spv.spectrum.factory
Class AbstractFileFactoryModule

java.lang.Object
  spv.spectrum.factory.AbstractFileFactoryModule

All Implemented Interfaces:

SpectrumFileFactoryModule

Direct Known Subclasses:

ASCIIFactoryModule, Fits2DTableAbstractFactoryModule, Fits3DTableAbstractFactoryModule, ImageAbstractFactoryModule, SDSSFactoryModule, SEDFactoryModule, SEDVOTableFactoryModule, SPCFactoryModule, STIS2DFactoryModule

public abstract class AbstractFileFactoryModule
extends java.lang.Object
implements SpectrumFileFactoryModule

Abstract superclass of all instrument-specific factory modules.

Version:

1.0 - 25Mar02, 1.1 - 21Jun02

Author:

Ivo Busko (Space Telescope Science Institute)

Field Summary

protected static java.lang.String	BIN_NUMBER_UNITS
protected static java.lang.String	C_BACK
static java.lang.String	C_DATA
protected static java.lang.String	C_DQ
static java.lang.String	C_ERROR
static java.lang.String	C_FLUX
protected static java.lang.String	C_GROSS
protected static java.lang.String	C_NELEM
protected static java.lang.String	C_NET
protected static java.lang.String	C_SPORDER
static java.lang.String	C_WAVELENGTH

Constructor Summary

AbstractFileFactoryModule()

Method Summary

void	addSSAPParameters(Spectrum sp, SpectrumSpecification ss) Adds SSAP parameters to the spectrum meta parameter list.
protected void	buildExtentMetaParameters(Spectrum sp) Populate meta parameters with extent values.
protected void	buildLocationMetaParameters(Spectrum sp) Populate meta parameters with location values.
protected SingleSpectrum	buildSingleSpectrum(SingleSpectrum sp, java.lang.String name, SpectrumSpecification ss, SpectrumHeader hdr, double[] wave, XUnits waveu, double[] flux, YUnits fluxu, double[] error, YUnits erroru, int[] dq, DQBits dqbits) Builds a SingleSpectrum instance.
protected SingleSpectrum	buildSingleSpectrum(SingleSpectrum sp, java.lang.String name, SpectrumSpecification ss, SpectrumHeader hdr, double[] wave, XUnits waveu, java.lang.String wavename, double[] flux, YUnits fluxu, java.lang.String fluxname, double[] error, YUnits erroru, java.lang.String errorname, int[] dq, DQBits dqbits) Builds a SingleSpectrum instance.
protected SingleSpectrum	buildSingleSpectrum(SingleSpectrum sp, java.lang.String name, SpectrumSpecification ss, SpectrumHeader hdr, double[] wave, XUnits waveu, java.lang.String wavename, double[] flux, YUnits fluxu, java.lang.String fluxname, double[] error, YUnits erroru, java.lang.String errorname, int[] dq, DQBits dqbits, java.lang.String emptyArrayErrorMessage) Builds a SingleSpectrum instance.
protected void	buildSpectralExtentMetaParameter(Spectrum sp) Populate meta parameters with spectral extent taken directly from the wavelength array.
protected void	buildTimeExtentMetaParameter(Spectrum sp, java.lang.String keyword) Populate meta parameters with time extent.
protected YUnits	fixIntensityUnits(YUnits units)
protected void	getGenericMetaParameter(Spectrum sp) Populate meta parameters with generic info.
protected void	getInstrumentPositionMetaParameter(Spectrum sp, java.lang.String ra, java.lang.String dec) Populate meta parameters with instrument position.
protected void	getPositionMetaParameter(Spectrum sp, java.lang.String ra, java.lang.String dec) Populate meta parameters with object position.
protected void	getTimeMetaParameter(Spectrum sp, java.lang.String start, java.lang.String end) Populate meta parameters with observation time.
protected java.lang.String	getUnits(nom.tam.fits.TableHDU hdu, java.lang.String colname) The JavaFITS library has a kludgy way of retrieving the physical units from a table column.
protected java.net.URL	getURL(java.lang.String filename) Returns the URL given a file name.
protected boolean	isFullD(double[] array) Returns true if array is not empty.
protected boolean	isFullI(int[] array) Returns true if array is not empty.
protected boolean	isTwoD(FitsFileAttributes ffa) Checks if a binary table carries arrays, or is a flat 2-D table.
abstract boolean	isValidInstrument(FitsFileAttributes ffa) Tests if a file contains spectra from a specific instrument.
abstract FileDescriptor	makeFileDescriptor(java.lang.String filename, nom.tam.fits.Fits fits) Creates a FileDescriptor object.
abstract Spectrum	makeSpectrum(SpectrumSpecification ss, nom.tam.fits.Fits fits) Creates a Spectrum object.
abstract SpectrumSpecification	makeSpectrumSpecification(java.net.URL url, nom.tam.fits.Fits fits) Returns a SpectrumSpecification object of the appropriate sub-type, given a completely specified file name.
protected void	maskAll(Spectrum sp) Masks all anomalies in the input spectrum.

