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

absolutePath - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractCoordinateTransform<T extends net.imglib2.realtransform.RealTransform> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AbstractCoordinateTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

AbstractCoordinateTransform(String, String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

AbstractCoordinateTransform(String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

AbstractCoordinateTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

AbstractCoordinateTransform(CoordinateTransform<T>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

AbstractCoordinateTransform(CoordinateTransform<T>, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

AbstractCoordinateTransformation<T extends net.imglib2.realtransform.AffineGet> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

AbstractCoordinateTransformation(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.AbstractCoordinateTransformation

AbstractLinearCoordinateTransform<T extends net.imglib2.realtransform.AffineGet,P> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AbstractLinearCoordinateTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearCoordinateTransform(String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearCoordinateTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearCoordinateTransform(String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearCoordinateTransform(String, String, String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearCoordinateTransform(AbstractLinearCoordinateTransform<T, P>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearCoordinateTransform(AbstractLinearCoordinateTransform<T, P>, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

AbstractLinearSpatialTransform<P> - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

AbstractLinearSpatialTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

AbstractLinearSpatialTransform(String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

AbstractMetadataTemplateParser<T extends N5Metadata> - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

Interface for metadata describing how spatial data are oriented in physical space.

AbstractMetadataTemplateParser(Gson, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

AbstractN5Builder - Class in org.janelia.saalfeldlab.n5.universe.options

AbstractN5DatasetMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

Abstract class for single-scale or multi-scale N5 metadata.

AbstractN5DatasetMetadata(String, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.AbstractN5DatasetMetadata

AbstractN5Metadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

Abstract class for single-scale or multi-scale N5 metadata.

AbstractN5Metadata(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.AbstractN5Metadata

AbstractN5SpatialDatasetMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

Abstract class for single-scale or multi-scale N5 metadata.

AbstractN5SpatialDatasetMetadata(String, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.AbstractN5SpatialDatasetMetadata

AbstractParametrizedFieldTransform<T extends net.imglib2.realtransform.RealTransform,S extends net.imglib2.type.numeric.RealType<S>> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AbstractParametrizedFieldTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

AbstractParametrizedFieldTransform(String, String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

AbstractParametrizedFieldTransform(String, String, String, String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

AbstractParametrizedRealFieldTransform<T extends net.imglib2.realtransform.RealTransform,P,V extends net.imglib2.type.numeric.NumericType<V>> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AbstractParametrizedRealFieldTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

AbstractParametrizedRealFieldTransform(String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

AbstractParametrizedTransform<T extends net.imglib2.realtransform.RealTransform,P> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AbstractParametrizedTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractParametrizedTransform(String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractParametrizedTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractParametrizedTransform(String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractParametrizedTransform(String, String, String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractParametrizedTransform(AbstractParametrizedTransform<T, P>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractParametrizedTransform(AbstractParametrizedTransform<T, P>, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

AbstractSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

AbstractSpatialTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractSpatialTransform

add(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

add(Axis) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

add(TransformGraph) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

add(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

Adds a node as a child of this node.

add(Predicate<ContainerMetadataNode>, ContainerTranslation) - Method in class org.janelia.saalfeldlab.n5.universe.translation.PiecewiseContainerTranslation

addAll(Collection<CoordinateSystem>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

addAll(Stream<CoordinateSystem>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

addChild(String, ContainerMetadataNode) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

addChild(NgffSingleScaleAxesMetadata) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

addChild(int, NgffSingleScaleAxesMetadata) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

addDefault(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

addDefaultGroupParser(N5MetadataParser<?>, boolean) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

Adds a group parser to the default list.

addDefaultGroupParser(N5MetadataParser<?>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

Prepends to the default group parser list.

addDefaultParser(N5MetadataParser<?>, boolean) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

Adds a parser to the current default list.

addDefaultParser(N5MetadataParser<?>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

Prepends to the default parser list.

addPath(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

Adds a node at the specified full path and any parent nodes along the path, if they do not already exist.

addPath(String, Function<String, N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

Adds a node at the specified full path and any parent nodes along the path, if they do not already exist.

addPathsRecursive() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

Adds path attributes to this node and recursively to its children.

addPathsRecursive(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

Adds path attributes to this node and recursively to its children.

addSpace(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

addTransform(CoordinateTransform<?>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

affine - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

affine - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

affine - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

AFFINE_TRANSFORM_KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

AffineCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AffineCoordinateTransform(BaseLinearCoordinateTransform<AffineGet>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

AffineCoordinateTransform(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

AffineCoordinateTransform(String, String, String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

AffineCoordinateTransform(String, N5Reader, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

AffineCoordinateTransform(String, String[], String[], double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

AffineCoordinateTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

AffineCoordinateTransformAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

AffineCoordinateTransformAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransformAdapter

affineFlat - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

AffineSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

AffineSpatialTransform(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

AffineSpatialTransform(N5Reader, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

AffineSpatialTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

affineToMatrix(AffineGet) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

AffineTransform3DJsonAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata

AffineTransform3DJsonAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.AffineTransform3DJsonAdapter

allPaths(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

allPaths(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

allSameAxisOrder(DatasetAttributes[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

ANGSTROM_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

apply(URI, N5Factory, Boolean) - Method in enum org.janelia.saalfeldlab.n5.universe.KeyValueAccessBackend

apply(RandomAccessibleInterval<T>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

apply(N5Reader, N5TreeNode) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser

apply(S) - Method in class org.janelia.saalfeldlab.n5.universe.translation.JqFunction

apply(ContainerMetadataNode) - Method in class org.janelia.saalfeldlab.n5.universe.translation.PiecewiseContainerTranslation

args - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

ARRAY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

arrayAxes(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.ArrayCoordinateSystem

ArrayCoordinateSystem - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes

ArrayCoordinateSystem() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.ArrayCoordinateSystem

ArrayCoordinateSystem(int) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.ArrayCoordinateSystem

ArrayCoordinateSystem(String, int) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.ArrayCoordinateSystem

asAffine(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

ATTOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

ATTOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

attributes - Variable in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

axes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

axes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisListMetadata

axes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

axes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

axes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

axesEquals(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

Returns true if these two spaces contain the same set of axes, in any order.

axesEquals(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

Returns true if these two spaces contain the same set of axes, in any order.

axesForSpace(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

axesFromIndexes(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

axesFromIndexes(int[], String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

axesFromLabels(String[], String[], int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

axesFromLabels(String[], String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

axesFromLabels(String[], int[], String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

axesFromLabels(String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

axesFromLabels(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

axesLabelsMatch(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

Axis - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

Axis(String, String, String, boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

see https://ngff.openmicroscopy.org/0.4/index.html#axes-md

Axis(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

see https://ngff.openmicroscopy.org/0.4/index.html#axes-md

Axis(String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

see https://ngff.openmicroscopy.org/0.4/index.html#axes-md

Axis(String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

see https://ngff.openmicroscopy.org/0.4/index.html#axes-md

AXIS_KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

AxisAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes

AxisAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.AxisAdapter

AxisMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata.axes

Metadata that labels and assigns types to axes.

axisOrdersForTransform(CoordinateTransform<?>[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

Builds a list of axes for intermediate results given a set of target axes and a list of transformations.

axisOrdersForTransform2(CoordinateTransform<?>[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

Builds a list of axes for intermediate results given a set of target axes and a list of transformations.

axisOrdersForTransformFirst(CoordinateTransform<?>[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

axisPermutationTransform(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

AxisSlicer - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

AxisSlicer(AxisMetadata) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

AxisUtils - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

AxisUtils() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

AxisUtils.DefaultAxisTypes - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

B

BaseLinearCoordinateTransform<T extends net.imglib2.realtransform.AffineGet> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

BaseLinearCoordinateTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(BaseLinearCoordinateTransform<T>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, String, String, String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, String, N5Reader, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, String, String[], String[], double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

BaseLinearCoordinateTransform(String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

basePath - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

BijectionCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

BijectionCoordinateTransform(String, String, String, RealCoordinateTransform<?>, RealCoordinateTransform<?>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BijectionCoordinateTransform

blockExists(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

blockExists(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

build(N5Reader, String, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

build(N5Reader, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

build() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

buildAxes(String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

buildAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

buildChild(int, N5DatasetMetadata) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

buildChildren(int, DatasetAttributes[], CoordinateTransformation<?>[], Axis[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

buildChildren() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

buildCosemMetadata(String, N5CosemMetadata, double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

builder() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

builder(boolean) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

Builder() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

buildForWriting(int, String, String, Axis[], String[], double[][], double[][]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata

Creates an OmeNgffMetadata object for writing.

buildGson(N, String, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

buildGson() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildGson(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

buildHelper(N, N5TreeNode) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

buildHelperN5(N5Reader, N5TreeNode, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

buildImpliedTransform(CoordinateSystem, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

buildJsonParameter() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

buildMetadata(int, String, DatasetAttributes[], OmeNgffMultiScaleMetadata) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

buildMetadata(int, String, OmeNgffMultiScaleMetadata.OmeNgffDataset[], DatasetAttributes[], CoordinateTransformation<?>[], OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata, Axis[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

buildMetadata(int, String, OmeNgffMultiScaleMetadata.OmeNgffDataset[], DatasetAttributes[], CoordinateTransformation<?>[], OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata, Axis[], boolean) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

buildN5(T, String, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

buildN5VMetadata(String, N5SingleScaleMetadata, String, double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

buildNgffMetadata(String, NgffSingleScaleAxesMetadata, double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

buildReader(String) - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

buildReader(KeyValueAccess, String) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5Builder

buildReader(KeyValueAccess, String) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

buildReader(KeyValueAccess, String) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr3Builder

buildRootScope() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

buildRootScope() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

Deprecated.

buildRootScope() - Static method in class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

buildScaleTranslationTransformList(double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

buildSpaces() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildSpaces(String, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildSpaces(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildTransform(double[], double[], Optional<AffineTransform3D>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

buildTransform(CoordinateTransformation<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformationUtils

buildTransform(P) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

buildTransform(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

buildTransform(RealRandomAccessible<RealComposite<T>>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

buildTransform(RealRandomAccessible<RealComposite<T>>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

buildTransform(P) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ParametrizedTransform

buildTransform(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

buildTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

buildTransform(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

buildTransform(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

buildTransform(P) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.transforms.ParametrizedTransform

buildTransform(double[], double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

buildTransform(double[][]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

buildTransform(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

buildTransform(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

buildTransformFromAxes(CoordinateSystem, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

buildTransformGraph() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildTransformGraph(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildTransformGraph(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildTransformGraph(String, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

buildWriter(String) - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

buildWriter(KeyValueAccess, String) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5Builder

buildWriter(KeyValueAccess, String) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

buildWriter(KeyValueAccess, String) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr3Builder

C

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions() and N5FactoryOptions.cacheAttributes(boolean)

cacheAttributes - Variable in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5Builder

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

Set the attributes caching behavior.

