"""
This script enables the user to convert spec2D FITS files
from SlicerIFU instruments into a 3D cube with a defined WCS.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
import time
from pypeit import msgs
from pypeit import par
from pypeit import inputfiles
from pypeit import utils
from pypeit.coadd3d import CoAdd3D
from pypeit.spectrographs.util import load_spectrograph
from pypeit.scripts import scriptbase
from IPython import embed
[docs]class CoAddDataCube(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Read in an array of spec2D files and convert '
'them into a datacube', width=width)
parser.add_argument('file', type = str, default=None, help='filename.coadd3d file')
parser.add_argument('--det', default=1, type=int, help="Detector")
parser.add_argument('-o', '--overwrite', default=False, action='store_true',
help='Overwrite any existing files/directories')
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 coadd_datacube_YYYYMMDD-HHMM.log')
return parser
[docs] @staticmethod
def main(args):
# Set the verbosity, and create a logfile if verbosity == 2
msgs.set_logfile_and_verbosity('coadd_datacube', args.verbosity)
# Check that a file has been provided
if args.file is None:
msgs.error('You must input a coadd3d file')
# Read in the relevant information from the .coadd3d file
coadd3dfile = inputfiles.Coadd3DFile.from_file(args.file)
spectrograph = load_spectrograph(coadd3dfile.config['rdx']['spectrograph'])
# Parameters
spectrograph_def_par = spectrograph.default_pypeit_par()
parset = par.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_def_par.to_config(),
merge_with=(coadd3dfile.cfg_lines,))
# If detector was passed as an argument override whatever was in the coadd3d file
if args.det is not None:
msgs.info("Restricting to detector={}".format(args.det))
parset['rdx']['detnum'] = int(args.det)
# Extract the options
ra_offsets = coadd3dfile.options['ra_offset']
dec_offsets = coadd3dfile.options['dec_offset']
skysub_frame = coadd3dfile.options['skysub_frame']
scale_corr = coadd3dfile.options['scale_corr']
# Instantiate CoAdd3d
tstart = time.time()
coadd = CoAdd3D.get_instance(coadd3dfile.filenames, parset, skysub_frame=skysub_frame,
scale_corr=scale_corr, ra_offsets=ra_offsets,
dec_offsets=dec_offsets, spectrograph=spectrograph,
det=args.det, overwrite=args.overwrite)
# Coadd the files
coadd.run()
msgs.info(utils.get_time_string(time.time()-tstart))