astro.fits
Class FitsTools

java.lang.Object
  astro.fits.FitsTools

public class FitsTools
extends Object

Some tools in dealing with FITS images.

Nested Class Summary

static class	FitsTools.Binning Flip according to the second and third command line argument
static class	FitsTools.Clip Reads the four extensions of an WiFSIP image, does clipping, flipping and tiling to produce a single output fits.
static class	FitsTools.ClipOne Reads one extensions of an WiFSIP image, does clipping to produce a single output fits.
static class	FitsTools.Dump Dumps the pixel values to stdout.
static class	FitsTools.E2V Reads the two extensions of an WiFSIP/Robotel image, does clipping, flipping and tiling to produce a single output fits.
static class	FitsTools.Flag Constructs a flag map from a weight map in a way that only values above a certain trashhold are set to 0, others to 1.
static class	FitsTools.Flip Flip according to the second and third command line argument
static class	FitsTools.Histogram Dumps the historgram to stdout.
static class	FitsTools.Limit Limits an image to ADU borders.
static class	FitsTools.Pixel Take the pixel at the given coordinates and print its value.
static class	FitsTools.SiraitV Transformas small IRAIT V-data.
static class	FitsTools.Size
static class	FitsTools.Split Splits a fits file given on the command line into its image hdu's, each image found saved to a fits file with a number indication at the end of the fits file name (extensionless).
static class	FitsTools.Stitcher Full use control on how to stitch quadrants together.
static class	FitsTools.Test
static class	FitsTools.TestFits Generates a test fits file, whose pixel value is adu=256*y+x.
static class	FitsTools.Weight Constructs a weight map from a normalized flat in a way that all values above a certain trashhold are set to a lower threshold.
static class	FitsTools.Wifsip Reads the four extensions of an WiFSIP image, does clipping, flipping and tiling to produce a single output fits.
static class	FitsTools.WifsipTime We read the comment to the simple keyword, extract the creation date out of it, parse it, subtract 34 seconds from it and write this as DATE-OBS to the header again.

Field Summary

static String	DATEKEY The FITS key denoting the yyyy-mm-tt of the observing date.
static List<String>	DATEKEYS A list of fits keys that might also indicate a date.
static String	DATEOBSKEY The FITS key denoting the yyyy-mm-tt of the observing date.
static String	FITSBITPIX The mandatory FITS key denoting the end of the header section.
static DateFormat	FITSDATE The default formatter used for FITS-header dates.
static DateFormat	FITSDATEMS
static String	FITSEND The mandatory FITS key denoting the end of the header section.
static String	FITSEXTENSION The extension for fits files.
static String	FITSNAXIS The mandatory FITS key denoting the end of the header section.
static String	FITSSCALE The FITS key denoting the scale of image data.
static String	FITSSCALEREM The FITS key denoting the scale of image data.
static String	FITSSIMPLE The mandatory FITS key denoting the end of the header section.
static String	FITSXTENSION The mandatory FITS key denoting the end of the header section.
static String	FITSZERO The FITS key denoting the zero point of image data.
static String	FITSZEROREM The FITS key denoting the zero point of image data.
static String	FITZEXTENSION The extension for compressed fits files.
static String	TIMEKEY The FITS key denoting the HH:MM:ss of the observing date.
static String	TIMEOBSKEY The FITS key denoting the HH:MM:ss of the observing date.
static String	XBIN Fits key for entering x-bin info to header.
static String	XORIGIN Fits key for entering x-pregap info to header.
static String	XTENSIONIMAGE The recognized extensions is an image
static String	YBIN Fits key for entering y-bin info to header.
static String	YORIGIN Fits key for entering y-pregap info to header.

Constructor Summary

FitsTools()

