Package loci.formats.services

Class JHDFServiceImpl

java.lang.Object
loci.common.services.AbstractService
loci.formats.services.JHDFServiceImpl
All Implemented Interfaces:
loci.common.services.Service, JHDFService
public class JHDFServiceImpl extends loci.common.services.AbstractService implements JHDFService
Utility class for working with HDF files.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private String
    currentFile
     
    private ch.systemsx.cisd.hdf5.IHDF5Reader
    hdfReader
    Root of the HDF5 file.
    private ch.systemsx.cisd.hdf5.IHDF5Writer
    hdfWriter
    Root of the HDF5 file.
    static final String
    NO_JHDF_MSG
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    JHDFServiceImpl()
    Default constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
    Closes and resets the service.
    void
    createGroup(String path)
    Writes an array as sub-slice into an existing HDF5 dataset
    boolean
    exists(String path)
    Checks if path in HDF5 file exists.
    int
    getElementSize(String path)
    Retrieves the Element Size of a dataset in Byte.
    String
    getFile()
    Retrieves the current initialized file path.
    List<String>
    getMember(String path)
    Retrieves the all members of a group.
    int[]
    getShape(String path)
    Retrieves the shape of a dataset.
    void
    initIntArray(String path, long[] dimensions, long bpp)
    Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.
    ch.systemsx.cisd.base.mdarray.MDByteArray
    readByteArray(String path)
    Reads a multi-dimensional byte array from path.
    ch.systemsx.cisd.base.mdarray.MDByteArray
    readByteBlockArray(String path, int[] offset, int[] size)
    Reads a multi-dimensional sub-block byte array from path.
    ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[]
    readCompoundArrayDataMap(String path)
    Reads Compound array of any type
    ch.systemsx.cisd.base.mdarray.MDIntArray
    readIntArray(String path)
    Reads a multi-dimensional int array from path.
    ch.systemsx.cisd.base.mdarray.MDIntArray
    readIntBlockArray(String path, int[] offset, int[] size)
    Reads a multi-dimensional sub-block int array from path.
    ch.systemsx.cisd.base.mdarray.MDShortArray
    readShortBlockArray(String path, int[] offset, int[] size)
    Reads a multi-dimensional sub-block short array from path.
    String[]
    readStringArray(String path)
    Reads String array array from path.
    void
    setFile(String file)
    Initializes the service on a given file path.
    void
    setFileForWrite(String file)
    Initializes the service on a given file path.
    void
    writeArraySlice(String path, ch.systemsx.cisd.base.mdarray.MDByteArray image, long[] offset)
    Writes an array as sub-slice into an existing HDF5 dataset
    void
    writeArraySlice(String path, ch.systemsx.cisd.base.mdarray.MDIntArray image, long[] offset)
    Writes an array as sub-slice into an existing HDF5 dataset
    void
    writeArraySlice(String path, ch.systemsx.cisd.base.mdarray.MDShortArray image, long[] offset)
    Writes an array as sub-slice into an existing HDF5 dataset

    Methods inherited from class loci.common.services.AbstractService

    checkClassDependency

    Methods inherited from class java.lang.Object

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

  • Field Details

    • NO_JHDF_MSG

      public static final String NO_JHDF_MSG

    • currentFile

      private String currentFile

    • hdfReader

      private ch.systemsx.cisd.hdf5.IHDF5Reader hdfReader
      Root of the HDF5 file.

    • hdfWriter

      private ch.systemsx.cisd.hdf5.IHDF5Writer hdfWriter
      Root of the HDF5 file.

  • Constructor Details

    • JHDFServiceImpl

      public JHDFServiceImpl()
      Default constructor.

  • Method Details

    • setFile

      public void setFile(String file) throws IOException
      Description copied from interface: JHDFService
      Initializes the service on a given file path.
      Specified by:
      setFile in interface JHDFService
      Parameters:
      file - Path to initialize the service with.
      Throws:
      IOException - If there is an error initializing the service with file.

    • setFileForWrite

      public void setFileForWrite(String file) throws IOException
      Description copied from interface: JHDFService
      Initializes the service on a given file path.
      Specified by:
      setFileForWrite in interface JHDFService
      Parameters:
      file - Path to initialize the service with.
      Throws:
      IOException - If there is an error initializing the service with file.

    • getFile

      public String getFile()
      Description copied from interface: JHDFService
      Retrieves the current initialized file path.
      Specified by:
      getFile in interface JHDFService
      Returns:
      Current initialized file path or null if the service has yet to be initialized or is closed.

    • getMember

      public List<String> getMember(String path)
      Description copied from interface: JHDFService
      Retrieves the all members of a group.
      Specified by:
      getMember in interface JHDFService
      Parameters:
      path - HDF path to the group.
      Returns:
      List of members.

    • getShape

      public int[] getShape(String path)
      Description copied from interface: JHDFService
      Retrieves the shape of a dataset.
      Specified by:
      getShape in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      Returns:
      int[] of shapes.

    • readByteArray

      public ch.systemsx.cisd.base.mdarray.MDByteArray readByteArray(String path)
      Description copied from interface: JHDFService
      Reads a multi-dimensional byte array from path.
      Specified by:
      readByteArray in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      Returns:
      MDByteArray array of bytes.

