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