Index (anchor-image-bean 0.2.1 API)

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

A

add(BoundingBoxEnclosed) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Adds a new BoundingBoxEnclosed to the arrangement.
add(BoundingBox) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Adds a new BoundingBox to the arrangement, with no padding.
addChannel(Channel, Logger) - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Adds a Channel to the aggregation.
addChannelAfterCheck(Channel) - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Adds a Channel to the aggregation - after checking channel has acceptable dimensions.
addDictionary(String, Dictionary) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds a Dictionary to the corresponding named-collection of dictionaries.
addObjectsFrom(NamedProvider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds all the ObjectCollections available in a NamedProvider using the corresponding identifiers.
addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds stacks and object-collections from a SharedObjects using the respective identifiers, and also adds a Dictionary.
addStack(String, Stack) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds a Stack to the corresponding named-collection of stacks.
addStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Adds a stack to the existing list of stack-providers.
addStacksFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds all the Stacks available in a NamedProvider using the corresponding identifiers.
aggregatedChannel() - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Retrieve or create a Channel with containing the aggregated values.
align(int, int, int) - Method in enum org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Determine the minimum value after alignment.
align(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
align(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for a smaller Extent so that it fits inside larger BoundingBox.
align(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for a smaller Extent so that it fits inside larger Extent.
Align - Class in org.anchoranalysis.image.bean.spatial.arrange.align: Align the bounding-box to the larger without resizing.
Align() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Align
Align(String, String, String) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Creates with alignment text for each axis.
alignAfterCheck(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
alignAfterCheck(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller BoundingBox so that it fits inside larger BoundingBox.
alignAfterCheck(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
alignAfterCheck(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
alignAfterCheck(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller Extent so that it fits inside larger BoundingBox.
alignAfterCheck(Extent, BoundingBox) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
alignAfterCheck(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
alignAfterCheck(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner: Determines a BoundingBox to use for smaller Extent so that it fits inside larger Extent.
alignAfterCheck(Extent, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
alignCorner(BoundingBox, Extent) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: The minimum corner at which the entity should be locate after alignment, ignoring the space to the left.
alignmentForDimension(String, String) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoices: Calculates how to align a particular axis.
AlignmentOnDimension - Enum in org.anchoranalysis.image.bean.nonbean.spatial.align: How the alignment will occur for a particular dimension.
alignX(String) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: How to align on the X-axis.
alignY(String) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: How to align on the Y-axis.
alignZ(String) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: How to align on the Z-axis.
AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed in square meters, or units thereof.
AreaPhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: Area expressed in pixels.
AreaPixels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
AreaPixels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels: Creates with a particular area value.
Arrange - Class in org.anchoranalysis.image.bean.provider.stack: Creates a stack that combines other stacks.
Arrange() - Constructor for class org.anchoranalysis.image.bean.provider.stack.Arrange
Arrange(boolean, boolean) - Constructor for class org.anchoranalysis.image.bean.provider.stack.Arrange: Shortcut to create with some explicit parameters.
ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange: When the position of a particular RGBStack cannot be determined, when combined with others onto a single plane.
ArrangeStackException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException: Create with a cause.
ArrangeStackException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException: Create with a message.
ArrangeStackException(String, Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException: Create with a message and cause.
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Single
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.StackArranger: Arranges stacks to that they fit together in a single raster.
arrangeStacks(Iterator<Extent>, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile
asExtent() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Creates an extent with identical width and height and depth (z-extent) of 1.
asExtent(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Creates an extent with identical width and height and a specific depth (z-extent).
aspectRatioInverted() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Returns the ratio of *image height to width*.
asPoint() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Exposes the padding as a Point3i.
AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction: Creates a DirectionVector that is a unit-vector along a particular image-axis.
AxisAlignedUnitVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector

B

BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider: A provider base-class that as well as providing type S, also provides a Stack.
BeanProviderAsStackBase() - Constructor for class org.anchoranalysis.image.bean.provider.BeanProviderAsStackBase
BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects voxels that are not off voxels.
BinaryNotOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects voxels that are not on voxels.
BinaryNotOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the off voxels.
BinaryOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
BinaryOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation: Selects only the on pixels.
BinaryOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
BinarySegmentation - Class in org.anchoranalysis.image.bean.segment.binary: Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
BinarySegmentation() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment: Parameters that are passed during a BinarySegmentation.
BinarySegmentationParameters() - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates with no intensity-histogram or resolution.
BinarySegmentationParameters(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates with a specific resolution, but no intensity-histogram.
BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: Creates with a specific resolution and intensity-histogram.
BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary: Uses an existing BinarySegmentation that is located by a unique identifier.
BinarySegmentationReference() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
binarySegmentations() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of BinarySegmentations, indexed by name.
BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary: Implementation of BinarySegmentation that performs global thresholding.
BinarySegmentationThreshold() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
BinarySegmentationUnary - Class in org.anchoranalysis.image.bean.segment.binary: An implementation of BinarySegmentation that delegates to one other BinarySegmentation.
BinarySegmentationUnary() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary
BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation: A base class for implementations of RelationToThreshold where the threshold is derived from a BinaryValuesInt.
BinaryVoxelsBase() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
BOTTOM - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the bottom in the Y-dimension.
BoundingBoxEnclosed - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Describes a BoundingBox that is optionally enclosed by a larger containing BoundingBox to given padding.
BoundingBoxEnclosed(BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: Create with a box that has no padding.
BoundingBoxEnclosed(BoundingBox, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed
BoxAligner - Class in org.anchoranalysis.image.bean.spatial.arrange.align: Aligns a smaller BoundingBox to fit inside a larger BoundingBox.
BoxAligner() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.BoxAligner
boxes() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Where to locate a respective image on a larger image.

C

calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class org.anchoranalysis.image.bean.spatial.ScaleCalculator: Calculates a scaling-factor for a source image/entity of particular dimensions.
calculateLevel(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel: Determines a voxel intensity that can be used for thresholding.
CalculateLevel - Class in org.anchoranalysis.image.bean.threshold: Calculates a threshold-level from a histogram.
CalculateLevel() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevel
calculateLevelFromDelegate(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary: Determines a voxel intensity that can be used for thresholding from the delegate calculateLevel.
CalculateLevelUnary - Class in org.anchoranalysis.image.bean.threshold: Implementation of CalculateLevel that calls a single delegate CalculateLevel.
CalculateLevelUnary() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
canEqual(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
Cell - Class in org.anchoranalysis.image.bean.spatial.arrange.tile: Indicates how to arrange one or more RGBStacks in a cell in a table.
Cell() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell
Cell(StackArranger, int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell
CENTER - org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Aligns to the center position along the axis.
CENTER - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the center (middle) in the respective dimension.
ChannelAggregator - Class in org.anchoranalysis.image.bean.channel: A method of aggregating the voxels from many identically-sized Channels into one.
ChannelAggregator() - Constructor for class org.anchoranalysis.image.bean.channel.ChannelAggregator
ChannelProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Channel and associated Stack.
ChannelProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProvider
ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider: Implementation of ChannelProvider that calls two ChannelProviders that must provide Channels of the same dimensions.
ChannelProviderBinary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider: Implementation of ChannelProvider that calls three ChannelProviders that must provide Channels of the same dimensions.
ChannelProviderTernary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of ChannelProvider that calls a single delegate ChannelProvider.
ChannelProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
channels() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Channels, indexed by name.
checkChannelType(Channel) - Method in class org.anchoranalysis.image.bean.nonbean.ConsistentChannelChecker: Checks that a channel has the same type (max value) as the others.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
checkUnsupported3D(Channel) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the implementation.
checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Throws an exception if object is present, as it is unsupported by the implementation.
checkUnsupportedSeeds(Optional<ObjectCollection>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Throws an exception if seeds is present, as it is unsupported by the implementation.
ColorProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a ColorList.
ColorProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ColorProvider
combine(List<RGBStack>, VoxelsResizer, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.StackArranger: Creates a new RGBStack of voxel data type unsigned byte that is a combination of other RGBStacks.
combine(List<RGBStack>, VoxelsResizer, ChannelFactorySingleType, OperationContext) - Method in class org.anchoranalysis.image.bean.spatial.arrange.StackArranger: Creates a new RGBStack that is a combination of other RGBStacks.
combinedStacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Exposes several entities that have natural Stack representations as a unified NamedProvider.
compareTo(ExtentToArrange) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Sorts in descending order by extent.
ConsistentChannelChecker - Class in org.anchoranalysis.image.bean.nonbean: Checks that all Channels have the same voxel-data-type.
ConsistentChannelChecker() - Constructor for class org.anchoranalysis.image.bean.nonbean.ConsistentChannelChecker
ConvertChannelTo<T> - Class in org.anchoranalysis.image.bean.channel: Creates a ChannelConverter for converting a channel to a particular type.
ConvertChannelTo() - Constructor for class org.anchoranalysis.image.bean.channel.ConvertChannelTo
ConvertChannelToWithHistogram<T> - Class in org.anchoranalysis.image.bean.channel: Creates a ChannelConverterAttached<Histogram, T> for converting a channel to a particular type, making use of a Histogram.
ConvertChannelToWithHistogram() - Constructor for class org.anchoranalysis.image.bean.channel.ConvertChannelToWithHistogram
copyImageInto(Stack, Stack, BoundingBox) - Static method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackCopierAtBox: Copies a source stack into a destination stack at a particular BoundingBox.
copyInitialize(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define and initializes.
copyProviderInitialize(Class<?>, NamedProviderStore<T>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class (which must be a Provider) from define and initializes each.
copyWithoutInitialize(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine: Copies objects of a particular class from the define without performing any initialization.
createConverter() - Method in class org.anchoranalysis.image.bean.channel.ConvertChannelTo: Creates the converter.
createConverter() - Method in class org.anchoranalysis.image.bean.channel.ConvertChannelToWithHistogram: Creates the converter.
createConverterFor(VoxelDataType) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles
createConverterFor(VoxelDataType) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Determines what kind of converter to use for a particular channel, to map it to an unsigned 8-bit channel.
createFromChannel(Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary: Creates a Channel given the entity provided by the delegate.
createFromHistogram(Histogram) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary: Creates a Histogram given the entity provided by the delegate.
createFromMask(Mask) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary: Creates a Mask given the entity provided by the delegate.
createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary: Creates a ObjectCollection given the entity provided by the delegate.
createFromStack(Stack) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary: Creates a Stack given the entity provided by the delegate.
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean: Creates a vector in a particular direction.
createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.Interpolator: Create a VoxelsResizer that can be used for resizing voxel-buffers.
createVoxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.None

