Class CompoundDS
- Object
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- hdf.object.HObject
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- hdf.object.Dataset
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- hdf.object.CompoundDS
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- All Implemented Interfaces:
CompoundDataFormat
,DataFormat
,MetaDataContainer
,Serializable
public abstract class CompoundDS extends Dataset implements CompoundDataFormat
A CompoundDS is a dataset with compound datatype.A compound datatype is an aggregation of one or more datatypes. Each member of a compound type has a name which is unique within that type, and a datatype of that member in a compound datum. Compound datatypes can be nested, i.e. members of a compound datatype can be some other compound datatype.
For more details on compound datatypes, see HDF5 User's Guide
Since Java cannot handle C-structured compound data, data in a compound dataset is loaded in to an Java List. Each element of the list is a data array that corresponds to a compound field. The data is read/written by compound field.
For example, if compound dataset "comp" has the following nested structure, and member datatypes
comp --> m01 (int) comp --> m02 (float) comp --> nest1 --> m11 (char) comp --> nest1 --> m12 (String) comp --> nest1 --> nest2 --> m21 (long) comp --> nest1 --> nest2 --> m22 (double)
The data object is a Java list of six arrays: {int[], float[], char[], Stirng[], long[] and double[]}.- Version:
- 1.1 9/4/2007
- Author:
- Peter X. Cao
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description protected boolean[]
isMemberSelected
The array to store flags to indicate if a member of this compound dataset is selected for read/write.protected Object[]
memberDims
The dimension sizes of each member.protected String[]
memberNames
The names of members of the compound dataset.protected int[]
memberOrders
Returns array containing the total number of elements of the members of this compound dataset.protected Datatype[]
memberTypes
The datatypes of compound members.protected int
numberOfMembers
The number of members of the compound dataset.static String
SEPARATOR
A single character to separate the names of nested compound fields.-
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, storageLayout
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Fields inherited from class hdf.object.HObject
fileFormat, linkTargetObjName, oid
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Constructor Summary
Constructors Constructor Description CompoundDS(FileFormat theFile, String dsName, String dsPath)
Constructs a CompoundDS object with the given file, dataset name and path.CompoundDS(FileFormat theFile, String dsName, String dsPath, long[] oid)
Deprecated.Not for public use in the future.
UsingCompoundDS(FileFormat, String, String)
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description Dataset
copy(Group pgroup, String name, long[] dims, Object data)
Deprecated.Not implemented for compound dataset.int
getMemberCount()
Returns the number of members of the compound dataset.int[]
getMemberDims(int i)
Returns the dimension sizes of the i-th member.String[]
getMemberNames()
Returns the names of the members of the compound dataset.int[]
getMemberOrders()
Returns array containing the total number of elements of the members of the compound dataset.Datatype[]
getMemberTypes()
Returns an array of datatype objects of compound members.int
getSelectedMemberCount()
Returns the number of selected members of the compound dataset.String[]
getSelectedMemberNames()
Returns an array of the names of the selected members of the compound dataset.int[]
getSelectedMemberOrders()
Returns array containing the total number of elements of the selected members of the compound dataset.Datatype[]
getSelectedMemberTypes()
Returns an array of datatype objects of selected compound members.boolean
isMemberSelected(int idx)
Checks if a member of the compound dataset is selected for read/write.void
selectMember(int idx)
Selects the i-th member for read/write.void
setAllMemberSelection(boolean selectAll)
Selects/deselects all members.-
Methods inherited from class hdf.object.Dataset
byteToString, clear, clearData, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDatatype, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStorage, getStorageLayout, getStride, getVirtualFilename, getVirtualMaps, getWidth, isInited, isString, isVirtual, readBytes, setConvertByteToString, setData, stringToByte, write
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Methods inherited from class hdf.object.HObject
close, debug, equals, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, hashCode, open, setLinkTargetObjName, setName, setPath, toString
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface hdf.object.DataFormat
clearData, convertFromUnsignedC, convertToUnsignedC, getCompression, getData, getDatatype, getDims, getFillValue, getHeight, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getStartDims, getStride, getWidth, init, isInited, read, setData, write, write
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Methods inherited from interface hdf.object.MetaDataContainer
getMetadata, hasAttribute, removeMetadata, updateMetadata, writeMetadata
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Field Detail
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SEPARATOR
public static final String SEPARATOR
A single character to separate the names of nested compound fields. An extended ASCII character, 0x95, is used to avoid common characters in compound names.- See Also:
- Constant Field Values
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numberOfMembers
protected int numberOfMembers
The number of members of the compound dataset.
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memberNames
protected String[] memberNames
The names of members of the compound dataset.
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memberOrders
protected int[] memberOrders
Returns array containing the total number of elements of the members of this compound dataset.For example, a compound dataset COMP has members of A, B and C as
COMP { int A; float B[5]; double C[2][3]; }
memberOrders is an integer array of {1, 5, 6} to indicate that member A has one element, member B has 5 elements, and member C has 6 elements.
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memberDims
protected transient Object[] memberDims
The dimension sizes of each member.The i-th element of the Object[] is an integer array (int[]) that contains the dimension sizes of the i-th member.
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memberTypes
protected Datatype[] memberTypes
The datatypes of compound members.
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isMemberSelected
protected boolean[] isMemberSelected
The array to store flags to indicate if a member of this compound dataset is selected for read/write.If a member is selected, the read/write will perform on the member. Applications such as HDFView will only display the selected members of the compound dataset.
For example, if a compound dataset has four members String[] memberNames = {"X", "Y", "Z", "TIME"}; and boolean[] isMemberSelected = {true, false, false, true}; members "X" and "TIME" are selected for read and write.
