org.janelia.saalfeldlab.n5.hdf5

Class N5HDF5Writer

java.lang.Object

org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader

org.janelia.saalfeldlab.n5.hdf5.N5HDF5Writer

All Implemented Interfaces:

Closeable, AutoCloseable, org.janelia.saalfeldlab.n5.GsonN5Reader, org.janelia.saalfeldlab.n5.GsonN5Writer, org.janelia.saalfeldlab.n5.N5Reader, org.janelia.saalfeldlab.n5.N5Writer

public class N5HDF5Writer
extends N5HDF5Reader
implements org.janelia.saalfeldlab.n5.GsonN5Writer

Best effort N5Writer implementation for HDF5 files.

Author:

Stephan Saalfeld

Nested Class Summary

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

Modifier and Type	Field and Description
protected ch.systemsx.cisd.hdf5.IHDF5Writer	writer

Fields inherited from class org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader

defaultBlockSize, FILE_SYSTEM_KEY_VALUE_ACCESS, gson, N5_JSON_ROOT_KEY, openDataSetCache, overrideBlockSize, reader, VERSION

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

NO_VERSION, VERSION, VERSION_KEY

Constructor Summary

Constructors

Constructor and Description
N5HDF5Writer(ch.systemsx.cisd.hdf5.IHDF5Writer writer, boolean overrideBlockSize, com.google.gson.GsonBuilder gsonBuilder, int... defaultBlockSize) Opens an N5HDF5Writer for a given HDF5 file.
N5HDF5Writer(ch.systemsx.cisd.hdf5.IHDF5Writer writer, boolean overrideBlockSize, int... defaultBlockSize) Opens an N5HDF5Writer for a given HDF5 file.
N5HDF5Writer(ch.systemsx.cisd.hdf5.IHDF5Writer writer, int... defaultBlockSize) Opens an N5HDF5Writer for a given HDF5 file.
N5HDF5Writer(String hdf5Path, boolean overrideBlockSize, com.google.gson.GsonBuilder gsonBuilder, int... defaultBlockSize) Opens an N5HDF5Writer for a given HDF5 file.
N5HDF5Writer(String hdf5Path, boolean overrideBlockSize, int... defaultBlockSize) Opens an N5HDF5Writer for a given HDF5 file.
N5HDF5Writer(String hdf5Path, int... defaultBlockSize) Opens an N5HDF5Writer for a given HDF5 file.

Method Summary

Modifier and Type	Method and Description
org.janelia.saalfeldlab.n5.DatasetAttributes	createDataset(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
void	createGroup(String pathName)
boolean	deleteBlock(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
boolean	deleteBlock(String pathName, long... gridPosition)
boolean	deleteChunk(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
boolean	deleteChunk(String pathName, long... gridPosition)
boolean	remove()
boolean	remove(String pathName)
boolean	removeAttribute(String pathName, String key)
<T> T	removeAttribute(String pathName, String key, Class<T> cls)
boolean	removeAttributes(String pathName, List<String> attributes)
<T> void	setAttribute(String pathName, String key, T attribute)
void	setAttributes(String groupPath, com.google.gson.JsonElement attributes)
void	setAttributes(String pathName, Map<String,?> attributes)
void	setDatasetAttributes(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
<T> void	writeBlock(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)
<T> void	writeChunk(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)
<T> void	writeRegion(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long[] min, long[] size, org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks, boolean writeFully)
<T> void	writeRegion(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long[] min, long[] size, org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks, boolean writeFully, ExecutorService exec)

Methods inherited from class org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader

blockExists, close, containsEscapeCharacters, cropBlockSize, datasetExists, doesOverrideBlockSize, exists, getAttribute, getAttribute, getAttributes, getAttributesKey, getDatasetAttributes, getDataType, getDefaultBlockSizeCopy, getFilename, getGson, getURI, list, listAttributes, normalizeHdf5PathLocation, readBlock, readChunk, reorder, reorder, toString

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.GsonN5Reader

createDatasetAttributes, getAttribute, getAttribute, getAttributes, getAttributesKey, getDatasetAttributes, getGson, listAttributes

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

createDataset, deleteChunks, setVersion, writeChunks, writeSerializedBlock

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

blockExists, close, datasetExists, deepList, deepList, deepList, deepList, deepList, deepListDatasets, deepListDatasets, deepListDatasets, deepListDatasets, deepListHelper, exists, getConvertedDatasetAttributes, getGroupSeparator, getURI, getVersion, groupPath, list, readBlock, readChunk, readChunks, readSerializedBlock

Field Detail

writer

protected ch.systemsx.cisd.hdf5.IHDF5Writer writer

Constructor Detail

N5HDF5Writer

public N5HDF5Writer(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                    boolean overrideBlockSize,
                    com.google.gson.GsonBuilder gsonBuilder,
                    int... defaultBlockSize)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5HDF5Writer for a given HDF5 file.

