def _goniometer(self):
'''
Create the goniometer model
'''
from dxtbx.model.goniometer import GoniometerFactory
return GoniometerFactory.single_axis()
def _goniometer(self):
"""
Create the goniometer model
"""
return GoniometerFactory.single_axis()
from dxtbx.datablock import DataBlockFactory, DataBlockDumper
from dxtbx.imageset import ImageSetFactory, ImageSweep, ImageSetData
from dxtbx.model.goniometer import GoniometerFactory
from dxtbx.model.scan import ScanFactory
import glob, os, sys
"""
Modification of AB's prepare_sweep.py.
Usage: libtbx.python prepare_sweep.py img_dir start_img, end_img savefile
"""
root = sys.argv[1]
start, end = int(sys.argv[2]), int(sys.argv[3])
g = GoniometerFactory.single_axis()
s = ScanFactory.make_scan((start, end), 0, (0, 1), [0] * (end - start + 1))
sw = ImageSetFactory.from_template(template=os.path.join(
root, "fft_frame_I_mf_####.cbf"),
scan=s,
goniometer=g,
image_range=(start, end))
dump = DataBlockDumper(DataBlockFactory.from_imageset(sw))
dump.as_file(sys.argv[4])
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)
assert (compare_tuples(xg.get_rotation_axis(), axis))
assert (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)
assert (compare_tuples(single.get_rotation_axis(), axis))
assert (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)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (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)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (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)
assert (compare_tuples(kappa.get_rotation_axis(), axis))
assert (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)
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 = 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')
cbf = 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
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
_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