Package nom.tam.fits

Class AsciiTable

java.lang.Object

nom.tam.fits.Data

nom.tam.fits.AbstractTableData

nom.tam.fits.AsciiTable

All Implemented Interfaces:

FitsElement, TableData

public class AsciiTable
extends AbstractTableData

This class represents the data in an ASCII table

Field Summary

Fields

Modifier and Type	Field	Description
private ByteParser	bp	The parser used to convert from buffer to data.
private byte[]	buffer	The byte buffer used to read/write the ASCII table
private ArrayDataInput	currInput	The actual stream used to input data
private java.lang.Object[]	data	An array of arrays giving the data in the table in binary numbers
private static int	DOUBLE_MAX_LENGTH
private static int	FLOAT_MAX_LENGTH
private static int	INT_MAX_LENGTH
private boolean[]	isNull	Markers indicating fields that are null
private int[]	lengths	The number of bytes in the field
private static java.util.logging.Logger	LOG
private static int	LONG_MAX_LENGTH
private static int	MAX_INTEGER_LENGTH
private int	nFields	The number of fields in the table
private int	nRows	The number of rows in the table
private java.lang.String[]	nulls	The null string for the field
private int[]	offsets	The offset from the beginning of the row at which the field starts
private int	rowLen	The number of bytes in a row
private java.lang.Class<?>[]	types	The type of data in the field

Fields inherited from class nom.tam.fits.Data

dataSize, fileOffset, input

Constructor Summary

Constructors

Constructor	Description
AsciiTable()	Create an empty ASCII table
AsciiTable(Header hdr)	Create an ASCII table given a header

Method Summary

Modifier and Type	Method	Description
(package private) int	addColInfo(int col, Cursor<java.lang.String,HeaderCard> iter)
int	addColumn(java.lang.Object newCol)	Add a column to the table without any associated header information.
int	addColumn(java.lang.Object newCol, int length)	This version of addColumn allows the user to override the default length associated with each column type.
int	addRow(java.lang.Object[] newRow)	Add a row at the end of the table.
void	deleteColumns(int start, int len)	Delete columns from the table.
void	deleteRows(int start, int len)	Delete rows from a FITS table
private void	ensureData()	be sure that the data is filled.
private boolean	extractElement(int offset, int length, java.lang.Object[] array, int col, int row, java.lang.String nullFld)	Move an element from the buffer into a data array.
void	fillHeader(Header hdr)	Fill in a header with information that points to this data.
private void	getBuffer(int size, long offset)	Read some data into the buffer.
java.lang.Object	getColumn(int col)	Get a column of data
java.lang.Object	getData()	Get the ASCII table information.
java.lang.Object	getElement(int row, int col)	Get a single element as a one-d array.
int	getNCols()	Get the number of columns in the table
int	getNRows()	Get the number of rows in the table
java.lang.Object[]	getRow(int row)	Get a row.
int	getRowLen()	Get the number of bytes in a row
protected long	getTrueSize()	Return the size of the data section
boolean	isNull(int row, int col)	See if an element is null.
private java.lang.Object	parseSingleElement(int row, int col)	Read a single element from the table.
private java.lang.Object[]	parseSingleRow(int row)	Read a single row from the table.
void	read(ArrayDataInput str)	Read in an ASCII table.
void	setColumn(int col, java.lang.Object newData)	Replace a column with new data.
void	setElement(int row, int col, java.lang.Object newData)	Modify an element in the table
void	setNull(int row, int col, boolean flag)	Mark (or unmark) an element as null.
(package private) void	setNullString(int col, java.lang.String newNull)	Set the null string for a columns.
void	setRow(int row, java.lang.Object[] newData)	Modify a row in the table
private java.lang.Object	singleElement(int row, int col)	Extract a single element from a table.
private java.lang.Object[]	singleRow(int row)	Extract a single row from a table.
void	updateAfterDelete(int oldNCol, Header hdr)	This is called after we delete columns.
void	write(ArrayDataOutput str)	Write the data to an output stream.

