def main(args):
"""
Args:
args:
Returns:
astropy.table.Table:
"""
import os
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
# 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
instruments_served = defs.pypeit_spectrographs
if args.spectrograph not in instruments_served:
raise ValueError(
'Instrument \'{0}\' unknown to PypeIt.\n'.format(
args.spectrograph) +
'\tOptions are: {0}\n'.format(', '.join(instruments_served)) +
'\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) #, write_bkg_pairs=args.background)
is_science = ps.fitstbl.find_frames('science')
msgs.info('Loaded spectrograph {0}'.format(ps.spectrograph.spectrograph))
# Unique configurations
setups, indx = ps.fitstbl.get_configuration_names(return_index=True)
answers = table.Table()
answers['setups'] = setups
passes, scifiles, cfgs = [], [], []
for setup, i in zip(setups, indx):
# Get the setup lines
cfg = ps.fitstbl.get_setup(i, config_only=False)
cfgs.append(cfg)
if setup == 'None':
print("There is a setup without science frames. Skipping...")
passes.append(False)
scifiles.append(None)
continue
in_cfg = ps.fitstbl['setup'] == setup
# TODO -- Make the snippet below, which is also in the init of PypeIt a method somewhere
config_specific_file = None
msgs.info(
'======================================================================='
)
msgs.info('Working on setup: {}'.format(setup))
msgs.info(str(cfg))
msgs.info(
'======================================================================='
)
# 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..')
passes.append(False)
scifiles.append(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: {}".format(
ps.fitstbl['filename'][in_cfg & is_science]))
scifiles.append(','.join(ps.fitstbl['filename'][in_cfg
& is_science]))
else:
msgs.warn("This setup has no science frames!")
scifiles.append('')
# Check!
passed = calibrations.check_for_calibs(par,
ps.fitstbl,
raise_error=False,
cut_cfg=in_cfg)
if not passed:
msgs.warn(
"Setup {} did not pass the calibration check!".format(setup))
#
passes.append(passed)
print('= RESULTS ============================================')
# Pass/fail
answers['pass'] = passes
# Parse the configs
pcfg = dict(disperser=[],
angle=[],
dichroic=[],
decker=[],
slitwid=[],
binning=[])
for cfg in cfgs:
# None?
if len(cfg) == 0:
for key in pcfg.keys():
pcfg[key].append(None)
continue
# Load it up
key0 = list(cfg.keys())[0]
subd = cfg[key0]['--'] # for convenience
pcfg['disperser'].append(subd['disperser']['name'])
pcfg['angle'].append(subd['disperser']['angle'])
pcfg['dichroic'].append(subd['dichroic'])
pcfg['decker'].append(subd['slit']['decker'])
pcfg['slitwid'].append(subd['slit']['slitwid'])
pcfg['binning'].append(subd['binning'])
# Add
for key in pcfg.keys():
answers[key] = pcfg[key]
# Sci files [put this last as it can get large]
answers['scifiles'] = scifiles
# Print
answers.pprint_all()
print(
'= ==================================================================================='
)
# Return
return answers, ps
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) #, write_bkg_pairs=args.background)
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 not args.save_setups:
shutil.rmtree('setup_files')
# Return objects used by unit tests
return answers, ps
def __init__(self,
pypeit_file,
verbosity=2,
overwrite=True,
reuse_masters=False,
logname=None,
show=False,
redux_path=None,
calib_only=False):
# Set up logging
self.logname = logname
self.verbosity = verbosity
self.pypeit_file = pypeit_file
self.msgs_reset()
# Load
cfg_lines, data_files, frametype, usrdata, setups, _ \
= parse_pypeit_file(pypeit_file, runtime=True)
self.calib_only = calib_only
# Spectrograph
cfg = ConfigObj(cfg_lines)
spectrograph_name = cfg['rdx']['spectrograph']
self.spectrograph = load_spectrograph(spectrograph_name)
msgs.info('Loaded spectrograph {0}'.format(self.spectrograph.name))
# --------------------------------------------------------------
# Get the full set of PypeIt parameters
# - Grab a science or standard file for configuration specific parameters
config_specific_file = None
for idx, row in enumerate(usrdata):
if ('science' in row['frametype']) or ('standard'
in row['frametype']):
config_specific_file = data_files[idx]
# search for arcs, trace if no scistd was there
if config_specific_file is None:
for idx, row in enumerate(usrdata):
if ('arc' in row['frametype']) or ('trace'
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]))
spectrograph_cfg_lines = self.spectrograph.config_specific_par(
config_specific_file).to_config()
# - Build the full set, merging with any user-provided
# parameters
self.par = PypeItPar.from_cfg_lines(cfg_lines=spectrograph_cfg_lines,
merge_with=cfg_lines)
msgs.info('Built full PypeIt parameter set.')
# Check the output paths are ready
if redux_path is not None:
self.par['rdx']['redux_path'] = redux_path
# TODO: Write the full parameter set here?
# --------------------------------------------------------------
# --------------------------------------------------------------
# Build the meta data
# - Re-initilize based on the file data
msgs.info('Compiling metadata')
self.fitstbl = PypeItMetaData(self.spectrograph,
self.par,
files=data_files,
usrdata=usrdata,
strict=True)
# - Interpret automated or user-provided data from the PypeIt
# file
self.fitstbl.finalize_usr_build(frametype, setups[0])
# --------------------------------------------------------------
# - Write .calib file (For QA naming amongst other things)
calib_file = pypeit_file.replace('.pypeit', '.calib')
self.fitstbl.write_calib(calib_file)
# Other Internals
self.overwrite = overwrite
# Currently the runtime argument determines the behavior for
# reuse_masters.
self.reuse_masters = reuse_masters
self.show = show
# Set paths
self.calibrations_path = os.path.join(
self.par['rdx']['redux_path'],
self.par['calibrations']['master_dir'])
# Check for calibrations
if not self.calib_only:
calibrations.check_for_calibs(
self.par,
self.fitstbl,
raise_error=self.par['calibrations']['raise_chk_error'])
# Report paths
msgs.info('Setting reduction path to {0}'.format(
self.par['rdx']['redux_path']))
msgs.info('Master calibration data output to: {0}'.format(
self.calibrations_path))
msgs.info('Science data output to: {0}'.format(self.science_path))
msgs.info('Quality assessment plots output to: {0}'.format(
self.qa_path))
# TODO: Is anything written to the qa dir or only to qa/PNGs?
# Should we have separate calibration and science QA
# directories?
# An html file wrapping them all too
# Init
# TODO: I don't think this ever used
self.det = None
self.tstart = None
self.basename = None
self.sciI = None
self.obstime = None