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
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 = detector_factory.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.e6))
def __init__(self, plots = False):
# Do we make scatterplots?
self.do_plots = plots
# 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_model(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.experiment import detector_factory
self.detector = detector_factory.make_detector("PAD", d1, d2,
matrix.col((0, 0, -110)), (pix_size_f, pix_size_s),
(npx_fast, npx_slow), (0, 2e20))
def __init__(self, plots = False):
# Do we make scatterplots?
self.do_plots = plots
# 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_model(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.experiment import detector_factory
self.detector = detector_factory.make_detector("PAD", d1, d2,
matrix.col((0, 0, -110)), (pix_size_f, pix_size_s),
(npx_fast, npx_slow), (0, 2e20))
if __name__ == '__main__':
# set the random seed to make the test reproducible
random.seed(1337)
# set up a simple detector frame with directions aligned with
# principal axes and sensor origin located on the z-axis at -110
d1 = matrix.col((1, 0, 0))
d2 = matrix.col((0, -1, 0))
#lim = (0,50)
npx_fast = 1475
npx_slow = 1679
pix_size_f = pix_size_s = 0.172
detector = detector_factory.make_detector("PAD", d1, d2,
matrix.col((0, 0, -110)), (pix_size_f, pix_size_s),
(npx_fast, npx_slow), (0, 2e20))
dp = DetectorParameterisationSinglePanel(detector)
beam = beam_factory().make_beam(
sample_to_source=-1*(matrix.col((0, 0, -110)) + 10 * d1 + 10 * d2),
wavelength=1.0)
# Test change of parameters
# =========================
# 1. shift detector plane so that the z-axis intercepts its centre
# at a distance of 100 along the initial normal direction. As the
# initial normal is along -z, we expect the frame to intercept the
# z-axis at -100.
if __name__ == '__main__':
# set the random seed to make the test reproducible
random.seed(1337)
# set up a simple detector frame with directions aligned with
# principal axes and sensor origin located on the z-axis at -110
d1 = matrix.col((1, 0, 0))
d2 = matrix.col((0, -1, 0))
#lim = (0,50)
npx_fast = 1475
npx_slow = 1679
pix_size_f = pix_size_s = 0.172
detector = detector_factory.make_detector("PAD", d1, d2,
matrix.col((0, 0, -110)),
(pix_size_f, pix_size_s),
(npx_fast, npx_slow), (0, 2e20))
dp = DetectorParameterisationSinglePanel(detector)
beam = beam_factory().make_beam(sample_to_source=-1 * (matrix.col(
(0, 0, -110)) + 10 * d1 + 10 * d2),
wavelength=1.0)
# Test change of parameters
# =========================
# 1. shift detector plane so that the z-axis intercepts its centre
# at a distance of 100 along the initial normal direction. As the
# initial normal is along -z, we expect the frame to intercept the
# z-axis at -100.
