All Classes Interface Summary Class Summary Enum Summary
| Class |
Description |
| AbstractAnimator |
Mother abstract class for animators that can animate the current view in a
ViewerFrame instance. |
| 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> |
|
| AbstractKeymapManager<T extends AbstractKeymapManager<T>> |
Manages a collection of Keymap. |
| AbstractLegacyViewerImgLoader<T,V extends net.imglib2.Volatile<T>> |
|
| AbstractSource<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| AbstractSpimSource<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| AbstractStyle<S extends AbstractStyle<S>> |
|
| AbstractStyleManager<M extends AbstractStyleManager<M,S>,S extends Style<S>> |
|
| AbstractTransformAnimator |
Mother abstract class for animators that animate the current view in a
ViewerFrame instance by modifying the viewer transform. |
| AbstractTransformedBoxModel |
A transformed box that can be modified and notifies listeners about changes.
|
| AbstractTransformedBoxModel.IntervalChangedListener |
|
| AbstractTransformedBoxSelectionDialog<R> |
|
| AbstractTransformedBoxSelectionDialog.OkCancelPanel |
A panel containing OK and Cancel buttons, and callback lists for both.
|
| AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel |
A panel that contains sliders to adjust timepoint, timepoint range, or
nothing.
|
| AbstractViewerPanel |
|
| AbstractViewerPanel.AlignPlane |
The planes which can be aligned with the viewer coordinate system: XY,
ZY, and XZ plane.
|
| AbstractViewerSetupImgLoader<T,V extends net.imglib2.Volatile<T>> |
|
| AccumulateProjector<A,B> |
|
| AccumulateProjectorARGB |
|
| AccumulateProjectorARGB.Factory |
|
| AccumulateProjectorFactory<A> |
|
| Affine3DHelpers |
Helpers to extract parts (rotation, scale, etc) from
AffineTransform3D.
|
| AffineTransform3DJsonSerializer |
|
| AlphaWeightedAccumulateProjectorARGB |
|
| AlphaWeightedAccumulateProjectorARGB.Factory |
|
| Appearance |
Appearance settings.
|
| Appearance.UpdateListener |
|
| AppearanceIO |
|
| AppearanceManager |
Manages the Appearance (save/load config file, propagate changes to
Prefs and LookAndFeel). |
| AppearanceSettingsPage |
|
| AttributesCaching |
|
| AWTUtils |
|
| AxisOrder |
|
| BasicViewerState |
Maintains the BigDataViewer state and implements ViewerState to
expose query and modification methods. |
| Bdv |
|
| BdvDefaultCards |
Default cards added to the card panel.
|
| BdvFunctions |
all show methods return a Bdv which can be used to add more stuff to the same window |
| BdvHandle |
Represents a BigDataViewer frame or panel and can be used to get to the bdv
internals.
|
| BdvHandleFrame |
|
| BdvHandlePanel |
|
| BdvN5Format |
|
| BdvOptions |
|
| BdvOptions.Values |
|
| BdvOverlay |
|
| BdvOverlaySource<O extends OverlayRenderer> |
|
| BdvPointsSource |
|
| BdvSource |
|
| BdvStackSource<T> |
|
| BdvVirtualChannelSource |
|
| BigDataViewer |
|
| BigDataViewerActions |
|
| BigDataViewerActions.Descriptions |
|
| BlendMode |
Blending modes.
|
| BlendModeSwitcher |
|
| BlendModeSwitcher.BlendModeChangeListener |
BlendModeChangeListeners are notified about blend mode changes.
|
| Bookmarks |
|
| BookmarksEditor |
|
| BookmarkTextOverlayAnimator |
Draw one line of text in the center or bottom right of the display.
|
| BoundedInterval |
A interval consisting of BoundedValue minimum and maximum that can
span any interval in a given range. |
| BoundedIntervalDouble |
A interval consisting of BoundedValueDouble minimum and maximum that can
span any interval in a given range. |
| BoundedRange |
A bounded range with minBound <= min <= max <= maxBound.
|
| BoundedValue |
A int variable that can take any value in a given range.
|
| BoundedValue.UpdateListener |
|
| BoundedValueDouble |
A double variable that can take any value in a given range.
|
| BoundedValueDouble.UpdateListener |
|
| BoundingBoxDialog |
Deprecated.
|
| BoundingBoxUtil |
|
| Bounds |
A range with minBound <= maxBound.