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Constructor Detail
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CompoundDS
public CompoundDS(FileFormat theFile, String dsName, String dsPath)
Constructs a CompoundDS object with the 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 dataset.dsName
- the name of the CompoundDS, e.g. "compDS".dsPath
- the full path of the CompoundDS, e.g. "/g1".
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CompoundDS
@Deprecated public CompoundDS(FileFormat theFile, String dsName, String dsPath, long[] oid)
Deprecated.Not for public use in the future.
UsingCompoundDS(FileFormat, String, String)
- Parameters:
theFile
- the file that contains the dataset.dsName
- the name of the CompoundDS, e.g. "compDS".dsPath
- the full path of the CompoundDS, e.g. "/g1".oid
- the oid of the CompoundDS.
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Method Detail
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getMemberCount
public final int getMemberCount()
Returns the number of members of the compound dataset.- Specified by:
getMemberCount
in interfaceCompoundDataFormat
- Returns:
- the number of members of the compound dataset.
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getSelectedMemberCount
public final int getSelectedMemberCount()
Returns the number of selected members of the compound dataset. Selected members are the compound fields which are selected for read/write.For example, in a compound datatype of {int A, float B, char[] C}, users can choose to retrieve only {A, C} from the dataset. In this case, getSelectedMemberCount() returns two.
- Specified by:
getSelectedMemberCount
in interfaceCompoundDataFormat
- Returns:
- the number of selected members.
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getMemberNames
public final String[] getMemberNames()
Returns the names of the members of the compound dataset. The names of compound members are stored in an array of Strings.For example, for a compound datatype of {int A, float B, char[] C} getMemberNames() returns ["A", "B", "C"}.
- Specified by:
getMemberNames
in interfaceCompoundDataFormat
- Returns:
- the names of compound members.
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getSelectedMemberNames
public final String[] getSelectedMemberNames()
Returns an array of the names of the selected members of the compound dataset.- Specified by:
getSelectedMemberNames
in interfaceCompoundDataFormat
- Returns:
- an array of the names of the selected members of the compound dataset.
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isMemberSelected
public final boolean isMemberSelected(int idx)
Checks if a member of the compound dataset is selected for read/write.- Specified by:
isMemberSelected
in interfaceCompoundDataFormat
- Parameters:
idx
- the index of compound member.- Returns:
- true if the i-th memeber is selected; otherwise returns false.
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selectMember
public final void selectMember(int idx)
Selects the i-th member for read/write.- Specified by:
selectMember
in interfaceCompoundDataFormat
- Parameters:
idx
- the index of compound member.
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setAllMemberSelection
public final void setAllMemberSelection(boolean selectAll)
Selects/deselects all members.- Specified by:
setAllMemberSelection
in interfaceCompoundDataFormat
- Parameters:
selectAll
- The indicator to select or deselect all members. If true, all members are selected for read/write. If false, no member is selected for read/write.
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getMemberOrders
public final int[] getMemberOrders()
Returns array containing the total number of elements of the members of the compound dataset.For example, a compound dataset COMP has members of A, B and C as
COMP { int A; float B[5]; double C[2][3]; }
getMemberOrders() will return an integer array of {1, 5, 6} to indicate that member A has one element, member B has 5 elements, and member C has 6 elements.- Specified by:
getMemberOrders
in interfaceCompoundDataFormat
- Returns:
- the array containing the total number of elements of the members of compound.
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getSelectedMemberOrders
public final int[] getSelectedMemberOrders()
Returns array containing the total number of elements of the selected members of the compound dataset.For example, a compound dataset COMP has members of A, B and C as
COMP { int A; float B[5]; double C[2][3]; }
If A and B are selected, getSelectedMemberOrders() returns an array of {1, 5}- Specified by:
getSelectedMemberOrders
in interfaceCompoundDataFormat
- Returns:
- array containing the total number of elements of the selected members of compound.
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getMemberDims
public final int[] getMemberDims(int i)
Returns the dimension sizes of the i-th member.For example, a compound dataset COMP has members of A, B and C as
COMP { int A; float B[5]; double C[2][3]; }
getMemberDims(2) returns an array of {2, 3}, while getMemberDims(1) returns an array of {5}, and getMemberDims(0) returns null.- Specified by:
getMemberDims
in interfaceCompoundDataFormat
- Parameters:
i
- the i-th member- Returns:
- the dimension sizes of the i-th member, null if the compound member is not an array.
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getMemberTypes
public final Datatype[] getMemberTypes()
Returns an array of datatype objects of compound members.Each member of a compound dataset has its own datatype. The datatype of a member can be atomic or other compound datatype (nested compound). Sub-classes set up the datatype objects at init().
- Specified by:
getMemberTypes
in interfaceCompoundDataFormat
- Returns:
- the array of datatype objects of the compound members.
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getSelectedMemberTypes
public final Datatype[] getSelectedMemberTypes()
Returns an array of datatype objects of selected compound members.- Specified by:
getSelectedMemberTypes
in interfaceCompoundDataFormat
- Returns:
- an array of datatype objects of selected compound members.
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copy
@Deprecated public Dataset copy(Group pgroup, String name, long[] dims, Object data) throws Exception
Deprecated.Not implemented for compound dataset.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 classDataset
- Parameters:
pgroup
- the group which the dataset is copied to.name
- the name of the new dataset.dims
- the dimension sizes of the the new dataset.data
- the data values of the subset to be copied.- Returns:
- the new dataset.
- Throws:
Exception
- if dataset can not be copied
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