Package hdf.object

Class Attribute

  • All Implemented Interfaces:
    CompoundDataFormat, DataFormat, MetaDataContainer, Serializable
    public class Attribute
extends Dataset
implements DataFormat, CompoundDataFormat
    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.

    For more details on attributes, HDF5 User's Guide

    The following code is an example of an attribute with 1D integer array of two elements. 

     // Example of creating a new attribute
 // The name of the new attribute
 String name = "Data range";
 // Creating an unsigned 1-byte integer datatype
 Datatype type = new Datatype(Datatype.CLASS_INTEGER, // class
                              1,                      // size in bytes
                              Datatype.ORDER_LE,      // byte order
                              Datatype.SIGN_NONE);    // unsigned
 // 1-D array of size two
 long[] dims = {2};
 // The value of the attribute
 int[] value = {0, 255};
 // Create a new attribute
 Attribute dataRange = new Attribute(name, type, dims);
 // Set the attribute value
 dataRange.setValue(value);
 // See FileFormat.writeAttribute() for how to attach an attribute to an object,
 @see hdf.object.FileFormat#writeAttribute(HObject, Attribute, boolean)
    For an atomic datatype, the value of an Attribute will be a 1D array of integers, floats and strings. For a compound datatype, it will be a 1D array of strings with field members separated by a comma. For example, "{0, 10.5}, {255, 20.0}, {512, 30.0}" is a compound attribute of {int, float} of three data points.
    Version:
    2.0 4/2/2018
    Author:
    Peter X. Cao, Jordan T. Henderson
    See Also:
    Datatype, Serialized Form

    • Field Detail

      • unsignedConverted

        protected boolean unsignedConverted
        Flag to indicate is the original unsigned C data is converted.

      • isScalar

        protected final boolean isScalar
        Flag to indicate if the attribute data is a single scalar point

      • numberOfMembers

        protected int numberOfMembers
        The number of members of the compound attribute.

      • memberNames

        protected String[] memberNames
        The names of the members of the compound attribute.

      • memberOrders

        protected int[] memberOrders
        Array containing the total number of elements of the members of this compound attribute.

        For example, a compound attribute 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.

      • 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.

      • memberTypes

        protected Datatype[] memberTypes
        The datatypes of the compound attribute's members.

      • isMemberSelected

        protected boolean[] isMemberSelected
        The array to store flags to indicate if a member of this compound attribute 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 attribute. 

         For example, if a compound attribute 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.

    • Constructor Detail

      • Attribute

        public Attribute​(HObject parentObj,
                 String attrName,
                 Datatype attrType,
                 long[] attrDims)
        Create an attribute with specified name, data type and dimension sizes. For scalar attribute, the dimension size can be either an array of size one or null, and the rank can be either 1 or zero. Attribute is a general class and is independent of file format, e.g., the implementation of attribute applies to both HDF4 and HDF5.

        The following example creates a string attribute with the name "CLASS" and value "IMAGE". 

         long[] attrDims = { 1 };
 String attrName = "CLASS";
 String[] classValue = { "IMAGE" };
 Datatype attrType = null;
 try {
     attrType = new H5Datatype(Datatype.CLASS_STRING, classValue[0].length() + 1, Datatype.NATIVE, Datatype.NATIVE);
 }
 catch (Exception ex) {}
 Attribute attr = new Attribute(attrName, attrType, attrDims);
 attr.setValue(classValue);
        Parameters:
        parentObj - the HObject to which this Attribute 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:
        Datatype

      • Attribute

        public Attribute​(HObject parentObj,
                 String attrName,
                 Datatype attrType,
                 long[] attrDims,
                 Object attrValue)
        Create an attribute with specific name and value. For scalar attribute, the dimension size can be either an array of size one or null, and the rank can be either 1 or zero. Attribute is a general class and is independent of file format, e.g., the implementation of attribute applies to both HDF4 and HDF5.

        The following example creates a string attribute with the name "CLASS" and value "IMAGE". 

         long[] attrDims = { 1 };
 String attrName = "CLASS";
 String[] classValue = { "IMAGE" };
 Datatype attrType = null;
 try {
     attrType = new H5Datatype(Datatype.CLASS_STRING, classValue[0].length() + 1, Datatype.NATIVE, Datatype.NATIVE);
 }
 catch (Exception ex) {}
 Attribute attr = new Attribute(attrName, attrType, attrDims, classValue);
        Parameters:
        parentObj - the HObject to which this Attribute 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
        attrValue - the value of the attribute, null if no value
        See Also:
        Datatype

    • 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 aid)
        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:
        aid - The object identifier.

      • getParentObject

        public HObject getParentObject()
        Returns the HObject to which this Attribute is currently "attached".
        Returns:
        the HObject to which this Attribute is currently "attached".

      • setParentObject

        public void setParentObject​(HObject pObj)
        Sets the HObject to which this Attribute is "attached".
        Parameters:
        pObj - the new HObject to which this Attribute is "attached".

      • getFillValue

        public Object getFillValue()
        Description copied from interface: DataFormat
        Returns the fill values for the data object.
        Specified by:
        getFillValue in interface DataFormat
        Returns:
        the fill values for the data object.

      • clearData

        public void clearData()
        Description copied from class: Dataset
        Clears the current data buffer in memory and forces the next read() to load the data from file.

        The function read() loads data from file into memory only if the data is not read. If data is already in memory, read() just returns the memory buffer. Sometimes we want to force read() to re-read data from file. For example, when the selection is changed, we need to re-read the data.

