uk.ac.starlink.splat.data

Class FITSSpecDataImpl

java.lang.Object

uk.ac.starlink.splat.data.AbstractSpecDataImpl

uk.ac.starlink.splat.data.FITSSpecDataImpl

All Implemented Interfaces:

Serializable, FITSHeaderSource, SpecDataImpl

public class FITSSpecDataImpl
extends AbstractSpecDataImpl
implements FITSHeaderSource

FITSSpecDataImpl - implementation of SpecDataImpl to access FITS spectra.

See Also:

"The Bridge Design Pattern", Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected uk.ac.starlink.ast.FrameSet	astref Reference to the AST frameset (also used when cloned).
protected boolean	cloned The state of the object.
protected nom.tam.fits.Header	clonedHeader Reference to cloned header cards.
protected double[]	data Reference to cloned data values.
protected double[]	errors Reference to cloned data errors.
protected nom.tam.fits.Fits	fitsref Reference to Fits object.
protected String	fullName The FITS file name.
protected int	hdunum Current HDU number.
protected nom.tam.fits.BasicHDU[]	hdurefs HDU references for the current Fits object.
protected nom.tam.fits.Header	header Reference to the header cards.
protected static int	MAX_HEADER_VALUE Maxiumum number of characters in a header string.
protected String	shortName Default symbolic name.

Fields inherited from class uk.ac.starlink.splat.data.AbstractSpecDataImpl

dataLabel, dataUnits, parentImpl

Constructor Summary

Constructors

Constructor and Description
FITSSpecDataImpl(String fileName) Constructor - open a FITS file by file name.
FITSSpecDataImpl(String fileName, int hdunum) Constructor - open a FITS file by file name.
FITSSpecDataImpl(String fileName, SpecData source) Constructor, creating an object by cloning another.
FITSSpecDataImpl(String fileName, SpecData source, int hdunum) Constructor, creating an object by cloning another.

Method Summary

Modifier and Type	Method and Description
protected uk.ac.starlink.ast.FrameSet	checkForNonStandardFormat(nom.tam.fits.Header header) Check for known non-standard formats (far too many of those it seems).
protected uk.ac.starlink.ast.FrameSet	createAstSet() Create an AST frameset from the FITS headers.
protected uk.ac.starlink.ast.FrameSet	dummyAstSet() Create a dummy AST frameset for the current HDU.
static void	dumpHeader(nom.tam.fits.Header header, PrintStream ps) Class utility: Print the header to a given stream.
protected void	finalize() Finalise object.
uk.ac.starlink.ast.FrameSet	getAst() Return reference to AST frameset describing coordinates of FITS headers.
double[]	getData() Return a copy of the spectrum data values.
protected double[]	getDataCopy() Get a copy of the FITS spectrum data in double precision.
protected int[]	getDataDims() Return an array of with length the number of dimensions of the original data and with each element set to the size of that dimension.
double[]	getDataErrors() Return a copy of the spectrum data errors.
String	getDataFormat() Return the data format.
int[]	getDims() Return the data array dimensionality.
nom.tam.fits.Header	getFitsHeaders() If available offer the FITs headers as a nom.tam.fits.Header object.
String	getFullName() Return the file name.
String	getProperty(String key) Return a keyed value from the FITS headers.
String	getShortName() Return a symbolic name.
static nom.tam.util.Cursor	getStandardIterator(nom.tam.fits.Header header) Get a Cursor iterator that is positioned after the standard FITS keywords.
boolean	isSDSSFITSHeader() Check if it's a SDSS FITS format
static boolean	isSDSSFITSHeader(nom.tam.fits.Header header)
nom.tam.fits.BasicHDU	makeHDU()
nom.tam.fits.BasicHDU	makeHDU(boolean useStandardIterator)
protected void	makeMemoryClone(SpecData source) Set up this object as a clone of another spectrum.
protected void	openForRead(String fileName) Open a named FITS file for reading.
void	save() Save spectrum to the associated disk-file.
protected void	saveAst(nom.tam.fits.Header header) Write an AST frameset that describes the coordinates of the spectrum into the file.
protected void	saveToFile() Create a new FITS file using the current configuration to populate it.

