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

A

AbstractShader - Class in bvv.core.shadergen

AbstractShader(String, String) - Constructor for class bvv.core.shadergen.AbstractShader

AbstractShader(StringBuilder, StringBuilder) - Constructor for class bvv.core.shadergen.AbstractShader

accept(Map<SegmentType, SegmentTemplate>, Map<SegmentType, Segment>, int) - Method in interface bvv.core.render.MultiVolumeShaderMip.SegmentConsumer

Runs the lambda that was handed over, offering access to available segments, their instances, and the current volume index.

add(int[]) - Method in class bvv.core.blockmath.RequiredBlocks

add(Localizable) - Method in class bvv.core.blockmath.RequiredBlocks

addGLEventListener(GLEventListener) - Method in class bvv.core.InteractiveGLDisplayCanvas

addGroup(SourceGroup) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

addHandler(Object) - Method in class bvv.core.InteractiveGLDisplayCanvas

Add new event handler.

addOverlayAnimator(OverlayAnimator) - Method in class bvv.core.VolumeViewerPanel

Add a new OverlayAnimator to the list of animators.

addressOf(Buffer) - Static method in class bvv.core.blocks.ByteUtils

addSource(SourceAndConverter<?>) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

addSources(Collection<SourceAndConverter<?>>) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

addTimePointListener(TimePointListener) - Method in class bvv.core.VolumeViewerPanel

Add a TimePointListener to notify about time-point changes.

addTimePointListener(TimePointListener, int) - Method in class bvv.core.VolumeViewerPanel

Add a TimePointListener to notify about time-point changes.

addTo(Bvv) - Method in class bvv.vistools.BvvOptions

When showing content using one of the BvvFunctions methods, this option can be given to specify that the content should be added to an existing window.

addTo() - Method in class bvv.vistools.BvvOptions.Values

affine(AffineTransform3D, Matrix4f) - Static method in class bvv.core.util.MatrixMath

Apply a AffineTransform3D to the specified matrix.

appearanceManager(AppearanceManager) - Method in class bvv.core.VolumeViewerOptions

Set the AppearanceManager to share appearance settings with other BigVolumeViewer windows.

axisOrder(AxisOrder) - Method in class bvv.vistools.BvvOptions

Specified when adding a stack.

axisOrder() - Method in class bvv.vistools.BvvOptions.Values

B

bestLevel(Vector3fc, Vector3f) - Method in class bvv.core.blockmath.MipmapSizes

Get best resolution level at source coordinates x.

BigVolumeViewer - Class in bvv.core

BigVolumeViewer(List<ConverterSetup>, List<SourceAndConverter<?>>, int, CacheControl, String, VolumeViewerOptions) - Constructor for class bvv.core.BigVolumeViewer

BIGVOLUMEVIEWER - Static variable in interface bvv.core.KeyConfigContexts

The action or behaviour applies to the BVV views.

BIGVOLUMEVIEWER - Static variable in interface bvv.core.KeyConfigScopes

BigVolumeViewerActions - Class in bvv.core

BigVolumeViewerActions() - Constructor for class bvv.core.BigVolumeViewerActions

BigVolumeViewerActions.Descriptions - Class in bvv.core

Command descriptions for commands re-used from BigVolumeViewerActions, CloseWindowActions, NavigationActions, TransformEventHandler3D.

BigVolumeViewerCommand - Class in bvv.core

BigVolumeViewerCommand() - Constructor for class bvv.core.BigVolumeViewerCommand

bind(GL3) - Method in class bvv.core.dither.DitherBuffer

bind(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

Bind this framebuffer and clear it.

bind(GL3, boolean) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

bind(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

Bind this framebuffer and clear it.

bind(GL3, boolean) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

bind(String, Segment, String) - Method in class bvv.core.shadergen.generate.Segment

bind(String, Segment) - Method in class bvv.core.shadergen.generate.Segment

bind(String, int, Segment, String) - Method in class bvv.core.shadergen.generate.Segment

bind(String, int, Segment) - Method in class bvv.core.shadergen.generate.Segment

bindSamplers(GpuContext) - Method in class bvv.core.render.MultiVolumeShaderMip

bindSamplers(GpuContext) - Method in class bvv.core.shadergen.AbstractShader

bindSamplers(GpuContext) - Method in interface bvv.core.shadergen.Shader

bindStagingBuffer(StagingBuffer) - Method in interface bvv.core.backend.GpuContext

bindStagingBuffer(StagingBuffer) - Method in class bvv.core.backend.jogl.JoglGpuContext

bindStagingBufferId(int) - Method in interface bvv.core.backend.GpuContext

bindStagingBufferId(int) - Method in class bvv.core.backend.jogl.JoglGpuContext

bindTexture(Texture) - Method in interface bvv.core.backend.GpuContext

bindTexture(Texture, int) - Method in interface bvv.core.backend.GpuContext

bindTexture(Texture) - Method in class bvv.core.backend.jogl.JoglGpuContext

bindTexture(Texture, int) - Method in class bvv.core.backend.jogl.JoglGpuContext

bindTextureId(int, int) - Method in interface bvv.core.backend.GpuContext

bindTextureId(int, int) - Method in class bvv.core.backend.jogl.JoglGpuContext

blockSize() - Method in class bvv.core.cache.CacheSpec

Get the size of a block without interpolation padding.

build() - Method in class bvv.core.shadergen.generate.SegmentedShaderBuilder

Bvv - Interface in bvv.vistools

Something that has a BvvHandle.

bvv.core - package bvv.core

bvv.core.backend - package bvv.core.backend

bvv.core.backend.jogl - package bvv.core.backend.jogl

bvv.core.blockmath - package bvv.core.blockmath

bvv.core.blocks - package bvv.core.blocks

bvv.core.cache - package bvv.core.cache

bvv.core.dither - package bvv.core.dither

bvv.core.multires - package bvv.core.multires

bvv.core.offscreen - package bvv.core.offscreen

bvv.core.render - package bvv.core.render

bvv.core.shadergen - package bvv.core.shadergen

bvv.core.shadergen.generate - package bvv.core.shadergen.generate

bvv.core.util - package bvv.core.util

bvv.vistools - package bvv.vistools

BvvFunctions - Class in bvv.vistools

all show methods return a Bvv which can be used to add more stuff to the same window

BvvFunctions() - Constructor for class bvv.vistools.BvvFunctions

BvvHandle - Class in bvv.vistools

Represents a BigVolumeViewer frame or panel and can be used to get to the bvv internals.

BvvHandle(BvvOptions) - Constructor for class bvv.vistools.BvvHandle

BvvHandleFrame - Class in bvv.vistools

bvvOptions - Variable in class bvv.vistools.BvvHandle

BvvOptions - Class in bvv.vistools

Optional parameters for BdvFunctions.

BvvOptions() - Constructor for class bvv.vistools.BvvOptions

BvvOptions.Values - Class in bvv.vistools

Read-only BvvOptions values.

BvvSource - Class in bvv.vistools

BvvSource(BvvHandle, int) - Constructor for class bvv.vistools.BvvSource

bvvSources - Variable in class bvv.vistools.BvvHandle

BvvStackSource<T> - Class in bvv.vistools

BvvStackSource(BvvHandle, int, T, List<ConverterSetup>, List<SourceAndConverter<T>>) - Constructor for class bvv.vistools.BvvStackSource

ByteToAddress() - Constructor for class bvv.core.blocks.CopySubArrayImp.ByteToAddress

ByteUtils - Class in bvv.core.blocks

ByteUtils() - Constructor for class bvv.core.blocks.ByteUtils

ByteUtils.Address - Interface in bvv.core.blocks

C

Cache() - Constructor for class bvv.core.blocks.TileAccess.Cache

cacheBlockSize(int[]) - Method in class bvv.core.VolumeViewerOptions

Sets the GPU cache tile size.

cacheBlockSize(int) - Method in class bvv.core.VolumeViewerOptions

Sets the GPU cache tile size.

cacheBlockSize(int[]) - Method in class bvv.vistools.BvvOptions

Sets the GPU cache tile size.

cacheBlockSize(int) - Method in class bvv.vistools.BvvOptions

Sets the GPU cache tile size.

cacheControl - Variable in class bvv.core.VolumeViewerPanel

cacheControls - Variable in class bvv.vistools.BvvHandle

CacheSpec - Class in bvv.core.cache

CacheSpec(Texture.InternalFormat, int, int, int) - Constructor for class bvv.core.cache.CacheSpec

CacheSpec(Texture.InternalFormat, int[]) - Constructor for class bvv.core.cache.CacheSpec

CacheSpec(Texture.InternalFormat, int[], int[], int[]) - Constructor for class bvv.core.cache.CacheSpec

canLoadCompletely(int[], int[], GridDataAccess<?>, boolean) - Method in class bvv.core.blocks.CopyGridBlock

canLoadCompletely(int[], boolean) - Method in class bvv.core.blocks.TileAccess

canLoadPartially(int[], int[], GridDataAccess<?>) - Method in class bvv.core.blocks.CopyGridBlock

canLoadPartially(int[]) - Method in class bvv.core.blocks.TileAccess

canvasSizeListeners() - Method in class bvv.core.InteractiveGLDisplayCanvas

CanvasSizeListeners can be added/removed here.

cards - Variable in class bvv.vistools.BvvHandle

Cells(AbstractCellImg<?, A, ? extends Cell<A>, ?>) - Constructor for class bvv.core.blocks.GridDataAccessImp.Cells

cellSize(int) - Method in interface bvv.core.blocks.GridDataAccess

Get the size of a standard cell in dimension d.

cellSize(int, int) - Method in interface bvv.core.blocks.GridDataAccess

From the position of a cell in the grid, compute the size of the cell in dimension d.

clearAttributes(ST) - Static method in class bvv.core.shadergen.generate.StringTemplateUtils

clearsubarray3d(T, int, int, int, int, int, int, int, int) - Method in interface bvv.core.blocks.CopySubArray

clearsubarray3d(ByteUtils.Address, int, int, int, int, int, int, int, int) - Method in class bvv.core.blocks.CopySubArrayImp.ByteToAddress

clearsubarray3d(ByteUtils.Address, int, int, int, int, int, int, int, int) - Method in class bvv.core.blocks.CopySubArrayImp.ShortToAddress

close() - Method in interface bvv.vistools.Bvv

close() - Method in class bvv.vistools.BvvHandle

close() - Method in class bvv.vistools.BvvHandleFrame

collapseCardPanel() - Method in class bvv.core.BigVolumeViewer

configDir - Static variable in class bvv.core.BigVolumeViewer

containsData() - Method in class bvv.core.cache.DefaultFillTask

containsData() - Method in interface bvv.core.cache.FillTask

copy(int[], int[], T, GridDataAccess<S>, CopySubArray<S, T>) - Method in class bvv.core.blocks.CopyGridBlock

Copy (non-aligned) block from cell grid.

copyBytes(byte[], long, long, long) - Static method in class bvv.core.blocks.ByteUtils

CopyGridBlock - Class in bvv.core.blocks

CopyGridBlock() - Constructor for class bvv.core.blocks.CopyGridBlock

copyShorts(short[], long, long, long) - Static method in class bvv.core.blocks.ByteUtils

CopySubArray<S,T> - Interface in bvv.core.blocks

copysubarray3d(S, int, int, int, int, int, T, int, int, int, int, int, int, int, int) - Method in interface bvv.core.blocks.CopySubArray

copysubarray3d(byte[], int, int, int, int, int, ByteUtils.Address, int, int, int, int, int, int, int, int) - Method in class bvv.core.blocks.CopySubArrayImp.ByteToAddress

copysubarray3d(short[], int, int, int, int, int, ByteUtils.Address, int, int, int, int, int, int, int, int) - Method in class bvv.core.blocks.CopySubArrayImp.ShortToAddress

CopySubArrayImp - Class in bvv.core.blocks

CopySubArrayImp() - Constructor for class bvv.core.blocks.CopySubArrayImp

CopySubArrayImp.ByteToAddress - Class in bvv.core.blocks

CopySubArrayImp.ShortToAddress - Class in bvv.core.blocks

createGLCanvas(int, int) - Static method in class bvv.core.InteractiveGLDisplayCanvas

Create a new InteractiveDisplayCanvas with a GLCanvas.

createGLJPanel(int, int) - Static method in class bvv.core.InteractiveGLDisplayCanvas

Create a new InteractiveDisplayCanvas with a GLJPanel.

currentAnimator - Variable in class bvv.core.VolumeViewerPanel

Current animator for viewer transform, or null.

D

dCam(double) - Method in class bvv.core.VolumeViewerOptions

Sets the distance from the camera to the z=0 plane.

dCam(double) - Method in class bvv.vistools.BvvOptions

Sets the distance from the camera to the z=0 plane.

dClip(double) - Method in class bvv.core.VolumeViewerOptions

dClip(double) - Method in class bvv.vistools.BvvOptions

dClipFar(double) - Method in class bvv.core.VolumeViewerOptions

Sets the visible distance from the z=0 plane away from the camera.

dClipFar(double) - Method in class bvv.vistools.BvvOptions

Sets the visible distance from the z=0 plane away from the camera.

dClipNear(double) - Method in class bvv.core.VolumeViewerOptions

Sets the visible distance from the z=0 plane towards the camera.

dClipNear(double) - Method in class bvv.vistools.BvvOptions

Sets the visible distance from the z=0 plane towards the camera.

DefaultFillTask - Class in bvv.core.cache

DefaultFillTask(ImageBlockKey<?>, Predicate<UploadBuffer>, BooleanSupplier) - Constructor for class bvv.core.cache.DefaultFillTask

fill.test() fills buffer and returns whether block data was complete

DefaultQuad - Class in bvv.core.util

DefaultQuad() - Constructor for class bvv.core.util.DefaultQuad

DefaultShader - Class in bvv.core.shadergen

DefaultShader(String, String) - Constructor for class bvv.core.shadergen.DefaultShader

DefaultSimpleStackManager - Class in bvv.core.render

DefaultSimpleStackManager() - Constructor for class bvv.core.render.DefaultSimpleStackManager

delete(Texture) - Method in interface bvv.core.backend.GpuContext

delete(Texture) - Method in class bvv.core.backend.jogl.JoglGpuContext

Descriptions() - Constructor for class bvv.core.BigVolumeViewerActions.Descriptions

display() - Method in class bvv.core.InteractiveGLDisplayCanvas

display - Variable in class bvv.core.VolumeViewerPanel

Canvas used for displaying the rendered image and overlays.

displayToGlobalCoordinates(double[]) - Method in class bvv.core.VolumeViewerPanel

Set gPos to the display coordinates at gPos transformed into the global coordinate system.

displayToGlobalCoordinates(P) - Method in class bvv.core.VolumeViewerPanel

Set gPos to the display coordinates at gPos transformed into the global coordinate system.

displayToGlobalCoordinates(double, double, RealPositionable) - Method in class bvv.core.VolumeViewerPanel

Set gPos to the display coordinates (x,y,0)^T transformed into the global coordinate system.

dither(GL3, int, int, int) - Method in class bvv.core.dither.DitherBuffer

DitherBuffer - Class in bvv.core.dither

DitherBuffer(int, int) - Constructor for class bvv.core.dither.DitherBuffer

DitherBuffer(int, int, int, int, int) - Constructor for class bvv.core.dither.DitherBuffer

DitherBuffer(int, int, int, int, int, IntFunction<Double>) - Constructor for class bvv.core.dither.DitherBuffer

DitherPattern - Class in bvv.core.dither

DitherPattern() - Constructor for class bvv.core.dither.DitherPattern

DitherPattern.DitherWeights - Class in bvv.core.dither

DitherWeights(float[][], float[]) - Constructor for class bvv.core.dither.DitherPattern.DitherWeights

ditherWidth(int) - Method in class bvv.core.VolumeViewerOptions

Sets the dither window width.

ditherWidth(int) - Method in class bvv.vistools.BvvOptions

Sets the dither window width.

DownSamplingScheme - Enum in bvv.core.multires

Down-sampling scheme for MultiResolutionStack3D.

draw(GL3, VolumeRenderer.RepaintType, OffScreenFrameBufferWithDepth, List<Stack3D<?>>, List<ConverterSetup>, Matrix4f, int, double) - Method in class bvv.core.render.VolumeRenderer

draw(GL3) - Method in class bvv.core.util.DefaultQuad

drawOverlays(Graphics) - Method in class bvv.core.VolumeViewerPanel

drawQuad(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

Render fullscreen quad with the texture.

drawQuad(GL3, int, int) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

drawQuad(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

Render fullscreen quad with the texture.

drawQuad(GL3, int, int) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

E

effectiveViewportHeight() - Method in class bvv.core.dither.DitherBuffer

effectiveViewportWidth() - Method in class bvv.core.dither.DitherBuffer

equals(Object) - Method in class bvv.core.cache.ImageBlockKey

equals(Object) - Method in class bvv.core.render.VolumeShaderSignature

equals(Object) - Method in class bvv.core.render.VolumeShaderSignature.VolumeSignature

expandAndFocusCardPanel() - Method in class bvv.core.BigVolumeViewer

F

fill(UploadBuffer) - Method in class bvv.core.cache.DefaultFillTask

fill(UploadBuffer) - Method in interface bvv.core.cache.FillTask

FillTask - Interface in bvv.core.cache

FindRequiredBlocks - Class in bvv.core.blockmath

FindRequiredBlocks() - Constructor for class bvv.core.blockmath.FindRequiredBlocks

findSuitableGridSize(CacheSpec, int) - Static method in class bvv.core.cache.TextureCache

Find suitable size of a 3D texture (in multiples of cacheSpec.paddedBlockSize()) such that it requires less than maxMemoryInMB, the texture is roughly square, and fits as many blocks as possible.

flush() - Method in class bvv.core.cache.PboChain

Finalize a batch of cache tile uploads.

format() - Method in class bvv.core.cache.CacheSpec

fragment(Segment) - Method in class bvv.core.shadergen.generate.SegmentedShaderBuilder

fragShift(int) - Method in class bvv.core.dither.DitherBuffer

frameTitle(String) - Method in class bvv.vistools.BvvOptions

Set the title of the BigDataViewer window.

freeSimpleVolumes(GpuContext) - Method in class bvv.core.render.DefaultSimpleStackManager

freeSimpleVolumes(GpuContext) - Method in interface bvv.core.render.SimpleStackManager

Free allocated resources associated to all stacks.

freeUnusedSimpleVolumes(GpuContext) - Method in class bvv.core.render.DefaultSimpleStackManager

Free allocated resources associated to all stacks that have not been requested since the last call to DefaultSimpleStackManager.freeUnusedSimpleVolumes(GpuContext).

freeUnusedSimpleVolumes(GpuContext) - Method in interface bvv.core.render.SimpleStackManager

Free allocated resources associated to all stacks that have not been requested since the last call to SimpleStackManager.freeUnusedSimpleVolumes(GpuContext).

fwd(int) - Method in interface bvv.core.blocks.GridDataAccess

G

GeomUtils - Class in bvv.core.blockmath

GeomUtils() - Constructor for class bvv.core.blockmath.GeomUtils

get(GL3) - Static method in class bvv.core.backend.jogl.JoglGpuContext

get() - Method in interface bvv.core.blocks.GridDataAccess

Get the primitive array with data of grid cell at current position.

get() - Method in class bvv.core.blocks.GridDataAccessImp.Cells

get() - Method in class bvv.core.blocks.GridDataAccessImp.VolatileCells

get(ResolutionLevel3D<?>, CacheSpec) - Method in class bvv.core.blocks.TileAccess.Cache

get(ImageBlockKey<?>) - Method in class bvv.core.cache.TextureCache

get(int, int, int) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

Get a value from the texture (downloaded by OffScreenFrameBuffer.unbind(GL3) or OffScreenFrameBuffer.getTexture(GL3))

get(int, int, int) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

Get a value from the texture (downloaded by OffScreenFrameBufferWithDepth.unbind(GL3) or OffScreenFrameBufferWithDepth.getTexture(GL3))

getAddress() - Method in interface bvv.core.blocks.ByteUtils.Address

getAddress() - Method in class bvv.core.cache.UploadBuffer

...tentative...

getAppearanceManager() - Method in class bvv.core.BigVolumeViewer

getAppearanceManager() - Method in class bvv.core.VolumeViewerOptions.Values

getBaseLevel() - Method in class bvv.core.blockmath.MipmapSizes

Highest required resolution (lowest level) for any visible block

getBaseLevel() - Method in class bvv.core.render.VolumeBlocks

Get the base resolution level for rendering the volume.

getBaseLevelVoxelSizeInWorldCoordinates() - Method in class bvv.core.render.VolumeBlocks

Get the size of a voxel at base resolution in world coordinates.

getBestLevel() - Method in class bvv.core.blockmath.RequiredBlock

getBigVolumeViewer() - Method in class bvv.vistools.BvvHandleFrame

getBlocks() - Method in class bvv.core.blockmath.RequiredBlocks

getBuffer() - Method in class bvv.core.cache.UploadBuffer

Stores data for uploading to texture tile.