|
| BoxDisplayModePanel |
|
| BoxRealRandomAccessible<T extends net.imglib2.type.Type<T>> |
|
| BoxSelectionOptions |
|
| BoxSelectionOptions.TimepointSelection |
|
| BoxSelectionOptions.Values |
|
| BoxSelectionPanel |
A JPanel containing X,Y,Z,... min/max sliders for adjusting a
Interval
|
| BoxSelectionPanel.Box |
Provides current interval and receives interval changes.
|
| BrightnessDialog |
Deprecated. |
| BrightnessDialog.ColorsPanel |
|
| BrightnessDialog.MinMaxPanel |
A panel containing min/max SliderPanels, view setup check-boxes and advanced settings. |
| BrightnessDialog.MinMaxPanels |
|
| BufferedImageOverlayRenderer |
|
| BufferedImageRenderResult |
|
| CacheArrayLoader<A extends net.imglib2.img.basictypeaccess.DataAccess> |
Provider of volatile Cell data.
|
| CacheControl |
This is the part of the VolatileGlobalCellCache interface that is
exposed to the renderer directly (that is, not via images). |
| CacheControl.CacheControls |
|
| CacheControl.Dummy |
|
| CardPanel |
CardPanel handles components in named Cards which can be expanded or collapsed.
|
| CatmaidImageLoader |
|
| CatmaidVolatileIntArrayLoader |
|
| ChangeAttributeId |
|
| ChangeViewSetupId |
|
| ChannelSources<T> |
Channels of an image as a collection of sources. |
| CloseWindowActions |
|
| CloseWindowActions.Descriptions |
|
| ColorIcon |
Adapted from http://stackoverflow.com/a/3072979/230513
|
| ConstantRandomAccessible<T> |
A RandomAccessible that has a given constant value everywhere.
|
| ConverterSetup |
Modify the range and color of the converter for a source.
|
| ConverterSetup.SetupChangeListener |
|
| ConverterSetupBounds |
Map from ConverterSetup to Bounds on the range bounds to put
on the range slider.
|
| ConverterSetupEditPanel |
A JPanel containing a ColorPanel and a
BoundedRangePanel.
|
| ConverterSetups |
|
| CreateInvalidVolatileCell<A> |
A CreateInvalid that produces empty cells of
VolatileArrayDataAccess type A, with the correct dimensions,
etc.
|
| CropDialog |
|
| CropImgLoader |
This ImgLoader provides views and transformations into a cropped
region of a data-set (provided by list of Sources). |
| 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> |
Types and creators for N5 DataType.
|
| DebugTilingOverlay |
Overlay to show how the display is tiled for rendering.
|
| DebugTilingOverlay.Tiles |
|
| DefaultEmptyArrayCreator<A extends net.imglib2.img.basictypeaccess.volatiles.VolatileArrayDataAccess<A>> |
|
| DefaultInterpolators<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| DefaultMipmapOrdering |
The standard mipmap ordering strategy for local hdf5 data.
|
| DefaultN5Properties |
|
| DelayedPackDialog |
A JDialog that delays pack() calls until the dialog is made visible.
|
| DimsAndExistence |
The dimensions of an image and a flag indicating whether that image
exists (can be loaded)
|
| DisplayMode |
|
| DisplaySettingsPanel |
This panel adds buttons to toggle fused, grouped, and
interpolation mode.
|
| EmptyArrayCreator<A> |
Produce empty, invalid VolatileAccess to be used as placeholder
invalid cell data.
|
| EmptyProjector<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| ExportMipmapInfo |
|
| ExportScalePyramid |
Write an image to a chunked mipmap representation.
|
| ExportScalePyramid.AfterEachPlane |
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>> |
Writing and reading back data for each resolution level.
|
| ExportScalePyramid.DefaultLoopbackHeuristic |
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 |
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.
|
| HDF5AccessHack |
|
| Hdf5ImageLoader |
|
| HelpDialog |
|
| IHDF5Access |
|
| 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> |
|
| ImarisVolatileByteArrayLoader |
|
| ImarisVolatileFloatArrayLoader |
|
| ImarisVolatileShortArrayLoader |
|
| InitializeViewerState |
|
| InteractiveDisplay |
|
| InteractiveDisplayCanvas |
|
| Interpolation |
Interpolation methods.
|
| InterpolationModeListener |
|
| IntervalAndTransform |
|
| IntervalBoundingBox |
|
| IntervalCorners |
Utilities for computing the corners of a RealInterval.
