public interface JHDFService
extends loci.common.services.Service
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
|
void setFile(java.lang.String file) throws java.io.IOException
file
- Path to initialize the service with.java.io.IOException
- If there is an error initializing the service with
file
.void setFileForWrite(java.lang.String file) throws java.io.IOException
file
- Path to initialize the service with.java.io.IOException
- If there is an error initializing the service with
file
.java.lang.String getFile()
null
if the service
has yet to be initialized or is closed.int[] getShape(java.lang.String path)
path
- HDF path to the dataset.java.util.List<java.lang.String> getMember(java.lang.String path)
path
- HDF path to the group.int getElementSize(java.lang.String path)
path
- HDF path to the group.ch.systemsx.cisd.base.mdarray.MDByteArray readByteArray(java.lang.String path)
path
- HDF path to the dataset.ch.systemsx.cisd.base.mdarray.MDIntArray readIntArray(java.lang.String path)
path
- HDF path to the dataset.ch.systemsx.cisd.base.mdarray.MDIntArray readIntBlockArray(java.lang.String path, int[] offset, int[] size)
path
- HDF path to the dataset.offset
- Offset of the block to read.size
- Output size of the array.ch.systemsx.cisd.base.mdarray.MDByteArray readByteBlockArray(java.lang.String path, int[] offset, int[] size)
path
- HDF path to the dataset.offset
- Offset of the block to read.size
- Output size of the array.ch.systemsx.cisd.base.mdarray.MDShortArray readShortBlockArray(java.lang.String path, int[] offset, int[] size)
path
- HDF path to the dataset.offset
- Offset of the block to read.size
- Output size of the array.java.lang.String[] readStringArray(java.lang.String path)
path
- HDF path to the dataset.ch.systemsx.cisd.hdf5.HDF5CompoundDataMap[] readCompoundArrayDataMap(java.lang.String path)
path
- HDF path to the dataset.boolean exists(java.lang.String path)
path
- path to HDF5 group or dataset.void initIntArray(java.lang.String path, long[] dimensions, long bpp)
path
- path to HDF5 a dataset.bpp
- bytes per pixel for the integer data type
bpp \in {1,2,4} == {Byte, Short, Integer}void writeArraySlice(java.lang.String path, ch.systemsx.cisd.base.mdarray.MDByteArray image, long[] offset)
path
- path to the (existing) HDF5 dataset.image
- the data stored as MDArray of pixel type Byteoffset
- dimensions, where to start writing the image. The image
will be written from offset to offset + image.dimensions()void writeArraySlice(java.lang.String path, ch.systemsx.cisd.base.mdarray.MDShortArray image, long[] offset)
path
- path to the (existing) HDF5 dataset.image
- the data stored as MDArray of pixel type Shortoffset
- dimensions, where to start writing the image. The image
will be written from offset to offset + image.dimensions()void writeArraySlice(java.lang.String path, ch.systemsx.cisd.base.mdarray.MDIntArray image, long[] offset)
path
- path to the (existing) HDF5 dataset.image
- the data stored as MDArray of pixel type intoffset
- dimensions, where to start writing the image. The image
will be written from offset to offset + image.dimensions()void createGroup(java.lang.String path) throws java.io.IOException
path
- path of the HDF5 group.java.io.IOException
void close() throws java.io.IOException
java.io.IOException
- If there is an error closing the file.Copyright © 2020 Open Microscopy Environment