def __init__(self, phi0, misset0, phi1, misset1):
"""Initialise the rotation axis and what have you from some
experimental results. N.B. all input values in DEGREES."""
# canonical: X = X-ray beam
# Z = rotation axis
# Y = Z ^ X
z = matrix.col([0, 0, 1])
# then calculate the rotation axis
R = (
(
z.axis_and_angle_as_r3_rotation_matrix(phi1, deg=True)
* matrix.sqr(xyz_matrix(misset1[0], misset1[1], misset1[2]))
)
* (
z.axis_and_angle_as_r3_rotation_matrix(phi0, deg=True)
* matrix.sqr(xyz_matrix(misset0[0], misset0[1], misset0[2]))
).inverse()
)
self._z = z
self._r = matrix.col(r3_rotation_axis_and_angle_from_matrix(R).axis)
self._M0 = matrix.sqr(xyz_matrix(misset0[0], misset0[1], misset0[2]))
return
def run(self, args=None):
"""Execute the script."""
# Parse the command line
params, options = self.parser.parse_args(args, show_diff_phil=True)
# Check the number of experiments is at least 2
experiments = flatten_experiments(params.input.experiments)
if len(experiments) < 2:
self.parser.print_help()
return
detectors = [experiment.detector[0] for experiment in experiments]
for pair in combinations(detectors, 2):
determine_axis(pair, params)
crystals = [experiment.crystal for experiment in experiments]
goniometers = [experiment.goniometer for experiment in experiments]
FUs = []
for c, g in zip(crystals, goniometers):
u = matrix.sqr(c.get_U())
f = matrix.sqr(g.get_fixed_rotation())
FUs.append(f * u)
for pair in combinations(FUs, 2):
R = pair[1] * pair[0].inverse()
rot = r3_rotation_axis_and_angle_from_matrix(R)
angle = rot.angle(deg=True)
axis = matrix.col(rot.axis)
if abs(angle) < 10:
continue
print("Axis: %8.5f %8.5f %8.5f" % axis.elems, "angle: %7.4f" % angle)
def __init__(self, phi0, misset0, phi1, misset1):
"""Initialise the rotation axis and what have you from some
experimental results. N.B. all input values in DEGREES."""
# canonical: X = X-ray beam
# Z = rotation axis
# Y = Z ^ X
z = matrix.col([0, 0, 1])
# then calculate the rotation axis
R = (
(
z.axis_and_angle_as_r3_rotation_matrix(phi1, deg=True)
* matrix.sqr(xyz_matrix(misset1[0], misset1[1], misset1[2]))
)
* (
z.axis_and_angle_as_r3_rotation_matrix(phi0, deg=True)
* matrix.sqr(xyz_matrix(misset0[0], misset0[1], misset0[2]))
).inverse()
)
self._z = z
self._r = matrix.col(r3_rotation_axis_and_angle_from_matrix(R).axis)
self._M0 = matrix.sqr(xyz_matrix(misset0[0], misset0[1], misset0[2]))
return
def difference_rotation_matrix_axis_angle(crystal_a, crystal_b, target_angle=0):
from cctbx import sgtbx
# assert crystal_a.get_space_group() == crystal_b.get_space_group()
space_group = crystal_b.get_space_group()
best_R_ab = None
best_cb_op = None
best_axis = None
best_angle = 1e8
# iterate over space group ops to find smallest differences
for i_op, op in enumerate(space_group.build_derived_laue_group().all_ops()):
if op.r().determinant() < 0:
continue
elif not op.t().is_zero():
continue
cb_op = sgtbx.change_of_basis_op(op.inverse())
crystal_b_sym = crystal_b.change_basis(cb_op)
U_a = crystal_a.get_U()
U_b = crystal_b_sym.get_U()
assert U_a.is_r3_rotation_matrix()
assert U_b.is_r3_rotation_matrix()
# the rotation matrix to transform from U_a to U_b
R_ab = U_b * U_a.transpose()
axis_angle = r3_rotation_axis_and_angle_from_matrix(R_ab)
axis = axis_angle.axis
angle = axis_angle.angle() * 180.0 / math.pi
for sign in (+1, -1):
