def exercise_similarity():
model_1 = crystal_model(real_space_a=(10,0,0),
real_space_b=(0,11,0),
real_space_c=(0,0,12),
space_group_symbol="P 1",
mosaicity=0.5)
model_2 = crystal_model(real_space_a=(10,0,0),
real_space_b=(0,11,0),
real_space_c=(0,0,12),
space_group_symbol="P 1",
mosaicity=0.5)
assert model_1.is_similar_to(model_2)
# mosaicity tests
model_1.set_mosaicity(-1)
model_2.set_mosaicity(-0.5)
assert model_1.is_similar_to(model_2) # test ignores negative mosaicity
model_1.set_mosaicity(0.5)
model_2.set_mosaicity(0.63) # outside tolerance
assert not model_1.is_similar_to(model_2)
model_2.set_mosaicity(0.625) #just inside tolerance
assert model_1.is_similar_to(model_2)
# orientation tests
R = model_2.get_U()
dr1 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0101, deg=True)
dr2 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0099, deg=True)
model_2.set_U(dr1 * R)
assert not model_1.is_similar_to(model_2) # outside tolerance
model_2.set_U(dr2 * R)
assert model_1.is_similar_to(model_2) # inside tolerance
# unit_cell.is_similar_to is tested elsewhere
return
def exercise():
from dials.algorithms.indexing import compare_orientation_matrices
from dxtbx.model.crystal import crystal_model
from cctbx import sgtbx
from scitbx import matrix
from scitbx.math import euler_angles as euler
# try and see if we can get back the original rotation matrix and euler angles
real_space_a = matrix.col((10,0,0))
real_space_b = matrix.col((0,10,10))
real_space_c = matrix.col((0,0,10))
euler_angles = (1.3, 5.6, 7.8)
R = matrix.sqr(
euler.xyz_matrix(euler_angles[0], euler_angles[1], euler_angles[2]))
crystal_a = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('P 1'))
crystal_b = crystal_model(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('P 1'))
assert approx_equal(crystal_b.get_U() * crystal_a.get_U().transpose(), R)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.is_identity_op()
assert approx_equal(best_R_ab, R)
# now see if we can deconvolute the original euler angles after applying
# a change of basis to one of the crystals
crystal_a = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group=sgtbx.space_group('I 2 3'))
crystal_b = crystal_model(R * real_space_a,
R * real_space_b,
R * real_space_c,
space_group=sgtbx.space_group('I 2 3'))
cb_op = sgtbx.change_of_basis_op('z,x,y')
crystal_b = crystal_b.change_basis(cb_op)
best_R_ab, best_axis, best_angle, best_cb_op = \
compare_orientation_matrices.difference_rotation_matrix_axis_angle(
crystal_a,
crystal_b)
best_euler_angles = euler.xyz_angles(best_R_ab)
assert approx_equal(best_euler_angles, euler_angles)
assert best_cb_op.c() == cb_op.inverse().c()
assert approx_equal(best_R_ab, R)
def tst_dump_empty_sweep(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
from uuid import uuid4
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
imageset.set_beam(Beam((1, 0, 0)))
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 3), (0.0, 1.0)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp%s.json' % uuid4().hex
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
self.check(experiments, experiments2)
print 'OK'
def tst_dump_empty_sweep(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
from uuid import uuid4
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
imageset.set_beam(Beam((1, 0, 0)))
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 3), (0.0, 1.0)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp%s.json' % uuid4().hex
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
self.check(experiments, experiments2)
print 'OK'
def to_crystal(filename):
''' Get the crystal model from the xparm file
Params:
filename The xparm/or integrate filename
Return:
The crystal model
'''
from rstbx.cftbx.coordinate_frame_converter import \
coordinate_frame_converter
from dxtbx.model.crystal import crystal_model
from cctbx.sgtbx import space_group, space_group_symbols
# Get the real space coordinate frame
cfc = coordinate_frame_converter(filename)
real_space_a = cfc.get('real_space_a')
real_space_b = cfc.get('real_space_b')
real_space_c = cfc.get('real_space_c')
sg = cfc.get('space_group_number')
space_group = space_group(space_group_symbols(sg).hall())
mosaicity = cfc.get('mosaicity')
# Return the crystal model
return crystal_model(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=space_group,
mosaicity=mosaicity)
def tst_from_datablock(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model.crystal import crystal_model
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 2), (0, 1)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
datablock = DataBlockFactory.from_imageset(imageset)
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert(len(experiments) == 1)
assert(experiments[0].imageset is not None)
assert(experiments[0].beam is not None)
assert(experiments[0].detector is not None)
assert(experiments[0].goniometer is not None)
assert(experiments[0].scan is not None)
assert(experiments[0].crystal is not None)
print 'OK'
pass
def __init__(self, obj):
from dxtbx.model.crystal import crystal_model
import cctbx.uctbx
from scitbx import matrix
# Get the crystal parameters
unit_cell_parameters = list(obj.handle['unit_cell'][0])
unit_cell = cctbx.uctbx.unit_cell(unit_cell_parameters)
U = list(obj.handle['orientation_matrix'][0].flatten())
U = matrix.sqr(U)
B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
A = U * B
Ai = A.inverse()
real_space_a = Ai[0:3]
real_space_b = Ai[3:6]
real_space_c = Ai[6:9]
# Get the space group symbol
space_group_symbol = obj.handle['unit_cell_group'][()]
# Create the model
self.model = crystal_model(
real_space_a,
real_space_b,
real_space_c,
space_group_symbol)
def to_crystal(filename):
''' Get the crystal model from the xparm file
Params:
filename The xparm/or integrate filename
Return:
The crystal model
'''
from rstbx.cftbx.coordinate_frame_converter import \
coordinate_frame_converter
from dxtbx.model.crystal import crystal_model
from cctbx.sgtbx import space_group, space_group_symbols
# Get the real space coordinate frame
cfc = coordinate_frame_converter(filename)
real_space_a = cfc.get('real_space_a')
real_space_b = cfc.get('real_space_b')
real_space_c = cfc.get('real_space_c')
sg = cfc.get('space_group_number')
space_group = space_group(space_group_symbols(sg).hall())
mosaicity = cfc.get('mosaicity')
# Return the crystal model
return crystal_model(real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=space_group,
mosaicity=mosaicity)
def tst_crystal(self):
from dxtbx.serialize.crystal import to_dict, from_dict
from dxtbx.model.crystal import crystal_model
from scitbx import matrix
real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))
c1 = crystal_model(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group_symbol="P 1 2/m 1",
mosaicity=0.1)
d = to_dict(c1)
c2 = from_dict(d)
eps = 1e-7
assert(abs(matrix.col(d['real_space_a']) - real_space_a) <= eps)
assert(abs(matrix.col(d['real_space_b']) - real_space_b) <= eps)
assert(abs(matrix.col(d['real_space_c']) - real_space_c) <= eps)
assert(d['space_group_hall_symbol'] == "-P 2y")
assert(d['mosaicity'] == 0.1)
assert(c1 == c2)
print 'OK'
def predict_once(args):
from dxtbx.model.experiment.experiment_list import Experiment
U = args[0]
A = U * B
direct_matrix = A.inverse()
cryst_model = crystal_model(
direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group,
)
experiment = Experiment(
imageset=sweep,
beam=sweep.get_beam(),
detector=sweep.get_detector(),
goniometer=sweep.get_goniometer(),
scan=sweep.get_scan(),
crystal=cryst_model,
)
predicted_reflections = flex.reflection_table.from_predictions(experiment)
miller_indices = predicted_reflections["miller_index"]
miller_set = miller.set(crystal_symmetry, miller_indices, anomalous_flag=True)
if params.d_min is not None:
resolution_sel = miller_set.d_spacings().data() > params.d_min
predicted_reflections = predicted_reflections.select(resolution_sel)
return len(predicted_reflections)
def tst_crystal_with_scan_points(self):
from dxtbx.serialize.crystal import to_dict, from_dict
from dxtbx.model.crystal import crystal_model
from scitbx import matrix
real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))
c1 = crystal_model(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group_symbol="P 1 2/m 1",
mosaicity=0.1)
A = c1.get_A()
c1.set_A_at_scan_points([A for i in range(5)])
d = to_dict(c1)
c2 = from_dict(d)
eps = 1e-9
for Acomp in (d['A_at_scan_points']):
for e1, e2 in zip(A, Acomp):
assert(abs(e1 - e2) <= eps)
assert(c1 == c2)
print 'OK'
def tst_from_datablock(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model.crystal import crystal_model
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 2), (0, 1)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
datablock = DataBlockFactory.from_imageset(imageset)
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert(len(experiments) == 1)
assert(experiments[0].imageset is not None)
assert(experiments[0].beam is not None)
assert(experiments[0].detector is not None)
assert(experiments[0].goniometer is not None)
assert(experiments[0].scan is not None)
assert(experiments[0].crystal is not None)
print 'OK'
def test_random(self):
"""Test random initial orientations, random parameter shifts and random
times"""
attempts = 100
failures = 0
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for i in range(attempts):
# make a new P1 random crystal and parameterise it
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)))
xl = crystal_model(a, b, c, space_group_symbol="P 1")
xl_op = TestOrientationModel(50, xl, self.image_range, 5)
