N5Factory (N5-Universe 3.0.2 API)

java.lang.Object
- org.janelia.saalfeldlab.n5.universe.N5Factory

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

N5FactoryWithCache
```
public class N5Factory
extends Object
implements Serializable
```
Factory for various N5 readers and writers. Implementation-specific parameters can be provided to the factory instance and will be used when such implementations are generated and ignored otherwise. Reasonable defaults are provided.

Author:

Stephan Saalfeld, John Bogovic, Igor Pisarev

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

N5Factory()

Constructors
Constructor and Description
`N5Factory()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`N5Factory`	`cacheAttributes(boolean cacheAttributes)` Deprecated. configure with `getOptions()` and `N5FactoryOptions.cacheAttributes(boolean)`
`protected com.google.cloud.storage.Storage`	`createGoogleCloudStorage()`
`static org.janelia.saalfeldlab.n5.N5Reader`	`createReader(String containerUri)` Creates an N5Reader at containerURI with default N5Factory configuration.
`protected software.amazon.awssdk.services.s3.S3Client`	`createS3(String uri)`
`static org.janelia.saalfeldlab.n5.N5Writer`	`createWriter(String containerUri)` Creates an N5 writer for the specified container URI with default N5Factory configuration.
`org.janelia.saalfeldlab.n5.KeyValueAccess`	`getKeyValueAccess(URI uri, boolean readOnly)` Test the provided `URI` to and return the appropriate `KeyValueAccess`.
`N5FactoryOptions`	`getOptions()`
`N5Factory`	`googleCloudConfiguration(Consumer<com.google.cloud.storage.StorageOptions.Builder> builderConfig)` This factory will use the gcsBuilderConfig to configure the Google Cloude Store `StorageOptions.Builder`, and thereby the Google Cloud `Storage` client.
`N5Factory`	`googleCloudProjectId(String projectId)`
`N5Factory`	`gsonBuilder(com.google.gson.GsonBuilder gsonBuilder)` Deprecated. configure with `getOptions()` and `N5FactoryOptions.gsonBuilder(GsonBuilder)`
`N5Factory`	`hdf5DefaultBlockSize(int... blockSize)` Deprecated. configure with `getOptions()` and `N5FactoryOptions.hdf5(Consumer)`
`N5Factory`	`hdf5OverrideBlockSize(boolean override)` Deprecated. configure with `getOptions()` and `N5FactoryOptions.hdf5(Consumer)`
`org.janelia.saalfeldlab.n5.N5Reader`	`openAWSS3Reader(String uri)` Deprecated. use `openReader(KeyValueAccessBackend, URI)` instead
`org.janelia.saalfeldlab.n5.N5Writer`	`openAWSS3Writer(String uri)` Deprecated. use `openWriter(KeyValueAccessBackend, String)` instead.
`org.janelia.saalfeldlab.n5.N5Reader`	`openFileSystemReader(String uri)` Deprecated. use `openReader(KeyValueAccessBackend, URI)` instead
`org.janelia.saalfeldlab.n5.N5Reader`	`openFSReader(String path)` Deprecated. use `openReader(StorageFormat, URI)` instead
`org.janelia.saalfeldlab.n5.N5Writer`	`openFSWriter(String path)` Deprecated. use `openWriter(StorageFormat, URI)` instead
`org.janelia.saalfeldlab.n5.N5Reader`	`openGoogleCloudReader(String uri)` Deprecated. use `openReader(KeyValueAccessBackend, URI)` instead
`org.janelia.saalfeldlab.n5.N5Writer`	`openGoogleCloudWriter(String uri)` Deprecated. use `openWriter(KeyValueAccessBackend, String)` instead.
`org.janelia.saalfeldlab.n5.N5Reader`	`openHDF5Reader(String path)` Deprecated. use `openReader(StorageFormat, URI)` instead
`org.janelia.saalfeldlab.n5.N5Writer`	`openHDF5Writer(String path)` Deprecated. use `openReader(StorageFormat, URI)` instead
`org.janelia.saalfeldlab.n5.N5Reader`	`openReader(KeyValueAccessBackend backend, String uri)` Open and N5Reader at the given URI given the specified `KeyValueAccessBackend`.
`org.janelia.saalfeldlab.n5.N5Reader`	`openReader(KeyValueAccessBackend backend, URI uri)` Open and N5Reader at the given URI given the specified `KeyValueAccessBackend`.
`org.janelia.saalfeldlab.n5.N5Reader`	`openReader(StorageFormat storage, org.janelia.saalfeldlab.n5.KeyValueAccess access, URI location)` Create an N5Reader at the `containerPath` requiring the specific `StorageFormat` and using `KeyValueAccess`.
`org.janelia.saalfeldlab.n5.N5Reader`	`openReader(StorageFormat format, String uri)` Open an `N5Reader` at the given URL, with best attempts to infer the appropriate `KeyValueAccessBackend`.
