def test_num_intervals(self, nintervals):
"""Test a range of different numbers of intervals"""
# Parameterise the detector with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50
det_p = TestDetectorModel(50, self.detector, self.image_range, nintervals)
# How many parameters?
num_param = det_p.num_free()
# apply a random parameter shift to the detector, on order of 2% of
# the initial values
p_vals = det_p.get_param_vals()
sigmas = [0.02 * p for p in p_vals]
new_vals = random_param_shift(p_vals, sigmas)
det_p.set_param_vals(new_vals)
# calculate state and gradients at image 50
det_p.compose()
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
# compare analytical and finite difference derivatives at image 50
an_ds_dp = det_p.get_ds_dp()
fd_ds_dp = get_fd_gradients(det_p, [1.e-7] * num_param)
param_names = det_p.get_param_names()
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
print "OK"
return
def test_ScanVaryingDetectorParameterisation(nintervals, plots=False):
"""Basic test of a ScanVaryingDetectorParameterisationSinglePanel
with a range of different numbers of intervals"""
vmp = _TestScanVaryingModelParameterisation()
# Parameterise the detector with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50
det_p = _TestDetectorModel(50, vmp.detector, vmp.image_range, nintervals)
# How many parameters?
num_param = det_p.num_free()
# apply a random parameter shift to the detector, on order of 2% of
# the initial values
p_vals = det_p.get_param_vals()
sigmas = [0.02 * p for p in p_vals]
new_vals = random_param_shift(p_vals, sigmas)
det_p.set_param_vals(new_vals)
# calculate state and gradients at image 50
det_p.compose()
null_mat = matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
# compare analytical and finite difference derivatives at image 50
an_ds_dp = det_p.get_ds_dp()
fd_ds_dp = get_fd_gradients(det_p, [1.0e-7] * num_param)
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_mat, eps=1.0e-6)
def test_ScanVaryingCrystalOrientationParameterisation_random(plots=False):
"""Test a ScanVaryingCrystalOrientationParameterisation with
random initial orientations, random parameter shifts and random times"""
vmp = _TestScanVaryingModelParameterisation()
attempts = 100
null_mat = matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
for i in range(attempts):
# make a new P1 random crystal and parameterise it
a = random.uniform(10, 50) * vmp.random_direction_close_to(
matrix.col((1, 0, 0)))
b = random.uniform(10, 50) * vmp.random_direction_close_to(
matrix.col((0, 1, 0)))
c = random.uniform(10, 50) * vmp.random_direction_close_to(
matrix.col((0, 0, 1)))
xl = Crystal(a, b, c, space_group_symbol="P 1")
xl_op = _TestOrientationModel(50, xl, vmp.image_range, 5)
# How many parameters?
num_param = xl_op.num_free()
# apply random parameter shifts to the orientation (2.0 mrad each
# checkpoint)
p_vals = xl_op.get_param_vals()
sigmas = [2.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# select random time point at which to make comparisons
t = random.uniform(*vmp.image_range)
xl_op.set_time_point(t)
# compare analytical and finite difference derivatives
xl_op_an_ds_dp = xl_op.get_ds_dp()
xl_op_fd_ds_dp = get_fd_gradients(xl_op,
[1.0e-6 * math.pi / 180] * num_param)
for j in range(num_param):
assert approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
null_mat,
eps=1.0e-6), textwrap.dedent("""\
Failure in try {i}
failure for parameter number {j}
of the orientation parameterisation
with fd_ds_dp =
{fd}
and an_ds_dp =
{an}
so that difference fd_ds_dp - an_ds_dp =
{diff}
""").format(
i=i,
j=j,
fd=xl_op_fd_ds_dp[j],
an=xl_op_an_ds_dp[j],
diff=xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j],
)
def test_ScanVaryingBeamParameterisation(nintervals, plots=False):
"""Basic test of a ScanVaryingBeamParameterisation
with a range of different numbers of intervals"""
vmp = _TestScanVaryingModelParameterisation()
# Parameterise the crystal with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50
beam_p = _TestBeamModel(50, vmp.beam, vmp.image_range, nintervals,
vmp.goniometer)
# How many parameters?
num_param = beam_p.num_free()
# apply a random parameter shift to the beam, on order of 2% of
# the initial values
p_vals = beam_p.get_param_vals()
sigmas = [0.02 * p for p in p_vals]
new_vals = random_param_shift(p_vals, sigmas)
beam_p.set_param_vals(new_vals)
# calculate state and gradients at image 50
beam_p.compose()
null_vec = matrix.col((0., 0., 0.))
# compare analytical and finite difference derivatives at image 50
an_ds_dp = beam_p.get_ds_dp()
fd_ds_dp = get_fd_gradients(beam_p, [1.e-7] * num_param)
param_names = beam_p.get_param_names()
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_vec, eps=1.e-6)
def test_ScanVaryingCrystalUnitCellParameterisation_intervals(
nintervals, plots=False):
"""Basic test of a ScanVaryingCrystalUnitCellParameterisation
with a range of different numbers of intervals"""
vmp = _TestScanVaryingModelParameterisation()
# Parameterise the crystal with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50
xl_ucp = _TestUnitCellModel(50, vmp.xl, vmp.image_range, nintervals)
