Class BinaryTableHDU

java.lang.Object

nom.tam.fits.BasicHDU<BinaryTable>

nom.tam.fits.TableHDU<BinaryTable>

nom.tam.fits.BinaryTableHDU

All Implemented Interfaces:

FitsElement

Direct Known Subclasses:

CompressedImageHDU, CompressedTableHDU

public class BinaryTableHDU
extends TableHDU<BinaryTable>

Binary table header/data unit.

See Also:

• BinaryTable
• AsciiTableHDU

Field Summary

Fields inherited from class BasicHDU

BITPIX_BYTE, BITPIX_DOUBLE, BITPIX_FLOAT, BITPIX_INT, BITPIX_LONG, BITPIX_SHORT

Modifier and Type	Field	Description
static final int	BITPIX_BYTE	Deprecated. Use Bitpix.VALUE_FOR_BYTE instead.
static final int	BITPIX_DOUBLE	Deprecated. Use Bitpix.VALUE_FOR_DOUBLE instead.
static final int	BITPIX_FLOAT	Deprecated. Use Bitpix.VALUE_FOR_FLOAT instead.
static final int	BITPIX_INT	Deprecated. Use Bitpix.VALUE_FOR_INT instead.
static final int	BITPIX_LONG	Deprecated. Use Bitpix.VALUE_FOR_LONG instead.
static final int	BITPIX_SHORT	Deprecated. Use Bitpix.VALUE_FOR_SHORT instead.

Constructor Summary

Constructors

Constructor	Description
BinaryTableHDU(Header hdr, BinaryTable datum)	Deprecated. (for internal use) Its visibility should be reduced to package level in the future.

Method Summary

Modifier and Type	Method	Description
int	addColumn(Object data)	Add a column to the table without any associated header information.
final boolean	convertToBits(int col)	Converts a column from FITS logical values to bits.
static BinaryTable	encapsulate(Object o)	Deprecated. (for internal use) Use BinaryTable.fromColumnMajor(Object[]) or BinaryTable.fromRowMajor(Object[][]) instead.
BinaryTable.ColumnDesc	getColumnDescriptor(int col)	Returns a copy of the column descriptor of a given column in this table
void	info(PrintStream stream)	Print out some information about this HDU.
static boolean	isData(Object o)	Deprecated. (for internal use) Will reduce visibility in the future
boolean	isHeader()	Deprecated. (for internal use) Will reduce visibility in the future
static boolean	isHeader(Header header)	Deprecated. (for internal use) Will reduce visibility in the future
static BinaryTable	manufactureData(Header header)	Deprecated. (for internal use) Will reduce visibility in the future
static Header	manufactureHeader(Data data)	Deprecated. (for internal use) Will reduce visibility in the future
void	setColumnName(int index, String name, String comment)	Sets the name / ID of a specific column in this table.
boolean	setComplexColumn(int index)	Convert a column in the table to complex.
static BinaryTableHDU	wrap(BinaryTable tab)	Wraps the specified table in an HDU, creating a header for it with the essential table description.
void	write(ArrayDataOutput out)	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 TableHDU

addRow, deleteColumnsIndexOne, deleteColumnsIndexOne, deleteColumnsIndexZero, deleteColumnsIndexZero, deleteRows, deleteRows, findColumn, getColumn, getColumn, getColumnFormat, getColumnMeta, getColumnMeta, getColumnName, getColumns, getDefaultColumnName, getElement, getNCols, getNRows, getRow, setColumn, setColumn, setColumnMeta, setColumnMeta, setColumnMeta, setColumnMeta, setColumnMeta, setColumnMeta, setColumnMeta, setCurrentColumn, setCurrentColumn, setElement, setRow