D

deriveFrom(Channel) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Creates from a Channel.
deriveFrom(RGBStack) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Derives a DisplayStack from a RGBStack.
deriveFrom(Stack) - Method in class org.anchoranalysis.image.bean.displayer.StackDisplayer: Derives a DisplayStack from a RGBStack.
describeBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay
dictionaries() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Named-store of Dictionarys.
DICTIONARY_IDENTIFIER - Static variable in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: The name of the dictionary added by ImageInitialization.addSharedObjectsDictionary(java.util.Optional<org.anchoranalysis.core.identifier.provider.store.SharedObjects>, java.util.Optional<org.anchoranalysis.core.value.Dictionary>).
dictionaryInitialization() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: The associated initialization for a DictionaryBean.
DimensionsProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide Dimensions.
DimensionsProvider() - Constructor for class org.anchoranalysis.image.bean.provider.DimensionsProvider
DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction: A bean that creates a DirectionVector.
DirectionVectorBean() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance: Implementation of UnitValueDistance that specifies a value in physical units, as described by particular recognized strings.
DistancePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance: Implementation of UnitValueDistance that specifies a value in voxels, ignoring any physical image resolution.
DistanceVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
DistanceVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels: Create with a particular value.
duplicateBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align

E

equals(Object) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: To correspond to ExtentToArrange.compareTo(ExtentToArrange).
equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
existingDimensions() - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: The Dimensions to use for the aggregation.
extent() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: The size of the larger image in which all the BoundingBoxes in list must fully reside.
ExtentToArrange - Class in org.anchoranalysis.image.bean.spatial.arrange.fill: A particular Extent to be arranged, with calculated aspect-ratio, and its unique index position.
ExtentToArrange(int, Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Create with a particular index and size.

