.style.StyleManager
rename(T, String) - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager: Try to set the name of profile to newName.
renderBox(Interval, AffineTransform3D, GeneralPath, GeneralPath) - Method in class bdv.viewer.overlay.RenderBoxHelper
renderBox(RealInterval, AffineTransform3D, GeneralPath, GeneralPath, GeneralPath) - Method in class bdv.tools.boundingbox.RenderBoxHelper
RenderBoxHelper - Class in bdv.tools.boundingbox: Helper for rendering overlay boxes.
RenderBoxHelper - Class in bdv.viewer.overlay: Helper for rendering overlay boxes.
RenderBoxHelper() - Constructor for class bdv.tools.boundingbox.RenderBoxHelper
RenderBoxHelper() - Constructor for class bdv.viewer.overlay.RenderBoxHelper
renderCanvas(Interval, GeneralPath) - Method in class bdv.viewer.overlay.RenderBoxHelper
renderOrderComparator - Static variable in interface bdv.viewer.render.MipmapOrdering
RenderOrderComparator() - Constructor for class bdv.viewer.render.MipmapOrdering.RenderOrderComparator
RenderResult - Interface in bdv.viewer.render: Provides the renderer with a target image (RandomAccessibleInterval<ARGBType>) to render to.
RenderTarget<R extends RenderResult> - Interface in bdv.viewer.render: Receiver for a rendered image (to be drawn onto a canvas later).
RenderThreadFactory(ThreadGroup) - Constructor for class bdv.viewer.ViewerPanel.RenderThreadFactory
renderTransformListeners() - Method in class bdv.viewer.AbstractViewerPanel: Add/remove TransformListeners to notify about viewer transformation changes.
renderTransformListeners() - Method in class bdv.viewer.ViewerPanel: Add/remove TransformListeners to notify about viewer transformation changes.
renewHintsAfterPaintingOnce() - Method in class bdv.viewer.render.MipmapOrdering.MipmapHints
reorder(int[]) - Static method in class bdv.img.hdf5.Util: Reorder long array representing column-major coordinate (imglib2) to row-major (hdf5).
reorder(int[], int[]) - Static method in class bdv.img.hdf5.Util: Reorder long array representing column-major coordinate (imglib2) to row-major (hdf5).
reorder(int[], long[]) - Static method in class bdv.img.hdf5.Util: Reorder long array representing column-major coordinate (imglib2) to row-major (hdf5).
reorder(long[]) - Static method in class bdv.img.hdf5.Util: Reorder long array representing column-major coordinate (imglib2) to row-major (hdf5).
reorder(long[], long[]) - Static method in class bdv.img.hdf5.Util: Reorder long array representing column-major coordinate (imglib2) to row-major (hdf5).
reproject(double, double, double) - Method in class bdv.tools.boundingbox.RenderBoxHelper: Reproject a point
requestFocusInWindow() - Method in class bdv.viewer.AbstractViewerPanel
requestRepaint() - Method in class bdv.viewer.render.MultiResolutionRenderer: Request a repaint of the display from the painter thread.
requestRepaint() - Method in class bdv.viewer.render.PainterThread: Request repaint.
requestRepaint() - Method in interface bdv.viewer.RequestRepaint: Repaint as soon as possible.
requestRepaint() - Method in class bdv.viewer.ViewerPanel: Repaint as soon as possible.
requestRepaint(Interval) - Method in class bdv.viewer.render.MultiResolutionRenderer: Request a repaint of the given interval of the display from the painter thread.
requestRepaint(Interval) - Method in class bdv.viewer.ViewerPanel
RequestRepaint - Interface in bdv.viewer
requiresMaskedSources() - Method in interface bdv.viewer.render.AccumulateProjectorFactory: Returns true if projectors created by this factory make use of alpha masks.
requiresMaskedSources() - Method in class bdv.viewer.render.AlphaWeightedAccumulateProjectorARGB.Factory
requiresRepaint() - Method in class bdv.tools.bookmarks.BookmarkTextOverlayAnimator
requiresRepaint() - Method in class bdv.viewer.animate.MessageOverlayAnimator
requiresRepaint() - Method in interface bdv.viewer.animate.OverlayAnimator: Returns true if the animator requires an immediate repaint to continue the animation.
requiresRepaint() - Method in class bdv.viewer.animate.TextOverlayAnimator
reset() - Method in class bdv.tools.transformation.ManualTransformationEditor: During an ongoing manual transformation, reset the transforming sources to their original transformations.
resetPropertyCaches() - Static method in class bdv.ui.UIUtils: Resets the caches for UIUtils.getUIScaleFactor(java.lang.Object).
resolution - Variable in class bdv.img.openconnectome.OpenConnectomeProject
resolutions - Variable in class bdv.AbstractCachedViewerSetupImgLoader
resolutions - Variable in class bdv.img.openconnectome.OpenConnectomeDataset
restoreFromXml(Element) - Method in class bdv.tools.bookmarks.Bookmarks
restoreFromXml(Element) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.

Restore the state of this SetupAssignments from XML.
restoreFromXml(Element) - Method in class bdv.tools.transformation.ManualTransformation
restoreFromXml(Element, ViewerState) - Method in class bdv.viewer.state.XmlIoViewerState
restoreSourceGroupsFromXml(Element, ViewerState) - Method in class bdv.viewer.state.XmlIoViewerState
restoreSourcesFromXml(Element, List<SourceState<?>>) - Method in class bdv.viewer.state.XmlIoViewerState
result - Variable in class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog
Result(boolean, TransformedBoxModel, int, int) - Constructor for class bdv.tools.boundingbox.TransformedBoxSelectionDialog.Result
Result(boolean, TransformedBox, int, int) - Constructor for class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result
retainAll(Collection<?>) - Method in class bdv.util.WrappedList
RGB_COLOR_MODEL - Static variable in class bdv.util.AWTUtils
ROTATE_LEFT - Static variable in class bdv.TransformEventHandler2D
ROTATE_LEFT - Static variable in class bdv.TransformEventHandler3D
ROTATE_LEFT_FAST - Static variable in class bdv.TransformEventHandler2D
ROTATE_LEFT_FAST - Static variable in class bdv.TransformEventHandler3D
ROTATE_LEFT_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
ROTATE_LEFT_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
ROTATE_LEFT_KEYS - Static variable in class bdv.TransformEventHandler2D
ROTATE_LEFT_KEYS - Static variable in class bdv.TransformEventHandler3D
ROTATE_LEFT_SLOW - Static variable in class bdv.TransformEventHandler2D
ROTATE_LEFT_SLOW - Static variable in class bdv.TransformEventHandler3D
ROTATE_LEFT_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
ROTATE_LEFT_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
ROTATE_RIGHT - Static variable in class bdv.TransformEventHandler2D
ROTATE_RIGHT - Static variable in class bdv.TransformEventHandler3D
ROTATE_RIGHT_FAST - Static variable in class bdv.TransformEventHandler2D
ROTATE_RIGHT_FAST - Static variable in class bdv.TransformEventHandler3D
ROTATE_RIGHT_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
ROTATE_RIGHT_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
ROTATE_RIGHT_KEYS - Static variable in class bdv.TransformEventHandler2D
ROTATE_RIGHT_KEYS - Static variable in class bdv.TransformEventHandler3D
ROTATE_RIGHT_SLOW - Static variable in class bdv.TransformEventHandler2D
ROTATE_RIGHT_SLOW - Static variable in class bdv.TransformEventHandler3D
ROTATE_RIGHT_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
ROTATE_RIGHT_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
RotationAnimator - Class in bdv.viewer.animate
RotationAnimator(AffineTransform3D, double, double, double[], long) - Constructor for class bdv.viewer.animate.RotationAnimator
run() - Method in class bdv.viewer.render.PainterThread
runOnApply - Variable in class bdv.ui.settings.SimpleSettingsPage
runOnCancel - Variable in class bdv.ui.settings.SimpleSettingsPage

S

save(Appearance, String) - Static method in class bdv.ui.appearance.AppearanceIO
SAVE_SETTINGS - Static variable in class bdv.BigDataViewerActions
SAVE_SETTINGS_KEYS - Static variable in class bdv.BigDataViewerActions
saveSettings() - Method in class bdv.BigDataViewer
saveSettings(String) - Method in class bdv.BigDataViewer
saveStyles() - Method in class bdv.ui.keymap.KeymapManager
saveStyles() - Method in interface bdv.ui.settings.style.StyleManager
saveStyles(File) - Method in class bdv.ui.keymap.AbstractKeymapManager
scale - Variable in class bdv.export.SubTaskProgressWriter
scaleBarBgColor() - Method in class bdv.ui.appearance.Appearance
scaleBarBgColor() - Static method in class bdv.util.Prefs
scaleBarBgColor(int) - Static method in class bdv.util.Prefs
scaleBarColor() - Method in class bdv.ui.appearance.Appearance
scaleBarColor() - Static method in class bdv.util.Prefs
scaleBarColor(int) - Static method in class bdv.util.Prefs
ScaleBarOverlayRenderer - Class in bdv.viewer.overlay
ScaleBarOverlayRenderer() - Constructor for class bdv.viewer.overlay.ScaleBarOverlayRenderer
screenScales(double[]) - Method in class bdv.util.BdvOptions: Set the number and scale factors for scaled screen images.
screenScales(double[]) - Method in class bdv.viewer.ViewerOptions: Set the number and scale factors for scaled screen images.
SCROLL_ROTATE - Static variable in class bdv.TransformEventHandler2D
SCROLL_ROTATE_FAST - Static variable in class bdv.TransformEventHandler2D
SCROLL_ROTATE_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
SCROLL_ROTATE_KEYS - Static variable in class bdv.TransformEventHandler2D
SCROLL_ROTATE_SLOW - Static variable in class bdv.TransformEventHandler2D
SCROLL_ROTATE_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
SCROLL_TRANSLATE - Static variable in class bdv.TransformEventHandler2D
SCROLL_TRANSLATE_FAST - Static variable in class bdv.TransformEventHandler2D
SCROLL_TRANSLATE_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
SCROLL_TRANSLATE_KEYS - Static variable in class bdv.TransformEventHandler2D
SCROLL_TRANSLATE_SLOW - Static variable in class bdv.TransformEventHandler2D
SCROLL_TRANSLATE_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
SCROLL_Z - Static variable in class bdv.TransformEventHandler3D
SCROLL_Z_FAST - Static variable in class bdv.TransformEventHandler3D
SCROLL_Z_FAST_KEYS - Static variable in class bdv.TransformEventHandler3D
SCROLL_Z_KEYS - Static variable in class bdv.TransformEventHandler3D
SCROLL_Z_SLOW - Static variable in class bdv.TransformEventHandler3D
SCROLL_Z_SLOW_KEYS - Static variable in class bdv.TransformEventHandler3D
SECTION - bdv.tools.boundingbox.TransformedBoxOverlay.BoxDisplayMode
select(StyleProfile<S>) - Method in class bdv.ui.settings.style.StyleProfileManager
select(T) - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileManager: Select the active profile.
SELECT_AXIS_X - Static variable in class bdv.TransformEventHandler3D
SELECT_AXIS_X_KEYS - Static variable in class bdv.TransformEventHandler3D
SELECT_AXIS_Y - Static variable in class bdv.TransformEventHandler3D
SELECT_AXIS_Y_KEYS - Static variable in class bdv.TransformEventHandler3D
SELECT_AXIS_Z - Static variable in class bdv.TransformEventHandler3D
SELECT_AXIS_Z_KEYS - Static variable in class bdv.TransformEventHandler3D
SelectAndEditProfileSettingsPage<T extends SelectAndEditProfileSettingsPage.Profile> - Class in bdv.ui.settings: A SettingsPage for the following common scenario: There are multiple "profiles" (e.g., keymaps, trackscheme styles, ...) to select from, and its possible to edit each individual profile.
SelectAndEditProfileSettingsPage(String, SelectAndEditProfileSettingsPage.ProfileManager<T>, SelectAndEditProfileSettingsPage.ProfileEditPanel<T>) - Constructor for class bdv.ui.settings.SelectAndEditProfileSettingsPage: Creates a new SelectAndEditProfileSettingsPage for the specified profile manager and the specified editor panel.
SelectAndEditProfileSettingsPage.Profile - Interface in bdv.ui.settings: Interface for the objects that are edited and selected in a SelectAndEditProfileSettingsPage.
SelectAndEditProfileSettingsPage.ProfileEditPanel<T> - Interface in bdv.ui.settings: Class that edits a profile of type T in a JPanel.
SelectAndEditProfileSettingsPage.ProfileManager<T extends SelectAndEditProfileSettingsPage.Profile> - Interface in bdv.ui.settings: Interface for classes that manage a collection of profiles.
selectBox(Bdv, AffineTransform3D, Interval, Interval) - Static method in class bdv.util.BdvFunctions
selectBox(Bdv, AffineTransform3D, Interval, Interval, BoxSelectionOptions) - Static method in class bdv.util.BdvFunctions
selectedStyle - Variable in class bdv.ui.settings.style.AbstractStyleManager
selectRealBox(Bdv, AffineTransform3D, RealInterval, RealInterval) - Static method in class bdv.util.BdvFunctions
selectRealBox(Bdv, AffineTransform3D, RealInterval, RealInterval, BoxSelectionOptions) - Static method in class bdv.util.BdvFunctions
selectSingleTimepoint() - Method in class bdv.tools.boundingbox.BoxSelectionOptions
selectSingleTimepoint(int, int) - Method in class bdv.tools.boundingbox.BoxSelectionOptions
selectTimepointRange() - Method in class bdv.tools.boundingbox.BoxSelectionOptions
selectTimepointRange(int, int) - Method in class bdv.tools.boundingbox.BoxSelectionOptions
SequenceDescriptionMinimal - Class in bdv.spimdata
SequenceDescriptionMinimal() - Constructor for class bdv.spimdata.SequenceDescriptionMinimal
SequenceDescriptionMinimal(SequenceDescriptionMinimal, BasicImgLoader) - Constructor for class bdv.spimdata.SequenceDescriptionMinimal: create copy of a SequenceDescriptionMinimal with replaced BasicImgLoader
SequenceDescriptionMinimal(TimePoints, Map<Integer, ? extends BasicViewSetup>, BasicImgLoader, MissingViews) - Constructor for class bdv.spimdata.SequenceDescriptionMinimal
serialize(AffineTransform3D, Type, JsonSerializationContext) - Method in class bdv.img.remote.AffineTransform3DJsonSerializer
set(boolean, Interval, AffineTransform3D) - Method in class bdv.viewer.overlay.IntervalAndTransform
set(int, E) - Method in class bdv.util.WrappedList
set(long, T) - Method in class bdv.img.cache.VolatileCachedCellImg.VolatileCachedCells
set(Appearance) - Method in class bdv.ui.appearance.Appearance
set(Keymap) - Method in class bdv.ui.keymap.Keymap
set(ViewerState) - Method in class bdv.viewer.BasicViewerState: Set this ViewerState to other.
set(M) - Method in class bdv.ui.settings.style.AbstractStyleManager
set(M) - Method in interface bdv.ui.settings.style.StyleManager
set(Interval) - Method in class bdv.util.ModifiableInterval
set(RealInterval) - Method in class bdv.util.ModifiableRealInterval
set(AffineTransform3D) - Method in interface bdv.TransformState: Set the transform.
SET_BOOKMARK - Static variable in class bdv.BigDataViewerActions
SET_BOOKMARK_KEYS - Static variable in class bdv.BigDataViewerActions
SET_CURRENT_SOURCE - Static variable in class bdv.viewer.NavigationActions
SET_CURRENT_SOURCE_KEYS_FORMAT - Static variable in class bdv.viewer.NavigationActions
setAccumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.viewer.BasicViewerState
setAccumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.viewer.SynchronizedViewerState
setAccumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in interface bdv.viewer.ViewerState: Set the AccumulateProjectorFactory.
setActive(boolean) - Method in class bdv.tools.transformation.ManualTransformationEditor
setActive(boolean) - Method in class bdv.util.BdvOverlaySource
setActive(boolean) - Method in class bdv.util.BdvSource
setActive(boolean) - Method in class bdv.util.BdvStackSource
setActive(boolean) - Method in class bdv.util.BdvVirtualChannelSource
setActive(boolean) - Method in class bdv.viewer.state.SourceGroup: Deprecated.