Modifier and Type	Method	Description
int	addRow(Object[] newRows)	Add a row to the end of the table.
void	deleteColumnsIndexOne(int column, int len)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to use TableData.deleteColumns(int, int) to edit tables before wrapping them in an HDU and editing the header as necessary to incorporate custom entries.
void	deleteColumnsIndexOne(int column, int len, String[] fields)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to use TableData.deleteColumns(int, int) to edit tables before wrapping them in an HDU and editing the header as necessary to incorporate custom entries.
void	deleteColumnsIndexZero(int column, int len)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to use TableData.deleteColumns(int, int) to edit tables before wrapping them in an HDU and editing the header as necessary to incorporate custom entries.
void	deleteColumnsIndexZero(int column, int len, IFitsHeader[] fields)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to use TableData.deleteColumns(int, int) to edit tables before wrapping them in an HDU and editing the header as necessary to incorporate custom entries.
void	deleteRows(int row)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to use TableData.deleteRows(int, int) to edit tables before wrapping them in an HDU and editing the header as necessary to incorporate custom entries.
void	deleteRows(int firstRow, int nRow)	Deprecated. It is not entirely foolproof for keeping the header in sync -- it is better to use TableData.deleteRows(int, int) to edit tables before wrapping them in an HDU and editing the header as necessary to incorporate custom entries.
int	findColumn(String colName)	Find the 0-based column index corresponding to a particular column name.
Object	getColumn(int col)	Returns the data for a particular column in as an array of elements.
Object	getColumn(String colName)	Returns the data for a particular column in as an array of elements.
String	getColumnFormat(int index0)	Get the FITS type of a column in the table.
String	getColumnMeta(int index0, String keyBase)	Convenience method for getting column metadata, as a string.
String	getColumnMeta(int index0, IFitsHeader keyBase)	Convenience method for getting column metadata, as a string.
String	getColumnName(int index0)	Gets the name of a column in the table, as it appears in this HDU's header.
Object[]	getColumns()	Returns the data for all columns in as an array.
static String	getDefaultColumnName(int col)	Returns the default name for a columns with the specified index, to use if no column name was explicitly defined
Object	getElement(int row, int col)	Returns a specific element from this table
int	getNCols()	Get the number of columns for this table
int	getNRows()	Get the number of rows for this table
Object[]	getRow(int row)	Returns a specific row from this table
void	setColumn(int col, Object newCol)	Update a column within a table.
void	setColumn(String colName, Object newCol)	Update a column within a table.
void	setColumnMeta(int index0, String key, Boolean value, String comment, boolean after)	Specify column metadata for a given column in a way that allows all of the column metadata for a given column to be organized together.
void	setColumnMeta(int index0, String key, Number value, int precision, String comment, boolean after)	Specify column metadata for a given column in a way that allows all of the column metadata for a given column to be organized together.
void	setColumnMeta(int index0, String key, Number value, String comment, boolean after)	Specify column metadata for a given column in a way that allows all of the column metadata for a given column to be organized together.
void	setColumnMeta(int index0, String key, String value, String comment)	Specify column metadata for a given column in a way that allows all of the column metadata for a given column to be organized together.
void	setColumnMeta(int index0, String key, String value, String comment, boolean after)	Deprecated. use TableHDU.setColumnMeta(int, IFitsHeader, String, String, boolean)
void	setColumnMeta(int index0, IFitsHeader key, Number value, String comment, boolean after)	Specify column metadata for a given column in a way that allows all of the column metadata for a given column to be organized together.
void	setColumnMeta(int index0, IFitsHeader key, String value, String comment, boolean after)	Specify column metadata for a given column in a way that allows all of the column metadata for a given column to be organized together.
void	setCurrentColumn(int col)	Deprecated. (for internal use) Will be removed int the future (no longer used).
void	setCurrentColumn(int col0, boolean after)	Deprecated. (for internal use) Will have private access in the future.
void	setElement(int row, int col, Object element)	Update a single element within the table.
void	setRow(int row, Object[] newRow)	Update a row within a table.

Methods inherited from class BasicHDU

addValue, addValue, addValue, addValue, addValue, addValue, addValue, addValue, calcChecksum, card, getAuthor, getAxes, getBitpix, getBitPix, getBlankValue, getBScale, getBUnit, getBZero, getCreationDate, getData, getDummyHDU, getEpoch, getEquinox, getFileOffset, getGroupCount, getHeader, getInstrument, getKernel, getMaximumValue, getMinimumValue, getObject, getObservationDate, getObserver, getOrigin, getParameterCount, getReference, getSize, getStoredChecksum, getStoredDatasum, getTelescope, getTrimmedString, getTrimmedString, read, reset, rewrite, rewriteable, setChecksum, verifyDataIntegrity, verifyIntegrity

