def __call__(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
s0 = self.beam.get_s0()
m2 = self.gonio.get_rotation_axis()
s0_length = matrix.col(self.beam.get_s0()).length()
for i in range(100):
# 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, phi, panel)
x1, x2 = bbox[0], bbox[1]
y1, y2 = bbox[2], bbox[3]
z1, z2 = bbox[4], bbox[5]
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
forward_fraction = self.transform_forward(bbox[4:], phi,
xcs.zeta())
# Calculate the transform fraction
reverse_fraction = self.transform_reverse(bbox[4:], phi,
xcs.zeta())
# Check the same points are non-zero
eps = 1e-7
for j in range(forward_fraction.all()[0]):
for i in range(forward_fraction.all()[1]):
if forward_fraction[j, i] > 0.0:
assert (reverse_fraction[i, j] > 0.0)
else:
assert (reverse_fraction[i, j] < eps)
# Test passed
print 'OK'
def __call__(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
s0 = self.beam.get_s0()
m2 = self.gonio.get_rotation_axis()
s0_length = matrix.col(self.beam.get_s0()).length()
for i in range(100):
# 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, phi, panel)
x1, x2 = bbox[0], bbox[1]
y1, y2 = bbox[2], bbox[3]
z1, z2 = bbox[4], bbox[5]
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
forward_fraction = self.transform_forward(bbox[4:], phi, xcs.zeta())
# Calculate the transform fraction
reverse_fraction = self.transform_reverse(bbox[4:], phi, xcs.zeta())
# Check the same points are non-zero
eps = 1e-7
for j in range(forward_fraction.all()[0]):
for i in range(forward_fraction.all()[1]):
if forward_fraction[j,i] > 0.0:
assert(reverse_fraction[i,j] > 0.0)
else:
assert(reverse_fraction[i,j] < eps)
# Test passed
print 'OK'
def tst_conservation_of_counts(self):
from scitbx import matrix
from random import uniform, seed
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.gaussian_rs import transform
from scitbx.array_family import flex
seed(0)
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()
# Create an s1 map
s1_map = transform.beam_vector_map(self.detector[0], self.beam, True)
for i in range(100):
# Get random x, y, z
x = uniform(300, 1800)
y = uniform(300, 1800)
z = uniform(500, 600)
# 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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
if abs(cs.zeta()) < 0.1:
continue
# The grid index generator
step_size = self.delta_divergence / self.grid_size
grid_index = transform.GridIndexGenerator(cs, x0, y0,
(step_size, step_size),
self.grid_size, s1_map)
# Create the image
#image = flex.double(flex.grid(z1 - z0, y1 - y0, x1 - x0), 1)
image = gaussian((z1 - z0, y1 - y0, x1 - x0), 10.0,
(z - z0, y - y0, x - x0), (2.0, 2.0, 2.0))
mask = flex.bool(flex.grid(image.all()), False)
for j in range(y1 - y0):
for i in range(x1 - x0):
inside = False
gx00, gy00 = grid_index(j, i)
gx01, gy01 = grid_index(j, i + 1)
gx10, gy10 = grid_index(j + 1, i)
gx11, gy11 = grid_index(j + 1, i + 1)
mingx = min([gx00, gx01, gx10, gx11])
maxgx = max([gx00, gx01, gx10, gx11])
mingy = min([gy00, gy01, gy10, gy11])
maxgy = max([gy00, gy01, gy10, gy11])
if (mingx >= 0 and maxgx < 2 * self.grid_size + 1
and mingy >= 0 and maxgy < 2 * self.grid_size + 1):
inside = True
for k in range(1, z1 - z0 - 1):
mask[k, j, i] = inside
# Transform the image to the grid
transformed = transform.TransformForwardNoModel(
self.spec, cs, bbox, 0, image.as_double(), mask)
grid = transformed.profile()
