def test_goniometer():
# Construct the object
g1 = Goniometer(rotation_axis=(1, 2, 3),
fixed_rotation_matrix=(1, 2, 3, 4, 5, 6, 7, 8, 9))
# Create a dictionary and get the object back
d = g1.to_dict()
g2 = Goniometer.from_dict(d)
assert g2 == g1
def __call__(self):
from dxtbx.model import Goniometer
# Construct the object
g1 = Goniometer(rotation_axis=(1, 2, 3),
fixed_rotation_matrix=(1, 2, 3, 4, 5, 6, 7, 8, 9))
# Create a dictionary and get the object back
d = g1.to_dict()
g2 = Goniometer.from_dict(d)
assert (g2 == g1)
print 'OK'
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 __call__(self):
from dxtbx.model import Goniometer
# Construct the object
g1 = Goniometer(
rotation_axis=(1, 2, 3),
fixed_rotation_matrix=(1, 2, 3, 4, 5, 6, 7, 8, 9))
# Create a dictionary and get the object back
d = g1.to_dict()
g2 = Goniometer.from_dict(d)
assert(g2 == g1)
print 'OK'
def tst_goniometer(self):
from dxtbx.model import Goniometer, GoniometerFactory
g1 = Goniometer((1, 0, 0), (1, 0, 0, 0, 1, 0, 0, 0, 1))
d = g1.to_dict()
g2 = GoniometerFactory.from_dict(d)
assert (d['rotation_axis'] == (1, 0, 0))
assert (d['fixed_rotation'] == (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert (g1 == g2)
# Test with a template and partial dictionary
d2 = {'rotation_axis': (0, 1, 0)}
g3 = GoniometerFactory.from_dict(d2, d)
assert (g3.get_rotation_axis() == (0, 1, 0))
assert (g3.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert (g2 != g3)
def test_goniometer():
g1 = Goniometer((1, 0, 0), (1, 0, 0, 0, 1, 0, 0, 0, 1))
d = g1.to_dict()
g2 = GoniometerFactory.from_dict(d)
assert d["rotation_axis"] == (1, 0, 0)
assert d["fixed_rotation"] == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert g1 == g2
assert "setting_rotation_at_scan_points" not in d
# Test with a template and partial dictionary
d2 = {"rotation_axis": (0, 1, 0)}
g3 = GoniometerFactory.from_dict(d2, d)
assert g3.get_rotation_axis() == (0, 1, 0)
assert g3.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert g2 != g3
def tst_from_sweep(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
filenames = ["filename_%01d.cbf" % (i + 1) for i in range(0, 2)]
imageset = Format.get_imageset(filenames,
beam=Beam(),
detector=Detector(),
goniometer=Goniometer(),
scan=Scan((1, 2), (0, 1)),
as_sweep=True)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1),
space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert (len(experiments) == 1)
assert (experiments[0].imageset is not None)
assert (experiments[0].beam is not None)
assert (experiments[0].detector is not None)
assert (experiments[0].goniometer is not None)
assert (experiments[0].scan is not None)
assert (experiments[0].crystal is not None)
print 'OK'
def random_gonio():
# make a random rotation axis with a random setting matrix
axis = matrix.col(flex.random_double_point_on_sphere())
fixed_rotation = matrix.sqr((1, 0, 0, 0, 1, 0, 0, 0, 1))
setting_rotation = matrix.sqr(flex.random_double_r3_rotation_matrix())
goniometer = Goniometer(axis, fixed_rotation, setting_rotation)
return goniometer
def tst_from_null_sweep(self):
from dxtbx.datablock import DataBlockFactory
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
sweep = ImageSweep(
NullReader(SweepFileList("template_%2d.cbf", (0, 10))))
sweep.set_beam(Beam((0, 0, 1)))
sweep.set_detector(Detector())
sweep.set_goniometer(Goniometer((1, 0, 0)))
sweep.set_scan(Scan((1, 10), (0, 0.1)))
# Create the datablock
datablock = DataBlockFactory.from_imageset(sweep)
assert (len(datablock) == 1)
datablock = datablock[0]
sweeps = datablock.extract_sweeps()
assert (len(sweeps) == 1)
assert (sweeps[0].get_beam() == sweep.get_beam())
assert (sweeps[0].get_detector() == sweep.get_detector())
assert (sweeps[0].get_goniometer() == sweep.get_goniometer())
assert (sweeps[0].get_scan() == sweep.get_scan())
print 'OK'
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 _goniometer_from_dict(obj):
''' Get the goniometer from a dictionary. '''
if 'axes' in obj and 'angles' in obj and 'scan_axis' in obj:
from dxtbx.model import MultiAxisGoniometer
return MultiAxisGoniometer.from_dict(obj)
from dxtbx.model import Goniometer
return Goniometer.from_dict(obj)
def test_experimentlist_dumper_dump_empty_sweep(tmpdir):
tmpdir.chdir()
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
filenames = ["filename_%01d.cbf" % (i+1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam = Beam((1, 0, 0)),