|
| InvokeOnEDT |
|
| KeyConfigContexts |
Constants that specify to what context an action or a behaviour applies.
|
| KeyConfigScopes |
The CommandDescription scope used for actions and behaviours defined in BigDataViewer
|
| Keymap |
|
| Keymap.UpdateListener |
|
| KeymapManager |
Manages a collection of Keymap. |
| KeymapSettingsPage |
|
| LabeledOptionButton |
|
| LegacyViewerImgLoader<T,V extends net.imglib2.Volatile<T>> |
|
| LegacyViewerImgLoaderExtWrapper<T,V extends net.imglib2.Volatile<T>,I extends LegacyViewerImgLoader<T,V> & mpicbg.spim.data.legacy.LegacyImgLoader<T>> |
|
| LegacyViewerImgLoaderWrapper<T,V extends net.imglib2.Volatile<T>,I extends LegacyViewerImgLoader<T,V>> |
|
| ManualSourceTransforms |
|
| ManualTransformActiveListener |
|
| ManualTransformation |
|
| ManualTransformationEditor |
|
| MaskUtils |
|
| MergeExample |
|
| MergePartitionList |
|
| MergeTools |
|
| MessageOverlayAnimator |
Draw lines of text in the lower right corner of the display.
|
| MessageOverlayAnimator.TextAnimator |
|
| MinMaxGroup |
A double interval.
|
| MinMaxGroup.UpdateListener |
|
| MipmapInfo |
Description of available mipmap levels for a BasicViewSetup.
|
| MipmapOrdering |
|
| MipmapOrdering.Level |
|
| MipmapOrdering.MipmapHints |
|
| MipmapOrdering.PrefetchOrderComparator |
|
| MipmapOrdering.RenderOrderComparator |
|
| MipmapTransforms |
|
| ModifiableInterval |
|
| ModifiableRealInterval |
|
| ModificationListener |
A ModificationListener to a SettingsPage is notified, when
any setting is changed. |
| MultiBoxOverlay |
Paint an overlay showing multiple transformed boxes (interval + transform).
|
| MultiBoxOverlay.IntervalAndTransform |
|
| MultiBoxOverlayRenderer |
|
| MultiResolutionRenderer |
A renderer that uses a coarse-to-fine rendering scheme.
|
| N5ImageLoader |
|
| N5Properties |
Provides metadata and resolves dataset path names for (`setupId`,
`timePointId` and multiresolution `level`) triples.
|
| NavigationActions |
|
| NavigationActions.Descriptions |
|
| OpenConnectomeDataset |
|
| OpenConnectomeImageLoader |
|
| OpenConnectomeProject |
oenconnecto.me project as specified by example at
|
| OpenConnectomeTokenInfo |
|
| OpenConnectomeVolatileArrayLoader |
|
| OverlayAnimator |
|
| OverlayRenderer |
Draw something to a Graphics canvas and receive notifications about
changes of the canvas size. |
| PainterThread |
Thread to repaint display.
|
| PainterThread.Paintable |
|
| Partition |
Partition describes one partition file of a dataset that is split across
multiple hdf5 files.
|
| PlaceHolderConverterSetup |
|
| PlaceHolderOverlayInfo |
|
| PlaceHolderOverlayInfo.VisibilityChangeListener |
|
| PlaceHolderSource |
|
| PointsOverlay |
|
| PreferencesDialog |
|
| Prefetcher |
|
| Prefs |
|
| Prefs.OverlayPosition |
|
| ProgressWriter |
|
| ProgressWriterConsole |
|
| ProgressWriterNull |
|
| ProjectorUtils |
|
| ProjectorUtils.ArrayData |
|
| ProposeMipmaps |
Propose number of mipmap levels, as well subsampling factors and chunk size
for each level.
|
| RandomAccessibleIntervalMipmapSource<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| RandomAccessibleIntervalMipmapSource4D<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| RandomAccessibleIntervalSource<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| RandomAccessibleIntervalSource4D<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| RandomAccessibleSource<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| RandomAccessibleSource4D<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| RangeSlider |
An extension of JSlider to select a range of values using two thumb controls.
|
| RealARGBColorConverterSetup |
|
| RealBoxSelectionPanel |
A JPanel containing X,Y,Z,... min/max sliders for adjusting a
RealInterval
|
| RealBoxSelectionPanel.RealBox |
Provides current interval and receives interval changes.
