def tst_scan(self):
from dxtbx.model import Scan, ScanFactory
from scitbx.array_family import flex
s1 = Scan((1, 3), (1.0, 0.2), flex.double([0.1, 0.1, 0.1]),
flex.double([0.1, 0.2, 0.3]))
d = s1.to_dict()
s2 = ScanFactory.from_dict(d)
assert (d['image_range'] == (1, 3))
assert (d['oscillation'] == (1.0, 0.2))
assert (d['exposure_time'] == [0.1, 0.1, 0.1])
assert (d['epochs'] == [0.1, 0.2, 0.3])
assert (s1 == s2)
# Test with a template and partial dictionary
d2 = {'exposure_time': [0.2, 0.2, 0.2]}
s3 = ScanFactory.from_dict(d2, d)
assert (s3.get_image_range() == (1, 3))
assert (s3.get_oscillation() == (1.0, 0.2))
assert (list(s3.get_exposure_times()) == [0.2, 0.2, 0.2])
assert (list(s3.get_epochs()) == [0.1, 0.2, 0.3])
assert (s2 != s3)
# Test with a partial epoch
d3 = {'image_range': (1, 10), 'epochs': [0.1, 0.2]}
s4 = ScanFactory.from_dict(d3, d)
assert (abs(s4.get_epochs()[2] - 0.3) < 1e-7)
assert (abs(s4.get_epochs()[9] - 1.0) < 1e-7)
print 'OK'
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 test_swap():
scan1 = Scan((1, 20), (0.0, 1.0))
scan2 = Scan((40, 60), (10.0, 2.0))
scan1.swap(scan2)
assert scan2.get_image_range() == (1, 20)
assert scan1.get_image_range() == (40, 60)
assert scan2.get_oscillation() == (0.0, 1.0)
assert scan1.get_oscillation() == (10.0, 2.0)
def test_scan():
from dxtbx.model import Scan
from scitbx.array_family import flex
s1 = Scan(image_range=(1, 20),
oscillation=(5.0, 0.1),
exposure_times=flex.double(range(20)),
epochs=flex.double(range(20, 40)))
d = s1.to_dict()
s2 = Scan.from_dict(d)
assert s1 == s2
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_scan_360_append(): scan1 = Scan((1, 360), (0.0, 1.0)) scan2 = Scan((361, 720), (0.0, 1.0)) scan = scan1 + scan2 eps = 1e-7 assert(scan.get_num_images() == 720) assert(abs(scan.get_oscillation()[0] - 0.0) < eps) assert(abs(scan.get_oscillation()[1] - 1.0) < eps) assert(scan.get_image_range() == (1, 720)) assert(scan.get_batch_range() == (1, 720)) scan1 = Scan((1, 360), (0.0, 1.0)) scan2 = Scan((361, 720), (360.0, 1.0)) scan = scan1 + scan2 eps = 1e-7 assert(scan.get_num_images() == 720) assert(abs(scan.get_oscillation()[0] - 0.0) < eps) assert(abs(scan.get_oscillation()[1] - 1.0) < eps) assert(scan.get_image_range() == (1, 720)) assert(scan.get_batch_range() == (1, 720)) from libtbx.test_utils import Exception_expected scan2.set_batch_offset(10) try: scan = scan1 + scan2 except Exception: pass else: raise Exception_expected
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_scan_360_append():
scan1 = Scan((1, 360), (0.0, 1.0))
scan2 = Scan((361, 720), (0.0, 1.0))
scan = scan1 + scan2
eps = 1e-7
assert scan.get_num_images() == 720
assert abs(scan.get_oscillation()[0] - 0.0) < eps
assert abs(scan.get_oscillation()[1] - 1.0) < eps
assert scan.get_image_range() == (1, 720)
assert scan.get_batch_range() == (1, 720)
scan1 = Scan((1, 360), (0.0, 1.0))
scan2 = Scan((361, 720), (360.0, 1.0))
scan = scan1 + scan2
eps = 1e-7
assert scan.get_num_images() == 720
assert abs(scan.get_oscillation()[0] - 0.0) < eps
assert abs(scan.get_oscillation()[1] - 1.0) < eps
assert scan.get_image_range() == (1, 720)
assert scan.get_batch_range() == (1, 720)
scan2.set_batch_offset(10)
with pytest.raises(RuntimeError):
scan = scan1 + scan2
class ScanFactory(object):
'''
A class to create a scan model from NXmx stuff
'''
def __init__(self, obj, detector_obj):
from dxtbx.model import Scan
from scitbx.array_family import flex
# Get the image and oscillation range
phi = obj.handle.file[obj.handle['depends_on'][()]]
image_range = (1, len(phi))
if len(phi) > 1:
oscillation = (float(phi[0]), float(phi[1]-phi[0]))
is_sweep = True
else:
oscillation = (float(phi[0]), 0.0)
is_sweep = False
# Get the exposure time
num_images = len(phi)
if "frame_time" in detector_obj.handle:
frame_time = float(detector_obj.handle['frame_time'][()])
exposure_time = flex.double(num_images, frame_time)
epochs = flex.double(num_images)
for i in range(1, len(epochs)):
epochs[i] = epochs[i-1] + exposure_time[i-1]
else:
exposure_time = flex.double(num_images, 0)
epochs = flex.double(num_images, 0)
if is_sweep is True:
# Construct the model
self.model = Scan(
image_range,
oscillation,
exposure_time,
epochs)
else:
self.model = []
for i, image in enumerate(range(image_range[0], image_range[1]+1)):
self.model.append(Scan(
(image, image),
oscillation,
exposure_time[i:i+1],
epochs[i:i+1]))
class ScanFactory(object):
'''
A class to create a scan model from NXmx stuff
'''
def __init__(self, obj, detector_obj):
from dxtbx.model import Scan
from scitbx.array_family import flex
# Get the image and oscillation range
phi = obj.handle.file[obj.handle['depends_on'][()]]
image_range = (1, len(phi))
if len(phi) > 1:
oscillation = (float(phi[0]), float(phi[1]-phi[0]))
is_sweep = True
else:
oscillation = (float(phi[0]), 0.0)
is_sweep = False
# Get the exposure time
num_images = len(phi)
if "frame_time" in detector_obj.handle:
frame_time = float(detector_obj.handle['frame_time'][()])
exposure_time = flex.double(num_images, frame_time)
epochs = flex.double(num_images)
for i in range(1, len(epochs)):
epochs[i] = epochs[i-1] + exposure_time[i-1]
else:
exposure_time = flex.double(num_images, 0)
epochs = flex.double(num_images, 0)
if is_sweep is True:
