"""
Script for coadding PypeIt 1d spectra
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
import os
from IPython import embed
import numpy as np
from astropy.io import fits
from astropy.time import Time
from pypeit import msgs
from pypeit import inputfiles
from pypeit import coadd1d
from pypeit import inputfiles
from pypeit.par import pypeitpar
from pypeit.scripts import scriptbase
from pypeit.spectrographs.util import load_spectrograph
## TODO: This is basically the exact same code as read_fluxfile in the fluxing
## script. Consolidate them? Make this a standard method in parse or io.
#def read_coaddfile(ifile):
# """
# Read a ``PypeIt`` coadd1d file, akin to a standard PypeIt file.
#
# The top is a config block that sets ParSet parameters. The name of the
# spectrograph is required.
#
# Args:
# ifile (:obj:`str`):
# Name of the coadd file
#
# Returns:
# :obj:`tuple`: Three objects are returned: a :obj:`list` with the
# configuration entries used to modify the relevant
# :class:`~pypeit.par.parset.ParSet` parameters, a :obj:`list` the names
# of spec1d files to be coadded, and a :obj:`list` with the object IDs
# aligned with each of the spec1d files.
# """
# # Read in the pypeit reduction file
# msgs.info('Loading the coadd1d file')
# lines = inputfiles.read_pypeit_file_lines(ifile)
# is_config = np.ones(len(lines), dtype=bool)
#
#
# # Parse the fluxing block
# spec1dfiles = []
# objids_in = []
# s, e = inputfiles.InputFile.find_block(lines, 'coadd1d')
# if s >= 0 and e < 0:
# msgs.error("Missing 'coadd1d end' in {0}".format(ifile))
# elif (s < 0) or (s==e):
# msgs.error("Missing coadd1d read or [coadd1d] block in in {0}. Check the input format for the .coadd1d file".format(ifile))
# else:
# for ctr, line in enumerate(lines[s:e]):
# prs = line.split(' ')
# spec1dfiles.append(prs[0])
# if ctr == 0 and len(prs) != 2:
# msgs.error('Invalid format for .coadd1d file.' + msgs.newline() +
# 'You must have specify a spec1dfile and objid on the first line of the coadd1d block')
# if len(prs) > 1:
# objids_in.append(prs[1])
# is_config[s-1:e+1] = False
#
# # Chck the sizes of the inputs
# nspec = len(spec1dfiles)
# if len(objids_in) == 1:
# objids = nspec*objids_in
# elif len(objids_in) == nspec:
# objids = objids_in
# else:
# msgs.error('Invalid format for .flux file.' + msgs.newline() +
# 'You must specify a single objid on the first line of the coadd1d block,' + msgs.newline() +
# 'or specify am objid for every spec1dfile in the coadd1d block.' + msgs.newline() +
# 'Run pypeit_coadd_1dspec --help for information on the format')
# # Construct config to get spectrograph
# cfg_lines = list(lines[is_config])
#
# # Return
# return cfg_lines, spec1dfiles, objids
[docs]def build_coadd_file_name(spec1dfiles, spectrograph):
"""Build the output file name for coadding.
The filename convention is coadd1d_<target>_<instrument name>_<YYYYMMDD>.fits or
coadd1d_<target>_<instrument name>_<YYYYMMDD>-<YYYYMMDD>.fits if the coadd included more than
one day's worth of data. The default location of the file will be along side the first spec1d file.
Currently instrument_name is taken from spectrograph.camera
Returns:
str: The name of the coadd output file.
"""
mjd_list = []
for f in spec1dfiles:
try:
mjd_list.append(float(fits.getheader(f)['MJD']))
except Exception as e:
msgs.error(f"Failed to read MJD from {f}: {e}")
start_mjd = np.min(mjd_list)
end_mjd = np.max(mjd_list)
start_date_portion = Time(start_mjd, format="mjd").strftime('%Y%m%d')
end_date_portion = Time(end_mjd, format="mjd").strftime('%Y%m%d')
date_portion = f"{start_date_portion}_{end_date_portion}"
instrument_name = spectrograph.camera
target = fits.getheader(spec1dfiles[0])['TARGET']
path = os.path.dirname(os.path.abspath(spec1dfiles[0]))
return os.path.join(path, f'coadd1d_{target}_{instrument_name}_{date_portion}.fits')
[docs]class CoAdd1DSpec(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Coadd 1D spectra produced by PypeIt',
width=width, formatter=scriptbase.SmartFormatter)
parser.add_argument('coadd1d_file', type=str,
help="R|File to guide coadding process.\n\n"
"------------------------\n"
" MultiSlit \n"
"------------------------\n\n"
"For coadding Multislit spectra the file must have the "
"following format (see docs for further details including the "
"use of paths): \n\n"
"F|[coadd1d]\n"
"F| coaddfile='output_filename.fits' # Optional\n"
"\n"
"F| coadd1d read\n"
"F| filename | obj_id\n"
"F| spec1dfile1 | objid1\n"
"F| spec1dfile2 | objid2\n"