F

featuresInitialization() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: The associated initialization for a FeatureRelatedBean.
filePaths() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Named-store of file-paths.
Fill - Class in org.anchoranalysis.image.bean.spatial.arrange.fill: Montages Extents together to completely fill the available space, while preserving aspect ratio.
Fill() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
Fill(int) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: Create with a particular number of rows.
Fill(int, boolean, int, double) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill
filter(ObjectCollection, Optional<Dimensions>) - Method in class org.anchoranalysis.image.bean.object.ObjectFilter: Filters an ObjectCollection to remove objects.
findMatch(ObjectCollection) - Method in class org.anchoranalysis.image.bean.object.ObjectMatcher: Finds matches for objects.
FitCombinedScaler - Class in org.anchoranalysis.image.bean.spatial.arrange.fill: Scales the size of images to match the target image, preserving aspect-ratio.

G

get() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
get() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
get() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
get() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange
get() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
get(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Gets the BoundingBox corresponding to a particular index.
getAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: How to align the box after it is grown, as much as possible.
getAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Indicates how to align the image across the three axes.
getAligner() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: How to align a smaller image inside a larger cell.
getAlignX() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the X-axis (i.e.
getAlignY() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Y-axis (i.e.
getAlignZ() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Z-axis: one of top, bottom, center, repeat.
getArrange() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Determines how the stacks in list are arranged.
getArrange() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: How to arrange any RGBStacks in this particular cell.
getAspectRatio() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: The aspect-ratio: width of extent divided by height.
getAsStack() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
getAsStack() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
getAsStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
getAxis() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector: Which axis the unit-vector will align with.
getBox() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: The BoundingBox in which the image should be placed.
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary: The delegate CalculateLevel.
getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
getCellDefault() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Used to define an individual cell, when no specific entry is found in cells for a particular cell.
getCells() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Defines the corresponding StackArranger for an individual cell in table.
getChannel() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary: The delegate ChannelProvider that is called.
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The first delegate ChannelProvider that is called.
getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The first delegate ChannelProvider that is called.
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The second delegate ChannelProvider that is called.
getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The second delegate ChannelProvider that is called.
getChannel3() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The third delegate ChannelProvider that is called.
getColumn() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The column in the table that the cell refers to (zero-indexed).
getEnclosing() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxEnclosed: An enclosing box (equal to or larger than box covering all screen-space used for this entity, including padding.
getExtent() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: The Extent.
getHeight() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in Y dimension.
getHistogram() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary: The delegate HistogramProvider that is called.
getId() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference: The identifier of the existing BinarySegmentation to use.
getIndex() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Index position.
getIntensityHistogram() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: A histogram of the intensity values of the voxels that are being segmented.
getInterpolator() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The interpolator to use for scaling images, if needed.
getList() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The stacks that are passed in respect order into arrange.
getMask() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary: The delegate Provider<Mask> that is called.
getNumberColumns() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of columns to use in the table produced when tiling.
getNumberRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The number of rows to use the montage, when sufficient images are available.
getNumberRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of rows to use in the table produced when tiling.
getObjects() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary: The delegate Provider<ObjectCollection> that is called.
getPaddingXY() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
getPaddingZ() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
getQuantileLower() - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the lower-limit for the intensity range to display.
getQuantileUpper() - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the upper-limit for the intensity range to display.
getResolution() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters: A Resolution associated with the image being segmented.
getRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The row in the table that the cell refers to (zero-indexed).
getScaleRoundingError() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Stores the difference that occurs between a discretized scaled width and what it should ideally be.
getSegment() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary: The delegate BinarySegmentation that may be called.
getSegment() - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary: The delegate SegmentChannelIntoObjects that is called.
getStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary: The delegate Provider<Stack> that is called.
getThresholder() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold: Performs the global thresholding.
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: A string indicating type of units to use, as per SpatialUnits.
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: How much each value represents e.g.
getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: How much each value represents e.g.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: The value in units of type unitType.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels: The distance in units of voxels.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: The volume in units of meters, with the unit described by unitType.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels: The volume in pixels.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: The volume in units of meters, with the unit described by unitType.
getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels: The volume in voxels.
getVoxelDataType() - Method in class org.anchoranalysis.image.bean.nonbean.ConsistentChannelChecker: The voxel-data-type that is consistent across all channels.
getWidth() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The width of the combined image in pixels.
getWidth() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in X dimension.
getWidthRatio() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: What fraction of the natural width of the elements should be used to determine the final width.
getX() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the x-axis.
getY() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the y-axis.
getZ() - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the z-axis.
Grow - Class in org.anchoranalysis.image.bean.spatial.arrange.align: Grow the bounding-box to fill larger as much as possible.
Grow() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
Grow(boolean) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Create to preserve the aspect-ratio or not.
Grow(boolean, Align) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.align.Grow
growWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Changes the width of the underlying Extent by adding growBy pixels.

