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 and Description
private java.lang.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 java.lang.String	NO_JHDF_MSG

Constructor Summary

Constructors

Constructor and Description
JHDFServiceImpl() Default constructor.

Method Summary

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

NO_JHDF_MSG

public static final java.lang.String NO_JHDF_MSG

currentFile

private java.lang.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 Detail

JHDFServiceImpl

public JHDFServiceImpl()

Default constructor.

Method Detail

setFile

public void setFile(java.lang.String file)
             throws java.io.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:

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

setFileForWrite

public void setFileForWrite(java.lang.String file)
                     throws java.io.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:

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

getFile

public java.lang.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 java.util.List<java.lang.String> getMember(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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 java.lang.String[] readStringArray(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.String path)
                 throws java.io.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:

java.io.IOException

exists

public boolean exists(java.lang.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 java.io.IOException

Description copied from interface: JHDFService

Closes and resets the service.

Specified by:

close in interface JHDFService

Throws:

java.io.IOException - If there is an error closing the file.