Method Summary

static nom.tam.fits.ImageHDU	bin(nom.tam.fits.ImageHDU l, int xbin, int ybin) Bins ADUs in an imageHDU to the given values.
static nom.tam.fits.ImageHDU	cap(nom.tam.fits.ImageHDU l, double cap, double low) Caps ADUs in an imageHDU whose values are above a certain threshold to a lower one.
static nom.tam.fits.ImageData	flag(nom.tam.fits.ImageHDU in, double trig) Extracts ADU's from an Image HDU and converts them to an integer flag map.
static nom.tam.fits.ImageHDU	flip(nom.tam.fits.ImageHDU in, boolean xflip, boolean yflip) We take a source HDU and flip it according to the flip indicators, where a positive value means leave unchanged, while negative values change the direction.
static <T extends nom.tam.fits.BasicHDU> T	getHduOfType(nom.tam.fits.Fits fits, Class<T> type, boolean ignorenull) Reads a fits file until a HDU is discovered that is of the provided type.
static <T extends nom.tam.fits.BasicHDU> T	getHduOfType(nom.tam.fits.Fits fits, Class<T> type, boolean ignorenull, int skip) Reads a fits file until a HDU is discovered that is of the provided type.
static Number	getRawValue(nom.tam.fits.Fits image, int x, int y) Scans an image hdu and retrieves the data there.
static Number	getRawValue(nom.tam.fits.ImageHDU image, int x, int y) Scans an image hdu and retrieves the data there.
static List<Number>	getRawWindow(nom.tam.fits.Fits file, Rectangle window) Extracts a window from an image hdu and returns non-scaled, raw, ADUs as a list of Numbers.
static List<Number>	getRawWindow(nom.tam.fits.ImageHDU image, Rectangle window) Extracts a window from an image hdu and returns ADUs as a list of Numbers.
static Dimension	getSize(nom.tam.fits.ImageHDU raw) Reads the header for the axes and returns a dimension object out of it, if image is two-dimensional.
static List<Number>	getTrueFrame(nom.tam.fits.ImageHDU hdu, Rectangle active, int thick) Extracts a frame at the inside of the active window.
static Number	getTrueValue(nom.tam.fits.Fits image, int x, int y) Scans an image hdu and retrieves the data there.
static Number	getTrueValue(nom.tam.fits.ImageHDU image, int x, int y) Scans an image hdu and retrieves the data there.
static List<Number>	getTrueWindow(nom.tam.fits.Fits file, Rectangle window) Extracts a window from an image hdu and returns zero-shifted and scaled ADUs as a list of Numbers.
static List<Number>	getTrueWindow(nom.tam.fits.ImageHDU image, Rectangle window) Extracts a window from an image hdu and returns ADUs as a list of Numbers.
static nom.tam.fits.ImageHDU	hilo(nom.tam.fits.ImageHDU l, double cap, double low) Caps ADUs in an imageHDU whose values are above a certain threshold to a lower one.
static nom.tam.fits.Fits	limit(nom.tam.fits.Fits raw, double min, double max) Limits ADUs in an image to the given values.
static nom.tam.fits.ImageData	limit(nom.tam.fits.ImageHDU l, double low, double hi) Limits ADUs in an imageHDU to the given values.
static boolean	saveAs(nom.tam.fits.Fits src, File as) To overcome the crude logic behind saving a fits file, we can do this here more easily.
static boolean	saveAs(nom.tam.fits.Fits src, String as) To overcome the crude logic behind saving a fits file, we can do this here more easily.
static nom.tam.fits.ImageHDU	scalarMultiply(nom.tam.fits.ImageHDU in, double scale) Multiplies the image with the given scalar.
static nom.tam.fits.ImageHDU	scalarOffset(nom.tam.fits.ImageHDU in, double offset) Multiplies the image with the given scalar.
static nom.tam.fits.ImageHDU	stitch(nom.tam.fits.ImageHDU left, nom.tam.fits.ImageHDU right, boolean rowpatch) Composes an image from two tiles and returns the union of both in a new ImageHDU.
static nom.tam.fits.Fits	transform(nom.tam.fits.Fits image, Function eval) Extracts ADU's from an Image HDU, transforms them according to the given function f(ADU), and constructs an Image HDU of likewise type.
static nom.tam.fits.ImageHDU	transform(nom.tam.fits.ImageHDU in, Function eval) Extracts ADU's from an Image HDU, transforms them according to the given function f(ADU), and constructs an Image HDU of likewise type.
static nom.tam.fits.ImageHDU	trim(nom.tam.fits.ImageHDU in, Rectangle active) We take a source image hdu and trim it to the given active area.

Methods inherited from class java.lang.Object

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

Field Detail

FITSEXTENSION

public static final String FITSEXTENSION

The extension for fits files.

See Also:

Constant Field Values

FITZEXTENSION

public static final String FITZEXTENSION

The extension for compressed fits files.

See Also:

Constant Field Values

FITSDATE

public static final DateFormat FITSDATE

The default formatter used for FITS-header dates.

FITSDATEMS

public static final DateFormat FITSDATEMS

FITSSIMPLE

public static final String FITSSIMPLE

The mandatory FITS key denoting the end of the header section.