Methods inherited from class nom.tam.fits.Data

getFileOffset, getKernel, getSize, reset, rewrite, rewriteable, setFileOffset

Methods inherited from class java.lang.Object

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

Field Detail

MAX_INTEGER_LENGTH

private static final int MAX_INTEGER_LENGTH

See Also:

Constant Field Values

FLOAT_MAX_LENGTH

private static final int FLOAT_MAX_LENGTH

See Also:

Constant Field Values

LONG_MAX_LENGTH

private static final int LONG_MAX_LENGTH

See Also:

Constant Field Values

INT_MAX_LENGTH

private static final int INT_MAX_LENGTH

See Also:

Constant Field Values

DOUBLE_MAX_LENGTH

private static final int DOUBLE_MAX_LENGTH

See Also:

Constant Field Values

LOG

private static final java.util.logging.Logger LOG

nRows

private int nRows

The number of rows in the table

nFields

private int nFields

The number of fields in the table

rowLen

private int rowLen

The number of bytes in a row

nulls

private java.lang.String[] nulls

The null string for the field

types

private java.lang.Class<?>[] types

The type of data in the field

offsets

private int[] offsets

The offset from the beginning of the row at which the field starts

lengths

private int[] lengths

The number of bytes in the field

buffer

private byte[] buffer

The byte buffer used to read/write the ASCII table

isNull

private boolean[] isNull

Markers indicating fields that are null

data

private java.lang.Object[] data

An array of arrays giving the data in the table in binary numbers

bp

private ByteParser bp

The parser used to convert from buffer to data.

currInput

private ArrayDataInput currInput

The actual stream used to input data

Constructor Detail

AsciiTable

public AsciiTable()

Create an empty ASCII table

AsciiTable

public AsciiTable(Header hdr)
           throws FitsException

Create an ASCII table given a header

Parameters:

hdr - The header describing the table

Throws:

FitsException - if the operation failed

Method Detail

addColInfo

int addColInfo(int col,
               Cursor<java.lang.String,HeaderCard> iter)
        throws HeaderCardException

Throws:

HeaderCardException

addColumn

public int addColumn(java.lang.Object newCol)
              throws FitsException

Description copied from interface: TableData

Add a column to the table without any associated header information. Users should be cautious of calling this routine directly rather than the corresponding routine in AsciiTableHDU since this routine knows nothing of the FITS header modifications required.

Parameters:

newCol - 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

addColumn

public int addColumn(java.lang.Object newCol,
                     int length)
              throws FitsException

This version of addColumn allows the user to override the default length associated with each column type.

Parameters:

newCol - The new column data

length - the requested length for the column

Returns:

the number of columns after this one is added.

Throws:

FitsException - if the operation failed

addRow

public int addRow(java.lang.Object[] newRow)
           throws FitsException

Description copied from interface: TableData

Add a row at the end of the table. Given the way the table is structured this will normally not be very efficient.Users should be cautious of calling this routine directly rather than the corresponding routine in AsciiTableHDU since this routine knows nothing of the FITS header modifications required.

Parameters:

newRow - An array of elements to be added. Each element of o should be an array of primitives or a String.

Returns:

the number of rows in the adapted table

Throws:

FitsException - if the operation failed

deleteColumns

public void deleteColumns(int start,
                          int len)
                   throws FitsException

Delete columns from the table.

Parameters:

start - The first, 0-indexed, column to be deleted.

len - The number of columns to be deleted.

Throws:

FitsException - if the operation failed

deleteRows

public void deleteRows(int start,
                       int len)
                throws FitsException

Delete rows from a FITS table

Parameters:

start - The first (0-indexed) row to be deleted.

len - The number of rows to be deleted.

Throws:

FitsException - if the operation failed

ensureData

private void ensureData()
                 throws FitsException

be sure that the data is filled. because the getData already tests null the getData is called without check.

Throws:

FitsException - if the operation failed

extractElement

private boolean extractElement(int offset,
                               int length,
                               java.lang.Object[] array,
                               int col,
                               int row,
                               java.lang.String nullFld)
                        throws FitsException

Move an element from the buffer into a data array.

Parameters:

offset - The offset within buffer at which the element starts.

length - The number of bytes in the buffer for the element.

array - An array of objects, each of which is a simple array.

col - Which element of array is to be modified?

row - Which index into that element is to be modified?

nullFld - What string signifies a null element?

Throws:

FitsException - if the operation failed

fillHeader

public void fillHeader(Header hdr)

Fill in a header with information that points to this data.

Specified by:

fillHeader in class Data

Parameters:

hdr - The header to be updated with information appropriate to the current table data.

getBuffer

private void getBuffer(int size,
                       long offset)
                throws java.io.IOException,
                       FitsException

Read some data into the buffer.

Throws:

java.io.IOException

FitsException

getColumn

public java.lang.Object getColumn(int col)
                           throws FitsException

Get a column of data

Parameters:

col - The 0-indexed column to be returned.

