def test_lris_blue_pypeit_overwrite():
f = os.path.join(os.environ['PYPEIT_DEV'],
'pypeit_files/keck_lris_blue_long_400_3400_d560.pypeit')
assert os.path.isfile(f), 'Could not find pypeit file.'
cfg_lines, data_files, frametype, usrdata, setups = parse_pypeit_file(
f, file_check=False)
# Change the dev path
for i in range(len(data_files)):
path_list = data_files[i].split('/')
for j, p in enumerate(path_list):
if p == 'RAW_DATA':
break
data_files[i] = os.path.join(os.environ['PYPEIT_DEV'],
'/'.join(path_list[j:]))
# Read the fits table with and without the user data
spectrograph = load_spectrograph('keck_lris_blue')
par = spectrograph.default_pypeit_par()
fitstbl = PypeItMetaData(spectrograph, par, files=data_files)
fitstbl_usr = PypeItMetaData(spectrograph,
par,
files=data_files,
usrdata=usrdata)
assert fitstbl['target'][
0] == 'unknown', 'Grating name changed in file header'
assert fitstbl_usr['target'][
0] == 'test', 'Grating name changed in pypeit file'
assert fitstbl['target'][0] != fitstbl_usr['target'][0], \
'Fits header value and input pypeit file value expected to be different.'
def test_lris_blue_pypeit_overwrite():
# JFH The RAW_DATA is at PYPEIT_DEV, but the github DEV suite where
# the pypeit files are at a different path. To fix this, I've just
# made pypeit_files directory in Cooked and copied this file over.
# KBW: I'd prefer that you put symlinks in the github dev suite:
# e.g.:
# cd $PYPEIT_DEV
# ln -s /Volumes/GoogleDrive/Team\ Drives/PHYS-GP-Hennawi/PypeIt/PypeIt-development-suite/RAW_DATA RAW_DATA
# Read the dev suite pypeit file
f = os.path.join(
os.environ['PYPEIT_DEV'],
'Cooked/pypeit_files/keck_lris_blue_long_400_3400_d560.pypeit')
if not os.path.isfile(f):
f = os.path.join(
os.environ['PYPEIT_DEV'],
'pypeit_files/keck_lris_blue_long_400_3400_d560.pypeit')
assert os.path.isfile(f), 'Could not find pypeit file.'
cfg_lines, data_files, frametype, usrdata, setups = parse_pypeit_file(
f, file_check=False)
# Change the dev path
for i in range(len(data_files)):
path_list = data_files[i].split('/')
for j, p in enumerate(path_list):
if p == 'RAW_DATA':
break
data_files[i] = os.path.join(os.environ['PYPEIT_DEV'],
'/'.join(path_list[j:]))
# Read the fits table with and without the user data
spectrograph = load_spectrograph('keck_lris_blue')
par = spectrograph.default_pypeit_par()
fitstbl = PypeItMetaData(spectrograph, par, file_list=data_files)
fitstbl_usr = PypeItMetaData(spectrograph,
par,
file_list=data_files,
usrdata=usrdata)
assert fitstbl['target'][
0] == 'unknown', 'Grating name changed in file header'
assert fitstbl_usr['target'][
0] == 'test', 'Grating name changed in pypeit file'
assert fitstbl['target'][0] != fitstbl_usr['target'][0], \
'Fits header value and input pypeit file value expected to be different.'
def build_fitstbl(self, strict=True):
"""
Construct the table with metadata for the frames to reduce.
Largely a wrapper for :func:`pypeit.core.load.create_fitstbl`.
Args:
strict (:obj:`bool`, optional):
Function will fault if :func:`fits.getheader` fails to
read the headers of any of the files in
:attr:`file_list`. Set to False to only report a
warning and continue.
