def xtomo_exchange(
self,
data,
data_white=None,
data_dark=None,
theta=None,
data_exchange_type=None,
source_name=None,
source_mode=None,
source_datetime=None,
beamline=None,
energy=None,
current=None,
actual_pixel_size=None,
experimenter_name=None,
experimenter_affiliation=None,
experimenter_email=None,
instrument_comment=None,
sample_name=None,
sample_comment=None,
acquisition_mode=None,
acquisition_comment=None,
sample_position_x=None,
sample_position_y=None,
sample_position_z=None,
sample_image_shift_x=None,
sample_image_shift_y=None,
image_exposure_time=None,
image_time=None,
image_theta=None,
hdf5_file_name=None,
axes="theta:y:x",
log="INFO",
):
"""
Write 3-D data to a data-exchange file.
Parameters
data : ndarray
3-D X-ray absorption tomography raw data.
Size of the dimensions should be:
[projections, slices, pixels].
data_white, data_dark : ndarray, optional
3-D white-field/dark_field data. Multiple
projections are stacked together to obtain
a 3-D matrix. 2nd and 3rd dimensions should
be the same as data: [shots, slices, pixels].
theta : ndarray, optional
Data acquisition angles corresponding
to each projection.
data_excahnge_type : str, optional
label defyining the type of data contained in data exchange file
for raw data tomography data use 'tomography_raw_projections'
source_name, source_mode, source_datetime : str, optional
label defining the source name, operation mode and date/time when these values were taken
beamline : str, optional
label defining the beamline name
energy, current : float, optional
X-ray energy and bean current
actual_pixel_size : float, optional
pixel size on the sample plane
experimenter_name, experimenter_affiliation, experimenter_email : str, optional
user name, affiliation and e-mail address
instrument_comment : str, optional
instrument comment
sample_name, sample_comment : str, optional
sample name and comment
acquisition_mode, acquisition_comment : str, optional
acquisition mode and comment
hd5_file_name : str
Output file.
Notes
-----
If file exists, does nothing
Examples
- Convert tomographic projection series (raw, dark, white) of tiff in data exchange:
>>> import dataexchange
>>> file_name = '/local/dataraid/databank/Anka/radios/image_.tif'
>>> dark_file_name = '/local/dataraid/databank/Anka/darks/image_.tif'
>>> white_file_name = '/local/dataraid/databank/Anka/flats/image_.tif'
>>> hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/Anka.h5'
>>> projections_start = 0
>>> projections_end = 3167
>>> white_start = 0
>>> white_end = 100
>>> dark_start = 0
>>> dark_end = 100
>>> sample_name = 'Anka'
>>>
>>> # Read raw data
>>> read = dataexchange.Import()
>>> data, white, dark, theta = read.xtomo_raw(file_name,
>>> projections_start = projections_start,
>>> projections_end = projections_end,
>>> white_file_name = white_file_name,
>>> white_start = white_start,
>>> white_end = white_end,
>>> dark_file_name = dark_file_name,
>>> dark_start = dark_start,
>>> dark_end = dark_end,
>>> projections_digits = 5,
>>> log='INFO'
>>> )
>>>
>>> # Save data
>>> write = dataexchange.Export()
>>> write.xtomo_exchange(data = data,
>>> data_white = white,
>>> data_dark = dark,
>>> theta = theta,
>>> hdf5_file_name = hdf5_file_name,
>>> data_exchange_type = 'tomography_raw_projections',
>>> sample_name = sample_name
>>> )
"""
if hdf5_file_name != None:
if os.path.isfile(hdf5_file_name):
self.logger.error("Data Exchange file: [%s] already exists", hdf5_file_name)
else:
# Create new folder.
dirPath = os.path.dirname(hdf5_file_name)
if not os.path.exists(dirPath):
os.makedirs(dirPath)
# Get the file_name in lower case.
lFn = hdf5_file_name.lower()
# Split the string with the delimeter '.'
end = lFn.split(".")