Set the group active (visible in fused mode) or inactive.
setActive(boolean) - Method in class bdv.viewer.state.SourceState: Deprecated.

Set the source active (visible in fused mode) or inactive
setBdvHandle(BdvHandle) - Method in class bdv.util.BdvSource
setBounds(ConverterSetup, Bounds) - Method in class bdv.viewer.ConverterSetupBounds
setBoundsInterval(Interval) - Method in class bdv.tools.boundingbox.BoxSelectionPanel
setBoundsInterval(RealInterval) - Method in class bdv.tools.boundingbox.RealBoxSelectionPanel
setBoxInterval(Interval) - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer: Update the box interval.
setCache(VolatileGlobalCellCache) - Method in class bdv.img.catmaid.CatmaidImageLoader
setCacheHints(CacheHints) - Method in class bdv.img.cache.VolatileCachedCellImg: Set hints on how to handle cell requests for this cache.
setCanvasSize(int, int) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
setCanvasSize(int, int) - Method in class bdv.tools.RecordMaxProjectionDialog
setCanvasSize(int, int) - Method in class bdv.tools.RecordMovieDialog
setCanvasSize(int, int) - Method in class bdv.util.BdvOverlay
setCanvasSize(int, int) - Method in interface bdv.viewer.OverlayRenderer: This is called, when the screen size of the canvas (the component displaying the image and generating mouse events) changes.
setCanvasSize(int, int) - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer
setCanvasSize(int, int, boolean) - Method in interface bdv.TransformEventHandler: This is called, when the screen size of the canvas (the component displaying the image and generating mouse events) changes.
setCanvasSize(int, int, boolean) - Method in class bdv.TransformEventHandler2D
setCanvasSize(int, int, boolean) - Method in class bdv.TransformEventHandler3D
setCardExpanded(Object, boolean) - Method in class bdv.ui.CardPanel: Set open state of a card
setCollapsed(boolean) - Method in class bdv.ui.splitpanel.SplitPanel: Un/collapse the UI-Panel.
setColor(int) - Method in class bdv.util.PlaceHolderConverterSetup
setColor(Color) - Method in class bdv.tools.brightness.ColorIcon
setColor(ARGBType) - Method in interface bdv.tools.brightness.ConverterSetup: Set the color for this converter.
setColor(ARGBType) - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
setColor(ARGBType) - Method in class bdv.util.BdvOverlaySource
setColor(ARGBType) - Method in class bdv.util.BdvPointsSource
setColor(ARGBType) - Method in class bdv.util.BdvSource
setColor(ARGBType) - Method in class bdv.util.BdvStackSource
setColor(ARGBType) - Method in class bdv.util.BdvVirtualChannelSource
setColor(ARGBType) - Method in class bdv.util.PlaceHolderConverterSetup
setCommandDescriptions(CommandDescriptions) - Method in class bdv.ui.keymap.KeymapManager
setCreatedSharedQueue(SharedQueue) - Method in class bdv.img.hdf5.Hdf5ImageLoader
setCreatedSharedQueue(SharedQueue) - Method in class bdv.img.n5.N5ImageLoader
setCreatedSharedQueue(SharedQueue) - Method in interface bdv.ViewerImgLoader: Use the given SharedQueue to asynchronously load blocks.
setCurrent() - Method in class bdv.util.BdvOverlaySource
setCurrent() - Method in class bdv.util.BdvSource
setCurrent() - Method in class bdv.util.BdvStackSource
setCurrent() - Method in class bdv.util.BdvVirtualChannelSource
setCurrent(boolean) - Method in class bdv.viewer.state.SourceGroup: Deprecated.

Set this group current (or not).
setCurrent(boolean) - Method in class bdv.viewer.state.SourceState: Deprecated.

