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.
0.03s - 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
----------------------------------------
0.02s - Spectrum calculated

<matplotlib.lines.Line2D object at 0x73c594a9c1a0>

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/latest/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/latest/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/latest/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/latest/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/latest/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
------------------ ---------- -----------------
2000.9499999999991   emission                34
 2000.999999999999   emission                39
2001.3099999999988   emission                70
2001.4899999999986   emission                88
2001.5599999999986   emission                95
2001.8299999999983   emission               122
2001.8599999999983   emission               125
2001.9399999999982   emission               133
2002.0399999999981   emission               143
               ...        ...               ...
2010.0799999999908 absorption               947
2010.5299999999904 absorption               992
2012.4099999999887 absorption              1180
2015.0099999999863 absorption              1440
2015.0399999999863 absorption              1443
2015.0999999999863 absorption              1449
 2015.419999999986 absorption              1481
2019.4399999999823 absorption              1883
2019.5599999999822 absorption              1895
2021.6099999999803 absorption              2100
Length = 215 rows
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/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 0x73c58f51f750>

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