Module org.hdfgroup.object

Package hdf.object.h4

Class H4SDS

Object

hdf.object.HObject

hdf.object.Dataset

hdf.object.ScalarDS

hdf.object.h4.H4SDS

All Implemented Interfaces:

DataFormat, MetaDataContainer, Serializable

public class H4SDS
extends ScalarDS
implements MetaDataContainer

H4SDS describes HDF4 Scientific Data Sets (SDS) and operations performed on the SDS. A SDS is a group of data structures used to store and describe multidimensional arrays of scientific data. The data contained in an SDS array has a data type associated with it. The standard data types supported by the SD interface include 32- and 64-bit floating-point numbers, 8-, 16- and 32-bit signed integers, 8-, 16- and 32-bit unsigned integers, and 8-bit characters. How to Select a Subset Dataset defines APIs for reading, writing and subsetting a dataset. No function is defined to select a subset of a data array. The selection is done in an implicit way. Function calls to dimension information such as getSelectedDims() return an array of dimension values, which is a reference to the array in the dataset object. Changes of the array outside the dataset object directly change the values of the array in the dataset object. It is like pointers in C. The following is an example of how to make a subset. In the example, the dataset is a 4-dimension with size of [200][100][50][10], i.e. dims[0]=200; dims[1]=100; dims[2]=50; dims[3]=10;
We want to select every other data point in dims[1] and dims[2]

     int rank = dataset.getRank();   // number of dimensions of the dataset
     long[] dims = dataset.getDims(); // the dimension sizes of the dataset
     long[] selected = dataset.getSelectedDims(); // the selected size of the dataet
     long[] start = dataset.getStartDims(); // the offset of the selection
     long[] stride = dataset.getStride(); // the stride of the dataset
     int[]  selectedIndex = dataset.getSelectedIndex(); // the selected dimensions for display

     // select dim1 and dim2 as 2D data for display,and slice through dim0
     selectedIndex[0] = 1;
     selectedIndex[1] = 2;
     selectedIndex[1] = 0;

     // reset the selection arrays
     for (int i=0; i<rank; i++) {
         start[i] = 0;
         selected[i] = 1;
         stride[i] = 1;
    }

    // set stride to 2 on dim1 and dim2 so that every other data point is selected.
    stride[1] = 2;
    stride[2] = 2;

    // set the selection size of dim1 and dim2
    selected[1] = dims[1]/stride[1];
    selected[2] = dims[1]/stride[2];

    // when dataset.read() is called, the slection above will be used since
    // the dimension arrays is passed by reference. Changes of these arrays
    // outside the dataset object directly change the values of these array
    // in the dataset object.

 

Version:

1.1 9/4/2007

Author:

Peter X. Cao

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DFTAG_NDG_NETCDF	tag for netCDF datasets.

Fields inherited from class hdf.object.ScalarDS

fillValue, imageDataRange, interlace, INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isDefaultImageOrder, isFillValueConverted, isImageDisplay, isTrueColor, palette, unsignedConverted

Fields inherited from class hdf.object.Dataset

chunkSize, compression, COMPRESSION_GZIP_TXT, convertByteToString, convertedBuf, data, datatype, dimNames, dims, filters, inited, isDataLoaded, isImage, isScalar, isText, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, space_type, startDims, storage, storageLayout

Fields inherited from class hdf.object.HObject

fileFormat, linkTargetObjName, oid, SEPARATOR

Constructor Summary

Constructors

Constructor	Description
H4SDS(FileFormat theFile, String name, String path)	Creates an H4SDS object with specific name and path.
H4SDS(FileFormat theFile, String name, String path, long[] oid)	Creates an H4SDS object with specific name, path and oid.

Method Summary

Modifier and Type	Method	Description
void	close(long id)	Closes access to the object.
Dataset	copy(Group pgroup, String dname, long[] dims, Object buff)	Creates a new dataset and writes the data buffer to the new dataset.
static H4SDS	create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object data)	Creates a new dataset.
static H4SDS	create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object fillValue, Object data)	Creates a new dataset.
Datatype	getDatatype()	Returns the datatype of the data object.
List	getMetadata()	Retrieves the object's metadata, such as attributes, from the file.
List	getMetadata(int... attrPropList)	Retrieves the object's metadata, such as attributes, from the file.
boolean	hasAttribute()	Check if the object has any attributes attached.
void	init()	Initializes the H4SDS such as dimension size of this dataset.
long	open()	Opens an existing object such as a dataset or group for access.
Object	read()	Reads the data from file.
byte[]	readBytes()	Reads the raw data of the dataset from file to a byte array.
void	removeMetadata(Object info)	Deletes an existing piece of metadata from this object.
void	updateMetadata(Object info)	Updates an existing piece of metadata attached to this object.
void	write(Object buf)	Writes a memory buffer to the object in the file.
void	writeMetadata(Object info)	Writes a specific piece of metadata (such as an attribute) into the file.