Set this source current (or not).
setCurrentGroup(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Make the group with the given index current.
setCurrentGroup(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setCurrentGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState: Make group the current group.
setCurrentGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState: Make group the current group.
setCurrentGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState: Make group the current group (optional operation).
setCurrentGroup(SourceGroup) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Make the given group current.
setCurrentGroupOrSource(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setCurrentSource(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Make the source with the given index current.
setCurrentSource(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setCurrentSource(Source<?>) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Make the given source current.
setCurrentSource(Source<?>) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setCurrentSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState: Make source the current source.
setCurrentSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState: Make source the current source.
setCurrentSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState: Make source the current source (optional operation).
setCurrentTimepoint(int) - Method in class bdv.viewer.BasicViewerState
setCurrentTimepoint(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Set the current timepoint index.
setCurrentTimepoint(int) - Method in class bdv.viewer.SynchronizedViewerState
setCurrentTimepoint(int) - Method in interface bdv.viewer.ViewerState: Set the current timepoint (optional operation).
setCurrentValue(double) - Method in class bdv.util.BoundedValueDouble
setCurrentValue(int) - Method in class bdv.util.BoundedValue
setCurrentViewerTransform(AffineTransform3D) - Method in class bdv.viewer.ViewerPanel: Deprecated.
Modify ViewerPanel.state() directly (state().setViewerTransform(t))
setDecimalFormat(String) - Method in class bdv.tools.brightness.SliderPanelDouble
setDepth(double) - Method in class bdv.tools.boundingbox.RenderBoxHelper
setDepth(double) - Method in class bdv.viewer.overlay.RenderBoxHelper
setDisplayMode(DisplayMode) - Method in class bdv.viewer.BasicViewerState
setDisplayMode(DisplayMode) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Set the DisplayMode.
setDisplayMode(DisplayMode) - Method in class bdv.viewer.SynchronizedViewerState
setDisplayMode(DisplayMode) - Method in class bdv.viewer.ViewerPanel: Set the DisplayMode.
setDisplayMode(DisplayMode) - Method in interface bdv.viewer.ViewerState: Set the DisplayMode (optional operation).
setDisplayMode(DisplayMode) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setDisplayRange(double, double) - Method in interface bdv.tools.brightness.ConverterSetup: Set the range of source values that is mapped to the full range of the target type.
setDisplayRange(double, double) - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
setDisplayRange(double, double) - Method in class bdv.util.BdvOverlaySource
setDisplayRange(double, double) - Method in class bdv.util.BdvSource
setDisplayRange(double, double) - Method in class bdv.util.BdvStackSource
setDisplayRange(double, double) - Method in class bdv.util.BdvVirtualChannelSource
setDisplayRange(double, double) - Method in class bdv.util.PlaceHolderConverterSetup
setDisplayRangeBounds(double, double) - Method in class bdv.util.BdvOverlaySource
setDisplayRangeBounds(double, double) - Method in class bdv.util.BdvSource
setDisplayRangeBounds(double, double) - Method in class bdv.util.BdvStackSource
setDisplayRangeBounds(double, double) - Method in class bdv.util.BdvVirtualChannelSource
setDividerSize(int) - Method in class bdv.ui.splitpanel.SplitPanel
setEditable(boolean) - Method in class bdv.tools.boundingbox.TransformedBoxEditor
setEnabled(boolean) - Method in class bdv.tools.boundingbox.BoxDisplayModePanel
setFillIntersection(boolean) - Method in class bdv.tools.boundingbox.TransformedBoxEditor: Only meaningful if BoxSourceType == NONE
setFixedTransform(AffineTransform3D) - Method in class bdv.tools.transformation.TransformedSource: Sets the fixed part of the extra transformation to the specified transform.
setFusedEnabled(boolean) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setGroupActive(int, boolean) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setGroupActive(SourceGroup, boolean) - Method in class bdv.viewer.BasicViewerState: Set group active or inactive.
setGroupActive(SourceGroup, boolean) - Method in class bdv.viewer.SynchronizedViewerState: Set group active or inactive.
setGroupActive(SourceGroup, boolean) - Method in interface bdv.viewer.ViewerState: Set group active or inactive (optional operation).
setGroupingEnabled(boolean) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setGroupName(int, String) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setGroupName(SourceGroup, String) - Method in class bdv.viewer.BasicViewerState: Set the name of a group.
setGroupName(SourceGroup, String) - Method in class bdv.viewer.SynchronizedViewerState: Set the name of a group.
setGroupName(SourceGroup, String) - Method in interface bdv.viewer.ViewerState: Set the name of a group (optional operation).
setGroupsActive(Collection<? extends SourceGroup>, boolean) - Method in class bdv.viewer.BasicViewerState: Set all groups in collection active or inactive.
setGroupsActive(Collection<? extends SourceGroup>, boolean) - Method in class bdv.viewer.SynchronizedViewerState: Set all groups in collection active or inactive.
setGroupsActive(Collection<? extends SourceGroup>, boolean) - Method in interface bdv.viewer.ViewerState: Set all groups in collection active or inactive (optional operation).
setHighlightedCornerListener(TransformedBoxOverlay.HighlightedCornerListener) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
setIncrementalTransform(AffineTransform3D) - Method in class bdv.tools.transformation.TransformedSource: Sets the incremental part of the extra transformation to the specified transform.
setInputMapsToBlock(Collection<String>) - Method in class bdv.tools.bookmarks.BookmarksEditor
setInterpolation(Interpolation) - Method in class bdv.viewer.BasicViewerState
setInterpolation(Interpolation) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Set the interpolation method.
setInterpolation(Interpolation) - Method in class bdv.viewer.SynchronizedViewerState
setInterpolation(Interpolation) - Method in class bdv.viewer.ViewerPanel: Set the Interpolation mode.
setInterpolation(Interpolation) - Method in interface bdv.viewer.ViewerState: Set the interpolation method (optional operation).
setIntersectionFillColor(Color) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
setInterval(Interval) - Method in interface bdv.tools.boundingbox.BoxSelectionPanel.Box
setInterval(RealInterval) - Method in class bdv.tools.boundingbox.AbstractTransformedBoxModel
setInterval(RealInterval) - Method in interface bdv.tools.boundingbox.RealBoxSelectionPanel.RealBox
setInterval(RealInterval) - Method in class bdv.tools.boundingbox.TransformedBoxModel
setInterval(RealInterval) - Method in class bdv.tools.boundingbox.TransformedRealBoxModel
setLookAndFeel(UIManager.LookAndFeelInfo) - Method in class bdv.ui.appearance.Appearance
setMinimumHeight(Component, int) - Static method in class bdv.ui.UIUtils: Set the minimum height of a component (leaving the minimum width untouched).
setMinimumWidth(Component, int) - Static method in class bdv.ui.UIUtils: Set the minimum width of a component (leaving the minimum height untouched).
setModified() - Method in interface bdv.ui.settings.ModificationListener
setName(String) - Method in class bdv.ui.keymap.Keymap: Sets the name of this Keymap.
setName(String) - Method in class bdv.ui.settings.style.AbstractStyle
setName(String) - Method in interface bdv.ui.settings.style.Style
setName(String) - Method in class bdv.viewer.state.SourceGroup: Deprecated.
setNumColummns(int) - Method in class bdv.tools.brightness.SliderPanel
setNumColummns(int) - Method in class bdv.tools.brightness.SliderPanelDouble
setNumFetcherThreads(int) - Method in class bdv.img.hdf5.Hdf5ImageLoader
setNumFetcherThreads(int) - Method in class bdv.img.n5.N5ImageLoader
setNumFetcherThreads(int) - Method in interface bdv.ViewerImgLoader: Set the number of fetcher threads that will be created to asynchronously load blocks.
setNumTimepoints(int) - Method in class bdv.viewer.BasicViewerState
setNumTimepoints(int) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Set the number of timepoints.
setNumTimepoints(int) - Method in class bdv.viewer.SynchronizedViewerState
setNumTimepoints(int) - Method in class bdv.viewer.ViewerPanel: Set the number of available timepoints.
setNumTimepoints(int) - Method in interface bdv.viewer.ViewerState: Set the number of timepoints (optional operation).
setOrigin(double, double) - Method in class bdv.tools.boundingbox.RenderBoxHelper
setOrigin(double, double) - Method in class bdv.viewer.overlay.RenderBoxHelper
setOutlineColor(Color) - Method in class bdv.tools.brightness.ColorIcon
setOverlayInfo(PlaceHolderOverlayInfo) - Method in class bdv.util.BdvOverlay
setPerspective(double) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay: Sets the perspective value.
setPerspective(double, double) - Method in class bdv.tools.boundingbox.TransformedBoxEditor: Sets up perspective projection for the overlay.
setPerspectiveProjection(boolean) - Method in class bdv.tools.boundingbox.RenderBoxHelper
setPoints(List<T>) - Method in class bdv.util.BdvPointsSource
setPoints(List<T>) - Method in class bdv.util.PointsOverlay
setPreferredHeight(Component, int) - Static method in class bdv.ui.UIUtils: Set the preferred height of a component (leaving the preferred width untouched).
setPreferredWidth(Component, int) - Static method in class bdv.ui.UIUtils: Set the preferred width of a component (leaving the preferred height untouched).
setProgress(double) - Method in interface bdv.export.ProgressWriter
setProgress(double) - Method in class bdv.export.ProgressWriterConsole
setProgress(double) - Method in class bdv.export.ProgressWriterNull
setProgress(double) - Method in class bdv.export.SubTaskProgressWriter
setRange(double, double) - Method in class bdv.util.BoundedIntervalDouble: Set the allowed range.
setRange(double, double) - Method in class bdv.util.BoundedValueDouble
setRange(int, int) - Method in class bdv.ui.rangeslider.RangeSlider: Sets both the lower and upper values in the range.
setRange(int, int) - Method in class bdv.util.BoundedInterval: Set the allowed range.
setRange(int, int) - Method in class bdv.util.BoundedValue
setRangeListener(SliderPanelDouble.RangeListener) - Method in class bdv.tools.brightness.SliderPanelDouble
setRenderResult(BufferedImageRenderResult) - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer: Set the RenderResult that is to be drawn on the canvas.
setRenderResult(R) - Method in interface bdv.viewer.render.RenderTarget: Set the RenderResult that is to be drawn on the canvas.
setRenderTime(long) - Method in class bdv.viewer.render.DebugTilingOverlay
setRenderTimePerPixelAndSource(double) - Method in class bdv.viewer.render.DebugTilingOverlay
setScale(double) - Method in class bdv.tools.boundingbox.RenderBoxHelper
setScale(double) - Method in class bdv.viewer.overlay.RenderBoxHelper
setScaleBarBgColor(int) - Method in class bdv.ui.appearance.Appearance
setScaleBarColor(int) - Method in class bdv.ui.appearance.Appearance
setScaleFactor(double) - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
setScaleFactor(double) - Method in interface bdv.viewer.render.RenderResult: Set the scale factor from target coordinates to screen resolution.
setSelectedStyle(Keymap) - Method in class bdv.ui.keymap.AbstractKeymapManager
setSelectedStyle(S) - Method in class bdv.ui.settings.style.AbstractStyleManager
setSelectedStyle(S) - Method in interface bdv.ui.settings.style.StyleManager
setShowMultibox(boolean) - Method in class bdv.ui.appearance.Appearance
setShowScaleBar(boolean) - Method in class bdv.ui.appearance.Appearance
setShowScaleBarInMovie(boolean) - Method in class bdv.ui.appearance.Appearance
setShowTextOverlay(boolean) - Method in class bdv.ui.appearance.Appearance
setShowTiles(boolean) - Method in class bdv.viewer.render.DebugTilingOverlay
setSingleSourceMode(boolean) - Method in class bdv.viewer.state.ViewerState: Deprecated.
replaced by ViewerState.setDisplayMode(DisplayMode)
setSourceActive(int, boolean) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setSourceActive(Source<?>, boolean) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
setSourceActive(SourceAndConverter<?>, boolean) - Method in class bdv.viewer.BasicViewerState: Set source active or inactive.
setSourceActive(SourceAndConverter<?>, boolean) - Method in class bdv.viewer.SynchronizedViewerState: Set source active or inactive.
setSourceActive(SourceAndConverter<?>, boolean) - Method in interface bdv.viewer.ViewerState: Set source active or inactive (optional operation).
setSourceInterval(Interval) - Method in class bdv.viewer.overlay.IntervalAndTransform
setSourceNameOverlayPosition(Prefs.OverlayPosition) - Method in class bdv.ui.appearance.Appearance
setSourceNameOverlayPosition(Prefs.OverlayPosition) - Method in class bdv.viewer.overlay.SourceInfoOverlayRenderer
setSourcesActive(Collection<? extends SourceAndConverter<?>>, boolean) - Method in class bdv.viewer.BasicViewerState: Set all sources in collection active or inactive.
setSourcesActive(Collection<? extends SourceAndConverter<?>>, boolean) - Method in class bdv.viewer.SynchronizedViewerState: Set all sources in collection active or inactive.
setSourcesActive(Collection<? extends SourceAndConverter<?>>, boolean) - Method in interface bdv.viewer.ViewerState: Set all sources in collection active or inactive (optional operation).
setSourceSize(double) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay: Sets the source size (estimated maximum dimension) in global coordinates.
setSourceToViewer(AffineTransform3D) - Method in class bdv.viewer.overlay.IntervalAndTransform
setSourceTransform(AffineTransform3D) - Method in class bdv.util.BdvOverlay
setSourceTransform(AffineTransform3D) - Method in class bdv.util.BdvPointsSource
setTiling(List<Tile>, double, int, int) - Method in class bdv.viewer.render.DebugTilingOverlay
setTime(long) - Method in class bdv.viewer.animate.AbstractAnimator: Sets the current time for the animation.
setTimepoint(int) - Method in class bdv.viewer.ViewerPanel: Show the specified time-point.
setTimePointsOrdered(List<TimePoint>) - Method in class bdv.viewer.overlay.SourceInfoOverlayRenderer
SettingsPage - Interface in bdv.ui.settings: A content page in a SettingsPanel.
SettingsPanel - Class in bdv.ui.settings: Main panel for preferences dialogs.
SettingsPanel() - Constructor for class bdv.ui.settings.SettingsPanel
setTransformAnimator(AbstractTransformAnimator) - Method in class bdv.viewer.AbstractViewerPanel
setTransformAnimator(AbstractTransformAnimator) - Method in class bdv.viewer.ViewerPanel
setTransformEventHandler(TransformEventHandler) - Method in class bdv.viewer.InteractiveDisplayCanvas: Set the TransformEventHandler that will be notified when component is resized.
setup - Variable in class bdv.util.BdvOverlaySource
setup - Variable in class bdv.util.BdvVirtualChannelSource
setup(CardPanel, AbstractViewerPanel, ConverterSetups) - Static method in class bdv.ui.BdvDefaultCards
setupAssignments - Variable in class bdv.BigDataViewer
setupAssignments - Variable in class bdv.util.BdvHandle
SetupAssignments - Class in bdv.tools.brightness: Deprecated.
SetupAssignments(ArrayList<ConverterSetup>, double, double) - Constructor for class bdv.tools.brightness.SetupAssignments: Deprecated.
SetupAssignments(ArrayList<ConverterSetup>, double, double, double, double) - Constructor for class bdv.tools.brightness.SetupAssignments: Deprecated.
SetupAssignments(List<ConverterSetup>, double, double) - Constructor for class bdv.tools.brightness.SetupAssignments: Deprecated.
SetupAssignments(List<ConverterSetup>, double, double, double, double) - Constructor for class bdv.tools.brightness.SetupAssignments: Deprecated.
SetupAssignments.UpdateListener - Interface in bdv.tools.brightness: Deprecated.
setupChangeListeners() - Method in interface bdv.tools.brightness.ConverterSetup: SetupChangeListeners can be added/removed here, and will be notified about changes to this ConverterSetup.
setupChangeListeners() - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
setupChangeListeners() - Method in class bdv.util.PlaceHolderConverterSetup
setUpdated() - Method in class bdv.viewer.render.awt.BufferedImageRenderResult
setUpdated() - Method in interface bdv.viewer.render.RenderResult: Notify that the target image data was changed.
setUpdateListener(MinMaxGroup.UpdateListener) - Method in class bdv.tools.brightness.MinMaxGroup: Set an MinMaxGroup.UpdateListener (usually a GUI component).
setUpdateListener(SetupAssignments.UpdateListener) - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.
setUpdateListener(BoundedValue.UpdateListener) - Method in class bdv.util.BoundedValue
setUpdateListener(BoundedValueDouble.UpdateListener) - Method in class bdv.util.BoundedValueDouble
setupId - Variable in class bdv.AbstractCachedViewerSetupImgLoader
setupId - Variable in class bdv.img.hdf5.ViewLevelId: The setup id (index within the timepoint).
SetupImgLoader(int) - Constructor for class bdv.img.imaris.ImarisImageLoader.SetupImgLoader
SetupImgLoader(int) - Constructor for class bdv.img.remote.RemoteImageLoader.SetupImgLoader
SetupImgLoader(int, DataTypeProperties<T, V, ?, ?>) - Constructor for class bdv.img.n5.N5ImageLoader.SetupImgLoader
SetupImgLoader(int, T, V) - Constructor for class bdv.img.n5.N5ImageLoader.SetupImgLoader
SetupImgLoader(Source<T>) - Constructor for class bdv.tools.crop.CropImgLoader.SetupImgLoader
SetupImgLoader(IHDF5Reader, HDF5Access, int, DataTypeProperties<T, V, ?, ?>, boolean) - Constructor for class bdv.img.hdf5.Hdf5ImageLoader.SetupImgLoader
setupImgLoaders - Variable in class bdv.img.remote.RemoteImageLoader: TODO
SetupImgLoaderWrapper(int) - Constructor for class bdv.spimdata.legacy.LegacyViewerImgLoaderExtWrapper.SetupImgLoaderWrapper
SetupImgLoaderWrapper(int) - Constructor for class bdv.spimdata.legacy.LegacyViewerImgLoaderWrapper.SetupImgLoaderWrapper
setupParametersChanged(ConverterSetup) - Method in interface bdv.tools.brightness.ConverterSetup.SetupChangeListener
setUpperValue(int) - Method in class bdv.ui.rangeslider.RangeSlider: Sets the upper value in the range.
setValue(int) - Method in class bdv.ui.rangeslider.RangeSlider: Sets the lower value in the range.
setViewer(RequestRepaint) - Method in interface bdv.tools.brightness.ConverterSetup: Deprecated.
setViewerState(ViewerState) - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer: Deprecated.
setViewerState(ViewerState) - Method in class bdv.viewer.overlay.ScaleBarOverlayRenderer: Deprecated.
setViewerState(ViewerState) - Method in class bdv.viewer.overlay.SourceInfoOverlayRenderer: Deprecated.
setViewerState(ViewerState) - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer: Update data to show in the box overlay.
setViewerState(ViewerState) - Method in class bdv.viewer.overlay.ScaleBarOverlayRenderer: Update data to show in the overlay.
setViewerState(ViewerState) - Method in class bdv.viewer.overlay.SourceInfoOverlayRenderer: Update data to show in the overlay.
setViewerTransform(AffineTransform3D) - Method in class bdv.viewer.BasicViewerState
setViewerTransform(AffineTransform3D) - Method in class bdv.viewer.state.ViewerState: Deprecated.

