def main():
file_name = "/local/data/databank/Diamond/projections_13429.hdf"
hdf5_file_name = "/local/data/databank/dataExchange/microCT/Diamond_2bin.h5"
mydata = Convert()
# Create minimal hdf5 file
if verbose:
print "Reading data ... "
mydata.nexus(
file_name,
hdf5_file_name=hdf5_file_name,
projections_start=20,
projections_end=1820,
projections_step=2,
white_start=11,
white_end=20,
dark_start=1,
dark_end=3,
sample_name="unknown",
)
# Add extra metadata if available / desired
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode="a")
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry(DataExchangeEntry.instrument(name={"value": "Diamond I12"}))
### Create HDF5 subgroup
### /measurement/instrument/source
f.add_entry(
DataExchangeEntry.source(
name={"value": "Diamond Light Source"},
date_time={"value": "2013-11-30T19:17:04+0100"},
beamline={"value": "JEEP I12"},
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry(DataExchangeEntry.experimenter(name={"value": "Michael Drakopoulos"}, role={"value": "Project PI"}))
f.close()
print "Done creating data exchange file: ", hdf5_file_name
def main():
file_name = '/local/data/databank/Diamond/projections_13429.hdf'
hdf5_file_name = '/local/data/databank/dataExchange/microCT/Diamond_2bin.h5'
mydata = Convert()
# Create minimal hdf5 file
if verbose: print "Reading data ... "
mydata.nexus(file_name,
hdf5_file_name = hdf5_file_name,
projections_start=20,
projections_end=1820,
projections_step=2,
white_start=11,
white_end=20,
dark_start=1,
dark_end=3,
sample_name = 'unknown'
)
# Add extra metadata if available / desired
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry( DataExchangeEntry.instrument(name={'value': 'Diamond I12'}) )
### Create HDF5 subgroup
### /measurement/instrument/source
f.add_entry( DataExchangeEntry.source(name={'value': "Diamond Light Source"},
date_time={'value': "2013-11-30T19:17:04+0100"},
beamline={'value': "JEEP I12"},
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"Michael Drakopoulos"},
role={'value':"Project PI"},
)
)
f.close()
print "Done creating data exchange file: ", hdf5_file_name
def main():
file_name = '/local/data/databank/TXM_26ID/Miller1/ABR_1SP_.tif'
#dark_file_name = '/local/data/databank/AS/Mayo_tooth_AS/BG__AFTER_.tif'
#white_file_name = '/local/data/databank/AS/Mayo_tooth_AS/BG__BEFORE_.tif'
hdf5_file_name = '/local/data/databank/dataExchange/TXM/TXM_APS26IDMiller1.h5'
sample_name = 'Teeth'
projections_start = 0
projections_end = 361
white_start = 0
white_end = 0
white_step = 1
dark_start = 0
dark_end = 0
dark_step = 1
verbose = True
if verbose: print "Input projection base name: ", file_name
#if verbose: print "Input white base name: ", white_file_name
#if verbose: print "Input dark base name: ", dark_file_name
if verbose: print "Output data exchange file name: ", hdf5_file_name
mydata = Convert()
# Create minimal hdf5 file
mydata.series_of_images(file_name,
hdf5_file_name,
projections_start,
projections_end,
#white_file_name = white_file_name,
white_start = white_start,
white_end = white_end,
white_step = white_step,
#dark_file_name = dark_file_name,
#dark_start = dark_start,
#dark_end = dark_end,
#dark_step = dark_step,
#sample_name = sample_name,
projections_digits = 4,
#white_digits = 2,
#dark_digits = 2,
projections_zeros = True,
verbose = False
)
if verbose: print "Done reading data ... "
# Add extra metadata if available
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry( DataExchangeEntry.instrument(name={'value': 'Australian Synchrotron Facility'}) )
# Create HDF5 subgroup
# /measurement/instrument/source
f.add_entry( DataExchangeEntry.source(name={'value': 'Australian Synchrotron FacilityI'},
date_time={'value': "2013-10-19T22:22:13+0100"},
beamline={'value': "Tomography"},
)
)
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"Sherry Mayo"},
role={'value':"Project PI"},
)
)
f.close()
if verbose: print "Done creating data exchange file: ", hdf5_file_name
def main():
file_name = '/local/data/databank/TXM_26ID/20130731_004_Stripe_Solder_Sample_Tip1_TomoScript_181imgs_p1s_b1.txrm'
