1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
# coding: utf-8
"""
Module to convert from (Bliss) .h5 to (Nexus Tomo-compliant) .nx format.
"""
class Tomo:
class H5:
"""HDF5 settings for tomography"""
VALID_CAMERA_NAMES: tuple[str, ...] = tuple()
# Camera names are now deduced using the `get_nx_detectors` and
# `guess_nx_detector` functions. Alternatively, a list of detector
# names can be provided (supports Unix shell-style wildcards), such as:
# ("pcolinux*", "basler", "frelon*", ...)
ROT_ANGLE_KEYS = (
"rotm",
"mhsrot",
"hsrot",
"mrsrot",
"hrsrot",
"srot",
"srot_eh2",
"diffrz",
"hrrz_trig",
"rot",
)
"""Keys used to find rotation angles."""
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."""
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_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_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)."""
DIODE_KEYS = ("fpico3",)
"""Keys used to store diode dataset."""
ACQ_EXPO_TIME_KEYS = ("acq_expo_time",)
"""Keys used to store acquisition exposure time."""
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'"""
ZSERIE_INIT_TITLES = ("tomo:zseries",)
"""Specific titles for z-series scans."""
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 = MULTITOMO_INIT_TITLES
"""Deprecated. Replaced by 'MULTITOMO_INIT_TITLES'"""
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."""
FLAT_TITLES = ("flat", "reference images", "ref", "refend")
"""Titles to determine flat field scans if 'technique/image_key' doesn't exists."""
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."""
ALIGNMENT_TITLES = ("static images", "ascan diffrz 180 0 4 0.1")
"""Titles to determine alignment scans if 'technique/image_key' doesn't exists."""
SAMPLE_X_PIXEL_SIZE_KEYS = ("technique/optic/sample_pixel_size",)
"""Possible paths to the pixel size along the x-axis."""
SAMPLE_Y_PIXEL_SIZE_KEYS = ("technique/optic/sample_pixel_size",)
"""Possible paths to the pixel size along the y-axis."""
DETECTOR_X_PIXEL_SIZE_KEYS = (
"technique/optic/optics_pixel_size",
"technique/scan/detector_pixel_size",
"technique/detector/{detector_name}/pixel_size",
"technique/detector/pixel_size",
)
DETECTOR_Y_PIXEL_SIZE_KEYS = (
"technique/optic/optics_pixel_size",
"technique/scan/detector_pixel_size",
"technique/detector/{detector_name}/pixel_size",
"technique/detector/pixel_size",
)
SAMPLE_DETECTOR_DISTANCE_KEYS = ("technique/scan/sample_detector_distance",)
"""Keys used to store the sample to detector distance."""
SOURCE_SAMPLE_DISTANCE_KEYS = ("technique/scan/source_sample_distance",)
"""Keys used to store the source to sample distance."""
MACHINE_CURRENT_KEYS = ("current",)
"""Keys used to store machine current values."""
class EDF:
"""EDF settings for tomography"""
MOTOR_POS = ("motor_pos",)
"""Keys for motor positions."""
MOTOR_MNE = ("motor_mne",)
"""Keys for motor names (mnemonics)."""
ROT_ANGLE = ("srot", "somega")
"""Keys used to find the rotation angle."""
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."""
MACHINE_CURRENT = ("srcur", "srcurrent")
"""Keys used to store machine current values."""
TO_IGNORE = ("_slice_",)
"""Fields to ignore when processing EDF files."""
DARK_NAMES = ("darkend", "dark")
"""Names identifying dark images in EDF files."""
REFS_NAMES = ("ref", "refHST")
"""Names identifying reference images in EDF files."""
|