Set the viewer transform.
setViewerTransform(AffineTransform3D) - Method in class bdv.viewer.SynchronizedViewerState
setViewerTransform(AffineTransform3D) - Method in interface bdv.viewer.ViewerState: Set the viewer transform (optional operation).
setVisible(boolean) - Method in class bdv.tools.boundingbox.BoundingBoxDialog: Deprecated.
setVisible(boolean) - Method in class bdv.tools.crop.CropDialog
setVisible(boolean) - Method in class bdv.tools.DelayedPackDialog
setVisible(boolean) - Method in class bdv.viewer.overlay.IntervalAndTransform
SharedQueue - Class in bdv.cache: Queue and threads for asynchronously loading data into a cache
SharedQueue - Class in bdv.util.volatiles: Deprecated.
This class lives now in bigdataviewer-core. Use bdv.cache.SharedQueue instead.
SharedQueue(int) - Constructor for class bdv.cache.SharedQueue
SharedQueue(int) - Constructor for class bdv.util.volatiles.SharedQueue: Deprecated.
SharedQueue(int, int) - Constructor for class bdv.cache.SharedQueue
SharedQueue(int, int) - Constructor for class bdv.util.volatiles.SharedQueue: Deprecated.
shareKeyPressedEvents(KeyPressedManager) - Method in class bdv.viewer.ViewerOptions: Set the KeyPressedManager to share KeyListener.keyPressed(java.awt.event.KeyEvent) events with other ui-behaviour windows.
shortLoader - Variable in class bdv.img.remote.RemoteImageLoader
show() - Static method in class bdv.util.BdvFunctions
show(BdvOptions) - Static method in class bdv.util.BdvFunctions
show(ChannelSources<T>) - Static method in class bdv.util.BdvFunctions
show(ChannelSources<T>, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(Source<T>) - Static method in class bdv.util.BdvFunctions
show(Source<T>, int) - Static method in class bdv.util.BdvFunctions
show(Source<T>, int, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(Source<T>, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(SourceAndConverter<T>) - Static method in class bdv.util.BdvFunctions
show(SourceAndConverter<T>, int) - Static method in class bdv.util.BdvFunctions
show(SourceAndConverter<T>, int, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(SourceAndConverter<T>, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(List<SourceAndConverter<T>>, int, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(AbstractSpimData<?>) - Static method in class bdv.util.BdvFunctions
show(AbstractSpimData<?>, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(RandomAccessible<T>, Interval, String) - Static method in class bdv.util.BdvFunctions
show(RandomAccessible<T>, Interval, String, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(RandomAccessibleInterval<ARGBType>, List<? extends VirtualChannels.VirtualChannel>, String) - Static method in class bdv.util.BdvFunctions
show(RandomAccessibleInterval<ARGBType>, List<? extends VirtualChannels.VirtualChannel>, String, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(RandomAccessibleInterval<T>, String) - Static method in class bdv.util.BdvFunctions
show(RandomAccessibleInterval<T>, String, BdvOptions) - Static method in class bdv.util.BdvFunctions
show(RealRandomAccessible<T>, Interval, String) - Static method in class bdv.util.BdvFunctions
show(RealRandomAccessible<T>, Interval, String, BdvOptions) - Static method in class bdv.util.BdvFunctions
SHOW_HELP - Static variable in class bdv.BigDataViewerActions
SHOW_HELP_KEYS - Static variable in class bdv.BigDataViewerActions
showAdvanced(boolean) - Method in class bdv.tools.brightness.BrightnessDialog.MinMaxPanel: Deprecated.
showAdvanced(boolean) - Method in class bdv.tools.brightness.BrightnessDialog.MinMaxPanels: Deprecated.
showCornerHandles(boolean) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
showDebugTileOverlay() - Method in class bdv.viewer.ViewerPanel: Display overlay to show how the display is tiled for rendering.
showMessage(String) - Method in class bdv.viewer.AbstractViewerPanel: Display the specified message in a text overlay for a short time.
showMessage(String) - Method in class bdv.viewer.ViewerPanel: Display the specified message in a text overlay for a short time.
showMultibox() - Method in class bdv.ui.appearance.Appearance
showMultibox() - Static method in class bdv.util.Prefs
showMultibox(boolean) - Static method in class bdv.util.Prefs
showOverlay(O, String) - Static method in class bdv.util.BdvFunctions
showOverlay(O, String, BdvOptions) - Static method in class bdv.util.BdvFunctions
showPage(String) - Method in class bdv.ui.settings.SettingsPanel: Shows the settings page with the specified path.
showPoints(List<? extends RealLocalizable>, String) - Static method in class bdv.util.BdvFunctions
showPoints(List<? extends RealLocalizable>, String, BdvOptions) - Static method in class bdv.util.BdvFunctions
showScaleBar() - Method in class bdv.ui.appearance.Appearance
showScaleBar() - Static method in class bdv.util.Prefs
showScaleBar(boolean) - Static method in class bdv.util.Prefs
showScaleBarInMovie() - Method in class bdv.ui.appearance.Appearance
showScaleBarInMovie() - Static method in class bdv.util.Prefs
showScaleBarInMovie(boolean) - Static method in class bdv.util.Prefs
showTextOverlay() - Method in class bdv.ui.appearance.Appearance
showTextOverlay() - Static method in class bdv.util.Prefs
showTextOverlay(boolean) - Static method in class bdv.util.Prefs
shutdown() - Method in class bdv.cache.SharedQueue
SimilarityTransformAnimator - Class in bdv.viewer.animate
SimilarityTransformAnimator(AffineTransform3D, AffineTransform3D, double, double, long) - Constructor for class bdv.viewer.animate.SimilarityTransformAnimator
SimpleCacheArrayLoader<A extends net.imglib2.img.basictypeaccess.DataAccess> - Interface in bdv.img.cache: Provider of volatile Cell data.
SimpleSettingsPage - Class in bdv.ui.settings: Helper class to easily put a JPanel as a page into a SettingsPanel.
SimpleSettingsPage(String, JPanel) - Constructor for class bdv.ui.settings.SimpleSettingsPage
SimpleVolatileProjector<A,B> - Class in bdv.viewer.render: An VolatileProjector, that renders a target 2D RandomAccessibleInterval by copying values from a source RandomAccessible.
SimpleVolatileProjector(RandomAccessible<A>, Converter<? super A, B>, RandomAccessibleInterval) - Constructor for class bdv.viewer.render.SimpleVolatileProjector: Create new projector with the given source and a converter from source to target pixel type.
SINGLE - bdv.tools.boundingbox.BoxSelectionOptions.TimepointSelection
SINGLE - bdv.viewer.DisplayMode
SingleSettingsPanel - Class in bdv.ui.settings: Main panel for preferences dialogs with a single page.
SingleSettingsPanel(SettingsPage) - Constructor for class bdv.ui.settings.SingleSettingsPanel
size() - Method in class bdv.util.DefaultInterpolators
size() - Method in class bdv.util.WrappedList
size() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
SliderPanel - Class in bdv.tools.brightness: A JSlider with a JSpinner next to it, both modifying the same value.
SliderPanel(String, BoundedValue, int) - Constructor for class bdv.tools.brightness.SliderPanel: Create a SliderPanel to modify a given value.
SliderPanelDouble - Class in bdv.tools.brightness: A JSlider with a JSpinner next to it, both modifying the same value.
SliderPanelDouble(String, BoundedValueDouble, double) - Constructor for class bdv.tools.brightness.SliderPanelDouble: Create a SliderPanelDouble to modify a given value.
SliderPanelDouble.RangeListener - Interface in bdv.tools.brightness
snapshot() - Method in class bdv.viewer.BasicViewerState: Get a snapshot of this ViewerState.
snapshot() - Method in class bdv.viewer.SynchronizedViewerState: Get a snapshot of this ViewerState.
snapshot() - Method in interface bdv.viewer.ViewerState: Get a snapshot of this ViewerState.
source - Variable in class bdv.tools.transformation.TransformedSource
Source<T> - Interface in bdv.viewer: Provides image data for all timepoints of one view setup.
SOURCE_ACTIVITY_CHANGED - bdv.viewer.ViewerStateChange
SOURCE_ACTVITY_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
SOURCE_TO_GROUP_ASSIGNMENT_CHANGED - bdv.viewer.ViewerStateChange
SOURCE_TO_GROUP_ASSIGNMENT_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
SourceAndConverter<T> - Class in bdv.viewer: Data source (for one view setup) and a converter to ARGBType.
SourceAndConverter(Source<T>, Converter<T, ARGBType>) - Constructor for class bdv.viewer.SourceAndConverter
SourceAndConverter(Source<T>, Converter<T, ARGBType>, SourceAndConverter<? extends Volatile<T>>) - Constructor for class bdv.viewer.SourceAndConverter
SourceAndConverter(SourceAndConverter<T>) - Constructor for class bdv.viewer.SourceAndConverter: copy constructor
SourceGroup - Class in bdv.viewer: A SourceGroup handle.
SourceGroup - Class in bdv.viewer.state: Deprecated.
SourceGroup() - Constructor for class bdv.viewer.SourceGroup
SourceGroup(SourceGroup) - Constructor for class bdv.viewer.state.SourceGroup: Deprecated.
SourceGroup(ViewerState, SourceGroup) - Constructor for class bdv.viewer.state.SourceGroup: Deprecated.
SourceGroup(String) - Constructor for class bdv.viewer.state.SourceGroup: Deprecated.
sourceGroupsToXml(List<SourceGroup>) - Method in class bdv.viewer.state.XmlIoViewerState
SourceGroupTree - Class in bdv.ui.sourcegrouptree: A JTree that shows the source-groups of a ViewerState and allows to modify activeness and currentness, to add/remove sources to/from groups, and to add/remove/rename groups.
SourceGroupTree(ViewerState) - Constructor for class bdv.ui.sourcegrouptree.SourceGroupTree
SourceGroupTree(ViewerState, InputTriggerConfig) - Constructor for class bdv.ui.sourcegrouptree.SourceGroupTree
SourceGroupTree.SourceGroupTreeTransferHandler - Class in bdv.ui.sourcegrouptree: TransferHandler for transferring sources into a group of a SourceGroupTree via cut/copy/paste and drag and drop.
SourceGroupTreeModel - Class in bdv.ui.sourcegrouptree
SourceGroupTreeModel(ViewerState) - Constructor for class bdv.ui.sourcegrouptree.SourceGroupTreeModel
SourceGroupTreeTransferHandler(SourceGroupTree, ViewerState) - Constructor for class bdv.ui.sourcegrouptree.SourceGroupTree.SourceGroupTreeTransferHandler
sourceIds - Variable in class bdv.viewer.state.SourceGroup: Deprecated.
SourceInfoOverlayRenderer - Class in bdv.viewer.overlay: Render current source name and current timepoint of a ViewerState into a Graphics2D.
SourceInfoOverlayRenderer() - Constructor for class bdv.viewer.overlay.SourceInfoOverlayRenderer
sourceInterval - Variable in class bdv.viewer.overlay.IntervalAndTransform
sourceMipmapOrdering - Variable in class bdv.tools.transformation.TransformedSource: This is either the TransformedSource.source itself, if it implements MipmapOrdering, or a DefaultMipmapOrdering.
sourceName - Variable in class bdv.viewer.overlay.SourceInfoOverlayRenderer
sourceNameOverlayPosition - Variable in class bdv.viewer.overlay.SourceInfoOverlayRenderer
sourceNameOverlayPosition() - Method in class bdv.ui.appearance.Appearance
sourceNameOverlayPosition() - Static method in class bdv.util.Prefs
sourceNameOverlayPosition(Prefs.OverlayPosition) - Static method in class bdv.util.Prefs
sourceOrder() - Method in class bdv.viewer.BasicViewerState: Returns a Comparator that compares sources according to the order in which they occur in the sources list.
sourceOrder() - Method in class bdv.viewer.SynchronizedViewerState: Returns a Comparator that compares sources according to the order in which they occur in the sources list.
sourceOrder() - Method in interface bdv.viewer.ViewerState: Returns a Comparator that compares sources according to the order in which they occur in the sources list.
sources(ViewerPanel) - Method in class bdv.viewer.NavigationActions: Deprecated.
SourceState<T> - Class in bdv.viewer.state: Deprecated.
SourceState(SourceAndConverter<T>, ViewerState) - Constructor for class bdv.viewer.state.SourceState: Deprecated.
SourceState(SourceAndConverter<T>, ViewerState, SourceAndConverter<?>) - Constructor for class bdv.viewer.state.SourceState: Deprecated.
SourceState(SourceState<T>, ViewerState) - Constructor for class bdv.viewer.state.SourceState: Deprecated.