Methods inherited from class uk.ac.starlink.splat.data.AbstractSpecDataImpl

getColumnNames, getCoordinateColumnName, getDataColumnName, getDataErrorColumnName, getDataLabel, getDataUnits, getObjectType, getParentImpl, getTime0, getTimeField, getTimeRefpos, getTimeScale, getTimeSystem, isFITSHeaderSource, setCoordinateColumnName, setDataColumnName, setDataErrorColumnName, setDataLabel, setDataUnits, setObjectType, setParentImpl, setTime0, setTimeField, setTimeRefpos, setTimeScale, setTimeSystem

Methods inherited from class java.lang.Object

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

Field Detail

fitsref

protected nom.tam.fits.Fits fitsref

Reference to Fits object.

hdurefs

protected nom.tam.fits.BasicHDU[] hdurefs

HDU references for the current Fits object.

hdunum

protected int hdunum

Current HDU number.

cloned

protected boolean cloned

The state of the object. Cloned is special and indicates that all values are memory resident, rather than backed up by the file.

data

protected double[] data

Reference to cloned data values.

errors

protected double[] errors

Reference to cloned data errors.

header

protected nom.tam.fits.Header header

Reference to the header cards.

clonedHeader

protected nom.tam.fits.Header clonedHeader

Reference to cloned header cards.

shortName

protected String shortName

Default symbolic name.

fullName

protected String fullName

The FITS file name.

astref

protected uk.ac.starlink.ast.FrameSet astref

Reference to the AST frameset (also used when cloned).

MAX_HEADER_VALUE

protected static final int MAX_HEADER_VALUE

Maxiumum number of characters in a header string.

See Also:

Constant Field Values

Constructor Detail

FITSSpecDataImpl

public FITSSpecDataImpl(String fileName)
                 throws SplatException

Constructor - open a FITS file by file name.

Throws:

SplatException

FITSSpecDataImpl

public FITSSpecDataImpl(String fileName,
                        int hdunum)
                 throws SplatException

Constructor - open a FITS file by file name.

Throws:

SplatException

FITSSpecDataImpl

public FITSSpecDataImpl(String fileName,
                        SpecData source)
                 throws SplatException

Constructor, creating an object by cloning another.

Throws:

SplatException

FITSSpecDataImpl

public FITSSpecDataImpl(String fileName,
                        SpecData source,
                        int hdunum)
                 throws SplatException

Constructor, creating an object by cloning another.

Throws:

SplatException

Method Detail

getData

public double[] getData()

Return a copy of the spectrum data values.

Specified by:

getData in interface SpecDataImpl

Specified by:

getData in class AbstractSpecDataImpl

getDataErrors

public double[] getDataErrors()

Return a copy of the spectrum data errors. TODO: need some mechanism for getting errors from another extension or FITS file.

Specified by:

getDataErrors in interface SpecDataImpl

Specified by:

getDataErrors in class AbstractSpecDataImpl

getDims

public int[] getDims()

Return the data array dimensionality.

Specified by:

getDims in interface SpecDataImpl

Specified by:

getDims in class AbstractSpecDataImpl

getShortName

public String getShortName()

Return a symbolic name. This is value of the "OBJECT" card, if present.

Specified by:

getShortName in interface SpecDataImpl

Specified by:

getShortName in class AbstractSpecDataImpl

getFullName

public String getFullName()

Return the file name.

Specified by:

getFullName in interface SpecDataImpl

Specified by:

getFullName in class AbstractSpecDataImpl

getAst

public uk.ac.starlink.ast.FrameSet getAst()

Return reference to AST frameset describing coordinates of FITS headers.

Specified by:

getAst in interface SpecDataImpl

Specified by:

getAst in class AbstractSpecDataImpl

getDataFormat

public String getDataFormat()

Return the data format.