# How many parameters?
num_param = xl_op.num_free()
# apply random parameter shifts to the orientation (2.0 mrad each
# checkpoint)
p_vals = xl_op.get_param_vals()
sigmas = [2.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# select random time point at which to make comparisons
t = random.uniform(*self.image_range)
xl_op.set_time_point(t)
# compare analytical and finite difference derivatives
xl_op_an_ds_dp = xl_op.get_ds_dp()
xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * \
num_param)
for j in range(num_param):
try:
assert(approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
null_mat, eps = 1.e-6))
except Exception:
failures += 1
print "for try", i
print "failure for parameter number", j
print "of the orientation parameterisation"
print "with fd_ds_dp = "
print xl_op_fd_ds_dp[j]
print "and an_ds_dp = "
print xl_op_an_ds_dp[j]
print "so that difference fd_ds_dp - an_ds_dp ="
print xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]
if failures == 0: print "OK"
def create_Bmat():
"""Create a random crystal model, in P1 for maximum generality. Return the
B matrix of this crystal"""
from dxtbx.model.crystal import crystal_model
vecs = map(random_vector_close_to, [(20, 0, 0), (0, 20, 0), (0, 0, 20)])
return crystal_model(*vecs, space_group_symbol="P 1").get_B()
def test_random(self):
"""Test random initial orientations, random parameter shifts and random
times"""
attempts = 100
failures = 0
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for i in range(attempts):
# make a new P1 random crystal and parameterise it
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)))
xl = crystal_model(a, b, c, space_group_symbol="P 1")
xl_op = TestOrientationModel(50, xl, self.image_range, 5)
# How many parameters?
num_param = xl_op.num_free()
# apply random parameter shifts to the orientation (2.0 mrad each
# checkpoint)
p_vals = xl_op.get_param_vals()
sigmas = [2.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# select random time point at which to make comparisons
t = random.uniform(*self.image_range)
xl_op.set_time_point(t)
# compare analytical and finite difference derivatives
xl_op_an_ds_dp = xl_op.get_ds_dp()
xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * \
num_param)
for j in range(num_param):
try:
assert(approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
null_mat, eps = 1.e-6))
except Exception:
failures += 1
print "for try", i
print "failure for parameter number", j
print "of the orientation parameterisation"
print "with fd_ds_dp = "
print xl_op_fd_ds_dp[j]
print "and an_ds_dp = "
print xl_op_an_ds_dp[j]
print "so that difference fd_ds_dp - an_ds_dp ="
print xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]
if failures == 0: print "OK"
def build_crystal(self):
vecs = map(self._build_cell_vec,
[self._params.crystal.a,
self._params.crystal.b,
self._params.crystal.c])
sg = self._params.crystal.space_group_symbol
self.crystal = crystal_model(*vecs, space_group_symbol = sg)
def generate_crystal(unit_cell, space_group):
from dxtbx.model.crystal import crystal_model
B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
U = random_rotation()
A = U * B
direct_matrix = A.inverse()
return crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
def dials_crystal_from_orientation(crystal_orientation,space_group):
dm = crystal_orientation.direct_matrix()
AA = col((dm[0],dm[1],dm[2]))
BB = col((dm[3],dm[4],dm[5]))
CC = col((dm[6],dm[7],dm[8]))
from dxtbx.model.crystal import crystal_model
cryst = crystal_model(real_space_a=AA, real_space_b=BB, real_space_c=CC,
space_group=space_group)
return cryst
def generate_crystal(unit_cell, space_group):
from dxtbx.model.crystal import crystal_model
B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
U = random_rotation()
A = U * B
direct_matrix = A.inverse()
return crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
def tst_equality(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
# Create a load of models
b1 = Beam()
d1 = Detector()
g1 = Goniometer()
s1 = Scan()
c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Create a load of models that look the same but aren't
b2 = Beam()
d2 = Detector()
g2 = Goniometer()
s2 = Scan()
c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Create an experiment
e1 = Experiment(
beam=b1, detector=d1, goniometer=g1,
scan=s1, crystal=c1, imageset=None)
# Create an experiment
e2 = Experiment(
beam=b1, detector=d1, goniometer=g1,
scan=s1, crystal=c1, imageset=None)
# Create an experiment
e3 = Experiment(
beam=b2, detector=d2, goniometer=g2,
scan=s2, crystal=c2, imageset=None)
# Check e1 equals e2 but not e3
assert(e1 == e2)
assert(e1 != e3)
assert(e2 != e3)
# Test passed
print 'OK'
def tst_equality(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
# Create a load of models
b1 = Beam()
d1 = Detector()
g1 = Goniometer()
s1 = Scan()
c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Create a load of models that look the same but aren't
b2 = Beam()
d2 = Detector()
g2 = Goniometer()
s2 = Scan()
c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Create an experiment
e1 = Experiment(
beam=b1, detector=d1, goniometer=g1,
scan=s1, crystal=c1, imageset=None)
# Create an experiment
e2 = Experiment(
beam=b1, detector=d1, goniometer=g1,
scan=s1, crystal=c1, imageset=None)
# Create an experiment
e3 = Experiment(
beam=b2, detector=d2, goniometer=g2,
scan=s2, crystal=c2, imageset=None)
# Check e1 equals e2 but not e3
assert(e1 == e2)
assert(e1 != e3)
assert(e2 != e3)
# Test passed
print 'OK'
def __init__(self,params):
import cPickle as pickle
from dxtbx.model.beam import beam_factory
from dxtbx.model.detector import detector_factory
from dxtbx.model.crystal import crystal_model
from cctbx.crystal_orientation import crystal_orientation,basis_type
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
from scitbx import matrix
self.experiments = ExperimentList()
self.unique_file_names = []
self.params = params
data = pickle.load(open(self.params.output.prefix+"_frame.pickle","rb"))
frames_text = data.split("\n")
for item in frames_text:
tokens = item.split(' ')
wavelength = float(tokens[order_dict["wavelength"]])
beam = beam_factory.simple(wavelength = wavelength)
detector = detector_factory.simple(
sensor = detector_factory.sensor("PAD"), # XXX shouldn't hard code for XFEL
distance = float(tokens[order_dict["distance"]]),
beam_centre = [float(tokens[order_dict["beam_x"]]), float(tokens[order_dict["beam_y"]])],
fast_direction = "+x",
slow_direction = "+y",
pixel_size = [self.params.pixel_size,self.params.pixel_size],
image_size = [1795,1795], # XXX obviously need to figure this out
)
reciprocal_matrix = matrix.sqr([float(tokens[order_dict[k]]) for k in [
'res_ori_1','res_ori_2','res_ori_3','res_ori_4','res_ori_5','res_ori_6','res_ori_7','res_ori_8','res_ori_9']])
ORI = crystal_orientation(reciprocal_matrix, basis_type.reciprocal)
direct = matrix.sqr(ORI.direct_matrix())
crystal = crystal_model(
real_space_a = matrix.row(direct[0:3]),
real_space_b = matrix.row(direct[3:6]),
real_space_c = matrix.row(direct[6:9]),
space_group_symbol = "P63", # XXX obviously another gap in the database paradigm
mosaicity = float(tokens[order_dict["half_mosaicity_deg"]]),
)
crystal.domain_size = float(tokens[order_dict["domain_size_ang"]])
#if isoform is not None:
# newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
# crystal.set_B(newB)
self.experiments.append(Experiment(beam=beam,
detector=None, #dummy for now
crystal=crystal))
self.unique_file_names.append(tokens[order_dict["unique_file_name"]])
self.show_summary()
def tst_contains(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
# Create a load of models
b1 = Beam()
d1 = Detector()
g1 = Goniometer()
s1 = Scan()
c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Create an experiment
e = Experiment(
beam=b1, detector=d1, goniometer=g1,
scan=s1, crystal=c1, imageset=None)
# Check experiment contains model
assert(b1 in e)
assert(d1 in e)
assert(g1 in e)
assert(s1 in e)
assert(c1 in e)
# Create a load of models that look the same but aren't
b2 = Beam()
d2 = Detector()
g2 = Goniometer()
s2 = Scan()
c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Check experiment doesn't contain model
assert(b2 not in e)
assert(d2 not in e)
assert(g2 not in e)
assert(s2 not in e)
assert(c2 not in e)
# Test passed
print 'OK'
def tst_contains(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
# Create a load of models
b1 = Beam()
d1 = Detector()
g1 = Goniometer()
s1 = Scan()
c1 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Create an experiment
e = Experiment(
beam=b1, detector=d1, goniometer=g1,
scan=s1, crystal=c1, imageset=None)
# Check experiment contains model
assert(b1 in e)
assert(d1 in e)
assert(g1 in e)
assert(s1 in e)
assert(c1 in e)
# Create a load of models that look the same but aren't
b2 = Beam()
d2 = Detector()
g2 = Goniometer()
s2 = Scan()
c2 = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), 0)
# Check experiment doesn't contain model
assert(b2 not in e)
assert(d2 not in e)
assert(g2 not in e)
assert(s2 not in e)
assert(c2 not in e)
# Test passed
print 'OK'
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 expt_crystal_maker(self):
"""Construct the crystal object for the experiments file."""