Methods inherited from class hdf.object.ScalarDS

addFilteredImageValue, clearData, convertFromUnsignedC, convertToUnsignedC, getFillValue, getFilteredImageValues, getImageDataRange, getInterlace, getNumberOfPalettes, getPalette, getPaletteName, isDefaultImageOrder, isImage, isImageDisplay, isTrueColor, readPalette, setImageDataRange, setIsImage, setIsImageDisplay, setPalette

Methods inherited from class hdf.object.Dataset

byteToString, clear, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDepth, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getSpaceType, getStartDims, getStorage, getStorageLayout, getStride, getVirtualFilename, getVirtualMaps, getWidth, isInited, isScalar, isString, isVirtual, refreshData, resetSelection, setConvertByteToString, setData, stringToByte, toString, toString, toString, write

Methods inherited from class hdf.object.HObject

createFullname, debug, equals, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, hashCode, setFullname, setLinkTargetObjName, setName, setPath, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface hdf.object.MetaDataContainer

clear

Field Details

DFTAG_NDG_NETCDF

public static final int DFTAG_NDG_NETCDF

tag for netCDF datasets. HDF4 library supports netCDF version 2.3.2. It only supports SDS APIs.

See Also:

• Constant Field Values

Constructor Details

H4SDS

public H4SDS(FileFormat theFile,
 String name,
 String path)

Creates an H4SDS object with specific name and path.

Parameters:

theFile - the HDF file.

name - the name of this H4SDS.

path - the full path of this H4SDS.

H4SDS

public H4SDS(FileFormat theFile,
 String name,
 String path,
 long[] oid)

Creates an H4SDS object with specific name, path and oid.

Parameters:

theFile - the HDF file.

name - the name of this H4SDS.

path - the full path of this H4SDS.

oid - the unique identifier of this data object.

Method Details

hasAttribute

public boolean hasAttribute()

Description copied from interface: MetaDataContainer

Check if the object has any attributes attached.

Specified by:

hasAttribute in interface MetaDataContainer

Returns:

true if it has any attributes, false otherwise.

getDatatype

public Datatype getDatatype()

Returns the datatype of the data object.

Specified by:

getDatatype in interface DataFormat

Overrides:

getDatatype in class Dataset

Returns:

the datatype of the data object.

copy

public Dataset copy(Group pgroup,
 String dname,
 long[] dims,
 Object buff)
             throws Exception

Description copied from class: Dataset

Creates a new dataset and writes the data buffer to the new dataset. This function allows applications to create a new dataset for a given data buffer. For example, users can select a specific interesting part from a large image and create a new image with the selection. The new dataset retains the datatype and dataset creation properties of this dataset.

Specified by:

copy in class Dataset

Parameters:

pgroup - the group which the dataset is copied to.

dname - the name of the new dataset.

dims - the dimension sizes of the the new dataset.

buff - the data values of the subset to be copied.

Returns:

the new dataset.

Throws:

Exception - if dataset can not be copied

readBytes

public byte[] readBytes()
                 throws hdf.hdflib.HDFException

Description copied from class: Dataset

Reads the raw data of the dataset from file to a byte array. readBytes() reads raw data to an array of bytes instead of array of its datatype. For example, for a one-dimension 32-bit integer dataset of size 5, readBytes() returns a byte array of size 20 instead of an int array of 5. readBytes() can be used to copy data from one dataset to another efficiently because the raw data is not converted to its native type, it saves memory space and CPU time.

Specified by:

readBytes in class Dataset

Returns:

the byte array of the raw data.

Throws:

hdf.hdflib.HDFException

read

public Object read()
            throws hdf.hdflib.HDFException,
OutOfMemoryError

Reads the data from file. read() reads the data from file to a memory buffer and returns the memory buffer. The dataset object does not hold the memory buffer. To store the memory buffer in the dataset object, one must call getData(). By default, the whole dataset is read into memory. Users can also select a subset to read. Subsetting is done in an implicit way.

Specified by:

read in interface DataFormat

Returns:

the data read from file.

