"""
This script generates an "observing log" for a directory with a set of files
to be reduced by PypeIt.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
import time
import os
from IPython import embed
import numpy as np
from pypeit.spectrographs import available_spectrographs
from pypeit.scripts import scriptbase
[docs]class ObsLog(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Construct an observing log for a set of files '
'from the provided spectrograph using '
'PypeItMetaData.', width=width)
parser.add_argument('spec', type=str,
help='A valid spectrograph identifier: {0}'.format(
', '.join(available_spectrographs)))
parser.add_argument('-r', '--root', default='current working directory', type=str,
help='Root to search for data files. You can provide the top-level '
'directory (e.g., /data/Kast) or the search string up through '
'the wildcard (.e.g, /data/Kast/b). Use the --extension option '
'to set the types of files to search for.')
parser.add_argument('-k', '--keys', default=False, action='store_true',
help='Do not produce the log; simply list the pypeit-specific '
'metadata keys available for this spectrograph and their '
'associated header cards. Metadata keys with header cards that '
'are None have no simple mapping between keyword and header '
'card.')
parser.add_argument('-c', '--columns', default='pypeit', type=str,
help='A comma-separated list of columns to include in the output '
'table. Each column must be a valid pypeit metadata keyword '
'specific to this spectrograph (run pypeit_obslog with the -k '
'argument to see the valid list). Additional valid keywords '
'are directory, filename, frametype, framebit, setup, calib, '
'and calibbit. If \'all\', all columns collected for the pypeit '
'metadata table are included. If \'pypeit\', the columns are '
'the same as those included in the pypeit file.')
parser.add_argument('-b', '--bad_frames', default=False, action='store_true',
help='Clean the output of bad frames that cannot be reduced by pypeit.')
parser.add_argument('-t', '--bad_types', default='keep', type=str,
help='Dictates how frames that could not be given a valid type should '
'be treated. Options are: "keep" to include them in the output, '
'"rm" to remove them from the output, "only" to only include the '
'frames with unknown types in the output (i.e, the frames with '
'determined types are excluded).')
parser.add_argument('-g', '--groupings', default=True, action='store_false',
help='Use this option to only determine the frame type. By default, '
'the script groups frames into expected configuration and '
'calibration groups, and it adds the default combination groups.')
parser.add_argument('-i', '--interact', default=False, action='store_true',
help='Once the metadata table is created, start an embedded IPython '
'session that you can use to interact with the table (an '
'Astropy.Table called fitstbl) directly.')
parser.add_argument('-s', '--sort', default='mjd', type=str,
help='Metadata keyword (pypeit-specific) to use to sort the output '
'table.')
parser.add_argument('-e', '--extension', default='.fits',
help='File extension; compression indicators (e.g. .gz) not required.')
parser.add_argument('-d', '--output_path', default='current working directory',
help='Path to top-level output directory.')
parser.add_argument('-o', '--overwrite', default=False, action='store_true',
help='Overwrite any existing files/directories')
parser.add_argument('-f', '--file', default=None, type=str,
help='Name for the ascii output file. Any leading directory path is '
'stripped; use -d to set the output directory. If None, the '
'table is just printed to stdout. If set to \'default\', the '
'file is set to [spectrograph].obslog. Note the file will *not* '
'be written if you also include the -i option to embed and '
'interact with the table (you can write the table using the '
'astropy.table.Table.write method in the embedded IPython '
'session). The table is always written in ascii format using '
'format=ascii.fixed_with for the call to '
'Astropy.table.Table.write .')
parser.add_argument('-G','--gui', default=False, action='store_true',
help='View the obs log in a GUI')
return parser
[docs] @staticmethod
def main(args):
from pypeit.spectrographs.util import load_spectrograph
from pypeit.pypeitsetup import PypeItSetup
# Check that input spectrograph is supported
if args.spec not in available_spectrographs:
raise ValueError('Instrument \'{0}\' unknown to PypeIt.\n'.format(args.spec)
+ '\tOptions are: {0}\n'.format(', '.join(available_spectrographs))
+ '\tSelect an available instrument or consult the documentation '
+ 'on how to add a new instrument.')
if args.gui:
from pypeit.scripts.setup_gui import SetupGUI
gui_args = SetupGUI.parse_args(["-s", args.spec, "-r", args.root, "-e", args.extension])
SetupGUI.main(gui_args)
if args.keys:
# Only print the metadata to header card mapping
load_spectrograph(args.spec).meta_key_map()
return
if args.bad_types not in ['keep', 'rm', 'only']:
raise ValueError(f'{args.bad_types} is not a valid keyword for the --bad_types '
f'argument.')
# Generate the metadata table
ps = PypeItSetup.from_file_root(args.root, args.spec,
extension=args.extension)
ps.run(setup_only=True, # This allows for bad headers
groupings=args.groupings,
clean_config=args.bad_frames)
# Check the file can be written (this is here because the spectrograph
# needs to be defined first)
_file = args.file
if _file == 'default':
_file = f'{ps.spectrograph.name}.obslog'
if _file is not None:
_odir, _file = os.path.split(_file)
_file = os.path.join(args.output_path, _file)
if not os.path.isdir(args.output_path):
os.makedirs(args.output_path)
if not args.interact and os.path.isfile(_file) and not args.overwrite:
raise FileExistsError(f'{_file} already exists. Use -o to overwrite.')
# Write/Print the data
#'{0}'.format(time.strftime("%a %d %b %Y %H:%M:%S",time.localtime())),
header = ['Auto-generated PypeIt Observing Log',
'{0}'.format(time.strftime("%Y-%m-%d",time.localtime())),
f'Root file string: {args.root}']
if args.bad_types == 'keep':
nrows = len(ps.fitstbl)
indx = np.ones(nrows, dtype=bool)
elif args.bad_types == 'rm':
indx = ps.fitstbl['frametype'] != 'None'
elif args.bad_types == 'only':
indx = ps.fitstbl['frametype'] == 'None'
else:
raise ValueError('CODING ERROR: Should never get here.')
fitstbl = ps.fitstbl.write(output='table' if args.interact else _file, rows=indx,
columns=args.columns, sort_col=args.sort,
overwrite=args.overwrite, header=header)
if args.interact:
embed()