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## CCD REDUCTION AND PRODUCING LIGHT CURVE FIGURES PROCESS USING PYTHON
## AUTHOR : QIANG CHEN chen@camk.edu.pl
## DATE   : 2020 Sep 26
##
# PYTHON ENVIRONMENT REQUIREMENT:
# - pip install astropy # reduction
# - pip install --no-deps ccdproc # reduction
# - pip install photutils # photometry
# - pip install astroalign # align the figure or coordinates arrays
# alternatively can use (CAMK):
#   source /home/chen/python-chen/chen3.6/bin/activate
#
# REFERENCE : CCD REDUCTION https://mwcraig.github.io/ccd-as-book/00-00-Preface.html
# REMAINS : 
# - Dark frames lack exposure choice, 300 sec make the bg negative!
# - pip install aplpy # I don't know how to use it
# - The bad pixels are not specified, will consider when needed
# - pip install drizzlepac # PYRAF, align the images 
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path = '/work/chuck/chen/obs/20190822'

1, create master bias
  Script  : make_master_bias.py
  Input   : path/*.fit
  Output  : path/reduced/combined_bias.fit

2, create master dark
  Script  : make_master_dark.py
  Input   : path/*.fit
  Output  : path/reduced/combined_dark_300.000.fit

3, carete master flat
  Script  : make_master_flat.py 
  Input   : path/*.fit
  Output  : path/reduced/flat_*.fit

4, reduce science figure
  Script  : calibrate_science_images.py 
  Input   : path/reduced/combined_bias.fit
            path/reduced/flat_*.fit
            path/reduced/combined_dark_300.000.fit
  Output  : path/reduced/light_*.fit

5.1 identify apperture parameters : fwhm, threshold
  Tips    : try to improve fwhm and threshold to select < 50 stars
  Script  : apperture_photometry_check.py
  Input   : path/reduced/*.fit
  Output  : path/reduced/stars_*.dat

5.2, apperture photometry
  Script  : aperture_photometry.py
  Input   : path/reduced/*.fit
  Output  : path/reduced/stars_*.dat

6, sorting stars of similar coordinates in the star data files
  Script  : stars_sorting_v2.py 
  Input   : path/reduced/stars_*.dat
  Output  : path/reduced/sorted_stars_{FILTER}*.dat
            path/reduced/sorted_ap_{FILTER}*.dat
            path/reduced/aligned_lightes_*_{FILTER}*.dat  

7.1 plot the light curve figures
  Script  : plot_light_curve.py
  Input   : path/reduced/sorted_stars_{FILTER}*.dat
            path/reduced/sorted_ap_{FILTER}*.dat
  Output  : path/reduced/sorted_stars_{FILTER}*.png
            path/reduced/sorted_ap_{FILTER}*.png
  Tips    : manualy find out which light curve figure looks like target object

7.2 plot the AB variable light curve
  Script  : plot_target_lightcurve.py
  Input   : path/reduced/sorted_stars_B18.dat 
            path/reduced/sorted_stars_V31.dat
  Output  : path/reduced/final_AB.png