"""
Trace slit edges for a set of images.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
from pypeit.scripts import scriptbase
[docs]
class TraceEdges(scriptbase.ScriptBase):
[docs]
@classmethod
def get_parser(cls, width=None):
from pypeit.spectrographs import available_spectrographs
parser = super().get_parser(description='Trace slit edges', width=width)
# Require either a pypeit file or a fits file
inp = parser.add_mutually_exclusive_group(required=True)
inp.add_argument('-f', '--pypeit_file', default=None, type=str,
help='PypeIt reduction file')
inp.add_argument('-t', '--trace_file', default=None, type=str, help='Image to trace')
parser.add_argument('-g', '--group', default=None,
help='If providing a pypeit file, use the trace images for this '
'calibration group. If None, use the first calibration group.')
parser.add_argument('-d', '--detector', type=str, default=None, nargs='*',
help='Detector(s) to process. If more than one, the list of detectors '
'must be one of the allowed mosaics hard-coded for the selected '
'spectrograph. Using "mosaic" for gemini_gmos, keck_deimos, or '
'keck_lris will use the default mosaic.')
parser.add_argument('-s', '--spectrograph', default=None, type=str,
help='A valid spectrograph identifier, which is only used if providing'
' files directly: {0}'.format(', '.join(available_spectrographs)))
parser.add_argument('-b', '--binning', default=None, type=str,
help='Image binning in spectral and spatial directions. Only used if '
'providing files directly; default is 1,1.')
parser.add_argument('-p', '--redux_path', type=str, default='current working directory',
help='Path to top-level output directory.')
parser.add_argument('-c', '--calib_dir', default='Calibrations',
help='Name for directory in output path for calibration file(s) '
'relative to the top-level directory.')
parser.add_argument('-o', '--overwrite', default=False, action='store_true',
help='Overwrite any existing files/directories')
parser.add_argument('--debug', type=int, default=0,
help='Debug level. (1) Show the result of each stage of the tracing '
'algorithm (previously the --show option). (2) Also show summary '
'plots related to the PCA decomposition and the slit and order '
'matching. (3) Also show the individual polynomial fits to the '
'detected edges.')
parser.add_argument('--show', default=False, action='store_true',
help='DEPRECATED! If set, the code will assume you mean to set '
'--debug 1.')
parser.add_argument('-v', '--verbosity', type=int, default=1,
help='Verbosity level between 0 [none] and 2 [all]. Default: 1. '
'Level 2 writes a log with filename trace_edges_YYYYMMDD-HHMM.log')
return parser
[docs]
@staticmethod
def main(args):
import time
from pathlib import Path
import numpy as np
from pypeit import msgs
from pypeit.spectrographs.util import load_spectrograph
from pypeit import edgetrace
from pypeit.pypeit import PypeIt
from pypeit.images import buildimage
from IPython import embed
# Set the verbosity, and create a logfile if verbosity == 2
msgs.set_logfile_and_verbosity('trace_edges', args.verbosity)
if args.show:
msgs.warn('"show" option is deprecated. Setting debug = 1.')
