def test_radius(setup):
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
s0 = setup["beam"].get_s0()
m2 = setup["gonio"].get_rotation_axis()
s0_length = matrix.col(setup["beam"].get_s0()).length()
width, height = setup["detector"][0].get_image_size()
radius12 = setup["delta_divergence"]
for i in range(1000):
# Get random x, y, z
x = random.uniform(0, 2000)
y = random.uniform(0, 2000)
z = random.uniform(0, 9)
# Get random s1, phi, panel
s1 = (matrix.col(setup["detector"][0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length)
phi = setup["scan"].get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = setup["calculate_bbox"](s1, z, panel)
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Check vertical edges
for j in range(bbox[2], bbox[3] + 1):
xyz1 = setup["detector"][0].get_pixel_lab_coord((bbox[0], j))
xyz2 = setup["detector"][0].get_pixel_lab_coord((bbox[1] + 1, j))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e31 = xcs.from_beam_vector_and_rotation_angle(
sdash1, phi)
e12, e22, e31 = xcs.from_beam_vector_and_rotation_angle(
sdash2, phi)
if bbox[0] > 0 and bbox[1] < width:
assert math.sqrt(e11**2 + e21**2) >= radius12
assert math.sqrt(e12**2 + e22**2) >= radius12
# Check horizontal edges
for i in range(bbox[0], bbox[1] + 1):
xyz1 = setup["detector"][0].get_pixel_lab_coord((i, bbox[2]))
xyz2 = setup["detector"][0].get_pixel_lab_coord((i, bbox[3] + 1))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e32 = xcs.from_beam_vector_and_rotation_angle(
sdash1, phi)
e12, e22, e32 = xcs.from_beam_vector_and_rotation_angle(
sdash2, phi)
if bbox[2] > 0 and bbox[3] < height:
assert math.sqrt(e11**2 + e21**2) >= radius12
assert math.sqrt(e12**2 + e22**2) >= radius12
def test_outer_bounds(setup):
assert len(setup["detector"]) == 1
s0 = setup["beam"].get_s0()
m2 = setup["gonio"].get_rotation_axis()
s0_length = matrix.col(setup["beam"].get_s0()).length()
width, height = setup["detector"][0].get_image_size()
zrange = setup["scan"].get_array_range()
for i in range(1000):
# Get random x, y, z
x = random.uniform(0, 2000)
y = random.uniform(0, 2000)
z = random.uniform(0, 9)
# Get random s1, phi, panel
s1 = (
matrix.col(setup["detector"][0].get_pixel_lab_coord((x, y))).normalize()
* s0_length
)
phi = setup["scan"].get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = setup["calculate_bbox"](s1, z, panel)
z1, z2 = bbox[4], bbox[5]
# Calculate the rotation angle for each point
phi_dash1 = setup["scan"].get_angle_from_array_index(z1, deg=False)
phi_dash2 = setup["scan"].get_angle_from_array_index(z2, deg=False)
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate reciprocal space coordinates at each point
e11, e21, e31 = xcs.from_beam_vector_and_rotation_angle(s1, phi_dash1)
e12, e22, e32 = xcs.from_beam_vector_and_rotation_angle(s1, phi_dash2)
# Check vertical edges
for j in range(bbox[2], bbox[3] + 1):
xyz1 = setup["detector"][0].get_pixel_lab_coord((bbox[0], j))
xyz2 = setup["detector"][0].get_pixel_lab_coord((bbox[1] + 1, j))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e3 = xcs.from_beam_vector_and_rotation_angle(sdash1, phi)
e12, e22, e3 = xcs.from_beam_vector_and_rotation_angle(sdash2, phi)
if bbox[0] > 0 and bbox[1] < width:
assert (
abs(e11) >= setup["delta_divergence"]
or abs(e21) >= setup["delta_divergence"]
)
assert (
abs(e12) >= setup["delta_divergence"]
or abs(e22) >= setup["delta_divergence"]
)
# Check horizontal edges
for i in range(bbox[0], bbox[1] + 1):
xyz1 = setup["detector"][0].get_pixel_lab_coord((i, bbox[2]))
xyz2 = setup["detector"][0].get_pixel_lab_coord((i, bbox[3] + 1))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e3 = xcs.from_beam_vector_and_rotation_angle(sdash1, phi)
e12, e22, e3 = xcs.from_beam_vector_and_rotation_angle(sdash2, phi)
if bbox[2] > 0 and bbox[3] < height:
assert (
abs(e11) >= setup["delta_divergence"]
or abs(e21) >= setup["delta_divergence"]
)
assert (
abs(e12) >= setup["delta_divergence"]
or abs(e22) >= setup["delta_divergence"]
)
# All e3 coords >= delta_mosaicity
if bbox[4] > zrange[0] and bbox[5] < zrange[1]:
assert abs(e31) >= setup["delta_mosaicity"]
assert abs(e32) >= setup["delta_mosaicity"]
def tst_outer_bounds(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
assert (len(self.detector) == 1)
s0 = self.beam.get_s0()
m2 = self.gonio.get_rotation_axis()
s0_length = matrix.col(self.beam.get_s0()).length()
width, height = self.detector[0].get_image_size()
zrange = self.scan.get_array_range()
for i in range(1000):
# Get random x, y, z
x = uniform(0, 2000)
