org.janelia.saalfeldlab.n5.zarr

Class N5ZarrReader

java.lang.Object

org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

org.janelia.saalfeldlab.n5.zarr.N5ZarrReader

All Implemented Interfaces:

AutoCloseable, org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer, org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.GsonN5Reader, org.janelia.saalfeldlab.n5.N5Reader

public class N5ZarrReader
extends ZarrKeyValueReader

Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org>, John Bogovic <bogovicj@janelia.hhmi.org>

Nested Class Summary

Nested classes/interfaces inherited from interface org.janelia.saalfeldlab.n5.N5Reader

org.janelia.saalfeldlab.n5.N5Reader.Version

Field Summary

Fields

Modifier and Type	Field and Description
protected static org.janelia.saalfeldlab.n5.N5Reader.Version	VERSION

Fields inherited from class org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

cache, cacheMeta, datasetAttributesMap, dimensionSeparator, gson, keyValueAccess, mapN5DatasetAttributes, mergeAttributes, uri, VERSION_ZERO, ZARR_FORMAT_KEY, ZARRAY_FILE, ZATTRS_FILE, ZGROUP_FILE

Fields inherited from interface org.janelia.saalfeldlab.n5.N5Reader

NO_VERSION, VERSION_KEY

Constructor Summary

Constructors

Constructor and Description
N5ZarrReader(String basePath) Opens an N5ZarrReader at a given base path.
N5ZarrReader(String basePath, boolean cacheMeta) Opens an N5ZarrReader at a given base path.
N5ZarrReader(String basePath, com.google.gson.GsonBuilder gsonBuilder) Opens an N5ZarrReader at a given base path with a custom GsonBuilder to support custom attributes.
N5ZarrReader(String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean cacheMeta) Opens an N5ZarrReader at a given base path with a custom GsonBuilder to support custom attributes.
N5ZarrReader(String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean mapN5DatasetAttributes, boolean mergeAttributes, boolean cacheMeta) Opens an N5ZarrReader at a given base path with a custom GsonBuilder to support custom attributes.

Method Summary

Methods inherited from class org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

addTypeAdapters, cacheMeta, combine, combineAll, createDatasetAttributes, datasetExists, exists, existsFromContainer, getAttribute, getAttribute, getAttributes, getAttributesFromContainer, getAttributesKey, getAttributesUnmapped, getCache, getConvertedDatasetAttributes, getDatasetAttributes, getGson, getJsonResource, getKeyValueAccess, getURI, getVersion, getVersion, getZArray, getZArrayAttributes, getZArrayAttributes, getZAttributes, getZGroup, groupExists, isDatasetFromAttributes, isDatasetFromContainer, isGroupFromAttributes, isGroupFromContainer, n5ToZarrDatasetAttributes, newCache, reverseAttrsWhenCOrder, toString, zarrToN5DatasetAttributes

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

existsFromContainer, hasDatasetAttributes, list, listFromContainer, normalGetDatasetAttributes

Methods inherited from interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

absoluteAttributesPath, absoluteGroupPath, blockExists, readBlock, readChunk, readChunks

Methods inherited from interface org.janelia.saalfeldlab.n5.GsonN5Reader

listAttributes

Methods inherited from interface org.janelia.saalfeldlab.n5.N5Reader

close, deepList, deepList, deepList, deepList, deepList, deepListDatasets, deepListDatasets, deepListDatasets, deepListDatasets, deepListHelper, getGroupSeparator, groupPath, readSerializedBlock

Field Detail

VERSION

protected static org.janelia.saalfeldlab.n5.N5Reader.Version VERSION

Constructor Detail

N5ZarrReader

public N5ZarrReader(String basePath,
                    com.google.gson.GsonBuilder gsonBuilder,
                    boolean mapN5DatasetAttributes,
                    boolean mergeAttributes,
                    boolean cacheMeta)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrReader at a given base path with a custom GsonBuilder to support custom attributes.

Parameters:

basePath - Zarr base path

gsonBuilder - the gson builder

mapN5DatasetAttributes - If true, getAttributes and variants of getAttribute methods will contain keys used by n5 datasets, and whose values are those for their corresponding zarr fields. For example, if true, the key "dimensions" (from n5) may be used to obtain the value of the key "shape" (from zarr).

mergeAttributes - If true, fields from .zgroup, .zarray, and .zattrs will be merged when calling getAttributes, and variants of getAttribute

cacheMeta - cache attributes and meta data Setting this to true avoids frequent reading and parsing of JSON encoded attributes and other meta data that requires accessing the store. This is most interesting for high latency backends. Changes of cached attributes and meta data by an independent writer on the same container will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be read or does not exist, if the N5 version of the container is not compatible with this implementation.

N5ZarrReader

public N5ZarrReader(String basePath,
                    com.google.gson.GsonBuilder gsonBuilder,
                    boolean cacheMeta)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrReader at a given base path with a custom GsonBuilder to support custom attributes.

Parameters:

basePath - Zarr base path

gsonBuilder -

cacheMeta - cache attributes and meta data Setting this to true avoids frequent reading and parsing of JSON encoded attributes and other meta data that requires accessing the store. This is most interesting for high latency backends. Changes of cached attributes and meta data by an independent writer on the same container will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be read or does not exist, if the N5 version of the container is not compatible with this implementation.

N5ZarrReader

public N5ZarrReader(String basePath,
                    boolean cacheMeta)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrReader at a given base path.

Parameters:

basePath - N5 base path

cacheMeta - cache attributes and meta data Setting this to true avoids frequent reading and parsing of JSON encoded attributes and other meta data that requires accessing the store. This is most interesting for high latency backends. Changes of cached attributes and meta data by an independent writer on the same container will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be read or does not exist, if the N5 version of the container is not compatible with this implementation.

N5ZarrReader

public N5ZarrReader(String basePath,
                    com.google.gson.GsonBuilder gsonBuilder)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrReader at a given base path with a custom GsonBuilder to support custom attributes.

Parameters:

basePath - N5 base path

gsonBuilder -

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be read or does not exist, if the N5 version of the container is not compatible with this implementation.

N5ZarrReader

public N5ZarrReader(String basePath)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrReader at a given base path.

Parameters:

basePath - N5 base path

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be read or does not exist, if the N5 version of the container is not compatible with this implementation.