Throws:

hdf.hdflib.HDFException - if object can not be read

OutOfMemoryError - if memory is exhausted

See Also:

• Dataset.getData()

write

public void write(Object buf)
           throws hdf.hdflib.HDFException

Writes a memory buffer to the object in the file.

Specified by:

write in interface DataFormat

Parameters:

buf - the data to write

Throws:

hdf.hdflib.HDFException - if data can not be written

getMetadata

public List getMetadata()
                 throws hdf.hdflib.HDFException

Retrieves the object's metadata, such as attributes, from the file. Metadata, such as attributes, is stored in a List.

Specified by:

getMetadata in interface MetaDataContainer

Returns:

the list of metadata objects.

Throws:

hdf.hdflib.HDFException - if the metadata can not be retrieved

writeMetadata

public void writeMetadata(Object info)
                   throws Exception

Writes a specific piece of metadata (such as an attribute) into the file. If an HDF(4&5) attribute exists in the file, this method updates its value. If the attribute does not exist in the file, it creates the attribute in the file and attaches it to the object. It will fail to write a new attribute to the object where an attribute with the same name already exists. To update the value of an existing attribute in the file, one needs to get the instance of the attribute by getMetadata(), change its values, then use writeMetadata() to write the value.

Specified by:

writeMetadata in interface MetaDataContainer

Parameters:

info - the metadata to write.

Throws:

Exception - if the metadata can not be written

removeMetadata

public void removeMetadata(Object info)
                    throws hdf.hdflib.HDFException

Deletes an existing piece of metadata from this object.

Specified by:

removeMetadata in interface MetaDataContainer

Parameters:

info - the metadata to delete.

Throws:

hdf.hdflib.HDFException - if the metadata can not be removed

updateMetadata

public void updateMetadata(Object info)
                    throws Exception

Updates an existing piece of metadata attached to this object.

Specified by:

updateMetadata in interface MetaDataContainer

Parameters:

info - the metadata to update.

Throws:

Exception - if the metadata can not be updated

open

public long open()

Description copied from class: HObject

Opens an existing object such as a dataset or group for access. The return value is an object identifier obtained by implementing classes such as H5.H5Dopen(). This function is needed to allow other objects to be able to access the object. For instance, H5File class uses the open() function to obtain object identifier for copyAttributes(long src_id, long dst_id) and other purposes. The open() function should be used in pair with close(long) function.

Specified by:

open in class HObject

Returns:

the object identifier if successful; otherwise returns a negative value.

See Also:

• HObject.close(long)

close

public void close(long id)

Description copied from class: HObject

Closes access to the object. Sub-classes must implement this interface because different data objects have their own ways of how the data resources are closed. For example, H5Group.close() calls the hdf.hdf5lib.H5.H5Gclose() method and closes the group resource specified by the group id.

Specified by:

close in class HObject

Parameters:

id - The object identifier.

init

public void init()

Initializes the H4SDS such as dimension size of this dataset.

Specified by:

init in interface DataFormat

create

public static H4SDS create(String name,
 Group pgroup,
 Datatype type,
 long[] dims,
 long[] maxdims,
 long[] chunks,
 int gzip,
 Object fillValue,
 Object data)
                    throws Exception

Creates a new dataset.

Parameters:

name - the name of the dataset to create.

pgroup - the parent group of the new dataset.

type - the datatype of the dataset.

dims - the dimension size of the dataset.

maxdims - the max dimension size of the dataset.

chunks - the chunk size of the dataset.

gzip - the level of the gzip compression.

fillValue - the default value.

data - the array of data values.

Returns:

the new dataset if successful. Otherwise returns null.

Throws:

Exception - if the dataset can not be created

create

public static H4SDS create(String name,
 Group pgroup,
 Datatype type,
 long[] dims,
 long[] maxdims,
 long[] chunks,
 int gzip,
 Object data)
                    throws Exception

Creates a new dataset.

Parameters:

name - the name of the dataset to create.

pgroup - the parent group of the new dataset.

type - the datatype of the dataset.

dims - the dimension size of the dataset.

maxdims - the max dimension size of the dataset.

chunks - the chunk size of the dataset.

gzip - the level of the gzip compression.

data - the array of data values.

Returns:

the new dataset if successful. Otherwise returns null.

Throws:

Exception - if the dataset can not be created

getMetadata

public List getMetadata(int... attrPropList)
                 throws Exception

Retrieves the object's metadata, such as attributes, from the file. Metadata, such as attributes, is stored in a List.

Parameters:

attrPropList - the list of properties to get

Returns:

the list of metadata objects.

Throws:

Exception - if the metadata can not be retrieved