def convert(params):
head_tail = os.path.split(params.old_projection_file_name)
new_hdf_file_name = head_tail[0] + os.sep + os.path.splitext(
head_tail[1])[0] + '.h5'
print('converting data file: %s in new format: %s' %
(params.old_projection_file_name, new_hdf_file_name))
print('using %s as dark and %s as white field' %
(params.old_dark_file_name, params.old_white_file_name))
exchange_base = "exchange"
tomo_grp = '/'.join([exchange_base, 'data'])
flat_grp = '/'.join([exchange_base, 'data_white'])
dark_grp = '/'.join([exchange_base, 'data_dark'])
theta_grp = '/'.join([exchange_base, 'theta'])
tomo = dxreader.read_hdf5(params.old_projection_file_name, tomo_grp)
flat = dxreader.read_hdf5(params.old_white_file_name, flat_grp)
dark = dxreader.read_hdf5(params.old_dark_file_name, dark_grp)
theta = dxreader.read_hdf5(params.old_projection_file_name, theta_grp)
# Open DataExchange file
f = dx.File(new_hdf_file_name, mode='w')
f.add_entry(dx.Entry.data(data={'value': tomo, 'units': 'counts'}))
f.add_entry(dx.Entry.data(data_white={'value': flat, 'units': 'counts'}))
f.add_entry(dx.Entry.data(data_dark={'value': dark, 'units': 'counts'}))
f.add_entry(dx.Entry.data(theta={'value': theta, 'units': 'degrees'}))
f.close()
def write_dxfile(fname, proj, theta, element):
experimenter_affiliation = "Argonne National Laboratory"
instrument_name = "2-ID-E XRF"
sample_name = "test data set"
flat = ones([1, proj.shape[1], proj.shape[2]]) * np.nanmax(proj)
dark = zeros([1, proj.shape[1], proj.shape[2]])
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(
dx.Entry.experimenter(affiliation={'value': experimenter_affiliation}))
f.add_entry(dx.Entry.instrument(name={'value': instrument_name}))
f.add_entry(dx.Entry.sample(name={'value': sample_name}))
f.add_entry(
dx.Entry.data(data={
'value': proj,
'element': element,
'units': 'counts'
}))
f.add_entry(dx.Entry.data(data_white={'value': flat, 'units': 'counts'}))
f.add_entry(dx.Entry.data(data_dark={'value': dark, 'units': 'counts'}))
f.add_entry(dx.Entry.data(theta={'value': theta, 'units': 'degrees'}))
f.close()
def save_dxhdf(self, data, element_names, thetas):
'''
saves all selected information to a new data exchange hdf5 file following the
dxfile definition at http://dxfile.readthedocs.io/
uncomment import dxfile.dxtomo as dx
'''
try:
fname = QtGui.QFileDialog.getSaveFileName()[0]
if fname == "":
raise IOError
experimenter_affiliation = "Argonne National Laboratory"
instrument_name = "2-ID-E XRF"
sample_name = "test data set"
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(
dx.Entry.experimenter(
affiliation={'value': experimenter_affiliation}))
f.add_entry(dx.Entry.instrument(name={'value': instrument_name}))
f.add_entry(dx.Entry.sample(name={'value': sample_name}))
f.add_entry(dx.Entry.data(data={
'value': data,
'units': 'ug/cm^2'
}))
f.add_entry(
dx.Entry.data(theta={
'value': thetas,
'units': 'degrees'
}))
# file_names = [x.encode('utf-8') for x in file_names]
# f.add_entry(dx.Entry.data(fnames={'value': file_names, 'units':'none'}))
element_names = [x.encode('utf-8') for x in element_names]
f.add_entry(
dx.Entry.data(elements={
'value': element_names,
'units': 'none'
}))
f.close()
except IOError:
print("ERROR saving sinogram stack")
except:
print("Something went horribly wrong.")
