"""
This script enables the user to view a 2D FITS file
and define the sky background regions interactively.
Run above the Science/ folder.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from pypeit.scripts import scriptbase
[docs]class SkySubRegions(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Display a spec2d frame and interactively '
'define the sky regions using a GUI. Run in the '
'same folder as your .pypeit file',
width=width)
parser.add_argument('file', type=str, default=None, help='spec2d file')
parser.add_argument('--det', default='1', type=str, help="Detector")
parser.add_argument('-o', '--overwrite', default=False, action='store_true',
help='Overwrite any existing files/directories')
parser.add_argument('-i', '--initial', default=False, action='store_true',
help='Use initial slit edges?')
parser.add_argument('-f', '--flexure', default=False, action='store_true',
help='Use flexure corrected slit edges?')
parser.add_argument('-s', '--standard', default=False, action='store_true',
help='List standard stars as well?')
parser.add_argument('-v', '--verbosity', type=int, default=1,
help='Verbosity level between 0 [none] and 2 [all]. Default: 1. '
'Level 2 writes a log with filename skysub_regions_YYYYMMDD-HHMM.log')
parser.add_argument('--try_old', default=False, action='store_true',
help='Attempt to load old datamodel versions. A crash may ensue..')
return parser
[docs] @staticmethod
def main(args):
from IPython import embed
from pypeit import spec2dobj
import os
import astropy.io.fits as fits
from pypeit import msgs
from pypeit import io
from pypeit.core.gui.skysub_regions import SkySubGUI
from pypeit.images import buildimage
from pypeit.images.detector_container import DetectorContainer
from pypeit.edgetrace import EdgeTraceSet
chk_version = not args.try_old
# Parse the detector name
try:
det = int(args.det)
except:
detname = args.det
else:
detname = DetectorContainer.get_name(det)
# Load it up
spec2DObj = spec2dobj.Spec2DObj.from_file(args.file, detname, chk_version=chk_version)
frame = spec2DObj.sciimg
hdr = fits.open(args.file)[0].header
fname = hdr['FILENAME']
calib_dir = hdr['CALIBDIR']
pypeline = hdr['PYPELINE']
specname = hdr['PYP_SPEC']
# Use the edges calibration frame to set the calibration key
key = EdgeTraceSet.calib_type.upper()
if key not in spec2DObj.calibs:
# TODO: Until I can figure out a better approach...
msgs.error(f'EdgeTrace calibration frame not recorded in {args.file}!')
calib_key, _ = EdgeTraceSet.parse_key_dir(spec2DObj.calibs[key], from_filename=True)
# Use the appropriate class to get the "detector" number
det = spec2DObj.detector.parse_name(detname)
# Setup for PypeIt imports
msgs.reset(verbosity=args.verbosity)
# Grab the slit edges
slits = spec2DObj.slits
# Get the spatial flexure
spat_flexure = None
if args.flexure:
spat_flexure = spec2DObj.sci_spat_flexure
# Derive an appropriate output filename
file_base = os.path.basename(fname)
regfile = buildimage.SkyRegions.construct_file_name(calib_key, calib_dir=calib_dir,
basename=io.remove_suffix(file_base))
# Finally, initialise the GUI
skyreg = SkySubGUI.initialize(det, frame, slits, pypeline, specname, outname=regfile,
overwrite=args.overwrite, runtime=False, printout=True,
initial=args.initial, flexure=spat_flexure)
# Get the results
msskyreg = skyreg.get_result()
if msskyreg is not None:
outfil = skyreg.get_outname()
setup, calib_id, detname = msskyreg.parse_calib_key(calib_key)
msskyreg.set_paths(calib_dir, setup, calib_id, detname)
msskyreg.to_file(file_path=outfil)
# Reset the defaults
skyreg.finalize()