# How many parameters?
num_param = xl_ucp.num_free()
# apply a random parameter shift to the unit cell, on order of 2% of
# the initial metrical matrix parameters
p_vals = xl_ucp.get_param_vals()
sigmas = [0.02 * p for p in p_vals]
new_vals = random_param_shift(p_vals, sigmas)
xl_ucp.set_param_vals(new_vals)
# calculate state and gradients at image 50
xl_ucp.compose()
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
# compare analytical and finite difference derivatives at image 50
an_ds_dp = xl_ucp.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_ucp, [1.e-7] * num_param)
param_names = xl_ucp.get_param_names()
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_mat, eps=1.e-6)
def test_num_intervals(self, nintervals):
"""Test a range of different numbers of intervals"""
# Parameterise the detector with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50
det_p = TestDetectorModel(50, self.detector, self.image_range, nintervals)
# How many parameters?
num_param = det_p.num_free()
# apply a random parameter shift to the detector, on order of 2% of
# the initial values
p_vals = det_p.get_param_vals()
sigmas = [0.02 * p for p in p_vals]
new_vals = random_param_shift(p_vals, sigmas)
det_p.set_param_vals(new_vals)
# calculate state and gradients at image 50
det_p.compose()
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
# compare analytical and finite difference derivatives at image 50
an_ds_dp = det_p.get_ds_dp()
fd_ds_dp = get_fd_gradients(det_p, [1.e-7] * num_param)
param_names = det_p.get_param_names()
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
print "OK"
return
def test_beam_parameters():
from scitbx import matrix
from dxtbx.model import BeamFactory
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation,
)
from dials.algorithms.refinement.refinement_helpers import (
get_fd_gradients,
random_param_shift,
)
# make a random beam vector and parameterise it
bf = BeamFactory()
s0 = bf.make_beam(matrix.col.random(3, 0.5, 1.5), wavelength=1.2)
s0p = BeamParameterisation(s0)
# Let's do some basic tests. First, can we change parameter values and
# update the modelled vector s0?
s0_old = matrix.col(s0.get_s0())
s0p.set_param_vals([1000 * 0.1, 1000 * 0.1, 0.8])
assert matrix.col(s0.get_s0()).angle(s0_old) == pytest.approx(0.1413033, abs=1e-6)
assert matrix.col(s0.get_s0()).length() == pytest.approx(0.8, abs=1e-6)
# random initial orientations and wavelengths with a random parameter shifts
attempts = 1000
failures = 0
for i in range(attempts):
# make a random beam vector and parameterise it
s0 = bf.make_beam(
matrix.col.random(3, 0.5, 1.5), wavelength=random.uniform(0.8, 1.5)
)
s0p = BeamParameterisation(s0)
# apply a random parameter shift
p_vals = s0p.get_param_vals()
p_vals = random_param_shift(p_vals, [1000 * pi / 9, 1000 * pi / 9, 0.01])
s0p.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
an_ds_dp = s0p.get_ds_dp()
fd_ds_dp = get_fd_gradients(s0p, [1.0e-5 * pi / 180, 1.0e-5 * pi / 180, 1.0e-6])
for j in range(3):
try:
assert list(fd_ds_dp[j] - an_ds_dp[j]) == pytest.approx(
(0, 0, 0), abs=1e-6
)
except Exception:
print("for try", i)
print("failure for parameter number", j)
print("with fd_ds_dp = ")
print(fd_ds_dp[j])
print("and an_ds_dp = ")
print(an_ds_dp[j])
print("so that difference fd_ds_dp - an_ds_dp =")
print(fd_ds_dp[j] - an_ds_dp[j])
raise
def test_random(self):
"""Test random initial orientations, random parameter shifts and random
times"""
attempts = 100
failures = 0
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for i in range(attempts):
# make a new P1 random crystal and parameterise it
a = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((1, 0, 0)))
b = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((0, 1, 0)))
c = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((0, 0, 1)))
xl = Crystal(a, b, c, space_group_symbol="P 1")
xl_op = TestOrientationModel(50, xl, self.image_range, 5)
# How many parameters?
num_param = xl_op.num_free()
# apply random parameter shifts to the orientation (2.0 mrad each
# checkpoint)
p_vals = xl_op.get_param_vals()
sigmas = [2.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# select random time point at which to make comparisons
t = random.uniform(*self.image_range)
xl_op.set_time_point(t)
# compare analytical and finite difference derivatives
xl_op_an_ds_dp = xl_op.get_ds_dp()
xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * \
num_param)
for j in range(num_param):
try:
assert (approx_equal(
(xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
null_mat,
eps=1.e-6))
except Exception:
failures += 1
print "for try", i
print "failure for parameter number", j
print "of the orientation parameterisation"
print "with fd_ds_dp = "
print xl_op_fd_ds_dp[j]
print "and an_ds_dp = "
print xl_op_an_ds_dp[j]
print "so that difference fd_ds_dp - an_ds_dp ="
print xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]
if failures == 0: print "OK"
def test_random(self):
"""Test random initial orientations, random parameter shifts and random
times"""
attempts = 100
failures = 0
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for i in range(attempts):
# make a new P1 random crystal and parameterise it
a = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((1, 0, 0)))
b = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((0, 1, 0)))
c = random.uniform(10,50) * \
self.random_direction_close_to(matrix.col((0, 0, 1)))
xl = crystal_model(a, b, c, space_group_symbol="P 1")
xl_op = TestOrientationModel(50, xl, self.image_range, 5)
