a2_real, b2_real, c2_real = sqr(
uctbx.unit_cell(
ucell2).orthogonalization_matrix()).transpose().as_list_of_lists()
C2 = Crystal(a2_real, b2_real, c2_real, symbol)
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.isotropic_ncells = False
if "eta" in args.perturb:
nbcryst.n_mos_domains = 1000
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:
def diffBragg_forward(CRYSTAL,
DETECTOR,
BEAM,
Famp,
energies,
fluxes,
oversample=0,
Ncells_abc=(50, 50, 50),
mos_dom=1,
mos_spread=0,
beamsize_mm=0.001,
device_Id=0,
show_params=True,
crystal_size_mm=None,
printout_pix=None,
verbose=0,
default_F=0,
interpolate=0,
profile="gauss",
spot_scale_override=None,
mosaicity_random_seeds=None,
nopolar=False,
diffuse_params=None,
cuda=False,
show_timings=False):
if cuda:
os.environ["DIFFBRAGG_USE_CUDA"] = "1"
CRYSTAL, Famp = nanoBragg_utils.ensure_p1(CRYSTAL, Famp)
nbBeam = NBbeam()
nbBeam.size_mm = beamsize_mm
nbBeam.unit_s0 = BEAM.get_unit_s0()
wavelengths = utils.ENERGY_CONV / np.array(energies)
nbBeam.spectrum = list(zip(wavelengths, fluxes))
nbCrystal = NBcrystal(init_defaults=False)
nbCrystal.isotropic_ncells = False
nbCrystal.dxtbx_crystal = CRYSTAL
nbCrystal.miller_array = Famp
nbCrystal.Ncells_abc = Ncells_abc
nbCrystal.symbol = CRYSTAL.get_space_group().info().type().lookup_symbol()
nbCrystal.thick_mm = crystal_size_mm
nbCrystal.xtal_shape = profile
nbCrystal.n_mos_domains = mos_dom
nbCrystal.mos_spread_deg = mos_spread
S = SimData()
S.detector = DETECTOR
npan = len(DETECTOR)
nfast, nslow = DETECTOR[0].get_image_size()
img_shape = npan, nslow, nfast
S.beam = nbBeam
S.crystal = nbCrystal
if mosaicity_random_seeds is not None:
S.mosaic_seeds = mosaicity_random_seeds
S.instantiate_diffBragg(verbose=verbose,
oversample=oversample,
interpolate=interpolate,
device_Id=device_Id,
default_F=default_F,
auto_set_spotscale=crystal_size_mm is not None
and spot_scale_override is None)
if spot_scale_override is not None:
S.update_nanoBragg_instance("spot_scale", spot_scale_override)
S.update_nanoBragg_instance("nopolar", nopolar)
if show_params:
S.D.show_params()
print("Spot scale=%f" % S.D.spot_scale)
if show_timings and verbose < 2:
S.D.verbose = 2
S.D.record_time = True
if diffuse_params is not None:
S.D.use_diffuse = True
S.D.gamma_miller_units = diffuse_params["gamma_miller_units"]
S.D.diffuse_gamma = diffuse_params["gamma"]
S.D.diffuse_sigma = diffuse_params["sigma"]
S.D.add_diffBragg_spots_full()
if show_timings:
S.D.show_timings()
t = time.time()
data = S.D.raw_pixels_roi.as_numpy_array().reshape(img_shape)
t = time.time() - t
if show_timings:
print("Took %f sec to recast and reshape" % t)
if printout_pix is not None:
S.D.raw_pixels_roi *= 0
p, f, s = printout_pix
S.D.printout_pixel_fastslow = f, s
S.D.show_params()
S.D.add_diffBragg_spots(printout_pix)
# free up memory
S.D.free_all()
S.D.free_Fhkl2()
if S.D.gpu_free is not None:
S.D.gpu_free()
return data