COSMICS SUPPRESSION

• Principles
• Use
• Parameters

Principles

• A spatial radius is chosen, which defines the region over which spectral similarity is supposed to be true. Over this region, usually twice the size of the spatial sampling, the integrals of the spectrum to be checked (and cleaned) and of the neighbours are computed. For instance, if the radius is given as 1, this means that one ring of neighbours will be used; then, seven integrals are computed : one for the central lens, six for the ring made of the six nearest lenses. They are used to normalise the peripheral spectra to the central spectrum integral value.
• The median of the spectra from the above normalised disk region is computed. This normalisation is used to be able to correct cosmic impacts even within high spatial gradient regions.
• The differential spectrum [Central spectrum]-[Median spectrum] is computed. This difference is then median-filtered, with a radius given by the user.
• The second-order difference between this filtered difference and the un-filtered difference is computed. This final spectrum is now holding only high spectral frequencies, and cosmic ray pixels may now be detected quite safely.
• A sigma-clipping is performed on this spectrum, and pixels above N times sigma are flagged.
• All the flagged pixels are replaced, in the original central spectrum, by the median value (the one obtained in the second step above). In fact, not only the flagged pixels, but their immediate neighbours too, up to a correction radius specified by the user, are replaced.

Use

• Click on [Cosmics] in the main menu, then on [Remove cosmics].The [Remove cosmics] window pops up.
• Enter the name of the [Input datacube], which is the object datacube you have wavelength-calibrated and flat-fielded in previous steps. You can type it in directly, or use the browse icon at the end of the field, or drag and drop it from the Reduction folder.
• Enter the name of the [Output datacube], that is the new datacube to be created after cosmics removal. Same input possibilities as above.
• Click on [Accept]. The result window opens, and trace the various steps of the elimination process. As a rule of thumb, expect to find something like 3000 cosmics over a one-hour exposure.

Parameters

• Spatial filtering radius : the radius of the neighbourhood over which similarities are to be searched for discriminating between lines and cosmics in spectra; to be given in lens ring units. Usually, it is wise to use a radius of 1, and the neighbouring disc will span over seven lenses, the one which is to be checked for cosmics, and the ring of six around it.
  
• Spectral filtering radius : the radius (in pixels) used for the median filtering of the first order difference between the central spectrum and the disc median.
  
• Sigma clipping factor : this is the factor to be multiplied by sigma to find and flag the bad pixels in the second-order difference.
  
• Maximum number of iterations : for the sigma-clipping operation.
  
• Spectral correction radius (pixels) : the radius around flagged bad pixels within which all pixels of the spectrum are to be replaced by median values.
  
• Debug : this switches the program to verbose mode, and more informations are recorded into the history file (see button [Start] in the left menu). In addition, the following options become then available :
  
• Median datacube : the name of the datacube which will hold the normalised disc medians for each of the original datacube.
  
• Residual datacube : the name of the datacube which will hold the second-order difference spectra for all the original spectra.
  
• Save values :
  All the input values (files names, etc...) are saved, and become the new default values for this user. They can be recalled at will, and are used each time the Remove cosmics window is opened.
  
• Recall values :
  The values saved by the user are loaded into the various input fields.
  
• Default values :
  The input fields are set to the general defaults values; for instance, the file names are set to blank.
  

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