`org.janelia.saalfeldlab.n5.N5Reader`	`openReader(StorageFormat format, URI uri)` Open an `N5Reader` at the given URL, with best attempts to infer the appropriate `KeyValueAccessBackend`.
`org.janelia.saalfeldlab.n5.N5Reader`	`openReader(String uri)` Open an `N5Reader` at the given URL, with best attempts to infer the appropriate `KeyValueAccessBackend` and `StorageFormat`.
`org.janelia.saalfeldlab.n5.N5Writer`	`openWriter(KeyValueAccessBackend backend, String uri)` Create or Open an N5Writer as the given uri and backend.
`org.janelia.saalfeldlab.n5.N5Writer`	`openWriter(KeyValueAccessBackend backend, URI uri)` Create or Open an N5Writer as the given uri and backend.
`org.janelia.saalfeldlab.n5.N5Writer`	`openWriter(StorageFormat storage, org.janelia.saalfeldlab.n5.KeyValueAccess access, URI location)` Create an N5Writer at the `location` requiring the specific `StorageFormat` and using `KeyValueAccess`.
`org.janelia.saalfeldlab.n5.N5Writer`	`openWriter(StorageFormat format, String uri)` Open an `N5Writer` at the given URL, with best attempts to infer the appropriate `KeyValueAccessBackend`.
`org.janelia.saalfeldlab.n5.N5Writer`	`openWriter(StorageFormat format, URI uri)` Open an `N5Writer` at the given URL, with best attempts to infer the appropriate `KeyValueAccessBackend`.
`org.janelia.saalfeldlab.n5.N5Writer`	`openWriter(String uri)` Open an `N5Writer` at the given URL, with best attempts to infer the appropriate `KeyValueAccessBackend` and `StorageFormat`.
`org.janelia.saalfeldlab.n5.N5Reader`	`openZarrReader(String path)` Deprecated. use `openReader(StorageFormat, URI)` instead
`org.janelia.saalfeldlab.n5.N5Writer`	`openZarrWriter(String path)` Deprecated. use `openWriter(StorageFormat, URI)`) instead
`N5Factory`	`options(Consumer<N5FactoryOptions> configureOptions)`
`N5Factory`	`preferredStorageFormat(StorageFormat format)` When N5Factory cannot determine the StorageFormat from the URI, it will attempt to try and create a reader/writer with all known StorageFormat values.
`N5Factory`	`s3Configuration(Consumer<software.amazon.awssdk.services.s3.S3ClientBuilder> builderConfig)` This factory will use the builderConfig to configure the `S3ClientBuilder`, and thereby the `S3Client`.
`N5Factory`	`s3UseCredentials()` Deprecated. configure with `s3Configuration`.
`N5Factory`	`setOptions(N5FactoryOptions options)`
`N5Factory`	`zarrDimensionSeparator(String separator)` Deprecated. configure with `getOptions()`, `N5FactoryOptions.zarr2(Consumer)`, `Zarr2Builder.dimensionSeparator(String)`
`N5Factory`	`zarrMapN5Attributes(boolean mapAttributes)` Deprecated. configure with `getOptions()`, `N5FactoryOptions.zarr2(Consumer)`, `Zarr2Builder.mapN5DatasetAttributes(boolean)`
`N5Factory`	`zarrMergeAttributes(boolean mergeAttributes)` Deprecated. configure with `getOptions()`, `N5FactoryOptions.zarr2(Consumer)`, `Zarr2Builder.mergeAttributes(boolean)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - N5Factory
```
public N5Factory()
```
- Method Detail
  - getOptions
```
public N5FactoryOptions getOptions()
```
  - setOptions
```
public N5Factory setOptions(N5FactoryOptions options)
```
  - options
```
public N5Factory options(Consumer<N5FactoryOptions> configureOptions)
```
  - s3UseCredentials
```
@Deprecated
public N5Factory s3UseCredentials()
```
    Deprecated. configure with s3Configuration.
  - hdf5DefaultBlockSize
```
public N5Factory hdf5DefaultBlockSize(int... blockSize)
```
    Deprecated. configure with getOptions() and N5FactoryOptions.hdf5(Consumer)
  - hdf5OverrideBlockSize
```
public N5Factory hdf5OverrideBlockSize(boolean override)
```
    Deprecated. configure with getOptions() and N5FactoryOptions.hdf5(Consumer)
  - gsonBuilder
```
public N5Factory gsonBuilder(com.google.gson.GsonBuilder gsonBuilder)
```
    Deprecated. configure with getOptions() and N5FactoryOptions.gsonBuilder(GsonBuilder)
  - cacheAttributes
```
public N5Factory cacheAttributes(boolean cacheAttributes)
```
    Deprecated. configure with getOptions() and N5FactoryOptions.cacheAttributes(boolean)
  - zarrDimensionSeparator
```
public N5Factory zarrDimensionSeparator(String separator)
```
    Deprecated. configure with getOptions(), N5FactoryOptions.zarr2(Consumer), Zarr2Builder.dimensionSeparator(String)
    