if abs(sign * angle - target_angle) < abs(best_angle - target_angle):
best_angle = sign * angle
best_axis = tuple(sign * a for a in axis)
best_R_ab = R_ab if sign > 0 else R_ab.inverse()
best_cb_op = cb_op if sign > 0 else cb_op.inverse()
return best_R_ab, best_axis, best_angle, best_cb_op
def difference_rotation_matrix_axis_angle(crystal_a, crystal_b, target_angle=0):
from cctbx import sgtbx
# assert crystal_a.get_space_group() == crystal_b.get_space_group()
space_group = crystal_b.get_space_group()
best_R_ab = None
best_cb_op = None
best_axis = None
best_angle = 1e8
# iterate over space group ops to find smallest differences
for i_op, op in enumerate(space_group.build_derived_laue_group().all_ops()):
if op.r().determinant() < 0:
continue
elif not op.t().is_zero():
continue
cb_op = sgtbx.change_of_basis_op(op.inverse())
crystal_b_sym = crystal_b.change_basis(cb_op)
U_a = matrix.sqr(crystal_a.get_U())
U_b = matrix.sqr(crystal_b_sym.get_U())
assert U_a.is_r3_rotation_matrix()
assert U_b.is_r3_rotation_matrix()
# the rotation matrix to transform from U_a to U_b
R_ab = U_b * U_a.transpose()
axis_angle = r3_rotation_axis_and_angle_from_matrix(R_ab)
axis = axis_angle.axis
angle = axis_angle.angle() * 180.0 / math.pi
for sign in (+1, -1):
if abs(sign * angle - target_angle) < abs(best_angle - target_angle):
best_angle = sign * angle
best_axis = tuple(sign * a for a in axis)
best_R_ab = R_ab if sign > 0 else R_ab.inverse()
best_cb_op = cb_op if sign > 0 else cb_op.inverse()
return best_R_ab, best_axis, best_angle, best_cb_op
def compute_Q(xparm_target, xparm_move):
_M = determine_rotation_to_dtrek(xparm_target)
a_t, b_t, c_t = parse_xds_xparm(xparm_target)
a_m, b_m, c_m = parse_xds_xparm(xparm_move)
m_t = matrix.sqr(a_t + b_t + c_t)
min_r = 180.0
min_ax = None
for op in ['X,Y,Z', '-X,-Y,Z', '-X,Y,-Z', 'X,-Y,-Z',
'Z,X,Y', 'Z,-X,-Y', '-Z,-X,Y', '-Z,X,-Y',
'Y,Z,X', '-Y,Z,-X', 'Y,-Z,-X', '-Y,-Z,X']:
op_m = op_to_mat(op)
m_m = op_m * matrix.sqr(a_m + b_m + c_m)
q = m_t.inverse() * m_m
if math.fabs(q.determinant() - 1) > 0.1:
print 'rejected %s' % op
continue
q_r = r3_rotation_axis_and_angle_from_matrix(q.inverse())
if math.fabs(q_r.angle(deg = True)) < min_r:
if q_r.angle(deg = True) >= 0:
min_ax = matrix.col(q_r.axis)
min_r = q_r.angle(deg = True)
else:
min_ax = - matrix.col(q_r.axis)
min_r = - q_r.angle(deg = True)
return (_M * min_ax).elems, min_r
def _reorient_coordinate_frame(self):
"""Align a DIALS experiment and data in a reflection table to the
PETS coordinate system. In that system, the s0 vector is aligned with
-Z, while the rotation axis is in the X-Z plane, close to +X"""
axis = matrix.col(self.experiment.goniometer.get_rotation_axis())
us0 = matrix.col(self.experiment.beam.get_unit_s0())
normal = us0.cross(-axis).normalize()
orthogonalised_axis = us0.cross(normal).normalize()
# Keep track of s1.us0 values to check reorientation
s1_dot_us0 = self.reflections["s1"].dot(us0)
R = align_reference_frame(us0, (0, 0, -1), orthogonalised_axis,
(1, 0, 0))
axis_angle = r3_rotation_axis_and_angle_from_matrix(R)
axis = axis_angle.axis
angle = axis_angle.angle(deg=False)
logger.info(
"Rotating experiment about axis ({:.4f}, {:.4f}, {:.4f}) by {:.3f}°"
.format(*axis, np.degrees(angle)))
self.experiment.detector.rotate_around_origin(axis, angle, deg=False)
self.experiment.crystal = rotate_crystal(self.experiment.crystal, R,
axis, angle)