Returns:

The column object -- typically as a 1-d array.

Throws:

FitsException - if the operation failed

getData

public java.lang.Object getData()
                         throws FitsException

Get the ASCII table information. This will actually do the read if it had previously been deferred

Specified by:

getData in class Data

Returns:

The table data as an Object[] array.

Throws:

FitsException - if the operation failed

getElement

public java.lang.Object getElement(int row,
                                   int col)
                            throws FitsException

Get a single element as a one-d array. We return String's as arrays for consistency though they could be returned as a scalar.

Parameters:

row - The 0-based row

col - The 0-based column

Returns:

The requested cell data.

Throws:

FitsException - when unable to get the data.

getNCols

public int getNCols()

Get the number of columns in the table

Returns:

The number of columns

getNRows

public int getNRows()

Get the number of rows in the table

Returns:

The number of rows.

getRow

public java.lang.Object[] getRow(int row)
                          throws FitsException

Get a row. If the data has not yet been read just read this row.

Parameters:

row - The 0-indexed row to be returned.

Returns:

A row of data.

Throws:

FitsException - if the operation failed

getRowLen

public int getRowLen()

Get the number of bytes in a row

Returns:

The number of bytes for a single row in the table.

getTrueSize

protected long getTrueSize()

Return the size of the data section

Specified by:

getTrueSize in class Data

Returns:

The size in bytes of the data section, not includeing the padding.

isNull

public boolean isNull(int row,
                      int col)

See if an element is null.

Parameters:

row - The 0-based row

col - The 0-based column

Returns:

if the given element has been nulled.

parseSingleElement

private java.lang.Object parseSingleElement(int row,
                                            int col)
                                     throws FitsException

Read a single element from the table. This returns an array of dimension 1.

Throws:

FitsException - if the operation failed

parseSingleRow

private java.lang.Object[] parseSingleRow(int row)
                                   throws FitsException

Read a single row from the table. This returns a set of arrays of dimension 1.

Throws:

FitsException - if the operation failed

read

public void read(ArrayDataInput str)
          throws FitsException

Read in an ASCII table. Reading is deferred if we are reading from a random access device

Specified by:

read in interface FitsElement

Specified by:

read in class Data

Parameters:

str - the stream to read from

Throws:

FitsException - if the operation failed

setColumn

public void setColumn(int col,
                      java.lang.Object newData)
               throws FitsException

Replace a column with new data.

Parameters:

col - The 0-based index to the column

newData - The column data. This is typically a 1-d array.

Throws:

FitsException - if the operation failed

setElement

public void setElement(int row,
                       int col,
                       java.lang.Object newData)
                throws FitsException

Modify an element in the table

Parameters:

row - the 0-based row

col - the 0-based column

newData - The new value for the column. Typically a primitive[1] array.

Throws:

FitsException - if the operation failed

setNull

public void setNull(int row,
                    int col,
                    boolean flag)

Mark (or unmark) an element as null. Note that if this FITS file is latter written out, a TNULL keyword needs to be defined in the corresponding header. This routine does not add an element for String columns.

Parameters:

row - The 0-based row.

col - The 0-based column.

flag - True if the element is to be set to null.

setNullString

void setNullString(int col,
                   java.lang.String newNull)

Set the null string for a columns. This is not a public method since we want users to call the method in AsciiTableHDU and update the header also.

setRow

public void setRow(int row,
                   java.lang.Object[] newData)
            throws FitsException

Modify a row in the table

Parameters:

row - The 0-based index of the row

newData - The new data. Each element of this array is typically a primitive[1] array.

Throws:

FitsException - if the operation failed

singleElement

private java.lang.Object singleElement(int row,
                                       int col)

Extract a single element from a table. This returns an array of length 1.

singleRow

private java.lang.Object[] singleRow(int row)

Extract a single row from a table. This returns an array of Objects each of which is an array of length 1.

updateAfterDelete

public void updateAfterDelete(int oldNCol,
                              Header hdr)
                       throws FitsException

This is called after we delete columns. The HDU doesn't know how to update the TBCOL entries.

Parameters:

oldNCol - The number of columns we had before deletion.

hdr - The associated header. @throws FitsException if the operation failed

Throws:

FitsException

write

public void write(ArrayDataOutput str)
           throws FitsException

Write the data to an output stream.

Specified by:

write in interface FitsElement

Specified by:

write in class Data

Parameters:

str - The output stream to be written to

Throws:

FitsException - if any IO exception is found or some inconsistency the FITS file arises.