Object
hdf.object.HObject
hdf.object.Dataset
hdf.object.CompoundDS
hdf.object.h5.H5CompoundDS
- All Implemented Interfaces:
CompoundDataFormat,DataFormat,MetaDataContainer,Serializable
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
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Field Summary
Fields inherited from class hdf.object.CompoundDS
flatNameList, flatTypeList, isMemberSelected, memberDims, memberNames, memberOrders, memberTypes, numberOfMembers, SEPARATORFields 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, storageLayoutFields inherited from class hdf.object.HObject
fileFormat, linkTargetObjName, oid -
Constructor Summary
ConstructorsConstructorDescriptionH5CompoundDS(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. -
Method Summary
Modifier and TypeMethodDescriptionvoidclear()Removes all of the elements from metadata list.voidclose(long did)Closes access to the object.protected ObjectconvertByteMember(Datatype dtype, byte[] byteData)Routine to convert datatypes that are read in as byte arrays to regular types.Converts the data values of this data object to appropriate Java integers if they are unsigned integers.Converts Java integer data values of this data object back to unsigned C-type integer data if they are unsigned integers.static Datasetcreate(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 Datasetcreate(String name, Group pgroup, long[] dims, String[] memberNames, Datatype[] memberDatatypes, int[] memberRanks, long[][] memberDims, Object data)Deprecated.Not for public use in the future.static Datasetcreate(String name, Group pgroup, long[] dims, String[] memberNames, Datatype[] memberDatatypes, int[] memberSizes, Object data)Deprecated.Not for public use in the future.Returns the datatype of the data object.Retrieves the object's metadata, such as attributes, from the file.getMetadata(int... attrPropList)Retrieves the object's metadata, such as attributes, from the file.longgetSize(long tid)Returns the size in bytes of a given datatype.getVirtualFilename(int index)Gets the source file name at index if dataset is virtual.intGets the number of source files if dataset is virtual.booleanCheck if the object has any attributes attached.voidinit()Retrieves datatype and dataspace information from file and sets the dataset in memory.booleanisString(long tid)Checks if a given datatype is a string.booleanChecks if dataset is virtual.longopen()Opens an existing object such as a dataset or group for access.read()Reads the data from file.byte[]Reads the raw data of the dataset from file to a byte array.voidremoveMetadata(Object info)Deletes an existing piece of metadata from this object.voidSets the name of the object.voidupdateMetadata(Object info)Updates an existing piece of metadata attached to this object.voidWrites the given data buffer into this dataset in a file.voidwriteMetadata(Object info)Writes a specific piece of metadata (such as an attribute) into the file.Methods inherited from class hdf.object.CompoundDS
convertCompoundByteMembers, copy, getFillValue, getMemberCount, getMemberDims, getMemberNames, getMemberOrders, getMemberTypes, getSelectedMemberCount, getSelectedMemberNames, getSelectedMemberOrders, getSelectedMemberTypes, isMemberSelected, resetSelection, selectMember, setAllMemberSelectionMethods inherited from class hdf.object.Dataset
byteToString, clearData, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDepth, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSpaceType, getStartDims, getStorage, getStorageLayout, getStride, getWidth, isInited, isScalar, setConvertByteToString, setData, stringToByte, toString, toString, writeMethods inherited from class hdf.object.HObject
createFullname, debug, equals, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, hashCode, setFullname, setLinkTargetObjName, setPath, toStringMethods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, waitMethods inherited from interface hdf.object.DataFormat
clearData, getCompression, getData, getDepth, getDims, getHeight, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSpaceType, getStartDims, getStride, getWidth, isInited, setData, write
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Constructor Details
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H5CompoundDS
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/".
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H5CompoundDS
Deprecated.Not for public use in the future.
UsingH5CompoundDS(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.
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Method Details
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open
Description copied from class:HObjectOpens 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:
openin classHObject- Returns:
- the object identifier if successful; otherwise returns a negative value.
- See Also:
HObject.close(long)
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close
Description copied from class:HObjectCloses 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. -
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();- Specified by:
initin interfaceDataFormat
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hasAttribute
Check if the object has any attributes attached.- Specified by:
hasAttributein interfaceMetaDataContainer- Returns:
- true if it has any attributes, false otherwise.
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getDatatype
Returns the datatype of the data object.- Specified by:
getDatatypein interfaceDataFormat- Overrides:
getDatatypein classDataset- Returns:
- the datatype of the data object.
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clear
Removes all of the elements from metadata list. The list should be empty after this call returns.- Specified by:
clearin interfaceMetaDataContainer- Overrides:
clearin classDataset
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readBytes
Description copied from class:DatasetReads 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. -
read
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. How to Select a Subset A selection is specified by three arrays: start, stride and count.- start: offset of a selection
- stride: determines how many elements to move in each dimension
- count: number of elements to select in each dimension
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 // dataset 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.getData() is called, the selection above will be used // since // the dimension arrays are passed by reference. Changes of these arrays // outside the dataset object directly change the values of these array // in the dataset object.For CompoundDS, the memory data object is an java.util.List object. Each element of the list is a data array that corresponds to a compound field. For example, if compound dataset "comp" has the following nested structure, and member datatypescomp --> m01 (int) comp --> m02 (float) comp --> nest1 --> m11 (char) comp --> nest1 --> m12 (String) comp --> nest1 --> nest2 --> m21 (long) comp --> nest1 --> nest2 --> m22 (double)
getData() returns a list of six arrays: {int[], float[], char[], String[], long[] and double[]}.- Specified by:
readin interfaceDataFormat- Returns:
- the data read from file.
