Class CompressedTableData

java.lang.Object

nom.tam.fits.Data

nom.tam.fits.AbstractTableData

nom.tam.fits.BinaryTable

nom.tam.image.compression.hdu.CompressedTableData

All Implemented Interfaces:

Cloneable, FitsElement, TableData

public class CompressedTableData
extends BinaryTable

FITS representation of a compressed binary table. It itself is a binary table, but one in which each row represents the compressed image of one or more rows of the original table.

See Also:

• CompressedTableHDU

Nested Class Summary

Nested classes/interfaces inherited from class BinaryTable

BinaryTable.ColumnDesc

Modifier and Type	Class	Description
static class	BinaryTable.ColumnDesc	Describes the data type and shape stored in a binary table column.

Constructor Summary

Constructors

Constructor	Description
CompressedTableData()	Creates a new empty compressed table data to be initialized at a later point
CompressedTableData(Header header)	Creates a new compressed table data based on the prescription of the supplied header.

Method Summary

Modifier and Type	Method	Description
void	compress(Header header)	(for internal use) This should only be called by CompressedTableHDU, and should have reduced visibility accordingly.
long	defragment()	Defragments the heap area of this table, compacting the heap area, and returning the number of bytes by which the heap size has been reduced.
void	fillHeader(Header h)
void	prepareUncompressedData(ColumnTable<?> data)	Deprecated. (for internal use) This should only be called by CompressedTableHDU, and its visibility will be reduced accordingly in the future, not to mention that it should take a BinaryTable as its argument.

Methods inherited from class BinaryTable

addBitsColumn, addColumn, addColumn, addComplexColumn, addFlattenedColumn, addRow, addStringColumn, addVariableSizeColumn, compact, containsHeap, convertToBits, copy, createColumnDataFor, deleteColumns, deleteRows, fromColumnMajor, fromRowMajor, get, getArrayElement, getArrayElementAs, getBases, getColumn, getData, getDescriptor, getDescriptor, getDescriptor, getDimens, getDouble, getElement, getFlatColumns, getFlattenedColumn, getLogical, getLong, getModelRow, getNCols, getNRows, getNumber, getRawElement, getRow, getSizes, getString, getTypes, indexOf, parseTDims, read, reserveHeapSpace, reserveRowSpace, set, setColumn, setComplexColumn, setElement, setFlattenedColumn, setRow, toHDU, updateAfterDelete, write