getBvvHandle() - Method in interface bvv.vistools.Bvv

getBvvHandle() - Method in class bvv.vistools.BvvHandle

getBvvHandle() - Method in class bvv.vistools.BvvSource

getBytesPerElement() - Method in enum bvv.core.backend.Texture.InternalFormat

getCacheBlockSize() - Method in class bvv.core.VolumeViewerOptions.Values

getCacheControl() - Method in class bvv.core.multires.SpimDataStacks

getCacheControl() - Method in interface bvv.core.multires.Stacks

getCardPanel() - Method in class bvv.core.VolumeViewerFrame

getCardPanel() - Method in class bvv.vistools.BvvHandle

getCode() - Method in class bvv.core.shadergen.generate.Segment

getCommandDescriptions(CommandDescriptions) - Method in class bvv.core.BigVolumeViewerActions.Descriptions

getComponent() - Method in class bvv.core.InteractiveGLDisplayCanvas

Implementing classes extend Component and return this.

getContentState() - Method in class bvv.core.cache.UploadBuffer

Was stored image block data complete?

getConverterSetups() - Method in class bvv.core.BigVolumeViewer

getConverterSetups() - Method in class bvv.core.VolumeViewerFrame

getConverterSetups() - Method in class bvv.core.VolumeViewerPanel

getConverterSetups() - Method in class bvv.vistools.BvvHandle

getConverterSetups() - Method in class bvv.vistools.BvvStackSource

getDCam() - Method in class bvv.core.render.RenderData

getDCam() - Method in class bvv.core.VolumeViewerOptions.Values

getDClipFar() - Method in class bvv.core.render.RenderData

getDClipFar() - Method in class bvv.core.VolumeViewerOptions.Values

getDClipNear() - Method in class bvv.core.render.RenderData

getDClipNear() - Method in class bvv.core.VolumeViewerOptions.Values

getDefaultSegments(boolean) - Static method in class bvv.core.render.MultiVolumeShaderMip

getDepthImg() - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

getDepthTexture() - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

getDisplay() - Method in class bvv.core.VolumeViewerPanel

Get the viewer canvas.

getDisplayComponent() - Method in class bvv.core.VolumeViewerPanel

Get the AWT Component of the viewer canvas.

getDitherBuffer() - Method in class bvv.core.dither.DitherBuffer

getDitherWidth() - Method in class bvv.core.VolumeViewerOptions.Values

getDownSamplingScheme() - Method in interface bvv.core.multires.MultiResolutionStack3D

getDrel(Vector3fc, Vector3f) - Method in class bvv.core.blockmath.MipmapSizes

getFillTasks() - Method in class bvv.core.render.VolumeBlocks

Sets up RequiredBlocks (internally) and creates a list of FillTasks for the cache to process.

getFragmentShaderCode() - Method in class bvv.core.shadergen.AbstractShader

getFragmentShaderCode() - Method in interface bvv.core.shadergen.Shader

getFrameTitle() - Method in class bvv.vistools.BvvOptions.Values

getGridPos() - Method in class bvv.core.blockmath.RequiredBlock

getGridPositions() - Method in class bvv.core.blockmath.RequiredBlocks

getHeight() - Method in class bvv.core.InteractiveGLDisplayCanvas

getHeight() - Method in class bvv.core.offscreen.OffScreenFrameBuffer

getHeight() - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

getHeight() - Method in class bvv.core.VolumeViewerOptions.Values

getImage() - Method in interface bvv.core.multires.ResolutionLevel3D

Get the image data for this resolution level.

getImage() - Method in interface bvv.core.multires.SimpleStack3D

Get the image data.

getImg() - Method in class bvv.core.offscreen.OffScreenFrameBuffer

getIms() - Method in class bvv.core.render.SimpleVolume

getIms() - Method in class bvv.core.render.VolumeBlocks

getInputTriggerConfig() - Method in class bvv.core.VolumeViewerOptions.Values

getInputTriggerConfig() - Method in class bvv.core.VolumeViewerPanel

getInputTriggerConfig() - Method in class bvv.vistools.BvvOptions.Values

getKey() - Method in class bvv.core.cache.DefaultFillTask

getKey() - Method in interface bvv.core.cache.FillTask

getKeybindings() - Method in class bvv.core.VolumeViewerFrame

getKeybindings() - Method in class bvv.vistools.BvvHandle

getKeybindings() - Method in class bvv.vistools.BvvHandleFrame

getKeymapManager() - Method in class bvv.core.BigVolumeViewer

getKeymapManager() - Method in class bvv.core.VolumeViewerOptions.Values

getKeyPressedManager() - Method in class bvv.core.VolumeViewerOptions.Values

getLevel() - Method in interface bvv.core.multires.ResolutionLevel3D

Get the index of this resolution level in the MultiResolutionStack3D By default, index 0 is the full resolution, and resolution level at index i>j has lower resolution (more down-sampled) than index j.

getLevelTransform() - Method in interface bvv.core.multires.ResolutionLevel3D

Get the transformation from image coordinates of this level to image coordinates of level 0 (full resolution).

getLookupTexture() - Method in class bvv.core.render.VolumeBlocks

getLutBlockScales(int) - Method in class bvv.core.render.VolumeBlocks

Set up lutBlockScales array for shader.

getManualTransformEditor() - Method in class bvv.core.BigVolumeViewer

getManualTransformEditor() - Method in class bvv.vistools.BvvHandle

getManualTransformEditor() - Method in class bvv.vistools.BvvHandleFrame

getMax() - Method in class bvv.core.blockmath.RequiredBlocks

getMaxAllowedStepInVoxels() - Method in class bvv.core.VolumeViewerOptions.Values

getMaxCacheSizeInMB() - Method in class bvv.core.VolumeViewerOptions.Values

getMaxNumTiles() - Method in class bvv.core.cache.TextureCache

getMaxRenderMillis() - Method in class bvv.core.VolumeViewerOptions.Values

getMin() - Method in class bvv.core.blockmath.RequiredBlocks

getMsgOverlay() - Method in class bvv.core.VolumeViewerOptions.Values

getNumDitherSamples() - Method in class bvv.core.VolumeViewerOptions.Values

getNumSourceGroups() - Method in class bvv.core.VolumeViewerOptions.Values

getNumTimepoints() - Method in class bvv.core.multires.SpimDataStacks

getNumTimepoints() - Method in interface bvv.core.multires.Stacks

getNumTimepoints() - Method in class bvv.vistools.BvvSource

getOffset() - Method in class bvv.core.cache.UploadBuffer

Starting offset for tile in buffer.

getOffset3f() - Method in class bvv.core.render.LookupTextureARGB

getOptionValues() - Method in class bvv.core.VolumeViewerPanel

getPboIdHack(StagingBuffer) - Method in class bvv.core.backend.jogl.JoglGpuContext

getPixelType() - Method in class bvv.core.render.VolumeShaderSignature.VolumeSignature

getPosition() - Method in interface bvv.core.blocks.GridDataAccess

getPrimitiveType(Object) - Static method in class bvv.core.blocks.TileAccess

getProgramIdHack(Shader) - Method in class bvv.core.backend.jogl.JoglGpuContext

getPv() - Method in class bvv.core.render.RenderData

getR() - Method in interface bvv.core.multires.ResolutionLevel3D

Get per-dimension down-sampling factors with respect to full resolution.

getRenderHeight() - Method in class bvv.core.VolumeViewerOptions.Values

getRenderTransformWorldToScreen() - Method in class bvv.core.render.RenderData

getRenderWidth() - Method in class bvv.core.VolumeViewerOptions.Values

getRequiredBlocks(ConvexPolytope, int[], long[], long[]) - Static method in class bvv.core.blockmath.FindRequiredBlocks

Given an interval split into regular blocks of size blockSize.

getRequiredLevelBlocksFrustum(Matrix4fc, int[], long[], long[]) - Static method in class bvv.core.blockmath.FindRequiredBlocks

Backproject NDC (-1,-1,-1) ... (1,1,1) to source image and find overlapping blocks.

getS() - Method in interface bvv.core.multires.ResolutionLevel3D

Get per-dimension scale factors with respect to full resolution.

getScreenHeight() - Method in class bvv.core.render.RenderData

getScreenWidth() - Method in class bvv.core.render.RenderData

getSetupAssignments() - Method in class bvv.core.BigVolumeViewer

Deprecated.

Instead getViewer().state() returns the ViewerState that can be modified directly.

getSetupAssignments() - Method in class bvv.vistools.BvvHandle

Deprecated.

getSf() - Method in class bvv.core.blockmath.MipmapSizes

getSimpleVolume(GpuContext, SimpleStack3D<?>) - Method in class bvv.core.render.DefaultSimpleStackManager

getSimpleVolume(GpuContext, SimpleStack3D<?>) - Method in interface bvv.core.render.SimpleStackManager

getSize() - Method in class bvv.core.InteractiveGLDisplayCanvas

getSize3f() - Method in class bvv.core.render.LookupTextureARGB

getSizeInBytes() - Method in interface bvv.core.backend.StagingBuffer

getSn() - Method in class bvv.core.blockmath.MipmapSizes

getSourceInfoOverlayRenderer() - Method in class bvv.core.VolumeViewerPanel

getSourceLevelMax() - Method in class bvv.core.render.VolumeBlocks

getSourceLevelMin() - Method in class bvv.core.render.VolumeBlocks

getSourceMax() - Method in class bvv.core.render.SimpleVolume

getSources() - Method in class bvv.vistools.BvvStackSource

getSourceStackType(Source<?>) - Static method in class bvv.core.multires.SourceStacks

getSourceStackType() - Method in class bvv.core.render.VolumeShaderSignature.VolumeSignature

getSourceTransform() - Method in interface bvv.core.multires.Stack3D

Get the transformation from image coordinates to world coordinates.

getSourceTransform() - Method in class bvv.vistools.BvvOptions.Values

getSplitPanel() - Method in class bvv.core.VolumeViewerFrame

getSplitPanel() - Method in class bvv.vistools.BvvHandle

getStack(int, int, boolean) - Method in class bvv.core.multires.SpimDataStacks

getStack(int, int, boolean) - Method in interface bvv.core.multires.Stacks

getStack3D(Source<T>, int) - Static method in class bvv.core.multires.SourceStacks

getState() - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Use VolumeViewerPanel.state() instead. Get a copy of the current ViewerState.

getStitchBuffer() - Method in class bvv.core.dither.DitherBuffer

getTexColorBuffer() - Method in class bvv.core.offscreen.OffScreenFrameBuffer

getTexture(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

getTexture(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

getTextureCache() - Method in class bvv.core.render.VolumeBlocks

getTextureIdHack(Texture) - Method in class bvv.core.backend.jogl.JoglGpuContext

getTimepoint() - Method in class bvv.core.render.RenderData

getTransformBehaviours() - Method in class bvv.core.VolumeViewerFrame

Get Behaviours hook where TransformEventHandler behaviours are installed.

