org.janelia.saalfeldlab.n5.zarr

Class ZarrKeyValueWriter

java.lang.Object

org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueWriter

All Implemented Interfaces:

AutoCloseable, org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer, org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer, org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer, org.janelia.saalfeldlab.n5.GsonN5Reader, org.janelia.saalfeldlab.n5.GsonN5Writer, org.janelia.saalfeldlab.n5.N5Reader, org.janelia.saalfeldlab.n5.N5Writer

Direct Known Subclasses:

N5ZarrWriter

public class ZarrKeyValueWriter
extends ZarrKeyValueReader
implements org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

Zarr KeyValueAccess implementation.

Author:

Stephan Saalfeld, John Bogovic

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	ZarrKeyValueWriter.ZarrJsonElements Stores JsonObjects to be written to .zattrs, .zgroup, and .zarray.

Nested classes/interfaces inherited from interface org.janelia.saalfeldlab.n5.N5Writer

org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T>

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

org.janelia.saalfeldlab.n5.N5Reader.Version

Field Summary

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

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

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

NO_VERSION, VERSION, VERSION_KEY

Constructor Summary

Constructors

Constructor and Description
ZarrKeyValueWriter(org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess, String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean mapN5DatasetAttributes, boolean mergeAttributes, String dimensionSeparator, boolean cacheAttributes) Opens an ZarrKeyValueWriter at a given base path with a custom GsonBuilder to support custom attributes.

Method Summary

Modifier and Type	Method and Description
protected static ZarrKeyValueWriter.ZarrJsonElements	build(com.google.gson.JsonObject obj, com.google.gson.Gson gson)
protected static ZarrKeyValueWriter.ZarrJsonElements	build(com.google.gson.JsonObject obj, com.google.gson.Gson gson, boolean mapN5Attributes) Creates a ZarrKeyValueWriter.ZarrJsonElements object from a JsonObject containing attributes.
ZarrDatasetAttributes	createDataset(String path, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
void	createGroup(String path)
protected void	deleteJsonResource(String normalPath, String jsonName)
protected static boolean	hasRequiredArrayKeys(com.google.gson.JsonObject obj)
protected void	initializeGroup(String normalPath) Creates a .zgroup file containing the zarr_format at the given path and all parent paths.
boolean	isCompatible(org.janelia.saalfeldlab.n5.N5Reader.Version version)
protected static void	move(com.google.gson.JsonObject src, Supplier<com.google.gson.JsonObject> dstSup, String... keys)
static byte[]	padCrop(byte[] src, int[] srcBlockSize, int[] dstBlockSize, int nBytes, int nBits, byte[] fill_value)
protected static void	redirectCompression(com.google.gson.JsonObject src, com.google.gson.Gson gson, com.google.gson.JsonObject dest)
protected static void	redirectDatasetAttribute(com.google.gson.JsonObject src, String srcKey, com.google.gson.JsonObject dest, String destKey)
protected void	redirectDatasetAttribute(com.google.gson.JsonObject src, String srcKey, ZarrKeyValueWriter.ZarrJsonElements zarrElems, String destKey, ZarrDatasetAttributes dsetAttrs)
protected void	redirectDatasetAttribute(com.google.gson.JsonObject src, String key, ZarrKeyValueWriter.ZarrJsonElements zarrElems, ZarrDatasetAttributes dsetAttrs)
protected static void	redirectDataType(com.google.gson.JsonObject src, com.google.gson.JsonObject dest)
protected void	redirectGroupDatasetAttribute(com.google.gson.JsonObject src, String srcKey, ZarrKeyValueWriter.ZarrJsonElements zarrElems, String destKey, ZarrDatasetAttributes dsetAttrs)
boolean	removeAttribute(String pathName, String key)
<T> T	removeAttribute(String pathName, String key, Class<T> cls)
void	setAttributes(String path, Map<String,?> attributes)
void	setDatasetAttributes(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
void	setVersion(String path)
protected void	setVersion(String path, boolean create)
void	setZArrayAttributes(String pathName, ZArrayAttributes attributes) Write the contents of the attributes argument to the .zarray file at the given pathName.
protected void	setZGroup(String pathName, org.janelia.saalfeldlab.n5.N5Reader.Version version)
protected void	writeJson(String normalPath, String jsonName, com.google.gson.JsonElement attributes)
protected void	writeJsonResource(String normalPath, String jsonName, Object attributes)
protected void	writeZArray(String normalGroupPath, com.google.gson.JsonElement attributes)
protected void	writeZAttrs(String normalGroupPath, com.google.gson.JsonElement attributes)
protected void	writeZGroup(String normalGroupPath, com.google.gson.JsonElement attributes)

