def __init__(self, plots = False):
# Do we make scatterplots?
self.do_plots = plots
# Let's say we have a scan of 100 images
self.image_range = (1, 100)
# Make a random P1 crystal
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)))
self.xl = crystal_model(a, b, c, space_group_symbol = "P 1")
# Make a beam with wavelength in the range 0.8--1.2 and s0 direction close
# to 0,0,1
s0 = random.uniform(0.8, 1.2) * \
self.random_direction_close_to(matrix.col((0, 0, 1)))
self.beam = Beam(s0)
# Make a standard goniometer model along X
self.goniometer = Goniometer((1,0,0))
# Make a simple single panel detector
d1 = matrix.col((1, 0, 0))
d2 = matrix.col((0, -1, 0))
npx_fast = 1475
npx_slow = 1679
pix_size_f = pix_size_s = 0.172
from dxtbx.model.experiment import detector_factory
self.detector = detector_factory.make_detector("PAD", d1, d2,
matrix.col((0, 0, -110)), (pix_size_f, pix_size_s),
(npx_fast, npx_slow), (0, 2e20))
def test_goniometer():
'''A test class for the goniometer class.'''
axis = (1, 0, 0)
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
xg = Goniometer(axis, fixed)
assert (len(xg.get_rotation_axis()) == 3)
assert (len(xg.get_fixed_rotation()) == 9)
assert (compare_tuples(xg.get_rotation_axis(), axis))
assert (compare_tuples(xg.get_fixed_rotation(), fixed))
single = goniometer_factory.single_axis()
assert (len(single.get_rotation_axis()) == 3)
assert (len(single.get_fixed_rotation()) == 9)
assert (compare_tuples(single.get_rotation_axis(), axis))
assert (compare_tuples(single.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 0.0, 0.0, '-y', 'omega')
assert (len(kappa.get_rotation_axis()) == 3)
assert (len(kappa.get_fixed_rotation()) == 9)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (compare_tuples(kappa.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 0.0, 0.0, '-y', 'omega')
assert (len(kappa.get_rotation_axis()) == 3)
assert (len(kappa.get_fixed_rotation()) == 9)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (compare_tuples(kappa.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 0.0, 0.0, '-y', 'phi')
assert (len(kappa.get_rotation_axis()) == 3)
assert (len(kappa.get_fixed_rotation()) == 9)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (compare_tuples(kappa.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 30.0, 0.0, '-y', 'omega')
assert (len(kappa.get_rotation_axis()) == 3)
assert (len(kappa.get_fixed_rotation()) == 9)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (not compare_tuples(kappa.get_fixed_rotation(), fixed))
import libtbx.load_env
import os
dxtbx_dir = libtbx.env.dist_path('dxtbx')
image = os.path.join(dxtbx_dir, 'tests', 'phi_scan_001.cbf')
cbf = goniometer_factory.imgCIF(image)
kappa = goniometer_factory.kappa(50.0, -10.0, 30.0, 0.0, '-y', 'phi')
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
image = os.path.join(dxtbx_dir, 'tests', 'omega_scan.cbf')
cbf = goniometer_factory.imgCIF(image)
kappa = goniometer_factory.kappa(50.0, -10.0, 30.0, 20.0, '-y', 'omega')
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
print 'OK'
def test_goniometer():
'''A test class for the goniometer class.'''
