autoproc_steps.py

Reduction steps called by autoproc.py

Pipeline Input Parameters

The following structure is used to pass commonly used pipeline variables throughout each steps. See autoproc.py at line 153 and autopipedefaults for usage and definition.

pipevar = { 'autoastrocommand':'autoastrometry', 
            'getsedcommand':'get_SEDs', 
            'sexcommand':'sex', 
            'swarpcommand':'swarp', 
            'rmifiles':0, 
            'prefix':'', 
            'datadir':'' , 
            'imworkingdir':'', 
            'overwrite':0 , 
            'verbose':1,
            'flatfail':'', 
            'fullastrofail':'',
            'pipeautopath':'',
            'refdatapath':'', 
            'defaultspath':'' 
          }

Functions

autopipedefaults - set commonly used variables to use throughout each step.
autopipeprepare - update image headers and performs bias/dark subtraction.
autopipeimflatten - flatten data using flat with matching filter name.
autopipemakesky - combine sky flats based on filter type (sigma clipping for sources).
autopipeskysub - subtract both master sky and median.
autopipeskysubmed - subtract median, does NOT use master sky.
autopipecrcleanim - remove cosmic rays.
autopipeastrometry - calculate astrometry of image files to fix WCS coordinates.
autopipestack - create flux scale and stack images with SWarp.

Functions are called in the same order as above, see autoproc.py at line 240 (snippet below).

for step in steps:        
  if step == 'prepare': ap.autopipeprepare(pipevar=pipevar)
  if step == 'flatten': ap.autopipeimflatten(pipevar=pipevar)
  if step == 'makesky' and nomastersky == False: ap.autopipemakesky(pipevar=pipevar)
  if step == 'skysub' and nomastersky == False:  ap.autopipeskysub(pipevar=pipevar)
  if step == 'skysub' and nomastersky == True:  ap.autopipeskysubmed(pipevar=pipevar)    
  if step == 'crclean' and nocrclean == False: ap.autopipecrcleanim(pipevar=pipevar)
  if step == 'astrometry': ap.autopipeastrometry(pipevar=pipevar),
  if step == 'stack'     : ap.autopipestack(pipevar=pipevar, customcat=customcat, customcatfilt=customcatfilt)

##autopipedefaults <> autopipedefaults(pipevar)

Sets commonly used variables for pipeautoproc to use throughout each step. Uses pipeautoproc.par to set variables, otherwise set to default values. Saves in a dictionary.

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

##autopipeprepare <> autopipeprepare(pipevar)

Runs pipeprepare on every valid file and saves files with prefix p. Changes header with more manageable keywords and does bias/dark subtraction if bias/dark master exists (compares header keywords in files and bias/dark master).

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

Saved in pipevar['datadir'] with prefix defined in pipevar['prefix'].

####Output files

Saved to pipevar['imworkingdir'] with p prefix.

####Dependencies

autoproc_depend.pipeprepare

##autopipeimflatten <> autopipeimflatten(pipevar)

Flattens data using flat with matching filter name, and Saves files with prefix f. Flat files that don't match any filter are stored in pipevar['flatfail'].

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

prepared files: In pipevar['imworkingdir'] with p prefix.
flat files: In pipevar['imworkingdir'] containing flat in filename.

####Output files

Saved to pipevar['imworkingdir'] with f prefix.

####Dependencies

autoproc_depend.flatpipeproc.

##autopipemakesky <> autopipemakesky(pipevar)

Combine sky flats based on filter type (sigma clipping for sources, at least 2 files per filter). See skypipecombine.

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

Stored in pipevar['imworkingdir'] with fp prefix.

####Output files

Saved to pipevar['imworkingdir'] with sky- prefix.

##autopipeskysub <> autopipeskysub(pipevar)

Subtracts master sky flat from data and subtracts median.

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

flattened files: Stored in pipevar['imworkingdir'] with fp prefix.
sky files: Stored in pipevar['imworkingdir'] containing sky- in filename.

####Output files

Saved to pipevar['imworkingdir'] with s prefix.

####Dependencies

autoproc_depend.skypipeproc.

##autopipeskysubmed <> autopipeskysubmed(pipevar)

Subtracts median ONLY, does NOT use master sky.

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

Stored in pipevar['imworkingdir'] with fp prefix.

####Output files

Saved to pipevar['imworkingdir'] with s prefix.

##autopipecrcleanim <> autopipecrcleanim(pipevar)

Removes cosmic rays

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

Stored in pipevar['imworkingdir'] with sfp prefix.

####Output files

Saved to pipevar['imworkingdir'] with z prefix.

####Dependencies

autoproc_depend.cosmiczap.

##autopipeastrometry <> autopipeastrometry(pipevar)

Calculates astrometry of image files to fix WCS coordinates (shift and rotation) in header. Using fast astrometry solver (vlt_autoastrometry.py) with pair-distance matching and asterism matching. Returns file with corrected WCS coordinates saved with a prefix. Runs Scamp for additional astrometry corrections, twice, once for basic individual LOOSE correction, second correct all together. Uses distortion of 3 as default, but uses 7 if distortion parameters high (i.e. RATIR H2RG).

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

Stored in pipevar['imworkingdir'] with zsfp prefix.

####Output files

Saved to pipevar['imworkingdir'] with a prefix.

