def test_indexing():
from dials.algorithms.profile_model.modeller import CircleSampler
width = 1000
height = 1000
scan_range = (2, 12)
depth = scan_range[1] - scan_range[0]
nz = 2
sampler = CircleSampler((width, height), scan_range, nz)
zstep = depth / nz
eps = 1e-10
dt = 2 * math.pi / 8
r2 = sampler.r2()
xp = [width / 2.0
] + [width / 2.0 + r2 * math.cos(i * dt) for i in range(8)]
yp = [height / 2.0
] + [height / 2.0 + r2 * math.sin(i * dt) for i in range(8)]
zind = [[k] * 9 for k in range(nz)]
zind = [i for j in zind for i in j]
zp = [(z + 0.5) * zstep + scan_range[0] for z in zind]
for x0, y0, z0, i in zip(xp, yp, zp, range(len(sampler))):
x1, y1, z1 = sampler.coord(i)
assert (abs(x0 - x1) <= eps)
assert (abs(y0 - y1) <= eps)
assert (abs(z0 - z1) <= eps)
def tst_indexing(self):
from dials.algorithms.profile_model.modeller import CircleSampler
from math import sin, cos, pi
width = 1000
height = 1000
scan_range = (2, 12)
depth = scan_range[1] - scan_range[0]
nz = 2
sampler = CircleSampler((width, height), scan_range, nz)
zstep = depth / nz
eps = 1e-10
dt = 2 * pi / 8
r2 = sampler.r2()
xp = [width / 2.0] + [width / 2.0 + r2 * cos(i * dt) for i in range(8)]
yp = [height / 2.0] + [height / 2.0 + r2 * sin(i * dt) for i in range(8)]
zind = [[k] * 9 for k in range(nz)]
zind = [i for j in zind for i in j]
zp = [(z + 0.5) * zstep + scan_range[0] for z in zind]
for x0, y0, z0, i in zip(xp, yp, zp, range(len(sampler))):
x1, y1, z1 = sampler.coord(i)
assert(abs(x0 - x1) <= eps)
assert(abs(y0 - y1) <= eps)
assert(abs(z0 - z1) <= eps)
print 'OK'
def tst_getters(self):
from math import sqrt
from dials.algorithms.profile_model.modeller import CircleSampler
width = 1000
height = 1000
scan_range = (2, 12)
depth = scan_range[1] - scan_range[0]
nz = 2
sampler = CircleSampler((width, height), scan_range, nz)
image_size = sampler.image_size()
scan_range = sampler.scan_range()
image_centre = sampler.image_centre()
r0 = sampler.r0()
r1 = sampler.r1()
r2 = sampler.r2()
size = len(sampler)
assert(width == image_size[0])
assert(height == image_size[1])
assert(width // 2 == image_centre[0])
assert(height // 2 == image_centre[1])
assert(r0 == min([width // 2, height // 2]))
assert(r1 == r0 / 3.0)
assert(r2 == r1 * sqrt(5.0))
assert(9 * nz == size)
print 'OK'
def tst_getters(self):
from math import sqrt
from dials.algorithms.profile_model.modeller import CircleSampler
width = 1000
height = 1000
scan_range = (2, 12)
depth = scan_range[1] - scan_range[0]
nz = 2
sampler = CircleSampler((width, height), scan_range, nz)
image_size = sampler.image_size()
scan_range = sampler.scan_range()
image_centre = sampler.image_centre()
r0 = sampler.r0()
r1 = sampler.r1()
r2 = sampler.r2()
size = len(sampler)
assert (width == image_size[0])
assert (height == image_size[1])
assert (width // 2 == image_centre[0])
assert (height // 2 == image_centre[1])
assert (r0 == min([width // 2, height // 2]))
assert (r1 == r0 / 3.0)
assert (r2 == r1 * sqrt(5.0))
assert (9 * nz == size)
print 'OK'
def tst_weights(self):
from dials.algorithms.profile_model.modeller import CircleSampler
from math import exp, log
from scitbx import matrix
width = 1000
height = 1000
scan_range = (2, 12)
depth = scan_range[1] - scan_range[0]
nz = 1
sampler = CircleSampler((width, height), scan_range, nz)
# Check the weight at the coord in 1.0
eps = 1e-7
for i in range(len(sampler)):
coord = sampler.coord(i)
weight = sampler.weight(i, 0, coord)
assert(abs(weight - 1.0) < eps)
r0 = sampler.r0()
r1 = sampler.r1()
r2 = sampler.r2()