|
| RealRandomAccessibleIntervalSource<T extends net.imglib2.type.Type<T>> |
|
| RealRandomAccessibleSource<T extends net.imglib2.type.Type<T>> |
A Source wrapping some RealRandomAccessible. |
| RecordMaxProjectionDialog |
|
| RecordMovieDialog |
|
| RemoteImageLoader |
|
| RemoteImageLoaderMetaData |
|
| RemoteVolatileShortArrayLoader |
|
| RenderBoxHelper |
Helper for rendering overlay boxes.
|
| RenderBoxHelper |
Helper for rendering overlay boxes.
|
| RenderResult |
Provides the renderer with a target image
( RandomAccessibleInterval<ARGBType>) to render to. |
| RenderTarget<R extends RenderResult> |
Receiver for a rendered image (to be drawn onto a canvas later).
|
| RequestRepaint |
|
| RotationAnimator |
|
| ScaleBarOverlayRenderer |
|
| SelectAndEditProfileSettingsPage<T extends SelectAndEditProfileSettingsPage.Profile> |
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.Profile |
|
| SelectAndEditProfileSettingsPage.ProfileEditPanel<T> |
Class that edits a profile of type T in a JPanel.
|
| SelectAndEditProfileSettingsPage.ProfileManager<T extends SelectAndEditProfileSettingsPage.Profile> |
Interface for classes that manage a collection of profiles.
|
| SequenceDescriptionMinimal |
|
| SettingsPage |
|
| SettingsPanel |
Main panel for preferences dialogs.
|
| SetupAssignments |
Deprecated. |
| SetupAssignments.UpdateListener |
|
| SharedQueue |
Queue and threads for asynchronously loading data into a cache
|
| SharedQueue |
Deprecated.
|
| SimilarityTransformAnimator |
|
| SimpleCacheArrayLoader<A extends net.imglib2.img.basictypeaccess.DataAccess> |
Provider of volatile Cell data.
|
| SimpleSettingsPage |
|
| SimpleVolatileProjector<A,B> |
An VolatileProjector, that renders a target 2D
RandomAccessibleInterval by copying values from a source
RandomAccessible. |
| SingleSettingsPanel |
Main panel for preferences dialogs with a single page.
|
| SliderPanel |
|
| SliderPanelDouble |
|
| SliderPanelDouble.RangeListener |
|
| Source<T> |
Provides image data for all timepoints of one view setup.
|
| SourceAndConverter<T> |
Data source (for one view setup) and a converter to ARGBType.
|
| SourceGroup |
A SourceGroup handle.
|
| SourceGroup |
Deprecated. |
| 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.SourceGroupTreeTransferHandler |
TransferHandler for transferring sources into a group of a SourceGroupTree via cut/copy/paste and drag and drop.
|
| SourceGroupTreeModel |
|
| SourceInfoOverlayRenderer |
|
| SourceState<T> |
Deprecated. |
| SourcesTransferable |
Drag and Drop Transferable for a collection of sources.
|
| SourcesTransferable.SourceList |
|
| 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. |
| SourceTableModel |
|
| SourceToConverterSetupBimap |
Associates ConverterSetups to sources (SourceAndConverter).
|
| SpimDataMinimal |
|
| SpimSource<T extends net.imglib2.type.numeric.NumericType<T>> |
|
| SplitPanel |
A JSplitPane with a ViewerPanel on the left and a
CardPanel on the right.
|
| Style<S extends Style<S>> |
|
| StyleManager<M extends StyleManager<M,S>,S extends Style<S>> |
|
| StyleProfile<S extends Style<S>> |
|
| StyleProfileManager<M extends StyleManager<M,S>,S extends Style<S>> |
|
| SubTaskProgressWriter |
|
| SynchronizedViewerState |
Maintains the BigDataViewer state and implements ViewerState to
expose query and modification methods. |
| TextOverlayAnimator |
Draw one line of text in the center or bottom right of the display.
|
| TextOverlayAnimator.TextPosition |
|
| TimePointListener |
|
| ToggleDialogAction |
|
| TransformedBox |
A transformed box (to display in a TransformedBoxOverlay).
|
| TransformedBoxEditor |
Installs an interactive box selection tool on a BDV.
|
| TransformedBoxEditor.BoxSourceType |
|
| TransformedBoxModel |
|
| TransformedBoxOverlay |
|
| TransformedBoxOverlay.BoxDisplayMode |
Specifies whether to show 3D wireframe box (FULL), or only
intersection with viewer plane (SECTION).
