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Source code for dxtbx.model.goniometer
from __future__ import absolute_import, division, print_function
import math
from builtins import object, range
import libtbx.phil
from scitbx.array_family import flex
import pycbf
from dxtbx_model_ext import Goniometer, KappaGoniometer, MultiAxisGoniometer
__all__ = [
"Goniometer",
"GoniometerFactory",
"KappaGoniometer",
"MultiAxisGoniometer",
"goniometer_phil_scope",
]
goniometer_phil_scope = libtbx.phil.parse(
"""
goniometer
.expert_level = 1
.short_caption = "Goniometer overrides"
{
axis = None
.type = floats(size=3)
.help = "Override the axis for a single axis goniometer. Equivalent to"
"providing a single 3D vector to 'axes'."
.short_caption="Goniometer axis"
axes = None
.type = floats
.help = "Override the goniometer axes. Axes must be provided in the"
"order crystal-to-goniometer, i.e. for a Kappa goniometer"
"phi,kappa,omega"
.short_caption="Goniometer axes"
angles = None
.type = floats
.help = "Override the goniometer angles. Axes must be provided in the"
"order crystal-to-goniometer, i.e. for a Kappa goniometer"
"phi,kappa,omega"
.short_caption = "Goniometer angles"
names = None
.type = str
.help = "The multi axis goniometer axis names"
.short_caption = "The axis names"
scan_axis = None
.type = int
.help = "The scan axis"
.short_caption = "The scan axis"
fixed_rotation = None
.type = floats(size=9)
.help = "Override the fixed rotation matrix"
.short_caption = "Fixed rotation matrix"
setting_rotation = None
.type = floats(size=9)
.help = "Override the setting rotation matrix"
.short_caption = "Setting rotation matrix"
invert_rotation_axis = False
.type = bool
.help = "Invert the rotation axis"
.short_caption = "Invert rotation axis"
}
"""
)
[docs]class GoniometerFactory(object):
"""A factory class for goniometer objects, which will encapsulate
some standard goniometer designs to make it a little easier to get
started with all of this - for cases when we are not using a CBF.
When we have a CBF just use that factory method and everything will be
peachy."""
[docs] @staticmethod
def single_axis_goniometer_from_phil(params, reference=None):
"""
Generate or overwrite a single axis goniometer
"""
# Check the axis parameter and copy from axes if required
if params.goniometer.axis is None:
params.goniometer.axis = params.goniometer.axes
if params.goniometer.axis is not None and len(params.goniometer.axis) != 3:
raise RuntimeError("Single axis goniometer requires 3 axis values")
# Check the angles parameter
if params.goniometer.angles is not None:
raise RuntimeError("Single axis goniometer requires angles == None")
# Check the names parameter
if params.goniometer.names is not None:
raise RuntimeError("Single axis goniometer requires names == None")
# Init the gonionmeter
if reference is None:
goniometer = Goniometer()
else:
goniometer = reference
# Set the parameters
if params.goniometer.axis is not None:
goniometer.set_rotation_axis_datum(params.goniometer.axis)
if params.goniometer.fixed_rotation is not None:
goniometer.set_fixed_rotation(params.goniometer.fixed_rotation)
if params.goniometer.setting_rotation is not None:
goniometer.set_setting_rotation(params.goniometer.setting_rotation)
if params.goniometer.invert_rotation_axis is True:
rotation_axis = goniometer.get_rotation_axis_datum()
goniometer.set_rotation_axis_datum([-x for x in rotation_axis])
# Return the model
return goniometer
[docs] @staticmethod
def multi_axis_goniometer_from_phil(params, reference=None):
# Check the axes parameter
if params.goniometer.axes is not None:
if len(params.goniometer.axes) % 3:
raise RuntimeError(
"Number of values for axes parameter must be multiple of 3."
)
# Check the fixed rotation
if params.goniometer.fixed_rotation is not None:
raise RuntimeError("Multi-axis goniometer requires fixed_rotation == None")
# Check the setting rotation
if params.goniometer.setting_rotation is not None:
raise RuntimeError(
"Multi-axis goniometer requires setting_rotation == None"
)
# Check the input
if reference is None:
if params.goniometer.axes is None:
raise RuntimeError("No axes set")
# Create the axes
axes = flex.vec3_double(
params.goniometer.axes[i * 3 : (i * 3) + 3]
for i in range(len(params.goniometer.axes) // 3)
)
# Invert the rotation axis
if params.goniometer.invert_rotation_axis is True:
axes = flex.vec3_double([[-x for x in v] for v in axes])
# Create the angles
if params.goniometer.angles is not None:
angles = params.goniometer.angles
if len(angles) != len(axes):
raise RuntimeError("Number of angles must match axes")
else:
angles = flex.double([0] * len(axes))
# Create the names
if params.goniometer.names is not None:
names = params.goniometer.names
if len(names) != len(axes):
raise RuntimeError("Number of names must match axes")
else:
names = flex.std_string([""] * len(axes))
# Create the scan axis
if params.goniometer.scan_axis is not None:
scan_axis = params.goniometer.scan_axis
else:
scan_axis = 0
# Create the model
goniometer = MultiAxisGoniometer(axes, angles, names, scan_axis)
else:
goniometer = reference
# Set the axes
if params.goniometer.axes is not None:
axes = flex.vec3_double(
params.goniometer.axes[i * 3 : (i * 3) + 3]
for i in range(len(params.goniometer.axes) // 3)
)
if len(goniometer.get_axes()) != len(axes):
raise RuntimeError(
"Number of axes must match the current goniometer (%s)"
% len(goniometer.get_axes())
)
goniometer.set_axes(axes)
# Invert rotation axis
if params.goniometer.invert_rotation_axis is True:
axes = flex.vec3_double(
[[-x for x in v] for v in goniometer.get_axes()]
)
goniometer.set_axes(axes)
# Set the angles
if params.goniometer.angles is not None:
if len(goniometer.get_angles()) != len(params.goniometer.angles):
raise RuntimeError(
"Number of angles must match the current goniometer (%s)"
% len(goniometer.get_angles())
)
goniometer.set_angles(params.goniometer.angles)
# Set the namess
if params.goniometer.names is not None:
if len(goniometer.get_names()) != len(params.goniometer.names):
raise RuntimeError(
"Number of names must match the current goniometer (%s)"
% len(goniometer.get_names())
)
goniometer.set_names(params.goniometer.names)
# Set the scan axis
if params.goniometer.scan_axis is not None:
raise RuntimeError("Can not override scan axis")
# Return the model
return goniometer
[docs] @staticmethod
def from_phil(params, reference=None):
"""
Convert the phil parameters into a goniometer model
"""
if params.goniometer.axis and params.goniometer.axes:
raise ValueError("Only one of axis or axes should be set")
if reference is not None:
if isinstance(reference, MultiAxisGoniometer):
goniometer = GoniometerFactory.multi_axis_goniometer_from_phil(
params, reference
)
else:
goniometer = GoniometerFactory.single_axis_goniometer_from_phil(
params, reference
)
else:
if params.goniometer.axes and len(params.goniometer.axes) > 3:
goniometer = GoniometerFactory.multi_axis_goniometer_from_phil(params)
elif params.goniometer.axis or params.goniometer.axes:
goniometer = GoniometerFactory.single_axis_goniometer_from_phil(params)
else:
return None
return goniometer
[docs] @staticmethod
def from_dict(d, t=None):
"""Convert the dictionary to a goniometer model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The goniometer model
"""
if d is None and t is None:
return None
joint = t.copy() if t else {}
joint.update(d)
# Create the model from the joint dictionary
if {"axes", "angles", "scan_axis"}.issubset(joint):
return MultiAxisGoniometer.from_dict(joint)
return Goniometer.from_dict(joint)
[docs] @staticmethod
def make_goniometer(rotation_axis, fixed_rotation):
return Goniometer(
tuple(map(float, rotation_axis)), tuple(map(float, fixed_rotation))
)
[docs] @staticmethod
def make_kappa_goniometer(alpha, omega, kappa, phi, direction, scan_axis):
omega_axis = (1, 0, 0)
phi_axis = (1, 0, 0)
c = math.cos(alpha * math.pi / 180)
s = math.sin(alpha * math.pi / 180)
if direction == "+y":
kappa_axis = (c, s, 0.0)
elif direction == "+z":
kappa_axis = (c, 0.0, s)
elif direction == "-y":
kappa_axis = (c, -s, 0.0)
elif direction == "-z":
kappa_axis = (c, 0.0, -s)
else:
raise RuntimeError("Invalid direction")
if scan_axis == "phi":
scan_axis = 0
else:
scan_axis = 2
axes = flex.vec3_double((phi_axis, kappa_axis, omega_axis))
angles = flex.double((phi, kappa, omega))
names = flex.std_string(("PHI", "KAPPA", "OMEGA"))
return GoniometerFactory.make_multi_axis_goniometer(
axes, angles, names, scan_axis
)
[docs] @staticmethod
def make_multi_axis_goniometer(axes, angles, names, scan_axis):
return MultiAxisGoniometer(axes, angles, names, scan_axis)
[docs] @staticmethod
def single_axis():
"""Construct a single axis goniometer which is canonical in the
CBF reference frame."""