pass
def main():
fname = './demo.h5'
experimenter_name = "Francesco De Carlo"
experimenter_affiliation = "Argonne National Laboratory"
experimenter_email = "*****@*****.**"
instrument_comment = "32-ID TXM"
sample_name = 'sample_name'
size = 180
theta = range(0, 180, 180 / size)
if (fname != None):
if os.path.isfile(fname):
print "Data Exchange file already exists: ", fname
else:
# Create new folder.
dirPath = os.path.dirname(fname)
if not os.path.exists(dirPath):
os.makedirs(dirPath)
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(
dx.Entry.experimenter(name={'value': experimenter_name}))
f.add_entry(
dx.Entry.experimenter(
affiliation={'value': experimenter_affiliation}))
f.add_entry(
dx.Entry.experimenter(email={'value': experimenter_email}))
f.add_entry(
dx.Entry.instrument(comment={'value': instrument_comment}))
f.add_entry(dx.Entry.sample(name={'value': sample_name}))
f.add_entry(
dx.Entry.data(theta={
'value': theta,
'units': 'degrees'
}))
f.close()
else:
print "Nothing to do ..."
def write_dxfile(fname, proj, theta, elem):
experimenter_affiliation = "Argonne National Laboratory"
instrument_name = "2-ID-E XRF"
sample_name = "test data set"
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(
dx.Entry.experimenter(affiliation={'value': experimenter_affiliation}))
f.add_entry(dx.Entry.instrument(name={'value': instrument_name}))
f.add_entry(dx.Entry.sample(name={'value': sample_name}))
f.add_entry(dx.Entry.data(data={'value': proj, 'units': 'ug/cm^2'}))
f.add_entry(dx.Entry.data(theta={'value': theta, 'units': 'degrees'}))
elem = [x.encode('utf-8') for x in elem]
f.add_entry(dx.Entry.data(elements={'value': elem, 'units': 'ug/cm^2'}))
f.close()
# Write ground_truth
ground_truth = discrete_phantom(phantom, ccd_x, prop='mass_atten')
fname_gt='tomobank/phantoms/' + tomobank_id + '/' + tomobank_id + '_ground_truth'
dxchange.write_tiff(ground_truth, fname=fname_gt, dtype='float32')
# Save into a data-exchange file.
if os.path.isfile(fname):
print ("Data Exchange file already exists: ", fname)
else:
# Create new folder.
dirPath = os.path.dirname(fname)
if not os.path.exists(dirPath):
os.makedirs(dirPath)
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(dx.Entry.experimenter(affiliation={'value': experimenter_affiliation}))
f.add_entry(dx.Entry.experimenter(email={'value': experimenter_email}))
f.add_entry(dx.Entry.instrument(name={'value': instrument_name}))
f.add_entry(dx.Entry.sample(name={'value': sample_name}))
f.add_entry(dx.Entry.data(data={'value': proj, 'units':'counts'}))
f.add_entry(dx.Entry.data(data_white={'value': flat, 'units':'counts'}))
f.add_entry(dx.Entry.data(data_dark={'value': dark, 'units':'counts'}))
f.add_entry(dx.Entry.data(theta={'value': theta, 'units':'degrees'}))
f.add_entry(dx.Entry.data(ground_truth={'value': ground_truth, 'units':'counts'}))
f.add_entry(dx.Entry.acquisition(start_date={'value': start_date}))
f.add_entry(dx.Entry.acquisition(end_date={'value': end_date}))
def save_dx(fname, proj, flat, dark, theta):
sample_name = fname
experiment_prosal = 'GUP-53902'
experiment_title = 'Investigating the Phase and Kirkendall Pore Evolution in Ti-coated Ni Wires using X-Ray Tomographic Microscopy'
experimenter_name = 'Ashley Paz y Puente'
experimenter_role = 'PI'
experimenter_affiliation = 'Northwestern University, University of Cincinnati'
experimenter_phone = '847-467-5416'