# Write the Data Exchange HDF5 file.
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode="w")
self.logger.info("Creating Data Exchange File [%s]", hdf5_file_name)
# Create core HDF5 dataset in exchange group for projections_theta_range
# deep stack of x,y images /exchange/data
self.logger.info("Adding projections to Data Exchange File [%s]", hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
data={"value": data, "units": "counts", "description": "transmission", "axes": axes}
)
)
# f.add_entry( DataExchangeEntry.data(data={'value': data, 'units':'counts', 'description': 'transmission', 'axes':'theta:y:x', 'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} }))
if theta != None:
f.add_entry(DataExchangeEntry.data(theta={"value": theta, "units": "degrees"}))
self.logger.info("Adding theta to Data Exchange File [%s]", hdf5_file_name)
else:
self.logger.warning("theta is not defined")
if data_dark != None:
self.logger.info("Adding dark fields to Data Exchange File [%s]", hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
data_dark={"value": data_dark, "units": "counts", "axes": "theta_dark:y:x"}
)
)
# f.add_entry( DataExchangeEntry.data(data_dark={'value': data_dark, 'units':'counts', 'axes':'theta_dark:y:x', 'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} }))
else:
self.logger.warning("data dark is not defined")
if data_white != None:
self.logger.info("Adding white fields to Data Exchange File [%s]", hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
data_white={"value": data_white, "units": "counts", "axes": "theta_white:y:x"}
)
)
# f.add_entry( DataExchangeEntry.data(data_white={'value': data_white, 'units':'counts', 'axes':'theta_white:y:x', 'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} }))
else:
self.logger.warning("data white is not defined")
if data_exchange_type != None:
self.logger.info("Adding data type to Data Exchange File [%s]", hdf5_file_name)
f.add_entry(DataExchangeEntry.data(title={"value": data_exchange_type}))
if source_name != None:
f.add_entry(DataExchangeEntry.source(name={"value": source_name}))
if source_mode != None:
f.add_entry(DataExchangeEntry.source(mode={"value": source_mode}))
if source_datetime != None:
f.add_entry(DataExchangeEntry.source(datetime={"value": source_datetime}))
if beamline != None:
f.add_entry(DataExchangeEntry.source(beamline={"value": beamline}))
if energy != None:
f.add_entry(
DataExchangeEntry.monochromator(
energy={"value": energy, "units": "keV", "dataset_opts": {"dtype": "d"}}
)
)
if current != None:
f.add_entry(
DataExchangeEntry.source(
current={"value": current, "units": "mA", "dataset_opts": {"dtype": "d"}}
)
)
if actual_pixel_size != None:
f.add_entry(
DataExchangeEntry.detector(
actual_pixel_size_x={
"value": actual_pixel_size,
"units": "microns",
"dataset_opts": {"dtype": "d"},
},
actual_pixel_size_y={
"value": actual_pixel_size,
"units": "microns",
"dataset_opts": {"dtype": "d"},
},
)
)
if experimenter_name != None:
f.add_entry(DataExchangeEntry.experimenter(name={"value": experimenter_name}))
if experimenter_affiliation != None:
f.add_entry(DataExchangeEntry.experimenter(affiliation={"value": experimenter_affiliation}))
if experimenter_email != None:
f.add_entry(DataExchangeEntry.experimenter(email={"value": experimenter_email}))
if instrument_comment != None:
f.add_entry(DataExchangeEntry.instrument(comment={"value": instrument_comment}))
if sample_name == None:
sample_name = end[0]
f.add_entry(
DataExchangeEntry.sample(
name={"value": sample_name},
description={
"value": "Sample name assigned by the HDF5 converter and based on the HDF5 file name"
},
)
)
else:
f.add_entry(DataExchangeEntry.sample(name={"value": sample_name}))
if sample_comment != None:
f.add_entry(DataExchangeEntry.sample(comment={"value": sample_comment}))
if acquisition_mode != None:
f.add_entry(DataExchangeEntry.acquisition(mode={"value": acquisition_mode}))
if acquisition_comment != None:
f.add_entry(DataExchangeEntry.acquisition(comment={"value": acquisition_comment}))
if sample_position_x != None:
f.add_entry(
DataExchangeEntry.acquisition(
sample_position_x={
"value": sample_position_x,
"units": "microns",
"dataset_opts": {"dtype": "d"},
}
)
)
if sample_position_y != None:
f.add_entry(
DataExchangeEntry.acquisition(
sample_position_y={
"value": sample_position_y,
"units": "microns",
"dataset_opts": {"dtype": "d"},
}
)
)
if sample_position_z != None:
f.add_entry(
DataExchangeEntry.acquisition(
sample_position_z={
"value": sample_position_z,
"units": "microns",
"dataset_opts": {"dtype": "d"},
}
)
)
if sample_image_shift_x != None:
f.add_entry(
DataExchangeEntry.acquisition(
sample_image_shift_x={
"value": sample_image_shift_x,
"units": "microns",
"dataset_opts": {"dtype": "d"},
}
)
)
if sample_image_shift_y != None:
f.add_entry(
DataExchangeEntry.acquisition(
sample_image_shift_y={
"value": sample_image_shift_y,
"units": "microns",
"dataset_opts": {"dtype": "d"},
}
)
)
if image_exposure_time != None:
f.add_entry(
DataExchangeEntry.acquisition(
image_exposure_time={
"value": image_exposure_time,
"units": "s",
"dataset_opts": {"dtype": "d"},
}
)
)
if image_time != None:
f.add_entry(DataExchangeEntry.acquisition(image_time={"value": image_time}))
if image_theta != None:
f.add_entry(DataExchangeEntry.acquisition(image_theta={"value": image_theta, "units": "degrees"}))
f.close()
self.logger.info("DONE!!!!. Created Data Exchange File [%s]", hdf5_file_name)
else:
self.logger.warning("Nothing to do ...")