Methods inherited from class java.lang.Object

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

Field Detail

C_FLUX

public static final java.lang.String C_FLUX

C_DATA

public static final java.lang.String C_DATA

C_ERROR

public static final java.lang.String C_ERROR

C_WAVELENGTH

public static final java.lang.String C_WAVELENGTH

C_SPORDER

protected static final java.lang.String C_SPORDER

C_NELEM

protected static final java.lang.String C_NELEM

C_GROSS

protected static final java.lang.String C_GROSS

C_BACK

protected static final java.lang.String C_BACK

C_NET

protected static final java.lang.String C_NET

C_DQ

protected static final java.lang.String C_DQ

BIN_NUMBER_UNITS

protected static final java.lang.String BIN_NUMBER_UNITS

Constructor Detail

AbstractFileFactoryModule

public AbstractFileFactoryModule()

Method Detail

makeSpectrum

public abstract Spectrum makeSpectrum(SpectrumSpecification ss,
                                      nom.tam.fits.Fits fits)
                               throws nom.tam.fits.FitsException,
                                      java.io.IOException,
                                      SpectrumException

Creates a Spectrum object.

Specified by:

makeSpectrum in interface SpectrumFileFactoryModule

Parameters:

ss - the spectrum specification

fits - the associated Fits object, or null if any

Returns:

the spectrum object

Throws:

java.io.IOException

nom.tam.fits.FitsException

SpectrumException

makeSpectrumSpecification

public abstract SpectrumSpecification makeSpectrumSpecification(java.net.URL url,
                                                                nom.tam.fits.Fits fits)
                                                         throws nom.tam.fits.FitsException,
                                                                java.io.IOException

Returns a SpectrumSpecification object of the appropriate sub-type, given a completely specified file name.

Specified by:

makeSpectrumSpecification in interface SpectrumFileFactoryModule

Parameters:

url - the URL with the file name complete will all specifications necessary to locate a valid spectrum, such as FITS extension, row selector, image section, etc.

fits - the associated Fits object, or null if any

Returns:

the SpectrumSpecification object of the appropriate sub-type

Throws:

java.io.IOException

nom.tam.fits.FitsException

makeFileDescriptor

public abstract FileDescriptor makeFileDescriptor(java.lang.String filename,
                                                  nom.tam.fits.Fits fits)
                                           throws nom.tam.fits.FitsException,
                                                  java.io.IOException,
                                                  SpectrumException

Creates a FileDescriptor object. The file name cannot have any constructs such as FITS extension specifiers, row/column selectors or image sections.

Specified by:

makeFileDescriptor in interface SpectrumFileFactoryModule

Parameters:

filename - the file name

fits - the associated Fits object, or null if any

Returns:

the FileDescripto object of the appropriate sub-type

Throws:

java.io.IOException

nom.tam.fits.FitsException

SpectrumException

isValidInstrument

public abstract boolean isValidInstrument(FitsFileAttributes ffa)
                                   throws nom.tam.fits.FitsException,
                                          java.io.IOException

Tests if a file contains spectra from a specific instrument.

