"""
This script examines a set of files and indicates which do and
which do not have sufficient calibs
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from pypeit.scripts import scriptbase
from pypeit.spectrographs import available_spectrographs
[docs]class ChkForCalibs(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description="Script to check for calibrations",
width=width)
parser.add_argument('root', type=str, default=None,
help='File path+root, e.g. /data/Kast/b ')
parser.add_argument('-s', '--spectrograph', default=None, type=str,
help='A valid spectrograph identifier: {0}'.format(
', '.join(available_spectrographs)))
parser.add_argument('-e', '--extension', default='.fits',
help='File extension; compression indicators (e.g. .gz) not required.')
parser.add_argument('--save_setups', default=False, action='store_true',
help='If not toggled, remove setup_files/ folder and its files.')
return parser
[docs] @staticmethod
def main(args):
"""
Args:
args:
Returns:
`astropy.table.Table`_:
"""
import os
from IPython import embed
import numpy as np
from astropy import table
from pypeit.pypeitsetup import PypeItSetup
from pypeit import calibrations
from pypeit import msgs
from pypeit.par import PypeItPar
import shutil
# Check that the spectrograph is provided if using a file root
if args.root is not None:
if args.spectrograph is None:
raise ValueError('Must provide spectrograph identifier with file root.')
# Check that input spectrograph is supported
if args.spectrograph not in available_spectrographs:
raise ValueError('Instrument \'{0}\' unknown to PypeIt.\n'.format(args.spectrograph)
+ '\tOptions are: {0}\n'.format(', '.join(available_spectrographs))
+ '\tSelect an available instrument or consult the documentation '
+ 'on how to add a new instrument.')
# Initialize PypeItSetup based on the arguments
ps = PypeItSetup.from_file_root(args.root, args.spectrograph, extension=args.extension)
# Run the setup
ps.run(setup_only=True)
is_science = ps.fitstbl.find_frames('science')
msgs.info('Loaded spectrograph {0}'.format(ps.spectrograph.name))
# Unique configurations
uniq_cfg = ps.fitstbl.unique_configurations(copy=True)
# Setup the table. Need to use object type for strings so that
# they're not truncated.
answers = table.Table()
answers['setups'] = list(uniq_cfg.keys())
# Add the configuration columns
for setup, setup_dict in uniq_cfg.items():
for key, value in setup_dict.items():
answers[key] = np.empty(len(answers), dtype=object) if isinstance(value, str) \
else type(value)(0)
break
answers['pass'] = False
answers['scifiles'] = np.empty(len(answers), dtype=object)
for i, setup in enumerate(uniq_cfg.keys()):
for setup_key, setup_value in uniq_cfg[setup].items():
answers[setup_key] = setup_value
if setup == 'None':
print("There is a setup without science frames. Skipping...")
answers['pass'][i] = False
answers['scifiles'][i] = None
continue
msgs.info('=======================================================================')
msgs.info('Working on setup: {}'.format(setup))
msgs.info(str(uniq_cfg[setup]))
msgs.info('=======================================================================')
# TODO: Make the snippet below, which is also in the init of
# PypeIt a method somewhere
in_cfg = ps.fitstbl['setup'] == setup
config_specific_file = None
# Grab a science/standard frame
data_files = [os.path.join(row['directory'], row['filename'])
for row in ps.fitstbl[in_cfg]]
for idx, row in enumerate(ps.fitstbl[in_cfg]):
if 'science' in row['frametype'] or 'standard' in row['frametype']:
config_specific_file = data_files[idx]
if config_specific_file is not None:
msgs.info('Setting configuration-specific parameters using {0}'.format(
os.path.split(config_specific_file)[1]))
else:
msgs.warn('No science or standard frame. Punting..')
answers['pass'][i] = False
answers['scifiles'][i] = None
continue
#
spectrograph_cfg_lines \
= ps.spectrograph.config_specific_par(config_specific_file).to_config()
# - Build the full set, merging with any user-provided
# parameters
par = PypeItPar.from_cfg_lines(cfg_lines=spectrograph_cfg_lines)
# Print science frames
if np.any(in_cfg & is_science):
msgs.info('Your science frames are: {0}'.format(
ps.fitstbl['filename'][in_cfg & is_science].tolist()))
answers['scifiles'][i] \
= ', '.join(ps.fitstbl['filename'][in_cfg & is_science].tolist())
else:
msgs.warn("This setup has no science frames!")
answers['scifiles'][i] = ''
# Check!
answers['pass'][i] = calibrations.check_for_calibs(par, ps.fitstbl,
raise_error=False, cut_cfg=in_cfg)
if not answers['pass'][i]:
msgs.warn("Setup {} did not pass the calibration check!".format(setup))
print('= RESULTS ============================================')
# Print
answers.pprint_all()
print('======================================================')
# Remove setup_files
if args.save_setups:
# TODO: This is nearly an exact copy of the code in
# `pypeit/scripts/setup.py`. Consolidate somehow?
# Output directory is hard-coded to be 'setup_files'
output_path = Path().resolve() / '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)
# 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)
# Return objects used by unit tests
return answers, ps