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
def flexBeam_sim_colors(CRYSTAL,
DETECTOR,
BEAM,
Famp,
energies,
fluxes,
pids=None,
cuda=False,
oversample=0,
Ncells_abc=(50, 50, 50),
mos_dom=1,
mos_spread=0,
beamsize_mm=0.001,
device_Id=0,
omp=False,
show_params=False,
crystal_size_mm=0.01,
printout_pix=None,
time_panels=True,
verbose=0,
default_F=0,
interpolate=0,
recenter=True,
profile="gauss",
spot_scale_override=None,
background_raw_pixels=None,
include_noise=False,
add_water=False,
add_air=False,
water_path_mm=0.005,
air_path_mm=0,
rois_perpanel=None,
adc_offset=0,
readout_noise=3,
psf_fwhm=0,
gain=1,
mosaicity_random_seeds=None):
"""
:param CRYSTAL: dxtbx Crystal model
:param DETECTOR: dxtbx detector model
:param BEAM: dxtbx beam model
:param Famp: cctbx miller array (amplitudes)
:param energies: list of energies to simulate the scattering
:param fluxes: list of pulse fluences per energy (same length as energies)
:param pids: panel ids to simulate on (None means all panels)
:param cuda: whether to use GPU (only works for nvidia builds)
:param oversample: pixel oversample factor (0 means nanoBragg will decide)
:param Ncells_abc: number of unit cells along each crystal direction in the mosaic block
:param mos_dom: number of mosaic domains in used to sample mosaic spread (texture)
:param mos_spread: mosaicity in degrees (spherical cap width)
:param beamsize_mm: focal size of the beam
:param device_Id: cuda device id (ignore if cuda=False)
:param omp: whether to use open mp (required open MP build configuration)
:param show_params: show the nanoBragg parameters
:param crystal_size_mm: size of the crystal (increases the intensity of the spots)
:param printout_pix: debug pixel position : tuple of (pixel_fast_coord, pixel_slow_coord)
:param time_panels: show timing info
:param verbose: verbosity level for nanoBragg (0-10), 0 is quiet
:param default_F: default amplitude value for nanoBragg
:param interpolate: whether to interpolate for small mosaic domains
:param recenter: recenter for tilted cameras, deprecated
:param profile: profile shape, can be : gauss, round, square, or tophat
:param spot_scale_override: scale the simulated scattering bythis amounth (overrides value based on crystal thickness)
:param background_raw_pixels: dictionary of {panel_id: raw_pixels}, add these background pixels to the simulated Bragg
:param include_noise: add noise to simulated pattern
:param add_water: add water to similated pattern
:param add_air: add ait to simulated pattern
:param water_path_mm: length of water the beam travels through
:param air_path_mm: length of air the beam travels through
:param rois_perpanel: regions of intererest on each panel
:param adc_offset: add this value to each pixel in simulated pattern
:param readout_noise: readout noise level (usually 3-5 ADU)
:param psf_fwhm: point spread kernel FWHM
:param gain: photon gain
:param mosaicity_random_seeds: random seeds to simulating mosaic texture
:return: list of [(panel_id0,simulated pattern0), (panel_id1, simulated_pattern1), ...]
"""
if pids is None:
pids = range(len(DETECTOR))
if background_raw_pixels is None:
background_raw_pixels = {pid: None for pid in pids}
if rois_perpanel is None:
rois_perpanel = {pid: None for pid in pids}
nbBeam = NBbeam()
nbBeam.size_mm = beamsize_mm
nbBeam.unit_s0 = BEAM.get_unit_s0()
wavelengths = ENERGY_CONV / np.array(energies)
nbBeam.spectrum = list(zip(wavelengths, fluxes))
nbCrystal = NBcrystal()
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
panel_images = []
tinit = time.time()
S = SimData()
S.detector = DETECTOR
S.beam = nbBeam
S.crystal = nbCrystal
S.using_cuda = cuda
S.using_omp = omp
S.add_air = add_air
S.air_path_mm = air_path_mm
S.add_water = add_water
S.water_path_mm = water_path_mm
S.readout_noise = readout_noise
S.gain = gain
S.psf_fwhm = psf_fwhm
S.include_noise = include_noise
if mosaicity_random_seeds is not None:
S.mosaic_seeds = mosaicity_random_seeds
S.instantiate_nanoBragg(verbose=verbose,
oversample=oversample,
interpolate=interpolate,
device_Id=device_Id,
default_F=default_F,
adc_offset=adc_offset)
if printout_pix is not None:
S.update_nanoBragg_instance("printout_pixel_fastslow", printout_pix)
if spot_scale_override is not None:
S.update_nanoBragg_instance("spot_scale", spot_scale_override)
for pid in pids:
t_panel = time.time()
S.background_raw_pixels = background_raw_pixels[pid]
S.panel_id = pid
S.rois = rois_perpanel[pid]
S.generate_simulated_image()
if show_params:
S.D.show_params()
print('spot scale: %2.7g' % S.D.spot_scale)
panel_image = S.D.raw_pixels.as_numpy_array()
panel_images.append([pid, panel_image])
S.D.raw_pixels *= 0
if time_panels:
tdone = time.time() - tinit
t_panel = time.time() - t_panel
print(
'Panel %d took %.4f seconds (Total sim time = %.4f seconds)' %
(pid, t_panel, tdone))
S.D.free_all()
return panel_images
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
# Setup the simulation and create a realistic image
# with background and noise
# <><><><><><><><><><><><><><><><><><><><><><><><><>
nbcryst = NBcrystal(init_defaults=True)
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)
def flexBeam_sim_colors(CRYSTAL,
DETECTOR,
BEAM,
Famp,
energies,
fluxes,
pids=None,
cuda=False,
oversample=0,
Ncells_abc=(50, 50, 50),
mos_dom=1,
mos_spread=0,
beamsize_mm=0.001,
device_Id=0,
omp=False,
show_params=False,
crystal_size_mm=0.01,
printout_pix=None,
time_panels=True,
verbose=0,
default_F=0,
interpolate=0,
recenter=True,
profile="gauss",
spot_scale_override=None,
background_raw_pixels=None,
include_noise=False,
add_water=False,
add_air=False,
water_path_mm=0.005,
air_path_mm=0,
rois_perpanel=None,
adc_offset=0,
readout_noise=3,
psf_fwhm=0,
gain=1,
mosaicity_random_seeds=None):
if pids is None:
pids = range(len(DETECTOR))
if background_raw_pixels is None:
background_raw_pixels = {pid: None for pid in pids}
if rois_perpanel is None:
rois_perpanel = {pid: None for pid in pids}
nbBeam = NBbeam()
nbBeam.size_mm = beamsize_mm
nbBeam.unit_s0 = BEAM.get_unit_s0()
wavelengths = ENERGY_CONV / np.array(energies)
nbBeam.spectrum = list(zip(wavelengths, fluxes))
nbCrystal = NBcrystal()
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
panel_images = []
for pid in pids:
tinit = time.time()
S = SimData()
S.detector = DETECTOR
S.beam = nbBeam
S.crystal = nbCrystal
S.panel_id = pid
S.using_cuda = cuda
S.using_omp = omp
S.add_air = add_air
S.air_path_mm = air_path_mm
S.add_water = add_water
S.water_path_mm = water_path_mm
S.background_raw_pixels = background_raw_pixels[pid]
S.rois = rois_perpanel[pid]
S.readout_noise = readout_noise
S.gain = gain
S.psf_fwhm = psf_fwhm
S.include_noise = include_noise
if mosaicity_random_seeds is not None:
S.mosaic_seeds = mosaicity_random_seeds
S.instantiate_nanoBragg(verbose=verbose,
oversample=oversample,
interpolate=interpolate,
device_Id=device_Id,
default_F=default_F,
adc_offset=adc_offset)
if recenter:
S.update_nanoBragg_instance(
"beam_center_mm",
DETECTOR[int(pid)].get_beam_centre(BEAM.get_s0()))
if printout_pix is not None:
S.update_nanoBragg_instance("printout_pixel_fastslow",
printout_pix)
if spot_scale_override is not None:
S.update_nanoBragg_instance("spot_scale", spot_scale_override)
S.generate_simulated_image()
if show_params:
S.D.show_params()
print('spot scale: %2.7g' % S.D.spot_scale)
panel_image = S.D.raw_pixels.as_numpy_array()
panel_images.append([pid, panel_image])
S.D.free_all()
if time_panels:
tdone = time.time() - tinit
print('Panel %d took %.4f seconds' % (pid, tdone))
del S.D
return panel_images