def test_multi_axis_goniometer():
from libtbx.test_utils import approx_equal
from scitbx.array_family import flex
alpha = 50
omega = -10
kappa = 30
phi = 20
direction = '-y'
from dxtbx.model.goniometer import KappaGoniometer
kappa_omega_scan = KappaGoniometer(
alpha, omega, kappa, phi, direction, 'omega')
axes = (kappa_omega_scan.get_phi_axis(), kappa_omega_scan.get_kappa_axis(),
kappa_omega_scan.get_omega_axis())
angles = (kappa_omega_scan.get_phi_angle(), kappa_omega_scan.get_kappa_angle(),
kappa_omega_scan.get_omega_angle())
# First test a kappa goniometer with omega as the scan axis
axes = flex.vec3_double(axes)
angles = flex.double(angles)
names = flex.std_string(('phi', 'kappa', 'omega'))
scan_axis = 2
multi_axis_omega_scan = goniometer_factory.multi_axis(
axes, angles, names, scan_axis)
assert approx_equal(multi_axis_omega_scan.get_fixed_rotation(), kappa_omega_scan.get_fixed_rotation())
assert approx_equal(multi_axis_omega_scan.get_rotation_axis(), kappa_omega_scan.get_rotation_axis())
recycle_omega = MultiAxisGoniometer.from_dict(multi_axis_omega_scan.to_dict())
assert approx_equal(recycle_omega.get_axes(), multi_axis_omega_scan.get_axes())
assert approx_equal(recycle_omega.get_angles(), multi_axis_omega_scan.get_angles())
assert recycle_omega.get_scan_axis() == multi_axis_omega_scan.get_scan_axis()
# Now test a kappa goniometer with phi as the scan axis
kappa_phi_scan = KappaGoniometer(
alpha, omega, kappa, phi, direction, 'phi')
scan_axis = 0
multi_axis_phi_scan = goniometer_factory.multi_axis(
axes, angles, names, scan_axis)
assert approx_equal(multi_axis_phi_scan.get_fixed_rotation(), kappa_phi_scan.get_fixed_rotation())
from scitbx import matrix
assert approx_equal(matrix.sqr(multi_axis_phi_scan.get_setting_rotation()) * multi_axis_phi_scan.get_rotation_axis(), kappa_phi_scan.get_rotation_axis())
recycle_phi = MultiAxisGoniometer.from_dict(multi_axis_phi_scan.to_dict())
assert approx_equal(recycle_phi.get_axes(), multi_axis_phi_scan.get_axes())
assert approx_equal(recycle_phi.get_angles(), multi_axis_phi_scan.get_angles())
assert recycle_phi.get_scan_axis() == multi_axis_phi_scan.get_scan_axis()
s = easy_pickle.dumps(multi_axis_phi_scan)
recycle = easy_pickle.loads(s)
assert recycle == multi_axis_phi_scan
assert approx_equal(recycle.get_axes(), multi_axis_phi_scan.get_axes())
assert approx_equal(recycle.get_angles(), multi_axis_phi_scan.get_angles())
assert recycle.get_scan_axis() == multi_axis_phi_scan.get_scan_axis()
recycle.set_angles((0,90,180))
assert approx_equal(recycle.get_angles(), (0, 90, 180))
new_axes = (0.9, 0.1, 0.0), (0.6427876096865394, -0.766044443118978, 0.0), (1.0, 0.0, 0.0)
new_axes = flex.vec3_double(
((0.99996, -0.00647, -0.00659), (0.91314, 0.27949, -0.29674),
(1.00000, -0.00013, -0.00064)))
recycle.set_axes(new_axes)
assert approx_equal(recycle.get_axes(), new_axes)
# Check exception is raised if scan axis is out range
try: goniometer_factory.multi_axis(axes, angles, names, 3)
except RuntimeError, e: pass
else: raise Exception_expected
# Single axis is just a special case of a multi axis goniometer
single_axis = goniometer_factory.multi_axis(
flex.vec3_double(((1,0,0),)), flex.double((0,)), flex.std_string(('PHI',)), 0)
assert single_axis.get_fixed_rotation() == (1,0,0,0,1,0,0,0,1)
