H5CompoundDS (HDFView 3.99)

Object
- hdf.object.HObject
- - hdf.object.Dataset
  - - hdf.object.CompoundDS
    - - hdf.object.h5.H5CompoundDS

All Implemented Interfaces:

CompoundDataFormat, DataFormat, MetaDataContainer, Serializable
```
public class H5CompoundDS
extends CompoundDS
```
The H5CompoundDS class defines an HDF5 dataset of compound datatypes.
An HDF5 dataset is an object composed of a collection of data elements, or raw data, and metadata that stores a description of the data elements, data layout, and all other information necessary to write, read, and interpret the stored data.
A HDF5 compound datatype is similar to a struct in C or a common block in Fortran: it is a collection of one or more atomic types or small arrays of such types. Each member of a compound type has a name which is unique within that type, and a byte offset that determines the first byte (smallest byte address) of that member in a compound datum.
For more information on HDF5 datasets and datatypes, read the HDF5 User's Guide.
There are two basic types of compound datasets: simple compound data and nested compound data. Members of a simple compound dataset have atomic datatypes. Members of a nested compound dataset are compound or array of compound data.
Since Java does not understand C structures, we cannot directly read/write compound data values as in the following C example.
```
 typedef struct s1_t {
         int    a;
         float  b;
         double c;
         } s1_t;
     s1_t       s1[LENGTH];
     ...
     H5Dwrite(..., s1);
     H5Dread(..., s1);
 
```
Values of compound data fields are stored in java.util.Vector object. We read and write compound data by fields instead of compound structure. As for the example above, the java.util.Vector object has three elements: int[LENGTH], float[LENGTH] and double[LENGTH]. Since Java understands the primitive datatypes of int, float and double, we will be able to read/write the compound data by field.
Version:

1.1 9/4/2007

Author:

Peter X. Cao

See Also:

Serialized Form

Field Summary
- Fields inherited from class hdf.object.CompoundDS
  isMemberSelected, memberDims, memberNames, memberOrders, memberTypes, numberOfMembers, separator
- Fields inherited from class hdf.object.Dataset
  chunkSize, compression, compression_gzip_txt, convertByteToString, convertedBuf, data, datatype, dimNames, dims, filters, inited, isDataLoaded, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, startDims, storage, storage_layout
- Fields inherited from class hdf.object.HObject
  fileFormat, linkTargetObjName, oid

Constructor Summary

Constructors
Constructor and Description
`H5CompoundDS(FileFormat theFile, String theName, String thePath)` Constructs an instance of a HDF5 compound dataset with given file, dataset name and path.
`H5CompoundDS(FileFormat theFile, String theName, String thePath, long[] oid)` Deprecated. Not for public use in the future. Using `H5CompoundDS(FileFormat, String, String)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`clear()` Clears memory held by the dataset, such as the data buffer.
`void`	`close(long did)` Closes access to the object.
`Object`	`convertFromUnsignedC()` Converts the data values of this data object to appropriate Java integers if they are unsigned integers.
`Object`	`convertToUnsignedC()` Converts Java integer data values of this data object back to unsigned C-type integer data if they are unsigned integers.
`static Dataset`	`create(String name, Group pgroup, long[] dims, long[] maxdims, long[] chunks, int gzip, String[] memberNames, Datatype[] memberDatatypes, int[] memberRanks, long[][] memberDims, Object data)` Creates a simple compound dataset in a file with/without chunking and compression.
`static Dataset`	`create(String name, Group pgroup, long[] dims, String[] memberNames, Datatype[] memberDatatypes, int[] memberRanks, long[][] memberDims, Object data)` Deprecated. Not for public use in the future. Using `create(String, Group, long[], long[], long[], int, String[], Datatype[], int[], long[][], Object)`
`static Dataset`	`create(String name, Group pgroup, long[] dims, String[] memberNames, Datatype[] memberDatatypes, int[] memberSizes, Object data)` Deprecated. Not for public use in the future. Using `create(String, Group, long[], long[], long[], int, String[], Datatype[], int[], long[][], Object)`
`Datatype`	`getDatatype()` Returns the datatype of the data object.
`Object`	`getFillValue()` Returns the fill values for the data object.
`List<Attribute>`	`getMetadata()` Retrieves the object's metadata, such as attributes, from the file.
`List<Attribute>`	`getMetadata(int... attrPropList)`
`long`	`getSize(long tid)` Returns the size in bytes of a given datatype.
`String`	`getVirtualFilename(int index)`
`int`	`getVirtualMaps()`
`boolean`	`hasAttribute()` Check if the object has any attributes attached.
`void`	`init()` Retrieves datatype and dataspace information from file and sets the dataset in memory.
`boolean`	`isString(long tid)` Checks if a given datatype is a string.
`boolean`	`isVirtual()`
`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`	`setName(String newName)` Sets the name of the object.
`void`	`updateMetadata(Object info)` Updates an existing piece of metadata attached to this object.
`void`	`write(Object buf)` Writes the given data buffer into this dataset in a file.
`void`	`writeMetadata(Object info)` Writes a specific piece of metadata (such as an attribute) into the file.