experimenter_email = '*****@*****.**'
experimenter_facility_user_id = '233967'
instrument_name = '2-BM micro-CT'
instrument_comment = 'A Hutch'
attenuator_name = 'filter'
attenuator_description = '1mm C, 4mm Glass, 1mm Si'
monochromator_name = 'DMM'
monochromator_description = '2.657mrad USArm; 1.349_monoY -9.999'
detector_name = 'PCO.edge'
detector_shutter_mode = 'rolling'
detector_exposure_time = 0.020
detector_description = 'sample to detector distance = 50 mm'
objective_magnification = 10
scintillator_name = 'LuAG'
scintillator_scintillating_thickness = 20
sample_detector_distance = 0.050
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(dx.Entry.sample( name={'value':sample_name}))
f.add_entry(dx.Entry.experiment( proposal={'value':experiment_prosal}))
f.add_entry(dx.Entry.experiment( title={'value':experiment_title}))
f.add_entry(dx.Entry.experimenter(name={'value':experimenter_name}))
f.add_entry(dx.Entry.experimenter(role={'value':experimenter_role}))
f.add_entry(dx.Entry.experimenter(affiliation={'value':experimenter_affiliation}))
f.add_entry(dx.Entry.experimenter(phone={'value':experimenter_phone}))
f.add_entry(dx.Entry.experimenter(email={'value':experimenter_email}))
f.add_entry(dx.Entry.experimenter(facility_user_id={'value':experimenter_facility_user_id}))
f.add_entry(dx.Entry.instrument(name={'value':instrument_name}))
f.add_entry(dx.Entry.instrument(comment={'value':instrument_comment}))
f.add_entry(dx.Entry.monochromator( name={'value':monochromator_name}))
f.add_entry(dx.Entry.monochromator( description={'value':monochromator_description}))
f.add_entry(dx.Entry.attenuator( name={'value':attenuator_name}))
f.add_entry(dx.Entry.attenuator( description={'value':attenuator_description}))
f.add_entry(dx.Entry.detector(name={'value':detector_name}))
f.add_entry(dx.Entry.detector(description={'value':detector_description}))
f.add_entry(dx.Entry.detector(exposure_time={'value':detector_exposure_time}))
f.add_entry(dx.Entry.detector(shutter_mode={'value':detector_shutter_mode}))
f.add_entry(dx.Entry.objective(magnification={'value':objective_magnification}))
f.add_entry(dx.Entry.scintillator(name={'value':scintillator_name}))
f.add_entry(dx.Entry.scintillator(scintillating_thickness={'value':scintillator_scintillating_thickness, 'units':'um'}))
f.add_entry(dx.Entry.data(data={'value': proj, 'units':'counts'}))
f.add_entry(dx.Entry.data(data_white={'value': flat, 'units':'counts'}))
f.add_entry(dx.Entry.data(data_dark={'value': dark, 'units':'counts'}))
f.add_entry(dx.Entry.data(theta={'value': theta, 'units':'degrees'}))
f.close()
def main():
fname = './demo.h5'
ccd_x, ccd_y = 128, 128
sample_name = 'sample_name'
sample_description = 'sample description'
sample_preparation_date = iso_time()
sample_chemical_formula = 'H2O'
sample_mass = '1234'
sample_concentration = '1234'
sample_environment = '1234'
sample_temperature = '1234'
sample_temperature_set = '1234'
sample_pressure = '1234'
sample_thickness = '1234'
sample_tray = 'A5'
sample_comment = 'sample comment'
experiment_prosal = '1234'
experiment_activity = '5678'
experiment_safety = '9012'
experiment_title = '4D Dynamics of Stress Corrosion Cracking in High Performance Aluminum Alloy'
experimenter_name = 'Joe'
experimenter_role = 'PI'
experimenter_affiliation = 'Argonne National Laboratory'
experimenter_address = '9700 S. Cass Av.'