See Also:

Constant Field Values

FITSXTENSION

public static final String FITSXTENSION

The mandatory FITS key denoting the end of the header section.

See Also:

Constant Field Values

FITSBITPIX

public static final String FITSBITPIX

The mandatory FITS key denoting the end of the header section.

See Also:

Constant Field Values

FITSNAXIS

public static final String FITSNAXIS

The mandatory FITS key denoting the end of the header section.

See Also:

Constant Field Values

FITSZERO

public static final String FITSZERO

The FITS key denoting the zero point of image data.

See Also:

Constant Field Values

FITSSCALE

public static final String FITSSCALE

The FITS key denoting the scale of image data.

See Also:

Constant Field Values

FITSEND

public static final String FITSEND

The mandatory FITS key denoting the end of the header section.

See Also:

Constant Field Values

DATEKEY

public static final String DATEKEY

The FITS key denoting the yyyy-mm-tt of the observing date.

See Also:

Constant Field Values

DATEOBSKEY

public static final String DATEOBSKEY

The FITS key denoting the yyyy-mm-tt of the observing date.

See Also:

Constant Field Values

TIMEKEY

public static final String TIMEKEY

The FITS key denoting the HH:MM:ss of the observing date.

See Also:

Constant Field Values

TIMEOBSKEY

public static final String TIMEOBSKEY

The FITS key denoting the HH:MM:ss of the observing date.

See Also:

Constant Field Values

DATEKEYS

public static final List<String> DATEKEYS

A list of fits keys that might also indicate a date.

XTENSIONIMAGE

public static final String XTENSIONIMAGE

The recognized extensions is an image

See Also:

Constant Field Values

FITSZEROREM

public static final String FITSZEROREM

The FITS key denoting the zero point of image data.

See Also:

Constant Field Values

FITSSCALEREM

public static final String FITSSCALEREM

The FITS key denoting the scale of image data.

See Also:

Constant Field Values

XORIGIN

public static final String XORIGIN

Fits key for entering x-pregap info to header.

See Also:

Constant Field Values

XBIN

public static final String XBIN

Fits key for entering x-bin info to header.

See Also:

Constant Field Values

YORIGIN

public static final String YORIGIN

Fits key for entering y-pregap info to header.

See Also:

Constant Field Values

YBIN

public static final String YBIN

Fits key for entering y-bin info to header.

See Also:

Constant Field Values

Constructor Detail

FitsTools

public FitsTools()

Method Detail

getHduOfType

public static <T extends nom.tam.fits.BasicHDU> T getHduOfType(nom.tam.fits.Fits fits,
                                                               Class<T> type,
                                                               boolean ignorenull)
                                                    throws nom.tam.fits.FitsException,
                                                           IOException

Reads a fits file until a HDU is discovered that is of the provided type.

Parameters:

ignorenull - Ignore empty HDU's

Throws:

nom.tam.fits.FitsException

IOException

getHduOfType

public static <T extends nom.tam.fits.BasicHDU> T getHduOfType(nom.tam.fits.Fits fits,
                                                               Class<T> type,
                                                               boolean ignorenull,
                                                               int skip)
                                                    throws nom.tam.fits.FitsException,
                                                           IOException

Reads a fits file until a HDU is discovered that is of the provided type.

Parameters:

ignorenull - Ignore empty HDU's

Throws:

nom.tam.fits.FitsException

IOException

getTrueValue

public static Number getTrueValue(nom.tam.fits.Fits image,
                                  int x,
                                  int y)
                           throws nom.tam.fits.FitsException,
                                  IOException

Scans an image hdu and retrieves the data there. The instance returned is of the instance of the FITS data, except for (unsigned)byte, where it is returned as a Short

Throws:

nom.tam.fits.FitsException

IOException

getTrueValue

public static Number getTrueValue(nom.tam.fits.ImageHDU image,
                                  int x,
                                  int y)
                           throws nom.tam.fits.FitsException

Scans an image hdu and retrieves the data there. The instance returned is of the instance of the FITS data, except for (unsigned)byte, where it is returned as a Short. It simply shuffels primitives to objects, not correcting for scale or zero.