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.CachedGsonKeyValueN5Writer

remove, writeAndCacheAttributes, writeAttributes

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

cacheMeta, datasetExists, exists, existsFromContainer, getAttribute, getAttribute, getAttributes, getAttributesFromContainer, getCache, getDatasetAttributes, groupExists, hasDatasetAttributes, isDatasetFromAttributes, isDatasetFromContainer, isGroupFromAttributes, isGroupFromContainer, list, listFromContainer, newCache, normalGetDatasetAttributes

Methods inherited from interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

deleteBlock, deleteChunk, deleteChunks, initializeContainer, removeAttributes, setAttributes, writeAttributes, writeBlock, writeChunk, writeChunks, writeRegion, writeRegion

Methods inherited from interface org.janelia.saalfeldlab.n5.N5Writer

createDataset, deleteBlock, deleteChunk, remove, setAttribute, setVersion, writeSerializedBlock

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

absoluteAttributesPath, absoluteGroupPath, blockExists, getKeyValueAccess, readBlock, readChunk, readChunks

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

createDatasetAttributes, getAttributesKey, getGson, listAttributes

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

close, deepList, deepList, deepList, deepList, deepList, deepListDatasets, deepListDatasets, deepListDatasets, deepListDatasets, deepListHelper, getConvertedDatasetAttributes, getGroupSeparator, getURI, getVersion, groupPath, readSerializedBlock

Constructor Detail

ZarrKeyValueWriter

public ZarrKeyValueWriter(org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess,
                          String basePath,
                          com.google.gson.GsonBuilder gsonBuilder,
                          boolean mapN5DatasetAttributes,
                          boolean mergeAttributes,
                          String dimensionSeparator,
                          boolean cacheAttributes)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Opens an ZarrKeyValueWriter at a given base path with a custom GsonBuilder to support custom attributes. If the base path does not exist, it will be created. If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

keyValueAccess -

basePath - n5 base path

gsonBuilder -

cacheAttributes - cache attributes Setting this to true avoids frequent reading and parsing of JSON encoded attributes, this is most interesting for high latency file systems. Changes of attributes by an independent writer will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created.

Method Detail

isCompatible

public boolean isCompatible(org.janelia.saalfeldlab.n5.N5Reader.Version version)

setVersion

public void setVersion(String path)
                throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setVersion in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

Specified by:

setVersion in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setVersion

protected void setVersion(String path,
                          boolean create)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

initializeGroup

protected void initializeGroup(String normalPath)
                        throws org.janelia.saalfeldlab.n5.N5Exception

Creates a .zgroup file containing the zarr_format at the given path and all parent paths.

Parameters:

normalPath -

Throws:

org.janelia.saalfeldlab.n5.N5Exception

createGroup

public void createGroup(String path)
                 throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

createGroup in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

Specified by:

createGroup in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

createGroup in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

createDataset

public ZarrDatasetAttributes createDataset(String path,
                                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
                                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

createDataset in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttributes

public void setAttributes(String path,
                          Map<String,?> attributes)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

removeAttribute

public boolean removeAttribute(String pathName,
                               String key)
                        throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

removeAttribute in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

removeAttribute in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

removeAttribute

public <T> T removeAttribute(String pathName,
                             String key,
                             Class<T> cls)
                      throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

removeAttribute in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

removeAttribute in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setDatasetAttributes

public void setDatasetAttributes(String pathName,
                                 org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
                          throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setDatasetAttributes in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setZArrayAttributes

public void setZArrayAttributes(String pathName,
                                ZArrayAttributes attributes)
                         throws org.janelia.saalfeldlab.n5.N5Exception

Write the contents of the attributes argument to the .zarray file at the given pathName. Overwrites and existing .zarray.

