"""
This script generates files to setup a PypeIt run
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
import argparse
from IPython import embed
from pypeit.scripts import scriptbase
from pypeit.spectrographs.util import available_spectrographs
[docs]
class Setup(scriptbase.ScriptBase):
[docs]
@classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Parse data files to construct a pypeit file in '
'preparation for reduction using \'run_pypeit\'',
width=width, default_log_file=True)
# TODO: Spectrograph should be a required argument
parser.add_argument('-s', '--spectrograph', default=None, type=str,
help='A valid spectrograph identifier: {0}'.format(
', '.join(available_spectrographs)))
parser.add_argument('-r', '--root', default='current working directory', type=str, nargs='+',
help='Root to search for data files. You can provide the top-level '
'directory (e.g., /data/Kast) or the search string up through '
'the wildcard (.e.g, /data/Kast/b). Use the --extension option '
'to set the types of files to search for.')
parser.add_argument('-e', '--extension', default=None,
help='File extension to use. Must include the period (e.g., ".fits") '
'and it must be one of the allowed extensions for this '
'spectrograph. If None, root directory will be searched for '
'all files with any of the allowed extensions.')
parser.add_argument('-d', '--output_path', default='current working directory',
help='Path to top-level output directory.')
parser.add_argument('-o', '--overwrite', default=False, action='store_true',
help='Overwrite any existing files/directories')
parser.add_argument('-c', '--cfg_split', default=None, type=str,
help='Generate the PypeIt files and folders by input configuration. '
'To write all unique configurations identifed, use \'all\', '
'otherwise provide the list of configuration letters; e.g., '
'\'A,B\' or \'B,D,E\' or \'E\'.')
parser.add_argument('-b', '--background', default=False, action='store_true',
help='Include the background-pair columns for the user to edit')
parser.add_argument('-f', '--flexure', default=False, action='store_true',
help='Include the manual spatial shift (flexure) column for the user to edit')
parser.add_argument('-m', '--manual_extraction', default=False, action='store_true',
help='Include the manual extraction column for the user to edit')
parser.add_argument('-k', '--keep_bad_frames', default=False, action='store_true',
help='Keep all frames, even if they are identified as having '
'bad/unrecognized configurations that cannot be reduced by '
'pypeit. (This is the opposite of the --bad_frames option in '
'pypeit_obslog; i.e., you have to tell pypeit_setup to keep '
'these frames, whereas you have to tell pypeit_obslog to remove '
'them.')
parser.add_argument('-p', '--param_block_file', default=None, type=str,
help='File containing the additional PypeIt user parameters to be '
'added to the parameter block of the generated reduction file')
parser.add_argument('-G', '--gui', default=False, action='store_true',
help='Run setup in a GUI')
# NOTE: These are only used to prevent updates to some of the automated
# document building just based on changes in the pypeit version or the
# date. These should *not* show up when users run `pypeit_setup -h` due
# to the use of `help=argparse.SUPPRESS`.
parser.add_argument('--version_override', type=str, default=None, help=argparse.SUPPRESS)
parser.add_argument('--date_override', type=str, default=None, help=argparse.SUPPRESS)
return parser
[docs]
@classmethod
def main(cls, args):
import time
from pathlib import Path
from pypeit import log
from pypeit.pypeitsetup import PypeItSetup
from pypeit.calibrations import Calibrations
if args.spectrograph is None:
if args.gui is False:
raise IOError('spectrograph is a required argument. Use the -s, --spectrograph '
'command-line option.')
else:
# Check that input spectrograph is supported
if args.spectrograph not in available_spectrographs:
raise ValueError(f'Instrument "{args.spectrograph}" unknown to PypeIt.\n'
f'\tOptions are: {", ".join(available_spectrographs)}\n'
'\tSelect an available instrument or consult the documentation '
'on how to add a new instrument.')
if args.gui:
# Start the GUI
from pypeit.setup_gui.controller import start_gui
start_gui(args)
else:
# Initialize the log
cls.init_log(args)
# Initialize PypeItSetup based on the arguments
ps = PypeItSetup.from_file_root(args.root, args.spectrograph, extension=args.extension)
# Add any additional user parameters
if args.param_block_file is not None:
if (user_par_fn := Path(args.param_block_file)).exists():
with open(user_par_fn, 'r', encoding='utf-8') as user_par_fobj:
user_cfgs = [l.rstrip() for l in user_par_fobj.readlines()]
ps.append_user_cfg(user_cfgs)
else:
log.warning(f"Could not open param_block file {args.param_block_file}. "
"Not adding any additional user parameters to the .pypeit file.")
# Run the setup
ps.run(setup_only=True, clean_config=not args.keep_bad_frames)
# Print selected files
output_path = Path(args.output_path).absolute()
if args.cfg_split is None:
# Output directory is hard-coded to be 'setup_files'
output_path /= 'setup_files'
if not output_path.exists():
output_path.mkdir(parents=True)
# Write the sorted file,
sorted_file = output_path / ps.pypeit_file.replace('.pypeit', '.sorted')
ps.fitstbl.write_sorted(sorted_file, write_bkg_pairs=args.background,
write_manual=args.manual_extraction)
# the calib file,
calib_file = sorted_file.with_suffix('.calib')
caldir = calib_file.parent / ps.par['calibrations']['calib_dir']
Calibrations.association_summary(calib_file, ps.fitstbl, ps.spectrograph, caldir,
overwrite=True)
# and the obslog file
obslog_file = sorted_file.with_suffix('.obslog')
header = ['Auto-generated PypeIt Observing Log',
f'{0}'.format(time.strftime("%a %d %b %Y %H:%M:%S", time.localtime()))]
ps.fitstbl.write(output=obslog_file, columns='pypeit', sort_col='mjd', overwrite=True,
header=header)
else:
if not output_path.exists():
output_path.mkdir(parents=True)
# Write the pypeit files.
configs = [item.strip() for item in args.cfg_split.split(',')]
pypeit_files = ps.fitstbl.write_pypeit(output_path=output_path, cfg_lines=ps.user_cfg,
write_bkg_pairs=args.background,
write_manual=args.manual_extraction,
write_shift = args.flexure,
configs=configs,
version_override=args.version_override,
date_override=args.date_override)
# Write the calib file for each written pypeit file.
setups = [Path(p).absolute().name.split('.')[0].split('_')[-1] for p in pypeit_files]
for i, setup in enumerate(setups):
indx = ps.fitstbl.find_configuration(setup)
calib_file = Path(pypeit_files[i]).absolute().with_suffix('.calib')
caldir = calib_file.parent / ps.par['calibrations']['calib_dir']
Calibrations.association_summary(calib_file, ps.fitstbl, ps.spectrograph,
caldir, subset=indx, overwrite=True)