def test_set_batch_offsets():
"""Test for namesake function"""
scan = Scan(image_range=[1, 200], oscillation=[0.0, 1.0])
exp1 = Experiment(scan=scan)
exp2 = Experiment()
set_batch_offsets([exp2, exp1], [0, 101])
assert exp1.scan.get_batch_offset() == 101
def test_experimentlist_with_identifiers():
from dxtbx.model import Beam, Detector, Goniometer, Scan
# Initialise a list of experiments
experiments = ExperimentList()
experiments.append(
Experiment(beam=Beam(s0=(0, 0, -1)),
detector=Detector(),
identifier="bacon"))
experiments.append(
Experiment(beam=Beam(s0=(0, 0, -1)),
detector=Detector(),
identifier="sausage"))
with pytest.raises(Exception):
experiments.append(
Experiment(beam=Beam(), detector=Detector(), identifier="bacon"))
d = experiments.to_dict()
e2 = ExperimentListDict(d).decode()
assert experiments[0].identifier == e2[0].identifier
assert experiments[1].identifier == e2[1].identifier
assert tuple(experiments.identifiers()) == ("bacon", "sausage")
experiments[0].identifier = "spam"
assert tuple(experiments.identifiers()) == ("spam", "sausage")
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 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 test_sort_tables_to_experiments_order_single_dataset_files():
"""Test reflection table sorting when tables contain a single dataset."""
# Reflection tables in the wrong order
reflection_tables = [
mock_reflection_file_object(id_=1).data,
mock_reflection_file_object(id_=0).data,
]
experiments = ExperimentList()
experiments.append(Experiment(identifier=str(0)))
experiments.append(Experiment(identifier=str(1)))
refls = sort_tables_to_experiments_order(reflection_tables, experiments)
# Check that reflection tables are rearranged
assert refls[0] is reflection_tables[1]
assert refls[1] is reflection_tables[0]
assert list(refls[0].experiment_identifiers().values()) == ["0"]
assert list(refls[1].experiment_identifiers().values()) == ["1"]
# Reflection tables in correct order
reflection_tables = [
mock_reflection_file_object(id_=0).data,
mock_reflection_file_object(id_=1).data,
]
experiments = ExperimentList()
experiments.append(Experiment(identifier=str(0)))
experiments.append(Experiment(identifier=str(1)))
refls = sort_tables_to_experiments_order(reflection_tables, experiments)
# Check that nothing has been changed
assert refls[0] is reflection_tables[0]
assert refls[1] is reflection_tables[1]
assert list(refls[0].experiment_identifiers().values()) == ["0"]
assert list(refls[1].experiment_identifiers().values()) == ["1"]
def _make_input_for_exclude_tests(exclude_images=True):
"""Generate input data, that upon exclusion should leave only the first
reflection."""