Returns:
:obj:`astropy.table.Table`: Table with the metadata for each
fits file to reduce. Note this is different from
:attr:`fitstbl` which is a :obj:`PypeItMetaData` object
"""
# Build and sort the table
self.fitstbl = PypeItMetaData(self.spectrograph, par=self.par, files=self.file_list,
usrdata=self.usrdata, strict=strict)
# Sort by the time
if 'time' in self.fitstbl.keys():
self.fitstbl.sort('time')
# Add this to the completed steps
self.steps.append(inspect.stack()[0][3])
# Return the table
return self.fitstbl.table
def get_master_dirkey(self, iFile=None):
# Do some checks
if self.spectrograph is None or self.par is None:
msgs.error()
idx = self.check_index(iFile)
# Get the master dir
if self.par['calibrations']['master_dir'] == 'default':
mdir = os.path.join(self.par['rdx']['redux_path'], 'Masters')
else:
mdir = self.par['calibrations']['master_dir']
if not os.path.exists(mdir):
mdir_base = os.path.join(os.getcwd(), os.path.basename(mdir))
msgs.warn('Master file dir: {0} does not exist. Using {1}'.format(
mdir, mdir_base))
mdir = mdir_base
# Get the base name
file_base = self.get_basename(iFile=iFile)
ftdict = dict({file_base: 'science'})
fitstbl = PypeItMetaData(self.spectrograph,
self.par,
files=[self.data_files[idx]],
usrdata=Table(self.usrdata[idx]),
strict=True)
fitstbl.finalize_usr_build(ftdict, self.setups[0])
mkey = fitstbl.master_key(0, det=self.det)
# Return the result
return mdir, mkey
def read_old_fitstbl(spectrograph, f):
fitstbl = PypeItMetaData(spectrograph, data=Table.read(f))
type_bits = np.zeros(len(fitstbl), dtype=fitstbl.bitmask.minimum_dtype())
for bit in fitstbl.bitmask.keys():
type_bits[fitstbl[bit]] = fitstbl.bitmask.turn_on(
type_bits[fitstbl[bit]], flag=bit)
fitstbl.set_frame_types(type_bits)
return fitstbl
def main(args):
# Load fits file
cfg_lines, data_files, frametype, usrdata, setups = parse_pypeit_file(args.file, runtime=False)
# Get the raw fits file name
sciIdx = get_science_frame(usrdata)
fname = data_files[sciIdx]
# Load the spectrograph
cfg = ConfigObj(cfg_lines)
spectrograph_name = cfg['rdx']['spectrograph']
spectrograph = load_spectrograph(spectrograph_name, ifile=data_files[sciIdx])
msgs.info('Loaded spectrograph {0}'.format(spectrograph.spectrograph))
spectrograph_cfg_lines = spectrograph.config_specific_par(fname).to_config()
par = PypeItPar.from_cfg_lines(cfg_lines=spectrograph_cfg_lines, merge_with=cfg_lines)
# Get the master key
file_base = os.path.basename(fname)
ftdict = dict({file_base: 'science'})
fitstbl = PypeItMetaData(spectrograph, par, files=[data_files[sciIdx]], usrdata=Table(usrdata[sciIdx]), strict=True)
fitstbl.finalize_usr_build(ftdict, setups[0])
mkey = fitstbl.master_key(0, det=args.det)
# Load the frame data
rawimage, _, _, datasec, _ = spectrograph.get_rawimage(fname, args.det)
rawimage = procimg.trim_frame(rawimage, datasec < 1)
frame = spectrograph.orient_image(rawimage, args.det)
# Set paths
if par['calibrations']['caldir'] == 'default':
mdir = os.path.join(par['rdx']['redux_path'], 'Masters')
else:
mdir = par['calibrations']['caldir']
if not os.path.exists(mdir):
mdir_base = os.path.join(os.getcwd(), os.path.basename(mdir))
msgs.warn('Master file dir: {0} does not exist. Using {1}'.format(mdir, mdir_base))
mdir = mdir_base
# Load the tslits_dict
trc_file = os.path.join(mdir, MasterFrame.construct_file_name('Edges', mkey)) + '.gz'
tslits_dict = edgetrace.EdgeTraceSet.from_file(trc_file).convert_to_tslits_dict()
