def sim_spots(F):
a_real = (79, 0, 0)
b_real = (0, 79, 0)
c_real = (0, 0, 38)
C = Crystal(a_real, b_real, c_real, 'P43212')
nbcryst = NBcrystal(init_defaults=True)
nbcryst.dxtbx_crystal = C # simulate ground truth
nbcryst.thick_mm = 0.1
nbcryst.Ncells_abc = 10, 10, 10
nbcryst.miller_array = F
print("Ground truth ncells = %f" % (nbcryst.Ncells_abc[0]))
# ground truth detector
from simtbx.nanoBragg.sim_data import SimData
DET_gt = SimData.simple_detector(150, 0.177, (600, 600))
# initialize the simulator
SIM = SimData(use_default_crystal=True)
SIM.detector = DET_gt
SIM.crystal = nbcryst
SIM.instantiate_diffBragg(oversample=0)
SIM.D.default_F = 0
SIM.D.progress_meter = False
SIM.D.add_diffBragg_spots()
SIM.D.F000 = 0
SPOTS = SIM.D.raw_pixels.as_numpy_array()
SIM.D.free_all()
SIM.D.free_Fhkl2()
return SPOTS
ETA_ABC_GT = args.eta
nbcryst.anisotropic_mos_spread_deg = ETA_ABC_GT
NCELLS_GT = 12, 12, 11
else:
NCELLS_GT = 12, 12, 11
nbcryst.Ncells_abc = NCELLS_GT
SIM = SimData(use_default_crystal=True)
#SIM.detector = SimData.simple_detector(150, 0.1, (513, 512))
if "eta" in args.perturb:
shape = 513 * 3, 512 * 3
#detdist = 70
else:
shape = 513, 512
detdist = 150
SIM.detector = SimData.simple_detector(detdist, 0.1, shape)
SIM.crystal = nbcryst
SIM.instantiate_diffBragg(oversample=0, auto_set_spotscale=True)
SIM.D.default_F = 0
SIM.D.F000 = 0
SIM.D.progress_meter = False
SIM.water_path_mm = 0.005
SIM.air_path_mm = 0.1
SIM.add_air = True
SIM.add_Water = True
SIM.include_noise = True
SIM.D.verbose = 2
SIM.D.add_diffBragg_spots()
SIM.D.verbose = 0
spots = SIM.D.raw_pixels.as_numpy_array()
SIM._add_background()
a_real, b_real, c_real = sqr(
uctbx.unit_cell(
ucell).orthogonalization_matrix()).transpose().as_list_of_lists()
C = Crystal(a_real, b_real, c_real, symbol)
# make a nanoBragg crystal to pass to diffBragg
nbcryst = NBcrystal()
nbcryst.dxtbx_crystal = C
nbcryst.n_mos_domains = 1
nbcryst.thick_mm = 0.01
nbcryst.Ncells_abc = (7, 7, 7)
# make an instance of diffBRagg, use the simData wrapper
SIM = SimData(use_default_crystal=True)
# overwrite the default detector with a smaller pixels one
SIM.detector = SimData.simple_detector(220, 0.1, (1000, 1000))
SIM.crystal = nbcryst
SIM.instantiate_diffBragg(oversample=0,
verbose=0,
interpolate=0,
default_F=1e3,
auto_set_spotscale=True)
# D is an instance of diffBragg with reasonable parameters
# and our dxtbx crystal created above
D = SIM.D
if args.curvatures:
D.compute_curvatures = True
# STEP 1: simulate the un-perturbed image:
D.refine(rot_idx)
nbcryst.dxtbx_crystal = C # simulate ground truth
nbcryst.thick_mm = 0.1
nbcryst.Ncells_abc = Ncells_gt # ground truth Ncells
nbcryst.mos_spread_deg = MOS_SPREAD
if args.aniso is not None:
nbcryst.anisotropic_mos_spread_deg = ANISO_MOS_SPREAD
assert nbcryst.has_anisotropic_mosaicity
else:
assert not nbcryst.has_anisotropic_mosaicity
nbcryst.n_mos_domains = N_MOS_DOMAINS
nbcryst.miller_array = miller_array_GT
print("Ground truth ncells = %f" % (nbcryst.Ncells_abc[0]))
# ground truth detector
DET_gt = SimData.simple_detector(150, 0.177, (600, 600))
# initialize the simulator
SIM = SimData()
if args.aniso is None:
SIM.Umats_method = 2
else:
SIM.Umats_method = 3
SIM.detector = DET_gt
