Object
hdf.object.HObject
hdf.object.Dataset
hdf.object.CompoundDS
hdf.object.h5.H5CompoundAttr
- All Implemented Interfaces:
Attribute
,CompoundDataFormat
,DataFormat
,H5Attribute
,Serializable
The H5CompoundAttr class defines an HDF5 attribute of compound datatypes.
An attribute is a (name, value) pair of metadata attached to a primary data object such as a dataset, group
or named datatype.
Like a dataset, an attribute has a name, datatype and dataspace.
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 attributes and datatypes, read the
HDF5 Attributes in HDF5 User
Guide
There are two basic types of compound attributes: simple compound data and nested compound data. Members of
a simple compound attribute have atomic datatypes. Members of a nested compound attribute 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:
- 1.0 6/15/2021
- Author:
- Allen Byrne
- See Also:
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Field Summary
Modifier and TypeFieldDescriptionprotected HObject
The HObject to which this NC2Attribute is attached, Attribute interfaceFields inherited from class hdf.object.CompoundDS
flatNameList, flatTypeList, 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, isImage, isNULL, isScalar, isText, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, space_type, startDims, storage, storageLayout
Fields inherited from class hdf.object.HObject
fileFormat, linkTargetObjName, oid
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Constructor Summary
ConstructorDescriptionH5CompoundAttr
(HObject parentObj, String attrName, Datatype attrType, long[] attrDims) Create an attribute with specified name, data type and dimension sizes.H5CompoundAttr
(HObject parentObj, String attrName, Datatype attrType, long[] attrDims, Object attrValue) Create an attribute with specific name and value. -
Method Summary
Modifier and TypeMethodDescriptionAttributeCommonIO
(long attr_id, H5File.IO_TYPE ioType, Object objBuf) The general read and write attribute operations for hdf5 object data.Read a subset of an attribute for hdf5 object data.void
close
(long aid) Closes access to the object.protected Object
convertByteMember
(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.final Object
Retrieves the attribute data from the file.final Datatype
Returns the datatype of the attribute.final long[]
Returns the array that contains the dimension sizes of the data value of the attribute.final String
Returns the name of the object.final int
Returns the selected size of the rows and columns of the attribute.final int
Returns the rank (number of dimensions) of the attribute.final int
Returns the space type for the attribute.getData()
Returns the data buffer of the attribute in memory.Returns the datatype of the data object.Returns the HObject to which this Attribute is currently "attached".getProperty
(String key) get a property for a given key.get all property keys.void
init()
Retrieves datatype and dataspace information from file and sets the attribute in memory.boolean
Check if attribute's dataspace is a NULLboolean
Check if attribute is a single scalar pointlong
open()
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.void
Not for public use in the future.void
setParentObject
(HObject pObj) Sets the HObject to which this Attribute is "attached".void
setProperty
(String key, Object value) set a property for the attribute.toAttributeString
(String delimiter) Returns a string representation of the data value.toAttributeString
(String delimiter, int maxItems) Returns a string representation of the data value.protected String
Returns a string representation of the dataset object.void
Writes the given data buffer into this attribute in a file.void
Writes the memory buffer of this dataset to file.void
writeAttribute
(Object buf) Writes the given data buffer into this attribute in a file.Methods inherited from class hdf.object.CompoundDS
convertCompoundByteMembers, copy, getFillValue, getMemberCount, getMemberDims, getMemberNames, getMemberOrders, getMemberTypes, getSelectedMemberCount, getSelectedMemberNames, getSelectedMemberOrders, getSelectedMemberTypes, isMemberSelected, resetSelection, selectMember, setAllMemberSelection
Methods inherited from class hdf.object.Dataset
byteToString, clear, clearData, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getDepth, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getSpaceType, getStartDims, getStorage, getStorageLayout, getStride, getVirtualFilename, getVirtualMaps, getWidth, isInited, isNULL, isScalar, isString, isVirtual, refreshData, setConvertByteToString, setData, stringToByte, 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.DataFormat
clearData, getCompression, getDepth, getDims, getHeight, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSpaceType, getStartDims, getStride, getWidth, isInited, refreshData, setData, write
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Field Details
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parentObject
The HObject to which this NC2Attribute is attached, Attribute interface
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Constructor Details
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H5CompoundAttr
Create an attribute with specified name, data type and dimension sizes.- Parameters:
parentObj
- the HObject to which this H5CompoundAttr is attached.attrName
- the name of the attribute.attrType
- the datatype of the attribute.attrDims
- the dimension sizes of the attribute, null for scalar attribute- See Also:
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H5CompoundAttr
public H5CompoundAttr(HObject parentObj, String attrName, Datatype attrType, long[] attrDims, Object attrValue) Create an attribute with specific name and value.- Parameters:
parentObj
- the HObject to which this H5CompoundAttr is attached.attrName
- the name of the attribute.attrType
- the datatype of the attribute.attrDims
- the dimension sizes of the attribute, null for scalar attributeattrValue