    Deprecated method to set dimensions separator for zarr 2 writers.
    
    Parameters:
    
    separator - to use for Zarr2 dimension separator
  - zarrMapN5Attributes
```
public N5Factory zarrMapN5Attributes(boolean mapAttributes)
```
    Deprecated. configure with getOptions(), N5FactoryOptions.zarr2(Consumer), Zarr2Builder.mapN5DatasetAttributes(boolean)
    
    Value to set for the [mapN5DatasetAttributes] parameter of ZarrKeyValueReader. NOTE: this is only used for Zarr2 readers, not Zarr3
    
    Parameters:
    
    mapAttributes - see ZarrKeyValueReader.getAttributes(String)
  - zarrMergeAttributes
```
public N5Factory zarrMergeAttributes(boolean mergeAttributes)
```
    Deprecated. configure with getOptions(), N5FactoryOptions.zarr2(Consumer), Zarr2Builder.mergeAttributes(boolean)
    
    Value to set for the [mergeAttributes] parameter of ZarrKeyValueReader. NOTE: this is only used for Zarr2 readers, not Zarr3
    
    Parameters:
    
    mergeAttributes - see ZarrKeyValueReader.getAttributes(String)
  - googleCloudProjectId
```
public N5Factory googleCloudProjectId(String projectId)
```
  - preferredStorageFormat
```
public N5Factory preferredStorageFormat(StorageFormat format)
```
    When N5Factory cannot determine the StorageFormat from the URI, it will attempt to try and create a reader/writer with all known StorageFormat values. The order of th StorageFormat will dictate which will formats will be attempted first. Some URI's may be valid for multiple StorageFormat types. (e.g. N5 and Zarr Writer at a new location). This format will be tried first if specified.
    
    Parameters:
    
    format - the storage format to try first.
    
