def test_calc_crystal_frame_vectors_single_axis_gonio(
test_reflection_table, test_experiment_singleaxisgonio
):
"""Test the namesake function, to check that the vectors are correctly rotated
into the crystal frame."""
rt, exp = test_reflection_table, test_experiment_singleaxisgonio
reflection_table = calc_crystal_frame_vectors(rt, exp)
# s0c and s1c are normalised. s0c points towards the source.
# as the crystal rotates about the x axis, the s0 vector moves in the y-z plane towards -y
expected_s0c = [
(0.0, 0.0, -1.0),
(0.0, -1.0 / sqrt(2.0), -1.0 / sqrt(2.0)),
(0.0, -1.0, 0.0),
]
for v1, v2 in zip(reflection_table["s0c"], expected_s0c):
assert v1 == pytest.approx(v2)
# the s1c vector should have fixed x-component, rotating in the y-z plane towards +y
expected_s1c = [
(1.0 / sqrt(2.0), 0.0, 1.0 / sqrt(2.0)),
(1.0 / sqrt(2.0), 0.5, 0.5),
(1.0 / sqrt(2.0), 1.0 / sqrt(2.0), 0.0),
]
for v1, v2 in zip(reflection_table["s1c"], expected_s1c):
assert v1 == pytest.approx(v2)
# now test redefined coordinates so that the lab x-axis is along the
# z-axis in the crystal frame
alignment_axis = (1.0, 0.0, 0.0)
reflection_table["s1c"] = align_axis_along_z(
alignment_axis, reflection_table["s1c"]
)
reflection_table["s0c"] = align_axis_along_z(
alignment_axis, reflection_table["s0c"]
)
expected_s0c_realigned = [
(1.0, 0.0, 0.0),
(1.0 / sqrt(2.0), -1.0 / sqrt(2.0), 0.0),
(0.0, -1.0, 0.0),
]
for v1, v2 in zip(reflection_table["s0c"], expected_s0c_realigned):
assert v1 == pytest.approx(v2)
expected_s1c_realigned = [
(-1.0 / sqrt(2.0), 0.0, 1.0 / sqrt(2.0)),
(-0.5, 0.5, 1.0 / sqrt(2.0)),
(0.0, 1.0 / sqrt(2.0), 1.0 / sqrt(2.0)),
]
for v1, v2 in zip(reflection_table["s1c"], expected_s1c_realigned):
assert v1 == pytest.approx(v2)
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 create(cls, params, experiment, reflection_table, for_multi=False):
"""Perform reflection_table preprocessing and create a SingleScaler."""
cls.ensure_experiment_identifier(experiment, reflection_table)
logger.info(
"The scaling model type being applied is %s. \n",
experiment.scaling_model.id_,
)
try:
reflection_table = cls.filter_bad_reflections(
reflection_table,
partiality_cutoff=params.cut_data.partiality_cutoff,
min_isigi=params.cut_data.min_isigi,
intensity_choice=params.reflection_selection.intensity_choice,
)
except ValueError:
raise BadDatasetForScalingException
# combine partial measurements of same reflection, to handle those reflections
# that were split by dials.integrate - changes size of reflection table.
reflection_table = sum_partial_reflections(reflection_table)
if "inverse_scale_factor" not in reflection_table:
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
elif (reflection_table["inverse_scale_factor"].count(0.0) ==
reflection_table.size()):
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
reflection_table = choose_initial_scaling_intensities(
reflection_table, params.reflection_selection.intensity_choice)
excluded_for_scaling = reflection_table.get_flags(
reflection_table.flags.excluded_for_scaling)
user_excluded = reflection_table.get_flags(
reflection_table.flags.user_excluded_in_scaling)
reasons = Reasons()
reasons.add_reason("user excluded", user_excluded.count(True))
reasons.add_reason("excluded for scaling",
excluded_for_scaling.count(True))
n_excluded = (excluded_for_scaling | user_excluded).count(True)
if n_excluded == reflection_table.size():
logger.info(
"All reflections were determined to be unsuitable for scaling."