assert single_axis.get_setting_rotation() == (1,0,0,0,1,0,0,0,1)
assert single_axis.get_rotation_axis() == (1,0,0)
print 'OK'
def test_multi_axis_goniometer():
from libtbx.test_utils import approx_equal
from scitbx.array_family import flex
alpha = 50
omega = -10
kappa = 30
phi = 20
direction = '-y'
from dxtbx.model.goniometer import KappaGoniometer
kappa_omega_scan = KappaGoniometer(alpha, omega, kappa, phi, direction,
'omega')
axes = (kappa_omega_scan.get_phi_axis(), kappa_omega_scan.get_kappa_axis(),
kappa_omega_scan.get_omega_axis())
angles = (kappa_omega_scan.get_phi_angle(),
kappa_omega_scan.get_kappa_angle(),
kappa_omega_scan.get_omega_angle())
# First test a kappa goniometer with omega as the scan axis
axes = flex.vec3_double(axes)
angles = flex.double(angles)
names = flex.std_string(('phi', 'kappa', 'omega'))
scan_axis = 2
multi_axis_omega_scan = goniometer_factory.multi_axis(
axes, angles, names, scan_axis)
assert approx_equal(multi_axis_omega_scan.get_fixed_rotation(),
kappa_omega_scan.get_fixed_rotation())
assert approx_equal(multi_axis_omega_scan.get_rotation_axis(),
kappa_omega_scan.get_rotation_axis())
recycle_omega = MultiAxisGoniometer.from_dict(
multi_axis_omega_scan.to_dict())
assert approx_equal(recycle_omega.get_axes(),
multi_axis_omega_scan.get_axes())
assert approx_equal(recycle_omega.get_angles(),
multi_axis_omega_scan.get_angles())
assert recycle_omega.get_scan_axis(
) == multi_axis_omega_scan.get_scan_axis()
# Now test a kappa goniometer with phi as the scan axis
kappa_phi_scan = KappaGoniometer(alpha, omega, kappa, phi, direction,
'phi')
scan_axis = 0
multi_axis_phi_scan = goniometer_factory.multi_axis(
axes, angles, names, scan_axis)
assert approx_equal(multi_axis_phi_scan.get_fixed_rotation(),
kappa_phi_scan.get_fixed_rotation())
from scitbx import matrix
assert approx_equal(
matrix.sqr(multi_axis_phi_scan.get_setting_rotation()) *
multi_axis_phi_scan.get_rotation_axis_datum(),
kappa_phi_scan.get_rotation_axis())
assert approx_equal(multi_axis_phi_scan.get_rotation_axis(),
kappa_phi_scan.get_rotation_axis())
recycle_phi = MultiAxisGoniometer.from_dict(multi_axis_phi_scan.to_dict())
assert approx_equal(recycle_phi.get_axes(), multi_axis_phi_scan.get_axes())
assert approx_equal(recycle_phi.get_angles(),
multi_axis_phi_scan.get_angles())
assert recycle_phi.get_scan_axis() == multi_axis_phi_scan.get_scan_axis()
s = easy_pickle.dumps(multi_axis_phi_scan)
recycle = easy_pickle.loads(s)
assert recycle == multi_axis_phi_scan
assert approx_equal(recycle.get_axes(), multi_axis_phi_scan.get_axes())
assert approx_equal(recycle.get_angles(), multi_axis_phi_scan.get_angles())
assert recycle.get_scan_axis() == multi_axis_phi_scan.get_scan_axis()
recycle.set_angles((0, 90, 180))
assert approx_equal(recycle.get_angles(), (0, 90, 180))
new_axes = (0.9, 0.1, 0.0), (0.6427876096865394, -0.766044443118978,
0.0), (1.0, 0.0, 0.0)
new_axes = flex.vec3_double(
((0.99996, -0.00647, -0.00659), (0.91314, 0.27949, -0.29674),
(1.00000, -0.00013, -0.00064)))
recycle.set_axes(new_axes)
assert approx_equal(recycle.get_axes(), new_axes)
# Check exception is raised if scan axis is out range
try:
goniometer_factory.multi_axis(axes, angles, names, 3)
except RuntimeError, e:
pass
def test_multi_axis_goniometer():
from libtbx.test_utils import approx_equal
from scitbx.array_family import flex
