def test_instantiate(fitstbl):
par = pypeitpar.PypeItPar()
spectrograph = load_kast_blue_masters(get_spectrograph=True)[0]
caliBrate = calibrations.MultiSlitCalibrations(fitstbl,
par['calibrations'],
spectrograph)
print(caliBrate)
def test_instantiate(fitstbl):
par = pypeitpar.PypeItPar()
spectrograph = load_spectrograph('shane_kast_blue')
caliBrate = calibrations.MultiSlitCalibrations(fitstbl,
par['calibrations'],
spectrograph,
data_path('Masters'))
def multi_caliBrate(fitstbl):
det = 1
spectrograph = load_kast_blue_masters(get_spectrograph=True)[0]
# Par
def_par = spectrograph.default_pypeit_par()
# Grab a science file for configuration specific parameters
for idx, row in enumerate(fitstbl):
if 'science' in row['frametype']:
sci_file = os.path.join(row['directory'], row['filename'])
break
par = spectrograph.config_specific_par(def_par, sci_file)
#
calib_par = par['calibrations']
calib_par['badpix'] = False
calib_par['biasframe']['useframe'] = 'overscan'
redux_path = data_path('') if os.getenv('PYPEIT_DEV') is None \
else os.path.join(os.getenv('PYPEIT_DEV'), 'Cooked')
multi_caliBrate = calibrations.MultiSlitCalibrations(fitstbl,
calib_par,
spectrograph,
redux_path=redux_path,
save_masters=False,
write_qa=False)
# Find the first science row
frame = fitstbl.find_frames('science', index=True)[0]
# Set
multi_caliBrate.set_config(frame, det, par=calib_par)
return multi_caliBrate
def multi_caliBrate(fitstbl):
spectrograph = load_spectrograph('shane_kast_blue')
# Grab a science file for configuration specific parameters
for idx, row in enumerate(fitstbl):
if 'science' in row['frametype']:
sci_file = os.path.join(row['directory'], row['filename'])
break
# Par
par = spectrograph.config_specific_par(sci_file)
#
calib_par = par['calibrations']
calib_par['badpix'] = False
calib_par['biasframe']['useframe'] = 'none' # Only use overscan
multi_caliBrate = calibrations.MultiSlitCalibrations(
fitstbl, calib_par, spectrograph)
return reset_calib(multi_caliBrate)
def multi_caliBrate(fitstbl):
# Grab a science file for configuration specific parameters
for idx, row in enumerate(fitstbl):
if 'science' in row['frametype']:
sci_file = os.path.join(row['directory'], row['filename'])
break
# Par
spectrograph = load_spectrograph('shane_kast_blue')
par = spectrograph.config_specific_par(sci_file)
turn_off = dict(use_biasimage=False)
par.reset_all_processimages_par(**turn_off)
#
calib_par = par['calibrations']
calib_par['bpm_usebias'] = False
#calib_par['biasframe']['useframe'] = 'none' # Only use overscan
calib_par['slitedges']['sync_predict'] = 'nearest'
multi_caliBrate = calibrations.MultiSlitCalibrations(
fitstbl, calib_par, spectrograph, data_path('Masters'))
return reset_calib(multi_caliBrate)
def __init__(self, pypeit_file, verbosity=2, overwrite=True, reuse_masters=False, logname=None,
show=False, redux_path=None):
# Load
cfg_lines, data_files, frametype, usrdata, setups = parse_pypeit_file(pypeit_file, runtime=True)
self.pypeit_file = pypeit_file
# Spectrograph
cfg = ConfigObj(cfg_lines)
spectrograph_name = cfg['rdx']['spectrograph']
self.spectrograph = load_spectrograph(spectrograph_name)
# Par
# Defaults
spectrograph_def_par = self.spectrograph.default_pypeit_par()
# Grab a science file for configuration specific parameters
sci_file = None
for idx, row in enumerate(usrdata):
if 'science' in row['frametype']:
sci_file = data_files[idx]
break
# Set
spectrograph_cfg_lines = self.spectrograph.config_specific_par(spectrograph_def_par, sci_file).to_config()
self.par = PypeItPar.from_cfg_lines(cfg_lines=spectrograph_cfg_lines, merge_with=cfg_lines)
# Fitstbl
self.fitstbl = PypeItMetaData(self.spectrograph, self.par, file_list=data_files,
usrdata=usrdata, strict=True)
# The following could be put in a prepare_to_run() method in PypeItMetaData
if 'setup' not in self.fitstbl.keys():
self.fitstbl['setup'] = setups[0]
self.fitstbl.get_frame_types(user=frametype) # This sets them using the user inputs
self.fitstbl.set_defaults() # Only does something if values not set in PypeIt file
self.fitstbl._set_calib_group_bits()
self.fitstbl._check_calib_groups()