# How many parameters?
num_param = xl_op.num_free()
# apply random parameter shifts to the orientation (2.0 mrad each
# checkpoint)
p_vals = xl_op.get_param_vals()
sigmas = [2.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# select random time point at which to make comparisons
t = random.uniform(*self.image_range)
xl_op.set_time_point(t)
# compare analytical and finite difference derivatives
xl_op_an_ds_dp = xl_op.get_ds_dp()
xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * \
num_param)
for j in range(num_param):
try:
assert(approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
null_mat, eps = 1.e-6))
except Exception:
failures += 1
print "for try", i
print "failure for parameter number", j
print "of the orientation parameterisation"
print "with fd_ds_dp = "
print xl_op_fd_ds_dp[j]
print "and an_ds_dp = "
print xl_op_an_ds_dp[j]
print "so that difference fd_ds_dp - an_ds_dp ="
print xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]
if failures == 0: print "OK"
def test():
goniometer = random_gonio()
gonp = GoniometerParameterisation(goniometer)
# Let's do some basic tests. First, can we change parameter values and
# update the laboratory frame rotation axis?
e_lab = matrix.col(goniometer.get_rotation_axis())
gonp.set_param_vals([1000 * 0.1, 1000 * 0.1])
assert matrix.col(goniometer.get_rotation_axis()).angle(
e_lab) == pytest.approx(0.1413033)
# random goniometers and random parameter shifts
attempts = 1000
for i in range(attempts):
# make a random goniometer and parameterise it
goniometer = random_gonio()
gonp = GoniometerParameterisation(goniometer)
# apply a random parameter shift
p_vals = gonp.get_param_vals()
p_vals = random_param_shift(p_vals,
[1000 * math.pi / 9, 1000 * math.pi / 9])
gonp.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
an_ds_dp = gonp.get_ds_dp()
fd_ds_dp = get_fd_gradients(
gonp, [1.0e-5 * math.pi / 180, 1.0e-5 * math.pi / 180])
null_mat = matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
for j in range(2):
try:
assert approx_equal((fd_ds_dp[j] - an_ds_dp[j]),
null_mat,
eps=1.0e-6)
except Exception:
print("for try", i)
print("failure for parameter number", j)
print("with fd_ds_dp = ")
print(fd_ds_dp[j])
print("and an_ds_dp = ")
print(an_ds_dp[j])
print("so that difference fd_ds_dp - an_ds_dp =")
print(fd_ds_dp[j] - an_ds_dp[j])
raise
a = random.uniform(10, 50) * random_direction_close_to(
matrix.col((1, 0, 0)))
b = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 1, 0)))
c = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 0, 1)))
xl = crystal_model(a, b, c, space_group_symbol="P 1")
xl_op = CrystalOrientationParameterisation(xl)
xl_ucp = CrystalUnitCellParameterisation(xl)
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
# compare analytical and finite difference derivatives
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi / 180] * 3)
for e, f in zip(an_ds_dp, fd_ds_dp):
assert (approx_equal((e - f), null_mat, eps=1.e-6))
an_ds_dp = xl_ucp.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_ucp, [1.e-7] * xl_ucp.num_free())
for e, f in zip(an_ds_dp, fd_ds_dp):
assert (approx_equal((e - f), null_mat, eps=1.e-6))
# random initial orientations with a random parameter shift at each
attempts = 100
failures = 0
for i in range(attempts):
# make a random P1 crystal and parameterise it
a = random.uniform(10, 50) * random_direction_close_to(
random.gauss(0, 1.0), deg = True)
# make a random P1 crystal and parameterise it
a = random.uniform(10,50) * random_direction_close_to(matrix.col((1, 0, 0)))
b = random.uniform(10,50) * random_direction_close_to(matrix.col((0, 1, 0)))
c = random.uniform(10,50) * random_direction_close_to(matrix.col((0, 0, 1)))
xl = crystal_model(a, b, c, space_group_symbol="P 1")
xl_op = CrystalOrientationParameterisation(xl)
xl_ucp = CrystalUnitCellParameterisation(xl)
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
# compare analytical and finite difference derivatives
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * 3)
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
an_ds_dp = xl_ucp.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_ucp, [1.e-7] * xl_ucp.num_free())
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
# random initial orientations with a random parameter shift at each
attempts = 100
failures = 0
for i in range(attempts):
# make a random P1 crystal and parameterise it
a = random.uniform(10,50) * random_direction_close_to(matrix.col((1, 0, 0)))
def test_num_intervals(self, nintervals):
"""Test a range of different numbers of intervals"""
# Parameterise the crystal with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50, but actually
# will try various time points in the test
xl_op = TestOrientationModel(50, self.xl, self.image_range, nintervals)
