JHDFService (Bio-Formats API)

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

All Methods Instance Methods Abstract Methods
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

- Method Detail
  - setFile
```
void setFile(java.lang.String file)
      throws java.io.IOException
```
    Initializes the service on a given file path.
    
    Parameters:
    
    file - Path to initialize the service with.
    
    Throws:
    
    java.io.IOException - If there is an error initializing the service with file.
  - setFileForWrite
```
void setFileForWrite(java.lang.String file)
              throws java.io.IOException
```
    Initializes the service on a given file path.
    
    Parameters:
    
    file - Path to initialize the service with.
    
    Throws:
    
    java.io.IOException - If there is an error initializing the service with file.
  - getFile
```
java.lang.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(java.lang.String path)
```
    Retrieves the shape of a dataset.
    
    Parameters:
    
    path - HDF path to the dataset.
    
    Returns:
    
    int[] of shapes.
  - getMember
```
java.util.List<java.lang.String> getMember(java.lang.String path)
```
    Retrieves the all members of a group.
    
    Parameters:
    
    path - HDF path to the group.
    
    Returns:
    
    List of members.
  - getElementSize
```
int getElementSize(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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
```
java.lang.String[] readStringArray(java.lang.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(java.lang.String path)
```
    Reads Compound array of any type
    
    Parameters:
    
    path - HDF path to the dataset.
    
    Returns:
    
    HDF5CompoundDataMap[] compound array map.
  - exists
```
boolean exists(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.String path)
          throws java.io.IOException
```
    Writes an array as sub-slice into an existing HDF5 dataset
    
    Parameters:
    
    path - path of the HDF5 group.
    
    Throws:
    
    java.io.IOException
  - close
```
void close()
    throws java.io.IOException
```
    Closes and resets the service.
    
    Throws:
    
    java.io.IOException - If there is an error closing the file.

Interface JHDFService

Method Summary

Method Detail

setFile

setFileForWrite

getFile

getShape

getMember

getElementSize

readByteArray

readIntArray

readIntBlockArray

readByteBlockArray

readShortBlockArray

readStringArray

readCompoundArrayDataMap

exists

initIntArray

writeArraySlice

writeArraySlice

writeArraySlice

createGroup

close