def get_baseline(s, var="radiance", Iunit=None):
"""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 :py:data:`~radis.spectrum.utils.SPECTRAL_QUANTITIES`
Returns
-------
baseline: Spectrum
Spectrum object where intenisity is the baseline of s is computed by peakutils
See Also
--------
:py:func:`~radis.spectrum.operations.sub_baseline`
"""
import peakutils
w1, I1 = s.get(var=var, Iunit=Iunit)
baseline = peakutils.baseline(I1, deg=1, max_it=500)
baselineSpectrum = Spectrum.from_array(w1,
baseline,
var,
unit=Iunit,
name=s.get_name() + "_baseline")
return baselineSpectrum
def experimental_spectrum(w,
I,
wunit='nm',
Iunit='counts',
conditions=None,
cond_units=None,
name=None): # -> Spectrum:
''' Convert (w, I) into a Spectrum object that has unit conversion and plotting
capabilities. Convolution is not available as the spectrum is assumed to
be measured experimentally (hence deconvolution of the slit function would
be required)
Parameters
----------
w, I: np.array
wavelength and intensity
wunit: 'nm', 'cm-1'
wavespace unit
Iunit: str
intensity unit (can be 'counts', 'mW/cm2/sr/nm', etc...). Default
'counts' (default Winspec output)
Other Parameters
----------------
conditions: dict
(optional) calculation conditions to be stored with Spectrum
cond_units: dict
(optional) calculation conditions units
name: str
(optional) give a name
See Also
--------
:func:`~radis.spectrum.spectrum.calculated_spectrum`,
:func:`~radis.spectrum.spectrum.transmittance_spectrum`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_array`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_txt`,
:func:`~radis.tools.database.load_spec`
'''
return Spectrum.from_array(np.array(w),
np.array(I),
'radiance',
waveunit=wunit,
unit=Iunit,
conditions=conditions,
cond_units=cond_units,
name=name)
def transmittance_spectrum(w,
T,
wunit='nm',
Tunit='I/I0',
conditions=None,
cond_units=None,
name=None): # -> Spectrum:
''' Convert (w, I) into a Spectrum object that has unit conversion, plotting
and slit convolution capabilities
Parameters
----------
w, I: np.array
wavelength and transmittance (no slit)
wunit: 'nm', 'cm-1'
wavespace unit
Iunit: str
intensity unit. Default 'I/I0'
Other Parameters
----------------
conditions: dict
(optional) calculation conditions to be stored with Spectrum
cond_units: dict
(optional) calculation conditions units
name: str
(optional) give a name
See Also
--------
:func:`~radis.spectrum.models.calculated_spectrum`,
:func:`~radis.spectrum.models.experimental_spectrum`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_array`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_txt`,
:func:`~radis.tools.database.load_spec`
'''
return Spectrum.from_array(np.array(w),
np.array(T),
'transmittance_noslit',
waveunit=wunit,
unit=Tunit,
conditions=conditions,
cond_units=cond_units,
name=name)
def calculated_spectrum(
w,
I,
wunit="nm",
Iunit="mW/cm2/sr/nm",
conditions=None,
cond_units=None,
populations=None,
name=None,
): # -> Spectrum:
"""Convert ``(w, I)`` into a :py:class:`~radis.spectrum.spectrum.Spectrum`
object that has unit conversion, plotting and slit convolution capabilities
Parameters
----------
w: np.array
wavelength, or wavenumber
I: np.array
intensity (no slit)
wunit: ``'nm'``, ``'cm-1'``, ``'nm_vac'``
wavespace unit: wavelength in air (``'nm'``), wavenumber
(``'cm-1'``), or wavelength in vacuum (``'nm_vac'``). Default ``'nm'``.
