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wave rms refactor #1672

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merged 16 commits into from
Oct 1, 2023
Merged

wave rms refactor #1672

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804a451
refactored in wavecalib.py and autoid.py
debora-pe Sep 13, 2023
7120c9c
edit pypeitpar
debora-pe Sep 13, 2023
8833ff9
Merge branch 'develop' into rms_refactor
debora-pe Sep 13, 2023
f5c3d29
minor change
debora-pe Sep 13, 2023
0f9c8de
fix QA
debora-pe Sep 13, 2023
861ac97
fix bug
debora-pe Sep 14, 2023
71d36f7
changes to the spectrographs
debora-pe Sep 15, 2023
0fe4451
Merge branch 'develop' into rms_refactor
debora-pe Sep 18, 2023
12eb635
comments
debora-pe Sep 20, 2023
222545b
more comments
debora-pe Sep 20, 2023
254c7f8
added docstring
debora-pe Sep 20, 2023
1207c19
fix small bug
debora-pe Sep 20, 2023
92195df
fix some spectrographs
debora-pe Sep 25, 2023
a110d41
all use fwhm_fromlines
debora-pe Sep 29, 2023
d896dab
Merge branch 'develop' into rms_refactor
debora-pe Sep 29, 2023
ad36b23
Merge branch 'develop' into rms_refactor
debora-pe Sep 30, 2023
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8 changes: 4 additions & 4 deletions pypeit/core/arc.py
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Expand Up @@ -179,7 +179,7 @@ def fit2darc_global_qa(pypeitFit, nspec, outfile=None):

# Finish
if outfile is not None:
plt.savefig(outfile, dpi=800)
plt.savefig(outfile, dpi=300)
plt.close()
else:
plt.show()
Expand Down Expand Up @@ -291,9 +291,9 @@ def fit2darc_orders_qa(pypeitFit, nspec, outfile=None):

ax1.set_ylabel(r'Res. [pix]')

ax0.text(0.1, 0.9, r'RMS={0:.3f} Pixel'.format(rms_order / np.abs(dwl)), ha="left", va="top",
ax0.text(0.1, 0.8, r'RMS={0:.3f} Pixel'.format(rms_order / np.abs(dwl)), ha="left", va="top",
transform=ax0.transAxes)
ax0.text(0.1, 0.8, r'$\Delta\lambda$={0:.3f} Pixel/$\AA$'.format(np.abs(dwl)), ha="left", va="top",
ax0.text(0.1, 0.9, r'$\Delta\lambda$={0:.3f} $\AA$/Pixel'.format(np.abs(dwl)), ha="left", va="top",
transform=ax0.transAxes)
ax0.get_yaxis().set_label_coords(-0.15, 0.5)

Expand All @@ -311,7 +311,7 @@ def fit2darc_orders_qa(pypeitFit, nspec, outfile=None):

# Finish
if outfile is not None:
plt.savefig(outfile, dpi=800)
plt.savefig(outfile, dpi=200)
plt.close()
else:
plt.show()
Expand Down
552 changes: 309 additions & 243 deletions pypeit/core/wavecal/autoid.py
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26 changes: 15 additions & 11 deletions pypeit/par/pypeitpar.py
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Expand Up @@ -2507,7 +2507,7 @@ class WavelengthSolutionPar(ParSet):
def __init__(self, reference=None, method=None, echelle=None, ech_nspec_coeff=None, ech_norder_coeff=None, ech_sigrej=None, lamps=None,
sigdetect=None, fwhm=None, fwhm_fromlines=None, fwhm_spat_order=None, fwhm_spec_order=None,
reid_arxiv=None, nreid_min=None, cc_thresh=None, cc_local_thresh=None, nlocal_cc=None,
rms_threshold=None, match_toler=None, func=None, n_first=None, n_final=None,
rms_thresh_frac_fwhm=None, match_toler=None, func=None, n_first=None, n_final=None,
sigrej_first=None, sigrej_final=None, numsearch=None,
nfitpix=None, refframe=None,
nsnippet=None, use_instr_flag=None, wvrng_arxiv=None,
Expand Down Expand Up @@ -2626,12 +2626,13 @@ def __init__(self, reference=None, method=None, echelle=None, ech_nspec_coeff=No
descr['fwhm'] = 'Spectral sampling of the arc lines. This is the FWHM of an arcline in ' \
'binned pixels of the input arc image'

