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Java library for reading and writing FITS files. FITS, the Flexible Image Transport System, is the format commonly used in the archiving and transport of astronomical data.
package nom.tam.fits;
import static nom.tam.fits.header.Standard.NAXISn;
import static nom.tam.fits.header.Standard.TFIELDS;
import static nom.tam.fits.header.Standard.TFORMn;
import static nom.tam.fits.header.Standard.TTYPEn;
import java.util.logging.Logger;
import nom.tam.fits.header.GenericKey;
import nom.tam.fits.header.IFitsHeader;
/*
* #%L
* nom.tam FITS library
* %%
* Copyright (C) 2004 - 2015 nom-tam-fits
* %%
* This is free and unencumbered software released into the public domain.
*
* Anyone is free to copy, modify, publish, use, compile, sell, or
* distribute this software, either in source code form or as a compiled
* binary, for any purpose, commercial or non-commercial, and by any
* means.
*
* In jurisdictions that recognize copyright laws, the author or authors
* of this software dedicate any and all copyright interest in the
* software to the public domain. We make this dedication for the benefit
* of the public at large and to the detriment of our heirs and
* successors. We intend this dedication to be an overt act of
* relinquishment in perpetuity of all present and future rights to this
* software under copyright law.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
* OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
* ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
* #L%
*/
/**
* This class allows FITS binary and ASCII tables to be accessed via a common
* interface.
*/
public abstract class TableHDU extends BasicHDU {
private static final Logger LOG = Logger.getLogger(TableHDU.class.getName());
/**
* Create the TableHDU. Note that this will normally only be invoked by
* subclasses in the FITS package.
*
* @param hdr
* the header
* @param td
* The data for the table.
*/
protected TableHDU(Header hdr, T td) {
super(hdr, td);
}
/**
* Add a column to the table without any associated header information.
*
* @param 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).
* @return the number of columns in the adapted table
* @throws FitsException
* if the operation failed
*/
public int addColumn(Object newCol) throws FitsException {
int nCols = getNCols();
this.myHeader.addValue(TFIELDS, nCols);
return nCols;
}
/**
* Add a row to the end of the table. If this is the first row, then this
* will add appropriate columns for each of the entries. The rows to add
* must be supplied as column based array of arrays.
*
* @return the number of rows in the adapted table
* @param newRows
* rows to add to the table
* @throws FitsException
* if the operation failed
*/
public int addRow(Object[] newRows) throws FitsException {
int row = this.myData.addRow(newRows);
this.myHeader.addValue(NAXISn.n(2), getNRows());
return row;
}
/**
* @return the stems of the keywords that are associated with table columns.
* Users can supplement this with their own and call the appropriate
* deleteColumns fields.
*/
protected abstract IFitsHeader[] columnKeyStems();
/**
* Delete a set of columns from a table.
*
* @param column
* The one-indexed start column.
* @param len
* The number of columns to delete.
* @throws FitsException
* if the operation failed
*/
public void deleteColumnsIndexOne(int column, int len) throws FitsException {
deleteColumnsIndexZero(column - 1, len);
}
/**
* Delete a set of columns from a table.
*
* @param column
* The one-indexed start column.
* @param len
* The number of columns to delete.
* @param fields
* Stems for the header fields to be removed for the table.
* @throws FitsException
* if the operation failed
*/
public void deleteColumnsIndexOne(int column, int len, String[] fields) throws FitsException {
deleteColumnsIndexZero(column - 1, len, GenericKey.create(fields));
}
/**
* Delete a set of columns from a table.
*
* @param column
* The one-indexed start column.
* @param len
* The number of columns to delete.
* @throws FitsException
* if the operation failed
*/
public void deleteColumnsIndexZero(int column, int len) throws FitsException {
deleteColumnsIndexZero(column, len, columnKeyStems());
}
/**
* Delete a set of columns from a table.
*
* @param column
* The zero-indexed start column.
* @param len
* The number of columns to delete.
* @param fields
* Stems for the header fields to be removed for the table.