- the value of the attribute, null if no value- See Also:
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Method Details
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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. -
close
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. -
init
Retrieves datatype and dataspace information from file and sets the attribute in memory. The init() is designed to support lazy operation in a attribute 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 attribute (start, stride and count) to the default, which is the entire attribute 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 attribute. getData() at step 4) reads the values of whole attribute into memory.dset = (Dataset) file.get(NAME_DATASET); // 1) get datatype and dataspace information from file attr.init(); rank = attr.getAttributeRank(); // rank = 2, a 2D attribute count = attr.getSelectedDims(); start = attr.getStartDims(); dims = attr.getAttributeDims(); // 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 = attr.getAttributeData(); // 4) reset selection to the whole attribute attr.init(); // 5) clean the memory data buffer attr.clearData(); // 6) Read the whole attribute data = attr.getAttributeData();
- Specified by:
init
in interfaceDataFormat
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getDatatype
Returns the datatype of the data object.- Specified by:
getDatatype
in interfaceDataFormat
- Overrides:
getDatatype
in classDataset
- Returns:
- the datatype of the data object.
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getData
Returns the data buffer of the attribute in memory. If data is already loaded into memory, returns the data; otherwise, calls read() to read data from file into a memory buffer and returns the memory buffer. The whole attribute is read into memory. Users can also select a subset from the whole data. 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 = attribute.getRank(); // number of dimensions of the attribute long[] dims = attribute.getDims(); // the dimension sizes of the attribute long[] selected = attribute.getSelectedDims(); // the selected size of the attribute long[] start = attribute.getStartDims(); // the offset of the selection long[] stride = attribute.getStride(); // the stride of the attribute int[] selectedIndex = attribute.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[2] = 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 H5CompoundAttr.getData() is called, the selection above will be used since // the dimension arrays are passed by reference. Changes of these arrays // outside the attribute object directly change the values of these array // in the attribute object.
For H5CompoundAttr, 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 attribute "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:
getData
in interfaceDataFormat
- Overrides:
getData
in classDataset
- Returns:
- the memory buffer of the attribute.
- Throws:
Exception
- if object can not be readOutOfMemoryError
- if memory is exhausted
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readBytes
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. -
read
Reads the data from file. read() reads the data from file to a memory buffer and returns the memory buffer. The attribute object does not hold the memory buffer. To store the memory buffer in the attribute object, one must call getData(). By default, the whole attribute is read into memory. For CompoundAttr, 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:
read
in interfaceDataFormat
- Returns:
- the data read from file.
- Throws:
Exception
- if object can not be read- See Also:
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write
Writes the given data buffer into this attribute in a file. The data buffer is a vector that contains the data values of compound fields. The data is written into file as one data blob.- Specified by:
write
in 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:CompoundDS
Routine to convert datatypes that are read in as byte arrays to regular types.- Overrides:
convertByteMember
in 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:
convertFromUnsignedC
in interfaceDataFormat
- Returns:
- the converted data buffer.
- See Also:
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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:
convertToUnsignedC
in interfaceDataFormat
- Returns:
- the converted data buffer.
- See Also:
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getParentObject
Returns the HObject to which this Attribute is currently "attached".- Specified by:
getParentObject
in interfaceAttribute
- Returns:
- the HObject to which this Attribute is currently "attached".
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setParentObject
Sets the HObject to which this Attribute is "attached".- Specified by:
setParentObject
in interfaceAttribute
- Parameters:
pObj
- the new HObject to which this Attribute is "attached".
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setProperty
set a property for the attribute.- Specified by:
setProperty
in interfaceAttribute
- Parameters:
key
- the attribute Map keyvalue
- the attribute Map value
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getProperty
get a property for a given key.- Specified by:
getProperty
in interfaceAttribute
- Parameters:
key
- the attribute Map key- Returns:
- the property
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getPropertyKeys
get all property keys.- Specified by:
getPropertyKeys
in interfaceAttribute
- Returns:
- the Collection of property keys
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getAttributeName
Returns the name of the object. For example, "Raster Image #2".- Specified by:
getAttributeName
in interfaceAttribute
- Returns:
- The name of the object.
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getAttributeData
Retrieves the attribute data from the file.- Specified by:
getAttributeData
in interfaceAttribute
- Returns:
- the attribute data.