H

hashCode() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
hashCode() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: To correspond to ExtentToArrange.equals(Object).
hashCode() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
hasNoPadding() - Method in class org.anchoranalysis.image.bean.spatial.Padding: Whether no padding exists.
HistogramProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Histogram.
HistogramProvider() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProvider
HistogramProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of HistogramProvider that calls a single delegate HistogramProvider.
HistogramProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
histograms() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Histograms, indexed by name.

I

ImageBean<T> - Class in org.anchoranalysis.image.bean: A bean that must be initialized with ImageInitialization before usage.
ImageBean() - Constructor for class org.anchoranalysis.image.bean.ImageBean: Create with default initializer and assigner.
ImageInitialization - Class in org.anchoranalysis.image.bean.nonbean.init: The state used to initialize a ImageBean.
ImageInitialization(SharedObjects) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Create with shared-objects.
ImageInitialization(SharedObjects, Optional<ImageSizeSuggestion>) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Create with shared-objects and a resizing suggestion.
ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator: Resizes with an interpolator that uses Lanczos resampling as implemented in Imglib2.
ImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator: Resizes with an interpolator that uses linear interpolation as implemented in Imglib2.
ImgLib2Linear() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
IntensityQuantiles - Class in org.anchoranalysis.image.bean.displayer: Implementation of StackDisplayer that converts to unsigned-8bit by taking the upper and lower quantiles of the intensity range.
IntensityQuantiles() - Constructor for class org.anchoranalysis.image.bean.displayer.IntensityQuantiles
Interpolator - Class in org.anchoranalysis.image.bean.interpolator: Defines a particular type of interpolation method that can be used for resizing images.
Interpolator() - Constructor for class org.anchoranalysis.image.bean.interpolator.Interpolator
isCreateShort() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: If true, the created raster has unsigned short voxel data type.
isForceRGB() - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Iff true, ensures every stack is converted into 3 channels.
isPreserveAspectRatio() - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Whether to preserve the aspect-ratio of the smaller image when growing.
isVaryNumberImagesPerRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: When true the number of Extents per row is allowed vary, to sensibly fill space.
iterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement

L

LEFT - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the left in the X-dimension/

M

MaskProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide a Mask and associated Stack.
MaskProvider() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProvider
MaskProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of MaskProvider that calls a single delegate MaskProvider.
MaskProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProviderUnary
masks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Masks, indexed by name.
MAX - org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Aligns to the maximum position along the axis.
maybeDropResolution(Dimensions) - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Removes the Resolution component in Dimensions.
MIN - org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Aligns to the minimum position along the axis.
modelDirectory() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Directory where machine-learning models can be found.

N

None - Class in org.anchoranalysis.image.bean.interpolator: An implementation of Interpolator that performs no interpolation.
None() - Constructor for class org.anchoranalysis.image.bean.interpolator.None

O

ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider: Base class for beans that implement Provider to provide an ObjectCollection.
ObjectCollectionProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider: Implementation of ObjectCollectionProvider that calls a single delegate Provider<ObjectCollection>.
ObjectCollectionProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
ObjectFilter - Class in org.anchoranalysis.image.bean.object: Base class for filtering an ObjectCollection to remove objects according to a criteria.
ObjectFilter() - Constructor for class org.anchoranalysis.image.bean.object.ObjectFilter
ObjectMatcher - Class in org.anchoranalysis.image.bean.object: Matches an object with other objects.
ObjectMatcher() - Constructor for class org.anchoranalysis.image.bean.object.ObjectMatcher
objects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of ObjectCollections, indexed by name.
onInitialization(ImageInitialization) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean: Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel - package org.anchoranalysis.image.bean.channel: Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.displayer - package org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator: Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean - package org.anchoranalysis.image.bean.nonbean: Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init: Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment: Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.align - package org.anchoranalysis.image.bean.nonbean.spatial.align: Non-bean classes to help specify the position of one entity relative to the others.
org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange: Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object: Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider: Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack: A provider of Stacks.
org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment: Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary: Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object: Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial: Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange: Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.arrange.align - package org.anchoranalysis.image.bean.spatial.arrange.align: Aligning a BoundingBox to fit inside another BoundingBox.
org.anchoranalysis.image.bean.spatial.arrange.fill - package org.anchoranalysis.image.bean.spatial.arrange.fill: Montages images together to completely fill the available space, while preserving aspect ratio.
org.anchoranalysis.image.bean.spatial.arrange.overlay - package org.anchoranalysis.image.bean.spatial.arrange.overlay: Combining other images through overlaying.
org.anchoranalysis.image.bean.spatial.arrange.tile - package org.anchoranalysis.image.bean.spatial.arrange.tile: Combining other images through tiling.
org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction: Beans to specify a direction.
org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold: Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation: Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance: Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent: Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area: Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume: Converting quantities of volume between units.
Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange.overlay: Overlays one image on the other.
Overlay() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay
Overlay(String, String, String) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Creates with alignment text for each axis.
Overlay(Align) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay

P

Padding - Class in org.anchoranalysis.image.bean.spatial: Padding (whitespace of certain extent) placed around an object in XY direction and in Z direction.
Padding() - Constructor for class org.anchoranalysis.image.bean.spatial.Padding
populate(BeanInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Adds diverse entities from a Define into the corresponding name-collections.
PopulateStoreFromDefine<V extends BeanInitialization> - Class in org.anchoranalysis.image.bean.nonbean.init: Helps populates a NamedProviderStore from the contents of a Define.
PopulateStoreFromDefine(Define, BeanInitializer<?>, Logger) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
PositionChoices - Class in org.anchoranalysis.image.bean.nonbean.spatial.align: The choices of text that may describe the position of an entity along a particular axis.
PositionChoices(String, String, String) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoices
PositionChoices(String, String, String, Optional<String>) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoices
PositionChoicesConstants - Class in org.anchoranalysis.image.bean.nonbean.spatial.align: A constant set of text strings used to indicate particular choices.
process(Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: Creates a Channel given the two entities provided by the delegates.
process(Channel, Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: Creates a Channel given the two entities provided by the delegates.

R

relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
REPEAT - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: The choice which will cause a single-slice in the z-dimension to be duplicated across the z-dimension to match the z-size onto which it is projected.
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance using a DirectionVector.
resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance using the direction between two points of type Point3d.
resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance using the direction between two points of type Point3i.
resolveForAxis(Optional<UnitConverter>, Axis) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance: Resolves the distance in a direction aligned to a particular axis.
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueExtent: Resolves a measurement of area/volume (in whatever units) to units corresponding to the image pixels/voxels.
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
retrieveCreateAggregatedChannel() - Method in class org.anchoranalysis.image.bean.channel.ChannelAggregator: Retrieve or create an aggregated-channel of type outputType.
RIGHT - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the right in the X-dimension/