Methods inherited from class hdf.object.CompoundDS
copy, getMemberCount, getMemberDims, getMemberNames, getMemberOrders, getMemberTypes, getSelectedMemberCount, getSelectedMemberOrders, getSelectedMemberTypes, isMemberSelected, selectMember, setAllMemberSelection

Methods inherited from class hdf.object.Dataset
byteToString, clearData, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getStartDims, getStorage, getStorageLayout, getStride, getWidth, isInited, setConvertByteToString, setData, stringToByte, write

Methods inherited from class hdf.object.HObject
debug, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, setLinkTargetObjName, setPath, toString

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface hdf.object.DataFormat
clearData, getCompression, getData, getDims, getHeight, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getStartDims, getStride, getWidth, isInited, setData, write

- Constructor Detail
  - H5CompoundDS
```
public H5CompoundDS(FileFormat theFile,
                    String theName,
                    String thePath)
```
    Constructs an instance of a HDF5 compound dataset with given file, dataset name and path.
    The dataset object represents an existing dataset in the file. For example, new H5CompoundDS(file, "dset1", "/g0/") constructs a dataset object that corresponds to the dataset,"dset1", at group "/g0/".
    This object is usually constructed at FileFormat.open(), which loads the file structure and object information into memory. It is rarely used elsewhere.
    
    Parameters:
    
    theFile - the file that contains the data object.
    
    theName - the name of the data object, e.g. "dset".
    
    thePath - the full path of the data object, e.g. "/arrays/".
  - H5CompoundDS
```
@Deprecated
public H5CompoundDS(FileFormat theFile,
                                String theName,
                                String thePath,
                                long[] oid)
```
    Deprecated. Not for public use in the future.
    Using H5CompoundDS(FileFormat, String, String)
    
    Parameters:
    
    theFile - the file that contains the data object.
    
    theName - the name of the data object, e.g. "dset".
    
    thePath - the full path of the data object, e.g. "/arrays/".
    
    oid - the oid of the data object.
- Method Detail
  - 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 did)
```
    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:
    
    did - The object identifier.
  - init
```
public void init()
```
    Retrieves datatype and dataspace information from file and sets the dataset in memory.
    The init() is designed to support lazy operation in a dataset object. When a data object is retrieved from file, the datatype, dataspace and raw data are not loaded into memory. When it is asked to read the raw data from file, init() is first called to get the datatype and dataspace information, then load the raw data from file.
    init() is also used to reset the selection of a dataset (start, stride and count) to the default, which is the entire dataset for 1D or 2D datasets. In the following example, init() at step 1) retrieves datatype and dataspace information from file. getData() at step 3) reads only one data point. init() at step 4) resets the selection to the whole dataset. getData() at step 4) reads the values of whole dataset into memory.
```
 dset = (Dataset) file.get(NAME_DATASET);

