def from_file(par_file):
params = config.read(par_file)
# Try known first-level keys
for key in ['TELESCOPE', 'Telescope', 'telescope']:
if key in params.keys():
return Telescope(**params[key])
# Try full parameter set
try:
return Telescope(**params)
except TypeError:
raise RuntimeError(f"Could not identify parameters for initializing a Telescope instance in parameter "
f"file {par_file}")
def from_file(par_file):
params = config.read(par_file)
# Try known first-level keys
for key in ['DETECTOR', 'Detector', 'detector']:
if key in params.keys():
return Detector(**params[key])
# Try full parameter set
try:
return Detector(**params)
except TypeError:
raise RuntimeError(
f"Could not identify parameters for initializing a Detector instance in parameter "
f"file {par_file}")
def gather_header_information(path,
instrument,
par_file=None,
list_file=None,
sort_by=None):
"""Sets up the data reduction parameter file and file list.
Args:
path (str):
Path to the files.
instrument (str):
Name of the instrument that took the data. This must be covered by config/instruments.cfg.
par_file (str, optional):
Name of the output default parameter file for the reduction.
list_file (str):
Name of the output file that contains all the file names and header information.
sort_by (str, optional):
Header card that is used for the sorting of files.
"""
# Defaults
header_cards = [
'OBSTYPE', 'OBJECT', 'FILTER', 'EXPTIME', 'nFRAMES', 'DATE'
]
dtypes = [str, str, str, float, int, str]
instrument_config_file = os.path.join(os.path.dirname(__file__),
'../config/instruments.cfg')
# Read config
configs = config.read(instrument_config_file)
instrument = configs['INSTRUMENTS'][instrument]
instrument_header_cards = configs[instrument]
# Double check whether all aliases are defined
for card in header_cards:
try:
instrument_header_cards[card]
except KeyError:
logger.info(
f"Dropping header card {card} from setup identification, as there is no description in the config file."
f"\nCheck out {instrument_config_file} for details.")
header_cards.remove(card)
# Apply fall back values
if path is None:
path = '../reduction'
if list_file is None:
list_file = 'files.tab'
if par_file is None:
par_file = 'reduction.yaml'
# Find files
if '*' in path:
files = glob.glob(path)
else:
files = glob.glob(os.path.join(path, '*fits'))
if len(files):
logger.info(f"Found {len(files)} file(s)")
files.sort()
else:
logger.error(f"Found no files in {path}!")
raise RuntimeError(f"Found no files in {path}!")
# Initialize output file information table
table = Table(names=['FILE'] + header_cards, dtype=[str] + dtypes)
# Read data from files
for file in files:
logger.info(f"Retrieving header information from file {file}")
hdr = fits.getheader(file)
new_row = [os.path.basename(file)]
for card in header_cards:
try:
new_row.append(hdr[instrument_header_cards[card]])
except KeyError:
logger.info(
f"Skipping file {os.path.basename(file)} due to at least one missing header card "
f"({instrument_header_cards[card]}).")
