def make_images(data, tag):
pixel_size = 0.1 # mm/pixel
detector = DetectorFactory.simple(
'PAD', 100,
(pixel_size * data.focus()[1] / 2, pixel_size * data.focus()[2] / 2),
'+x', '-y', (pixel_size, pixel_size),
(data.focus()[2], data.focus()[1]), (-1, 1e6 - 1), [], None)
beam = BeamFactory.simple(1.0)
sf = ScanFactory()
scan = sf.make_scan(image_range=(1, 180),
exposure_times=0.1,
oscillation=(0, 1.0),
epochs=range(180),
deg=True)
# write images in each of three directions
for slice_id in [0, 1, 2]:
for idx in xrange(data.focus()[slice_id]):
if slice_id == 0: # slow
data_slice = data[idx:idx + 1, :, :]
data_slice.reshape(flex.grid(data.focus()[1], data.focus()[2]))
filename = "fft_frame_%s_mf_%04d.cbf" % (tag, idx)
elif slice_id == 1: # med
data_slice = data[:, idx:idx + 1, :]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[2]))
filename = "fft_frame_%s_sf_%04d.cbf" % (tag, idx)
elif slice_id == 2: # fast
data_slice = data[:, :, idx:idx + 1]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[1]))
filename = "fft_frame_%s_sm_%04d.cbf" % (tag, idx)
print['slow', 'med', 'fast'][slice_id], idx
FormatCBFMini.as_file(detector, beam, None, scan, data_slice,
filename)
def get_values(invert_y):
beam = BeamFactory.simple(wavelength=1)
if invert_y:
y_direction = "-y"
else:
y_direction = "+y"
detector = DetectorFactory.simple(
sensor=DetectorFactory.sensor("PAD"),
distance=100,
beam_centre=[50, 50],
fast_direction="+x",
slow_direction=y_direction,
pixel_size=[0.1, 0.1],
image_size=[1000, 1000],
)[0]
wavelength = beam.get_wavelength()
thickness = 0.5
table = attenuation_coefficient.get_table("Si")
mu = table.mu_at_angstrom(wavelength) / 10.0
t0 = thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
v1 = detector.pixel_to_millimeter((0, 0))
v2 = detector.pixel_to_millimeter((1000, 1000))
return v1, v2
def make_images(data, tag):
pixel_size = 0.1
detector = DetectorFactory.simple(
'PAD', 100,
(pixel_size * data.focus()[1] / 2, pixel_size * data.focus()[2] / 2),
'+x', '-y', (pixel_size, pixel_size),
(data.focus()[2], data.focus()[1]), (-1, 1e6 - 1), [], None)
beam = BeamFactory.simple(1.0)
for slice_id in [0, 1, 2]:
for idx in xrange(data.focus()[slice_id]):
if slice_id == 0: # slow
data_slice = data[idx:idx + 1, :, :]
data_slice.reshape(flex.grid(data.focus()[1], data.focus()[2]))
filename = "fft_frame_%s_mf_%04d.cbf" % (tag, idx)
elif slice_id == 1: # med
data_slice = data[:, idx:idx + 1, :]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[2]))
filename = "fft_frame_%s_sf_%04d.cbf" % (tag, idx)
elif slice_id == 2: # fast
data_slice = data[:, :, idx:idx + 1]
data_slice.reshape(flex.grid(data.focus()[0], data.focus()[1]))
filename = "fft_frame_%s_sm_%04d.cbf" % (tag, idx)
print['slow', 'med', 'fast'][slice_id], idx
FormatCBFMini.as_file(detector, beam, None, None, data_slice,
filename)
def __init__(self):
#unit cell and space group for lysozyme
known_symmetry = crystal.symmetry("78,78,37,90,90,90", "P43212")
data = two_color_still_sim.two_color_still_sim(symm=known_symmetry,
rot=None)
self.data = data
wavelength1 = 12398 / 7400 #wavelength for 2 color experiment in Angstroms
wavelength2 = 12398 / 7500 #wavelength for 2 color experiment in Angstroms
#get detector with a single panel
detector = detector_factory.simple('SENSOR_UNKNOWN', 125,
(97.075, 97.075), '+x', '-y',
(0.11, 0.11), (1765, 1765))
self.detector = detector
beam1 = beam_factory.simple_directional((0, 0, 1), wavelength1)
beam2 = beam_factory.simple_directional((0, 0, 1), wavelength2)
beams = [beam1, beam2]
self.beams = beams
hkl_list = data.hkl_list
self.hkl_list = hkl_list
A = data.A
self.A = A
two_color_sim = data.ewald_proximity_test(beams, hkl_list, A, detector)
self.two_color_sim = two_color_sim
def test_unique_hkl():
'''tests the uniqueness of hkl values associated with each experiment for
100 simulated randomly oriented thermolysin diffraction images prior to indexing.'''