a, b, c = self.ucell.parameters()[0:3]
direct_matrix = self.ori.direct_matrix()
real_a = direct_matrix[0:3]
real_b = direct_matrix[3:6]
real_c = direct_matrix[6:9]
lattice = self.ucell.lattice_symmetry_group()
self.crystal = crystal.crystal_model(real_a, real_b, real_c, space_group=lattice)
self.crystal.set_mosaicity(self.data['mosaicity'])
self.crystal._ML_half_mosaicity_deg = self.data['ML_half_mosaicity_deg'][0]
self.crystal._ML_domain_size_ang = self.data['ML_domain_size_ang'][0]
if self.data['identified_isoform'] is not None:
self.crystal.identified_isoform = self.data['identified_isoform']
def exercise_similarity():
model_1 = crystal_model(real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
mosaicity=0.5)
model_2 = crystal_model(real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
mosaicity=0.5)
assert model_1.is_similar_to(model_2)
# mosaicity tests
model_1.set_mosaicity(-1)
model_2.set_mosaicity(-0.5)
assert model_1.is_similar_to(model_2) # test ignores negative mosaicity
model_1.set_mosaicity(0.5)
model_2.set_mosaicity(0.63) # outside tolerance
assert not model_1.is_similar_to(model_2)
model_2.set_mosaicity(0.625) #just inside tolerance
assert model_1.is_similar_to(model_2)
# orientation tests
R = model_2.get_U()
dr1 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0101,
deg=True)
dr2 = matrix.col((1, 0, 0)).axis_and_angle_as_r3_rotation_matrix(0.0099,
deg=True)
model_2.set_U(dr1 * R)
assert not model_1.is_similar_to(model_2) # outside tolerance
model_2.set_U(dr2 * R)
assert model_1.is_similar_to(model_2) # inside tolerance
# unit_cell.is_similar_to is tested elsewhere
return
def from_dict(d):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
Returns:
The crystal model
'''
from dxtbx.model.crystal import crystal_model
# If None, return None
if d is None:
return None
# Check the version and id
if str(d['__id__']) != "crystal":
raise ValueError("\"__id__\" does not equal \"crystal\"")
# Extract from the dictionary
real_space_a = d['real_space_a']
real_space_b = d['real_space_b']
real_space_c = d['real_space_c']
# str required to force unicode to ascii conversion
space_group = str("Hall:" + d['space_group_hall_symbol'])
mosaicity = d['mosaicity']
xl = crystal_model(real_space_a, real_space_b, real_space_c,
space_group_symbol=space_group,
mosaicity=mosaicity)
# New parameters for maximum likelihood values
try:
xl._ML_half_mosaicity_deg = d['ML_half_mosaicity_deg']
except KeyError:
pass
try:
xl._ML_domain_size_ang = d['ML_domain_size_ang']
except KeyError:
pass
# Extract scan point setting matrices, if present
try:
A_at_scan_points = d['A_at_scan_points']
xl.set_A_at_scan_points(A_at_scan_points)
except KeyError:
pass
return xl
def trumpet_wrapper(result, postx, file_name, params, out):
from scitbx import matrix
from dxtbx.model.beam import beam_factory
beam = beam_factory.make_beam(s0=(0, 0, -1. / result["wavelength"]))
from dxtbx.model.experiment import experiment_list
from dxtbx.model import crystal
obs_to_plot = postx.observations_original_index_pair1_selected # XXX uses a private interface
HKL = obs_to_plot.indices()
i_sigi = obs_to_plot.data() / obs_to_plot.sigmas()
direct_matrix = result["current_orientation"][0].direct_matrix()
real_a = direct_matrix[0:3]
real_b = direct_matrix[3:6]
real_c = direct_matrix[6:9]
SG = obs_to_plot.space_group()
crystal = crystal.crystal_model(real_a, real_b, real_c, space_group=SG)
q = experiment_list.Experiment(beam=beam, crystal=crystal)
TPL = trumpet_plot()
from xfel.cxi.data_utils import reduction
RED = reduction(filename=file_name,
experiment=q,
HKL=HKL,
i_sigi=i_sigi,
measurements=obs_to_plot,
params=params)
TPL.set_reduction(RED)
# first plot: before postrefinement
TPL.reduction.experiment.crystal.set_A(
matrix.sqr(result["current_orientation"][0].reciprocal_matrix()))
TPL.set_refined(
dict(half_mosaic_rotation_deg=result["ML_half_mosaicity_deg"][0],
mosaic_domain_size_ang=result["ML_domain_size_ang"][0]))
TPL.plot_one_model(nrow=0, out=out)
# second plot after postrefinement
values = postx.get_parameter_values()
TPL.reduction.experiment.crystal.set_A(
postx.refined_mini.refinery.get_eff_Astar(values))
TPL.refined["red_curve_domain_size_ang"] = 1 / values.RS
TPL.refined[
"partiality_array"] = postx.refined_mini.refinery.get_partiality_array(
values)
TPL.plot_one_model(nrow=1, out=out)
TPL.show()
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")
def get_random_predictions():
""" Return a DIALS reflection table representing predictions using the given models.
Assumes a Ewald proximity model for mosaicity """
# The U matrix to calculate A*
rot = flex.random_double_r3_rotation_matrix()
A = sqr(rot) * sqr(uc.reciprocal().orthogonalization_matrix())
A_inv = A.inverse()
# Use the matrix to create a crystal model
a = col(A_inv[:3])
b = col(A_inv[3:6])
c = col(A_inv[6:])
cm = crystal_model(a, b, c, space_group=spgrp)
# This DIALS object has no gonio or scan which will identify it as a still
expt = Experiment(beam=beam, detector=detector, goniometer=None, scan=None, crystal=cm)
# Predict the reflections
return flex.reflection_table.from_predictions(expt)
def prepare_dxtbx_models(self,setting_specific_ai,sg,isoform=None):
from dxtbx.model.beam import beam_factory
beam = beam_factory.simple(wavelength = self.inputai.wavelength)
from dxtbx.model.detector import detector_factory
detector = detector_factory.simple(
sensor = detector_factory.sensor("PAD"),
distance = setting_specific_ai.distance(),
beam_centre = [setting_specific_ai.xbeam(), setting_specific_ai.ybeam()],
fast_direction = "+x",
slow_direction = "+y",
pixel_size = [self.pixel_size,self.pixel_size],
image_size = [self.inputpd['size1'],self.inputpd['size1']],
)
direct = matrix.sqr(setting_specific_ai.getOrientation().direct_matrix())
from dxtbx.model.crystal import crystal_model
crystal = crystal_model(
real_space_a = matrix.row(direct[0:3]),
real_space_b = matrix.row(direct[3:6]),
real_space_c = matrix.row(direct[6:9]),
space_group_symbol = sg,
mosaicity = setting_specific_ai.getMosaicity()
)
if isoform is not None:
newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
crystal.set_B(newB)
from dxtbx.model.experiment.experiment_list import Experiment, ExperimentList
experiments = ExperimentList()
experiments.append(Experiment(beam=beam,
detector=detector,
crystal=crystal))
print beam
print detector
print crystal
return experiments
def trumpet_wrapper(result, postx, file_name, params, out):
from scitbx import matrix
from dxtbx.model.beam import beam_factory
beam = beam_factory.make_beam(s0=(0,0,-1./result["wavelength"]))
from dxtbx.model.experiment import experiment_list
from dxtbx.model import crystal
obs_to_plot = postx.observations_original_index_pair1_selected # XXX uses a private interface
HKL=obs_to_plot.indices()
i_sigi=obs_to_plot.data()/obs_to_plot.sigmas()
direct_matrix = result["current_orientation"][0].direct_matrix()
real_a = direct_matrix[0:3]
real_b = direct_matrix[3:6]
real_c = direct_matrix[6:9]
SG = obs_to_plot.space_group()
crystal = crystal.crystal_model(real_a, real_b, real_c, space_group=SG)
q = experiment_list.Experiment(beam=beam, crystal=crystal)
TPL = trumpet_plot()
from xfel.cxi.data_utils import reduction
RED = reduction(filename = file_name, experiment = q, HKL = HKL, i_sigi = i_sigi,
measurements = obs_to_plot, params = params)
TPL.set_reduction(RED)
# first plot: before postrefinement
TPL.reduction.experiment.crystal.set_A(matrix.sqr(result["current_orientation"][0].reciprocal_matrix()))
TPL.set_refined(dict(half_mosaic_rotation_deg=result["ML_half_mosaicity_deg"][0],
mosaic_domain_size_ang=result["ML_domain_size_ang"][0]))
TPL.plot_one_model(nrow=0,out=out)
# second plot after postrefinement
values = postx.get_parameter_values()
TPL.reduction.experiment.crystal.set_A(postx.refined_mini.refinery.get_eff_Astar(values))
TPL.refined["red_curve_domain_size_ang"]=1/values.RS
TPL.refined["partiality_array"]=postx.refined_mini.refinery.get_partiality_array(values)
TPL.plot_one_model(nrow=1,out=out)
TPL.show()
def tst_from_imageset(self):
from dxtbx.imageset import ImageSet, NullReader
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
imageset = ImageSet(NullReader(["filename.cbf"]))
imageset.set_beam(Beam(), 0)
imageset.set_detector(Detector(), 0)
crystal = crystal_model(
(1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert(len(experiments) == 1)
assert(experiments[0].imageset is not None)
assert(experiments[0].beam is not None)
assert(experiments[0].detector is not None)
assert(experiments[0].crystal is not None)
print 'OK'
def get_random_predictions():
"""Return a DIALS reflection table representing predictions using the given models.
