Class HDF5Reader

java.lang.Object
org.episteme.core.io.AbstractResourceReader<byte[]>
org.episteme.core.io.loaders.HDF5Reader
All Implemented Interfaces:
ResourceIO<byte[]>, ResourceReader<byte[]>
public class HDF5Reader extends AbstractResourceReader<byte[]>
Reader for HDF5 (Hierarchical Data Format) files. Supports compression and parallel I/O.
Since:
1.2
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • HDF5Reader

      public HDF5Reader()

  • Method Details

    • enableCompression

      public void enableCompression(String algorithm, int level)
      Enables compression for the HDF5 writer/reader.
      Parameters:
      algorithm - Compression algorithm: "gzip", "szip", "lzf", "blosc"
      level - Level (0-9 for gzip)

    • enableParallelIO

      public void enableParallelIO(long mpiCommHandle, long mpiInfoHandle)
      Enables parallel I/O for MPI-based execution.
      Parameters:
      mpiCommHandle - MPI Communicator handle (long)
      mpiInfoHandle - MPI Info handle (long)

    • loadFromSource

      public byte[] loadFromSource(String resourceId) throws Exception
      Specified by:
      loadFromSource in class AbstractResourceReader<byte[]>
      Throws:
      Exception

    • loadFromInputStream

      protected byte[] loadFromInputStream(InputStream is, String id) throws Exception
      Overrides:
      loadFromInputStream in class AbstractResourceReader<byte[]>
      Throws:
      Exception

    • getResourcePath

      public String getResourcePath()
      Description copied from interface: ResourceIO
      Returns the base path where this resource is located.

    • getResourceType

      public Class<byte[]> getResourceType()
      Description copied from interface: ResourceIO
      Returns the type of resource.

    • getName

      public String getName()
      Description copied from interface: ResourceIO
      Returns the display name of this resource handler. MUST be implemented with I18N support.
      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.
      Returns:
      the description

    • getLongDescription

      public String getLongDescription()
      Description copied from interface: ResourceIO
      Returns a long description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the long description

    • getCategory

      public String getCategory()
      Description copied from interface: ResourceIO
      Returns the category for grouping. MUST be implemented with I18N support.
      Returns:
      the category name

    • 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"}

      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").