; GBTIDL functions to setup data reduction parameters for a GBT on-off
; observing run. 
; use: @gbt_setup
;
;
print,'enter gbt_setup.pro'

;; compile 
.comp /Users/jhibbard/Desktop/data2/gbtpro/ottflux
.comp /Users/jhibbard/Desktop/data2/gbtpro/spcalflux
.comp /Users/jhibbard/Desktop/data2/gbtpro/accumscans
.comp /Users/jhibbard/Desktop/data2/gbtpro/write_spectra
.comp /Users/jhibbard/Desktop/data2/gbtpro/GBTreduce1
.comp /Users/jhibbard/Desktop/data2/gbtpro/GBTreduce

; raw data and summary file will be night-specific
rawdata='/Users/jhibbard/Desktop/data2/GBTrawdata/AGBT05C_029_02.raw.acs.fits'
Summaryfile='AGBT05C_029_02_summary.txt'
night_preface='02'
; the keep file can be the same for multiple nights
keepfile='AGBT05C_029_keep.fits'

;; Global reduction parameter values:
fitting_order=3                 ;; Default fit order for baseline subtraction.
                                ;;    This can be changed for individual sources
Nbox=20                         ;; Parameter for boxcar smoothing & 
                                ;;    decimation; in channels
default_region=[40,380,450,475,630,790] 
default_region=[50,300,500,790] ;; Default egion used for baseline subtraction. 
                                ;;    This needs to be in pixels, after any 
                                ;;    decimation by Nbox. 
                                ;;    This can be changed for individual sources
do_out=1                        ;; keep accumulated spectra and ps and ascii 
                                ;;    versions of final baseline subtracted data

;; Modify these based on your data: number of scans that have RFI,
;; number of calibration sources, number of target sources

Num_RFI_scans=6
Num_Calibs=3
Num_Sources=5

; define structures for setting up data reduction parameters
interference={scan: 0, ints:lonarr(128,/NOZERO)}
interference.ints=-1
rec = {target, name:"blank", scans:lonarr(256,/NOZERO), $
       Nbox:20, region:lonarr(128,/NOZERO), nfit:1, type:0}

rfi = replicate(interference, Num_RFI_scans)
calib = replicate({target}, Num_Calibs)
source = replicate({target}, Num_Sources)

;; initialize scans and regions
calib.scans=-1
calib.region=-1
calib.Nbox=Nbox
calib.region=default_region
calib.nfit=fitting_order
source.scans=-1
source.region=-1
source.Nbox=Nbox
source.region=default_region
source.nfit=fitting_order

print,'Define RFI parameters'
i=0
rfi[i].scan=15 & rfi[i].ints=[0,1,2] & i+=1
rfi[i].scan=25 & rfi[i].ints=[20,21,22] & i+=1
rfi[i].scan=39 & rfi[i].ints=[3,4,5,6,7] & i+=1
rfi[i].scan=51 & rfi[i].ints=[7,8,9,10,11,12] & i+=1
rfi[i].scan=62 & rfi[i].ints=[0,1,2,3] & i+=1
rfi[i].scan=72 & rfi[i].ints=[11,12,13,14] & i+=1

print,'Define Calibrator parameters'
;; first calibrator listed is the primary calibrator. Others are just
;; for comparison. type=0 for spectral line calibrators, type=1 for 
;; flux calibrators. For flux calibrators, the mean flux will be
;; calculated from the first to last element of region (in channels).
i=0
calib[i].name= 'UGC0317a' & calib[i].scans=[5] & calib[i].nfit=3 & calib[i].type=0 & i+=1
calib[i].name= 'UGC0317b' & calib[i].scans=[35] & calib[i].nfit=3 & calib[i].type=0 & i+=1
calib[i].name='3C48Line' & calib[i].scans=[62] & calib[i].nfit=3 
              calib[i].type=1 & calib[i].region=[200,600] & i+=1

print,'Define Source parameters'
;; here, region can be any size
i=0
source[i].name='J0031-0934' & source[i].scans=[7,9,11,25,27,29] &  i+=1
source[i].name='J0215-0846' & source[i].scans=[13,15,17,19,21,23] &  i+=1
source[i].name='J0236-005' & source[i].scans=[37,39,41,43,45,47,70,72] &  i+=1
source[i].name='HS2236+1344' & source[i].scans=[49,51,53,55,57,59] &  i+=1
source[i].name='J0133+1342' & source[i].scans=[64,66,68] &  i+=1

print, 'Done with setup. Reduce all data with GBTreduce.pro'
print, 'Syntax: GBTreduce, rawdata, rfi, calib, source, summaryfile, ', $
          'do_out, keepfile, night_preface'

GBTreduce, rawdata, rfi, calib, source, summaryfile, do_out, keepfile, night_preface

print, 'Review set-up parameters with GBTreduce1.pro (syntax: j=3 & GBTreduce1, source[j])'