detector = Detector(),
goniometer = Goniometer(),
scan = Scan((1,2), (0.0, 1.0)),
as_sweep=True)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp.json'
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
check(experiments, experiments2)
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 tst_contains(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
# Check all the models are found
for e in self.el:
assert(e.beam in self.el)
assert(e.detector in self.el)
assert(e.goniometer in self.el)
assert(e.scan in self.el)
# Create some more models
b = Beam()
d = Detector()
g = Goniometer()
s = Scan()
# Check that models not in are not found
assert(b not in self.el)
assert(d not in self.el)
assert(g not in self.el)
assert(s not in self.el)
# Test passed
print 'OK'
def test_experimentlist_factory_from_datablock():
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
filenames = ["filename_%01d.cbf" % (i+1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam = Beam(),
detector = Detector(),
goniometer = Goniometer(),
scan = Scan((1,2), (0,1)),
as_sweep=True)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
datablock = DataBlockFactory.from_imageset(imageset)
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert len(experiments) == 1
assert experiments[0].imageset is not None
assert experiments[0].beam is not None
assert experiments[0].detector is not None
assert experiments[0].goniometer is not None
assert experiments[0].scan is not None
assert experiments[0].crystal is not None
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 test_experimentlist_factory_from_datablock():
filenames = ["filename_%01d.cbf" % (i + 1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam=Beam(),
detector=Detector(),
goniometer=Goniometer(),
scan=Scan((1, 2), (0, 1)),
as_sequence=True,
)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
datablock = DataBlockFactory.from_imageset(imageset)
assert datablock[0].format_class()
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert len(experiments) == 1
assert experiments[0].imageset
assert experiments[0].beam
assert experiments[0].detector is not None
assert experiments[0].goniometer
assert experiments[0].scan
assert experiments[0].crystal
def tst_dump_empty_sweep(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
from uuid import uuid4
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
imageset.set_beam(Beam((1, 0, 0)))
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 3), (0.0, 1.0)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp%s.json' % uuid4().hex
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
self.check(experiments, experiments2)
print 'OK'
def tst_from_datablock(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model.crystal import crystal_model
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 2), (0, 1)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
datablock = DataBlockFactory.from_imageset(imageset)
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert(len(experiments) == 1)
assert(experiments[0].imageset is not None)
assert(experiments[0].beam is not None)
assert(experiments[0].detector is not None)
assert(experiments[0].goniometer is not None)
assert(experiments[0].scan is not None)
assert(experiments[0].crystal is not None)
print 'OK'
def __init__(self):
# Let's say we have a scan of 100 images
self.image_range = (1, 100)
# Make a random P1 crystal
a = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((1, 0, 0)))
b = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((0, 1, 0)))
c = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((0, 0, 1)))
self.xl = Crystal(a, b, c, space_group_symbol="P 1")
# Make a beam with wavelength in the range 0.8--1.2 and s0 direction close
# to 0,0,1
s0 = random.uniform(0.8, 1.2) * \
self.random_direction_close_to(matrix.col((0, 0, 1)))
self.beam = Beam(s0)
# Make a standard goniometer model along X
self.goniometer = Goniometer((1, 0, 0))
# Make a simple single panel detector
d1 = matrix.col((1, 0, 0))
d2 = matrix.col((0, -1, 0))
npx_fast = 1475
npx_slow = 1679
pix_size_f = pix_size_s = 0.172
from dxtbx.model import DetectorFactory
self.detector = DetectorFactory.make_detector("PAD", d1, d2,
matrix.col((0, 0, -110)),
(pix_size_f, pix_size_s),
(npx_fast, npx_slow),
(0, 2e20))
def tst_from_null_sweep(self):
from dxtbx.format.Format import Format