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

cacheAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr3Builder

CalibratedSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

CalibratedSpatialTransform(SpatialTransform, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.CalibratedSpatialTransform

CalibratedTransformMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CalibratedTransformMetadata(String, CalibratedSpatialTransform, Axis[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CalibratedTransformMetadata

CanonicalDatasetMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalDatasetMetadata(String, DatasetAttributes, double, double, ColorMetadata) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

CanonicalDatasetMetadata(String, DatasetAttributes, CanonicalDatasetMetadata.IntensityLimits, ColorMetadata) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

CanonicalDatasetMetadata(String, DatasetAttributes, ColorMetadata) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

CanonicalDatasetMetadata(String, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

CanonicalDatasetMetadata.IntensityLimits - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata.canonical

canonicalMetadata(HashMap<String, JsonElement>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

canonicalMetadata(HashMap<String, JsonElement>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

CanonicalMetadataAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalMetadataAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataAdapter

CanonicalMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

A parser for the "canonical" metadata dialect.

CanonicalMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

CanonicalMetadataParser(Predicate<CanonicalMetadata>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

CanonicalMetadataParser(N5Reader, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

Deprecated.

CanonicalMultichannelMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalMultichannelMetadata(String, MultiChannelMetadataCanonical) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultichannelMetadata

CanonicalMultiscaleMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalMultiscaleMetadata(String, MultiResolutionSpatialMetadataCanonical) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultiscaleMetadata

canonicalPath(N5TreeNode, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

canonicalPath(String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

CanonicalSpatialDatasetMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalSpatialDatasetMetadata(String, SpatialMetadataCanonical, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

CanonicalSpatialDatasetMetadata(String, SpatialMetadataCanonical, DatasetAttributes, CanonicalDatasetMetadata.IntensityLimits) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

CanonicalSpatialDatasetMetadata(String, SpatialMetadataCanonical, DatasetAttributes, CanonicalDatasetMetadata.IntensityLimits, ColorMetadata) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

CanonicalSpatialMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

CanonicalSpatialMetadata(String, SpatialMetadataCanonical) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

CanonicalSpatialMetadata(String, SpatialMetadataCanonical, CanonicalDatasetMetadata.IntensityLimits) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

CENTIMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

CENTISECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

CHANNEL - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

channelPattern - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

channelScaleLevelPattern - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

channelType - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

child(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

childRelative(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

children - Variable in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

childrenAttributes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

childrenList() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

childrenMetadata - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

cLabel - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

clear() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

clear() - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

ColorMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for metadata that describes

Common - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05

Common() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

ContainerMetadataNode - Class in org.janelia.saalfeldlab.n5.universe.container

ContainerMetadataNode() - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

ContainerMetadataNode(HashMap<String, JsonElement>, Map<String, ContainerMetadataNode>, Gson) - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

ContainerMetadataNode(JsonObject, Map<String, ContainerMetadataNode>, Gson) - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

ContainerMetadataNode(ContainerMetadataNode) - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

ContainerMetadataWriter - Class in org.janelia.saalfeldlab.n5.universe.container

ContainerMetadataWriter(N5Writer, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

ContainerMetadataWriter(N5Writer) - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

ContainerMetadataWriter(N5Writer, ContainerMetadataNode) - Constructor for class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

ContainerTranslation - Interface in org.janelia.saalfeldlab.n5.universe.translation

containerWriter - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

contains(T, T[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Returns true if any elements of array equal t

containsAny(Set<T>, T[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Returns true if any elements of array are contained in the set

CoordinateFieldCoordinateTransform<T extends net.imglib2.type.numeric.RealType<T>> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

CoordinateFieldCoordinateTransform(String, RealRandomAccessible<RealComposite<T>>, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

CoordinateFieldCoordinateTransform(String, N5Reader, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

CoordinateFieldCoordinateTransform(String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

CoordinateSystem - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

CoordinateSystem(String, int) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

CoordinateSystem(String, Axis[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

coordinateSystem() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CTNode

CoordinateSystems - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph

CoordinateSystems() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

CoordinateSystems(Collection<CoordinateSystem>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

CoordinateSystems(Stream<CoordinateSystem>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

CoordinateSystems(CoordinateSystem[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

coordinateSystems() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

CoordinateTransform<T extends net.imglib2.realtransform.RealTransform> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

CoordinateTransformAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

CoordinateTransformAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

CoordinateTransformAdapter(N5Reader) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

CoordinateTransformation<T extends net.imglib2.realtransform.AffineGet> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

An OME-NGFF coordinate transformation.

CoordinateTransformationAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

CoordinateTransformationAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

CoordinateTransformationAdapter(boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

coordinateTransformations - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

coordinateTransformations - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDataset

COORDINATETRANSFORMATIONS_KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

coordinateTransformToScaleAndTranslation(CoordinateTransformation<?>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

cOrder(DatasetAttributes) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

CosemMultiScaleParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMultiScaleMetadata.CosemMultiScaleParser

CosemTransform(String[], double[], double[], String[], String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

CosemTransform(String[], double[], double[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

create(CoordinateTransformation<?>) - Static method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformation

create(CoordinateTransform<?>) - Static method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

createGoogleCloudStorage() - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

createGroup(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

createGroup(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

createReader(String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Creates an N5Reader at containerURI with default N5Factory configuration.

createS3(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

createWriter(String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Creates an N5 writer for the specified container URI with default N5Factory configuration.

CTNode - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph

A node in a TransformGraph.

CTNode(CoordinateSystem) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CTNode

CTNode(CoordinateSystem, List<CoordinateTransform<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CTNode

CUBIC_INTERPOLATION - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

cumNeededAxes(CoordinateTransform<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

D

dataAxes(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

dataAxes(int, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

dataAxes(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

dataAxesStartEnd(int, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

dataAxis(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

DatasetAdapterV03 - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03

Ignores the coordinateTransformations, as those are not present in NGFF v0.3.

DatasetAdapterV03() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03.DatasetAdapterV03

datasetAttributes(Gson, JsonObject) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

datasetAttributes(JsonDeserializationContext, JsonElement) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

datasetAttributes(JsonDeserializationContext, JsonElement) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

datasets - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes

datasets - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

DAY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

DECIMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

DECISECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

DEFAULT_DOWNSAMPLING_FACTORS - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

DEFAULT_MAX - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

DEFAULT_MIN - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

DEFAULT_OFFSET - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

DEFAULT_PARSERS - Static variable in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

DEFAULT_RESOLUTION - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

DEFAULT_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

defaultArray(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

defaultArray(String, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

defaultAxes(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

defaultAxes(String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

defaultAxes(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

defaultAxes(int, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

defaultAxes(int, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

defaultAxes(int, int, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

defaultAxes() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

defaultAxis(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

defaultAxis(int, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

DefaultAxisMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

Default implementation of AxisMetadata.

DefaultAxisMetadata(String, String[], String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadata

DefaultAxisMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

DefaultAxisMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadataParser

defaultAxisTypes - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

defaultBlockSize - Variable in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

defaultBlockSize(int[]) - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

DefaultDatasetAxisMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

Default implementation of AxisMetadata.

DefaultDatasetAxisMetadata(String, String[], String[], String[], DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultDatasetAxisMetadata

DefaultDatasetAxisMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

DefaultDatasetAxisMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultDatasetAxisMetadataParser

defaultGroupParsers(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parser configuration depends on the n5 reader.

DefaultIndexedAxisMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

Default implementation of IndexedAxisMetadata.