axis = (1, 0, 0)
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
xg = Goniometer(axis, fixed)
assert(len(xg.get_rotation_axis()) == 3)
assert(len(xg.get_fixed_rotation()) == 9)
assert(compare_tuples(xg.get_rotation_axis(), axis))
assert(compare_tuples(xg.get_fixed_rotation(), fixed))
single = goniometer_factory.single_axis()
assert(len(single.get_rotation_axis()) == 3)
assert(len(single.get_fixed_rotation()) == 9)
assert(compare_tuples(single.get_rotation_axis(), axis))
assert(compare_tuples(single.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 0.0, 0.0, '-y', 'omega')
assert(len(kappa.get_rotation_axis()) == 3)
assert(len(kappa.get_fixed_rotation()) == 9)
assert(compare_tuples(kappa.get_rotation_axis(), axis))
assert(compare_tuples(kappa.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 0.0, 0.0, '-y', 'omega')
assert(len(kappa.get_rotation_axis()) == 3)
assert(len(kappa.get_fixed_rotation()) == 9)
assert(compare_tuples(kappa.get_rotation_axis(), axis))
assert(compare_tuples(kappa.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 0.0, 0.0, '-y', 'phi')
assert(len(kappa.get_rotation_axis()) == 3)
assert(len(kappa.get_fixed_rotation()) == 9)
assert(compare_tuples(kappa.get_rotation_axis(), axis))
assert(compare_tuples(kappa.get_fixed_rotation(), fixed))
kappa = goniometer_factory.kappa(50.0, 0.0, 30.0, 0.0, '-y', 'omega')
assert(len(kappa.get_rotation_axis()) == 3)
assert(len(kappa.get_fixed_rotation()) == 9)
assert(compare_tuples(kappa.get_rotation_axis(), axis))
assert(not compare_tuples(kappa.get_fixed_rotation(), fixed))
import libtbx.load_env
import os
dxtbx_dir = libtbx.env.dist_path('dxtbx')
image = os.path.join(dxtbx_dir, 'tests', 'phi_scan_001.cbf')
cbf = goniometer_factory.imgCIF(image)
kappa = goniometer_factory.kappa(50.0, -10.0, 30.0, 0.0, '-y', 'phi')
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
image = os.path.join(dxtbx_dir, 'tests', 'omega_scan.cbf')
cbf = goniometer_factory.imgCIF(image)
kappa = goniometer_factory.kappa(50.0, -10.0, 30.0, 20.0, '-y', 'omega')
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
print 'OK'
def test_comparison():
# Setting rotation for small random offset
offset_ax = matrix.col.random(3, -1.0, 1.0).normalize()
S = offset_ax.axis_and_angle_as_r3_rotation_matrix(angle=0.01, deg=True)
# Equal goniometers with scan-points set
g1 = Goniometer((1, 0, 0))
g1.set_setting_rotation(S)
g1.set_setting_rotation_at_scan_points([S] * 5)
g2 = Goniometer((1, 0, 0))
g2.set_setting_rotation(S)
g2.set_setting_rotation_at_scan_points([S] * 5)
assert g1 == g2
assert g1.is_similar_to(g2)
# Different setting matrix
g3 = Goniometer((1, 0, 0))
invS = S.inverse()
g3.set_setting_rotation(invS)
g3.set_setting_rotation_at_scan_points([invS] * 5)
assert g1 != g3
assert not g1.is_similar_to(g3)
def test_scan_varying():
axis = (1, 0, 0)
g = Goniometer(axis)
assert g.get_num_scan_points() == 0
assert g.get_setting_rotation_at_scan_points().size() == 0
with pytest.raises(RuntimeError):
g.get_setting_rotation_at_scan_point(0)
# set varying beam
num_scan_points = 11
S_static = matrix.sqr(g.get_setting_rotation())
S_as_scan_points = [S_static]
axis = matrix.col.random(3, -1.0, 1.0).normalize()
R = axis.axis_and_angle_as_r3_rotation_matrix(angle=0.01, deg=True)
for i in range(num_scan_points - 1):
S_as_scan_points.append(R * S_as_scan_points[-1])
g.set_setting_rotation_at_scan_points(S_as_scan_points)
assert g.get_num_scan_points() == 11
assert g.get_setting_rotation_at_scan_points().size() == 11
for t in range(num_scan_points):
S_t = matrix.sqr(g.get_setting_rotation_at_scan_point(t))
assert S_t == S_as_scan_points[t]
# also test setting as tuple
g.set_setting_rotation_at_scan_points(tuple(S_as_scan_points))
assert g.get_num_scan_points() == 11
assert g.get_setting_rotation_at_scan_points().size() == 11
# test resetting
g.reset_scan_points()
assert g.get_num_scan_points() == 0
assert g.get_setting_rotation_at_scan_points().size() == 0
def test_goniometer():
"""A test class for the goniometer class."""