# Derive an appropriate output filename
prefix = os.path.splitext(file_base)
if prefix[1] == ".gz":
prefix = os.path.splitext(prefix[0])[0]
else:
prefix = prefix[0]
outname = "{0:s}_skyregions.fits".format(prefix)
# Finally, initialise the GUI
skyreg = SkySubGUI.initialize(args.det, frame, tslits_dict, outname=outname, runtime=False, printout=True)
# Get the results
skyreg.get_result()
def test_add_reduce():
"""Test adding history entries for reducing an exposure"""
# Create a PypeItMetadata object to simulate
# what would be created in PypeIt::reduce_all
# This will contain two calibration groups, one
# that combines two frames and has no calibration
# frames, and another that combines and subtracts
# frames and has calibration frames
spectrograph = load_spectrograph('keck_deimos')
spectrograph_def_par = spectrograph.default_pypeit_par()
ftype_bitmask = FrameTypeBitMask()
science_value = ftype_bitmask.turn_on(np.int_(0),'science')
standard_value = ftype_bitmask.turn_on(np.int_(0),'standard')
arc_value = ftype_bitmask.turn_on(np.int_(0),'arc')
tilt_arc_science_value = ftype_bitmask.turn_on(np.int_(0), 'tilt') | arc_value | science_value
t = Table(names=['filename', 'frametype', 'framebit', 'target', 'calib', 'comb_id', 'bkg_id'],
rows=[['file1.fits','science', science_value, 'targ1', '1', '-1', '-1'],
['file2.fits','standard', standard_value, 'targ2', '1', '-1', '-1'],
['file3.fits','tilt/arc/science',tilt_arc_science_value, 'targ3', '2', '2', '3'],
['file4.fits','tilt/arc/science',tilt_arc_science_value, 'targ4', '2', '3', '2'],
['file5.fits','tilt/arc/science',tilt_arc_science_value, 'targ3', '2', '2', '3'],
['file6.fits','tilt/arc/science',tilt_arc_science_value, 'targ4', '2', '3', '2'],
['file7.fits','arc', arc_value, 'targ5', '2', '-1', '-1']])
metadata = PypeItMetaData(spectrograph, spectrograph_def_par, data=t)
metadata.set_calibration_groups()
#Create history entries for both calibration groups
history = History()
history.add_reduce(1, metadata, [0], [])
history.add_reduce(2, metadata, [2, 4], [3, 5])
# Verify we get the expected entries
expected_history = [' PypeIt Reducing target targ1',
'Combining frames:',
'"file1.fits"',
' PypeIt Reducing target targ3',
'Combining frames:',
'"file3.fits"',
'"file5.fits"',
'Subtracted background from frames:',
'"file4.fits"',
'"file6.fits"',
'Callibration frames:',
'tilt/arc/science "file3.fits"',
'tilt/arc/science "file4.fits"',
'tilt/arc/science "file5.fits"',
'tilt/arc/science "file6.fits"',
'arc "file7.fits"']
assert verify_history(history, expected_history)
def test_setup_keck_deimos_multiconfig():
root = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA', 'keck_deimos')
files = glob.glob(os.path.join(root, '830G_L_8100', '*fits*'))
files += glob.glob(os.path.join(root, '830G_L_8400', '*fits*'))
output_path = os.path.join(os.getcwd(), 'output')
if os.path.isdir(output_path):
shutil.rmtree(output_path)
os.makedirs(output_path)
ps = pypeitsetup.PypeItSetup(files, spectrograph_name='keck_deimos')
ps.run(setup_only=True, sort_dir=output_path)
# Write the automatically generated pypeit data
pypeit_files = ps.fitstbl.write_pypeit(output_path,
cfg_lines=ps.user_cfg,
write_bkg_pairs=True)
assert len(pypeit_files) == 2, 'Should have created two pypeit files'
# Test the pypeit files for the correct configuration and
# calibration group results
for f, s, c in zip(pypeit_files, ['A', 'B'], ['0', '1']):
