radis.spectrum.spectrum module¶

Summary¶

Spectrum class holder

Contains both the emission and absorption features calculated by a SpectrumFactory, or generated by another spectral code or an experiment and imported in RADIS. Allows use post-processing functions such as applying an instrumental slit, saving to disk, plot all spectral quantities with arbitrary units.

See the The Spectrum object for the list of all post-processing functions, how to save a Spectrum, or how to generate a Spectrum from text.

Examples

Typical use:

from radis calculated_spectrum
s = calculated_spectrum(w, I, conditions={'case':'previously calculated by ##'})
s.plot('radiance_noslit')
s.apply_slit(0.5, shape='triangular')
s.plot('radiance')

Spectrum objects can be modified, stored, resampled, rescaled, or retrieved after they have been created, with store(), rescale_path_length(), rescale_mole_fraction(), resample(), store(), load_spec()

from radis import load_spec
s = load_spec('co_calculation.spec')
s.rescale_path_length(0.5)                  # calculate for new path_length
s.rescale_mole_fraction(0.02)   # calculate for new mole fraction
s.resample(w_new)               # resample on new wavespace
s.store('co_calculation2.spec')

References

[Spectrum]

See the Spectrum object page

apply_slit(slit_function, unit='nm', shape: ['triangular', 'trapezoidal', 'gaussian'] = 'triangular', center_wavespace=None, norm_by='area', mode='valid', plot_slit=False, store=True, slit_dispersion=None, slit_dispersion_threshold=0.01, auto_recenter_crop=True, assert_evenly_spaced=True, verbose=True, inplace=True, *args, **kwargs)[source]¶

Apply an instrumental slit function to all quantities in Spectrum. Slit function can be generated with usual shapes (see shape=) or imported from an experimental slit function (path to a text file or numpy array of shape n*2). Convoluted spectra are cut on the edge compared to non-convoluted spectra, to remove side effects. See mode= to change this behaviour.

Warning with units: read about 'unit' and 'return_unit' parameters.

Parameters:

slit_function (float or str or array) –

If float:
generate slit function with FWHM of slit function (in nm or cm-1 depending on unit=). A (top, base) tuple of (float, float) is required when asking for a trapezoidal slit function.

If .txt:
import experimental slit function from .txt file: format must be 2-columns with wavelengths and intensity (doesn’t have to be normalized)

If array:
format must be 2-columns with wavelengths and intensity (doesn’t have to be normalized) It is recommended to truncate the input slit function to its minimum useful spectral extension (see Notes of convolve_with_slit()).
unit ('nm' or 'cm-1') – unit of slit_function (FWHM, or imported file)
shape ('triangular', 'trapezoidal', 'gaussian', or any of SLIT_SHAPES) –

which shape to use when generating a slit. Will call,
respectively, triangular_slit(), trapezoidal_slit(), gaussian_slit(). Default ‘triangular’
center_wavespace (float, or None) – center of slit when generated (in unit). Not used if slit is imported.
norm_by ('area', 'max') – normalisation type: - 'area' normalizes the slit function to an area

of 1. It conserves energy, and keeps the same units.
- 'max' normalizes the slit function to a maximum of 1. The convoluted spectrum units change (they are multiplied by the spectrum waveunit, e.g: a radiance non convoluted in mW/cm2/sr/nm on a wavelength (nm). range will yield a convoluted radiance in mW/cm2/sr. Note that the slit is set to 1 in the Spectrum wavespace (i.e: a Spectrum calculated in cm-1 will have a slit set to 1 in cm-1).
Default 'area'
mode ('valid', 'same') –

'same' returns output of same length as initial spectra,
but boundary effects are still visible. 'valid' returns output of length len(spectra) - len(slit) + 1, for which lines outside of the calculated range have no impact. Default 'valid'.

Other Parameters:

assert_evenly_spaced (boolean, or 'resample') – for the convolution to be accurate, w should be evenly spaced. If assert_evenly_spaced=True, then we check this is the case, and raise an error if arrays is not evenly spaced. If 'resample', then we resample w and I if needed. Recommended, but it takes some time.
auto_recenter_crop (bool) – if True, recenter slit and crop zeros on the side when importing an experimental slit. Default True. See recenter_slit(), crop_slit()
plot_slit (boolean) – if True, plot slit
store (boolean) – if True, store slit in the Spectrum object so it can be retrieved with get_slit() and plot with plot_slit(). Default True
slit_dispersion (func of (lambda, in 'nm'), or None) – spectrometer reciprocal function : dÎ»/dx(Î») (in nm) If not None, then the slit_dispersion function is used to correct the slit function for the whole range. Can be important if slit function was measured far from the measured spectrum (e.g: a slit function measured at 632.8 nm will look broader at 350 nm because the spectrometer dispersion is higher at 350 nm. Therefore it should be corrected) Default None

Warning

slit dispersion function is assumed to be given in nm if your spectrum is stored in cm-1 the wavenumbers are converted to wavelengths before being forwarded to the dispersion function

See test_auto_correct_dispersion() for an example of the slit dispersion effect.

A Python implementation of the slit dispersion:
```
>>> def f(lbd):
>>>    return  w/(2*f)*(tan(Î¦)+sqrt((2*d/m/(w*1e-9)*cos(Î¦))^2-1))
```
Theoretical / References:
```
>>> dÎ»/dx ~ d/mf    # at first order
>>> dÎ»/dx = w/(2*f)*(tan(Î¦)+sqrt((2*d/m/(w)*cos(Î¦))^2-1))  # cf
```
with:
- Î¦: spectrometer angle (Â°)
- f: focal length (mm)
- m: order of dispersion
- d: grooves spacing (mm) = 1/gr with gr in (gr/mm)
See Laux 1999 “Experimental study and modeling of infrared air plasma radiation” for more information
slit_dispersion_warning_threshold (float) – if not None, check that slit dispersion is about constant (< threshold change) on the calculated range. Default 0.01 (1%). See offset_dilate_slit_function()
inplace (bool) – if True, adds convolved arrays directly in the Spectrum. If False, returns a new Spectrum with only the convolved arrays. Note: if you want a new Spectrum with both the convolved and non convolved quantities, use
```
s.copy().apply_slit()
```
*args, **kwargs – are forwarded to slit generation or import function
verbose (bool) – print stuff
energy_threshold (float) – tolerance fraction when resampling. Default 1e-3 (0.1%) If areas before and after resampling differ by more than that an error is raised.

Returns:

Spectrum – Allows chaining. If inplace=False, return a new Spectrum with the new spectral arrays only.

Return type:

same Spectrum, with new spectral arrays.

Notes

Units:

the slit function is first converted to the wavespace (wavelength/wavenumber) that the Spectrum is stored in, and applied to the spectral quantities in their native wavespace.

Implementation:

convolve_with_slit() is applied to all quantities in get_vars() that ends with _noslit. Generate a triangular instrumental slit function (or any other shape depending of shape=) with base slit_function_base (Uses the central wavelength of the spectrum for the slit function generation)

We deal with several special cases (which makes the code a little heavy, but the method very versatile):

when slit unit and spectrum unit arent the same
when spectrum is not evenly spaced

Examples

s.apply_slit(1.2, 'nm')

This applies the instrumental function to all available spectral arrays. To manually apply the slit to a particular spectral array, use take()

s.take('transmittance_noslit').apply_slit(1.2, 'nm')

See convolve_with_slit() for more details on Units and Normalization

The slit is made considering the “center wavelength” which is the mean wavelength of the full spectrum you are applying it to.

Examples using `radis.Spectrum.apply_slit`¶

Line Survey

Calculate a spectrum from ExoMol

Calculate a full range spectrum

Calculate non-LTE spectra of carbon-monoxide

GPU Accelerated Spectra

GPU Accelerated Spectra (recalc_gpu() demo)

Example of using RADIS from Matlab

argmax(value_only=False)[source]¶

Return wave position of maximum of the Spectrum

Equivalent to the following use of the function max():

s.max(value_only=value_only, return_wmax=True)[1]

Chain Editing and Lineshape Fitting a Spectrum

See also

max()

argmin(value_only=False)[source]¶

Return wave position of minimum of the Spectrum

Equivalent to the following use of the function min():

s.min(value_only=value_only, return_wmin=True)[1]

See also

min()

c[source]¶

cite(format='bibentry')[source]¶

Prints bibliographic references used to compute this spectrum, as stored in the references dictionary. Default references known to RADIS are listed in radis.db.references.doi.