DefaultIndexedAxisMetadata(String, String[], String[], String[], int[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultIndexedAxisMetadata

defaultLabel(int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

defaultN5ViewerAxes(N5SpatialDatasetMetadata) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

The default axes for dialects that store only spatial data (n5viewer and cosem), when time dimension is allowed.

defaultName(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

defaultShallowGroupParsers(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parser configuration depends on the n5 reader.

defaultSpaceName(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

deleteBlock(String, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

deleteBlock(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

deleteBlock(String, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

deleteBlock(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

deleteChunk(String, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

deleteChunk(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

deleteChunk(String, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

deleteChunk(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.AffineTransform3DJsonAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxesMetadataAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.AxisAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransformAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SpatialTransformAdapter

deserializeAxes(JsonObject, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

deserializeDatasets(JsonObject, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

diff(String, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

Returns a space containing the axes of this space not also part of the given space

dimension(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.FinalVoxelDimensions

dimensions(double[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.FinalVoxelDimensions

dimensionSeparator(String) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

dimensionSeparator(String) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr3Builder

dimensionSeparator - Variable in class org.janelia.saalfeldlab.n5.universe.options.ZarrBuilder

dimensionSeparator(String) - Method in class org.janelia.saalfeldlab.n5.universe.options.ZarrBuilder

discover(N5Reader, String, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discover(N5Reader, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discover(N5Reader, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discover(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discover(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverAndParseRecursive(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Recursively discovers and parses metadata for datasets that are children of the given base path using N5Reader.deepList(java.lang.String, java.util.function.Predicate<java.lang.String>).

discoverAndParseRecursive(String, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverAndParseRecursive(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverAndParseRecursive(N5TreeNode, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverAndParseRecursive(N5TreeNode, Predicate<String>, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverShallow(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverShallow(String, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverShallow(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverShallow(N5TreeNode, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

discoverShallow(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Discovers metadata present at the provided dataset without listing.

discoverShallow(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Discovers metadata present at the root without listing

discrete - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

DiscreteCoordinateTransform - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

DISPLACEMENT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

DisplacementFieldCoordinateTransform<T extends net.imglib2.type.numeric.RealType<T>> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

DisplacementFieldCoordinateTransform(String, RealRandomAccessible<RealComposite<T>>, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

DisplacementFieldCoordinateTransform(String, N5Reader, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

DisplacementFieldCoordinateTransform(String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

DisplacementFieldCoordinateTransform(String, String, String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

DisplacementFieldCoordinateTransform(String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

distance(Double[], RealLocalizable) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

distance(RealLocalizable, RealLocalizable) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

DOWN_AVERAGE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

DOWN_SAMPLE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

DOWNSAMPLING_FACTORS_KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

downsamplingFactors(long, long[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

downsamplingFactors(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

downsamplingFactorsKey - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

downsamplingFactorsKeyStrict - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

downsamplingFactorsStrict() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

E

edges() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CTNode

equals(Object) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

equals(Object) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

equals(FinalVoxelDimensions, FinalVoxelDimensions) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.FinalVoxelDimensions

equals(Object) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CTNode

EXAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

EXASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

exists(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

exists(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

F

F_ORDER - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

FEMTOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

FEMTOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

field - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

FIELD_TO_NULL_CHECK - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

fields - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

FIELDS_TO_NULL_CHECK - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

fillPermutation(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Replaces "-1"s in the input permutation array with the largest value.

filter - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

filterRecursive(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

FinalVoxelDimensions - Class in org.janelia.saalfeldlab.n5.universe.metadata

FinalVoxelDimensions(String, double...) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.FinalVoxelDimensions

findFieldTransformStrict(N5Reader, String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

findImagePlusPermutation(AxisMetadata) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Finds and returns a permutation p such that source[p[i]] equals target[i]

findImagePlusPermutation(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Finds and returns a permutation p such that source[p[i]] equals xyczt

findImagePlusSpatialPermutation(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

findNgffPermutation(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata

Finds and returns a permutation p such that source[p[i]] equals xyczt

findPermutation(T[], T[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Finds and returns a permutation p such that source[p[i]] equals target[i]

findPixelToPhysicalTransformCheckSelfRef(N5Reader, String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

Returns the first coordinate transformation found at this group that is either not a ParametrizedTransform, or is a ParametrizedTransform that does not reference this group.

findPixelToPhysicalTransformStrict(N5Reader, String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

flatSpace() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

flatten() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

flatten(double[][]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

Returns a "row-major" flattened array, i.e., the first index is contiguous in the output.

flattenColMajor(double[][]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

Returns a "row-major" flattened array, i.e., the first index is contiguous in the output.

flattenLeaves() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

flattenN5Tree(N5TreeNode) - Static method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

flatTransforms() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

FOOT_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

fOrder(DatasetAttributes) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

fOrderedScale() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

fOrderedTranslation() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

fromFlatList(String, String[], String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

Generates a tree based on the output of N5Reader.deepList(java.lang.String, java.util.function.Predicate<java.lang.String>), returning the root node.

fromFlatList(N5TreeNode, String[], String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

Generates a tree based on the output of N5Reader.deepList(java.lang.String, java.util.function.Predicate<java.lang.String>), returning the root node.

fromParsers(N5MetadataParser<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

fromString(String) - Static method in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

fwdFun - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

G

GenericMetadataGroup<T extends N5Metadata> - Class in org.janelia.saalfeldlab.n5.universe.metadata

GenericMetadataGroup(String, T[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.GenericMetadataGroup

get(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils.DefaultAxisTypes

getAffine() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

getAttributes(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.AbstractN5DatasetMetadata

getAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultDatasetAxisMetadata

getAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

getAttributes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5DatasetMetadata

Return the dataset attributes if this metadata object represents a single dataset.

getAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

getAttributes(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

getAttributesKey() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getAttributesKey() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

getAxes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisListMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CalibratedTransformMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

getAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

getAxis(int) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

getAxis(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

getAxis(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

getAxisLabels() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

getAxisLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadata

getAxisLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

getAxisLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

getAxisLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

getAxisLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

getAxisNames() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

getAxisTypes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

getAxisTypes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

getAxisTypes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadata

getAxisTypes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

getAxisTypes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

getAxisTypes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

getAxisTypes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

getBaseWriter() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

getCacheAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

getCanonicalPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

getChild(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getChild(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getChildPathsRecursive(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getChildren() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultichannelMetadata

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultiscaleMetadata

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiChannelMetadataCanonical

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonical

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.GenericMetadataGroup

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

getChildrenMetadata() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataGroup

Note: This is NOT gauranteeed to be sorted.

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

getChildrenMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

getChildrenStream() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getCollection() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

getColor() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

getColor() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ColorMetadata

getColor() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.IntColorMetadata

getColor() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.RGBAColorMetadata

getColorMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

getContainerAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getCoordinateSystems() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

getCoordinateTransformations() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

getCoordinateTransformations() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

getCoordinateTransformations() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

getCosemTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

getCost() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

getDatasets() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

getDatasets() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

getDefaultBlockSize() - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

getDefaultType(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

getDefaultTypes(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

getDefaultUnit(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

getDescendant(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

getDescendants(Predicate<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

getDimensionSeparator() - Method in class org.janelia.saalfeldlab.n5.universe.options.ZarrBuilder

getDoubleArray(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

getDoubleArray(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

getDoubleArray2(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

getDoubleArray2(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

getDownsamplingFactors() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

getEnd() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

getField() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

getFields() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

getForward() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BijectionCoordinateTransform

getGson() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getGson() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

getGson() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

getGson() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

getGsonBuilder() - Method in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

getHdf5Builder() - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

getIndex() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

getIndexedAxes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisMetadata

getIndexedAxis(int) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisMetadata

getIndexes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultIndexedAxisMetadata

getIndexes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisListMetadata

getIndexes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisMetadata

getIndexes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

getInput(CoordinateTransform<?>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

getInput() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getInput() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getInput() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getInputAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

getInputAxes(CoordinateTransform<?>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

getInputAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getInputAxes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getInputAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getInputSpaceObj() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getInstance() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils.DefaultAxisTypes

getInterpolation() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

getInverse() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BijectionCoordinateTransform

getInverseTranslationFunction() - Method in class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

getInvertibleTransform(N5Reader) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.InvertibleCoordinateTransform

getInvertibleTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.InvertibleCoordinateTransform

getJsonParameter() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform

getJsonParameter() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

getKeyValueAccess(URI, boolean) - Static method in enum org.janelia.saalfeldlab.n5.universe.KeyValueAccessBackend

Test the provided URI to and return the appropriate KeyValueAccess.

getKeyValueAccess(URI, boolean) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Test the provided URI to and return the appropriate KeyValueAccess.

getMapN5DatasetAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

getMergeAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

getMetadata() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

getMetadataMapN5(N5Reader, String, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getMetadataTree() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

getN5Builder() - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

getName() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

getName() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

getName() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata

getName() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getName() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getName() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getNode(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getNodeName() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

getOffset() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

getOptions() - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

getOrig() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

getOutput(CoordinateTransform<?>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

getOutput() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getOutput() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getOutput() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getOutputAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

getOutputAxes(CoordinateTransform<?>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

getOutputAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getOutputAxes() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getOutputAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getOutputSpaceObj() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getOverrideBlockSize() - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

getParameterPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

getParameterPath() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ParametrizedTransform

getParameterPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

getParameterPath() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.transforms.ParametrizedTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

getParameters(N5Reader) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ParametrizedTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

getParameters(N5Reader) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.transforms.ParametrizedTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

getParameters(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

getParent(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getParentPath() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.AbstractN5Metadata

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadata

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CalibratedTransformMetadata

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiChannelMetadataCanonical

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonical

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

getPath() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

getPath() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultichannelMetadata

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultiscaleMetadata

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiChannelMetadataCanonical

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonical

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.GenericMetadataGroup

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

getPaths() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataGroup

getPaths() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

getPixelResolution() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

getReaderFromCache(StorageFormat, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

getScale() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.ScaleCoordinateTransformation

getScale() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

getSpace(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

getSpaceFromAxes(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

Returns the first space that contains exactly the given axis labels, in the given order.

getSpaceNodes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

getSpacesContainingAxes(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

Returns all spaces that contain the given axis labels, in any order.

getSpacesFromAxes(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

Returns all spaces that contains exactly the given axis labels, in the given order.

getSpacesOld(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

getSpatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

getSpatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

getSpatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.CalibratedSpatialTransform

getStart() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

getStorageFromNestedScheme(String) - Static method in enum org.janelia.saalfeldlab.n5.universe.StorageFormat

getStringNullable(JsonElement) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

Gets a String from a JsonElement if possible, returning null if the element is JsonNull.