Parameters:

pathName - the group / dataset path

attributes - ZArray attributes

Throws:

org.janelia.saalfeldlab.n5.N5Exception - the exception

setZGroup

protected void setZGroup(String pathName,
                         org.janelia.saalfeldlab.n5.N5Reader.Version version)
                  throws IOException

Throws:

IOException

deleteJsonResource

protected void deleteJsonResource(String normalPath,
                                  String jsonName)
                           throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeJson

protected void writeJson(String normalPath,
                         String jsonName,
                         com.google.gson.JsonElement attributes)
                  throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeJsonResource

protected void writeJsonResource(String normalPath,
                                 String jsonName,
                                 Object attributes)
                          throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeZArray

protected void writeZArray(String normalGroupPath,
                           com.google.gson.JsonElement attributes)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeZGroup

protected void writeZGroup(String normalGroupPath,
                           com.google.gson.JsonElement attributes)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeZAttrs

protected void writeZAttrs(String normalGroupPath,
                           com.google.gson.JsonElement attributes)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

padCrop

public static byte[] padCrop(byte[] src,
                             int[] srcBlockSize,
                             int[] dstBlockSize,
                             int nBytes,
                             int nBits,
                             byte[] fill_value)

redirectDatasetAttribute

protected void redirectDatasetAttribute(com.google.gson.JsonObject src,
                                        String key,
                                        ZarrKeyValueWriter.ZarrJsonElements zarrElems,
                                        ZarrDatasetAttributes dsetAttrs)

redirectDatasetAttribute

protected static void redirectDatasetAttribute(com.google.gson.JsonObject src,
                                               String srcKey,
                                               com.google.gson.JsonObject dest,
                                               String destKey)

redirectDatasetAttribute

protected void redirectDatasetAttribute(com.google.gson.JsonObject src,
                                        String srcKey,
                                        ZarrKeyValueWriter.ZarrJsonElements zarrElems,
                                        String destKey,
                                        ZarrDatasetAttributes dsetAttrs)

redirectGroupDatasetAttribute

protected void redirectGroupDatasetAttribute(com.google.gson.JsonObject src,
                                             String srcKey,
                                             ZarrKeyValueWriter.ZarrJsonElements zarrElems,
                                             String destKey,
                                             ZarrDatasetAttributes dsetAttrs)

redirectDataType

protected static void redirectDataType(com.google.gson.JsonObject src,
                                       com.google.gson.JsonObject dest)

redirectCompression

protected static void redirectCompression(com.google.gson.JsonObject src,
                                          com.google.gson.Gson gson,
                                          com.google.gson.JsonObject dest)

build

protected static ZarrKeyValueWriter.ZarrJsonElements build(com.google.gson.JsonObject obj,
                                                           com.google.gson.Gson gson)

build

protected static ZarrKeyValueWriter.ZarrJsonElements build(com.google.gson.JsonObject obj,
                                                           com.google.gson.Gson gson,
                                                           boolean mapN5Attributes)

Creates a ZarrKeyValueWriter.ZarrJsonElements object from a JsonObject containing attributes.

Used when re-directing attributes to the appropriate zarr metadata files according to attribute keys.

Parameters:

obj - the json attributes object

gson - the json

mapN5Attributes - if true, map n5 attribute keys to corresponding zarr attribute keys

Returns:

hasRequiredArrayKeys

protected static boolean hasRequiredArrayKeys(com.google.gson.JsonObject obj)

move

protected static void move(com.google.gson.JsonObject src,
                           Supplier<com.google.gson.JsonObject> dstSup,
                           String... keys)