def run(args):
from dials.util.options import OptionParser
from dials.util.options import flatten_datablocks
from dials.util.options import flatten_experiments
import libtbx.load_env
usage = "%s [options] datablock.json" %(
libtbx.env.dispatcher_name)
import os
if 'DIALS_EXPORT_DO_NOT_CHECK_FORMAT' in os.environ:
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_datablocks=True,
read_experiments=True,
check_format=False,
epilog=help_message)
else:
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_datablocks=True,
read_experiments=True,
check_format=True,
epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
datablocks = flatten_datablocks(params.input.datablock)
experiments = flatten_experiments(params.input.experiments)
if (len(datablocks) == 0 and len(experiments) == 0):
parser.print_help()
exit(0)
if len(datablocks) == 0 and len(experiments) > 0:
imagesets = experiments.imagesets()
crystal = experiments[0].crystal
else:
imagesets = []
crystal = None
for datablock in datablocks:
imagesets.extend(datablock.extract_imagesets())
assert len(imagesets) == 1, len(imagesets)
imageset = imagesets[0]
gonio = imageset.get_goniometer()
if not params.detector_distance:
detector = imageset.get_detector()
if len(detector) > 1:
params.detector_distance = detector.hierarchy().get_directed_distance()
else:
params.detector_distance = detector[0].get_directed_distance()
if gonio is not None and not isinstance(gonio, MultiAxisGoniometer):
from dxtbx.model.goniometer import GoniometerFactory
gonio = GoniometerFactory.multi_axis(
axes=flex.vec3_double((gonio.get_rotation_axis(),)),
angles=flex.double((0,)),
names=flex.std_string(('GON_OMEGA',)),
scan_axis=0)
imageset.set_goniometer(gonio)
if isinstance(gonio, MultiAxisGoniometer):
if params.angle:
assert len(params.angle) == len(gonio.get_angles())
else:
for angle in gonio.get_angles():
params.angle.append(angle)
import wxtbx.app
a = wxtbx.app.CCTBXApp(0)
a.settings = params
f = ExperimentViewer(
None, -1, "Experiment viewer", size=(1024,768))
f.load_imageset(imageset, crystal=crystal)
f.Show()
a.SetTopWindow(f)
a.MainLoop()
def run(args):
import os
from dials.util.options import OptionParser, flatten_experiments
usage = "dials.geometry_viewer [options] models.expt"
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_experiments=True,
check_format=False,
epilog=help_message,
)
params, options = parser.parse_args(quick_parse=True, show_diff_phil=True)
if "DIALS_EXPORT_DO_NOT_CHECK_FORMAT" in os.environ:
print(
"\nWarning: use of DIALS_EXPORT_DO_NOT_CHECK_FORMAT environment variable"
"\nis no longer recommended, the recommended command is require_images=False"
)
if not params.require_images or "DIALS_EXPORT_DO_NOT_CHECK_FORMAT" in os.environ:
check_format = False
else:
check_format = True
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_experiments=True,
check_format=check_format,
epilog=help_message,
)
try:
params, options = parser.parse_args(show_diff_phil=False)
except Exception as e:
print(e)
print(
"dials.geometry_viewer help: Error in parsing data may be due to missing \n"
"files. If so, this may be overcome by require_images=False\n")
sys.exit()
experiments = flatten_experiments(params.input.experiments)
if len(experiments) == 0:
parser.print_help()
exit(0)
imagesets = experiments.imagesets()
crystal = experiments[0].crystal
assert len(imagesets) == 1, len(imagesets)
imageset = imagesets[0]
gonio = imageset.get_goniometer()
if not params.detector_distance:
detector = imageset.get_detector()
if len(detector) > 1:
params.detector_distance = detector.hierarchy(
).get_directed_distance()
else:
params.detector_distance = detector[0].get_directed_distance()
if gonio is not None and not isinstance(gonio, MultiAxisGoniometer):
from dxtbx.model.goniometer import GoniometerFactory
gonio = GoniometerFactory.multi_axis(
axes=flex.vec3_double((gonio.get_rotation_axis(), )),
angles=flex.double((0, )),
names=flex.std_string(("GON_OMEGA", )),
scan_axis=0,
)
imageset.set_goniometer(gonio)
if isinstance(gonio, MultiAxisGoniometer):
if params.angle:
assert len(params.angle) == len(gonio.get_angles())
else:
for angle in gonio.get_angles():
params.angle.append(angle)
import wxtbx.app
a = wxtbx.app.CCTBXApp(0)
a.settings = params
f = ExperimentViewer(None, -1, "Experiment viewer", size=(1024, 768))
f.load_imageset(imageset, crystal=crystal)
f.Show()
a.SetTopWindow(f)
a.MainLoop()
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())
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:
GoniometerFactory.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)
((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, e:
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)
print 'OK'
def test_goniometer_from_phil():
from dxtbx.model.goniometer import GoniometerFactory
from dxtbx.model.goniometer import goniometer_phil_scope
from libtbx.phil import parse
params = goniometer_phil_scope.fetch(
parse('''