# How many parameters?
num_param = xl_op.num_free()
# shift the parameters away from zero
p_vals = xl_op.get_param_vals()
sigmas = [1.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# recalc state and gradients at image 50
xl_op.compose()
p_vals = xl_op.get_param_vals()
#print "Shifted parameter vals", p_vals
# compare analytical and finite difference derivatives at image 50
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * num_param)
param_names = xl_op.get_param_names()
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
# Now test gradients at equally spaced time points across the whole
# range
num_points = 50
smooth_at = []
phi1_data = []
phi2_data = []
phi3_data = []
step_size = (self.image_range[1] - self.image_range[0]) / num_points
for t in [self.image_range[0] + e * step_size \
for e in range(num_points + 1)]:
# collect data for plot
smooth_at.append(t)
phi1_data.append(xl_op._smoother.value_weight(t, xl_op._param[0])[0])
phi2_data.append(xl_op._smoother.value_weight(t, xl_op._param[1])[0])
phi3_data.append(xl_op._smoother.value_weight(t, xl_op._param[2])[0])
xl_op.set_time_point(t)
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * num_param)
#print t
#print "Gradients:"
#for s, a, f in zip(param_names, an_ds_dp, fd_ds_dp):
# print s
# print a
# print f
# print "diff:", a-f
# print
#
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
if self.do_plots:
try:
import matplotlib.pyplot as plt
plt.ion()
plt.clf()
plt.subplot(311)
plt.cla()
plt.scatter(smooth_at, phi1_data)
plt.title("Phi1")
plt.xlabel("image number")
plt.ylabel("Phi1 (mrad)")
plt.subplot(312)
plt.cla()
plt.scatter(smooth_at, phi2_data)
plt.title("Phi2")
plt.xlabel("image number")
plt.ylabel("Phi2 (mrad)")
plt.subplot(313)
plt.cla()
plt.scatter(smooth_at, phi3_data)
plt.title("Phi3")
plt.xlabel("image number")
plt.ylabel("Phi3 (mrad)")
plt.suptitle("Parameter smoothing with %d intervals" % nintervals)
plt.draw()
except ImportError as e:
print "pyplot not available", e
print "OK"
def test_ScanVaryingCrystalOrientationParameterisation_intervals(
nintervals, plots=False):
"""Test a ScanVaryingCrystalOrientationParameterisation with
a range of different numbers of intervals"""
vmp = _TestScanVaryingModelParameterisation()
# Parameterise the crystal with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50, but actually
# will try various time points in the test
xl_op = _TestOrientationModel(50, vmp.xl, vmp.image_range, nintervals)
# How many parameters?
num_param = xl_op.num_free()
# shift the parameters away from zero
p_vals = xl_op.get_param_vals()
sigmas = [1.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# recalc state and gradients at image 50
xl_op.compose()
p_vals = xl_op.get_param_vals()
# print "Shifted parameter vals", p_vals
# compare analytical and finite difference derivatives at image 50
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.0e-6 * math.pi / 180] * num_param)
null_mat = matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_mat, eps=1.0e-6)
# Now test gradients at equally spaced time points across the whole
# range
num_points = 50
smooth_at = []
phi1_data = []
phi2_data = []
phi3_data = []
step_size = (vmp.image_range[1] - vmp.image_range[0]) / num_points
for t in [
vmp.image_range[0] + e * step_size for e in range(num_points + 1)
]:
# collect data for plot
smooth_at.append(t)
phi1_data.append(xl_op._smoother.value_weight(t, xl_op._param[0])[0])
phi2_data.append(xl_op._smoother.value_weight(t, xl_op._param[1])[0])
phi3_data.append(xl_op._smoother.value_weight(t, xl_op._param[2])[0])
xl_op.set_time_point(t)
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op,
[1.0e-6 * math.pi / 180] * num_param)
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_mat, eps=1.0e-6)
if plots:
import matplotlib.pyplot as plt
plt.ion()
plt.clf()
plt.subplot(311)
plt.cla()
plt.scatter(smooth_at, phi1_data)
plt.title("Phi1")
plt.xlabel("image number")
plt.ylabel("Phi1 (mrad)")
plt.subplot(312)
plt.cla()
plt.scatter(smooth_at, phi2_data)
plt.title("Phi2")
plt.xlabel("image number")
plt.ylabel("Phi2 (mrad)")
plt.subplot(313)
plt.cla()
plt.scatter(smooth_at, phi3_data)
plt.title("Phi3")
plt.xlabel("image number")
plt.ylabel("Phi3 (mrad)")
plt.suptitle("Parameter smoothing with %d intervals" % nintervals)
plt.draw()
det = Detector(random_panel())
dp = DetectorParameterisationSinglePanel(det)
# apply a random parameter shift
p_vals = dp.get_param_vals()
p_vals = random_param_shift(
p_vals,
[10, 10, 10, 1000. * pi / 18, 1000. * pi / 18, 1000. * pi / 18])
dp.set_param_vals(p_vals)
# obtain current sensor state
#state = dp.get_state()
