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test_refl1d.py
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test_refl1d.py
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import itertools
import warnings
import pytest
import numpy as np
from test_discovery import get_test_data, get_polarised_test_data
from refl1d import abeles
from refl1d.reflectivity import reflectivity_amplitude, magnetic_amplitude
from refl1d.names import Stack, QProbe, Experiment, SLD
# abeles.refl is a Python calculator, reflectivity_amplitude uses
# a C extension
backends = [abeles.refl, reflectivity_amplitude]
tests_backends = list(itertools.product(get_test_data(), backends))
ids = [f"{t[0][0]}-{t[1]}" for t in tests_backends]
@pytest.mark.parametrize("nsd, backend", tests_backends, ids=ids)
def test_refl1d(nsd, backend):
"""
Run validation for refl1d.
Parameters
----------
nsd: tuple
test_name, slabs, data
backend: {abeles.refl, reflectivity_amplitude}
function for reflectance calculation
"""
# NCOLS of data:
# 2 - test kernel only
# 3 - test kernel and chi2 calculation
# 4 - test resolution smearing and chi2 calculation
test_name, slabs, data = nsd
if data.shape[1] == 4:
# resolution smeared
if backend == reflectivity_amplitude:
# no way of setting backend for resolution smearing tests
return
resolution_test(slabs, data)
elif data.shape[1] < 4:
# no resolution data, just test kernel
kernel_test(slabs, data, backend)
def kernel_test(slabs, data, backend):
"""
Test the reflectivity kernels for ref1d.
Parameters
----------
slabs: np.ndarray
Slab representation of the system
data: np.ndarray
Q, R arrays
backend: {abeles.refl, reflectivity_amplitude}
function for reflectance calculation
"""
r = backend(
data[:, 0] / 2.0,
slabs[:, 0],
slabs[:, 1],
irho=slabs[:, 2],
sigma=slabs[1:, 3],
)
R = (r * np.conj(r)).real
assert R.shape == data[:, 1].shape
np.testing.assert_allclose(R, data[:, 1], rtol=8e-5)
def resolution_test(slabs, data):
stk = Stack()
for i, slab in enumerate(slabs[::-1]):
m = SLD(f"layer {i}", rho=slab[1], irho=slab[2])
stk |= m(thickness=slab[0], interface=slab[-1])
probe = QProbe(Q=data[:, 0], dQ=data[:, 3])
probe.oversample(21, seed=1)
try:
M = Experiment(stk, probe)
_, R = M.reflectivity()
np.testing.assert_allclose(R, data[:, 1], rtol=0.033)
except AssertionError:
# Probe oversampling did not work.
# make our own oversampling with a linearly spaced array
warnings.warn(
"QProbe oversampling didn't work. Trying linearly spaced points",
RuntimeWarning,
)
argmin = np.argmin(data[:, 0])
argmax = np.argmax(data[:, 0])
probe.calc_Qo = np.linspace(
data[argmin, 0] - 3.5 * data[argmin, 3],
data[argmax, 0] + 3.5 * data[argmax, 3],
21 * len(data),
)
M = Experiment(stk, probe)
_, R = M.reflectivity()
np.testing.assert_allclose(R, data[:, 1], rtol=0.033)
pol_backends = [
magnetic_amplitude,
]
pol_tests_backends = list(
itertools.product(get_polarised_test_data(), pol_backends)
)
pol_ids = [f"{t[0][0]}-{t[1]}" for t in pol_tests_backends]
@pytest.mark.parametrize("nsd, backend", pol_tests_backends, ids=pol_ids)
def test_pol_refl1d(nsd, backend):
"""
Run validation for refl1d (polarised beam).
Parameters
----------
nsd: tuple
test_name, slabs, data, AGUIDE, H
backend: {abeles.refl, reflectivity_amplitude}
function for reflectance calculation
"""
test_name, slabs, data, AGUIDE, H = nsd
Rmm, Rmp, Rpm, Rpp = pol_kernel_test(slabs[::-1], data, AGUIDE, H, backend)
def pol_kernel_test(slabs, data, AGUIDE, H, backend):
"""
Test the reflectivity kernels for ref1d.
Parameters
----------
slabs: np.ndarray
Slab representation of the system
data: np.ndarray
Q, R arrays
backend: {abeles.refl, reflectivity_amplitude}
function for reflectance calculation
"""
kz = data[:, 0] / 2.0 # = Qz / 2
rmm, rmp, rpm, rpp = backend(
kz,
slabs[:, 0], # thickness
slabs[:, 1], # SLDn
irho=slabs[:, 2], # SLDi,
thetaM=slabs[:, 3], # thetaM
rhoM=slabs[:, 4], # SLDm,
sigma=slabs[:-1, 5], # sigma
Aguide=AGUIDE, # AGUIDE
H=H, # applied field H
)
Rmm, Rmp, Rpm, Rpp = [(r * np.conj(r)).real for r in [rmm, rmp, rpm, rpp]]
assert Rmm.shape == data[:, 1].shape
np.testing.assert_allclose(Rmm, data[:, 1], rtol=8e-5)
np.testing.assert_allclose(Rmp, data[:, 2], rtol=8e-5)
np.testing.assert_allclose(Rpm, data[:, 3], rtol=8e-5)
np.testing.assert_allclose(Rpp, data[:, 4], rtol=8e-5)
return Rmm, Rmp, Rpm, Rpp
if __name__ == "__main__":
for nsd, backend in tests_backends:
test_refl1d(nsd, backend)
for nsd, backend in pol_tests_backends:
test_pol_refl1d(nsd, backend)