gapick - Finding optimal set of PSF stars¶
Overview¶
gapick - [g]enetic [a]lgorithm PICK (after daophot PICK), is command line and python module for
finding PSF stars set which minimizes goal function: mean of allstar errors for all good stars in field.
The “good stars” are those which passes filtering against magnitude (brighter than minimal threshold --max-ph-mag)
and against aperture photometry error (error lower than threshold --max-ph-err).
The mineralization process is implemented as genetic algorithm, where individual is some subset of initial PSF stars candidates.
gapick command line tool is automatically installed with pip installation of astwro package. Python function interface is available as follows:
from astwro.tools import gapick
gapick.main(arguments)
Arguments of astwro.tools.gapick.main() corresponds to long version of command line arguments, eg command line:
$ gapick gapick --overwite --out_dir results i.fits
is equivalent to:
from astwro.tools import gapick
gapick.main(overwrite=True, out_dir='results', image='i.fits')
image is only positional argument of commandline.
Parameters¶
Commandline parameters help is displayed with --help option:
$ gapick --help
usage: gapick [-h] [--all-stars-file FILE] [--psf-stars-file FILE]
[--frames-av n] [--frames-sum n] [--photo-opt FILE]
[--photo-is r] [--photo-os r] [--photo-ap r [r ...]]
[--stars-to-pick n] [--faintest-to-pick MAG] [--fine]
[--max-psf-err-mult x] [--max-ph-err x] [--max-ph-mag m]
[--parallel n] [--out_dir output_dir] [--overwrite]
[--ga_init_prob x] [--ga_max_iter n] [--ga_pop n]
[--ga_cross_prob x] [--ga_mut_prob x] [--ga_mut_str x]
[--loglevel level] [--no_stdout] [--no_progress] [--version]
[image]
Find best PSF stars using GA to minimize mean error 2nd version of PSF fit
applied to all stars by allstar. Minimized function is the mean of allstar's
chi value calculated on sigma-clipped (sigma=4.0) list of all stars. Results
will be stored in --dir directory if provided. List of stars will be output to
stdout until suppressed by -no_stdout
positional arguments:
image FITS image file (default: astwro sample image for
tests)
optional arguments:
-h, --help show this help message and exit
--all-stars-file FILE, -c FILE
all stars input file in one of daophot's formats
(default: obtained by daophot FIND)
--psf-stars-file FILE, -l FILE
PSF candidates input file in one of daophot's formats,
the result of algorithm is a subset of those stars
(default: obtained by daophot PICK)
--frames-av n frames ave - parameter of daophot FIND when --all-
stars-file not provided (default: 1)
--frames-sum n frames summed - parameter of daophot FIND when --all-
stars-file not provided (default: 1)
--photo-opt FILE, -O FILE
photo.opt file for aperture photometry (default: none)
--photo-is r PHOTOMETRY inner sky radius, overwrites photo.opt,
(default: from --photo-opt or 35)
--photo-os r PHOTOMETRY outher sky radius, overwrites photo.opt,
(default: from --photo-opt or 50)
--photo-ap r [r ...] PHOTOMETRY apertures radius (up to 12), overwrites
photo.opt, (default: from --photo-opt or 8)
--stars-to-pick n, -P n
number of stars to PICK as candidates when --stars-to-
pick not provided (default: 100)
--faintest-to-pick MAG
faintest magnitude to PICK as candidates when --stars-
to-pick not provided (default: 20)
--fine, -f fine tuned PSF calculation (3 iter) for crowded
fields, without this option no neighbourssubtraction
will be performed
--max-psf-err-mult x threshold for PSF errors of candidates - multipler of
average error; candidates with PSF error greater than
x*av_err will be rejected (default 3.0)
--max-ph-err x threshold for photometry error of stars for processing
by allstar; stars for which aperture photometry
(daophot PHOTO) error is greater than x will be
excluded form allstar run and have no effect on
quality measurment (default 0.1)
--max-ph-mag m threshold for photometry magnitude of stars for
processing by allstar; stars for which aperture
photometry (daophot PHOTO) magnitude is greater than m
(fainter than m) will be excluded form allstar run and
have no effect on quality measurement (default 20)
--parallel n, -p n how many parallel processes can be forked; n=1 avoids
parallelism (default: 8)
--out_dir output_dir, -d output_dir
output directory; directory will be created and result
files will be stored there; directory should not exist
or --overwrite flag should be set (default: do not
produce output files)
--overwrite, -o if directory specified by --out_dir parameter exists,
then ALL its content WILL BE DELETED
--ga_init_prob x, -I x
what portion of candidates is used to initialize GA
individuals; e.g. if there is 100 candidates, each of
them will be chosen to initialize individual genome
with probability x; in other words if x=0.3 first
population in GA will contain individuals with around
30 stars each; try to make size of first population
stars similar to expected number of resulting PDF
stars (default: 0.3)
--ga_max_iter n, -i n
maximum number of iterations of generic algorithm -
generations (default: 50)
--ga_pop n, -n n population size of GA (default: 80)
--ga_cross_prob x crossover probability of GA (default: 0.5)
--ga_mut_prob x mutation probability of GA - probability to became a
mutant (default: 0.2)
--ga_mut_str x mutation strength of GA - probability of every bit
flip in mutant (default: 0.05)
--loglevel level, -L level
logging level: debug, info, warning, error, critical
(default: info)
--no_stdout, -t suppress printing result (list of best choice of PSF
stars) to stdout at finish
--no_progress, -b suppress showing progress bar
--version, -v show version and exit
Note
Run gapick --help for actual set of parameters which can slightly differ from above.