axis = (1, 0, 0)
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
return GoniometerFactory.make_goniometer(axis, fixed)
[docs] @staticmethod
def single_axis_reverse():
"""Construct a single axis goniometer which is canonical in the
CBF reference frame, but reversed in rotation."""
axis = (-1, 0, 0)
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
return GoniometerFactory.make_goniometer(axis, fixed)
[docs] @staticmethod
def known_axis(axis):
"""Return an goniometer instance for a known rotation axis, assuming
that nothing is known about the fixed element of the rotation axis."""
assert len(axis) == 3
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
return Goniometer(axis, fixed)
[docs] @staticmethod
def kappa(alpha, omega, kappa, phi, direction, scan_axis):
"""Return a kappa goniometer where omega is the primary axis (i,e.
aligned with X in the CBF coordinate frame) and has the kappa arm
with angle alpha attached to it, aligned with -z, +y, +z or -y at
omega = 0, that being the direction, which in turn has phi fixed to it
which should initially be coincident with omega. We also need to know
which axis is being used for the scan i.e. phi or omega. All angles
should be given in degrees. This will work by first constructing the
rotation axes and then composing them to the scan axis and fixed
component of the rotation."""
return GoniometerFactory.make_kappa_goniometer(
alpha, omega, kappa, phi, direction, scan_axis
)
[docs] @staticmethod
def multi_axis(axes, angles, names, scan_axis):
""""""
return GoniometerFactory.make_multi_axis_goniometer(
axes, angles, names, scan_axis
)
[docs] @staticmethod
def imgCIF(cif_file):
"""Initialize a goniometer model from an imgCIF file."""
# FIXME in here work out how to get the proper setting matrix if != 1
cbf_handle = pycbf.cbf_handle_struct()
cbf_handle.read_file(cif_file.encode(), pycbf.MSG_DIGEST)
return GoniometerFactory.imgCIF_H(cbf_handle)
[docs] @staticmethod
def imgCIF_H(cbf_handle):
"""Initialize a goniometer model from an imgCIF file handle, where
it is assumed that the file has already been read."""
# find the goniometer axes and dependencies
axis_names = flex.std_string()
depends_on = flex.std_string()
axes = flex.vec3_double()
angles = flex.double()
scan_axis = None
cbf_handle.find_category(b"axis")
for i in range(cbf_handle.count_rows()):
cbf_handle.find_column(b"equipment")
if cbf_handle.get_value() == b"goniometer":
cbf_handle.find_column(b"id")
axis_names.append(cbf_handle.get_value())
axis = []
for i in range(3):
cbf_handle.find_column(b"vector[%i]" % (i + 1))
axis.append(float(cbf_handle.get_value()))
axes.append(axis)
cbf_handle.find_column(b"depends_on")
depends_on.append(cbf_handle.get_value())
cbf_handle.next_row()
# find the starting angles of each goniometer axis and figure out which one
# is the scan axis (i.e. non-zero angle_increment)
cbf_handle.find_category(b"diffrn_scan_axis")
for i in range(cbf_handle.count_rows()):
cbf_handle.find_column(b"axis_id")
axis_name = cbf_handle.get_value()
if axis_name.decode() not in axis_names:
cbf_handle.next_row()
continue
cbf_handle.find_column(b"angle_start")
axis_angle = float(cbf_handle.get_value())
cbf_handle.find_column(b"angle_increment")
increment = float(cbf_handle.get_value())
angles.append(axis_angle)
if abs(increment) > 0:
assert (
scan_axis is None
), "More than one scan axis is defined: not currently supported"
scan_axis = flex.first_index(axis_names, axis_name)
cbf_handle.next_row()
assert axes.size() == angles.size()
if scan_axis is None:
# probably a still shot -> scan axis arbitrary as no scan
scan_axis = 0
# figure out the order of the axes from the depends_on values
order = flex.size_t()
for i in range(axes.size()):
if depends_on[i] == ".":
o = 0
else:
o = flex.first_index(axis_names, depends_on[i]) + 1
assert o not in order
order.append(o)
# multi-axis gonio requires axes in order as viewed from crystal to gonio base
# i.e. the reverse of the order we have from cbf header
order = order.reversed()
axes = axes.select(order)
angles = angles.select(order)
axis_names = axis_names.select(order)
scan_axis = axes.size() - scan_axis - 1
# construct a multi-axis goniometer
gonio = GoniometerFactory.multi_axis(axes, angles, axis_names, scan_axis)
return gonio
