Coverage for src/recon3d/constants.py: 100%
19 statements
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1"""
2This module stores constant values in a single location for recon3d.
4This module defines various constants and conversion factors that are used
5throughout the recon3d application. It provides a centralized location for
6these constants, making the code more maintainable and easier to understand.
8Classes
9-------
10Constants
11 Creates all constants used in this module.
13Conversions
14 Unit conversions.
16SkimageConnectivity
17 Connectivity level to be used with skimage.measure.label function in 3D.
19CC3DConnectivity
20 Connectivity level to be used with cc3d.connected_components function in 3D.
22Attributes
23----------
24MODULE_NAME : str
25 The name of the module.
26"""
28from typing import NamedTuple, Final
29import numpy as np
31MODULE_NAME: Final[str] = "recon3d"
34class Constants(NamedTuple):
35 """
36 Creates all constants used in this module.
38 This class defines a set of constants that are used throughout the module.
39 It utilizes the `NamedTuple` from the `typing` module to create immutable
40 constants.
42 Attributes
43 ----------
44 YML_SCHEMA_VERSION : float
45 The version of the YAML schema.
46 module_short_name : str
47 The short name of the module.
48 module_prompt : str
49 The prompt string for the module.
50 KNUD_THOMSEN_FACTOR : float
51 The Knud Thomsen factor for the surface area of a scalene ellipsoid.
52 """
54 YML_SCHEMA_VERSION: float = 1.0
55 module_short_name: str = MODULE_NAME
56 module_prompt: str = MODULE_NAME + ">"
57 KNUD_THOMSEN_FACTOR: float = 1.6075 # for surface area of scalene ellipsoid
59 # def __init__(self) -> None:
60 # self.YML_SCHEMA_VERSION = 1.0 # Good
63class Conversions(NamedTuple):
64 """
65 Unit conversions.
67 This class defines constants for converting between radians and degrees.
68 It utilizes the `NamedTuple` from the `typing` module to create immutable
69 constants.
71 Attributes
72 ----------
73 RAD_TO_DEG : float
74 Conversion factor from radians to degrees.
75 DEG_TO_RAD : float
76 Conversion factor from degrees to radians.
77 """
79 RAD_TO_DEG: float = 180 / np.pi
80 DEG_TO_RAD: float = 1 / RAD_TO_DEG
83class SkimageConnectivity(NamedTuple):
84 """
85 Connectivity level to be used with skimage.measure.label function in 3D.
87 This class defines constants for different levels of connectivity that can
88 be used with the `skimage.measure.label` function in 3D image processing.
89 It utilizes the `NamedTuple` from the `typing` module to create immutable
90 constants.
92 Attributes
93 ----------
94 FACE_NEIGHBORS : int
95 Connectivity level with 6 face neighbors.
96 FACE_EDGE_NEIGHBORS : int
97 Connectivity level with 6 face neighbors and 12 edge neighbors.
98 FACE_EDGE_VERTEX_NEIGHBORS : int
99 Connectivity level with 6 face neighbors, 12 edge neighbors, and 8 vertex neighbors.
100 """
102 FACE_NEIGHBORS = 1
103 FACE_EDGE_NEIGHBORS = 2
104 FACE_EDGE_VERTEX_NEIGHBORS = 3
107class CC3DConnectivity(NamedTuple):
108 """
109 Connectivity level to be used with cc3d.connect_components function in 3D.
111 This class defines constants for different levels of connectivity that can
112 be used with the `cc3d.connected_components` function.
113 It utilizes the `NamedTuple` from the `typing` module to create immutable
114 constants.
116 Attributes
117 ----------
118 FACE_NEIGHBORS : int
119 Connectivity level with 6 face neighbors.
120 FACE_EDGE_NEIGHBORS : int
121 Connectivity level with 6 face neighbors and 12 edge neighbors.
122 FACE_EDGE_VERTEX_NEIGHBORS : int
123 Connectivity level with 6 face neighbors, 12 edge neighbors, and 8 vertex neighbors.
124 """
126 FACE_NEIGHBORS = 6
127 FACE_EDGE_NEIGHBORS = 18
128 FACE_EDGE_VERTEX_NEIGHBORS = 26