"F| spec1dfile3 | objid3\n"
"F| ... \n"
"F| coadd1d end\n"
"\n OR the coadd1d read/end block can look like \n\n"
"F| coadd1d read\n"
"F| filename | obj_id\n"
"F| spec1dfile1 | objid \n"
"F| spec1dfile2 | \n"
"F| spec1dfile3 | \n"
"F| ... \n"
"F| coadd1d end\n"
"\n"
"That is the coadd1d block must be a two column list of\n"
"spec1dfiles and objids, but you can specify only a single "
"objid for all spec1dfiles on the first line\n\n"
"Where: \n"
"\n"
"spec1dfile: full path to a PypeIt spec1dfile\n\n"
"objid: the object identifier. To determine the objids inspect "
"the spec1d_*.txt files or run pypeit_show_1dspec spec1dfile "
"--list\n\n"
"------------------------\n"
" Echelle \n"
"------------------------\n\n"
"For coadding Echelle spectra the file must have the following "
"format (see docs for further details): \n\n"
"F|[coadd1d]\n"
"F| coaddfile='output_filename.fits' # Optional\n"
"\n"
"F| coadd1d read\n"
"F| filename | obj_id | sensfile | setup_id \n"
"F| spec1dfile1 | objid1 | sensfile1 | setup_id1\n"
"F| spec1dfile2 | objid2 | sensfile2 | setup_id2\n"
"F| spec1dfile3 | objid3 | sensfile3 | setup_id3\n"
"F| ... \n"
"F| coadd1d end\n"
"\n OR the coadd1d read/end block can look like \n\n"
"F| coadd1d read\n"
"F| filename | obj_id | sensfile | setup_id\n"
"F| spec1dfile1 | objid1 | sensfile | setup_id\n"
"F| spec1dfile2 | | | \n"
"F| spec1dfile3 | | | \n"
"F| ... \n"
"F| coadd1d end\n"
"\n"
"That is the coadd1d block is a four column list of\n"
"spec1dfiles, objids, sensitivity function files, and setup_ids, "
"but you can specify only a single objid, sensfile, and setup_id "
"for all spec1dfiles on the first line\n\n"
"Here: \n"
"\n"
"spec1dfile: full path to a PypeIt spec1dfile\n\n"
"objid: the object identifier (see details above)\n\n"
"sensfile: full path to a PypeIt sensitivity function file for "
"the echelle setup in question\n\n"
"setup_id: string identifier for the echelle setup in question, "
"i.e. 'VIS', 'NIR', or 'UVB'\n\n"
"If the coaddfile is not given the output file will be placed "
"in the same directory as the first spec1d file.\n\n")
parser.add_argument("--debug", default=False, action="store_true", help="show debug plots?")
parser.add_argument("--show", default=False, action="store_true",
help="show QA during coadding process")
parser.add_argument("--par_outfile", default='coadd1d.par',
help="Output to save the parameters")
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 coadd_1dspec_YYYYMMDD-HHMM.log')
#parser.add_argument("--test_spec_path", type=str, help="Path for testing")
return parser
[docs] @staticmethod
def main(args):
""" Runs the 1d coadding steps
"""
# Set the verbosity, and create a logfile if verbosity == 2
msgs.set_logfile_and_verbosity('coadd_1dspec', args.verbosity)
# Load the file
#config_lines, spec1dfiles, objids = read_coaddfile(args.coadd1d_file)
coadd1dFile = inputfiles.Coadd1DFile.from_file(args.coadd1d_file)
# Append path for testing
#if args.test_spec_path is not None:
# spec1dfiles = [os.path.join(args.test_spec_path, ifile) for ifile in spec1dfiles]
# Read in spectrograph from spec1dfile header
header = fits.getheader(coadd1dFile.filenames[0])
spectrograph = load_spectrograph(header['PYP_SPEC'])
# Parameters
spectrograph_def_par = spectrograph.default_pypeit_par()
par = pypeitpar.PypeItPar.from_cfg_lines(cfg_lines=spectrograph_def_par.to_config(),
merge_with=(coadd1dFile.cfg_lines,))
# Check that sensfunc column is populated if this is echelle
if spectrograph.pypeline == 'Echelle' and coadd1dFile.sensfiles is None:
msgs.error("To coadd echelle spectra, the 'sensfile' column must present in your .coadd1d file")
# Write the par to disk
print("Writing the parameters to {}".format(args.par_outfile))
par.to_config(args.par_outfile)
# TODO This needs to come out of the parset
coaddfile = par['coadd1d']['coaddfile']
# Testing?
#if args.test_spec_path is not None:
# if sensfile is not None:
# sensfile = os.path.join(args.test_spec_path, sensfile)
# coaddfile = os.path.join(args.test_spec_path, coaddfile)
if coaddfile is None:
coaddfile = build_coadd_file_name(coadd1dFile.filenames, spectrograph)
# Instantiate
coAdd1d = coadd1d.CoAdd1D.get_instance(coadd1dFile.filenames,
coadd1dFile.objids,
spectrograph=spectrograph,
par=par['coadd1d'],
sensfuncfile=coadd1dFile.sensfiles,
setup_id=coadd1dFile.setup_id,
debug=args.debug, show=args.show,
chk_version=par['rdx']['chk_version'])
# Run
coAdd1d.run()
# Save to file
coAdd1d.save(coaddfile)
msgs.info('Coadding complete')