 // 1) get datatype and dataspace information from file
 dset.init();
 rank = dset.getRank(); // rank = 2, a 2D dataset
 count = dset.getSelectedDims();
 start = dset.getStartDims();
 dims = dset.getDims();

 // 2) select only one data point
 for (int i = 0; i < rank; i++) {
     start[0] = 0;
     count[i] = 1;
 }

 // 3) read one data point
 data = dset.getData();

 // 4) reset selection to the whole dataset
 dset.init();

 // 5) clean the memory data buffer
 dset.clearData();

 // 6) Read the whole dataset
 data = dset.getData();
 
```
  - hasAttribute
```
public boolean hasAttribute()
```
    Description copied from interface: MetaDataContainer
    
    Check if the object has any attributes attached.
    
    Returns:
    
    true if it has any attributes, false otherwise.
  - getDatatype
```
public Datatype getDatatype()
```
    Description copied from interface: DataFormat
    
    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.
  - getFillValue
```
public Object getFillValue()
```
    Description copied from interface: DataFormat
    
    Returns the fill values for the data object.
    
    Returns:
    
    the fill values for the data object.
  - clear
```
public void clear()
```
    Description copied from class: Dataset
    
    Clears memory held by the dataset, such as the data buffer.
    
    Overrides:
    
    clear in class Dataset
  - readBytes
```
public byte[] readBytes()
                 throws hdf.hdf5lib.exceptions.HDF5Exception
```
    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.hdf5lib.exceptions.HDF5Exception
  - read
```
public Object read()
            throws Exception
```
    Description copied from interface: DataFormat
    
    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.
    
    Returns:
    
    the data read from file.
    
    Throws:
    
    Exception - if object can not be read
    
    See Also:
    
    DataFormat.getData()
  - write
```
public void write(Object buf)
           throws hdf.hdf5lib.exceptions.HDF5Exception
```
    Writes the given data buffer into this dataset in a file.
    The data buffer is a vector that contains the data values of compound fields. The data is written into file field by field.
    
    Parameters:
    
    buf - The vector that contains the data values of compound fields.
    
    Throws:
    
    hdf.hdf5lib.exceptions.HDF5Exception - If there is an error at the HDF5 library level.
  - convertFromUnsignedC
```
public Object convertFromUnsignedC()
```
    Description copied from interface: DataFormat
    
    Converts the data values of this data object to appropriate Java integers if they are unsigned integers.
    
    Returns:
    
    the converted data buffer.
    
    See Also:
    
    Dataset.convertToUnsignedC(Object), Dataset.convertFromUnsignedC(Object, Object)
  - convertToUnsignedC
```
public Object convertToUnsignedC()
```
    Description copied from interface: DataFormat
    
    Converts Java integer data values of this data object back to unsigned C-type integer data if they are unsigned integers.
    
    Returns:
    
    the converted data buffer.
    
    See Also:
    
    Dataset.convertToUnsignedC(Object), Dataset.convertToUnsignedC(Object, Object)
  - getMetadata
```
public List<Attribute> getMetadata()
                            throws hdf.hdf5lib.exceptions.HDF5Exception
```
    Description copied from interface: MetaDataContainer
    
    Retrieves the object's metadata, such as attributes, from the file.
    Metadata, such as attributes, is stored in a List.
    
    Returns:
    
    the list of metadata objects.
    
    Throws:
    
    hdf.hdf5lib.exceptions.HDF5Exception
  - getMetadata
```
public List<Attribute> getMetadata(int... attrPropList)
                            throws hdf.hdf5lib.exceptions.HDF5Exception
```
    Throws:
    
    hdf.hdf5lib.exceptions.HDF5Exception
  - writeMetadata
```
public void writeMetadata(Object info)
                   throws Exception
```
    Description copied from interface: MetaDataContainer
    
    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.
    
    Parameters:
    
    info - the metadata to write.
    
    Throws:
    
    Exception - if the metadata can not be written
  - removeMetadata
```
public void removeMetadata(Object info)
                    throws hdf.hdf5lib.exceptions.HDF5Exception
```
    Description copied from interface: MetaDataContainer
    
    Deletes an existing piece of metadata from this object.
    
    Parameters:
    
    info - the metadata to delete.
    
    Throws:
    
    hdf.hdf5lib.exceptions.HDF5Exception
  - updateMetadata
```
public void updateMetadata(Object info)
                    throws hdf.hdf5lib.exceptions.HDF5Exception
```
    Description copied from interface: MetaDataContainer
    
    Updates an existing piece of metadata attached to this object.
    
