def build_beam(self):
if self._params.beam.wavelength.random:
wavelength = random.uniform(
*self._params.beam.wavelength.range)
else: wavelength = self._params.beam.wavelength.value
assert self._params.beam.direction.method in ['inclination',
'close_to',
'exactly']
if self._params.beam.direction.method == 'inclination':
if self._params.beam.direction.inclination.random:
inclination = random.gauss(0.,
self._params.beam.direction.inclination.angle)
else: inclination = \
self._params.beam.direction.inclination.angle
beam_dir = matrix.col((0, 0, 1)).rotate(
matrix.col((0, 1, 0)), inclination, deg=True)
elif self._params.beam.direction.method == 'close_to':
temp = self._params.beam.direction.close_to.direction
beam_dir = random_vector_close_to(temp,
sd = self._params.beam.direction.close_to.sd)
elif self._params.beam.direction.method == 'exactly':
beam_dir = matrix.col(self._params.beam.direction.exactly)
self.beam = beam_factory.make_beam(unit_s0 = beam_dir,
wavelength = wavelength)
def __init__(self, test_nave_model = False):
# Set up experimental models with regular geometry
from dxtbx.model.experiment import beam_factory
from dxtbx.model.experiment import goniometer_factory
from dxtbx.model.experiment import detector_factory
from dxtbx.model.crystal import crystal_model
# Beam along the Z axis
self.beam = beam_factory.make_beam(unit_s0 = matrix.col((0, 0, 1)),
wavelength = 1.0)
# Goniometer (used only for index generation) along X axis
self.goniometer = goniometer_factory.known_axis(matrix.col((1, 0, 0)))
# Detector fast, slow along X, -Y; beam in the centre, 200 mm distance
dir1 = matrix.col((1, 0, 0))
dir2 = matrix.col((0, -1, 0))
n = matrix.col((0, 0, 1))
centre = matrix.col((0, 0, 200))
npx_fast = npx_slow = 1000
pix_size = 0.2
origin = centre - (0.5 * npx_fast * pix_size * dir1 +
0.5 * npx_slow * pix_size * dir2)
self.detector = detector_factory.make_detector("PAD",
dir1, dir2, origin,
(pix_size, pix_size),
(npx_fast, npx_slow),
(0, 1.e6))
# Cubic 100 A^3 crystal
a = matrix.col((100, 0, 0))
b = matrix.col((0, 100, 0))
c = matrix.col((0, 0, 100))
self.crystal = crystal_model(a, b, c, space_group_symbol = "P 1")
if test_nave_model:
self.crystal._ML_half_mosaicity_deg = 500
self.crystal._ML_domain_size_ang = 0.2
# Collect these models in an Experiment (ignoring the goniometer)
from dxtbx.model.experiment.experiment_list import Experiment
self.experiment = Experiment(beam=self.beam, detector=self.detector,
goniometer=None, scan=None, crystal=self.crystal, imageset=None)
# Generate some reflections
self.reflections = self.generate_reflections()
return
from dxtbx.model.experiment import beam_factory, goniometer_factory
### local functions
def random_direction_close_to(vector):
return vector.rotate_around_origin(
matrix.col((random.random(), random.random(), random.random())).normalize(),
random.gauss(0, 1.0),
deg=True,
)
### Create models
# make a beam vector close to the Z axis
direction = random_direction_close_to(matrix.col((0, 0, 1)))
mybeam = beam_factory.make_beam(direction, 1.5)
# make a random P1 crystal
a = random.uniform(10, 20) * random_direction_close_to(matrix.col((1, 0, 0)))
b = random.uniform(10, 20) * random_direction_close_to(matrix.col((0, 1, 0)))
c = random.uniform(10, 20) * random_direction_close_to(matrix.col((0, 0, 1)))
crystal_model(a, b, c, space_group_symbol="P 1")
# make a dumb goniometer that rotates around X
mygonio = goniometer_factory.known_axis((1, 0, 0))
# generate some indices
resolution = 2.0
indices = full_sphere_indices(
unit_cell=mycrystal.get_unit_cell(),
resolution_limit=resolution,
from dxtbx.model.crystal import crystal_model
from dxtbx.model.experiment import beam_factory, goniometer_factory
### local functions
def random_direction_close_to(vector):
return vector.rotate_around_origin(matrix.col(
(random.random(),
random.random(),
random.random())).normalize(),
random.gauss(0, 1.0), deg = True)
### Create models
# make a beam vector close to the Z axis
direction = random_direction_close_to(matrix.col((0, 0, 1)))
mybeam = beam_factory.make_beam(direction, 1.5)
# make a random P1 crystal
a = random.uniform(10,20) * random_direction_close_to(matrix.col((1, 0, 0)))
b = random.uniform(10,20) * random_direction_close_to(matrix.col((0, 1, 0)))
c = random.uniform(10,20) * random_direction_close_to(matrix.col((0, 0, 1)))
crystal_model(a, b, c, space_group_symbol="P 1")
# make a dumb goniometer that rotates around X
mygonio = goniometer_factory.known_axis((1, 0, 0))
# generate some indices
resolution = 2.0
indices = full_sphere_indices(
unit_cell = mycrystal.get_unit_cell(),
resolution_limit = resolution,