# 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.logname = logname
self.overwrite = overwrite
# Currently the runtime argument determines the behavior for reuse_masters. There is also a reuse_masters
# parameter in the parset but it is currently ignored.
self.reuse_masters=reuse_masters
self.show = show
# Make the output directories
self.par['rdx']['redux_path'] = os.getcwd() if redux_path is None else redux_path
msgs.info("Setting reduction path to {:s}".format(self.par['rdx']['redux_path']))
paths.make_dirs(self.spectrograph.spectrograph, self.par['calibrations']['caldir'],
self.par['rdx']['scidir'], self.par['rdx']['qadir'],
overwrite=self.overwrite, redux_path=self.par['rdx']['redux_path'])
# Instantiate Calibrations class
self.caliBrate \
= calibrations.MultiSlitCalibrations(self.fitstbl, self.par['calibrations'], self.spectrograph,
redux_path=self.par['rdx']['redux_path'],
reuse_masters=self.reuse_masters,
save_masters=True, write_qa=True,
show=self.show)
# Init
self.verbosity = verbosity
# TODO: I don't think this ever used
self.frame = None
self.det = None
self.tstart = None
self.basename = None
self.sciI = None
self.obstime = None
def __init__(self,
pypeit_file,
verbosity=2,
overwrite=True,
reuse_masters=False,
logname=None,
show=False,
redux_path=None):
# Load
cfg_lines, data_files, frametype, usrdata, setups \
= parse_pypeit_file(pypeit_file, runtime=True)
self.pypeit_file = pypeit_file
# Spectrograph
cfg = ConfigObj(cfg_lines)
spectrograph_name = cfg['rdx']['spectrograph']
self.spectrograph = load_spectrograph(spectrograph_name,
ifile=data_files[0])
msgs.info('Loaded spectrograph {0}'.format(
self.spectrograph.spectrograph))
# --------------------------------------------------------------
# Get the full set of PypeIt parameters
# - Grab a science or standard file for configuration specific parameters
scistd_file = None
for idx, row in enumerate(usrdata):
if ('science' in row['frametype']) or ('standard'
in row['frametype']):
scistd_file = data_files[idx]
break
# - Configuration specific parameters for the spectrograph
if scistd_file is not None:
msgs.info(
'Setting configuration-specific parameters using {0}'.format(
os.path.split(scistd_file)[1]))
spectrograph_cfg_lines = self.spectrograph.config_specific_par(
scistd_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.logname = logname
self.overwrite = overwrite
# Currently the runtime argument determines the behavior for
# reuse_masters.
self.reuse_masters = reuse_masters
self.show = show
# Set paths
if self.par['calibrations']['caldir'] == 'default':
self.calibrations_path = os.path.join(
self.par['rdx']['redux_path'], 'Masters')
else:
self.calibrations_path = self.par['calibrations']['caldir']
# 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?
# Instantiate Calibrations class
self.caliBrate \
= calibrations.MultiSlitCalibrations(self.fitstbl, self.par['calibrations'],
self.spectrograph,
caldir=self.calibrations_path,
qadir=self.qa_path,
reuse_masters=self.reuse_masters,
show=self.show)
# Init
self.verbosity = verbosity
# TODO: I don't think this ever used
self.frame = None
self.det = None
self.tstart = None
self.basename = None
self.sciI = None
self.obstime = None
def test_reuse(multi_caliBrate, fitstbl):
"""
Test that Calibrations appropriately reuses existing calibrations frames.
