def read_aps_32id(fname, proj=None, sino=None):
"""
Read APS 32-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
tomo_grp = os.path.join('exchange', 'data')
flat_grp = os.path.join('exchange', 'data_white')
dark_grp = os.path.join('exchange', 'data_dark')
tomo = tio.read_hdf5(fname, tomo_grp, slc=(proj, sino))
flat = tio.read_hdf5(fname, flat_grp, slc=(None, sino))
dark = tio.read_hdf5(fname, dark_grp, slc=(None, sino))
return tomo, flat, dark
def read_aps_7bm(fname, proj=None, sino=None):
"""
Read APS 7-BM standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
array
Projection angles in radian.
"""
tomo_grp = '/'.join(['exchange', 'data'])
theta_grp = '/'.join(['exchange', 'theta'])
tomo = tio.read_hdf5(fname, tomo_grp, slc=(proj, sino))
theta = tio.read_hdf5(fname, theta_grp, slc=(proj, ))
return tomo, theta
def read_aps_7bm(fname, proj=None, sino=None):
"""
Read APS 7-BM standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
array
Projection angles in radian.
"""
tomo_grp = os.path.join('exchange', 'data')
theta_grp = os.path.join('exchange', 'theta')
tomo = tio.read_hdf5(fname, tomo_grp, slc=(proj, sino))
theta = tio.read_hdf5(fname, theta_grp, slc=(proj, ))
return tomo, theta
def read_lnls_imx(folder, proj=None, sino=None):
"""
Read LNLS IMX standard data format.
Parameters
----------
folder : str
Path to sample folder (containing tomo.h5, flat.h5, dark.h5)
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
folder = os.path.abspath(folder)
tomo_name = os.path.join(folder, 'tomo.h5')
flat_name = os.path.join(folder, 'tomo_flat_before.h5')
dark_name = os.path.join(folder, 'tomo_dark_before.h5')
tomo = tio.read_hdf5(tomo_name, 'images', slc=(proj, sino))
flat = tio.read_hdf5(flat_name, 'flats', slc=(None, sino))
dark = tio.read_hdf5(dark_name, 'darks', slc=(None, sino))
return tomo, flat, dark
def read_lnls_imx(folder, proj=None, sino=None):
"""
Read LNLS IMX standard data format.
Parameters
----------
folder : str
Path to sample folder (containing tomo.h5, flat.h5, dark.h5)
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
folder = os.path.abspath(folder)
tomo_name = os.path.join(folder, 'tomo.h5')
flat_name = os.path.join(folder, 'tomo_flat_before.h5')
dark_name = os.path.join(folder, 'tomo_dark_before.h5')
tomo = tio.read_hdf5(tomo_name, 'images', slc=(proj, sino))
flat = tio.read_hdf5(flat_name, 'flats', slc=(None, sino))
dark = tio.read_hdf5(dark_name, 'darks', slc=(None, sino))
return tomo, flat, dark
def read_aps_32id(fname, exchange_rank=0, proj=None, sino=None,
dtype=None, shared=True):
"""
Read APS 32-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
exchange_rank : int, optional
exchange_rank is added to "exchange" to point tomopy to the data
to recontruct. if rank is not set then the data are raw from the
detector and are located under exchange = "exchange/...", to process
data that are the result of some intemedite processing step then
exchange_rank = 1, 2, ... will direct tomopy to process
"exchange1/...",
proj : {sequence, int} or np.slice, optional
Specify projections to read. (start, end, step)
sino : {sequence, int} or np.slice, optional
Specify sinograms to read. (start, end, step)
dtype : numpy datatype, optional
Convert data to this datatype on read if specified.
shared : bool, optional
If True, read proj data into shared memory location. Defaults to False.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
if exchange_rank > 0:
exchange_base = 'exchange{:d}'.format(int(exchange_rank))
else:
exchange_base = "exchange"
tomo_grp = '/'.join([exchange_base, 'data'])
flat_grp = '/'.join([exchange_base, 'data_white'])
dark_grp = '/'.join([exchange_base, 'data_dark'])
tomo = tio.read_hdf5(fname, tomo_grp, (proj, sino), dtype, shared)
flat = tio.read_hdf5(fname, flat_grp, (None, sino), dtype)
dark = tio.read_hdf5(fname, dark_grp, (None, sino), dtype)
return tomo, flat, dark
def read_aps_32id(fname, exchange_rank=0, proj=None, sino=None,
dtype=None, shared=True):
"""
Read APS 32-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
exchange_rank : int, optional
exchange_rank is added to "exchange" to point tomopy to the data
to recontruct. if rank is not set then the data are raw from the
detector and are located under exchange = "exchange/...", to process
data that are the result of some intemedite processing step then
exchange_rank = 1, 2, ... will direct tomopy to process
"exchange1/...",
proj : {sequence, int} or np.slice, optional
Specify projections to read. (start, end, step)
sino : {sequence, int} or np.slice, optional
Specify sinograms to read. (start, end, step)
dtype : numpy datatype, optional
Convert data to this datatype on read if specified.