if exclude_images:
exclude_images = [["0:360:720"], ["1:360:720"]]
expt1 = Experiment(scan=Scan(image_range=(0, 720), oscillation=(0.0, 1.0)))
expt2 = Experiment(scan=Scan(image_range=(0, 720), oscillation=(0.0,
-1.0)))
refls1 = flex.reflection_table()
refls2 = flex.reflection_table()
refls1["xyzobs.mm.value"] = flex.vec3_double([
(0.0, 0.0, 10.0 * math.pi / 180.0), (0.0, 0.0, 370.0 * math.pi / 180.0)
])
refls1["xyzobs.px.value"] = flex.vec3_double([(0.0, 0.0, 10.0),
(0.0, 0.0, 370.0)])
refls1["i"] = flex.int([0, 1])
refls2["xyzobs.mm.value"] = flex.vec3_double([
(0.0, 0.0, -10.0 * math.pi / 180.0),
(0.0, 0.0, -370.0 * math.pi / 180.0)
])
refls2["xyzobs.px.value"] = flex.vec3_double([(0.0, 0.0, 10.0),
(0.0, 0.0, 370.0)])
refls2["i"] = flex.int([0, 1])
expts = ExperimentList([expt1, expt2])
tables = [refls1, refls2]
expts, tables = assign_unique_identifiers(expts, tables)
return exclude_images, expts, tables
def experiments():
"""Make a list of three empty experiments"""
experiments = ExperimentList()
experiments.append(Experiment())
experiments.append(Experiment())
experiments.append(Experiment())
return experiments
def test_get_image_ranges():
"""Test for namesake function"""
scan = Scan(image_range=[1, 200], oscillation=[0.0, 1.0])
exp1 = Experiment(scan=scan)
exp2 = Experiment()
experiments = [exp1, exp2]
image_ranges = get_image_ranges(experiments)
assert image_ranges == [(1, 200), (0, 0)]
def test_calculate_batch_offsets():
"""Test offset calculation. Offset is next number ending in 01 bigger than
previous batch numbers which is not consecutive"""
scan = Scan(image_range=[1, 200], oscillation=[0.0, 1.0])
exp1 = Experiment(scan=scan)
exp2 = Experiment()
offsets = calculate_batch_offsets([exp1, exp2])
assert offsets == [0, 301]
def test_get_batch_ranges():
"""Test for namesake function"""
scan = Scan(image_range=[1, 200], oscillation=[0.0, 1.0])
exp1 = Experiment(scan=scan)
exp2 = Experiment(scan=scan)
batch_offsets = [0, 300]
experiments = [exp1, exp2]
batch_ranges = get_batch_ranges(experiments, batch_offsets)
assert batch_ranges == [(1, 200), (301, 500)]
def save_opt_det(phil_params, x, ref_params, SIM):
opt_det = get_optimized_detector(x, ref_params, SIM)
El = ExperimentList()
E = Experiment()
E.detector = opt_det
El.append(E)
El.as_file(phil_params.geometry.optimized_detector_name)
print("Saved detector model to %s" %
phil_params.geometry.optimized_detector_name)
def test_select_remove_on_experiment_identifiers():
table = flex.reflection_table()
table["id"] = flex.int([0, 1, 2, 3])
experiments = ExperimentList()
experiments.append(Experiment(identifier="abcd"))
experiments.append(Experiment(identifier="efgh"))
experiments.append(Experiment(identifier="ijkl"))
experiments.append(Experiment(identifier="mnop"))
table.experiment_identifiers()[0] = "abcd"
table.experiment_identifiers()[1] = "efgh"
table.experiment_identifiers()[2] = "ijkl"
table.experiment_identifiers()[3] = "mnop"
table.assert_experiment_identifiers_are_consistent(experiments)
table = table.remove_on_experiment_identifiers(["efgh"])
del experiments[1]
table.assert_experiment_identifiers_are_consistent(experiments)
assert list(table.experiment_identifiers().keys()) == [0, 2, 3]
assert list(
table.experiment_identifiers().values()) == ["abcd", "ijkl", "mnop"]
table = table.select_on_experiment_identifiers(["abcd", "mnop"])
del experiments[1] # now ijkl
table.assert_experiment_identifiers_are_consistent(experiments)
assert list(table.experiment_identifiers().keys()) == [0, 3]