SIM.crystal = nbcryst
SIM.instantiate_diffBragg(oversample=1, verbose=0)
SIM.D.refine(eta_diffBragg_id)
SIM.D.initialize_managers()
SIM.D.spot_scale = 100000
SIM.D.default_F = 0
SIM.D.progress_meter = False
n_ucell_params = len(UcellMan.variables)
assert np.allclose(UcellMan.B_recipspace, C.get_B())
# STEP4:
# make a nanoBragg crystal to pass to diffBragg
nbcryst = NBcrystal(init_defaults=True)
nbcryst.dxtbx_crystal = C
nbcryst.n_mos_domains = 1
nbcryst.thick_mm = 0.01
nbcryst.Ncells_abc = (7, 7, 7)
# STEP5: make an instance of diffBRagg, use the simData wrapper
SIM = SimData()
# overwrite the default detector to use smaller pixels
img_sh = 700, 700
SIM.detector = SimData.simple_detector(300, 0.1, img_sh)
SIM.crystal = nbcryst
SIM.instantiate_diffBragg(oversample=0, verbose=0, auto_set_spotscale=True)
# D is an instance of diffBragg with sensible parameters
# and our dxtbx crystal created above
D = SIM.D
D.progress_meter = True
# STEP6:
# initialize the derivative managers for the unit cell parameters
for i_param in range(n_ucell_params):
D.refine(UCELL_ID_OFFSET + i_param)
for i in range(n_ucell_params):
D.set_ucell_derivative_matrix(UCELL_ID_OFFSET + i,
UcellMan.derivative_matrices[i])
if args.curvatures:
C2.rotate_around_origin(rot_axis, rot_ang) assert np.allclose(C2.get_U(), C.get_U()) C2.rotate_around_origin(col(perturb_rot_axis), perturb_rot_ang) # Setup the simulation and create a realistic image # with background and noise # <><><><><><><><><><><><><><><><><><><><><><><><><> nbcryst = NBcrystal() nbcryst.dxtbx_crystal = C # simulate ground truth nbcryst.thick_mm = 0.1 nbcryst.Ncells_abc = 12, 12, 11 nbcryst.isotropic_ncells = False SIM = SimData(use_default_crystal=True) #SIM.detector = SimData.simple_detector(150, 0.1, (513, 512)) SIM.detector = SimData.simple_detector(150, 0.1, (513, 512)) SIM.crystal = nbcryst SIM.instantiate_diffBragg(oversample=0, auto_set_spotscale=True) SIM.D.default_F = 0 SIM.D.F000 = 0 SIM.D.progress_meter = False SIM.water_path_mm = 0.005 SIM.air_path_mm = 0.1 SIM.add_air = True SIM.add_Water = True SIM.include_noise = True SIM.D.add_diffBragg_spots() spots = SIM.D.raw_pixels.as_numpy_array() SIM._add_background() SIM.D.readout_noise_adu = args.readout
rotation = Rotation.random(num=1, random_state=101)[0]
Q = rec(rotation.as_quat(), n=(4, 1))
rot_ang, rot_axis = Q.unit_quaternion_as_axis_and_angle()
C.rotate_around_origin(rot_axis, rot_ang)
# make a nanoBragg crystal to pass to diffBragg
nbcryst = NBcrystal(init_defaults=True)
nbcryst.dxtbx_crystal = C
nbcryst.n_mos_domains = 1
nbcryst.thick_mm = 0.01
nbcryst.Ncells_abc = (7, 7, 7)
# make an instance of diffBRagg, use the simData wrapper
SIM = SimData(use_default_crystal=True)
# overwrite the default detector with a smaller pixels one
SIM.detector = SimData.simple_detector(300, 0.1, (700, 700))
SIM.crystal = nbcryst
Fcell = 1e6
SIM.instantiate_diffBragg(oversample=0,
verbose=0,
interpolate=0,
default_F=Fcell)
# D is an instance of diffBragg with reasonable parameters
# and our dxtbx crystal created above
D = SIM.D
D.progress_meter = True
# initialize the derivative manager for Fcell
fcell = 11 # internal index of fcell manager within diffBragg
D.refine(fcell)