* @throws FitsException
* if the operation failed
*/
public void deleteColumnsIndexZero(int column, int len, IFitsHeader[] fields) throws FitsException {
if (column < 0 || len < 0 || column + len > getNCols()) {
throw new FitsException("Illegal columns deletion request- Start:" + column + " Len:" + len + " from table with " + getNCols() + " columns");
}
if (len == 0) {
return;
}
int ncol = getNCols();
this.myData.deleteColumns(column, len);
// Get rid of the keywords for the deleted columns
for (int col = column; col < column + len; col += 1) {
for (IFitsHeader field : fields) {
this.myHeader.deleteKey(field.n(col + 1));
}
}
// Shift the keywords for the columns after the deleted columns
for (int col = column + len; col < ncol; col += 1) {
for (IFitsHeader field : fields) {
IFitsHeader oldKey = field.n(col + 1);
IFitsHeader newKey = field.n(col + 1 - len);
if (this.myHeader.containsKey(oldKey)) {
this.myHeader.replaceKey(oldKey, newKey);
}
}
}
// Update the number of fields.
this.myHeader.addValue(TFIELDS, getNCols());
// Give the data sections a chance to update the header too.
this.myData.updateAfterDelete(ncol, this.myHeader);
}
/**
* Remove all rows from the table starting at some specific index from the
* table. Inspired by a routine by R. Mathar but re-implemented using the
* DataTable and changes to AsciiTable so that it can be done easily for
* both Binary and ASCII tables.
*
* @param row
* the (0-based) index of the first row to be deleted.
* @throws FitsException
* if an error occurs.
*/
public void deleteRows(final int row) throws FitsException {
deleteRows(row, getNRows() - row);
}
/**
* Remove a number of adjacent rows from the table. This routine was
* inspired by code by R.Mathar but re-implemented using changes in the
* ColumnTable class abd AsciiTable so that we can do it for all FITS
* tables.
*
* @param firstRow
* the (0-based) index of the first row to be deleted. This is
* zero-based indexing: 0<=firstrow< number of rows.
* @param nRow
* the total number of rows to be deleted.
* @throws FitsException
* If an error occurs in the deletion.
*/
public void deleteRows(final int firstRow, int nRow) throws FitsException {
// Just ignore invalid requests.
if (nRow <= 0 || firstRow >= getNRows() || firstRow <= 0) {
return;
}
/* correct if more rows are requested than available */
if (nRow > getNRows() - firstRow) {
nRow = getNRows() - firstRow;
}
this.myData.deleteRows(firstRow, nRow);
this.myHeader.setNaxis(2, getNRows());
}
/**
* Find the 0-based column index corresponding to a particular column name.
*
* @return index of the column
* @param colName
* the name of the column
*/
public int findColumn(String colName) {
for (int i = 0; i < getNCols(); i += 1) {
String val = this.myHeader.getStringValue(TTYPEn.n(i + 1));
if (val != null && val.trim().equals(colName)) {
return i;
}
}
return -1;
}
/**
* @return a specific column from the table using 0-based column indexing.
* @param col
* column index to get
* @throws FitsException
* if the operation failed
*/
public Object getColumn(int col) throws FitsException {
return this.myData.getColumn(col);
}
/**
* @return a specific column of the table where the column name is specified
* using the TTYPEn keywords in the header.
* @param colName
* The name of the column to be extracted.
* @throws FitsException
* if the operation failed
*/
public Object getColumn(String colName) throws FitsException {
return getColumn(findColumn(colName));
}
/**
* Get the FITS type of a column in the table.
*
* @param index
* The 0-based index of the column.
* @return The FITS type.
* @throws FitsException
* if an invalid index was requested.
*/
public String getColumnFormat(int index) throws FitsException {
int flds = this.myHeader.getIntValue(TFIELDS, 0);
if (index < 0 || index >= flds) {
throw new FitsException("Bad column index " + index + " (only " + flds + " columns)");
}
return this.myHeader.getStringValue(TFORMn.n(index + 1)).trim();
}
/**
* Convenience method for getting column data. Note that this works only for
* metadata that returns a string value. This is equivalent to
* getStringValue(type+index);
*
* @return meta data string value
* @param index
* index of the colum
* @param type
* the key type to get
*/
public String getColumnMeta(int index, String type) {
return this.myHeader.getStringValue(type + (index + 1));
}
/**
* Get the name of a column in the table.
*
* @param index
* The 0-based column index.
* @return The column name.
*/
public String getColumnName(int index) {
String ttype = this.myHeader.getStringValue(TTYPEn.n(index + 1));
if (ttype != null) {
ttype = ttype.trim();
}
return ttype;
}
/**
* @return all of the columns of the table.
* @throws FitsException
* if the operation failed
*/
public Object[] getColumns() throws FitsException {
Object[] result = new Object[getNCols()];
for (int i = 0; i < result.length; i += 1) {
result[i] = getColumn(i);
}
return result;
}
/**
* @return a specific element of the table using 0-based indices.
* @param row
* the row index of the element
* @param col
* the column index of the element
* @throws FitsException
* if the operation failed
*/
public Object getElement(int row, int col) throws FitsException {
return this.myData.getElement(row, col);
}
/**
* Get the number of columns for this table
*
* @return The number of columns in the table.
*/
public int getNCols() {
return this.myData.getNCols();
}
/**
* Get the number of rows for this table
*
* @return The number of rows in the table.
