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Replace deprecated scipy.integrate.quadrature in the TestLineShapes #457

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merged 5 commits into from
Aug 7, 2024
Merged

Replace deprecated scipy.integrate.quadrature in the TestLineShapes #457

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054e270
Replace deprecated scipy.integrate.quadrature with GaussianQuadrature…
vsnever Aug 2, 2024
177038f
Merge branch 'development' into test/remove_deprecated_scipy_quadrature
vsnever Aug 2, 2024
08a14b7
Replace GaussianQuadrature with scipy.integrate.quad in test_lineshap…
vsnever Aug 2, 2024
95197e5
Define relative_tolerance in test_stark_broadened_line() and compare …
vsnever Aug 2, 2024
1e08f1e
Remove print() in test_lineshapes.py.
vsnever Aug 2, 2024
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17 changes: 7 additions & 10 deletions cherab/core/tests/test_lineshapes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

import numpy as np
from scipy.special import erf, hyp2f1
from scipy.integrate import quadrature
from scipy.integrate import quad

from raysect.core import Point3D, Vector3D
from raysect.core.math.function.float import Arg1D, Constant1D
Expand Down Expand Up @@ -296,7 +296,7 @@ def test_stark_broadened_line(self):
line = Line(deuterium, 0, (6, 2)) # D-delta line
target_species = self.plasma.composition.get(line.element, line.charge)
wavelength = 656.104
integrator = GaussianQuadrature(relative_tolerance=1.e-5)
integrator = GaussianQuadrature(relative_tolerance=1.e-8)
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1.e-8 is used in the quad calls too, please consider using a variable instead (e.g. relative_tolerance), if the values are supposed to be equal here and below. It could save some trouble in the future.

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Thanks, @Mateasek. I added the relative_tolerance variable. Also, in this case it is better to check for relative error rather than absolute error, so I changed that too.

stark_line = StarkBroadenedLine(line, wavelength, target_species, self.plasma, self.atomic_data, integrator=integrator)

# spectrum parameters
Expand Down Expand Up @@ -373,14 +373,11 @@ def stark_lineshape_sigma_minus(x):
lorentz_weight = np.exp(np.poly1d(weight_poly_coeff[::-1])(np.log(fwhm_lorentz / fwhm_full)))

for i in range(bins):
lorentz_bin = 0.5 * sin_sqr * quadrature(stark_lineshape_pi, wavelengths[i], wavelengths[i + 1],
rtol=integrator.relative_tolerance)[0] / delta
lorentz_bin += (0.25 * sin_sqr + 0.5 * cos_sqr) * quadrature(stark_lineshape_sigma_plus, wavelengths[i], wavelengths[i + 1],
rtol=integrator.relative_tolerance)[0] / delta
lorentz_bin += (0.25 * sin_sqr + 0.5 * cos_sqr) * quadrature(stark_lineshape_sigma_minus, wavelengths[i], wavelengths[i + 1],
rtol=integrator.relative_tolerance)[0] / delta
ref_value = lorentz_bin * lorentz_weight + gaussian[i] * (1. - lorentz_weight)
self.assertAlmostEqual(ref_value, spectrum.samples[i], delta=1e-9,
lorentz_bin = 0.5 * sin_sqr * quad(stark_lineshape_pi, wavelengths[i], wavelengths[i + 1], epsrel=1.e-8)[0]
lorentz_bin += (0.25 * sin_sqr + 0.5 * cos_sqr) * quad(stark_lineshape_sigma_plus, wavelengths[i], wavelengths[i + 1], epsrel=1.e-8)[0]
lorentz_bin += (0.25 * sin_sqr + 0.5 * cos_sqr) * quad(stark_lineshape_sigma_minus, wavelengths[i], wavelengths[i + 1], epsrel=1.e-8)[0]
ref_value = lorentz_bin / delta * lorentz_weight + gaussian[i] * (1. - lorentz_weight)
self.assertAlmostEqual(ref_value, spectrum.samples[i], delta=1e-8,
msg='StarkBroadenedLine.add_line() method gives a wrong value at {} nm.'.format(wavelengths[i]))

def test_beam_emission_multiplet(self):
Expand Down
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