Iunit: str
intensity unit (can be 'counts', 'mW/cm2/sr/nm', etc...). Default
'mW/cm2/sr/nm' (note that non-convoluted Specair spectra are in 'mW/cm2/sr/µm')
Other Parameters
----------------
conditions: dict
(optional) calculation conditions to be stored with Spectrum. Default ``None``
cond_units: dict
(optional) calculation conditions units. Default ``None``
populations: dict
populations to be stored in Spectrum. Default ``None``
name: str
(optional) give a name
Examples
--------
::
# w, I are numpy arrays for wavelength and radiance
from radis import calculated_spectrum
s = calculated_spectrum(w, I, wunit='nm', Iunit='W/cm2/sr/nm') # creates 'radiance_noslit'
See Also
--------
:func:`~radis.spectrum.models.transmittance_spectrum`,
:func:`~radis.spectrum.models.experimental_spectrum`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_array`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_txt`,
:func:`~radis.tools.database.load_spec`
"""
return Spectrum.from_array(
np.array(w),
np.array(I),
"radiance_noslit",
waveunit=wunit,
unit=Iunit,
conditions=conditions,
cond_units=cond_units,
populations=populations,
name=name,
)
def experimental_spectrum(w,
I,
wunit="nm",
Iunit="counts",
conditions={},
cond_units=None,
name=None): # -> Spectrum:
"""Convert ``(w, I)`` into a :py:class:`~radis.spectrum.spectrum.Spectrum`
object that has unit conversion and plotting
capabilities. Convolution is not available as the spectrum is assumed to
have be measured experimentally (hence it is already convolved with the slit function)
Parameters
----------
w: np.array
wavelength, or wavenumber
I: np.array
intensity
wunit: ``'nm'``, ``'cm-1'``, ``'nm_vac'``
wavespace unit: wavelength in air (``'nm'``), wavenumber
(``'cm-1'``), or wavelength in vacuum (``'nm_vac'``). Default ``'nm'``.
Iunit: str
intensity unit (can be 'counts', 'mW/cm2/sr/nm', etc...). Default
'counts' (default Winspec output)
Other Parameters
----------------
conditions: dict
(optional) calculation conditions to be stored with Spectrum
cond_units: dict
(optional) calculation conditions units
name: str
(optional) give a name
Examples
--------
Load and plot an experimental spectrum::
from numpy import loadtxt
from radis import experimental_spectrum
w, I = loadtxt('my_file.txt').T # assuming 2 columns
s = experimental_spectrum(w, I, Iunit='mW/cm2/sr/nm') # creates 'radiance'
s.plot()
See Also
--------
:func:`~radis.spectrum.models.calculated_spectrum`,
:func:`~radis.spectrum.models.transmittance_spectrum`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_array`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_txt`,
:func:`~radis.tools.database.load_spec`
"""
if np.shape(w) != np.shape(I):
raise ValueError(
"Wavelength {0} and intensity {1} do not have the same shape".
format(np.shape(w), np.shape(I)))
return Spectrum.from_array(
np.array(w),
np.array(I),
"radiance",
waveunit=wunit,
unit=Iunit,
conditions=conditions,
cond_units=cond_units,
name=name,
)
def transmittance_spectrum(w,
T,
wunit="nm",
Tunit="",
conditions=None,
cond_units=None,
name=None): # -> Spectrum:
"""Convert ``(w, I)`` into a :py:class:`~radis.spectrum.spectrum.Spectrum`
object that has unit conversion, plotting and slit convolution capabilities
Parameters
----------
w: np.array
wavelength, or wavenumber
T: np.array
transmittance (no slit)
wunit: ``'nm'``, ``'cm-1'``, ``'nm_vac'``
wavespace unit: wavelength in air (``'nm'``), wavenumber
(``'cm-1'``), or wavelength in vacuum (``'nm_vac'``). Default ``'nm'``.