    Returns:
    
    this N5Factory
  - s3Configuration
```
public N5Factory s3Configuration(Consumer<software.amazon.awssdk.services.s3.S3ClientBuilder> builderConfig)
```
    This factory will use the builderConfig to configure the S3ClientBuilder, and thereby the S3Client.
    
    Returns:
    
    this N5Factory
  - googleCloudConfiguration
```
public N5Factory googleCloudConfiguration(Consumer<com.google.cloud.storage.StorageOptions.Builder> builderConfig)
```
    This factory will use the gcsBuilderConfig to configure the Google Cloude Store StorageOptions.Builder, and thereby the Google Cloud Storage client.
    
    Returns:
    
    this N5Factory
  - createS3
```
protected software.amazon.awssdk.services.s3.S3Client createS3(String uri)
```
  - createGoogleCloudStorage
```
protected com.google.cloud.storage.Storage createGoogleCloudStorage()
```
  - getKeyValueAccess
```
@Nullable
public org.janelia.saalfeldlab.n5.KeyValueAccess getKeyValueAccess(URI uri,
                                                                             boolean readOnly)
```
    Test the provided URI to and return the appropriate KeyValueAccess. If no appropriate KeyValueAccess is found, may be null
    This differs subtly from KeyValueAccessBackend.getKeyValueAccess(URI, boolean) in that the resulting KeyValueAccess may use configured fields from this N5Factory.
    
    Parameters:
    
    uri - to create a KeyValueAccess from.
    
    Returns:
    
    the KeyValueAccess and container path, or null if none are valid
  - openFSReader
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Reader openFSReader(String path)
```
    Deprecated. use openReader(StorageFormat, URI) instead
    
    Open an N5Reader over an N5 Container.
    NOTE: The name seems to imply that this will open any N5Reader, over a FileSystemKeyValueAccess however that is misleading. Instead this will open any N5Container that is a valid StorageFormat.N5. This is partially why it is deprecated, as well as the redundant implementation with openReader(StorageFormat, URI).
    
    Parameters:
    
    path - path to the n5 root folder
    
    Returns:
    
    the N5Reader
  - openZarrReader
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Reader openZarrReader(String path)
```
    Deprecated. use openReader(StorageFormat, URI) instead
    
    Open an N5Reader for Zarr.
    For more options of the Zarr backend study the N5ZarrReader constructors.}
    
    Parameters:
    
    path - path to the zarr directory
    
    Returns:
    
    the N5Reader
  - openHDF5Reader
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Reader openHDF5Reader(String path)
```
    Deprecated. use openReader(StorageFormat, URI) instead
    
    Open an N5Reader for HDF5. Close the reader when you do not need it any more.
    For more options of the HDF5 backend study the N5HDF5Reader constructors.
    
    Parameters:
    
    path - path to the hdf5 file
    
    Returns:
    
    the N5Reader
  - openGoogleCloudReader
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Reader openGoogleCloudReader(String uri)
```
    Deprecated. use openReader(KeyValueAccessBackend, URI) instead
    
    Open an N5Reader for Google Cloud.
    
    Parameters:
    
    uri - uri to the google cloud object
    
    Returns:
    
    the N5Reader
  - openAWSS3Reader
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Reader openAWSS3Reader(String uri)
```
    Deprecated. use openReader(KeyValueAccessBackend, URI) instead
    
    Open an N5Reader for AWS S3.
    
    Parameters:
    
    uri - uri to the amazon s3 object
    
    Returns:
    
    the N5Reader
  - openFileSystemReader
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Reader openFileSystemReader(String uri)
```
    Deprecated. use openReader(KeyValueAccessBackend, URI) instead
    
    Open an N5Reader over a FileSytem.
    
    Parameters:
    
    uri - uri to the N5Reader
    
    Returns:
    
    the N5Reader
  - openReader
```
public org.janelia.saalfeldlab.n5.N5Reader openReader(String uri)
```
    Open an N5Reader at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend and StorageFormat.
    
