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java.lang.Objectncsa.hdf.object.HObject
ncsa.hdf.object.Dataset
ncsa.hdf.object.ScalarDS
ncsa.hdf.object.h4.H4SDS
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
- See Also:
- Serialized Form
Field Summary static int
DFTAG_NDG_NETCDF
tag for netCDF datasets.
Fields inherited from class ncsa.hdf.object.ScalarDS imageDataRange, interlace, INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isImage, isText, isTrueColor, isUnsigned, nativeDatatype, palette, unsignedConverted
Fields inherited from class ncsa.hdf.object.Dataset chunkSize, compression, data, datatype, dimNames, dims, H5Z_FILTER_CONFIG_DECODE_ENABLED, H5Z_FILTER_CONFIG_ENCODE_ENABLED, rank, selectedDims, selectedIndex, selectedStride, startDims
Fields inherited from class ncsa.hdf.object.HObject hasAttribute, oid, separator
Constructor Summary H4SDS(FileFormat fileFormat, java.lang.String name, java.lang.String path)
H4SDS(FileFormat fileFormat, 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 this object.Dataset
copy(Group pgroup, java.lang.String dname, long[] dims, java.lang.Object buff)
Copy this dataset to another group.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 of this dataset.java.util.List
getMetadata()
Loads the metadata such as attributes and type of the the data object into memory if the metadata is not loaded.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.void
init()
Initializes the H4SDS such as dimension size of this dataset.int
open()
Opens access to this object.java.lang.Object
read()
Loads and returns the data value from file.byte[]
readBytes()
Read data values of this dataset into byte array.byte[][]
readPalette(int idx)
read 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)
Write data values into file.void
writeMetadata(java.lang.Object info)
Saves a specific metadata into file.
Methods inherited from class ncsa.hdf.object.ScalarDS clearData, convertFromUnsignedC, convertToUnsignedC, getImageDataRange, getInterlace, getNativeDataType, isImage, isText, isTrueColor, isUnsigned, setPalette
Methods inherited from class ncsa.hdf.object.Dataset byteToString, convertFromUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getData, getDimNames, getDims, getHeight, getRank, getSelectedDims, getSelectedIndex, getStartDims, getStride, getWidth, setData, stringToByte, write
Methods inherited from class ncsa.hdf.object.HObject equalsOID, getFID, getFile, getFileFormat, getName, getOID, getPath, hasAttribute, setName, setPath, toString
Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Field Detail 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 fileFormat, java.lang.String name, java.lang.String path)
H4SDS
public H4SDS(FileFormat fileFormat, java.lang.String name, java.lang.String path, long[] oid)
- Creates an H4SDS object with specific name and path.
- Parameters:
fileFormat
- 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 readPalette
public byte[][] readPalette(int idx)
- Description copied from class:
ScalarDS
- read specific image palette from file.
- Specified by:
readPalette
in classScalarDS
- Parameters:
idx
- the palette index to read.
getPaletteRefs
public byte[] getPaletteRefs()
- Description copied from class:
ScalarDS
- returns the byte array of palette refs. returns null if there is no palette attribute attached to this dataset.
- Specified by:
getPaletteRefs
in classScalarDS
getDatatype
public Datatype getDatatype()
- Description copied from class:
Dataset
- returns the datatype of this dataset.
- Specified by:
getDatatype
in classDataset
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
- Copy this dataset to another group.
- Specified by:
copy
in classDataset
- 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 to be copied.- Returns:
- the new dataset.
- Throws:
java.lang.Exception
readBytes
public byte[] readBytes() throws HDFException
- Description copied from class:
Dataset
- Read data values of this dataset into byte array. readBytes() loads data as arry 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 a int array of 5.
readBytes() is most used for copy data values, at which case, data do not need to be changed or displayed.
- Specified by:
readBytes
in classDataset
- Throws:
HDFException
read
public java.lang.Object read() throws HDFException
- Description copied from class:
Dataset
- Loads and returns the data value from file.
- Specified by:
read
in classDataset
- Throws:
HDFException
write
public void write(java.lang.Object buf) throws HDFException
- Description copied from class:
Dataset
- Write data values into file.
- Specified by:
write
in classDataset
- Parameters:
buf
- the data to write- Throws:
HDFException
getMetadata
public java.util.List getMetadata() throws HDFException
- Description copied from interface:
DataFormat
- Loads the metadata such as attributes and type of the the data object into memory if the metadata is not loaded. If the metadata is loaded, it returns the metadata. The metadata is stored as a collection of metadata ojbects in a List.
- Returns:
- the list of metadata objects.
- Throws:
HDFException
- See Also:
List
writeMetadata
public void writeMetadata(java.lang.Object info) throws java.lang.Exception
- Description copied from interface:
DataFormat
- Saves a specific metadata into file. If the metadata exists, it updates its value. If the metadata does not exists, it creates and attach the new metadata to the object and saves it into file.
- Parameters:
info
- the specific metadata.- 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 access to this object.
Sub-classes have to implement this interface so that different data objects have their own ways of how the data resources are opened.
- Specified by:
open
in classHObject
- Returns:
- the interface identifier for access this object.
close
public void close(int id)
- Description copied from class:
HObject
- Closes access to this object.
- Specified by:
close
in classHObject
- Parameters:
id
- the object identifier. Sub-classes have to implement this interface so that different data objects have their own ways of how the data resources are closed.
init
public void init()
- Initializes the H4SDS such as dimension size of this dataset.
- Specified by:
init
in classDataset
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 library to retrieve the associated palette.
- Specified by:
getPalette
in classScalarDS
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.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
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