Parameters:: format (default 'bibentry'. See more in habanero.content_negotiation())

Examples

from radis import calc_spectrum
s = calc_spectrum(
    1900,
    2300,  # cm-1
    molecule="CO",
    isotope="1,2,3",
    pressure=1.01325,  # bar
    Tvib=2000,  #
    Trot=300,
    mole_fraction=0.1,
    path_length=1,  # cm
    databank="hitran",
)
s.cite()

Returns :

Used for algorithm
------------------
@article{van_den_Bekerom_2021,
    doi = {10.1016/j.jqsrt.2020.107476},
    url = {https://doi.org/10.1016%2Fj.jqsrt.2020.107476},
    year = 2021,
    month = {mar},
    publisher = {Elsevier {BV}},
    volume = {261},
    pages = {107476},
    author = {D.C.M. van den Bekerom and E. Pannier},
    title = {A discrete integral transform for rapid spectral synthesis},
    journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}
}

Used for calculation, rovibrational energies
--------------------------------------------
@article{Pannier_2019,
    doi = {10.1016/j.jqsrt.2018.09.027},
    url = {https://doi.org/10.1016%2Fj.jqsrt.2018.09.027},
    year = 2019,
    month = {jan},
    publisher = {Elsevier {BV}},
    volume = {222-223},
    pages = {12--25},
    author = {Erwan Pannier and Christophe O. Laux},
    title = {{RADIS}: A nonequilibrium line-by-line radiative code for {CO}2 and {HITRAN}-like database species},
    journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}
}

Used for data retrieval
-----------------------
@article{Ginsburg_2019,
    doi = {10.3847/1538-3881/aafc33},
    url = {https://doi.org/10.3847%2F1538-3881%2Faafc33},
    year = 2019,
    month = {feb},
    publisher = {American Astronomical Society},
    volume = {157},
    number = {3},
    pages = {98},
    author = {Adam Ginsburg and Brigitta M. Sip{\H{o}}cz and C. E. Brasseur and Philip S. Cowperthwaite and Matthew W. Craig and Christoph Deil and James Guillochon and Giannina Guzman and Simon Liedtke and Pey Lian Lim and Kelly E. Lockhart and Michael Mommert and Brett M. Morris and Henrik Norman and Madhura Parikh and Magnus V. Persson and Thomas P. Robitaille and Juan-Carlos Segovia and Leo P. Singer and Erik J. Tollerud and Miguel de Val-Borro and Ivan Valtchanov and Julien Woillez and},
    title = {astroquery: An Astronomical Web-querying Package in Python},
    journal = {The Astronomical Journal}
}

Used for line database
----------------------
@article{Gordon_2017,
    doi = {10.1016/j.jqsrt.2017.06.038},
    url = {https://doi.org/10.1016%2Fj.jqsrt.2017.06.038},
    year = 2017,
    month = {dec},
    publisher = {Elsevier {BV}},
    volume = {203},
    pages = {3--69},
    author = {I.E. Gordon and L.S. Rothman and C. Hill and R.V. Kochanov and Y. Tan and P.F. Bernath and M. Birk and V. Boudon and A. Campargue and K.V. Chance and B.J. Drouin and J.-M. Flaud and R.R. Gamache and J.T. Hodges and D. Jacquemart and V.I. Perevalov and A. Perrin and K.P. Shine and M.-A.H. Smith and J. Tennyson and G.C. Toon and H. Tran and V.G. Tyuterev and A. Barbe and A.G. Cs{\'{a}}sz{\'{a}}r and V.M. Devi and T. Furtenbacher and J.J. Harrison and J.-M. Hartmann and A. Jolly and T.J. Johnson and T. Karman and I. Kleiner and A.A. Kyuberis and J. Loos and O.M. Lyulin and S.T. Massie and S.N. Mikhailenko and N. Moazzen-Ahmadi and H.S.P. Müller and O.V. Naumenko and A.V. Nikitin and O.L. Polyansky and M. Rey and M. Rotger and S.W. Sharpe and K. Sung and E. Starikova and S.A. Tashkun and J. Vander Auwera and G. Wagner and J. Wilzewski and P. Wcis{\l}o and S. Yu and E.J. Zak},
    title = {The {HITRAN}2016 molecular spectroscopic database},
    journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}
}

Used for partition function
---------------------------
@article{Gamache_2021,
    doi = {10.1016/j.jqsrt.2021.107713},
    url = {https://doi.org/10.1016%2Fj.jqsrt.2021.107713},
    year = 2021,
    month = {sep},
    publisher = {Elsevier {BV}},
    volume = {271},
    pages = {107713},
    author = {Robert R. Gamache and Bastien Vispoel and Michaël Rey and Andrei Nikitin and Vladimir Tyuterev and Oleg Egorov and Iouli E. Gordon and Vincent Boudon},
    title = {Total internal partition sums for the {HITRAN}2020 database},
    journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}
}
@article{Kochanov_2016,
    doi = {10.1016/j.jqsrt.2016.03.005},
    url = {https://doi.org/10.1016%2Fj.jqsrt.2016.03.005},
    year = 2016,
    month = {jul},
    publisher = {Elsevier {BV}},
    volume = {177},
    pages = {15--30},
    author = {R.V. Kochanov and I.E. Gordon and L.S. Rothman and P. Wcis{\l}o and C. Hill and J.S. Wilzewski},
    title = {{HITRAN} Application Programming Interface ({HAPI}): A comprehensive approach to working with spectroscopic data},
    journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}
}

Used for spectroscopic constants
--------------------------------
@article{Guelachvili_1983,
    doi = {10.1016/0022-2852(83)90203-5},
    url = {https://doi.org/10.1016%2F0022-2852%2883%2990203-5},
    year = 1983,
    month = {mar},
    publisher = {Elsevier {BV}},
    volume = {98},
    number = {1},
    pages = {64--79},
    author = {G. Guelachvili and D. de Villeneuve and R. Farrenq and W. Urban and J. Verges},
    title = {Dunham coefficients for seven isotopic species of {CO}},
    journal = {Journal of Molecular Spectroscopy}
}

Other Examples¶

Cite all references used

See also

RefTracker, doi

compare_with(other, spectra_only=False, plot=True, wunit='default', verbose=True, rtol=1e-05, ignore_nan=False, ignore_outliers=False, normalize=False, **kwargs)[source]¶

Compare Spectrum with another Spectrum object.

Parameters:

other (type Spectrum) – another Spectrum to compare with
spectra_only (boolean, or str) – if True, only compares spectral quantities (in the same waveunit) and not lines or conditions. If str, compare a particular quantity name. If False, compare everything (including lines and conditions and populations). Default False
plot (boolean) – if True, use plot_diff to plot all quantities for the 2 spectra and the difference between them. Default True.
wunit ("nm", "cm-1", "default") – in which wavespace to compare (and plot). If "default", natural wavespace of first Spectrum is taken.
rtol (float) – relative difference to use for spectral quantities comparison
ignore_nan (boolean) – if True, nans are ignored when comparing spectral quantities
ignore_outliers (boolean, or float) –

if not False, outliers are discarded. i.e, output is determined by:
```
out = (~np.isclose(I, Ie, rtol=rtol, atol=0)).sum()/len(I) < ignore_outliers
```
normalize (bool) – Normalize the spectra to be plotted

Other Parameters:

kwargs (dict) – arguments are forwarded to plot_diff()

Returns:

equals – return True if spectra are equal (respective to tolerance defined by rtol and other input conditions)

Return type:

boolean

Examples

Compare two Spectrum objects, or specifically the transmittance:

s1.compare_with(s2)
s1.compare_with(s2, 'transmittance')

Note that you can also simply use s1 == s2, that uses compare_with() internally:

s1 == s2       # will return True or False

See also

compare_spectra()

cond_units[source]¶

conditions[source]¶

computation conditions, or experimental parameters, or any metadata you need to store with the Spectrum object.

Type:: dict

copy(copy_lines=True, quantity='all', copy_arrays=True)[source]¶

Returns a copy of this Spectrum object (performs a smart deepcopy)

Parameters:

copy_lines (bool) – default True
quantity (‘all’, or one of ‘radiance_noslit’, ‘absorbance’, etc.) – if not ‘all’, copy only one quantity. Default 'all'
copy_arrays (bool) – if False, returned array’s quantity is a pointer to the original Spectrum. Faster, but warning, changing them will then change the original Spectrum. Default True

Examples

crop(wmin=None, wmax=None, wunit='default', inplace=True)[source]¶

Crop spectrum to wmin-wmax range in wunit (inplace)

Parameters:

wmin, wmax (float, or None) – boundaries of spectral range (in wunit)
wunit ('nm', 'cm-1', 'nm_vac') – which waveunit to use for wmin, wmax. If default: use the default Spectrum wavespace defined with get_waveunit().

