# reduction notes for 2009Sep04 wiro longslit

# read in all images to rfits
files a*.fit > allfiles.txt

# replace .fit with .fits in output file list
sed -e "s/.fit/.fits/" allfiles.txt > allout.txt

rfits @allfiles.txt 0 @allout.txt

# overscan and trim all images   bt.fits

#produce output file name with _bt suffix
sed -e "s/.fits/_bt.fits/" allout.txt > trimout.txt

imdel @trimout.txt ver-
ccdproc @allout.txt outp=@trimout.txt biassec=[10:50,*] trimsec=[56:2099,741:1020] interact+

# make master bias image and
# optionally reomve bias by subtracting master bias from all images here


# produce a list of science images in science.txt and list of flat images in flats.txt
# this unix head and tail comands only works if your flats are nicely seggregated from the
# rest of the images

!tail -n 71 trimout.txt  > science.txt
!head -n 14 trimout.txt | tail -n 5   > flats.txt


# combine flats
imdel masterflat.fits ver-
imcomb @flats.txt outp=masterflat.fits comb=average rejec=avsigclip weight=median scale=mode statsec=[400:600,50:200]

# run resp[onse on masteflat
#imdel Response.fits ver+
response calib=masterflat.fits normal=masterflat.fits respons=Response.fits interac+ func=leg order=15

# or copy flat Response.fits from xxxx to use here
#cp ../2009Sep03/Response.fits .

# optionally create a master sky flat and use Illum to make
# an illumination image.  

# divide science images by normalized master flat (i.e., response image)
sed -e "s/_bt/_btf/" science.txt > science_f.txt
imarith @science.txt / Response.fits @science_f.txt

# if you made an Illum flat, divide by this image now too.  

# and dispaxis and extract spectra for each star
hedit @science_f.txt field=DISPAXIS value=1 add+ verif- show+ update+

emacs stars.txt & ; list of stars for which to extract spectra
emacs stars_ex.txt & ; MT names of stars
emacs arcs.txt & ; arc files for each star


imdel @stars_ex.txt verify-
apall @stars.txt outp=@stars_ex.txt referen="" interac+ find+ recent+ resize+ trace+ fittr+ backgr=fit b_sampl='-30:-20,20:30' b_order=3 t_order=3

# extract arc spectral for each star using same apertures
apall @arcs.txt outp=@arcs.txt referen=@stars.txt  interac- edit- find- recent- resize- trace- fittr+ backgr=none

# identify lines in first arc

identify a016_btf.0001.fits  

sed -e "s/.fits/.0001.fits/" arcs.txt > arcs_ex.txt

reidentify a016_btf.0001.fits @arcs_ex.txt coord=linelists$cuar.dat interac+
#rms=0.021 typically

# 
# assign reference spectra
cp arcs_ex.txt arcs_ex2.txt ; edit if necessary to assign spectra
#emacs arcs_ex2.txt & 

sed -e "s/.fits/.0001.fits/" stars_ex.txt > stars_ex2.txt 

refspectra @stars_ex2.txt refer=@arcs_ex2.txt select=match verb+ 

# clean spectra with splot before transforming


# apply wavelenth solutions
sed -e "s/.0001/_w.0001/" stars_ex2.txt  > stars_disp.txt

imdel  @stars_disp.txt ver-
dispcor @stars_ex2.txt @stars_disp.txt verbos+ linear+



ls *_w*.fits | grep -v 0001 > contin.txt
sed -e "s/_w/_wc/" contin.txt > contin_out.txt


# continuum normalize
del @contin_out.txt ver-

continuum @contin.txt @contin_out.txt  type=ratio replace- interac+ order=15 func=cheb high_re=2.2 low_rej=2