def generated_single_exp():
"""Generate an experiment object."""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
scan = Scan(image_range=[0, 60], oscillation=[0.0, 1.0])
beam = Beam(s0=(0.0, 0.0, 1.01))
goniometer = Goniometer((1.0, 0.0, 0.0))
detector = Detector()
experiments.append(
Experiment(
beam=beam,
scan=scan,
goniometer=goniometer,
detector=detector,
crystal=crystal,
))
experiments[0].identifier = "0"
return experiments
def from_dict(d, t=None):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The crystal model
'''
# If None, return None
if d == None:
if t == None: return None
else: return from_dict(t, None)
elif t != None:
d = dict(t.items() + d.items())
# Create the model from the dictionary
if 'ML_half_mosaicity_deg' in d:
assert 'ML_domain_size_ang' in d
if d['ML_half_mosaicity_deg'] is None or d['ML_domain_size_ang'] is None:
assert d['ML_half_mosaicity_deg'] is None and d['ML_domain_size_ang'] is None
else:
if 'mosaicity' in d and d['mosaicity'] > 0:
print "Warning, two kinds of mosaicity found. Using Sauter2014 model"
from dxtbx.model import MosaicCrystalSauter2014
return MosaicCrystalSauter2014.from_dict(d)
if 'mosaicity' in d:
from dxtbx.model import MosaicCrystalKabsch2010
return MosaicCrystalKabsch2010.from_dict(d)
else:
from dxtbx.model import Crystal
return Crystal.from_dict(d)
def generated_exp(n=1, space_group="P 2", assign_ids=False, id_=None):
"""Generate an experiment list with two experiments."""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [15.0, 0.0, 0.0],
"real_space_b": [0.0, 10.0, 0.0],
"real_space_c": [0.0, 0.0, 20.0],
"space_group_hall_symbol": space_group,
}
crystal = Crystal.from_dict(exp_dict)
scan = Scan(image_range=[0, 90], oscillation=[0.0, 1.0])
beam = Beam(s0=(0.0, 0.0, 1.01))
if assign_ids:
experiments.append(
Experiment(identifier="0", beam=beam, scan=scan, crystal=crystal)
)
elif id_:
experiments.append(
Experiment(identifier=str(id_), beam=beam, scan=scan, crystal=crystal)
)
else:
experiments.append(Experiment(beam=beam, scan=scan, crystal=crystal))
if n > 1:
for i in range(1, n):
if assign_ids:
experiments.append(
Experiment(identifier=str(i), beam=beam, scan=scan, crystal=crystal)
)
else:
experiments.append(Experiment(beam=beam, scan=scan, crystal=crystal))
return experiments
def generate_test_input():
(reflections,
ms) = load_data("test_dataset_mu0p2_smalldetector_P4_rot0.pickle")
# json.dump(datablock, open(datablock_json, 'w'))
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [20.0, 0.0, 0.0],
"real_space_b": [0.0, 20.0, 0.0],
"real_space_c": [0.0, 0.0, 15.0],
"space_group_hall_symbol": " P 4",
}
experiments.crystal = Crystal.from_dict(exp_dict)
experiments.scan = Scan(image_range=[0, 360], oscillation=[0.0, 1.0])
experiments.beam = Beam(s0=(0.0, 0.0, 1.01))
experiments.goniometer = Goniometer((1.0, 0.0, 0.0))
phil_scope = phil.parse(
"""
include scope dials_scratch.jbe.scaling_code.scaling_options.phil_scope
""",
process_includes=True,
)
optionparser = OptionParser(phil=phil_scope, check_format=False)
parameters, _ = optionparser.parse_args(args=None,
quick_parse=True,
show_diff_phil=False)
parameters.__inject__("scaling_method", "aimless")
parameters.scaling_options.__inject__("multi_mode", False)
return (reflections, experiments, parameters)
def generated_exp(n=1):
"""Generate an experiment list with two experiments."""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
scan = Scan(image_range=[0, 90], oscillation=[0.0, 1.0])
beam = Beam(s0=(0.0, 0.0, 1.01))
goniometer = Goniometer((1.0, 0.0, 0.0))
detector = Detector()
experiments.append(
Experiment(
beam=beam,
scan=scan,
goniometer=goniometer,
detector=detector,
crystal=crystal,
))
if n > 1:
for _ in range(n - 1):
experiments.append(
Experiment(
beam=beam,
scan=scan,
goniometer=goniometer,
detector=detector,
crystal=crystal,
))
return experiments
def mock_exp(mock_scaling_component, idval=0):
"""Mock experiments object for initialising a scaler."""