getTransformEventHandler() - Method in class bvv.core.VolumeViewerPanel

getTransformEventHandlerFactory() - Method in class bvv.core.VolumeViewerOptions.Values

getTriggerbindings() - Method in class bvv.core.VolumeViewerFrame

getTriggerbindings() - Method in class bvv.vistools.BvvHandle

getTriggerbindings() - Method in class bvv.vistools.BvvHandleFrame

getType() - Method in interface bvv.core.multires.Typed

getUniform1f(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform1f(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform1f(String) - Method in interface bvv.core.shadergen.Shader

getUniform1fv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform1fv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform1fv(String) - Method in interface bvv.core.shadergen.Shader

getUniform1i(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform1i(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform1i(String) - Method in interface bvv.core.shadergen.Shader

getUniform1iv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform1iv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform1iv(String) - Method in interface bvv.core.shadergen.Shader

getUniform2f(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform2f(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform2f(String) - Method in interface bvv.core.shadergen.Shader

getUniform2fv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform2fv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform2fv(String) - Method in interface bvv.core.shadergen.Shader

getUniform2i(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform2i(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform2i(String) - Method in interface bvv.core.shadergen.Shader

getUniform2iv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform2iv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform2iv(String) - Method in interface bvv.core.shadergen.Shader

getUniform3f(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform3f(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform3f(String) - Method in interface bvv.core.shadergen.Shader

getUniform3fv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform3fv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform3fv(String) - Method in interface bvv.core.shadergen.Shader

getUniform3i(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform3i(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform3i(String) - Method in interface bvv.core.shadergen.Shader

getUniform3iv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform3iv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform3iv(String) - Method in interface bvv.core.shadergen.Shader

getUniform4f(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform4f(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform4f(String) - Method in interface bvv.core.shadergen.Shader

getUniform4fv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform4fv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform4fv(String) - Method in interface bvv.core.shadergen.Shader

getUniform4i(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform4i(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform4i(String) - Method in interface bvv.core.shadergen.Shader

getUniform4iv(String) - Method in class bvv.core.shadergen.AbstractShader

getUniform4iv(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniform4iv(String) - Method in interface bvv.core.shadergen.Shader

getUniformMatrix3f(String) - Method in class bvv.core.shadergen.AbstractShader

getUniformMatrix3f(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniformMatrix3f(String) - Method in interface bvv.core.shadergen.Shader

getUniformMatrix4f(String) - Method in class bvv.core.shadergen.AbstractShader

getUniformMatrix4f(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniformMatrix4f(String) - Method in interface bvv.core.shadergen.Shader

getUniformSampler(String) - Method in class bvv.core.shadergen.AbstractShader

getUniformSampler(Segment, String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUniformSampler(String) - Method in interface bvv.core.shadergen.Shader

getUniformSetter(Shader) - Method in interface bvv.core.backend.GpuContext

getUniformSetter(Shader) - Method in class bvv.core.backend.jogl.JoglGpuContext

getUniqueName(String) - Method in class bvv.core.shadergen.AbstractShader

getUniqueName(String) - Method in class bvv.core.shadergen.DefaultShader

getUniqueName(String) - Method in class bvv.core.shadergen.generate.SegmentedShader

getUnusedSetupId(BigDataViewer) - Static method in class bvv.vistools.BvvFunctions

getUnusedSetupId(SetupAssignments) - Static method in class bvv.vistools.BvvFunctions

getVertexShaderCode() - Method in class bvv.core.shadergen.AbstractShader

getVertexShaderCode() - Method in interface bvv.core.shadergen.Shader

getViewer() - Method in class bvv.core.BigVolumeViewer

getViewerFrame() - Method in class bvv.core.BigVolumeViewer

getViewerPanel() - Method in class bvv.core.VolumeViewerFrame

getViewerPanel() - Method in class bvv.vistools.BvvHandle

getVisibilityAndGrouping() - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.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.

getVolumeSignatures() - Method in class bvv.core.render.VolumeShaderSignature

getVolumeTexture() - Method in class bvv.core.render.SimpleVolume

getVolumeViewerOptions() - Method in class bvv.vistools.BvvOptions.Values

getVoxelSizeInWorldCoordinates() - Method in class bvv.core.render.SimpleVolume

Get the size of a voxel in world coordinates.

getWeights(int, int, int, int, int, int, int, double, int[], int[]) - Static method in class bvv.core.dither.DitherPattern

getWidth() - Method in class bvv.core.InteractiveGLDisplayCanvas

getWidth() - Method in class bvv.core.offscreen.OffScreenFrameBuffer

getWidth() - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

getWidth() - Method in class bvv.core.VolumeViewerOptions.Values

GpuContext - Interface in bvv.core.backend

GridDataAccess<T> - Interface in bvv.core.blocks

Access to data at positions in a cell grid.

GridDataAccessImp - Class in bvv.core.blocks

GridDataAccessImp.Cells<T,A extends net.imglib2.img.basictypeaccess.array.ArrayDataAccess<?>> - Class in bvv.core.blocks

Access to primitive data of Cells in a CellImg.

GridDataAccessImp.VolatileCells<T,A extends net.imglib2.img.basictypeaccess.volatiles.VolatileArrayDataAccess<?>> - Class in bvv.core.blocks

Access to primitive data of volatile Cells in a CellImg.

H

hashCode() - Method in class bvv.core.cache.ImageBlockKey

hashCode() - Method in class bvv.core.render.VolumeShaderSignature

hashCode() - Method in class bvv.core.render.VolumeShaderSignature.VolumeSignature

hasPlaceHolderSources - Variable in class bvv.vistools.BvvHandle

hasPreferredSize() - Method in class bvv.vistools.BvvOptions.Values

height(int) - Method in class bvv.core.VolumeViewerOptions

Set height of VolumeViewerPanel canvas.

homogPlane(HyperPlane) - Static method in class bvv.core.util.MatrixMath

HotLoadingUtils - Class in bvv.core.util

Utility to support hot-loading shaders during development (e.g., when running from IDE).

HotLoadingUtils() - Constructor for class bvv.core.util.HotLoadingUtils

HotLoadingUtils.ShaderHotLoader - Class in bvv.core.util

hyperPlane(Vector4f) - Static method in class bvv.core.util.MatrixMath

I

image() - Method in class bvv.core.cache.ImageBlockKey

ImageBlockKey<T> - Class in bvv.core.cache

Identifies a particular block in a particular image.

ImageBlockKey(T, int, int, int) - Constructor for class bvv.core.cache.ImageBlockKey

ImageBlockKey(T, int[]) - Constructor for class bvv.core.cache.ImageBlockKey

imgSize(int) - Method in interface bvv.core.blocks.GridDataAccess

Get the image size in dimension d in pixels.

init(Matrix4fc, int, List<? extends ResolutionLevel3D<?>>) - Method in class bvv.core.blockmath.MipmapSizes

init(TextureCache.StagedTasks) - Method in class bvv.core.cache.PboChain

Initialize a new batch of cache tile uploads.

init(int[], int[], int) - Method in class bvv.core.render.LookupTextureARGB

Reinitialize the lut data.

init(MultiResolutionStack3D<?>, TextureCache, int, Matrix4fc) - Method in class bvv.core.render.VolumeBlocks

init(GL3) - Method in class bvv.core.render.VolumeRenderer

init(int[]) - Method in class bvv.core.render.VolumeTextureRGBA8

Reinitialize.

init(int[]) - Method in class bvv.core.render.VolumeTextureU16

Reinitialize.

init(int[]) - Method in class bvv.core.render.VolumeTextureU8

Reinitialize.

inputTriggerConfig(InputTriggerConfig) - Method in class bvv.core.VolumeViewerOptions

Set the InputTriggerConfig from which keyboard and mouse action mapping is loaded.

inputTriggerConfig(InputTriggerConfig) - Method in class bvv.vistools.BvvOptions

Set the InputTriggerConfig from which keyboard and mouse action mapping is loaded.

insert(String, Segment...) - Method in class bvv.core.shadergen.generate.Segment

insert(String, Collection<Segment>) - Method in class bvv.core.shadergen.generate.Segment

install(Actions, BigVolumeViewer) - Static method in class bvv.core.BigVolumeViewerActions

Create BigVolumeViewer actions and install them in the specified Actions.

instantiate() - Method in class bvv.core.shadergen.generate.SegmentTemplate

InteractiveGLDisplayCanvas<C extends Component & com.jogamp.opengl.GLAutoDrawable> - Class in bvv.core

Wraps a Component (either GLJPanel or GLCanvas) that is used to display rendered images using JOGL.

InteractiveGLDisplayCanvas.CanvasSizeListener - Interface in bvv.core

Receive notifications about changes of the canvas size.

invalidate(Source<?>) - Static method in class bvv.core.multires.SourceStacks

invalidate() - Method in class bvv.vistools.BvvStackSource

isAbove(HyperPlane, double[]) - Static method in class bvv.core.blockmath.GeomUtils

isAbove(HyperPlane, RealLocalizable) - Static method in class bvv.core.blockmath.GeomUtils

isCurrent() - Method in class bvv.vistools.BvvSource

isCurrent() - Method in class bvv.vistools.BvvStackSource

isInside(ConvexPolytope, double[]) - Static method in class bvv.core.blockmath.GeomUtils

isInside(ConvexPolytope, RealLocalizable) - Static method in class bvv.core.blockmath.GeomUtils

isModified() - Method in class bvv.core.util.HotLoadingUtils.ShaderHotLoader

isPlaceHolderSource() - Method in class bvv.vistools.BvvSource

isPlaceHolderSource() - Method in class bvv.vistools.BvvStackSource

isSupportedType(Object) - Static method in class bvv.core.blocks.TileAccess

isVisible() - Method in class bvv.core.blockmath.MipmapSizes

Is any part of the volume visible?

J

JoglGpuContext - Class in bvv.core.backend.jogl

JoglSetUniforms - Class in bvv.core.backend.jogl

K

K - Variable in class bvv.core.dither.DitherPattern.DitherWeights

KeyConfigContexts - Interface in bvv.core

Constants that specify to what context an action or a behaviour applies.

KeyConfigScopes - Interface in bvv.core

The CommandDescription scope used for actions and behaviours defined in BigVolumeViewer

keymapManager(KeymapManager) - Method in class bvv.core.VolumeViewerOptions

Set the KeymapManager to share keymap settings with other BigVolumeViewer windows.

L

loadAndPatchSnippet(Class<?>, String, List<String>) - Static method in class bvv.core.shadergen.generate.StringTemplateUtils

loadSettings() - Method in class bvv.core.BigVolumeViewer

loadSettings(String) - Method in class bvv.core.BigVolumeViewer

loadTile(int[], UploadBuffer) - Method in class bvv.core.blocks.TileAccess

Load data for the tile at gridPos into buffer.

