uk.ac.starlink.fits

Class FitsTableBuilder

java.lang.Object

uk.ac.starlink.table.formats.DocumentedTableBuilder

uk.ac.starlink.fits.FitsTableBuilder

All Implemented Interfaces:

Documented, DocumentedIOHandler, MultiTableBuilder, TableBuilder

public class FitsTableBuilder
extends DocumentedTableBuilder
implements MultiTableBuilder

Implementation of the TableBuilder interface which gets StarTables from FITS files.

The table implementation used by uncompressed binary FITS tables stored on disk maps the file into memory (MappedByteBuffer) rather than reading the stream as such; this makes table construction very fast and cheap on memory, regardless of storage policy. This behaviour can be inhibited by referring to the file location as a URL (e.g. "file:spec23.fits" rather than "spec23.fits"), which fools the handler into thinking that it can't be mapped.

Limited support is provided for the HEALPix-FITS convention; the relevant HealpixTableInfo table parameters are added, but any BAD_DATA keyword value is ignored, and the 1024-element array-valued column variant of the format is not understood.

Author:

Mark Taylor (Starlink)

Constructor Summary

Constructors

Constructor and Description
FitsTableBuilder() Default constructor.
FitsTableBuilder(WideFits wide) Constructor.

Method Summary

Modifier and Type	Method and Description
static StarTable	attemptReadTable(InputStream in, boolean wantRandom, DataSource datsrc, WideFits wide, long[] pos, StoragePolicy policy) Reads the next header, and returns a StarTable based on it if it represents a table.
boolean	canImport(DataFlavor flavor) Returns true for a flavor with the MIME type "application/fits".
boolean	canStream() Indicates whether this handler can read tables from a stream.
boolean	docIncludesExample() Indicates whether the serialization of some (short) example table should be added to the user documentation for this handler.
static StarTable	findNamedTable(InputStream in, DataSource datsrc, String name, WideFits wide, long[] pos, StoragePolicy policy) Looks through the HDUs in a given FITS stream and if it finds one which has a given name, attempts to make a table out of it.
String	getFormatName() Returns "FITS".
String	getXmlDescription() Returns user-directed documentation in XML format.
StarTable	makeStarTable(DataSource datsrc, boolean wantRandom, StoragePolicy policy) Creates a StarTable from a DataSource which refers to a FITS file or stream.
TableSequence	makeStarTables(DataSource datsrc, StoragePolicy policy) Constructs a sequence of StarTables based on a given DataSource.
void	streamStarTable(InputStream in, TableSink sink, String extnum) Reads a FITS table from an input stream and writes it to a sink.

Methods inherited from class uk.ac.starlink.table.formats.DocumentedTableBuilder

getExtensions, looksLikeFile

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.starlink.table.TableBuilder

looksLikeFile

Methods inherited from interface uk.ac.starlink.table.formats.DocumentedIOHandler

matchesExtension, readText, toLink

Constructor Detail

FitsTableBuilder

public FitsTableBuilder()

Default constructor.

FitsTableBuilder

public FitsTableBuilder(WideFits wide)

Constructor.

Parameters:

wide - convention for representing extended columns; use null to avoid use of extended columns

Method Detail

getFormatName

public String getFormatName()

Returns "FITS".

Specified by:

getFormatName in interface TableBuilder

Returns:

one-word description of this handler's format

makeStarTable

public StarTable makeStarTable(DataSource datsrc,
                               boolean wantRandom,
                               StoragePolicy policy)
                        throws IOException

Creates a StarTable from a DataSource which refers to a FITS file or stream. If the source has a position attribute, it will be interpreted in one of two ways:

• If it's an integer, it will be interpreted as the index of the HDU holding the table. The first HDU is number 0 (though being primary this one can't hold a table), the first extension is number 1, etc.
• Otherwise it's interpreted as the name of the extension. Either of the forms "EXTNAME" or "EXTNAME-EXTVER" is permitted, where EXTNAME and EXTVER are the values of the corresponding FITS header cards, as per the FITS standard.

If the EXTNAME happens to be in the form of a positive integer, this means you can't refer to the extension by name. Too bad.

If there is no position attribute, the first HDU which does hold a table is used.

Specified by:

makeStarTable in interface TableBuilder

Parameters:

datsrc - the source of the FITS table data

wantRandom - whether a random-access table is preferred

policy - a StoragePolicy object which may be used to supply scratch storage if the builder needs it

Returns:

a new StarTable based on datsrc, or null if it doesn't look like a FITS table

Throws:

TableFormatException - if the table is not of a kind that can be handled by this handler

IOException - if an unexpected I/O error occurs during processing

makeStarTables

public TableSequence makeStarTables(DataSource datsrc,
                                    StoragePolicy policy)
                             throws IOException

Description copied from interface: MultiTableBuilder

Constructs a sequence of StarTables based on a given DataSource. If the source is not recognised or this object does not know how to make tables from it, then a TableFormatException should be thrown. If this builder thinks it should be able to handle the source but an error occurs during processing, an IOException can be thrown.