args.debug = 1
if args.pypeit_file is not None:
pypeit_file = Path(args.pypeit_file).absolute()
if not pypeit_file.exists():
msgs.error(f'File does not exist: {pypeit_file}')
redux_path = pypeit_file.parent if args.redux_path is None \
else Path(args.redux_path).absolute()
rdx = PypeIt(str(pypeit_file), redux_path=str(redux_path))
detectors = rdx.par['rdx']['detnum'] if args.detector is None else args.detector
# Save the spectrograph
spec = rdx.spectrograph
# Get the calibration group to use
group = np.unique(rdx.fitstbl['calib'])[0] if args.group is None else args.group
if group not in np.unique(rdx.fitstbl['calib']):
msgs.error(f'Invalid calibration group: {group}')
# Find the rows in the metadata table with trace frames in the
# specified calibration group
tbl_rows = rdx.fitstbl.find_frames('trace', calib_ID=int(group), index=True)
setup = rdx.fitstbl['setup'][tbl_rows[0]]
calib_id = rdx.fitstbl['calib'][tbl_rows[0]]
# Save the binning
binning = rdx.fitstbl['binning'][tbl_rows[0]]
# Save the full file paths
files = rdx.fitstbl.frame_paths(tbl_rows)
# Trace image processing parameters
proc_par = rdx.par['calibrations']['traceframe']
# Slit tracing parameters
trace_par = rdx.par['calibrations']['slitedges']
# Use the bias frames to set the BPM
bpm_usebias = rdx.par['calibrations']['bpm_usebias']
# Get the bias files, if requested
bias_files = rdx.fitstbl.find_frame_files('bias', calib_ID=int(group))
bias_par = rdx.par['calibrations']['biasframe']
if len(bias_files) == 0:
bias_files = None
# Get the dark files, if requested
dark_files = rdx.fitstbl.find_frame_files('dark', calib_ID=int(group))
dark_par = rdx.par['calibrations']['darkframe']
if len(dark_files) == 0:
dark_files = None
# Lamp-off files
lampoff_files = rdx.fitstbl.find_frame_files('lampoffflats', calib_ID=int(group))
lampoff_par = rdx.par['calibrations']['lampoffflatsframe']
if len(lampoff_files) == 0:
lampoff_files = None
# Set the QA path
qa_path = rdx.qa_path
else:
detectors = args.detector
spec = load_spectrograph(args.spectrograph)
setup = 'A' # Dummy value
calib_id = '1' # Dummy value
binning = '1,1' if args.binning is None else args.binning
trace_file = Path(args.trace_file).absolute()
if not trace_file.exists():
msgs.error(f'File does not exist: {trace_file}')
files = [str(trace_file)]
redux_path = trace_file.parent if args.redux_path is None \
else Path(args.redux_path).absolute()
par = spec.default_pypeit_par()
proc_par = par['calibrations']['traceframe']
trace_par = par['calibrations']['slitedges']
bpm_usebias = par['calibrations']['bpm_usebias']
bias_files = None
bias_par = None
dark_files = None
dark_par = None
lampoff_files = None
lampoff_par = None
# Set the QA path
qa_path = redux_path / 'QA'
if detectors is None:
detectors = np.arange(spec.ndet)+1
elif isinstance(detectors, (int, tuple)):
detectors = [detectors]
elif any([isinstance(d,str) for d in detectors]):
detectors = [eval(d) for d in detectors]
calib_dir = redux_path / args.calib_dir
for det in detectors:
# Get the bias frame
if bias_files is None:
proc_par['process']['use_biasimage'] = False
msbias = None
else:
msbias = buildimage.buildimage_fromlist(spec, det, bias_par, bias_files)
# Get the bad-pixel mask
msbpm = spec.bpm(files[0], det, msbias=msbias if bpm_usebias else None)
# Save a copy
original_bpm = msbpm.copy()
# Get the dark frame
if dark_files is None:
proc_par['process']['use_darkimage'] = False
msdark = None
else:
msdark = buildimage.buildimage_fromlist(spec, det, dark_par, dark_files,
bias=msbias)
# Build the trace image
msbpm = original_bpm.copy() # Reset bpm
traceImage = buildimage.buildimage_fromlist(spec, det, proc_par, files, bias=msbias,
bpm=msbpm, dark=msdark, setup=setup,
calib_id=calib_id, calib_dir=calib_dir)
# Subtract the lamp-off flats, if they exist
if lampoff_files is not None:
msbpm = original_bpm.copy() # Reset bpm
lampoff_flat = buildimage.buildimage_fromlist(spec, det, lampoff_par,
lampoff_files, dark=msdark,
bias=msbias, bpm=msbpm)
traceImage = traceImage.sub(lampoff_flat)
# Trace the slit edges
t = time.perf_counter()
edges = edgetrace.EdgeTraceSet(traceImage, spec, trace_par, auto=True,
debug=args.debug, qa_path=qa_path)
if not edges.success:
msgs.warn(f'Edge tracing for detector {det} failed. Continuing...')
continue
msgs.info(f'Tracing for detector {det} finished in { time.perf_counter()-t:.1f} s.')
# Write the two calibration frames
edges.to_file()
edges.get_slits().to_file()
return 0