JHDFServiceImpl (Bio-Formats API)

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 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 String`	`NO_JHDF_MSG`

Constructor Summary

Constructors
Constructor and Description

JHDFServiceImpl()
Default constructor.

Constructors
Constructor and Description
`JHDFServiceImpl()` Default constructor.

Method Summary

All Methods Instance Methods Concrete Methods
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

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 String NO_JHDF_MSG
```
    See Also:
    
    Constant Field Values
  - 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 Detail
  - JHDFServiceImpl
```
public JHDFServiceImpl()
```
    Default constructor.
- Method Detail
  - 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.

Class JHDFServiceImpl

Field Summary

Constructor Summary

Method Summary

Methods inherited from class loci.common.services.AbstractService

Methods inherited from class java.lang.Object

Field Detail

NO_JHDF_MSG

currentFile

hdfReader

hdfWriter

Constructor Detail

JHDFServiceImpl

Method Detail

setFile

setFileForWrite

getFile

getMember

getShape

readByteArray

readIntArray

readIntBlockArray

readByteBlockArray

readShortBlockArray

readStringArray

readCompoundArrayDataMap

getElementSize

initIntArray

writeArraySlice

writeArraySlice

writeArraySlice

createGroup

exists

close