white_file_name = '/local/data/databank/TXM_26ID/20130731_001_Background_Reference_20imgs_p5s_b1.xrm'
hdf5_file_name = '/local/data/databank/dataExchange/TXM/20130731_004_Stripe_Solder_Sample_Tip1_nx.h5'
log_file = '/local/data/databank/dataExchange/TXM/20130731_004_Stripe_Solder_Sample_Tip1.log'
mydata = Convert()
# Create minimal hdf5 file
if verbose: print "Reading data ... "
mydata.stack(file_name,
hdf5_file_name=hdf5_file_name,
white_file_name=white_file_name,
sample_name='Stripe_Solder_Sample_Tip1')
# Add extra metadata if available / desired
reader = xradia.xrm()
array = dstruct
reader.read_txrm(file_name, array)
# Read angles
n_angles = np.shape(array.exchange.angles)
if verbose: print "Done reading ", n_angles, " angles"
theta = np.zeros(n_angles)
theta = array.exchange.angles[:]
# Save any other available metadata in a log file
f = open(log_file, 'w')
f.write('Data creation date: \n')
f.write(str(array.information.file_creation_datetime))
f.write('\n')
f.write('=======================================\n')
f.write('Sample name: \n')
f.write(str(array.information.sample.name))
f.write('\n')
f.write('=======================================\n')
f.write('Experimenter name: \n')
f.write(str(array.information.experimenter.name))
f.write('\n')
f.write('=======================================\n')
f.write('X-ray energy: \n')
f.write(str(array.exchange.energy))
f.write(str(array.exchange.energy_units))
f.write('\n')
f.write('=======================================\n')
f.write('Angles: \n')
f.write(str(array.exchange.angles))
f.write('\n')
f.write('=======================================\n')
f.write('Data axes: \n')
f.write(str(array.exchange.data_axes))
f.write('\n')
f.write('=======================================\n')
f.write('x distance: \n')
f.write(str(array.exchange.x))
f.write('\n')
f.write('=======================================\n')
f.write('x units: \n')
f.write(str(array.exchange.x_units))
f.write('\n')
f.write('=======================================\n')
f.write('y distance: \n')
f.write(str(array.exchange.y))
f.write('\n')
f.write('=======================================\n')
f.write('y units: \n')
f.write(str(array.exchange.y_units))
f.write('\n')
f.close()
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry(DataExchangeEntry.instrument(name={'value': 'APS-CNM 26-ID'}))
### Create HDF5 subgroup
### /measurement/instrument/source
f.add_entry(
DataExchangeEntry.source(
name={'value': "Advanced Photon Source"},
date_time={'value': "2013-07-31T19:42:13+0100"},
beamline={'value': "26-ID"},
))
# Create HDF5 subgroup
# /measurement/instrument/monochromator
f.add_entry(
DataExchangeEntry.monochromator(
type={'value': 'Unknown'},
energy={
'value': float(array.exchange.energy[0]),
'units': 'keV',
'dataset_opts': {
'dtype': 'd'
}
},
mono_stripe={'value': 'Unknown'},
))
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry(
DataExchangeEntry.experimenter(
name={'value': "Robert Winarski"},
role={'value': "Project PI"},
))
# Create HDF5 subgroup
# /measurement/sample
f.add_entry(
DataExchangeEntry.data(theta={
'value': theta,
'units': 'degrees'
}))
f.close()
print "Done creating data exchange file: ", hdf5_file_name
def main():
file_name = '/local/data/databank/TXM_26ID/Miller1/ABR_1SP_.tif'
#dark_file_name = '/local/data/databank/AS/Mayo_tooth_AS/BG__AFTER_.tif'
#white_file_name = '/local/data/databank/AS/Mayo_tooth_AS/BG__BEFORE_.tif'
hdf5_file_name = '/local/data/databank/dataExchange/TXM/TXM_APS26IDMiller1.h5'
sample_name = 'Teeth'
projections_start = 0
projections_end = 361
white_start = 0
white_end = 0
white_step = 1
dark_start = 0
dark_end = 0
dark_step = 1
verbose = True
if verbose: print "Input projection base name: ", file_name
#if verbose: print "Input white base name: ", white_file_name
#if verbose: print "Input dark base name: ", dark_file_name
if verbose: print "Output data exchange file name: ", hdf5_file_name
mydata = Convert()
# Create minimal hdf5 file
mydata.series_of_images(
file_name,
hdf5_file_name,
projections_start,
projections_end,
#white_file_name = white_file_name,
white_start=white_start,
white_end=white_end,
white_step=white_step,
#dark_file_name = dark_file_name,