assert list(table.experiment_identifiers().values()) == ["abcd", "mnop"]
# reset 'id' column such that they are numbered 0 .. n-1
table.reset_ids()
table.assert_experiment_identifiers_are_consistent(experiments)
assert list(table.experiment_identifiers().keys()) == [0, 1]
assert list(table.experiment_identifiers().values()) == ["abcd", "mnop"]
# test that the function doesn't fail if no identifiers set
table1 = copy.deepcopy(table)
for k in table1.experiment_identifiers().keys():
del table1.experiment_identifiers()[k]
table1.reset_ids()
assert list(table1.experiment_identifiers().keys()) == []
# Test exception is raised if bad choice
with pytest.raises(KeyError):
table.remove_on_experiment_identifiers(["efgh"])
with pytest.raises(KeyError):
table.select_on_experiment_identifiers(["efgh"])
table = flex.reflection_table()
table["id"] = flex.int([0, 1, 2, 3])
# Test exception is raised if identifiers map not set
with pytest.raises(KeyError):
table.remove_on_experiment_identifiers(["efgh"])
with pytest.raises(KeyError):
table.select_on_experiment_identifiers(["abcd", "mnop"])
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_experiment_consistent(dials_regression):
# Create a sequence
sequence_filenames = os.path.join(dials_regression, "centroid_test_data",
"centroid*.cbf")
sequence = ImageSetFactory.new(sorted(glob(sequence_filenames)))[0]
# Create experiment with sequence and good scan
e = Experiment(imageset=sequence, scan=sequence.get_scan())
assert e.is_consistent()
# Create experiment with sequence and defective scan
scan = sequence.get_scan()
scan.set_image_range((1, 1))
e = Experiment(imageset=sequence, scan=scan)
def tst_equality(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import Crystal
# Create a load of models
b1 = Beam()
d1 = Detector()
g1 = Goniometer()
s1 = Scan()
c1 = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
# Create a load of models that look the same but aren't
b2 = Beam()
d2 = Detector()
g2 = Goniometer()
s2 = Scan()
c2 = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
# Create an experiment
e1 = Experiment(beam=b1,
detector=d1,
goniometer=g1,
scan=s1,
crystal=c1,
imageset=None)
# Create an experiment
e2 = Experiment(beam=b1,
detector=d1,
goniometer=g1,
scan=s1,
crystal=c1,
imageset=None)
# Create an experiment
e3 = Experiment(beam=b2,
detector=d2,
goniometer=g2,
scan=s2,
crystal=c2,
imageset=None)
# Check e1 equals e2 but not e3
assert (e1 == e2)
assert (e1 != e3)
assert (e2 != e3)
# Test passed
print 'OK'
def test_experiment_consistent(dials_data):
# Create a sequence
sequence_filenames = dials_data("centroid_test_data").listdir(
"centroid*.cbf")
sequence = ImageSetFactory.new(
sorted(f.strpath for f in sequence_filenames))[0]
# Create experiment with sequence and good scan
e = Experiment(imageset=sequence, scan=sequence.get_scan())
assert e.is_consistent()
# Create experiment with sequence and defective scan
scan = sequence.get_scan()
scan.set_image_range((1, 1))
e = Experiment(imageset=sequence, scan=scan)
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_sweep_and_crystal(imageset, crystal, load_models=True):
""" Create an experiment list from sweep and crystal. """
if load_models:
return ExperimentList([
Experiment(
imageset=imageset,
beam=imageset.get_beam(),
detector=imageset.get_detector(),
goniometer=imageset.get_goniometer(),
scan=imageset.get_scan(),
crystal=crystal,
)
])
else:
return ExperimentList(
[Experiment(imageset=imageset, crystal=crystal)])
def test_correct(space_group_symbol):
sgi = sgtbx.space_group_info(space_group_symbol)