# Following does not work (https://github.com/cctbx/dxtbx/issues/454)
# self.experiment.beam.rotate_around_origin(axis, angle, deg=False)
# Set unit s0 and polarization normal directly instead (preserving inconsistent
# beam, if that's what we have).
new_us0 = (R *
matrix.col(self.experiment.beam.get_unit_s0())).normalize()
new_p_norm = (R * matrix.col(
self.experiment.beam.get_polarization_normal())).normalize()
self.experiment.beam.set_unit_s0(new_us0)
self.experiment.beam.set_polarization_normal(new_p_norm)
# Rotating the goniometer is also complicated. See https://github.com/cctbx/dxtbx/pull/451
new_datum = (R * matrix.col(
self.experiment.goniometer.get_rotation_axis_datum())).normalize()
new_F = (R *
matrix.sqr(self.experiment.goniometer.get_fixed_rotation()) *
R.transpose())
new_S = (
R * matrix.sqr(self.experiment.goniometer.get_setting_rotation()) *
R.transpose())
self.experiment.goniometer.set_rotation_axis_datum(new_datum)
self.experiment.goniometer.set_setting_rotation(new_S)
self.experiment.goniometer.set_fixed_rotation(new_F)
# Re-calculate s1 vectors and reciprocal lattice points with new geometry
el = ExperimentList()
el.append(self.experiment)
self.reflections.map_centroids_to_reciprocal_space(el, calculated=True)
error = flex.abs(s1_dot_us0 - self.reflections["s1"].dot(new_us0))
if flex.max(error) > 1e-10:
raise RuntimeError("Failed to rotate experiment correctly")
def derive_axis_angle(xparm0, xparm1): xparm0 = find_xparm(xparm0) xparm1 = find_xparm(xparm1) from scitbx.math import r3_rotation_axis_and_angle_from_matrix import math ub0 = xparm_to_ub(xparm0) ub1 = xparm_to_ub(xparm1) R = ub1 * ub0.inverse() axis_angle = r3_rotation_axis_and_angle_from_matrix(R) axis = axis_angle.axis angle = axis_angle.angle() * 180.0 / math.pi return axis, angle, R
def determine_effective_scan_axis(gonio):
x = gonio.rotate_vector(0.0, 1, 0, 0)
y = gonio.rotate_vector(0.0, 0, 1, 0)
z = gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = gonio.rotate_vector(1.0, 1, 0, 0)
y1 = gonio.rotate_vector(1.0, 0, 1, 0)
z1 = gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
rot = r3_rotation_axis_and_angle_from_matrix(RA)
return rot.axis, rot.angle(deg = True)
def cbf_gonio_to_effective_axis_fixed_old(cbf_gonio):
'''Given a cbf goniometer handle, first determine the real rotation
axis, then determine the fixed component of rotation which is rotated
about this axis.'''
# First construct the real rotation axis, as the difference in rotating
# the identity matrix at the end of the scan and the beginning.
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0)
y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0)
z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
rot = r3_rotation_axis_and_angle_from_matrix(RA)
# Then, given this, determine the component of the scan which is fixed -
# which will need to be with respect to the unrotated axis. N.B. this
# will not be unique, but should be correct modulo a free rotation about
# the shifted axis.
start = cbf_gonio.get_rotation_range()[0]
# want positive rotations => if negative invert axis
axis = matrix.col(rot.axis)
angle = rot.angle()
if angle < 0:
axis = -1 * axis
# common sense would suggest in here that if the angle is -ve should
# be made +ve - works OK for omega scans but not phi scans, probably
# incomplete goniometer definition problem...
# start = -start
S = axis.axis_and_angle_as_r3_rotation_matrix(start, deg=True)
return axis, S.inverse() * R
def cbf_gonio_to_effective_axis_fixed_old(cbf_gonio):
'''Given a cbf goniometer handle, first determine the real rotation
axis, then determine the fixed component of rotation which is rotated
about this axis.'''
