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 test_rescaling_function(verbose=True, *args, **kwargs):
""" Test rescaling functions """
from radis.test.utils import getTestFile
s = Spectrum.from_txt(
getTestFile("calc_N2C_spectrum_Trot1200_Tvib3000.txt"),
quantity="radiance_noslit",
waveunit="nm",
unit="mW/cm2/sr/µm", # Specair units: mW/cm2/sr/µm
conditions={
"Tvib": 3000,
"Trot": 1200,
"path_length": 1, # arbitrary
"medium": "air",
},
populations={"molecules": {
"N2C": 1e13
}}, # arbitrary
# (just an example)
)
s.update(optically_thin=True)
s.rescale_path_length(10)
assert np.isclose(
s.get_radiance_noslit(Iunit="mW/cm2/sr/nm")[0], 352.57305783248)
def test_rescaling_function(verbose=True, *args, **kwargs):
''' Test rescaling functions '''
from radis.test.utils import getTestFile
s = Spectrum.from_txt(
getTestFile('calc_N2C_spectrum_Trot1200_Tvib3000.txt'),
quantity='radiance_noslit',
waveunit='nm',
unit='mW/cm2/sr/µm', # Specair units: mW/cm2/sr/µm
conditions={
'Tvib': 3000,
'Trot': 1200,
'path_length': 1, # arbitrary
'medium': 'air',
},
populations={'molecules': {
'N2C': 1e13
}}, # arbitrary
# (just an example)
)
s.update(optically_thin=True)
s.rescale_path_length(10)
assert np.isclose(
s.get_radiance_noslit(Iunit='mW/cm2/sr/nm')[0], 352.57305783248)
def get_baseline(s, var='radiance', wunit='nm', medium='air', Iunit=None):
'''Calculate and returns a baseline
Parameters
----------
s: Spectrum
Spectrum which needs a baseline
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, wunit=wunit, medium=medium)
baseline = peakutils.baseline(I1, deg=1, max_it=500)
baselineSpectrum = Spectrum.from_array(w1,
baseline,
var,
waveunit=wunit,
unit=Iunit,
conditions={'medium': medium},
name=s.get_name() + '_baseline')
return baselineSpectrum
def test_klarenaar_validation_case(verbose=True,
plot=False,
warnings=True,
*args,
**kwargs):
""" Reproduce the Klarenaar 2018 validation case, as given in the
[RADIS-2018]_ article.
References
----------
Klarenaar et al, "Time evolution of vibrational temperatures in a CO 2 glow
discharge measured with infrared absorption spectroscopy", doi 10.1088/1361-6595/aa902e,
and the references there in.
"""
setup_test_line_databases()
# %% Data from Dang, adapted by Klarenaar
s_exp = Spectrum.from_txt(
getValidationCase(
join(
"test_CO2_3Tvib_vs_klarenaar_data",
"klarenaar_2017_digitized_data.csv",
)),
"transmittance_noslit",
waveunit="cm-1",
unit="I/I0",
delimiter=",",
name="Klarenaar 2017",
)
# %% Calculate Klarenaar test case conditions
sf = SpectrumFactory(
2284.2,
2284.6,
wstep=0.001, # cm-1
pressure=20 * 1e-3, # bar
db_use_cached=True,
cutoff=1e-25,
molecule="CO2",
isotope="1,2",
path_length=10, # cm-1
# warning! 10% in mass fraction -> less in mole fraction
mole_fraction=0.1 * 28.97 / 44.07,
broadening_max_width=1, # cm-1
medium="vacuum",
export_populations="vib",
)
sf.warnings["MissingSelfBroadeningWarning"] = "ignore"
# sf.load_databank('HITEMP-CO2-DUNHAM')
sf.load_databank("HITEMP-CO2-TEST")
# Calculate with Klarenaar fitted values
T12 = 517
T3 = 2641
Trot = 491
s = sf.non_eq_spectrum((T12, T12, T3),
Trot,
Ttrans=Trot,
vib_distribution="treanor",
name="RADIS")
if plot:
plot_diff(s, s_exp, "transmittance_noslit")
# plt.savefig('test_CO2_3Tvib_vs_klarenaar.png')
assert get_residual(s, s_exp, "transmittance_noslit",
ignore_nan=True) < 0.003
return True
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 test_klarenaar_validation_case(verbose=True, plot=False, warnings=True,
*args, **kwargs):
''' Reproduce the Klarenaar 2018 validation case, as given in the
[RADIS-2018]_ article.