Assumes a Ewald proximity model for mosaicity"""
# The U matrix to calculate A*
rot = flex.random_double_r3_rotation_matrix()
A = sqr(rot) * sqr(uc.reciprocal().orthogonalization_matrix())
A_inv = A.inverse()
# Use the matrix to create a crystal model
a = col(A_inv[:3])
b = col(A_inv[3:6])
c = col(A_inv[6:])
cm = crystal_model(a, b, c, space_group=spgrp)
# This DIALS object has no gonio or scan which will identify it as a still
expt = Experiment(beam=beam,
detector=detector,
goniometer=None,
scan=None,
crystal=cm)
# Predict the reflections
return flex.reflection_table.from_predictions(expt)
def tst_from_imageset(self):
from dxtbx.imageset import ImageSet, NullReader
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
imageset = ImageSet(NullReader(["filename.cbf"]))
imageset.set_beam(Beam(), 0)
imageset.set_detector(Detector(), 0)
crystal = crystal_model(
(1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert(len(experiments) == 1)
assert(experiments[0].imageset is not None)
assert(experiments[0].beam is not None)
assert(experiments[0].detector is not None)
assert(experiments[0].crystal is not None)
print 'OK'
def __init__(self, obj):
from dxtbx.model.crystal import crystal_model
import cctbx.uctbx
from scitbx import matrix
# Get the crystal parameters
unit_cell_parameters = list(obj.handle['unit_cell'][0])
unit_cell = cctbx.uctbx.unit_cell(unit_cell_parameters)
U = list(obj.handle['orientation_matrix'][0].flatten())
U = matrix.sqr(U)
B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
A = U * B
Ai = A.inverse()
real_space_a = Ai[0:3]
real_space_b = Ai[3:6]
real_space_c = Ai[6:9]
# Get the space group symbol
space_group_symbol = obj.handle['unit_cell_group'][()]
# Create the model
self.model = crystal_model(real_space_a, real_space_b, real_space_c,
space_group_symbol)
def predict_once(args):
from dxtbx.model.experiment.experiment_list import Experiment
U = args[0]
A = U * B
direct_matrix = A.inverse()
cryst_model = crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
experiment = Experiment(imageset=sweep,
beam=sweep.get_beam(),
detector=sweep.get_detector(),
goniometer=sweep.get_goniometer(),
scan=sweep.get_scan(),
crystal=cryst_model)
predicted_reflections = flex.reflection_table.from_predictions(
experiment)
miller_indices = predicted_reflections['miller_index']
miller_set = miller.set(
crystal_symmetry, miller_indices, anomalous_flag=True)
if params.d_min is not None:
resolution_sel = miller_set.d_spacings().data() > params.d_min
predicted_reflections = predicted_reflections.select(resolution_sel)
return len(predicted_reflections)
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))
def test1():
dials_regression = libtbx.env.find_in_repositories(
relative_path="dials_regression", test=os.path.isdir)
# use a datablock that contains a CS-PAD detector description
data_dir = os.path.join(dials_regression, "refinement_test_data",
"hierarchy_test")
datablock_path = os.path.join(data_dir, "datablock.json")
assert os.path.exists(datablock_path)
# load models
from dxtbx.datablock import DataBlockFactory
datablock = DataBlockFactory.from_serialized_format(datablock_path,
check_format=False)
im_set = datablock[0].extract_imagesets()[0]
from copy import deepcopy
detector = deepcopy(im_set.get_detector())
beam = im_set.get_beam()
# we'll invent a crystal, goniometer and scan for this test
from dxtbx.model.crystal import crystal_model
crystal = crystal_model((40., 0., 0.), (0., 40., 0.), (0., 0., 40.),
space_group_symbol="P1")
from dxtbx.model.experiment import goniometer_factory
goniometer = goniometer_factory.known_axis((1., 0., 0.))
# Build a mock scan for a 180 degree sweep
from dxtbx.model.scan import scan_factory
sf = scan_factory()
scan = sf.make_scan(image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=range(1800),
deg=True)
sweep_range = scan.get_oscillation_range(deg=False)
im_width = scan.get_oscillation(deg=False)[1]
assert sweep_range == (0., pi)
assert approx_equal(im_width, 0.1 * pi / 180.)
from dxtbx.model.experiment.experiment_list import ExperimentList, Experiment
# Build an experiment list
experiments = ExperimentList()
experiments.append(
Experiment(beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal,
imageset=None))
# simulate some reflections
refs, ref_predictor = generate_reflections(experiments)
# move the detector quadrants apart by 2mm both horizontally and vertically
from dials.algorithms.refinement.parameterisation \
import DetectorParameterisationHierarchical
det_param = DetectorParameterisationHierarchical(detector, level=1)
det_p_vals = det_param.get_param_vals()
p_vals = list(det_p_vals)
p_vals[1] += 2
p_vals[2] -= 2
p_vals[7] += 2
p_vals[8] += 2
p_vals[13] -= 2
p_vals[14] += 2
p_vals[19] -= 2
p_vals[20] -= 2
det_param.set_param_vals(p_vals)
# reparameterise the detector at the new perturbed geometry
det_param = DetectorParameterisationHierarchical(detector, level=1)
# parameterise other models
from dials.algorithms.refinement.parameterisation.beam_parameters import \
BeamParameterisation
from dials.algorithms.refinement.parameterisation.crystal_parameters import \
CrystalOrientationParameterisation, CrystalUnitCellParameterisation
beam_param = BeamParameterisation(beam, goniometer)
xlo_param = CrystalOrientationParameterisation(crystal)
xluc_param = CrystalUnitCellParameterisation(crystal)
# fix beam
beam_param.set_fixed([True] * 3)
# fix crystal
xluc_param.set_fixed([True] * 6)
xlo_param.set_fixed([True] * 3)
# parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.prediction_parameters import \
XYPhiPredictionParameterisation
from dials.algorithms.refinement.parameterisation.parameter_report import \
ParameterReporter
pred_param = XYPhiPredictionParameterisation(experiments, [det_param],
[beam_param], [xlo_param],
[xluc_param])
param_reporter = ParameterReporter([det_param], [beam_param], [xlo_param],
[xluc_param])
# reflection manager and target function
from dials.algorithms.refinement.target import \
LeastSquaresPositionalResidualWithRmsdCutoff
from dials.algorithms.refinement.reflection_manager import ReflectionManager
refman = ReflectionManager(refs, experiments, nref_per_degree=20)
# set a very tight rmsd target of 1/10000 of a pixel
target = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments,
ref_predictor,
refman,
pred_param,
restraints_parameterisation=None,
frac_binsize_cutoff=0.0001)
# minimisation engine
from dials.algorithms.refinement.engine \
import LevenbergMarquardtIterations as Refinery
refinery = Refinery(target=target,
prediction_parameterisation=pred_param,
log=None,
verbosity=0,
track_step=False,
track_gradient=False,
track_parameter_correlation=False,
max_iterations=20)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(reflections=refs,
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
verbosity=0)
history = refiner.run()
assert history.reason_for_termination == "RMSD target achieved"
#compare detector with original detector
orig_det = im_set.get_detector()
refined_det = refiner.get_experiments()[0].detector
from scitbx import matrix
import math
for op, rp in zip(orig_det, refined_det):
# compare the origin vectors by...
o1 = matrix.col(op.get_origin())
o2 = matrix.col(rp.get_origin())
# ...their relative lengths
assert approx_equal(math.fabs(o1.length() - o2.length()) / o1.length(),
0,
eps=1e-5)
# ...the angle between them
assert approx_equal(o1.accute_angle(o2), 0, eps=1e-5)
print "OK"
return
def from_dict(d):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
Returns:
The crystal model
'''
from dxtbx.model.crystal import crystal_model
# If None, return None
if d is None:
return None
# Check the version and id
if str(d['__id__']) != "crystal":
raise ValueError("\"__id__\" does not equal \"crystal\"")
# Extract from the dictionary
real_space_a = d['real_space_a']
real_space_b = d['real_space_b']
real_space_c = d['real_space_c']
# str required to force unicode to ascii conversion
space_group = str("Hall:" + d['space_group_hall_symbol'])
mosaicity = d['mosaicity']
xl = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group_symbol=space_group,
mosaicity=mosaicity)
# New parameters for maximum likelihood values
try:
xl._ML_half_mosaicity_deg = d['ML_half_mosaicity_deg']
except KeyError:
pass
try:
xl._ML_domain_size_ang = d['ML_domain_size_ang']
except KeyError:
pass
# Isoforms used for stills
try:
xl.identified_isoform = d['identified_isoform']
except KeyError:
pass
# Extract scan point setting matrices, if present
try:
A_at_scan_points = d['A_at_scan_points']
xl.set_A_at_scan_points(A_at_scan_points)
except KeyError:
pass
# Extract covariance of B, if present
try:
cov_B = d['B_covariance']
xl.set_B_covariance(cov_B)
except KeyError:
pass
return xl
def __init__(self, params):
import cPickle as pickle
from dxtbx.model import BeamFactory
from dxtbx.model import DetectorFactory
from dxtbx.model.crystal import crystal_model
from cctbx.crystal_orientation import crystal_orientation, basis_type
from dxtbx.model import Experiment, ExperimentList
from scitbx import matrix
self.experiments = ExperimentList()
self.unique_file_names = []
self.params = params
data = pickle.load(
open(self.params.output.prefix + "_frame.pickle", "rb"))
frames_text = data.split("\n")
for item in frames_text:
tokens = item.split(' ')
wavelength = float(tokens[order_dict["wavelength"]])
beam = BeamFactory.simple(wavelength=wavelength)
detector = DetectorFactory.simple(
sensor=DetectorFactory.sensor(
"PAD"), # XXX shouldn't hard code for XFEL
distance=float(tokens[order_dict["distance"]]),
beam_centre=[
float(tokens[order_dict["beam_x"]]),
float(tokens[order_dict["beam_y"]])
],
fast_direction="+x",
slow_direction="+y",
pixel_size=[self.params.pixel_size, self.params.pixel_size],
image_size=[1795,
1795], # XXX obviously need to figure this out
)
reciprocal_matrix = matrix.sqr([
float(tokens[order_dict[k]]) for k in [
'res_ori_1', 'res_ori_2', 'res_ori_3', 'res_ori_4',
'res_ori_5', 'res_ori_6', 'res_ori_7', 'res_ori_8',
'res_ori_9'
]
])
ORI = crystal_orientation(reciprocal_matrix, basis_type.reciprocal)
direct = matrix.sqr(ORI.direct_matrix())
crystal = crystal_model(
real_space_a=matrix.row(direct[0:3]),
real_space_b=matrix.row(direct[3:6]),
real_space_c=matrix.row(direct[6:9]),
space_group_symbol=self.params.target_space_group.type().
lookup_symbol(),
mosaicity=float(tokens[order_dict["half_mosaicity_deg"]]),
)
crystal.domain_size = float(tokens[order_dict["domain_size_ang"]])
#if isoform is not None:
# newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
# crystal.set_B(newB)
self.experiments.append(
Experiment(
beam=beam,
detector=None, #dummy for now
crystal=crystal))
self.unique_file_names.append(
tokens[order_dict["unique_file_name"]])
self.show_summary()
from cctbx.uctbx import unit_cell
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)
# make a random P1 crystal and parameterise it
a = random.uniform(10, 50) * random_direction_close_to(
matrix.col((1, 0, 0)))
b = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 1, 0)))
c = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 0, 1)))
xl = crystal_model(a, b, c, space_group_symbol="P 1")
xl_op = CrystalOrientationParameterisation(xl)
xl_ucp = CrystalUnitCellParameterisation(xl)
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
# compare analytical and finite difference derivatives
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi / 180] * 3)
for e, f in zip(an_ds_dp, fd_ds_dp):
assert (approx_equal((e - f), null_mat, eps=1.e-6))
an_ds_dp = xl_ucp.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_ucp, [1.e-7] * xl_ucp.num_free())
for e, f in zip(an_ds_dp, fd_ds_dp):
def run(args):
import libtbx.load_env
from libtbx.utils import Sorry
usage = "%s [options] experiments.json indexed.pickle" % libtbx.env.dispatcher_name
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_reflections=True,
read_experiments=True,
check_format=False,
epilog=help_message,
)
params, options = parser.parse_args(show_diff_phil=True)
reflections = flatten_reflections(params.input.reflections)
experiments = flatten_experiments(params.input.experiments)
if len(experiments) == 0 and len(reflections) == 0:
parser.print_help()
return
elif len(experiments.crystals()) > 1:
raise Sorry("Only one crystal can be processed at a time")
if params.change_of_basis_op is None:
raise Sorry("Please provide a change_of_basis_op.")
reference_crystal = None
if params.reference is not None:
from dxtbx.serialize import load
reference_experiments = load.experiment_list(params.reference, check_format=False)
assert len(reference_experiments.crystals()) == 1
reference_crystal = reference_experiments.crystals()[0]
if len(experiments) and params.change_of_basis_op is libtbx.Auto:
if reference_crystal is not None:
from dials.algorithms.indexing.compare_orientation_matrices import (
difference_rotation_matrix_and_euler_angles,
)
cryst = experiments.crystals()[0]
R, euler_angles, change_of_basis_op = difference_rotation_matrix_and_euler_angles(cryst, reference_crystal)
print "Change of basis op: %s" % change_of_basis_op
print "Rotation matrix to transform input crystal to reference::"
print R.mathematica_form(format="%.3f", one_row_per_line=True)
print "Euler angles (xyz): %.2f, %.2f, %.2f" % euler_angles
elif len(reflections):
assert len(reflections) == 1
# always re-map reflections to reciprocal space
from dials.algorithms.indexing import indexer
refl_copy = flex.reflection_table()
for i, imageset in enumerate(experiments.imagesets()):
if "imageset_id" in reflections[0]:
sel = reflections[0]["imageset_id"] == i
else:
sel = reflections[0]["id"] == i
refl = indexer.indexer_base.map_spots_pixel_to_mm_rad(
reflections[0].select(sel), imageset.get_detector(), imageset.get_scan()
)
indexer.indexer_base.map_centroids_to_reciprocal_space(
refl, imageset.get_detector(), imageset.get_beam(), imageset.get_goniometer()
)
refl_copy.extend(refl)
# index the reflection list using the input experiments list
refl_copy["id"] = flex.int(len(refl_copy), -1)
from dials.algorithms.indexing import index_reflections
index_reflections(refl_copy, experiments, tolerance=0.2)
hkl_expt = refl_copy["miller_index"]
hkl_input = reflections[0]["miller_index"]
change_of_basis_op = derive_change_of_basis_op(hkl_input, hkl_expt)
# reset experiments list since we don't want to reindex this
experiments = []
else:
change_of_basis_op = sgtbx.change_of_basis_op(params.change_of_basis_op)
if len(experiments):
experiment = experiments[0]
cryst_orig = copy.deepcopy(experiment.crystal)
cryst_reindexed = cryst_orig.change_basis(change_of_basis_op)
if params.space_group is not None:
a, b, c = cryst_reindexed.get_real_space_vectors()
cryst_reindexed = crystal_model(a, b, c, space_group=params.space_group.group())
experiment.crystal.update(cryst_reindexed)
print "Old crystal:"
print cryst_orig
print
print "New crystal:"
print cryst_reindexed
print
print "Saving reindexed experimental models to %s" % params.output.experiments
dump.experiment_list(experiments, params.output.experiments)
if len(reflections):
assert len(reflections) == 1
reflections = reflections[0]
miller_indices = reflections["miller_index"]
if params.hkl_offset is not None:
h, k, l = miller_indices.as_vec3_double().parts()
h += params.hkl_offset[0]
k += params.hkl_offset[1]
l += params.hkl_offset[2]
miller_indices = flex.miller_index(h.iround(), k.iround(), l.iround())
non_integral_indices = change_of_basis_op.apply_results_in_non_integral_indices(miller_indices)
if non_integral_indices.size() > 0:
print "Removing %i/%i reflections (change of basis results in non-integral indices)" % (
non_integral_indices.size(),
miller_indices.size(),
)
sel = flex.bool(miller_indices.size(), True)
sel.set_selected(non_integral_indices, False)
miller_indices_reindexed = change_of_basis_op.apply(miller_indices.select(sel))
reflections["miller_index"].set_selected(sel, miller_indices_reindexed)
reflections["miller_index"].set_selected(~sel, (0, 0, 0))
print "Saving reindexed reflections to %s" % params.output.reflections
easy_pickle.dump(params.output.reflections, reflections)
def test1():
dials_regression = libtbx.env.find_in_repositories(
relative_path="dials_regression",
test=os.path.isdir)
# use a datablock that contains a CS-PAD detector description
data_dir = os.path.join(dials_regression, "refinement_test_data",
"hierarchy_test")
datablock_path = os.path.join(data_dir, "datablock.json")
assert os.path.exists(datablock_path)
# load models
from dxtbx.datablock import DataBlockFactory
datablock = DataBlockFactory.from_serialized_format(datablock_path, check_format=False)
im_set = datablock[0].extract_imagesets()[0]
from copy import deepcopy
detector = deepcopy(im_set.get_detector())
beam = im_set.get_beam()
# we'll invent a crystal, goniometer and scan for this test
from dxtbx.model.crystal import crystal_model
crystal = crystal_model((40.,0.,0.) ,(0.,40.,0.), (0.,0.,40.),
space_group_symbol = "P1")
from dxtbx.model.experiment import goniometer_factory
goniometer = goniometer_factory.known_axis((1., 0., 0.))
# Build a mock scan for a 180 degree sweep
from dxtbx.model.scan import scan_factory
sf = scan_factory()
scan = sf.make_scan(image_range = (1,1800),
exposure_times = 0.1,
oscillation = (0, 0.1),
epochs = range(1800),
deg = True)
sweep_range = scan.get_oscillation_range(deg=False)
im_width = scan.get_oscillation(deg=False)[1]
assert sweep_range == (0., pi)
assert approx_equal(im_width, 0.1 * pi / 180.)
from dxtbx.model.experiment.experiment_list import ExperimentList, Experiment
# Build an experiment list
experiments = ExperimentList()
experiments.append(Experiment(
beam=beam, detector=detector, goniometer=goniometer,
scan=scan, crystal=crystal, imageset=None))
# simulate some reflections
refs, ref_predictor = generate_reflections(experiments)
# move the detector quadrants apart by 2mm both horizontally and vertically
from dials.algorithms.refinement.parameterisation \
import DetectorParameterisationHierarchical
det_param = DetectorParameterisationHierarchical(detector, level=1)
det_p_vals = det_param.get_param_vals()
p_vals = list(det_p_vals)
p_vals[1] += 2
p_vals[2] -= 2
p_vals[7] += 2
p_vals[8] += 2
p_vals[13] -= 2
p_vals[14] += 2
p_vals[19] -= 2
p_vals[20] -= 2
det_param.set_param_vals(p_vals)
# reparameterise the detector at the new perturbed geometry
det_param = DetectorParameterisationHierarchical(detector, level=1)
# parameterise other models
from dials.algorithms.refinement.parameterisation.beam_parameters import \
BeamParameterisation
from dials.algorithms.refinement.parameterisation.crystal_parameters import \
CrystalOrientationParameterisation, CrystalUnitCellParameterisation
beam_param = BeamParameterisation(beam, goniometer)
xlo_param = CrystalOrientationParameterisation(crystal)
xluc_param = CrystalUnitCellParameterisation(crystal)
# fix beam
beam_param.set_fixed([True]*3)
# fix crystal
xluc_param.set_fixed([True]*6)
xlo_param.set_fixed([True]*3)
# parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.prediction_parameters import \
XYPhiPredictionParameterisation
from dials.algorithms.refinement.parameterisation.parameter_report import \
ParameterReporter
pred_param = XYPhiPredictionParameterisation(experiments,
[det_param], [beam_param], [xlo_param], [xluc_param])
param_reporter = ParameterReporter([det_param], [beam_param],
[xlo_param], [xluc_param])
# reflection manager and target function
from dials.algorithms.refinement.target import \
LeastSquaresPositionalResidualWithRmsdCutoff
from dials.algorithms.refinement.reflection_manager import ReflectionManager
refman = ReflectionManager(refs, experiments, nref_per_degree=20)
# set a very tight rmsd target of 1/10000 of a pixel
target = LeastSquaresPositionalResidualWithRmsdCutoff(experiments,
ref_predictor, refman, pred_param, restraints_parameterisation=None,
frac_binsize_cutoff=0.0001)
# minimisation engine
from dials.algorithms.refinement.engine \
import LevenbergMarquardtIterations as Refinery
refinery = Refinery(target = target,
prediction_parameterisation = pred_param,
log = None,
verbosity = 0,
track_step = False,
track_gradient = False,
track_parameter_correlation = False,
max_iterations = 20)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(reflections=refs,
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
verbosity=0)
history = refiner.run()
assert history.reason_for_termination == "RMSD target achieved"
#compare detector with original detector
orig_det = im_set.get_detector()
refined_det = refiner.get_experiments()[0].detector
from scitbx import matrix
import math
for op, rp in zip(orig_det, refined_det):
