!
! prepare.prg ::  prepare flat field and wavelength solution
!
! convert into midas
! rotate
! create median bias
! subtract median bias
!


DEFINE/PARAM p1 ? N "Enter grism number:" 
 !! above you can append a range for the grism number, so midas will
 !! check that the number is not crap

load/lut heat

set/context long


!! copy line catalog into current dir, midas sometimes does not like
!! the remote location...
!!

$ cp /scisoft/midas/calib/data/spec/line/hear.tbl stdlines.tbl


!! set default parameters
!!

@@ defaultpars{p1}



!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! fits -> bdf
!!

$ls *.fits > in.cat
$ls *.fits | sed s/fits/bdf/ > out.cat
! $paste in.cat out.cat

indisk/fits in.cat out.cat

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! rotate, to have lambda from sx to dx
!!
!!    overwrites original images
!!    restores descriptors start and step
!!


$ls *.bdf | awk '{print "rotate/clock "$1" r"$1}' > rclock.prg

write/out rotating images ... 
@@ rclock

$cat rclock.prg | awk '{print "mv "$3,$2}' > mv.sh

$sh mv.sh


crea/icat all

exec/cat write/descr all.cat start 1,1
exec/cat write/descr all.cat  step 1,1
exec/cat copy/dd all.cat ESO.TEL.AIRM.END all.cat o_airm

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! create median bias frame
!!
!!   get cursor to stop processing
!!

crea/icat bias *Dark*.bdf
$vi bias.cat                 !! edit catalog to remove unwanted (e.g. dark)

COMBINE/LONG bias bias MEDIAN
load bias scale=-3
STAT/IMAGE bias plot=p excess=0,300

write/out this BIAS will be subtracted from frames
write/out exit from display to continue
get/cur

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! subtract bias from all images
!!
exec/cat compute/ima all.cat = all.cat - bias

!! goto end

flatfield:
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! create master flat field
!!
!!    trim
!!    create median
!!    normalize
!!    show
!!    
!!
CREATE/ICAT flat *FlatSpec*.bdf

$vi flat.cat

!! trim flat field
!!
PREPARE/LONG flat.cat tflat



CREATE/ICAT flat tflat*.bdf
COMBINE/LONG flat medflat median

!!  normalization: the degree of the polynomial is decided by
!!    set/long fdeg=xxx
!!
NORMALIZE/FLAT medflat masterflat 0
!!                                ^            ^
!!                                bias level
!!

load masterflat cuts=f,ihap scale=-2

write/out frames will be divided by this master flat
write/out     exit from display to continue ...
get/cur

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! trim objects and HeAr
!!
write/out trimming HeAr
!!
!!crea/icat spectra *Spectrum*bdf
!!prepare/long spectra.cat obj
!!   crea/icat spectra obj*bdf


!!!!!!!!
trimhear:

crea/icat hear *HeAr*bdf
!! edit HeAr catalog, leave just the best arc
$vi hear.cat
prepare/long hear.cat hear
   crea/icat hear hear*bdf


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!
!! divide objects and HeAr by master flatfield
!!   and check final result
!!
!!exec/cat compute/ima spectra.cat = spectra.cat / masterflat
!!exec/cat load spectra.cat cuts=f,ihap scale=-2

!! Actually dividing the hear by the masterflat can create spurious
!! lines (e.g. grism 2 of EFOSC), so better not do it!
!!
!!exec/cat compute/ima    hear.cat =    hear.cat / masterflat
!!exec/cat load hear.cat cuts=f,ihap scale=-2

!! 
!! create master HeAr frame, and show
!!
avera/ima masterhear = hear.cat ? ? median

load masterhear cuts=f,ihap scale=-2



!! calibrate in lambda, based on a guess session
!!

!! override some parameters with reference session
!!
$cp ~/midwork/initial_{p1}.tbl refsess.tbl
$cp ~/midwork/initial_{p1}COE.tbl refsessCOE.tbl
init/long refsess



@@ waveguess



end: