def write_example(filename):
# --- prepare data ---
# Generate fake raw data
rawdata = np.ones(180 * 256 * 256, np.uint16).reshape(180, 256, 256)
rawdata_white = np.ones(2 * 256 * 256, np.uint16).reshape(2, 256, 256)
rawdata_dark = np.zeros(10 * 256 * 256, np.uint16).reshape(10, 256, 256)
# Generate fake normalized data
normalizeddata = np.ones(180 * 256 * 256, \
np.float64).reshape(180, 256, 256)
# Generate fake reconstructed data
reconstructeddata = np.ones(256 * 256 * 256, \
np.float64).reshape(256, 256, 256)
# x, y and z ranges
x = np.arange(128)
y = np.arange(128)
z = np.arange(180);
# Fabricated theta values
theta = (z / float(180)) * 180.0
theta_white = (0.0, 180.0)
theta_dark = (0.0, 0.0, 0.0, 0.0, 0.0, 180.0, 180.0, 180.0, 180.0, 180.0)
# Fabricated data_shift_x and data_shift_y value
data_shift_x = np.random.randint(-100, 100, size=180)
data_shift_y = np.random.randint(-100, 100, size=180)
# --- create file ---
print filename
# Open DataExchange file
f = DataExchangeFile(filename, mode='w')
# Create core HDF5 dataset in exchange group for 180 deep stack
# of x,y images /exchange/data
f.add_entry( DataExchangeEntry.data(data={'value': rawdata, 'units':'counts', 'description': 'transmission', 'axes':'theta:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(title={'value': 'tomography_raw_projections'}))
f.add_entry( DataExchangeEntry.data(data_dark={'value':rawdata_dark, 'units':'counts', 'axes':'theta_dark:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(data_white={'value': rawdata_white, 'units':'counts', 'axes':'theta_white:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(theta={'value': theta, 'units':'degrees'}))
f.add_entry( DataExchangeEntry.data(theta_dark={'value': theta_dark, 'units':'degrees'}))
f.add_entry( DataExchangeEntry.data(theta_white={'value': theta_white, 'units':'degrees'}))
f.add_entry( DataExchangeEntry.data(data_shift_x={'value': data_shift_x}))
f.add_entry( DataExchangeEntry.data(data_shift_y={'value': data_shift_y}))
# Exchange HDF5 group
# /exchange_2
# this will be the out_put of the normalization process
f.add_entry( DataExchangeEntry.data(root='exchange_2', title={'value': 'tomography normalized projections'}) )
f.add_entry( DataExchangeEntry.data(root='exchange_2', data={'value': normalizeddata, 'units':'counts', 'axes':'theta:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(root='exchange_2', theta={'value': theta, 'units':'degrees'}))
# Exchange HDF5 group
# /exchange_3
# this will be the out_put of the reconstruction process
f.add_entry( DataExchangeEntry.data(root='exchange_3', title={'value': 'tomography reconstructions'}) )
f.add_entry( DataExchangeEntry.data(root='exchange_3', data={'value': reconstructeddata, 'units':'density', 'axes':'z:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
# Create HDF5 group measurement
# /measuremen
f.add_entry( DataExchangeEntry.instrument(name={'value': 'APS 2-BM'}) )
# Create HDF5 subgroup
# /measurement/instrument/source
f.add_entry( DataExchangeEntry.source(name={'value': 'APS'},
date_time={'value': "2012-07-31T21:15:23+0600"},
beamline={'value': "2-BM"},
current={'value': 101.199, 'units': 'mA', 'dataset_opts': {'dtype': 'd'}},
energy={'value': 7.0, 'units':'GeV', 'dataset_opts': {'dtype': 'd'}},
mode={'value':'TOPUP'}
)
)
# Create HDF5 subgroup
# /measurement/instrument/attenuator
f.add_entry( DataExchangeEntry.attenuator(thickness={'value': 1e-3, 'units': 'm', 'dataset_opts': {'dtype': 'd'}},