    Parameters:
    
    uri - the root location of the store
    
    Returns:
    
    the N5Reader
  - openReader
```
public org.janelia.saalfeldlab.n5.N5Reader openReader(StorageFormat format,
                                                      String uri)
```
    Open an N5Reader at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.
    
    Parameters:
    
    format - of the data store this N5Reader is accessing
    
    uri - the root location of the store
    
    Returns:
    
    the N5Reader
  - openReader
```
public org.janelia.saalfeldlab.n5.N5Reader openReader(StorageFormat format,
                                                      URI uri)
```
    Open an N5Reader at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.
    
    Parameters:
    
    format - of the data store this N5Reader is accessing
    
    uri - the root location of the store
    
    Returns:
    
    the N5Reader
  - openReader
```
public org.janelia.saalfeldlab.n5.N5Reader openReader(KeyValueAccessBackend backend,
                                                      String uri)
```
    Open and N5Reader at the given URI given the specified KeyValueAccessBackend.
    
    Parameters:
    
    backend - key-value access
    
    uri - location of reader
    
    Returns:
    
    the N5Reader
  - openReader
```
public org.janelia.saalfeldlab.n5.N5Reader openReader(KeyValueAccessBackend backend,
                                                      URI uri)
```
    Open and N5Reader at the given URI given the specified KeyValueAccessBackend.
    
    Parameters:
    
    backend - key-value access
    
    uri - location of reader
    
    Returns:
    
    the N5Reader
  - openReader
```
public org.janelia.saalfeldlab.n5.N5Reader openReader(@Nullable
                                                      StorageFormat storage,
                                                      org.janelia.saalfeldlab.n5.KeyValueAccess access,
                                                      URI location)
```
    Create an N5Reader at the containerPath requiring the specific StorageFormat and using KeyValueAccess.
    
    Parameters:
    
    storage - of the underlying data store this N5Reader is over
    
    access - to the key-value backend of the underlying data
    
    location - root URI of the resulting N5Reader
    
    Returns:
    
    the N5Reader
  - openFSWriter
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Writer openFSWriter(String path)
```
    Deprecated. use openWriter(StorageFormat, URI) instead
    
    Open an N5Writer for N5 Container.
    NOTE: The name seems to imply that this will open any N5Writer, over a FileSystemKeyValueAccess however that is misleading. Instead this will open any N5Container that is a valid StorageFormat.N5. This is partially why it is deprecated, as well as the redundant implementation with openWriter(StorageFormat, URI).
    
    Parameters:
    
    path - path to the n5 directory
    
    Returns:
    
    the N5Writer
  - openZarrWriter
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Writer openZarrWriter(String path)
```
    Deprecated. use openWriter(StorageFormat, URI)) instead
    
    Open an N5Writer for Zarr.
    For more options of the Zarr backend study the N5ZarrWriter constructors.
    
    Parameters:
    
    path - path to the zarr directory
    
    Returns:
    
    the N5Writer
  - openHDF5Writer
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Writer openHDF5Writer(String path)
```
    Deprecated. use openReader(StorageFormat, URI) instead
    
    Open an N5Writer for HDF5. Don't forget to close the writer after writing to close the file and make it available to other processes.
    For more options of the HDF5 backend study the N5HDF5Writer constructors.
    
    Parameters:
    
    path - path to the hdf5 file
    
    Returns:
    
    the N5HDF5Writer
  - openGoogleCloudWriter
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Writer openGoogleCloudWriter(String uri)
```
    Deprecated. use openWriter(KeyValueAccessBackend, String) instead.
    
    Open an N5Writer for Google Cloud.
    
    Parameters:
    
    uri - uri to the google cloud object
    
    Returns:
    
    the N5GoogleCloudStorageWriter
  - openAWSS3Writer
```
@Deprecated
public org.janelia.saalfeldlab.n5.N5Writer openAWSS3Writer(String uri)
```
    Deprecated. use openWriter(KeyValueAccessBackend, String) instead.
    