        Specified by:
        clearData in interface DataFormat
        Overrides:
        clearData in class Dataset
        See Also:
        Dataset.getData(), DataFormat.read()

      • setProperty

        public void setProperty​(String key,
                        Object value)
        set a property for the attribute.
        Parameters:
        key - the attribute Map key
        value - the attribute Map value

      • getProperty

        public Object getProperty​(String key)
        get a property for a given key.
        Parameters:
        key - the attribute Map key
        Returns:
        the property

      • getPropertyKeys

        public Collection<String> getPropertyKeys()
        get all property keys.
        Returns:
        the Collection of property keys

      • isScalar

        public boolean isScalar()
        Returns:
        true if the data is a single scalar point; otherwise, returns false.

      • read

        public Object read()
            throws Exception,
                   OutOfMemoryError
        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.

        Specified by:
        read in interface DataFormat
        Returns:
        the data read from file.
        Throws:
        Exception - if object can not be read
        OutOfMemoryError - if memory is exhausted
        See Also:
        DataFormat.getData()

      • write

        public void write​(Object buf)
           throws Exception
        Description copied from interface: DataFormat
        Writes a memory buffer to the object in the file.
        Specified by:
        write in interface DataFormat
        Parameters:
        buf - the data to write
        Throws:
        Exception - if data can not be written

      • getSelectedMemberCount

        public int getSelectedMemberCount()
        Returns the number of selected members of the compound attribute. 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 attribute. In this case, getSelectedMemberCount() returns two.

        Specified by:
        getSelectedMemberCount in interface CompoundDataFormat
        Returns:
        the number of selected members.

      • getMemberNames

        public String[] getMemberNames()
        Returns the names of the members of the compound attribute. 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 interface CompoundDataFormat
        Returns:
        the names of compound members.

      • isMemberSelected

        public boolean isMemberSelected​(int idx)
        Checks if a member of the compound attribute is selected for read/write.
        Specified by:
        isMemberSelected in interface CompoundDataFormat
        Parameters:
        idx - the index of compound member.
        Returns:
        true if the i-th memeber is selected; otherwise returns false.

      • setAllMemberSelection

        public void setAllMemberSelection​(boolean selectAll)
        Selects/deselects all members.
        Specified by:
        setAllMemberSelection in interface CompoundDataFormat
        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.

      • getMemberOrders

        public int[] getMemberOrders()
        Returns array containing the total number of elements of the members of the compound attribute.

        For example, a compound attribute 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 interface CompoundDataFormat
        Returns:
        the array containing the total number of elements of the members of the compound attribute.

      • getSelectedMemberOrders

        public int[] getSelectedMemberOrders()
        Returns array containing the total number of elements of the selected members of the compound attribute.

        For example, a compound attribute 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 interface CompoundDataFormat
        Returns:
        array containing the total number of elements of the selected members of the compound attribute.

      • getMemberDims

        public int[] getMemberDims​(int i)
        Returns the dimension sizes of the i-th member.

        For example, a compound attribute 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 interface CompoundDataFormat
        Parameters:
        i - the i-th member
        Returns:
        the dimension sizes of the i-th member, null if the compound member is not an array.

      • getMemberTypes

        public Datatype[] getMemberTypes()
        Returns an array of datatype objects of compound members.

        Each member of a compound attribute has its own datatype. The datatype of a member can be atomic or other compound datatype (nested compound). The datatype objects are setup at init().

        Specified by:
        getMemberTypes in interface CompoundDataFormat
        Returns:
        the array of datatype objects of the compound members.

      • getMetadata

        public List getMetadata()
                 throws Exception
        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.

        Specified by:
        getMetadata in interface MetaDataContainer
        Returns:
        the list of metadata objects.
        Throws:
        Exception - if the metadata can not be retrieved

      • writeMetadata

        public void writeMetadata​(Object metadata)
                   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.
        Specified by:
        writeMetadata in interface MetaDataContainer
        Parameters:
        metadata - the metadata to write.
        Throws:
        Exception - if the metadata can not be written

      • removeMetadata

        public void removeMetadata​(Object metadata)
                    throws Exception
        Description copied from interface: MetaDataContainer
        Deletes an existing piece of metadata from this object.
        Specified by:
        removeMetadata in interface MetaDataContainer
        Parameters:
        metadata - the metadata to delete.
        Throws:
        Exception - if the metadata can not be removed

      • updateMetadata

        public void updateMetadata​(Object metadata)
                    throws Exception
        Description copied from interface: MetaDataContainer
        Updates an existing piece of metadata attached to this object.
        Specified by:
        updateMetadata in interface MetaDataContainer
        Parameters:
        metadata - the metadata to update.
        Throws:
        Exception - if the metadata can not be updated

      • readBytes

        public byte[] readBytes()
                 throws Exception
        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:
        Exception - if data can not be read

      • copy

        public Dataset copy​(Group pgroup,
                    String name,
                    long[] dims,
                    Object data)
             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.
        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

      • equals

        public boolean equals​(Object obj)
        Returns whether this Attribute is equal to the specified HObject by comparing various properties.
        Overrides:
        equals in class HObject
        Parameters:
        obj - The object
        Returns:
        true if the object is equal

      • toString

        public String toString​(String delimiter)
        Returns a string representation of the data value of the attribute. 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.

        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.

      • toString

        public String toString​(String delimiter,
                       int maxItems)
        Returns a string representation of the data value of the attribute. 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.

        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.