|
| TransformedBoxOverlay.HighlightedCornerListener |
|
| TransformedBoxOverlaySource |
A BDV source (and converter etc) representing a TransformedBox.
|
| TransformedBoxSelectionDialog |
|
| TransformedBoxSelectionDialog.Result |
|
| TransformedRealBoxModel |
|
| TransformedRealBoxSelectionDialog |
|
| TransformedRealBoxSelectionDialog.Result |
|
| TransformedSource<T> |
A Source that wraps another Source and allows to decorate it
with an extra AffineTransform3D. |
| TransformEventHandler |
Change a transformation in response to user input (mouse events, key events, etc.)
|
| TransformEventHandler2D |
|
| TransformEventHandler2D.Descriptions |
|
| TransformEventHandler3D |
|
| TransformEventHandler3D.Descriptions |
|
| TransformEventHandlerFactory |
Factory for TransformEventHandler.
|
| TransformListener<A> |
|
| TransformState |
|
| TranslationAnimator |
An animator that just executes a constant speed translation of the current
viewpoint to a target location, keeping all other view parameters constant.
|
| UIUtils |
AWT/Swing helpers.
|
| UIUtils.TextPosition |
|
| Util |
|
| ViewerFrame |
|
| ViewerImgLoader |
|
| ViewerOptions |
|
| ViewerOptions.Values |
|
| ViewerPanel |
A JPanel for viewing multiple of Sources. |
| ViewerPanel.RenderThreadFactory |
|
| ViewerSetupImgLoader<T,V extends net.imglib2.Volatile<T>> |
|
| ViewerState |
Deprecated. |
| ViewerState |
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
|
| ViewerStateChange |
|
| ViewerStateChangeListener |
|
| ViewLevelId |
|
| VirtualChannels |
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.VirtualChannel |
|
| VisibilityAndGrouping |
Deprecated.
|
| VisibilityAndGrouping.Event |
Deprecated. |
| VisibilityAndGrouping.UpdateListener |
Deprecated. |
| VisibilityAndGroupingDialog |
Deprecated. |
| VisibilityAndGroupingDialog.GroupingPanel |
|
| VisibilityAndGroupingDialog.ModePanel |
|
| VisibilityAndGroupingDialog.VisibilityPanel |
|
| VolatileCachedCellImg<T extends net.imglib2.type.NativeType<T>,A extends net.imglib2.img.basictypeaccess.DataAccess> |
A LazyCellImg for Volatile accesses.
|
| VolatileCachedCellImg.Get<T> |
|
| VolatileCachedCellImg.VolatileCachedCells<T> |
|
| VolatileGlobalCellCache |
|
| VolatileGlobalCellCache.Key |
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> |
|
| VolatileProjector |
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>> |
Deprecated.
|
| VolatileRandomAccessibleIntervalView<T,V extends net.imglib2.Volatile<T>> |
|
| VolatileRandomAccessibleView<T,V extends net.imglib2.Volatile<T>> |
|
| VolatileSource<T extends net.imglib2.type.numeric.NumericType<T>,V extends net.imglib2.Volatile<T> & net.imglib2.type.numeric.NumericType<V>> |
|
| VolatileSpimSource<V extends net.imglib2.Volatile<?> & net.imglib2.type.numeric.NumericType<V>> |
|
| VolatileTypeMatcher |
|
| VolatileView<T,V extends net.imglib2.Volatile<T>> |
|
| VolatileViewData<T,V extends net.imglib2.Volatile<T>> |
|
| VolatileViews |
Wrap view cascades ending in CachedCellImg as volatile views.
|
| WrapBasicImgLoader |
|
| WrappedList<E> |
A List wrapper that forwards all calls to another List. |
| WriteSequenceToHdf5 |
Create a hdf5 files containing image data from all views and all timepoints
in a chunked, mipmaped representation.
|
| WriteSequenceToN5 |
|
| XmlIoCatmaidImageLoader |
|
| XmlIoHdf5ImageLoader |
|
| XmlIoImarisImageLoader |
|
| XmlIoN5ImageLoader |
|
| XmlIoOpenConnectomeImageLoader |
|
| XmlIoRemoteImageLoader |
|
| XmlIoSpimDataMinimal |
|
| XmlIoSpimDataMinimalLegacy |
|
| XmlIoTransformedSources |
|
| XmlIoViewerState |
|