Iunit: str
intensity unit. Default ``""`` (adimensionned)
Other Parameters
----------------
conditions: dict
(optional) calculation conditions to be stored with Spectrum
cond_units: dict
(optional) calculation conditions units
name: str
(optional) give a name
Examples
--------
::
# w, T are numpy arrays for wavelength and transmittance
from radis import transmittance_spectrum
s2 = transmittance_spectrum(w, T, wunit='nm') # creates 'transmittance_noslit'
See Also
--------
:func:`~radis.spectrum.models.calculated_spectrum`,
:func:`~radis.spectrum.models.experimental_spectrum`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_array`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_txt`,
:func:`~radis.tools.database.load_spec`
"""
return Spectrum.from_array(
np.array(w),
np.array(T),
"transmittance_noslit",
waveunit=wunit,
unit=Tunit,
conditions=conditions,
cond_units=cond_units,
name=name,
)
def test_broadening_vs_hapi(rtol=1e-2,
verbose=True,
plot=False,
*args,
**kwargs):
"""
Test broadening against HAPI and tabulated data
We're looking at CO(0->1) line 'R1' at 2150.86 cm-1
"""
from hapi import absorptionCoefficient_Voigt, db_begin, fetch, tableList
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
T = 3000
p = 0.0001
wstep = 0.001
wmin = 2150 # cm-1
wmax = 2152 # cm-1
broadening_max_width = 10 # cm-1
# %% HITRAN calculation
# -----------
# Generate HAPI database locally
hapi_data_path = join(dirname(__file__),
__file__.replace(".py", "_HAPIdata"))
db_begin(hapi_data_path)
if not "CO" in tableList(): # only if data not downloaded already
fetch("CO", 5, 1, wmin - broadening_max_width / 2,
wmax + broadening_max_width / 2)
# HAPI doesnt correct for side effects
# Calculate with HAPI
nu, coef = absorptionCoefficient_Voigt(
SourceTables="CO",
Environment={
"T": T,
"p": p / 1.01325,
}, # K # atm
WavenumberStep=wstep,
HITRAN_units=False,
)
s_hapi = Spectrum.from_array(nu,
coef,
"abscoeff",
"cm-1",
"cm-1",
conditions={"Tgas": T},
name="HAPI")
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope=[1],
warnings={
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"HighTemperatureWarning": "ignore",
"GaussianBroadeningWarning": "ignore",
},
) # 0.2)
sf.load_databank(path=join(hapi_data_path, "CO.data"),
format="hitran",
parfuncfmt="hapi")
# s = pl.non_eq_spectrum(Tvib=T, Trot=T, Ttrans=T)
s = sf.eq_spectrum(Tgas=T, name="RADIS")
if plot: # plot broadening of line of largest linestrength
sf.plot_broadening(i=sf.df1.S.idxmax())
# Plot and compare
res = abs(get_residual_integral(s, s_hapi, "abscoeff"))
if plot:
plot_diff(
s,
s_hapi,
var="abscoeff",
title="{0} bar, {1} K (residual {2:.2g}%)".format(p, T, res * 100),
show_points=False,
)
plt.xlim((wmin, wmax))
if verbose:
printm("residual:", res)
assert res < rtol
def test_broadening(rtol=1e-2, verbose=True, plot=False, *args, **kwargs):
'''
Test broadening against HAPI and tabulated data
We're looking at CO(0->1) line 'R1' at 2150.86 cm-1
'''
from radis.io.hapi import db_begin, fetch, tableList, absorptionCoefficient_Voigt
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
T = 3000
p = 0.0001
wstep = 0.001
wmin = 2150 # cm-1
wmax = 2152 # cm-1
broadening_max_width = 10 # cm-1
# %% HITRAN calculation
# -----------
# Generate HAPI database locally
db_begin(join(dirname(__file__), __file__.replace('.py', '_HAPIdata')))
if not 'CO' in tableList(): # only if data not downloaded already
fetch('CO', 5, 1, wmin - broadening_max_width / 2,
wmax + broadening_max_width / 2)
# HAPI doesnt correct for side effects
# Calculate with HAPI
nu, coef = absorptionCoefficient_Voigt(
SourceTables='CO',
Environment={
'T': T, # K
'p': p / 1.01325, # atm
},
WavenumberStep=wstep,
HITRAN_units=False)
s_hapi = Spectrum.from_array(nu,
coef,
'abscoeff',
'cm-1',
'cm_1',
conditions={'Tgas': T},
name='HAPI')
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope=[1],
warnings={
'MissingSelfBroadeningWarning': 'ignore',
'NegativeEnergiesWarning': 'ignore',
'HighTemperatureWarning': 'ignore',
'GaussianBroadeningWarning': 'ignore'
}) # 0.2)
sf.load_databank('HITRAN-CO-TEST')
# s = pl.non_eq_spectrum(Tvib=T, Trot=T, Ttrans=T)
s = sf.eq_spectrum(Tgas=T, name='RADIS')
if plot: # plot broadening of line of largest linestrength
sf.plot_broadening(i=sf.df1.S.idxmax())
# Plot and compare
res = abs(get_residual_integral(s, s_hapi, 'abscoeff'))
if plot:
plot_diff(s,
s_hapi,
var='abscoeff',
title='{0} bar, {1} K (residual {2:.2g}%)'.format(
p, T, res * 100),
show_points=False)
plt.xlim((wmin, wmax))
if verbose:
printm('residual:', res)
assert res < rtol
def concat_spectra(s1, s2, var=None):
"""Concatenate two spectra ``s1`` and ``s2`` side by side.