    • readIntArray

      public ch.systemsx.cisd.base.mdarray.MDIntArray readIntArray(String path)
      Description copied from interface: JHDFService
      Reads a multi-dimensional int array from path.
      Specified by:
      readIntArray in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      Returns:
      MDIntArray array of int.

    • readIntBlockArray

      public ch.systemsx.cisd.base.mdarray.MDIntArray readIntBlockArray(String path, int[] offset, int[] size)
      Description copied from interface: JHDFService
      Reads a multi-dimensional sub-block int array from path.
      Specified by:
      readIntBlockArray in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      offset - Offset of the block to read.
      size - Output size of the array.
      Returns:
      MDIntArray array of int.

    • readByteBlockArray

      public ch.systemsx.cisd.base.mdarray.MDByteArray readByteBlockArray(String path, int[] offset, int[] size)
      Description copied from interface: JHDFService
      Reads a multi-dimensional sub-block byte array from path.
      Specified by:
      readByteBlockArray in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      offset - Offset of the block to read.
      size - Output size of the array.
      Returns:
      MDIntArray array of int.

    • readShortBlockArray

      public ch.systemsx.cisd.base.mdarray.MDShortArray readShortBlockArray(String path, int[] offset, int[] size)
      Description copied from interface: JHDFService
      Reads a multi-dimensional sub-block short array from path.
      Specified by:
      readShortBlockArray in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      offset - Offset of the block to read.
      size - Output size of the array.
      Returns:
      MDIntArray array of int.

    • readStringArray

      public String[] readStringArray(String path)
      Description copied from interface: JHDFService
      Reads String array array from path.
      Specified by:
      readStringArray in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      Returns:
      String[] array.

    • readCompoundArrayDataMap

      public ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[] readCompoundArrayDataMap(String path)
      Description copied from interface: JHDFService
      Reads Compound array of any type
      Specified by:
      readCompoundArrayDataMap in interface JHDFService
      Parameters:
      path - HDF path to the dataset.
      Returns:
      HDF5CompoundDataMap[] compound array map.

    • getElementSize

      public int getElementSize(String path)
      Description copied from interface: JHDFService
      Retrieves the Element Size of a dataset in Byte.
      Specified by:
      getElementSize in interface JHDFService
      Parameters:
      path - HDF path to the group.
      Returns:
      List of members.

    • initIntArray

      public void initIntArray(String path, long[] dimensions, long bpp)
      Description copied from interface: JHDFService
      Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.
      Specified by:
      initIntArray in interface JHDFService
      Parameters:
      path - path to HDF5 a dataset.
      bpp - bytes per pixel for the integer data type bpp \in {1,2,4} == {Byte, Short, Integer}

    • writeArraySlice

      public void writeArraySlice(String path, ch.systemsx.cisd.base.mdarray.MDByteArray image, long[] offset)
      Description copied from interface: JHDFService
      Writes an array as sub-slice into an existing HDF5 dataset
      Specified by:
      writeArraySlice in interface JHDFService
      Parameters:
      path - path to the (existing) HDF5 dataset.
      image - the data stored as MDArray of pixel type Byte
      offset - dimensions, where to start writing the image. The image will be written from offset to offset + image.dimensions()

    • writeArraySlice

      public void writeArraySlice(String path, ch.systemsx.cisd.base.mdarray.MDShortArray image, long[] offset)
      Description copied from interface: JHDFService
      Writes an array as sub-slice into an existing HDF5 dataset
      Specified by:
      writeArraySlice in interface JHDFService
      Parameters:
      path - path to the (existing) HDF5 dataset.
      image - the data stored as MDArray of pixel type Short
      offset - dimensions, where to start writing the image. The image will be written from offset to offset + image.dimensions()

    • writeArraySlice

      public void writeArraySlice(String path, ch.systemsx.cisd.base.mdarray.MDIntArray image, long[] offset)
      Description copied from interface: JHDFService
      Writes an array as sub-slice into an existing HDF5 dataset
      Specified by:
      writeArraySlice in interface JHDFService
      Parameters:
      path - path to the (existing) HDF5 dataset.
      image - the data stored as MDArray of pixel type int
      offset - dimensions, where to start writing the image. The image will be written from offset to offset + image.dimensions()

    • createGroup

      public void createGroup(String path) throws IOException
      Description copied from interface: JHDFService
      Writes an array as sub-slice into an existing HDF5 dataset
      Specified by:
      createGroup in interface JHDFService
      Parameters:
      path - path of the HDF5 group.
      Throws:
      IOException

    • exists

      public boolean exists(String path)
      Description copied from interface: JHDFService
      Checks if path in HDF5 file exists.
      Specified by:
      exists in interface JHDFService
      Parameters:
      path - path to HDF5 group or dataset.
      Returns:
      boolean true if path exists in HDF5 file else false.

    • close

      public void close() throws IOException
      Description copied from interface: JHDFService
      Closes and resets the service.
      Specified by:
      close in interface JHDFService
      Throws:
      IOException - If there is an error closing the file.