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

Class H5ScalarDS

Object
hdf.object.HObject
hdf.object.Dataset
hdf.object.ScalarDS
hdf.object.h5.H5ScalarDS
All Implemented Interfaces:
DataFormat, MetaDataContainer, Serializable
public class H5ScalarDS extends ScalarDS
H5ScalarDS describes a multi-dimension array of HDF5 scalar or atomic data types, such as byte, int, short, long, float, double and string, and operations performed on the scalar dataset.

The library predefines a modest number of datatypes. For details, read HDF5 Datatypes

Version:
1.1 9/4/2007
Author:
Peter X. Cao
See Also:
Serialized Form

  • Constructor Details

    • H5ScalarDS

      public H5ScalarDS​(FileFormat theFile, String theName, String thePath)
      Constructs an instance of a H5 scalar dataset with given file, dataset name and path.

      For example, in H5ScalarDS(h5file, "dset", "/arrays/"), "dset" is the name of the dataset, "/arrays" is the group path of the dataset.

      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/".

    • H5ScalarDS

      @Deprecated public H5ScalarDS​(FileFormat theFile, String theName, String thePath, long[] oid)
      Deprecated.
      Not for public use in the future.
      Using H5ScalarDS(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.

  • 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:
      HObject.close(long)

    • close

      public void close​(long did)
      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:
      did - The object identifier.

    • init

      public void 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();

    • hasAttribute

      public boolean hasAttribute()
      Description copied from interface: MetaDataContainer
      Check if the object has any attributes attached.
      Returns:
      true if it has any attributes, false otherwise.

    • getDatatype

      public Datatype getDatatype()
      Description copied from interface: DataFormat
      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.

    • clear

      public void clear()
      Description copied from class: Dataset
      Clears memory held by the dataset, such as the data buffer.
      Overrides:
      clear in class Dataset

    • 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 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.

      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 dataset 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 = 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 ScalarDS, the memory data buffer is a one-dimensional array of byte, short, int, float, double or String type based on the datatype of the dataset.

      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 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)
      getData() returns a list of six arrays: {int[], float[], char[], String[], long[] and double[]}.
      Returns:
      the data read from file.
      Throws:
      Exception - if object can not be read
      See Also:
      Dataset.getData(), DataFormat.read()

    • write

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

    • getMetadata

      public List<Attribute> getMetadata() throws hdf.hdf5lib.exceptions.HDF5Exception
      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.

      Returns:
      the list of metadata objects.
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception

    • getMetadata

      public List<Attribute> getMetadata​(int... attrPropList) throws hdf.hdf5lib.exceptions.HDF5Exception
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception

    • writeMetadata

      public void writeMetadata​(Object info) 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.
      Parameters:
      info - the metadata to write.
      Throws:
      Exception - if the metadata can not be written

    • removeMetadata

      public void removeMetadata​(Object info) throws hdf.hdf5lib.exceptions.HDF5Exception
      Description copied from interface: MetaDataContainer
      Deletes an existing piece of metadata from this object.
      Parameters:
      info - the metadata to delete.
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception

    • updateMetadata

      public void updateMetadata​(Object info) throws hdf.hdf5lib.exceptions.HDF5Exception
      Description copied from interface: MetaDataContainer
      Updates an existing piece of metadata attached to this object.
      Parameters:
      info - the metadata to update.
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception

    • setName

      public void setName​(String newName) throws Exception
      Description copied from class: HObject
      Sets the name of the object. setName (String newName) changes the name of the object in the file.
      Overrides:
      setName in class HObject
      Parameters:
      newName - The new name of the object.
      Throws:
      Exception - if name is root or contains separator

    • create

      public static Dataset create​(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object data) throws Exception
      Throws:
      Exception

    • create

      public static Dataset create​(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object fillValue, Object data) throws Exception
      Creates a scalar dataset in a file with/without chunking and compression.

      The following example shows how to create a string dataset using this function. 