LookupTextureARGB - Class in bvv.core.render

LookupTextureARGB() - Constructor for class bvv.core.render.LookupTextureARGB

M

main(String[]) - Static method in class bvv.core.BigVolumeViewer

maintain(GpuContext) - Method in class bvv.core.cache.PboChain

Maps and unmaps Pbos and uploads to texture.

makeLut(int) - Method in class bvv.core.render.VolumeBlocks

makePattern(int, int, int[], int[]) - Static method in class bvv.core.dither.DitherPattern

makeShader(int) - Static method in class bvv.core.dither.DitherPattern

map(StagingBuffer) - Method in interface bvv.core.backend.GpuContext

map(StagingBuffer) - Method in class bvv.core.backend.jogl.JoglGpuContext

MatrixMath - Class in bvv.core.util

maxAllowedStepInVoxels(double) - Method in class bvv.core.VolumeViewerOptions

maxAllowedStepInVoxels(double) - Method in class bvv.vistools.BvvOptions

maxCacheSizeInMB(int) - Method in class bvv.core.VolumeViewerOptions

Sets the max memory to use for the GPU cache texture in MB.

maxCacheSizeInMB(int) - Method in class bvv.vistools.BvvOptions

Sets the max memory to use for the GPU cache texture in MB.

maxRenderMillis(int) - Method in class bvv.core.VolumeViewerOptions

Set target per-frame time in milliseconds.

maxRenderMillis - Variable in class bvv.core.VolumeViewerPanel

maxRenderMillis(int) - Method in class bvv.vistools.BvvOptions

Set target per-frame time in milliseconds.

MinMax - Enum in bvv.core.shadergen

MipmapSizes - Class in bvv.core.blockmath

MipmapSizes() - Constructor for class bvv.core.blockmath.MipmapSizes

msgOverlay(MessageOverlayAnimator) - Method in class bvv.core.VolumeViewerOptions

msgOverlay - Variable in class bvv.core.VolumeViewerPanel

Fade-out overlay of recent messages.

MultiResolutionStack3D<T> - Interface in bvv.core.multires

A 3D stack with multiple resolution levels.

MultiVolumeShaderMip - Class in bvv.core.render

MultiVolumeShaderMip(VolumeShaderSignature, boolean, double, Map<SegmentType, SegmentTemplate>, MultiVolumeShaderMip.SegmentConsumer, String) - Constructor for class bvv.core.render.MultiVolumeShaderMip

MultiVolumeShaderMip(VolumeShaderSignature, boolean, double) - Constructor for class bvv.core.render.MultiVolumeShaderMip

MultiVolumeShaderMip.SegmentConsumer - Interface in bvv.core.render

Functional interface to be able to use and integrate custom segments.

N

ndcTransform(int) - Method in class bvv.core.dither.DitherBuffer

nextTimePoint() - Method in class bvv.core.VolumeViewerPanel

Show the next time-point.

nextTimestamp() - Method in class bvv.core.cache.TextureCache

numDimensions() - Method in interface bvv.core.multires.ResolutionLevel3D

numDimensions() - Method in interface bvv.core.multires.Stack3D

numDitherSamples(int) - Method in class bvv.core.VolumeViewerOptions

Sets the number of dither samples.

numDitherSamples(int) - Method in class bvv.vistools.BvvOptions

Sets the number of dither samples.

numSourceGroups(int) - Method in class bvv.core.VolumeViewerOptions

Set how many source groups there are initially.

numSourceGroups(int) - Method in class bvv.vistools.BvvOptions

Set how many source groups there are initially.

numSteps() - Method in class bvv.core.dither.DitherBuffer

numVolumes() - Method in class bvv.core.render.VolumeShaderSignature

O

offscreen - Variable in class bvv.core.VolumeViewerPanel

OffScreenFrameBuffer - Class in bvv.core.offscreen

Render to texture.

OffScreenFrameBuffer(int, int) - Constructor for class bvv.core.offscreen.OffScreenFrameBuffer

Use GL_RGB32F as internalFormat.

OffScreenFrameBuffer(int, int, int) - Constructor for class bvv.core.offscreen.OffScreenFrameBuffer

OffScreenFrameBuffer(int, int, int, boolean, boolean) - Constructor for class bvv.core.offscreen.OffScreenFrameBuffer

OffScreenFrameBufferWithDepth - Class in bvv.core.offscreen

Render to texture.

OffScreenFrameBufferWithDepth(int, int) - Constructor for class bvv.core.offscreen.OffScreenFrameBufferWithDepth

Use GL_RGB32F as internalFormat.

OffScreenFrameBufferWithDepth(int, int, int) - Constructor for class bvv.core.offscreen.OffScreenFrameBufferWithDepth

onMouseMoved() - Method in class bvv.core.VolumeViewerPanel

options() - Static method in class bvv.core.VolumeViewerOptions

Create default VolumeViewerOptions.

options - Variable in class bvv.core.VolumeViewerPanel

options() - Static method in interface bvv.vistools.Bvv

options() - Static method in class bvv.vistools.BvvOptions

Create default BvvOptions.

optionsFromValues() - Method in class bvv.core.VolumeViewerOptions.Values

optionsFromValues() - Method in class bvv.vistools.BvvOptions.Values

origNumTimepoints - Variable in class bvv.vistools.BvvHandle

overlayAnimators - Variable in class bvv.core.VolumeViewerPanel

A list of currently incomplete (see OverlayAnimator.isComplete()) animators.

overlays() - Method in class bvv.core.InteractiveGLDisplayCanvas

P

paddedBlockSize() - Method in class bvv.core.cache.CacheSpec

Get the size of a padded block.

padOffset() - Method in class bvv.core.cache.CacheSpec

Get the offset in a padded block, where the (actual, unpadded) block data starts.

paint() - Method in class bvv.core.VolumeViewerPanel

painterThread - Variable in class bvv.core.VolumeViewerPanel

Thread that triggers repainting of the display.

parallel(TextureCache, PboChain, GpuContext, ForkJoinPool, Collection<? extends FillTask>) - Static method in class bvv.core.cache.ProcessFillTasks

PboChain - Class in bvv.core.cache

PboChain(int, int, TextureCache) - Constructor for class bvv.core.cache.PboChain

perspective(double, double, double, double, double, double, Matrix4f) - Static method in class bvv.core.util.MatrixMath

Setup projection frustum transformation such that the (BDV) screen plane at distance dCam exactly touches the frustum sides.

pos() - Method in class bvv.core.cache.ImageBlockKey

pos(int[]) - Method in class bvv.core.cache.ImageBlockKey

pos(int) - Method in class bvv.core.cache.ImageBlockKey

preferredSize(int, int) - Method in class bvv.vistools.BvvOptions

Set preferred size of ViewerPanel canvas.

previousTimePoint() - Method in class bvv.core.VolumeViewerPanel

Show the previous time-point.

ProcessFillTasks - Class in bvv.core.cache

ProcessFillTasks() - Constructor for class bvv.core.cache.ProcessFillTasks

putTile(int[], TextureCache.Tile, int) - Method in class bvv.core.render.LookupTextureARGB

R

ready() - Method in class bvv.core.cache.PboChain

registerCustomSampler(int, String, Texture) - Method in class bvv.core.render.MultiVolumeShaderMip

Deprecated.

replace by setUniform( index, name, texture )

registerTexture(Texture, int) - Method in class bvv.core.backend.jogl.JoglGpuContext

removeAllSources() - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

removeCustomUniformForVolume(int, String) - Method in class bvv.core.render.MultiVolumeShaderMip

Deprecated.

removeFromBdv() - Method in class bvv.vistools.BvvSource

removeFromBdv() - Method in class bvv.vistools.BvvStackSource

removeGroup(SourceGroup) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

removeHandler(Object) - Method in class bvv.core.InteractiveGLDisplayCanvas

Remove an event handler.

removeSource(Source<?>) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

removeSources(Collection<Source<?>>) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly

removeTimePointListener(TimePointListener) - Method in class bvv.core.VolumeViewerPanel

Remove a TimePointListener.

render(GL3, RenderData) - Method in interface bvv.core.VolumeViewerPanel.RenderScene

RenderData - Class in bvv.core.render

RenderData(Matrix4fc, int, AffineTransform3D, double, double, double, double, double) - Constructor for class bvv.core.render.RenderData

RenderData() - Constructor for class bvv.core.render.RenderData

renderer - Variable in class bvv.core.VolumeViewerPanel

Renders the current state to gl context.

renderHeight(int) - Method in class bvv.core.VolumeViewerOptions

Sets the height of offscreen canvas.

renderHeight(int) - Method in class bvv.vistools.BvvOptions

Sets the height of offscreen canvas.

renderTransformListeners() - Method in class bvv.core.VolumeViewerPanel

Add/remove TransformListeners to notify about viewer transformation changes.

renderWidth(int) - Method in class bvv.core.VolumeViewerOptions

Sets the width of offscreen canvas.

renderWidth(int) - Method in class bvv.vistools.BvvOptions

Sets the width of offscreen canvas.

repeat(String, int) - Method in class bvv.core.shadergen.generate.Segment

repeat(List<String>, int) - Method in class bvv.core.shadergen.generate.Segment

requestFocusInWindow() - Method in class bvv.core.InteractiveGLDisplayCanvas

requestRepaint() - Method in class bvv.core.VolumeViewerPanel

Repaint as soon as possible.

requestRepaint(VolumeRenderer.RepaintType) - Method in class bvv.core.VolumeViewerPanel

RequiredBlock - Class in bvv.core.blockmath

RequiredBlock(int[], int) - Constructor for class bvv.core.blockmath.RequiredBlock

RequiredBlocks - Class in bvv.core.blockmath

RequiredBlocks(int) - Constructor for class bvv.core.blockmath.RequiredBlocks

ResolutionLevel3D<T> - Interface in bvv.core.multires

One resolution level of a MultiResolutionStack3D This may be used as part of a cache key, so equals() and hashCode() should be overridden such that ResolutionLevel3Ds referring the same image data are equal.

resolutions() - Method in interface bvv.core.multires.MultiResolutionStack3D

Returns the list of all resolution levels.

run(String, int, int, int, int, int, int, int, int, double, double) - Static method in class bvv.core.BigVolumeViewer

run() - Method in class bvv.core.BigVolumeViewerCommand

S

saveSettings() - Method in class bvv.core.BigVolumeViewer

saveSettings(String) - Method in class bvv.core.BigVolumeViewer

scaleClippingPolytope(ConvexPolytope, int[]) - Static method in class bvv.core.blockmath.FindRequiredBlocks

Creates a clipping polytope in grid space from clip by scaling with inverse blockSize.

sceneBuf - Variable in class bvv.core.VolumeViewerPanel

screen(double, double, double, Matrix4f) - Static method in class bvv.core.util.MatrixMath

Set matrix to the "bdv screen transformation": translate the origin from the upper-left corner to the center of the screen (in XY).

screenPerspective(double, double, double, double, double, Matrix4f) - Static method in class bvv.core.util.MatrixMath

Setup view and projection frustum transformation such that a camera looks at (the center of) the (BDV) screen plane.

screenPerspective(double, double, double, double, double, double, Matrix4f) - Static method in class bvv.core.util.MatrixMath

Setup view and projection frustum transformation such that a camera looks at (the center of) the (BDV) screen plane.

