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.
Calculating Equilibrium Spectrum
Physical Conditions
----------------------------------------
   Tgas                 700 K
   isotope              1,2,3
   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
   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 0x7208578aea50>

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/master/radis/spectrum/spectrum.py:4372: 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/master/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/master/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/master/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/master/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
------------------ ---------- -----------------
2000.8899999999992   emission                28
 2001.019999999999   emission                41
 2001.119999999999   emission                51
2001.2999999999988   emission                69
2001.5299999999986   emission                92
2001.6899999999985   emission               108
2001.7699999999984   emission               116
2001.9399999999982   emission               133
2002.0199999999982   emission               141
               ...        ...               ...
2011.2199999999898 absorption              1061
2013.9799999999873 absorption              1337
 2014.299999999987 absorption              1369
2014.8199999999865 absorption              1421
2015.0899999999863 absorption              1448
2017.3399999999842 absorption              1673
 2017.469999999984 absorption              1686
2018.9999999999827 absorption              1839
2019.5599999999822 absorption              1895
2026.0199999999763 absorption              2541
Length = 290 rows
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/master/radis/tools/plot_tools.py:614: UserWarning: Couldn't add Ruler tool (still an experimental feature in RADIS : please report the error !)
  warn(

<matplotlib.patches.Rectangle object at 0x72085f1039d0>

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