def side_effect_config_table(*args):
"""Side effect to mock configure reflection table
call during initialisation."""
return args[0]
exp = MagicMock()
exp.identifier = str(idval)
exp.scaling_model.components = {"scale": mock_scaling_component}
exp.scaling_model.consecutive_refinement_order = ["scale"]
exp.scaling_model.is_scaled = False
exp.scaling_model.configdict = {}
exp.scaling_model.configure_reflection_table.side_effect = side_effect_config_table
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
exp.crystal = Crystal.from_dict(exp_dict)
exp.scan.get_oscillation.return_value = (0, 1.0)
exp.beam.get_sample_to_source_direction.return_value = (0.0, 0.0, -1.0)
exp.goniometer.get_rotation_axis.return_value = (0.0, 0.0, 1.0)
return exp
def example_crystal():
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 1.0],
"space_group_hall_symbol": "-P 2yb",
}
crystal = Crystal.from_dict(exp_dict)
return crystal
def test_ModelEvaluation(dials_regression, tmpdir):
# thaumatin
data_dir = os.path.join(dials_regression, "indexing_test_data",
"i04_weak_data")
pickle_path = os.path.join(data_dir, "full.pickle")
sweep_path = os.path.join(data_dir, "experiments_import.json")
input_reflections = flex.reflection_table.from_file(pickle_path)
input_experiments = load.experiment_list(sweep_path, check_format=False)
input_reflections = input_reflections.select(
input_reflections["xyzobs.px.value"].parts()[2] < 100)
input_reflections.centroid_px_to_mm(input_experiments[0].detector,
scan=input_experiments[0].scan)
input_reflections.map_centroids_to_reciprocal_space(
input_experiments[0].detector,
input_experiments[0].beam,
goniometer=input_experiments[0].goniometer,
)
input_reflections["imageset_id"] = flex.size_t(input_reflections.size(), 0)
input_reflections["id"] = flex.int(input_reflections.size(), -1)
refine_params = refine_phil.fetch().extract()
evaluator = model_evaluation.ModelEvaluation(
refinement_params=refine_params)
experiments = copy.deepcopy(input_experiments)
reflections = copy.deepcopy(input_reflections)
experiments[0].crystal = Crystal.from_dict(
dict([
("__id__", "crystal"),
(
"real_space_a",
(20.007058080503633, 49.721143642677994, 16.636052132572846),
),
(
"real_space_b",
(-15.182202482876685, 24.93846318493148, -50.7116866438356),
),
(
"real_space_c",
(-135.23051191036296, 41.14539066294313, 55.41374425160883),
),
("space_group_hall_symbol", " P 1"),
]))
assign_indices = AssignIndicesGlobal()
assign_indices(reflections, experiments)
result = evaluator.evaluate(experiments, reflections)
assert result is not None
assert result.n_indexed == 7313
assert result.fraction_indexed == pytest.approx(0.341155066244)
assert result.rmsds == pytest.approx(
(0.10215787570953785, 0.12954412140128563, 0.0010980583382102509))
def aligned_lyso_crystal():
from dxtbx.model import Crystal
cryst_descr = {
'__id__': 'crystal',
'real_space_a': (79, 0, 0),
'real_space_b': (0, 79, 0),
'real_space_c': (0, 0, 38),
'space_group_hall_symbol': '-P 4 2'
}
C = Crystal.from_dict(cryst_descr)
return C
def single_exp():
"""Generate an experiment object."""
crystal = Crystal.from_dict({
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
})
scan = Scan(image_range=[0, 60], oscillation=[0.0, 1.0])
return Experiment(scan=scan, crystal=crystal)
def test_exp_P1():
"""Create a mock experiments object."""
exp = Experiment()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 1.0],
"space_group_hall_symbol": " P 1",
}
crystal = Crystal.from_dict(exp_dict)
exp.crystal = crystal
return exp
def test_exp(idval=0):
"""Test experiments object."""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
experiments.append(Experiment(crystal=crystal))
experiments[0].identifier = str(idval)
return experiments
def generated_exp(n=1):
"""Generate an experiment list with two experiments."""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
for i in range(n):
experiments.append(
Experiment(
scan=Scan(image_range=[1, 25], oscillation=[0.0, 1.0]),
crystal=Crystal.from_dict(exp_dict),
identifier=str(i),
))
return experiments
def example_array(reflections):
"""Generate a miller array for a test."""