def xtomo_exchange(self,
data,
data_white=None,
data_dark=None,
theta=None,
data_exchange_type=None,
source_name=None,
source_mode=None,
source_datetime=None,
beamline=None,
energy=None,
current=None,
actual_pixel_size=None,
experimenter_name=None,
experimenter_affiliation=None,
experimenter_email=None,
instrument_comment=None,
sample_name=None,
sample_comment=None,
acquisition_mode=None,
acquisition_comment=None,
sample_position_x=None,
sample_position_y=None,
sample_position_z=None,
sample_image_shift_x=None,
sample_image_shift_y=None,
hdf5_file_name=None,
axes='theta:y:x',
log='INFO'):
"""
Write 3-D data to a data-exchange file.
Parameters
data : ndarray
3-D X-ray absorption tomography raw data.
Size of the dimensions should be:
[projections, slices, pixels].
data_white, data_dark : ndarray, optional
3-D white-field/dark_field data. Multiple
projections are stacked together to obtain
a 3-D matrix. 2nd and 3rd dimensions should
be the same as data: [shots, slices, pixels].
theta : ndarray, optional
Data acquisition angles corresponding
to each projection.
data_excahnge_type : str, optional
label defyining the type of data contained in data exchange file
for raw data tomography data use 'tomography_raw_projections'
source_name, source_mode, source_datetime : str, optional
label defining the source name, operation mode and date/time when these values were taken
beamline : str, optional
label defining the beamline name
energy, current : float, optional
X-ray energy and bean current
actual_pixel_size : float, optional
pixel size on the sample plane
experimenter_name, experimenter_affiliation, experimenter_email : str, optional
user name, affiliation and e-mail address
instrument_comment : str, optional
instrument comment
sample_name, sample_comment : str, optional
sample name and comment
acquisition_mode, acquisition_comment : str, optional
acquisition mode and comment
hd5_file_name : str
Output file.
Notes
-----
If file exists, does nothing
Examples
- Convert tomographic projection series (raw, dark, white) of tiff in data exchange:
>>> import dataexchange
>>> file_name = '/local/dataraid/databank/Anka/radios/image_.tif'
>>> dark_file_name = '/local/dataraid/databank/Anka/darks/image_.tif'
>>> white_file_name = '/local/dataraid/databank/Anka/flats/image_.tif'
>>> hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/Anka.h5'
>>> projections_start = 0
>>> projections_end = 3167
>>> white_start = 0
>>> white_end = 100
>>> dark_start = 0
>>> dark_end = 100
>>> sample_name = 'Anka'
>>>
>>> # Read raw data
>>> read = dataexchange.Import()
>>> data, white, dark, theta = read.xtomo_raw(file_name,
>>> projections_start = projections_start,
>>> projections_end = projections_end,
>>> white_file_name = white_file_name,
>>> white_start = white_start,
>>> white_end = white_end,
>>> dark_file_name = dark_file_name,
>>> dark_start = dark_start,
>>> dark_end = dark_end,
>>> projections_digits = 5,
>>> log='INFO'
>>> )
>>>
>>> # Save data
>>> write = dataexchange.Export()
>>> write.xtomo_exchange(data = data,
>>> data_white = white,
>>> data_dark = dark,
>>> theta = theta,
>>> hdf5_file_name = hdf5_file_name,
>>> data_exchange_type = 'tomography_raw_projections',
>>> sample_name = sample_name
>>> )
"""
if (hdf5_file_name != None):
if os.path.isfile(hdf5_file_name):
self.logger.error("Data Exchange file: [%s] already exists",
hdf5_file_name)
else:
# Create new folder.
dirPath = os.path.dirname(hdf5_file_name)
if not os.path.exists(dirPath):
os.makedirs(dirPath)
# Get the file_name in lower case.
lFn = hdf5_file_name.lower()
# Split the string with the delimeter '.'
end = lFn.split('.')