experimenter_phone = '1-123-456-7890'
experimenter_email = '*****@*****.**'
experimenter_facility_user_id = '1234'
instrument_name = '32-ID TXM'
instrument_comment = 'nice instrument'
source_name = 'APS'
source_datetime = iso_time()
source_beamline = 'U18'
source_current = '100'
source_energy = '123'
source_pulse_energy = '45'
source_pulse_width = '67'
source_mode = 'top-up'
source_beam_intensity_incident = '123'
source_beam_intensity_transmitted = '456'
attenuator_name = 'filter'
attenuator_description = 'a nice filter'
attenuator_thickness = 1
attenuator_transmission = 0.754
monochromator_name = 'mono'
monochromator_description = 'a nice mono'
monochromator_energy = 27.5
monochromator_energy_units = 'keV'
monochromator_energy_error = '456'
monochromator_mono_stripe = 'Au/Ag'
mirror_name = 'mirror'
mirror_description = 'a nice mirror'
mirror_angle = 2.657
mirror_angle_units = 'rad'
detector_name = 'camera'
detector_description = 'a nice camera'
detector_manufacturer = 'a nice company'
detector_model = '123'
detector_serial_number = '456'
detector_firmware_version = '789'
detector_software_version = '012'
detector_bit_dept = '16'
detector_pixel_size_x = 0.65e-4
detector_pixel_size_y = 0.65e-4
detector_actual_pixel_size_x = 1.2
detector_actual_pixel_size_y = 1.2
detector_dimension_x = ccd_x
detector_dimension_y = ccd_y
detector_binning_x = 1
detector_binning_y = 1
detector_operating_temperature = 12
detector_exposure_time = 0.2
detector_delay_time = 0.001
detector_stabilization_time = 0.0001
detector_frame_rate = 160
detector_shutter_mode = 'global'
detector_output_data = '/exchange'
detector_counts_per_joule = '123'
detector_basis_vectors = '456'
detector_corner_position = '789'
detector_roi_name = 'roi'
detector_roi_description = 'a nice roi'
detector_roi_min_x = 0
detector_roi_min_y = 0
detector_roi_size_x = ccd_x
detector_roi_size_y = ccd_y
objective_name = 'objective'
objective_description = 'a nice objective'
objective_manufacturer = 'a nice company'
objective_model = 'a nice model'
objective_magnification = 1.5
objective_numerical_aperture = 0.8
scintillator_name = 'scintillator'
scintillator_description = 'a nice scintillator'
scintillator_manufacturer = 'a nice company'
scintillator_serial_number = '123'
scintillator_scintillating_thickness = 456
scintillator_substrate_thickness = 789
sample_stack_name = 'sample stack'
sample_stack_description = 'a nice sample stack'
sample_stack_setup_sample_x = 1
sample_stack_setup_sample_y = 2
sample_stack_setup_sample_z = 3
sample_stack_setup_sample_xx = 11
sample_stack_setup_sample_zz = 33
sample_detector_distance = 60
interferometer_name = 'interferometer'
interferometer_description = 'a nice interferometer'
interferometer_setup_grid_start = 123
interferometer_setup_grid_end = 456
interferometer_setup_number_of_grid_periods = 789
interferometer_setup_number_of_grid_steps = 123
process_name = 'the best process'
acquisition_sample_position_x = np.random.rand(180)
acquisition_sample_position_y = np.random.rand(180)
acquisition_sample_position_z = np.random.rand(180)
acquisition_sample_image_shift_x = np.random.rand(180)
acquisition_sample_image_shift_y = np.random.rand(180)
acquisition_image_theta = range(0, 180, 1)
acquisition_scan_index = range(0, 180, 1)
acquisition_scan_date = [iso_time() for x in range(180)]
acquisition_image_date = [iso_time() for x in range(180)]
acquisition_time_stamp = [iso_time() for x in range(180)]
acquisition_image_number = range(0, 180, 1)
acquisition_image_exposure_time = np.ones(180) * detector_exposure_time
acquisition_image_is_complete = np.ones(180)
acquisition_shutter = np.ones(180)
acquisition_image_type = np.ones(180)
acquisition_start_date = iso_time()
acquisition_end_date = iso_time()
acquisition_setup_number_of_projections = 180
acquisition_setup_number_of_darks = 10
acquisition_setup_number_of_whites = 10
acquisition_setup_number_of_inter_whites = 1
acquisition_setup_white_frequency = 1
acquisition_setup_sample_in = 0
acquisition_setup_sample_out = 4
acquisition_setup_rotation_start_angle = 0
acquisition_setup_rotation_end_angle = 180
acquisition_setup_rotation_speed = 0.750
acquisition_setup_angular_step = (
acquisition_setup_rotation_end_angle -
acquisition_setup_rotation_start_angle) / 180
acquisition_setup_mode = 'fly scan'
acquisition_setup_comment = 'a nice fly scan'
data = np.random.rand(180, ccd_y, ccd_x)
data_white = np.ones((acquisition_setup_number_of_whites, ccd_y,
ccd_x)) # Array filled with zeros
data_dark = np.zeros((acquisition_setup_number_of_darks, ccd_y,
ccd_x)) # Array filled with zeros
theta = range(0, 180, 1)
if (fname != None):
if os.path.isfile(fname):
print "Data Exchange file already exists: ", fname
else:
