def tst_set_mosflm_beam_centre(detector):
from scitbx import matrix
from dxtbx.model import Beam
wavelength = 1
panel = detector[0]
detector_normal = matrix.col(panel.get_normal())
origin = matrix.col(panel.get_origin())
fast_axis = matrix.col(panel.get_fast_axis())
slow_axis = matrix.col(panel.get_slow_axis())
image_size = panel.get_image_size_mm()
s0 = (1.0 / wavelength) * detector_normal
beam = Beam(-s0.normalize(), wavelength)
beam_centre = matrix.col(panel.get_beam_centre(beam.get_s0()))
origin_shift = matrix.col((1, 0.5))
new_beam_centre = beam_centre + origin_shift
new_mosflm_beam_centre = tuple(reversed(new_beam_centre))
from dxtbx.model.detector_helpers import set_mosflm_beam_centre
set_mosflm_beam_centre(detector, beam, new_mosflm_beam_centre)
assert (matrix.col(panel.get_beam_centre(beam.get_s0())) - matrix.col(
tuple(reversed(new_mosflm_beam_centre)))).length() < 1e-6
def test_set_mosflm_beam_centre(detector):
wavelength = 1.0
panel = detector[0]
detector_normal = matrix.col(panel.get_normal())
_ = matrix.col(panel.get_origin())
_ = matrix.col(panel.get_fast_axis())
_ = matrix.col(panel.get_slow_axis())
_ = panel.get_image_size_mm()
s0 = (1.0 / wavelength) * detector_normal
beam = Beam(-s0.normalize(), wavelength)
beam_centre = matrix.col(panel.get_beam_centre(beam.get_s0()))
origin_shift = matrix.col((1, 0.5))
new_beam_centre = beam_centre + origin_shift
new_mosflm_beam_centre = tuple(reversed(new_beam_centre))
set_mosflm_beam_centre(detector, beam, new_mosflm_beam_centre)
assert (
matrix.col(panel.get_beam_centre(beam.get_s0()))
- matrix.col(tuple(reversed(new_mosflm_beam_centre)))
).length() < 1e-6
# test resolution methods
beam = Beam(direction=(0, 0, 1), wavelength=1.0)
d_min1 = detector.get_max_resolution(beam.get_s0())
d_min2 = detector.get_max_inscribed_resolution(beam.get_s0())
assert d_min1 < d_min2
def tst_set_direction_wavelength():
"""Test setting direction and wavelength"""
from scitbx import matrix
direction = matrix.col((0.013142, 0.002200, 1.450476))
unit_direction = direction.normalize()
wavelength = 0.689400
# Create the beam
b = Beam(direction, wavelength)
eps = 1e-7
# Check direction is a unit vector
assert (abs(matrix.col(b.get_direction()).length() - 1) <= eps)
assert (abs(matrix.col(b.get_direction()) - unit_direction) <= eps)
# Check wavelength is correct
assert (abs(b.get_wavelength() - wavelength) <= eps)
# Check s0 is in direction and has length 1/wavelength
assert (abs(matrix.col(b.get_s0()).length() - 1.0 / wavelength) <= eps)
assert (abs(-matrix.col(b.get_s0()).normalize() - unit_direction) <= eps)
# Test passed
print "OK"
def tst_set_mosflm_beam_centre(detector):
from scitbx import matrix
from dxtbx.model import Beam
wavelength = 1
panel = detector[0]
detector_normal = matrix.col(panel.get_normal())
origin = matrix.col(panel.get_origin())
fast_axis = matrix.col(panel.get_fast_axis())
slow_axis = matrix.col(panel.get_slow_axis())
image_size = panel.get_image_size_mm()
s0 = (1.0/wavelength) * detector_normal
beam = Beam(-s0.normalize(), wavelength)
beam_centre = matrix.col(panel.get_beam_centre(beam.get_s0()))
origin_shift = matrix.col((1, 0.5))
new_beam_centre = beam_centre + origin_shift
new_mosflm_beam_centre = tuple(reversed(new_beam_centre))
from dxtbx.model.detector_helpers import set_mosflm_beam_centre
set_mosflm_beam_centre(detector, beam, new_mosflm_beam_centre)
assert (matrix.col(panel.get_beam_centre(beam.get_s0())) -
matrix.col(tuple(reversed(new_mosflm_beam_centre)))).length() < 1e-6
print 'OK'