Modifier and Type	Method	Description
int	addBitsColumn(Object o)	Adds a column of bits.
int	addColumn(Object o)	Adds a new column with the specified data array, with some default mappings.
int	addColumn(BinaryTable.ColumnDesc descriptor)	Adds a new empty column to the table to the specification.
int	addComplexColumn(Object o, Class<?> decimalType)	Adds a column of complex values stored as the specified decimal type of components in the FITS.
int	addFlattenedColumn(Object o, int... dims)	Deprecated. (for internal use) No longer used, will be removed in the future
int	addRow(Object[] o)	Adds a row to the table.
int	addStringColumn(String[] o)	Adds a column of string values (one per row), optimized for storage size.
int	addVariableSizeColumn(Object o)	Adds a new variable-length data column, populating it with the specified data object.
void	compact()	Discard the information about the original heap size (if this table was read from an input), and instead use the real size of the actual heap (plus reserved space around it) when writing to an output.
final boolean	containsHeap()	Checks if this table contains a heap for storing variable length arrays (VLAs).
boolean	convertToBits(int col)	Converts a column from FITS logical values to bits.
BinaryTable	copy()	Returns an independent copy of the binary table.
static void	createColumnDataFor(BinaryTable table)	Deprecated. (for internal use) It may become a private method in the future.
void	deleteColumns(int start, int len)	Removes a set of consecutive columns from this table, without updating assocu=iated the header information for the columns that were removed.
void	deleteRows(int row, int len)	Removes a set of consecutive rows from this table without updating any associated header information for an encompassing HDU.
static BinaryTable	fromColumnMajor(Object[] columns)	Creates a binary table from existing data in column-major format order.
static BinaryTable	fromRowMajor(Object[][] table)	Creates a binary table from existing table data in row-major format.
Object	get(int row, int col)	Returns a table element using the usual Java boxing for primitive scalar (singleton) entries, or packaging complex values as ComplexValue, or as appropriate primitive or object arrays.
Object	getArrayElement(int row, int col)	Returns a table element as an array of the FITS storage type.
Object	getArrayElementAs(int row, int col, Class<?> asType)	Returns a numerical table element as an array of a specific underlying other numerical type.
Class<?>[]	getBases()	Deprecated. (for internal use) Ambiguous, use BinaryTable.ColumnDesc.getElementClass() instead.
Object	getColumn(int col)	Returns the data for a particular column in as an array of elements.
ColumnTable<?>	getData()	Returns the underlying Java representation of the data contained in this HDU's data segment.
BinaryTable.ColumnDesc	getDescriptor(int column)	Returns the column descriptor of a given column in this table
BinaryTable.ColumnDesc	getDescriptor(String name)	Returns the (first) column descriptor whose name matches the specified value.
static BinaryTable.ColumnDesc	getDescriptor(Header header, int col)	Extracts a column descriptor from the FITS header for a given column index
int[][]	getDimens()	Deprecated. (for internal use) Use BinaryTable.ColumnDesc.getEntryShape() to access the shape of Java elements individually for columns instead.
final double	getDouble(int row, int col)	Returns the decimal value, if possible, of a scalar table entry.
Object	getElement(int row, int col)	Returns a table element as a Java array.
Object[]	getFlatColumns()	Deprecated. (for internal use) It may be private in the future.
Object	getFlattenedColumn(int col)	Deprecated. (for internal use) It may be reduced to private visibility in the future.
final Boolean	getLogical(int row, int col)	Returns the boolean value, if possible, for scalar elements.
final long	getLong(int row, int col)	Returns a 64-bit integer value, if possible, of a scalar table entry.
Object[]	getModelRow()	Deprecated. (for internal use) Use BinaryTable.getElement(int, int) instead for low-level reading of tables in deferred mode.
int	getNCols()	Returns the number of columns contained in this table.
int	getNRows()	Returns the number of columns contained in this table.
final Number	getNumber(int row, int col)	Returns the numerical value, if possible, for scalar elements.
Object	getRawElement(int row, int col)	Deprecated. (for internal use) Will reduce visibility in the future.
Object[]	getRow(int row)	Returns an array of elements in a particualr table row.
int[]	getSizes()	Deprecated. (for internal use) Use BinaryTable.ColumnDesc.getElementCount() instead.
final String	getString(int row, int col)	Returns the string value, if possible, for scalar elements.
char[]	getTypes()	Deprecated. (for internal use) Use BinaryTable.ColumnDesc.getElementClass() instead.
int	indexOf(String name)	Returns the Java index of the first column by the specified name.
static int[]	parseTDims(String tdims)	Deprecated. (for internal use) It may be reduced to private visibility in the future.
void	read(ArrayDataInput in)	Reads the data or skips over it for reading later, depending on whether reading from a stream or a random acessible input, respectively.
void	reserveHeapSpace(int bytes)	Reserves space in the file at the end of the heap for future heap growth (e.g. different/longer or new VLA entries).
void	reserveRowSpace(int rows)	Reserves space for future addition of rows at the end of the regular table.
void	set(int row, int col, Object o)	The Swiss-army knife of setting table entries, including Java boxing, and with some support for automatic type conversions.
void	setColumn(int col, Object o)	Sets new data for a table column.
boolean	setComplexColumn(int index)	Convert a column from float/double to float complex/double complex.
void	setElement(int row, int col, Object o)	Consider using the more Java-friendly BinaryTable.set(int, int, Object) with implicit scalar type conversions.
void	setFlattenedColumn(int col, Object data)	Deprecated. (for internal use) It may be reduced to private visibility in the future.
void	setRow(int row, Object[] data)	Sets new data for a table row.
BinaryTableHDU	toHDU()	Returns an approprotae HDU object that encapsulates this FITS data, and contains the minimal mandatory header description for that data.
void	updateAfterDelete(int oldNcol, Header hdr)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to (re)wrap tables in a new HDU after column deletions, and then edit the new header as necessary to incorporate custom entries.
void	write(ArrayDataOutput os)	Writes the contents of the element to a data sink, adding padding as necessary if the element (such as a header or data segment) is expected to complete the FITS block of 2880 bytes.