Modifier and Type	Method	Description
void	addValue(String key, boolean val, String comment)	Add information to the header.
void	addValue(String key, double val, String comment)	Add information to the header.
void	addValue(String key, int val, String comment)	Add information to the header.
void	addValue(String key, String val, String comment)	Add information to the header.
void	addValue(IFitsHeader key, boolean val)	Add information to the header.
void	addValue(IFitsHeader key, double val)	Add information to the header.
void	addValue(IFitsHeader key, int val)	Add information to the header.
void	addValue(IFitsHeader key, String val)	Add information to the header.
long	calcChecksum()	Deprecated. Use BasicHDU.verifyIntegrity() instead when appropriate.
HeaderCardBuilder	card(IFitsHeader key)	Returns a header card builder for filling the header cards using the builder pattern.
String	getAuthor()	Return the name of the person who compiled the information in the data associated with this header.
int[]	getAxes()	In FITS files the index represented by NAXIS1 is the index that changes most rapidly.
Bitpix	getBitpix()	Return the Bitpix enum type for this HDU.
final int	getBitPix()	Deprecated. (for internal use) Will reduce visibility or remove entirely in the future.
long	getBlankValue()	Deprecated. This is only applicable to ImageHDU or RandomGroupsHDU with integer type data and not for other HDU or data types.
double	getBScale()	Deprecated. This is only applicable to ImageHDU or RandomGroupsHDU with integer type data and not for other HDU or data types.
String	getBUnit()	Deprecated. This is only applicable to ImageHDU or RandomGroupsHDU and not for other HDU or data types.
double	getBZero()	Deprecated. This is only applicable to ImageHDU or RandomGroupsHDU with integer type data and not for other HDU or data types.
Date	getCreationDate()	Get the FITS file creation date as a Date object.
BinaryTable	getData()	Returns the data component of this HDU.
static NullDataHDU	getDummyHDU()	Deprecated. Use NullDataHDU instead.
double	getEpoch()	Deprecated. use BasicHDU.getEquinox() instead
double	getEquinox()	Get the equinox in years for the celestial coordinate system in which positions given in either the header or data are expressed.
long	getFileOffset()	Returns the byte offset at which this element starts ina file.
int	getGroupCount()	Deprecated. Should not be exposed outside of RandomGroupsHDU -- will reduce visibility in the future/
Header	getHeader()	Returns the FITS header component of this HDU
String	getInstrument()	Get the name of the instrument which was used to acquire the data in this FITS file.
final Object	getKernel()	Returns the underlying Java object (usually an array of some type) that stores the data internally.
double	getMaximumValue()	Return the minimum valid value in the array.
double	getMinimumValue()	Return the minimum valid value in the array.
String	getObject()	Get the name of the observed object in this FITS file.
Date	getObservationDate()	Get the FITS file observation date as a Date object.
String	getObserver()	Get the name of the person who acquired the data in this FITS file.
String	getOrigin()	Get the name of the organization which created this FITS file.
int	getParameterCount()	Deprecated. Should not be exposed outside of RandomGroupsHDU -- will reduce visibility in the future.
String	getReference()	Return the citation of a reference where the data associated with this header are published.
long	getSize()	Returns the size of this elements in the FITS representation.
long	getStoredChecksum()	Deprecated. Not very useful, since it has no meaning other than ensuring that the checksum of the HDU yields (int) -1 (that is 0xffffffff) after including this value for the CHECKSUM keyword in the header.
long	getStoredDatasum()	Returns the FITS checksum for the HDU's data that is stored in the header of this HDU under the DATASUM keyword.
String	getTelescope()	Get the name of the telescope which was used to acquire the data in this FITS file.
String	getTrimmedString(String keyword)	Deprecated. (for internal use) Will reduced visibility in the future.
String	getTrimmedString(IFitsHeader keyword)	Deprecated. (for internal use) Will reduced visibility in the future.
void	read(ArrayDataInput stream)	Read a FITS element from the input, starting at the current position.
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.
void	setChecksum()	Computes the checksums for this HDU and stores the CHECKSUM and DATASUM values in the header.
boolean	verifyDataIntegrity()	Checks that the HDUs data checksum is correct.
boolean	verifyIntegrity()	Checks the HDU's integrity, using the recorded CHECKSUM and/or DATASUM keywords if present.

Methods inherited from class Object

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

Constructor Details

BinaryTableHDU

@Deprecated
public BinaryTableHDU(Header hdr,
 BinaryTable datum)

Deprecated.

(for internal use) Its visibility should be reduced to package level in the future.

Creates a new binary table HDU from the specified FITS header and associated table data

Parameters:

hdr - the FITS header describing the data and any user-specific keywords

datum - the corresponding data object

Method Details

wrap

public static BinaryTableHDU wrap(BinaryTable tab)
                           throws FitsException

Wraps the specified table in an HDU, creating a header for it with the essential table description. Users may want to complete the table description with optional FITS keywords such as TTYPEn, TUNITn etc. It is strongly recommended that the table structure (rows or columns) isn't altered after the table is encompassed in an HDU, since there is no guarantee that the header description will be kept in sync.

Parameters:

tab - the binary table to wrap into a new HDU

Returns:

A new HDU encompassing and describing the supplied table.

Throws:

FitsException - if the table structure is invalid, and cannot be described in a header (should never really happen, but we keep the possibility open to it).

Since:

1.18

See Also:

• BinaryTable.toHDU()

encapsulate

@Deprecated
public static BinaryTable encapsulate(Object o)
                               throws FitsException

Deprecated.

(for internal use) Use BinaryTable.fromColumnMajor(Object[]) or BinaryTable.fromRowMajor(Object[][]) instead. Will reduce visibility in the future.

