COSREJ-Reject cosmic rays from a set of supposedly identical spectra

Description:

Given an image whose cross-sections are a set of spectra of the same object all with exactly the same wavelength to pixel mapping (in other words a set of spectra that should be identical, other than for signal to noise effects and possible differences in their total counts due to differing exposure times etc), COSREJ attempts to remove any cosmic rays or other obvious features that might be contaminating some (but not the majority) of the spectra.

Parameters:

IMAGE

A 2-D image in which all the cross sections are a set of similar spectra. Note that each pixel of each spectrum is compared with the corresponding pixels in the other spectra, so they should be properly aligned - probably already scrunched.

XSTART

COSREJ scales up each spectrum to the same mean value. To do this it calculates the mean for each spectrum between the limits sepcified for XSTART and XEND (which are given in terms of the X-axis values, not necessarily in pixels). Normally, you would use the whole spectrum, but there may be end effects you'd prefer to avoid.

XEND

COSREJ scales up each spectrum to the same mean value. To do this it calculates the mean for each spectrum between the limits sepcified for XSTART and XEND (which are given in terms of the X-axis values, not necessarily in pixels). Normally, you would use the whole spectrum, but there may be end effects you'd prefer to avoid.

CRSIG

Each pixel in each spectrum is compared with the equivalent pixels in the other spectra, and any that differ from the mean of the other pixels by more than a given factor (CRSIG) times the standard deviation of the other pixels are rejected. This is repeated until either only two pixels are left, or until no pixels are rejected in a pass through the remaining pixels. The rejected pixels are set to the mean value of the remaining unrejected pixels. If you're only trying to get rid of gross effects like cosmic rays, CRSIG values around 10 should be satisfactory. The value is unlikely to be critical.

WMEAN

COSREJ can create a `spectrum' with one element for each spectrum in the original image, where each element is the mean value used for that spectrum. This might possibly be used to scale the resulting image using, for example, ISYDIV. Such a spectrum is produced only if WMEAN is set.

MSPECT

If WMEAN is set, MSPECT is the name of the `mean spectrum' generated. This is a file containing nothing but a data array containing the mean values for the spectra in the image.

OUTPUT

The name of the resulting image. The data produced in OUTPUT is the same as that for IMAGE, except that the cosmic rays have been processed out. If OUTPUT and IMAGE are the same, the operation is performed in situ.

See also:

FIGARO: BCLEAN, CLEAN, MEDFILT, MEDSKY, TIPPEX.
KAPPA: FFCLEAN, CHPIX, FILLBAD, GLITCH, MEDIAN, MSTATS, ZAPLIN.

Source comments:

 C O S R E J

 Name:
    COSREJ

 Function:
    Remove cosmic rays from a set of similar spectra.

 Description:
    Given an image whose cross-sections are a set of spectra of the
    same object all with exactly the same wavelength to pixel mapping
    (in other words a set of spectra that should be identical, other
    than for signal to noise effects and possible differences in
    their total counts due to differing exposure times etc), this
    routine attempts to remove any cosmic rays or other obvious
    features that might be contaminating some (but not the majority)
    of the spectra.  First, the mean value for each spectrum over a
    specified range is calculated and this is used to reduce each
    spectrum to the same mean value.  Each pixel in each spectrum is
    compared with the equivalent pixels in the other spectra, and any
    that differ from the mean of the other pixels by more than a
    given factor (the CRSIG parameter) times the standard deviation
    of the other pixels are rejected.  This is repeated until either
    only two pixels are left, or until no pixels are rejected in a
    pass through the remaining pixels.  The rejected pixels are set
    to the mean value of the remaining unrejected pixels.  Finally,
    the spectra are rescaled to their original mean values.  If
    requested, the program can create a `spectrum' with one element
    for each spectrum in the original image, where each element is
    the mean value used for that spectrum.  This might possibly be
    used to scale the resulting image using, for example, ISYDIV.

 Command parameters:
    IMAGE    The name of the image in which the spectra are held.
    XSTART   The first x-value of the range to be used to calculate
             the mean value for each spectrum.
    XEND     The last x-value of the range to be used to calculate
             the mean value for each spectrum.
    CRSIG    The cutoff sigma value to be used.
    MSPECT   The name of the mean spectrum produced, if WMEAN is yes.
    OUTPUT   The name of the resulting image with the cosmic rays removed.

 Command keywords:
    WMEAN    Yes if a spectrum of mean values is to be produced.

 Error array handling: Ignored.

 Data quality / flagged value handling:
    Not explicitly performed.  Relies on standard DSA processing.

 Files used:
    BADPIX.DAT  Contains a list of the cosmic rays removed from the data.

    8th  Sept  1987.   Original version DJA / AAO