# Create new folder.
dirPath = os.path.dirname(fname)
if not os.path.exists(dirPath):
os.makedirs(dirPath)
# Open DataExchange file
f = dx.File(fname, mode='w')
# Write the Data Exchange HDF5 file.
f.add_entry(dx.Entry.sample(name={'value': sample_name}))
f.add_entry(
dx.Entry.sample(description={'value': sample_description}))
f.add_entry(
dx.Entry.sample(
preparation_date={'value': sample_preparation_date}))
f.add_entry(
dx.Entry.sample(
chemical_formula={'value': sample_chemical_formula}))
f.add_entry(dx.Entry.sample(mass={'value': sample_mass}))
f.add_entry(
dx.Entry.sample(concentration={'value': sample_concentration}))
f.add_entry(
dx.Entry.sample(environment={'value': sample_environment}))
f.add_entry(
dx.Entry.sample(temperature={'value': sample_temperature}))
f.add_entry(
dx.Entry.sample(
temperature_set={'value': sample_temperature_set}))
f.add_entry(dx.Entry.sample(pressure={'value': sample_pressure}))
f.add_entry(dx.Entry.sample(thickness={'value': sample_thickness}))
f.add_entry(dx.Entry.sample(tray={'value': sample_tray}))
f.add_entry(dx.Entry.sample(comment={'value': sample_comment}))
f.add_entry(
dx.Entry.experiment(proposal={'value': experiment_prosal}))
f.add_entry(
dx.Entry.experiment(activity={'value': experiment_activity}))
f.add_entry(
dx.Entry.experiment(safety={'value': experiment_safety}))
f.add_entry(dx.Entry.experiment(title={'value': experiment_title}))
f.add_entry(
dx.Entry.experimenter(name={'value': experimenter_name}))
f.add_entry(
dx.Entry.experimenter(role={'value': experimenter_role}))
f.add_entry(
dx.Entry.experimenter(
affiliation={'value': experimenter_affiliation}))
f.add_entry(
dx.Entry.experimenter(address={'value': experimenter_address}))
f.add_entry(
dx.Entry.experimenter(phone={'value': experimenter_phone}))
f.add_entry(
dx.Entry.experimenter(email={'value': experimenter_email}))
f.add_entry(
dx.Entry.experimenter(
facility_user_id={'value': experimenter_facility_user_id}))
f.add_entry(dx.Entry.instrument(name={'value': instrument_name}))
f.add_entry(
dx.Entry.instrument(comment={'value': instrument_comment}))
f.add_entry(dx.Entry.source(name={'value': source_name}))
f.add_entry(dx.Entry.source(datetime={'value': source_datetime}))
f.add_entry(dx.Entry.source(beamline={'value': source_beamline}))
f.add_entry(dx.Entry.source(current={'value': source_current}))
f.add_entry(dx.Entry.source(energy={'value': source_energy}))
f.add_entry(
dx.Entry.source(pulse_energy={'value': source_pulse_energy}))
f.add_entry(
dx.Entry.source(pulse_width={'value': source_pulse_width}))
f.add_entry(dx.Entry.source(mode={'value': source_mode}))
f.add_entry(
dx.Entry.source(beam_intensity_incident={
'value': source_beam_intensity_incident
}))
f.add_entry(
dx.Entry.source(beam_intensity_transmitted={
'value': source_beam_intensity_transmitted
}))
f.add_entry(dx.Entry.attenuator(name={'value': attenuator_name}))
f.add_entry(
dx.Entry.attenuator(
description={'value': attenuator_description}))
f.add_entry(
dx.Entry.attenuator(thickness={
'value': attenuator_thickness,