defaults['fwhm_fromlines'] = False
defaults['fwhm_fromlines'] = True
dtypes['fwhm_fromlines'] = bool
descr['fwhm_fromlines'] = 'Estimate spectral resolution in each slit using the arc lines. '\
'If True, the estimated FWHM will override ``fwhm`` only in '\
'the determination of the wavelength solution (`i.e.`, not in '\
'WaveTilts).'
'the determination of the wavelength solution (including the ' \
'calculation of the threshold for the solution RMS, see ' \
'``rms_thresh_frac_fwhm``), but not for the wave tilts calibration.' \

defaults['fwhm_spat_order'] = 0
dtypes['fwhm_spat_order'] = int
Expand Down Expand Up @@ -2698,12 +2699,15 @@ def __init__(self, reference=None, method=None, echelle=None, ech_nspec_coeff=No
'be added to it to make it odd.'

# These are the parameters used for the iterative fitting of the arc lines
defaults['rms_threshold'] = 0.15
dtypes['rms_threshold'] = float
descr['rms_threshold'] = 'Maximum RMS (in binned pixels) for keeping a slit/order solution. ' \
'Used for echelle spectrographs, the \'reidentify\' method, and when re-analyzing a slit with the redo_slits parameter.' \
'In a future PR, we will refactor the code to always scale this threshold off the measured FWHM of the arc lines.'

defaults['rms_thresh_frac_fwhm'] = 0.15
dtypes['rms_thresh_frac_fwhm'] = float
descr['rms_thresh_frac_fwhm'] = 'Maximum RMS (expressed as fraction of the FWHM) for keeping ' \
'a slit/order solution. If ``fwhm_fromlines`` is True, ' \
'FWHM will be computed from the arc lines in each slits ' \
'(the median value among all the slits is used), otherwise ``fwhm`` ' \
'will be used. This parameter is used for the \'holy-grail\', ' \
'\'reidentify\', and \'echelle\' methods and when re-analyzing ' \
'a slit using the ``redo_slits`` parameter. '

defaults['match_toler'] = 2.0
dtypes['match_toler'] = float
Expand Down Expand Up @@ -2785,7 +2789,7 @@ def from_dict(cls, cfg):
'ech_norder_coeff', 'ech_sigrej', 'ech_separate_2d', 'lamps', 'sigdetect',
'fwhm', 'fwhm_fromlines', 'fwhm_spat_order', 'fwhm_spec_order',
'reid_arxiv', 'nreid_min', 'cc_thresh', 'cc_local_thresh',
'nlocal_cc', 'rms_threshold', 'match_toler', 'func', 'n_first','n_final',
'nlocal_cc', 'rms_thresh_frac_fwhm', 'match_toler', 'func', 'n_first','n_final',
'sigrej_first', 'sigrej_final', 'numsearch', 'nfitpix',
'refframe', 'nsnippet', 'use_instr_flag', 'wvrng_arxiv',
'redo_slits', 'qa_log']
Expand Down
4 changes: 2 additions & 2 deletions pypeit/spectrographs/bok_bc.py
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Expand Up @@ -231,9 +231,9 @@ def default_pypeit_par(cls):
par['calibrations']['wavelengths']['lamps'] = ['NeI', 'ArI', 'ArII', 'HeI']
# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths']['rms_threshold'] = 0.5
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.19
par['calibrations']['wavelengths']['sigdetect'] = 5.
par['calibrations']['wavelengths']['fwhm']= 5.0
par['calibrations']['wavelengths']['fwhm']= 2.6

