def tst_set_mosflm_beam_centre(detector):
from scitbx import matrix
from dxtbx.model import Beam
wavelength = 1
panel = detector[0]
detector_normal = matrix.col(panel.get_normal())
origin = matrix.col(panel.get_origin())
fast_axis = matrix.col(panel.get_fast_axis())
slow_axis = matrix.col(panel.get_slow_axis())
image_size = panel.get_image_size_mm()
s0 = (1.0 / wavelength) * detector_normal
beam = Beam(-s0.normalize(), wavelength)
beam_centre = matrix.col(panel.get_beam_centre(beam.get_s0()))
origin_shift = matrix.col((1, 0.5))
new_beam_centre = beam_centre + origin_shift
new_mosflm_beam_centre = tuple(reversed(new_beam_centre))
from dxtbx.model.detector_helpers import set_mosflm_beam_centre
set_mosflm_beam_centre(detector, beam, new_mosflm_beam_centre)
assert (matrix.col(panel.get_beam_centre(beam.get_s0())) - matrix.col(
tuple(reversed(new_mosflm_beam_centre)))).length() < 1e-6
print 'OK'
def tst_set_mosflm_beam_centre(detector):
from scitbx import matrix
from dxtbx.model import Beam
wavelength = 1
panel = detector[0]
detector_normal = matrix.col(panel.get_normal())
origin = matrix.col(panel.get_origin())
fast_axis = matrix.col(panel.get_fast_axis())
slow_axis = matrix.col(panel.get_slow_axis())
image_size = panel.get_image_size_mm()
s0 = (1.0/wavelength) * detector_normal
beam = Beam(-s0.normalize(), wavelength)
beam_centre = matrix.col(panel.get_beam_centre(beam.get_s0()))
origin_shift = matrix.col((1, 0.5))
new_beam_centre = beam_centre + origin_shift
new_mosflm_beam_centre = tuple(reversed(new_beam_centre))
from dxtbx.model.detector_helpers import set_mosflm_beam_centre
set_mosflm_beam_centre(detector, beam, new_mosflm_beam_centre)
assert (matrix.col(panel.get_beam_centre(beam.get_s0())) -
matrix.col(tuple(reversed(new_mosflm_beam_centre)))).length() < 1e-6
print 'OK'
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 tst_set_direction_wavelength(): """Test setting direction and wavelength""" from scitbx import matrix direction = matrix.col((0.013142, 0.002200, 1.450476)) unit_direction = direction.normalize() wavelength = 0.689400 # Create the beam b = Beam(direction, wavelength) eps = 1e-7 # Check direction is a unit vector assert(abs(matrix.col(b.get_direction()).length() - 1) <= eps) assert(abs(matrix.col(b.get_direction()) - unit_direction) <= eps) # Check wavelength is correct assert(abs(b.get_wavelength() - wavelength) <= eps) # Check s0 is in direction and has length 1/wavelength assert(abs(matrix.col(b.get_s0()).length() - 1.0 / wavelength) <= eps) assert(abs(-matrix.col(b.get_s0()).normalize() - unit_direction) <= eps) # Test passed print "OK"
def tst_resolution(detector):
from dxtbx.model import Beam
beam = Beam(direction=(0, 0, 1), wavelength=1.0)
d_min1 = detector.get_max_resolution(beam.get_s0())
d_min2 = detector.get_max_inscribed_resolution(beam.get_s0())
assert d_min1 < d_min2
def test_experimentlist_with_identifiers():
# 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")
experiments.append(Experiment(identifier="bacon"))
experiments.select_on_experiment_identifiers(["spam", "bacon"])
assert list(experiments.identifiers()) == ["spam", "bacon"]
experiments.append(Experiment(identifier="ham"))
experiments.append(Experiment(identifier="jam"))
experiments.remove_on_experiment_identifiers(["spam", "jam"])
assert list(experiments.identifiers()) == ["bacon", "ham"]
