def read_pixel_size(params):
'''
Read the pixel size and magnification from the HDF file.
Use to compute the effective pixel size.
'''
log.info(' *** auto pixel size reading')
if params.pixel_size_auto != True:
log.info(' *** *** OFF')
return params
if check_item_exists_hdf(params.file_name,
'/measurement/instrument/detection_system/objective/resolution'):
params.pixel_size = config.param_from_dxchange(params.file_name,
'/measurement/instrument/detection_system/objective/resolution')
log.info(' *** *** effective pixel size = {:6.4e} microns'.format(params.pixel_size))
return(params)
log.warning(' *** tomoScan resolution parameter not found. Try old format')
pixel_size = config.param_from_dxchange(params.file_name,
'/measurement/instrument/detector/pixel_size_x')
mag = config.param_from_dxchange(params.file_name,
'/measurement/instrument/detection_system/objective/magnification')
#Handle case where something wasn't read right
if not (pixel_size and mag):
log.warning(' *** *** problem reading pixel size from the HDF file')
return params
#What if pixel size isn't in microns, but in mm or m?
for i in range(3):
if pixel_size < 0.5:
pixel_size *= 1e3
else:
break
params.pixel_size = pixel_size / mag
log.info(' *** *** effective pixel size = {:6.4e} microns'.format(params.pixel_size))
return params
def read_bright_ratio(params):
'''Read the ratio between the bright exposure and other exposures.
'''
log.info(' *** *** %s' % params.flat_correction_method)
if params.flat_correction_method != 'standard' or (
not params.scintillator_auto):
log.warning(' *** *** skip finding exposure ratio')
params.bright_exp_ratio = 1
return params
log.info(' *** *** Find bright exposure ratio params from the HDF file')
try:
if check_item_exists_hdf(
params.file_name,
'/measurement/instrument/detector/different_flat_exposure'):
diff_bright_exp = config.param_from_dxchange(
params.file_name,
'/measurement/instrument/detector/different_flat_exposure',
attr=None,
scalar=False,
char_array=True)
if diff_bright_exp.lower() == 'same':
log.error(' *** *** used same flat and data exposures')
params.bright_exp_ratio = 1
return params
if check_item_exists_hdf(
params.file_name,
'/measurement/instrument/detector/exposure_time_flat'):
bright_exp = config.param_from_dxchange(
params.file_name,
'/measurement/instrument/detector/exposure_time_flat',
attr=None,
scalar=True,
char_array=False)
else:
bright_exp = config.param_from_dxchange(
params.file_name,
'/measurement/instrument/detector/brightfield_exposure_time',
attr=None,
scalar=True,
char_array=False)
log.info(' *** *** %f' % bright_exp)
norm_exp = config.param_from_dxchange(
params.file_name,
'/measurement/instrument/detector/exposure_time',
attr=None,
scalar=True,
char_array=False)
log.info(' *** *** %f' % norm_exp)
params.bright_exp_ratio = bright_exp / norm_exp
log.info(' *** *** found bright exposure ratio of {0:6.4f}'.format(
params.bright_exp_ratio))
except:
log.warning(' *** *** problem getting bright exposure ratio. Use 1.')
params.bright_exp_ratio = 1
return params
def read_scintillator(params):
'''Read the scintillator type and thickness from the HDF file.
'''
if params.scintillator_auto:
log.info(' *** auto reading scintillator params')
dataset_name = '/measurement/instrument/detection_system/scintillator/scintillating_thickness'
val = config.param_from_dxchange(params.file_name,
dataset_name,
attr=None,
scalar=True,
char_array=False)
params.scintillator_thickness = float(val)
log.info(' *** *** scintillator thickness = {:f}'.format(
params.scintillator_thickness))
tomoscan_path = '/measurement/instrument/detection_system/scintillator/name'
scint_material_string = ''
try:
scint_material_string = config.param_from_dxchange(
params.file_name, tomoscan_path, scalar=False, char_array=True)
except KeyError:
log.warning(
' *** *** scintillator material not in tomoscan form. Try old format'
)
if not scint_material_string:
old_path = '/measurement/instrument/detection_system/scintillator/description'
try:
scint_material_string = config.param_from_dxchange(
params.file_name, old_path, scalar=False, char_array=True)
except KeyError:
log.warning(' *** *** no scintillator material found')
return (params)
if scint_material_string.lower().startswith('luag'):
params.scintillator_material = 'LuAG_Ce'
elif scint_material_string.lower().startswith('lyso'):
params.scintillator_material = 'LYSO_Ce'
elif scint_material_string.lower().startswith('yag'):
params.scintillator_material = 'YAG_Ce'
else:
log.warning(' *** *** scintillator {:s} not recognized!'.format(
scint_material_string))
log.info(' *** *** using scintillator {:s}'.format(
params.scintillator_material))
# Run the initialization for beam hardening. Needed in case
# rotation_axis must be computed later.
# if params.beam_hardening_method.lower() == 'standard':
# beamhardening.initialize(params)
return params
def read_filter_materials_old(params):
'''Read the beam filter configuration from the HDF file.
If params.filter_1_material and/or params.filter_2_material are
'auto', then try to read the filter configuration recorded during
acquisition in the HDF5 file.
Parameters
==========
params
The global parameter object, should have *filter_1_material*,
*filter_1_thickness*, *filter_2_material*, and
*filter_2_thickness* attributes.
