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 import Crystal
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
crystal = Crystal(real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=space_group)
if (mosaicity is not None):
crystal.set_mosaicity(mosaicity)
return crystal
def tst_crystal(self):
from dxtbx.model import Crystal, CrystalFactory
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(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")
c1.set_mosaicity(0.1)
d = c1.to_dict()
c2 = CrystalFactory.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 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 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
if mosaicity is None:
from dxtbx.model import Crystal
crystal = Crystal(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=space_group,
)
else:
from dxtbx.model import MosaicCrystalKabsch2010
crystal = MosaicCrystalKabsch2010(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group=space_group,
)
crystal.set_mosaicity(mosaicity)
return crystal
def prepare_dxtbx_models(self, setting_specific_ai, sg, isoform=None):
from dxtbx.model import BeamFactory
beam = BeamFactory.simple(wavelength=self.inputai.wavelength)
from dxtbx.model import DetectorFactory
detector = DetectorFactory.simple(
sensor=DetectorFactory.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 import Crystal
crystal = Crystal(
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,
)
crystal.set_mosaicity(setting_specific_ai.getMosaicity())
if isoform is not None:
newB = matrix.sqr(isoform.fractionalization_matrix()).transpose()
crystal.set_B(newB)
from dxtbx.model import Experiment, ExperimentList
experiments = ExperimentList()
experiments.append(
Experiment(beam=beam, detector=detector, crystal=crystal))
print beam
print detector
print crystal
return experiments
class construct_reflection_table_and_experiment_list(object):
def __init__(self,
pickle,
img_location,
pixel_size,
proceed_without_image=False):
# unpickle pickle file and keep track of image location
if img_location is None:
if proceed_without_image:
self.img_location = []
else:
raise Sorry, "No image found at specified location. Override by setting proceed_without_image to False" \
+ "to produce experiment lists that may only be read when check_format is False."
else:
self.img_location = [img_location]
# pickle can be already unpickled, if so, loading it will fail with an AttributeError. A load
# error will fail with EOFError
try:
self.data = easy_pickle.load(pickle)
except EOFError:
self.data = None
self.pickle = None
except AttributeError:
self.data = pickle
self.pickle = None
else:
self.pickle = pickle
if self.data is not None:
self.length = len(self.data['observations'][0].data())
self.pixel_size = pixel_size
# extract things from pickle file
def unpack_pickle(self):
"""Extract all relevant information from an integration pickle file."""
# crystal-dependent
self.ori = self.data['current_orientation'][0]
self.ucell = self.data['current_orientation'][0].unit_cell()
# experiment-dependent
self.wavelength = self.data['wavelength']
self.det_dist = self.data['distance']
# observation-dependent
self.observations = self.data['observations'][0]
self.predictions = self.data['mapped_predictions'][0]
if 'fuller_kapton_absorption_correction' in self.data:
self.fuller_correction = self.data[
'fuller_kapton_absorption_correction'][0]
if 'fuller_kapton_absorption_correction_sigmas' in self.data:
self.fuller_correction_sigmas = self.data[
'fuller_kapton_absorption_correction_sigmas'][0]
# construct the experiments and experiment_list objects
def expt_beam_maker(self):
"""Construct the beam object for the experiments file."""
self.beam = BeamFactory.simple(self.wavelength)
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(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 'identified_isoform' in self.data.keys(
) and self.data['identified_isoform'] is not None:
self.crystal.identified_isoform = self.data['identified_isoform']
def expt_detector_maker(self):
"""Construct the detector object for the experiments file. This function generates a monolithic flattening of the
CSPAD detector if not supplied with an image file."""
self.distance = self.data['distance']
self.xbeam, self.ybeam = self.data['xbeam'], self.data['ybeam']
if len(self.img_location) > 0 and not dxtbx.load(
self.img_location[0])._image_file.endswith("_00000.pickle"):
self.detector = dxtbx.load(self.img_location[0])._detector()
else:
self.detector = DetectorFactory.simple(
'SENSOR_UNKNOWN', self.distance, (self.xbeam, self.ybeam),
'+x', '-y', (self.pixel_size, self.pixel_size), (1765, 1765))
def expt_gonio_maker(self):
"""XFEL data consisting of stills is expected to have been generated by an experiment without a goniometer -- use placeholder None."""
self.goniometer = None
def expt_imageset_maker(self):
"""Construct the imageset object for the experiments file."""
if len(self.img_location) == 0:
self.imageset = None
return
self.filename = self.img_location
self.format = FormatMultiImage.FormatMultiImage()
self.reader = imageset.MultiFileReader(self.format, self.filename)
self.imageset = imageset.ImageSet(self.reader)
def expt_scan_maker(self):
"""XFEL data consisting of stills is expected not to contain scans -- use placeholder None."""