       H5File file = new H5File("test.h5", H5File.CREATE);
 int max_str_len = 120;
 Datatype strType = new H5Datatype(Datatype.CLASS_STRING, max_str_len, Datatype.NATIVE, Datatype.NATIVE);
 int size = 10000;
 long dims[] = { size };
 long chunks[] = { 1000 };
 int gzip = 9;
 String strs[] = new String[size];

 for (int i = 0; i < size; i++)
     strs[i] = String.valueOf(i);

 file.open();
 file.createScalarDS("/1D scalar strings", null, strType, dims, null, chunks, gzip, strs);

 try {
     file.close();
 }
 catch (Exception ex) {
 }
      Parameters:
      name - the name of the dataset to create.
      pgroup - parent group where the new dataset is created.
      type - the datatype of the dataset.
      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). No compression if gzip<=0.
      fillValue - the default data value.
      data - the array of data values.
      Returns:
      the new scalar dataset if successful; otherwise returns null.
      Throws:
      Exception - if there is a failure.

    • 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

    • getPalette

      public byte[][] getPalette()
      Description copied from class: ScalarDS
      Returns the palette of this scalar dataset or null if palette does not exist.

      A Scalar dataset can be displayed as spreadsheet data or an image. When a scalar dataset is displayed as an image, the palette or color table may be needed to translate a pixel value to color components (for example, red, green, and blue). Some scalar datasets have no palette and some datasets have one or more than one palettes. If an associated palette exists but is not loaded, this interface retrieves the palette from the file and returns the palette. If the palette is loaded, it returns the palette. It returns null if there is no palette associated with the dataset.

      Current implementation only supports palette model of indexed RGB with 256 colors. Other models such as YUV", "CMY", "CMYK", "YCbCr", "HSV will be supported in the future.

      The palette values are stored in a two-dimensional byte array and are arranges by color components of red, green and blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue components respectively.

      Sub-classes have to implement this interface. HDF4 and HDF5 images use different libraries to retrieve the associated palette.

      Specified by:
      getPalette in class ScalarDS
      Returns:
      the 2D palette byte array.

    • getPaletteName

      public String getPaletteName​(int idx)
      Description copied from class: ScalarDS
      Get the name of a specific image palette from file.

      A scalar dataset may have multiple palettes attached to it. getPaletteName(int idx) returns the name of a specific palette identified by its index.

      Overrides:
      getPaletteName in class ScalarDS
      Parameters:
      idx - the index of the palette to retrieve the name.
      Returns:
      The name of the palette

    • readPalette

      public byte[][] readPalette​(int idx)
      Description copied from class: ScalarDS
      Reads a specific image palette from file.

      A scalar dataset may have multiple palettes attached to it. readPalette(int idx) returns a specific palette identified by its index.

      Specified by:
      readPalette in class ScalarDS
      Parameters:
      idx - the index of the palette to read.
      Returns:
      the image palette

    • getPaletteRefs

      public byte[] getPaletteRefs()
      Description copied from class: ScalarDS
      Returns the byte array of palette refs.

      A palette reference is an object reference that points to the palette dataset.

      For example, Dataset "Iceberg" has an attribute of object reference "Palette". The arrtibute "Palette" has value "2538" that is the object reference of the palette data set "Iceberg Palette".

      Specified by:
      getPaletteRefs in class ScalarDS
      Returns:
      null if there is no palette attribute attached to this dataset.

    • extend

      public void extend​(long[] newDims) throws hdf.hdf5lib.exceptions.HDF5Exception
      H5Dset_extent verifies that the dataset is at least of size size, extending it if necessary. The dimensionality of size is the same as that of the dataspace of the dataset being changed. This function can be applied to the following datasets: 1) Any dataset with unlimited dimensions 2) A dataset with fixed dimensions if the current dimension sizes are less than the maximum sizes set with maxdims (see H5Screate_simple)
      Parameters:
      newDims - the dimension target size
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception - If there is an error at the HDF5 library level.

    • isVirtual

      public boolean isVirtual()
      Overrides:
      isVirtual in class Dataset

    • getVirtualFilename

      public String getVirtualFilename​(int index)
      Overrides:
      getVirtualFilename in class Dataset

    • getVirtualMaps

      public int getVirtualMaps()
      Overrides:
      getVirtualMaps in class Dataset