- Throws:
Exception- if object can not be read- See Also:
Dataset.getData(),DataFormat.read()
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write
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.- Specified by:
writein interfaceDataFormat- Parameters:
buf- The vector that contains the data values of compound fields.- Throws:
Exception- If there is an error at the HDF5 library level.
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convertByteMember
Description copied from class:CompoundDSRoutine to convert datatypes that are read in as byte arrays to regular types.- Overrides:
convertByteMemberin classCompoundDS- Parameters:
dtype- the datatype to convert tobyteData- the bytes to convert- Returns:
- the converted object
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convertFromUnsignedC
Converts the data values of this data object to appropriate Java integers if they are unsigned integers.- Specified by:
convertFromUnsignedCin interfaceDataFormat- Returns:
- the converted data buffer.
- See Also:
Dataset.convertToUnsignedC(Object),Dataset.convertFromUnsignedC(Object, Object)
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convertToUnsignedC
Converts Java integer data values of this data object back to unsigned C-type integer data if they are unsigned integers.- Specified by:
convertToUnsignedCin interfaceDataFormat- Returns:
- the converted data buffer.
- See Also:
Dataset.convertToUnsignedC(Object),Dataset.convertToUnsignedC(Object, Object)
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getMetadata
Retrieves the object's metadata, such as attributes, from the file. Metadata, such as attributes, is stored in a List.- Specified by:
getMetadatain interfaceMetaDataContainer- Returns:
- the list of metadata objects.
- Throws:
hdf.hdf5lib.exceptions.HDF5Exception- if the metadata can not be retrieved
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getMetadata
public List<Attribute> getMetadata(int... attrPropList) throws hdf.hdf5lib.exceptions.HDF5ExceptionRetrieves 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:
hdf.hdf5lib.exceptions.HDF5Exception- if the metadata can not be retrieved
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writeMetadata
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:
writeMetadatain interfaceMetaDataContainer- Parameters:
info- the metadata to write.- Throws:
Exception- if the metadata can not be written
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removeMetadata
Deletes an existing piece of metadata from this object.- Specified by:
removeMetadatain interfaceMetaDataContainer- Parameters:
info- the metadata to delete.- Throws:
hdf.hdf5lib.exceptions.HDF5Exception- if the metadata can not be removed
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updateMetadata
Updates an existing piece of metadata attached to this object.- Specified by:
updateMetadatain interfaceMetaDataContainer- Parameters:
info- the metadata to update.- Throws:
hdf.hdf5lib.exceptions.HDF5Exception- if the metadata can not be updated
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setName
Description copied from class:HObjectSets the name of the object. setName (String newName) changes the name of the object in the file. -
create
@Deprecated public static Dataset create(String name, Group pgroup, long[] dims, String[] memberNames, Datatype[] memberDatatypes, int[] memberSizes, Object data) throws ExceptionDeprecated.Not for public use in the future.
Usingcreate(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 datatypememberDatatypes- the datatypes of the compound datatypememberSizes- the dim sizes of the membersdata- 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.
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create
@Deprecated public static Dataset create(String name, Group pgroup, long[] dims, String[] memberNames, Datatype[] memberDatatypes, int[] memberRanks, long[][] memberDims, Object data) throws ExceptionDeprecated.Not for public use in the future.
Usingcreate(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 datatypememberDatatypes- the datatypes of the compound datatypememberRanks- the ranks of the membersmemberDims- the dim sizes of the membersdata- 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.
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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 ExceptionCreates 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, Datatype.NATIVE, Datatype.NATIVE); mdtypes[1] = new H5Datatype(Datatype.CLASS_FLOAT, 4, Datatype.NATIVE, Datatype.NATIVE); mdtypes[2] = new H5Datatype(Datatype.CLASS_STRING, STR_LEN, Datatype.NATIVE, Datatype.NATIVE); 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 datatypememberDatatypes- the datatypes of the compound datatypememberRanks- the ranks of the membersmemberDims- the dim sizes of the membersdata- 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.
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isString
Description copied from class:DatasetChecks if a given datatype is a string. Sub-classes must replace this default implementation. -
getSize
Description copied from class:DatasetReturns the size in bytes of a given datatype. Sub-classes must replace this default implementation. -
isVirtual
Description copied from class:DatasetChecks if dataset is virtual. Sub-classes must replace this default implementation. -
getVirtualFilename
Description copied from class:DatasetGets the source file name at index if dataset is virtual. Sub-classes must replace this default implementation.- Overrides:
getVirtualFilenamein classDataset- Parameters:
index- index of the source file name if dataset is virtual.- Returns:
- filename if the dataset is virtual; otherwise returns null.
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getVirtualMaps
Description copied from class:DatasetGets the number of source files if dataset is virtual. Sub-classes must replace this default implementation.- Overrides:
getVirtualMapsin classDataset- Returns:
- the list size if the dataset is virtual; otherwise returns negative.
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Using
H5CompoundDS(FileFormat, String, String)