Parameters:

writer - HDF5 writer

overrideBlockSize - true if you want this N5HDF5Writer to use the defaultBlockSize instead of the chunk-size for reading datasets

gsonBuilder - custom GsonBuilder to support custom attributes

defaultBlockSize - for all dimensions > defaultBlockSize.length, and for all dimensions with defaultBlockSize[i] <= 0, the size of the dataset will be used

Throws:

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

N5HDF5Writer

public N5HDF5Writer(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                    boolean overrideBlockSize,
                    int... defaultBlockSize)
             throws IOException

Opens an N5HDF5Writer for a given HDF5 file.

Parameters:

writer - HDF5 writer

overrideBlockSize - true if you want this N5HDF5Writer to use the defaultBlockSize instead of the chunk-size for reading datasets

defaultBlockSize - for all dimensions > defaultBlockSize.length, and for all dimensions with defaultBlockSize[i] <= 0, the size of the dataset will be used

Throws:

IOException - the exception

N5HDF5Writer

public N5HDF5Writer(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                    int... defaultBlockSize)
             throws IOException

Opens an N5HDF5Writer for a given HDF5 file.

Parameters:

writer - HDF5 writer

defaultBlockSize - for all dimensions > defaultBlockSize.length, and for all dimensions with defaultBlockSize[i] <= 0, the size of the dataset will be used

Throws:

IOException - the exception

N5HDF5Writer

public N5HDF5Writer(String hdf5Path,
                    boolean overrideBlockSize,
                    com.google.gson.GsonBuilder gsonBuilder,
                    int... defaultBlockSize)

Opens an N5HDF5Writer for a given HDF5 file.

Parameters:

hdf5Path - HDF5 writer

overrideBlockSize - true if you want this N5HDF5Writer to use the defaultBlockSize instead of the chunk-size for reading datasets

gsonBuilder - custom GsonBuilder to support custom attributes

defaultBlockSize - for all dimensions > defaultBlockSize.length, and for all dimensions with defaultBlockSize[i] <= 0, the size of the dataset will be used

N5HDF5Writer

public N5HDF5Writer(String hdf5Path,
                    boolean overrideBlockSize,
                    int... defaultBlockSize)

Opens an N5HDF5Writer for a given HDF5 file.

Parameters:

hdf5Path - HDF5 file name

overrideBlockSize - true if you want this N5HDF5Writer to use the defaultBlockSize instead of the chunk-size for reading datasets

defaultBlockSize - for all dimensions > defaultBlockSize.length, and for all dimensions with defaultBlockSize[i] <= 0, the size of the dataset will be used

N5HDF5Writer

public N5HDF5Writer(String hdf5Path,
                    int... defaultBlockSize)

Opens an N5HDF5Writer for a given HDF5 file.

Parameters:

hdf5Path - HDF5 file name

defaultBlockSize - for all dimensions > defaultBlockSize.length, and for all dimensions with defaultBlockSize[i] <= 0, the size of the dataset will be used

Method Detail

createDataset

public org.janelia.saalfeldlab.n5.DatasetAttributes createDataset(String pathName,
                                                                  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

createGroup

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

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttribute

public <T> void setAttribute(String pathName,
                             String key,
                             T attribute)
                      throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttributes

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

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttributes

public void setAttributes(String groupPath,
                          com.google.gson.JsonElement attributes)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.GsonN5Writer

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

removeAttribute

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

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.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

removeAttributes

public boolean removeAttributes(String pathName,
                                List<String> attributes)
                         throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeChunk

public <T> void writeChunk(String pathName,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeBlock

public <T> void writeBlock(String pathName,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeRegion

public <T> void writeRegion(String datasetPath,
                            org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                            long[] min,
                            long[] size,
                            org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks,
                            boolean writeFully)
                     throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeRegion

public <T> void writeRegion(String datasetPath,
                            org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                            long[] min,
                            long[] size,
                            org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks,
                            boolean writeFully,
                            ExecutorService exec)
                     throws org.janelia.saalfeldlab.n5.N5Exception,
                            InterruptedException,
                            ExecutionException

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

InterruptedException

ExecutionException

deleteChunk

public boolean deleteChunk(String pathName,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

deleteChunk

public boolean deleteChunk(String datasetPath,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

deleteBlock

public boolean deleteBlock(String pathName,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

deleteBlock

public boolean deleteBlock(String datasetPath,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

remove

public boolean remove()

Specified by:

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

remove

public boolean remove(String pathName)
               throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception