def setup_class(cls):
ex_dir_ = os.path.dirname(__file__) + '/../../../examples'
# Load beam
beam = ps.Beam(ex_dir_ + '/input/beam/amo86615.beam')
# Load and initialize the detector
np.random.seed(0)
det = ps.Epix10kDetector(
geom=ex_dir_ + '/input/lcls/xcsx35617/'
'Epix10ka2M::CalibV1/XcsEndstation.0:Epix10ka2M.0/geometry/0-end.data',
run_num=0,
beam=beam,
cameraConfig='fixedMedium')
cls.det = det
cls.pos_recip = det.pixel_position_reciprocal
# Ref Particle
cls.particle_0 = ps.Particle()
cls.particle_0.create_from_atoms([ # Angstrom
("O", cst.vecx),
("O", 2 * cst.vecy),
("O", 3 * cst.vecz),
])
cls.pattern_0 = pg.calculate_diffraction_pattern_gpu(
cls.pos_recip, cls.particle_0, return_type="complex_field")
# Second Particle
cls.part_coord_1 = np.array((0.5, 0.2, 0.1)) # Angstrom
cls.particle_1 = ps.Particle()
cls.particle_1.create_from_atoms([ # Angstrom
("O", cst.vecx + cls.part_coord_1),
("O", 2 * cst.vecy + cls.part_coord_1),
("O", 3 * cst.vecz + cls.part_coord_1),
])
cls.part_coord_1 *= 1e-10 # Angstrom -> meter
cls.pattern_1 = pg.calculate_diffraction_pattern_gpu(
cls.pos_recip, cls.particle_1, return_type="complex_field")
# Flat Field
cls.flatField = np.ones(
(cls.det.panel_num, cls.det.panel_pixel_num_x[0],
cls.det.panel_pixel_num_y[0])) * 1.0
cls.I0width = 0.03
cls.I0min = 0
cls.I0max = 150000
cls.bauf = BuildAutoRangeFrames(cls.det, cls.I0width, cls.I0min,
cls.I0max, cls.flatField)
cls.bauf.makeFrame()
geom=input_dir+'/lcls/amo86615/PNCCD::CalibV1/Camp.0:pnCCD.1/geometry/0-end.data'
pdbfile=input_dir+'/pdb/3iyf.pdb'
# Load beam
beam = ps.Beam(beamfile)
increase_factor = 1e5
print('BEFORE: # of photons per pulse = {}'.format(beam.get_photons_per_pulse()))
print('>>> Increasing the number of photons per pulse by a factor {}'.format(increase_factor))
beam.set_photons_per_pulse(increase_factor*beam.get_photons_per_pulse())
print('AFTER : # of photons per pulse = {}'.format(beam.get_photons_per_pulse()))
#beam._n_phot = 1e14 # detector normal
#beam._n_phot = 1e17 # detector saturates
#beam._n_phot = 1e20 # detector gets fried
# Load and initialize the detector
det = ps.Epix10kDetector(geom=geom, run_num=0, beam=beam, cameraConfig='fixedMedium')
increase_factor = 0.5
print('BEFORE: detector distance = {} m'.format(det.distance))
print('>>> Increasing the detector distance by a factor of {}'.format(increase_factor))
det.distance = increase_factor*det.distance
print('AFTER : detector distance = {} m'.format(det.distance))
# Create particle object(s)
particle = ps.Particle()
particle.read_pdb(pdbfile, ff='WK')
# Perform SPI experiment
tic = time.time()
experiment = ps.SPIExperiment(det, beam, particle)
dp_photons = experiment.generate_image_stack() # generate diffraction field