copy constructor
sourcesToXml(List<SourceState<?>>) - Method in class bdv.viewer.state.XmlIoViewerState
SourcesTransferable - Class in bdv.ui: Drag and Drop Transferable for a collection of sources.
SourcesTransferable(Collection<SourceAndConverter<?>>) - Constructor for class bdv.ui.SourcesTransferable
SourcesTransferable.SourceList - Class in bdv.ui
SourceTable - Class in bdv.ui.sourcetable: A JTable that shows the sources of a ViewerState and allows to modify activeness, currentness, as well as the color of the corresponding ConverterSetup.
SourceTable(ViewerState, ConverterSetups) - Constructor for class bdv.ui.sourcetable.SourceTable
SourceTable(ViewerState, ConverterSetups, InputTriggerConfig) - Constructor for class bdv.ui.sourcetable.SourceTable
SourceTableModel - Class in bdv.ui.sourcetable
SourceTableModel(ViewerState, ConverterSetups) - Constructor for class bdv.ui.sourcetable.SourceTableModel
SourceToConverterSetupBimap - Interface in bdv.viewer: Associates ConverterSetups to sources (SourceAndConverter).
sourceToViewer - Variable in class bdv.viewer.overlay.IntervalAndTransform
sourceTransform - Variable in class bdv.tools.transformation.TransformedSource: Extra transformation.
sourceTransform - Variable in class bdv.util.BdvOverlay
sourceTransform(double...) - Method in class bdv.util.BdvOptions: Set the transform of the BdvSource to be created to account for the given calibration (scaling of the source axes).
sourceTransform(AffineTransform3D) - Method in class bdv.util.BdvOptions: Set the transform of the BdvSource to be created.
SOURCETRANSFORM_AFFINE_TAG - Static variable in class bdv.tools.transformation.XmlIoTransformedSources
SOURCETRANSFORM_TAG - Static variable in class bdv.tools.transformation.XmlIoTransformedSources
SOURCETRANSFORM_TYPE_ATTRIBUTE_NAME - Static variable in class bdv.tools.transformation.XmlIoTransformedSources
SOURCETRANSFORM_TYPE_VALUE_AFFINE - Static variable in class bdv.tools.transformation.XmlIoTransformedSources
SOURCETRANSFORMS_TAG - Static variable in class bdv.tools.transformation.XmlIoTransformedSources
SpimDataMinimal - Class in bdv.spimdata
SpimDataMinimal() - Constructor for class bdv.spimdata.SpimDataMinimal
SpimDataMinimal(SpimDataMinimal, BasicImgLoader) - Constructor for class bdv.spimdata.SpimDataMinimal: create copy of a SpimDataMinimal with replaced BasicImgLoader
SpimDataMinimal(File, SequenceDescriptionMinimal, ViewRegistrations) - Constructor for class bdv.spimdata.SpimDataMinimal
spimSource - Variable in class bdv.viewer.SourceAndConverter: provides image data for all timepoints of one view.
SpimSource<T extends net.imglib2.type.numeric.NumericType<T>> - Class in bdv
SpimSource(AbstractSpimData<?>, int, String) - Constructor for class bdv.SpimSource
split(List<TimePoint>, List<? extends BasicViewSetup>, int, int, String) - Static method in class bdv.img.hdf5.Partition: Split a sequence into partitions, each containing a specified number of timepoints and setups.
splitEdge(double[], double[], GeneralPath, GeneralPath) - Method in class bdv.viewer.overlay.RenderBoxHelper
splitInputStackIntoSourceStacks(RandomAccessible<T>, Interval, AxisOrder) - Static method in enum bdv.util.AxisOrder
splitInputStackIntoSourceStacks(RandomAccessibleInterval<T>, AxisOrder) - Static method in enum bdv.util.AxisOrder
splitPanel - Variable in class bdv.util.BdvHandle
SplitPanel - Class in bdv.ui.splitpanel: A JSplitPane with a ViewerPanel on the left and a CardPanel on the right.
SplitPanel(AbstractViewerPanel, CardPanel) - Constructor for class bdv.ui.splitpanel.SplitPanel
state() - Method in class bdv.viewer.AbstractViewerPanel: Get the ViewerState.
state() - Method in class bdv.viewer.ViewerPanel: Get the ViewerState.
stateFromXml(Element) - Method in class bdv.viewer.ViewerPanel
stateToXml() - Method in class bdv.viewer.ViewerPanel
stop() - Method in class bdv.viewer.ViewerPanel: Stop the ViewerPanel.painterThread and shutdown rendering ExecutorService.
storeCachedAttributes(CachedGsonKeyValueN5Reader) - Static method in class bdv.export.n5.meta.AttributesCaching
storeProfile(T) - Method in interface bdv.ui.settings.SelectAndEditProfileSettingsPage.ProfileEditPanel
storeSliderSize() - Method in class bdv.tools.brightness.BrightnessDialog.MinMaxPanel: Deprecated.
stride() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
Style<S extends Style<S>> - Interface in bdv.ui.settings.style
styleForName(String) - Method in class bdv.ui.settings.style.AbstractStyleManager
StyleManager<M extends StyleManager<M,S>,S extends Style<S>> - Interface in bdv.ui.settings.style
StyleProfile<S extends Style<S>> - Class in bdv.ui.settings.style
StyleProfile(S, boolean) - Constructor for class bdv.ui.settings.style.StyleProfile
StyleProfileManager<M extends StyleManager<M,S>,S extends Style<S>> - Class in bdv.ui.settings.style
StyleProfileManager(M, M) - Constructor for class bdv.ui.settings.style.StyleProfileManager
subList(int, int) - Method in class bdv.util.WrappedList
SubTaskProgressWriter - Class in bdv.export
SubTaskProgressWriter(ProgressWriter, double, double) - Constructor for class bdv.export.SubTaskProgressWriter
suggestPoTBlockSize(double[], int) - Static method in class bdv.export.ProposeMipmaps: Propose block size such that each dimension is power-of-two, number of elements is as big as possible, but not larger than maxNumElements and the block (scaled by the voxelSize) is as close to square as possible given constraints 1 and 2.
suggestPoTBlockSize(double[], long[], int) - Static method in class bdv.export.ProposeMipmaps: Propose block size such that each dimension is power-of-two, number of elements is as big as possible, but not larger than maxNumElements and the block (scaled by the voxelSize) is as close to square as possible given constraints 1 and 2. Additionally, the full size[] of the image limits the number of bits spent in a particular dimension.
SUM - bdv.viewer.BlendMode
supportsColor() - Method in interface bdv.tools.brightness.ConverterSetup
supportsColor() - Method in class bdv.tools.brightness.RealARGBColorConverterSetup
supportsColor() - Method in class bdv.util.PlaceHolderConverterSetup
switchToNextMode() - Method in class bdv.viewer.BlendModeSwitcher
SynchronizedViewerState - Class in bdv.viewer: Maintains the BigDataViewer state and implements ViewerState to expose query and modification methods.
SynchronizedViewerState(ViewerState) - Constructor for class bdv.viewer.SynchronizedViewerState

T

targetRenderNanos(long) - Method in class bdv.util.BdvOptions: Set target rendering time in nanoseconds.
targetRenderNanos(long) - Method in class bdv.viewer.ViewerOptions: Set target rendering time in nanoseconds.
text - Variable in class bdv.viewer.animate.MessageOverlayAnimator.TextAnimator
text - Variable in class bdv.viewer.animate.TextOverlayAnimator
TextAnimator(String, long) - Constructor for class bdv.viewer.animate.MessageOverlayAnimator.TextAnimator
TextOverlayAnimator - Class in bdv.viewer.animate: Draw one line of text in the center or bottom right of the display.
TextOverlayAnimator(String, long) - Constructor for class bdv.viewer.animate.TextOverlayAnimator
TextOverlayAnimator(String, long, TextOverlayAnimator.TextPosition) - Constructor for class bdv.viewer.animate.TextOverlayAnimator
TextOverlayAnimator(String, long, TextOverlayAnimator.TextPosition, double, double) - Constructor for class bdv.viewer.animate.TextOverlayAnimator
TextOverlayAnimator(String, long, TextOverlayAnimator.TextPosition, double, double, Font) - Constructor for class bdv.viewer.animate.TextOverlayAnimator
TextOverlayAnimator.TextPosition - Enum in bdv.viewer.animate
texts - Variable in class bdv.viewer.animate.MessageOverlayAnimator
Tiles(List<Tile>, double, int, int) - Constructor for class bdv.viewer.render.DebugTilingOverlay.Tiles
time(ViewerPanel) - Method in class bdv.viewer.NavigationActions: Deprecated.
timeDimension() - Method in enum bdv.util.AxisOrder
timePointChanged(int) - Method in class bdv.util.PlaceHolderOverlayInfo
timePointChanged(int) - Method in interface bdv.viewer.TimePointListener
timepointId - Variable in class bdv.img.hdf5.ViewLevelId: The timepoint id (index).
TimePointListener - Interface in bdv.viewer
timePointListeners() - Method in class bdv.viewer.AbstractViewerPanel: Add/remove TimePointListener to notify about time-point changes.
timePointListeners() - Method in class bdv.viewer.ViewerPanel: Add/remove TimePointListener to notify about time-point changes.
timepointSelectionPanel - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
timepointSelectionPanel - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
TimepointSelectionPanel(AbstractViewerPanel, BoxSelectionOptions) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel
timePointsOrdered - Variable in class bdv.viewer.overlay.SourceInfoOverlayRenderer
timepointString - Variable in class bdv.viewer.overlay.SourceInfoOverlayRenderer
title(String) - Method in class bdv.tools.boundingbox.BoxSelectionOptions
toArray() - Method in class bdv.util.WrappedList
toArray(T[]) - Method in class bdv.util.WrappedList
toggle() - Method in class bdv.tools.transformation.ManualTransformationEditor
TOGGLE_BLEND_MODE - Static variable in class bdv.viewer.NavigationActions
TOGGLE_BLEND_MODE_KEYS - Static variable in class bdv.viewer.NavigationActions
TOGGLE_FUSED_MODE - Static variable in class bdv.viewer.NavigationActions
TOGGLE_FUSED_MODE_KEYS - Static variable in class bdv.viewer.NavigationActions
TOGGLE_GROUPING - Static variable in class bdv.viewer.NavigationActions
TOGGLE_GROUPING_KEYS - Static variable in class bdv.viewer.NavigationActions
TOGGLE_INTERPOLATION - Static variable in class bdv.viewer.NavigationActions
TOGGLE_INTERPOLATION_KEYS - Static variable in class bdv.viewer.NavigationActions
TOGGLE_SOURCE_VISIBILITY - Static variable in class bdv.viewer.NavigationActions
TOGGLE_SOURCE_VISIBILITY_KEYS_FORMAT - Static variable in class bdv.viewer.NavigationActions
toggleActiveGroupOrSource(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
toggleDialogAction(Dialog, String, String...) - Method in class bdv.BigDataViewerActions: Deprecated.
toggleDialogAction(Actions, Dialog, String, String...) - Static method in class bdv.BigDataViewerActions
ToggleDialogAction - Class in bdv.tools
ToggleDialogAction(String, Dialog) - Constructor for class bdv.tools.ToggleDialogAction
toggleInterpolation() - Method in class bdv.viewer.ViewerPanel: Switch to next interpolation mode.
toggleInterpolation(ViewerState) - Static method in class bdv.viewer.NavigationActions
toggleManualTransformation() - Method in class bdv.BigDataViewer
TOP_CENTER - bdv.ui.UIUtils.TextPosition
TOP_CENTER - bdv.util.Prefs.OverlayPosition
TOP_RIGHT - bdv.ui.UIUtils.TextPosition
TOP_RIGHT - bdv.util.Prefs.OverlayPosition
toPrefs() - Method in class bdv.ui.appearance.AppearanceManager: Deprecated.
Prefs will be replaced eventually by directly using Appearance in BDV
toString() - Method in class bdv.img.hdf5.DimsAndExistence
toString() - Method in class bdv.img.MipmapInfo
toString() - Method in class bdv.ui.appearance.Appearance
toString() - Method in class bdv.util.BoundedRange
toString() - Method in class bdv.util.Bounds
toString() - Method in class bdv.util.WrappedList
toString() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
toString(AffineTransform3D) - Static method in class bdv.util.Affine3DHelpers: Pretty-print the matrix content of an affine transform.
toXml() - Method in class bdv.tools.bookmarks.Bookmarks
toXml() - Method in class bdv.tools.brightness.SetupAssignments: Deprecated.