#par['calibrations']['wavelengths']['n_first'] = 3
#par['calibrations']['wavelengths']['n_final'] = 5
Expand Down
8 changes: 4 additions & 4 deletions pypeit/spectrographs/gemini_flamingos.py
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Expand Up @@ -109,9 +109,9 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution with arc lines
par['calibrations']['wavelengths']['rms_threshold'] = 0.5
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.1
par['calibrations']['wavelengths']['sigdetect']=5
par['calibrations']['wavelengths']['fwhm'] = 5
par['calibrations']['wavelengths']['fwhm'] = 5.
par['calibrations']['wavelengths']['n_first']=2
par['calibrations']['wavelengths']['n_final']=4
par['calibrations']['wavelengths']['lamps'] = ['OH_NIRES']
Expand Down Expand Up @@ -276,9 +276,9 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution with arc lines
par['calibrations']['wavelengths']['rms_threshold'] = 1.0
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.05 # this needs to be updated
par['calibrations']['wavelengths']['sigdetect']=3
par['calibrations']['wavelengths']['fwhm'] = 20
par['calibrations']['wavelengths']['fwhm'] = 20 # we don't know this value, no dataset in the repo
par['calibrations']['wavelengths']['n_first']=2
par['calibrations']['wavelengths']['n_final']=4
par['calibrations']['wavelengths']['lamps'] = ['ArI', 'ArII', 'ThAr', 'NeI']
Expand Down
4 changes: 2 additions & 2 deletions pypeit/spectrographs/gemini_gmos.py
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Expand Up @@ -263,7 +263,8 @@ def default_pypeit_par(cls):
par['calibrations']['slitedges']['fit_order'] = 3

# 1D wavelength solution
par['calibrations']['wavelengths']['rms_threshold'] = 0.40 # Might be grating dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.08 # Might be grating dependent..
par['calibrations']['wavelengths']['fwhm'] = 5.
par['calibrations']['wavelengths']['sigdetect'] = 5. # Doesn't work for reddest chip
par['calibrations']['wavelengths']['lamps'] = ['CuI', 'ArI', 'ArII']
par['calibrations']['wavelengths']['method'] = 'full_template'
Expand Down Expand Up @@ -325,7 +326,6 @@ def config_specific_par(self, scifile, inp_par=None):

# Allow for various binning
binning = parse.parse_binning(self.get_meta_value(headarr, 'binning'))
par['calibrations']['wavelengths']['fwhm_fromlines'] = True

return par

Expand Down
6 changes: 3 additions & 3 deletions pypeit/spectrographs/gemini_gnirs.py
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Expand Up @@ -322,8 +322,8 @@ def config_specific_par(self, scifile, inp_par=None):
par['calibrations']['slitedges']['fit_min_spec_length'] = 0.5

# Wavelengths
par['calibrations']['wavelengths']['rms_threshold'] = 1.0 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.4
par['calibrations']['wavelengths']['sigdetect'] = 10.0
par['calibrations']['wavelengths']['lamps'] = ['OH_GNIRS']
# par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[0]['nonlinear'] * self.detector[0]['saturation']
par['calibrations']['wavelengths']['n_first'] = 2
Expand Down Expand Up @@ -354,7 +354,7 @@ def config_specific_par(self, scifile, inp_par=None):
par['calibrations']['slitedges']['sync_predict'] = 'nearest'

# Wavelengths
par['calibrations']['wavelengths']['rms_threshold'] = 1.0 # Might be grating dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.05
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['lamps'] = ['Ar_IR_GNIRS']
# par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[0]['nonlinear'] * self.detector[0]['saturation']
Expand Down
1 change: 0 additions & 1 deletion pypeit/spectrographs/keck_deimos.py
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Expand Up @@ -395,7 +395,6 @@ def config_specific_par(self, scifile, inp_par=None):
# Wavelength FWHM
binning = parse.parse_binning(self.get_meta_value(headarr, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 6.0 / binning[1]
par['calibrations']['wavelengths']['fwhm_fromlines'] = True

