astro.fits
Class CrosstalkDark

java.lang.Object
  util.PropertyContainer
      util.PropertyResources
          util.PropertyBundles
              astro.fits.CrosstalkDark

All Implemented Interfaces:

Cloneable, Initializable, LocalizedSupplying, PropertySupplying, ResourceSupplying

public class CrosstalkDark
extends PropertyBundles

Small class to prepare the WiFSIP crosstalk measures for further processing. This starts with two dark frames taken between the crosstalk frames. These dark frames are already averaged and split into single-extension fits files, known to this class as the two arrays #DARK1 and #DARK2. We then take a measurement file (an out-of-focus image of Regulus spanning most of a single amplifier quadrant). From the sky estimate (either mode, median, or average of the image), we scale the two dark (α, β) such that we match this sky estimate, e.g. for amplifier 0 we have dark1-mode=2263, dark2-mod=3743. For reg_2amp, all of them taken just before DARK1 and way before dark 2, we get a sky estimate that is lower than 2263, thus we get negative β and an α > 1 (BC: α+β=1), for reg_1 and reg_3 accordingly 0< α,β< 1 and for reg4, taken after both darks, we expect β > 1 and α < 0.

Nested Class Summary

static class	CrosstalkDark.Scale The known possible scaling values.
static class	CrosstalkDark.Scalings Reads properties - normally none are sufficient - and prints the scaling factors for each quadrant and file for sanity checks.
static class	CrosstalkDark.Subtract Creates dark-subtracted fits from the input list by scaling the two master darks to match the background estimate.

Nested classes/interfaces inherited from class util.PropertyResources

PropertyResources.URLResource

Field Summary

private List<nom.tam.fits.ImageHDU>	dark1 The list of early dark HDU, one per amplifier section.
private List<nom.tam.fits.ImageHDU>	dark2 The list of late dark HDU, one per amplifier section.
private static String	DEFDARK1 The default list of early dark images.
private static String	DEFDARK2 The default list of late dark images.
private static String	DEFFITS The default list of fits files.
private static String	DEFILLU The default list of illuminated quadrants.
private static double	DEFLOWER The default upper bound for reject, times sigma.
private static int	DEFREJECT The default number of maximum rejection loops.
private static String	DEFSCALE The default scaling algorithm.
private static double	DEFUPPER The default upper bound for reject, times sigma.
private Map<File,Integer>	illu For each file the quadrant index with the illuminated section.
static String	KEY_DARK1 The list of early dark images, one per amplifier.
static String	KEY_DARK2 The list of late dark images, one per amplifier.
static String	KEY_FITS The list of images in the order they are processed.
static String	KEY_ILLU The amplifier index in alpha beta where the illuminated image is.
static String	KEY_LOWER The lower bound for reject (remove all at least xsigma below av.)
static String	KEY_REJECT The default number of iterative rejection steps.
static String	KEY_SCALE The scaling item: AVERGAE, MODE or median.
static String	KEY_UPPER The upper bound for reject (remove all at least xsigma above av.)
private VectorG	scale1 The 4Vector of scaling values in the early darks.
private VectorG	scale2 The 4Vector of scaling values in the early darks.

Fields inherited from class util.PropertyBundles

KEY_LOCALECOUNTRY, KEY_LOCALELANGUAGE, KEY_RESOURCEBUNDLES

Fields inherited from class util.PropertyResources

KEY_NOINITONCREATE, localurl, locate, POSTFIX_DIR, POSTFIX_EXT, POSTFIX_FILE, POSTFIX_LIST, POSTFIX_URL, urlset

Fields inherited from class util.PropertyContainer

KEY_LISTSEPARATOR, KEY_MAPKEYVALUECHAR, KEY_MAPSEPARATOR

Fields inherited from interface util.ResourceSupplying

KEY_URLRESOURCES, KEY_URLUSECONFIG, KEY_URLUSECURRENT, KEY_URLUSEHOME

Fields inherited from interface util.PropertySupplying

CONFIG, KEY_CLASS

Constructor Summary

CrosstalkDark(Map<String,String> prop)
Constructs and defaults a new crosstalk-dark fitter.

