def read_elettra_syrmep(fname, ind_tomo):
"""
Read Elettra SYRMEP standard data format.
Parameters
----------
fname : str
Path to data folder.
ind_tomo : list of int
Indices of the projection files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
fname = os.path.abspath(fname)
tomo_name = os.path.join(fname, 'tomo_')
flat_name = os.path.join(fname, 'flat_')
dark_name = os.path.join(fname, 'dark_')
tomo = dio.Reader(tomo_name).tiff(stack=True, ind=ind_tomo, digit=4)
flat = dio.Reader(flat_name).tiff(stack=True, ind=range(1, 11), digit=4)
dark = dio.Reader(dark_name).tiff(stack=True, ind=range(1, 11), digit=4)
return tomo, flat, dark
def read_aps_32id(fname, proj=None, sino=None):
"""
Read APS 32-ID standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
proj : slice, optional
Specifies the projections to read from a slice object.
sino : slice, optional
Specifies the sinograms to read from a slice object.
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 = dio.Reader(fname, proj, sino).hdf5(tomo_grp)
flat = dio.Reader(fname, dim2=sino).hdf5(flat_grp)
dark = dio.Reader(fname, dim2=sino).hdf5(dark_grp)
return tomo, flat, dark
def read_diamond_l12(fname, ind_tomo):
"""
Read Diamond Light Source L12 (JEEP) standard data format.
Parameters
----------
fname : str
Path to data folder.
ind_tomo : list of int
Indices of the projection files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
"""
fname = os.path.abspath(fname)
tomo_name = os.path.join(fname, 'im_')
flat_name = os.path.join(fname, 'flat_')
tomo = dio.Reader(tomo_name).tiff(stack=True, ind=ind_tomo, digit=6)
flat = dio.Reader(flat_name).tiff(stack=True, ind=range(0, 1), digit=6)
return tomo, flat
def read_aps_13bm(fname, format, proj=None, sino=None):
"""
Read APS 13-BM standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
format : str
Data format. 'spe' or 'netcdf4'
proj : slice, optional
Specifies the projections to read from a slice object.
sino : slice, optional
Specifies the sinograms to read from a slice object.
Returns
-------
ndarray
3D tomographic data.
"""
if format is 'spe':
tomo = dio.Reader(fname, sino).spe()
elif format is 'netcdf4':
tomo = dio.Reader(fname, proj, sino).netcdf4('array_data')
return tomo
def read_aps_7bm(fname, proj=None, sino=None):
"""
Read APS 7-BM standard data format.
Parameters
----------
fname : str
Path to hdf5 file.
proj : slice, optional
Specifies the projections to read from a slice object.
sino : slice, optional
Specifies the sinograms to read from a slice object.
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 = dio.Reader(fname, proj, sino).hdf5(tomo_grp)
theta = dio.Reader(fname, proj).hdf5(theta_grp)
return tomo, theta
def read_als_832(fname, ind_tomo=None):
"""
Read ALS 8.3.2 standard data format.
Parameters
----------
fname : str
Path to file name without indices and extension.
ind_tomo : list of int, optional
Indices of the projection files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
# File definitions.
fname = os.path.abspath(fname)
tomo_name = fname + '_0000_'
flat_name = fname + 'bak_'
dark_name = fname + 'drk_'
log_file = fname + '.sct'
# Read metadata from ALS log file.
contents = open(log_file, 'r')
for line in contents:
if '-nangles' in line:
nproj = int(re.findall(r'\d+', line)[0])
if '-num_bright_field' in line:
nflat = int(re.findall(r'\d+', line)[0])
if '-num_dark_fields' in line:
ndark = int(re.findall(r'\d+', line)[0])
contents.close()
if ind_tomo is None:
ind_tomo = range(0, nproj)
tomo = dio.Reader(tomo_name).tiff(
stack=True, ind=ind_tomo, digit=4)
white = dio.Reader(flat_name).tiff(
stack=True, ind=range(0, nflat), digit=4)
dark = dio.Reader(dark_name).tiff(
stack=True, ind=range(0, ndark), digit=4)
return tomo, white, dark
def read_sls_tomcat(fname, ind_tomo=None):
"""
Read SLS TOMCAT standard data format.