# Get the sums and ensure they're the same
eps = 1e-7
sum_grid = flex.sum(grid)
sum_image = flex.sum(flex.double(flex.select(image, flags=mask)))
assert (abs(sum_grid - sum_image) <= eps)
mask = flex.bool(flex.grid(image.all()), True)
transformed = transform.TransformForwardNoModel(
self.spec, cs, bbox, 0, image.as_double(), mask)
grid = transformed.profile()
# Boost the bbox to make sure all intensity is included
x0, x1, y0, y1, z0, z1 = bbox
bbox2 = (x0 - 10, x1 + 10, y0 - 10, y1 + 10, z0 - 10, z1 + 10)
# Do the reverse transform
transformed = transform.TransformReverseNoModel(
self.spec, cs, bbox2, 0, grid)
image2 = transformed.profile()
# Check the sum of pixels are the same
sum_grid = flex.sum(grid)
sum_image = flex.sum(image2)
assert (abs(sum_grid - sum_image) <= eps)
# Do the reverse transform
transformed = transform.TransformReverseNoModel(
self.spec, cs, bbox, 0, grid)
image2 = transformed.profile()
from dials.algorithms.statistics import pearson_correlation_coefficient
cc = pearson_correlation_coefficient(image.as_1d().as_double(),
image2.as_1d())
assert (cc >= 0.99)
# if cc < 0.99:
# print cc, bbox
# from matplotlib import pylab
# pylab.plot(image.as_numpy_array()[(z1-z0)/2,(y1-y0)/2,:])
# pylab.show()
# pylab.plot(image2.as_numpy_array()[(z1-z0)/2,(y1-y0)/2,:])
# pylab.show()
# pylab.plot((image.as_double()-image2).as_numpy_array()[(z1-z0)/2,(y1-y0)/2,:])
# pylab.show()
# Test passed
print 'OK'
def test_forward_no_model(dials_data):
sequence = load.imageset(
dials_data("centroid_test_data").join("sweep.json").strpath)
# Get the models
beam = sequence.get_beam()
detector = sequence.get_detector()
gonio = sequence.get_goniometer()
scan = sequence.get_scan()
scan.set_image_range((0, 1000))
# Set some parameters
sigma_divergence = beam.get_sigma_divergence(deg=False)
mosaicity = 0.157 * math.pi / 180
n_sigma = 3
grid_size = 20
delta_divergence = n_sigma * sigma_divergence
step_size = delta_divergence / grid_size
delta_divergence2 = delta_divergence + step_size * 0.5
delta_mosaicity = n_sigma * mosaicity
# Create the bounding box calculator
calculate_bbox = BBoxCalculator3D(beam, detector, gonio, scan,
delta_divergence2, delta_mosaicity)
# Initialise the transform
spec = transform.TransformSpec(beam, detector, gonio, scan,
sigma_divergence, mosaicity, n_sigma + 1,
grid_size)
# tst_conservation_of_counts(self):
random.seed(0)
assert len(detector) == 1
s0 = beam.get_s0()
m2 = gonio.get_rotation_axis()
s0_length = matrix.col(beam.get_s0()).length()
# Create an s1 map
s1_map = transform.beam_vector_map(detector[0], beam, True)
for i in range(100):
# Get random x, y, z
x = random.uniform(300, 1800)
y = random.uniform(300, 1800)
z = random.uniform(500, 600)
# Get random s1, phi, panel
s1 = matrix.col(detector[0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length
phi = scan.get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = calculate_bbox(s1, z, panel)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
if abs(cs.zeta()) < 0.1:
continue
# The grid index generator
step_size = delta_divergence / grid_size
grid_index = transform.GridIndexGenerator(cs, x0, y0,
(step_size, step_size),
grid_size, s1_map)
# Create the image
# image = flex.double(flex.grid(z1 - z0, y1 - y0, x1 - x0), 1)
image = gaussian((z1 - z0, y1 - y0, x1 - x0), 10.0,
(z - z0, y - y0, x - x0), (2.0, 2.0, 2.0))
mask = flex.bool(flex.grid(image.all()), False)