# Construct the model
self.model = Scan(
image_range,
oscillation,
exposure_time,
epochs)
else:
self.model = []
for i, image in enumerate(range(image_range[0], image_range[1]+1)):
self.model.append(Scan(
(image, image),
oscillation,
exposure_time[i:i+1],
epochs[i:i+1]))
def __call__(self):
from dxtbx.model import Scan
from scitbx.array_family import flex
s1 = Scan(
image_range=(1, 20),
oscillation=(5.0, 0.1),
exposure_times=flex.double(range(20)),
epochs=flex.double(range(20,40)))
d = s1.to_dict()
s2 = Scan.from_dict(d)
assert(s1 == s2)
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_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_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 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 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 from_dict(d, t=None):
''' Convert the dictionary to a scan model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The scan model
'''
from dxtbx.model import Scan
from scitbx.array_family import flex # import dependency
# 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())
if not isinstance(d['exposure_time'], list):
d['exposure_time'] = [d['exposure_time']]
# Create the model from the dictionary
return Scan.from_dict(d)
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 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 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_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_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 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_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 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 test_valid_image_ranges():
scan = Scan((1, 100), (0.0, 1.0))
scan.set_valid_image_ranges("0", [(1,80)])
scan.set_valid_image_ranges("1", [(1,50)])
assert list(scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(scan.get_valid_image_ranges("1")) == [(1, 50)]
scan.set_valid_image_ranges("0", [(1,50), (80, 100)])
assert list(scan.get_valid_image_ranges("0")) == [(1, 50), (80, 100)]
assert list(scan.get_valid_image_ranges("2")) == []
def convert_stills_to_sweep(self, imageset):
from dxtbx.model import Scan
assert self.params.geometry.scan.oscillation is not None
for i in range(len(imageset)):
self.override_beam(
imageset.get_beam(index=i),
self.params.geometry.beam)
self.override_detector(
imageset.get_detector(index=i),
self.params.geometry.detector)
self.override_goniometer(
imageset.get_goniometer(index=i),
self.params.geometry.goniometer)
beam = imageset.get_beam(index=0)
detector = imageset.get_detector(index=0)
goniometer = imageset.get_goniometer(index=0)
for i in range(1, len(imageset)):
assert beam.is_similar_to(
imageset.get_beam(index=i),
wavelength_tolerance = self.params.input.tolerance.beam.wavelength,
direction_tolerance = self.params.input.tolerance.beam.direction,
polarization_normal_tolerance = self.params.input.tolerance.beam.polarization_normal,
polarization_fraction_tolerance = self.params.input.tolerance.beam.polarization_fraction)
assert detector.is_similar_to(
imageset.get_detector(index=i),
fast_axis_tolerance = self.params.input.tolerance.detector.fast_axis,
slow_axis_tolerance = self.params.input.tolerance.detector.slow_axis,
origin_tolerance = self.params.input.tolerance.detector.origin)
assert goniometer.is_similar_to(
imageset.get_goniometer(index=i),
rotation_axis_tolerance = self.params.input.tolerance.goniometer.rotation_axis,
fixed_rotation_tolerance = self.params.input.tolerance.goniometer.fixed_rotation,
setting_rotation_tolerance = self.params.input.tolerance.goniometer.setting_rotation)
assert beam is not None
assert detector is not None
assert goniometer is not None
if self.params.geometry.scan.image_range is not None:
image_range = self.params.geometry.scan.image_range
else:
image_range = (1, len(imageset))
oscillation = self.params.geometry.scan.oscillation
scan = Scan(image_range=image_range, oscillation=oscillation)
from dxtbx.sweep_filenames import template_regex
from dxtbx.imageset import ImageSetFactory
indices = list(range(image_range[0], image_range[1]+1))
template = template_regex(imageset.get_path(0))[0]
if template is None:
paths = [imageset.get_path(i) for i in range(len(imageset))]
assert len(set(paths)) == 1
template = paths[0]
new_sweep = ImageSetFactory.make_sweep(
template = template,
indices = indices,
format_class = imageset.reader().get_format_class(),
beam = beam,
detector = detector,
goniometer = goniometer,
scan = scan)
return new_sweep
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_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 tst_swap(): scan1 = Scan((1, 20), (0.0, 1.0)) scan2 = Scan((40, 60), (10.0, 2.0)) scan1.swap(scan2) assert(scan2.get_image_range() == (1, 20)) assert(scan1.get_image_range() == (40, 60)) assert(scan2.get_oscillation() == (0.0, 1.0)) assert(scan1.get_oscillation() == (10.0, 2.0)) print 'OK'
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_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 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 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 _scan_from_dict(obj): ''' Get the scan from a dictionary. ''' from dxtbx.model import Scan return Scan.from_dict(obj)