def tst_set_direction_wavelength(): """Test setting direction and wavelength""" from scitbx import matrix direction = matrix.col((0.013142, 0.002200, 1.450476)) unit_direction = direction.normalize() wavelength = 0.689400 # Create the beam b = Beam(direction, wavelength) eps = 1e-7 # Check direction is a unit vector assert(abs(matrix.col(b.get_direction()).length() - 1) <= eps) assert(abs(matrix.col(b.get_direction()) - unit_direction) <= eps) # Check wavelength is correct assert(abs(b.get_wavelength() - wavelength) <= eps) # Check s0 is in direction and has length 1/wavelength assert(abs(matrix.col(b.get_s0()).length() - 1.0 / wavelength) <= eps) assert(abs(-matrix.col(b.get_s0()).normalize() - unit_direction) <= eps) # Test passed print "OK"
def tst_resolution(detector):
from dxtbx.model import Beam
beam = Beam(direction=(0, 0, 1), wavelength=1.0)
d_min1 = detector.get_max_resolution(beam.get_s0())
d_min2 = detector.get_max_inscribed_resolution(beam.get_s0())
assert d_min1 < d_min2
def tst_resolution(detector): from dxtbx.model import Beam beam = Beam(direction=(0,0,1), wavelength=1.0) d_min1 = detector.get_max_resolution(beam.get_s0()) d_min2 = detector.get_max_inscribed_resolution(beam.get_s0()) assert d_min1 < d_min2 print 'OK'
def test_setting_direction_and_wavelength():
direction = matrix.col((0.013142, 0.002200, 1.450476))
unit_direction = direction.normalize()
wavelength = 0.689400
# Create the beam
b = Beam(direction, wavelength)
eps = 1e-7
# Check direction is a unit vector
assert matrix.col(b.get_direction()).length() == pytest.approx(1)
assert abs(matrix.col(b.get_direction()) - unit_direction) <= eps
# Check wavelength is correct
assert b.get_wavelength() == pytest.approx(wavelength)
# Check s0 is in direction and has length 1/wavelength
assert matrix.col(b.get_s0()).length() == pytest.approx(1.0 / wavelength)
assert abs(-matrix.col(b.get_s0()).normalize() - unit_direction) <= eps
def test_beam_with_scan_points():
b1 = Beam((1, 0, 0), 2, 0.1, 0.1)
s0_static = matrix.col(b1.get_s0())
b1.set_s0_at_scan_points([s0_static] * 5)
d = b1.to_dict()
b2 = BeamFactory.from_dict(d)
for s0comp in d["s0_at_scan_points"]:
assert matrix.col(s0comp) == s0_static
for s0comp in b2.get_s0_at_scan_points():
assert matrix.col(s0comp) == s0_static
assert b1 == b2
def test_beam_with_scan_points():
from dxtbx.model import Beam, BeamFactory
b1 = Beam((1, 0, 0), 2, 0.1, 0.1)
from scitbx import matrix
s0_static = matrix.col(b1.get_s0())
b1.set_s0_at_scan_points([s0_static] * 5)
d = b1.to_dict()
b2 = BeamFactory.from_dict(d)
for s0comp in d['s0_at_scan_points']:
assert matrix.col(s0comp) == s0_static
for s0comp in b2.get_s0_at_scan_points():
assert matrix.col(s0comp) == s0_static
assert b1 == b2
def tst_scan_varying():
from scitbx import matrix
direction = matrix.col((0.013142, 0.002200, 1.450476))
unit_direction = direction.normalize()
wavelength = 0.689400
s0 = -unit_direction * 1.0 / wavelength
# Create the beam
b = Beam(s0)
assert b.get_num_scan_points() == 0
assert b.get_s0_at_scan_points().size() == 0
try:
b.get_s0_at_scan_point(0) # should raise RuntimeError
except RuntimeError:
pass
# set varying beam
num_scan_points = 11
s0_static = matrix.col(b.get_s0())
s0_as_scan_points = [s0_static]
axis = matrix.col.random(3, -1., 1.).normalize()
for i in range(num_scan_points - 1):
s0_as_scan_points.append(s0_as_scan_points[-1].rotate_around_origin(
axis, angle=0.01, deg=True))
b.set_s0_at_scan_points(s0_as_scan_points)
assert b.get_num_scan_points() == 11
assert b.get_s0_at_scan_points().size() == 11
for t in range(num_scan_points):
s0_t = matrix.col(b.get_s0_at_scan_point(t))
assert s0_t == s0_as_scan_points[t]
# also test setting as tuple
b.set_s0_at_scan_points(tuple(s0_as_scan_points))
assert b.get_num_scan_points() == 11
assert b.get_s0_at_scan_points().size() == 11
# test resetting
b.reset_scan_points()
assert b.get_num_scan_points() == 0
assert b.get_s0_at_scan_points().size() == 0
print 'OK'