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

Class OmeNgffMetadata

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.OmeNgffMetadata

All Implemented Interfaces:

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

public class OmeNgffMetadata
extends SpatialMultiscaleMetadata<NgffSingleScaleAxesMetadata>

Field Summary

Fields

Modifier and Type	Field and Description
OmeNgffMultiScaleMetadata[]	multiscales
String	version

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

basePath, childrenMetadata

Constructor Summary

Constructors

Constructor and Description
OmeNgffMetadata(String path, OmeNgffMultiScaleMetadata[] multiscales)

Method Summary

Modifier and Type	Method and Description
static OmeNgffMetadata	buildForWriting(int numDimensions, String name, String version, Axis[] axes, String[] scalePaths, double[][] scales, double[][] translations) Creates an OmeNgffMetadata object for writing.
static int[]	findNgffPermutation(String[] axisLabels) Finds and returns a permutation p such that source[p[i]] equals xyczt
static <T,M extends AxisMetadata & N5Metadata> net.imglib2.RandomAccessibleInterval<T>	permuteForNgff(net.imglib2.RandomAccessibleInterval<T> img, M meta)

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

getChildrenMetadata, getPath, getPaths, sortScaleMetadata, units

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, units

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

getChildrenMetadata, getPaths

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

getName, getPath

Field Detail

multiscales

public final OmeNgffMultiScaleMetadata[] multiscales

version

public final transient String version

Constructor Detail

OmeNgffMetadata

public OmeNgffMetadata(String path,
                       OmeNgffMultiScaleMetadata[] multiscales)

Method Detail

buildForWriting

public static OmeNgffMetadata buildForWriting(int numDimensions,
                                              String name,
                                              String version,
                                              Axis[] axes,
                                              String[] scalePaths,
                                              double[][] scales,
                                              double[][] translations)

Creates an OmeNgffMetadata object for writing. See AxisUtils.defaultAxes(String...) for convenient creation of axes.

Parameters:

numDimensions - number of dimensions

name - a name for this dataset

version - the OME-Zarr version

axes - an array of axes (length numDimensions)

scalePaths - relative paths to children containing scale level arrays

scales - array of absolute resolutions. size: [numScales][numDimensions]

translations - array of translations. size: [numScales][numDimensions]. May be null.

Returns:

OmeNgffMetadata

permuteForNgff

public static <T,M extends AxisMetadata & N5Metadata> net.imglib2.RandomAccessibleInterval<T> permuteForNgff(net.imglib2.RandomAccessibleInterval<T> img,
                                                                                                             M meta)

findNgffPermutation

public static int[] findNgffPermutation(String[] axisLabels)

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

Parameters:

axisLabels - the axis labels

Returns:

the permutation array