S

ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial: Calculating a scaling-factor from dimensions.
ScaleCalculator() - Constructor for class org.anchoranalysis.image.bean.spatial.ScaleCalculator
scaleToMatchRow(double, int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: Changes the size of the image to match a row that has a total width of rowWidth, preserving aspect-ratio.
scaleToWidth(List<List<ExtentToArrange>>, boolean, int) - Static method in class org.anchoranalysis.image.bean.spatial.arrange.fill.FitCombinedScaler: Calculates the size of the combined image to use for the montage, and scales the associated Extent each to match.
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects: Segments a channel to produce an object-collection.
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary: Creates an ObjectCollection given the segmentation-results provided by the delegate.
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation: Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary
SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment: Performs some kind of segmentation on an image.
SegmentationBean() - Constructor for class org.anchoranalysis.image.bean.segment.SegmentationBean
SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.segment: When a segmentation cannot successfully complete.
SegmentationFailedException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.segment.SegmentationFailedException: Create with a message only.
SegmentationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.segment.SegmentationFailedException: Create with a message and a cause.
SegmentationFailedException(Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.segment.SegmentationFailedException: Create with a cause only.
SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object: A base class for algorithms to segment a channel into one or more objects.
SegmentChannelIntoObjects() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object: Implementation of SegmentChannelIntoObjects that calls a single delegate SegmentChannelIntoObjects.
SegmentChannelIntoObjectsUnary() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary: Performs a binary-segmentation, in a similar manner to BinarySegmentation.segment(org.anchoranalysis.image.voxel.VoxelsUntyped, org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters, java.util.Optional<org.anchoranalysis.image.voxel.object.ObjectMask>) but with the delegate as additional argument.
setAlign(Align) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: How to align the box after it is grown, as much as possible.
setAlign(Align) - Method in class org.anchoranalysis.image.bean.spatial.arrange.overlay.Overlay: Indicates how to align the image across the three axes.
setAligner(BoxAligner) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: How to align a smaller image inside a larger cell.
setAlignX(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the X-axis (i.e.
setAlignY(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Y-axis (i.e.
setAlignZ(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Align: Indicates how to align the image across the Z-axis: one of top, bottom, center, repeat.
setArrange(StackArranger) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Determines how the stacks in list are arranged.
setArrange(StackArranger) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: How to arrange any RGBStacks in this particular cell.
setAxis(String) - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector: Which axis the unit-vector will align with.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelUnary: The delegate CalculateLevel.
setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
setCellDefault(StackArranger) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Used to define an individual cell, when no specific entry is found in cells for a particular cell.
setCells(List<Cell>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Defines the corresponding StackArranger for an individual cell in table.
setChannel(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary: The delegate ChannelProvider that is called.
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The first delegate ChannelProvider that is called.
setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The first delegate ChannelProvider that is called.
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary: The second delegate ChannelProvider that is called.
setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The second delegate ChannelProvider that is called.
setChannel3(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary: The third delegate ChannelProvider that is called.
setColumn(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The column in the table that the cell refers to (zero-indexed).
setCreateShort(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: If true, the created raster has unsigned short voxel data type.
setForceRGB(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: Iff true, ensures every stack is converted into 3 channels.
setHeight(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in Y dimension.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary: The delegate HistogramProvider that is called.
setId(String) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference: The identifier of the existing BinarySegmentation to use.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The interpolator to use for scaling images, if needed.
setList(List<Provider<Stack>>) - Method in class org.anchoranalysis.image.bean.provider.stack.Arrange: The stacks that are passed in respect order into arrange.
setMask(Provider<Mask>) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary: The delegate Provider<Mask> that is called.
setNumberColumns(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of columns to use in the table produced when tiling.
setNumberRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The number of rows to use the montage, when sufficient images are available.
setNumberRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: The number of rows to use in the table produced when tiling.
setObjects(Provider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary: The delegate Provider<ObjectCollection> that is called.
setPaddingXY(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
setPaddingZ(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
setPreserveAspectRatio(boolean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.align.Grow: Whether to preserve the aspect-ratio of the smaller image when growing.
setQuantileLower(double) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the lower-limit for the intensity range to display.
setQuantileUpper(double) - Method in class org.anchoranalysis.image.bean.displayer.IntensityQuantiles: The lower quantile to use as the upper-limit for the intensity range to display.
setRow(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.tile.Cell: The row in the table that the cell refers to (zero-indexed).
setSegment(BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationUnary: The delegate BinarySegmentation that may be called.
setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary: The delegate SegmentChannelIntoObjects that is called.
setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary: The delegate Provider<Stack> that is called.
setThresholder(Thresholder) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold: Performs the global thresholding.
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: A string indicating type of units to use, as per SpatialUnits.
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: How much each value represents e.g.
setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: How much each value represents e.g.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical: The value in units of type unitType.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels: The distance in units of voxels.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical: The volume in units of meters, with the unit described by unitType.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels: The volume in pixels.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical: The volume in units of meters, with the unit described by unitType.
setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels: The volume in voxels.
setVaryNumberImagesPerRow(boolean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: When true the number of Extents per row is allowed vary, to sensibly fill space.
setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: The width of the combined image in pixels.
setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY: Size in X dimension.
setWidthRatio(double) - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.Fill: What fraction of the natural width of the elements should be used to determine the final width.
setX(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the x-axis.
setY(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the y-axis.
setZ(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Component of the vector along the z-axis.
sharedObjects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: Objects shared between different components, a form of shared memory between them.
Single - Class in org.anchoranalysis.image.bean.spatial.arrange: A single Stack arranged as-is.
Single() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Single
SizeXY - Class in org.anchoranalysis.image.bean.spatial: The size of an entity in the X and Y dimensions.
SizeXY() - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
SizeXY(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
SizeXY(Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY: Create form an Extent.
SpecifyVector - Class in org.anchoranalysis.image.bean.spatial.direction: Specifies each axis-component of a vector in a particular direction.
SpecifyVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector
SpecifyVector(double, double, double) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector
SpecifyVector(DirectionVector) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.SpecifyVector: Create from a DirectionVector.
StackArrangement - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: A list of BoundingBoxes that indicate where to locate corresponding Stacks on a unified larger image.
StackArrangement(Extent) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Create with the overall Extent and no boxes.
StackArrangement(Extent, List<BoundingBoxEnclosed>) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
StackArrangement(Extent, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement: Create with a single BoundingBox.
StackArranger - Class in org.anchoranalysis.image.bean.spatial.arrange: Base class for a method that determines positions for RGBStacks when combined onto a single plane.
StackArranger() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.StackArranger
StackCopierAtBox - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange: Copies a source stack into a destination stack at a particular BoundingBox.
StackDisplayer - Class in org.anchoranalysis.image.bean.displayer: Converts from a Channel or Stack to a DisplayStack so that it can be displayed.
StackDisplayer() - Constructor for class org.anchoranalysis.image.bean.displayer.StackDisplayer
StackProvider - Class in org.anchoranalysis.image.bean.provider.stack: Base class for beans that implement Provider to provide a Stack.
StackProvider() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProvider
StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack: Implementation of StackProvider that calls a single delegate Provider<Stack>.
StackProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
stacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A collection of Stacks, indexed by name.
suggestedSize() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitialization: A suggested input on how to resize an image, if one is provided.