Specified by:

isValidInstrument in interface SpectrumFileFactoryModule

Parameters:

ffa - attributes of the FITS file

Returns:

true if the file matches the instrument, false otherwise.

Throws:

nom.tam.fits.FitsException

java.io.IOException

addSSAPParameters

public void addSSAPParameters(Spectrum sp,
                              SpectrumSpecification ss)

Adds SSAP parameters to the spectrum meta parameter list.

Specified by:

addSSAPParameters in interface SpectrumFileFactoryModule

Parameters:

sp - the spectrum to be updated

ss - the spectrum specification holding SSAP parameters

buildSingleSpectrum

protected SingleSpectrum buildSingleSpectrum(SingleSpectrum sp,
                                             java.lang.String name,
                                             SpectrumSpecification ss,
                                             SpectrumHeader hdr,
                                             double[] wave,
                                             XUnits waveu,
                                             double[] flux,
                                             YUnits fluxu,
                                             double[] error,
                                             YUnits erroru,
                                             int[] dq,
                                             DQBits dqbits)
                                      throws SpectrumException

Builds a SingleSpectrum instance. The wavelength and flux array get their standard names.

Parameters:

sp - the empty instance to be built

name - the name

ss - the spectrum specification

hdr - the header

wave - the wavelenth array

waveu - the units associated with the wavelength array

flux - the flux array

fluxu - the units associated with the flux array

error - the error array

erroru - the units associated with the error array

dq - the data quality array

dqbits - the DQBits object associated with the dq array

Returns:

the SingleSpectrum instance

Throws:

SpectrumException

buildSingleSpectrum

protected SingleSpectrum buildSingleSpectrum(SingleSpectrum sp,
                                             java.lang.String name,
                                             SpectrumSpecification ss,
                                             SpectrumHeader hdr,
                                             double[] wave,
                                             XUnits waveu,
                                             java.lang.String wavename,
                                             double[] flux,
                                             YUnits fluxu,
                                             java.lang.String fluxname,
                                             double[] error,
                                             YUnits erroru,
                                             java.lang.String errorname,
                                             int[] dq,
                                             DQBits dqbits)
                                      throws SpectrumException

Builds a SingleSpectrum instance.

Parameters:

sp - the empty instance to be built

name - the spectrum name

ss - the spectrum specification

hdr - the header

wave - the wavelenth array

waveu - the units associated with the wavelength array

wavename - the name of the wavelength array

flux - the flux array

fluxu - the units associated with the flux array

fluxname - the name of the flux array

error - the error array

erroru - the units associated with the error array

errorname - the name of the error array

dq - the data quality array

dqbits - the DQBits object associated with the dq array

Returns:

the SingleSpectrum instance

Throws:

SpectrumException

buildSingleSpectrum

protected SingleSpectrum buildSingleSpectrum(SingleSpectrum sp,
                                             java.lang.String name,
                                             SpectrumSpecification ss,
                                             SpectrumHeader hdr,
                                             double[] wave,
                                             XUnits waveu,
                                             java.lang.String wavename,
                                             double[] flux,
                                             YUnits fluxu,
                                             java.lang.String fluxname,
                                             double[] error,
                                             YUnits erroru,
                                             java.lang.String errorname,
                                             int[] dq,
                                             DQBits dqbits,
                                             java.lang.String emptyArrayErrorMessage)
                                      throws SpectrumException

Builds a SingleSpectrum instance.

This method includes a check for very long spectra. With more than 20,000 or so data points, plotting becomes painfully slow (bug in GeneralPath Java2D class). This method inserts data break points in the input arrays in case the input arrays exceed a given size.

