nom.tam.fits

Class BinaryTable

java.lang.Object

nom.tam.fits.Data

nom.tam.fits.AbstractTableData

nom.tam.fits.BinaryTable

All Implemented Interfaces:

FitsElement, TableData

Direct Known Subclasses:

CompressedImageData, CompressedTableData

public class BinaryTable
extends AbstractTableData

This class defines the methods for accessing FITS binary table data.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	BinaryTable.ColumnDesc Collect all of the information we are using to describe a column into a single object.
protected static class	BinaryTable.SaveState Opaque state to pass to ColumnTable

Field Summary

Fields inherited from class nom.tam.fits.Data

dataSize, fileOffset, input

Constructor Summary

Constructors

Constructor and Description
BinaryTable() Create a null binary table data segment.
BinaryTable(ColumnTable<?> tabIn) Create a binary table from an existing ColumnTable
BinaryTable(Header myHeader) Create a binary table from given header information.
BinaryTable(Object[] o) Create a binary table from existing data in column order.
BinaryTable(Object[][] data) Create a binary table from existing data in row order.

Method Summary

Modifier and Type	Method and Description
protected void	addByteVaryingColumn()
int	addColumn(Object o) Add a column to the table without any associated header information.
int	addFlattenedColumn(Object o, int[] dims) Add a column where the data is already flattened.
int	addRow(Object[] o) Add a row at the end of the table.
static void	createColumnDataFor(BinaryTable table) TODO: this is only for internal access!
protected ColumnTable<BinaryTable.SaveState>	createColumnTable(Object[] arrCol, int[] sizes)
void	deleteColumns(int start, int len) Delete a set of columns.
void	deleteRows(int row, int len) Delete rows from a table.
void	fillHeader(Header h) Update a FITS header to reflect the current state of the data.
Class<?>[]	getBases()
Object	getColumn(int col) Get a given column
ColumnTable<BinaryTable.SaveState>	getData()
int[][]	getDimens()
Object	getElement(int i, int j) Get a particular element from the table.
Object[]	getFlatColumns()
Object	getFlattenedColumn(int col)
int	getHeapOffset()
int	getHeapSize()
Object[]	getModelRow()
int	getNCols() Get the number of columns in the table.
int	getNRows() Get the number of rows in the table
Object	getRawElement(int i, int j)
Object[]	getRow(int row) Get a given row
int[]	getSizes()
static int[]	getTDims(String tdims) Parse the TDIMS value.
long	getTrueSize() Get the size of the data in the HDU sans padding.
char[]	getTypes()
void	read(ArrayDataInput i) Read the data -- or defer reading on random access.
protected void	readHeap(ArrayDataInput input) Read the heap which contains the data for variable length arrays.
protected void	readTrueData(ArrayDataInput i) Read table, heap and padding
void	setColumn(int col, Object xcol) Replace a column in the table.
void	setElement(int i, int j, Object o) Replace a single element within the table.
void	setFlattenedColumn(int col, Object data) Set a column with the data already flattened.
void	setRow(int row, Object[] data) Replace a row in the table.
void	updateAfterDelete(int oldNcol, Header hdr) Update the header after a deletion.
protected boolean	validColumn(int j) Check if the column number is valid.
protected boolean	validRow(int i) Check to see if this is a valid row.
void	write(ArrayDataOutput os) Write the table, heap and padding.

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

Constructor Detail

BinaryTable

public BinaryTable()

Create a null binary table data segment.

BinaryTable

public BinaryTable(ColumnTable<?> tabIn)

Create a binary table from an existing ColumnTable

Parameters:

tabIn - the column table to create the binary table from

BinaryTable

public BinaryTable(Header myHeader)
            throws FitsException

Create a binary table from given header information.

Parameters:

myHeader - A header describing what the binary table should look like.

Throws:

FitsException - if the specified header is not usable for a binary table

BinaryTable

public BinaryTable(Object[] o)
            throws FitsException

Create a binary table from existing data in column order.

Parameters:

o - array of columns

Throws:

FitsException - if the data for the columns could not be used as coulumns

BinaryTable

public BinaryTable(Object[][] data)
            throws FitsException

Create a binary table from existing data in row order.

Parameters:

data - The data used to initialize the binary table.

Throws:

FitsException - if the data could not be converted to a binary table

Method Detail

createColumnDataFor

public static void createColumnDataFor(BinaryTable table)
                                throws FitsException

TODO: this is only for internal access!

Parameters:

table - the table to create the column data.

Throws:

FitsException - if the data could not be created.

getTDims

public static int[] getTDims(String tdims)

Parse the TDIMS value. If the TDIMS value cannot be deciphered a one-d array with the size given in arrsiz is returned.

Parameters:

tdims - The value of the TDIMSn card.

Returns:

An int array of the desired dimensions. Note that the order of the tdims is the inverse of the order in the TDIMS key.

addColumn

public int addColumn(Object o)
              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:

o - 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

addFlattenedColumn

public int addFlattenedColumn(Object o,
                              int[] dims)
                       throws FitsException

Add a column where the data is already flattened.

Parameters:

o - The new column data. This should be a one-dimensional primitive array.

dims - The dimensions of one row of the column.

Returns:

the new column size

Throws:

FitsException - if the array could not be flattened

addRow

public int addRow(Object[] o)
           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:

o - 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 a set of columns. Note that this does not fix the header, so users should normally call the routine in TableHDU. * @throws FitsException if the operation failed

Throws:

FitsException

deleteRows

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

Delete rows from a table.

Parameters:

row - The 0-indexed start of the rows to be deleted.

len - The number of rows to be deleted. * @throws FitsException if the operation failed

Throws:

FitsException

fillHeader

public void fillHeader(Header h)
                throws FitsException

Update a FITS header to reflect the current state of the data. * @throws FitsException if the operation failed

Parameters:

h - header to fill with the data from the current data object

Throws:

FitsException - if the operation fails

getBases

public Class<?>[] getBases()

Returns:

the types in the table, not the underlying types (e.g., for varying length arrays or booleans).

getColumn

public Object getColumn(int col)
                 throws FitsException

Get a given column

Parameters:

col - The index of the column. * @throws FitsException if the operation failed

Throws:

FitsException

getData

public ColumnTable<BinaryTable.SaveState> getData()
                                           throws FitsException

Specified by:

getData in class Data

Returns:

the data array object.

Throws:

FitsException - if the data could not be gathered .

getDimens

public int[][] getDimens()

getElement

public Object getElement(int i,
                         int j)
                  throws FitsException

Get a particular element from the table.

Parameters:

i - The row of the element.

j - The column of the element. * @throws FitsException if the operation failed

Throws:

FitsException

getFlatColumns

public Object[] getFlatColumns()

getFlattenedColumn

public Object getFlattenedColumn(int col)
                          throws FitsException

Parameters:

col - the column to flatten

Returns:

column in flattened format. For large tables getting a column in standard format can be inefficient because a separate object is needed for each row. Leaving the data in flattened format means that only a single object is created.

Throws:

FitsException - if the column could not be flattened

getHeapOffset

public int getHeapOffset()

Returns:

the offset to the heap

getHeapSize

public int getHeapSize()

Returns:

the size of the heap -- including the offset from the end of the table data.

getModelRow

public Object[] getModelRow()

Returns:

a row that may be used for direct i/o to the table.

getNCols

public int getNCols()

Get the number of columns in the table.

getNRows

public int getNRows()

Get the number of rows in the table

getRawElement

public Object getRawElement(int i,
                            int j)
                     throws FitsException

Parameters:

i - The row of the element.

j - The column of the element.

Returns:

a particular element from the table but do no processing of this element (e.g., dimension conversion or extraction of variable length array elements/)

Throws:

FitsException - if the operation failed

getRow

public Object[] getRow(int row)
                throws FitsException

Get a given row

Parameters:

row - The index of the row to be returned.

Returns:

A row of data. * @throws FitsException if the operation failed

Throws:

FitsException

getSizes

public int[] getSizes()

getTrueSize

public long getTrueSize()

Get the size of the data in the HDU sans padding.

getTypes

public char[] getTypes()

read

public void read(ArrayDataInput i)
          throws FitsException

Read the data -- or defer reading on random access. * @throws FitsException if the operation failed

Specified by:

read in interface FitsElement

Specified by:

read in class Data

Parameters:

i - The input data stream

Throws:

FitsException - if the read was unsuccessful.

setColumn

public void setColumn(int col,
                      Object xcol)
               throws FitsException

Replace a column in the table.

Parameters:

col - The index of the column to be replaced.

xcol - The new data for the column

Throws:

FitsException - Thrown if the data does not match the current column description.

setElement

public void setElement(int i,
                       int j,
                       Object o)
                throws FitsException

Replace a single element within the table.

Parameters:

i - The row of the data.

j - The column of the data.

o - The replacement data. * @throws FitsException if the operation failed

Throws:

FitsException

setFlattenedColumn

public void setFlattenedColumn(int col,
                               Object data)
                        throws FitsException

Set a column with the data already flattened.

Parameters:

col - The index of the column to be replaced.

data - The new data array. This should be a one-d primitive array.

Throws:

FitsException - Thrown if the type of length of the replacement data differs from the original.

setRow

public void setRow(int row,
                   Object[] data)
            throws FitsException

Replace a row in the table.

Parameters:

row - The index of the row to be replaced.

data - The new values for the row.

Throws:

FitsException - Thrown if the new row cannot match the existing data.

updateAfterDelete

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

Update the header after a deletion.

Throws:

FitsException - if the operation failed

write

public void write(ArrayDataOutput os)
           throws FitsException

Write the table, heap and padding. * @throws FitsException if the operation failed

Specified by:

write in interface FitsElement

Specified by:

write in class Data

Parameters:

os - The output stream on which to write the data.

Throws:

FitsException - if the write was unsuccessful.

addByteVaryingColumn

protected void addByteVaryingColumn()
                             throws TableException

Throws:

TableException

createColumnTable

protected ColumnTable<BinaryTable.SaveState> createColumnTable(Object[] arrCol,
                                                               int[] sizes)
                                                        throws TableException

Throws:

TableException

readHeap

protected void readHeap(ArrayDataInput input)
                 throws FitsException

Read the heap which contains the data for variable length arrays. A. Kovacs (4/1/08) Separated heap reading, s.t. the heap can be properly initialized even if in deferred read mode. columnToArray() checks and initializes the heap as necessary.

Parameters:

input - stream to read from.

Throws:

FitsException - if the heap could not be read from the stream

readTrueData

protected void readTrueData(ArrayDataInput i)
                     throws FitsException

Read table, heap and padding

Parameters:

i - the stream to read the data from.

Throws:

FitsException - if the reading failed

validColumn

protected boolean validColumn(int j)

Check if the column number is valid.

Parameters:

j - The Java index (first=0) of the column to check.

Returns:

true if the column is valid

validRow

protected boolean validRow(int i)

Check to see if this is a valid row.

Parameters:

i - The Java index (first=0) of the row to check.

Returns:

true if the row is valid