'units': 'mm'
}))
f.add_entry(
dx.Entry.attenuator(
transmission={'value': attenuator_transmission}))
f.add_entry(
dx.Entry.monochromator(name={'value': monochromator_name}))
f.add_entry(
dx.Entry.monochromator(
description={'value': monochromator_description}))
f.add_entry(
dx.Entry.monochromator(
energy={
'value': monochromator_energy,
'units': monochromator_energy_units
}))
f.add_entry(
dx.Entry.monochromator(
energy_error={'value': monochromator_energy_error}))
f.add_entry(
dx.Entry.monochromator(
mono_stripe={'value': monochromator_mono_stripe}))
f.add_entry(dx.Entry.mirror(name={'value': mirror_name}))
f.add_entry(
dx.Entry.mirror(description={'value': mirror_description}))
f.add_entry(
dx.Entry.mirror(angle={
'value': mirror_angle,
'units': mirror_angle_units
}))
f.add_entry(dx.Entry.detector(name={'value': detector_name}))
f.add_entry(
dx.Entry.detector(description={'value': detector_description}))
f.add_entry(
dx.Entry.detector(
manufacturer={'value': detector_manufacturer}))
f.add_entry(dx.Entry.detector(model={'value': detector_model}))
f.add_entry(
dx.Entry.detector(
serial_number={'value': detector_serial_number}))
f.add_entry(
dx.Entry.detector(
firmware_version={'value': detector_firmware_version}))
f.add_entry(
dx.Entry.detector(
software_version={'value': detector_software_version}))
f.add_entry(
dx.Entry.detector(bit_dept={'value': detector_bit_dept}))
f.add_entry(
dx.Entry.detector(pixel_size_x={
'value': detector_pixel_size_x,
'units': 'm'
}))
f.add_entry(
dx.Entry.detector(pixel_size_y={
'value': detector_pixel_size_y,
'units': 'm'
}))
f.add_entry(
dx.Entry.detector(actual_pixel_size_x={
'value': detector_actual_pixel_size_x,
'units': 'um'
}))
f.add_entry(
dx.Entry.detector(actual_pixel_size_y={
'value': detector_actual_pixel_size_y,
'units': 'um'
}))
f.add_entry(
dx.Entry.detector(dimension_x={'value': detector_dimension_x}))
f.add_entry(
dx.Entry.detector(dimension_y={'value': detector_dimension_y}))
f.add_entry(
dx.Entry.detector(binning_x={'value': detector_binning_x}))
f.add_entry(
dx.Entry.detector(binning_y={'value': detector_binning_y}))
f.add_entry(
dx.Entry.detector(operating_temperature={
'value': detector_operating_temperature
}))
f.add_entry(
dx.Entry.detector(
exposure_time={'value': detector_exposure_time}))
f.add_entry(
dx.Entry.detector(delay_time={'value': detector_delay_time}))
f.add_entry(
dx.Entry.detector(
stabilization_time={'value': detector_stabilization_time}))
f.add_entry(
dx.Entry.detector(frame_rate={'value': detector_frame_rate}))
f.add_entry(
dx.Entry.detector(
shutter_mode={'value': detector_shutter_mode}))
f.add_entry(
dx.Entry.detector(output_data={'value': detector_output_data}))
f.add_entry(
dx.Entry.detector(
counts_per_joule={'value': detector_counts_per_joule}))
f.add_entry(
dx.Entry.detector(
basis_vectors={'value': detector_basis_vectors}))
f.add_entry(
dx.Entry.detector(
corner_position={'value': detector_corner_position}))
f.add_entry(dx.Entry.roi(name={'value': detector_roi_name}))
f.add_entry(