# Objects FWHM
# Find objects
Expand Down
3 changes: 1 addition & 2 deletions pypeit/spectrographs/keck_esi.py
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Expand Up @@ -91,9 +91,8 @@ def default_pypeit_par(cls):
# Wavelengths
# 1D wavelength solution
# This is for 1x1
par['calibrations']['wavelengths']['rms_threshold'] = 0.30
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.103
par['calibrations']['wavelengths']['fwhm'] = 2.9
par['calibrations']['wavelengths']['fwhm_fromlines'] = True
#
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['lamps'] = ['CuI', 'ArI', 'NeI', 'HgI', 'XeI', 'ArII']
Expand Down
2 changes: 1 addition & 1 deletion pypeit/spectrographs/keck_hires.py
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Expand Up @@ -115,7 +115,7 @@ def default_pypeit_par(cls):
# 1D wavelength solution
par['calibrations']['wavelengths']['lamps'] = ['ThAr']
# This is for 1x1 binning. TODO GET BINNING SORTED OUT!!
par['calibrations']['wavelengths']['rms_threshold'] = 0.50
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.1
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['n_final'] = 4 #[3] + 13 * [4] + [3]
# This is for 1x1 binning. Needs to be divided by binning for binned data!!
Expand Down
5 changes: 2 additions & 3 deletions pypeit/spectrographs/keck_lris.py
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Expand Up @@ -75,7 +75,7 @@ def default_pypeit_par(cls):
# Remove slits that are too short
par['calibrations']['slitedges']['minimum_slit_length'] = 3.
# 1D wavelengths
par['calibrations']['wavelengths']['rms_threshold'] = 0.20 # Might be grism dependent
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.05 # Might be grism dependent
# Set the default exposure time ranges for the frame typing
par['calibrations']['biasframe']['exprng'] = [None, 0.001]
par['calibrations']['darkframe']['exprng'] = [999999, None] # No dark frames
Expand Down Expand Up @@ -136,7 +136,6 @@ def config_specific_par(self, scifile, inp_par=None):
# Wave FWHM
binning = parse.parse_binning(self.get_meta_value(scifile, 'binning'))
par['calibrations']['wavelengths']['fwhm'] = 8.0 / binning[0]
par['calibrations']['wavelengths']['fwhm_fromlines'] = True
# Arc lamps list from header
par['calibrations']['wavelengths']['lamps'] = ['use_header']

Expand Down Expand Up @@ -843,7 +842,7 @@ def default_pypeit_par(cls):
par['calibrations']['slitedges']['fit_min_spec_length'] = 0.2

# 1D wavelength solution -- Additional parameters are grism dependent
par['calibrations']['wavelengths']['rms_threshold'] = 0.20 # Might be grism dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.06 # Might be grism dependent..
par['calibrations']['wavelengths']['sigdetect'] = 10.0

#par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[0]['nonlinear'] * self.detector[0]['saturation']
Expand Down
4 changes: 1 addition & 3 deletions pypeit/spectrographs/keck_mosfire.py
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Expand Up @@ -84,7 +84,7 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths']['rms_threshold'] = 0.30 #0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.11 #0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect']=5.0
par['calibrations']['wavelengths']['fwhm']= 5.0
par['calibrations']['wavelengths']['n_final']= 4
Expand Down Expand Up @@ -210,7 +210,6 @@ def config_specific_par(self, scifile, inp_par=None):
# using OH lines
if 'long2pos_specphot' not in decker and filter in supported_filters:
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths']['fwhm_fromlines'] = True
par['calibrations']['wavelengths']['sigdetect'] = 10.
# templates
if filter == 'Y':
Expand All @@ -233,7 +232,6 @@ def config_specific_par(self, scifile, inp_par=None):
elif 'long2pos_specphot' in decker and filter in supported_filters:
par['calibrations']['wavelengths']['lamps'] = ['Ar_IR_MOSFIRE', 'Ne_IR_MOSFIRE']
par['calibrations']['wavelengths']['method'] = 'full_template'
par['calibrations']['wavelengths']['fwhm_fromlines'] = True
# templates
if filter == 'Y':
par['calibrations']['wavelengths']['reid_arxiv'] = 'keck_mosfire_arcs_Y.fits'
Expand Down
3 changes: 1 addition & 2 deletions pypeit/spectrographs/keck_nires.py
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Expand Up @@ -80,10 +80,9 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths']['rms_threshold'] = 0.30
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.136
par['calibrations']['wavelengths']['sigdetect']=5.0
par['calibrations']['wavelengths']['fwhm']= 2.2 # Measured
par['calibrations']['wavelengths']['fwhm_fromlines'] = True
par['calibrations']['wavelengths']['n_final']= [3,4,4,4,4]
par['calibrations']['wavelengths']['lamps'] = ['OH_NIRES']
#par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[0]['nonlinear'] * self.detector[0]['saturation']
Expand Down
4 changes: 2 additions & 2 deletions pypeit/spectrographs/keck_nirspec.py
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Expand Up @@ -70,9 +70,9 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths']['rms_threshold'] = 0.20 #0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.06 #0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect']=5.0
par['calibrations']['wavelengths']['fwhm']= 5.0
par['calibrations']['wavelengths']['fwhm']= 3.5
par['calibrations']['wavelengths']['n_final']= 4
par['calibrations']['wavelengths']['lamps'] = ['OH_NIRES']
#par['calibrations']['wavelengths']['nonlinear_counts'] = self.detector[0]['nonlinear'] * self.detector[0]['saturation']
Expand Down
8 changes: 3 additions & 5 deletions pypeit/spectrographs/lbt_luci.py
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Expand Up @@ -329,10 +329,9 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths'][
'rms_threshold'] = 0.20 # 0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.05 # 0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['fwhm'] = 5.0
par['calibrations']['wavelengths']['fwhm'] = 4.5
par['calibrations']['wavelengths']['n_final'] = 4
par['calibrations']['wavelengths']['lamps'] = ['OH_NIRES']
#par['calibrations']['wavelengths']['nonlinear_counts'] = \
Expand Down Expand Up @@ -444,8 +443,7 @@ def default_pypeit_par(cls):