# compare analytical and finite difference derivatives.
an_ds_dp = dp.get_ds_dp(multi_state_elt=0)
fd_ds_dp = get_fd_gradients(dp, [1.e-6] * 3 + [1.e-4 * pi / 180] * 3)
for j in range(6):
try:
assert (approx_equal((fd_ds_dp[j] - an_ds_dp[j]),
matrix.sqr(
(0., 0., 0., 0., 0., 0., 0., 0., 0.)),
eps=1.e-6))
except AssertionError:
failures += 1
print "for try", i
print "failure for parameter number", j
print "with fd_ds_dp = "
print fd_ds_dp[j]
print "and an_ds_dp = "
print an_ds_dp[j]
def test():
import random
import textwrap
from cctbx.uctbx import unit_cell
from libtbx.test_utils import approx_equal
def random_direction_close_to(vector):
return vector.rotate_around_origin(
matrix.col((random.random(), random.random(),
random.random())).normalize(),
random.gauss(0, 1.0),
deg=True,
)
# make a random P1 crystal and parameterise it
a = random.uniform(10, 50) * random_direction_close_to(
matrix.col((1, 0, 0)))
b = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 1, 0)))
c = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 0, 1)))
xl = Crystal(a, b, c, space_group_symbol="P 1")
xl_op = CrystalOrientationParameterisation(xl)
xl_ucp = CrystalUnitCellParameterisation(xl)
null_mat = matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
# compare analytical and finite difference derivatives
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.0e-6 * pi / 180] * 3)
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_mat, eps=1.0e-6)
an_ds_dp = xl_ucp.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_ucp, [1.0e-7] * xl_ucp.num_free())
for e, f in zip(an_ds_dp, fd_ds_dp):
assert approx_equal((e - f), null_mat, eps=1.0e-6)
# random initial orientations with a random parameter shift at each
attempts = 100
for i in range(attempts):
# make a random P1 crystal and parameterise it
a = random.uniform(10, 50) * random_direction_close_to(
matrix.col((1, 0, 0)))
b = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 1, 0)))
c = random.uniform(10, 50) * random_direction_close_to(
matrix.col((0, 0, 1)))
xl = Crystal(a, b, c, space_group_symbol="P 1")
xl_op = CrystalOrientationParameterisation(xl)
xl_uc = CrystalUnitCellParameterisation(xl)
# apply a random parameter shift to the orientation
p_vals = xl_op.get_param_vals()
p_vals = random_param_shift(
p_vals, [1000 * pi / 9, 1000 * pi / 9, 1000 * pi / 9])
xl_op.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
xl_op_an_ds_dp = xl_op.get_ds_dp()
xl_op_fd_ds_dp = get_fd_gradients(xl_op, [1.0e-5 * pi / 180] * 3)
# apply a random parameter shift to the unit cell. We have to
# do this in a way that is respectful to metrical constraints,
# so don't modify the parameters directly; modify the cell
# constants and extract the new parameters
cell_params = xl.get_unit_cell().parameters()
cell_params = random_param_shift(cell_params, [1.0] * 6)
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(xl.get_space_group())
S.set_orientation(orientation=newB)
X = S.forward_independent_parameters()
xl_uc.set_param_vals(X)
xl_uc_an_ds_dp = xl_ucp.get_ds_dp()
# now doing finite differences about each parameter in turn
xl_uc_fd_ds_dp = get_fd_gradients(xl_ucp, [1.0e-7] * xl_ucp.num_free())
for j in range(3):
assert approx_equal((xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j]),
null_mat,
eps=1.0e-6), textwrap.dedent("""\
Failure in try {i}
failure for parameter number {j}
of the orientation parameterisation
with fd_ds_dp =
{fd}
and an_ds_dp =
{an}
so that difference fd_ds_dp - an_ds_dp =
{diff}
""").format(
i=i,
j=j,
fd=xl_op_fd_ds_dp[j],
an=xl_op_an_ds_dp[j],
diff=xl_op_fd_ds_dp[j] - xl_op_an_ds_dp[j],
)
for j in range(xl_ucp.num_free()):
assert approx_equal((xl_uc_fd_ds_dp[j] - xl_uc_an_ds_dp[j]),
null_mat,
eps=1.0e-6), textwrap.dedent("""\
Failure in try {i}
failure for parameter number {j}
of the unit cell parameterisation
with fd_ds_dp =
{fd}
and an_ds_dp =
{an}
so that difference fd_ds_dp - an_ds_dp =
{diff}
""").format(
i=i,
j=j,
fd=xl_uc_fd_ds_dp[j],
an=xl_uc_an_ds_dp[j],
diff=xl_uc_fd_ds_dp[j] - xl_uc_an_ds_dp[j],
)
def test_num_intervals(self, nintervals):
"""Test a range of different numbers of intervals"""
# Parameterise the crystal with the image range and five intervals. Init
# TestOrientationModel to explore gradients at image 50, but actually
# will try various time points in the test
xl_op = TestOrientationModel(50, self.xl, self.image_range, nintervals)