# compare the origin vectors by...
o1 = matrix.col(op.get_origin())
o2 = matrix.col(rp.get_origin())
# ...their relative lengths
assert approx_equal(
math.fabs(o1.length() - o2.length()) / o1.length(), 0, eps=1e-5)
# ...the angle between them
assert approx_equal(o1.accute_angle(o2), 0, eps=1e-5)
print "OK"
return
def run(space_group_info):
datablock_json = os.path.join(dials_regression, "indexing_test_data",
"i04_weak_data", "datablock_orig.json")
datablock = load.datablock(datablock_json, check_format=False)[0]
sweep = datablock.extract_imagesets()[0]
sweep._indices = sweep._indices[:20]
sweep.set_scan(sweep.get_scan()[:20])
import random
space_group = space_group_info.group()
unit_cell = space_group_info.any_compatible_unit_cell(
volume=random.uniform(1e4, 1e6))
crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group=space_group)
crystal_symmetry.show_summary()
# the reciprocal matrix
B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
U = random_rotation()
A = U * B
direct_matrix = A.inverse()
cryst_model = crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
experiment = Experiment(imageset=sweep,
beam=sweep.get_beam(),
detector=sweep.get_detector(),
goniometer=sweep.get_goniometer(),
scan=sweep.get_scan(),
crystal=cryst_model)
predicted_reflections = flex.reflection_table.from_predictions(experiment)
use_fraction = 0.3
use_sel = flex.random_selection(
len(predicted_reflections),
int(use_fraction * len(predicted_reflections)))
predicted_reflections = predicted_reflections.select(use_sel)
miller_indices = predicted_reflections['miller_index']
miller_set = miller.set(crystal_symmetry,
miller_indices,
anomalous_flag=True)
predicted_reflections['xyzobs.mm.value'] = predicted_reflections[
'xyzcal.mm']
predicted_reflections['id'] = flex.int(len(predicted_reflections), 0)
from dials.algorithms.indexing.indexer import indexer_base
indexer_base.map_centroids_to_reciprocal_space(predicted_reflections,
sweep.get_detector(),
sweep.get_beam(),
sweep.get_goniometer())
# check that local and global indexing worked equally well in absence of errors
result = compare_global_local(experiment, predicted_reflections,
miller_indices)
assert result.misindexed_local == 0
assert result.misindexed_global == 0
a, b, c = cryst_model.get_real_space_vectors()
relative_error = 0.02
a *= (1 + relative_error)
b *= (1 + relative_error)
c *= (1 + relative_error)
cryst_model2 = crystal_model(a, b, c, space_group=space_group)
experiment.crystal = cryst_model2
result = compare_global_local(experiment, predicted_reflections,
miller_indices)
# check that the local indexing did a better job given the errors in the basis vectors
#assert result.misindexed_local < result.misindexed_global
assert result.misindexed_local == 0
assert result.correct_local > result.correct_global
# usually the number misindexed is much smaller than this
assert result.misindexed_local < (0.001 * len(result.reflections_local))
# the reciprocal matrix
A = cryst_model.get_A()
A = random_rotation(angle_max=0.03) * A
direct_matrix = A.inverse()
cryst_model2 = crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
experiment.crystal = cryst_model2
result = compare_global_local(experiment, predicted_reflections,
miller_indices)
# check that the local indexing did a better job given the errors in the basis vectors
assert result.misindexed_local <= result.misindexed_global, (
result.misindexed_local, result.misindexed_global)
assert result.misindexed_local < 0.01 * result.correct_local
assert result.correct_local > result.correct_global
# usually the number misindexed is much smaller than this
assert result.misindexed_local < (0.001 * len(result.reflections_local))
def exercise_crystal_model():
real_space_a = matrix.col((10,0,0))
real_space_b = matrix.col((0,11,0))
real_space_c = matrix.col((0,0,12))
model = crystal_model(real_space_a=(10,0,0),
real_space_b=(0,11,0),
real_space_c=(0,0,12),
space_group_symbol="P 1")
assert isinstance(model.get_unit_cell(), uctbx.unit_cell)
assert model.get_unit_cell().parameters() == (
10.0, 11.0, 12.0, 90.0, 90.0, 90.0)
assert approx_equal(model.get_A(), (1/10, 0, 0, 0, 1/11, 0, 0, 0, 1/12))
assert approx_equal(model.get_A().inverse(), (10, 0, 0, 0, 11, 0, 0, 0, 12))
assert approx_equal(model.get_B(), model.get_A())
assert approx_equal(model.get_U(), (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert approx_equal(model.get_real_space_vectors(),
(real_space_a, real_space_b, real_space_c))
assert approx_equal(model.get_mosaicity(), 0)
model2 = crystal_model(real_space_a=(10,0,0),
real_space_b=(0,11,0),
real_space_c=(0,0,12),
space_group_symbol="P 1")
assert model == model2
model2.set_mosaicity(0.01)
assert model != model2
# rotate 45 degrees about x-axis
R1 = matrix.sqr((1, 0, 0,
0, math.cos(math.pi/4), -math.sin(math.pi/4),
0, math.sin(math.pi/4), math.cos(math.pi/4)))
# rotate 30 degrees about y-axis
R2 = matrix.sqr((math.cos(math.pi/6), 0, math.sin(math.pi/6),
0, 1, 0,
-math.sin(math.pi/6), 0, math.cos(math.pi/6)))
# rotate 60 degrees about z-axis
R3 = matrix.sqr((math.cos(math.pi/3), -math.sin(math.pi/3), 0,
math.sin(math.pi/3), math.cos(math.pi/3), 0,
0, 0, 1))
R = R1 * R2 * R3
model.set_U(R)
# B is unchanged
assert approx_equal(model.get_B(), (1/10, 0, 0, 0, 1/11, 0, 0, 0, 1/12))
assert approx_equal(model.get_U(), R)
assert approx_equal(model.get_A(), model.get_U() * model.get_B())
a_, b_, c_ = model.get_real_space_vectors()
assert approx_equal(a_, R * real_space_a)
assert approx_equal(b_, R * real_space_b)
assert approx_equal(c_, R * real_space_c)
s = StringIO()
print >> s, model
assert not show_diff(s.getvalue().replace("-0.0000", " 0.0000"), """\
Crystal:
Unit cell: (10.000, 11.000, 12.000, 90.000, 90.000, 90.000)
Space group: P 1
U matrix: {{ 0.4330, -0.7500, 0.5000},
{ 0.7891, 0.0474, -0.6124},
{ 0.4356, 0.6597, 0.6124}}
B matrix: {{ 0.1000, 0.0000, 0.0000},
{ 0.0000, 0.0909, 0.0000},
{ 0.0000, 0.0000, 0.0833}}
A = UB: {{ 0.0433, -0.0682, 0.0417},
{ 0.0789, 0.0043, -0.0510},
{ 0.0436, 0.0600, 0.0510}}
""")
model.set_B((1/12, 0, 0, 0, 1/12, 0, 0, 0, 1/12))
assert approx_equal(model.get_unit_cell().parameters(),
(12, 12, 12, 90, 90, 90))
U = matrix.sqr((
0.3455, -0.2589, -0.9020, 0.8914, 0.3909, 0.2293, 0.2933, -0.8833, 0.3658))
B = matrix.sqr((1/13, 0, 0, 0, 1/13, 0, 0, 0, 1/13))
model.set_A(U * B)
assert approx_equal(model.get_A(), U * B)
assert approx_equal(model.get_U(), U, 1e-4)
assert approx_equal(model.get_B(), B, 1e-5)
model3 = crystal_model(
real_space_a=(10,0,0),
real_space_b=(0,11,0),
real_space_c=(0,0,12),
space_group=sgtbx.space_group_info("P 222").group(),
mosaicity=0.01)
assert model3.get_space_group().type().hall_symbol() == " P 2 2"
assert model != model3
#
sgi_ref = sgtbx.space_group_info(number=230)
model_ref = crystal_model(
real_space_a=(44,0,0),
real_space_b=(0,44,0),
real_space_c=(0,0,44),
space_group=sgi_ref.group())
assert approx_equal(model_ref.get_U(), (1,0,0,0,1,0,0,0,1))
assert approx_equal(model_ref.get_B(), (1/44,0,0,0,1/44,0,0,0,1/44))
assert approx_equal(model_ref.get_A(), model_ref.get_B())
assert approx_equal(model_ref.get_unit_cell().parameters(),
(44,44,44,90,90,90))
a_ref, b_ref, c_ref = model_ref.get_real_space_vectors()
cb_op_to_primitive = sgi_ref.change_of_basis_op_to_primitive_setting()
model_primitive = model_ref.change_basis(cb_op_to_primitive)
cb_op_to_reference = model_primitive.get_space_group().info()\
.change_of_basis_op_to_reference_setting()
a_prim, b_prim, c_prim = model_primitive.get_real_space_vectors()
#print cb_op_to_primitive.as_abc()
##'-1/2*a+1/2*b+1/2*c,1/2*a-1/2*b+1/2*c,1/2*a+1/2*b-1/2*c'
assert approx_equal(a_prim, -1/2 * a_ref + 1/2 * b_ref + 1/2 * c_ref)
assert approx_equal(b_prim, 1/2 * a_ref - 1/2 * b_ref + 1/2 * c_ref)
assert approx_equal(c_prim, 1/2 * a_ref + 1/2 * b_ref - 1/2 * c_ref)
#print cb_op_to_reference.as_abc()
##b+c,a+c,a+b
assert approx_equal(a_ref, b_prim + c_prim)
assert approx_equal(b_ref, a_prim + c_prim)
assert approx_equal(c_ref, a_prim + b_prim)
assert approx_equal(
model_primitive.get_U(),
[-0.5773502691896258, 0.40824829046386285, 0.7071067811865476,
0.5773502691896257, -0.4082482904638631, 0.7071067811865476,
0.5773502691896257, 0.8164965809277259, 0.0])
assert approx_equal(
model_primitive.get_B(),
[0.0262431940540739, 0.0, 0.0, 0.00927837023781507, 0.02783511071344521,
0.0, 0.01607060866333063, 0.01607060866333063, 0.03214121732666125])
assert approx_equal(
model_primitive.get_A(), (0, 1/44, 1/44, 1/44, 0, 1/44, 1/44, 1/44, 0))
assert approx_equal(
model_primitive.get_unit_cell().parameters(),
[38.1051177665153, 38.1051177665153, 38.1051177665153,
109.47122063449069, 109.47122063449069, 109.47122063449069])
assert model_ref != model_primitive
model_ref_recycled = model_primitive.change_basis(cb_op_to_reference)
assert approx_equal(model_ref.get_U(), model_ref_recycled.get_U())