    Parameters:
    
    info - the metadata to update.
    
    Throws:
    
    hdf.hdf5lib.exceptions.HDF5Exception
  - setName
```
public void setName(String newName)
             throws Exception
```
    Description copied from class: HObject
    
    Sets the name of the object. setName (String newName) changes the name of the object in the file.
    
    Overrides:
    
    setName in class HObject
    
    Parameters:
    
    newName - The new name of the object.
    
    Throws:
    
    Exception - if name is root or contains separator
  - create
```
@Deprecated
public static Dataset create(String name,
                                         Group pgroup,
                                         long[] dims,
                                         String[] memberNames,
                                         Datatype[] memberDatatypes,
                                         int[] memberSizes,
                                         Object data)
                                  throws Exception
```
    Deprecated. Not for public use in the future.
    Using create(String, Group, long[], long[], long[], int, String[], Datatype[], int[], long[][], Object)
    
    Parameters:
    
    name - the name of the dataset to create.
    
    pgroup - parent group where the new dataset is created.
    
    dims - the dimension size of the dataset.
    
    memberNames - the names of compound datatype
    
    memberDatatypes - the datatypes of the compound datatype
    
    memberSizes - the dim sizes of the members
    
    data - list of data arrays written to the new dataset, null if no data is written to the new dataset.
    
    Returns:
    
    the new compound dataset if successful; otherwise returns null.
    
    Throws:
    
    Exception - if there is a failure.
  - create
```
@Deprecated
public static Dataset create(String name,
                                         Group pgroup,
                                         long[] dims,
                                         String[] memberNames,
                                         Datatype[] memberDatatypes,
                                         int[] memberRanks,
                                         long[][] memberDims,
                                         Object data)
                                  throws Exception
```
    Deprecated. Not for public use in the future.
    Using create(String, Group, long[], long[], long[], int, String[], Datatype[], int[], long[][], Object)
    
    Parameters:
    
    name - the name of the dataset to create.
    
    pgroup - parent group where the new dataset is created.
    
    dims - the dimension size of the dataset.
    
    memberNames - the names of compound datatype
    
    memberDatatypes - the datatypes of the compound datatype
    
    memberRanks - the ranks of the members
    
    memberDims - the dim sizes of the members
    
    data - list of data arrays written to the new dataset, null if no data is written to the new dataset.
    
    Returns:
    
    the new compound dataset if successful; otherwise returns null.
    
    Throws:
    
    Exception - if the dataset can not be created.
  - create
```
public static Dataset create(String name,
                             Group pgroup,
                             long[] dims,
                             long[] maxdims,
                             long[] chunks,
                             int gzip,
                             String[] memberNames,
                             Datatype[] memberDatatypes,
                             int[] memberRanks,
                             long[][] memberDims,
                             Object data)
                      throws Exception
```
    Creates a simple compound dataset in a file with/without chunking and compression.
    This function provides an easy way to create a simple compound dataset in file by hiding tedious details of creating a compound dataset from users.
    This function calls H5.H5Dcreate() to create a simple compound dataset in file. Nested compound dataset is not supported. The required information to create a compound dataset includes the name, the parent group and data space of the dataset, the names, datatypes and data spaces of the compound fields. Other information such as chunks, compression and the data buffer is optional.
    The following example shows how to use this function to create a compound dataset in file.
```
 H5File file = null;
 String message = "";
 Group pgroup = null;
 int[] DATA_INT = new int[DIM_SIZE];
 float[] DATA_FLOAT = new float[DIM_SIZE];
 String[] DATA_STR = new String[DIM_SIZE];
 long[] DIMs = { 50, 10 };
 long[] CHUNKs = { 25, 5 };

 try {
     file = (H5File) H5FILE.open(fname, H5File.CREATE);
     file.open();
     pgroup = (Group) file.get("/");
 }
 catch (Exception ex) {
 }

