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 generate_test_experiments(n=2):
experiments = ExperimentList()
exp_dict = {
"__id__": "crystal",
"real_space_a": [1.0, 0.0, 0.0],
"real_space_b": [0.0, 1.0, 0.0],
"real_space_c": [0.0, 0.0, 2.0],
"space_group_hall_symbol": " C 2y",
}
crystal = Crystal.from_dict(exp_dict)
scan = Scan(image_range=[1, 10], oscillation=[0.0, 1.0])
experiments.append(
Experiment(crystal=crystal,
scan=scan,
scaling_model=get_scaling_model()))
experiments[0].identifier = "0"
if n > 1:
for i in range(n - 1):
experiments.append(
Experiment(crystal=crystal,
scan=scan,
scaling_model=get_scaling_model()))
experiments[i + 1].identifier = str(i + 1)
return experiments
def 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_experimentlist_dumper_dump_empty_sweep(tmpdir):
tmpdir.chdir()
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)
filename = "temp.json"
experiments.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
check(experiments, experiments2)
def test_experimentlist_factory_from_sweep():
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
assert experiments[0].beam
assert experiments[0].detector is not None
assert experiments[0].goniometer
assert experiments[0].scan
assert experiments[0].crystal
def scan():
image_range = (0, 1000)
oscillation = (0, 0.1)
scan = Scan(image_range, oscillation)
scan.set_batch_offset(100)
return scan
def convert_stills_to_sweep(self, imageset):
from dxtbx.model import Scan
assert self.params.geometry.scan.oscillation is not None
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)):
b_i = imageset.get_beam(i)
d_i = imageset.get_detector(i)
g_i = imageset.get_goniometer(i)
assert (beam is None and b_i is None) or 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 None
and d_i is None) or 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 None
and g_i is None) or 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,
)
oscillation = self.params.geometry.scan.oscillation
from dxtbx.sweep_filenames import template_regex_from_list
from dxtbx.imageset import ImageSetFactory
template, indices = template_regex_from_list(imageset.paths())
image_range = (min(indices), max(indices))
assert (image_range[1] + 1 - image_range[0]) == len(indices)
scan = Scan(image_range=image_range, oscillation=oscillation)
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 make_scan_experiment(image_range=(1, 100), expid="0"):
"""Make an experiment with a scan"""
return Experiment(scan=Scan(image_range, (0.0, 1.0)), identifier=expid)
def test_scan():
'''Test pickling the scan data object.'''
obj1 = Scan((1, 2), (1, 1))
obj2 = pickle_then_unpickle(obj1)
assert obj1 == obj2
def test_experiment():
d = {
"__id__":
"crystal",
"real_space_a":
[14.963210089244596, -22.599814679318, 51.02946725220764],
"real_space_b":
[-19.963976860932235, -51.503385430151205, -16.955728379753463],
"real_space_c":
[135.29560393219694, -34.371677531924206, -54.89475471853507],
"space_group_hall_symbol":
" P 4",
"A_at_scan_points": [[
0.004481726844090139,
-0.005980612987053365,
0.006013325470974739,
-0.006768741824936281,
-0.015428970379357122,
-0.0015280122438480544,
0.01528745348419002,
-0.005078101688718203,
-0.0024394384982453095,
]],
}
crystal = CrystalFactory.from_dict(d)
beam_d = {
"direction": [-2.4882593300783137e-06, -0.0, 0.9999999999969044],
"transmission": 1.0,
"polarization_normal": [0.0, 1.0, 0.0],
"divergence": 0.0,
"polarization_fraction": 0.999,
"flux": 0.0,
"sigma_divergence": 0.0,
"wavelength": 0.9762499999999994,
}
beam = BeamFactory.from_dict(beam_d)
scan = Scan(image_range=[0, 1], oscillation=[0.0, 0.01])
detector_dict = {
"hierarchy": {
"origin": [0.0, 0.0, 0.0],
"fast_axis": [1.0, 0.0, 0.0],
"name": "",
"raw_image_offset": [0, 0],
"slow_axis": [0.0, 1.0, 0.0],
"material": "",
"mask": [],
"thickness": 0.0,
"mu": 0.0,
"gain": 1.0,
"trusted_range": [0.0, 0.0],
"image_size": [0, 0],
"px_mm_strategy": {
"type": "SimplePxMmStrategy"
},
"identifier": "",
"type": "",
"children": [{
"panel": 0
}],
"pixel_size": [0.0, 0.0],
},
"panels": [{
"origin":
[-210.66631009735772, 205.7063614421482, -263.8386975038205],
"fast_axis": [
0.9999973940105483,
-0.0016357501034268717,
-0.0015925745544149894,
],
"name":
"Panel",
"raw_image_offset": [0, 0],
"slow_axis": [
-0.0016426481736367285,
-0.999989234013669,
-0.004339765400707805,
],
"material":
"Si",
"mask": [
[488, 1, 494, 2527],
[982, 1, 988, 2527],
[1476, 1, 1482, 2527],
[1970, 1, 1976, 2527],
[1, 196, 2463, 212],
[1, 408, 2463, 424],
[1, 620, 2463, 636],
[1, 832, 2463, 848],
[1, 1044, 2463, 1060],
[1, 1256, 2463, 1272],
[1, 1468, 2463, 1484],
[1, 1680, 2463, 1696],
[1, 1892, 2463, 1908],
[1, 2104, 2463, 2120],
[1, 2316, 2463, 2332],
],
"thickness":
0.32,
"mu":
3.9220322752480934,
"gain":
1.0,
"trusted_range": [-1.0, 161977.0],
"image_size": [2463, 2527],
"px_mm_strategy": {
"type": "ParallaxCorrectedPxMmStrategy"
},
"identifier":
"",
"type":
"SENSOR_PAD",
"pixel_size": [0.17200000000000001, 0.17200000000000001],
}],
}
detector = DetectorFactory.from_dict(detector_dict)
expt = Experiment(beam=beam, crystal=crystal, scan=scan, detector=detector)
return expt