from dxtbx.imageset import ImageSweep
from dxtbx.model import Beam, Detector, Goniometer, Scan
filenames = ["template_%2d.cbf" % (i+1) for i in range(0, 10)]
sweep = Format.get_imageset(
filenames,
beam = Beam((0, 0, 1)),
detector = Detector(),
goniometer = Goniometer((1, 0, 0)),
scan = Scan((1, 10), (0, 0.1)))
# Create the datablock
datablock = DataBlockFactory.from_imageset(sweep)
assert(len(datablock) == 1)
datablock = datablock[0]
sweeps = datablock.extract_sweeps()
assert(len(sweeps) == 1)
assert(sweeps[0].get_beam() == sweep.get_beam())
assert(sweeps[0].get_detector() == sweep.get_detector())
assert(sweeps[0].get_goniometer() == sweep.get_goniometer())
assert(sweeps[0].get_scan() == sweep.get_scan())
print 'OK'
def test_goniometer():
from dxtbx.model import Goniometer, GoniometerFactory
g1 = Goniometer((1, 0, 0), (1, 0, 0, 0, 1, 0, 0, 0, 1))
d = g1.to_dict()
g2 = GoniometerFactory.from_dict(d)
assert d['rotation_axis'] == (1, 0, 0)
assert d['fixed_rotation'] == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert g1 == g2
assert 'setting_rotation_at_scan_points' not in d
# Test with a template and partial dictionary
d2 = {'rotation_axis': (0, 1, 0)}
g3 = GoniometerFactory.from_dict(d2, d)
assert g3.get_rotation_axis() == (0, 1, 0)
assert g3.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert g2 != g3
def experiment_list():
from dxtbx.model import Beam, Detector, Goniometer, Scan
# Initialise a list of experiments
experiments = ExperimentList()
# Create a few beams
b1 = Beam()
b2 = Beam()
b3 = Beam()
# Create a few detectors
d1 = Detector()
d2 = Detector()
d3 = Detector()
# Create a few goniometers
g1 = Goniometer()
g2 = Goniometer()
g3 = Goniometer()
# Create a few scans
s1 = Scan()
s2 = Scan()
s3 = Scan()
# Create a list of models
b = [b1, b2, b3, b2, b1]
d = [d1, d2, d3, d2, d1]
g = [g1, g2, g3, g2, g1]
s = [s1, s2, s3, s2, s1]
ident = ["sausage", "eggs", "bacon", "toast", "beans"]
# Populate with various experiments
for i in range(5):
experiments.append(Experiment(
beam=b[i],
detector=d[i],
goniometer=g[i],
scan=s[i],
identifier=ident[i]))
# Return the list of experiments
return experiments
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 __init__(self, obj):
from dxtbx.model import Goniometer
# Get the rotation axis
rotation_axis = construct_vector(
obj.handle.file,
obj.handle.file[obj.handle['depends_on'][()]].name)
# Construct the model
self.model = Goniometer(tuple(rotation_axis))
def tst_contains(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 an experiment
e = Experiment(beam=b1,
detector=d1,
goniometer=g1,
scan=s1,
crystal=c1,
imageset=None)
# Check experiment contains model
assert (b1 in e)
assert (d1 in e)
assert (g1 in e)
assert (s1 in e)
assert (c1 in e)
# 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")
# Check experiment doesn't contain model
assert (b2 not in e)
assert (d2 not in e)
assert (g2 not in e)
assert (s2 not in e)
assert (c2 not in e)
# Test passed
print 'OK'
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 test_experiment_is_still():
experiment = Experiment()
assert experiment.is_still()
experiment.goniometer = Goniometer()
assert experiment.is_still()
experiment.scan = Scan()
assert experiment.is_still()
experiment.scan = Scan((1, 1000), (0, 0.05))
assert not experiment.is_still()
# Specifically test the bug from dxtbx#4 triggered by ending on 0°
experiment.scan = Scan((1, 1800), (-90, 0.05))
assert not experiment.is_still()
def test_experimentlist_imagesequence_decode(mocker):
# These models are shared between experiments
beam = Beam(s0=(0, 0, -1))
detector = Detector()
gonio = Goniometer()
# Construct the experiment list
experiments = ExperimentList()
for i in range(3):
experiments.append(
Experiment(
beam=beam,
detector=detector,
scan=ScanFactory.make_scan(
image_range=(i + 1, i + 1),
exposure_times=[1],
oscillation=(0, 0),
epochs=[0],
),
goniometer=gonio,
))
# Convert experiment list to dict and manually insert a shared imageset
d = experiments.to_dict()
d["imageset"].append({
"__id__": "ImageSequence",
"template": "Puck3_10_1_####.cbf.gz"
})
for e in d["experiment"]:
e["imageset"] = 0
# Monkeypatch this function as we don't actually have an imageset
make_sequence = mocker.patch.object(ExperimentListDict, "_make_sequence")
# Ensure that if make_sequence is called more than once it returns a different
# value each time
make_sequence.side_effect = lambda *args, **kwargs: mocker.MagicMock()
