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COSMOS includes programs to (1) calculate and adjust the mapping between the CCD focal plane and the science plane (wavelength vs slit coordinate) (2) reduce data, (3) provide quick-look capabilities, as well as some utility programs. All programs have a specified set of input parameters which may be entered on the command line. If more than one input parameter is required, they are denoted by flags and may be entered in any order. Alternately, if no parameters are specified, the program will prompt for them. Most programs have an associated parameter file, whose name is program.par. The parameters in each parameter file are listed with each program. Parameter files may be edited with the utility program editpar. Parameter files must be located in the directory specified by the environment variable COSMOS_PAR_DIR. IRAF routines which are part of the COSMOS packages follow IRAF conventions for input parameters and parameter files. However, although each of the routines with names irafroutine8 does have a parameter file, one should instead use the IRAF routine epar to edit the parameter file for the standard IRAF program irafroutine.

Utility Programs

  • defineobs  define or edit an observation definition file
  • editpar  edit program parameter files
  • setcosdir  GUI to set the value of COSMOS_IMAGE_DIR

Setup/Alignment Programs

  • adjust-offset  make manual corrections to dewar offset files
  • align-mask  adjust dewar offset files using mask image

Mapping Programs

Display/Visualization Programs

  • apertures  calculate positions of mask apertures using observation definition file
  • mosaic  combine all 8 CCD frames into one image
  • spectral-lines  calculate positions of spectral lines using observation definition file
  • spectral-map  calculate positions of spectral lines using a spectral map

Reduction Programs

  • badorders  constructs bad pixel maps to mask zero and higher order spectra
  • biasflat  do bias and flat field corrections of frames
  • extract  extract 1-d or 2-d spectra from one or multiple frames, with optional cosmic ray rejection
  • extract-2dspec  extract 2-d spectra
  • ldss3-pattern  removes pattern noise from LDSS3 frames
  • process-2spec  2-d spectral reduction pipeline
  • Sflats   construct a spectroscopic flat field frame
  • spec2big  converts extracted spectra from extensions format to equispec format
  • stitch  combine multiple LDSS3 FITS files into one file
  • subsky  subtract sky from spectral frame
  • sumspec  sum spectral files, with optional cosmic ray rejection

Quick Look and Analysis Programs

  • quick-list  produce a short slit list for quick-look reductions
  • viewspectra  view and analyze 1-d or 2-d spectra

IRAF Routines

  • display8  display a mosaic of all 8 CCD chips

Miscellaneous Programs

Program Syntax

adjust-map  -m mapfile -f framename[s][-d n]
adjust-offset  offsetfile delx dely [delth scale]
align-mask  -o observset -f framename
apertures  -o observset -b binning
badorders  -o observset [-i input_badpixel_file] -f output_badpixel_file
biasflat  [-b biasfile] [-f flatfile] framename[s]
display8*  framename buffer[z1 = lower-intensity z2 = upper-intensity]
defineobs  [observset]
editpar  program
extract-2dspec  -m mapfile -f framename
ifu-image  framename
ldss3-pattern  framename
map-spectra  observset
mosaic  framename
process-2spec  [spectrum set]
Sflats  -m mapfile -f flatfile[s] [-o outputfile] [-z badpixfile]
spec2big  framename
spectral-lines  -o observset -l linefile -b binning[-c] [-e]
spectral-map  -m mapfile -l linefile -b binning[-c] [-e]
stitch  framename
sumspec  -o outputfile(_1spec or _2spec) inputfiles
subsky  -f framename -m mapfile [-z badpixfile] [-d]

* IRAF routine

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