"""
# In case of previous data or failures
if os.path.isdir(multi_caliBrate.master_dir):
shutil.rmtree(multi_caliBrate.master_dir)
os.makedirs(multi_caliBrate.master_dir)
# Perform the calibrations and check that the data are correctly
# stored in memory
multi_caliBrate.shape = (2048, 350)
multi_caliBrate.get_bpm()
# Make them all
# assert list(multi_caliBrate_reuse.calib_dict.keys()) == ['A_1_01'], 'Incorrect master key'
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) == ['bpm'], \
# 'Incorrect list of master types in memory'
msarc = multi_caliBrate.get_arc()
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) == ['bpm', 'arc'], \
# 'Incorrect list of master types in memory'
msarc = multi_caliBrate.get_tiltimg()
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) == ['bpm', 'arc', 'tiltimg'], \
# 'Incorrect list of master types in memory'
multi_caliBrate.get_slits()
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) == ['bpm', 'arc', 'tiltimg', 'trace'], \
# 'Incorrect list of master types in memory'
multi_caliBrate.get_wv_calib()
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) \
# == ['bpm', 'arc', 'tiltimg','trace', 'wavecalib'], \
# 'Incorrect list of master types in memory'
multi_caliBrate.get_tilts()
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) \
# == ['bpm', 'arc', 'tiltimg', 'trace', 'wavecalib', 'wavetilts'], \
# 'Incorrect list of master types in memory'
multi_caliBrate.get_flats()
# assert list(multi_caliBrate_reuse.calib_dict['A_1_01'].keys()) \
# == ['bpm', 'arc', 'tiltimg', 'trace', 'wavecalib', 'wavetilts',
# 'flatimages'], \
# 'Incorrect list of master types in memory'
# Reset
#reset_calib(multi_caliBrate_reuse)
spectrograph = load_spectrograph('shane_kast_blue')
par = spectrograph.default_pypeit_par()
multi_caliBrate_reuse = calibrations.MultiSlitCalibrations(
fitstbl, par['calibrations'], spectrograph, data_path('Masters'))
multi_caliBrate_reuse.reuse_masters = True
reset_calib(multi_caliBrate_reuse)
# Read the calibrations
# - These don't source a master file
multi_caliBrate_reuse.shape = (2048, 350)
multi_caliBrate_reuse.get_bpm()
# - The arc is the first sourced master
assert 'arc' not in multi_caliBrate_reuse.master_key_dict.keys(), \
'arc master key should not be defined yet'
_msarc = multi_caliBrate_reuse.get_arc()
assert multi_caliBrate_reuse.msarc is not None, 'Should find cached data.'
_msarc = multi_caliBrate_reuse.get_tiltimg()
assert multi_caliBrate_reuse.mstilt is not None, 'Should find cached data.'
# JXP took these out of the class
#assert os.path.isfile(multi_caliBrate_reuse.arcImage.master_file_path), \
# 'Should find master file.'
#assert multi_caliBrate_reuse.arcImage.load() is not None, \
# 'Load should not return None'
# - Make sure the rest of the steps complete
multi_caliBrate_reuse.get_slits()
multi_caliBrate_reuse.get_wv_calib()
multi_caliBrate_reuse.get_tilts()
multi_caliBrate_reuse.get_flats()
# Clean-up
shutil.rmtree(multi_caliBrate_reuse.master_dir)
