Package nom.tam.fits
Class BinaryTable
- java.lang.Object
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- nom.tam.fits.Data
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- nom.tam.fits.AbstractTableData
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- nom.tam.fits.BinaryTable
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- 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.
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Nested Class Summary
Nested Classes Modifier and Type Class 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
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Field Summary
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Fields inherited from class nom.tam.fits.Data
dataSize, fileOffset, input
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Constructor Summary
Constructors Constructor Description BinaryTable()
Create a null binary table data segment.BinaryTable(java.lang.Object[] o)
Create a binary table from existing data in column order.BinaryTable(java.lang.Object[][] data)
Create a binary table from existing data in row order.BinaryTable(Header myHeader)
Create a binary table from given header information.BinaryTable(ColumnTable<?> tabIn)
Create a binary table from an existing ColumnTable
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addByteVaryingColumn()
int
addColumn(java.lang.Object o)
Add a column to the table without any associated header information.int
addFlattenedColumn(java.lang.Object o, int[] dims)
Add a column where the data is already flattened.int
addRow(java.lang.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(java.lang.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.java.lang.Class<?>[]
getBases()
java.lang.Object
getColumn(int col)
Get a given columnColumnTable<BinaryTable.SaveState>
getData()
int[][]
getDimens()
java.lang.Object
getElement(int i, int j)
Get a particular element from the table.java.lang.Object[]
getFlatColumns()
java.lang.Object
getFlattenedColumn(int col)
int
getHeapOffset()
int
getHeapSize()
java.lang.Object[]
getModelRow()
int
getNCols()
Get the number of columns in the table.int
getNRows()
Get the number of rows in the tablejava.lang.Object
getRawElement(int i, int j)
java.lang.Object[]
getRow(int row)
Get a given rowint[]
getSizes()
static int[]
getTDims(java.lang.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 paddingvoid
setColumn(int col, java.lang.Object xcol)
Replace a column in the table.void
setElement(int i, int j, java.lang.Object o)
Replace a single element within the table.void
setFlattenedColumn(int col, java.lang.Object data)
Set a column with the data already flattened.void
setRow(int row, java.lang.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
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Constructor Detail
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BinaryTable
public BinaryTable()
Create a null binary table data segment.
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BinaryTable
public BinaryTable(ColumnTable<?> tabIn)
Create a binary table from an existing ColumnTable- Parameters:
tabIn
- the column table to create the binary table from
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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
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BinaryTable
public BinaryTable(java.lang.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
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BinaryTable
public BinaryTable(java.lang.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
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Method Detail
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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.
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getTDims
public static int[] getTDims(java.lang.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.
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addColumn
public int addColumn(java.lang.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
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addFlattenedColumn
public int addFlattenedColumn(java.lang.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
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addRow
public int addRow(java.lang.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
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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
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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
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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- Throws:
FitsException
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getBases
public java.lang.Class<?>[] getBases()
- Returns:
- the types in the table, not the underlying types (e.g., for varying length arrays or booleans).
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getColumn
public java.lang.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
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getData
public ColumnTable<BinaryTable.SaveState> getData() throws FitsException
- Specified by:
getData
in classData
- Returns:
- the data array object.
- Throws:
FitsException
- if the data could not be gathered .
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getDimens
public int[][] getDimens()
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getElement
public java.lang.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
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getFlatColumns
public java.lang.Object[] getFlatColumns()
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getFlattenedColumn
public java.lang.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
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getHeapOffset
public int getHeapOffset()
- Returns:
- the offset to the heap
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getHeapSize
public int getHeapSize()
- Returns:
- the size of the heap -- including the offset from the end of the table data.
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getModelRow
public java.lang.Object[] getModelRow()
- Returns:
- a row that may be used for direct i/o to the table.
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getNCols
public int getNCols()
Get the number of columns in the table.
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getNRows
public int getNRows()
Get the number of rows in the table
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getRawElement
public java.lang.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
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getRow
public java.lang.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
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getSizes
public int[] getSizes()
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getTrueSize
public long getTrueSize()
Get the size of the data in the HDU sans padding.
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getTypes
public char[] getTypes()
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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 interfaceFitsElement
- Specified by:
read
in classData
- Parameters:
i
- The input data stream- Throws:
FitsException
- if the read was unsuccessful.
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setColumn
public void setColumn(int col, java.lang.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.
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setElement
public void setElement(int i, int j, java.lang.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
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setFlattenedColumn
public void setFlattenedColumn(int col, java.lang.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.
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setRow
public void setRow(int row, java.lang.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.
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updateAfterDelete
public void updateAfterDelete(int oldNcol, Header hdr) throws FitsException
Update the header after a deletion.- Throws:
FitsException
- if the operation failed
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write
public void write(ArrayDataOutput os) throws FitsException
Write the table, heap and padding. * @throws FitsException if the operation failed- Specified by:
write
in interfaceFitsElement
- Specified by:
write
in classData
- Parameters:
os
- The output stream on which to write the data.- Throws:
FitsException
- if the write was unsuccessful.
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addByteVaryingColumn
protected void addByteVaryingColumn() throws TableException
- Throws:
TableException
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createColumnTable
protected ColumnTable<BinaryTable.SaveState> createColumnTable(java.lang.Object[] arrCol, int[] sizes) throws TableException
- Throws:
TableException
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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
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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
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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
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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
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