Other Parameters:

inplace (bool) – if True, modifies the Spectrum object directly. Else, returns a copy. Default True.

Returns:

s – Cropped Spectrum. If inplace=True, Spectrum has been updated directly anyway. Allows chaining

Return type:

Spectrum

Examples

Crop to experimental Spectrum, and compare:

from radis import calc_spectrum, load_spec, plot_diff
s = calc_spectrum(...)
s_exp = load_spec('typical_result.spec')
s.crop(s_exp.get_wavelength.min(), s_exp.get_wavelength.max(), 'nm')
plot_diff(s_exp, s)

Chain Editing and Lineshape Fitting a Spectrum

Load an experimental spectrum

See also

radis.spectrum.operations.crop()

file[source]¶

fit_model(model, plot=False, confidence=0.9545, verbose=False, debug=False)[source]¶

Fit a lineshape model to the spectrum.

The model can be a simple lineshape model among Gaussian1D, Lorentz1D, Voigt1D,

or a combination of multiple models.

Parameters:

model (astropy.modeling.Model or a list of models) – model to fit to the spectrum. If a list is given, a sum of models is fitted
plot (bool) – if True, plot the difference between the model and the spectrum

Other Parameters:

confidence (0.6827, 0.9545, or 0.9973) – confidence interval to use.

Returns:

g_fit – the fitted model
y_err – uncertainty on the fitted parameters calculated as the square root of the diagonal of the covariance matrix

Examples

from astropy.modeling import models
s = radis.test_spectrum().crop(2201.7, 2205.1)
g_fit, y_err = s.fit_model(models.Lorentz1D(), plot=True)

Example with 6 Voigt lines:

from astropy.modeling import models
s = radis.test_spectrum().crop(2201.7, 2225.1)
g_fit_list, y_err = s.fit_model([models.Voigt1D() for _ in range(6)], plot=True)

Other Examples¶

Chain Editing and Lineshape Fitting a Spectrum

Fit Multiple Voigt Lineshapes

classmethod from_array(w, I, quantity, wunit=None, Iunit=None, waveunit=None, unit=None, *args, **kwargs)[source]¶

Construct Spectrum from 2 arrays.

Parameters:

w, I (array) – waverange and vector
quantity (str) – spectral quantity name
wunit ('nm', 'cm-1', 'nm_vac') – unit of waverange: wavelength in air ('nm' or 'nm_air'), wavenumber ('cm-1'), or wavelength in vacuum ('nm_vac'). If None, then w must be a dimensioned array.
Iunit (str) – spectral quantity unit (arbitrary). Ex: 'mW/cm2/sr/nm' for radiance_noslit If None, then I must be a dimensioned array.
*args, **kwargs – see Spectrum doc

Other Parameters:

conditions (dict) – physical conditions and calculation parameters
cond_units (dict) – units for conditions
populations (dict) – a dictionary of all species, and levels. Should be compatible with other radiative codes such as Specair output. Suggested format: {molecules: {isotopes: {elec state: rovib levels}}} e.g:
```
{'CO2':{1: 'X': df}}   # with df a Pandas Dataframe
```
lines (pandas Dataframe) – all lines in databank (necessary for using line_survey()). Warning if you want to play with the lines content: The signification of columns in lines may be specific to a database format. Plus, some additional columns may have been added by the calculation (e.g: Ei and S for emission integral and linestrength in SpectrumFactory). Refer to the code to know what they mean (and their units)

Returns:

creates a Spectrum object

Return type:

Spectrum

Examples

Create a spectrum:

from radis import Spectrum
s = Spectrum.from_array(w, I, 'radiance_noslit',
                       wunit='nm', unit='mW/cm2/sr/nm')

Dimensioned arrays can also be used directly

import astropy.units as u
w = np.linspace(200, 300) * u.nm
I = np.random.rand(len(w)) * u.mW/u.cm**2/u.sr/u.nm
s = Spectrum.from_array(w, I, 'radiance_noslit')

To create a spectrum with absorption and emission components (e.g: radiance_noslit and transmittance_noslit, or emisscoeff and abscoeff) call the Spectrum class directly. Ex:

from radis import Spectrum
s = Spectrum({'abscoeff': (w, A), 'emisscoeff': (w, E)},
             units={'abscoeff': 'cm-1', 'emisscoeff':'W/cm2/sr/nm'},
             wunit='nm')

classmethod from_hdf5(file, wmin=None, wmax=None, wunit=None, columns=None, engine='pytables')[source]¶

Generates a Spectrum from an HDF5 file. Uses hdf2spec()

Other Parameters:

wmin, wmax (float) – range of wmin, wmax to load , using wunit (if None, load everything)
columns (list of str) – spectral arrays to load (if None, load everything)

Examples

Spectrum.from_hdf5("rad_hdf.h5", wmin=2100, wmax=2200, columns=['abscoeff', 'emisscoeff'])

See also

to_hdf5()

classmethod from_mat(file, quantity, wunit, unit, data_key=None, w_name='nu', I_name=None, index=None, *args, **kwargs)[source]¶

Construct Spectrum from Matlab .mat file.

Parameters:

file (str) – file name
quantity (str) – spectral quantity name
wunit ('nm', 'cm-1', 'nm_vac') – unit of waverange: wavelength in air ('nm'), wavenumber ('cm-1'), or wavelength in vacuum ('nm_vac').
unit (str) – spectral quantity unit
index (int) – index within Matlab .mat array.
data_key (str) – data key to use within Matlab .mat array. If None, guess.
w_name, I_name (str) – key to use to parse the data[data_key] array and return waverange and quantity.
*args, **kwargs – the following inputs are forwarded to loadmat(): 'simplify_cells', 'skiprows' The rest if forwarded to Spectrum and will be registered as a Spectrum condition. see Spectrum doc

Returns:

s – creates a Spectrum object

Return type:

Spectrum

Examples

Chain Editing and Lineshape Fitting a Spectrum

Fit Multiple Voigt Lineshapes

Notes

Internally, the scipy loadmat() function is used and corresponds to

data = scipy.io.loadmat(file, **kwloadmat)
data = data[data_key]
w, I = data[w_name], data[I_name]

Special keywords can be given to kwloadmat. See docs of kwargs.

See also

from_array(), load_spec()

classmethod from_spec(file)[source]¶: Generates a Spectrum from a .spec [json] file. Uses load_spec()

classmethod from_specutils(spectrum, var='radiance')[source]¶

Convert a specutils Spectrum1D to a radis Spectrum object.

Parameters:

spectrum (a specutils specutils.spectra.spectrum1d.Spectrum1D)
var (str) – spectral array, default "radiance"

Examples

Taken from the Specutils website (https://specutils.readthedocs.io/en/stable/#getting-started-with-specutils)

from astropy.io import fits
from astropy import units as u
from specutils import Spectrum1D

f = fits.open('https://data.sdss.org/sas/dr16/sdss/spectro/redux/26/spectra/1323/spec-1323-52797-0012.fits')
# The spectrum is in the second HDU of this file.
specdata = f[1].data

lamb = 10**specdata['loglam'] * u.AA
flux = specdata['flux'] * 10**-17 * u.Unit('erg cm-2 s-1 AA-1')
spec = Spectrum1D(spectral_axis=lamb, flux=flux)

from radis import Spectrum
s = Spectrum.from_specutils(spec)
s.plot(wunit='nm')

Post-process using Specutils

See also

to_specutils()

classmethod from_txt(file, quantity, wunit, unit, waveunit=None, *args, **kwargs)[source]¶

Construct Spectrum from txt file.