 Vector data = new Vector();
 data.add(0, DATA_INT);
 data.add(1, DATA_FLOAT);
 data.add(2, DATA_STR);

 // create groups
 Datatype[] mdtypes = new H5Datatype[3];
 String[] mnames = { "int", "float", "string" };
 Dataset dset = null;
 try {
     mdtypes[0] = new H5Datatype(Datatype.CLASS_INTEGER, 4, -1, -1);
     mdtypes[1] = new H5Datatype(Datatype.CLASS_FLOAT, 4, -1, -1);
     mdtypes[2] = new H5Datatype(Datatype.CLASS_STRING, STR_LEN, -1, -1);
     dset = file.createCompoundDS("/CompoundDS", pgroup, DIMs, null, CHUNKs, 9, mnames, mdtypes, null, data);
 }
 catch (Exception ex) {
     failed(message, ex, file);
     return 1;
 }
 
```
    Parameters:
    
    name - the name of the dataset to create.
    
    pgroup - parent group where the new dataset is created.
    
    dims - the dimension size of the dataset.
    
    maxdims - the max dimension size of the dataset. maxdims is set to dims if maxdims = null.
    
    chunks - the chunk size of the dataset. No chunking if chunk = null.
    
    gzip - GZIP compression level (1 to 9). 0 or negative values if no compression.
    
    memberNames - the names of compound datatype
    
    memberDatatypes - the datatypes of the compound datatype
    
    memberRanks - the ranks of the members
    
    memberDims - the dim sizes of the members
    
    data - list of data arrays written to the new dataset, null if no data is written to the new dataset.
    
    Returns:
    
    the new compound dataset if successful; otherwise returns null.
    
    Throws:
    
    Exception - if there is a failure.
  - isString
```
public boolean isString(long tid)
```
    Description copied from class: Dataset
    
    Checks if a given datatype is a string. Sub-classes must replace this default implementation.
    
    Overrides:
    
    isString in class Dataset
    
    Parameters:
    
    tid - The data type identifier.
    
    Returns:
    
    true if the datatype is a string; otherwise returns false.
  - getSize
```
public long getSize(long tid)
```
    Description copied from class: Dataset
    
    Returns the size in bytes of a given datatype. Sub-classes must replace this default implementation.
    
    Overrides:
    
    getSize in class Dataset
    
    Parameters:
    
    tid - The data type identifier.
    
    Returns:
    
    The size of the datatype
  - isVirtual
```
public boolean isVirtual()
```
    Overrides:
    
    isVirtual in class Dataset
  - getVirtualFilename
```
public String getVirtualFilename(int index)
```
    Overrides:
    
    getVirtualFilename in class Dataset
  - getVirtualMaps
```
public int getVirtualMaps()
```
    Overrides:
    
    getVirtualMaps in class Dataset

Class H5CompoundDS

Field Summary

Fields inherited from class hdf.object.CompoundDS

Fields inherited from class hdf.object.Dataset

Fields inherited from class hdf.object.HObject

Constructor Summary

Method Summary

Methods inherited from class hdf.object.CompoundDS

Methods inherited from class hdf.object.Dataset

Methods inherited from class hdf.object.HObject

Methods inherited from class Object

Methods inherited from interface hdf.object.DataFormat

Constructor Detail

H5CompoundDS

H5CompoundDS

Method Detail

open

close

init

hasAttribute

getDatatype

getFillValue

clear

readBytes

read

write

convertFromUnsignedC

convertToUnsignedC

getMetadata

getMetadata

writeMetadata

removeMetadata

updateMetadata

setName

create

create

create

isString

getSize

isVirtual

getVirtualFilename

getVirtualMaps