Returns
=======
params
An equivalent object to the *params* input, optionally with
*filter_1_material*, *filter_1_thickness*, *filter_2_material*,
and *filter_2_thickness* attributes modified to reflect the HDF5
file.
'''
log.info(' *** auto reading filter configuration')
# Read the relevant data from disk
filter_path = '/measurement/instrument/filters/Filter_{idx}_Material'
param_path = 'filter_{idx}_{attr}'
for idx_filter in (1, 2):
filter_param = getattr(
params, param_path.format(idx=idx_filter, attr='material'))
if filter_param == 'auto':
# Read recorded filter condition from the HDF5 file
filter_str = config.param_from_dxchange(
params.file_name,
filter_path.format(idx=idx_filter),
char_array=True,
scalar=False)
if filter_str is None:
log.warning(
' *** *** Could not load filter %d configuration from HDF5 file.'
% idx_filter)
material, thickness = _filter_str_to_params('Open')
else:
material, thickness = _filter_str_to_params(filter_str)
# Update the params with the loaded values
setattr(params, param_path.format(idx=idx_filter, attr='material'),
material)
setattr(params, param_path.format(idx=idx_filter,
attr='thickness'), thickness)
log.info(' *** *** Filter %d: (%s %f)' %
(idx_filter, material, thickness))
return params
def read_scintillator(params):
'''Read the scintillator type and thickness from DXchange.
'''
if params.scintillator_auto and params.beam_hardening_method.lower(
) == 'standard':
log.info(' *** *** Find scintillator params from DXchange')
params.scintillator_thickness = float(
config.param_from_dxchange(
params.file_name,
'/measurement/instrument/detection_system/scintillator/scintillating_thickness',
attr=None,
scalar=True,
char_array=False))
log.info(' *** *** scintillator thickness = {:f}'.format(
params.scintillator_thickness))
scint_material_string = config.param_from_dxchange(
params.file_name,
'/measurement/instrument/detection_system/scintillator/description',
scalar=False,
char_array=True)
if scint_material_string.lower().startswith('luag'):
params.scintillator_material = 'LuAG_Ce'
elif scint_material_string.lower().startswith('lyso'):
params.scintillator_material = 'LYSO_Ce'
elif scint_material_string.lower().startswith('yag'):
params.scintillator_material = 'YAG_Ce'
else:
log.warning(' *** *** scintillator {:s} not recognized!'.format(
scint_material_string))
log.warning(' *** *** using scintillator {:s}'.format(
params.scintillator_material))
#Run the initialization for beam hardening. Needed in case rotation_axis must
#be computed later.
if params.beam_hardening_method.lower() == 'standard':
beamhardening.initialize(params)
return params
def read_filter_materials_tomoscan(params):
'''Read the beam filter configuration from the HDF file.
If params.filter_{n}_auto for n in [1,2,3] is True,
then try to read the filter configuration recorded during
acquisition in the HDF5 file.
Parameters
==========
params
The global parameter object, should have *filter_n_material*,
*filter_n_thickness*, and *filter_n_auto* for n in [1,2,3]
Returns
=======
params
An equivalent object to the *params* input, optionally with
*filter_n_material* and *filter_n_thickness*
attributes modified to reflect the HDF5 file.
'''
log.info(' *** auto reading filter configuration')
# Read the relevant data from disk
filter_path = '/measurement/instrument/attenuator_{idx}'
param_path = 'filter_{idx}_{attr}'
for idx_filter in range(1, 4, 1):
if not check_item_exists_hdf(params.file_name,
filter_path.format(idx=idx_filter)):
log.warning(
' *** *** Filter {idx} not found in HDF file. Set this filter to none'
.format(idx=idx_filter))
setattr(params, param_path.format(idx=idx_filter, attr='material'),
'Al')
setattr(params, param_path.format(idx=idx_filter,
attr='thickness'), 0.0)
continue
filter_auto = getattr(params,
param_path.format(idx=idx_filter, attr='auto'))
if filter_auto != 'True' and filter_auto != True:
log.warning(
' *** *** do not auto read filter {n}'.format(n=idx_filter))
continue
log.warning(' *** *** auto reading parameters for filter {0}'.format(
idx_filter))
# See if there are description and thickness fields
if check_item_exists_hdf(
params.file_name,
filter_path.format(idx=idx_filter) + '/description'):
filt_material = config.param_from_dxchange(
params.file_name,
filter_path.format(idx=idx_filter) + '/description',
char_array=True,
scalar=False)
filt_thickness = int(
config.param_from_dxchange(params.file_name,
filter_path.format(idx=idx_filter) +
'/thickness',
char_array=False,
scalar=True))
else:
#The filter info is just the raw string from the filter unit.
log.warning(
' *** *** filter {idx} info must be read from the raw string'.
format(idx=idx_filter))
filter_str = config.param_from_dxchange(
params.file_name,
filter_path.format(idx=idx_filter) + '/setup/filter_unit_text',
char_array=True,
scalar=False)
if filter_str is None:
log.warning(
' *** *** Could not load filter %d configuration from HDF5 file.'
% idx_filter)
filt_material, filt_thickness = _filter_str_to_params('Open')
else:
filt_material, filt_thickness = _filter_str_to_params(
filter_str)
# Update the params with the loaded values
setattr(params, param_path.format(idx=idx_filter, attr='material'),
filt_material)
setattr(params, param_path.format(idx=idx_filter, attr='thickness'),
filt_thickness)
log.info(' *** *** Filter %d: (%s %f)' %
(idx_filter, filt_material, filt_thickness))
return params