def sph_harm_table(reflection_table, lmax):
"""Calculate the spherical harmonic table for a spherical
harmonic absorption correction."""
theta_phi = calc_theta_phi(reflection_table["s0c"])
theta_phi_2 = calc_theta_phi(reflection_table["s1c"])
sph_h_t = create_sph_harm_table(theta_phi, theta_phi_2, lmax)
return sph_h_t
def test_create_sph_harm_table(test_reflection_table, mock_exp):
"""Simple test for the spherical harmonic table, constructing the table step
by step, and verifying the values of a few easy-to-calculate entries.
This also acts as a test for the calc_theta_phi function as well."""
rt, exp = test_reflection_table, mock_exp
reflection_table = calc_crystal_frame_vectors(rt, exp)
theta_phi = calc_theta_phi(reflection_table["s0c"])
expected = [
(pi / 2.0, 0.0),
(pi / 2.0, -1.0 * pi / 4.0),
(pi / 2.0, -1.0 * pi / 2.0),
]
for v1, v2 in zip(theta_phi, expected):
assert v1 == pytest.approx(v2)
theta_phi_2 = calc_theta_phi(reflection_table["s1c"])
expected = [
(pi / 4.0, 0.0),
(pi / 4.0, -1.0 * pi / 4.0),
(pi / 4.0, -1.0 * pi / 2.0),
]
for v1, v2 in zip(theta_phi_2, expected):
assert v1 == pytest.approx(v2)
sph_h_t = create_sph_harm_table(theta_phi, theta_phi_2, 2)
Y10 = ((3.0 / (8.0 * pi)) ** 0.5) / 2.0
Y20 = -1.0 * ((5.0 / (256.0 * pi)) ** 0.5)
assert sph_h_t[1, 0] == pytest.approx(Y10)
assert sph_h_t[1, 1] == pytest.approx(Y10)
assert sph_h_t[1, 2] == pytest.approx(Y10)
assert sph_h_t[5, 0] == pytest.approx(Y20)
assert sph_h_t[5, 1] == pytest.approx(Y20)
assert sph_h_t[5, 2] == pytest.approx(Y20)
def test_create_sph_harm_table(test_reflection_table, mock_exp):
"""Simple test for the spherical harmonic table, constructing the table step
by step, and verifying the values of a few easy-to-calculate entries.
This also acts as a test for the calc_theta_phi function as well."""
rt, exp = test_reflection_table, mock_exp
reflection_table = calc_crystal_frame_vectors(rt, exp)
theta_phi = calc_theta_phi(reflection_table["s0c"])
assert approx_equal(
list(theta_phi),
[(pi / 2.0, 0.0), (pi / 2.0, -1.0 * pi / 4.0), (pi / 2.0, -1.0 * pi / 2.0)],
)
theta_phi_2 = calc_theta_phi(reflection_table["s1c"])
assert approx_equal(
list(theta_phi_2),
[(pi / 4.0, 0.0), (pi / 4.0, -1.0 * pi / 4.0), (pi / 4.0, -1.0 * pi / 2.0)],
)
sph_h_t = create_sph_harm_table(theta_phi, theta_phi_2, 2)
Y10 = ((3.0 / (8.0 * pi)) ** 0.5) / 2.0
Y20 = -1.0 * ((5.0 / (256.0 * pi)) ** 0.5)
assert approx_equal(sph_h_t[1, 0], Y10)
assert approx_equal(sph_h_t[1, 1], Y10)
assert approx_equal(sph_h_t[1, 2], Y10)
assert approx_equal(sph_h_t[5, 0], Y20)
assert approx_equal(sph_h_t[5, 1], Y20)
assert approx_equal(sph_h_t[5, 2], Y20)
def test_create_sph_harm_table(test_reflection_table, test_experiment_singleaxisgonio):
"""Simple test for the spherical harmonic table, constructing the table step
by step, and verifying the values of a few easy-to-calculate entries.