shared : bool, optional
If True, read proj data into shared memory location. Defaults to False.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
if exchange_rank > 0:
exchange_base = 'exchange{:d}'.format(int(exchange_rank))
else:
exchange_base = "exchange"
tomo_grp = '/'.join([exchange_base, 'data'])
flat_grp = '/'.join([exchange_base, 'data_white'])
dark_grp = '/'.join([exchange_base, 'data_dark'])
tomo = tio.read_hdf5(fname, tomo_grp, (proj, sino), dtype, shared)
flat = tio.read_hdf5(fname, flat_grp, (None, sino), dtype)
dark = tio.read_hdf5(fname, dark_grp, (None, sino), dtype)
return tomo, flat, dark
def read_aps_13id(fname, group='/xrfmap/roimap/sum_cor', proj=None, sino=None):
"""
Read APS 13-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
group : str, optional
Path to the group inside hdf5 file where data is located.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
"""
tomo = tio.read_hdf5(fname, group, slc=(None, proj, sino))
tomo = np.swapaxes(tomo, 0, 1)
tomo = np.swapaxes(tomo, 1, 2).copy()
return tomo
def read_aps_13id(
fname, group='/xrfmap/roimap/sum_cor', proj=None, sino=None):
"""
Read APS 13-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
group : str, optional
Path to the group inside hdf5 file where data is located.
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
"""
tomo = tio.read_hdf5(fname, group, slc=(None, proj, sino))
tomo = np.swapaxes(tomo, 0, 1)
tomo = np.swapaxes(tomo, 1, 2).copy()
return tomo
def read_aps_32id(fname, exchange_rank=0, proj=None, sino=None):
"""
Read APS 32-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
exchange_rank : int, optional
exchange_rank is added to "exchange" to point tomopy to the data
to recontruct. if rank is not set then the data are raw from the
detector and are located under exchange = "exchange/...", to process
data that are the result of some intemedite processing step then
exchange_rank = 1, 2, ... will direct tomopy to process
"exchange1/...",
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
if exchange_rank > 0:
exchange_base = 'exchange{:d}'.format(int(exchange_rank))
else:
exchange_base = "exchange"
tomo_grp = '/'.join([exchange_base, 'data'])
flat_grp = '/'.join([exchange_base, 'data_white'])
dark_grp = '/'.join([exchange_base, 'data_dark'])
tomo = tio.read_hdf5(fname, tomo_grp, slc=(proj, sino))
flat = tio.read_hdf5(fname, flat_grp, slc=(None, sino))
dark = tio.read_hdf5(fname, dark_grp, slc=(None, sino))
return tomo, flat, dark
def read_aps_32id(fname, exchange_rank=0, proj=None, sino=None):
"""
Read APS 32-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
exchange_rank : int, optional
exchange_rank is added to "exchange" to point tomopy to the data
to recontruct. if rank is not set then the data are raw from the
detector and are located under exchange = "exchange/...", to process
data that are the result of some intemedite processing step then
exchange_rank = 1, 2, ... will direct tomopy to process
"exchange1/...",
proj : {sequence, int}, optional
Specify projections to read. (start, end, step)
sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
if exchange_rank > 0:
exchange_base = 'exchange{:d}'.format(int(exchange_rank))
else:
exchange_base = "exchange"
tomo_grp = '/'.join([exchange_base, 'data'])
flat_grp = '/'.join([exchange_base, 'data_white'])
dark_grp = '/'.join([exchange_base, 'data_dark'])
tomo = tio.read_hdf5(fname, tomo_grp, slc=(proj, sino))
flat = tio.read_hdf5(fname, flat_grp, slc=(None, sino))
dark = tio.read_hdf5(fname, dark_grp, slc=(None, sino))
return tomo, flat, dark