loci.formats.services

Interface JHDFService

All Superinterfaces:

Service

All Known Implementing Classes:

JHDFServiceImpl

public interface JHDFService
extends Service

Utility class for working with NetCDF/HDF files.

Source code:

Trac, Gitweb

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes and resets the service.
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.
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.

Method Detail

setFile

void setFile(String file)
             throws IOException

Initializes the service on a given file path.

Parameters:

file - Path to initialize the service with.

Throws:

IOException - If there is an error initializing the service with file.

getFile

String getFile()

Retrieves the current initialized file path.

Returns:

Current initialized file path or null if the service has yet to be initialized or is closed.

getShape

int[] getShape(String path)

Retrieves the shape of a dataset.

Parameters:

path - HDF path to the dataset.

Returns:

int[] of shapes.

getMember

List<String> getMember(String path)

Retrieves the all members of a group.

Parameters:

path - HDF path to the group.

Returns:

List of members.

getElementSize

int getElementSize(String path)

Retrieves the Element Size of a dataset in Byte.

Parameters:

path - HDF path to the group.

Returns:

List of members.

readByteArray

ch.systemsx.cisd.base.mdarray.MDByteArray readByteArray(String path)

Reads a multi-dimensional byte array from path.

Parameters:

path - HDF path to the dataset.

Returns:

MDByteArray array of bytes.

readIntArray

ch.systemsx.cisd.base.mdarray.MDIntArray readIntArray(String path)

Reads a multi-dimensional int array from path.

Parameters:

path - HDF path to the dataset.

Returns:

MDIntArray array of int.

readIntBlockArray

ch.systemsx.cisd.base.mdarray.MDIntArray readIntBlockArray(String path,
                                                         int[] offset,
                                                         int[] size)

Reads a multi-dimensional sub-block int array from path.

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

ch.systemsx.cisd.base.mdarray.MDByteArray readByteBlockArray(String path,
                                                           int[] offset,
                                                           int[] size)

Reads a multi-dimensional sub-block byte array from path.

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

ch.systemsx.cisd.base.mdarray.MDShortArray readShortBlockArray(String path,
                                                             int[] offset,
                                                             int[] size)

Reads a multi-dimensional sub-block short array from path.

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

String[] readStringArray(String path)

Reads String array array from path.

Parameters:

path - HDF path to the dataset.

Returns:

String[] array.

readCompoundArrayDataMap

ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[] readCompoundArrayDataMap(String path)

Reads Compound array of any type

Parameters:

path - HDF path to the dataset.

Returns:

HDF5CompoundDataMap[] compound array map.

exists

boolean exists(String path)

Checks if path in HDF5 file exists.

Parameters:

path - path to HDF5 group or dataset.

Returns:

boolean true if path exists in HDF5 file else false.

close

void close()
           throws IOException

Closes and resets the service.

Throws:

IOException - If there is an error closing the file.