If the position of the data source is not null, then this method should return a sequence containing a single table, the one which would be returned by the makeStarTable method with that position.

Specified by:

makeStarTables in interface MultiTableBuilder

Parameters:

datsrc - the DataSource containing the table resource

policy - a StoragePolicy object which may be used to supply scratch storage if the builder needs it

Returns:

an array of StarTables read from datsrc

Throws:

TableFormatException - if the table is not of a kind that can be handled by this handler

IOException - if an unexpected I/O error occurs during processing

canImport

public boolean canImport(DataFlavor flavor)

Returns true for a flavor with the MIME type "application/fits".

Specified by:

canImport in interface TableBuilder

Parameters:

flavor - the DataFlavor whose suitability as stream input is to be assessed

Returns:

true iff this builder reckons it stands a good chance of turning a stream of type flavor into a StarTable

streamStarTable

public void streamStarTable(InputStream in,
                            TableSink sink,
                            String extnum)
                     throws IOException

Reads a FITS table from an input stream and writes it to a sink.

Specified by:

streamStarTable in interface TableBuilder

Parameters:

in - input stream containing the FITS data

sink - destination for table data

extnum - may contain a string representation of the HDU number in which the required table is found (otherwise the first table HDU will be used)

Throws:

TableFormatException - if the table can't be streamed or the data is malformed

IOException - if some other error occurs

canStream

public boolean canStream()

Description copied from class: DocumentedTableBuilder

Indicates whether this handler can read tables from a stream.

Specified by:

canStream in class DocumentedTableBuilder

Returns:

true iff this handler can read from streams

docIncludesExample

public boolean docIncludesExample()

Description copied from interface: DocumentedIOHandler

Indicates whether the serialization of some (short) example table should be added to the user documentation for this handler. Binary formats, or instances for which the Documented.getXmlDescription() method already includes some example output, should return false.

Specified by:

docIncludesExample in interface DocumentedIOHandler

Returns:

true if the user documentation would benefit from the addition of an example serialization

getXmlDescription

public String getXmlDescription()

Description copied from interface: Documented

Returns user-directed documentation in XML format.

The output should be a sequence of one or more <P> elements, using XHTML-like XML. Since rendering may be done in a number of contexts however, use of the full range of XHTML elements is discouraged. Where possible, the content should stick to simple markup such as the elements P, A, UL, OL, LI, DL, DT, DD EM, STRONG, I, B, CODE, TT, PRE.

Specified by:

getXmlDescription in interface Documented

Returns:

XML description of this object

findNamedTable

public static StarTable findNamedTable(InputStream in,
                                       DataSource datsrc,
                                       String name,
                                       WideFits wide,
                                       long[] pos,
                                       StoragePolicy policy)
                                throws IOException

Looks through the HDUs in a given FITS stream and if it finds one which has a given name, attempts to make a table out of it. The supplied name is checked against the EXTNAME header value (if present), and if that fails, against EXTNAME-EXTVER (if EXTVER is present too). Matching is case-insensitive.

Parameters:

in - stream to read from, positioned at the start of an HDU (before the header)

datsrc - a DataSource which can supply the data in strm

name - target extension name or name-version

wide - convention for representing extended columns; use null to avoid use of extended columns

pos - a 1-element array holding the position in datsrc at which strm is positioned - it's an array so it can be updated by this routine (sorry)

policy - storage policy, or null for default (normally not used)

Returns:

a new table

Throws:

IOException

attemptReadTable

public static StarTable attemptReadTable(InputStream in,
                                         boolean wantRandom,
                                         DataSource datsrc,
                                         WideFits wide,
                                         long[] pos,
                                         StoragePolicy policy)
                                  throws IOException

Reads the next header, and returns a StarTable based on it if it represents a table. If a StarTable is returned, it may not be safe to use the supplied input stream subsequently for other purposes. If the next HDU is some non-table type, null is returned and the stream is advanced to the end of that HDU; in this case the stream may continue to be used (e.g. for further calls to this method).

On exit, the first element of the pos array contains the position after the current HDU.

Parameters:

in - stream to read from, positioned at the start of an HDU (before the header)

wantRandom - whether a random-access table is preferred

datsrc - a DataSource which can supply the data in strm

wide - convention for representing extended columns; use null to avoid use of extended columns

pos - a 1-element array holding the position in datsrc at which strm is positioned - it's an array so it can be updated by this routine (sorry)

policy - storage policy, or null for default (normally not used)

Returns:

a StarTable made from the HDU at the start of strm or null

Throws:

IOException