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CalibratedTransformMetadata

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.AbstractCoordinateTransformation

getTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformation

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.IdentityCoordinateTransformation

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.ScaleCoordinateTransformation

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TranslationCoordinateTransformation

getTransform(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

getTransform(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

getTransform(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BijectionCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BijectionCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

getTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getTransform(N5Reader) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.InverseCoordinateTransform

getTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.LinearCoordinateTransform

getTransform(N5Reader) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ParametrizedTransform

getTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.RealCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.RealTransformCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

getTransform(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

getTransform(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.CalibratedSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.IdentitySpatialTransform

getTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.transforms.LinearSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SequenceSpatialTransform

getTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.transforms.SpatialTransform

getTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

getTransformations() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

getTransformations() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SequenceSpatialTransform

getTransformNoSubsets() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

getTransforms() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

getTranslated() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

getTranslation() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TranslationCoordinateTransformation

getTranslation() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

getTranslation() - Method in class org.janelia.saalfeldlab.n5.universe.translation.ImportedTranslations

getTranslation() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

getTranslationFunction() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

getType() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

getType() - Method in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

getType() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.AbstractCoordinateTransformation

getType() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformation

getType() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

getType() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

getType() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getTypesToClasses() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

getUnit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

getUnit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.CalibratedSpatialTransform

getUnits() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

getUnits() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

getUnits() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadata

getUnits() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata

getUnits() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

getUnits() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

getUnits() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

getURI() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

getURI() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

getUrl() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

getVectorAxisIndex() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

getVectorAxisIndex() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

getVectorAxisIndex() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

getVectorAxisIndex() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

getWriterFromCache(StorageFormat, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

getZarr2Builder() - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

getZarr3Builder() - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

GIGAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

GIGASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

googleCloudConfiguration(Consumer<StorageOptions.Builder>) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

This factory will use the gcsBuilderConfig to configure the Google Cloude Store StorageOptions.Builder, and thereby the Google Cloud Storage client.

googleCloudProjectId(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

GROUP_PARSERS - Static variable in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

groupPath(String...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

groupPath(String...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

gson - Variable in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

gson - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

gson - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

gson - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

gsonBuilder() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

gsonBuilder() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions() and N5FactoryOptions.gsonBuilder(GsonBuilder)

gsonBuilder - Variable in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5Builder

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

Set the default GsonBuilder.

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

gsonBuilder(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr3Builder

gsonBuilder(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

guessStorageFromKeys(URI, KeyValueAccess) - Static method in enum org.janelia.saalfeldlab.n5.universe.StorageFormat

guessStorageFromUri(URI) - Static method in enum org.janelia.saalfeldlab.n5.universe.StorageFormat

H

hasAllLabels(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

hasAxis(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

hashCode() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

hasSpace(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

hasSpace(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

Does this path run through the given space.

hdf5(Consumer<HDF5Builder>) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

Configure HDF5Builder to be used when the factory accesses an HDF5 container.

HDF5Builder - Class in org.janelia.saalfeldlab.n5.universe.options

hdf5DefaultBlockSize(int...) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions() and N5FactoryOptions.hdf5(Consumer)

hdf5OverrideBlockSize(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions() and N5FactoryOptions.hdf5(Consumer)

HECTOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

HECTOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

HOUR - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

I

IdentityCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

IdentityCoordinateTransform() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

IdentityCoordinateTransform(String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

IdentityCoordinateTransform(String, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

IdentityCoordinateTransform(IdentityCoordinateTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

IdentityCoordinateTransform(IdentityCoordinateTransform, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

IdentityCoordinateTransformation - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

IdentityCoordinateTransformation() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.IdentityCoordinateTransformation

IdentitySpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

IdentitySpatialTransform() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.IdentitySpatialTransform

ImportedTranslations - Class in org.janelia.saalfeldlab.n5.universe.translation

ImportedTranslations() - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.ImportedTranslations

INCH_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

IndexedAxis - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

IndexedAxis(String, String, String, int) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

IndexedAxisListMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.axes

Default implementation of IndexedAxisMetadata.

IndexedAxisListMetadata(IndexedAxis[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxisListMetadata

IndexedAxisMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata.axes

Metadata that labels and assigns types to axes.

indexes(Axis[], Predicate<Axis>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

indexes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultIndexedAxisMetadata

indexesOfType(String) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

indexesOfType(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

indexOf(String) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata

indexOf(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

inferDownsamplingFactorsFromDataset(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

inferSpacesFromAxes() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

inferSpacesFromAxes(CoordinateSystems) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

If this object does not have input_space or output_space defined, attempts to infer the space name, given * input_axes or output_axes, if they are defined.

input - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

inputAxes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

inputAxesLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

inputHasAxis(CoordinateTransform<?>, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

inputIndexesFromAxisOrders(CoordinateTransform<?>[], List<String[]>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

inputIsSubspace(CoordinateTransform<?>, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

inputSpaceObj - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

IntColorMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

A ColorMetadata that stores color as a single int.

IntColorMetadata(int) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.IntColorMetadata

IntensityLimits(double, double) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata.IntensityLimits

IntensityMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for metadata that describes

interpolation - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

interpolator(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

interpretParameters() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

intersection(String, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

InverseCoordinateTransform<T extends net.imglib2.realtransform.RealTransform,C extends CoordinateTransform<T>> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

InverseCoordinateTransform(String, C) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.InverseCoordinateTransform

InverseCoordinateTransform(C) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.InverseCoordinateTransform

InvertibleCoordinateTransform<T extends net.imglib2.realtransform.InvertibleRealTransform> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

InvertibleTreeTranslation - Class in org.janelia.saalfeldlab.n5.universe.translation

InvertibleTreeTranslation(ContainerMetadataNode, Gson, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

invertPermutation(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

invFun - Variable in class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

isAffine() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

isDataset() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

isIdentityPermutation(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

isLabelMultiset() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

isSubspaceOf(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

isSubspaceOf(String[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

Is a a subset of b.

isSubspaceOf(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

isSuperspaceOf(String[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

Is a a super set of b.

isSuperspaceOf(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

isSuperspaceOf(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

isType(String) - Method in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

isValid(CoordinateTransform<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

Checks if the list of transformations is valid.

isValid() - Method in class org.janelia.saalfeldlab.n5.universe.translation.JqFunction

J

JqContainerTranslation - Class in org.janelia.saalfeldlab.n5.universe.translation

JqContainerTranslation(String, Gson) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.JqContainerTranslation

JqFunction<S,T> - Class in org.janelia.saalfeldlab.n5.universe.translation

JqFunction(String, Gson, Class<T>) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.JqFunction

JqFunction(String, Gson, T) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.JqFunction

JqPredicate<S> - Class in org.janelia.saalfeldlab.n5.universe.translation

JqPredicate(String, Gson) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.JqPredicate

JqUtils - Class in org.janelia.saalfeldlab.n5.universe.translation

JqUtils() - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

K

KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

KEY - Static variable in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransform

KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

KeyValueAccessBackend - Enum in org.janelia.saalfeldlab.n5.universe

Enum to discover and provide KeyValueAccess for N5Readers and N5Writers.

KILOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

KILOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

kwargs - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

L

LINEAR_INTERPOLATION - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

LinearCoordinateTransform<T extends net.imglib2.realtransform.AffineGet> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

LinearSpatialTransform - Interface in org.janelia.saalfeldlab.n5.universe.metadata.transforms

list(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

list(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

listAttributes(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

load(Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

load(File) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

loadFile(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

M

main(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

main(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

main(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

main(String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SpatialTransformAdapter

makeDefault(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

makeDefaultAxis(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

makeDefaultSpace(String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

makeDefaultSpace(String, String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

makeDfieldSpace(String, String, String, String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

makeSpace(String, String, String, String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

mapN5DatasetAttributes - Variable in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

mapN5DatasetAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

MatrixCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

MatrixCoordinateTransform() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.MatrixCoordinateTransform

max - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata.IntensityLimits

max(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

maxForDataType(DataType) - Static method in interface org.janelia.saalfeldlab.n5.universe.metadata.IntensityMetadata

maxIntensity() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

maxIntensity() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

maxIntensity() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.IntensityMetadata

maxIntensity() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

maxKey - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

maxKeyStrict - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

maxStrict() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

MEGAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

MEGASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

mergeAttributes - Variable in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

mergeAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.Zarr2Builder

metadata - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

metadataForThisScale(String, M, String, double[], double[], double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

MetadataUtils - Class in org.janelia.saalfeldlab.n5.universe.metadata

MetadataUtils() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

METER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

method - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

MICRO - Static variable in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

MICROMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

MICROSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

MILE_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

MILLIMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

MILLISECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

min - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata.IntensityLimits

min(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

minIntensity() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata

minIntensity() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialMetadata

minIntensity() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.IntensityMetadata

minIntensity() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

minKey - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

minKeyStrict - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

minStrict() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

MINUTE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

modifySpatialTransform(String, AffineGet) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

modifySpatialTransform(String, AffineGet) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

modifySpatialTransform(String, AffineGet) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

modifySpatialTransform(String, AffineGet) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialModifiable

modifySpatialTransform(String, double[], double[]) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialModifiable

movingPoints - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

MU - Static variable in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

mul(double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

mul(double[], long[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

MultiChannelMetadataCanonical - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

MultiChannelMetadataCanonical(String, CanonicalMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiChannelMetadataCanonical

MultiResolutionSpatialMetadataCanonical - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

MultiResolutionSpatialMetadataCanonical(String, CalibratedTransformMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonical

MultiResolutionSpatialMetadataCanonicalParser - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

Interface for metadata describing how spatial data are oriented in physical space.