assert approx_equal(model_ref.get_B(), model_ref_recycled.get_B())
assert approx_equal(model_ref.get_A(), model_ref_recycled.get_A())
assert approx_equal(model_ref.get_unit_cell().parameters(),
model_ref_recycled.get_unit_cell().parameters())
assert model_ref == model_ref_recycled
#
uc = uctbx.unit_cell((58.2567, 58.1264, 39.7093, 46.9077, 46.8612, 62.1055))
sg = sgtbx.space_group_info(symbol="P1").group()
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
cb_op_to_minimum = cs.change_of_basis_op_to_minimum_cell()
# the reciprocal matrix
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
U = random_rotation()
direct_matrix = (U * B).inverse()
model = crystal_model(direct_matrix[:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=sg)
assert uc.is_similar_to(model.get_unit_cell())
uc_minimum = uc.change_basis(cb_op_to_minimum)
model_minimum = model.change_basis(cb_op_to_minimum)
assert uc_minimum.is_similar_to(model_minimum.get_unit_cell())
assert model_minimum != model
model_minimum.update(model)
assert model_minimum == model
#
from scitbx.math import euler_angles
A_static = model.get_A()
A_as_scan_points = [A_static]
num_scan_points = 11
for i in range(num_scan_points-1):
A_as_scan_points.append(
A_as_scan_points[-1] * matrix.sqr(euler_angles.xyz_matrix(0.1,0.2,0.3)))
model.set_A_at_scan_points(A_as_scan_points)
model_minimum = model.change_basis(cb_op_to_minimum)
assert model.num_scan_points == model_minimum.num_scan_points == num_scan_points
M = matrix.sqr(cb_op_to_minimum.c_inv().r().transpose().as_double())
M_inv = M.inverse()
for i in range(num_scan_points):
A_orig = model.get_A_at_scan_point(i)
A_min = model_minimum.get_A_at_scan_point(i)
assert A_min == A_orig * M_inv
def write_par_file(file_name, experiment):
from scitbx import matrix
from dxtbx.model.crystal import crystal_model
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from dials.command_line.refine_bravais_settings import short_space_group_name
imageset = experiment.imageset
detector = imageset.get_detector()
goniometer = imageset.get_goniometer()
beam = imageset.get_beam()
scan = imageset.get_scan()
R_to_mosflm = align_reference_frame(beam.get_s0(), (1.0, 0.0, 0.0),
goniometer.get_rotation_axis(),
(0.0, 0.0, 1.0))
cryst = experiment.crystal
cryst = cryst.change_basis(
cryst.get_space_group().info()\
.change_of_basis_op_to_reference_setting())
A = cryst.get_A()
A_inv = A.inverse()
real_space_a = R_to_mosflm * A_inv.elems[:3]
real_space_b = R_to_mosflm * A_inv.elems[3:6]
real_space_c = R_to_mosflm * A_inv.elems[6:9]
cryst_mosflm = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group=cryst.get_space_group(),
mosaicity=cryst.get_mosaicity())
A_mosflm = cryst_mosflm.get_A()
U_mosflm = cryst_mosflm.get_U()
B_mosflm = cryst_mosflm.get_B()
UB_mosflm = U_mosflm * B_mosflm
uc_params = cryst_mosflm.get_unit_cell().parameters()
assert U_mosflm.is_r3_rotation_matrix(), U_mosflm
symmetry = cryst_mosflm.get_space_group().type().number()
beam_centre = tuple(reversed(detector[0].get_beam_centre(beam.get_s0())))
distance = detector[0].get_directed_distance()
polarization = R_to_mosflm * matrix.col(beam.get_polarization_normal())
rotation = matrix.col(goniometer.get_rotation_axis())
if (rotation.angle(matrix.col(detector[0].get_fast_axis())) <
rotation.angle(matrix.col(detector[0].get_slow_axis()))):
direction = 'FAST'
else:
direction = 'SLOW'
rotation = R_to_mosflm * rotation
with open(file_name, 'wb') as f: #
print >> f, '# parameter file for BEST'
print >> f, 'TITLE From DIALS'
print >> f, 'DETECTOR PILA'
print >> f, 'SITE Not set'
print >> f, 'DIAMETER %6.2f' % (max(
detector[0].get_image_size()) * detector[0].get_pixel_size()[0])
print >> f, 'PIXEL %s' % detector[0].get_pixel_size()[0]
print >> f, 'ROTAXIS %4.2f %4.2f %4.2f' % rotation.elems, direction
print >> f, 'POLAXIS %4.2f %4.2f %4.2f' % polarization.elems
print >> f, 'GAIN 1.00' # correct for Pilatus images
print >> f, 'CMOSAIC %.2f' % experiment.profile.sigma_m()
print >> f, 'PHISTART %.2f' % scan.get_oscillation_range()[0]
print >> f, 'PHIWIDTH %.2f' % scan.get_oscillation()[1]
print >> f, 'DISTANCE %7.2f' % distance
print >> f, 'WAVELENGTH %.5f' % beam.get_wavelength()
print >> f, 'POLARISATION %7.5f' % beam.get_polarization_fraction()
print >> f, 'SYMMETRY %s' % short_space_group_name(
cryst.get_space_group())
print >> f, 'UB %9.2f %9.2f %9.2f' % UB_mosflm[:3]
print >> f, ' %9.2f %9.2f %9.2f' % UB_mosflm[3:6]
print >> f, ' %9.2f %9.2f %9.2f' % UB_mosflm[6:]
print >> f, 'CELL %8.2f %8.2f %8.2f %6.2f %6.2f %6.2f' % uc_params
print >> f, 'RASTER 13 13 7 3 4'
print >> f, 'SEPARATION 2.960 2.960'
print >> f, 'BEAM %8.3f %8.3f' % beam_centre
print >> f, '# end of parameter file for BEST'
def extract_varying_crystal(integrate_lp, experiments):
'''Extract a varying crystal model from an INTEGRATE.LP file (static
in blocks with step changes) and write it to the provided
experiments
'''
if len(experiments) > 1:
print "Can only read a varying crystal model for a single " +\
"experiment. Skipping."
return
experiment = experiments[0]
# read required records from the file. Relies on them being in the
# right order as we read through once
xds_axis = None
xds_beam = None
blocks, a_axis, b_axis, c_axis = [], [], [], []
with open(integrate_lp) as f:
for record in f:
if record.lstrip().startswith("ROTATION_AXIS="):
xds_axis = record.split("ROTATION_AXIS=")[1].split()
break
for record in f:
if record.lstrip().startswith("INCIDENT_BEAM_DIRECTION="):
xds_beam = record.split("INCIDENT_BEAM_DIRECTION=")[1].split()
break
for record in f:
if record.lstrip().startswith("PROCESSING OF IMAGES"):
blocks.append(record.split("PROCESSING OF IMAGES")[1])
continue
if record.lstrip().startswith("COORDINATES OF UNIT CELL A-AXIS"):
a_axis.append(record.split("COORDINATES OF UNIT CELL A-AXIS")[1])
continue
if record.lstrip().startswith("COORDINATES OF UNIT CELL B-AXIS"):
b_axis.append(record.split("COORDINATES OF UNIT CELL B-AXIS")[1])
continue
if record.lstrip().startswith("COORDINATES OF UNIT CELL C-AXIS"):
c_axis.append(record.split("COORDINATES OF UNIT CELL C-AXIS")[1])
continue
# sanity checks
msg = "INTEGRATE.LP is not in the expected format"
nblocks = len(blocks)
try:
assert len(a_axis) == len(b_axis) == len(c_axis) == nblocks
assert (xds_axis, xds_beam).count(None) == 0
except AssertionError:
print msg
return
# conversions to numeric
try:
blocks = [map(int, block.split("...")) for block in blocks]
a_axis = [map(float, axis.split()) for axis in a_axis]
b_axis = [map(float, axis.split()) for axis in b_axis]
c_axis = [map(float, axis.split()) for axis in c_axis]
xds_beam = [float(e) for e in xds_beam]
xds_axis = [float(e) for e in xds_axis]
except ValueError:
print msg
return
# coordinate frame conversions
from scitbx import matrix
dbeam = matrix.col(experiment.beam.get_direction())
daxis = matrix.col(experiment.goniometer.get_rotation_axis())
xbeam = matrix.col(xds_beam).normalize()
xaxis = matrix.col(xds_axis).normalize()
# want to align XDS -s0 vector...
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
R = align_reference_frame(- xbeam, dbeam, xaxis, daxis)
# Make a static crystal for each block
from dxtbx.model.crystal import crystal_model
crystals = []
sg = experiment.crystal.get_space_group()
for a, b, c in zip(a_axis, b_axis, c_axis):
a = R * matrix.col(a)
b = R * matrix.col(b)
c = R * matrix.col(c)
crystals.append(crystal_model(a, b, c, space_group=sg))
# construct a list of scan points
A_list = []
for block, crystal in zip(blocks, crystals):
A = crystal.get_A()
for im in range(block[0], block[1] + 1):
A_list.append(A)
# Need a final scan point at the end of the final image
A_list.append(A)
# set the scan-varying crystal
experiment.crystal.set_A_at_scan_points(A_list)
return
def test_refinement():
'''Test a refinement run'''
dials_regression = libtbx.env.find_in_repositories(
relative_path="dials_regression",
test=os.path.isdir)
# Get a beam and detector from a datablock. This one has a CS-PAD, but that
# is irrelevant
data_dir = os.path.join(dials_regression, "refinement_test_data",
"hierarchy_test")
datablock_path = os.path.join(data_dir, "datablock.json")
assert os.path.exists(datablock_path)
# load models
from dxtbx.datablock import DataBlockFactory
datablock = DataBlockFactory.from_serialized_format(datablock_path, check_format=False)
im_set = datablock[0].extract_imagesets()[0]
from copy import deepcopy
detector = deepcopy(im_set.get_detector())
beam = im_set.get_beam()
# Invent a crystal, goniometer and scan for this test
from dxtbx.model.crystal import crystal_model
crystal = crystal_model((40.,0.,0.) ,(0.,40.,0.), (0.,0.,40.),
space_group_symbol = "P1")
orig_xl = deepcopy(crystal)
from dxtbx.model.experiment import goniometer_factory
goniometer = goniometer_factory.known_axis((1., 0., 0.))
