loci.formats.services

Interface JHDFService

All Superinterfaces:

loci.common.services.Service

All Known Implementing Classes:

JHDFServiceImpl

public interface JHDFService
extends loci.common.services.Service

Utility class for working with NetCDF/HDF files.

Method Summary

Modifier and Type	Method and 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

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.

setFileForWrite

void setFileForWrite(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.

initIntArray

void initIntArray(String path,
                  long[] dimensions,
                  long bpp)

Creates an HDF5 dataset in path consisting of integers specified by bytes per pixel bpp.

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

void writeArraySlice(String path,
                     ch.systemsx.cisd.base.mdarray.MDByteArray image,
                     long[] offset)

Writes an array as sub-slice into an existing HDF5 dataset

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

void writeArraySlice(String path,
                     ch.systemsx.cisd.base.mdarray.MDShortArray image,
                     long[] offset)

Writes an array as sub-slice into an existing HDF5 dataset

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

void writeArraySlice(String path,
                     ch.systemsx.cisd.base.mdarray.MDIntArray image,
                     long[] offset)

Writes an array as sub-slice into an existing HDF5 dataset

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

void createGroup(String path)
          throws IOException

Writes an array as sub-slice into an existing HDF5 dataset

Parameters:

path - path of the HDF5 group.

Throws:

IOException

close

void close()
    throws IOException

Closes and resets the service.

Throws:

IOException - If there is an error closing the file.