def tst_resolution(detector): from dxtbx.model import Beam beam = Beam(direction=(0,0,1), wavelength=1.0) d_min1 = detector.get_max_resolution(beam.get_s0()) d_min2 = detector.get_max_inscribed_resolution(beam.get_s0()) assert d_min1 < d_min2 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 test_set_mosflm_beam_centre(detector):
wavelength = 1.0
panel = detector[0]
detector_normal = matrix.col(panel.get_normal())
_ = matrix.col(panel.get_origin())
_ = matrix.col(panel.get_fast_axis())
_ = matrix.col(panel.get_slow_axis())
_ = panel.get_image_size_mm()
s0 = (1.0 / wavelength) * detector_normal
beam = Beam(-s0.normalize(), wavelength)
beam_centre = matrix.col(panel.get_beam_centre(beam.get_s0()))
origin_shift = matrix.col((1, 0.5))
new_beam_centre = beam_centre + origin_shift
new_mosflm_beam_centre = tuple(reversed(new_beam_centre))
set_mosflm_beam_centre(detector, beam, new_mosflm_beam_centre)
assert (
matrix.col(panel.get_beam_centre(beam.get_s0()))
- matrix.col(tuple(reversed(new_mosflm_beam_centre)))
).length() < 1e-6
# test resolution methods
beam = Beam(direction=(0, 0, 1), wavelength=1.0)
d_min1 = detector.get_max_resolution(beam.get_s0())
d_min2 = detector.get_max_inscribed_resolution(beam.get_s0())
assert d_min1 < d_min2
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 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 tst_set_models(imageset):
# Create some other models
beam = Beam((1, 0, 0), 0.5)
detector = Detector(
Panel(
"UNKNOWN",
"Panel",
(1, 0, 0),
(0, 1, 0),
(0, 0, 1),
(0.1, 0.1),
(1000, 1000),
(0, 1),
))
# Override sequence models
imageset.set_beam(beam)
imageset.set_detector(detector)
# Ensure this doens't interfere with reading
for i in imageset:
pass
# Get the models back and check they're ok
beam2 = imageset.get_beam()
detector2 = imageset.get_detector()
assert beam2 == beam
assert detector2 == detector
# Get the models from an index back and check they're not the same
beam2 = imageset.get_beam(0)
detector2 = imageset.get_detector(0)
assert beam2 != beam
assert detector2 != detector
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 tst_from_phil():
from libtbx.phil import parse
from dxtbx.model.beam import beam_phil_scope, BeamFactory
from scitbx import matrix
direction = matrix.col((0.013142, 0.002200, 1.450476))
unit_direction = direction.normalize()
wavelength = 0.689400
reference = Beam(direction, wavelength)
params1 = beam_phil_scope.fetch(parse("""
beam {
wavelength = 1.0
direction = (0, 0, 1)
}
""")).extract()
params2 = beam_phil_scope.fetch(parse("""
beam {
wavelength = 1.0
}
""")).extract()
# Create the beam
b1 = BeamFactory.from_phil(params1)
b2 = BeamFactory.from_phil(params2, reference)
try:
b3 = BeamFactory.from_phil(params2)
passed = True
except Exception:
passed = False
assert passed == False
print 'OK'
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 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 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 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 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 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 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 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 test_from_phil():
from libtbx.phil import parse
from dxtbx.model.beam import beam_phil_scope, BeamFactory
from scitbx import matrix
direction = matrix.col((0.013142, 0.002200, 1.450476))
unit_direction = direction.normalize()
wavelength = 0.689400
reference = Beam(direction, wavelength)
params1 = beam_phil_scope.fetch(
parse("""
beam {
wavelength = 1.0
direction = (0, 0, 1)
}
""")).extract()
