def pack_data_exchange():
f = DataExchangeFile(CXP.io.data_exchange_filename, mode='w')
sim = DataExchangeEntry.simulation(
name={'value': 'Simulated Ptycho Data.'},
energy={
'value': CXP.experiment.energy,
'units': 'keV'
},
focusing_optic={'value': CXP.experiment.optic},
probe_modes={'value': CXP.reconstruction.probe_modes},
noise_model={'value': CXP.simulation.noise_model},
gaussian_noise_level={'value': CXP.simulation.gaussian_noise_level},
total_photons={'value': CXP.simulation.total_photons},
beam_stop={'value': CXP.simulation.beam_stop},
beam_stop_size={'value': CXP.simulation.beam_stop_size},
beam_stop_attenuation={'value': CXP.simulation.beam_stop_attenuation},
defocus={'value': CXP.simulation.defocus},
position_jitter={
'value': CXP.reconstruction.initial_position_jitter_radius,
'units': 'pixels'
})
f.add_entry(sim)
sample = DataExchangeEntry.sample(
root='/simulation',
name={'value': 'ground truth sample complex amplitude'},
data={
'value': cxph.sample.data[0],
'units': 'sqrt(counts)'
},
)
f.add_entry(sample)
probe = DataExchangeEntry.sample(
root='/simulation',
entry_name='probe',
)
for mode in range(CXP.reconstruction.probe_modes):
setattr(probe, 'mode_{:d}'.format(mode), {
'value': cxph.input_probe.modes[mode].data[0],
'units': 'counts'
})
f.add_entry(probe)
detector = DataExchangeEntry.detector(
root='/simulation',
x_pixel_size={'value': CXP.experiment.dx_d},
y_pixel_size={'value': CXP.experiment.dx_d},
x_dimension={'value': CXP.experiment.px},
y_dimension={'value': CXP.experiment.py},
distance={'value': CXP.experiment.z},
basis_vectors={
'value': [[0, -CXP.experiment.dx_d, 0],
[-CXP.experiment.dx_d, 0, 0]]
},
corner_position={'value': [0, 0, 0]})
f.add_entry(detector)
data = DataExchangeEntry.data(
name={'value': 'simulated_data'},
data={
'value': sp.array(cxph.det_mod.data),
'axes': 'translation:y:x',
'units': 'counts',
'dataset_opts': {
'compression': 'gzip',
'compression_opts': 4
}
},
translation={'value': '/exchange/sample/geometry/translation'})
f.add_entry(data)
# Get scan positions into dex format
pos = sp.zeros((cxph.positions.total, 3))
y, x = cxph.positions.correct
for i in range(cxph.positions.total):
pos[i, 0], pos[i, 1] = x[i] * CXP.dx_s, y[i] * CXP.dx_s
positions = DataExchangeEntry.translation(
root='/exchange/sample/geometry',
name={'value': 'ptychography scan positions'},
scan_type={'value': CXP.measurement.ptycho_scan_type},
data={
'value': pos,
'units': 'm'
})
f.add_entry(positions)
f.close()
def pack_data_exchange():
f = DataExchangeFile(CXP.io.data_exchange_filename, mode='w')
sim = DataExchangeEntry.simulation(
name={'value': 'Simulated Ptycho Data.'},
energy={'value': CXP.experiment.energy, 'units':'keV'},
focusing_optic={'value': CXP.experiment.optic},
probe_modes={'value':CXP.reconstruction.probe_modes},
noise_model={'value': CXP.simulation.noise_model},
gaussian_noise_level={'value': CXP.simulation.gaussian_noise_level},
total_photons={'value': CXP.simulation.total_photons},
beam_stop={'value': CXP.simulation.beam_stop},
beam_stop_size={'value':CXP.simulation.beam_stop_size},
beam_stop_attenuation={'value':CXP.simulation.beam_stop_attenuation},
defocus = {'value':CXP.simulation.defocus},
position_jitter={'value': CXP.reconstruction.initial_position_jitter_radius, 'units':'pixels'}
)
f.add_entry(sim)
sample = DataExchangeEntry.sample(
root='/simulation',
name={'value':'ground truth sample complex amplitude'},
data={'value': cxph.sample.data[0], 'units':'sqrt(counts)'},
)
f.add_entry(sample)
probe = DataExchangeEntry.sample(
root='/simulation',
entry_name='probe',
)
for mode in range(CXP.reconstruction.probe_modes):
setattr(probe, 'mode_{:d}'.format(mode), {'value': cxph.input_probe.modes[mode].data[0], 'units':'counts'})
f.add_entry(probe)
detector = DataExchangeEntry.detector(
root='/simulation',
x_pixel_size={'value': CXP.experiment.dx_d},
y_pixel_size={'value': CXP.experiment.dx_d},
x_dimension={'value': CXP.experiment.px},
y_dimension={'value': CXP.experiment.py},
distance={'value': CXP.experiment.z},
basis_vectors={'value': [[0,-CXP.experiment.dx_d,0],[-CXP.experiment.dx_d,0,0]]},
corner_position={'value': [0,0,0]}
)
f.add_entry(detector)
data = DataExchangeEntry.data(
name={'value': 'simulated_data'},
data={'value': sp.array(cxph.det_mod.data), 'axes':'translation:y:x', 'units':'counts',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4}},
translation={'value':'/exchange/sample/geometry/translation'}
)
f.add_entry(data)
# Get scan positions into dex format
pos = sp.zeros((cxph.positions.total, 3))
y, x = cxph.positions.correct
for i in range(cxph.positions.total):
pos[i,0], pos[i, 1] = x[i]*CXP.dx_s, y[i]*CXP.dx_s
positions = DataExchangeEntry.translation(
root='/exchange/sample/geometry',
name={'value':'ptychography scan positions'},
scan_type={'value': CXP.measurement.ptycho_scan_type},
data={'value': pos, 'units': 'm'}
)
f.add_entry(positions)
f.close()
