org.janelia.saalfeldlab.n5.universe.metadata

Class N5SingleScaleMetadataParser

java.lang.Object

org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser

All Implemented Interfaces:

BiFunction<org.janelia.saalfeldlab.n5.N5Reader,N5TreeNode,Optional<N5SingleScaleMetadata>>, N5MetadataParser<N5SingleScaleMetadata>, N5MetadataWriter<N5SingleScaleMetadata>

public class N5SingleScaleMetadataParser
extends Object
implements N5MetadataParser<N5SingleScaleMetadata>, N5MetadataWriter<N5SingleScaleMetadata>

Default N5MetadataParser for N5SingleScaleMetadata.

This parser provides default values for all metadata fields when values for the corresponding keys are not found, i.e., it returns empty metadata only when parsing throws an exception. As a result, this parser should appear as the last element of parser lists that are passed to N5DatasetDiscoverer.

When downsamplingFactors are specified, this parser assumes downsampling was performed using averaging and includes an offset to the resulting spatial transformation. Specifically, for a downsamplling factor of f, this parser yields an offset of (f-1)/2.

Author:

Caleb Hulbert, John Bogovic

Field Summary

Fields

Modifier and Type	Field and Description
static String	AFFINE_TRANSFORM_KEY
static Pattern	channelPattern
static Pattern	channelScaleLevelPattern
static String	DOWNSAMPLING_FACTORS_KEY
static String	PIXEL_RESOLUTION_KEY
static Pattern	scaleLevelPattern

Constructor Summary

Constructors

Constructor and Description
N5SingleScaleMetadataParser()

Method Summary

Modifier and Type	Method and Description
static net.imglib2.realtransform.AffineTransform3D	buildTransform(double[] downsamplingFactors, double[] pixelResolution, Optional<net.imglib2.realtransform.AffineTransform3D> extraTransformOpt)
static Optional<double[]>	inferDownsamplingFactorsFromDataset(String dataset)
Optional<N5SingleScaleMetadata>	parseMetadata(org.janelia.saalfeldlab.n5.N5Reader n5, N5TreeNode node) Called by the N5DatasetDiscoverer while discovering the N5 tree and filling the metadata for datasets or groups.
Optional<FinalVoxelDimensions>	validateAndReturnN5vPixelResoution(org.janelia.saalfeldlab.n5.N5Reader n5, String group) Checks whether the given group is an n5v scale level: /c[0-9]+/s[0-9]+, and if so, returns a FinalVoxelDimensions.
void	writeMetadata(N5SingleScaleMetadata t, org.janelia.saalfeldlab.n5.N5Writer n5, String group) Writes metadata to a dataset or group in an N5 container.

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.N5MetadataParser

apply, parseDatasetAttributes, parseMetadata

Methods inherited from interface java.util.function.BiFunction

andThen

Field Detail

DOWNSAMPLING_FACTORS_KEY

public static final String DOWNSAMPLING_FACTORS_KEY

See Also:

Constant Field Values

PIXEL_RESOLUTION_KEY

public static final String PIXEL_RESOLUTION_KEY

See Also:

Constant Field Values

AFFINE_TRANSFORM_KEY

public static final String AFFINE_TRANSFORM_KEY

See Also:

Constant Field Values

channelPattern

public static final Pattern channelPattern

scaleLevelPattern

public static final Pattern scaleLevelPattern

channelScaleLevelPattern

public static final Pattern channelScaleLevelPattern

Constructor Detail

N5SingleScaleMetadataParser

public N5SingleScaleMetadataParser()

Method Detail

buildTransform

public static net.imglib2.realtransform.AffineTransform3D buildTransform(double[] downsamplingFactors,
                                                                         double[] pixelResolution,
                                                                         Optional<net.imglib2.realtransform.AffineTransform3D> extraTransformOpt)

inferDownsamplingFactorsFromDataset

public static Optional<double[]> inferDownsamplingFactorsFromDataset(String dataset)

parseMetadata

public Optional<N5SingleScaleMetadata> parseMetadata(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                     N5TreeNode node)

Description copied from interface: N5MetadataParser

Called by the N5DatasetDiscoverer while discovering the N5 tree and filling the metadata for datasets or groups.

The metadata parsing is done in the bottom-up fashion, so the children of the given node have already been processed and should already contain valid metadata (if any).

Specified by:

parseMetadata in interface N5MetadataParser<N5SingleScaleMetadata>

Parameters:

n5 - the reader

node - list of tree nodes

Returns:

the metadata

validateAndReturnN5vPixelResoution

public Optional<FinalVoxelDimensions> validateAndReturnN5vPixelResoution(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                                         String group)

Checks whether the given group is an n5v scale level: /c[0-9]+/s[0-9]+, and if so, returns a FinalVoxelDimensions.

Parameters:

n5 - the reader

group - the group name

Returns:

an optional containing voxelDimensions if they exists and is consistent

writeMetadata

public void writeMetadata(N5SingleScaleMetadata t,
                          org.janelia.saalfeldlab.n5.N5Writer n5,
                          String group)
                   throws Exception

Description copied from interface: N5MetadataWriter

Writes metadata to a dataset or group in an N5 container.

Specified by:

writeMetadata in interface N5MetadataWriter<N5SingleScaleMetadata>

Parameters:

t - metadata

n5 - the n5 writer

group - the path relative to the container root of the group or dataset

Throws:

Exception - the exception