Post-process using Specutils

Find peaks or uncertainties using the specutils library. A Radis Spectrum object can easily be converted to a specutils specutils.spectra.spectrum1d.Spectrum1D using to_specutils().

Below, we create a noisy spectrum based on a synthetic CO spectrum, we convert it to specutils, add uncertainties by targeting a noisy region, then determine the lines using find_lines_threshold() :

import astropy.units as u
import numpy as np

from radis import spectrum_test

""" We create a synthetic CO spectrum"""

s = (
    spectrum_test(molecule="CO", wavenum_min=2000, wavenum_max=2030)
    .apply_slit(1.5, "nm")
    .take("radiance")
)
s.trim()  # removes nans created by the slit convolution boundary effects
noise = np.random.normal(0.0, s.max().value * 0.03, len(s))
s_exp = s + noise

s_exp.plot()

--------------------------------------------------------------------------------
CO - HITRAN - Downloading database
--------------------------------------------------------------------------------

Download:
- All files already downloaded.

Caching to HDF5/H5 format:
- All files already cached.
0.02s - Loaded database
Calculating Equilibrium Spectrum
Physical Conditions
----------------------------------------
   Tgas                 700 K
   isotope              1,2,3
   medium               air
   mole_fraction        0.1
   path_length          1 cm
   pressure             1.01325 bar
   self_absorption      True
   species              CO
   state                X
   wavenum_max          2030.0000 cm-1
   wavenum_min          2000.0000 cm-1
Computation Parameters
----------------------------------------
   Tref                 296 K
   add_at_used          numpy
   broadening_method    voigt_poly
   cutoff               1e-27 cm-1/(#.cm-2)
   dbformat             hitran
   dbpath               /home/docs/.radisdb/hitran/CO.h5
   diluent              air
   folding_thresh       1e-06
   include_neighbouring_lines  True
   isatom               False
   isneutral            None
   lbfunc               None
   memory_mapping_engine  auto
   neighbour_lines      0 cm-1
   optimization         simple
   parsum_mode          full summation
   pfsource             default
   potential_lowering   None
   pseudo_continuum_threshold  0
   sparse_ldm           True
   truncation           50 cm-1
   waveunit             cm-1
   wstep                0.01 cm-1
   zero_padding         3001
----------------------------------------
0.01s - Spectrum calculated

<matplotlib.lines.Line2D object at 0x79def42501a0>

Determine the noise level by selecting a noisy region from the graph above :

spectrum = s_exp.to_specutils()

from specutils import SpectralRegion
from specutils.manipulation import noise_region_uncertainty
from specutils.spectra import Spectrum1D

noise_region = SpectralRegion(2010.5 / u.cm, 2009.5 / u.cm)
spectrum = noise_region_uncertainty(spectrum, noise_region)
if not isinstance(spectrum, Spectrum1D):
    spectrum = Spectrum1D(
        flux=spectrum.flux,
        spectral_axis=spectrum.spectral_axis,
        uncertainty=getattr(spectrum, "uncertainty", None),
        wcs=getattr(spectrum, "wcs", None),
        mask=getattr(spectrum, "mask", None),
        meta=getattr(spectrum, "meta", None),
    )

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/develop/radis/spectrum/spectrum.py:4385: AstropyDeprecationWarning: The Spectrum1D class is deprecated and may be removed in a future version.
        Use Spectrum instead.
  return Spectrum1D(
/home/docs/checkouts/readthedocs.org/user_builds/radis/conda/develop/lib/python3.14/site-packages/astropy/nddata/mixins/ndslicing.py:68: AstropyDeprecationWarning: The Spectrum1D class is deprecated and may be removed in a future version.
        Use Spectrum instead.
  return self.__class__(**kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/radis/conda/develop/lib/python3.14/site-packages/specutils/spectra/spectrum.py:582: AstropyDeprecationWarning: The Spectrum1D class is deprecated and may be removed in a future version.
        Use Spectrum instead.
  return self.__class__(**alt_kwargs)
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/develop/examples/2_Experimental_spectra/plot_specutils_processing.py:47: AstropyDeprecationWarning: The Spectrum1D class is deprecated and may be removed in a future version.
        Use Spectrum instead.
  spectrum = Spectrum1D(

Find lines :

from specutils.fitting import find_lines_threshold

lines = find_lines_threshold(spectrum, noise_factor=2)

print(lines)


s_exp.plot(lw=2, show_ruler=True)
import matplotlib.pyplot as plt

for line in lines.to_pandas().line_center.values:
    plt.axvline(line, color="r", zorder=-1)
s.plot(nfig="same")
plt.axvspan(noise_region.lower.value, noise_region.upper.value, color="b", alpha=0.1)

/home/docs/checkouts/readthedocs.org/user_builds/radis/conda/develop/lib/python3.14/site-packages/specutils/analysis/flux.py:289: AstropyUserWarning: Spectrum is not below the threshold signal-to-noise 0.01. This may indicate you have not continuum subtracted this spectrum (or that you have but it has high SNR features).

If you want to suppress this warning either type 'specutils.conf.do_continuum_function_check = False' or see http://docs.astropy.org/en/stable/config/#adding-new-configuration-items for other ways to configure the warning.
  warnings.warn(message, AstropyUserWarning)
   line_center     line_type  line_center_index
      1 / cm
------------------ ---------- -----------------
2000.7899999999993   emission                18
2001.3099999999988   emission                70
2002.0099999999982   emission               140
 2002.129999999998   emission               152
 2002.149999999998   emission               154
 2002.279999999998   emission               167
2002.4199999999978   emission               181
2002.7699999999975   emission               216
2002.9299999999973   emission               232
               ...        ...               ...
 2005.389999999995 absorption               478
2009.5999999999913 absorption               899
2014.9099999999864 absorption              1430
 2019.669999999982 absorption              1906
2021.3699999999806 absorption              2076
  2021.92999999998 absorption              2132
 2024.229999999978 absorption              2362
2025.7699999999766 absorption              2516
2026.6099999999758 absorption              2600
2026.6299999999758 absorption              2602
Length = 208 rows
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/develop/radis/tools/plot_tools.py:615: UserWarning: Couldn't add Ruler tool (still an experimental feature in RADIS : please report the error !)
  warn(

<matplotlib.patches.Rectangle object at 0x79deef78d450>

Note: we can also create a RADIS spectrum object from Specutils specutils.spectra.spectrum1d.Spectrum1D :

from radis import Spectrum

s2 = Spectrum.from_specutils(spectrum)

s2.plot(Iunit="mW/cm2/sr/nm", wunit="nm")
s_exp.plot(Iunit="mW/cm2/sr/nm", wunit="nm", nfig="same")
assert s_exp == s2