MultiResolutionSpatialMetadataCanonicalParser(Gson, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonicalParser

MultiscaleDataset() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes.MultiscaleDataset

MultiscaleMetadata<T extends N5DatasetMetadata & SpatialMetadata> - Class in org.janelia.saalfeldlab.n5.universe.metadata

An abstract class for a SpatialMetadataGroup whose children contain the same data sampled at different resolutions.

MultiscaleMetadata(String, T[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

MultiScaleParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5MultiScaleMetadata.MultiScaleParser

multiscales - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata

MultiscalesAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

MultiscalesAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

MultiscalesAdapter(boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

N

n5(Consumer<N5Builder>) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

Configure N5Builder to be used when the factory accesses an N5 container.

N5Builder - Class in org.janelia.saalfeldlab.n5.universe.options

N5CosemMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

Janelia COSEM's implementation of a N5SingleScaleMetadata.

N5CosemMetadata(String, N5CosemMetadata.CosemTransform, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

N5CosemMetadata.CosemTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata

N5CosemMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata

The N5MetadataParser for N5CosemMetadata.

N5CosemMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser

N5CosemMultiScaleMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

Janelia COSEM's implementation of a MultiscaleMetadata.

N5CosemMultiScaleMetadata(String, N5CosemMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMultiScaleMetadata

N5CosemMultiScaleMetadata.CosemMultiScaleParser - Class in org.janelia.saalfeldlab.n5.universe.metadata

N5DatasetDiscoverer - Class in org.janelia.saalfeldlab.n5.universe

This class aids in detecting and parsing datasets in an N5 container.

N5DatasetDiscoverer(N5Reader, ExecutorService) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

N5DatasetDiscoverer(N5Reader, ExecutorService, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

N5DatasetDiscoverer(N5Reader, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Creates an N5 discoverer.

N5DatasetDiscoverer(N5Reader, ExecutorService, Predicate<N5TreeNode>, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

N5DatasetDiscoverer(N5Reader, ExecutorService, Optional<Comparator<? super String>>, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

N5DatasetDiscoverer(N5Reader, ExecutorService, Optional<Comparator<? super String>>, Predicate<N5TreeNode>, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Creates an N5 discoverer.

N5DatasetDiscoverer(N5Reader, ExecutorService, Optional<Comparator<? super String>>, Predicate<N5TreeNode>, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Creates an N5 discoverer.

N5DatasetMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for metadata that corresponds to an N5 dataset.

N5DefaultSingleScaleMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

This class merely serves as a marker that all its values are default values.

N5DefaultSingleScaleMetadata(String, AffineTransform3D, double[], double[], double[], String, DatasetAttributes, Double, Double, boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5DefaultSingleScaleMetadata

N5DefaultSingleScaleMetadata(String, AffineTransform3D, double[], double[], double[], String, DatasetAttributes, boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5DefaultSingleScaleMetadata

N5DefaultSingleScaleMetadata(String, AffineTransform3D, double[], double[], double[], String, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5DefaultSingleScaleMetadata

N5Factory - Class in org.janelia.saalfeldlab.n5.universe

Factory for various N5 readers and writers.

N5Factory() - Constructor for class org.janelia.saalfeldlab.n5.universe.N5Factory

N5FactoryOptions - Class in org.janelia.saalfeldlab.n5.universe.options

N5FactoryOptions() - Constructor for class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

N5FactoryWithCache - Class in org.janelia.saalfeldlab.n5.universe

N5FactoryWithCache() - Constructor for class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

N5GenericSingleScaleMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata

A parser for N5SingleScaleMetadata with whose keys can be specified.

N5GenericSingleScaleMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

N5GenericSingleScaleMetadataParser(String, String, String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

N5GenericSingleScaleMetadataParser.Builder - Class in org.janelia.saalfeldlab.n5.universe.metadata

N5Metadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Base interfaces for metadata stored with N5.

N5MetadataGroup<T extends N5Metadata> - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Base interfaces for metadata corresponding to an n5 group.

N5MetadataParser<T extends N5Metadata> - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for reading metadata from N5 containers.

N5MetadataUtils - Class in org.janelia.saalfeldlab.n5.universe

N5MetadataUtils() - Constructor for class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

N5MetadataWriter<T extends N5Metadata> - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for writing metadata to an N5 container.

N5MultiScaleMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

An implementation of MultiscaleMetadata whose children are instances of N5SingleScaleMetadata.

N5MultiScaleMetadata(String, N5SingleScaleMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5MultiScaleMetadata

N5MultiScaleMetadata.MultiScaleParser - Class in org.janelia.saalfeldlab.n5.universe.metadata

N5SingleScaleMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

Metadata representing an N5Dataset that implements SpatialMetadata and IntensityMetadata.

N5SingleScaleMetadata(String, AffineTransform3D, double[], double[], double[], String, DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

N5SingleScaleMetadata(String, AffineTransform3D, double[], double[], double[], String, DatasetAttributes, boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

N5SingleScaleMetadata(String, AffineTransform3D, double[], double[], double[], String, DatasetAttributes, Double, Double, boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

N5SingleScaleMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata

Default N5MetadataParser for N5SingleScaleMetadata.

N5SingleScaleMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

N5SpatialDatasetMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata

N5TreeNode - Class in org.janelia.saalfeldlab.n5.universe

A node representing a dataset or group in an N5 container, and stores its corresponding N5Metadata, and child nodes if any exist.

N5TreeNode(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.N5TreeNode

N5ViewerDatasetMetadataWriter - Class in org.janelia.saalfeldlab.n5.universe.metadata

N5ViewerDatasetMetadataWriter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5ViewerDatasetMetadataWriter

N5ViewerMultiscaleMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata

N5ViewerMultiscaleMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.N5ViewerMultiscaleMetadataParser

name - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

name - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

name - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

name - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

NANOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

NANOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

NEAREST_INTERPOLATION - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

newBuilder(Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

NgffMultiScaleGroupAttributes - Class in org.janelia.saalfeldlab.n5.universe.metadata

NgffMultiScaleGroupAttributes() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes

NgffMultiScaleGroupAttributes.MultiscaleDataset - Class in org.janelia.saalfeldlab.n5.universe.metadata

NgffSingleScaleAxesMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

NgffSingleScaleAxesMetadata(String, double[], double[], DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

NgffSingleScaleAxesMetadata(String, double[], double[], Axis[], DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

normalizeGroupPath(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

normalizeIndexes(int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Converters an array of integers to a normalized array of integers such that the smallest integer is mapped to 0, the second smallest to 1 ... and the largest is mapped to N-1, where N is the number of unique integers in the array.

numDimensions() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

numDimensions() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.FinalVoxelDimensions

numDimensions - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

O

offset(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

offset - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

offsetKey - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

offsetKeyStrict - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

offsetStrict() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

OmeNgffDataset() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDataset

OmeNgffDownsamplingMetadata() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

OmeNgffMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

OmeNgffMetadata(String, OmeNgffMultiScaleMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata

OmeNgffMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

OmeNgffMetadataParser(boolean) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

OmeNgffMetadataParser(N5Reader) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

OmeNgffMetadataParser() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

OmeNgffMultiScaleMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

OmeNgffMultiScaleMetadata(OmeNgffMultiScaleMetadata, NgffSingleScaleAxesMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

OmeNgffMultiScaleMetadata(int, String, String, String, String, Axis[], OmeNgffMultiScaleMetadata.OmeNgffDataset[], CoordinateTransformation<?>[], DatasetAttributes[], OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

OmeNgffMultiScaleMetadata(int, String, String, String, String, Axis[], OmeNgffMultiScaleMetadata.OmeNgffDataset[], CoordinateTransformation<?>[], DatasetAttributes[], OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata, NgffSingleScaleAxesMetadata[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

OmeNgffMultiScaleMetadata.OmeNgffDataset - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

OmeNgffMultiScaleMetadataMutable - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

OmeNgffMultiScaleMetadataMutable() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

OmeNgffMultiScaleMetadataMutable(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

OmeNgffV03MetadataProcessor - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03

OmeNgffV03MetadataProcessor() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03.OmeNgffV03MetadataProcessor

open(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

open(N5Reader, String, String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

open(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openAWSS3Reader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(KeyValueAccessBackend, URI) instead

openAWSS3Writer(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openWriter(KeyValueAccessBackend, String) instead.

openFileSystemReader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(KeyValueAccessBackend, URI) instead

openFSReader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(StorageFormat, URI) instead

openFSWriter(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openWriter(StorageFormat, URI) instead

openGoogleCloudReader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(KeyValueAccessBackend, URI) instead

openGoogleCloudWriter(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openWriter(KeyValueAccessBackend, String) instead.

openGraph(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openGraph(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openGraph(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openGraph(N5Reader, String, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openGraph(N5Reader, String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openGraphImpliedSpaces(N5Reader, String, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openHDF5Reader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(StorageFormat, URI) instead

openHDF5Writer(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(StorageFormat, URI) instead

openJson(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openReader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open an N5Reader at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend and StorageFormat.

openReader(StorageFormat, String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open an N5Reader at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.

openReader(StorageFormat, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open an N5Reader at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.

openReader(KeyValueAccessBackend, String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open and N5Reader at the given URI given the specified KeyValueAccessBackend.

openReader(KeyValueAccessBackend, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open and N5Reader at the given URI given the specified KeyValueAccessBackend.

openReader(StorageFormat, KeyValueAccess, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Create an N5Reader at the containerPath requiring the specific StorageFormat and using KeyValueAccess.

openReader(StorageFormat, KeyValueAccess, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

openReference(String, N5Reader, String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openTransformN5(String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

openWriter(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open an N5Writer at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend and StorageFormat.