break
if len(new_row) == len(table.columns):
table.add_row(new_row)
# Sort table entries by default properties and user request
table.sort('FILE')
table.sort('OBSTYPE')
if sort_by:
table.sort(sort_by)
# Identify instrument setups
setups = identify_instrument_setups(table)
table.add_column(setups)
# Save table
logger.info(f"Writing header information to {list_file}")
table.write(list_file, format='ascii.fixed_width', overwrite=True)
# Write dummy parameter file for the reduction
_, ext = os.path.splitext(par_file)
if 'yaml' in ext:
logger.info(
f"Creating default reduction YAML parameter file {par_file}")
par_file_content = f"PATHS:\n filePath: {path}\n fileList: {list_file}\n outDir: Science/\n tmpDir: tmp/" \
f"\n\nFLAT:\n masterFlatFile: MasterFlat.fits" \
f"\n\nSKY:\n method: scalar"
else:
logger.info(
f"Creating default reduction INI parameter file {par_file}")
par_file_content = f"[PATHS]\nfilePath = {path}\nfileList = {list_file}\noutDir = Science/\ntmpDir = tmp/" \
f"\n\n[FLAT]\nmasterFlatFile = MasterFlat.fits" \
f"\n\n[SKY]\nmethod = scalar"
with open(par_file, 'w+') as par_file:
par_file.write(par_file_content)
def main():
# Parse args
parser = GeneralArgParser()
args = parser.parse_args()
if args.debug:
logger.setLevel('DEBUG')
logger.debug(args)
if args.gui:
start()
# Execute the script of the corresponding command
if args.command is 'generate':
# Read parameters from file and generate exposures
target, telescope, detector, parameters = get_objects(args.parfile,
debug=args.debug)
generate_exposure(target=target,
telescope=telescope,
detector=detector,
debug=args.debug,
**parameters)
elif args.command is 'reduce':
# In setup mode
if args.setup:
run.setup(path=args.path,
instrument=args.instrument,
par_file=args.parfile,
list_file=args.filelist,
sort_by=args.sortby)
# Else start reduction following the parameter file
else:
params = config.read(args.parfile)
run.full_reduction(params, debug=args.debug)
elif args.command is 'ssa':
# Prepare path information and execute reconstruction
if args.tmpdir is not None and not os.path.isdir(args.tmpdir):
os.mkdir(args.tmpdir)
ssa(args.files,
mode=args.mode,
tmp_dir=args.tmpdir,
outfile=args.outfile,
box_indexes=args.box_indexes,
debug=args.debug)
elif args.command is 'holography':
# Read parameters from file and execute reconstruction
defaults_file = os.path.join(os.path.dirname(__file__),
'../config/holography.cfg')
defaults_file = os.path.abspath(defaults_file)
params = config.read(defaults_file)
params = config.update_from_file(params, args.parfile)
holography(params,
mode=params['OPTIONS']['reconstructionMode'],
debug=args.debug)
elif args.command is 'aperture':
if args.mode == 'psf1d':
logger.info("Extract 1D PSF profile")
analysis.get_psf_1d(args.file,
args.index,
args.radius,
args.out_file,
args.normalize,
debug=args.debug)
elif args.mode == 'variance':
logger.info("Extract 1D PSF variation")
analysis.get_psf_variation(args.file, args.index, args.radius,
args.out_file, args.normalize,
args.debug)
else:
logger.warning(f"Aperture mode {args.mode} not recognized!")
elif args.command is 'extract':
if args.out_file is None:
args.out_file = 'sources_' + os.path.basename(
args.file_name).replace('.fits', '.dat')
extract_sources(image=args.file_name,
noise_threshold=args.noise_threshold,
fwhm=args.fwhm,
image_var=args.var,
write_to=args.out_file)
elif args.command == 'plot':
plot = Plot.from_file(file_name=args.file,
extension=args.extension,
columns=args.columns,
format=args.format,
layout=args.layout,
debug=args.debug)
plot.apply_layout(layout=args.layout)
plot.save()
plot.show()
elif args.command is 'apodization':
get_resolution_parameters(wavelength=args.wavelength,
diameter=args.diameter,
pixel_scale=args.pixel_scale)
def test_read(self):
config = read(self.par_file)
def get_objects(parameter_file, debug=False):
"""Get objects from parameter file.
Args:
parameter_file (str):
File from which the objects are instantiated.
debug (bool, optional):
Show debugging information.
Returns:
target (Target object):
telescope (Telescope object):
detector (Detector object):
parameters (dict):
Dictionary containing the parameters parsed toward generate exposure beyond the three objects.
"""
# Set logger level
if debug:
logger.setLevel('DEBUG')
# Check whether files exist
if not os.path.isfile(parameter_file):
raise FileNotFoundError(f"Parameter file {parameter_file} not found!")
