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 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"
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
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)
def _get_beam(self):
return BeamFactory.simple_directional((0, 0, 1), WAVELEN_LOW)
params.indexing.two_color.avg_energy = parameters.ENERGY_LOW * .5 + parameters.ENERGY_HIGH * .5
params.indexing.stills.refine_all_candidates = False
params.indexing.stills.refine_candidates_with_known_symmetry = False
params.indexing.refinement_protocol.mode = "ignore"
params.indexing.stills.rmsd_min_px = 20000
params.indexing.stills.candidate_outlier_rejection = False
params.indexing.refinement_protocol.n_macro_cycles = 1
params.indexing.multiple_lattice_search.max_lattices = 1
params.indexing.basis_vector_combinations.max_refine = 10000000000
#params.indexing.basis_vector_combinations.max_combinations = 150
params.refinement.reflections.outlier.algorithm = "null"
# ====================================================================
BEAM_LOW = BeamFactory.simple_directional((0, 0, 1),
parameters.WAVELEN_LOW)
BEAM_HIGH = BeamFactory.simple_directional((0, 0, 1),
parameters.WAVELEN_HIGH)
if __name__ == "__main__":
show_hits = False
if not HAS_TWO_COLOR:
print("Need to install the module cxi_xdr_xes")
sys.exit()
pickle_fname = sys.argv[1]
image_fname = sys.argv[2]
print('Loading reflections')
with open(pickle_fname, 'r') as f:
found_refl = cPickle.load(f)
refl_select = spot_utils.ReflectionSelect(found_refl)