Parameters:

file (str) – file name
quantity (str) – spectral quantity name
wunit ('nm', 'cm-1', 'nm_vac') – unit of waverange: wavelength in air ('nm'), wavenumber ('cm-1'), or wavelength in vacuum ('nm_vac').
unit (str) – spectral quantity unit
*args, **kwargs – the following inputs are forwarded to loadtxt: 'delimiter', 'skiprows' The rest if forwarded to Spectrum. see Spectrum doc

Other Parameters:

delimiter (',', etc.) – see numpy.loadtxt()
skiprows (int) – see numpy.loadtxt()
argsort (bool) – sorts the arrays in file by wavespace. Convenient way to load a file where points have been manually added at the end. Default False.
*Optional Spectrum parameters*
conditions (dict) – physical conditions and calculation parameters
cond_units (dict) – units for conditions
populations (dict) – a dictionary of all species, and levels. Should be compatible with other radiative codes such as Specair output. Suggested format: {molecules: {isotopes: {elec state: rovib levels}}} e.g:
```
{'CO2':{1: 'X': df}}   # with df a Pandas Dataframe
```
lines (pandas Dataframe) – all lines in databank (necessary for using line_survey()). Warning if you want to play with the lines content: The signification of columns in lines may be specific to a database format. Plus, some additional columns may have been added by the calculation (e.g: Ei and S for emission integral and linestrength in SpectrumFactory). Refer to the code to know what they mean (and their units)

Returns:

s – creates a Spectrum object

Return type:

Spectrum

Examples

Generate an experimental spectrum from txt. In that example the delimiter key is forwarded to loadtxt():

from radis import Spectrum
s = Spectrum.from_txt('spectrum.csv', 'radiance', wunit='nm',
                          unit='W/cm2/sr/nm', delimiter=',')

To create a spectrum with absorption and emission components (e.g: radiance_noslit and transmittance_noslit, or emisscoeff and abscoeff) call the Spectrum class directly. Ex:

from radis import Spectrum
s = Spectrum({'abscoeff': (w, A), 'emisscoeff': (w, E)},
             units={'abscoeff': 'cm-1', 'emisscoeff':'W/cm2/sr/nm'},
             wunit='nm')

Notes

Internally, the numpy loadtxt() function is used and transposed:

w, I = np.loadtxt(file).T

You can use 'delimiter' and ‘skiprows' as arguments.

generate_perf_profile()[source]¶

Generate a visual/interactive performance profile diagram using tuna

Note

requires a profiler key with in Spectrum.conditions

Warning

deprecated in favor of print_perf_profile()

Examples

s = calc_spectrum(...)
s.generate_perf_profile()

See typical output in https://github.com/radis/radis/pull/325

https://user-images.githubusercontent.com/16088743/128018032-6049be72-1881-46ac-9d7c-1ed89f9c4f42.png

Note

You can also profile with tuna directly:

python -m cProfile -o program.prof your_radis_script.py
tuna your_radis_script.py

See also

print_perf_profile()

get(var: ['abscoeff', 'absorbance', 'emissivity_noslit', 'transmittance_noslit', 'radiance_noslit'], wunit='default', Iunit='default', copy=True, trim_nan=False, return_units=False)[source]¶

Retrieve a spectral quantity from a Spectrum object. You can select wavespace unit, intensity unit, or propagation medium.

Parameters:

var (variable ('absorbance', 'transmittance', 'xsection' etc.)) – Should be a defined quantity among CONVOLUTED_QUANTITIES or NON_CONVOLUTED_QUANTITIES. To get the full list of spectral arrays defined in this Spectrum object use the get_vars() method.
wunit ('nm', 'cm', 'nm_vac'.) – wavespace unit: wavelength in air ('nm'), wavenumber ('cm-1'), or wavelength in vacuum ('nm_vac'). if "default", default unit for waveunit is used. See get_waveunit().
Iunit (unit for variable var) – if "default", default unit for quantity var is used. See the units attribute. For var="radiance", one can use per wavelength (~ ‘W/m2/sr/nm’) or per wavenumber (~ ‘W/m2/sr/cm-1’) units

Note

if using default, the returned unit may be different from Spectrum.units[var]. e.g, for a Spectrum with radiance stored in ‘mW/cm2/sr/nm’, getting it with wunit='cm-1', Iunit='default' will return Iunit in ‘mW/cm2/sr/cm-1’ for consistency. Use return_units to be sure about which units are used.

Other Parameters:

copy (bool) – if True, returns a copy of the stored quantity (modifying it wont change the Spectrum object). Default True.
trim_nan (bool) – if True, removes nan on the sides of the spectral array (and corresponding wavespace). Default False.
return_units (bool) – if True, return dimensioned Astropy arrays. Is using return_units = 'as_str', return wunit and Iunit as extra variables, i.e, w, I, wunit, Iunit = s.get(..., return_units='as_str') Default False

Returns:

w, I – wavespace, quantity (ex: wavelength, radiance_noslit). For numpy users, note that these are copies (values) of the Spectrum quantity and not a view (reference): if you modify them the Spectrum is not changed

Return type:

array-like

Examples

Get transmittance in cm-1:

w, I = s.get('transmittance_noslit', wunit='cm-1')

Get radiance (in wavelength in air):

_, R = s.get('radiance_noslit', wunit='nm', Iunit='W/cm2/sr/nm')

Use with return_units to get dimensioned Astropy Quantities

w, R  = s.get('radiance_noslit', return_units=True)

get_baseline(algorithm='als', **kwargs)[source]¶

Calculate and returns a baseline

Parameters:

s (Spectrum) – Spectrum which needs a baseline
var (str) – on which spectral quantity to read the baseline. Default 'radiance'. See SPECTRAL_QUANTITIES
algorithm (‘als’, ‘polynomial’) – Asymmetric least square or Polynomial fit
**kwargs (dict) – additional parameters to send to the algorithm. By default, for ‘polynomial’:

**kwargs = **{“deg”: 1, “max_it”:500}

for ‘als’:

**kwargs = {“asymmetry_param”: 0.05,
“smoothness_param”: 1e6}

Returns:

baseline – Spectrum object where intensity is the baseline of s

Return type:

Spectrum

Examples

Remove a baseline

See also

get_baseline()

get_conditions()[source]¶: Get all physical / computational parameters.

See also

print_conditions(), the Spectrum page

get_integral(var, wunit='default', Iunit='default', **kwargs)[source]¶

Returns integral of variable ‘var’ over waverange.

Parameters:

var (str) – spectral quantity to integrate
wunit (str) – over which waverange to integrated. If default, use the default Spectrum wavespace defined with get_waveunit().
Iunit (str) – default 'default'

Warning

this is the unit of the quantity, not the unit of the integral. Don’t forget to multiply by wunit

Other Parameters:

kwargs (**dict) – forwarded to get()

Returns:

integral – integral in [Iunit]*[wunit]

Return type:

float

See also

get_power(), the Spectrum page

get_name()[source]¶

Return Spectrum name.

If not defined, returns either the file name if Spectrum was loaded from a file, or the 'spectrum{id}' with the Python id object

get_populations(molecule=None, isotope=None, electronic_state=None, show_warning=True)[source]¶

Return populations that are featured in the spectrum, either as upper or lower levels.

Parameters:

molecule (str, or None) – if None, only one molecule must be defined. Else, an error is raised
isotope (int, or None) – isotope number. if None, only one isotope must be defined. Else, an error is raised
electronic_state (str) – if None, only one electronic state must be defined. Else, an error is raised
show_warning (bool) – if False, turns off warning about meaning of populations, see Notes and discussion on https://github.com/radis/radis/issues/508.

Returns:

pandas dataframe of levels, where levels are the index,
and ‘Evib’ and ‘nvib’ are featured

Notes

Structure:

{molecule: {isotope: {electronic_state: {'vib': pandas Dataframe,    # (copy of) vib levels
                                         'rovib': pandas Dataframe,  # (copy of) rovib levels
                                         'Ia': float    # isotopic abundance
                                         }}}}

(If Spectrum generated with RADIS, structure should match that of SpectrumFactory.get_populations())

Examples

An example on how different are populations used for partition function and spectrum calculations

#%% CO2 example
# For instance, plot populations of a given vibrational level, v1,v2,v3=(0,1,0)
import radis
s = radis.test_spectrum(molecule="CO2", Tvib=3000, Trot=1000,
                        export_lines=True,
                        export_populations="rovib",
                        isotope=1)
pops = s.get_populations("CO2")["rovib"]

import matplotlib.pyplot as plt
pops.query("v1==0 & v2==1 & v3==0").plot("j", "n",
                                         label="pops. used to compute partition functions")
s.lines.query("v1l==0 & v2l==1 & v3l==0").plot("jl", "nl", ax=plt.gca(), kind="scatter", color="r",
                                               label="pops. of visible absorbing lines")
plt.legend()
plt.xlim((0,70))

See populations of computed levels

See also

plot_populations(), line_survey()

get_power(unit='mW/cm2/sr')[source]¶

Returns integrated radiance (no slit) power density.