# First construct the real rotation axis, as the difference in rotating
# the identity matrix at the end of the scan and the beginning.
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0)
y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0)
z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
rot = r3_rotation_axis_and_angle_from_matrix(RA)
# Then, given this, determine the component of the scan which is fixed -
# which will need to be with respect to the unrotated axis. N.B. this
# will not be unique, but should be correct modulo a free rotation about
# the shifted axis.
start = cbf_gonio.get_rotation_range()[0]
# want positive rotations => if negative invert axis
axis = matrix.col(rot.axis)
angle = rot.angle()
if angle < 0:
axis = -1 * axis
# common sense would suggest in here that if the angle is -ve should
# be made +ve - works OK for omega scans but not phi scans, probably
# incomplete goniometer definition problem...
# start = -start
S = axis.axis_and_angle_as_r3_rotation_matrix(start, deg=True)
return axis, S.inverse() * R
def run(self):
'''Execute the script.'''
from dials.util.options import flatten_experiments
# Parse the command line
params, options = self.parser.parse_args(show_diff_phil=True)
# Check the number of experiments is at least 2
experiments = flatten_experiments(params.input.experiments)
if len(experiments) < 2:
self.parser.print_help()
return
detectors = [experiment.detector[0] for experiment in experiments]
from itertools import combinations
for pair in combinations(detectors, 2):
determine_axis(pair, params)
from scitbx import matrix
from scitbx.math import r3_rotation_axis_and_angle_from_matrix
crystals = [experiment.crystal for experiment in experiments]
goniometers = [experiment.goniometer for experiment in experiments]
FUs = []
for c, g in zip(crystals, goniometers):
u = matrix.sqr(c.get_U())
f = matrix.sqr(g.get_fixed_rotation())
FUs.append(f * u)
for pair in combinations(FUs, 2):
R = pair[1] * pair[0].inverse()
rot = r3_rotation_axis_and_angle_from_matrix(R)
angle = rot.angle(deg=True)
axis = matrix.col(rot.axis)
if abs(angle) < 10:
continue
print('Axis: %8.5f %8.5f %8.5f' % axis.elems,
'angle: %7.4f' % angle)
def cbf_gonio_to_effective_axis(cbf_gonio): '''Given a cbf goniometer handle, determine the real rotation axis.''' x = cbf_gonio.rotate_vector(0.0, 1, 0, 0) y = cbf_gonio.rotate_vector(0.0, 0, 1, 0) z = cbf_gonio.rotate_vector(0.0, 0, 0, 1) R = matrix.rec(x + y + z, (3, 3)).transpose() x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0) y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0) z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1) R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose() RA = R1 * R.inverse() axis = r3_rotation_axis_and_angle_from_matrix(RA).axis return axis
def cbf_gonio_to_effective_axis(cbf_gonio):
'''Given a cbf goniometer handle, determine the real rotation axis.'''
x = cbf_gonio.rotate_vector(0.0, 1, 0, 0)
y = cbf_gonio.rotate_vector(0.0, 0, 1, 0)
z = cbf_gonio.rotate_vector(0.0, 0, 0, 1)
R = matrix.rec(x + y + z, (3, 3)).transpose()
x1 = cbf_gonio.rotate_vector(1.0, 1, 0, 0)
y1 = cbf_gonio.rotate_vector(1.0, 0, 1, 0)
z1 = cbf_gonio.rotate_vector(1.0, 0, 0, 1)
R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
RA = R1 * R.inverse()
axis = r3_rotation_axis_and_angle_from_matrix(RA).axis
return axis
def align_experiments(
experiments: ExperimentList,
params: libtbx.phil.scope_extract,
) -> ExperimentList:
if len(experiments) > 1:
logger.info(
"Only the first experiment will be used to determine the detector axes"
)
expt = experiments[0]
detector = expt.detector
if len(detector) > 1:
logger.info(
"Only the first panel will be used to determine the detector axes")
panel = detector[0]
xds_x, xds_y = read_xds_inp(params.input.xds_inp)
R = align_reference_frame(panel.get_fast_axis(), xds_x,
panel.get_slow_axis(), xds_y)
axis_angle = r3_rotation_axis_and_angle_from_matrix(R)
axis = axis_angle.axis
angle = axis_angle.angle()
logger.info(
f"Rotating experiment{'s' if len(experiments) else ''} about axis {axis} by {np.degrees(angle)}°"
)
for expt in experiments:
expt.detector.rotate_around_origin(axis, angle, deg=False)
expt.beam.rotate_around_origin(axis, angle, deg=False)
# https://github.com/cctbx/dxtbx/issues/447
# expt.goniometer.rotate_around_origin(axis, angle, deg=False)
rotation_axis = matrix.col(expt.goniometer.get_rotation_axis())
expt.goniometer.set_rotation_axis(R * rotation_axis)
if expt.crystal is not None:
expt.crystal = rotate_crystal(expt.crystal, R, axis, angle)
return experiments
def find_U_matrix(found_vectors, crystal, beam_energy=8, optimise_U=True,
refl='orient', angle_accuracy = 0.5):
"""Given a Crystal class object with a cif file loaded into it, this
function returns the U matrix as a dnp array.
