def main():
from simtbx.nanoBragg.sim_data import SimData
import sys
if "--cuda" in sys.argv:
import os
os.environ["DIFFBRAGG_USE_CUDA"] = "1"
S = SimData(use_default_crystal=True)
S.instantiate_diffBragg()
S.D.nopolar = True
S.D.oversample = 3
S.D.add_diffBragg_spots()
S._add_background()
diff_img = S.D.raw_pixels.as_numpy_array()
S.D.raw_pixels *= 0
S.D.add_nanoBragg_spots()
S._add_background()
nano_img = S.D.raw_pixels.as_numpy_array()
import numpy as np
assert np.allclose(diff_img, nano_img, atol=1e-9)
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
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()
SIM.D.readout_noise_adu = args.readout
SIM._add_noise()
# 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)
D.initialize_managers()
D.set_value(rot_idx, 0)
D.use_cuda = args.cuda
#D.printout_pixel_fastslow = 786, 567
D.add_diffBragg_spots()
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
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
SIM.water_path_mm = 0.15
SIM.air_path_mm = 0.1
SIM.add_air = True
SIM.add_water = True
SIM.include_noise = True
SIM.D.use_cuda = args.cuda
SIM.D.compute_curvatures = args.curvatures
SIM.D.add_diffBragg_spots()
if args.aniso is None:
# 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)
D.initialize_managers()
#roi = ((0, 699), (0, 699))
#rX = slice(roi[0][0], roi[0][1], 1)
#rY = slice(roi[1][0], roi[1][1], 1)