Parameters:: Iunit (str) – power unit.
Returns:: P – radiated power in unit
Return type:: float

Examples

s.get_power('W/cm2/sr')

See also

get_integral(), the Spectrum page

get_quantities(which=None)[source]¶: Returns all spectral quantities stored in this object (convoluted or non convoluted). Wrapper to get_vars()

get_radiance(Iunit='mW/cm2/sr/nm', copy=True)[source]¶

Return radiance in whatever unit, and can even convert from ~1/nm to ~1/cm-1 (and the other way round)

Other Parameters:: copy (boolean) – if True, returns a copy of the stored waverange (modifying it wont change the Spectrum object). Default True.

get_radiance_noslit(Iunit='mW/cm2/sr/nm', copy=True)[source]¶

Return radiance (non convoluted) in whatever unit, and can even convert from ~1/nm to ~1/cm-1 (and the other way round)

Other Parameters:: copy (boolean) – if True, returns a copy of the stored waverange (modifying it wont change the Spectrum object). Default True.

get_rovib_levels(molecule=None, isotope=None, electronic_state=None, first=None)[source]¶

Return rovibrational levels calculated in the spectrum (energies, populations)

Parameters:

molecule (str, or None) – if None, only one molecule must be defined. Else, an error is raised
isotope (int, or None) – isotope number. if None, only one isotope must be defined. Else, an error is raised
electronic_state (str) – if None, only one electronic state must be defined. Else, an error is raised
first (int, or ‘all’ or None) – only show the first N levels. If None or ‘all’, all levels are shown

Returns:

out – pandas dataframe of levels, where levels are the index, and ‘Evib’ and ‘nvib’ are featured

Return type:

pandas DataFrame

get_slit(wunit='same')[source]¶

Get slit function that was applied to the Spectrum.

Returns:: wslit, Islit – slit function with wslit in Spectrum waveunit. See get_waveunit()
Return type:: array

get_vars(which=None)[source]¶: Returns all spectral quantities stored in this object (convoluted or non convoluted)

get_vib_levels(molecule=None, isotope=None, electronic_state=None, first=None)[source]¶

Return vibrational levels in the spectrum (energies, populations)

Parameters:

molecule (str, or None) – if None, only one molecule must be defined. Else, an error is raised
isotope (int, or None) – isotope number. if None, only one isotope must be defined. Else, an error is raised
electronic_state (str) – if None, only one electronic state must be defined. Else, an error is raised
first (int, or ‘all’ or None) – only show the first N levels. If None or ‘all’, all levels are shown

Returns:

out – pandas dataframe of levels, where levels are the index, and ‘Evib’ and ‘nvib’ are featured

Return type:

pandas DataFrame

get_wavelength(medium='air', which=None, copy=True)[source]¶

Return wavelength in defined medium.

Parameters:: medium ('air', 'vacuum') – returns wavelength as seen in air, or vacuum. Default 'air'. See vacuum2air(), air2vacuum()
Other Parameters:: copy (boolean) – if True, returns a copy of the stored waverange (modifying it wont change the Spectrum object). Default True.
Returns:: w – (a copy of) spectrum wavelength for convoluted or non convoluted quantities
Return type:: array_like

See also

the Spectrum page

get_wavenumber(which=None, copy=True)[source]¶

Return wavenumber (if the same for all quantities)

Other Parameters:: copy (boolean) – if True, returns a copy of the stored waverange (modifying it wont change the Spectrum object). Default True.
Returns:: w – (a copy of) spectrum wavenumber for convoluted or non convoluted quantities
Return type:: array_like

get_waveunit()[source]¶: Returns whether this spectrum is defined in wavelength (nm) or wavenumber (cm-1)

has_nan(ignore_wavespace=True) → bool[source]¶

Parameters:: s (Spectrum) – radis Spectrum.
Returns:: b – returns whether Spectrum has nan
Return type:: bool

Note

print(s) will also show which spectral quantities have ````nan.

is_at_equilibrium(check='warn', verbose=False)[source]¶

Returns whether this spectrum is at (thermal) equilibrium. Reads the thermal_equilibrium key in Spectrum conditions. It does not imply chemical equilibrium (mole fractions are still arbitrary)

If they are defined, also check that the following assertions are True:

Tvib = Trot = Tgas self_absorption = True overpopulation = None

If they are not, still trust the value in Spectrum conditions, but raise a warning.

Other Parameters:

check ('warn', 'error', 'ignore') – what to do if Spectrum conditions dont match the given equilibrium state: raise a warning, raise an error, or just ignore and dont even check. Default 'warn'.
verbose (bool) – if True, print why is the spectrum is not at equilibrium, if applicable.

is_optically_thin()[source]¶

Returns whether the spectrum is optically thin, based on the value on the self_absorption key in conditions.

If not given, raises an error

line_survey(overlay=None, wunit='cm-1', Iunit='hitran', medium='air', cutoff=None, plot='S', lineinfo=['int', 'A', 'El'], barwidth='hwhm_voigt', yscale='log', writefile=None, *args, **kwargs)[source]¶

Plot Line Survey (all linestrengths used for calculation) Output in: Plotly (html)

Parameters:

overlay (tuple (w, I, [name], [units]), or list or tuples) – plot (w, I) on a secondary axis. Useful to compare linestrength with calculated / measured data:
```
LineSurvey(overlay='abscoeff')
```
wunit ('nm', 'cm-1') – wavelength / wavenumber units
Iunit ('hitran', 'splot') – Linestrength output units:
- 'hitran': (cm-1/(molecule/cm-2))
- 'splot' : (cm-1/atm) (Spectraplot units [2])
Note: if not None, cutoff criteria is applied in this unit. Not used if plot is not ‘S’
medium ('air', 'vacuum') – show wavelength either in air or vacuum. Default 'air'
plot (str) – what to plot. Default 'S' (scaled line intensity). But it can be any key in the lines, such as population ('nu'), or Einstein coefficient ('A')
lineinfo (list, or 'all') – extra line information to plot. Should be a column name in the databank (s.lines). For instance: 'int', 'selbrd', etc… Default ['int']

Other Parameters:

writefile (str) – if not None, a valid filename to save the plot under .html format.
If None, use the fig object returned to show the plot.
- yscale ('log', 'linear') – Default 'log'
- barwidth (float or str) –
  
  if float, width of bars, in wunit, as a fraction of full-range; i.e.
  barwidth=0.01
  makes bars span 1% of the full range. if str, uses the column as width. Example
  barwidth = 'hwhm_voigt'
  returns:
  
  fig (a Plotly figure.) – If using a Jupyter Notebook, the plot will appear. Else, use writefile to export to an html file.
  
  Plot in Plotly. See Output in [1]_

An example using the SpectrumFactory to generate a spectrum:

from radis import SpectrumFactory
sf = SpectrumFactory(
                     wavenum_min=2380,
                     wavenum_max=2400,
                     mole_fraction=400e-6,
                     path_length=100,  # cm
                     isotope=[1],
                     export_lines=True,    # required for LineSurvey!
                     db_use_cached=True)
sf.load_databank('HITRAN-CO2-TEST')
s = sf.eq_spectrum(Tgas=1500)
s.apply_slit(0.5)
s.line_survey(overlay='radiance_noslit', barwidth=0.01, lineinfo="all")  # or barwidth='hwhm_voigt'

See the output in Examples

Line Survey

LineSurvey(), the Spectrum page

lines[source]¶

informations on emitting or absorbing lines that contribute to the spectrum.

Other Examples¶

Get max position wmax

s = radis.test_spectrum()
max, wmax = s.max(return_wmax=True)

Note that the later can also be achieved with argmax()

wmax = s.argmax()

Chain Editing and Lineshape Fitting a Spectrum

Post-process using Specutils

See also

argmax()

min(value_only=True, return_wmin=False)[source]¶

Minimum of the Spectrum, if only one spectral quantity is available

s.min()

Returns a dimensioned quantity by default, with the default unit of the spectrum. If value_only=False, a float is returned, without dimensions.

If there are multiple arrays in your Spectrum, use take(), e.g.

s.take('radiance').min()

Other Examples¶

Get min position wmin

s = radis.test_spectrum()
min, wmin = s.min(return_wmin=True)

Note that the later can also be achieved with argmin()

wmax = s.argmin()

See also

argmin()

name[source]¶

normalize(normalize_how='max', wrange=(), wunit=None, inplace=False, force=False, verbose=False, return_norm=False)[source]¶

Normalise the Spectrum, if only one spectral quantity is available.

Parameters:

normalize_how ('max', 'area', 'mean') – how to normalize. 'max' is the default but may not be suited for very noisy experimental spectra. 'area' will normalize the integral to 1. 'mean' will normalize by the mean amplitude value
wrange (tuple of floats, float) – normalize on this range if a tuple, else normalise at that point. If an empty tuple, use the entire range.
wunit ("nm", "cm-1", "nm_vac") – unit of the normalisation range above. If None, use the spectrum default waveunit.
inplace (bool) – if True, changes the Spectrum.

