def parser(options=None):
# TODO: Add argument that specifies the log file
parser = argparse.ArgumentParser(
description="Script to setup a PypeIt run [v3]")
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('-r',
'--root',
type=str,
default=None,
help='File path+root, e.g. /data/Kast/b ')
#group.add_argument('-p', '--pypeit_file', type=str, default=None,
# help='PypeIt file to use')
parser.add_argument('-s',
'--spectrograph',
default=None,
type=str,
help='A valid spectrograph identifier: {0}'.format(
', '.join(valid_spectrographs())))
parser.add_argument(
'-e',
'--extension',
default='.fits',
help='File extension; compression indicators (e.g. .gz) not required.')
parser.add_argument('-d',
'--output_path',
default=None,
help='Path to top-level output directory. '
'Default is the current working directory.')
parser.add_argument('-o',
'--overwrite',
default=False,
action='store_true',
help='Overwrite any existing files/directories')
parser.add_argument(
'-c',
'--cfg_split',
default=None,
type=str,
help=
'Generate the PypeIt files and folders by input configuration. [all or A,B or B,D,E or E]'
)
parser.add_argument(
'-b',
'--background',
default=False,
action='store_true',
help='Include the background-pair columns for the user to edit')
parser.add_argument('-v',
'--verbosity',
type=int,
default=2,
help='Level of verbosity from 0 to 2; default is 2.')
# parser.add_argument('-q', '--quick', default=False, help='Quick reduction',
# action='store_true')
# parser.add_argument('-c', '--cpus', default=False,
# help='Number of CPUs for parallel processing', action='store_true')
# parser.print_help()
return parser.parse_args() if options is None else parser.parse_args(
options)
def main(args):
import os
import pdb as debugger
from pypeit import msgs
from pypeit.pypeitsetup import PypeItSetup
# 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 = valid_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.')
# Get the output directory
output_path = os.getcwd() if args.output_path is None else args.output_path
sort_dir = os.path.join(output_path, 'setup_files')
# Initialize PypeItSetup based on the arguments
if args.root is not None:
ps = PypeItSetup.from_file_root(args.root,
args.spectrograph,
extension=args.extension,
output_path=sort_dir)
else:
# Should never reach here
raise IOError('Need to set -r !!')
# Run the setup
ps.run(setup_only=True, sort_dir=sort_dir, write_bkg_pairs=args.background)
# Use PypeItMetaData to write the complete PypeIt file
if args.cfg_split is not None:
pypeit_file = os.path.join(output_path,
'{0}.pypeit'.format(args.spectrograph))
config_list = [item.strip() for item in args.cfg_split.split(',')]
ps.fitstbl.write_pypeit(pypeit_file,
cfg_lines=ps.user_cfg,
write_bkg_pairs=args.background,
configs=config_list)
return 0
def parser(options=None):
import argparse
from pypeit.spectrographs.util import valid_spectrographs
parser = argparse.ArgumentParser()
# 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',
default=None,
type=int,
help='Only analyze the specified detector; otherwise analyze all.')
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(valid_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',
default=None,
help='Path to top-level output directory. '
'Default is the current working directory.')
parser.add_argument(
'-m',
'--master_dir',
default='Masters',
help='Name for directory in output path for Master 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',
default=False,
action='store_true',
help='Run in debug mode.')
parser.add_argument(
'--show',
default=False,
action='store_true',
help='Show the stages of trace refinements (only for the new code).')
return parser.parse_args() if options is None else parser.parse_args(
options)
lines += p.to_rst_table()
lines += ['']
lines += ['Instrument-Specific Default Configuration']
lines += ['+++++++++++++++++++++++++++++++++++++++++']
lines += ['']
lines += textwrap.wrap('The following provides the changes to the global default parameters '
'provided above for each instrument. That is, if one were to include '
'these in the PypeIt file, you would be reproducing the effect of the '
'`default_pypeit_par` method specific to each derived '
':class:`pypeit.spectrographs.spectrograph.Spectrograph` class.', 72)
lines += ['']
spectrographs = valid_spectrographs()
for spec in spectrographs:
s = load_spectrograph(spec)
lines += [ ' '.join([s.telescope['name'], s.camera]) ]
lines += [ '-'*len(lines[-1]) ]
lines += [ 'Alterations to the default parameters are::' ]
lines += ['']
sl = s.default_pypeit_par().to_config(include_descr=False, exclude_defaults=True)
lines += [ ' ' + l for l in sl ]
lines += ['']
lines += ['']
output_rst = os.path.join(pypeit_root, 'doc', 'pypeit_par.rst')
with open(output_rst, 'w') as f:
f.write('\n'.join(lines))