Args:
found_vectors: A list of Vector class objects representing the momentum
transfer vectors of the measured Bragg peaks.
crystal: A Crystal class object.
beam_energy: The beam energy in keV.
optimise_U: If True the function optimises the U matrix before
returning can be set to False if in Jython because requires scipy.
refl: The filter applied to the Bragg reflections read from the cif file.
angle_accuracy: The accuracy required for two angle to be considered equal.
Returns:
U: The U matrix as a dnp object.
"""
# First gets all the allowed momentum transfer vectors of the crystal.
grouped_reflections = f.group_reflections(crystal, beam_energy, refl=refl)
all_vectors = []
for group in grouped_reflections:
group_vectors = f.momentum_transfer_vectors(group, crystal)
all_vectors += group_vectors
# Find the target vectors.
target_vectors = finding_the_targets(found_vectors, all_vectors, crystal, angle_accuracy)
found_vectors_copy = copy.deepcopy(found_vectors)
# Find and apply the first rotation.
rotation1 = get_rotator(found_vectors[0], target_vectors[0])
found_vectors = rotate_list(rotation1, found_vectors)
# Find the second rotation
rotation2 = get_second_rotator(target_vectors[0], found_vectors[1],
target_vectors[1])
U = rotation2 * rotation1
# Optimising the U matrix
def diff(array, data, vectors):
"""This is a function used to optimise the U matrix. It evaluates the
difference between the rotated set of vectors and their corosponding
vectors in reciprical space.
"""
x = array[0]
y = array[1]
z = array[2]
angle = array[3]
axis = Vector([x, y, z])
U = Rotator(scm.r3_rotation_axis_and_angle_as_matrix(axis, angle))
data = rotate_list(U, data)
index_list=[]
for i, dat in enumerate(data):
diffs = []
dat = dat
for j, vector in enumerate(vectors):
diffs.append((dat-vector).length())
index = diffs.index(min(dnp.abs(diffs)))
index_list.append(index)
targets = [0]*len(data)
for i, idx in enumerate(index_list):
targets[i] = vectors[idx]
total = 0
for i, dat in enumerate(data):
total += dnp.abs((dat - targets[i]).length())
return total
if not optimise_U:
return U
elif optimise_U:
# The array gives a first estimate for the arguments for the diff
# function.
U_axis_angle = scm.r3_rotation_axis_and_angle_from_matrix(U)
axis = Vector(U_axis_angle.axis)
array = dnp.array([axis[0], axis[1], axis[2], U_axis_angle.angle()])
import scipy.optimize
optimise = scipy.optimize.minimize(diff, array, (found_vectors_copy,
all_vectors),
bounds=[(-1, 1), (-1, 1), (-1, 1),
(-dnp.pi, dnp.pi)])
if optimise['success']:
new_axis = Vector((optimise.x[0], optimise.x[1], optimise.x[2]))
new_U = Rotator(scm.r3_rotation_axis_and_angle_as_matrix(new_axis,
optimise.x[3]))
return new_U
else:
print optimise
print diff(array, found_vectors_copy, all_vectors)
new_axis = Vector((optimise.x[0], optimise.x[1], optimise.x[2]))
new_U = Rotator(scm.r3_rotation_axis_and_angle_as_matrix(new_axis,
optimise.x[3]))
new_U_axis_angle = scm.r3_rotation_axis_and_angle_from_matrix(
new_U)
array = dnp.array([new_axis[0], new_axis[1], new_axis[2],
new_U_axis_angle.angle()])
print 'U matrix optimisation failed.'