Other Parameters:

force (boolean) – By default, normalizing some parameters such as transmittance is forbidden because considered non-physical. Use force=True if you really want to.

Examples

s.normalize("max", (4200, 4800), inplace=True).plot()

If there are multiple arrays in your Spectrum, use take(), e.g.

s.take('radiance').normalize(wrange=(4200, 4800)).plot()

offset(offset: Spectrum, unit: float, inplace: str = True) → Spectrum[source]¶

Offset the spectrum by a wavelength or wavenumber (inplace)

Parameters:

offset (float) – Constant to add to all quantities in the Spectrum.
unit (‘nm’ or ‘cm-1’) – unit for offset

Other Parameters:

inplace (bool) – if True, modifies the Spectrum object directly. Else, returns a copy. Default True.

Returns:

s – Offset Spectrum. If inplace=True, Spectrum has been updated directly anyway. Allows chaining.

Return type:

Spectrum

Examples

s.offset(5, 'nm')

plot(var: ['abscoeff', 'absorbance', 'emissivity_noslit', 'transmittance_noslit', 'radiance_noslit'] = None, wunit='default', Iunit='default', show_points=False, nfig=None, yscale='linear', show_medium='vacuum_only', normalize=False, force=False, plot_by_parts=False, show=True, show_ruler=False, **kwargs)[source]¶

Plot a Spectrum object.

Note

default plotting library and templates can be edited in radis.config [“plot”]

Parameters:

var (variable (absorbance, transmittance, transmittance_noslit, xsection, etc.)) – For full list see get_vars(). If None, plot the first thing in the Spectrum. Default None.
wunit ('default', 'nm', 'cm-1', 'nm_vac',) – wavelength air, wavenumber, or wavelength vacuum. If 'default', Spectrum get_waveunit() is used.
Iunit (unit for variable) – if default, default unit for quantity var is used. for radiance, one can use per wavelength (~ W/m2/sr/nm) or per wavenumber (~ W/m2/sr/cm-1) units

Other Parameters:

show_points (boolean) – show calculated points. Default True.
nfig (int, None, or ‘same’) – plot on a particular figure. ‘same’ plots on current figure. For instance:
```
s1.plot()
s2.plot(nfig='same')
```
show_medium (bool, 'vacuum_only') – if True and wunit are wavelengths, plot the propagation medium in the xaxis label ([air] or [vacuum]). If 'vacuum_only', plot only if wunit=='nm_vac'. Default 'vacuum_only' (prevents from inadvertently plotting spectra with different propagation medium on the same graph).
yscale (‘linear’, ‘log’) – plot yscale
normalize (boolean, or tuple.) – option to normalize quantity to 1 (ex: for radiance). Default False
plot_by_parts (bool) – if True, look for discontinuities in the wavespace and plot the different parts without connecting lines. Useful for experimental spectra produced by overlapping step-and-glue. Additional parameters read from kwargs : split_threshold and cutwings. See more in split_and_plot_by_parts().
force (bool) – plotting on an existing figure is forbidden if labels are not the same. Use force=True to ignore that.
show (bool) – show figure. Default False. Will still show the figure in interactive mode, e.g, %matplotlib inline in a Notebook.
show_ruler (bool) – if True, add a ruler tool to the Matplotlib toolbar. Convenient to measure distances between peaks, etc.

Warning

still experimental ! Try it, feedback welcome !
**kwargs (**dict) – kwargs forwarded as argument to plot (e.g: lineshape attributes: lw=3, color='r')

Returns:

line plot

Return type:

line

Examples

Plot an experimental_spectrum() in arbitrary units:

s = experimental_spectrum(..., Iunit='mW/cm2/sr/nm')
s.plot(Iunit='W/cm2/sr/cm-1')

See more examples in the plot Spectral quantities page.

Atomic spectrum #1: Partition functions and potential lowering

Calculate a spectrum from ExoMol

Calculate a full range spectrum

Calculate a large spectrum by part

Calculate non-LTE spectra of carbon-monoxide

Chain Editing and Lineshape Fitting a Spectrum

Load an experimental spectrum

Remove a baseline

Post-process using Specutils

Example #3: non-equilibrium spectrum (Tvib, Trot, x_CO)

GPU Accelerated Spectra (recalc_gpu() demo)

Use different plot themes

See also

plot_diff(), the Spectrum page

plot_populations(what=None, nunit='', correct_for_abundance=False, **kwargs)[source]¶

Plots vib populations if given and format is valid.

Parameters:

what (‘vib’, ‘rovib’, None) – if None plot everything
nunit (‘’, ‘cm-3’) – plot either in a fraction of vibrational levels, or a molecule number in in cm-3
correct_for_abundance (boolean) – if True, multiplies each population by the isotopic abundance (as it is done during the calculation of emission integral)
kwargs (**dict) – are forwarded to the plot

Examples

See populations of computed levels

See also

get_populations(), line_survey()

plot_slit(wunit=None, waveunit=None)[source]¶

Plot slit function that was applied to the Spectrum.

If dispersion was used (see apply_slit()) the different slits are built again and plotted too (dotted).

Parameters:: wunit ('nm', 'cm-1', or None) – plot slit in wavelength or wavenumber. If None, use the unit the slit in which the slit function was given. Default None
Returns:: fix, ax – figure and ax
Return type:: matplotlib objects

Examples

s = radis.test_spectrum()
s.apply_slit((0.4, 0.6), "nm")  # add trapezoidal slit function
s.plot_slit()   # plot the slit function that was applied

See also

the Spectrum page

populations[source]¶

populations of rovibrational levels used to compute partition functions of the spectrum

print_conditions(**kwargs)[source]¶

Prints all physical / computational parameters.

Parameters:: kwargs (dict) – refer to print_conditions()

Examples

s = radis.test_spectrum()
s.print_conditions()

You can also simply print the Spectrum object directly:

s = radis.test_spectrum()
print(s)

Both syntaxes above will return (in radis==0.15):

# output >>

    Spectrum Name:  CO-hitran-700K-#3680
    Spectral Quantities
    ----------------------------------------
       abscoeff     [cm-1]  (40,002 points)
       absorbance   (40,002 points)
       emissivity_noslit    (40,002 points)
       transmittance_noslit         (40,002 points)
       radiance_noslit      [mW/cm2/sr/cm-1]        (40,002 points)
    Physical Conditions
    ----------------------------------------
       Tgas                 700 K
       Trot                 700 K
       Tvib                 700 K
       isotope              1,2,3
       mole_fraction        0.1
       molecule             CO
       overpopulation       None
       path_length          1 cm
       pressure_mbar        1013.25 mbar
       rot_distribution     boltzmann
       self_absorption      True
       state                X
       thermal_equilibrium  True
       vib_distribution     boltzmann
       wavenum_max          2300.0000 cm-1
       wavenum_min          1900.0000 cm-1
    Computation Parameters
    ----------------------------------------
       NwG                  3
       NwL                  5
       Tref                 296 K
       broadening_method    voigt
       cutoff               1e-27 cm-1/(#.cm-2)
       dbformat             hitran
       dbpath               C:\Users\erwan\.radisdb\hitran\CO.hdf5
       default_output_unit  cm-1
       diluents             {'air': 0.9}
       folding_thresh       1e-06
       include_neighbouring_lines  True
       memory_mapping_engine  auto
       neighbour_lines      0 cm-1
       optimization         simple
       parfuncfmt           hapi
       parsum_mode          full summation
       profiler             {'spectrum_calculation': {'check_line_databank': ...
       pseudo_continuum_threshold  0
       radis_version        0.14
       sparse_ldm           True
       spectral_points      40000.0
       truncation           50 cm-1
       waveunit             cm-1
       wstep                0.01 cm-1
       zero_padding         40002
    Config parameters
    ----------------------------------------
       DEFAULT_DOWNLOAD_PATH  ~/.radisdb
       GRIDPOINTS_PER_LINEWIDTH_ERROR_THRESHOLD  1
       GRIDPOINTS_PER_LINEWIDTH_WARN_THRESHOLD  3
       SPARSE_WAVERANGE     auto
    Information
    ----------------------------------------
       calculation_time     0.11549490000000162 s
       chunksize            None
       db_use_cached        True
       dxG                  0.1375350788016573
       dxL                  0.20180288881201608
       export_lines         False
       export_populations   None
       export_rovib_fraction  True
       levelsfmt            None
       lines_calculated     742
       lines_cutoff         0
       lines_in_continuum   0
       load_energies        False
       lvl_use_cached       True
       parfuncpath          None
       total_lines          742
       warning_broadening_threshold  0.01
       warning_linestrength_cutoff  0.01
       wavenum_max_calc     2300.0000 cm-1
       wavenum_min_calc     1900.0000 cm-1
    ----------------------------------------

print_perf_profile(number_format='{:.3f}', precision=16)[source]¶

Prints Profiler output dictionary in a structured manner.