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
ms = cs.build_miller_set(anomalous_flag=True, d_min=1).expand_to_p1()
# the reciprocal matrix
B = scitbx.matrix.sqr(cs.unit_cell().fractionalization_matrix()).transpose()
crystal = Crystal(B, sgtbx.space_group())
expts = ExperimentList([Experiment(crystal=crystal)])
refl = flex.reflection_table()
refl["miller_index"] = ms.indices()
refl["rlp"] = B.elems * ms.indices().as_vec3_double()
refl["imageset_id"] = flex.int(len(refl))
refl["xyzobs.mm.value"] = flex.vec3_double(len(refl))
non_primitive_basis.correct(expts, refl, assign_indices.AssignIndicesGlobal())
cs_corrected = expts.crystals()[0].get_crystal_symmetry()
assert cs_corrected.change_of_basis_op_to_primitive_setting().is_identity_op()
assert (
cs.change_of_basis_op_to_primitive_setting().apply(ms.indices())
== refl["miller_index"]
)
def test_experiment_consistent(dials_regression): from dxtbx.imageset import ImageSetFactory from dxtbx.model import Scan # Create a sweep sweep_filenames = os.path.join(dials_regression, 'centroid_test_data', 'centroid*.cbf') sweep = ImageSetFactory.new(sorted(glob(sweep_filenames)))[0] # Create experiment with sweep and good scan e = Experiment(imageset=sweep, scan=sweep.get_scan()) assert e.is_consistent() # Create experiment with sweep and defective scan scan = sweep.get_scan() scan.set_image_range((1, 1)) e = Experiment(imageset=sweep, scan=scan)
def test_change_of_basis_ops_to_minimum_cell_mpro():
input_ucs = [
(46.023, 55.001, 64.452, 64.744, 78.659, 89.824),
(44.747, 53.916, 62.554, 114.985, 99.610, 90.736),
]
# Setup the input experiments and reflection tables
expts = ExperimentList()
for uc in input_ucs:
uc = uctbx.unit_cell(uc)
sg = sgtbx.space_group_info("P1").group()
B = scitbx.matrix.sqr(uc.fractionalization_matrix()).transpose()
expts.append(
Experiment(crystal=Crystal(B, space_group=sg, reciprocal=True)))
# Actually run the method we are testing
cb_ops = change_of_basis_ops_to_minimum_cell(
expts,
max_delta=5,
relative_length_tolerance=0.05,
absolute_angle_tolerance=2)
expts.change_basis(cb_ops, in_place=True)
assert symmetry.unit_cells_are_similar_to(
expts,
median_unit_cell(expts),
relative_length_tolerance=0.05,
absolute_angle_tolerance=2,
)
def test_as_miller_array():
table = flex.reflection_table()
table["intensity.1.value"] = flex.double([1.0, 2.0, 3.0])
table["intensity.1.variance"] = flex.double([0.25, 1.0, 4.0])
table["miller_index"] = flex.miller_index([(1, 0, 0), (2, 0, 0),
(3, 0, 0)])
crystal = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group=sgtbx.space_group_info("P 222").group(),
)
experiment = Experiment(crystal=crystal)
iobs = table.as_miller_array(experiment, intensity="1")
assert list(iobs.data()) == list(table["intensity.1.value"])
assert list(iobs.sigmas()) == list(flex.sqrt(
table["intensity.1.variance"]))
with pytest.raises(KeyError):
_ = table.as_miller_array(experiment, intensity="2")
table["intensity.2.value"] = flex.double([1.0, 2.0, 3.0])
with pytest.raises(KeyError):
_ = table.as_miller_array(experiment, intensity="2")
def test_slice_experiments():
image_range = (0, 1000)
oscillation = (0, 0.1)
scan = Scan(image_range, oscillation)
experiments = ExperimentList([Experiment(scan=scan)])
sliced_image_range = [(1, 5)]
sliced_experiments = slice_experiments(experiments, sliced_image_range)
assert sliced_experiments[0].scan.get_image_range() == sliced_image_range[0]
copy.deepcopy(sliced_experiments)
def test_interpret_images_to_doses_options():
"""Test handling of command line options for experiments input."""
