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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. 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 paramater 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

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

Setup/Alignment Programs

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

Mapping Programs

map-spectra contruct spectral maps
adjust-map use a comparison arc to adjust spectral maps

Display/Visualization Programs

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

Reduction Programs

stitch combine multiple LDSS3 FITS files into one file
biasflat do bias and flat field corrections of frames
Sflats construct a spectroscopic flat field frame
subsky subtract sky from spectral frame
extract-2dspec extract 2-d spectra
extract extract 1-d or 2-d spectra from one or multiple frames, with optional cosmic ray rejection
sumspec sum spectral files, with optional cosmoc ray rejection
process-2spec 2-d spectral reduction pipeline

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
imcombine8 perform imcombine of all 8 ccd chips

Miscellaneous Programs

ifu-image contruct image of ifu input

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

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

extract

imcombine8* inputfile,inputfile outputfile

ifu-image framename

map-spectra observset

mosaic framename

quick-list

process-2spec [spectrum set]

setcosdir

Sflats -m mapfile -f flatfile[s] [-o outputfile] [-z badpixfile]

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]

viewspectra

Note: * = IRAF routine