Example

Spectrum.print_perf_profile()

# output >>
    spectrum_calculation      0.189s ████████████████
        check_line_databank              0.000s
        check_non_eq_param               0.042s ███
        fetch_energy_5                   0.015s █
        calc_weight_trans                0.008s
        reinitialize                     0.002s
            copy_database                    0.000s
            memory_usage_warning             0.002s
            reset_population                 0.000s
        calc_noneq_population            0.041s ███
            part_function                    0.035s ██
            population                       0.006s
        scaled_non_eq_linestrength       0.005s
            map_part_func                    0.001s
            corrected_population_se          0.003s
        calc_emission_integral           0.006s
        applied_linestrength_cutoff      0.002s
        calc_lineshift                   0.001s
        calc_hwhm                        0.007s
        generate_wavenumber_arrays       0.001s
        calc_line_broadening             0.074s ██████
            precompute_LDM_lineshapes        0.012s
            LDM_Initialized_vectors          0.000s
            LDM_closest_matching_line        0.001s
            LDM_Distribute_lines             0.001s
            LDM_convolve                     0.060s █████
            others                           0.001s
        calc_other_spectral_quan         0.003s
        generate_spectrum_obj            0.000s
        others                           -0.016s

Other Parameters:: precision (int, optional) – total number of blocks. Default 16.

See also

generate_perf_profile()

recalc_gpu(var='abscoeff', wunit='default', Iunit='default', pressure=None, Tgas=None, mole_fraction=None, path_length=None, slit_function=None)[source]¶

Recalculate the spectrum based on new input parameters. Can only be called for spectrum objects produced by eq_spectrum_gpu(). This method is used internally by eq_spectrum_gpu_interactive(). Parameters may be passed as arguments, or updated directly in conditions, after which spectrum.recalc_gpu() may be called without passing arguments.

Parameters:

var (variable (absorbance, transmittance, transmittance_noslit, xsection, etc.)) – For full list see get_vars(). If None, plot the first thing in the Spectrum. Default None.
wunit ('nm', 'cm-1', 'nm_vac' or None) – wavelength in air ('nm'), wavenumber ('cm-1'), or wavelength in vacuum ('nm_vac'). If None, 'wavespace' must be defined in conditions.
Iunit (unit for variable) – if default, default unit for quantity var is used. for radiance, one can use per wavelength (~ W/m2/sr/nm) or per wavenumber (~ W/m2/sr/cm-1) units
pressure (float, optional) – Pressure in [bar]
Tgas (float, optional) – Equilibrium temperature in [K]
mole_fraction (float, optional) – Mole fraction
path_length (float, optional) – Absroption length in [cm]
slit_function (float, optional) – Slit FWHM in [cm-1]

Returns:

new_y – The recalculated array specified by the var keyword.

Return type:

numpy.ndarray[np.fltoat32]

Examples

s = sf.eq_spectrum_gpu(
    Tgas=1100.0,  # K
    pressure=1,  # bar
    mole_fraction=0.8,
    path_length=0.2,  # cm
)

I = []
for T in [300.0, 1000.0, 2000.0]:
    I.append(s.recalc_gpu('radiance', Tgas=T)

references[source]¶

resample(w_new, unit='same', out_of_bounds='nan', energy_threshold='default', print_conservation=False, inplace=True, if_conflict_drop=None, **kwargs)[source]¶

Resample spectrum over a new wavelength/wavenumber range.

Warning

This may result in information loss. Resampling is done with oversampling and spline interpolation. These parameters can be adjusted, and energy conservation ensured with the appropriate parameters.

To minimize information loss, always resample the high-resolution spectrum over the low-resolution spectrum, i.e.

s_highres.resample(s_lowres)

Fills with 'nan' or transparent medium (transmittance 1, radiance 0) when out of bound (see out_of_bounds)

Parameters:

w_new (array, or Spectrum) – new wavespace to resample the spectrum on. Must be inclosed in the current wavespace (we won’t extrapolate) One can also give a Spectrum directly:
```
s1.resample(s2.get_wavenumber())
s1.resample(s2)            # also valid
```
unit ('same', 'nm', 'cm-1', 'nm_vac') – unit of new wavespace. It 'same' it is assumed to be the current waveunit. Default 'same'. The spectrum waveunit is changed to this unit after resampling (i.e: a spectrum calculated and stored in cm-1 but resampled in nm will be stored in nm from now on). If 'nm', wavelength in air. If 'nm_vac', wavelength in vacuum.
out_of_bounds ('transparent', 'nan', 'error') – what to do if resampling is out of bounds. 'transparent': fills with transparent medium. ‘nan’: fill with nan. 'error': raises an error. Default 'nan'
medium ('air', 'vacuum', or 'default') – in which medium is the new waverange is calculated if it is given in ‘nm’. Ignored if unit=’cm-1’

Other Parameters:

energy_threshold (float or None or 'default') -- if energy conservation (integrals on the intersecting range) is above this threshold, raise an error. If ``None, dont check for energy conservation. If 'default', look up the value in radis.config [“RESAMPLING_TOLERANCE_THRESHOLD”] Default 'default'
print_conservation (boolean) – if True, prints energy conservation. Default False.
inplace (boolean) – if True, modifies the Spectrum object directly. Else, returns a copy. Default True.
**kwargs (**dict) – all other arguments are sent to radis.misc.signal.resample()

Returns:

Spectrum – object has been modified anyway.

Return type:

resampled Spectrum object. If using inplace=True, the Spectrum

Examples

Convert a Spectrum in wavenumber to wavelengths:

s_nm = s.resample(s.get_wavelength(), "nm", inplace=False)

resample_even(energy_threshold=0.005, print_conservation=False, inplace=True)[source]¶

Resample spectrum over the same waverange, but evenly spaced.

Warning

This may result in information loss. Resampling is done with oversampling and spline interpolation. These parameters can be adjusted, and energy conservation ensured with the appropriate parameters.

Parameters:

energy_threshold (float or None) – if energy conservation (integrals on the intersecting range) is above this threshold, raise an error. If None, dont check for energy conservation Default 5e-3 (0.5%)
print_conservation (boolean) – if True, prints energy conservation. Default False.
inplace (boolean) – if True, modifies the Spectrum object directly. Else, returns a copy. Default True.
**kwargs (**dict) – all other arguments are sent to radis.misc.signal.resample()

Returns:

Spectrum – object has been modified anyway.

Return type:

resampled Spectrum object. If using inplace=True, the Spectrum

Examples

rescale_mole_fraction(new_mole_fraction, old_mole_fraction=None, inplace=True, ignore_warnings=False, force=False, verbose=True)[source]¶

Update spectrum with new molar fraction Convoluted values (with slit) are dropped in the process.

Parameters:

new_mole_fraction (float) – new mole fraction
old_mole_fraction (float, or None) – if None, current mole fraction (conditions[‘mole_fraction’]) is used

Other Parameters:

inplace (boolean) – if True, modifies the Spectrum object directly. Else, returns a copy. Default True.
force (boolean) – if False, won’t allow rescaling to 0 (not to loose information). Default False

Returns:

s – Cropped Spectrum. If inplace=True, Spectrum has been updated directly anyway. Allows chaining

Return type:

Spectrum

Examples

s.rescale_mole_fraction(0.2)

Notes

Implementation:

similar to rescale_path_length() but we have to scale abscoeff & emisscoeff Note that this is valid only for small changes in mole fractions. Then, the change in line broadening becomes significant

See also

the Spectrum page

rescale_path_length(new_path_length, old_path_length=None, inplace=True, force=False)[source]¶

Rescale spectrum to new path length. Starts from absorption coefficient and emission coefficient, and solves the RTE again for the new path length Convoluted values (with slit) are dropped in the process.