- Throws:
Exception
- if the data can not be retrievedOutOfMemoryError
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getAttributeDatatype
Returns the datatype of the attribute.- Specified by:
getAttributeDatatype
in interfaceAttribute
- Returns:
- the datatype of the attribute.
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getAttributeSpaceType
Returns the space type for the attribute. It returns a negative number if it failed to retrieve the type information from the file.- Specified by:
getAttributeSpaceType
in interfaceAttribute
- Returns:
- the space type for the attribute.
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getAttributeRank
Returns the rank (number of dimensions) of the attribute. It returns a negative number if it failed to retrieve the dimension information from the file.- Specified by:
getAttributeRank
in interfaceAttribute
- Returns:
- the number of dimensions of the attribute.
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getAttributePlane
Returns the selected size of the rows and columns of the attribute. It returns a negative number if it failed to retrieve the size information from the file.- Specified by:
getAttributePlane
in interfaceAttribute
- Returns:
- the selected size of the rows and colums of the attribute.
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getAttributeDims
Returns the array that contains the dimension sizes of the data value of the attribute. It returns null if it failed to retrieve the dimension information from the file.- Specified by:
getAttributeDims
in interfaceAttribute
- Returns:
- the dimension sizes of the attribute.
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isAttributeNULL
Description copied from interface:Attribute
Check if attribute's dataspace is a NULL- Specified by:
isAttributeNULL
in interfaceAttribute
- Returns:
- true if the dataspace is a NULL; otherwise, returns false.
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isAttributeScalar
Description copied from interface:Attribute
Check if attribute is a single scalar point- Specified by:
isAttributeScalar
in interfaceAttribute
- Returns:
- true if the data is a single scalar point; otherwise, returns false.
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setAttributeData
Not for public use in the future. setData() is not safe to use because it changes memory buffer of the dataset object. Dataset operations such as write/read will fail if the buffer type or size is changed.- Specified by:
setAttributeData
in interfaceAttribute
- Parameters:
d
- the object data -must be an array of Objects
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writeAttribute
Writes the memory buffer of this dataset to file.- Specified by:
writeAttribute
in interfaceAttribute
- Throws:
Exception
- if buffer can not be written
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writeAttribute
Writes the given data buffer into this attribute in a file. The data buffer is a vector that contains the data values of compound fields. The data is written into file as one data blob.- Specified by:
writeAttribute
in interfaceAttribute
- Parameters:
buf
- The vector that contains the data values of compound fields.- Throws:
Exception
- If there is an error at the library level.
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toAttributeString
Returns a string representation of the data value. For example, "0, 255". For a compound datatype, it will be a 1D array of strings with field members separated by the delimiter. For example, "{0, 10.5}, {255, 20.0}, {512, 30.0}" is a compound attribute of {int, float} of three data points.- Specified by:
toAttributeString
in interfaceAttribute
- Parameters:
delimiter
- The delimiter used to separate individual data points. It can be a comma, semicolon, tab or space. For example, toString(",") will separate data by commas.- Returns:
- the string representation of the data values.
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toAttributeString
Returns a string representation of the data value. For example, "0, 255". For a compound datatype, it will be a 1D array of strings with field members separated by the delimiter. For example, "{0, 10.5}, {255, 20.0}, {512, 30.0}" is a compound attribute of {int, float} of three data points.- Specified by:
toAttributeString
in interfaceAttribute
- Parameters:
delimiter
- The delimiter used to separate individual data points. It can be a comma, semicolon, tab or space. For example, toString(",") will separate data by commas.maxItems
- The maximum number of Array values to return- Returns:
- the string representation of the data values.
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toString
Description copied from class:Dataset
Returns a string representation of the dataset object.- Overrides:
toString
in classDataset
- Parameters:
theData
- The Object datatheType
- The type of the data in the Objectdelimiter
- The delimiter used to separate individual data points. It can be a comma, semicolon, tab or space. For example, toString(",") will separate data by commas.count
- The maximum number of Array values to return- Returns:
- the string representation of the dataset object.
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AttributeCommonIO
public Object AttributeCommonIO(long attr_id, H5File.IO_TYPE ioType, Object objBuf) throws Exception The general read and write attribute operations for hdf5 object data.- Specified by:
AttributeCommonIO
in interfaceH5Attribute
- Parameters:
attr_id
- the attribute to accessioType
- the type of IO operationobjBuf
- the data buffer to use for write operation- Returns:
- the attribute data
- Throws:
Exception
- if the data can not be retrieved
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AttributeSelection
Read a subset of an attribute for hdf5 object data.- Specified by:
AttributeSelection
in interfaceH5Attribute
- Returns:
- the selected attribute data
- Throws:
Exception
- if the data can not be retrieved
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