return U
else:
raise Exception("""optimise_U must be a boolean type""")
def run(args):
import libtbx.load_env
from scitbx import matrix
from cctbx.sgtbx import lattice_symmetry_group
from scitbx.math import r3_rotation_axis_and_angle_from_matrix
usage = "%s [options] experiment_0.json ..." % \
libtbx.env.dispatcher_name
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_experiments=True,
check_format=False,
epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
experiments = params.input.experiments
# check input
space_group = None
for experiment in experiments:
assert(len(experiment.data.goniometers()) == 1)
assert(len(experiment.data.crystals()) == 1)
crystal = experiment.data.crystals()[0]
if space_group is None:
space_group = crystal.get_space_group()
else:
assert(crystal.get_space_group() == space_group)
reference_U = None
reference_space_group = None
for j, experiment in enumerate(experiments):
goniometer = experiment.data.goniometers()[0]
F = matrix.sqr(goniometer.get_fixed_rotation())
crystal = experiment.data.crystals()[0]
U = matrix.sqr(crystal.get_U())
B = matrix.sqr(crystal.get_B())
UB = F * U * B
UBt = UB.transpose().elems
a, b, c = matrix.col(UBt[0:3]), matrix.col(UBt[3:6]), matrix.col(UBt[6:9])
axis = matrix.col(goniometer.get_rotation_axis())
from math import pi
r2d = 180 / pi
abc = [a, b, c]
abc_names = 'abc'
distances = [(r2d * (min(axis.angle(_a), pi - axis.angle(_a))), k)
for k, _a in enumerate(abc)]
close = sorted(distances)[0]
if reference_U is None:
reference_U = U
reference_space_group = lattice_symmetry_group(crystal.get_unit_cell(),
max_delta=0.0)
print '%s possible lattice ops' % len(reference_space_group.all_ops())
print 'Experiment %d' % j
print 'Closest (original) axis: %s* %.2f' % \
(abc_names[close[1]], close[0])
results = []
for op in reference_space_group.all_ops():
R = B * matrix.sqr(op.r().as_double()).transpose() * B.inverse()
relative = (U * R).inverse() * reference_U
rot = r3_rotation_axis_and_angle_from_matrix(relative)
results.append((abs(rot.angle()), op.r().as_hkl(), rot))
results.sort()
print 'Best reindex op for experiment %d: %12s (%.3f)' % \
(j, results[0][1], 180.0 * results[0][2].angle() / pi)
if results[0][0] > (5 * pi / 180.0):
print 'Rotation: axis: %.4f %.4f %.4f' % results[0][2].axis
print ' angle: %.4f degrees' % \
(180.0 * results[0][2].angle() / pi)
def run(args):
import libtbx.load_env
from scitbx import matrix
from cctbx.sgtbx import lattice_symmetry_group
from scitbx.math import r3_rotation_axis_and_angle_from_matrix
usage = "%s [options] experiment_0.expt ..." % libtbx.env.dispatcher_name
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_experiments=True,
check_format=False,
epilog=help_message,
)
params, options = parser.parse_args(show_diff_phil=True)
experiments = params.input.experiments
# check input
space_group = None
for experiment in experiments:
assert len(experiment.data.goniometers()) == 1
assert len(experiment.data.crystals()) == 1
crystal = experiment.data.crystals()[0]
if space_group is None:
space_group = crystal.get_space_group()
else:
assert crystal.get_space_group() == space_group
reference_U = None
reference_space_group = None
for j, experiment in enumerate(experiments):
goniometer = experiment.data.goniometers()[0]
F = matrix.sqr(goniometer.get_fixed_rotation())
crystal = experiment.data.crystals()[0]
U = matrix.sqr(crystal.get_U())
B = matrix.sqr(crystal.get_B())
UB = F * U * B
UBt = UB.transpose().elems
a, b, c = matrix.col(UBt[0:3]), matrix.col(UBt[3:6]), matrix.col(
UBt[6:9])
axis = matrix.col(goniometer.get_rotation_axis())
from math import pi
r2d = 180 / pi
abc = [a, b, c]
abc_names = "abc"