axis = (1, 0, 0)
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
xg = Goniometer(axis, fixed)
assert len(xg.get_rotation_axis()) == 3
assert len(xg.get_fixed_rotation()) == 9
_compare_tuples(xg.get_rotation_axis(), axis)
_compare_tuples(xg.get_fixed_rotation(), fixed)
single = GoniometerFactory.single_axis()
assert len(single.get_rotation_axis()) == 3
assert len(single.get_fixed_rotation()) == 9
_compare_tuples(single.get_rotation_axis(), axis)
_compare_tuples(single.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 0.0, 0.0, "-y", "omega")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
_compare_tuples(kappa.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 0.0, 0.0, "-y", "omega")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
_compare_tuples(kappa.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 0.0, 0.0, "-y", "phi")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
_compare_tuples(kappa.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 30.0, 0.0, "-y", "omega")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
with pytest.raises(AssertionError):
_compare_tuples(kappa.get_fixed_rotation(), fixed)
import libtbx.load_env
dxtbx_dir = libtbx.env.dist_path("dxtbx")
image = os.path.join(dxtbx_dir, "tests", "phi_scan_001.cbf")
assert GoniometerFactory.imgCIF(image)
kappa = GoniometerFactory.kappa(50.0, -10.0, 30.0, 0.0, "-y", "phi")
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
image = os.path.join(dxtbx_dir, "tests", "omega_scan.cbf")
assert GoniometerFactory.imgCIF(image)
kappa = GoniometerFactory.kappa(50.0, -10.0, 30.0, 20.0, "-y", "omega")
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
def test_goniometer():
"""A test class for the goniometer class."""
axis = (1, 0, 0)
fixed = (1, 0, 0, 0, 1, 0, 0, 0, 1)
xg = Goniometer(axis, fixed)
assert len(xg.get_rotation_axis()) == 3
assert len(xg.get_fixed_rotation()) == 9
_compare_tuples(xg.get_rotation_axis(), axis)
_compare_tuples(xg.get_fixed_rotation(), fixed)
single = GoniometerFactory.single_axis()
assert len(single.get_rotation_axis()) == 3
assert len(single.get_fixed_rotation()) == 9
_compare_tuples(single.get_rotation_axis(), axis)
_compare_tuples(single.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 0.0, 0.0, "-y", "omega")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
_compare_tuples(kappa.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 0.0, 0.0, "-y", "omega")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
_compare_tuples(kappa.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 0.0, 0.0, "-y", "phi")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
_compare_tuples(kappa.get_fixed_rotation(), fixed)
kappa = GoniometerFactory.kappa(50.0, 0.0, 30.0, 0.0, "-y", "omega")
assert len(kappa.get_rotation_axis()) == 3
assert len(kappa.get_fixed_rotation()) == 9
_compare_tuples(kappa.get_rotation_axis(), axis)
with pytest.raises(AssertionError):
_compare_tuples(kappa.get_fixed_rotation(), fixed)
image = Path(__file__).parent / "phi_scan_001.cbf"
assert GoniometerFactory.imgCIF(str(image))
kappa = GoniometerFactory.kappa(50.0, -10.0, 30.0, 0.0, "-y", "phi")
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2
image = Path(__file__).parent / "omega_scan.cbf"
assert GoniometerFactory.imgCIF(str(image))
kappa = GoniometerFactory.kappa(50.0, -10.0, 30.0, 20.0, "-y", "omega")
s = easy_pickle.dumps(kappa)
kappa2 = easy_pickle.loads(s)
assert kappa == kappa2