This also acts as a test for the calc_theta_phi function as well."""
rt, exp = test_reflection_table, test_experiment_singleaxisgonio
reflection_table = calc_crystal_frame_vectors(rt, exp)
reflection_table["s0c"] = align_axis_along_z(
(1.0, 0.0, 0.0), reflection_table["s0c"]
)
reflection_table["s1c"] = align_axis_along_z(
(1.0, 0.0, 0.0), reflection_table["s1c"]
)
theta_phi = calc_theta_phi(reflection_table["s0c"])
# so s0c vectors realigned in xyz is
# (1.0, 0.0, 0.0),
# (1.0 / sqrt(2.0), -1.0 / sqrt(2.0), 0.0),
# (0.0, -1.0, 0.0),
# physics conventions, theta from 0 to pi, phi from 0 to 2pi
expected = [
(pi / 2.0, 0.0),
(pi / 2.0, 7.0 * pi / 4.0),
(pi / 2.0, 3.0 * pi / 2.0),
]
for v1, v2 in zip(theta_phi, expected):
assert v1 == pytest.approx(v2)
theta_phi_2 = calc_theta_phi(reflection_table["s1c"])
expected = [
(pi / 4.0, pi),
(pi / 4.0, 3 * pi / 4.0),
(pi / 4.0, 1.0 * pi / 2.0),
]
for v1, v2 in zip(theta_phi_2, expected):
assert v1 == pytest.approx(v2)
sph_h_t = create_sph_harm_table(theta_phi, theta_phi_2, 2)
Y10 = ((3.0 / (8.0 * pi)) ** 0.5) / 2.0
Y20 = -1.0 * ((5.0 / (256.0 * pi)) ** 0.5)
assert sph_h_t[1, 0] == pytest.approx(Y10)
assert sph_h_t[1, 1] == pytest.approx(Y10)
assert sph_h_t[1, 2] == pytest.approx(Y10)
assert sph_h_t[5, 0] == pytest.approx(Y20)
assert sph_h_t[5, 1] == pytest.approx(Y20)
assert sph_h_t[5, 2] == pytest.approx(Y20)
def test_equality_of_two_harmonic_table_methods(dials_regression, run_in_tmpdir):
from dials_scaling_ext import calc_theta_phi, calc_lookup_index
from dxtbx.serialize import load
from dials.util.options import OptionParser
from libtbx import phil
from dials.algorithms.scaling.scaling_library import create_scaling_model
data_dir = os.path.join(dials_regression, "xia2-28")
pickle_path = os.path.join(data_dir, "20_integrated.pickle")
sequence_path = os.path.join(data_dir, "20_integrated_experiments.json")
phil_scope = phil.parse(
"""
include scope dials.command_line.scale.phil_scope
""",
process_includes=True,
)
optionparser = OptionParser(phil=phil_scope, check_format=False)
params, _ = optionparser.parse_args(args=[], quick_parse=True)
params.model = "physical"
lmax = 2
params.physical.lmax = lmax
reflection_table = flex.reflection_table.from_file(pickle_path)
experiments = load.experiment_list(sequence_path, check_format=False)
experiments = create_scaling_model(params, experiments, [reflection_table])
experiment = experiments[0]
# New method
reflection_table["phi"] = (
reflection_table["xyzobs.px.value"].parts()[2]
* experiment.scan.get_oscillation()[1]
)
reflection_table = calc_crystal_frame_vectors(reflection_table, experiment)
theta_phi_0 = calc_theta_phi(reflection_table["s0c"]) # array of tuples in radians
theta_phi_1 = calc_theta_phi(reflection_table["s1c"])
points_per_degree = 2
s0_lookup_index = calc_lookup_index(theta_phi_0, points_per_degree)
s1_lookup_index = calc_lookup_index(theta_phi_1, points_per_degree)
print(list(s0_lookup_index[0:20]))
print(list(s1_lookup_index[0:20]))
coefficients_list = create_sph_harm_lookup_table(lmax, points_per_degree)
experiment.scaling_model.components["absorption"].data = {
"s0_lookup": s0_lookup_index,
"s1_lookup": s1_lookup_index,
}
experiment.scaling_model.components[
"absorption"
].coefficients_list = coefficients_list
assert experiment.scaling_model.components["absorption"]._mode == "memory"
experiment.scaling_model.components["absorption"].update_reflection_data()
absorption = experiment.scaling_model.components["absorption"]
harmonic_values_list = absorption.harmonic_values[0]
experiment.scaling_model.components["absorption"].parameters = flex.double(
[0.1, -0.1, 0.05, 0.02, 0.01, -0.05, 0.12, -0.035]
)
scales, derivatives = experiment.scaling_model.components[
"absorption"
].calculate_scales_and_derivatives()
# Old method:
old_data = {"sph_harm_table": create_sph_harm_table(theta_phi_0, theta_phi_1, lmax)}