*/
public int getNRows() {
return this.myData.getNRows();
}
/**
* @return a specific row of the table.
* @param row
* the index of the row to retreive
* @throws FitsException
* if the operation failed
*/
public Object[] getRow(int row) throws FitsException {
return this.myData.getRow(row);
}
/**
* Update a column within a table. The new column should have the same
* format ast the column being replaced.
*
* @param col
* index of the column to replace
* @param newCol
* the replacement column
* @throws FitsException
* if the operation failed
*/
public void setColumn(int col, Object newCol) throws FitsException {
this.myData.setColumn(col, newCol);
}
/**
* Update a column within a table. The new column should have the same
* format as the column being replaced.
*
* @param colName
* name of the column to replace
* @param newCol
* the replacement column
* @throws FitsException
* if the operation failed
*/
public void setColumn(String colName, Object newCol) throws FitsException {
setColumn(findColumn(colName), newCol);
}
/**
* 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.
*
* @param index
* The 0-based index of the column
* @param key
* The column key. I.e., the keyword will be key+(index+1)
* @param value
* The value to be placed in the header.
* @param comment
* The comment for the header
* @param after
* Should the header card be after the current column metadata
* block (true), or immediately before the TFORM card (false). @throws
* FitsException if the operation failed
* @throws FitsException
* if the header could not be updated
*/
public void setColumnMeta(int index, IFitsHeader key, String value, String comment, boolean after) throws FitsException {
setCurrentColumn(index, after);
this.myHeader.addValue(key.n(index + 1).key(), value, comment);
}
public void setColumnMeta(int index, String key, boolean value, String comment, boolean after) throws FitsException {
setCurrentColumn(index, after);
this.myHeader.addValue(key + (index + 1), value, comment);
}
public void setColumnMeta(int index, String key, double value, String comment, boolean after) throws FitsException {
setCurrentColumn(index, after);
this.myHeader.addValue(key + (index + 1), value, comment);
}
public void setColumnMeta(int index, String key, double value, int precision, String comment, boolean after) throws FitsException {
setCurrentColumn(index, after);
this.myHeader.addValue(key + (index + 1), value, precision, comment);
}
public void setColumnMeta(int index, String key, long value, String comment, boolean after) throws FitsException {
setCurrentColumn(index, after);
this.myHeader.addValue(key + (index + 1), value, comment);
}
public void setColumnMeta(int index, String key, String value, String comment) throws FitsException {
setColumnMeta(index, key, value, comment, true);
}
/**
* 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.
*
* @param index
* The 0-based index of the column
* @param key
* The column key. I.e., the keyword will be key+(index+1)
* @param value
* The value to be placed in the header.
* @param comment
* The comment for the header
* @param after
* Should the header card be after the current column metadata
* block (true), or immediately before the TFORM card (false). @throws
* FitsException if the operation failed
* @throws FitsException
* if the header could not be updated
* @deprecated use
* {@link #setColumnMeta(int, IFitsHeader, String, String, boolean)}
*/
@Deprecated
public void setColumnMeta(int index, String key, String value, String comment, boolean after) throws FitsException {
setCurrentColumn(index, after);
this.myHeader.addValue(key + (index + 1), value, comment);
}
public void setColumnName(int index, String name, String comment) throws FitsException {
setColumnMeta(index, TTYPEn, name, comment, true);
}
/**
* Set the cursor in the header to point after the metadata for the
* specified column
*
* @param col
* The 0-based index of the column
*/
public void setCurrentColumn(int col) {
setCurrentColumn(col, true);
}
/**
* Set the cursor in the header to point either before the TFORM value or
* after the column metadat
*
* @param col
* The 0-based index of the column
* @param after
* True if the cursor should be placed after the existing column
* metadata or false if the cursor is to be placed before the
* TFORM value. If no corresponding TFORM is found, the cursoe
* will be placed at the end of current header.
*/
public void setCurrentColumn(int col, boolean after) {
if (after) {
this.myHeader.positionAfterIndex(TFORMn, col + 1);
} else {
this.myHeader.findCard(TFORMn.n(col + 1));
}
}
/**
* Update a single element within the table.
*
* @param row
* the row index
* @param col
* the column index
* @param element
* the replacement element
* @throws FitsException
* if the operation failed
*/
public void setElement(int row, int col, Object element) throws FitsException {
this.myData.setElement(row, col, element);
}
/**
* Update a row within a table.
*
* @param row
* row index
* @param newRow
* the replacement row
* @throws FitsException
* if the operation failed
*/
public void setRow(int row, Object[] newRow) throws FitsException {
this.myData.setRow(row, newRow);
}
}
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