# How many parameters?
num_param = xl_op.num_free()
# shift the parameters away from zero
p_vals = xl_op.get_param_vals()
sigmas = [1.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xl_op.set_param_vals(new_vals)
# recalc state and gradients at image 50
xl_op.compose()
p_vals = xl_op.get_param_vals()
#print "Shifted parameter vals", p_vals
# compare analytical and finite difference derivatives at image 50
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * num_param)
param_names = xl_op.get_param_names()
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
# Now test gradients at equally spaced time points across the whole
# range
num_points = 50
smooth_at = []
phi1_data = []
phi2_data = []
phi3_data = []
step_size = (self.image_range[1] - self.image_range[0]) / num_points
for t in [self.image_range[0] + e * step_size \
for e in range(num_points + 1)]:
# collect data for plot
smooth_at.append(t)
phi1_data.append(xl_op._smoother.value_weight(t, xl_op._param[0])[0])
phi2_data.append(xl_op._smoother.value_weight(t, xl_op._param[1])[0])
phi3_data.append(xl_op._smoother.value_weight(t, xl_op._param[2])[0])
xl_op.set_time_point(t)
an_ds_dp = xl_op.get_ds_dp()
fd_ds_dp = get_fd_gradients(xl_op, [1.e-6 * pi/180] * num_param)
#print t
#print "Gradients:"
#for s, a, f in zip(param_names, an_ds_dp, fd_ds_dp):
# print s
# print a
# print f
# print "diff:", a-f
# print
#
for e, f in zip(an_ds_dp, fd_ds_dp):
assert(approx_equal((e - f), null_mat, eps = 1.e-6))
if self.do_plots:
try:
import matplotlib.pyplot as plt
plt.ion()
plt.clf()
plt.subplot(311)
plt.cla()
plt.scatter(smooth_at, phi1_data)
plt.title("Phi1")
plt.xlabel("image number")
plt.ylabel("Phi1 (mrad)")
plt.subplot(312)
plt.cla()
plt.scatter(smooth_at, phi2_data)
plt.title("Phi2")
plt.xlabel("image number")
plt.ylabel("Phi2 (mrad)")
plt.subplot(313)
plt.cla()
plt.scatter(smooth_at, phi3_data)
plt.title("Phi3")
plt.xlabel("image number")
plt.ylabel("Phi3 (mrad)")
plt.suptitle("Parameter smoothing with %d intervals" % nintervals)
plt.draw()
except ImportError as e:
print "pyplot not available", e
print "OK"
failures = 0
for i in range(attempts):
# make a random beam vector and parameterise it
s0 = bf.make_beam(matrix.col.random(3, 0.5, 1.5),
wavelength=random.uniform(0.8,1.5))
s0p = BeamParameterisation(s0)
# apply a random parameter shift
p_vals = s0p.get_param_vals()
p_vals = random_param_shift(p_vals, [1000*pi/9, 1000*pi/9, 0.01])
s0p.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
an_ds_dp = s0p.get_ds_dp()
fd_ds_dp = get_fd_gradients(s0p, [1.e-5 * pi/180, 1.e-5 * pi/180, 1.e-6])
for j in range(3):
try:
assert(approx_equal((fd_ds_dp[j] - an_ds_dp[j]),
matrix.col((0., 0., 0.)), eps = 1.e-6))
except Exception:
failures += 1
print "for try", i
print "failure for parameter number", j
print "with fd_ds_dp = "
print fd_ds_dp[j]
print "and an_ds_dp = "
print an_ds_dp[j]
print "so that difference fd_ds_dp - an_ds_dp ="
print fd_ds_dp[j] - an_ds_dp[j]
def test_beam_parameters():
from dxtbx.model import BeamFactory
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation,
)
from dials.algorithms.refinement.refinement_helpers import (
get_fd_gradients,
random_param_shift,
)
# make a random beam vector and parameterise it
bf = BeamFactory()
s0 = bf.make_beam(matrix.col.random(3, 0.5, 1.5), wavelength=1.2)
s0p = BeamParameterisation(s0)
# Let's do some basic tests. First, can we change parameter values and
# update the modelled vector s0?
s0_old = matrix.col(s0.get_s0())
s0p.set_param_vals([1000 * 0.1, 1000 * 0.1, 0.8])
assert matrix.col(s0.get_s0()).angle(s0_old) == pytest.approx(0.1413033, abs=1e-6)
assert matrix.col(s0.get_s0()).length() == pytest.approx(0.8, abs=1e-6)
# random initial orientations and wavelengths with a random parameter shifts
attempts = 1000
for i in range(attempts):
# make a random beam vector and parameterise it
sample_to_source = matrix.col.random(3, 0.5, 1.5).normalize()
beam = bf.make_beam(sample_to_source, wavelength=random.uniform(0.8, 1.5))
# Ensure consistent polarization (https://github.com/cctbx/dxtbx/issues/454)
beam.set_polarization_normal(sample_to_source.ortho().normalize())
s0p = BeamParameterisation(beam)
# apply a random parameter shift
p_vals = s0p.get_param_vals()
p_vals = random_param_shift(p_vals, [1000 * pi / 9, 1000 * pi / 9, 0.01])
s0p.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
an_ds_dp = s0p.get_ds_dp()
fd_ds_dp = get_fd_gradients(s0p, [1.0e-5 * pi / 180, 1.0e-5 * pi / 180, 1.0e-6])
for j in range(3):
try:
assert list(fd_ds_dp[j] - an_ds_dp[j]) == pytest.approx(
(0, 0, 0), abs=1e-6
)
except Exception:
print("for try", i)
print("failure for parameter number", j)
print("with fd_ds_dp = ")
print(fd_ds_dp[j])
print("and an_ds_dp = ")
print(an_ds_dp[j])
print("so that difference fd_ds_dp - an_ds_dp =")
print(fd_ds_dp[j] - an_ds_dp[j])
raise
# Ensure the polarization normal vector remains orthogonal to the beam
# (https://github.com/dials/dials/issues/1939)
assert (
abs(
matrix.col(beam.get_unit_s0()).dot(
matrix.col(beam.get_polarization_normal())
)
)
< 1e-10
)
# create random initial position
det = Detector(random_panel())
dp = DetectorParameterisationSinglePanel(det)
# apply a random parameter shift
p_vals = dp.get_param_vals()
p_vals = random_param_shift(p_vals, [10, 10, 10, 1000.*pi/18,
1000.*pi/18, 1000.*pi/18])
dp.set_param_vals(p_vals)
# obtain current sensor state
#state = dp.get_state()
