Programs
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 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
- adjust-map use a comparison arc to adjust spectral maps
- map-spectra construct spectral maps
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
- ifu-image construct 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
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
extract
ifu-image framename
ldss3-pattern framename
map-spectra observset
mosaic framename
quick-list
process-2spec [spectrum set]
setcosdir
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]
viewspectra
* IRAF routine