# TODO: All of this front-end stuff, pulled from pypeit.py, should
# be put into a function.
# Read the pypeit file
cfg_lines, data_files, frametype, usrdata, setups = parse_pypeit_file(
f, runtime=True)
# Spectrograph
cfg = ConfigObj(cfg_lines)
spectrograph = load_spectrograph(cfg['rdx']['spectrograph'])
# Configuration-specific parameters
for idx, row in enumerate(usrdata):
if 'science' in row['frametype'] or 'standard' in row['frametype']:
break
spectrograph_cfg_lines = spectrograph.config_specific_par(
data_files[idx]).to_config()
# PypeIt parameters
par = PypeItPar.from_cfg_lines(cfg_lines=spectrograph_cfg_lines,
merge_with=cfg_lines)
# Metadata
fitstbl = PypeItMetaData(spectrograph,
par,
files=data_files,
usrdata=usrdata,
strict=True)
fitstbl.finalize_usr_build(frametype, setups[0])
assert np.all(fitstbl['setup'] == s), 'Setup is wrong'
assert np.all(fitstbl['calib'] == c), 'Calibration group is wrong'
# Clean-up
shutil.rmtree(output_path)
def load_metadata(self, fits_file):
"""
Load the fitstbl from disk (a binary FITS table)
Args:
fits_file (str): Name of PypeItMetaData file
Returns:
obj:`PypeItMetaData`: The so-called fitstbl
"""
self.fitstbl = PypeItMetaData(self.spectrograph, self.par, data=Table.read(fits_file))
msgs.info("Loaded fitstbl from {:s}".format(fits_file))
return self.fitstbl.table
def test_read_combid():
# ------------------------------------------------------------------
# In case of failed tests
setup_dir = data_path('setup_files')
if os.path.isdir(setup_dir):
shutil.rmtree(setup_dir)
config_dir = data_path('shane_kast_blue_A')
if os.path.isdir(config_dir):
shutil.rmtree(config_dir)
# ------------------------------------------------------------------
# Generate the pypeit file with the comb_id
droot = data_path('b')
pargs = Setup.parse_args([
'-r', droot, '-s', 'shane_kast_blue', '-c=all', '-b',
'--extension=fits.gz', '--output_path={:s}'.format(data_path(''))
])
Setup.main(pargs)
shutil.rmtree(setup_dir)
pypeit_file = os.path.join(config_dir, 'shane_kast_blue_A.pypeit')
cfg_lines, data_files, frametype, usrdata, setups, _ = parse_pypeit_file(
pypeit_file)
# Get the spectrograph
spectrograph = None
for l in cfg_lines:
if 'spectrograph' in l:
spectrograph = load_spectrograph(l.split(' ')[-1])
break
assert spectrograph is not None, 'Did not appropriately read spectrograph'
# Set the metadata
pmd = PypeItMetaData(spectrograph,
spectrograph.default_pypeit_par(),
files=data_files,
usrdata=usrdata,
strict=False)
indx = pmd['filename'] == 'b27.fits.gz'
assert pmd['comb_id'][indx] == [1], 'Incorrect combination group ID'
assert pmd['comb_id'][np.where(~indx)
[0]][0] == -1, 'Incorrect combination group ID'
shutil.rmtree(config_dir)
def dummy_fitstbl(nfile=10,
spectro_name='shane_kast_blue',
directory='',
notype=False):
"""
Generate a dummy fitstbl for testing
Parameters
----------
nfile : int, optional
Number of files to mimic
spectro_name : str, optional
Name of spectrograph to mimic
notype : bool (optional)
If True, do not add image type info to the fitstbl
Returns
-------
fitstbl : PypeItMetaData
"""
fitsdict = {}
fitsdict['index'] = np.arange(nfile)
fitsdict['directory'] = [directory] * nfile
fitsdict['filename'] = ['b{:03d}.fits.gz'.format(i) for i in range(nfile)]
# TODO: The below will fail at 60
dates = ['2015-01-23T00:{:02d}:11.04'.format(i) for i in range(nfile)]
ttime = time.Time(dates, format='isot')
fitsdict['mjd'] = ttime.mjd
fitsdict['target'] = ['Dummy'] * nfile
fitsdict['ra'] = ['00:00:00'] * nfile
fitsdict['dec'] = ['+00:00:00'] * nfile
fitsdict['exptime'] = [300.] * nfile