Serialize the state of this SetupAssignments to XML.
toXml() - Method in class bdv.tools.transformation.ManualTransformation
toXml(CatmaidImageLoader, File) - Method in class bdv.img.catmaid.XmlIoCatmaidImageLoader
toXml(Hdf5ImageLoader, File) - Method in class bdv.img.hdf5.XmlIoHdf5ImageLoader
toXml(ImarisImageLoader, File) - Method in class bdv.img.imaris.XmlIoImarisImageLoader
toXml(N5ImageLoader, File) - Method in class bdv.img.n5.XmlIoN5ImageLoader
toXml(N5ImageLoader, URI) - Method in class bdv.img.n5.XmlIoN5ImageLoader
toXml(OpenConnectomeImageLoader, File) - Method in class bdv.img.openconnectome.XmlIoOpenConnectomeImageLoader
toXml(RemoteImageLoader, File) - Method in class bdv.img.remote.XmlIoRemoteImageLoader
toXml(ManualSourceTransforms) - Method in class bdv.tools.transformation.XmlIoTransformedSources
toXml(ViewerState) - Method in class bdv.viewer.state.XmlIoViewerState
toXmlAffine(AffineTransform3D) - Method in class bdv.tools.transformation.XmlIoTransformedSources
transform(Collection<SourceAndConverter<?>>) - Method in class bdv.tools.transformation.ManualTransformationEditor: Initiate a manual transformation modifying the given sourcesToTransform.
transformBoundingBoxReal(RealInterval, AffineTransform3D) - Static method in class bdv.tools.boundingbox.BoundingBoxUtil
transformChanged(A) - Method in interface bdv.viewer.TransformListener
transformChanged(AffineTransform3D) - Method in class bdv.tools.boundingbox.TransformedBoxOverlay
transformChanged(AffineTransform3D) - Method in class bdv.tools.transformation.ManualTransformationEditor
transformChanged(AffineTransform3D) - Method in class bdv.util.PlaceHolderOverlayInfo
TransformedBox - Interface in bdv.tools.boundingbox: A transformed box (to display in a TransformedBoxOverlay).
TransformedBoxEditor - Class in bdv.tools.boundingbox: Installs an interactive box selection tool on a BDV.
TransformedBoxEditor(InputTriggerConfig, AbstractViewerPanel, ConverterSetups, int, TriggerBehaviourBindings, AbstractTransformedBoxModel) - Constructor for class bdv.tools.boundingbox.TransformedBoxEditor
TransformedBoxEditor(InputTriggerConfig, AbstractViewerPanel, ConverterSetups, int, TriggerBehaviourBindings, AbstractTransformedBoxModel, String, TransformedBoxEditor.BoxSourceType) - Constructor for class bdv.tools.boundingbox.TransformedBoxEditor
TransformedBoxEditor.BoxSourceType - Enum in bdv.tools.boundingbox
TransformedBoxModel - Class in bdv.tools.boundingbox
TransformedBoxModel(ModifiableInterval, AffineTransform3D) - Constructor for class bdv.tools.boundingbox.TransformedBoxModel
TransformedBoxModel(Interval, AffineTransform3D) - Constructor for class bdv.tools.boundingbox.TransformedBoxModel
TransformedBoxOverlay - Class in bdv.tools.boundingbox: A BDV OverlayRenderer showing a TransformedBox.
TransformedBoxOverlay(TransformedBox) - Constructor for class bdv.tools.boundingbox.TransformedBoxOverlay
TransformedBoxOverlay(Interval) - Constructor for class bdv.tools.boundingbox.TransformedBoxOverlay
TransformedBoxOverlay.BoxDisplayMode - Enum in bdv.tools.boundingbox: Specifies whether to show 3D wireframe box (FULL), or only intersection with viewer plane (SECTION).
TransformedBoxOverlay.HighlightedCornerListener - Interface in bdv.tools.boundingbox
TransformedBoxOverlaySource - Class in bdv.tools.boundingbox: A BDV source (and converter etc) representing a TransformedBox.
TransformedBoxOverlaySource(String, TransformedBoxOverlay, TransformedBox, AbstractViewerPanel, ConverterSetups, int) - Constructor for class bdv.tools.boundingbox.TransformedBoxOverlaySource
TransformedBoxSelectionDialog - Class in bdv.tools.boundingbox
TransformedBoxSelectionDialog(AbstractViewerPanel, ConverterSetups, int, InputTriggerConfig, TriggerBehaviourBindings, AffineTransform3D, Interval, Interval, BoxSelectionOptions) - Constructor for class bdv.tools.boundingbox.TransformedBoxSelectionDialog
TransformedBoxSelectionDialog.Result - Class in bdv.tools.boundingbox
TransformedRealBoxModel - Class in bdv.tools.boundingbox
TransformedRealBoxModel(ModifiableRealInterval, AffineTransform3D) - Constructor for class bdv.tools.boundingbox.TransformedRealBoxModel
TransformedRealBoxModel(RealInterval, AffineTransform3D) - Constructor for class bdv.tools.boundingbox.TransformedRealBoxModel
TransformedRealBoxSelectionDialog - Class in bdv.tools.boundingbox
TransformedRealBoxSelectionDialog(AbstractViewerPanel, ConverterSetups, int, InputTriggerConfig, TriggerBehaviourBindings, AffineTransform3D, RealInterval, RealInterval, BoxSelectionOptions) - Constructor for class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
TransformedRealBoxSelectionDialog.Result - Class in bdv.tools.boundingbox
TransformedSource<T> - Class in bdv.tools.transformation: A Source that wraps another Source and allows to decorate it with an extra AffineTransform3D.
TransformedSource(Source<T>) - Constructor for class bdv.tools.transformation.TransformedSource: Instantiates a new TransformedSource wrapping the specified source with the identity transform.
TransformedSource(Source<T>, TransformedSource<?>) - Constructor for class bdv.tools.transformation.TransformedSource
TransformedSource(Source<T>, TransformedSource<?>, String) - Constructor for class bdv.tools.transformation.TransformedSource
TransformedSource(Source<T>, String) - Constructor for class bdv.tools.transformation.TransformedSource
TransformEventHandler - Interface in bdv: Change a transformation in response to user input (mouse events, key events, etc.)
TransformEventHandler2D - Class in bdv: A TransformEventHandler that changes an AffineTransform3D through a set of Behaviours.
TransformEventHandler2D(TransformState) - Constructor for class bdv.TransformEventHandler2D
TransformEventHandler2D.Descriptions - Class in bdv
TransformEventHandler3D - Class in bdv: A TransformEventHandler that changes an AffineTransform3D through a set of Behaviours.
TransformEventHandler3D(TransformState) - Constructor for class bdv.TransformEventHandler3D
TransformEventHandler3D.Descriptions - Class in bdv
transformEventHandlerFactory(TransformEventHandlerFactory) - Method in class bdv.util.BdvOptions
transformEventHandlerFactory(TransformEventHandlerFactory) - Method in class bdv.viewer.ViewerOptions
TransformEventHandlerFactory - Interface in bdv: Factory for TransformEventHandler.
TransformListener<A> - Interface in bdv.viewer
transformListeners() - Method in class bdv.viewer.AbstractViewerPanel: Add/remove TransformListeners to notify about viewer transformation changes.
transformListeners() - Method in class bdv.viewer.render.awt.BufferedImageOverlayRenderer: Add/remove TransformListeners to notify about viewer transformation changes.
transformListeners() - Method in class bdv.viewer.ViewerPanel: Add/remove TransformListeners to notify about viewer transformation changes.
transforms - Variable in class bdv.tools.transformation.ManualSourceTransforms
TransformState - Interface in bdv
TranslationAnimator - Class in bdv.viewer.animate: An animator that just executes a constant speed translation of the current viewpoint to a target location, keeping all other view parameters constant.
TranslationAnimator(AffineTransform3D, double[], long) - Constructor for class bdv.viewer.animate.TranslationAnimator
tryFetchTokenInfo(String, String, int) - Static method in class bdv.img.openconnectome.OpenConnectomeImageLoader: Try to fetch information for a token from an OpenConnectome volume cutout service, e.g.
tryFetchTokenList(String, int) - Static method in class bdv.img.openconnectome.OpenConnectomeImageLoader: Try to fetch the list of public tokens from an OpenConnectome volume cutout service, e.g.
tryInitTransform() - Method in class bdv.util.BdvHandle
tryLoadArray(int, int, int, int[], long[]) - Method in class bdv.img.openconnectome.OpenConnectomeVolatileArrayLoader
tryLoadSettings(String) - Method in class bdv.BigDataViewer
type - Variable in class bdv.AbstractViewerSetupImgLoader
type - Variable in class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
type - Variable in class bdv.util.AbstractSource
type - Variable in class bdv.util.RealRandomAccessibleSource
type() - Method in class bdv.img.n5.DataTypeProperties

U

UIUtils - Class in bdv.ui: AWT/Swing helpers.
UIUtils() - Constructor for class bdv.ui.UIUtils
UIUtils.TextPosition - Enum in bdv.ui
uninstall() - Method in class bdv.tools.boundingbox.TransformedBoxEditor
update() - Method in class bdv.tools.brightness.BrightnessDialog.MinMaxPanel: Deprecated.
update() - Method in interface bdv.tools.brightness.MinMaxGroup.UpdateListener
update() - Method in interface bdv.tools.brightness.SetupAssignments.UpdateListener: Deprecated.
update() - Method in class bdv.tools.brightness.SliderPanel
update() - Method in class bdv.tools.brightness.SliderPanelDouble
update() - Method in class bdv.tools.VisibilityAndGroupingDialog: Deprecated.
update() - Method in interface bdv.util.BoundedValue.UpdateListener
update() - Method in interface bdv.util.BoundedValueDouble.UpdateListener
update(int) - Method in class bdv.viewer.VisibilityAndGrouping: Deprecated.
updateInterval(double, double) - Method in class bdv.tools.brightness.MinMaxGroup
updateInterval(double, double) - Method in class bdv.util.BoundedIntervalDouble: This is called when the min or max values change.
updateInterval(int, int) - Method in class bdv.util.BoundedInterval: This is called when the min or max values change.
updateListeners - Variable in class bdv.viewer.VisibilityAndGrouping: Deprecated.
updateListeners() - Method in class bdv.ui.appearance.Appearance
updateListeners() - Method in class bdv.ui.keymap.Keymap
updateLookAndFeel() - Method in class bdv.ui.appearance.AppearanceManager
updateSelection() - Method in class bdv.tools.boundingbox.BoxSelectionPanel
updateSelection() - Method in class bdv.tools.boundingbox.RealBoxSelectionPanel
updateSetupParameters() - Method in interface bdv.util.VirtualChannels.VirtualChannel
updateSliders(Interval) - Method in class bdv.tools.boundingbox.BoxSelectionPanel
updateSliders(RealInterval) - Method in class bdv.tools.boundingbox.RealBoxSelectionPanel
updateUI() - Method in class bdv.ui.rangeslider.RangeSlider: Overrides the superclass method to install the UI delegate to draw two thumbs.
updateUI() - Method in class bdv.ui.settings.SettingsPanel
updateUI() - Method in class bdv.ui.sourcegrouptree.SourceGroupTree
updateUI() - Method in class bdv.ui.sourcetable.SourceTable
updateUI() - Method in class bdv.ui.splitpanel.SplitPanel
updateUI() - Method in class bdv.ui.viewermodepanel.DisplaySettingsPanel
updateUI() - Method in class bdv.ui.viewermodepanel.LabeledOptionButton
updateVirtualScreenSize(int, int) - Method in class bdv.viewer.overlay.MultiBoxOverlayRenderer: Update the screen interval.
updateVisibility() - Method in interface bdv.util.VirtualChannels.VirtualChannel
userStyles - Variable in class bdv.ui.settings.style.AbstractStyleManager
useVolatileIfAvailable(boolean) - Method in class bdv.viewer.ViewerOptions: Set whether volatile versions of sources should be used if available.
Util - Class in bdv.img.hdf5
Util() - Constructor for class bdv.img.hdf5.Util

