def compute_zeta(self, experiment):
"""
Compute zeta for each reflection.
:param experiment: The experimental models
:return: Zeta for each reflection
"""
from dials.algorithms.profile_model.gaussian_rs import zeta_factor
m2 = experiment.goniometer.get_rotation_axis()
s0 = experiment.beam.get_s0()
self["zeta"] = zeta_factor(m2, s0, self["s1"])
return self["zeta"]
def compute_zeta(self, experiment):
'''
Compute zeta for each reflection.
:param experiment: The experimental models
:return: Zeta for each reflection
'''
from dials.algorithms.profile_model.gaussian_rs import zeta_factor
m2 = experiment.goniometer.get_rotation_axis()
s0 = experiment.beam.get_s0()
self['zeta'] = zeta_factor(m2, s0, self['s1'])
return self['zeta']
def compute_zeta_multi(self, experiments):
"""
Compute zeta for each reflection.
:param experiments: The list of experiments
:return: Zeta for each reflection
"""
from dials.algorithms.profile_model.gaussian_rs import zeta_factor
m2 = cctbx.array_family.flex.vec3_double(len(experiments))
s0 = cctbx.array_family.flex.vec3_double(len(experiments))
for i, e in enumerate(experiments):
m2[i] = e.goniometer.get_rotation_axis()
s0[i] = e.beam.get_s0()
self["zeta"] = zeta_factor(m2, s0, self["s1"], self["id"])
return self["zeta"]
def compute_zeta_multi(self, experiments):
'''
Compute zeta for each reflection.
:param experiments: The list of experiments
:return: Zeta for each reflection
'''
from dials.algorithms.profile_model.gaussian_rs import zeta_factor
m2 = flex.vec3_double(len(experiments))
s0 = flex.vec3_double(len(experiments))
for i, e in enumerate(experiments):
m2[i] = e.goniometer.get_rotation_axis()
s0[i] = e.beam.get_s0()
self['zeta'] = zeta_factor(m2, s0, self['s1'], self['id'])
return self['zeta']
def compute_zeta_multi(self, experiments):
'''
Compute zeta for each reflection.
:param experiments: The list of experiments
:return: Zeta for each reflection
'''
from dials.algorithms.profile_model.gaussian_rs import zeta_factor
m2 = flex.vec3_double(len(experiments))
s0 = flex.vec3_double(len(experiments))
for i, e in enumerate(experiments):
m2[i] = e.goniometer.get_rotation_axis()
s0[i] = e.beam.get_s0()
self['zeta'] = zeta_factor(m2, s0, self['s1'], self['id'])
return self['zeta']
def get_reflections(experiments):
from dials.algorithms.profile_model.gaussian_rs import zeta_factor
from dials.algorithms.spot_prediction import PixelToMillerIndex
from collections import defaultdict
from dials.algorithms.spot_prediction import ScanStaticRayPredictor
from math import floor, sqrt, pi
from dials.array_family import flex
reflection_pixels = defaultdict(list)
transform = PixelToMillerIndex(
experiments[0].beam,
experiments[0].detector,
experiments[0].goniometer,
experiments[0].scan,
experiments[0].crystal,
)
xsize, ysize = experiments[0].detector[0].get_image_size()
z0 = experiments[0].scan.get_array_range()[0]
image = experiments[0].imageset[0][0]
mask = flex.bool(image.accessor())
for j in range(ysize):
print(j)
for i in range(xsize):
h = transform.h(0, i + 0.5, j + 0.5, z0 + 0.5)
hkl = tuple(map(lambda x: int(floor(x + 0.5)), h))
d = sqrt(sum(map(lambda a: (a[0] - a[1]) ** 2, zip(h, hkl))))
if d < 0.3:
foreground = True
else:
foreground = False
mask[j, i] = foreground
reflection_pixels[hkl].append((j, i, foreground))
# from matplotlib import pylab
# pylab.imshow(mask.as_numpy_array())
# pylab.show()
I = []
V = []
T = []
predictor = ScanStaticRayPredictor(
experiments[0].beam.get_s0(),
experiments[0].goniometer.get_rotation_axis(),
experiments[0].goniometer.get_fixed_rotation(),
experiments[0].goniometer.get_setting_rotation(),
(-2 * pi, 2 * pi),
)
UB = experiments[0].crystal.get_A()
phi0 = experiments[0].scan.get_angle_from_array_index(z0 + 0.5, deg=False)
m2 = experiments[0].goniometer.get_rotation_axis()
s0 = experiments[0].beam.get_s0()
for hkl, pixel_list in reflection_pixels.iteritems():
rays = predictor(hkl, UB)
if len(rays) == 0:
continue
elif len(rays) == 1:
dphi = rays[0].angle - phi0
else:
dphi0 = ((rays[0].angle - phi0) + pi) % (2 * pi) - pi
dphi1 = ((rays[1].angle - phi0) + pi) % (2 * pi) - pi
if abs(dphi0) < abs(dphi1):
dphi = dphi0
s1 = rays[0].s1
else:
dphi = dphi1
s1 = rays[1].s1
if abs(dphi) > 5 * pi / 180.0:
continue
try:
zeta = zeta_factor(m2, s0, s1)
except Exception:
continue
dphi *= zeta
I_sum = 0
B_sum = 0
I_count = 0
B_count = 0
for j, i, foreground in pixel_list:
data = image[j, i]
if foreground:
I_sum += data
I_count += 1
else:
B_sum += data
B_count += 1
B = B_sum / B_count
I.append(I_sum - B * I_count)
V.append(I_sum + B * I_count * (1 + I_count / B_count))
T.append(dphi * 180 / pi)
print(min(T), max(T))
IOS = []
TN = []
for i, v, t in zip(I, V, T):
if i > 0 and v > 0:
IOS.append(i / sqrt(v))
TN.append(t)
from matplotlib import pylab
pylab.hist(TN, bins=20, weights=IOS)
pylab.xlabel("DPHI (degrees)")
pylab.show()
