ncsa.hdf.object.h4
Class H4SDS

java.lang.Object
  ncsa.hdf.object.HObject
      ncsa.hdf.object.Dataset
          ncsa.hdf.object.ScalarDS
              ncsa.hdf.object.h4.H4SDS

All Implemented Interfaces:

java.io.Serializable, DataFormat

public class H4SDS
extends ScalarDS

H4SDS describes HDF4 Scientific Data Sets (SDS) and operations performed on the SDS. A SDS, is a group of data structures used to store and describe multidimensional arrays of scientific data.

The data contained in an SDS array has a data type associated with it. The standard data types supported by the SD interface include 32- and 64-bit floating-point numbers, 8-, 16- and 32-bit signed integers, 8-, 16- and 32-bit unsigned integers, and 8-bit characters.

How to Select a Subset

Dataset defines APIs for read, write and subet a dataset. No function is defined to select a subset of a data array. The selection is done in an implicit way. Function calls to dimension information such as getSelectedDims() return an array of dimension values, which is a reference to the array in the dataset object. Changes of the array outside the dataset object directly change the values of the array in the dataset object. It is like pointers in C.

The following is an example of how to make a subset. In the example, the dataset is a 4-dimension with size 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 points in dims[1] and dims[2]

     int rank = dataset.getRank();   // number of dimension of the dataset
     long[] dims = dataset.getDims(); // the dimension sizes of the dataset
     long[] selected = dataset.getSelectedDims(); // the selected size of the dataet
     long[] start = dataset.getStartDims(); // the off set 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

 





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






Field Summary




static int
DFTAG_NDG_NETCDF



          tag for netCDF datasets.



static long
serialVersionUID



           


 
Fields inherited from class ncsa.hdf.object.ScalarDS
INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isFillValueConverted
 
Fields inherited from class ncsa.hdf.object.HObject
separator
 



Constructor Summary
H4SDS(FileFormat theFile,
      java.lang.String name,
      java.lang.String path)



           
H4SDS(FileFormat theFile,
      java.lang.String name,
      java.lang.String path,
      long[] oid)



          Creates an H4SDS object with specific name and path.
 



Method Summary




 void
close(int id)



          Closes access to the object.



 Dataset
copy(Group pgroup,
     java.lang.String dname,
     long[] dims,
     java.lang.Object buff)



          Creates a new dataset and writes the data buffer to the new dataset.



static H4SDS
create(java.lang.String name,
       Group pgroup,
       Datatype type,
       long[] dims,
       long[] maxdims,
       long[] chunks,
       int gzip,
       java.lang.Object data)



          Creates a new dataset.



 Datatype
getDatatype()



          Returns the datatype object of the dataset.



 java.util.List
getMetadata()



          Retrieves the metadata such as attributes from file.



 java.util.List
getMetadata(int... attrPropList)



           



 byte[][]
getPalette()



          Returns the palette of this scalar dataset or null if palette does not
 exist.



 byte[]
getPaletteRefs()



          Returns the byte array of palette refs.



 boolean
hasAttribute()



          Check if the object has any attributes attached.



 void
init()



          Initializes the H4SDS such as dimension size of this dataset.



 int
open()



          Opens an existing object such as dataset or group for access.



 java.lang.Object
read()



          Reads the data from file.



 byte[]
readBytes()



          Reads the raw data of the dataset from file to a byte array.



 byte[][]
readPalette(int idx)



          Reads a specific image palette from file.



 void
removeMetadata(java.lang.Object info)



          Deletes an existing metadata from this data object.



 void
write(java.lang.Object buf)



          Writes a memory buffer to the dataset in file.



 void
writeMetadata(java.lang.Object info)



          Writes a specific metadata (such as attribute) into file.


 
Methods inherited from class ncsa.hdf.object.ScalarDS
clearData, convertFromUnsignedC, convertToUnsignedC, getFillValue, getImageDataRange, getInterlace, getPaletteName, isDefaultImageOrder, isImage, isImageDisplay, isText, isTrueColor, isUnsigned, setIsImage, setIsImageDisplay, setPalette
 
Methods inherited from class ncsa.hdf.object.Dataset
byteToString, clear, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDimNames, getDims, getHeight, getMaxDims, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStride, getWidth, isEnumConverted, isString, setConvertByteToString, setData, setEnumConverted, stringToByte, write
 
Methods inherited from class ncsa.hdf.object.HObject
equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, setLinkTargetObjName, setName, setPath, toString
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 





Field Detail



serialVersionUID
public static final long serialVersionUID


See Also:
Constant Field Values




DFTAG_NDG_NETCDF
public static final int DFTAG_NDG_NETCDF

tag for netCDF datasets.
  HDF4 library supports netCDF version 2.3.2. It only supports SDS APIs.


See Also:
Constant Field Values





Constructor Detail



H4SDS
public H4SDS(FileFormat theFile,
             java.lang.String name,
             java.lang.String path)





H4SDS
public H4SDS(FileFormat theFile,
             java.lang.String name,
             java.lang.String path,
             long[] oid)

Creates an H4SDS object with specific name and path.
 