openWriter(KeyValueAccessBackend, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Create or Open an N5Writer as the given uri and backend.

openWriter(KeyValueAccessBackend, String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Create or Open an N5Writer as the given uri and backend.

openWriter(StorageFormat, String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open an N5Writer at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.

openWriter(StorageFormat, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Open an N5Writer at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.

openWriter(StorageFormat, KeyValueAccess, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Create an N5Writer at the location requiring the specific StorageFormat and using KeyValueAccess.

openWriter(StorageFormat, KeyValueAccess, URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

openZarrReader(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openReader(StorageFormat, URI) instead

openZarrWriter(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

use N5Factory.openWriter(StorageFormat, URI)) instead

options(Consumer<N5FactoryOptions>) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

order - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

ordering - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

org.janelia.saalfeldlab.n5.universe - package org.janelia.saalfeldlab.n5.universe

org.janelia.saalfeldlab.n5.universe.container - package org.janelia.saalfeldlab.n5.universe.container

org.janelia.saalfeldlab.n5.universe.metadata - package org.janelia.saalfeldlab.n5.universe.metadata

org.janelia.saalfeldlab.n5.universe.metadata.axes - package org.janelia.saalfeldlab.n5.universe.metadata.axes

org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms - package org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms

org.janelia.saalfeldlab.n5.universe.metadata.canonical - package org.janelia.saalfeldlab.n5.universe.metadata.canonical

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03 - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05 - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations - package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

org.janelia.saalfeldlab.n5.universe.metadata.transforms - package org.janelia.saalfeldlab.n5.universe.metadata.transforms

org.janelia.saalfeldlab.n5.universe.options - package org.janelia.saalfeldlab.n5.universe.options

org.janelia.saalfeldlab.n5.universe.translation - package org.janelia.saalfeldlab.n5.universe.translation

originalPath(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

Returns the path in the original container given the path in the translated container.

output - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

outputAxes - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

outputAxesLabels() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

outputHasAxis(CoordinateTransform<?>, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

outputIndexesFromAxisOrders(CoordinateTransform<?>[], List<String[]>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

outputIsSubspace(CoordinateTransform<?>, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

outputIsSuperspace(CoordinateTransform<?>, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

outputMatchesAny(CoordinateTransform<?>, Set<String>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

outputMatchesAny(CoordinateTransform<?>, String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

outputSpaceObj - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

overrideBlockSize - Variable in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

overrideBlockSize(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.options.HDF5Builder

P

ParametrizedTransform<T extends net.imglib2.realtransform.RealTransform,P> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

ParametrizedTransform<T,P> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.transforms

parse(Gson, JsonElement) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

parse(Gson, JsonElement) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataTemplateCanonical

parse(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

parse(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

PARSEC_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

parseDatasetAttributes(N5Reader, N5TreeNode) - Static method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser

parseFromMap(Gson, HashMap<String, JsonElement>, BiFunction<Gson, JsonElement, Optional<S>>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

parseFromMap(Gson, HashMap<String, JsonElement>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

parseFromMap(Gson, HashMap<String, JsonElement>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonicalParser

parseFromMap(Gson, HashMap<String, JsonElement>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataTemplateCanonical

parseFromObj(Gson, JsonObject, BiFunction<Gson, HashMap<String, JsonElement>, Optional<S>>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultAxisMetadataParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.DefaultDatasetAxisMetadataParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

parseMetadata(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

Deprecated.

parseMetadata(N5TreeNode, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

Deprecated.

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMultiScaleMetadata.CosemMultiScaleParser

Called by the N5DatasetDiscoverer while discovering the N5 tree and filling the metadata for datasets or groups.

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

parseMetadata(N5Reader, N5TreeNode) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser

Called by the N5DatasetDiscoverer while discovering the N5 tree and filling the metadata for datasets or groups.

parseMetadata(N5Reader, String) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5MultiScaleMetadata.MultiScaleParser

Called by the N5DatasetDiscoverer while discovering the N5 tree and filling the metadata for datasets or groups.

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5ViewerMultiscaleMetadataParser

Called by the N5DatasetDiscoverer while discovering the N5 tree and filling the metadata for datasets or groups.

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

parseMetadata(N5Reader, N5TreeNode, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

parseMetadata(N5Reader, N5TreeNode, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parses metadata for a node using the given parsers, stopping after the first success.

parseMetadata(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadata(N5Reader, String, boolean) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadata(N5Reader, String, boolean, ExecutorService, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadata(N5Reader, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

parseMetadata(N5Reader, String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

parseMetadata(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

parseMetadata(N5TreeNode, String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

parseMetadataRecursive(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parses metadata for the given node and all children in parallel using this object's executor.

parseMetadataRecursive(N5TreeNode, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parses metadata for the given node and all children in parallel using this object's executor.

parseMetadataRecursive(N5TreeNode, Consumer<N5TreeNode>, boolean) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parses metadata for the given node and all children in parallel using this object's executor.

parseMetadataShallow(N5Reader, N5TreeNode, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Parses metadata for a node using the given parsers, stopping after the first success.

parseMetadataTree(R, N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

parseMetadataTree(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadataTree(N5Reader, String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadataTree(N5Reader, ExecutorService) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadataTree(N5Reader, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadataTree(N5Reader, ExecutorService, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseMetadataTree(N5Reader, String, ExecutorService, List<N5MetadataParser<?>>, List<N5MetadataParser<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

PARSERS - Static variable in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

parseUri(String) - Static method in enum org.janelia.saalfeldlab.n5.universe.StorageFormat

parseVectorAxisIndex(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

parseVectorAxisIndex(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

parseVectorAxisIndex(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

parseVectorAxisIndex(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

path - Variable in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

path - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes.MultiscaleDataset

path - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDataset

path(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

path(CoordinateSystem, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

path - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

pathFromAxes(String, String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

pathFromAxes(String[], String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

pathFromAxes(String[], String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

paths(CoordinateSystem, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

pathToChild(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

Returns a stream of nodes for the given path.

permute(List<T>, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permute(T[], T[], int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Permutes an input array into a destination array.

permute(long[], int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permute(int[], int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permute(double[], int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permute(RandomAccessibleInterval<T>, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Permutes the dimensions of a RandomAccessibleInterval using the given permutation vector, where the ith value in p gives destination of the ith input dimension in the output.

permuteCosemMetadata(N5CosemMetadata, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

permuteForImagePlus(RandomAccessibleInterval<T>, M) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permuteForImagePlus(int[], M) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permuteForNgff(RandomAccessibleInterval<T>, M) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata

permuteImageAndMetadataForImagePlus(RandomAccessibleInterval<T>, M) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permuteImageAndMetadataForImagePlus(int[], RandomAccessibleInterval<T>, M) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

permuteN5vMetadata(N5SingleScaleMetadata, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

permuteNgffMetadata(NgffSingleScaleAxesMetadata, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

permuteSpatialMetadata(M, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

PETAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

PETASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

PICOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

PICOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

PiecewiseContainerTranslation - Class in org.janelia.saalfeldlab.n5.universe.translation

PiecewiseContainerTranslation() - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.PiecewiseContainerTranslation

PIXEL_RESOLUTION_KEY - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

positionAxisIndex - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

positionAxisIndex - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

pow(double[], int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

Element-wise power.

preConcatenate(AffineTransform3D, AffineGet) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

preConcatenate(AffineTransform3D, AffineGet) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

preferredStorageFormat(StorageFormat) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

When N5Factory cannot determine the StorageFormat from the URI, it will attempt to try and create a reader/writer with all known StorageFormat values.

preserve_range - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

printRecursive() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

R

readBlock(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

readBlock(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

readChunk(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

readChunk(String, DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

readProcess(OmeNgffMultiScaleMetadata.OmeNgffDataset[], DatasetAttributes[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03.OmeNgffV03MetadataProcessor

Estimates implied coordinate transformations from the sizes of the array for each scale.

RealCoordinateTransform<T extends net.imglib2.realtransform.RealTransform> - Interface in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

RealTransformCoordinateTransform<T extends net.imglib2.realtransform.RealTransform> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

RealTransformCoordinateTransform(String, String[], String[], T) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.RealTransformCoordinateTransform

RealTransformCoordinateTransform(String, String, String, T) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.RealTransformCoordinateTransform

RealTransformCoordinateTransform(String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.RealTransformCoordinateTransform

ReferencedCoordinateTransform<T extends net.imglib2.realtransform.RealTransform> - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

ReferencedCoordinateTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

relativePath(String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

Returns a relative group path from the child absolute path group path child the parent absolute group path.

remove(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

remove() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

remove(URI) - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

remove(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5FactoryWithCache

remove(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

remove(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

remove() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

removeAllChildren() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

removeAttribute(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

removeAttribute(String, String, Class<T>) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

removeAttribute(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

removeAttribute(String, String, Class<T>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

removeAttributes(String, List<String>) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

removeAttributes(String, List<String>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

removeDimension(int, AffineGet) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

removeLeadingSlash(String) - Static method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

Removes the leading slash from a given path and returns the corrected path.

resetGroupParsers() - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

resetParsers() - Static method in class org.janelia.saalfeldlab.n5.universe.N5MetadataUtils

resolution(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

resolutionKey - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

resolutionKeyStrict - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

resolutionStrict() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

resolveAbsoluePath(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedTransform

resolveAbsoluePath(String) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ParametrizedTransform

resolveImports(String) - Static method in class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

reverse - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

reverse(N5Reader) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

reversedCopy(T[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

Creates a new array containing all elements of the input array in reversed order.

reversedCopy(JsonArray) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

reverseDimensions(RandomAccessibleInterval<T>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

reverseParameters(JsonObject) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

reverseParameters(CoordinateTransformation<?>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

