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 tst_conservation_of_counts(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.gaussian_rs import transform
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()
# 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(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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
# 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.TransformForward(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)
# Test passed
print 'OK'
def test_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 some parameters
sigma_divergence = beam.get_sigma_divergence(deg=False)
mosaicity = 0.157 * math.pi / 180
n_sigma = 3
grid_size = 7
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):
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(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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
# 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.TransformForward(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
# Test passed
# tst_transform_with_background(self):
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(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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
# 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))
background = flex.random_double(len(image))
background.resize(image.accessor())
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.TransformForward(spec, cs, bbox, 0,
image.as_double(),
background.as_double(), mask)
igrid = transformed.profile()
bgrid = transformed.background()
# Get the sums and ensure they're the same
eps = 1e-7
sum_igrid = flex.sum(igrid)
sum_bgrid = flex.sum(bgrid)
sum_image = flex.sum(flex.double(flex.select(image, flags=mask)))
sum_bkgrd = flex.sum(flex.double(flex.select(background, flags=mask)))
try:
assert abs(sum_igrid - sum_image) <= eps
assert abs(sum_bgrid - sum_bkgrd) <= eps
except Exception:
print("Failed for: ", (x, y, z))
raise
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_forward(dials_data):
from dials.model.serialize import load
from dials.algorithms.profile_model.gaussian_rs import transform
from dials.algorithms.profile_model.gaussian_rs import BBoxCalculator3D
sweep = load.sweep(
dials_data("centroid_test_data").join("sweep.json").strpath)
# Get the models
beam = sweep.get_beam()
detector = sweep.get_detector()
gonio = sweep.get_goniometer()
scan = sweep.get_scan()
# beam.set_direction((0.0, 0.0, 1.0))
# gonio.set_rotation_axis((1.0, 0.0, 0.0))
# detector.set_frame((1.0, 0.0, 0.0),
# (0.0, 1.0, 0.0),
# (-150, -150, -200))
# Set some parameters
sigma_divergence = beam.get_sigma_divergence(deg=False)
mosaicity = 0.157 * math.pi / 180
n_sigma = 3
grid_size = 7
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):
from scitbx import matrix
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.gaussian_rs import transform
from scitbx.array_family import flex
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(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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
# 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.TransformForward(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
# Test passed
# def tst_transformed_centroid(self):
# from scitbx import matrix
# from random import uniform
# from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
# from dials.algorithms.profile_model.gaussian_rs import transform
# from scitbx.array_family import flex
# from time import time
# 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, beam, True)
# # Get random x, y, z
# x = random.uniform(300, 1800)
# y = random.uniform(300, 1800)
# z = random.uniform(-10, 0)
# # Get random s1, phi, panel
# s1 = matrix.col(detector.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)
# # 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 = gaussian((z1 - z0, y1 - y0, x1 - x0), 10.0,
# (z - z0, y - y0, x - x0), (2.0, 2.0, 2.0))
# print x, y, z, bbox
# print (z1 - z0, y1 - y0, x1 - x0), (z - z0, y - y0, x - x0)
# 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
# #image[k,j,i] *= inside
# from matplotlib import pylab
# pylab.imshow(image.as_numpy_array()[(z1 - z0) / 2,:,:], interpolation='none')
# pylab.show()
# # Transform the image to the grid
# grid = transform(cs, bbox, image, mask)
# from matplotlib import pylab
# pylab.imshow(grid.as_numpy_array()[7,:,:], interpolation='none')
# pylab.show()
# # 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)
# # Check the centroid
# sz = grid_size * 2 + 1
# grid_x = flex.double(flex.grid(sz, sz, sz))
# grid_y = flex.double(flex.grid(sz, sz, sz))
# grid_z = flex.double(flex.grid(sz, sz, sz))
# for k in range(sz):
# for j in range(sz):
# for i in range(sz):
# grid_x[k,j,i] = i + 0.5
# grid_y[k,j,i] = j + 0.5
# grid_z[k,j,i] = k + 0.5
#
# sum_grid_x = flex.sum(grid * grid_x)
# sum_grid_y = flex.sum(grid * grid_y)
# sum_grid_z = flex.sum(grid * grid_z)
# xc = sum_grid_x / sum_grid
# yc = sum_grid_y / sum_grid
# zc = sum_grid_z / sum_grid
# print xc, yc, zc
# assert(abs(xc - grid_size + 0.5) <= 0.5)
# assert(abs(yc - grid_size + 0.5) <= 0.5)
# assert(abs(zc - grid_size + 0.5) <= 0.5)
# # Test passed
# print 'OK'
# tst_transform_with_background(self):
from scitbx import matrix
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.gaussian_rs import transform
from scitbx.array_family import flex
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(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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
# 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))
background = flex.random_double(len(image))
background.resize(image.accessor())
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.TransformForward(spec, cs, bbox, 0,
image.as_double(),
background.as_double(), mask)
igrid = transformed.profile()
bgrid = transformed.background()
# Get the sums and ensure they're the same
eps = 1e-7
sum_igrid = flex.sum(igrid)
sum_bgrid = flex.sum(bgrid)
sum_image = flex.sum(flex.double(flex.select(image, flags=mask)))
sum_bkgrd = flex.sum(flex.double(flex.select(background, flags=mask)))
try:
assert abs(sum_igrid - sum_image) <= eps
assert abs(sum_bgrid - sum_bkgrd) <= eps
except Exception:
print("Failed for: ", (x, y, z))
raise
def tst_conservation_of_counts(self):
from scitbx import matrix
from random import uniform
from dials.algorithms.profile_model.gaussian_rs import CoordinateSystem
from dials.algorithms.profile_model.gaussian_rs import transform
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()
# 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(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)
x0, x1, y0, y1, z0, z1 = bbox
# Create the coordinate system
cs = CoordinateSystem(m2, s0, s1, phi)
# 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.TransformForward(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
# 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"