experiment.scaling_model.components["absorption"].data = old_data
assert experiment.scaling_model.components["absorption"]._mode == "speed"
experiment.scaling_model.components["absorption"].update_reflection_data()
old_harmonic_values = absorption.harmonic_values[0]
for i in range(0, 8):
print(i)
assert list(harmonic_values_list[i]) == pytest.approx(
list(old_harmonic_values.col(i).as_dense_vector()), abs=0.01
)
experiment.scaling_model.components["absorption"].parameters = flex.double(
[0.1, -0.1, 0.05, 0.02, 0.01, -0.05, 0.12, -0.035]
)
scales_1, derivatives_1 = experiment.scaling_model.components[
"absorption"
].calculate_scales_and_derivatives()
assert list(scales_1) == pytest.approx(list(scales), abs=0.001)
assert list(scales_1) != [1.0] * len(scales_1)
def test_equality_of_two_harmonic_table_methods(dials_data):
location = dials_data("l_cysteine_dials_output", pathlib=True)
refl = location / "20_integrated.pickle"
expt = location / "20_integrated_experiments.json"
phil_scope = phil.parse(
"""
include scope dials.command_line.scale.phil_scope
""",
process_includes=True,
)
parser = ArgumentParser(phil=phil_scope, check_format=False)
params, _ = parser.parse_args(args=[], quick_parse=True)
params.model = "physical"
lmax = 2
params.physical.lmax = lmax
reflection_table = flex.reflection_table.from_file(refl)
experiments = load.experiment_list(expt, check_format=False)
experiments = create_scaling_model(params, experiments, [reflection_table])
experiment = experiments[0]
# New method
reflection_table["phi"] = (reflection_table["xyzobs.px.value"].parts()[2] *
experiment.scan.get_oscillation()[1])
reflection_table = calc_crystal_frame_vectors(reflection_table, experiment)
reflection_table["s1c"] = align_axis_along_z((1.0, 0.0, 0.0),
reflection_table["s1c"])
reflection_table["s0c"] = align_axis_along_z((1.0, 0.0, 0.0),
reflection_table["s0c"])
theta_phi_0 = calc_theta_phi(
reflection_table["s0c"]) # array of tuples in radians
theta_phi_1 = calc_theta_phi(reflection_table["s1c"])
points_per_degree = 4
s0_lookup_index = calc_lookup_index(theta_phi_0, points_per_degree)
s1_lookup_index = calc_lookup_index(theta_phi_1, points_per_degree)
print(list(s0_lookup_index[0:20]))
print(list(s1_lookup_index[0:20]))
coefficients_list = create_sph_harm_lookup_table(lmax, points_per_degree)
experiment.scaling_model.components["absorption"].data = {
"s0_lookup": s0_lookup_index,
"s1_lookup": s1_lookup_index,
}
experiment.scaling_model.components[
"absorption"].coefficients_list = coefficients_list
assert experiment.scaling_model.components["absorption"]._mode == "memory"
experiment.scaling_model.components["absorption"].update_reflection_data()
absorption = experiment.scaling_model.components["absorption"]
harmonic_values_list = absorption.harmonic_values[0]
experiment.scaling_model.components["absorption"].parameters = flex.double(
[0.1, -0.1, 0.05, 0.02, 0.01, -0.05, 0.12, -0.035])
scales, derivatives = experiment.scaling_model.components[
"absorption"].calculate_scales_and_derivatives()
# Old method:
old_data = {
"sph_harm_table": create_sph_harm_table(theta_phi_0, theta_phi_1, lmax)
}
experiment.scaling_model.components["absorption"].data = old_data
assert experiment.scaling_model.components["absorption"]._mode == "speed"
experiment.scaling_model.components["absorption"].update_reflection_data()
old_harmonic_values = absorption.harmonic_values[0]
for i in range(0, 8):
print(i)
assert list(harmonic_values_list[i]) == pytest.approx(list(
old_harmonic_values.col(i).as_dense_vector()),
abs=0.01)
experiment.scaling_model.components["absorption"].parameters = flex.double(
[0.1, -0.1, 0.05, 0.02, 0.01, -0.05, 0.12, -0.035])
scales_1, derivatives_1 = experiment.scaling_model.components[
"absorption"].calculate_scales_and_derivatives()
assert list(scales_1) == pytest.approx(list(scales), abs=0.001)
assert list(scales_1) != [1.0] * len(scales_1)