Methods inherited from class Data

calcChecksum, detach, getFileOffset, getKernel, getSize, isDeferred, isEmpty, reset, rewrite, rewriteable

Modifier and Type	Method	Description
long	calcChecksum()	Computes and returns the FITS checksum for this data, for example to compare against the stored DATASUM in the FITS header (e.g. via BasicHDU.getStoredDatasum()).
void	detach()	Detaches this data object from the input (if any), such as a file or stream, but not before loading data from the previously assigned input into memory.
long	getFileOffset()	Returns the byte offset at which this element starts ina file.
final Object	getKernel()	Same as Data.getData().
long	getSize()	Returns the size of this elements in the FITS representation.
boolean	isDeferred()	Checks if the data should be assumed to be in deferred read mode.
boolean	isEmpty()	Checks if the data content is currently empty, i.e. no actual data is currently stored in memory.
boolean	reset()	Reset the input stream to point to the beginning of this element
void	rewrite()	Rewrite the contents of the element in place.
boolean	rewriteable()	Checks if we can write this element back to its source.

Methods inherited from class Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface TableData

addRowEntries, setRowEntries

Modifier and Type	Method	Description
default int	addRowEntries(Object... entries)	Like TableData.addRow(Object[]), but with a vararg list of row entries.
default void	setRowEntries(int row, Object... entries)	Like TableData.setRow(int, Object[]) but with vararg list of entries.

Constructor Details

CompressedTableData

public CompressedTableData()

Creates a new empty compressed table data to be initialized at a later point

CompressedTableData

public CompressedTableData(Header header)
                    throws FitsException

Creates a new compressed table data based on the prescription of the supplied header.

Parameters:

header - The header that describes the compressed table

Throws:

FitsException - If the header is invalid or could not be accessed.

Method Details

compress

public void compress(Header header)
              throws FitsException

(for internal use) This should only be called by CompressedTableHDU, and should have reduced visibility accordingly.

Parameters:

header - the compressed header

Throws:

FitsException - if the table cannot be compressed.

defragment

public long defragment()
                throws FitsException

Description copied from class: BinaryTable

Defragments the heap area of this table, compacting the heap area, and returning the number of bytes by which the heap size has been reduced. When tables with variable-sized columns are modified, the heap may retain old data as columns are removed or elements get replaced with new data of different size. The data order in the heap may also get jumbled, causing what would appear to be sequential reads to jump all over the heap space with the caching. And, depending on how the heap was constructed in the first place, it may not be optimal for the row-after-row table access that is the most typical use case.

This method rebuilds the heap by taking elements in table read order (by rows, and columns) and puts them on a new heap.

For best squential read performance, you should defragment all tables that have been built column-by-column before writing them to a FITS file. The only time defragmentation is really not needed is if the table was built row-by-row, with no modifications to variable-length content after the fact.

Overrides:

defragment in class BinaryTable

Returns:

the number of bytes by which the heap has shrunk as a result of defragmentation.

Throws:

FitsException - if there was an error accessing the heap or the main data table comntaining the heap locators. In case of an error the table content may be left in a damaged state.

See Also:

• BinaryTable.compact()
• BinaryTable.setElement(int, int, Object)
• BinaryTable.addColumn(Object)
• BinaryTable.deleteColumns(int, int)
• BinaryTable.setColumn(int, Object)

fillHeader

public void fillHeader(Header h)
                throws FitsException

Overrides:

fillHeader in class BinaryTable

Throws:

FitsException

prepareUncompressedData

@Deprecated
public void prepareUncompressedData(ColumnTable<?> data)
                             throws FitsException

Deprecated.

(for internal use) This should only be called by CompressedTableHDU, and its visibility will be reduced accordingly in the future, not to mention that it should take a BinaryTable as its argument.

Parameters:

data - The original (uncompressed) table data.

Throws:

FitsException