# Copyright(c) 2002-2009 Association of Universities for Research in Astronomy, Inc.
#
# GMOS example reductions script: Typical reduction of MOS data
#
# This data processing was done to aid the data quality assessment performed
# by the Gemini staff. The data processing is not designed to give the best
# possible result. Better signal-to-noise and better cleaning for cosmic-ray
# hits and bad pixels will most likely be possible. The user of these data
# is encouraged to use the provided co-added images only as guide lines and
# to re-reduce the data to obtain the best possible reduction.
#
# Gemini GMOS data reduction script
# Observation UT date: 2001dec22 
# Data processor:   Inger Jorgensen
# Data reduction date: 2002feb25
#
# Brief data description: MOS observations from the queue program GN-2001B-Q-10
#
# Update: Illustrate the use of the automatic slit edge finding feature (v1.7)

# Define various directories containing raw data and calibration data
set raw=/net/sabrina/staging2/gmos/2001dec22/
set gcalib=../../2001dec25/Basecalib/

# set up the logfile for this reduction
gmos.logfile="GN-2001B-Q-10_log5.txt"

# The bias image has been made with gbias and has been overscan
# 	subtracted and trimmed

# Make the flat field
# To let GSCUT find the edges automatically, fl_usegrad is set to yes.
# Then, since we will later let GSCUT find the slit edges automatically, 
# we need to keep the 'combflat' image.
gsflat N20011221S139,N20011221S142,N20011221S143 rgN20011221S139_flat.fits \
    order=29 rawpath=raw$ bias=gcalib$N20011217S153_bias.fits \
    mdfdir=/usr/dataproc/gmos/GN-2001B-distrib/GN-2001B-Q-10/ \
    fl_usegrad+ combflat=rgN20011221S139_comb.fits fl_keep+ fl_over+

# In this wavelength range the flats contain a pair of emission lines
# (due to a yet unidentified emission line source in the ISS)
# Set the pixels in those lines to one to avoid introducing spurious
# features
imreplace rgN20011221S139_flat.fits[sci,1][1430:3890,*] 1 low=1.02 upper=INDEF

# Reduce the science observations, the name of the output image is 
# defined by the default value outpref="gs"
# Steps in gsreduce 
#    subtract off the bias 
#    clean for cosmic ray hits
#    mosaic the 3 detectors 
#    interpolate accross the chip gaps to aid later reduction steps
#    flat field correction 
#    cut the images into slitlets
#    run gsappwave to get an approximate wavelength calibration in the 
#       header of the output image

# Set the instrumental resolution for gscrrej which is called from gsreduce
gscrrej.datares=7.

# Update the _comb frame created by GSFLAT above with the location of
# the slit edges.
gscut rgN20011221S139_comb.fits fl_update+ gradimage=rgN20011221S139_comb

# Reduce the spectra
# 'refimage' contains information on the slit locations that was just found
# by GSCUT.
gsreduce N20011221S140,N20011221S141 rawpath=raw$ \
    bias=gcalib$N20011217S153_bias.fits flat=rgN20011221S139_flat.fits \
    mdfdir=/usr/dataproc/gmos/GN-2001B-distrib/GN-2001B-Q-10/  fl_gscrrej+ \
    refimage=rgN20011221S139_comb.fits fl_over+

# Reduce the CuAr spectrum. The CuAr is not flat fielded.
gsreduce N20011221S016 rawpath=raw$ \
    fl_flat- fl_dark- bias=gcalib$N20011217S153_bias.fits \
    mdfdir=/usr/dataproc/gmos/GN-2001B-distrib/GN-2001B-Q-10/ \
    refimage=rgN20011221S139_comb.fits fl_over+

# Establish the wavelength calibration
# This step requires a bit of interactions since the automatic line
# id fails in about 20% of the cases, with this version of gswavelength 
# Improvements are planned for future releases of gswavelength
# For MOS data, the step parameter must be set equal to 2 so that the 
# distortion in the spatial direction can be properly determined
gswavelength gsN20011221S016.fits coordlist="linelists$cuar.dat" \
    fwidth=13 cradius=13 minsep=5 aiddebug=s order=4 match=-10 \
    fitcxord=4 fitcyord=4 step=2

# Transform the CuAr spectrum, for checking that the transformation is ok
# Output image name is defined by the default value outpref="t"
gstransform gsN20011221S016 wavtran=gsN20011221S016

# Inspect the transformed arc by using imexamine on each of the SCI 
# extensions
for(i=1;i<=37;i+=1) {
  imexa("tgsN20011221S016[SCI,"//str(i)//"]")
}

# Transform the science exposures
gstransform gsN20011221S140,gsN20011221S141 wavtran=gsN20011221S016

# Skysubtract the science exposures. Output image names are defined by the
# default value outpref="s"
gsskysub tgsN20011221S140,tgsN20011221S141 mos_sample=0.8 fl_inter+

# Inspect the sky subtracted spectra by imexamine on each of the SCI 
# extensions
for(i=1;i<=37;i+=1) {
  imexa("stgsN20011221S140[SCI,"//str(i)//"]")
}
for(i=1;i<=37;i+=1) {
  imexa("stgsN20011221S141[SCI,"//str(i)//"]")

# Test gsextract works, adjust the paramegers tsum and tstep to make
# it possible to trace faint objects
# Run the task interactively to make sure all the faint objects are 
# traced correctly
gsextract stgsN20011221S141 tnsum=100 tstep=100 fl_inter+

# GEXTRACT may be repeated for the other image stgsN20011221S140

# Inspect the extracted spectra
for(i=1;i<=37;i+=1) {
  splot("estgsN20011221S141[SCI,"//str(i)//"]")
}

# Flux calibrate 1D spectra, this only works correctly if the 
# sensitivity function covers the full wavelength range spanned
# but the different slitlets in the MOS observation. This is not
# normally the case.
gscalibrate estgsN20011221S141 sfunction=../Basecalib_spec_old/sens

# Inspect the flux calibrated spectra
for(i=1;i<=37;i+=1) {
  splot("cestgsN20011221S141[SCI,"//str(i)//"]")
}