0.7.288: complete_run.ini EXTALL=TRUE: all sky exposures are ignored

[larnoldgithub]

Apart from producing the tmp/*o_pp.fits, APERO completly ignored the SKY exposures. SKY exposure odometers are completly absent from red/, which is an issue for several programs which had requested a SKY expesure. I thought EXTALL means all :)

[larnoldgithub]

manually doing: apero_extract_spirou.py 23BQ06-Sep25 2899621o_pp.fits for example does extract the spectrum of a SKY.

TRG_TYPE= 'SKY ' / target or sky object

[njcuk9999]

So this is by design, currently we do not need to use the sky files for a "normal" apero run. [Note in v0.8 we actually we extract sky files as we will build a mask as part of the reductions]

I would ask you to look at the sequences in the documentation for what the keywords mean in general.

http://apero.exoplanets.ca/auto/recipe_sequences/spirou/sequences.html

For "full_seq" (used inside complete_run.ini) indeed there is a EXTALL (Entry 21 in the table)

You'll note that: {files}=[OBJ_DARK, OBJ_FP, POLAR_DARK, POLAR_FP]

If you look at the DPRTYPE APERO gives a SKY file it is not one of these (its is DARK_DARK_SKY) thus you need to use a different sequence to reduce those files: http://apero.exoplanets.ca/auto/recipe_sequences/spirou/sequence_eng_seq.html

The eng_seq has EXT_SKY so set that to True and you'll get all skys extracted (note you may also want to combine this with the pp_seq_opt and set PP_SKY=True if not using the full_seq to preprocess all files.

Note in a custom run.ini file you could add both the full_seq and eng_seq options and thus always get all sky extracted.

i.e.

# Stuff before this

# Run the preprocessing recipes
RUN_PP = True

# Run the reference calibration recipes
RUN_DARKREF = True
RUN_BADREF = True
RUN_LOCREFCAL = True
RUN_LOCREFSCI = True
RUN_SHAPEREF = True
RUN_SHAPELREF = True
RUN_FLATREF = True
RUN_THERM_REFI = True
RUN_LEAKREF = True
RUN_WAVEREF = True
RUN_THERM_REFT = True

# Run the night calibration recipes
RUN_BAD = True
RUN_LOCCAL = True
RUN_LOCSCI = True
RUN_SHAPE = True
RUN_FF = True
RUN_THERM_I = True
RUN_WAVE = True
RUN_THERM_T = True

# Run the extraction recipes
RUN_EXTALL = True

# Run the telluric recipes
RUN_MKTELLU1 = True
RUN_MKTMOD1 = True
RUN_MKTFIT1 = True
RUN_MKTEMP1 = True
RUN_MKTELLU2 = True
RUN_MKTMOD2 = True
RUN_MKTFIT2 = True
RUN_MKTEMP2 = True
RUN_FTFIT1 = True
RUN_FTTEMP1 = True
RUN_FTFIT2 = True
RUN_FTTEMP2 = True

# Run the radial velocity recipes
RUN_CCF = True

# Run the polar recipes
RUN_POLAR = True

# Run the postprocessing recipes
RUN_POSTALL = True

# stuff after this

And then add the stuff for eng_seq e.g. what is in other_run.ini

# Stuff before this

# Run the extraction recipes (from eng_seq from other_run.ini)
RUN_EXT_HC1HC1 = False
RUN_EXT_FPFP = False
RUN_EXT_FF = False
RUN_EXT_DFP = False
RUN_EXT_SKY = False
RUN_EXT_LFC = False
RUN_EXT_FPD = False
RUN_EXT_LFCFP = False
RUN_EXT_FPLFC = False
RUN_EXT_EVERY = False

# stuff after this

Then at the bottom of this combined run.ini you can add both sequences. Don't forget to add the skips for both as well!

# -----------------------------------------------------------------------------
# Run information
# -----------------------------------------------------------------------------
#
#   Format:
#
#   id##### = command
#
#   Must start with "id" followed by a number
#     The number identifies the order to process in
#
#   If command is a sequence will process all in defined sequence
#      valid sequences are:
#           pp_seq, pp_seq_opt, full_seq,
#           limited_seq, ref_seq, calib_seq,
#           tellu_seq, science_seq, eng_seq

id00000 = full_seq
id00001 = eng_seq