Parameters:

o - data to encapsulate

Returns:

Encapsulate data in a BinaryTable data type

Throws:

FitsException - if the type of the data is not usable as data

isData

@Deprecated
public static boolean isData(Object o)

Deprecated.

(for internal use) Will reduce visibility in the future

Check if this data object is consistent with a binary table.

Parameters:

o - a column table object, an Object[][], or an Object[]. This routine doesn't check that the dimensions of arrays are properly consistent.

Returns:

true if the data object can be represented as a FITS binary table, otherwise false.

isHeader

@Deprecated
public static boolean isHeader(Header header)

Deprecated.

(for internal use) Will reduce visibility in the future

Check that this is a valid binary table header.

Parameters:

header - to validate.

Returns:

true if this is a binary table header.

manufactureData

@Deprecated
public static BinaryTable manufactureData(Header header)
                                   throws FitsException

Deprecated.

(for internal use) Will reduce visibility in the future

Prepares a data object into which the actual data can be read from an input subsequently or at a later time.

Parameters:

header - The FITS header that describes the data

Returns:

A data object that support reading content from a stream.

Throws:

FitsException - if the data could not be prepared to prescriotion.

manufactureHeader

@Deprecated
public static Header manufactureHeader(Data data)
                                throws FitsException

Deprecated.

(for internal use) Will reduce visibility in the future

Parameters:

data - the data used to build the binary table. This is typically some kind of array of objects.

Returns:

a newly created binary table HDU from the supplied data.

Throws:

FitsException - if there was a problem with the data.

addColumn

public int addColumn(Object data)
              throws FitsException

Description copied from class: TableHDU

Add a column to the table without any associated header information.

Overrides:

addColumn in class TableHDU<BinaryTable>

Parameters:

data - the new column information. the newCol should be an Object[] where type of all of the constituents is identical. The length of data should match the other columns. Note: It is valid for data to be a 2 or higher dimensionality primitive array. In this case the column index is the first (in Java speak) index of the array. E.g., if called with int[30][20][10], the number of rows in the table should be 30 and this column will have elements which are 2-d integer arrays with TDIM = (10,20).

Returns:

the number of columns in the adapted table

Throws:

FitsException - if the operation failed

info

public void info(PrintStream stream)

Description copied from class: BasicHDU

Print out some information about this HDU.

Specified by:

info in class BasicHDU<BinaryTable>

Parameters:

stream - the printstream to write the info on

isHeader

@Deprecated
public boolean isHeader()

Deprecated.

(for internal use) Will reduce visibility in the future

Check that this HDU has a valid header.

Returns:

true if this HDU has a valid header.

getColumnDescriptor

public BinaryTable.ColumnDesc getColumnDescriptor(int col)

Returns a copy of the column descriptor of a given column in this table

Parameters:

col - the zero-based column index

Returns:

a copy of the column's descriptor

Since:

1.18

See Also:

• BinaryTable.getDescriptor(int)

setColumnName

public void setColumnName(int index,
 String name,
 String comment)
                   throws IndexOutOfBoundsException,
HeaderCardException

Description copied from class: TableHDU

Sets the name / ID of a specific column in this table. Naming columns is generally a good idea so that people can figure out what sort of data actually appears in specific table columns.

Overrides:

setColumnName in class TableHDU<BinaryTable>

Parameters:

index - the 0-based column index

name - the name or ID we want to assing to the column

comment - Any additional comment we would like to store alongside in the FITS header. (The comment may be truncated or even ommitted, depending on space constraints in the FITS header.

Throws:

IndexOutOfBoundsException - if the table has no column matching the index

HeaderCardException - if there was a problem wil adding the associated descriptive FITS header keywords to this table's header.

See Also:

• TableHDU.getColumnName(int)
• TableHDU.getDefaultColumnName(int)

convertToBits

public final boolean convertToBits(int col)
                            throws FitsException

Converts a column from FITS logical values to bits. Null values (allowed in logical columns) will map to false. It is legal to call this on a column that is already containing bits.

Parameters:

col - The zero-based index of the column to be reset.

Returns:

Whether the conversion was possible. *

Throws:

FitsException - if the header could not be updated

Since:

1.18

setComplexColumn

public boolean setComplexColumn(int index)
                         throws FitsException

Convert a column in the table to complex. Only tables with appropriate types and dimensionalities can be converted. It is legal to call this on a column that is already complex.

Parameters:

index - The zero-based index of the column to be converted.

Returns:

Whether the column can be converted

Throws:

FitsException - if the header could not be updated

See Also:

• setComplexColumn(int)

write

public void write(ArrayDataOutput out)
           throws FitsException

Description copied from interface: FitsElement

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.

Specified by:

write in interface FitsElement

Overrides:

write in class BasicHDU<BinaryTable>

Parameters:

out - The data sink.

Throws:

FitsException - if the write was unsuccessful.