distances = [(r2d * (min(axis.angle(_a), pi - axis.angle(_a))), k)
for k, _a in enumerate(abc)]
close = sorted(distances)[0]
if reference_U is None:
reference_U = U
reference_space_group = lattice_symmetry_group(
crystal.get_unit_cell(), max_delta=0.0)
print("%s possible lattice ops" %
len(reference_space_group.all_ops()))
print("Experiment %d" % j)
print("Closest (original) axis: %s* %.2f" %
(abc_names[close[1]], close[0]))
results = []
for op in reference_space_group.all_ops():
R = B * matrix.sqr(op.r().as_double()).transpose() * B.inverse()
relative = (U * R).inverse() * reference_U
rot = r3_rotation_axis_and_angle_from_matrix(relative)
results.append((abs(rot.angle()), op.r().as_hkl(), rot))
results.sort()
print("Best reindex op for experiment %d: %12s (%.3f)" %
(j, results[0][1], 180.0 * results[0][2].angle() / pi))
if results[0][0] > (5 * pi / 180.0):
print("Rotation: axis: %.4f %.4f %.4f" % results[0][2].axis)
print(" angle: %.4f degrees" %
(180.0 * results[0][2].angle() / pi))
def find_U_matrix(found_vectors, crystal, beam_energy=8, optimise_U=True):
"""Given a Crystal class object with a cif file loaded into it, this
function returns the U matrix as a dnp array.
Args:
found_vectors: A list of Vector class objects representing the momentum
transfer vectors of the measured Bragg peaks.
crystal: A Crystal class object.
beam_energy: The beam energy in keV.
optimise_U: If True the function optimises the U matrix before
returning can be set to False if in Jython because requires scipy.
Returns:
U: The U matrix as a dnp object.
"""
# First gets all the allowed momentum transfer vectors of the crystal.
grouped_reflections = f.group_reflections(crystal, beam_energy)
all_vectors = []
for group in grouped_reflections:
group_vectors = f.momentum_transfer_vectors(group, crystal)
all_vectors += group_vectors
# Find the target vectors.
target_vectors = finding_the_targets(found_vectors, all_vectors)
found_vectors_copy = copy.deepcopy(found_vectors)
U = Rotator((1,0,0,0,1,0,0,0,1))
print U
# Optimising the U matrix
def diff(array, data, vectors):
"""This is a function used to optimise the U matrix. It evaluates
"""
x = array[0]
y = array[1]
z = array[2]
# z = 1.0
angle = array[3]
axis = Vector([x, y, z])
U = Rotator(scm.r3_rotation_axis_and_angle_as_matrix(axis, angle))
data = rotate_list(U, data)
index_list=[]
for i, dat in enumerate(data):
diffs = []
dat = dat
for j, vector in enumerate(vectors):
diffs.append((dat-vector).length())
index = diffs.index(min(dnp.abs(diffs)))
index_list.append(index)
targets = [0]*len(data)
for i, idx in enumerate(index_list):
targets[i] = vectors[idx]
total = 0
for i, dat in enumerate(data):
total += (dat - targets[i]).length()
return total*1000
if not optimise_U:
return U
elif optimise_U:
U_axis_angle = scm.r3_rotation_axis_and_angle_from_matrix(U)
axis = Vector(U_axis_angle.axis)
# The array gives a first estimate for the arguments for the diff
# function.
array = dnp.array([axis[0], axis[1], axis[2], U_axis_angle.angle()])
print 'old diff', diff(array, found_vectors_copy, all_vectors)
import scipy.optimize
optimise = scipy.optimize.basinhopping(diff, array, minimizer_kwargs={'args':(found_vectors_copy,
all_vectors)})
print optimise
new_axis = Vector((optimise.x[0], optimise.x[1], optimise.x[2]))
new_U = Rotator(scm.r3_rotation_axis_and_angle_as_matrix(new_axis.normalize(),
optimise.x[3]))
new_U_axis_angle = scm.r3_rotation_axis_and_angle_from_matrix(
new_U)
print 'new diff', diff(optimise, found_vectors_copy, all_vectors)
print 'old ax', axis
print 'new ax',new_axis
return new_U
else:
raise Exception("""optimise_U must be a boolean type""")