alpha = 50
omega = -10
kappa = 30
phi = 20
direction = "-y"
from dxtbx.model.goniometer import KappaGoniometer
kappa_omega_scan = KappaGoniometer(alpha, omega, kappa, phi, direction,
"omega")
axes = (
kappa_omega_scan.get_phi_axis(),
kappa_omega_scan.get_kappa_axis(),
kappa_omega_scan.get_omega_axis(),
)
angles = (
kappa_omega_scan.get_phi_angle(),
kappa_omega_scan.get_kappa_angle(),
kappa_omega_scan.get_omega_angle(),
)
# First test a kappa goniometer with omega as the scan axis
axes = flex.vec3_double(axes)
angles = flex.double(angles)
names = flex.std_string(("phi", "kappa", "omega"))
scan_axis = 2
multi_axis_omega_scan = GoniometerFactory.multi_axis(
axes, angles, names, scan_axis)
assert approx_equal(
multi_axis_omega_scan.get_fixed_rotation(),
kappa_omega_scan.get_fixed_rotation(),
)
assert approx_equal(multi_axis_omega_scan.get_rotation_axis(),
kappa_omega_scan.get_rotation_axis())
recycle_omega = MultiAxisGoniometer.from_dict(
multi_axis_omega_scan.to_dict())
assert approx_equal(recycle_omega.get_axes(),
multi_axis_omega_scan.get_axes())
assert approx_equal(recycle_omega.get_angles(),
multi_axis_omega_scan.get_angles())
assert recycle_omega.get_scan_axis(
) == multi_axis_omega_scan.get_scan_axis()
# Now test a kappa goniometer with phi as the scan axis
kappa_phi_scan = KappaGoniometer(alpha, omega, kappa, phi, direction,
"phi")
scan_axis = 0
multi_axis_phi_scan = GoniometerFactory.multi_axis(axes, angles, names,
scan_axis)
assert approx_equal(multi_axis_phi_scan.get_fixed_rotation(),
kappa_phi_scan.get_fixed_rotation())
assert approx_equal(
matrix.sqr(multi_axis_phi_scan.get_setting_rotation()) *
multi_axis_phi_scan.get_rotation_axis_datum(),
kappa_phi_scan.get_rotation_axis(),
)
assert approx_equal(multi_axis_phi_scan.get_rotation_axis(),
kappa_phi_scan.get_rotation_axis())
recycle_phi = MultiAxisGoniometer.from_dict(multi_axis_phi_scan.to_dict())
assert approx_equal(recycle_phi.get_axes(), multi_axis_phi_scan.get_axes())
assert approx_equal(recycle_phi.get_angles(),
multi_axis_phi_scan.get_angles())
assert recycle_phi.get_scan_axis() == multi_axis_phi_scan.get_scan_axis()
s = easy_pickle.dumps(multi_axis_phi_scan)
recycle = easy_pickle.loads(s)
assert recycle == multi_axis_phi_scan
assert approx_equal(recycle.get_axes(), multi_axis_phi_scan.get_axes())
assert approx_equal(recycle.get_angles(), multi_axis_phi_scan.get_angles())
assert recycle.get_scan_axis() == multi_axis_phi_scan.get_scan_axis()
recycle.set_angles((0, 90, 180))
assert approx_equal(recycle.get_angles(), (0, 90, 180))
new_axes = flex.vec3_double((
(0.99996, -0.00647, -0.00659),
(0.91314, 0.27949, -0.29674),
(1.00000, -0.00013, -0.00064),
))
recycle.set_axes(new_axes)
assert approx_equal(recycle.get_axes(), new_axes)
# Check exception is raised if scan axis is out range
try:
GoniometerFactory.multi_axis(axes, angles, names, 3)
except RuntimeError:
pass
else:
raise Exception_expected
# Single axis is just a special case of a multi axis goniometer
single_axis = GoniometerFactory.multi_axis(flex.vec3_double(((1, 0, 0), )),
flex.double((0, )),
flex.std_string(("PHI", )), 0)
assert single_axis.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert single_axis.get_setting_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert single_axis.get_rotation_axis() == (1, 0, 0)