Specified by:

getDataFormat in interface SpecDataImpl

Specified by:

getDataFormat in class AbstractSpecDataImpl

save

public void save()
          throws SplatException

Save spectrum to the associated disk-file.

Specified by:

save in interface SpecDataImpl

Specified by:

save in class AbstractSpecDataImpl

Throws:

SplatException

getProperty

public String getProperty(String key)

Return a keyed value from the FITS headers. Returns "" if not found.

Specified by:

getProperty in interface SpecDataImpl

Overrides:

getProperty in class AbstractSpecDataImpl

getFitsHeaders

public nom.tam.fits.Header getFitsHeaders()

Description copied from interface: FITSHeaderSource

If available offer the FITs headers as a nom.tam.fits.Header object.

Specified by:

getFitsHeaders in interface FITSHeaderSource

finalize

protected void finalize()
                 throws Throwable

Finalise object. Free any resources associated with member variables.

Overrides:

finalize in class Object

Throws:

Throwable

openForRead

protected void openForRead(String fileName)
                    throws SplatException

Open a named FITS file for reading.

Parameters:

fileName - The name of the FITS file, including any HDU reference (format file.fits[0]).

Throws:

SplatException

makeHDU

public nom.tam.fits.BasicHDU makeHDU()
                              throws nom.tam.fits.FitsException

Returns:

A new FITS HDU using the current configuration to populate it. Will only succeed for clone spectra.

Throws:

nom.tam.fits.FitsException

makeHDU

public nom.tam.fits.BasicHDU makeHDU(boolean useStandardIterator)
                              throws nom.tam.fits.FitsException

Throws:

nom.tam.fits.FitsException

saveToFile

protected void saveToFile()
                   throws SplatException

Create a new FITS file using the current configuration to populate it. Will only succeed for clone spectra.

Throws:

SplatException

saveAst

protected void saveAst(nom.tam.fits.Header header)

Write an AST frameset that describes the coordinates of the spectrum into the file.

getDataCopy

protected double[] getDataCopy()
                        throws nom.tam.fits.FitsException

Get a copy of the FITS spectrum data in double precision.

Throws:

nom.tam.fits.FitsException

createAstSet

protected uk.ac.starlink.ast.FrameSet createAstSet()

Create an AST frameset from the FITS headers. If fails then a simple null mapping is used instead.

checkForNonStandardFormat

protected uk.ac.starlink.ast.FrameSet checkForNonStandardFormat(nom.tam.fits.Header header)

Check for known non-standard formats (far too many of those it seems). For now we recognise SDSS, which uses a log(wavelength) scale.

isSDSSFITSHeader

public boolean isSDSSFITSHeader()

Check if it's a SDSS FITS format

isSDSSFITSHeader

public static boolean isSDSSFITSHeader(nom.tam.fits.Header header)

dummyAstSet

protected uk.ac.starlink.ast.FrameSet dummyAstSet()

Create a dummy AST frameset for the current HDU. Used when FITS headers fail to describe any additional coordinates and reproduce just an N-dimensional grid based coordinate system, where N is the dimensionality of the underlying data.

Returns:

reference to dummy AST frameset.

getDataDims

protected int[] getDataDims()

Return an array of with length the number of dimensions of the original data and with each element set to the size of that dimension. Note in SPLAT multidimensional data is assumed to be in column major order, so we need to reverse the order of these dimensions.

makeMemoryClone

protected void makeMemoryClone(SpecData source)

Set up this object as a clone of another spectrum. The resultant state is a memory-only resident one, until the save method is called, when the actual file is created and the contents are written.

getStandardIterator

public static nom.tam.util.Cursor getStandardIterator(nom.tam.fits.Header header)

Get a Cursor iterator that is positioned after the standard FITS keywords. If none are found then the iterator is positioned at the end.

Parameters:

header - Header that you want an iterator for.

Returns:

a Cursor iterator positioned at the end of the standard headers.

dumpHeader

public static void dumpHeader(nom.tam.fits.Header header,
                              PrintStream ps)

Class utility: Print the header to a given stream.

Parameters:

ps - the stream to which the card images are dumped.