flex.set_random_seed(42) # the meaning of life
known_symmetry = crystal.symmetry("78,78,37,90,90,90", "P43212")
detector = detector_factory.simple('SENSOR_UNKNOWN', 125, (97.075, 97.075),
'+x', '-y', (0.11, 0.11), (1765, 1765))
wavelength1 = 12398 / 7400 #wavelength for 2 color experiment in Angstroms
wavelength2 = 12398 / 7500 #wavelength for 2 color experiment in Angstroms
beam1 = beam_factory.simple_directional((0, 0, 1), wavelength1)
beam2 = beam_factory.simple_directional((0, 0, 1), wavelength2)
beams = [beam1, beam2]
for i in range(100):
data = two_color_still_sim.two_color_still_sim(known_symmetry,
rot=None)
hkl_list = data.hkl_list
A = data.A
sim_data = data.ewald_proximity_test(beams, hkl_list, A, detector)
refl = sim_data.get('reflection_table')
refl1 = refl.select(refl['set_id'] == 0)
refl2 = refl.select(refl['set_id'] == 1)
# unit test to make sure all miller indices are unique for each experiment id
assert len(refl1['miller_index']) == len(set(refl1['miller_index']))
assert len(refl2['miller_index']) == len(set(refl2['miller_index']))
print "ok"
def test_detector():
"""A test class for the detector class."""
assert DetectorFactory.simple(
"CCD",
100.0,
(45.0, 52.0),
"+x",
"-y",
(0.172, 0.172),
(516, 590),
(0, 1024),
[],
)
assert DetectorFactory.two_theta(
"CCD",
60.0,
(35.0, 34.0),
"+x",
"+y",
"+x",
30,
(0.07, 0.07),
(1042, 1042),
(0, 1024),
[],
)
image = Path(__file__).parent / "phi_scan_001.cbf"
assert DetectorFactory.imgCIF(str(image), "CCD")
def test_detector():
"""A test class for the detector class."""
assert DetectorFactory.simple(
"CCD",
100.0,
(45.0, 52.0),
"+x",
"-y",
(0.172, 0.172),
(516, 590),
(0, 1024),
[],
)
assert DetectorFactory.two_theta(
"CCD",
60.0,
(35.0, 34.0),
"+x",
"+y",
"+x",
30,
(0.07, 0.07),
(1042, 1042),
(0, 1024),
[],
)
dxtbx_dir = libtbx.env.dist_path("dxtbx")
image = os.path.join(dxtbx_dir, "tests", "phi_scan_001.cbf")
# xparm = os.path.join(dxtbx_dir, "tests", "example-xparm.xds")
assert DetectorFactory.imgCIF(image, "CCD")
def _construct_detector(distance):
return DetectorFactory.simple(
sensor="PAD",
distance=distance,
beam_centre=(216.87, 211.32),
fast_direction="+x",
slow_direction="-y",
pixel_size=(0.172, 0.172),
image_size=(2463, 2527),
trusted_range=(-1, 1e8),
)
def _construct_detector(distance):
return DetectorFactory.simple(
sensor="PAD",
distance=distance,
beam_centre=(41.20, 51.69),
fast_direction="+x",
slow_direction="-y",
pixel_size=(0.172, 0.172),
image_size=(487, 619),
trusted_range=(-1, 1e8),
)
def test_detector():
'''A test class for the detector class.'''
