process_sphere_irdis_template.script

;; Example script to process SPHERE IRDIS DBI/CI data through pipeline. 
;; Will produce oifits files.

save_dir='~/data/sphere_data/HD142527_SAM/IRDIS/Analysis/'
data_dir='~/data/sphere_data/HD142527_SAM/IRDIS/Raw/'
prefix='SPHERE_IRDIFS_IRDIS_OBS137_'

frames=54+findgen(48) ;; files with the same number will be processed together, negative numbers note targets
tsize=[0.01+fltarr(4),-0.02+fltarr(4),0.03+fltarr(4),0.04+fltarr(4),0.05+fltarr(4),-0.06+fltarr(4),$
	0.07+fltarr(4),0.08+fltarr(4),0.09+fltarr(4),-0.10+fltarr(4),0.11+fltarr(4),0.12+fltarr(4)] ;; files with the same number will be processed together, negative numbers note targets

jobname='' ;;just a name thats added to the output files
extn='.fits'

;; discard_sigma defines criteria for automatic frame rejection. 
;; The 5 entries are the number of sigma to reject based on:
;;   [x position, y position, total flux, peak flux]
;; if there is a 5th entry, it repeats the peak flux calculation using 
;;  only discard_sigma[4] percent of frames to get the mean and st.dev.
;; Negative numbers mean no rejection! 
discard_sigma=[-2., -2., 5., -3.6, -0.7] 


flatpath='../Cal/sphere_irdis_flat.idlvar'

skies='../Cal/'+['SPHERE_IRDIFS_IRDIS_SKY103_0010.fits','SPHERE_IRDIFS_IRDIS_SKY103_0011.fits']

cd,save_dir

;;cube the data
qbe_sphere,data_dir, jobname, flatpath, frames,skies, tsize,extn=extn,prefix=prefix,cutsize=256,discard_sigma=discard_sigma,/centre_once_per_cube
;;get the visibilities and closure phases
calc_bispect_gpi, save_dir+"cubeinfo"+jobname+".idlvar" , root_dir="~/code/masking/"
;;calibrate the data
calibrate_v2_cp_gpi,save_dir+"cubeinfo"+jobname+".idlvar",/save_python,root_dir='~/code/masking/',/skip_cp_rejection,/cal4src

;; Fit a binary model to the data and calculate detection limits
binary_grid,'HD142527_0000_mrg.oifits' ;; you will have to change the filename here to your output oifits

end