T

threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
threshold(VoxelsUntyped) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Like Thresholder.threshold(VoxelsUntyped) but using default binary-values.
threshold(VoxelsUntyped, BinaryValuesByte) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Like Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder: Thresholds voxels (across a range of values) so that they have only binary range (i.e.
threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
Thresholder - Class in org.anchoranalysis.image.bean.threshold: Thresholds voxels to create a binary-voxels using global thresholding.
Thresholder() - Constructor for class org.anchoranalysis.image.bean.threshold.Thresholder
ThresholderGlobal - Class in org.anchoranalysis.image.bean.threshold: Performs global thresholding.
ThresholderGlobal() - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
ThresholderGlobal(CalculateLevel) - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
Tile - Class in org.anchoranalysis.image.bean.spatial.arrange.tile: A higher-level aggregate structure that arranges other StackArrangers in a tabular pattern.
Tile() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile
Tile(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.tile.Tile: Creates for a particular number of columns and rows.
TOP - Static variable in class org.anchoranalysis.image.bean.nonbean.spatial.align.PositionChoicesConstants: Align to the top in the Y-dimension.
toString() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.StackArrangement
toString() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange
toString() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels

U

uniqueName() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
UnitValueArea - Class in org.anchoranalysis.image.bean.unitvalue.extent.area: A base class for a value that describes an area measurement on the image.
UnitValueArea() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
UnitValueDistance - Class in org.anchoranalysis.image.bean.unitvalue.distance: Base class for methods to specify a distance along a vector in an image.
UnitValueDistance() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
UnitValueException - Exception in org.anchoranalysis.image.bean.nonbean: When a failure occurs converting from one type of units to another.
UnitValueException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.UnitValueException: Create with a cause.
UnitValueException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.UnitValueException: Create with a message.
UnitValueExtent - Class in org.anchoranalysis.image.bean.unitvalue.extent: A base class for a value that describes an area or volume measurement, which can then be resolved to a number of voxels.
UnitValueExtent() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueExtent
UnitValueVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume: A base class for a value that describes a volume measurement on the image.
UnitValueVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.UnitValueVolume

V

valueOf(String) - Static method in enum org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.anchoranalysis.image.bean.nonbean.spatial.align.AlignmentOnDimension: Returns an array containing the constants of this enum type, in the order they are declared.
VolumePhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume: Volume expressed in cubic meters, or units thereof.
VolumePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
VolumeVoxels - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume: Volume expressed in voxels.
VolumeVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
VolumeVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
voxelsResizer() - Method in class org.anchoranalysis.image.bean.interpolator.Interpolator: Memoizes a call to Interpolator.createVoxelsResizer().

W

width() - Method in class org.anchoranalysis.image.bean.spatial.arrange.fill.ExtentToArrange: The size in the X-dimension.

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