Method Summary

private static double	averageIndex(VectorG v, int i0) Takes the statistical mean over all indices in the vector except the one stated in i0.
void	darkCorrectAll() Does a scaling on all crosstalk fits to remove the dark background.
private VectorG[]	getAlphBeta(File amp) For a fits file, read its scaling factors and return the alpha and beta scaling to all its quadrants as a length-of-two array of 4-Vectors.
private VectorG	getDarkScaling(List<nom.tam.fits.ImageHDU> dark) Tries to read a list of dark, single-extension images, belonging to a single dark, ordered by amplifier.
private CrosstalkDark.Scale	getScaleFactor() Converts a string to the appropriate scaling.
private double	getScaling(nom.tam.fits.ImageHDU data, CrosstalkDark.Scale how) Takes a single Image HDU, calculates the ADU statistic and returns the scaling factor, i.e.
void	init() On init, we read the dark images and get their scaling factors.
private static String	pretty(VectorG v) Converts an alpha or beta vector to a pretty print.
private List<nom.tam.fits.ImageHDU>	readDarkList(List<String> dark) Tries to read a list of dark, single-extension images, belonging to a single dark, ordered by amplifier.
private VectorG	readWifsip(File amp) Reads all four extension of a fits file, calculates for each the scaling factor, and return those as a four-vector.
private nom.tam.fits.Fits	subtractScaledDark(File f, VectorG alpha, VectorG beta) From a file f we read all HDUs and scale them such that the dark sky is (partly) removed.

Methods inherited from class util.PropertyBundles

clone, getLocalized, getLocalized, getLocalizedString, getLocalizedString, loadResource

Methods inherited from class util.PropertyResources

createFrom, createFrom, createFrom, getApplet, getAsResources, getLocalClassLoader, getPropertiesToKey, getPropertiesToKey, getResource, getResourceAsStream, getResourceFromKey, getResources, keyCreate, keyCreate, reload, setApplet

Methods inherited from class util.PropertyContainer

augment, augment, augment, defaultBoolean, defaultChar, defaultDouble, defaultFloat, defaultInt, defaultLong, defaultObject, defaultObject, defaultProperties, defaultProperty, getAsBoolean, getAsChar, getAsDouble, getAsEnums, getAsFloat, getAsInt, getAsList, getAsLong, getAsMap, getAsMap, getAsObject, getAsObject, getProperties, getProperty, has, isNew, parseObject, reload, removeProperty, rescanned, setObject, setProperties, setProperty, stringProperties, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface util.ResourceSupplying

getResource, getResourceAsStream, getResources

Methods inherited from interface util.PropertySupplying

defaultBoolean, defaultChar, defaultDouble, defaultFloat, defaultInt, defaultLong, defaultObject, defaultObject, defaultProperties, defaultProperty, getAsBoolean, getAsChar, getAsDouble, getAsFloat, getAsInt, getAsList, getAsLong, getAsMap, getAsObject, getAsObject, getProperties, getProperty, has, parseObject, removeProperty, setObject, setProperty, stringProperties

Field Detail

KEY_DARK1

public static final String KEY_DARK1

The list of early dark images, one per amplifier.

See Also:

Constant Field Values

KEY_DARK2

public static final String KEY_DARK2

The list of late dark images, one per amplifier.

See Also:

Constant Field Values

KEY_SCALE

public static final String KEY_SCALE

The scaling item: AVERGAE, MODE or median.

See Also:

Constant Field Values

KEY_FITS

public static final String KEY_FITS

The list of images in the order they are processed.

See Also:

Constant Field Values

KEY_REJECT

public static final String KEY_REJECT

The default number of iterative rejection steps.

See Also:

Constant Field Values

KEY_UPPER

public static final String KEY_UPPER

The upper bound for reject (remove all at least xsigma above av.)

See Also:

Constant Field Values

KEY_LOWER

public static final String KEY_LOWER

The lower bound for reject (remove all at least xsigma below av.)

See Also:

Constant Field Values

KEY_ILLU

public static final String KEY_ILLU

The amplifier index in alpha beta where the illuminated image is.

See Also:

Constant Field Values

DEFSCALE

private static final String DEFSCALE

The default scaling algorithm.

DEFREJECT

private static final int DEFREJECT

The default number of maximum rejection loops.

