def get_goniometer_shadow_masker(self, goniometer=None):
from dials.util.masking import GoniometerShadowMaskGenerator
from scitbx.array_family import flex
import math
coords = flex.vec3_double(((0, 0, 0), ))
alpha = flex.double_range(0, 190, step=10) * math.pi / 180
r = flex.double(alpha.size(), 40)
x = flex.double(r.size(), 107.61)
y = -r * flex.sin(alpha)
z = -r * flex.cos(alpha)
coords.extend(flex.vec3_double(x, y, z))
coords.extend(
flex.vec3_double((
# fixed
(107.49, 7.84, 39.49),
(107.39, 15.69, 38.97),
(107.27, 23.53, 38.46),
(107.16, 31.37, 37.94),
(101.76, 33.99, 36.25),
(96.37, 36.63, 34.56),
(90.98, 39.25, 33.00),
(85.58, 41.88, 31.18),
(80.89, 47.06, 31.00),
(76.55, 51.51, 31.03),
(72.90, 55.04, 31.18),
(66.86, 60.46, 31.67),
(62.10, 64.41, 32.25),
)))
alpha = flex.double_range(180, 370, step=10) * math.pi / 180
r = flex.double(alpha.size(), 33)
x = (flex.sqrt(flex.pow2(r * flex.sin(alpha)) + 89.02**2) *
flex.cos((50 * math.pi / 180) -
flex.atan(r / 89.02 * flex.sin(alpha))))
y = (flex.sqrt(flex.pow2(r * flex.sin(alpha)) + 89.02**2) *
flex.sin((50 * math.pi / 180) -
flex.atan(r / 89.02 * flex.sin(alpha))))
z = -r * flex.cos(alpha)
coords.extend(flex.vec3_double(x, y, z))
coords.extend(
flex.vec3_double((
# fixed
(62.10, 64.41, -32.25),
(66.86, 60.46, -31.67),
(72.90, 55.04, -31.18),
(76.55, 51.51, -31.03),
(80.89, 47.06, -31.00),
(85.58, 41.88, -31.18),
(90.98, 39.25, -33.00),
(96.37, 36.63, -34.56),
(101.76, 33.99, -36.25),
(107.16, 31.37, -37.94),
(107.27, 23.53, -38.46),
(107.39, 15.69, -38.97),
(107.49, 7.84, -39.49),
(107.61, 0.00, -40.00))))
# I23 end station coordinate system:
# X-axis: positive direction is facing away from the storage ring (from
# sample towards goniometer)
# Y-axis: positive direction is vertically up
# Z-axis: positive direction is in the direction of the beam (from
# sample towards detector)
# K-axis (kappa): at an angle of +50 degrees from the X-axis
# K & phi rotation axes: clockwise rotation is positive (right hand
# thumb rule)
# Omega-axis: along the X-axis; clockwise rotation is positive
# End station x-axis is parallel to ImgCIF x-axis
# End station z-axis points in opposite direction to ImgCIF definition
# (ImgCIF: The Z-axis is derived from the source axis which goes from
# the sample to the source)
# Consequently end station y-axis (to complete set following right hand
# rule) points in opposite direction to ImgCIF y-axis.
# Kappa arm aligned with -y in ImgCIF convention
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from scitbx import matrix
R = align_reference_frame(matrix.col((1, 0, 0)), matrix.col((1, 0, 0)),
matrix.col((0, 1, 0)), matrix.col(
(0, -1, 0)))
coords = R.elems * coords
if goniometer is None:
goniometer = self.get_goniometer()
return GoniometerShadowMaskGenerator(goniometer, coords,
flex.size_t(len(coords), 1))
def get_goniometer_shadow_masker(self, goniometer=None):
from dials.util.masking import GoniometerShadowMaskGenerator
from scitbx.array_family import flex
import math
coords = flex.vec3_double((
(0,0,0),
))
alpha = flex.double_range(0, 190, step=10) * math.pi / 180
r = flex.double(alpha.size(), 40)
x = flex.double(r.size(), 107.61)
y = -r*flex.sin(alpha)
z = -r*flex.cos(alpha)
coords.extend(flex.vec3_double(x, y, z))
coords.extend(flex.vec3_double((
# fixed
(107.49, 7.84, 39.49),
(107.39, 15.69, 38.97),
(107.27, 23.53, 38.46),
(107.16, 31.37, 37.94),
(101.76, 33.99, 36.25),
(96.37, 36.63, 34.56),
(90.98, 39.25, 33.00),
(85.58, 41.88, 31.18),
(80.89, 47.06, 31.00),
(76.55, 51.51, 31.03),
(72.90, 55.04, 31.18),
(66.86, 60.46, 31.67),
(62.10, 64.41, 32.25),
)))
alpha = flex.double_range(180, 370, step=10) * math.pi / 180
r = flex.double(alpha.size(), 33)
x = (flex.sqrt(flex.pow2(r * flex.sin(alpha)) + 89.02**2) * flex.cos((50 * math.pi/180) - flex.atan(r/89.02 * flex.sin(alpha))))
y = (flex.sqrt(flex.pow2(r * flex.sin(alpha)) + 89.02**2) * flex.sin((50 * math.pi/180) - flex.atan(r/89.02 * flex.sin(alpha))))
z = -r*flex.cos(alpha)
coords.extend(flex.vec3_double(x, y, z))
coords.extend(flex.vec3_double((
# fixed
(62.10, 64.41, -32.25),
(66.86, 60.46, -31.67),
(72.90, 55.04, -31.18),
(76.55, 51.51, -31.03),
(80.89, 47.06, -31.00),
(85.58, 41.88, -31.18),
(90.98, 39.25, -33.00),
(96.37, 36.63, -34.56),
(101.76, 33.99, -36.25),
(107.16, 31.37, -37.94),
(107.27, 23.53, -38.46),
(107.39, 15.69, -38.97),
(107.49, 7.84, -39.49),
(107.61, 0.00, -40.00)
)))
# I23 end station coordinate system:
# X-axis: positive direction is facing away from the storage ring (from
# sample towards goniometer)
# Y-axis: positive direction is vertically up
# Z-axis: positive direction is in the direction of the beam (from
# sample towards detector)
# K-axis (kappa): at an angle of +50 degrees from the X-axis
# K & phi rotation axes: clockwise rotation is positive (right hand
# thumb rule)
# Omega-axis: along the X-axis; clockwise rotation is positive
# End station x-axis is parallel to ImgCIF x-axis
# End station z-axis points in opposite direction to ImgCIF definition
# (ImgCIF: The Z-axis is derived from the source axis which goes from
# the sample to the source)
# Consequently end station y-axis (to complete set following right hand
# rule) points in opposite direction to ImgCIF y-axis.
# Kappa arm aligned with -y in ImgCIF convention
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from scitbx import matrix
R = align_reference_frame(matrix.col((1,0,0)), matrix.col((1,0,0)),
matrix.col((0,1,0)), matrix.col((0,-1,0)))
coords = R.elems * coords
if goniometer is None:
goniometer = self.get_goniometer()
return GoniometerShadowMaskGenerator(
goniometer, coords, flex.size_t(len(coords), 1))