Parameters:

sp - the empty instance to be built

name - the spectrum name

ss - the spectrum specification

hdr - the header

wave - the wavelenth array

waveu - the units associated with the wavelength array

wavename - the name of the wavelength array

flux - the flux array

fluxu - the units associated with the flux array

fluxname - the name of the flux array

error - the error array

erroru - the units associated with the error array

errorname - the name of the error array

dq - the data quality array

dqbits - the DQBits object associated with the dq array

emptyArrayErrorMessage - error message for empty ydata array condition

Returns:

the SingleSpectrum instance

Throws:

SpectrumException

fixIntensityUnits

protected YUnits fixIntensityUnits(YUnits units)

getUnits

protected java.lang.String getUnits(nom.tam.fits.TableHDU hdu,
                                    java.lang.String colname)

The JavaFITS library has a kludgy way of retrieving the physical units from a table column. This method is basicaly a capsule to hide the nastiness away. Why not provide a plain getUnits method ?

Parameters:

hdu - the HDU that contains the table

colname - the column name

Returns:

the units associated with the given column. If no columnn is found, returns the "UNITLESS" string.

isFullD

protected boolean isFullD(double[] array)

Returns true if array is not empty. Empty array is signaled by all its elements having the same stored value.

Returns:

true if array is not empty

isFullI

protected boolean isFullI(int[] array)

Returns true if array is not empty. Empty array is signaled by all its elements having the same stored value.

Returns:

true if array is not empty

getURL

protected java.net.URL getURL(java.lang.String filename)

Returns the URL given a file name.

Parameters:

filename - the file name

Returns:

the URL

maskAll

protected void maskAll(Spectrum sp)

Masks all anomalies in the input spectrum.

Parameters:

sp - the spectrum to be masked

isTwoD

protected boolean isTwoD(FitsFileAttributes ffa)
                  throws nom.tam.fits.FitsException,
                         java.io.IOException

Checks if a binary table carries arrays, or is a flat 2-D table.

Parameters:

ffa - the file attributes object

Returns:

true if no array columns exist

Throws:

nom.tam.fits.FitsException

java.io.IOException

getGenericMetaParameter

protected void getGenericMetaParameter(Spectrum sp)

Populate meta parameters with generic info.

Parameters:

sp - spectrum whose meta parameters are to be updated

getPositionMetaParameter

protected void getPositionMetaParameter(Spectrum sp,
                                        java.lang.String ra,
                                        java.lang.String dec)

Populate meta parameters with object position.

This method populates both the nominal and the instrument positions. Subclasses should call explictly method getInstrumentPositionMetaParameter if different header keywords are used for each one.

Parameters:

sp - spectrum whose meta parameters are to be updated

ra - R.A. keyword in header

dec - DEC keyword in header

getInstrumentPositionMetaParameter

protected void getInstrumentPositionMetaParameter(Spectrum sp,
                                                  java.lang.String ra,
                                                  java.lang.String dec)

Populate meta parameters with instrument position.

Parameters:

sp - spectrum whose meta parameters are to be updated

ra - R.A. keyword in header

dec - DEC keyword in header

getTimeMetaParameter

protected void getTimeMetaParameter(Spectrum sp,
                                    java.lang.String start,
                                    java.lang.String end)

Populate meta parameters with observation time.

Parameters:

sp - the spectrum whose meta parameters are to be updated

start - the header keyword with start time

end - the header keyword with end time

buildSpectralExtentMetaParameter

protected void buildSpectralExtentMetaParameter(Spectrum sp)

Populate meta parameters with spectral extent taken directly from the wavelength array.

Parameters:

sp - the spectrum whose meta parameters are to be updated

buildTimeExtentMetaParameter

protected void buildTimeExtentMetaParameter(Spectrum sp,
                                            java.lang.String keyword)

Populate meta parameters with time extent.

Parameters:

sp - the spectrum whose meta parameters are to be updated

keyword - the header keyword with the exposure time

buildLocationMetaParameters

protected void buildLocationMetaParameters(Spectrum sp)

Populate meta parameters with location values.

Parameters:

sp - the spectrum whose meta parameters are to be updated

buildExtentMetaParameters

protected void buildExtentMetaParameters(Spectrum sp)

Populate meta parameters with extent values.

Parameters:

sp - the spectrum whose meta parameters are to be updated