See Also:

Constant Field Values

DEFUPPER

private static final double DEFUPPER

The default upper bound for reject, times sigma.

See Also:

Constant Field Values

DEFLOWER

private static final double DEFLOWER

The default upper bound for reject, times sigma.

See Also:

Constant Field Values

DEFDARK1

private static final String DEFDARK1

The default list of early dark images.

See Also:

Constant Field Values

DEFDARK2

private static final String DEFDARK2

The default list of late dark images.

See Also:

Constant Field Values

DEFILLU

private static final String DEFILLU

The default list of illuminated quadrants.

See Also:

Constant Field Values

DEFFITS

private static final String DEFFITS

The default list of fits files.

See Also:

Constant Field Values

dark1

private List<nom.tam.fits.ImageHDU> dark1

The list of early dark HDU, one per amplifier section.

scale1

private VectorG scale1

The 4Vector of scaling values in the early darks.

dark2

private List<nom.tam.fits.ImageHDU> dark2

The list of late dark HDU, one per amplifier section.

scale2

private VectorG scale2

The 4Vector of scaling values in the early darks.

illu

private Map<File,Integer> illu

For each file the quadrant index with the illuminated section.

Constructor Detail

CrosstalkDark

public CrosstalkDark(Map<String,String> prop)

Constructs and defaults a new crosstalk-dark fitter.

Method Detail

init

public void init()

On init, we read the dark images and get their scaling factors.

Specified by:

init in interface Initializable

Overrides:

init in class PropertyResources

darkCorrectAll

public void darkCorrectAll()
                    throws nom.tam.fits.FitsException,
                           IOException

Does a scaling on all crosstalk fits to remove the dark background. Quadrants with the amplifier visible are estimated by averageing the dark from alpha-beta of all other quadrants.

Throws:

nom.tam.fits.FitsException

IOException

averageIndex

private static final double averageIndex(VectorG v,
                                         int i0)

Takes the statistical mean over all indices in the vector except the one stated in i0.

subtractScaledDark

private nom.tam.fits.Fits subtractScaledDark(File f,
                                             VectorG alpha,
                                             VectorG beta)
                                      throws nom.tam.fits.FitsException,
                                             IOException

From a file f we read all HDUs and scale them such that the dark sky is (partly) removed.

Throws:

nom.tam.fits.FitsException

IOException

readWifsip

private VectorG readWifsip(File amp)
                    throws nom.tam.fits.FitsException,
                           IOException

Reads all four extension of a fits file, calculates for each the scaling factor, and return those as a four-vector.

Throws:

nom.tam.fits.FitsException

IOException

getAlphBeta

private VectorG[] getAlphBeta(File amp)
                       throws nom.tam.fits.FitsException,
                              IOException

For a fits file, read its scaling factors and return the alpha and beta scaling to all its quadrants as a length-of-two array of 4-Vectors.

Throws:

nom.tam.fits.FitsException

IOException

readDarkList

private List<nom.tam.fits.ImageHDU> readDarkList(List<String> dark)
                                          throws nom.tam.fits.FitsException,
                                                 IOException

Tries to read a list of dark, single-extension images, belonging to a single dark, ordered by amplifier.

Throws:

nom.tam.fits.FitsException

IOException

getDarkScaling

private VectorG getDarkScaling(List<nom.tam.fits.ImageHDU> dark)
                        throws nom.tam.fits.FitsException,
                               IOException

Tries to read a list of dark, single-extension images, belonging to a single dark, ordered by amplifier.

Throws:

nom.tam.fits.FitsException

IOException

getScaling

private double getScaling(nom.tam.fits.ImageHDU data,
                          CrosstalkDark.Scale how)
                   throws nom.tam.fits.FitsException,
                          IOException

Takes a single Image HDU, calculates the ADU statistic and returns the scaling factor, i.e. the median, mode, or average according to the algortihm requested. The image hdu maus have a non-null data section.

Throws:

nom.tam.fits.FitsException

IOException

getScaleFactor

private final CrosstalkDark.Scale getScaleFactor()

Converts a string to the appropriate scaling.

pretty

private static String pretty(VectorG v)

Converts an alpha or beta vector to a pretty print.