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 1.0],
"space_group_hall_symbol": "-P 2yb",
}
crystal = Crystal.from_dict(exp_dict)
ms = miller.set(
crystal_symmetry=crystal.get_crystal_symmetry(),
indices=reflections["miller_index"],
anomalous_flag=False,
)
ma = miller.array(ms, data=reflections["intensity"])
ma.set_sigmas(reflections["variance"]**0.5)
return ma
def generate_test_experiments(n=2):
"""Make a test experiment list"""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
for i in range(n):
experiments.append(
Experiment(
crystal=Crystal.from_dict(exp_dict),
scan=Scan(image_range=[1, 10], oscillation=[0.0, 1.0]),
scaling_model=get_scaling_model(),
identifier=str(i),
))
return experiments
def generated_exp(n=1, scan=True, image_range=[0, 10]):
"""Generate an experiment list with two experiments."""
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
if scan:
scan = Scan(image_range=image_range, oscillation=[0.0, 1.0])
else:
scan = None
beam = Beam(s0=(0.0, 0.0, 1.01))
goniometer = Goniometer((1.0, 0.0, 0.0))
goniometer_2 = Goniometer((1.0, 1.0, 0.0))
detector = Detector()
experiments.append(
Experiment(
beam=beam,
scan=scan,
goniometer=goniometer,
detector=detector,
crystal=crystal,
)
)
experiments[0].identifier = "0"
if n > 1:
for i in range(0, n - 1):
experiments.append(
Experiment(
beam=beam,
scan=scan,
goniometer=goniometer_2,
detector=detector,
crystal=crystal,
)
)
experiments[i + 1].identifier = str(i + 1)
return experiments
def from_dict(d, t=None):
"""Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The crystal model
"""
if d is None and t is None:
return None
joint = t.copy() if t else {}
joint.update(d)
# Create the model from the dictionary
if "ML_half_mosaicity_deg" in joint:
assert "ML_domain_size_ang" in joint
if (joint["ML_half_mosaicity_deg"] is None
or joint["ML_domain_size_ang"] is None):
assert (joint["ML_half_mosaicity_deg"] is None
and joint["ML_domain_size_ang"] is None)
else:
if joint.get("mosaicity", 0) > 0:
print(
"Warning, two kinds of mosaicity found. Using Sauter2014 model"
)
from dxtbx.model import MosaicCrystalSauter2014
return MosaicCrystalSauter2014.from_dict(joint)
if "mosaicity" in joint:
from dxtbx.model import MosaicCrystalKabsch2010
return MosaicCrystalKabsch2010.from_dict(joint)
else:
from dxtbx.model import Crystal
return Crystal.from_dict(joint)
def from_dict(d, t=None):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The crystal model
'''
from dxtbx.model import Crystal
# If None, return None
if d == None:
if t == None: return None
else: return from_dict(t, None)
elif t != None:
d = dict(t.items() + d.items())
# Create the model from the dictionary
return Crystal.from_dict(d)
def test_Result():
rmsds = (0.0269546226916153, 0.03159452239902618, 0.004208711548775884)
fraction_indexed = 0.9683976336148051
model_likelihood = 0.95846970346759
n_indexed = 19152
crystal = Crystal.from_dict(
dict([
("__id__", "crystal"),
(
"real_space_a",
(-45.031874961773504, -14.833784919966813,
-48.766092343826806),
),
(
"real_space_b",
(-32.15263553253188, 3.8725711269478085, 59.82290857456796),
),
(
"real_space_c",
(29.6683003477066, 59.732569113301565, -13.880892871529552),
),
("space_group_hall_symbol", " P 1"),
]))
result = model_evaluation.Result(
rmsds=rmsds,
fraction_indexed=fraction_indexed,
model_likelihood=model_likelihood,
n_indexed=n_indexed,
crystal=crystal,
)
assert result.rmsds == rmsds
assert result.fraction_indexed == fraction_indexed
assert result.model_likelihood == model_likelihood
assert result.n_indexed == n_indexed
assert result.crystal == crystal
def generate_test_experiments(n=2):
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
scan = Scan(image_range=[1, 10], oscillation=[0.0, 1.0])
experiments.append(
Experiment(crystal=crystal, scan=scan, scaling_model=get_scaling_model())
)
experiments[0].identifier = "0"
if n > 1:
for i in range(n - 1):
experiments.append(
Experiment(
crystal=crystal, scan=scan, scaling_model=get_scaling_model()
)
)
experiments[i + 1].identifier = str(i + 1)
return experiments
def test_filtered_arrays_from_experiments_reflections():
"""Test the creating of a miller array from crystal and reflection table."""