V

valueForPathChanged(TreePath, Object) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
valueOf(String) - Static method in enum bdv.tools.boundingbox.BoxSelectionOptions.TimepointSelection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.tools.boundingbox.TransformedBoxEditor.BoxSourceType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.tools.boundingbox.TransformedBoxOverlay.BoxDisplayMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.ui.UIUtils.TextPosition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.util.AxisOrder: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.util.Prefs.OverlayPosition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.viewer.AbstractViewerPanel.AlignPlane: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.viewer.animate.TextOverlayAnimator.TextPosition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.viewer.BlendMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.viewer.DisplayMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.viewer.Interpolation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bdv.viewer.ViewerStateChange: Returns the enum constant of this type with the specified name.
values - Variable in class bdv.tools.boundingbox.BoxSelectionOptions
values - Variable in class bdv.util.BdvOptions
values - Variable in class bdv.viewer.ViewerOptions
values() - Static method in enum bdv.tools.boundingbox.BoxSelectionOptions.TimepointSelection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.tools.boundingbox.TransformedBoxEditor.BoxSourceType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.tools.boundingbox.TransformedBoxOverlay.BoxDisplayMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.ui.UIUtils.TextPosition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.util.AxisOrder: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.util.Prefs.OverlayPosition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.viewer.AbstractViewerPanel.AlignPlane: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.viewer.animate.TextOverlayAnimator.TextPosition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.viewer.BlendMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.viewer.DisplayMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.viewer.Interpolation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bdv.viewer.ViewerStateChange: Returns an array containing the constants of this enum type, in the order they are declared.
Values() - Constructor for class bdv.tools.boundingbox.BoxSelectionOptions.Values
Values() - Constructor for class bdv.viewer.ViewerOptions.Values
viewer - Variable in class bdv.BigDataViewer
viewer - Variable in class bdv.tools.boundingbox.TransformedBoxSelectionDialog
viewer - Variable in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog
viewer - Variable in class bdv.util.BdvHandle
VIEWER_TRANSFORM_CHANGED - bdv.viewer.ViewerStateChange
viewerFrame - Variable in class bdv.BigDataViewer
ViewerFrame - Class in bdv.viewer: A JFrame containing a ViewerPanel and associated InputActionBindings.
ViewerFrame(List<SourceAndConverter<?>>, int, CacheControl) - Constructor for class bdv.viewer.ViewerFrame
ViewerFrame(List<SourceAndConverter<?>>, int, CacheControl, KeymapManager, AppearanceManager, ViewerOptions) - Constructor for class bdv.viewer.ViewerFrame
ViewerImgLoader - Interface in bdv
ViewerOptions - Class in bdv.viewer: Optional parameters for ViewerPanel.
ViewerOptions() - Constructor for class bdv.viewer.ViewerOptions
ViewerOptions.Values - Class in bdv.viewer: Read-only ViewerOptions values.
ViewerPanel - Class in bdv.viewer: A JPanel for viewing multiple of Sources.
ViewerPanel(List<SourceAndConverter<?>>, int, CacheControl) - Constructor for class bdv.viewer.ViewerPanel
ViewerPanel(List<SourceAndConverter<?>>, int, CacheControl, ViewerOptions) - Constructor for class bdv.viewer.ViewerPanel
ViewerPanel.RenderThreadFactory - Class in bdv.viewer
ViewerSetupImgLoader<T,V extends net.imglib2.Volatile<T>> - Interface in bdv
ViewerState - Class in bdv.viewer.state: Deprecated.
ViewerState - Interface in bdv.viewer: Reading and writing the BigDataViewer state: interpolation and display mode contained sources and source groups activeness / currentness of sources and groups current timepoint and transformation
ViewerState(ViewerState) - Constructor for class bdv.viewer.state.ViewerState: Deprecated.

copy constructor
ViewerState(SynchronizedViewerState) - Constructor for class bdv.viewer.state.ViewerState: Deprecated.
ViewerState(List<SourceAndConverter<?>>, int) - Constructor for class bdv.viewer.state.ViewerState: Deprecated.
ViewerState(List<SourceAndConverter<?>>, List<SourceGroup>, int) - Constructor for class bdv.viewer.state.ViewerState: Deprecated.
VIEWERSTATE_CURRENTGROUP_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_CURRENTSOURCE_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_CURRENTTIMEPOINT_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_DISPLAYMODE_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_DISPLAYMODE_VALUE_FUSED - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_DISPLAYMODE_VALUE_FUSEDGROUP - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_DISPLAYMODE_VALUE_GROUP - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_DISPLAYMODE_VALUE_SINGLE - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_GROUP_ACTIVE_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_GROUP_NAME_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_GROUP_SOURCEID_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_GROUP_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_GROUPS_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_INTERPOLATION_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_INTERPOLATION_VALUE_NEARESTNEIGHBOR - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_INTERPOLATION_VALUE_NLINEAR - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_SOURCE_ACTIVE_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_SOURCE_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_SOURCES_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
VIEWERSTATE_TAG - Static variable in class bdv.viewer.state.XmlIoViewerState
ViewerStateChange - Enum in bdv.viewer: Types of BigDataViewer state changes that ViewerStateChangeListeners can be notified about.
viewerStateChanged(ViewerStateChange) - Method in class bdv.tools.VisibilityAndGroupingDialog.GroupingPanel: Deprecated.
viewerStateChanged(ViewerStateChange) - Method in class bdv.tools.VisibilityAndGroupingDialog.ModePanel: Deprecated.
viewerStateChanged(ViewerStateChange) - Method in class bdv.tools.VisibilityAndGroupingDialog.VisibilityPanel: Deprecated.
viewerStateChanged(ViewerStateChange) - Method in class bdv.util.PlaceHolderOverlayInfo
viewerStateChanged(ViewerStateChange) - Method in class bdv.viewer.ViewerPanel
viewerStateChanged(ViewerStateChange) - Method in interface bdv.viewer.ViewerStateChangeListener
ViewerStateChangeListener - Interface in bdv.viewer: ViewerStateChangeListeners are notified about BigDataViewer state changes.
ViewLevelId - Class in bdv.img.hdf5
ViewLevelId(int, int, int) - Constructor for class bdv.img.hdf5.ViewLevelId
ViewLevelId(ViewId, int) - Constructor for class bdv.img.hdf5.ViewLevelId
VirtualChannels - Class in bdv.util: The current application for VirtualChannel sources is the following scenario: We have a labeling and want to display it using lookup tables to convert labels to ARGBType.
VirtualChannels() - Constructor for class bdv.util.VirtualChannels
VirtualChannels.VirtualChannel - Interface in bdv.util
virtualScreenInterval - Variable in class bdv.viewer.overlay.MultiBoxOverlayRenderer: scaled screenImage interval for MultiBoxOverlayRenderer.box rendering
VISIBILITY_AND_GROUPING - Static variable in class bdv.BigDataViewerActions
VISIBILITY_AND_GROUPING_KEYS - Static variable in class bdv.BigDataViewerActions
VISIBILITY_CHANGED - bdv.viewer.ViewerStateChange
VISIBILITY_CHANGED - Static variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
visibilityAndGrouping - Variable in class bdv.viewer.VisibilityAndGrouping.Event: Deprecated.
VisibilityAndGrouping - Class in bdv.viewer: Deprecated.
This is not necessary anymore, because ViewerState can be modified directly. (See ViewerPanel.state().) Manage visibility and currentness of sources and groups, as well as grouping of sources, and display mode.
VisibilityAndGrouping(ViewerState) - Constructor for class bdv.viewer.VisibilityAndGrouping: Deprecated.
VisibilityAndGrouping.Event - Class in bdv.viewer: Deprecated.
VisibilityAndGrouping.UpdateListener - Interface in bdv.viewer: Deprecated.
VisibilityAndGroupingDialog - Class in bdv.tools: Deprecated.
VisibilityAndGroupingDialog(Frame, ViewerState) - Constructor for class bdv.tools.VisibilityAndGroupingDialog: Deprecated.
VisibilityAndGroupingDialog(Frame, VisibilityAndGrouping) - Constructor for class bdv.tools.VisibilityAndGroupingDialog: Deprecated.
VisibilityAndGroupingDialog.GroupingPanel - Class in bdv.tools: Deprecated.
VisibilityAndGroupingDialog.ModePanel - Class in bdv.tools: Deprecated.
VisibilityAndGroupingDialog.VisibilityPanel - Class in bdv.tools: Deprecated.
visibilityChanged() - Method in interface bdv.util.PlaceHolderOverlayInfo.VisibilityChangeListener
visibilityChanged(VisibilityAndGrouping.Event) - Method in interface bdv.viewer.VisibilityAndGrouping.UpdateListener: Deprecated.
visibilityChangeListeners() - Method in class bdv.util.PlaceHolderOverlayInfo: Register VisibilityChangeListeners, that will be notified when the visibility of the source represented by this PlaceHolderOverlayInfo changes.
VisibilityPanel(ViewerState, BooleanSupplier) - Constructor for class bdv.tools.VisibilityAndGroupingDialog.VisibilityPanel: Deprecated.
VolatileCachedCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess> - Class in bdv.img.cache: A LazyCellImg for Volatile accesses.
VolatileCachedCellImg(CellGrid, Fraction, Function<NativeImg<T, ? super A>, T>, CacheHints, VolatileCachedCellImg.Get<Cell<A>>) - Constructor for class bdv.img.cache.VolatileCachedCellImg: Deprecated.
Construct with a VolatileCache using VolatileCachedCellImg(CellGrid, NativeType, CacheHints, VolatileCache).
VolatileCachedCellImg(CellGrid, T, CacheHints, VolatileCachedCellImg.Get<Cell<A>>) - Constructor for class bdv.img.cache.VolatileCachedCellImg: Deprecated.
Construct with a VolatileCache using VolatileCachedCellImg(CellGrid, NativeType, CacheHints, VolatileCache).
VolatileCachedCellImg(CellGrid, T, CacheHints, VolatileCache<Long, Cell<A>>) - Constructor for class bdv.img.cache.VolatileCachedCellImg
VolatileCachedCellImg.Get<T> - Interface in bdv.img.cache
VolatileCachedCellImg.VolatileCachedCells<T> - Class in bdv.img.cache
VolatileCachedCells(long[], VolatileCachedCellImg.Get<T>, CacheHints) - Constructor for class bdv.img.cache.VolatileCachedCellImg.VolatileCachedCells
VolatileGlobalCellCache - Class in bdv.img.cache
VolatileGlobalCellCache(int, int) - Constructor for class bdv.img.cache.VolatileGlobalCellCache: Create a new global cache with a new fetch queue served by the specified number of fetcher threads.
VolatileGlobalCellCache(BlockingFetchQueues<Callable<?>>) - Constructor for class bdv.img.cache.VolatileGlobalCellCache: Create a new global cache with the specified fetch queue.
VolatileGlobalCellCache.Key - Class in bdv.img.cache: Key for a cell identified by timepoint, setup, level, and index (flattened spatial coordinate).
VolatileHierarchyProjector<A extends net.imglib2.Volatile<?>,B extends net.imglib2.type.operators.SetZero> - Class in bdv.viewer.render: VolatileProjector for a hierarchy of Volatile inputs.
VolatileHierarchyProjector(List<? extends RandomAccessible<A>>, Converter<? super A, B>, RandomAccessibleInterval) - Constructor for class bdv.viewer.render.VolatileHierarchyProjector
VolatileHierarchyProjector(List<? extends RandomAccessible<A>>, Converter<? super A, B>, RandomAccessibleInterval, byte[]) - Constructor for class bdv.viewer.render.VolatileHierarchyProjector
VolatileProjector - Interface in bdv.viewer.render: Render a 2D target copying pixels from a nD source.
VolatileRandomAccessibleIntervalMipmapSource<T extends net.imglib2.type.numeric.NumericType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> - Class in bdv.util: Deprecated.
use VolatileSource
VolatileRandomAccessibleIntervalMipmapSource(RandomAccessibleIntervalMipmapSource<T>, Supplier<V>, SharedQueue) - Constructor for class bdv.util.VolatileRandomAccessibleIntervalMipmapSource: Deprecated.
VolatileRandomAccessibleIntervalMipmapSource(RandomAccessibleIntervalMipmapSource<T>, V, SharedQueue) - Constructor for class bdv.util.VolatileRandomAccessibleIntervalMipmapSource: Deprecated.
VolatileRandomAccessibleIntervalView<T,V extends net.imglib2.Volatile<T>> - Class in bdv.util.volatiles
VolatileRandomAccessibleIntervalView(VolatileViewData<T, V>) - Constructor for class bdv.util.volatiles.VolatileRandomAccessibleIntervalView
VolatileRandomAccessibleView<T,V extends net.imglib2.Volatile<T>> - Class in bdv.util.volatiles
VolatileRandomAccessibleView(VolatileViewData<T, V>) - Constructor for class bdv.util.volatiles.VolatileRandomAccessibleView
VolatileSource<T extends net.imglib2.type.numeric.NumericType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> - Class in bdv.util
VolatileSource(Source<T>, Supplier<V>, SharedQueue) - Constructor for class bdv.util.VolatileSource
VolatileSource(Source<T>, V, SharedQueue) - Constructor for class bdv.util.VolatileSource
volatileSourceAndConverter - Variable in class bdv.viewer.SourceAndConverter
VolatileSpimSource<V extends net.imglib2.Volatile<?> & net.imglib2.type.numeric.NumericType<V>> - Class in bdv
VolatileSpimSource(AbstractSpimData<?>, int, String) - Constructor for class bdv.VolatileSpimSource
volatileType - Variable in class bdv.AbstractViewerSetupImgLoader
volatileType - Variable in class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
volatileType() - Method in class bdv.img.n5.DataTypeProperties
VolatileTypeMatcher - Class in bdv.util.volatiles
VolatileTypeMatcher() - Constructor for class bdv.util.volatiles.VolatileTypeMatcher
VolatileView<T,V extends net.imglib2.Volatile<T>> - Interface in bdv.util.volatiles: Something that provides VolatileViewData.
VolatileViewData<T,V extends net.imglib2.Volatile<T>> - Class in bdv.util.volatiles: Metadata associated with a VolatileView.
VolatileViewData(RandomAccessible<V>, CacheControl, T, V) - Constructor for class bdv.util.volatiles.VolatileViewData
VolatileViews - Class in bdv.util.volatiles: Wrap view cascades ending in CachedCellImg as volatile views.
VolatileViews() - Constructor for class bdv.util.volatiles.VolatileViews
voxelDimensions - Variable in class bdv.util.AbstractSource
voxelDimensions - Variable in class bdv.util.RealRandomAccessibleSource
voxelres - Variable in class bdv.img.openconnectome.OpenConnectomeDataset