References
----------
Klarenaar et al, "Time evolution of vibrational temperatures in a CO 2 glow
discharge measured with infrared absorption spectroscopy", doi 10.1088/1361-6595/aa902e,
and the references there in.
'''
setup_test_line_databases()
try:
# %% Data from Dang, adapted by Klarenaar
s_exp = Spectrum.from_txt(getValidationCase(join('test_CO2_3Tvib_vs_klarenaar_data',
'klarenaar_2017_digitized_data.csv')),
'transmittance_noslit', waveunit='cm-1', unit='I/I0',
delimiter=',',
name='Klarenaar 2017')
# %% Calculate Klarenaar test case conditions
sf = SpectrumFactory(2284.2, 2284.6,
wstep=0.001, # cm-1
pressure=20*1e-3, # bar
db_use_cached=True,
cutoff=1e-25,
molecule='CO2',
isotope='1,2',
path_length=10, # cm-1
# warning! 10% in mass fraction -> less in mole fraction
mole_fraction=0.1*28.97/44.07,
broadening_max_width=1, # cm-1
medium='vacuum',
export_populations='vib',
)
sf.warnings['MissingSelfBroadeningWarning'] = 'ignore'
# sf.load_databank('HITEMP-CO2-DUNHAM')
sf.load_databank('HITEMP-CO2-TEST')
# Calculate with Klarenaar fitted values
T12 = 517
T3 = 2641
Trot = 491
s = sf.non_eq_spectrum((T12, T12, T3), Trot, Ttrans=Trot,
vib_distribution='treanor',
name='RADIS')
if plot:
plot_diff(s, s_exp, 'transmittance_noslit')
# plt.savefig('test_CO2_3Tvib_vs_klarenaar.png')
assert get_residual(s, s_exp, 'transmittance_noslit', ignore_nan=True) < 0.003
return True
except DatabankNotFound as err:
assert IgnoreMissingDatabase(err, __file__, warnings)
def substract_spectra(s1, s2, var=None, wunit='nm'):
'''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
wunit: str
'nm'or 'cm-1'
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
Iunit = s1.units[var]
wunit = s1.get_waveunit()
medium = s1.get_medium()
# Resample
if wunit == 'nm':
s2 = s2.resample(s1.get_wavelength(), 'nm', inplace=False)
elif wunit == 'cm-1':
s2 = s2.resample(s1.get_wavenumber(), 'cm-1', inplace=False)
else:
raise ValueError('Unexpected wunit: {0}'.format(wunit))
# Substract
w1, I1 = s1.get(var=var, Iunit=Iunit, wunit=wunit, medium=medium)
w2, I2 = s2.get(var=var, Iunit=Iunit, wunit=wunit, medium=medium)
name = s1.get_name() + '-' + s2.get_name()
sub = Spectrum.from_array(w1,
I1 - I2,
var,
waveunit=wunit,
unit=Iunit,
conditions={'medium': medium},
name=name)
# warn("Conditions of the left spectrum were copied in the substraction.", Warning)
return sub
def add_spectra(s1, s2, var=None, wunit='nm', 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
wunit: str
'nm'or 'cm-1'
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`")
# Use same units
Iunit = s1.units[var]
wunit = s1.get_waveunit()
medium = s1.get_medium()
# Resample
if wunit == 'nm':
s2 = s2.resample(s1.get_wavelength(), 'nm', inplace=False)
elif wunit == 'cm-1':
s2 = s2.resample(s1.get_wavenumber(), 'cm-1', inplace=False)
else:
raise ValueError('Unexpected wunit: {0}'.format(wunit))
# Add
w1, I1 = s1.get(var=var, Iunit=Iunit, wunit=wunit, medium=medium)
w2, I2 = s2.get(var=var, Iunit=Iunit, wunit=wunit, medium=medium)
name = s1.get_name() + '+' + s2.get_name()
sub = Spectrum.from_array(w1,
I1 + I2,
var,
waveunit=wunit,
unit=Iunit,
conditions={'medium': medium},
name=name)
# warn("Conditions of the left spectrum were copied in the substraction.", Warning)
return sub