# Write the Data Exchange HDF5 file.
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='w')
self.logger.info("Creating Data Exchange File [%s]",
hdf5_file_name)
# Create core HDF5 dataset in exchange group for projections_theta_range
# deep stack of x,y images /exchange/data
self.logger.info(
"Adding projections to Data Exchange File [%s]",
hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
data={
'value': data,
'units': 'counts',
'description': 'transmission',
'axes': axes
}))
# f.add_entry( DataExchangeEntry.data(data={'value': data, 'units':'counts', 'description': 'transmission', 'axes':'theta:y:x', 'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} }))
if (theta != None):
f.add_entry(
DataExchangeEntry.data(theta={
'value': theta,
'units': 'degrees'
}))
self.logger.info("Adding theta to Data Exchange File [%s]",
hdf5_file_name)
else:
self.logger.warning("theta is not defined")
if (data_dark != None):
self.logger.info(
"Adding dark fields to Data Exchange File [%s]",
hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
data_dark={
'value': data_dark,
'units': 'counts',
'axes': 'theta_dark:y:x'
}))
# f.add_entry( DataExchangeEntry.data(data_dark={'value': data_dark, 'units':'counts', 'axes':'theta_dark:y:x', 'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} }))
else:
self.logger.warning("data dark is not defined")
if (data_white != None):
self.logger.info(
"Adding white fields to Data Exchange File [%s]",
hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
data_white={
'value': data_white,
'units': 'counts',
'axes': 'theta_white:y:x'
}))
# f.add_entry( DataExchangeEntry.data(data_white={'value': data_white, 'units':'counts', 'axes':'theta_white:y:x', 'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} }))
else:
self.logger.warning("data white is not defined")
if (data_exchange_type != None):
self.logger.info(
"Adding data type to Data Exchange File [%s]",
hdf5_file_name)
f.add_entry(
DataExchangeEntry.data(
title={'value': data_exchange_type}))
if (source_name != None):
f.add_entry(
DataExchangeEntry.source(name={'value': source_name}))
if (source_mode != None):
f.add_entry(
DataExchangeEntry.source(mode={'value': source_mode}))
if (source_datetime != None):
f.add_entry(
DataExchangeEntry.source(
datetime={'value': source_datetime}))
if (beamline != None):
f.add_entry(
DataExchangeEntry.source(beamline={'value': beamline}))
if (energy != None):
f.add_entry(
DataExchangeEntry.monochromator(
energy={
'value': energy,
'units': 'keV',
'dataset_opts': {
'dtype': 'd'
}
}))
if (current != None):
f.add_entry(
DataExchangeEntry.source(
current={
'value': current,
'units': 'mA',
'dataset_opts': {
'dtype': 'd'
}
}))
if (actual_pixel_size != None):
f.add_entry(
DataExchangeEntry.detector(actual_pixel_size_x={
'value': actual_pixel_size,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
},
actual_pixel_size_y={
'value':
actual_pixel_size,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
}))
if (experimenter_name != None):
f.add_entry(
DataExchangeEntry.experimenter(
name={'value': experimenter_name}))
if (experimenter_affiliation != None):
f.add_entry(
DataExchangeEntry.experimenter(
affiliation={'value': experimenter_affiliation}))
if (experimenter_email != None):
f.add_entry(
DataExchangeEntry.experimenter(
email={'value': experimenter_email}))
if (instrument_comment != None):
f.add_entry(
DataExchangeEntry.instrument(
comment={'value': instrument_comment}))
if (sample_name == None):
sample_name = end[0]
f.add_entry(
DataExchangeEntry.sample(
name={'value': sample_name},
description={
'value':
'Sample name assigned by the HDF5 converter and based on the HDF5 file name'
}))
else:
f.add_entry(
DataExchangeEntry.sample(name={'value': sample_name}))
if (sample_comment != None):
f.add_entry(
DataExchangeEntry.sample(
comment={'value': sample_comment}))
if (acquisition_mode != None):
f.add_entry(
DataExchangeEntry.acquisition(
mode={'value': acquisition_mode}))
if (acquisition_comment != None):
f.add_entry(
DataExchangeEntry.acquisition(
comment={'value': acquisition_comment}))
if (sample_position_x != None):
f.add_entry(
DataExchangeEntry.acquisition(
sample_position_x={
'value': sample_position_x,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
}))
if (sample_position_y != None):
f.add_entry(
DataExchangeEntry.acquisition(
sample_position_y={
'value': sample_position_y,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
}))
if (sample_position_z != None):
f.add_entry(
DataExchangeEntry.acquisition(
sample_position_z={
'value': sample_position_z,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
}))
if (sample_image_shift_x != None):
f.add_entry(
DataExchangeEntry.acquisition(
sample_image_shift_x={
'value': sample_image_shift_x,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
}))
if (sample_image_shift_y != None):
f.add_entry(
DataExchangeEntry.acquisition(
sample_image_shift_y={
'value': sample_image_shift_y,
'units': 'microns',
'dataset_opts': {
'dtype': 'd'
}
}))
f.close()
self.logger.info("DONE!!!!. Created Data Exchange File [%s]",
hdf5_file_name)
else:
self.logger.warning("Nothing to do ...")