    Open an N5Writer for AWS S3.
    
    Parameters:
    
    uri - uri to the s3 object
    
    Returns:
    
    the N5Writer
  - openWriter
```
public org.janelia.saalfeldlab.n5.N5Writer openWriter(String uri)
```
    Open an N5Writer at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend and StorageFormat.
    
    Parameters:
    
    uri - the root location of the store
    
    Returns:
    
    the N5Writer
  - openWriter
```
public org.janelia.saalfeldlab.n5.N5Writer openWriter(KeyValueAccessBackend backend,
                                                      URI uri)
```
    Create or Open an N5Writer as the given uri and backend.
    
    Parameters:
    
    backend - key-value access
    
    uri - location of writer
    
    Returns:
    
    the N5Writer
  - openWriter
```
public org.janelia.saalfeldlab.n5.N5Writer openWriter(KeyValueAccessBackend backend,
                                                      String uri)
```
    Create or Open an N5Writer as the given uri and backend.
    
    Parameters:
    
    backend - key-value access
    
    uri - location of writer
    
    Returns:
    
    the N5Writer
  - openWriter
```
public org.janelia.saalfeldlab.n5.N5Writer openWriter(StorageFormat format,
                                                      String uri)
```
    Open an N5Writer at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.
    
    Parameters:
    
    format - of the data store for this N5Writer
    
    uri - the root location of the store
    
    Returns:
    
    the N5Writer
  - openWriter
```
public org.janelia.saalfeldlab.n5.N5Writer openWriter(StorageFormat format,
                                                      URI uri)
```
    Open an N5Writer at the given URL, with best attempts to infer the appropriate KeyValueAccessBackend.
    
    Parameters:
    
    format - of the data store for this N5Writer
    
    uri - the root location of the store
    
    Returns:
    
    the N5Writer
  - openWriter
```
public org.janelia.saalfeldlab.n5.N5Writer openWriter(@Nullable
                                                      StorageFormat storage,
                                                      org.janelia.saalfeldlab.n5.KeyValueAccess access,
                                                      URI location)
```
    Create an N5Writer at the location requiring the specific StorageFormat and using KeyValueAccess.
    
    Parameters:
    
    storage - of the underlying data store this N5Writer is over
    
    access - to the key-value backend of the underlying data
    
    location - root location of the resulting N5Writer
    
    Returns:
    
    the N5Writer
  - createWriter
```
public static org.janelia.saalfeldlab.n5.N5Writer createWriter(String containerUri)
```
    Creates an N5 writer for the specified container URI with default N5Factory configuration.
    
    Parameters:
    
    containerUri - location of the N5 container
    
    Returns:
    
    an N5Writer instance for the given containerURI
  - createReader
```
public static org.janelia.saalfeldlab.n5.N5Reader createReader(String containerUri)
```
    Creates an N5Reader at containerURI with default N5Factory configuration.
    
    Parameters:
    
    containerUri - location of the N5 container
    
    Returns:
    
    an N5Reader instance for the given containerURI

Class N5Factory

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

N5Factory

Method Detail

getOptions

setOptions

options

s3UseCredentials

hdf5DefaultBlockSize

hdf5OverrideBlockSize

gsonBuilder

cacheAttributes

zarrDimensionSeparator

zarrMapN5Attributes

zarrMergeAttributes

googleCloudProjectId

preferredStorageFormat

s3Configuration

googleCloudConfiguration

createS3

createGoogleCloudStorage

getKeyValueAccess

openFSReader

openZarrReader

openHDF5Reader

openGoogleCloudReader

openAWSS3Reader

openFileSystemReader

openReader

openReader

openReader

openReader

openReader

openReader

openFSWriter

openZarrWriter

openHDF5Writer

openGoogleCloudWriter

openAWSS3Writer

openWriter

openWriter

openWriter

openWriter

openWriter

openWriter

createWriter

createReader