# coding: utf-8
# /*##########################################################################
#
# Copyright (c) 2015-2020 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
"""
module to convert from (bliss) .h5 to (nexus tomo compliant) .nx
"""
__authors__ = ["H. Payno"]
__license__ = "MIT"
__date__ = "13/05/2020"
[docs]class Tomo:
[docs] class H5:
"""HDF5 settings for tomography"""
VALID_CAMERA_NAMES = None
# now camera names are deduce using converter `get_nx_detectors`
# and `guess_nx_detector` functions. But you can provide A LIST of
# detector name (unix shell-style wildcards are managed) like
# ("pcolinux*", "basler", "frelon*", ...)
ROT_ANGLE_KEYS = (
"rotm",
"mhsrot",
"hsrot",
"mrsrot",
"hrsrot",
"srot",
"srot_eh2",
"diffrz",
"hrrz_trig",
"rot",
)
X_TRANS_KEYS = ("sx", "d3tx", "tfx", "px")
"""Keys used to find the x translation"""
Y_TRANS_KEYS = ("sy", "d3ty", "hry", "py")
"""Keys used by bliss to store y translation"""
Z_TRANS_KEYS = ("sz", "d3tz", "hrz", "pz", "mrsz")
"""Keys used by bliss to store translation"""
Y_ROT_KEY = "instrument/positioners/yrot"
"""Key used by bliss to store the estimated center of rotation for half
acquisition"""
DIODE_KEYS = ("fpico3",)
"""keys used by bliss to store diode dataset"""
ACQ_EXPO_TIME_KEYS = ("acq_expo_time",)
INIT_TITLES = (
# "pcotomo:basic", seems to not be used anymore
"tomo:basic",
"tomo:fullturn",
"sequence_of_scans",
"tomo:halfturn",
"tomo:multiturn",
"tomo:helical",
)
"""if a scan starts by one of those string then is considered as
initialization scan"""
ZSERIE_INIT_TITLES = ("tomo:zseries",)
"""specific titles for zserie. Will extend DEFAULT_SCAN_TITLES"""
PCOTOMO_INIT_TITLES = ("tomo:pcotomo", "pcotomo:")
"""specific titles for pcotomo. Will extend DEFAULT_SCAN_TITLES"""
DARK_TITLES = ("dark images", "dark")
"""if a scan starts by one of those string then is considered as
dark scan"""
FLAT_TITLES = ("flat", "reference images", "ref", "refend")
"""if a scan starts by one of those string then is considered as
reference scan"""
PROJ_TITLES = ("projections", "ascan rot 0 ", "ascan diffrz 0 180 1600 0.1")
"""if a scan starts by one of those string then is considered as
projection scan"""
ALIGNMENT_TITLES = ("static images", "ascan diffrz 180 0 4 0.1")
"""if a scan starts by one of those string then is considered as
alignment scan"""
X_PIXEL_SIZE = ( # aka "sample" pixel size
"technique/optic/sample_pixel_size",
"technique/detector/pixel_size",
)
"""Possible path to th pixel size."""
Y_PIXEL_SIZE = ( # aka "sample" pixel size
"technique/optic/sample_pixel_size",
"technique/detector/pixel_size",
)
DISTANCE_KEYS = ("technique/scan/sample_detector_distance",)
"""keys used by bliss to store the sample to detector distance"""
MACHINE_ELECTRIC_CURRENT_KEYS = ("current",)
"""keys used by bliss to store the electric current"""
[docs] class EDF:
"""EDF settings for tomography"""
MOTOR_POS = ("motor_pos",)
MOTOR_MNE = ("motor_mne",)
ROT_ANGLE = (
"srot",
"somega",
)
X_TRANS = ("sx",)
Y_TRANS = ("sy",)
Z_TRANS = ("sz",)
MACHINE_ELECTRIC_CURRENT = ("srcur", "srcurrent")
# EDF_TO_IGNORE = ['HST', '_slice_']
TO_IGNORE = ("_slice_",)
DARK_NAMES = ("darkend", "dark")
REFS_NAMES = ("ref", "refHST")
[docs]class XRD3D(Tomo):
[docs] class H5(Tomo.H5):
positioners_path = "instrument/positioners/"
ROT_ANGLE_KEYS = (positioners_path + "diffrz", positioners_path + "rot")
ROCKING_KEYS = (
positioners_path + "diffty",
positioners_path + "instrument/positioners/dty",
)