dx.Entry.roi(description={'value': detector_roi_description}))
f.add_entry(dx.Entry.roi(min_x={'value': detector_roi_min_x}))
f.add_entry(dx.Entry.roi(min_y={'value': detector_roi_min_y}))
f.add_entry(dx.Entry.roi(size_x={'value': detector_roi_size_x}))
f.add_entry(dx.Entry.roi(size_y={'value': detector_roi_size_y}))
f.add_entry(dx.Entry.objective(name={'value': objective_name}))
f.add_entry(
dx.Entry.objective(
description={'value': objective_description}))
f.add_entry(
dx.Entry.objective(
manufacturer={'value': objective_manufacturer}))
f.add_entry(dx.Entry.objective(model={'value': objective_model}))
f.add_entry(
dx.Entry.objective(
magnification={'value': objective_magnification}))
f.add_entry(
dx.Entry.objective(
numerical_aperture={'value': objective_numerical_aperture
}))
f.add_entry(
dx.Entry.scintillator(name={'value': scintillator_name}))
f.add_entry(
dx.Entry.scintillator(
description={'value': scintillator_description}))
f.add_entry(
dx.Entry.scintillator(
manufacturer={'value': scintillator_manufacturer}))
f.add_entry(
dx.Entry.scintillator(
serial_number={'value': scintillator_serial_number}))
f.add_entry(
dx.Entry.scintillator(scintillating_thickness={
'value': scintillator_scintillating_thickness,
'units': 'um'
}))
f.add_entry(
dx.Entry.scintillator(substrate_thickness={
'value': scintillator_substrate_thickness,
'units': 'um'
}))
f.add_entry(
dx.Entry.sample_stack(name={'value': sample_stack_name}))
f.add_entry(
dx.Entry.sample_stack(
description={'value': sample_stack_description}))
f.add_entry(
dx.Entry.sample_stack_setup(sample_x={
'value': sample_stack_setup_sample_x,
'units': 'mm'
}))
f.add_entry(
dx.Entry.sample_stack_setup(sample_y={
'value': sample_stack_setup_sample_y,
'units': 'mm'
}))
f.add_entry(
dx.Entry.sample_stack_setup(sample_z={
'value': sample_stack_setup_sample_z,
'units': 'mm'
}))
f.add_entry(
dx.Entry.sample_stack_setup(sample_xx={
'value': sample_stack_setup_sample_xx,
'units': 'mm'
}))
f.add_entry(
dx.Entry.sample_stack_setup(sample_zz={
'value': sample_stack_setup_sample_zz,
'units': 'mm'
}))
f.add_entry(
dx.Entry.sample_stack_setup(sample_detector_distance={
'value': sample_detector_distance,
'units': 'mm'
}))
f.add_entry(
dx.Entry.interferometer(name={'value': interferometer_name}))
f.add_entry(
dx.Entry.interferometer(
description={'value': interferometer_description}))
f.add_entry(
dx.Entry.interferometer_setup(
grid_start={'value': interferometer_setup_grid_start}))
f.add_entry(
dx.Entry.interferometer_setup(
grid_end={'value': interferometer_setup_grid_end}))
f.add_entry(
dx.Entry.interferometer_setup(
number_of_grid_periods={
'value': interferometer_setup_number_of_grid_periods
}))
f.add_entry(
dx.Entry.interferometer_setup(
number_of_grid_steps={
'value': interferometer_setup_number_of_grid_steps
}))
f.add_entry(dx.Entry.process(name={'value': process_name}))
f.add_entry(
dx.Entry.acquisition(
sample_position_x={'value': acquisition_sample_position_x
}))
f.add_entry(
dx.Entry.acquisition(
sample_position_y={'value': acquisition_sample_position_y
