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java.lang.Objectncsa.hdf.object.HObject
ncsa.hdf.object.Dataset
ncsa.hdf.object.ScalarDS
ncsa.hdf.object.h5.H5ScalarDS
H5ScalarDS describes an 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 The Datatype Interface (H5T)
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
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 H5ScalarDS(FileFormat fileFormat, java.lang.String name, java.lang.String path)
H5ScalarDS(FileFormat fileFormat, java.lang.String name, java.lang.String path, long[] oid)
Constructs an H5ScalarDS object with specific name and path.
Method Summary void
close(int did)
Closes access to this object.Dataset
copy(Group pgroup, java.lang.String dstName, long[] dims, java.lang.Object buff)
Copy this dataset to another group.static H5ScalarDS
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()
Retrieve and initialize dimensions and member information.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
setName(java.lang.String newName)
Sets the name of the 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, setPath, toString
Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Constructor Detail H5ScalarDS
public H5ScalarDS(FileFormat fileFormat, java.lang.String name, java.lang.String path)
H5ScalarDS
public H5ScalarDS(FileFormat fileFormat, java.lang.String name, java.lang.String path, long[] oid)
- Constructs an H5ScalarDS object with specific name and path.
- Parameters:
fileFormat
- the HDF file.name
- the name of this H5ScalarDS.path
- the full path of this H5ScalarDS.oid
- the unique identifier of this data object.
Method Detail copy
public Dataset copy(Group pgroup, java.lang.String dstName, 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.dstName
- 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 HDF5Exception
- 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:
HDF5Exception
read
public java.lang.Object read() throws HDF5Exception
- Description copied from class:
Dataset
- Loads and returns the data value from file.
- Specified by:
read
in classDataset
- Throws:
HDF5Exception
write
public void write(java.lang.Object buf) throws HDF5Exception
- Description copied from class:
Dataset
- Write data values into file.
- Specified by:
write
in classDataset
- Parameters:
buf
- the data to write- Throws:
HDF5Exception
getMetadata
public java.util.List getMetadata() throws HDF5Exception
- 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:
HDF5Exception
- 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 HDF5Exception
- Description copied from interface:
DataFormat
- Deletes an existing metadata from this data object.
- Parameters:
info
- the metadata to delete.- Throws:
HDF5Exception
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 did)
- Description copied from class:
HObject
- Closes access to this object.
- Specified by:
close
in classHObject
- Parameters:
did
- 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()
- Retrieve and initialize dimensions and member information.
- 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
readPalette
public byte[][] readPalette(int idx)
- read specific image palette from file.
- Specified by:
readPalette
in classScalarDS
- Parameters:
idx
- the palette index to read- Returns:
- the palette data into two-dimension byte array, byte[3][256]
create
public static H5ScalarDS 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
getPaletteRefs
public byte[] getPaletteRefs()
- 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
setName
public void setName(java.lang.String newName) throws java.lang.Exception
- Sets the name of the data object.
- Overrides:
setName
in classHObject
- Parameters:
newName
- the new name of the object.- Throws:
java.lang.Exception
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