nxtomomill.settings.Tomo#

class nxtomomill.settings.Tomo[source]#

Bases: object

__init__()#

Methods

class EDF[source]#

Bases: object

EDF settings for tomography

DARK_NAMES = ('darkend', 'dark')#: Names identifying dark images in EDF files.

MACHINE_CURRENT = ('srcur', 'srcurrent')#: Keys used to store machine current values.

MOTOR_MNE = ('motor_mne',)#: Keys for motor names (mnemonics).

MOTOR_POS = ('motor_pos',)#: Keys for motor positions.

REFS_NAMES = ('ref', 'refHST')#: Names identifying reference images in EDF files.

ROT_ANGLE = ('srot', 'somega')#: Keys used to find the rotation angle.

TO_IGNORE = ('_slice_',)#: Fields to ignore when processing EDF files.

X_TRANS = ('sx',)#: Keys used to find x translation in EDF format.

Y_TRANS = ('sy',)#: Keys used to find y translation in EDF format.

Z_TRANS = ('sz',)#: Keys used to find z translation in EDF format.

class H5[source]#

Bases: object

HDF5 settings for tomography

ACQ_EXPO_TIME_KEYS = ('acq_expo_time',)#: Keys used to store acquisition exposure time.

ALIGNMENT_TITLES = ('static images', 'ascan diffrz 180 0 4 0.1')#: Titles to determine alignment scans if ‘technique/image_key’ doesn’t exists.

BACK_AND_FORTH_INIT_TITLES = ('tomo:backandforth', 'backandforthtomo:basic', 'backandforth', 'tomo:back_and_forth', 'back_and_forth')#: Specific titles for back and forth scans. Either the value of ‘technique/scan_category’ if exists else the value of ‘title’

DARK_TITLES = ('dark images', 'dark')#: Titles to determine dark field scans if ‘technique/image_key’ doesn’t exists.

DIODE_KEYS = ('fpico3',)#: Keys used to store diode dataset.

FLAT_TITLES = ('flat', 'reference images', 'ref', 'refend')#: Titles to determine flat field scans if ‘technique/image_key’ doesn’t exists.

INIT_TITLES = ('tomo:basic', 'tomo:fullturn', 'tomo:fulltomo', 'sequence_of_scans', 'tomo:halfturn', 'tomo:multiturn', 'tomo:helical', 'tomo:holotomo', 'holotomo_distance')#: Initialization scan titles. Either the value of ‘technique/scan_category’ if exists else the value of ‘title’

MACHINE_CURRENT_KEYS = ('current',)#: Keys used to store machine current values.

MULTITOMO_INIT_TITLES = ('tomo:pcotomo', 'pcotomo', 'tomo:multitomo', 'multitomo', 'multitomo:basic', 'tomo:multiturn', 'multiturn')#: Specific titles for multi-tomo scans (also known as PCO scans). Either the value of ‘technique/scan_category’ if exists else the value of ‘title’

PCOTOMO_INIT_TITLES = ('tomo:pcotomo', 'pcotomo', 'tomo:multitomo', 'multitomo', 'multitomo:basic', 'tomo:multiturn', 'multiturn')#: Deprecated. Replaced by ‘MULTITOMO_INIT_TITLES’

PROJ_TITLES = ('projections', 'ascan rot 0', 'ascan diffrz 0 180 1600 0.1')#: Titles to determine projection scans if ‘technique/image_key’ doesn’t exists.

ROT_ANGLE_KEYS = ('rotm', 'mhsrot', 'hsrot', 'mrsrot', 'hrsrot', 'srot', 'srot_eh2', 'diffrz', 'hrrz_trig', 'rot')#: Keys used to find rotation angles.

SAMPLE_DETECTOR_DISTANCE_KEYS = ('technique/scan/sample_detector_distance',)#: Keys used to store the sample to detector distance.

SAMPLE_U_KEYS = ('sau', 'sx', 'px', 'ntx', 'shtx', 'hrx', 'fake_su')#: Keys used to find the U translation above the center of rotation (direction is dependent of the rotation angle).

SAMPLE_V_KEYS = ('sav', 'sy', 'py', 'nty', 'shty', 'hry2', 'fake_sv')#: Keys used to find the V translation above the center of rotation (direction is dependent of the rotation angle).

SAMPLE_X_KEYS = ('samx', 'psx', 'sax', 'fake_sx')#: Keys used to find the X translation above the center of rotation (direction is independent of the rotation angle).

SAMPLE_X_PIXEL_SIZE_KEYS = ('technique/optic/sample_pixel_size',)#: Possible paths to the pixel size along the x-axis.

SAMPLE_Y_KEYS = ('samy', 'psv', 'say', 'fake_sy')#: Keys used to find the Y translation above the center of rotation (direction is independent of the rotation angle).

SAMPLE_Y_PIXEL_SIZE_KEYS = ('technique/optic/sample_pixel_size',)#: Possible paths to the pixel size along the y-axis.

SOURCE_SAMPLE_DISTANCE_KEYS = ('technique/scan/source_sample_distance',)#: Keys used to store the source to sample distance.

TRANSLATION_Y_KEYS = ('yrot', 'diffty', 'hry')#: Keys used to find the Y translation below the center of rotation.

TRANSLATION_Z_KEYS = ('sz', 'difftz', 'hrz', 'pz', 'ntz', 'samtz', 'mrsz')#: Keys used to find the Z translation below or above the center of rotation.

ZSERIE_INIT_TITLES = ('tomo:zseries',)#: Specific titles for z-series scans.