RGBAColorMetadata - Class in org.janelia.saalfeldlab.n5.universe.metadata

A ColorMetadata that stores rgba componenents as integers

RGBAColorMetadata(int, int, int, int) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.RGBAColorMetadata

root - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

rootOrig - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

rootTranslated - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

S

s3Configuration(Consumer<S3ClientBuilder>) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

This factory will use the builderConfig to configure the S3ClientBuilder, and thereby the S3Client.

s3UseCredentials() - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with s3Configuration.

scale - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

scale - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.ScaleCoordinateTransformation

scale - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

scale - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

scale - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

scale - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

ScaleCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

ScaleCoordinateTransform(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(String, String[], String[], double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(String, String, String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(String, String, String, N5Reader, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(ScaleCoordinateTransform, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(ScaleCoordinateTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransform(ScaleCoordinateTransform, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

ScaleCoordinateTransformation - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

ScaleCoordinateTransformation(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.ScaleCoordinateTransformation

ScaleCoordinateTransformation(ScaleCoordinateTransformation) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.ScaleCoordinateTransformation

scaleLevelPattern - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

ScaleOffsetCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

ScaleOffsetCoordinateTransform() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleOffsetCoordinateTransform

ScaleOffsetSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

ScaleOffsetSpatialTransform(double[], double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

ScaleOffsetSpatialTransform(N5Reader, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

ScaleOffsetSpatialTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

scalesAndTranslations(double[], double[], int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

ScaleSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

ScaleSpatialTransform(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

ScaleSpatialTransform(N5Reader, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

ScaleSpatialTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

scaleTranslationFromCoordinateTransformations(CoordinateTransformation<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

scaleTranslationTransforms(double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

Returns the most efficient transform given the input scale and translation parameters.

SECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

seqTest() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

SequenceCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

SequenceCoordinateTransform(CoordinateTransform<?>[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

SequenceCoordinateTransform(String, String, CoordinateTransform<?>[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

SequenceCoordinateTransform(String, String, String, CoordinateTransform<?>[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

SequenceCoordinateTransform(String, String, String, List<CoordinateTransform<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

SequenceSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

SequenceSpatialTransform(SpatialTransform[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SequenceSpatialTransform

serialize(AffineTransform3D, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.AffineTransform3DJsonAdapter

serialize(Axis, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.AxisAdapter

serialize(CoordinateTransformation<?>, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

serialize(OmeNgffMultiScaleMetadata, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

serialize(OmeNgffMultiScaleMetadata.OmeNgffDataset, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v03.DatasetAdapterV03

serialize(CoordinateTransform<?>, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

serialize(SpatialTransform, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SpatialTransformAdapter

serializeAsFlatArray() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

serializeFlatArray - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

setAttribute(String, String, T) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

setAttribute(String, String, T) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

setAttribute(String, String, T) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

setAttributes(String, Map<String, ?>) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

setAttributes(String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

setAttributes(String, Map<String, ?>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

setAttributes(String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

setAttributes(String, Map<String, ?>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

setDatasetAttributes(N5SingleScaleMetadata, N5DatasetMetadata) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

Returns a new N5SingleScaleMetadata equal to the baseMetadata, but with DatasetAttributes coming from datasetMetadata.ew

setDefaultIndex(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

setDefaultLabel(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

setDefaults(boolean, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

setDefaults(int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

setDefaultType() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

setDefaultUnit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.IndexedAxis

setFilter(Predicate<CanonicalMetadata>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

setGson(Gson) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

setInput(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

setMetadata(N5Metadata) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

setMetadataTree(ContainerMetadataNode) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

setN5Writer(N5Writer) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

setNameSpaces(String, String, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

setOptions(N5FactoryOptions) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

setOutput(CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

setPath(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadataMutable

setReverseParameters(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

setReverseParameters(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.MultiscalesAdapter

setSerializeAsFlatArray(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractLinearCoordinateTransform

setSpaces(CoordinateSystems) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

setTranslatedAttribute(String, String, T) - Method in class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

setTranslatedAttributes(String, Map<String, ?>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

setTranslatedAttributes(String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

setup(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser

Deprecated.

setup(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

sharedOptions - Variable in class org.janelia.saalfeldlab.n5.universe.options.AbstractN5Builder

slice(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

Slices at position 0 for the given label.

slice(String, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

slice(int, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

sliceOverride(String, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

sliceOverride(int, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

sliceType(String, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

Slices the first axis of the given type at the pr

sliceType(String, int, int) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisSlicer

sort(N5TreeNode, Comparator<? super String>, Consumer<N5TreeNode>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

sort(N5TreeNode, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

sort(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

sortAndTrimRecursive(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

sortAndTrimRecursive(N5TreeNode, Consumer<N5TreeNode>) - Method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

sortScaleMetadata(T[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

Sort the array according to scale level; If not all metadata are scale sets, no sorting is done.

SPACE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

space(String, String...) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

SPACE_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

spaceFrom(String[]) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

spaceFrom(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

spaces - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

SpacesTransforms - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05

SpacesTransforms(CoordinateSystem[], CoordinateTransform<?>[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

spaceType - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

SpatialMetadata - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for metadata describing how spatial data are oriented in physical space.

SpatialMetadataCanonical - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

Interface for metadata describing how spatial data are oriented in physical space.

SpatialMetadataCanonical(String, SpatialTransform, String, Axis[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

SpatialMetadataCanonical(String, CalibratedSpatialTransform, Axis[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

SpatialMetadataGroup<T extends SpatialMetadata> - Interface in org.janelia.saalfeldlab.n5.universe.metadata

Interface for a metadata whose children are each SpatialMetadata, and is itslef SpatialMetadata.

SpatialMetadataTemplateCanonical - Class in org.janelia.saalfeldlab.n5.universe.metadata.canonical

Interface for metadata describing how spatial data are oriented in physical space.

SpatialMetadataTemplateCanonical(Gson, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataTemplateCanonical

SpatialModifiable<T extends SpatialMetadata> - Interface in org.janelia.saalfeldlab.n5.universe.metadata

SpatialMultiscaleMetadata<T extends N5SpatialDatasetMetadata> - Class in org.janelia.saalfeldlab.n5.universe.metadata

An abstract class for a SpatialMetadataGroup whose children contain the same data sampled at different resolutions.

SpatialMultiscaleMetadata(String, T[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.SpatialMultiscaleMetadata

spatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CalibratedTransformMetadata

spatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

spatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata

spatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

spatialTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

spatialTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadata

spatialTransform() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

SpatialTransform - Interface in org.janelia.saalfeldlab.n5.universe.metadata.transforms

spatialTransform3D(AffineGet, Axis[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

spatialTransform3D(AffineGet, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

spatialTransform3d() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

spatialTransform3d() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadata

spatialTransform3d() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

SpatialTransformAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

SpatialTransformAdapter(N5Reader) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.SpatialTransformAdapter

spatialTransforms() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

spatialTransforms3d() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

squaredDistance(Double[], RealLocalizable) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

squaredDistance(RealLocalizable, RealLocalizable) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

StackedCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

StackedCoordinateTransform(String, String, String, List<CoordinateTransform<?>>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

StackedCoordinateTransform(String, String, String, CoordinateTransform<?>[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.StackedCoordinateTransform

StorageFormat - Enum in org.janelia.saalfeldlab.n5.universe

stringToJson(String, Gson) - Static method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

structureEquals(N5TreeNode) - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

subAffine(AffineGet, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

subSpace(String, String...) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

subTransforms(CoordinateSystem, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

Returns all transforms that have all input axis in the "input" CoordinateSystem and all output axis in the "output" CoordinateSystem.

superAffine(AffineGet, int, int[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

Returns an affine with a specified dimensionality that contains

T

targetPoints - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

TERAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

TERASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

test(URI) - Method in enum org.janelia.saalfeldlab.n5.universe.KeyValueAccessBackend

test(S) - Method in class org.janelia.saalfeldlab.n5.universe.translation.JqPredicate

test1() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateTransformAdapter

ThinPlateSplineCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

ThinPlateSplineCoordinateTransform(double[][], double[][]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(String, String, double[][], double[][]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(String, String, String, double[][], double[][]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(ThinplateSplineTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(String, String, ThinplateSplineTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(String, String, String, ThinplateSplineTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(ThinPlateR2LogRSplineKernelTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(String, String, ThinPlateR2LogRSplineKernelTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

ThinPlateSplineCoordinateTransform(String, String, String, ThinPlateR2LogRSplineKernelTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

TIME - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

TIME_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

timeType - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

tLabel - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

toAffine(CoordinateTransform<?>, int) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

toAffine3D(SequenceCoordinateTransform) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

toAffine3D(Collection<CoordinateTransform<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

toAffine3D(N5Reader, Collection<CoordinateTransform<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

toAffine3D(SequenceCoordinateTransform) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

toAffine3D(Collection<CoordinateTransform<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

toAffine3D(N5Reader, Collection<CoordinateTransform<?>>) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

toAffineTransform3d() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

toString() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

toString() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.ArrayCoordinateSystem

toString() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

toString() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

toString() - Method in class org.janelia.saalfeldlab.n5.universe.N5TreeNode

totalAffine3D(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

totalAffine3D() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

totalTransform(N5Reader, TransformGraph) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

totalTransform(N5Reader) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

totalTransform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

tps - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

tranformsToAffine(OmeNgffMultiScaleMetadata.OmeNgffDataset, CoordinateTransformation<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformationUtils

transform(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.AbstractMetadataTemplateParser

transform() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes.MultiscaleDataset

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.BaseLinearCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.InverseCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.RealTransformCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AffineSpatialTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleOffsetSpatialTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.ScaleSpatialTransform

transform - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

transform(String, String, ObjectMapper, Scope) - Method in class org.janelia.saalfeldlab.n5.universe.translation.JqUtils

TransformationUtils - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

TransformationUtils() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformationUtils

TransformAxes - Class in org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms

A transformation whose axes are labeled.