experiments = ExperimentList()
experiments.append(
Experiment(scan=Scan(image_range=(1, 10), oscillation=(0, 1.0))))
experiments.append(
Experiment(scan=Scan(image_range=(1, 20), oscillation=(0, 1.0))))
experiments.append(
Experiment(scan=Scan(image_range=(1, 10), oscillation=(0, 1.0))))
# Default
starting_doses, dpi = dials.pychef.interpret_images_to_doses_options(
experiments, dose_per_image=[1])
assert starting_doses == [0, 0, 0]
assert dpi == [1.0, 1.0, 1.0]
# Multi-sweep measurements on same crystal
starting_doses, dpi = dials.pychef.interpret_images_to_doses_options(
experiments, dose_per_image=[1], shared_crystal=True)
assert starting_doses == [0, 10, 30]
assert dpi == [1.0, 1.0, 1.0]
# Specify starting doses
starting_doses, dpi = dials.pychef.interpret_images_to_doses_options(
experiments,
dose_per_image=[1],
starting_doses=[0, 20, 0],
shared_crystal=False)
assert starting_doses == [0, 20, 0]
assert dpi == [1.0, 1.0, 1.0]
# Specify doses per image and shared crystal
starting_doses, dpi = dials.pychef.interpret_images_to_doses_options(
experiments, dose_per_image=[1.0, 2.0, 1.0], shared_crystal=True)
assert starting_doses == [0, 10, 50]
assert dpi == [1.0, 2.0, 1.0]
# Test error is raised if bad input values for starting doses or dose per image.
with pytest.raises(ValueError):
_, __ = dials.pychef.interpret_images_to_doses_options(
experiments, dose_per_image=[1.0], starting_doses=[0, 1])
with pytest.raises(ValueError):
_, __ = dials.pychef.interpret_images_to_doses_options(
experiments, dose_per_image=[1.0, 2.0])
def test_sort_tables_to_experiments_order_multi_dataset_files():
"""Test reflection table sorting when a table contains multiple datasets."""
# Reflection tables in the wrong order
reflection_tables = [
mock_two_reflection_file_object(ids=[1, 2]).data,
mock_reflection_file_object(id_=0).data,
]
experiments = ExperimentList()
experiments.append(Experiment(identifier=str(0)))
experiments.append(Experiment(identifier=str(1)))
experiments.append(Experiment(identifier=str(2)))
refls = sort_tables_to_experiments_order(reflection_tables, experiments)
# Check that reflection tables are rearranged
assert refls[0] is reflection_tables[1]
assert refls[1] is reflection_tables[0]
assert list(refls[0].experiment_identifiers().values()) == ["0"]
assert list(refls[1].experiment_identifiers().values()) == ["1", "2"]
def test_experiment_equality():
# Create a load of models
b1 = Beam()
d1 = Detector()
g1 = Goniometer()
s1 = Scan()
c1 = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
# Create a load of models that look the same but aren't
b2 = Beam()
d2 = Detector()
g2 = Goniometer()
s2 = Scan()
c2 = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
# Create an experiment
e1 = Experiment(beam=b1,
detector=d1,
goniometer=g1,
scan=s1,
crystal=c1,
imageset=None)
# Create an experiment
e2 = Experiment(beam=b1,
detector=d1,
goniometer=g1,
scan=s1,
crystal=c1,
imageset=None)
# Create an experiment
e3 = Experiment(beam=b2,
detector=d2,
goniometer=g2,
scan=s2,
crystal=c2,
imageset=None)
# Check e1 equals e2 but not e3
assert e1 == e2
assert e1 != e3
assert e2 != e3
def from_sweep_and_crystal(imageset, crystal):
''' Create an experiment list from sweep and crystal. '''
return ExperimentList([
Experiment(imageset=imageset,
beam=imageset.get_beam(),
detector=imageset.get_detector(),
goniometer=imageset.get_goniometer(),
scan=imageset.get_scan(),
crystal=crystal)
])
def from_stills_and_crystal(imageset, crystal, load_models=True):
"""Create an experiment list from stills and crystal."""
experiments = ExperimentList()
if load_models:
for i in range(len(imageset)):
experiments.append(
Experiment(
imageset=imageset[i:i + 1],
beam=imageset.get_beam(i),
detector=imageset.get_detector(i),
goniometer=imageset.get_goniometer(i),
scan=imageset.get_scan(i),
crystal=crystal,
))
else:
for i in range(len(imageset)):
experiments.append(
Experiment(imageset=imageset[i:i + 1], crystal=crystal))
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 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)