params2 = beam_phil_scope.fetch(
parse("""
beam {
wavelength = 1.0
}
""")).extract()
# Create the beam
b1 = BeamFactory.from_phil(params1)
b2 = BeamFactory.from_phil(params2, reference)
with pytest.raises(RuntimeError):
b3 = BeamFactory.from_phil(params2)
def __call__(self):
from dxtbx.model import Beam
# Construct the object
b1 = Beam(direction=(1, 2, 3),
wavelength=1.1,
divergence=0.01,
sigma_divergence=0.01,
polarization_normal=(4, 5, 6),
polarization_fraction=0.9)
# Create a dictionary and get the beam back
d = b1.to_dict()
b2 = Beam.from_dict(d)
assert (b2 == b1)
print 'OK'
def test_beam():
# Construct the object
b1 = Beam(
direction=(1, 2, 3),
wavelength=1.1,
divergence=0.01,
sigma_divergence=0.01,
polarization_normal=(4, 5, 6),
polarization_fraction=0.9,
flux=1.0,
transmission=1.0,
)
# Create a dictionary and get the beam back
d = b1.to_dict()
b2 = Beam.from_dict(d)
assert b2 == b1
def tst_set_s0():
"""Test setting s0"""
from scitbx import matrix
direction = matrix.col((0.013142, 0.002200, 1.450476))
unit_direction = direction.normalize()
wavelength = 0.689400
s0 = -unit_direction * 1.0 / wavelength
# Create the beam
b = Beam(s0)
eps = 1e-7
# Check direction is a unit vector
assert (abs(matrix.col(b.get_direction()).length() - 1) <= eps)
assert (abs(matrix.col(b.get_direction()) - unit_direction) <= eps)
# Check wavelength is correct
assert (abs(b.get_wavelength() - wavelength) <= eps)
# Check s0 is in direction and has length 1/wavelength
assert (abs(matrix.col(b.get_s0()).length() - 1.0 / wavelength) <= eps)
assert (abs(-matrix.col(b.get_s0()).normalize() - unit_direction) <= eps)
assert (abs(matrix.col(b.get_s0()) - s0) <= eps)
# Test passed
print "OK"
def __call__(self):
from dxtbx.model import Beam
# Construct the object
b1 = Beam(
direction=(1, 2, 3),
wavelength=1.1,
divergence=0.01,
sigma_divergence=0.01,
polarization_normal=(4, 5, 6),
polarization_fraction=0.9)
# Create a dictionary and get the beam back
d = b1.to_dict()
b2 = Beam.from_dict(d)
assert(b2 == b1)
print 'OK'
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_beam():
b1 = Beam((1, 0, 0), 2, 0.1, 0.1)
d = b1.to_dict()
b2 = BeamFactory.from_dict(d)
assert d["direction"] == (1, 0, 0)
assert d["wavelength"] == 2
assert d["divergence"] == pytest.approx(0.1)
assert d["sigma_divergence"] == pytest.approx(0.1)
assert b1 == b2
assert "s0_at_scan_points" not in d
# Test with a template and partial dictionary
d2 = {"direction": (0, 1, 0), "divergence": 0.2}
b3 = BeamFactory.from_dict(d2, d)
assert b3.get_sample_to_source_direction() == (0, 1, 0)
assert b3.get_wavelength() == 2
assert b3.get_divergence() == pytest.approx(0.2)
assert b3.get_sigma_divergence() == pytest.approx(0.1)
assert b2 != b3
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 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 load_models(obj):
try:
beam = Beam.from_dict(blist[obj['beam']])
except Exception:
beam = None
try:
dobj = dlist[obj['detector']]
detector = Detector.from_dict(dobj)
except Exception:
detector = None
try:
from dxtbx.serialize import goniometer
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 from_dict(d, t=None):
''' Convert the dictionary to a beam model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The beam model
'''
from dxtbx.model import Beam
# 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 Beam.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 _beam_from_dict(obj): ''' Get a beam from a dictionary. ''' from dxtbx.model import Beam return Beam.from_dict(obj)