for j in range(y1 - y0):
for i in range(x1 - x0):
inside = False
gx00, gy00 = grid_index(j, i)
gx01, gy01 = grid_index(j, i + 1)
gx10, gy10 = grid_index(j + 1, i)
gx11, gy11 = grid_index(j + 1, i + 1)
mingx = min([gx00, gx01, gx10, gx11])
maxgx = max([gx00, gx01, gx10, gx11])
mingy = min([gy00, gy01, gy10, gy11])
maxgy = max([gy00, gy01, gy10, gy11])
if (mingx >= 0 and maxgx < 2 * grid_size + 1 and mingy >= 0
and maxgy < 2 * grid_size + 1):
inside = True
for k in range(1, z1 - z0 - 1):
mask[k, j, i] = inside
# Transform the image to the grid
transformed = transform.TransformForwardNoModel(
spec, cs, bbox, 0, image.as_double(), mask)
grid = transformed.profile()
# Get the sums and ensure they're the same
eps = 1e-7
sum_grid = flex.sum(grid)
sum_image = flex.sum(flex.double(flex.select(image, flags=mask)))
assert abs(sum_grid - sum_image) <= eps
mask = flex.bool(flex.grid(image.all()), True)
transformed = transform.TransformForwardNoModel(
spec, cs, bbox, 0, image.as_double(), mask)
grid = transformed.profile()
# Boost the bbox to make sure all intensity is included
x0, x1, y0, y1, z0, z1 = bbox
bbox2 = (x0 - 10, x1 + 10, y0 - 10, y1 + 10, z0 - 10, z1 + 10)
# Do the reverse transform
transformed = transform.TransformReverseNoModel(
spec, cs, bbox2, 0, grid)
image2 = transformed.profile()
# Check the sum of pixels are the same
sum_grid = flex.sum(grid)
sum_image = flex.sum(image2)
assert abs(sum_grid - sum_image) <= eps
# Do the reverse transform
transformed = transform.TransformReverseNoModel(
spec, cs, bbox, 0, grid)
image2 = transformed.profile()
from dials.algorithms.statistics import pearson_correlation_coefficient
cc = pearson_correlation_coefficient(image.as_1d().as_double(),
image2.as_1d())
assert cc >= 0.99
def test_map_forward_reverse(dials_data):
sequence = load.imageset(
dials_data("centroid_test_data").join("sweep.json").strpath)
# Get the models
beam = sequence.get_beam()
detector = sequence.get_detector()
gonio = sequence.get_goniometer()
scan = sequence.get_scan()
# Set the delta_divergence/mosaicity
n_sigma = 3
sigma_divergence = 0.060 * math.pi / 180
mosaicity = 0.154 * math.pi / 180
delta_divergence = n_sigma * sigma_divergence
delta_mosaicity = n_sigma * mosaicity
# Set the grid size
grid_size = (4, 4, 4)
# Create the E3 fraction object
transform_forward = MapFramesForward(
scan.get_array_range()[0],
scan.get_oscillation(deg=False)[0],
scan.get_oscillation(deg=False)[1],
mosaicity,
n_sigma,
grid_size[2],
)
# Create the E3 fraction object
transform_reverse = MapFramesReverse(
scan.get_array_range()[0],
scan.get_oscillation(deg=False)[0],
scan.get_oscillation(deg=False)[1],
mosaicity,
n_sigma,
grid_size[2],
)
# Create the bounding box calculator
calculate_bbox = BBoxCalculator3D(beam, detector, gonio, scan,
delta_divergence, delta_mosaicity)
s0 = beam.get_s0()
m2 = gonio.get_rotation_axis()
s0_length = matrix.col(beam.get_s0()).length()
for i in range(100):
# 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(detector[0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length
phi = scan.get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = calculate_bbox(s1, phi, panel)
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
forward_fraction = transform_forward(bbox[4:], phi, xcs.zeta())
# Calculate the transform fraction
reverse_fraction = transform_reverse(bbox[4:], phi, xcs.zeta())
# Check the same points are non-zero
eps = 1e-7