# Build a mock scan for a 180 degree sweep
from dxtbx.model.scan import scan_factory
sf = scan_factory()
scan = sf.make_scan(image_range = (1,1800),
exposure_times = 0.1,
oscillation = (0, 0.1),
epochs = range(1800),
deg = True)
sweep_range = scan.get_oscillation_range(deg=False)
im_width = scan.get_oscillation(deg=False)[1]
assert sweep_range == (0., pi)
assert approx_equal(im_width, 0.1 * pi / 180.)
from dxtbx.model.experiment.experiment_list import ExperimentList, Experiment
# Build an experiment list
experiments = ExperimentList()
experiments.append(Experiment(
beam=beam, detector=detector, goniometer=goniometer,
scan=scan, crystal=crystal, imageset=None))
# simulate some reflections
refs, _ = generate_reflections(experiments)
# change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
# alpha and beta angles)
from dials.algorithms.refinement.parameterisation.crystal_parameters import \
CrystalUnitCellParameterisation
xluc_param = CrystalUnitCellParameterisation(crystal)
xluc_p_vals = xluc_param.get_param_vals()
cell_params = crystal.get_unit_cell().parameters()
cell_params = [a + b for a, b in zip(cell_params, [0.1, -0.1, 0.1, 0.1,
-0.1, 0.0])]
from cctbx.uctbx import unit_cell
from rstbx.symmetry.constraints.parameter_reduction import \
symmetrize_reduce_enlarge
from scitbx import matrix
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(crystal.get_space_group())
S.set_orientation(orientation=newB)
X = tuple([e * 1.e5 for e in S.forward_independent_parameters()])
xluc_param.set_param_vals(X)
# reparameterise the crystal at the perturbed geometry
xluc_param = CrystalUnitCellParameterisation(crystal)
# Dummy parameterisations for other models
beam_param = None
xlo_param = None
det_param = None
# parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.parameter_report import \
ParameterReporter
pred_param = TwoThetaPredictionParameterisation(experiments,
det_param, beam_param, xlo_param, [xluc_param])
param_reporter = ParameterReporter(det_param, beam_param,
xlo_param, [xluc_param])
# reflection manager
refman = TwoThetaReflectionManager(refs, experiments, nref_per_degree=20,
verbosity=2)
# reflection predictor
ref_predictor = TwoThetaExperimentsPredictor(experiments)
# target function
target = TwoThetaTarget(experiments, ref_predictor, refman, pred_param)
# minimisation engine
from dials.algorithms.refinement.engine \
import LevenbergMarquardtIterations as Refinery
refinery = Refinery(target = target,
prediction_parameterisation = pred_param,
log = None,
verbosity = 0,
track_step = False,
track_gradient = False,
track_parameter_correlation = False,
max_iterations = 20)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(reflections=refs,
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
verbosity=1)
history = refiner.run()
# compare crystal with original crystal
refined_xl = refiner.get_experiments()[0].crystal
#print refined_xl
assert refined_xl.is_similar_to(orig_xl, uc_rel_length_tolerance=0.001,
uc_abs_angle_tolerance=0.01)
#print "Unit cell esds:"
#print refined_xl.get_cell_parameter_sd()
return
def dump(experiments, directory):
'''
Dump the experiments in mosflm format
:param experiments: The experiments to dump
:param directory: The directory to write to
'''
for i, experiment in enumerate(experiments):
suffix = ""
if len(experiments) > 1:
suffix = "_%i" % (i + 1)
sub_dir = "%s%s" % (directory, suffix)
if not os.path.isdir(sub_dir):
os.makedirs(sub_dir)
detector = experiment.detector
beam = experiment.beam
scan = experiment.scan
goniometer = experiment.goniometer
# XXX imageset is getting the experimental geometry from the image files
# rather than the input experiments.json file
imageset = experiment.imageset
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
R_to_mosflm = align_reference_frame(beam.get_s0(), (1.0, 0.0, 0.0),
goniometer.get_rotation_axis(),
(0.0, 0.0, 1.0))
#print R_to_mosflm
cryst = experiment.crystal
cryst = cryst.change_basis(
cryst.get_space_group().info()\
.change_of_basis_op_to_reference_setting())
A = cryst.get_A()
A_inv = A.inverse()
real_space_a = R_to_mosflm * A_inv.elems[:3]
real_space_b = R_to_mosflm * A_inv.elems[3:6]
real_space_c = R_to_mosflm * A_inv.elems[6:9]
cryst_mosflm = crystal_model(real_space_a,
real_space_b,
real_space_c,
space_group=cryst.get_space_group(),
mosaicity=cryst.get_mosaicity())
A_mosflm = cryst_mosflm.get_A()
U_mosflm = cryst_mosflm.get_U()
assert U_mosflm.is_r3_rotation_matrix(), U_mosflm
w = beam.get_wavelength()
index_mat = os.path.join(sub_dir, "index.mat")
mosflm_in = os.path.join(sub_dir, "mosflm.in")
print "Exporting experiment to %s and %s" % (index_mat, mosflm_in)
with open(index_mat, "wb") as f:
print >> f, format_mosflm_mat(w * A_mosflm, U_mosflm,
cryst.get_unit_cell())
directory, template = os.path.split(imageset.get_template())
symmetry = cryst_mosflm.get_space_group().type().number()
beam_centre = tuple(
reversed(detector[0].get_beam_centre(beam.get_s0())))
distance = detector[0].get_directed_distance()
with open(mosflm_in, "wb") as f:
print >> f, write_mosflm_input(directory=directory,
template=template,
symmetry=symmetry,
beam_centre=beam_centre,
distance=distance,
mat_file="index.mat")
return
def run(space_group_info):
datablock_json = os.path.join(
dials_regression, "indexing_test_data",
"i04_weak_data", "datablock_orig.json")
datablock = load.datablock(datablock_json, check_format=False)[0]
sweep = datablock.extract_imagesets()[0]
sweep._indices = sweep._indices[:20]
sweep.set_scan(sweep.get_scan()[:20])
import random
space_group = space_group_info.group()
unit_cell = space_group_info.any_compatible_unit_cell(volume=random.uniform(1e4,1e6))
crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group=space_group)
crystal_symmetry.show_summary()
# the reciprocal matrix
B = matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
U = random_rotation()
A = U * B
direct_matrix = A.inverse()
cryst_model = crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
experiment = Experiment(imageset=sweep,
beam=sweep.get_beam(),
detector=sweep.get_detector(),
goniometer=sweep.get_goniometer(),
scan=sweep.get_scan(),
crystal=cryst_model)
predicted_reflections = flex.reflection_table.from_predictions(
experiment)
use_fraction = 0.3
use_sel = flex.random_selection(
len(predicted_reflections), int(use_fraction*len(predicted_reflections)))
predicted_reflections = predicted_reflections.select(use_sel)
miller_indices = predicted_reflections['miller_index']
miller_set = miller.set(
crystal_symmetry, miller_indices, anomalous_flag=True)
predicted_reflections['xyzobs.mm.value'] = predicted_reflections['xyzcal.mm']
predicted_reflections['id'] = flex.int(len(predicted_reflections), 0)
from dials.algorithms.indexing.indexer import indexer_base
indexer_base.map_centroids_to_reciprocal_space(
predicted_reflections, sweep.get_detector(), sweep.get_beam(),
sweep.get_goniometer())
# check that local and global indexing worked equally well in absence of errors
result = compare_global_local(experiment, predicted_reflections,
miller_indices)
assert result.misindexed_local == 0
assert result.misindexed_global == 0
a, b, c = cryst_model.get_real_space_vectors()
relative_error = 0.02
a *= (1+relative_error)
b *= (1+relative_error)
c *= (1+relative_error)
cryst_model2 = crystal_model(a, b, c, space_group=space_group)
experiment.crystal = cryst_model2
result = compare_global_local(experiment, predicted_reflections,
miller_indices)
# check that the local indexing did a better job given the errors in the basis vectors
#assert result.misindexed_local < result.misindexed_global
assert result.misindexed_local == 0
assert result.correct_local > result.correct_global
# usually the number misindexed is much smaller than this
assert result.misindexed_local < (0.001 * len(result.reflections_local))
# the reciprocal matrix
A = cryst_model.get_A()
A = random_rotation(angle_max=0.03) * A
direct_matrix = A.inverse()
cryst_model2 = crystal_model(direct_matrix[0:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=space_group)
experiment.crystal = cryst_model2
result = compare_global_local(experiment, predicted_reflections,
miller_indices)
# check that the local indexing did a better job given the errors in the basis vectors
assert result.misindexed_local <= result.misindexed_global, (
result.misindexed_local, result.misindexed_global)
assert result.misindexed_local < 0.01 * result.correct_local
assert result.correct_local > result.correct_global
# usually the number misindexed is much smaller than this
assert result.misindexed_local < (0.001 * len(result.reflections_local))