"""
Script to measure and correct for flexure in multi-slit data.
.. 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 pypeit import msgs
from pypeit import inputfiles
from pypeit.spectrographs.util import load_spectrograph
from pypeit.par import pypeitpar
from pypeit.core import flexure
from pypeit.scripts import scriptbase
#def read_flexfile(ifile):
# """
# Read a ``PypeIt`` flexure file, akin to a standard ``PypeIt`` file.
#
# The top is a config block that sets ParSet parameters.
#
# Args:
# ifile (:obj:`str`):
# Name of the flexure file
#
# Returns:
# :obj:`tuple`: Two objects are returned: a :obj:`list` with the
# configuration entries used to modify the relevant
# :class:`~pypeit.par.parset.ParSet` parameters and a :obj:`list` with the
# names of spec1d files to be flexure corrected.
# """
# # Read in the pypeit reduction file
# msgs.info('Loading the flexure 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, 'flexure')
# if s >= 0 and e < 0:
# msgs.error("Missing 'flexure end' in {0}".format(ifile))
# elif (s < 0) or (s == e):
# msgs.error(
# "Missing flexure read block in {0}. Check the input format for the .flex file".format(ifile))
# else:
# for ctr, line in enumerate(lines[s:e]):
# prs = line.split(' ')
# spec1dfiles.append(prs[0])
# if len(prs) > 1:
# msgs.error('Invalid format for .flex file.' + msgs.newline() +
# 'You must specify only spec1dfiles in the block ')
# is_config[s-1:e+1] = False
#
# # Chck the sizes of the inputs
# nspec = len(spec1dfiles)
#
# # Construct config to get spectrograph
# cfg_lines = list(lines[is_config])
#
# # Return
# return cfg_lines, spec1dfiles
# TODO: Maybe not a good idea to name this script the same as the
# flexure.MultiSlitFlexure class, but it is technically okay...
[docs]class MultiSlitFlexure(scriptbase.ScriptBase):
[docs] @classmethod
def get_parser(cls, width=None):
parser = super().get_parser(description='Calculate and apply flexure corrections for 1D '
'spectra produced by PypeIt.',
width=width, formatter=scriptbase.SmartFormatter)
parser.add_argument("flex_file", type=str,
help="R|File to guide flexure corrections for this multi-slit mode."
" This file must have the following format: \n\n"
"F|flexure read\n"
"F| filename\n"
"F| spec1dfile1\n"
"F| spec1dfile2\n"
"F| ... \n"
"F|flexure end\n"
"\n\n")
parser.add_argument("outroot", type=str,
help='Output fileroot for the flexure fits saved as FITS.')
parser.add_argument("--clobber", default=True,
action="store_true", help="Clobber output files")
parser.add_argument("--debug", default=False,
action="store_true", help="show debug plots?")
return parser
[docs] @staticmethod
def main(args):
from astropy.io import fits
# Load the file
flexFile = inputfiles.FlexureFile.from_file(args.flex_file)
# Read in spectrograph from spec1dfile header
header = fits.getheader(flexFile.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=(flexFile.cfg_lines,))
# Loop to my loop
for filename in flexFile.filenames:
# Instantiate
mdFlex = flexure.MultiSlitFlexure(s1dfile=filename)
# Initalize
msgs.info("Setup")
mdFlex.init(spectrograph, par['flexure'])
# INITIAL SKY LINE STUFF
msgs.info("Measuring sky lines")
mdFlex.measure_sky_lines()
# FIT SURFACES
msgs.info("Fitting the surface")
mdFlex.fit_mask_surfaces()
# Apply
msgs.info("Applying flexure correction")
mdFlex.update_fit()
# REFIT FOR QA PLOTS
msgs.info("Generate QA")
mask = header['TARGET'].strip()
fnames = header['FILENAME'].split('.')
root = mask+'_'+fnames[2]
mdFlex.qa_plots('./', root)
# Write
msgs.info("Write to disk")
mdFlex.to_file(args.outroot+root+'.fits', overwrite=args.clobber)
# Apply??
print("All done!!")