# Decode the dict to get a new experiment list
experiments2 = ExperimentListDict(d).decode()
# This function should only be called once per imageset
make_sequence.assert_called_once()
# Verify that this experiment is as we expect
assert len(experiments2) == 3
assert len(experiments2.imagesets()) == 1
assert len(experiments2.goniometers()) == 1
assert len(experiments2.detectors()) == 1
assert len(experiments2.beams()) == 1
assert len(experiments2.scans()) == 3
for expt in experiments2:
assert expt.imageset is experiments2.imagesets()[0]
def test_experiment_contains():
# 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 an experiment
e = Experiment(beam=b1,
detector=d1,
goniometer=g1,
scan=s1,
crystal=c1,
imageset=None)
# Check experiment contains model
assert b1 in e
assert d1 in e
assert g1 in e
assert s1 in e
assert c1 in e
# 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")
# Check experiment doesn't contain model
assert b2 not in e
assert d2 not in e
assert g2 not in e
assert s2 not in e
assert c2 not in e
def tst_null_reader_sweep(self):
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
template = 'hello_world_%d.cbf'
paths = [template % 1]
# Create the null reader
reader = NullReader(SweepFileList(template, (0, 1)))
# Create the imageset
imageset = ImageSweep(reader)
# Try to get an item
try:
imageset[0]
assert(False)
except Exception:
print 'OK'
# Try to slice the imageset
imageset2 = imageset[0:1]
print 'OK'
# Try some functions which should work
assert(len(imageset) == 1)
assert(imageset == imageset)
assert(imageset.indices() == [0])
assert(imageset.is_valid())
assert(imageset.get_template() == template)
print 'OK'
# Get the image paths
assert(imageset.paths() == paths)
assert(imageset.get_path(0) == paths[0])
print 'OK'
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1,1), (0, 1)))
assert(isinstance(imageset.get_beam(), Beam))
assert(isinstance(imageset.get_detector(), Detector))
assert(isinstance(imageset.get_goniometer(), Goniometer))
assert(isinstance(imageset.get_scan(), Scan))
print 'OK'
def tst_indices(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
# Get the models
b = [e.beam for e in self.el]
d = [e.detector for e in self.el]
g = [e.goniometer for e in self.el]
s = [e.scan for e in self.el]
# Check indices of beams
assert(self.el.indices(b[0]) == [0, 4])
assert(self.el.indices(b[1]) == [1, 3])
assert(self.el.indices(b[2]) == [2])
assert(self.el.indices(b[3]) == [1, 3])
assert(self.el.indices(b[4]) == [0, 4])
# Check indices of detectors
assert(self.el.indices(d[0]) == [0, 4])
assert(self.el.indices(d[1]) == [1, 3])
assert(self.el.indices(d[2]) == [2])
assert(self.el.indices(d[3]) == [1, 3])
assert(self.el.indices(d[4]) == [0, 4])
# Check indices of goniometer
assert(self.el.indices(g[0]) == [0, 4])
assert(self.el.indices(g[1]) == [1, 3])
assert(self.el.indices(g[2]) == [2])
assert(self.el.indices(g[3]) == [1, 3])
assert(self.el.indices(g[4]) == [0, 4])
# Check indices of scans
assert(self.el.indices(s[0]) == [0, 4])
assert(self.el.indices(s[1]) == [1, 3])
assert(self.el.indices(s[2]) == [2])
assert(self.el.indices(s[3]) == [1, 3])
assert(self.el.indices(s[4]) == [0, 4])
# Check some models not in the list
assert(len(self.el.indices(Beam())) == 0)
assert(len(self.el.indices(Detector())) == 0)
assert(len(self.el.indices(Goniometer())) == 0)
assert(len(self.el.indices(Scan())) == 0)
# Test passed
print 'OK'
def from_dict(d, t=None):
''' Convert the dictionary to a goniometer model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The goniometer model
'''
from dxtbx.model import Goniometer
# 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 Goniometer.from_dict(d)
def load_models(obj):
try:
beam = Beam.from_dict(blist[obj['beam']])
except Exception:
beam = None
try:
dobj = dlist[obj['detector']]
if 'hierarchy' in dobj:
detector = HierarchicalDetector.from_dict(dobj)
else:
detector = Detector.from_dict(dobj)
except Exception:
detector = None
try:
gonio = Goniometer.from_dict(glist[obj['goniometer']])
except Exception:
gonio = None
try:
scan = Scan.from_dict(slist[obj['scan']])
except Exception:
scan = None
return beam, detector, gonio, scan
def _goniometer_from_dict(obj): ''' Get the goniometer from a dictionary. ''' from dxtbx.model import Goniometer return Goniometer.from_dict(obj)