r = r2 / (2.0*r1)
expected = exp(-4.0*r*r*log(2.0))
for i in range(1, 9):
coord = sampler.coord(i)
weight = sampler.weight(0, 0, coord)
assert(abs(weight - expected) < eps)
r = r2 / (2.0*(r2 - r1))
expected = exp(-4.0*r*r*log(2.0))
for i in range(1, 9):
coord = sampler.coord(0)
weight = sampler.weight(i, 0, coord)
assert(abs(weight - expected) < eps)
for i in range(1, 9):
coord1 = matrix.col(sampler.coord(0))
coord2 = matrix.col(sampler.coord(i))
coord = coord1 + r1 * (coord2 - coord1) / r2
weight = sampler.weight(0, 0, coord)
assert(abs(weight - 0.5) < eps)
weight = sampler.weight(i, 0, coord)
assert(abs(weight - 0.5) < eps)
print 'OK'
def tst_weights(self):
from dials.algorithms.profile_model.modeller import CircleSampler
from math import exp, log
from scitbx import matrix
width = 1000
height = 1000
scan_range = (2, 12)
depth = scan_range[1] - scan_range[0]
nz = 1
sampler = CircleSampler((width, height), scan_range, nz)
# Check the weight at the coord in 1.0
eps = 1e-7
for i in range(len(sampler)):
coord = sampler.coord(i)
weight = sampler.weight(i, coord)
assert (abs(weight - 1.0) < eps)
r0 = sampler.r0()
r1 = sampler.r1()
r2 = sampler.r2()
r = r2 / (2.0 * r1)
expected = exp(-4.0 * r * r * log(2.0))
for i in range(1, 9):
coord = sampler.coord(i)
weight = sampler.weight(0, coord)
assert (abs(weight - expected) < eps)
r = r2 / (2.0 * (r2 - r1))
expected = exp(-4.0 * r * r * log(2.0))
for i in range(1, 9):
coord = sampler.coord(0)
weight = sampler.weight(i, coord)
assert (abs(weight - expected) < eps)
for i in range(1, 9):
coord1 = matrix.col(sampler.coord(0))
coord2 = matrix.col(sampler.coord(i))
coord = coord1 + r1 * (coord2 - coord1) / r2
weight = sampler.weight(0, coord)
assert (abs(weight - 0.5) < eps)
weight = sampler.weight(i, coord)
assert (abs(weight - 0.5) < eps)
print 'OK'
def test_weights():
from scitbx import matrix
from dials.algorithms.profile_model.modeller import CircleSampler
width = 1000
height = 1000
scan_range = (2, 12)
nz = 1
sampler = CircleSampler((width, height), scan_range, nz)
# Check the weight at the coord in 1.0
eps = 1e-7
for i in range(len(sampler)):
coord = sampler.coord(i)
weight = sampler.weight(i, 0, coord)
assert abs(weight - 1.0) < eps
r1 = sampler.r1()
r2 = sampler.r2()
r = r2 / (2.0 * r1)
expected = math.exp(-4.0 * r * r * math.log(2.0))
for i in range(1, 9):
coord = sampler.coord(i)
weight = sampler.weight(0, 0, coord)
assert abs(weight - expected) < eps
r = r2 / (2.0 * (r2 - r1))
expected = math.exp(-4.0 * r * r * math.log(2.0))
for i in range(1, 9):
coord = sampler.coord(0)
weight = sampler.weight(i, 0, coord)
assert abs(weight - expected) < eps
for i in range(1, 9):
coord1 = matrix.col(sampler.coord(0))
coord2 = matrix.col(sampler.coord(i))
coord = coord1 + r1 * (coord2 - coord1) / r2
weight = sampler.weight(0, 0, coord)
assert abs(weight - 0.5) < eps
weight = sampler.weight(i, 0, coord)
assert abs(weight - 0.5) < eps
def test_getters():
from dials.algorithms.profile_model.modeller import CircleSampler
width = 1000
height = 1000
scan_range = (2, 12)
nz = 2
sampler = CircleSampler((width, height), scan_range, nz)
image_size = sampler.image_size()
image_centre = sampler.image_centre()
r0 = sampler.r0()
r1 = sampler.r1()
r2 = sampler.r2()
size = len(sampler)
assert width == image_size[0]
assert height == image_size[1]
assert width // 2 == image_centre[0]
assert height // 2 == image_centre[1]
assert r0 == min([width // 2, height // 2])
assert r1 == r0 / 3.0
assert r2 == r1 * math.sqrt(5.0)
assert 9 * nz == size
