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Programs

Introduction

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. Some programs are intended to replace common IRAF routines, so that one need not run IRAF simultaneously while doing reductions. 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, with a few noted exceptions,  denoted by flags and may  be entered in any order. Alternately, if no parameters are specified, many programs 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. Image files must be located in the directory specified by the environment variable COSMOS_IMAGE_DIR

Utility Programs

• defineobs  define or edit an observation definition file
• editpar  edit program parameter files
• fitsheader print out the header of a fits file

Setup/Alignment Programs

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

Mapping Programs

• map-spectra  construct spectral maps
• adjust-map  use a comparison arc to adjust spectral maps

Display/Visualization Programs

• display display image frames in a ds9 window
• mark-slits use an observation definition or map file to mark predicted slit locations on a ds9 display
• whatsthat identifies slit and wavelength within a spectral image in a ds9 window

the following programs are now seldom needed but are retained for completeness

• 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
• apertures calculate positions of apertures using observation definition file

Reduction Programs

• badorders  constructs bad pixel maps to mask zero and higher order spectra
• biasflat  do bias and flat field corrections of frames
• extract-spec  extract 1-d or 2-d spectra from one or a set of 8 frames, with optional cosmic ray rejection
• 1dspec perform 1-d optimal extraction on a set of 2-d spectra
• process-spec  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

Shortcut aliases

·      scd directory_name:    alias for:   setenv COSMOS_IMAGE_DIR directory_name

·      lcd:                                    alias for:   ls $COSMOS_IMAGE_DIR

 

 

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