W

width() - Method in class bdv.viewer.render.ProjectorUtils.ArrayData
width(int) - Method in class bdv.viewer.ViewerOptions: Set width of ViewerPanel canvas.
withFused(boolean) - Method in enum bdv.viewer.DisplayMode
withGrouping(boolean) - Method in enum bdv.viewer.DisplayMode
withMax(double) - Method in class bdv.util.BoundedRange
withMaxBound(double) - Method in class bdv.util.BoundedRange
withMin(double) - Method in class bdv.util.BoundedRange
withMinBound(double) - Method in class bdv.util.BoundedRange
wrapAsVolatile(RandomAccessible<T>) - Static method in class bdv.util.volatiles.VolatileViews
wrapAsVolatile(RandomAccessible<T>, SharedQueue) - Static method in class bdv.util.volatiles.VolatileViews
wrapAsVolatile(RandomAccessible<T>, SharedQueue, CacheHints) - Static method in class bdv.util.volatiles.VolatileViews
wrapAsVolatile(RandomAccessible<T>, SharedQueue) - Static method in class bdv.util.volatiles.VolatileViews: Deprecated.
Use bdv.cache.SharedQueue instead of bdv.util.volatiles.SharedQueue
wrapAsVolatile(RandomAccessible<T>, SharedQueue, CacheHints) - Static method in class bdv.util.volatiles.VolatileViews: Deprecated.
Use bdv.cache.SharedQueue instead of bdv.util.volatiles.SharedQueue
wrapAsVolatile(RandomAccessibleInterval<T>) - Static method in class bdv.util.volatiles.VolatileViews
wrapAsVolatile(RandomAccessibleInterval<T>, SharedQueue) - Static method in class bdv.util.volatiles.VolatileViews
wrapAsVolatile(RandomAccessibleInterval<T>, SharedQueue, CacheHints) - Static method in class bdv.util.volatiles.VolatileViews
wrapAsVolatile(RandomAccessibleInterval<T>, SharedQueue) - Static method in class bdv.util.volatiles.VolatileViews: Deprecated.
Use bdv.cache.SharedQueue instead of bdv.util.volatiles.SharedQueue
wrapAsVolatile(RandomAccessibleInterval<T>, SharedQueue, CacheHints) - Static method in class bdv.util.volatiles.VolatileViews: Deprecated.
Use bdv.cache.SharedQueue instead of bdv.util.volatiles.SharedQueue
WrapBasicImgLoader - Class in bdv.spimdata
WrapBasicImgLoader(BasicImgLoader, Map<Integer, ?>) - Constructor for class bdv.spimdata.WrapBasicImgLoader
wrapImgLoaderIfNecessary(AbstractSpimData<?>) - Static method in class bdv.spimdata.WrapBasicImgLoader: If the image loader of spimData is not a ViewerImgLoader, then replace it with a wrapper that presents it as ViewerImgLoader.
WrappedList<E> - Class in bdv.util: A List wrapper that forwards all calls to another List.
WrappedList(List<E>) - Constructor for class bdv.util.WrappedList
wrapWithTransformedSource(SourceAndConverter<T>) - Static method in class bdv.BigDataViewer: Decorate source with an extra transformation, that can be edited manually in this viewer.
writeBlock(D, DataBlock<?>) - Method in interface bdv.export.ExportScalePyramid.DatasetIO: Write the given dataBlock to the dataset.
writeHdf5File(AbstractSequenceDescription<?, ?, ?>, int[][], int[][], boolean, File, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, int, ProgressWriter) - Static method in class bdv.export.WriteSequenceToHdf5: Create a hdf5 file containing image data from all views and all timepoints in a chunked, mipmaped representation.
writeHdf5File(AbstractSequenceDescription<?, ?, ?>, Map<Integer, ExportMipmapInfo>, boolean, File, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, int, ProgressWriter) - Static method in class bdv.export.WriteSequenceToHdf5: Create a hdf5 file containing image data from all views and all timepoints in a chunked, mipmaped representation.
writeHdf5PartitionFile(AbstractSequenceDescription<?, ?, ?>, Map<Integer, ExportMipmapInfo>, boolean, Partition, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, int, ProgressWriter) - Static method in class bdv.export.WriteSequenceToHdf5: Create a hdf5 partition file containing image data for a subset of views and timepoints in a chunked, mipmaped representation.
writeHdf5PartitionLinkFile(AbstractSequenceDescription<?, ?, ?>, Map<Integer, ExportMipmapInfo>) - Static method in class bdv.export.WriteSequenceToHdf5: Create a hdf5 master file linking to image data from all views and all timepoints.
writeHdf5PartitionLinkFile(AbstractSequenceDescription<?, ?, ?>, Map<Integer, ExportMipmapInfo>, ArrayList<Partition>, File) - Static method in class bdv.export.WriteSequenceToHdf5: Create a hdf5 master file linking to image data from all views and all timepoints.
writeN5File(AbstractSequenceDescription<?, ?, ?>, Map<Integer, ExportMipmapInfo>, Compression, File, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, int, ProgressWriter) - Static method in class bdv.export.n5.WriteSequenceToN5: Create a n5 group containing image data from all views and all timepoints in a chunked, mipmaped representation.
writeScalePyramid(RandomAccessibleInterval<T>, T, ExportMipmapInfo, ExportScalePyramid.DatasetIO<D, T>, ExecutorService, int, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, ProgressWriter) - Static method in class bdv.export.ExportScalePyramid: Write an image to a chunked mipmap representation.
WriteSequenceToHdf5 - Class in bdv.export: Create a hdf5 files containing image data from all views and all timepoints in a chunked, mipmaped representation.
WriteSequenceToHdf5() - Constructor for class bdv.export.WriteSequenceToHdf5
WriteSequenceToN5 - Class in bdv.export.n5
WriteSequenceToN5() - Constructor for class bdv.export.n5.WriteSequenceToN5
writeViewToHdf5PartitionFile(RandomAccessibleInterval<UnsignedShortType>, int, int, ExportMipmapInfo, boolean, boolean, Hdf5BlockWriterThread, ExecutorService, int, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, ProgressWriter) - Static method in class bdv.export.WriteSequenceToHdf5: Deprecated.
writeViewToHdf5PartitionFile(RandomAccessibleInterval<UnsignedShortType>, Partition, int, int, ExportMipmapInfo, boolean, boolean, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, int, ProgressWriter) - Static method in class bdv.export.WriteSequenceToHdf5: Deprecated.
writeViewToHdf5PartitionFile(RandomAccessibleInterval<T>, T, int, int, ExportMipmapInfo, boolean, boolean, Hdf5BlockWriterThread, ExecutorService, int, ExportScalePyramid.LoopbackHeuristic, ExportScalePyramid.AfterEachPlane, ProgressWriter) - Static method in class bdv.export.WriteSequenceToHdf5: Write a single view to a hdf5 partition file, in a chunked, mipmaped representation.

X

XmlIoCatmaidImageLoader - Class in bdv.img.catmaid
XmlIoCatmaidImageLoader() - Constructor for class bdv.img.catmaid.XmlIoCatmaidImageLoader
XmlIoHdf5ImageLoader - Class in bdv.img.hdf5
XmlIoHdf5ImageLoader() - Constructor for class bdv.img.hdf5.XmlIoHdf5ImageLoader
XmlIoImarisImageLoader - Class in bdv.img.imaris
XmlIoImarisImageLoader() - Constructor for class bdv.img.imaris.XmlIoImarisImageLoader
XmlIoN5ImageLoader - Class in bdv.img.n5
XmlIoN5ImageLoader() - Constructor for class bdv.img.n5.XmlIoN5ImageLoader
XmlIoOpenConnectomeImageLoader - Class in bdv.img.openconnectome
XmlIoOpenConnectomeImageLoader() - Constructor for class bdv.img.openconnectome.XmlIoOpenConnectomeImageLoader
XmlIoRemoteImageLoader - Class in bdv.img.remote
XmlIoRemoteImageLoader() - Constructor for class bdv.img.remote.XmlIoRemoteImageLoader
XmlIoSpimDataMinimal - Class in bdv.spimdata
XmlIoSpimDataMinimal() - Constructor for class bdv.spimdata.XmlIoSpimDataMinimal
XmlIoSpimDataMinimalLegacy - Class in bdv.spimdata.legacy
XmlIoSpimDataMinimalLegacy() - Constructor for class bdv.spimdata.legacy.XmlIoSpimDataMinimalLegacy
XmlIoTransformedSources - Class in bdv.tools.transformation
XmlIoTransformedSources() - Constructor for class bdv.tools.transformation.XmlIoTransformedSources
XmlIoViewerState - Class in bdv.viewer.state
XmlIoViewerState() - Constructor for class bdv.viewer.state.XmlIoViewerState
XY - bdv.util.AxisOrder
XY - bdv.viewer.AbstractViewerPanel.AlignPlane
XYC - bdv.util.AxisOrder
XYCT - bdv.util.AxisOrder
XYCZ - bdv.util.AxisOrder
XYCZT - bdv.util.AxisOrder
XYT - bdv.util.AxisOrder
XYTC - bdv.util.AxisOrder
XYZ - bdv.util.AxisOrder
XYZC - bdv.util.AxisOrder
XYZCT - bdv.util.AxisOrder
XYZT - bdv.util.AxisOrder
XYZTC - bdv.util.AxisOrder
XZ - bdv.viewer.AbstractViewerPanel.AlignPlane

Z

zDimension() - Method in enum bdv.util.AxisOrder
ZOOM_FAST - Static variable in class bdv.TransformEventHandler2D
ZOOM_FAST_KEYS - Static variable in class bdv.TransformEventHandler2D
ZOOM_NORMAL - Static variable in class bdv.TransformEventHandler2D
ZOOM_NORMAL - Static variable in class bdv.TransformEventHandler3D
ZOOM_NORMAL_KEYS - Static variable in class bdv.TransformEventHandler2D
ZOOM_NORMAL_KEYS - Static variable in class bdv.TransformEventHandler3D
ZOOM_SLOW - Static variable in class bdv.TransformEventHandler2D
ZOOM_SLOW_KEYS - Static variable in class bdv.TransformEventHandler2D
ZY - bdv.viewer.AbstractViewerPanel.AlignPlane

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