# compare analytical and finite difference derivatives.
an_ds_dp = dp.get_ds_dp(multi_state_elt=0)
fd_ds_dp = get_fd_gradients(dp,
[1.e-6] * 3 + [1.e-4 * pi/180] * 3)
for j in range(6):
try:
assert(approx_equal((fd_ds_dp[j] - an_ds_dp[j]),
matrix.sqr((0., 0., 0.,
0., 0., 0.,
0., 0., 0.)), eps = 1.e-6))
except AssertionError:
failures += 1
print "for try", i
print "failure for parameter number", j
print "with fd_ds_dp = "
print fd_ds_dp[j]
print "and an_ds_dp = "
print an_ds_dp[j]
def test():
# set the random seed to make the test reproducible
random.seed(1337)
# set up a simple detector frame with directions aligned with
# principal axes and sensor origin located on the z-axis at -110
d1 = matrix.col((1, 0, 0))
d2 = matrix.col((0, -1, 0))
# lim = (0,50)
npx_fast = 1475
npx_slow = 1679
pix_size_f = pix_size_s = 0.172
detector = DetectorFactory.make_detector(
"PAD",
d1,
d2,
matrix.col((0, 0, -110)),
(pix_size_f, pix_size_s),
(npx_fast, npx_slow),
(0, 2e20),
)
dp = DetectorParameterisationSinglePanel(detector)
beam = BeamFactory().make_beam(
sample_to_source=-1 * (matrix.col((0, 0, -110)) + 10 * d1 + 10 * d2),
wavelength=1.0,
)
# Test change of parameters
# =========================
# 1. shift detector plane so that the z-axis intercepts its centre
# at a distance of 100 along the initial normal direction. As the
# initial normal is along -z, we expect the frame to intercept the
# z-axis at -100.
p_vals = dp.get_param_vals()
p_vals[0:3] = [100.0, 0.0, 0.0]
dp.set_param_vals(p_vals)
detector = dp._model
assert len(detector) == 1
panel = detector[0]
v1 = matrix.col(panel.get_origin())
v2 = matrix.col((0.0, 0.0, 1.0))
assert approx_equal(v1.dot(v2), -100.0)
# 2. rotate frame around its initial normal by +90 degrees. Only d1
# and d2 should change. As we rotate clockwise around the initial
# normal (-z direction) then d1 should rotate onto the original
# direction d2, and d2 should rotate to negative of the original
# direction d1
p_vals[3] = 1000.0 * pi / 2 # set tau1 value
dp.set_param_vals(p_vals)
detector = dp._model
assert len(detector) == 1
panel = detector[0]
assert approx_equal(
matrix.col(panel.get_fast_axis()).dot(dp._initial_state["d1"]), 0.0)
assert approx_equal(
matrix.col(panel.get_slow_axis()).dot(dp._initial_state["d2"]), 0.0)
assert approx_equal(
matrix.col(panel.get_normal()).dot(dp._initial_state["dn"]), 1.0)
# 3. no rotation around initial normal, +10 degrees around initial
# d1 direction and +10 degrees around initial d2. Check d1 and d2
# match paper calculation
p_vals[3] = 0.0 # tau1
p_vals[4] = 1000.0 * pi / 18 # tau2
p_vals[5] = 1000.0 * pi / 18 # tau3
dp.set_param_vals(p_vals)
# paper calculation values
v1 = matrix.col((cos(pi / 18), 0, sin(pi / 18)))
v2 = matrix.col((
sin(pi / 18)**2,
-cos(pi / 18),
sqrt((2 * sin(pi / 36) * sin(pi / 18))**2 - sin(pi / 18)**4) -
sin(pi / 18),
))
detector = dp._model
assert len(detector) == 1
panel = detector[0]
assert approx_equal(matrix.col(panel.get_fast_axis()).dot(v1), 1.0)
assert approx_equal(matrix.col(panel.get_slow_axis()).dot(v2), 1.0)
# 4. Test fixing and unfixing of parameters
p_vals = [
100.0, 0.0, 0.0, 1000.0 * pi / 18, 1000.0 * pi / 18, 1000.0 * pi / 18
]
dp.set_param_vals(p_vals)
f = dp.get_fixed()
f[0:3] = [True] * 3
dp.set_fixed(f)
p_vals2 = [0.0, 0.0, 0.0]
dp.set_param_vals(p_vals2)
assert dp.get_param_vals(only_free=False) == [
100.0, 0.0, 0.0, 0.0, 0.0, 0.0
]
an_ds_dp = dp.get_ds_dp()
assert len(an_ds_dp) == 3
f[0:3] = [False] * 3
dp.set_fixed(f)
p_vals = dp.get_param_vals()
p_vals2 = [a + b for a, b in zip(p_vals, [-10.0, 1.0, 1.0, 0.0, 0.0, 0.0])]
dp.set_param_vals(p_vals2)
assert dp.get_param_vals() == [90.0, 1.0, 1.0, 0.0, 0.0, 0.0]
# 5. Tests of the calculation of derivatives
# Now using parameterisation in mrad
# random initial orientations with a random parameter shift at each
attempts = 100
for i in range(attempts):
# create random initial position
det = Detector(random_panel())
dp = DetectorParameterisationSinglePanel(det)
# apply a random parameter shift
p_vals = dp.get_param_vals()
p_vals = random_param_shift(
p_vals,
[10, 10, 10, 1000.0 * pi / 18, 1000.0 * pi / 18, 1000.0 * pi / 18])
dp.set_param_vals(p_vals)
# compare analytical and finite difference derivatives.
an_ds_dp = dp.get_ds_dp(multi_state_elt=0)
fd_ds_dp = get_fd_gradients(dp, [1.0e-6] * 3 + [1.0e-4 * pi / 180] * 3)
for j in range(6):
assert approx_equal(
(fd_ds_dp[j] - an_ds_dp[j]),
matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)),
eps=1.0e-6,
), textwrap.dedent("""\
Failure comparing analytical with finite difference derivatives.