Parameters
----------
fname : str
Path to file name without indices and extension.
ind_tomo : list of int, optional
Indices of the projection files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
# File definitions.
fname = os.path.abspath(fname)
log_file = fname + '.log'
# Read metadata from ALS log file.
contents = open(log_file, 'r')
for line in contents:
ls = line.split()
if len(ls) > 1:
if (ls[0] == 'Number' and ls[2] == 'projections'):
nproj = int(ls[4])
elif (ls[0] == 'Number' and ls[2] == 'flats'):
nflat = int(ls[4])
elif (ls[0] == 'Number' and ls[2] == 'darks'):
ndark = int(ls[4])
contents.close()
if ind_tomo is None:
ind_tomo = range(ndark + nflat + 1, ndark + nflat + nproj)
ind_flat = range(ndark + 1, ndark + nflat)
ind_dark = range(1, ndark)
tomo = dio.Reader(fname).tiff(stack=True, ind=ind_tomo, digit=4)
flat = dio.Reader(fname).tiff(stack=True, ind=ind_flat, digit=4)
dark = dio.Reader(fname).tiff(stack=True, ind=ind_dark, digit=4)
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 : slice, optional
Specifies the projections to read from a slice object.
sino : slice, optional
Specifies the sinograms to read from a slice object.
Returns
-------
ndarray
3D tomographic data.
"""
tomo = dio.Reader(fname, None, proj, sino).hdf5(group)
tomo = np.swapaxes(tomo, 0, 1)
tomo = np.swapaxes(tomo, 1, 2).copy()
return tomo
def read_aus_microct(fname, ind_tomo, ind_flat, ind_dark):
"""
Read Australian Synchrotron Micro Computed Tomography standard
data format.
Parameters
----------
fname : str
Path to data folder.
ind_tomo : list of int
Indices of the projection files to read.
ind_flat : list of int
Indices of the flat field files to read.
ind_dark : list of int
Indices of the dark field files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
fname = os.path.abspath(fname)
tomo_name = os.path.join(fname, 'SAMPLE_T_')
flat_name = os.path.join(fname, 'BG__BEFORE_')
dark_name = os.path.join(fname, 'DF__BEFORE_')
tomo = dio.Reader(tomo_name).tiff(stack=True, ind=ind_tomo, digit=4)
flat = dio.Reader(flat_name).tiff(stack=True, ind=ind_flat, digit=2)
dark = dio.Reader(dark_name).tiff(stack=True, ind=ind_dark, digit=2)
return tomo, flat, dark
def read_petra3_p05(fname, ind_tomo, ind_flat, ind_dark):
"""
Read Petra-III P05 standard data format.
Parameters
----------
fname : str
Path to data folder.
ind_tomo : list of int
Indices of the projection files to read.
ind_flat : list of int
Indices of the flat field files to read.
ind_dark : list of int
Indices of the dark field files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
fname = os.path.abspath(fname)
tomo_name = os.path.join(fname, 'scan_0002', 'ccd', 'pco01', 'ccd_')
flat_name = os.path.join(fname, 'scan_0001', 'ccd', 'pco01', 'ccd_')
dark_name = os.path.join(fname, 'scan_0003', 'ccd', 'pco01', 'ccd_')
tomo = dio.Reader(tomo_name).tiff(stack=True, ind=ind_tomo, digit=4)
flat = dio.Reader(flat_name).tiff(stack=True, ind=ind_flat, digit=4)
dark = dio.Reader(dark_name).tiff(stack=True, ind=ind_dark, digit=4)
return tomo, flat, dark
def read_anka_tomotopo(fname, ind_tomo, ind_flat, ind_dark):
"""
Read ANKA TOMO-TOMO standard data format.
Parameters
----------
fname : str
Path to data folder name without indices and extension.
ind_tomo : list of int, optional
Indices of the projection files to read.
ind_flat : list of int, optional
Indices of the flat field files to read.
ind_dark : list of int, optional
Indices of the dark field files to read.
Returns
-------
ndarray
3D tomographic data.
ndarray
3d flat field data.
ndarray
3D dark field data.
"""
fname = os.path.abspath(fname)
tomo_name = os.path.join(fname, 'radios', 'image_')
flat_name = os.path.join(fname, 'flats', 'image_')
dark_name = os.path.join(fname, 'darks', 'image_')
tomo = dio.Reader(tomo_name).tiff(stack=True, ind=ind_tomo, digit=5)
flat = dio.Reader(flat_name).tiff(stack=True, ind=ind_flat, digit=5)
dark = dio.Reader(dark_name).tiff(stack=True, ind=ind_dark, digit=5)
return tomo, flat, dark