y = uniform(0, 2000)
z = uniform(0, 9)
# Get random s1, phi, panel
s1 = matrix.col(self.detector[0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length
phi = self.scan.get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = self.calculate_bbox(s1, z, panel)
x1, x2 = bbox[0], bbox[1]
y1, y2 = bbox[2], bbox[3]
z1, z2 = bbox[4], bbox[5]
# Calculate the rotation angle for each point
phi_dash1 = self.scan.get_angle_from_array_index(z1, deg=False)
phi_dash2 = self.scan.get_angle_from_array_index(z2, deg=False)
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate reciprocal space coordinates at each point
e11, e21, e31 = xcs.from_beam_vector_and_rotation_angle(
s1, phi_dash1)
e12, e22, e32 = xcs.from_beam_vector_and_rotation_angle(
s1, phi_dash2)
# Check vertical edges
for j in range(bbox[2], bbox[3] + 1):
xyz1 = self.detector[0].get_pixel_lab_coord((bbox[0], j))
xyz2 = self.detector[0].get_pixel_lab_coord((bbox[1] + 1, j))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e3 = xcs.from_beam_vector_and_rotation_angle(
sdash1, phi)
e12, e22, e3 = xcs.from_beam_vector_and_rotation_angle(
sdash2, phi)
if bbox[0] > 0 and bbox[1] < width:
assert (abs(e11) >= self.delta_divergence
or abs(e21) >= self.delta_divergence)
assert (abs(e12) >= self.delta_divergence
or abs(e22) >= self.delta_divergence)
# Check horizontal edges
for i in range(bbox[0], bbox[1] + 1):
xyz1 = self.detector[0].get_pixel_lab_coord((i, bbox[2]))
xyz2 = self.detector[0].get_pixel_lab_coord((i, bbox[3] + 1))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e3 = xcs.from_beam_vector_and_rotation_angle(
sdash1, phi)
e12, e22, e3 = xcs.from_beam_vector_and_rotation_angle(
sdash2, phi)
if bbox[2] > 0 and bbox[3] < height:
assert (abs(e11) >= self.delta_divergence
or abs(e21) >= self.delta_divergence)
assert (abs(e12) >= self.delta_divergence
or abs(e22) >= self.delta_divergence)
# All e3 coords >= delta_mosaicity
if bbox[4] > zrange[0] and bbox[5] < zrange[1]:
assert (abs(e31) >= self.delta_mosaicity)
assert (abs(e32) >= self.delta_mosaicity)
print 'OK'
def tst_outer_bounds(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
assert(len(self.detector) == 1)
s0 = self.beam.get_s0()
m2 = self.gonio.get_rotation_axis()
s0_length = matrix.col(self.beam.get_s0()).length()
width, height = self.detector[0].get_image_size()
zrange = self.scan.get_array_range()
for i in range(1000):
# Get random x, y, z
x = uniform(0, 2000)
y = uniform(0, 2000)
z = uniform(0, 9)
# Get random s1, phi, panel
s1 = matrix.col(self.detector[0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length
phi = self.scan.get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = self.calculate_bbox(s1, z, panel)
x1, x2 = bbox[0], bbox[1]
y1, y2 = bbox[2], bbox[3]
z1, z2 = bbox[4], bbox[5]
# Calculate the rotation angle for each point
phi_dash1 = self.scan.get_angle_from_array_index(z1, deg = False)
phi_dash2 = self.scan.get_angle_from_array_index(z2, deg = False)
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate reciprocal space coordinates at each point
e11, e21, e31 = xcs.from_beam_vector_and_rotation_angle(s1, phi_dash1)
e12, e22, e32 = xcs.from_beam_vector_and_rotation_angle(s1, phi_dash2)
# Check vertical edges
for j in range(bbox[2], bbox[3] + 1):
xyz1 = self.detector[0].get_pixel_lab_coord((bbox[0], j))
xyz2 = self.detector[0].get_pixel_lab_coord((bbox[1] + 1, j))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e3 = xcs.from_beam_vector_and_rotation_angle(sdash1, phi)
e12, e22, e3 = xcs.from_beam_vector_and_rotation_angle(sdash2, phi)
if bbox[0] > 0 and bbox[1] < width:
assert(abs(e11) >= self.delta_divergence or
abs(e21) >= self.delta_divergence)
assert(abs(e12) >= self.delta_divergence or
abs(e22) >= self.delta_divergence)
# Check horizontal edges
for i in range(bbox[0], bbox[1] + 1):
xyz1 = self.detector[0].get_pixel_lab_coord((i, bbox[2]))
xyz2 = self.detector[0].get_pixel_lab_coord((i, bbox[3] + 1))
sdash1 = matrix.col(xyz1).normalize() * s0_length
sdash2 = matrix.col(xyz2).normalize() * s0_length
e11, e21, e3 = xcs.from_beam_vector_and_rotation_angle(sdash1, phi)
e12, e22, e3 = xcs.from_beam_vector_and_rotation_angle(sdash2, phi)
if bbox[2] > 0 and bbox[3] < height:
assert(abs(e11) >= self.delta_divergence or
abs(e21) >= self.delta_divergence)
assert(abs(e12) >= self.delta_divergence or
abs(e22) >= self.delta_divergence)
# All e3 coords >= delta_mosaicity
if bbox[4] > zrange[0] and bbox[5] < zrange[1]:
assert(abs(e31) >= self.delta_mosaicity)
assert(abs(e32) >= self.delta_mosaicity)
print 'OK'