Parameters:
theFile - the HDF file.
name - the name of this H4SDS.
path - the full path of this H4SDS.
oid - the unique identifier of this data object.





Method Detail



hasAttribute
public boolean hasAttribute()

Description copied from interface: DataFormat
Check if the object has any attributes attached.



Returns:
true if it has any attribute(s), false otherwise.





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.





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.





getDatatype
public Datatype getDatatype()

Description copied from class: Dataset
Returns the datatype object of the dataset.


Specified by:
getDatatype in class Dataset



Returns:
the datatype object of the dataset.





copy
public Dataset copy(Group pgroup,
                    java.lang.String dname,
                    long[] dims,
                    java.lang.Object buff)
             throws java.lang.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.
dname - 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:
java.lang.Exception





readBytes
public byte[] readBytes()
                 throws HDFException

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 an one-dimension 32-bit integer dataset of
 size 5, the readBytes() returns of 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:
HDFException





read
public java.lang.Object read()
                      throws HDFException

Description copied from class: Dataset
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 memobry 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
 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: determining how many elements to move in each dimension
 
count: number of elements to select in each dimension
 
 getStartDims(), getStartDims() 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 dimension of the dataset
 long[] dims = dataset.getDims(); // the dimension sizes of the dataset
 long[] selected = dataset.getSelectedDims(); // the selected size of the dataet
 long[] start = dataset.getStartDims(); // the off set 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 points are 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 slection 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 an one-dimensional array of byte,
 short, int, float, double or String type based on the datatype of the
 dataset.
 

 For CompoundDS, the meory 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 memeber 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[],
 Stirng[], long[] and double[]}.


Specified by:
read in class Dataset



Returns:
the data read from file.
Throws:
HDFException
See Also:
#getData()}





write
public void write(java.lang.Object buf)
           throws HDFException

Description copied from class: Dataset
Writes a memory buffer to the dataset in file.


Specified by:
write in class Dataset


Parameters:
buf - the data to write
Throws:
HDFException





getMetadata
public java.util.List getMetadata()
                           throws HDFException

Description copied from interface: DataFormat
Retrieves the metadata such as attributes from file.
 

 Metadata such as attributes are stored in a List.



Returns:
the list of metadata objects.
Throws:
HDFException





writeMetadata
public void writeMetadata(java.lang.Object info)
                   throws java.lang.Exception

Description copied from interface: DataFormat
Writes a specific metadata (such as attribute) into file.
 
 

 If an HDF(4&5) attribute exists in file, the method updates its value. 
 If the attribute does not exists in file, it creates the attribute in 
 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 file, one needs to get 
 the instance of the attribute by getMetadata(), change its values, 
 and use writeMetadata() to write the value.


Parameters:
info - the metadata to write.
Throws:
java.lang.Exception





removeMetadata
public void removeMetadata(java.lang.Object info)
                    throws HDFException

Description copied from interface: DataFormat
Deletes an existing metadata from this data object.


Parameters:
info - the metadata to delete.
Throws:
HDFException





open
public int open()

Description copied from class: HObject
Opens an existing object such as 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(int src_id, int
 dst_id) and other purposes. The open() function should be used in pair
 with close(int) function.


Specified by:
open in class HObject



Returns:
the object identifier if successful; otherwise returns a negative
         value.
See Also:
HObject.close(int)





close
public void close(int id)

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 ncsa.hdf.hdf5lib.H5.H5Gclose()
 method and closes the group resource specified by the group id.


Specified by:
close in class HObject


Parameters:
id - The object identifier.





init
public void init()

Initializes the H4SDS such as dimension size of this dataset.


Specified by:
init in class Dataset








getPalette
public byte[][] getPalette()

Description copied from class: ScalarDS
Returns the palette of this scalar dataset or null if palette does not
 exist.
 

 Scalar dataset can be displayed as spreadsheet data or image. When a
 scalar dataset is chosen to display 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 not loaded, this interface retrieves the palette from
 the file and returns the palette. If the palette is loaded, it returnd
 the palette. It returns null if there is no palette assciated 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 arrange
 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.





create
public static H4SDS create(java.lang.String name,
                           Group pgroup,
                           Datatype type,
                           long[] dims,
                           long[] maxdims,
                           long[] chunks,
                           int gzip,
                           java.lang.Object data)
                    throws java.lang.Exception

Creates a new dataset.


Parameters:
name - the name of the dataset to create.
pgroup - the parent group of the new dataset.
type - the datatype of the dataset.
dims - the dimension size of the dataset.
maxdims - the max dimension size of the dataset.
chunks - the chunk size of the dataset.
gzip - the level of the gzip compression.
data - the array of data values.
Returns:
the new dataset if successful. Otherwise returns null.
Throws:
java.lang.Exception





getMetadata
public java.util.List getMetadata(int... attrPropList)
                           throws java.lang.Exception



Throws:
java.lang.Exception