Segment - Class in bvv.core.shadergen.generate

SegmentedShader - Class in bvv.core.shadergen.generate

SegmentedShaderBuilder - Class in bvv.core.shadergen.generate

SegmentedShaderBuilder() - Constructor for class bvv.core.shadergen.generate.SegmentedShaderBuilder

SegmentTemplate - Class in bvv.core.shadergen.generate

SegmentTemplate(String, String...) - Constructor for class bvv.core.shadergen.generate.SegmentTemplate

SegmentTemplate(String, List<String>) - Constructor for class bvv.core.shadergen.generate.SegmentTemplate

SegmentTemplate(Class<?>, String, String...) - Constructor for class bvv.core.shadergen.generate.SegmentTemplate

SegmentTemplate(Class<?>, String, List<String>) - Constructor for class bvv.core.shadergen.generate.SegmentTemplate

SegmentType - Enum in bvv.core.shadergen.generate

sequential(TextureCache, PboChain, GpuContext, Collection<? extends FillTask>) - Static method in class bvv.core.cache.ProcessFillTasks

set(RenderData) - Method in class bvv.core.render.RenderData

set(float) - Method in interface bvv.core.shadergen.Uniform1f

set(float[]) - Method in interface bvv.core.shadergen.Uniform1fv

set(int) - Method in interface bvv.core.shadergen.Uniform1i

set(int[]) - Method in interface bvv.core.shadergen.Uniform1iv

set(int[][]) - Method in interface bvv.core.shadergen.Uniform1iv

set(float, float) - Method in interface bvv.core.shadergen.Uniform2f

set(Vector2fc) - Method in interface bvv.core.shadergen.Uniform2f

set(RealInterval, MinMax) - Method in interface bvv.core.shadergen.Uniform2f

set(float[]) - Method in interface bvv.core.shadergen.Uniform2fv

set(float[][]) - Method in interface bvv.core.shadergen.Uniform2fv

set(int, int) - Method in interface bvv.core.shadergen.Uniform2i

set(Vector2ic) - Method in interface bvv.core.shadergen.Uniform2i

set(int[]) - Method in interface bvv.core.shadergen.Uniform2iv

set(int[][]) - Method in interface bvv.core.shadergen.Uniform2iv

set(float, float, float) - Method in interface bvv.core.shadergen.Uniform3f

set(Vector3fc) - Method in interface bvv.core.shadergen.Uniform3f

set(RealInterval, MinMax) - Method in interface bvv.core.shadergen.Uniform3f

set(float[]) - Method in interface bvv.core.shadergen.Uniform3fv

set(float[][]) - Method in interface bvv.core.shadergen.Uniform3fv

set(int, int, int) - Method in interface bvv.core.shadergen.Uniform3i

set(Vector3ic) - Method in interface bvv.core.shadergen.Uniform3i

set(int[]) - Method in interface bvv.core.shadergen.Uniform3iv

set(int[][]) - Method in interface bvv.core.shadergen.Uniform3iv

set(float, float, float, float) - Method in interface bvv.core.shadergen.Uniform4f

set(Vector4fc) - Method in interface bvv.core.shadergen.Uniform4f

set(RealInterval, MinMax) - Method in interface bvv.core.shadergen.Uniform4f

set(float[]) - Method in interface bvv.core.shadergen.Uniform4fv

set(float[][]) - Method in interface bvv.core.shadergen.Uniform4fv

set(int, int, int, int) - Method in interface bvv.core.shadergen.Uniform4i

set(Vector4ic) - Method in interface bvv.core.shadergen.Uniform4i

set(int[]) - Method in interface bvv.core.shadergen.Uniform4iv

set(int[][]) - Method in interface bvv.core.shadergen.Uniform4iv

set(Matrix3fc) - Method in interface bvv.core.shadergen.UniformMatrix3f

set(Matrix4fc) - Method in interface bvv.core.shadergen.UniformMatrix4f

set(Texture) - Method in interface bvv.core.shadergen.UniformSampler

setActive(boolean) - Method in class bvv.vistools.BvvSource

setActive(boolean) - Method in class bvv.vistools.BvvStackSource

setBaseLevel(int) - Method in class bvv.core.render.VolumeBlocks

Set the base resolution level for rendering the volume.

setBdvHandle(BvvHandle) - Method in class bvv.vistools.BvvSource

setBestLevel(int) - Method in class bvv.core.blockmath.RequiredBlock

setBytes(byte, long, long) - Static method in class bvv.core.blocks.ByteUtils

setCamParams(double, double) - Method in class bvv.core.VolumeViewerPanel

setCamParams(double, double, double) - Method in class bvv.core.VolumeViewerPanel

setCanvasSize(int, int) - Method in interface bvv.core.InteractiveGLDisplayCanvas.CanvasSizeListener

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 bvv.core.VolumeViewerPanel

setColor(ARGBType) - Method in class bvv.vistools.BvvSource

setColor(ARGBType) - Method in class bvv.vistools.BvvStackSource

setContentState(TextureCache.ContentState) - Method in class bvv.core.cache.UploadBuffer

Called by FillTask to say whether stored image block data was complete.

setConverter(int, ConverterSetup) - Method in class bvv.core.render.MultiVolumeShaderMip

setCurrent() - Method in class bvv.vistools.BvvSource

setCurrent() - Method in class bvv.vistools.BvvStackSource

setCurrentViewerTransform(AffineTransform3D) - Method in class bvv.core.VolumeViewerPanel

Deprecated.

Modify VolumeViewerPanel.state() directly (state().setViewerTransform(t))

setCustomFloatArrayUniformForVolume(int, String, int, float[]) - Method in class bvv.core.render.MultiVolumeShaderMip

Deprecated.

replace by setUniform( index, name, elementSize, value )

setCustomIntArrayUniformForVolume(int, String, int, int[]) - Method in class bvv.core.render.MultiVolumeShaderMip

Deprecated.

replace by setUniform( index, name, elementSize, value )

setCustomUniformForVolume(int, String, Object) - Method in class bvv.core.render.MultiVolumeShaderMip

Deprecated.

replace by setUniform( index, name, value )

setDegrade(Double) - Method in class bvv.core.render.MultiVolumeShaderMip

Note that this will only take effect after MultiVolumeShaderMip.setProjectionViewMatrix(Matrix4fc, double) (added for use by scenery)

setDepthTexture(Texture2D) - Method in class bvv.core.render.MultiVolumeShaderMip

setDepthTextureName(String) - Method in class bvv.core.render.MultiVolumeShaderMip

setDisplayMode(DisplayMode) - Method in class bvv.core.VolumeViewerPanel

Set the DisplayMode.

setDisplayRange(double, double) - Method in class bvv.vistools.BvvSource

setDisplayRange(double, double) - Method in class bvv.vistools.BvvStackSource

setDisplayRangeBounds(double, double) - Method in class bvv.vistools.BvvSource

setDisplayRangeBounds(double, double) - Method in class bvv.vistools.BvvStackSource

setDither(DitherBuffer, int) - Method in class bvv.core.render.MultiVolumeShaderMip

setEffectiveViewportSize(int, int) - Method in class bvv.core.render.MultiVolumeShaderMip

setMaxAllowedStepInVoxels(double) - Method in class bvv.core.VolumeViewerPanel

setNumTimepoints(int) - Method in class bvv.core.VolumeViewerPanel

Set the number of available timepoints.

setPosition(int, int) - Method in interface bvv.core.blocks.GridDataAccess

setPosition(int[]) - Method in interface bvv.core.blocks.GridDataAccess

setProjectionViewMatrix(Matrix4fc, double) - Method in class bvv.core.render.MultiVolumeShaderMip

setRenderScene(VolumeViewerPanel.RenderScene) - Method in class bvv.core.VolumeViewerPanel

setShorts(short, long, long) - Static method in class bvv.core.blocks.ByteUtils

setSourceStackType(Source<?>, SourceStacks.SourceStackType) - Static method in class bvv.core.multires.SourceStacks

setTimepoint(int) - Method in class bvv.core.VolumeViewerPanel

Show the specified time-point.

setTransformAnimator(AbstractTransformAnimator) - Method in class bvv.core.VolumeViewerPanel

setTransformEventHandler(TransformEventHandler) - Method in class bvv.core.InteractiveGLDisplayCanvas

Set the TransformEventHandler that will be notified when component is resized.

setUniform(int, String, Object) - Method in class bvv.core.render.MultiVolumeShaderMip

Set uniform name to the given value, where the uniform type is inferred from the type of value.

setUniform(int, String, int, Object) - Method in class bvv.core.render.MultiVolumeShaderMip

Set uniform array name to the given value, where the uniform type is inferred from the type of value.

setUniform1f(String, float) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform1f(String, float) - Method in interface bvv.core.backend.SetUniforms

setUniform1fv(String, int, float[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform1fv(String, int, float[]) - Method in interface bvv.core.backend.SetUniforms

setUniform1i(String, int) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform1i(String, int) - Method in interface bvv.core.backend.SetUniforms

setUniform1iv(String, int, int[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform1iv(String, int, int[]) - Method in interface bvv.core.backend.SetUniforms

setUniform2f(String, float, float) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform2f(String, float, float) - Method in interface bvv.core.backend.SetUniforms

setUniform2fv(String, int, float[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform2fv(String, int, float[]) - Method in interface bvv.core.backend.SetUniforms

setUniform2i(String, int, int) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform2i(String, int, int) - Method in interface bvv.core.backend.SetUniforms

setUniform2iv(String, int, int[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform2iv(String, int, int[]) - Method in interface bvv.core.backend.SetUniforms

setUniform3f(String, float, float, float) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform3f(String, float, float, float) - Method in interface bvv.core.backend.SetUniforms

setUniform3fv(String, int, float[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform3fv(String, int, float[]) - Method in interface bvv.core.backend.SetUniforms

setUniform3i(String, int, int, int) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform3i(String, int, int, int) - Method in interface bvv.core.backend.SetUniforms

setUniform3iv(String, int, int[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform3iv(String, int, int[]) - Method in interface bvv.core.backend.SetUniforms

setUniform4f(String, float, float, float, float) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform4f(String, float, float, float, float) - Method in interface bvv.core.backend.SetUniforms

setUniform4fv(String, int, float[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform4fv(String, int, float[]) - Method in interface bvv.core.backend.SetUniforms

setUniform4i(String, int, int, int, int) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform4i(String, int, int, int, int) - Method in interface bvv.core.backend.SetUniforms

setUniform4iv(String, int, int[]) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniform4iv(String, int, int[]) - Method in interface bvv.core.backend.SetUniforms

setUniformMatrix3f(String, boolean, FloatBuffer) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniformMatrix3f(String, boolean, FloatBuffer) - Method in interface bvv.core.backend.SetUniforms

setUniformMatrix4f(String, boolean, FloatBuffer) - Method in class bvv.core.backend.jogl.JoglSetUniforms

setUniformMatrix4f(String, boolean, FloatBuffer) - Method in interface bvv.core.backend.SetUniforms