}))
f.add_entry(
dx.Entry.acquisition(
sample_position_z={'value': acquisition_sample_position_z
}))
f.add_entry(
dx.Entry.acquisition(sample_image_shift_x={
'value': acquisition_sample_image_shift_x
}))
f.add_entry(
dx.Entry.acquisition(sample_image_shift_y={
'value': acquisition_sample_image_shift_y
}))
f.add_entry(
dx.Entry.acquisition(
image_theta={'value': acquisition_image_theta}))
f.add_entry(
dx.Entry.acquisition(
scan_index={'value': acquisition_scan_index}))
f.add_entry(
dx.Entry.acquisition(
scan_date={'value': acquisition_scan_date}))
f.add_entry(
dx.Entry.acquisition(
image_date={'value': acquisition_image_date}))
f.add_entry(
dx.Entry.acquisition(
time_stamp={'value': acquisition_time_stamp}))
f.add_entry(
dx.Entry.acquisition(
image_number={'value': acquisition_image_number}))
f.add_entry(
dx.Entry.acquisition(image_exposure_time={
'value': acquisition_image_exposure_time
}))
f.add_entry(
dx.Entry.acquisition(
image_is_complete={'value': acquisition_image_is_complete
}))
f.add_entry(
dx.Entry.acquisition(shutter={'value': acquisition_shutter}))
f.add_entry(
dx.Entry.acquisition(
image_type={'value': acquisition_image_type}))
f.add_entry(
dx.Entry.acquisition(
start_date={'value': acquisition_start_date}))
f.add_entry(
dx.Entry.acquisition(end_date={'value': acquisition_end_date}))
f.add_entry(
dx.Entry.acquisition_setup(
number_of_projections={
'value': acquisition_setup_number_of_projections
}))
f.add_entry(
dx.Entry.acquisition_setup(
number_of_darks={
'value': acquisition_setup_number_of_darks
}))
f.add_entry(
dx.Entry.acquisition_setup(
number_of_whites={
'value': acquisition_setup_number_of_whites
}))
f.add_entry(
dx.Entry.acquisition_setup(
number_of_inter_whites={
'value': acquisition_setup_number_of_inter_whites
}))
f.add_entry(
dx.Entry.acquisition_setup(
white_frequency={
'value': acquisition_setup_white_frequency
}))
f.add_entry(
dx.Entry.acquisition_setup(
sample_in={'value': acquisition_setup_sample_in}))
f.add_entry(
dx.Entry.acquisition_setup(
sample_out={'value': acquisition_setup_sample_out}))
f.add_entry(
dx.Entry.acquisition_setup(
rotation_start_angle={
'value': acquisition_setup_rotation_start_angle
}))
f.add_entry(
dx.Entry.acquisition_setup(
rotation_end_angle={
'value': acquisition_setup_rotation_end_angle
}))
f.add_entry(
dx.Entry.acquisition_setup(
rotation_speed={'value': acquisition_setup_rotation_speed
}))
f.add_entry(
dx.Entry.acquisition_setup(
angular_step={'value': acquisition_setup_angular_step}))
f.add_entry(
dx.Entry.acquisition_setup(
mode={'value': acquisition_setup_mode}))
f.add_entry(
dx.Entry.acquisition_setup(
comment={'value': acquisition_setup_comment}))
f.add_entry(dx.Entry.data(data={'value': data, 'units': 'counts'}))
f.add_entry(
dx.Entry.data(data_white={
'value': data_white,
'units': 'counts'
}))
f.add_entry(
dx.Entry.data(data_dark={
'value': data_dark,
'units': 'counts'
}))
f.add_entry(
dx.Entry.data(theta={
'value': theta,
'units': 'degrees'
}))
f.close()
else:
print "Nothing to do ..."