#dark_start = dark_start,
#dark_end = dark_end,
#dark_step = dark_step,
#sample_name = sample_name,
projections_digits=4,
#white_digits = 2,
#dark_digits = 2,
projections_zeros=True,
verbose=False)
if verbose: print "Done reading data ... "
# Add extra metadata if available
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry(
DataExchangeEntry.instrument(
name={'value': 'Australian Synchrotron Facility'}))
# Create HDF5 subgroup
# /measurement/instrument/source
f.add_entry(
DataExchangeEntry.source(
name={'value': 'Australian Synchrotron FacilityI'},
date_time={'value': "2013-10-19T22:22:13+0100"},
beamline={'value': "Tomography"},
))
# /measurement/experimenter
f.add_entry(
DataExchangeEntry.experimenter(
name={'value': "Sherry Mayo"},
role={'value': "Project PI"},
))
f.close()
if verbose: print "Done creating data exchange file: ", hdf5_file_name
def main():
file_name = '/local/data/databank/TXM_26ID/20130731_004_Stripe_Solder_Sample_Tip1_TomoScript_181imgs_p1s_b1.txrm'
white_file_name = '/local/data/databank/TXM_26ID/20130731_001_Background_Reference_20imgs_p5s_b1.xrm'
hdf5_file_name = '/local/data/databank/dataExchange/TXM/20130731_004_Stripe_Solder_Sample_Tip1_nx.h5'
log_file = '/local/data/databank/dataExchange/TXM/20130731_004_Stripe_Solder_Sample_Tip1.log'
mydata = Convert()
# Create minimal hdf5 file
if verbose: print "Reading data ... "
mydata.stack(file_name,
hdf5_file_name = hdf5_file_name,
white_file_name = white_file_name,
sample_name = 'Stripe_Solder_Sample_Tip1'
)
# Add extra metadata if available / desired
reader = xradia.xrm()
array = dstruct
reader.read_txrm(file_name,array)
# Read angles
n_angles = np.shape(array.exchange.angles)
if verbose: print "Done reading ", n_angles, " angles"
theta = np.zeros(n_angles)
theta = array.exchange.angles[:]
# Save any other available metadata in a log file
f = open(log_file,'w')
f.write('Data creation date: \n')
f.write(str(array.information.file_creation_datetime))
f.write('\n')
f.write('=======================================\n')
f.write('Sample name: \n')
f.write(str(array.information.sample.name))
f.write('\n')
f.write('=======================================\n')
f.write('Experimenter name: \n')
f.write(str(array.information.experimenter.name))
f.write('\n')
f.write('=======================================\n')
f.write('X-ray energy: \n')
f.write(str(array.exchange.energy))
f.write(str(array.exchange.energy_units))
f.write('\n')
f.write('=======================================\n')
f.write('Angles: \n')
f.write(str(array.exchange.angles))
f.write('\n')
f.write('=======================================\n')
f.write('Data axes: \n')
f.write(str(array.exchange.data_axes))
f.write('\n')
f.write('=======================================\n')
f.write('x distance: \n')
f.write(str(array.exchange.x))
f.write('\n')
f.write('=======================================\n')
f.write('x units: \n')
f.write(str(array.exchange.x_units))
f.write('\n')
f.write('=======================================\n')
f.write('y distance: \n')
f.write(str(array.exchange.y))
f.write('\n')
f.write('=======================================\n')
f.write('y units: \n')
f.write(str(array.exchange.y_units))
f.write('\n')
f.close()
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry( DataExchangeEntry.instrument(name={'value': 'APS-CNM 26-ID'}) )
### Create HDF5 subgroup
### /measurement/instrument/source
f.add_entry( DataExchangeEntry.source(name={'value': "Advanced Photon Source"},
date_time={'value': "2013-07-31T19:42:13+0100"},
beamline={'value': "26-ID"},
)
)
# Create HDF5 subgroup
# /measurement/instrument/monochromator
f.add_entry( DataExchangeEntry.monochromator(type={'value': 'Unknown'},
energy={'value': float(array.exchange.energy[0]), 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
mono_stripe={'value': 'Unknown'},
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"Robert Winarski"},
role={'value':"Project PI"},
)
)
# Create HDF5 subgroup
# /measurement/sample
f.add_entry( DataExchangeEntry.data(theta={'value': theta, 'units':'degrees'}))
f.close()
print "Done creating data exchange file: ", hdf5_file_name