d = DetectorFactory.simple('CCD', 100.0, (45.0, 52.0), '+x', '-y',
(0.172, 0.172), (516, 590), (0, 1024), [])
t = DetectorFactory.two_theta(
'CCD', 60.0, (35.0, 34.0), '+x', '+y', '+x', 30,
(0.07, 0.07), (1042, 1042), (0, 1024), [])
import libtbx.load_env
import os
dxtbx_dir = libtbx.env.dist_path('dxtbx')
image = os.path.join(dxtbx_dir, 'tests', 'phi_scan_001.cbf')
xparm = os.path.join(dxtbx_dir, 'tests', 'example-xparm.xds')
c = DetectorFactory.imgCIF(image, 'CCD')
def get_basis():
'''gets the input basis vectors of 100 simulated diffraction images'''
flex.set_random_seed(42)
known_symmetry = crystal.symmetry("78,78,37,90,90,90", "P43212")
detector = detector_factory.simple('SENSOR_UNKNOWN', 125, (97.075, 97.075),
'+x', '-y', (0.11, 0.11), (1765, 1765))
wavelength1 = 12398 / 7400 #wavelength for 2 color experiment in Angstroms
wavelength2 = 12398 / 7500 #wavelength for 2 color experiment in Angstroms
beam1 = beam_factory.simple_directional((0, 0, 1), wavelength1)
beam2 = beam_factory.simple_directional((0, 0, 1), wavelength2)
a_basis = []
b_basis = []
c_basis = []
unique_vectors = []
# refiner resets random number seed so in order to get the same 100 images
#generated each time the random seed is set
# the implementation is as follows
sims = [merge_close_spots.merge_close_spots() for i in range(2)]
for data in sims:
A = data.A
A_inv = A.inverse()
a = col(A_inv[:3])
b = col(A_inv[3:6])
c = col(A_inv[6:])
a_basis.append(a)
b_basis.append(b)
c_basis.append(c)
res = data.two_color_sim
info = data.spot_proximity(res)
refl = info[0]
candidate_basis_vectors = index(refl, detector, known_symmetry,
[beam1, beam2])
unique_vectors.append(candidate_basis_vectors)
return a_basis, b_basis, c_basis, unique_vectors
def test_indexed_hkl():
'''tests the uniqueness of hkl values associated with each experiment for
100 simulated randomly oriented thermolysin diffraction images indexed using
two color indexer'''
flex.set_random_seed(42)
known_symmetry = crystal.symmetry("78,78,37,90,90,90", "P43212")
detector = detector_factory.simple('SENSOR_UNKNOWN', 125, (97.075, 97.075),
'+x', '-y', (0.11, 0.11), (1765, 1765))
wavelength1 = 12398 / 7400 #wavelength for 2 color experiment in Angstroms
wavelength2 = 12398 / 7500 #wavelength for 2 color experiment in Angstroms
beam1 = beam_factory.simple_directional((0, 0, 1), wavelength1)
beam2 = beam_factory.simple_directional((0, 0, 1), wavelength2)
a_basis = []
b_basis = []
c_basis = []
# refiner resets random number seed so in order to get the same 100 images
#generated each time the random seed is set
# the implementation is as follows
# gets simulated images
sims = [merge_close_spots.merge_close_spots() for i in range(2)]
for data in sims:
A = data.A
A_inv = A.inverse()
a = col(A_inv[:3])
b = col(A_inv[3:6])
c = col(A_inv[6:])
crystinp = Crystal(a, b, c, space_group=known_symmetry.space_group())
a_basis.append(a)
b_basis.append(b)
c_basis.append(c)
res = data.two_color_sim
info = data.spot_proximity(res)
refl = info[0]
result = index(refl, detector, known_symmetry, [beam1, beam2])
cm = result.refined_experiments.crystals()[0]