self.scan = None
def assemble_experiments(self):
self.unpack_pickle()
self.expt_beam_maker()
self.expt_crystal_maker()
self.expt_detector_maker()
self.expt_gonio_maker()
self.expt_imageset_maker()
self.expt_scan_maker()
self.experiment = Experiment(beam=self.beam,
crystal=self.crystal,
detector=self.detector,
goniometer=self.goniometer,
imageset=self.imageset,
scan=self.scan)
self.experiment_list = ExperimentList([self.experiment])
def experiments_to_json(self, path_name=None):
if path_name is None:
loc = os.path.dirname(self.pickle)
else:
loc = path_name
name = os.path.basename(self.pickle).split(".pickle")[0]
expt_name = int_pickle_to_filename(name, "idx-", "_experiments.json")
experiments = os.path.join(loc, expt_name)
dumper = experiment_list.ExperimentListDumper(self.experiment_list)
dumper.as_json(experiments)
# construct the reflection table
def refl_table_maker(self):
self.reflections = flex.reflection_table()
def refl_bkgd_maker(self):
self.reflections['background.mean'] = sciflex.double(self.length)
self.reflections['background.mse'] = sciflex.double(self.length)
def refl_bbox_maker(self):
self.reflections['bbox'] = flex.int6(self.length)
def refl_correlation_maker(self):
self.reflections['correlation.ideal.profile'] = sciflex.double(
self.length)
def refl_entering_maker(self):
self.reflections['entering'] = flex.bool(self.length)
def refl_flags_maker(self):
self.reflections['flags'] = flex.size_t(self.length, 1)
def refl_id_maker(self):
self.reflections['id'] = sciflex.size_t(self.length)
def refl_intensities_maker(self):
self.reflections['intensity.sum.value'] = self.observations.data()
self.reflections['intensity.sum.variance'] = self.observations.sigmas(
)**2
def refl_lp_maker(self):
self.reflections['lp'] = sciflex.double(self.length)
def refl_millers_maker(self):
self.reflections['miller_index'] = self.observations._indices
def refl_nbackgroundforeground_maker(self):
self.reflections['n_background'] = sciflex.size_t(self.length)
self.reflections['n_foreground'] = sciflex.size_t(self.length)
def refl_panel_maker(self):
self.reflections['panel'] = sciflex.size_t(self.length, 0)
def refl_profile_maker(self):
self.reflections['profile.correlation'] = sciflex.double(self.length)
def refl_s1_maker(self):
from scitbx.matrix import col
self.reflections['s1'] = sciflex.vec3_double(self.length)
for idx in xrange(self.length):
coords = col(self.detector[0].get_pixel_lab_coord(
self.reflections['xyzobs.px.value'][idx][0:2])).normalize()
self.reflections['s1'][idx] = tuple(coords)
def refl_xyzcal_maker(self):
self.reflections['xyzcal.px'] = sciflex.vec3_double(
self.predictions.parts()[1],
self.predictions.parts()[0], sciflex.double(self.length, 0.0))
self.reflections[
'xyzcal.mm'] = self.pixel_size * self.reflections['xyzcal.px']
def refl_xyzobs_maker(self):
self.reflections['xyzobs.px.value'] = sciflex.vec3_double(
self.predictions.parts()[1],
self.predictions.parts()[0], sciflex.double(self.length, 0.5))
self.reflections['xyzobs.px.variance'] = sciflex.vec3_double(
self.length, (0.0, 0.0, 0.0))
def refl_zeta_maker(self):
self.reflections['zeta'] = sciflex.double(self.length)
def refl_kapton_correction_maker(self):
if hasattr(self, 'fuller_correction'):
self.reflections[
'kapton_absorption_correction'] = self.fuller_correction
if hasattr(self, 'fuller_correction_sigmas'):
self.reflections[
'kapton_absorption_correction_sigmas'] = self.fuller_correction_sigmas
def assemble_reflections(self):
self.refl_table_maker()
self.refl_bkgd_maker()
self.refl_bbox_maker()
self.refl_correlation_maker()
self.refl_entering_maker()
self.refl_flags_maker()
self.refl_id_maker()
self.refl_intensities_maker()
self.refl_millers_maker()
self.refl_nbackgroundforeground_maker()
self.refl_panel_maker()
self.refl_xyzcal_maker()
self.refl_xyzobs_maker()
self.refl_zeta_maker()
self.refl_kapton_correction_maker()
self.refl_s1_maker(
) # depends on successful completion of refl_xyz_obs_maker
def reflections_to_pickle(self, path_name=None):
if path_name is None:
loc = os.path.dirname(self.pickle)
else:
loc = path_name
name = os.path.basename(self.pickle).split(".pickle")[0]
refl_name = int_pickle_to_filename(name, "idx-", "_integrated.pickle")
reflections = os.path.join(loc, refl_name)
self.reflections.as_pickle(reflections)
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(real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1")
# This doesn't work as python class uctbx.unit_cell(uctbx_ext.unit_cell)
# so C++ and python classes are different types
#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(
matrix.sqr(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(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(),
matrix.sqr(model.get_U()) * matrix.sqr(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(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())
model3.set_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(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 = map(matrix.col, 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 = map(matrix.col,
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(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 = matrix.sqr(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 = matrix.sqr(model.get_A_at_scan_point(i))
A_min = matrix.sqr(model_minimum.get_A_at_scan_point(i))
assert approx_equal(A_min, A_orig * M_inv)
def exercise_similarity():
model_1 = Crystal(real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1")
model_1.set_mosaicity(0.5)
model_2 = Crystal(real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1")
model_2.set_mosaicity(0.5)
assert model_1.is_similar_to(model_2)
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(0.62) #just inside tolerance
# orientation tests
R = matrix.sqr(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 import Crystal
# 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'])
xl = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group_symbol=space_group)
# 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
# Extract mosaicity, if present
try:
mosaicity = d['mosaicity']
xl.set_mosaicity(mosaicity)
except KeyError:
pass
return xl