for j in range(forward_fraction.all()[0]):
for i in range(forward_fraction.all()[1]):
if forward_fraction[j, i] > 0.0:
assert reverse_fraction[i, j] > 0.0
else:
assert reverse_fraction[i, j] < eps
def test_map_frames_forward(dials_data):
sequence = load.imageset(
dials_data("centroid_test_data").join("sweep.json").strpath)
# Get the models
beam = sequence.get_beam()
detector = sequence.get_detector()
gonio = sequence.get_goniometer()
scan = sequence.get_scan()
# Set the delta_divergence/mosaicity
n_sigma = 3
sigma_divergence = 0.060 * math.pi / 180
mosaicity = 0.154 * math.pi / 180
delta_divergence = n_sigma * sigma_divergence
delta_mosaicity = n_sigma * mosaicity
# Set the grid size
grid_size = (4, 4, 4)
# Create the E3 fraction object
transform = MapFramesForward(
scan.get_array_range()[0],
scan.get_oscillation(deg=False)[0],
scan.get_oscillation(deg=False)[1],
mosaicity,
n_sigma,
grid_size[2],
)
# Create the bounding box calculator
calculate_bbox = BBoxCalculator3D(beam, detector, gonio, scan,
delta_divergence, delta_mosaicity)
assert len(detector) == 1
s0 = beam.get_s0()
m2 = gonio.get_rotation_axis()
s0_length = matrix.col(beam.get_s0()).length()
for i in range(100):
# 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(detector[0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length
phi = scan.get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = calculate_bbox(s1, z, panel)
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
fraction = transform(bbox[4:], phi, xcs.zeta())
# Ensure the minimum and maximum are 0 < 1
fmax = flex.max(fraction)
fmin = flex.min(fraction)
assert fmax <= (
1.0 + 5e-15) and fmax > 0.0, f"{fmax:.16f} not between 0 and 1"
assert fmin >= 0.0 and fmin <= 1.0
# Ensure the fraction for each image frame adds up to 1.0 for
# all those frames completely within the grid
for j in range(1, fraction.all()[0] - 1):
tot = flex.sum(fraction[j:j + 1, :])
assert abs(tot - 1.0) < 1e-7
# Ensure the frames follow a progression through the grid. I.e,
# check that values increase then decrease and don't jump around
for j in range(fraction.all()[0]):
f = fraction[j:j + 1, :]
last = f[0]
rev = False
for i in range(1, len(f)):
curr = f[1]
if rev is False:
if curr < last:
rev = True
else:
assert curr <= last
last = curr
def __call__(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from scitbx.array_family import flex
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()
for i in range(100):
# 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]
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
fraction = self.transform(bbox[4:], phi, xcs.zeta())
# Ensure the minimum and maximum are 0 < 1
fmax = flex.max(fraction)
fmin = flex.min(fraction)
assert (fmax <= (1.0 + 5e-15)
and fmax > 0.0), "%.16f not between 0 and 1" % fmax
assert (fmin >= 0.0 and fmin <= 1.0)
# Ensure the fraction for each image frame adds up to 1.0 for
# all those frames completely within the grid
for j in range(1, fraction.all()[0] - 1):
tot = flex.sum(fraction[j:j + 1, :])
assert (abs(tot - 1.0) < 1e-7)
# Ensure the frames follow a progression through the grid. I.e,
# check that values increase then decrease and don't jump around
for j in range(fraction.all()[0]):
f = fraction[j:j + 1, :]
last = f[0]
rev = False
for i in range(1, len(f)):
curr = f[1]
if rev == False:
if curr < last:
rev = True
else:
assert (curr <= last)
last = curr
# Test passed
print 'OK'
def test_map_frames_reverse(dials_data):
from dials.model.serialize import load
from dials.algorithms.profile_model.gaussian_rs.transform import MapFramesReverse
from dials.algorithms.profile_model.gaussian_rs import BBoxCalculator3D
sequence = load.sequence(
dials_data("centroid_test_data").join("sweep.json").strpath)
# Get the models
beam = sequence.get_beam()
detector = sequence.get_detector()
gonio = sequence.get_goniometer()
scan = sequence.get_scan()
# Set the delta_divergence/mosaicity
n_sigma = 3
sigma_divergence = 0.060 * math.pi / 180
mosaicity = 0.154 * math.pi / 180
delta_divergence = n_sigma * sigma_divergence
delta_mosaicity = n_sigma * mosaicity
# Set the grid size
grid_size = (4, 4, 4)
# Create the E3 fraction object
transform = MapFramesReverse(
scan.get_array_range()[0],
scan.get_oscillation(deg=False)[0],
scan.get_oscillation(deg=False)[1],
mosaicity,
n_sigma,
grid_size[2],
)
# Create the bounding box calculator
calculate_bbox = BBoxCalculator3D(beam, detector, gonio, scan,
delta_divergence, delta_mosaicity)
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from scitbx.array_family import flex
s0 = beam.get_s0()
m2 = gonio.get_rotation_axis()
s0_length = matrix.col(beam.get_s0()).length()
for i in range(100):
# 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(detector[0].get_pixel_lab_coord(
(x, y))).normalize() * s0_length
phi = scan.get_angle_from_array_index(z, deg=False)
panel = 0
# Calculate the bounding box
bbox = calculate_bbox(s1, phi, panel)
x1, x2 = bbox[0], bbox[1]
y1, y2 = bbox[2], bbox[3]
z1, z2 = bbox[4], bbox[5]
if x1 == 0 or y1 == 0 or z1 == 0:
continue
if x2 == 2000 or y2 == 2000 or z2 == 9:
continue
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
fraction = transform(bbox[4:], phi, xcs.zeta())
# Ensure the minimum and maximum are 0 < 1
fmax = flex.max(fraction)
fmin = flex.min(fraction)
assert fmax <= 1.0 and fmax > 0.0
assert fmin >= 0.0 and fmin <= 1.0
# Ensure the fraction for image adds up to 1.0 for
# all those images completely within the image
for v3 in range(fraction.all()[0]):
tot = flex.sum(fraction[v3:v3 + 1, :])
assert abs(tot - 1.0) < 1e-7
# Ensure the frames follow a progression through the grid. I.e,
# check that values increase then decrease and don't jump around
for v3 in range(fraction.all()[0]):
f = fraction[v3:v3 + 1, :]
last = f[0]
rev = False
for i in range(1, len(f)):
curr = f[1]
if rev is False:
if curr < last:
rev = True
else:
assert curr <= last
last = curr
def __call__(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from scitbx.array_family import flex
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()
for i in range(100):
# 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]
# Create the XDS coordinate system
xcs = CoordinateSystem(m2, s0, s1, phi)
# Calculate the transform fraction
fraction = self.transform(bbox[4:], phi, xcs.zeta())
# Ensure the minimum and maximum are 0 < 1
fmax = flex.max(fraction)
fmin = flex.min(fraction)
assert(fmax <= (1.0 + 5e-15) and fmax > 0.0), "%.16f not between 0 and 1" % fmax
assert(fmin >= 0.0 and fmin <= 1.0)
# Ensure the fraction for each image frame adds up to 1.0 for
# all those frames completely within the grid
for j in range(1, fraction.all()[0]-1):
tot = flex.sum(fraction[j:j+1,:])
assert(abs(tot - 1.0) < 1e-7)
# Ensure the frames follow a progression through the grid. I.e,
# check that values increase then decrease and don't jump around
for j in range(fraction.all()[0]):
f = fraction[j:j+1,:]
last = f[0]
rev = False
for i in range(1,len(f)):
curr = f[1]
if rev == False:
if curr < last:
rev = True
else:
assert(curr <= last)
last = curr
# Test passed
print 'OK'
def tst_conservation_of_counts(self):
from scitbx import matrix
from random import uniform, seed
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.gaussian_rs import transform
from scitbx.array_family import flex
seed(0)
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()
# Create an s1 map
s1_map = transform.beam_vector_map(self.detector[0], self.beam, True)
for i in range(100):
# Get random x, y, z
x = uniform(300, 1800)
y = uniform(300, 1800)
z = uniform(500, 600)
# 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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
if abs(cs.zeta()) < 0.1:
continue
# The grid index generator
step_size = self.delta_divergence / self.grid_size
grid_index = transform.GridIndexGenerator(cs, x0, y0, (step_size, step_size), self.grid_size, s1_map)
# Create the image
# image = flex.double(flex.grid(z1 - z0, y1 - y0, x1 - x0), 1)
image = gaussian((z1 - z0, y1 - y0, x1 - x0), 10.0, (z - z0, y - y0, x - x0), (2.0, 2.0, 2.0))
mask = flex.bool(flex.grid(image.all()), False)
for j in range(y1 - y0):
for i in range(x1 - x0):
inside = False
gx00, gy00 = grid_index(j, i)
gx01, gy01 = grid_index(j, i + 1)
gx10, gy10 = grid_index(j + 1, i)
gx11, gy11 = grid_index(j + 1, i + 1)
mingx = min([gx00, gx01, gx10, gx11])
maxgx = max([gx00, gx01, gx10, gx11])
mingy = min([gy00, gy01, gy10, gy11])
maxgy = max([gy00, gy01, gy10, gy11])
if mingx >= 0 and maxgx < 2 * self.grid_size + 1 and mingy >= 0 and maxgy < 2 * self.grid_size + 1:
inside = True
for k in range(1, z1 - z0 - 1):
mask[k, j, i] = inside
# Transform the image to the grid
transformed = transform.TransformForwardNoModel(self.spec, cs, bbox, 0, image.as_double(), mask)
grid = transformed.profile()
# Get the sums and ensure they're the same
eps = 1e-7
sum_grid = flex.sum(grid)
sum_image = flex.sum(flex.double(flex.select(image, flags=mask)))
assert abs(sum_grid - sum_image) <= eps
mask = flex.bool(flex.grid(image.all()), True)
transformed = transform.TransformForwardNoModel(self.spec, cs, bbox, 0, image.as_double(), mask)
grid = transformed.profile()
# Boost the bbox to make sure all intensity is included
x0, x1, y0, y1, z0, z1 = bbox
bbox2 = (x0 - 10, x1 + 10, y0 - 10, y1 + 10, z0 - 10, z1 + 10)
# Do the reverse transform
transformed = transform.TransformReverseNoModel(self.spec, cs, bbox2, 0, grid)
image2 = transformed.profile()
# Check the sum of pixels are the same
sum_grid = flex.sum(grid)
sum_image = flex.sum(image2)
assert abs(sum_grid - sum_image) <= eps
# Do the reverse transform
transformed = transform.TransformReverseNoModel(self.spec, cs, bbox, 0, grid)
image2 = transformed.profile()
from dials.algorithms.statistics import pearson_correlation_coefficient
cc = pearson_correlation_coefficient(image.as_1d().as_double(), image2.as_1d())
assert cc >= 0.99
# if cc < 0.99:
# print cc, bbox
# from matplotlib import pylab
# pylab.plot(image.as_numpy_array()[(z1-z0)/2,(y1-y0)/2,:])
# pylab.show()
# pylab.plot(image2.as_numpy_array()[(z1-z0)/2,(y1-y0)/2,:])
# pylab.show()
# pylab.plot((image.as_double()-image2).as_numpy_array()[(z1-z0)/2,(y1-y0)/2,:])
# pylab.show()
# Test passed
print "OK"
