Module org.hdfgroup.object

Package hdf.object.fits

Class FitsDataset

Object

hdf.object.HObject

hdf.object.Dataset

hdf.object.ScalarDS

hdf.object.fits.FitsDataset

All Implemented Interfaces:

DataFormat, MetaDataContainer, Serializable

public class FitsDataset
extends ScalarDS

FitsDataset 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)

Version:

1.1 9/4/2007

Author:

Peter X. Cao

See Also:

Serialized Form

Field Summary

Fields inherited from class hdf.object.ScalarDS

fillValue, imageDataRange, interlace, INTERLACE_LINE, INTERLACE_PIXEL, INTERLACE_PLANE, isDefaultImageOrder, isFillValueConverted, isImage, isImageDisplay, isText, isTrueColor, palette, unsignedConverted

Fields inherited from class hdf.object.Dataset

chunkSize, compression, COMPRESSION_GZIP_TXT, convertByteToString, convertedBuf, data, datatype, dimNames, dims, filters, inited, isDataLoaded, maxDims, nPoints, originalBuf, rank, selectedDims, selectedIndex, selectedStride, startDims, storage, storageLayout

Fields inherited from class hdf.object.HObject

fileFormat, linkTargetObjName, oid, SEPARATOR

Constructor Summary

Constructors

Constructor	Description
FitsDataset(FileFormat fileFormat, nom.tam.fits.BasicHDU hdu, String dName, long[] oid)	Constructs an FitsDataset object with specific netcdf variable.

Method Summary

Modifier and Type	Method	Description
void	close(long did)	Closes access to the object.
Dataset	copy(Group pgroup, String dstName, long[] dims, Object buff)	Creates a new dataset and writes the data buffer to the new dataset.
static FitsDataset	create(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object data)	Creates a new dataset.
Datatype	getDatatype()	Returns the datatype of the data object.
List	getMetadata()	Retrieves the object's metadata, such as attributes, from the file.
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()
long	open()	Opens an existing object such as a dataset or group for access.
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(Object info)	Deletes an existing piece of metadata from this object.
void	setName(String newName)	Sets the name of the object.
void	updateMetadata(Object info)	Updates an existing piece of metadata attached to this object.
void	write(Object buf)	Writes a memory buffer to the object in the file.
void	writeMetadata(Object info)	Writes a specific piece of metadata (such as an attribute) into the file.

Methods inherited from class hdf.object.ScalarDS

addFilteredImageValue, clearData, convertFromUnsignedC, convertToUnsignedC, getFillValue, getFilteredImageValues, getImageDataRange, getInterlace, getPaletteName, isDefaultImageOrder, isImage, isImageDisplay, isTrueColor, setImageDataRange, setIsImage, setIsImageDisplay, setPalette

Methods inherited from class hdf.object.Dataset

byteToString, clear, convertFromUnsignedC, convertFromUnsignedC, convertToUnsignedC, convertToUnsignedC, getChunkSize, getCompression, getConvertByteToString, getData, getDimNames, getDims, getFilters, getHeight, getMaxDims, getOriginalClass, getRank, getSelectedDims, getSelectedIndex, getSize, getStartDims, getStorage, getStorageLayout, getStride, getVirtualFilename, getVirtualMaps, getWidth, isInited, isString, isVirtual, setConvertByteToString, setData, stringToByte, write

Methods inherited from class hdf.object.HObject

createFullname, debug, equals, equals, equalsOID, getFID, getFile, getFileFormat, getFullName, getLinkTargetObjName, getName, getOID, getPath, hashCode, setFullname, setLinkTargetObjName, setPath, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

FitsDataset

public FitsDataset(FileFormat fileFormat,
nom.tam.fits.BasicHDU hdu,
String dName,
long[] oid)

Constructs an FitsDataset object with specific netcdf variable.

Parameters:

fileFormat - the netcdf file.

hdu - the BasicHDU.

dName - the name for this dataset.

oid - the unique identifier for this dataset.

Method Details

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.

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 Exception

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:

Exception - if data can not be read

read

public Object read()
            throws Exception

Description copied from interface: DataFormat

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.

Returns:

the data read from file.

Throws:

Exception - if object can not be read

See Also:

DataFormat.getData()

write

public void write(Object buf)
           throws Exception

Description copied from interface: DataFormat

Writes a memory buffer to the object in the file.

Parameters:

buf - the data to write

Throws:

Exception - if data can not be written

getMetadata

public List getMetadata()
                 throws Exception

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:

Exception - if the metadata can not be retrieved

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 Exception

Description copied from interface: MetaDataContainer

Deletes an existing piece of metadata from this object.

Parameters:

info - the metadata to delete.

Throws:

Exception - if the metadata can not be removed

updateMetadata

public void updateMetadata(Object info)
                    throws Exception

Description copied from interface: MetaDataContainer

Updates an existing piece of metadata attached to this object.

Parameters:

info - the metadata to update.

Throws:

Exception - if the metadata can not be updated

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()

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.

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

create

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

Exception - if there is an error

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 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.

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

getMetadata

public List getMetadata(int... attrPropList)
                 throws Exception

Throws:

Exception