Parameters:

new_path_length (float) – new path length
old_path_length (float, or None) – if None, current path length (conditions[‘path_length’]) is used

Other Parameters:

inplace (boolean) – if True, modifies the Spectrum object directly. Else, returns a copy. Default True.
force (boolean) – if False, won’t allow rescaling to 0 (not to loose information). Default False

Returns:

s – Cropped Spectrum. If inplace=True, Spectrum has been updated directly anyway. Allows chaining

Return type:

Spectrum

Examples

for path in [0.1, 10, 100]:
    s.rescale_path_length(10, inplace=False).plot(nfig='same')

Additionally, you can also use astropy units in the input arguments, for example:

# preparing a test spectrum :
import radis
s = radis.test_spectrum()

# rescaling :
import astropy.units as u
s.rescale_path_length(1 * u.km).plot()

Notes

Implementation:

To deal with all the input cases, we first make a list of what has to be recomputed, and what has to be recalculated

See also

the Spectrum page

save(*args, **kwargs)[source]¶

Alias to Spectrum.store.

See Spectrum.store for documentation

savetxt(filename, var, wunit='default', Iunit='default')[source]¶

Export spectral quantity var to filename.

(note that by doing this you will loose additional information, such: as the calculation conditions or the units. You better save a Spectrum object under a .spec file with store() and load it afterwards with load_spec())

Parameters:

filename (str) – file name
var (str) – which spectral variable ot export

Other Parameters:

wunit, Iunit, medium (str) – see get() for more information

Notes

Export variable as:

np.savetxt(filename, np.vstack(self.get(var, wunit=wunit, Iunit=Iunit,
                                    medium=medium)).T, header=header)

See also

store(), save(), the Spectrum page

sort(inplace=True)[source]¶

Sort the Spectrum by wavelength / wavenumber.

Parameters:: inplace (bool, optional) – if True, modifies the Spectrum object directly. The default is True.
Returns:: s – sorted Spectrum. If inplace=True, Spectrum has been updated directly anyway. Allows chaining.
Return type:: Spectrum

Examples

store(path, discard=['lines', 'populations'], compress=True, add_info=None, add_date=None, if_exists_then='error', verbose=True)[source]¶

Save a Spectrum object in JSON format. Object can be recovered with load_spec(). If many Spectrum are saved in a same folder you can view their properties with the SpecDatabase structure.

Parameters:

path (path to folder (database) or file) – if a folder, file is saved to database and name is generated automatically. if a file name, then Spectrum is saved to this file and the later formatting options dont apply
file (str) – explicitly give a filename to save
compress (boolean) – if False, save under text format, readable with any editor. if True, saves under binary format. Faster and takes less space. If 2, removes all quantities that can be regenerated with s.update(), e.g, transmittance if abscoeff and path length are given, radiance if emisscoeff and abscoeff are given in non-optically thin case, etc. Default True.
add_info (list) – append these parameters and their values if they are in conditions example:
```
add_info = ['Tvib', 'Trot']
```
discard (list of str) – parameters to exclude, for instance to save some memory for instance Default [lines, populations]: retrieved Spectrum looses the line_survey() ability, and plot_populations() (but it saves tons of memory!)
if_exists_then ('increment', 'replace', 'error', 'ignore') – what to do if file already exists. If increment an incremental digit is added. If replace file is replaced (yeah). If 'ignore' no file is created. If error (or anything else) an error is raised. Default error

Return type:

Returns filename used

Notes

If many spectra are stored in a folder, it may be time to set up a SpecDatabase structure to easily see all Spectrum conditions and get Spectrum that suits specific parameters.

Examples

Store a spectrum in compressed mode, regenerate quantities after loading:

from radis import load_spec
s.store('test.spec', compress=True)   # s is a Spectrum
s2 = load_spec('test.spec')
s2.update()                           # regenerate missing quantities

Examples using `radis.spectrum.spectrum.Spectrum.store`¶

Example #1: Temperature fit

take(var, copy_lines=False, copy_arrays=True)[source]¶

Parameters:

var (str) – spectral quantity ('absorbance', 'transmittance', 'xsection' etc.)

Other Parameters:

copy_lines (bool) – if True, export s.lines. Default False
copy_arrays (bool) – if False, returned array’s quantity is a pointer to the original Spectrum. Faster, but warning, changing them will then change the original Spectrum. Default True

Returns:

s – same Spectrum with only the var spectral quantity

Return type:

Spectrum

Examples

Use take to chain other commands

s.take('radiance').normalize().plot()

to_hdf5(file, engine='pytables')[source]¶

Stores the Spectrum under HDF5 format. Uses spec2hdf()

Examples

s.to_hdf5('spec01.h5')

See also

from_hdf5()

to_json(*args, **kwargs)[source]¶

Alias to Spectrum.store(compress=False).

See Spectrum. store() for documentation

to_pandas(copy=True)[source]¶

Convert a Spectrum to a Pandas DataFrame

Returns:: pd.DataFrame – units are stored in attributes df.attrs
Return type:: pandas DataFrame where columns are spectral arrays, and

Notes

Pandas does not support units yet. pint-pandas is an advanced project but not fully working. See discussion in https://github.com/pandas-dev/pandas/issues/10349

For the moment, we store units as metadata

to_specutils(var=None, wunit='default', Iunit='default')[source]¶

Convert a radis Spectrum object to specutils specutils.spectra.spectrum1d.Spectrum1D

Parameters:

var (‘radiance’, ‘radiance_noslit’, etc.) – which spectral array to convert. If None and only one spectral array is defined, use it.
wunit ('nm', 'cm', 'nm_vac'.) – wavespace unit: wavelength in air ('nm'), wavenumber ('cm-1'), or wavelength in vacuum ('nm_vac'). if "default", default unit for waveunit is used. See get_waveunit().

Note

specutils handles wavelengths in vacuum only. If using 'nm' wavelengths will be converted to wavelengths in vacuum. We recommend using 'nm_air' or 'nm_vac' to avoid any confusion.
Iunit (unit for variable var) – if "default", default unit for quantity var is used. See the units attribute. For var="radiance", one can use per wavelength (~ ‘W/m2/sr/nm’) or per wavenumber (~ ‘W/m2/sr/cm-1’) units

Note

nan that may have been added on the wings of the spectra if a slit has been applied are removed using trim_nan parameter of get() . The waverange in the 1DSpectrum object may therefore be cropped.

Examples

spectrum = s.to_specutils()

Add uncertainties by reading a spectrum noise region with SpectralRegion and noise_region_uncertainty()

from specutils import SpectralRegion
from specutils.manipulation import noise_region_uncertainty
noise_region = SpectralRegion(2012 / u.cm, 2009 / u.cm)
spectrum = noise_region_uncertainty(spectrum, noise_region)

Find lines out of the noise using find_lines_threshold()

from specutils.fitting import find_lines_threshold
lines = find_lines_threshold(spectrum)

Chain Editing and Lineshape Fitting a Spectrum

Post-process using Specutils

See also

from_specutils()

trim(inplace=True)[source]¶

Remove nan common to all arrays on each side of the Spectrum.

Returns a smaller Spectrum (inplace or not).

Returns:: s – directly anyway. Allows chaining.
Return type:: Spectrum : trimmed Spectrum. If inplace=True, Spectrum has been updated

units[source]¶

units for spectral quantities.

Type:: dict

update(quantity='all', optically_thin='default', verbose=True)[source]¶

Calculate missing quantities: ex: if path_length and emisscoeff are given, recalculate radiance_noslit.

Parameters:

spec (Spectrum)
quantity (str) – name of the spectral quantity to recompute. If ‘same’, only the quantities in the Spectrum are recomputed. If ‘all’, then all quantities that can be derived are recomputed. Default ‘all’.
optically_thin (True, False, or ‘default’) – determines whether to calculate radiance with or without self absorption. If ‘default’, the value is determined from the self_absorption key in Spectrum.conditions. If not given, False is taken. Default ‘default’ Also updates the self_absorption value in conditions (creates it if doesnt exist

Examples

Initialize a spectrum from the absorption coefficient, retrieve the transmittance or the emission coefficient :

s = Spectrum.from_array([1900.  , 1900.01, 1900.02, 1900.03, 1900.04, 1900.05, 1900.06,
                         1900.07, 1900.08, 1900.09],
                        [2.71414065e-06, 2.88341489e-06, 3.06942277e-06, 3.27445689e-06,
                         3.50121831e-06, 3.75290756e-06, 4.03334037e-06, 4.34709612e-06,
                         4.69971017e-06, 5.09792551e-06],
                        'abscoeff',
                        wunit='cm-1',
                        Iunit='cm-1',
                        conditions={'path_length':1, # cm
                                    'thermal_equilibrium':True,
                                    'Tgas':700,  # K
                                    })
s.update('transmittance_noslit')
s.update('emisscoeff')

See also

the Spectrum page

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