# Read parameter file
params = config.read(parameter_file)
# Create objects from the parameters
target = Target(**params['TARGET'])
logger.debug(f"Initialized Target instance:\n{target}")
telescope = Telescope(**params['TELESCOPE'])
logger.debug(f"Initialized Telescope instance:\n{telescope}")
detector = Detector(**params['DETECTOR'])
logger.debug(f"Initialized Detector instance:\n{detector}")
# Extract and interpret other kez word parameters
if 'KWARGS' in params:
parameters = params['KWARGS']
elif 'PARAMETERS' in params:
parameters = params['PARAMETERS']
else:
parameters = {}
# Interpret str-type key word arguments
for key in parameters.keys():
if isinstance(parameters[key], str):
try:
parameters[key] = eval(parameters[key])
logger.debug(
f"Kwarg {key} evaluated as {parameters[key]} ({type(parameters[key])})"
)
except SyntaxError:
parameters[key] = Quantity(parameters[key])
logger.debug(
f"Kwarg {key} evaluated as {parameters[key]} ({type(parameters[key])})"
)
except NameError:
logger.debug(
f"Kwarg {key} not evaluated {parameters[key]} ({type(parameters[key])})"
)
return target, telescope, detector, parameters
def setup(path, instrument, par_file=None, list_file=None, sort_by=None):
"""Sets up the data reduction parameter file and file list.
Args:
path (str):
Path to the files.
instrument (str):
Name of the instrument that took the data. This must be covered by config/instruments.cfg.
par_file (str, optional):
Name of the output default parameter file for the reduction.
list_file (str):
Name of the output file that contains all the file names and header information.
sort_by (str, optional):
Header card that is used for the sorting of files.
"""
# Defaults
default_cards = ['OBSTYPE', 'OBJECT', 'FILTER', 'EXPTIME', 'nFRAMES', 'DATE']
dtypes = [str, str, str, float, int, str]
instrument_config_file = os.path.join(os.path.dirname(__file__), '../config/instruments.cfg')
# Read config
configs = config.read(instrument_config_file)
instrument_cards = configs[instrument.upper()]
# Double check whether all aliases are defined
cards = []
for card in default_cards:
try:
cards.append(instrument_cards[card])
except KeyError:
logger.info(
f"Dropping header card {card} from setup identification, as there is no description in the config file."
f"\nCheck out {instrument_config_file} for details.")
cards.append(None)
for card, dtype, header_card in zip(cards, dtypes, default_cards):
if card is None:
cards.remove(card)
dtypes.remove(dtype)
default_cards.remove(header_card)
# Apply fall back values
if path is None:
path = '.'
if list_file is None:
list_file = 'files.tab'
if par_file is None:
par_file = 'reduction.yaml'
# Find files
if '*' in path:
files = glob.glob(path)
else:
files = glob.glob(os.path.join(path, '*fits'))
if len(files):
logger.info(f"Found {len(files)} file(s)")
files.sort()
else:
logger.error(f"Found no files in {path}!")
raise RuntimeError(f"Found no files in {path}!")
# Initialize a file archive
raw_files = FileArchive(files, cards=cards, dtypes=dtypes, names=default_cards, sort_by=sort_by)
raw_files.identify_setups(['FILTER', 'EXPTIME'])
raw_files.write_table(file_name=list_file)
# Write dummy parameter file for the reduction
_, ext = os.path.splitext(par_file)
if 'yaml' in ext:
logger.info(f"Creating default reduction YAML parameter file {par_file}")
par_file_content = f"PATHS:\n filePath: {path}\n fileList: {list_file}\n outDir: Science/\n tmpDir: tmp/" \
f"\n prefix: r" \
f"\n\nFLAT:\n masterFlatFile: MasterFlat.fits" \
f"\n\nSKY:\n method: scalar"
else:
logger.info(f"Creating default reduction INI parameter file {par_file}")
par_file_content = f"[PATHS]\nfilePath = {path}\nfileList = {list_file}\noutDir = Science/\ntmpDir = tmp/" \
f"\nprefix = r" \
f"\n\n[FLAT]\nmasterFlatFile = MasterFlat.fits" \
f"\n\n[SKY]\nmethod = scalar"
with open(par_file, 'w+') as par_file:
par_file.write(par_file_content)