####Dependencies

autoproc_depend.astrometry, vlt_autoastrometry.py, SCAMP, SExtractor.

####Usage of vlt_autoastrometry.py

See autoproc_depend.py at line 541, pipevar['autoastrocommand'] is vlt_autoastrometry.py as defined in pipeautoproc.par.

head = pf.getheader(file)
        
targ = head['TARGNAME']
sat  = head['SATURATE']
        
if 'flat' in targ: continue
  cmd = 'python ' + pipevar['autoastrocommand'] + ' ' + file + ' -l ' + str(sat)

##autopipestack <> autopipestack(pipevar)

Does zeropoint correction on each individual frame using sextractor and get_SEDs. Creates flux scale (newflxsc) from how close to median of zeropoint values. Uses flux scale to stack images in swarp (has moved bad zeropoint values and bad newflxsc values to marked folders - badzptfit/ and badflxsc/) and calculates absolute zeropoint correction of coadd. Saves zeropoint plot as zpt_(FILTER).ps.

####Params

pipevar {dict}: (Input pipeline parameters)[#pipeline-input-parameters].

####Input files

Stored in pipevar['imworkingdir'] with a prefix.

####Output files

Saved to pipevar['imworkingdir'] with coadd prefix as .fits and .weight.fits.

####Dependencies

SWarp, get_SEDs.py, autoproc_depend.calc_zpt, autoproc_depend.findsexobj (SExtractor), autoproc_depend.identify_matches.

####Usage of autoproc_depend.findsexobj

See autoproc_depend.py at line 745.

for sfile in stacklist:
 head = pf.getheader(sfile)
 ipixscl = head['PIXSCALE']
 apd.findsexobj(sfile, 3.0, pipevar,pix=ipixscl,aperture=20.0, quiet=quiet)

NOTE: stacklist is a list of files that meet the following conditions:

same filter (head['FILTER'])
same target (head['TARGNAME'])
head['ASTRRMS1'] in (2.0e-4, 5.0e-6)
head['ASTRRMS2'] in (2.0e-4, 5.0e-6)

See autoproc_depend.py at line 924.

head   = pf.getheader(outfl)
pixscl = head['PIXSCALE']
try:
 apd.findsexobj(outfl, 10.0, pipevar, pix=pixscl, aperture=20.0, wtimage=outwt, quiet=quiet)

NOTE: outfl is the fits file coadded with the flux scale using SWarp (see line 903).

See autoproc_depend.py at line 930.

head   = pf.getheader(outfl)
cpsfdi = 1.34 * float(head['SEEPIX'])
           
# Run sextractor again on new coadd file
apd.findsexobj(outfl, 3.0, pipevar, pix=pixscl, aperture=cpsfdi, wtimage=outwt, quiet=quiet)

####Usage of get_SEDs.py

See autoproc_depend.py at line 805.

# If custom catalog not provided, catalog doesn't include filter, or 
# no objects from catalog found in image then
# use get_SEDs.py to make catalog using 2MASS + (SDSS or APASS or USNOB1)
if nocustomcat:
  # Create catalog star file 
  # (python get_SEDs.py imfile filter catfile USNOB_THRESH alloptstars)
  sedcmd = 'python ' + pipevar['getsedcommand'] + ' ' + imfile + ' ' +\
                         filter + ' ' + catfile + " 15 True "+ qtcmd

####Usage of SWarp

See autoproc_depend.py at line 903.

stackcmd = pipevar['swarpcommand']
# Keywords to carry through
stackcmd += ' -COPY_KEYWORDS OBJECT,TARGNAME,FILTER,' +\
                   'INSTRUME,PIXSCALE,WAVELENG,DATE-OBS,AIRMASS,FLATFLD,FLATTYPE '
# Create output variables that will be used by SWarp
outfl = pipevar['imworkingdir'] + 'coadd' + targ + '_'+ re.sub(r'[^\w]', '', medtime)+'_'+ filter + '.fits'
outwt = pipevar['imworkingdir'] + 'coadd' + targ + '_'+ re.sub(r'[^\w]', '', medtime)+'_'+ filter + '.weight.fits'
            
if pipevar['verbose'] > 0:
  stackcmd += ' -VERBOSE_TYPE NORMAL '
else:
  stackcmd = stackcmd + ' -VERBOSE_TYPE QUIET '
            
# Coadd with flux scale
stackcmd = stackcmd + ' -SUBTRACT_BACK N -WRITE_XML N -IMAGEOUT_NAME ' +\
                       outfl + ' -WEIGHTOUT_NAME ' + outwt +\
                       ' -FSCALE_KEYWORD NEWFLXSC ' + newtextslist

####Usage of autoproc_depend.calc_zpt

See autoproc_depend.py at line 839.

zpt, scats, rmss = apd.calc_zpt(np.array([refmag]), np.array([obskpm]), np.array([obswts]), sigma=3.0)

See autoproc_depend.py at line 1029.

czpts, cscats, crmss = apd.calc_zpt(np.array([refmag]), np.array([obskpm]), 
                                   np.array([obswts]), sigma=1.0,
                                   plotter=pipevar['imworkingdir']+'zpt_'+filter+'.ps')

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autoproc_steps.py

Pipeline Input Parameters

Functions

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