org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff

Class OmeNgffMultiScaleMetadata

java.lang.Object

org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata<T>

org.janelia.saalfeldlab.n5.universe.metadata.SpatialMultiscaleMetadata<NgffSingleScaleAxesMetadata>

org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMultiScaleMetadata

All Implemented Interfaces:

N5Metadata, N5MetadataGroup<NgffSingleScaleAxesMetadata>, SpatialMetadata, SpatialMetadataGroup<NgffSingleScaleAxesMetadata>

Direct Known Subclasses:

OmeNgffMultiScaleMetadataMutable

public class OmeNgffMultiScaleMetadata
extends SpatialMultiscaleMetadata<NgffSingleScaleAxesMetadata>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	OmeNgffMultiScaleMetadata.OmeNgffDataset
static class	OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata

Field Summary

Fields

Modifier and Type	Field and Description
Axis[]	axes
org.janelia.saalfeldlab.n5.DatasetAttributes[]	childrenAttributes
CoordinateTransformation<?>[]	coordinateTransformations
OmeNgffMultiScaleMetadata.OmeNgffDataset[]	datasets
OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata	metadata
String	name
String	type
String	version

Fields inherited from class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

basePath, childrenMetadata

Constructor Summary

Constructors

Constructor and Description
OmeNgffMultiScaleMetadata(int nd, String path, String name, String type, String version, Axis[] axes, OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets, CoordinateTransformation<?>[] coordinateTransformations, org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes, OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata)
OmeNgffMultiScaleMetadata(int nd, String path, String name, String type, String version, Axis[] axes, OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets, CoordinateTransformation<?>[] coordinateTransformations, org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes, OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata, NgffSingleScaleAxesMetadata[] childrenMetadata)
OmeNgffMultiScaleMetadata(OmeNgffMultiScaleMetadata other, NgffSingleScaleAxesMetadata[] children)

Method Summary

Modifier and Type	Method and Description
static boolean	allSameAxisOrder(org.janelia.saalfeldlab.n5.DatasetAttributes[] multiscaleDatasetAttributes)
N5SingleScaleMetadata	buildChild(int nd, N5DatasetMetadata datasetMeta)
NgffSingleScaleAxesMetadata[]	buildChildren()
NgffSingleScaleAxesMetadata[]	buildChildren(int nd, org.janelia.saalfeldlab.n5.DatasetAttributes[] datasetAttributes, CoordinateTransformation<?>[] coordinateTransformations, Axis[] axes)
static NgffSingleScaleAxesMetadata[]	buildMetadata(int nd, String path, org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes, OmeNgffMultiScaleMetadata multiscales)
static NgffSingleScaleAxesMetadata[]	buildMetadata(int nd, String path, OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets, org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes, CoordinateTransformation<?>[] transforms, OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata, Axis[] axes)
static NgffSingleScaleAxesMetadata[]	buildMetadata(int nd, String path, OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets, org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes, CoordinateTransformation<?>[] transforms, OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata, Axis[] axes, boolean reverseParameters)
static boolean	cOrder(org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
static Axis[]	defaultAxes()
static boolean	fOrder(org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
Axis[]	getAxes()
String[]	getCanonicalPaths()
NgffSingleScaleAxesMetadata[]	getChildrenMetadata() Note: This is NOT gauranteeed to be sorted.
CoordinateTransformation<?>[]	getCoordinateTransformations()
OmeNgffMultiScaleMetadata.OmeNgffDataset[]	getDatasets()
String[]	units()

Methods inherited from class org.janelia.saalfeldlab.n5.universe.metadata.MultiscaleMetadata

getPath, getPaths, sortScaleMetadata

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup

spatialTransform, spatialTransform3d, spatialTransforms, spatialTransforms3d, unit