# Wavelengths
# 1D wavelength solution
par['calibrations']['wavelengths'][
'rms_threshold'] = 0.20 # 0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.04 # 0.20 # Might be grating dependent..
par['calibrations']['wavelengths']['sigdetect'] = 5.0
par['calibrations']['wavelengths']['fwhm'] = 5.0
par['calibrations']['wavelengths']['n_final'] = 4
Expand Down
8 changes: 4 additions & 4 deletions pypeit/spectrographs/lbt_mods.py
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Expand Up @@ -324,7 +324,7 @@ def default_pypeit_par(cls):

# 1D wavelength solution
par['calibrations']['wavelengths']['sigdetect'] = 5.
par['calibrations']['wavelengths']['rms_threshold'] = 0.4
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.09
par['calibrations']['wavelengths']['fwhm'] = 10.
#par['calibrations']['wavelengths']['lamps'] = ['XeI','ArII','ArI','NeI','KrI']]
par['calibrations']['wavelengths']['lamps'] = ['ArI','NeI','KrI','XeI']
Expand Down Expand Up @@ -488,7 +488,7 @@ def default_pypeit_par(cls):

# 1D wavelength solution
par['calibrations']['wavelengths']['sigdetect'] = 10.
par['calibrations']['wavelengths']['rms_threshold'] = 0.4
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.09
par['calibrations']['wavelengths']['lamps'] = ['XeI','KrI','ArI','HgI']

# slit
Expand Down Expand Up @@ -645,7 +645,7 @@ def default_pypeit_par(cls):

# 1D wavelength solution
par['calibrations']['wavelengths']['sigdetect'] = 5.
par['calibrations']['wavelengths']['rms_threshold'] = 1.0
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.22
par['calibrations']['wavelengths']['fwhm'] = 10.
#par['calibrations']['wavelengths']['lamps'] = ['XeI','ArII','ArI','NeI','KrI']]
par['calibrations']['wavelengths']['lamps'] = ['ArI','NeI','KrI','XeI']
Expand Down Expand Up @@ -807,7 +807,7 @@ def default_pypeit_par(cls):

# 1D wavelength solution
par['calibrations']['wavelengths']['sigdetect'] = 10.
par['calibrations']['wavelengths']['rms_threshold'] = 0.4
par['calibrations']['wavelengths']['rms_thresh_frac_fwhm'] = 0.09
par['calibrations']['wavelengths']['lamps'] = ['XeI','KrI','ArI','HgI']

# slit
Expand Down
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