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"""Setup experimental geometry for refinement test cases"""
from __future__ import annotations
import random
from dxtbx.model import BeamFactory, Crystal, DetectorFactory, GoniometerFactory
from libtbx.phil import command_line, parse
from scitbx import matrix
# Local functions
def random_vector_close_to(vector, sd=0.5):
return matrix.col(vector).rotate_around_origin(
matrix.col((random.random(), random.random(), random.random())).normalize(),
random.gauss(0, sd),
deg=True,
)
class Extract:
"""Parse and extract geometry model from PHIL"""
def __init__(
self, master_phil, local_overrides="", cmdline_args=None, verbose=False
):
self._verbose = verbose
arg_interpreter = command_line.argument_interpreter(master_phil=master_phil)
user_phil = parse(local_overrides)
cmdline_phils = []
if cmdline_args:
for arg in cmdline_args:
cmdline_phils.append(arg_interpreter.process(arg))
working_phil = master_phil.fetch(sources=[user_phil] + cmdline_phils)
self._params = working_phil.extract().geometry.parameters
self.set_seed()
self.build_goniometer()
self.build_crystal()
self.build_beam()
self.build_detector()
# write changes back to the PHIL object
temp = working_phil.extract()
temp.geometry.parameters = self._params
self.phil = master_phil.format(python_object=temp)
def set_seed(self):
if self._params.random_seed is not None:
random.seed(self._params.random_seed)
# set the flex random seed too
from dials.array_family import flex
flex.set_random_seed(self._params.random_seed)
if self._verbose:
msg = "Random seed set to %d while building models"
print(msg % self._params.random_seed)
def build_goniometer(self):
self.goniometer = GoniometerFactory.known_axis(self._params.goniometer.axis)
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(
0.0, self._params.beam.direction.inclination.angle
)
else:
inclination = self._params.beam.direction.inclination.angle
beam_dir = matrix.col((0, 0, 1)).rotate_around_origin(
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 = BeamFactory.make_beam(unit_s0=beam_dir, wavelength=wavelength)
def build_detector(self):
assert self._params.detector.directions.method in ["close_to", "exactly"]
if self._params.detector.directions.method == "close_to":
temp = self._params.detector.directions.close_to.dir1
dir1 = random_vector_close_to(
temp, sd=self._params.detector.directions.close_to.sd
)
n = random_vector_close_to(
self._params.detector.directions.close_to.norm,
sd=self._params.detector.directions.close_to.sd,
)
elif self._params.detector.directions.method == "exactly":
temp = self._params.detector.directions.exactly.dir1
dir1 = matrix.col(temp)
n = matrix.col(self._params.detector.directions.exactly.norm)
dir2 = n.cross(dir1).normalize()
assert self._params.detector.centre.method in ["close_to", "exactly"]
if self._params.detector.centre.method == "close_to":
centre = random_vector_close_to(
self._params.detector.centre.close_to.value,
sd=self._params.detector.centre.close_to.sd,
)
elif self._params.detector.centre.method == "exactly":
temp = self._params.detector.centre.exactly.value
centre = matrix.col(temp)
origin = centre - (
0.5 * self._params.detector.npx_fast * self._params.detector.pix_size * dir1
+ 0.5
* self._params.detector.npx_slow
* self._params.detector.pix_size
* dir2
)
self.detector = DetectorFactory.make_detector(
"PAD",
dir1,
dir2,
origin,
(self._params.detector.pix_size, self._params.detector.pix_size),
(self._params.detector.npx_fast, self._params.detector.npx_slow),
(0, 1.0e6),
)
@staticmethod
def _build_cell_vec(vec):
if vec.length.random:
length = random.uniform(*vec.length.range)
else:
length = vec.length.value
assert vec.direction.method in ["close_to", "exactly"]
if vec.direction.method == "close_to":
x = random_vector_close_to(
vec.direction.close_to.direction, sd=vec.direction.close_to.sd
)
elif vec.direction.method == "exactly":
x = matrix.col(vec.direction.exactly.direction)
return length * x
def build_crystal(self):
vecs = [
self._build_cell_vec(axis)
for axis in (
self._params.crystal.a,
self._params.crystal.b,
self._params.crystal.c,
)
]
sg = self._params.crystal.space_group_symbol
self.crystal = Crystal(*vecs, space_group_symbol=sg)
|