refl = generate_integrated_test_reflections()
refl["miller_index"] = flex.miller_index([(1, 0, 0), (2, 0, 0), (3, 0, 0),
(4, 0, 0), (5, 0, 0), (6, 0, 0)])
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
experiments.append(Experiment(crystal=crystal))
miller_set = filtered_arrays_from_experiments_reflections(
experiments, [refl])[0]
assert isinstance(miller_set, miller.set)
assert list(miller_set.data()) == [4.6, 2.4, 2.5] # same as calling filter
# for export on scale intensity reducer.
# now try for prf
del refl["intensity.scale.value"]
miller_set = filtered_arrays_from_experiments_reflections(
experiments, [refl])[0]
assert isinstance(miller_set, miller.set)
assert list(miller_set.data()) == [1.0, 2.0, 3.0] # same as calling filter
# for export on prf + sum intensity reducer.
# now just for sum
del refl["intensity.prf.value"]
miller_set = filtered_arrays_from_experiments_reflections(
experiments, [refl])[0]
assert isinstance(miller_set, miller.set)
assert list(miller_set.data()) == [11.0, 12.0, 13.0,
14.0] # same as calling
# filter for export on prf intensity reducer.
# Now try with a bad dataset - should be filtered.
refl = generate_integrated_test_reflections()
refl["miller_index"] = flex.miller_index([(1, 0, 0), (2, 0, 0), (3, 0, 0),
(4, 0, 0), (5, 0, 0), (6, 0, 0)])
# Trigger filtering on prf/sum, but when prf is bad - should proceed with sum
refl.unset_flags(flex.bool(6, True), refl.flags.integrated_prf)
del refl["intensity.scale.value"]
refl2 = generate_integrated_test_reflections()
refl2["partiality"] = flex.double(6, 0.0)
experiments = ExperimentList()
experiments.append(Experiment(crystal=crystal))
experiments.append(Experiment(crystal=crystal))
miller_sets = filtered_arrays_from_experiments_reflections(
experiments, [refl, refl2], outlier_rejection_after_filter=True)
assert len(miller_sets) == 1
with pytest.raises(AssertionError):
miller_sets = filtered_arrays_from_experiments_reflections(
experiments, [refl, refl2], return_batches=True)
experiments = ExperimentList()
experiments.append(Experiment(crystal=crystal))
experiments.append(Experiment(crystal=crystal))
refl2 = generate_integrated_test_reflections()
refl2["partiality"] = flex.double(6, 0.0)
with pytest.raises(ValueError):
refl["partiality"] = flex.double(6, 0.0)
_ = filtered_arrays_from_experiments_reflections(
experiments, [refl, refl2])
def test_ModelRank():
results = [
model_evaluation.Result(
rmsds=(0.0269546226916153, 0.03159452239902618, 0.004208711548775884),
fraction_indexed=0.9683976336148051,
model_likelihood=0.95846970346759,
n_indexed=19152,
crystal=Crystal.from_dict(
dict(
[
("__id__", "crystal"),
(
"real_space_a",
(
-45.031874961773504,
-14.833784919966813,
-48.766092343826806,
),
),
(
"real_space_b",
(-32.15263553253188, 3.8725711269478085, 59.82290857456796),
),
(
"real_space_c",
(29.6683003477066, 59.732569113301565, -13.880892871529552),
),
("space_group_hall_symbol", " P 1"),
]
)
),
hkl_offset=None,
),
model_evaluation.Result(
rmsds=(0.0341397658828684, 0.027401396596305812, 0.00427723439147068),
