# There are a few basic steps to the reduction process, often referred to as "OTZF": Overscan, Trim, Zero, Flat.
# [ Note: We no longer need to do corrections for dark leakage, fringing, and non-uniform illuminations.  
# Corrections for fringing and non-uniform illuminations are only important for I (or z) band. ]

# 0. Preliminary Tasks
# Copy raw data to a processing directory (e.g., "proc/").
# Remove undesired images from the processing directory: pointing images, focus images, images with low flux counts, high seeing, etc.
# Do your processing work below in a different directory, a directory where you place a copy of the raw data (i.e., don't overwrite the raw data).

# 1. Update headers to indicate what type of image each fits file represents.
hedit @bias.list ccdtype bias add+ verify-
hedit @bias.list imagetype zero add+ verify-
hedit @object.r.list ccdtype object add+ verify-
hedit @object.r.list imagetype object add+ verify-
hedit @flat.list ccdtype flat add+ verify-
hedit @flat.list imagetype flat add+ verify-

# 2. Combine bias images using zerocombine.  

task prevu=/d/crow1/tools/iraf/galphot/sep00/prevu.cl
zerocombine input=@bias.list output=masterbias.fit combine=average reject=minmax ccdtype=zero process=no delete=no clobber=no

# 3. Determine the overscan and trim sections.

disp a023 1
implot a023
:l 1000 1100
:c 1000 1100
# [ typing 'e' twice will define a zoomed-in box and 'r' replots; I found biassec=[2150:2200,1:2048] trimsec=[55:2100,1:2048] ]

# 4. Overscan-subtract and trim the flats and objects. 

ccdproc @flat.list ccdtype=flat fixpix=no overscan=yes trim=yes zerocor=yes darkcor=no flatcor=no biassec=[2150:2200,1:2048] trimsec=[55:2100,1:2048] zero=masterbias
ccdproc @object.r.list ccdtype=object fixpix=no overscan=yes trim=yes zerocor=yes darkcor=no flatcor=no biassec=[2150:2200,1:2048] trimsec=[55:2100,1:2048] zero=masterbias

# 5. Combine flats. MAKE SURE TO COMBINE SEPARATE FILTERS SEPARATELY. 

flatcombine input=@flat.list output=master_r_flat.fit combine=median reject=avsigclip ccdtype=flat subsets=yes process=no delete=no clobber=no scale=mode

# 6. Flat-field your object frames for flats

ccdproc @object.r.list ccdtype=object fixpix=no overscan=no trim=no zerocor=no darkcor=no flatcor=yes flat=master_r_flat