Package nom.tam.fits

Class BinaryTable

    • 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​(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
      • 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
    • 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​(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.
      • 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
      • 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
      • 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
      • 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
        Throws:
        FitsException
      • getBases

        public java.lang.Class<?>[] getBases()
        Returns:
        the types in the table, not the underlying types (e.g., for varying length arrays or booleans).
      • 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
      • getDimens

        public int[][] getDimens()
      • 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
      • getFlatColumns

        public java.lang.Object[] getFlatColumns()
      • 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
      • 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 java.lang.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 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
      • 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
      • 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,
                              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.
      • 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
      • 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.
      • 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.
      • 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.
      • 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