fraction_indexed=0.9849825554937554,
model_likelihood=0.9562237490188447,
n_indexed=19480,
crystal=Crystal.from_dict(
dict(
[
("__id__", "crystal"),
(
"real_space_a",
(29.66830034770662, 59.73256911330157, -13.880892871529573),
),
(
"real_space_b",
(47.516210146598816, -48.77135532028254, 2.824076640788394),
),
(
"real_space_c",
(
-45.036407933560845,
-14.950807536025826,
-49.06808637024198,
),
),
("space_group_hall_symbol", " P 1"),
]
)
),
hkl_offset=None,
),
model_evaluation.Result(
rmsds=(0.30456791867888355, 0.15679214175133024, 0.009635577811258947),
fraction_indexed=0.33629974212469027,
model_likelihood=0.6574428619874397,
n_indexed=6651,
crystal=Crystal.from_dict(
dict(
[
("__id__", "crystal"),
(
"real_space_a",
(
-11.907050303571122,
34.85499418820148,
30.689745759790572,
),
),
(
"real_space_b",
(-56.943458237132, 19.90418665217566, -18.37834061045143),
),
(
"real_space_c",
(-41.63267941211685, -24.82747139443437, 44.5508337593274),
),
("space_group_hall_symbol", " P 1"),
]
)
),
hkl_offset=None,
),
]
ranker = model_evaluation.ModelRankWeighted()
ranker.extend(results)
assert list(ranker.score_by_fraction_indexed()) == pytest.approx(
[0.02449862002620243, 0.0, 1.550350501381241]
)
assert list(ranker.score_by_rmsd_xy()) == pytest.approx(
[0.0, 0.07598423386955666, 3.044108569529155]
)
assert list(ranker.score_by_volume()) == pytest.approx(
[0.44207271296753703, 0.45026641813391066, 0.0]
)
assert list(ranker.combined_scores()) == pytest.approx(
[0.19602846593366663, 0.20851345109588518, 11.670183660213905]
)
assert (
str(ranker)
== """\
+-------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
| unit_cell | volume | volume score | #indexed | % indexed | % indexed score | rmsd_xy | rmsd_xy score | overall score |
|-------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------|
| 68.02 68.03 68.12 109.6 109.5 109.3 | 242890 | 0.44 | 19152 | 97 | 0.02 | 0.04 | 0 | 0.2 |
| 68.12 68.15 68.26 109.5 109.4 109.4 | 244274 | 0.45 | 19480 | 98 | 0 | 0.04 | 0.08 | 0.21 |
| 47.94 63.06 65.84 75.2 71.6 74.5 | 178786 | 0 | 6651 | 34 | 1.55 | 0.34 | 3.04 | 11.67 |
+-------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+"""
)
best = ranker.best_model()
assert best.n_indexed == 19152
ranker = model_evaluation.ModelRankFilter()
ranker.extend(results)
best = ranker.best_model()
assert best.n_indexed == 19152
assert (
str(ranker)
== """\
+-------------------------------------+----------+-------------+--------------------+--------------+
| unit_cell | volume | n_indexed | fraction_indexed | likelihood |
|-------------------------------------+----------+-------------+--------------------+--------------|
| 68.02 68.03 68.12 109.6 109.5 109.3 | 242890 | 19152 | 97 | 0.96 |
| 68.12 68.15 68.26 109.5 109.4 109.4 | 244274 | 19480 | 98 | 0.96 |
| 47.94 63.06 65.84 75.2 71.6 74.5 | 178786 | 6651 | 34 | 0.66 |
+-------------------------------------+----------+-------------+--------------------+--------------+"""
)
def test_scale_script_prepare_input():
"""Test prepare_input method of scaling script."""