SetUniforms - Interface in bvv.core.backend

setUniforms(GpuContext) - Method in class bvv.core.render.MultiVolumeShaderMip

setUniforms(GpuContext) - Method in class bvv.core.shadergen.AbstractShader

setUniforms(GpuContext) - Method in interface bvv.core.shadergen.Shader

setUniformValueByType(Segment, String, int, Object) - Method in class bvv.core.shadergen.generate.SegmentedShader

(added for use by scenery)

setUniformValueByType(Segment, String, Object) - Method in class bvv.core.shadergen.generate.SegmentedShader

(added for use by scenery)

setupAssignments - Variable in class bvv.vistools.BvvHandle

setupId(int) - Method in class bvv.core.multires.SpimDataStacks

setupId(int) - Method in interface bvv.core.multires.Stacks

setups - Variable in class bvv.vistools.BvvHandle

setViewportWidth(int) - Method in class bvv.core.render.MultiVolumeShaderMip

setVolume(int, VolumeBlocks) - Method in class bvv.core.render.MultiVolumeShaderMip

setVolume(int, SimpleVolume) - Method in class bvv.core.render.MultiVolumeShaderMip

Shader - Interface in bvv.core.shadergen

ShaderHotLoader(String...) - Constructor for class bvv.core.util.HotLoadingUtils.ShaderHotLoader

ShaderHotLoader(boolean, String...) - Constructor for class bvv.core.util.HotLoadingUtils.ShaderHotLoader

shareKeyPressedEvents(KeyPressedManager) - Method in class bvv.core.VolumeViewerOptions

Set the KeyPressedManager to share KeyListener.keyPressed(java.awt.event.KeyEvent) events with other ui-behaviour windows.

ShortToAddress() - Constructor for class bvv.core.blocks.CopySubArrayImp.ShortToAddress

shouldSet(boolean) - Method in class bvv.core.backend.jogl.JoglSetUniforms

shouldSet(boolean) - Method in interface bvv.core.backend.SetUniforms

show(RandomAccessibleInterval<T>, String) - Static method in class bvv.vistools.BvvFunctions

show(BvvOptions) - Static method in class bvv.vistools.BvvFunctions

show(RandomAccessibleInterval<T>, String, BvvOptions) - Static method in class bvv.vistools.BvvFunctions

show(Source<T>) - Static method in class bvv.vistools.BvvFunctions

show(Source<T>, BvvOptions) - Static method in class bvv.vistools.BvvFunctions

show(Source<T>, int) - Static method in class bvv.vistools.BvvFunctions

show(Source<T>, int, BvvOptions) - Static method in class bvv.vistools.BvvFunctions

show(SourceAndConverter<T>) - Static method in class bvv.vistools.BvvFunctions

show(SourceAndConverter<T>, BvvOptions) - Static method in class bvv.vistools.BvvFunctions

show(SourceAndConverter<T>, int) - Static method in class bvv.vistools.BvvFunctions

show(SourceAndConverter<T>, int, BvvOptions) - Static method in class bvv.vistools.BvvFunctions

show(AbstractSpimData<?>) - Static method in class bvv.vistools.BvvFunctions

show(AbstractSpimData<?>, BvvOptions) - Static method in class bvv.vistools.BvvFunctions

showMessage(String) - Method in class bvv.core.VolumeViewerPanel

Display the specified message in a text overlay for a short time.

shrinkClippingPolytope(ConvexPolytope, int[]) - Static method in class bvv.core.blockmath.FindRequiredBlocks

Creates a new clipping polytope by shifting the planes of clip such that we only have to check the (0, 0) corner of cells.

signedDistance(HyperPlane, double[]) - Static method in class bvv.core.blockmath.GeomUtils

signedDistance(HyperPlane, RealLocalizable) - Static method in class bvv.core.blockmath.GeomUtils

SimpleStack3D<T> - Interface in bvv.core.multires

A simple 3D stack (not multi-resolution) This may be used as part of a cache key, so equals() and hashCode() should be overridden such that SimpleStack3Ds referring the same image data are equal.

SimpleStackManager - Interface in bvv.core.render

SimpleVolume - Class in bvv.core.render

TODO

SimpleVolume(Texture3D, AffineTransform3D, Vector3f, Vector3f) - Constructor for class bvv.core.render.SimpleVolume

sliderTime - Variable in class bvv.core.VolumeViewerPanel

SourceStacks - Class in bvv.core.multires

SourceStacks() - Constructor for class bvv.core.multires.SourceStacks

SourceStacks.SourceStackType - Enum in bvv.core.multires

sourceTransform(AffineTransform3D) - Method in class bvv.vistools.BvvOptions

Set the transform of the BdvSource to be created.

sourceTransform(double...) - Method in class bvv.vistools.BvvOptions

Set the transform of the BdvSource to be created to account for the given calibration (scaling of the source axes).

spec() - Method in class bvv.core.cache.TextureCache

SpimDataStacks - Class in bvv.core.multires

SpimDataStacks(AbstractSpimData<?>) - Constructor for class bvv.core.multires.SpimDataStacks

splitPanel - Variable in class bvv.vistools.BvvHandle

spo - Variable in class bvv.core.dither.DitherPattern.DitherWeights

Stack3D<T> - Interface in bvv.core.multires

A 3D stack (simple or multi-resolution) This may be used as part of a cache key, so equals() and hashCode() should be overridden such that Stack3Ds referring the same image data are equal.

Stacks - Interface in bvv.core.multires

StagingBuffer - Interface in bvv.core.backend

Handle to a staging buffer for texture data.

state() - Method in class bvv.core.cache.TextureCache.Tile

state - Variable in class bvv.core.VolumeViewerPanel

Currently rendered state (visible sources, transformation, timepoint, etc.)

state() - Method in class bvv.core.VolumeViewerPanel

Get the ViewerState.

stateFromXml(Element) - Method in class bvv.core.VolumeViewerPanel

stateToXml() - Method in class bvv.core.VolumeViewerPanel

stop() - Method in class bvv.core.VolumeViewerPanel

Stop the VolumeViewerPanel.painterThread.

StringTemplateUtils - Class in bvv.core.shadergen.generate

StringTemplateUtils() - Constructor for class bvv.core.shadergen.generate.StringTemplateUtils

T

texDepth() - Method in interface bvv.core.backend.Texture

texDepth() - Method in interface bvv.core.backend.Texture2D

texDepth() - Method in class bvv.core.cache.TextureCache

texDepth() - Method in class bvv.core.render.LookupTextureARGB

texDepth() - Method in class bvv.core.render.VolumeTextureRGBA8

texDepth() - Method in class bvv.core.render.VolumeTextureU16

texDepth() - Method in class bvv.core.render.VolumeTextureU8

texDims() - Method in interface bvv.core.backend.Texture

texDims() - Method in interface bvv.core.backend.Texture2D

texDims() - Method in interface bvv.core.backend.Texture3D

texHeight() - Method in interface bvv.core.backend.Texture

texHeight() - Method in class bvv.core.cache.TextureCache

texHeight() - Method in class bvv.core.render.LookupTextureARGB

texHeight() - Method in class bvv.core.render.VolumeTextureRGBA8

texHeight() - Method in class bvv.core.render.VolumeTextureU16

texHeight() - Method in class bvv.core.render.VolumeTextureU8

texInternalFormat() - Method in interface bvv.core.backend.Texture

texInternalFormat() - Method in class bvv.core.cache.TextureCache

texInternalFormat() - Method in class bvv.core.render.LookupTextureARGB

texInternalFormat() - Method in class bvv.core.render.VolumeTextureRGBA8

texInternalFormat() - Method in class bvv.core.render.VolumeTextureU16

texInternalFormat() - Method in class bvv.core.render.VolumeTextureU8

texMagFilter() - Method in interface bvv.core.backend.Texture

texMagFilter() - Method in class bvv.core.cache.TextureCache

texMagFilter() - Method in class bvv.core.render.LookupTextureARGB

texMagFilter() - Method in class bvv.core.render.VolumeTextureRGBA8

texMagFilter() - Method in class bvv.core.render.VolumeTextureU16

texMagFilter() - Method in class bvv.core.render.VolumeTextureU8

texMinFilter() - Method in interface bvv.core.backend.Texture

texMinFilter() - Method in class bvv.core.cache.TextureCache

texMinFilter() - Method in class bvv.core.render.LookupTextureARGB

texMinFilter() - Method in class bvv.core.render.VolumeTextureRGBA8

texMinFilter() - Method in class bvv.core.render.VolumeTextureU16

texMinFilter() - Method in class bvv.core.render.VolumeTextureU8

texSubImage3D(StagingBuffer, Texture3D, int, int, int, int, int, int, long) - Method in interface bvv.core.backend.GpuContext

texSubImage3D(Texture3D, int, int, int, int, int, int, Buffer) - Method in interface bvv.core.backend.GpuContext

texSubImage3D(StagingBuffer, Texture3D, int, int, int, int, int, int, long) - Method in class bvv.core.backend.jogl.JoglGpuContext

texSubImage3D(Texture3D, int, int, int, int, int, int, Buffer) - Method in class bvv.core.backend.jogl.JoglGpuContext

Texture - Interface in bvv.core.backend

Texture.InternalFormat - Enum in bvv.core.backend

Texture.MagFilter - Enum in bvv.core.backend

Texture.MinFilter - Enum in bvv.core.backend

Texture.Wrap - Enum in bvv.core.backend

Texture2D - Interface in bvv.core.backend

Texture3D - Interface in bvv.core.backend

TextureCache - Class in bvv.core.cache

Not thread-safe.