Note: their spectral range should not overlap
Returns
-------
s: Spectrum
Spectrum object with the same units and waveunits as ``s1``
Parameters
----------
s1, s2: Spectrum objects
Spectrum you want to concatenate
var: str
quantity to manipulate: 'radiance', 'transmittance', ... If ``None``,
get the unique spectral quantity of ``s1``, or the unique spectral
quantity of ``s2``, or raises an error if there is any ambiguity
Notes
-----
.. warning::
the output Spectrum has the sum of the spectral ranges of s1 and s2.
It won't be evenly spaced. This means that you cannot apply a slit without
side effects. Typically, you want to use this function for convolved
quantities only, such as experimental spectra. Else, use
:func:`~radis.los.slabs.MergeSlabs` with the options
``resample='full', out='transparent'``
See Also
--------
:func:`~radis.spectrum.operations.add_spectra`,
:func:`~radis.los.slabs.MergeSlabs`
"""
# Get variable
if var is None:
try:
var = _get_unique_var(
s2, var, inplace=False) # unique variable of 2nd spectrum
except KeyError:
var = _get_unique_var(
s1, var, inplace=False
) # if doesnt exist, unique variable of 1st spectrum
# if it fails, let it fail
# Make sure it is in both Spectra
if var not in s1.get_vars():
raise KeyError("Variable {0} not in Spectrum {1}".format(
var, s1.get_name()))
if var not in s2.get_vars():
raise KeyError("Variable {0} not in Spectrum {1}".format(
var, s1.get_name()))
if var in ["transmittance_noslit", "transmittance"]:
warn(
"It does not make much physical sense to sum transmittances. Are "
+
"you sure of what you are doing? See also // (MergeSlabs) and > " +
"(SerialSlabs)")
# Use same units
Iunit1 = s1.units[var]
wunit1 = s1.get_waveunit()
# Get the value, on the same wunit)
w1, I1 = s1.get(var=var,
copy=False) # @dev: faster to just get the stored value.
# it's copied in hstack() below anyway).
w2, I2 = s2.get(var=var, Iunit=Iunit1, wunit=wunit1)
if not (w1.max() < w2.min() or w2.max() > w1.min()):
raise ValueError(
"You cannot use concat_spectra for overlapping spectral ranges. " +
"Got: {0:.2f}-{1:.2f} and {2:.2f}-{3:.2f} {4}. ".format(
w1.min(), w1.max(), w2.min(), w2.max(), wunit1) +
"Use MergeSlabs instead, with the correct `out=` parameter " +
"for your case")
w_tot = hstack((w1, w2))
I_tot = hstack((I1, I2))
name = s1.get_name() + "&" + s2.get_name() # use "&" instead of "+"
concat = Spectrum.from_array(w_tot,
I_tot,
var,
waveunit=wunit1,
unit=Iunit1,
name=name)
return concat
def substract_spectra(s1, s2, var=None):
"""Return a new spectrum with ``s2`` substracted from ``s1``.
Equivalent to::
s1 - s2
Parameters
----------
s1, s2: Spectrum objects
Spectrum you want to substract
var: str
quantity to manipulate: 'radiance', 'transmittance', ... If ``None``,
get the unique spectral quantity of ``s1``, or the unique spectral
quantity of ``s2``, or raises an error if there is any ambiguity
Returns
-------
s: Spectrum
Spectrum object with the same units and waveunits as ``s1``
See Also
--------
:func:`~radis.spectrum.operations.add_spectra`
"""
# Get variable
if var is None:
try:
var = _get_unique_var(
s2, var, inplace=False) # unique variable of 2nd spectrum
except KeyError:
var = _get_unique_var(
s1, var, inplace=False
) # if doesnt exist, unique variable of 1st spectrum
# if it fails, let it fail
# Make sure it is in both Spectra
if var not in s1.get_vars():
raise KeyError("Variable {0} not in Spectrum {1}".format(
var, s1.get_name()))
if var not in s2.get_vars():
raise KeyError("Variable {0} not in Spectrum {1}".format(
var, s1.get_name()))
# Use same units
Iunit1 = s1.units[var]
wunit1 = s1.get_waveunit()
# Resample s2 on s1
s2 = s2.resample(s1, inplace=False)
# Substract
w1, I1 = s1.get(var=var, Iunit=Iunit1, wunit=wunit1)
w2, I2 = s2.get(var=var, Iunit=Iunit1, wunit=wunit1)
name = s1.get_name() + "-" + s2.get_name()
sub = Spectrum.from_array(w1,
I1 - I2,
var,
waveunit=wunit1,
unit=Iunit1,
name=name)
# warn("Conditions of the left spectrum were copied in the substraction.", Warning)
return sub
def add_spectra(s1, s2, var=None, force=False):
"""Return a new spectrum with ``s2`` added to ``s1``.
