def read_als_832h5(fname,
ind_tomo=None,
ind_flat=None,
ind_dark=None,
proj=None,
sino=None):
"""
Read ALS 8.3.2 hdf5 file with stacked datasets.
Parameters
----------
fname : str
Path to hdf5 file.
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.
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.
list of int
Indices of flat field data within tomography projection list
"""
with dxreader.find_dataset_group(fname) as dgroup:
dname = dgroup.name.split('/')[-1]
tomo_name = dname + '_0000_0000.tif'
flat_name = dname + 'bak_0000.tif'
dark_name = dname + 'drk_0000.tif'
# Read metadata from dataset group attributes
keys = list(dgroup.attrs.keys())
if 'nangles' in keys:
nproj = int(dgroup.attrs['nangles'])
if 'i0cycle' in keys:
inter_bright = int(dgroup.attrs['i0cycle'])
if 'num_bright_field' in keys:
nflat = int(dgroup.attrs['num_bright_field'])
else:
nflat = dxreader._count_proj(dgroup,
flat_name,
nproj,
inter_bright=inter_bright)
if 'num_dark_fields' in keys:
ndark = int(dgroup.attrs['num_dark_fields'])
else:
ndark = dxreader._count_proj(dgroup, dark_name, nproj)
# Create arrays of indices to read projections, flats and darks
if ind_tomo is None:
ind_tomo = list(range(0, nproj))
if proj is not None:
ind_tomo = ind_tomo[slice(*proj)]
ind_dark = list(range(0, ndark))
group_dark = [nproj - 1]
ind_flat = list(range(0, nflat))
if inter_bright > 0:
group_flat = list(range(0, nproj, inter_bright))
if group_flat[-1] != nproj - 1:
group_flat.append(nproj - 1)
elif inter_bright == 0:
group_flat = [0, nproj - 1]
else:
group_flat = None
tomo = dxreader.read_hdf5_stack(dgroup,
tomo_name,
ind_tomo,
slc=(None, sino))
flat = dxreader.read_hdf5_stack(dgroup,
flat_name,
ind_flat,
slc=(None, sino),
out_ind=group_flat)
dark = dxreader.read_hdf5_stack(dgroup,
dark_name,
ind_dark,
slc=(None, sino),
out_ind=group_dark)
return tomo, flat, dark, dxreader._map_loc(ind_tomo, group_flat)
def read_als_832h5(fname, ind_tomo=None, ind_flat=None, ind_dark=None,
proj=None, sino=None):
"""
Read ALS 8.3.2 hdf5 file with stacked datasets.
Parameters
----------
fname : str
Path to hdf5 file.
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.
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.
list of int
Indices of flat field data within tomography projection list
"""
with dxreader.find_dataset_group(fname) as dgroup:
dname = dgroup.name.split('/')[-1]
tomo_name = dname + '_0000_0000.tif'
flat_name = dname + 'bak_0000.tif'
dark_name = dname + 'drk_0000.tif'
# Read metadata from dataset group attributes
keys = list(dgroup.attrs.keys())
if 'nangles' in keys:
nproj = int(dgroup.attrs['nangles'])
if 'i0cycle' in keys:
inter_bright = int(dgroup.attrs['i0cycle'])
if 'num_bright_field' in keys:
nflat = int(dgroup.attrs['num_bright_field'])
else:
nflat = dxreader._count_proj(dgroup, flat_name, nproj,
inter_bright=inter_bright)
if 'num_dark_fields' in keys:
ndark = int(dgroup.attrs['num_dark_fields'])
else:
ndark = dxreader._count_proj(dgroup, dark_name, nproj)
# Create arrays of indices to read projections, flats and darks
if ind_tomo is None:
ind_tomo = list(range(0, nproj))
if proj is not None:
ind_tomo = ind_tomo[slice(*proj)]
ind_dark = list(range(0, ndark))
group_dark = [nproj - 1]
ind_flat = list(range(0, nflat))
if inter_bright > 0:
group_flat = list(range(0, nproj, inter_bright))
if group_flat[-1] != nproj - 1:
group_flat.append(nproj - 1)
elif inter_bright == 0:
group_flat = [0, nproj - 1]
else:
group_flat = None
tomo = dxreader.read_hdf5_stack(
dgroup, tomo_name, ind_tomo, slc=(None, sino))
flat = dxreader.read_hdf5_stack(
dgroup, flat_name, ind_flat, slc=(None, sino), out_ind=group_flat)
dark = dxreader.read_hdf5_stack(
dgroup, dark_name, ind_dark, slc=(None, sino), out_ind=group_dark)
return tomo, flat, dark, dxreader._map_loc(ind_tomo, group_flat)