fitsdict['dispname'] = ['600/4310'] * nfile
fitsdict['dichroic'] = ['560'] * nfile
fitsdict["binning"] = ['1,1'] * nfile
fitsdict["airmass"] = [1.0] * nfile
if spectro_name == 'shane_kast_blue':
fitsdict['numamplifiers'] = [1] * nfile
# Lamps
for i in range(1, 17):
fitsdict['lampstat{:02d}'.format(i)] = ['off'] * nfile
fitsdict['exptime'][0] = 0 # Bias
fitsdict['lampstat06'][1] = 'on' # Arc
fitsdict['exptime'][1] = 30 # Arc
fitsdict['lampstat01'][2] = 'on' # Trace, pixel, slit flat
fitsdict['lampstat01'][3] = 'on' # Trace, pixel, slit flat
fitsdict['exptime'][2] = 30 # flat
fitsdict['exptime'][3] = 30 # flat
fitsdict['ra'][4] = '05:06:36.6' # Standard
fitsdict['dec'][4] = '52:52:01.0'
fitsdict['airmass'][4] = 1.2
fitsdict['ra'][5] = '07:06:23.45' # Random object
fitsdict['dec'][5] = '+30:20:50.5'
fitsdict['decker'] = ['0.5 arcsec'] * nfile
# arrays
for k in fitsdict.keys():
fitsdict[k] = np.array(fitsdict[k])
spectrograph = load_spectrograph(spectro_name)
fitstbl = PypeItMetaData(spectrograph,
spectrograph.default_pypeit_par(),
data=fitsdict)
fitstbl['instrume'] = spectro_name
type_bits = np.zeros(len(fitstbl),
dtype=fitstbl.type_bitmask.minimum_dtype())
# Image typing
if not notype:
if spectro_name == 'shane_kast_blue':
#fitstbl['sci_ID'] = 1 # This links all the files to the science object
type_bits[0] = fitstbl.type_bitmask.turn_on(type_bits[0],
flag='bias')
type_bits[1] = fitstbl.type_bitmask.turn_on(type_bits[1],
flag='arc')
type_bits[1] = fitstbl.type_bitmask.turn_on(type_bits[1],
flag='tilt')
type_bits[2:4] = fitstbl.type_bitmask.turn_on(
type_bits[2:4], flag=['pixelflat', 'trace', 'illumflat'])
type_bits[4] = fitstbl.type_bitmask.turn_on(type_bits[4],
flag='standard')
type_bits[5:] = fitstbl.type_bitmask.turn_on(type_bits[5:],
flag='science')
fitstbl.set_frame_types(type_bits)
# Calibration groups
cfgs = fitstbl.unique_configurations(
ignore_frames=['bias', 'dark'])
fitstbl.set_configurations(cfgs)
fitstbl.set_calibration_groups(global_frames=['bias', 'dark'])
return fitstbl
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 __init__(self,
pypeit_file,
verbosity=2,
overwrite=True,
reuse_masters=False,
logname=None,
show=False,
redux_path=None,
calib_only=False):
# Load
cfg_lines, data_files, frametype, usrdata, setups \
= parse_pypeit_file(pypeit_file, runtime=True)
self.pypeit_file = pypeit_file
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.spectrograph))
# --------------------------------------------------------------
# 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.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
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
# # Instantiate Calibrations class
# if self.spectrograph.pypeline in ['MultiSlit', 'Echelle']:
# self.caliBrate \
# = calibrations.MultiSlitCalibrations(self.fitstbl, self.par['calibrations'],
# self.spectrograph, self.calibrations_path,
# qadir=self.qa_path,
# reuse_masters=self.reuse_masters,
# show=self.show,
# slitspat_num=self.par['rdx']['slitspatnum'])
# elif self.spectrograph.pypeline in ['IFU']:
# self.caliBrate \
# = calibrations.IFUCalibrations(self.fitstbl, self.par['calibrations'],
# self.spectrograph,
# self.calibrations_path,
# qadir=self.qa_path,
# reuse_masters=self.reuse_masters,
# show=self.show)
# else:
# msgs.error("No calibration available to support pypeline: {0:s}".format(self.spectrograph.pypeline))
# Init
self.verbosity = verbosity
# TODO: I don't think this ever used
self.det = None
self.tstart = None
self.basename = None
self.sciI = None
self.obstime = None