Equivalent to::
s1 + s2
.. warning::
we are just algebrically adding the quantities. If you want to merge
spectra while preserving the radiative transfer equation, see
:func:`~radis.los.slabs.MergeSlabs` and :func:`~radis.los.slabs.SerialSlabs`
Parameters
----------
s1, s2: Spectrum objects
Spectrum you want to substract
var: str
quantity to manipulate: 'radiance', 'transmittance', ... If ``None``,
get the unique spectral quantity of ``s1``, or the unique spectral
quantity of ``s2``, or raises an error if there is any ambiguity
Returns
-------
s: Spectrum
Spectrum object with the same units and waveunits as ``s1``
See Also
--------
:func:`~radis.los.slabs.MergeSlabs`,
:func:`~radis.spectrum.operations.substract_spectra`
"""
# Get variable
if var is None:
try:
var = _get_unique_var(
s2, var, inplace=False) # unique variable of 2nd spectrum
except KeyError:
var = _get_unique_var(
s1, var, inplace=False
) # if doesnt exist, unique variable of 1st spectrum
# if it fails, let it fail
# Make sure it is in both Spectra
if var not in s1.get_vars():
raise KeyError("Variable {0} not in Spectrum {1}".format(
var, s1.get_name()))
if var not in s2.get_vars():
raise KeyError("Variable {0} not in Spectrum {1}".format(
var, s1.get_name()))
if var in ["transmittance_noslit", "transmittance"] and not force:
raise ValueError(
"It does not make much physical sense to sum transmittances. Are "
+
"you sure of what you are doing? See also `//` (MergeSlabs), `>` "
+
"(SerialSlabs) and `concat_spectra`. If you're sure, use `force=True`"
)
# Get s1 units
Iunit1 = s1.units[var]
wunit1 = s1.get_waveunit()
# Resample s2 on s1
s2 = s2.resample(s1, inplace=False)
# Add, change output unit if needed.
w1, I1 = s1.get(var=var, Iunit=Iunit1, wunit=wunit1)
w2, I2 = s2.get(var=var, Iunit=Iunit1, wunit=wunit1)
name = s1.get_name() + "+" + s2.get_name()
sub = Spectrum.from_array(w1,
I1 + I2,
var,
waveunit=wunit1,
unit=Iunit1,
name=name)
# warn("Conditions of the left spectrum were copied in the substraction.", Warning)
return sub
def calculated_spectrum(w,
I,
wunit='nm',
Iunit='mW/cm2/sr/nm',
conditions=None,
cond_units=None,
populations=None,
name=None): # -> Spectrum:
''' Convert (w, I) into a Spectrum object that has unit conversion, plotting
and slit convolution capabilities
Parameters
----------
w, I: np.array
wavelength and intensity
wunit: 'nm', 'cm-1'
wavespace unit
Iunit: str
intensity unit (can be 'counts', 'mW/cm2/sr/nm', etc...). Default
'mW/cm2/sr/nm' (note that non-convoluted Specair spectra are in 'mW/cm2/sr/µm')
Other Parameters
----------------
conditions: dict
(optional) calculation conditions to be stored with Spectrum. Default ``None``
cond_units: dict
(optional) calculation conditions units. Default ``None``
populations: dict
populations to be stored in Spectrum. Default ``None``
name: str
(optional) give a name
See Also
--------
:func:`~radis.spectrum.spectrum.transmittance_spectrum`,
:func:`~radis.spectrum.spectrum.experimental_spectrum`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_array`,
:meth:`~radis.spectrum.spectrum.Spectrum.from_txt`,
:func:`~radis.tools.database.load_spec`
'''
return Spectrum.from_array(np.array(w),
np.array(I),
'radiance_noslit',
waveunit=wunit,
unit=Iunit,
conditions=conditions,
cond_units=cond_units,
populations=populations,
name=name)