TransformAxes(SpatialTransform, IndexedAxis[], IndexedAxis[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

TransformAxes(SpatialTransform, String...) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

TransformAxes(int[], String...) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

TransformAxes(String...) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxes

TransformAxesMetadataAdapter - Class in org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms

TransformAxesMetadataAdapter() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.axisTransforms.TransformAxesMetadataAdapter

TransformGraph - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph

TransformGraph() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

TransformGraph(List<CoordinateTransform<?>>, CoordinateSystems) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

TransformGraph(List<CoordinateTransform<?>>, List<CoordinateSystem>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

transformImage(N5Reader, String, String, String) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

TransformPath - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph

TransformPath(CoordinateTransform<?>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

TransformPath(TransformPath, CoordinateTransform<?>) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformPath

transforms - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.SpacesTransforms

TransformUtils - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

TransformUtils() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TransformUtils

translate - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

TranslatedMetadataWriter<T extends N5Metadata> - Class in org.janelia.saalfeldlab.n5.universe.translation

TranslatedMetadataWriter(N5Writer, String, String, N5MetadataWriter<T>) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedMetadataWriter

TranslatedMetadataWriter(N5Writer, String, N5MetadataWriter<T>) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedMetadataWriter

TranslatedN5Reader - Class in org.janelia.saalfeldlab.n5.universe.translation

TranslatedN5Reader(N5Reader, Gson, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

TranslatedN5Reader(GsonN5Reader, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

TranslatedN5Writer - Class in org.janelia.saalfeldlab.n5.universe.translation

TranslatedN5Writer(GsonN5Writer, Gson, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

TranslatedTreeMetadataParser - Class in org.janelia.saalfeldlab.n5.universe.translation

A parser for metadata that are translated into the "canonical" dialect.

TranslatedTreeMetadataParser(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

TranslatedTreeMetadataParser(String, Predicate<CanonicalMetadata>) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

TranslatedTreeMetadataParser(N5Reader, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

TranslatedTreeMetadataWriter - Class in org.janelia.saalfeldlab.n5.universe.translation

TranslatedTreeMetadataWriter(N5Writer, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataWriter

TranslatedTreeMetadataWriter(N5Writer, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataWriter

translation - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TranslationCoordinateTransformation

translation(Interval, double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

translation(Interval, double[], double[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.Common

translation - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

translation - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

translation - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

translation - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Reader

TranslationCoordinateTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations

TranslationCoordinateTransform(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(String, String[], String[], double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(String, String, String, double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(String, String, String, N5Reader, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(String, String, String, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(TranslationCoordinateTransform) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransform(TranslationCoordinateTransform, String[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

TranslationCoordinateTransformation - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations

TranslationCoordinateTransformation(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TranslationCoordinateTransformation

TranslationCoordinateTransformation(TranslationCoordinateTransformation) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TranslationCoordinateTransformation

TranslationSpatialTransform - Class in org.janelia.saalfeldlab.n5.universe.metadata.transforms

TranslationSpatialTransform(double[]) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

TranslationSpatialTransform(N5Reader, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

TranslationSpatialTransform(String) - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.transforms.TranslationSpatialTransform

TreeTranslation - Class in org.janelia.saalfeldlab.n5.universe.translation

TreeTranslation(ContainerMetadataNode, Gson, String) - Constructor for class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

trim(N5TreeNode) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

trim(N5TreeNode, Consumer<N5TreeNode>) - Static method in class org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer

Removes branches of the N5 container tree that do not contain any nodes that can be opened (nodes with metadata).

type - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

type - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.AbstractCoordinateTransformation

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.IdentityCoordinateTransformation

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.ScaleCoordinateTransformation

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.TranslationCoordinateTransformation

type - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

type - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractCoordinateTransform

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.IdentityCoordinateTransform

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ReferencedCoordinateTransform

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ScaleCoordinateTransform

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.SequenceCoordinateTransform

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

TYPE - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.TranslationCoordinateTransform

type - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractLinearSpatialTransform

type - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.transforms.AbstractSpatialTransform

typesToClasses - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.coordinateTransformations.CoordinateTransformationAdapter

U

union(String, CoordinateSystem) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem

unit - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis

Unit - Enum in org.janelia.saalfeldlab.n5.universe.metadata.axes

unit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CalibratedTransformMetadata

unit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.SpatialMetadataCanonical

unit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.FinalVoxelDimensions

unit(String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

unit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata

Unit - Class in org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes

Unit() - Constructor for class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

unit() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.NgffSingleScaleAxesMetadata

unit() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadata

unit() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

unitKey - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

unitKeyStrict - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser

units() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMultiscaleMetadata

units() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.canonical.MultiResolutionSpatialMetadataCanonical

units() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

units - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform

units() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

units() - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

unitStrict() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser.Builder

unknownAxis() - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

unknownType - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

updateChildrenDatasetAttributes(N5SingleScaleMetadata[], N5DatasetMetadata[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

updateChildrenMetadata(N5TreeNode, N5Metadata[], boolean) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

updateDownsamplingFactors(long, long[], long[], String[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

updateOriginal() - Method in class org.janelia.saalfeldlab.n5.universe.translation.InvertibleTreeTranslation

updateTransform(T) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

updateTransforms(Stream<T>) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems

updateTransforms() - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph

updateTranslated() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TreeTranslation

V

validateAndReturnN5vPixelResoution(N5Reader, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

Checks whether the given group is an n5v scale level: /c[0-9]+/s[0-9]+, and if so, returns a FinalVoxelDimensions.

validTranslation() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataParser

valueOf(String) - Static method in enum org.janelia.saalfeldlab.n5.universe.KeyValueAccessBackend

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.janelia.saalfeldlab.n5.universe.StorageFormat

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.janelia.saalfeldlab.n5.universe.KeyValueAccessBackend

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.janelia.saalfeldlab.n5.universe.metadata.axes.Unit

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.janelia.saalfeldlab.n5.universe.StorageFormat

Returns an array containing the constants of this enum type, in the order they are declared.

vectorAxisIndex - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedFieldTransform

vectorAxisIndex - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AbstractParametrizedRealFieldTransform

vectorAxisType - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

vectorAxisType - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

version - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata

version - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

version - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

W

weights - Variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.ThinPlateSplineCoordinateTransform

writeAllAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

writeAllAttributes(String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

Writes all attributes stored in the tree.

writeAllTranslatedAttributes() - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataWriter

writeAllTranslatedAttributes(String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataWriter

Writes all attributes stored in the node corresponding to the given pathName.

writeAttribute(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataWriter

writeBlock(String, DatasetAttributes, DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

writeBlock(String, DatasetAttributes, DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

writeChunk(String, DatasetAttributes, DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

writeChunk(String, DatasetAttributes, DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

writeDisplacementFieldTransform(N5Writer, String, RandomAccessibleInterval<T>, int[], Compression, CoordinateSystem[], CoordinateTransform<?>[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.DisplacementFieldCoordinateTransform

writeMetadata(N5CosemMetadata, N5Writer, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser

writeMetadata(T, N5Writer, String) - Method in interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataWriter

Writes metadata to a dataset or group in an N5 container.

writeMetadata(N5SingleScaleMetadata, N5Writer, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

writeMetadata(N5SingleScaleMetadata, N5Writer, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.N5ViewerDatasetMetadataWriter

writeMetadata(OmeNgffMetadata, N5Writer, String) - Method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadataParser

writeMetadata(T, N5Writer, String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedMetadataWriter

writePositionFieldTransform(N5Writer, String, RandomAccessibleInterval<T>, int[], Compression, CoordinateSystem[], CoordinateTransform[]) - Static method in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.CoordinateFieldCoordinateTransform

writer - Variable in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean, ExecutorService) - Method in class org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean, ExecutorService) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedN5Writer

writeTranslatedAttribute(String, String) - Method in class org.janelia.saalfeldlab.n5.universe.translation.TranslatedTreeMetadataWriter

X

xLabel - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

Y

YARD_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

yLabel - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

YOCTOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

YOCTOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

YOTTAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

YOTTASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

Z

zarr2(Consumer<Zarr2Builder>) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

Configure Zarr2Builder to be used when the factory accesses a Zarr2 container.

Zarr2Builder - Class in org.janelia.saalfeldlab.n5.universe.options

zarr3(Consumer<Zarr3Builder>) - Method in class org.janelia.saalfeldlab.n5.universe.options.N5FactoryOptions

Configure Zarr3Builder to be used when the factory accesses a Zarr3 container.

Zarr3Builder - Class in org.janelia.saalfeldlab.n5.universe.options

ZarrBuilder - Class in org.janelia.saalfeldlab.n5.universe.options

zarrDimensionSeparator(String) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions(), N5FactoryOptions.zarr2(Consumer), Zarr2Builder.dimensionSeparator(String)

zarrMapN5Attributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions(), N5FactoryOptions.zarr2(Consumer), Zarr2Builder.mapN5DatasetAttributes(boolean)

zarrMergeAttributes(boolean) - Method in class org.janelia.saalfeldlab.n5.universe.N5Factory

Deprecated.

configure with N5Factory.getOptions(), N5FactoryOptions.zarr2(Consumer), Zarr2Builder.mergeAttributes(boolean)

ZEPTOMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

ZEPTOSECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

ZETTAMETER_UNIT - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

ZETTASECOND - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.axes.Unit

zLabel - Static variable in class org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils

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