# test the components of the scaling script directly with a test reflection
# table, experiments list and params.
params, exp, reflections = generate_test_input()
# try to pass in unequal number of reflections and experiments
reflections.append(generate_test_reflections())
with pytest.raises(ValueError):
_ = ScalingAlgorithm(params, exp, reflections)
params, exp, reflections = generate_test_input()
# Try to use use_datasets when not identifiers set
params.dataset_selection.use_datasets = [0]
with pytest.raises(ValueError):
_ = ScalingAlgorithm(params, exp, reflections)
# Try to use use_datasets when not identifiers set
params.dataset_selection.use_datasets = None
params.dataset_selection.exclude_datasets = [0]
with pytest.raises(ValueError):
_ = ScalingAlgorithm(params, exp, reflections)
# Now make two experiments with identifiers and select on them
params, exp, reflections = generate_test_input(n=2)
exp[0].identifier = "0"
reflections[0].experiment_identifiers()[0] = "0"
exp[1].identifier = "1"
reflections[1].experiment_identifiers()[0] = "1"
list1 = ExperimentList().append(exp[0])
list2 = ExperimentList().append(exp[1])
reflections[0].assert_experiment_identifiers_are_consistent(list1)
reflections[1].assert_experiment_identifiers_are_consistent(list2)
params.dataset_selection.use_datasets = [0]
params, exp, script_reflections = prepare_input(params, exp, reflections)
assert len(script_reflections) == 1
# Try again, this time excluding
params, exp, reflections = generate_test_input(n=2)
exp[0].identifier = "0"
reflections[0].experiment_identifiers()[0] = "0"
exp[1].identifier = "1"
reflections[1].experiment_identifiers()[1] = "1"
params.dataset_selection.exclude_datasets = [0]
params, exp, script_reflections = prepare_input(params, exp, reflections)
assert len(script_reflections) == 1
assert script_reflections[0] is reflections[1]
# Try having two unequal space groups
params, exp, reflections = generate_test_input(n=2)
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " P 1",
}
crystal = Crystal.from_dict(exp_dict)
exp[0].crystal = crystal
with pytest.raises(ValueError):
_ = prepare_input(params, exp, reflections)
# Test cutting data
params, exp, reflections = generate_test_input(n=1)
params.cut_data.d_min = 1.5
params, _, script_reflections = prepare_input(params, exp, reflections)
r = script_reflections[0]
assert list(r.get_flags(r.flags.user_excluded_in_scaling)) == [
False,
False,
True,
True,
]
# Ensure that the user_excluded_in_scaling flags are reset before applying any new
# cutoffs by re-passing script_reflections to prepare_input
params.cut_data.d_min = None
params, _, script_reflections = prepare_input(params, exp,
script_reflections)
r = script_reflections[0]
assert list(r.get_flags(r.flags.user_excluded_in_scaling)) == [
False,
False,
False,
False,
]
params.cut_data.d_max = 1.25
params, _, script_reflections = prepare_input(params, exp, reflections)
r = script_reflections[0]
assert list(r.get_flags(r.flags.user_excluded_in_scaling)) == [
True,
True,
False,
False,
]
params, exp, reflections = generate_test_input(n=1)
reflections[0]["partiality"] = flex.double([0.5, 0.8, 1.0, 1.0])
params.cut_data.partiality_cutoff = 0.75
_, __, script_reflections = prepare_input(params, exp, reflections)
r = script_reflections[0]
assert list(r.get_flags(r.flags.user_excluded_in_scaling)) == [
True,
False,
False,
False,
]
from __future__ import division
import numpy as np
from simtbx.nanoBragg.anisotropic_mosaicity import AnisoUmats
from dxtbx.model import Crystal
cryst_dict = dict([('__id__', 'crystal'),
('real_space_a', (-48.93914505851325, -61.4985726090971,
0.23980318971727585)),
('real_space_b', (-27.63556200961052, 72.26768337463876,
13.81410546001183)),
('real_space_c', (-42.92524538136074, 33.14788397044063,
-259.2845460893375)),
('space_group_hall_symbol', '-P 6 2')])
cryst = Crystal.from_dict(cryst_dict)
# mosaicities in degrees
eta_a, eta_b, eta_c = 0.02, 0.1, 0.03
# Generate mosaic models with randomized sampling, no derivatives
Nmos = 1000
A = AnisoUmats(num_random_samples=Nmos)
# spherical cap model
U, Uprime, Udblprime = A.generate_Umats(eta=[eta_a, eta_a, eta_a],
crystal=cryst,
how=2,
verbose=True,
compute_derivs=True)
from simtbx.nanoBragg.tst_gaussian_mosaicity import plotter2
U_by2, _, _ = A.generate_Umats(eta_a / 2.,