Throws:

nom.tam.fits.FitsException

getRawValue

public static Number getRawValue(nom.tam.fits.Fits image,
                                 int x,
                                 int y)
                          throws nom.tam.fits.FitsException,
                                 IOException

Scans an image hdu and retrieves the data there. The instance returned is of the instance of the FITS data, except for (unsigned)byte, where it is returned as a Short

Throws:

nom.tam.fits.FitsException

IOException

getRawValue

public static Number getRawValue(nom.tam.fits.ImageHDU image,
                                 int x,
                                 int y)
                          throws nom.tam.fits.FitsException

Scans an image hdu and retrieves the data there. The instance returned is of the instance of the FITS data, except for (unsigned)byte, where it is returned as a Short. It simply shuffels primitives to objects, not correcting for scale or zero.

Throws:

nom.tam.fits.FitsException

bin

public static nom.tam.fits.ImageHDU bin(nom.tam.fits.ImageHDU l,
                                        int xbin,
                                        int ybin)
                                 throws nom.tam.fits.FitsException

Bins ADUs in an imageHDU to the given values.

Throws:

nom.tam.fits.FitsException

limit

public static nom.tam.fits.Fits limit(nom.tam.fits.Fits raw,
                                      double min,
                                      double max)
                               throws nom.tam.fits.FitsException,
                                      IOException

Limits ADUs in an image to the given values. Works on all image HDUs found

Throws:

nom.tam.fits.FitsException

IOException

limit

public static nom.tam.fits.ImageData limit(nom.tam.fits.ImageHDU l,
                                           double low,
                                           double hi)
                                    throws nom.tam.fits.FitsException

Limits ADUs in an imageHDU to the given values.

Throws:

nom.tam.fits.FitsException

cap

public static nom.tam.fits.ImageHDU cap(nom.tam.fits.ImageHDU l,
                                        double cap,
                                        double low)
                                 throws nom.tam.fits.FitsException

Caps ADUs in an imageHDU whose values are above a certain threshold to a lower one.

Throws:

nom.tam.fits.FitsException

hilo

public static nom.tam.fits.ImageHDU hilo(nom.tam.fits.ImageHDU l,
                                         double cap,
                                         double low)
                                  throws nom.tam.fits.FitsException

Caps ADUs in an imageHDU whose values are above a certain threshold to a lower one.

Throws:

nom.tam.fits.FitsException

trim

public static nom.tam.fits.ImageHDU trim(nom.tam.fits.ImageHDU in,
                                         Rectangle active)
                                  throws nom.tam.fits.FitsException

We take a source image hdu and trim it to the given active area. The active area is matched to the image such that an upper left corner of 5,3 means that in the input image hdu the x-index starts at 5 and the y-index at 3. So, an upper left corner of 0,0 corresponds to the lower left corner 1,1 according to fits definition. The width and height define the stretch of the active order, respectively.
The header of the trimmed image is minimal in that sense that it only carries the information on image size, if you want to retain the old header info, you have to merge. This is an example of such a minimal header:

 SIMPLE  =                    T / Java FITS
        BITPIX  =                  -32 
        NAXIS   =                    2 / Dimensionality   
        NAXIS1  =                 4066  
        NAXIS2  =                 4064 
        EXTEND  =                    T / Extensions are permitted 
        END
 

Parameters:

active - If null or fill size, return the original image. O therwise a new image is allocated.

Throws:

IllegalArgumentException - If the active size does not fit in the source one.

nom.tam.fits.FitsException

flip

public static nom.tam.fits.ImageHDU flip(nom.tam.fits.ImageHDU in,
                                         boolean xflip,
                                         boolean yflip)
                                  throws nom.tam.fits.FitsException

We take a source HDU and flip it according to the flip indicators, where a positive value means leave unchanged, while negative values change the direction.

Throws:

nom.tam.fits.FitsException

stitch

public static nom.tam.fits.ImageHDU stitch(nom.tam.fits.ImageHDU left,
                                           nom.tam.fits.ImageHDU right,
                                           boolean rowpatch)
                                    throws nom.tam.fits.FitsException

Composes an image from two tiles and returns the union of both in a new ImageHDU. In particular, if the rowpatch parameter is true, the image returned is composed of the first image followed by the second in x (= to the right). If rowpatch is true, the image is composed such that the second image is index-wise after the first, i.e. in standard fits notation on top.

Throws:

IllegalArgumentException - if the stitched edges are different.

nom.tam.fits.FitsException

transform

public static nom.tam.fits.Fits transform(nom.tam.fits.Fits image,
                                          Function eval)
                                   throws nom.tam.fits.FitsException,
                                          IOException

Extracts ADU's from an Image HDU, transforms them according to the given function f(ADU), and constructs an Image HDU of likewise type. This transformed HDU is returned.