Methods inherited from interface org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataGroup

getPaths

Methods inherited from interface org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata

getName, getPath

Field Detail

version

public final String version

name

public final String name

type

public final String type

axes

public final Axis[] axes

datasets

public final OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets

coordinateTransformations

public final CoordinateTransformation<?>[] coordinateTransformations

metadata

public final OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata

childrenAttributes

public transient org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes

Constructor Detail

OmeNgffMultiScaleMetadata

public OmeNgffMultiScaleMetadata(OmeNgffMultiScaleMetadata other,
                                 NgffSingleScaleAxesMetadata[] children)

OmeNgffMultiScaleMetadata

public OmeNgffMultiScaleMetadata(int nd,
                                 String path,
                                 String name,
                                 String type,
                                 String version,
                                 Axis[] axes,
                                 OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets,
                                 CoordinateTransformation<?>[] coordinateTransformations,
                                 org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes,
                                 OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata)

OmeNgffMultiScaleMetadata

public OmeNgffMultiScaleMetadata(int nd,
                                 String path,
                                 String name,
                                 String type,
                                 String version,
                                 Axis[] axes,
                                 OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets,
                                 CoordinateTransformation<?>[] coordinateTransformations,
                                 org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes,
                                 OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata,
                                 NgffSingleScaleAxesMetadata[] childrenMetadata)

Method Detail

getAxes

public Axis[] getAxes()

buildChild

public N5SingleScaleMetadata buildChild(int nd,
                                        N5DatasetMetadata datasetMeta)

buildMetadata

public static NgffSingleScaleAxesMetadata[] buildMetadata(int nd,
                                                          String path,
                                                          org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes,
                                                          OmeNgffMultiScaleMetadata multiscales)

buildMetadata

public static NgffSingleScaleAxesMetadata[] buildMetadata(int nd,
                                                          String path,
                                                          OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets,
                                                          org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes,
                                                          CoordinateTransformation<?>[] transforms,
                                                          OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata,
                                                          Axis[] axes)

buildMetadata

public static NgffSingleScaleAxesMetadata[] buildMetadata(int nd,
                                                          String path,
                                                          OmeNgffMultiScaleMetadata.OmeNgffDataset[] datasets,
                                                          org.janelia.saalfeldlab.n5.DatasetAttributes[] childrenAttributes,
                                                          CoordinateTransformation<?>[] transforms,
                                                          OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata metadata,
                                                          Axis[] axes,
                                                          boolean reverseParameters)

buildChildren

public NgffSingleScaleAxesMetadata[] buildChildren(int nd,
                                                   org.janelia.saalfeldlab.n5.DatasetAttributes[] datasetAttributes,
                                                   CoordinateTransformation<?>[] coordinateTransformations,
                                                   Axis[] axes)

buildChildren

public NgffSingleScaleAxesMetadata[] buildChildren()

getDatasets

public OmeNgffMultiScaleMetadata.OmeNgffDataset[] getDatasets()

getCoordinateTransformations

public CoordinateTransformation<?>[] getCoordinateTransformations()

getCanonicalPaths

public String[] getCanonicalPaths()

getChildrenMetadata

public NgffSingleScaleAxesMetadata[] getChildrenMetadata()

Description copied from interface: N5MetadataGroup

Note: This is NOT gauranteeed to be sorted. Sort with

Specified by:

getChildrenMetadata in interface N5MetadataGroup<NgffSingleScaleAxesMetadata>

Overrides:

getChildrenMetadata in class MultiscaleMetadata<NgffSingleScaleAxesMetadata>

Returns:

an array of the metadata for the children of this group

units

public String[] units()

Specified by:

units in interface SpatialMetadataGroup<NgffSingleScaleAxesMetadata>

Overrides:

units in class MultiscaleMetadata<NgffSingleScaleAxesMetadata>

cOrder

public static boolean cOrder(org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)

fOrder

public static boolean fOrder(org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)

allSameAxisOrder

public static boolean allSameAxisOrder(org.janelia.saalfeldlab.n5.DatasetAttributes[] multiscaleDatasetAttributes)

defaultAxes

public static Axis[] defaultAxes()