)
logger.info(reasons)
raise BadDatasetForScalingException(
"""Unable to use this dataset for scaling""")
else:
logger.info(
"Excluding %s/%s reflections\n%s",
n_excluded,
reflection_table.size(),
reasons,
)
if params.reflection_selection.method == "intensity_ranges":
reflection_table = quasi_normalisation(reflection_table,
experiment)
if (params.reflection_selection.method
in (None, Auto, "auto", "quasi_random")) or (
experiment.scaling_model.id_ == "physical"
and "absorption" in experiment.scaling_model.components):
if experiment.scan:
reflection_table = calc_crystal_frame_vectors(
reflection_table, experiment)
alignment_axis = (1.0, 0.0, 0.0)
reflection_table["s0c"] = align_axis_along_z(
alignment_axis, reflection_table["s0c"])
reflection_table["s1c"] = align_axis_along_z(
alignment_axis, reflection_table["s1c"])
try:
scaler = SingleScaler(params, experiment, reflection_table,
for_multi)
except BadDatasetForScalingException as e:
raise ValueError(e)
else:
return scaler
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)
def test_calc_crystal_frame_vectors_multi_axis_gonio(test_reflection_table):
"""Test the namesake function, to check that the vectors are correctly rotated
into the crystal frame."""
experiments = test_experiments_multiaxisgonio()
table = generate_reflection_table()
# for the first scan, the rotation axis is the (1,0,0) direction, like the
# single axis gonio test case above, so check that first.
table = calc_crystal_frame_vectors(table, experiments[0])
# s0c and s1c are normalised. s0c points towards the source.
# as the crystal rotates about the x axis, the s0 vector moves in the y-z plane towards -y
expected_s0c = [
(0.0, 0.0, -1.0),
(0.0, -1.0 / sqrt(2.0), -1.0 / sqrt(2.0)),
(0.0, -1.0, 0.0),
]
for v1, v2 in zip(table["s0c"], expected_s0c):
assert v1 == pytest.approx(v2)
# the s1c vector should have fixed x-component, rotating in the y-z plane towards +y
expected_s1c = [
(1.0 / sqrt(2.0), 0.0, 1.0 / sqrt(2.0)),
(1.0 / sqrt(2.0), 0.5, 0.5),
(1.0 / sqrt(2.0), 1.0 / sqrt(2.0), 0.0),
]
for v1, v2 in zip(table["s1c"], expected_s1c):
assert v1 == pytest.approx(v2)
# for second scan, the rotation axis is the (1,1,0) direction
table = generate_reflection_table().select(flex.bool([True, False, True]))
table = calc_crystal_frame_vectors(table, experiments[1])
# s0c and s1c are normalised. s0c points towards the source.
# as the crystal rotates about the (1,1,0) axis, the s0 vector rotates towards (1, -sqrt2, -1)
# the y-z plane towards -y
expected_s0c = [
(0.0, 0.0, -1.0),
(0.5, -1.0 / sqrt(2.0), -0.5),
]
for v1, v2 in zip(table["s0c"], expected_s0c):
assert v1 == pytest.approx(v2)
# the s1c vector should rotate to +y
expected_s1c = [
(1.0 / sqrt(2.0), 0.0, 1.0 / sqrt(2.0)),
(0.0, 1.0, 0.0),
]
for v1, v2 in zip(table["s1c"], expected_s1c):
assert v1 == pytest.approx(v2)
# now test redefined coordinates so that the lab x-axis is along the
# z-axis in the crystal frame
alignment_axis = (1.0, 0.0, 0.0)
table["s1c"] = align_axis_along_z(alignment_axis, table["s1c"])
table["s0c"] = align_axis_along_z(alignment_axis, table["s0c"])
expected_s0c_realigned = [
(1.0, 0.0, 0.0),
(0.5, -1.0 / sqrt(2.0), 0.5),
]
for v1, v2 in zip(table["s0c"], expected_s0c_realigned):
assert v1 == pytest.approx(v2)
# the s1c vector should rotate to +y
expected_s1c_realigned = [
(-1.0 / sqrt(2.0), 0.0, 1.0 / sqrt(2.0)),
(0.0, 1.0, 0.0),
]
for v1, v2 in zip(table["s1c"], expected_s1c_realigned):
assert v1 == pytest.approx(v2)