R, best_axis, best_angle, change_of_basis = difference_rotation_matrix_axis_angle(
crystal_a=cm, crystal_b=crystinp)
# cmd_line = command_line.argument_interpreter(master_params=master_phil_scope)
# working_phil = cmd_line.process_and_fetch(args=[])
params = master_phil_scope.extract()
params.refinement.parameterisation.beam.fix = "all"
params.refinement.parameterisation.detector.fix = "all"
params.indexing.known_symmetry.space_group = known_symmetry.space_group_info(
)
params.refinement.verbosity = 3
params.indexing.refinement_protocol.d_min_start = 3
params.indexing.refinement_protocol.n_macro_cycles = 1
params.indexing.known_symmetry.unit_cell = known_symmetry.unit_cell()
params.indexing.multiple_lattice_search.max_lattices = 1
params.indexing.debug = True
params.indexing.known_symmetry.absolute_angle_tolerance = 5.0
params.indexing.known_symmetry.relative_length_tolerance = 0.3
params.indexing.stills.rmsd_min_px = 3.5
expts = copy.deepcopy(result.refined_experiments)
expts.crystals()[0].change_basis(change_of_basis)
reflections_exp0 = result.refined_reflections.select(
result.refined_reflections['id'] == 0)
reflections_exp1 = result.refined_reflections.select(
result.refined_reflections['id'] == 1)
assert len(reflections_exp0['miller_index']) == len(
set(reflections_exp0['miller_index']))
assert len(reflections_exp1['miller_index']) == len(
set(reflections_exp1['miller_index']))
print "OK"
'reflection_table': refl,
'all_spots': spots,
'wavelength_1_spots': spots1,
'wavelength_2_spots': spots2,
'input_orientation': A
}
return sim_res
if __name__ == "__main__":
wavelength1 = 12398 / 7400 #wavelength for 2 color experiment in Angstroms
wavelength2 = 12398 / 7500 #wavelength for 2 color experiment in Angstroms
#get detector with a single panel
detector = detector_factory.simple('SENSOR_UNKNOWN', 125, (97.075, 97.075),
'+x', '-y', (0.11, 0.11), (1765, 1765))
#unit cell and space group for lysozyme
known_symmetry = crystal.symmetry("78,78,37,90,90,90", "P43212")
beam1 = beam_factory.simple_directional((0, 0, 1), wavelength1)
beam2 = beam_factory.simple_directional((0, 0, 1), wavelength2)
beams = [beam1, beam2]
flex.set_random_seed(42)
for i in range(5):
data = two_color_still_sim(known_symmetry, rot=None)
hkl_list = data.hkl_list
A = data.A
from math import sqrt
side_length = sqrt(diagonal.length()**2 / 2)
npx = int(round(side_length / pixel_size[0]))
beam_centre = [npx / 2 * pixel_size[0]] * 2
distance = detector[0].get_distance()
# Create a new single panel detector orthogonal to the beam, which intersects
# at the centre
from dxtbx.model.detector import DetectorFactory
detector2 = DetectorFactory.simple(
sensor="PAD",
distance=distance,
beam_centre=beam_centre,
fast_direction="+x",
slow_direction="-y",
pixel_size=pixel_size,
image_size=(npx, npx),
)
exp.detector = detector2
# Make the scan a full turn to ensure no reflections get thrown out during
# refinement for being outside the scan range
image_width_deg = scan.get_oscillation(deg=True)[1]
nimages = int(round(360.0 / image_width_deg))
image_width_deg = 360.0 / nimages
image_range = 1, nimages
epochs = [0] * nimages
exposure_times = 0.0
oscillation = (0, image_width_deg)