TextureCache(int[], CacheSpec) - Constructor for class bvv.core.cache.TextureCache

TextureCache.ContentState - Enum in bvv.core.cache

TextureCache.Tile - Class in bvv.core.cache

texWidth() - Method in interface bvv.core.backend.Texture

texWidth() - Method in class bvv.core.cache.TextureCache

texWidth() - Method in class bvv.core.render.LookupTextureARGB

texWidth() - Method in class bvv.core.render.VolumeTextureRGBA8

texWidth() - Method in class bvv.core.render.VolumeTextureU16

texWidth() - Method in class bvv.core.render.VolumeTextureU8

texWrap() - Method in interface bvv.core.backend.Texture

texWrap() - Method in class bvv.core.cache.TextureCache

texWrap() - Method in class bvv.core.render.LookupTextureARGB

texWrap() - Method in class bvv.core.render.VolumeTextureRGBA8

texWrap() - Method in class bvv.core.render.VolumeTextureU16

texWrap() - Method in class bvv.core.render.VolumeTextureU8

threadGroup - Variable in class bvv.core.VolumeViewerPanel

A ThreadGroup for (only) the threads used by this ViewerPanel, that is, at the moment only VolumeViewerPanel.painterThread.

TileAccess<S> - Class in bvv.core.blocks

Copy blocks from a ResolutionLevel3D source to an UploadBuffer.

TileAccess(GridDataAccess<S>, CopySubArray<S, ByteUtils.Address>, CacheSpec) - Constructor for class bvv.core.blocks.TileAccess

TileAccess.Cache - Class in bvv.core.blocks

Thread-local weak cache for TileAccess to avoid creating too many of them.

timepointId(int) - Method in class bvv.core.multires.SpimDataStacks

timepointId(int) - Method in interface bvv.core.multires.Stacks

timePointListeners - Variable in class bvv.core.VolumeViewerPanel

These listeners will be notified about changes to the current timepoint ViewerState.getCurrentTimepoint().

toString(HyperPlane) - Static method in class bvv.core.blockmath.GeomUtils

toString(ConvexPolytope) - Static method in class bvv.core.blockmath.GeomUtils

toString() - Method in class bvv.core.blockmath.RequiredBlocks

transformEventHandlerFactory(TransformEventHandlerFactory) - Method in class bvv.core.VolumeViewerOptions

transformListeners() - Method in class bvv.core.VolumeViewerPanel

Add/remove TransformListeners to notify about viewer transformation changes.

tryActivate(GpuContext) - Method in class bvv.core.cache.PboChain

Activate next Pbo if necessary and possible.

tryInitTransform() - Method in class bvv.vistools.BvvHandle

tryLoadSettings(String) - Method in class bvv.core.BigVolumeViewer

tryUpload(GpuContext) - Method in class bvv.core.cache.PboChain

Unmap and upload next Pbo if necessary.

Typed<T> - Interface in bvv.core.multires

U

unbind(GL3) - Method in class bvv.core.dither.DitherBuffer

unbind(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

Unbind this framebuffer (bind framebuffer 0) and download the texture into a float array.

unbind(GL3, boolean) - Method in class bvv.core.offscreen.OffScreenFrameBuffer

unbind(GL3) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

Unbind this framebuffer (bind framebuffer 0) and download the texture into a float array.

unbind(GL3, boolean) - Method in class bvv.core.offscreen.OffScreenFrameBufferWithDepth

Uniform1f - Interface in bvv.core.shadergen

Uniform1fv - Interface in bvv.core.shadergen

Uniform1i - Interface in bvv.core.shadergen

Uniform1iv - Interface in bvv.core.shadergen

Uniform2f - Interface in bvv.core.shadergen

Uniform2fv - Interface in bvv.core.shadergen

Uniform2i - Interface in bvv.core.shadergen

Uniform2iv - Interface in bvv.core.shadergen

Uniform3f - Interface in bvv.core.shadergen

Uniform3fv - Interface in bvv.core.shadergen

Uniform3i - Interface in bvv.core.shadergen

Uniform3iv - Interface in bvv.core.shadergen

Uniform4f - Interface in bvv.core.shadergen

Uniform4fv - Interface in bvv.core.shadergen

Uniform4i - Interface in bvv.core.shadergen

Uniform4iv - Interface in bvv.core.shadergen

UniformMatrix3f - Interface in bvv.core.shadergen

UniformMatrix4f - Interface in bvv.core.shadergen

UniformSampler - Interface in bvv.core.shadergen

unmap(StagingBuffer) - Method in interface bvv.core.backend.GpuContext

unmap(StagingBuffer) - Method in class bvv.core.backend.jogl.JoglGpuContext

upload(GpuContext) - Method in class bvv.core.render.LookupTextureARGB

upload(GpuContext, Buffer) - Method in class bvv.core.render.VolumeTextureRGBA8

upload(GpuContext, Buffer) - Method in class bvv.core.render.VolumeTextureU16

upload(GpuContext, Buffer) - Method in class bvv.core.render.VolumeTextureU8

UploadBuffer - Class in bvv.core.cache

UploadBuffer(Buffer, int) - Constructor for class bvv.core.cache.UploadBuffer

use(Shader) - Method in interface bvv.core.backend.GpuContext

use(Shader) - Method in class bvv.core.backend.jogl.JoglGpuContext

use(GpuContext) - Method in class bvv.core.render.MultiVolumeShaderMip

use(GpuContext) - Method in class bvv.core.shadergen.AbstractShader

use(GpuContext) - Method in interface bvv.core.shadergen.Shader

useAtTimestamp(int) - Method in class bvv.core.cache.TextureCache.Tile

V

valueOf(String) - Static method in enum bvv.core.backend.Texture.InternalFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.backend.Texture.MagFilter

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.backend.Texture.MinFilter

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.backend.Texture.Wrap

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.cache.TextureCache.ContentState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.multires.DownSamplingScheme

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.multires.SourceStacks.SourceStackType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.render.VolumeRenderer.RepaintType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.render.VolumeShaderSignature.PixelType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.shadergen.generate.SegmentType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bvv.core.shadergen.MinMax

Returns the enum constant of this type with the specified name.

values() - Static method in enum bvv.core.backend.Texture.InternalFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.backend.Texture.MagFilter

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.backend.Texture.MinFilter

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.backend.Texture.Wrap

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.cache.TextureCache.ContentState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.multires.DownSamplingScheme

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.multires.SourceStacks.SourceStackType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.render.VolumeRenderer.RepaintType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.render.VolumeShaderSignature.PixelType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.shadergen.generate.SegmentType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bvv.core.shadergen.MinMax

Returns an array containing the constants of this enum type, in the order they are declared.

values - Variable in class bvv.core.VolumeViewerOptions

Values() - Constructor for class bvv.core.VolumeViewerOptions.Values

values - Variable in class bvv.vistools.BvvOptions

vertex(Segment) - Method in class bvv.core.shadergen.generate.SegmentedShaderBuilder

viewer - Variable in class bvv.vistools.BvvHandle

viewerStateChanged(ViewerStateChange) - Method in class bvv.core.VolumeViewerPanel

visibilityAndGrouping - Variable in class bvv.core.VolumeViewerPanel

Manages visibility and currentness of sources and groups, as well as grouping of sources, and display mode.

VolatileCells(AbstractCellImg<?, A, ? extends Cell<A>, ?>) - Constructor for class bvv.core.blocks.GridDataAccessImp.VolatileCells

VolumeBlocks - Class in bvv.core.render

For setting up the volume for one frame, call methods in this order: VolumeBlocks.init(MultiResolutionStack3D, TextureCache, int, Matrix4fc) VolumeBlocks.getFillTasks() VolumeBlocks.makeLut(int) VolumeBlocks.getLutBlockScales(int) can be called at any point after init().

VolumeBlocks() - Constructor for class bvv.core.render.VolumeBlocks

VolumeRenderer - Class in bvv.core.render

VolumeRenderer(int, int, int, int, int, int[], int) - Constructor for class bvv.core.render.VolumeRenderer

VolumeRenderer.RepaintType - Enum in bvv.core.render

VolumeShaderSignature - Class in bvv.core.render

VolumeShaderSignature(List<VolumeShaderSignature.VolumeSignature>) - Constructor for class bvv.core.render.VolumeShaderSignature

VolumeShaderSignature.PixelType - Enum in bvv.core.render

VolumeShaderSignature.VolumeSignature - Class in bvv.core.render

VolumeSignature(SourceStacks.SourceStackType, VolumeShaderSignature.PixelType) - Constructor for class bvv.core.render.VolumeShaderSignature.VolumeSignature

VolumeTextureRGBA8 - Class in bvv.core.render

VolumeTextureRGBA8() - Constructor for class bvv.core.render.VolumeTextureRGBA8

VolumeTextureU16 - Class in bvv.core.render

VolumeTextureU16() - Constructor for class bvv.core.render.VolumeTextureU16

VolumeTextureU8 - Class in bvv.core.render

VolumeTextureU8() - Constructor for class bvv.core.render.VolumeTextureU8

VolumeViewerFrame - Class in bvv.core

A JFrame containing a VolumeViewerPanel and associated InputActionBindings.

VolumeViewerFrame(List<SourceAndConverter<?>>, int, CacheControl, VolumeViewerOptions) - Constructor for class bvv.core.VolumeViewerFrame

VolumeViewerFrame(List<SourceAndConverter<?>>, int, CacheControl, KeymapManager, AppearanceManager, VolumeViewerOptions) - Constructor for class bvv.core.VolumeViewerFrame

VolumeViewerOptions - Class in bvv.core

Optional parameters for VolumeViewerPanel.

VolumeViewerOptions() - Constructor for class bvv.core.VolumeViewerOptions

VolumeViewerOptions.Values - Class in bvv.core

Read-only ViewerOptions values.

VolumeViewerPanel - Class in bvv.core

VolumeViewerPanel(List<SourceAndConverter<?>>, int, CacheControl, VolumeViewerOptions) - Constructor for class bvv.core.VolumeViewerPanel

VolumeViewerPanel.RenderScene - Interface in bvv.core

W

watch(Class<?>, String) - Method in class bvv.core.util.HotLoadingUtils.ShaderHotLoader

watch(String) - Method in class bvv.core.util.HotLoadingUtils.ShaderHotLoader

width(int) - Method in class bvv.core.VolumeViewerOptions

Set width of VolumeViewerPanel canvas.

X

x() - Method in class bvv.core.cache.ImageBlockKey

x() - Method in class bvv.core.cache.TextureCache.Tile

Tile X coordinate in texture grid (padded blocks)

Y

y() - Method in class bvv.core.cache.ImageBlockKey

y() - Method in class bvv.core.cache.TextureCache.Tile

Tile Y coordinate in texture grid (padded blocks)

yAxisFlipped() - Method in class bvv.core.InteractiveGLDisplayCanvas

Z

z() - Method in class bvv.core.cache.ImageBlockKey

z() - Method in class bvv.core.cache.TextureCache.Tile

Tile Z coordinate in texture grid (padded blocks)

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