type={'value': 'Al'}
)
)
# Create HDF5 subgroup
# /measurement/instrument/monochromator
f.add_entry( DataExchangeEntry.monochromator(type={'value': 'Multilayer'},
energy={'value': 19.26, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
energy_error={'value': 1e-3, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
mono_stripe={'value': 'Ru/C'},
)
)
# Create HDF5 subgroup
# /measurement/instrument/detector
f.add_entry( DataExchangeEntry.detector(manufacturer={'value':'CooKe Corporation'},
model={'value': 'pco dimax'},
serial_number={'value': '1234XW2'},
bit_depth={'value': 12, 'dataset_opts': {'dtype': 'd'}},
x_pixel_size={'value': 6.7e-6, 'dataset_opts': {'dtype': 'f'}},
y_pixel_size={'value': 6.7e-6, 'dataset_opts': {'dtype': 'f'}},
x_dimensions={'value': 2048, 'dataset_opts': {'dtype': 'i'}},
y_dimensions={'value': 2048, 'dataset_opts': {'dtype': 'i'}},
x_binning={'value': 1, 'dataset_opts': {'dtype': 'i'}},
y_binning={'value': 1, 'dataset_opts': {'dtype': 'i'}},
operating_temperature={'value': 270, 'units':'K', 'dataset_opts': {'dtype': 'f'}},
exposure_time={'value': 170, 'units':'ms', 'dataset_opts': {'dtype': 'd'}},
frame_rate={'value': 3, 'dataset_opts': {'dtype': 'i'}},
output_data={'value':'/exchange'}
)
)
f.add_entry( DataExchangeEntry.roi(name={'value':'Center Third'},
x1={'value':256, 'dataset_opts': {'dtype': 'i'}},
x2={'value':1792, 'dataset_opts': {'dtype': 'i'}},
y1={'value':256, 'dataset_opts': {'dtype': 'i'}},
y2={'value':1792, 'dataset_opts': {'dtype': 'i'}},
)
)
f.add_entry(DataExchangeEntry.objective(manufacturer={'value':'Zeiss'},
model={'value':'Plan-NEOFLUAR 1004-072'},
magnification={'value':20, 'dataset_opts': {'dtype': 'd'}},
numerical_aperture={'value':0.5, 'dataset_opts': {'dtype': 'd'}},
)
)
f.add_entry(DataExchangeEntry.scintillator(manufacturer={'value':'Crytur'},
serial_number={'value':'12'},
name={'value':'YAG polished'},
type={'value':'YAG on YAG'},
scintillating_thickness={'value':5e-6, 'dataset_opts': {'dtype': 'd'}},
substrate_thickness={'value':1e-4, 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/sample
f.add_entry( DataExchangeEntry.sample( name={'value':'Hornby_b'},
description={'value':'test sample'},
preparation_date={'value':'2011-07-31T21:15:23+0600'},
chemical_formula={'value':'unknown'},
mass={'value':0.25, 'units':'g', 'dataset_opts': {'dtype': 'd'}},
enviroment={'value':'air'},
temperature={'value':120.0, 'units':'Celsius', 'dataset_opts': {'dtype': 'd'}},
temperature_set={'value':130.0, 'units':'Celsius', 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/sample/geometry/translation
f.add_entry( DataExchangeEntry.translation(root='/measurement/sample/geometry',
distances={'value':[0,0,0],'axes':'z:y:x', 'units':'m', 'dataset_opts': {'dtype': 'd'}}
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"John Doe"},
role={'value':"Project PI"},
affiliation={'value':"University of California, Berkeley"},
address={'value':"EPS UC Berkeley CA 94720 4767 USA"},
phone={'value':"+1 123 456 0000"},
email={'value':"*****@*****.**"},
facility_user_id={'value':"a123456"},
)
)
# Create HDF5 subgroup
# /measurement/experiment
f.add_entry( DataExchangeEntry.experiment( proposal={'value':"1234"},
activity={'value':"e11218"},
safety={'value':"9876"},
)
)
# --- All done ---
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()
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()
