Module org.hdfgroup.object
Package hdf.object.h5

Class H5ScalarAttr

Object
hdf.object.HObject
hdf.object.Dataset
hdf.object.ScalarDS
hdf.object.h5.H5ScalarAttr
All Implemented Interfaces:
Attribute, DataFormat, H5Attribute, Serializable
public class H5ScalarAttr extends ScalarDS implements H5Attribute
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 H5ScalarAttr(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.
Version:
1.0 6/15/2021
Author:
Allen Byrne
See Also:

  • Field Details

    • parentObject

      protected HObject parentObject
      The HObject to which this NC2Attribute is attached, Attribute interface

    • isNativeDatatype

      protected boolean isNativeDatatype
      flag to indicate if the datatype in file is the same as dataype in memory

  • Constructor Details

    • H5ScalarAttr

      public H5ScalarAttr(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 H5ScalarAttr(attrName, attrType, attrDims);
 attr.setValue(classValue);
      Parameters:
      parentObj - the HObject to which this H5ScalarAttr 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:

    • H5ScalarAttr

      public H5ScalarAttr(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 H5ScalarAttr(attrName, attrType, attrDims, classValue);
      Parameters:
      parentObj - the HObject to which this H5ScalarAttr 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:

  • Method Details

    • 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:

    • 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.

    • init

      public void 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.
      Specified by:
      init in interface DataFormat

    • getDatatype

      public Datatype getDatatype()
      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.

    • getData

      public Object getData() throws Exception, OutOfMemoryError
      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.
      1. start: offset of a selection
      2. stride: determines how many elements to move in each dimension
      3. count: number of elements to select in each dimension
      getStartDims(), getStride() and getSelectedDims() returns the start, stride and count arrays respectively. Applications can make a selection by changing the values of the arrays. The following example shows how to make a subset. In the example, the attribute is a 4-dimensional array of [200][100][50][10], i.e. dims[0]=200; dims[1]=100; dims[2]=50; dims[3]=10;
      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 H5ScalarAttr.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 H5ScalarAttr, the memory data buffer is a one-dimensional array of byte, short, int, float, double or String type based on the datatype of the attribute.
      Specified by:
      getData in interface DataFormat
      Overrides:
      getData in class Dataset
      Returns:
      the memory buffer of the attribute.
      Throws:
      Exception - if object can not be read
      OutOfMemoryError - if memory is exhausted

    • copy

      public Dataset copy(Group pgroup, String dstName, long[] dims, Object buff) 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.
      dstName - the name of the new dataset.
      dims - the dimension sizes of the the new dataset.
      buff - the data values of the subset to be copied.
      Returns:
      the new dataset.
      Throws:
      Exception - if dataset can not be copied

    • 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
      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 ScalarAttr, the memory data buffer is a one-dimensional array of byte, short, int, float, double or String type based on the datatype of the attribute.
      Specified by:
      read in interface DataFormat
      Returns:
      the data read from file.
      Throws:
      Exception - if object can not be read
      See Also:

    • write

      public void write(Object buf) throws Exception
      Writes the given data buffer into this attribute in a file.
      Specified by:
      write in interface DataFormat
      Parameters:
      buf - The buffer that contains the data values.
      Throws:
      Exception - If there is an error at the HDF5 library level.

    • getParentObject

      public HObject getParentObject()
      Returns the HObject to which this Attribute is currently "attached".
      Specified by:
      getParentObject in interface Attribute
      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".
      Specified by:
      setParentObject in interface Attribute
      Parameters:
      pObj - the new HObject to which this Attribute is "attached".

    • setProperty

      public void setProperty(String key, Object value)
      set a property for the attribute.
      Specified by:
      setProperty in interface 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.
      Specified by:
      getProperty in interface Attribute
      Parameters:
      key - the attribute Map key
      Returns:
      the property

    • getPropertyKeys

      public Collection<String> getPropertyKeys()
      get all property keys.
      Specified by:
      getPropertyKeys in interface Attribute
      Returns:
      the Collection of property keys

    • getAttributeName

      public final String getAttributeName()
      Returns the name of the object. For example, "Raster Image #2".
      Specified by:
      getAttributeName in interface Attribute
      Returns:
      The name of the object.

    • getAttributeData

      public final Object getAttributeData() throws Exception, OutOfMemoryError
      Retrieves the attribute data from the file.
      Specified by:
      getAttributeData in interface Attribute
      Returns:
      the attribute data.
      Throws:
      Exception - if the data can not be retrieved
      OutOfMemoryError

    • getAttributeDatatype

      public final Datatype getAttributeDatatype()
      Returns the datatype of the attribute.
      Specified by:
      getAttributeDatatype in interface Attribute
      Returns:
      the datatype of the attribute.

    • getAttributeSpaceType

      public final int 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 interface Attribute
      Returns:
      the space type for the attribute.

    • getAttributeRank

      public final int 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 interface Attribute
      Returns:
      the number of dimensions of the attribute.

    • getAttributePlane

      public final int 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 interface Attribute
      Returns:
      the selected size of the rows and colums of the attribute.

    • getAttributeDims

      public final long[] 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 interface Attribute
      Returns:
      the dimension sizes of the attribute.

    • isAttributeScalar

      public boolean isAttributeScalar()
      Specified by:
      isAttributeScalar in interface Attribute
      Returns:
      true if the data is a single scalar point; otherwise, returns false.

    • setAttributeData

      public void setAttributeData(Object d)
      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 interface Attribute
      Parameters:
      d - the object data -must be an array of Objects

    • writeAttribute

      public void writeAttribute() throws Exception
      Writes the memory buffer of this dataset to file.
      Specified by:
      writeAttribute in interface Attribute
      Throws:
      Exception - if buffer can not be written

    • writeAttribute

      public void writeAttribute(Object buf) throws Exception
      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 interface Attribute
      Parameters:
      buf - The vector that contains the data values of compound fields.
      Throws:
      Exception - If there is an error at the library level.

    • toAttributeString

      public String toAttributeString(String delimiter)
      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 interface Attribute
      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.

    • toAttributeString

      public String toAttributeString(String delimiter, int maxItems)
      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 interface Attribute
      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.

    • 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 interface H5Attribute
      Parameters:
      attr_id - the attribute to access
      ioType - the type of IO operation
      objBuf - the data buffer to use for write operation
      Returns:
      the attribute data
      Throws:
      Exception - if the data can not be retrieved

    • AttributeSelection

      public Object AttributeSelection() throws Exception
      Read a subset of an attribute for hdf5 object data.
      Specified by:
      AttributeSelection in interface H5Attribute
      Returns:
      the selected attribute data
      Throws:
      Exception - if the data can not be retrieved