Class NativeHDF5Reader

java.lang.Object

org.episteme.core.io.AbstractResourceReader<NativeRealDoubleMatrixStorage>

org.episteme.nativ.physics.loaders.hdf5.NativeHDF5Reader

All Implemented Interfaces:

AutoCloseable, ResourceIO<NativeRealDoubleMatrixStorage>, ResourceReader<NativeRealDoubleMatrixStorage>

public class NativeHDF5Reader
extends AbstractResourceReader<NativeRealDoubleMatrixStorage>
implements AutoCloseable

High-performance HDF5 reader using Panama for zero-copy data transfer.

Constructor Summary

Constructors

Constructor	Description
NativeHDF5Reader()
NativeHDF5Reader(Path path)

Method Summary

Modifier and Type	Method	Description
void	close()
String	getCategory()	Returns the category for grouping.
long[]	getDatasetDimensions(String datasetName)
String	getDescription()	Returns a short description of this resource handler.
String	getLongDescription()	Returns a long description of this resource handler.
String	getName()	Returns the display name of this resource handler.
String	getResourcePath()	Returns the base path where this resource is located.
Class<NativeRealDoubleMatrixStorage>	getResourceType()	Returns the type of resource.
String[]	getSupportedExtensions()	Returns the supported file extensions (e.g., ".h5", ".fits").
String[]	getSupportedVersions()	Returns the supported versions of the format this reader/writer handles.
protected NativeRealDoubleMatrixStorage	loadFromSource(String resourceId)
static NativeRealDoubleMatrixStorage	open(String path)	Opens an HDF5 file and reads the dataset named "data".
void	readBlock(String datasetName, NativeRealDoubleMatrixStorage matrix, int startRow, int startCol, int rowCount, int colCount)	Reads a block of data from the dataset using hyperslabs.
void	readMatrix(String datasetName, NativeRealDoubleMatrixStorage matrix)

Methods inherited from class AbstractResourceReader

clearCache, getMiniCatalog, getSampleDataPath, isUsingFallback, load, loadAll, loadAllFromSource, loadFromFallback, loadFromInputStream, setCacheEnabled

Methods inherited from class Object

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

Methods inherited from interface ResourceIO

getExpectedResourceFiles, isFileBased, isOutput

Methods inherited from interface ResourceReader

isInput

Constructor Details

NativeHDF5Reader

public NativeHDF5Reader()

NativeHDF5Reader

public NativeHDF5Reader(Path path)

Method Details

open

public static NativeRealDoubleMatrixStorage open(String path)
                                          throws Exception

Opens an HDF5 file and reads the dataset named "data".

Throws:

Exception

getName

public String getName()

Description copied from interface: ResourceIO

Returns the display name of this resource handler. MUST be implemented with I18N support.

Specified by:

getName in interface ResourceIO<NativeRealDoubleMatrixStorage>

Returns:

the display name

getDescription

public String getDescription()

Description copied from interface: ResourceIO

Returns a short description of this resource handler. MUST be implemented with I18N support.

Specified by:

getDescription in interface ResourceIO<NativeRealDoubleMatrixStorage>

Returns:

the description

getCategory

public String getCategory()

Description copied from interface: ResourceIO

Returns the category for grouping. MUST be implemented with I18N support.

Specified by:

getCategory in interface ResourceIO<NativeRealDoubleMatrixStorage>

Returns:

the category name

getResourceType

public Class<NativeRealDoubleMatrixStorage> getResourceType()

Description copied from interface: ResourceIO

Returns the type of resource.

Specified by:

getResourceType in interface ResourceIO<NativeRealDoubleMatrixStorage>

getResourcePath

public String getResourcePath()

Description copied from interface: ResourceIO

Returns the base path where this resource is located.

Specified by:

getResourcePath in interface ResourceIO<NativeRealDoubleMatrixStorage>

getLongDescription

public String getLongDescription()

Description copied from interface: ResourceIO

Returns a long description of this resource handler. MUST be implemented with I18N support.

Specified by:

getLongDescription in interface ResourceIO<NativeRealDoubleMatrixStorage>

Returns:

the long description

getSupportedVersions

public String[] getSupportedVersions()

Description copied from interface: ResourceIO

Returns the supported versions of the format this reader/writer handles.

Each implementation MUST override this method to declare which versions of the underlying format are supported. The returned array should contain version strings in the format's standard notation (e.g., "3.0", "2.1", "Level 3 Version 2").

Examples:

• MathML: {"3.0", "2.0"}
• SBML: {"Level 3 Version 2", "Level 3 Version 1", "Level 2 Version 5"}
• PhyloXML: {"1.10", "1.00"}

Specified by:

getSupportedVersions in interface ResourceIO<NativeRealDoubleMatrixStorage>

Returns:

array of supported version strings, never null (empty array if version-agnostic)

getSupportedExtensions

public String[] getSupportedExtensions()

Description copied from interface: ResourceIO

Returns the supported file extensions (e.g., ".h5", ".fits").

Specified by:

getSupportedExtensions in interface ResourceIO<NativeRealDoubleMatrixStorage>

loadFromSource

protected NativeRealDoubleMatrixStorage loadFromSource(String resourceId)
                                                throws Exception

Specified by:

loadFromSource in class AbstractResourceReader<NativeRealDoubleMatrixStorage>

Throws:

Exception

getDatasetDimensions

public long[] getDatasetDimensions(String datasetName)

readMatrix

public void readMatrix(String datasetName,
 NativeRealDoubleMatrixStorage matrix)

readBlock

public void readBlock(String datasetName,
 NativeRealDoubleMatrixStorage matrix,
 int startRow,
 int startCol,
 int rowCount,
 int colCount)

Reads a block of data from the dataset using hyperslabs.

close

public void close()

Specified by:

close in interface AutoCloseable