Failure in try {i}
failure for parameter number {j}
of the orientation parameterisation
with fd_ds_dp =
{fd}
and an_ds_dp =
{an}
so that difference fd_ds_dp - an_ds_dp =
{diff}
""").format(i=i,
j=j,
fd=fd_ds_dp[j],
an=an_ds_dp[j],
diff=fd_ds_dp[j] - an_ds_dp[j])
# 5. Test a multi-panel detector with non-coplanar panels.
# place a beam at the centre of the single panel detector (need a
# beam to initialise the multi-panel detector parameterisation)
lim = det[0].get_image_size_mm()
shift1 = lim[0] / 2.0
shift2 = lim[1] / 2.0
beam_centre = (matrix.col(det[0].get_origin()) +
shift1 * matrix.col(det[0].get_fast_axis()) +
shift2 * matrix.col(det[0].get_slow_axis()))
beam = BeamFactory().make_beam(sample_to_source=-1.0 * beam_centre,
wavelength=1.0)
multi_panel_detector = make_multi_panel(det)
# parameterise this detector
dp = DetectorParameterisationMultiPanel(multi_panel_detector, beam)
# ensure the beam still intersects the central panel
intersection = multi_panel_detector.get_ray_intersection(beam.get_s0())
assert intersection[0] == 4
# record the offsets and dir1s, dir2s
offsets_before_shift = dp._offsets
dir1s_before_shift = dp._dir1s
dir2s_before_shift = dp._dir2s
# apply a random parameter shift (~10 mm distances, ~50 mrad angles)
p_vals = dp.get_param_vals()
p_vals = random_param_shift(p_vals, [10, 10, 10, 50, 50, 50])
# reparameterise the detector
dp = DetectorParameterisationMultiPanel(multi_panel_detector, beam)
# record the offsets and dir1s, dir2s
offsets_after_shift = dp._offsets
dir1s_after_shift = dp._dir1s
dir2s_after_shift = dp._dir2s
# ensure the offsets, dir1s and dir2s are the same. This means that
# each panel in the detector moved with the others as a rigid body
for a, b in zip(offsets_before_shift, offsets_after_shift):
assert approx_equal(a, b, eps=1.0e-10)
for a, b in zip(dir1s_before_shift, dir1s_after_shift):
assert approx_equal(a, b, eps=1.0e-10)
for a, b in zip(dir2s_before_shift, dir2s_after_shift):
assert approx_equal(a, b, eps=1.0e-10)
attempts = 5
for i in range(attempts):
multi_panel_detector = make_multi_panel(det)
# parameterise this detector
dp = DetectorParameterisationMultiPanel(multi_panel_detector, beam)
p_vals = dp.get_param_vals()
# apply a random parameter shift
p_vals = random_param_shift(
p_vals,
[10, 10, 10, 1000.0 * pi / 18, 1000.0 * pi / 18, 1000.0 * pi / 18])
dp.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
# get_fd_gradients will implicitly only get gradients for the
# 1st panel in the detector, so explicitly get the same for the
# analytical gradients
for j in range(9):
an_ds_dp = dp.get_ds_dp(multi_state_elt=j)
fd_ds_dp = get_fd_gradients(dp, [1.0e-7] * dp.num_free(),
multi_state_elt=j)
for k in range(6):
assert approx_equal(
(fd_ds_dp[k] - matrix.sqr(an_ds_dp[k])),
matrix.sqr((0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)),
eps=1.0e-5,
out=None,
), textwrap.dedent("""\
Failure comparing analytical with finite difference derivatives.
Failure in try {i}
for panel number {j]
failure for parameter number {k}
of the orientation parameterisation
with fd_ds_dp =
{fd}
and an_ds_dp =
{an}
so that difference fd_ds_dp - an_ds_dp =
{diff}
""").format(
i=i,
j=j,
k=k,
fd=fd_ds_dp[k],
an=an_ds_dp[k],
diff=fd_ds_dp[k] - matrix.sqr(an_ds_dp[k]),
)
attempts = 1000
failures = 0
for i in range(attempts):
# make a random goniometer and parameterise it
goniometer = random_gonio()
gonp = GoniometerParameterisation(goniometer)
# apply a random parameter shift
p_vals = gonp.get_param_vals()
p_vals = random_param_shift(p_vals, [1000 * pi / 9, 1000 * pi / 9])
gonp.set_param_vals(p_vals)
# compare analytical and finite difference derivatives
an_ds_dp = gonp.get_ds_dp()
fd_ds_dp = get_fd_gradients(gonp, [1.e-5 * pi / 180, 1.e-5 * pi / 180])
null_mat = matrix.sqr((0., 0., 0., 0., 0., 0., 0., 0., 0.))
for j in range(2):
try:
assert (approx_equal((fd_ds_dp[j] - an_ds_dp[j]),
null_mat,
eps=1.e-6))
except Exception:
failures += 1
print "for try", i
print "failure for parameter number", j
print "with fd_ds_dp = "
print fd_ds_dp[j]
print "and an_ds_dp = "
print an_ds_dp[j]