Throws:

nom.tam.fits.FitsException

IOException

flag

public static nom.tam.fits.ImageData flag(nom.tam.fits.ImageHDU in,
                                          double trig)
                                   throws nom.tam.fits.FitsException

Extracts ADU's from an Image HDU and converts them to an integer flag map. If ADU is above trig, set flag to zero, otherwise to 1 (bad oixel map). Works only on float images.

Throws:

nom.tam.fits.FitsException

scalarMultiply

public static nom.tam.fits.ImageHDU scalarMultiply(nom.tam.fits.ImageHDU in,
                                                   double scale)
                                            throws nom.tam.fits.FitsException

Multiplies the image with the given scalar.

Throws:

nom.tam.fits.FitsException

scalarOffset

public static nom.tam.fits.ImageHDU scalarOffset(nom.tam.fits.ImageHDU in,
                                                 double offset)
                                          throws nom.tam.fits.FitsException

Multiplies the image with the given scalar.

Throws:

nom.tam.fits.FitsException

transform

public static nom.tam.fits.ImageHDU transform(nom.tam.fits.ImageHDU in,
                                              Function eval)
                                       throws nom.tam.fits.FitsException

Extracts ADU's from an Image HDU, transforms them according to the given function f(ADU), and constructs an Image HDU of likewise type. This transformed HDU is returned.

Throws:

nom.tam.fits.FitsException

getSize

public static Dimension getSize(nom.tam.fits.ImageHDU raw)
                         throws nom.tam.fits.FitsException

Reads the header for the axes and returns a dimension object out of it, if image is two-dimensional.

Throws:

nom.tam.fits.FitsException

getRawWindow

public static List<Number> getRawWindow(nom.tam.fits.Fits file,
                                        Rectangle window)
                                 throws nom.tam.fits.FitsException,
                                        IOException

Extracts a window from an image hdu and returns non-scaled, raw, ADUs as a list of Numbers. Order is index=x*height+y. The number of elements in the list returned is always width*height of the window. If count extraction fails at any point, null is returned.

Parameters:

window - If null, entire HDU is read.

Returns:

A List of Numbers or null.

Throws:

nom.tam.fits.FitsException

IOException

getRawWindow

public static List<Number> getRawWindow(nom.tam.fits.ImageHDU image,
                                        Rectangle window)
                                 throws nom.tam.fits.FitsException

Extracts a window from an image hdu and returns ADUs as a list of Numbers. Order is index=x*height+y. The number of elements in the list returned is always width*height of the window. If count extraction fails at any point, null is returned.

Parameters:

window - If null, entire HDU is read.

Returns:

A List of Numbers or null.

Throws:

nom.tam.fits.FitsException

getTrueWindow

public static List<Number> getTrueWindow(nom.tam.fits.Fits file,
                                         Rectangle window)
                                  throws nom.tam.fits.FitsException,
                                         IOException

Extracts a window from an image hdu and returns zero-shifted and scaled ADUs as a list of Numbers. Order is index=x*height+y. The number of elements in the list returned is always width*height of the window. If count extraction fails at any point, null is returned.

Parameters:

window - If null, entire HDU is read.

Returns:

A List of Numbers or null.

Throws:

nom.tam.fits.FitsException

IOException

getTrueWindow

public static List<Number> getTrueWindow(nom.tam.fits.ImageHDU image,
                                         Rectangle window)
                                  throws nom.tam.fits.FitsException

Extracts a window from an image hdu and returns ADUs as a list of Numbers. Order is index=x*height+y. The number of elements in the list returned is always width*height of the window. If count extraction fails at any point, null is returned.

Parameters:

window - If null, entire HDU is read.

Returns:

A List of Numbers or null.

Throws:

nom.tam.fits.FitsException

getTrueFrame

public static List<Number> getTrueFrame(nom.tam.fits.ImageHDU hdu,
                                        Rectangle active,
                                        int thick)
                                 throws nom.tam.fits.FitsException

Extracts a frame at the inside of the active window. The thickness is the number of rectangular circumferences added to the ADU list.

Throws:

nom.tam.fits.FitsException

saveAs

public static boolean saveAs(nom.tam.fits.Fits src,
                             File as)
                      throws IOException

To overcome the crude logic behind saving a fits file, we can do this here more easily.

Throws:

IOException

saveAs

public static boolean saveAs(nom.tam.fits.Fits src,
                             String as)
                      throws IOException

To overcome the crude logic behind saving a fits file, we can do this here more easily.

Throws:

IOException