Coverage for src/abm_initialization_collection/sample/get_sample_indices.py: 100%
19 statements
« prev ^ index » next coverage.py v7.1.0, created at 2024-07-26 20:12 +0000
1from abm_initialization_collection.coordinate.make_grid_coordinates import (
2 make_hex_grid_coordinates,
3 make_rect_grid_coordinates,
4)
7def get_sample_indices(
8 grid: str,
9 bounds: tuple[int, int, int],
10 resolution: float,
11 scale_xy: float,
12 scale_z: float,
13) -> list:
14 """
15 Get sample indices with given bounds for selected grid type.
17 Parameters
18 ----------
19 grid : {'rect', 'hex'}
20 Type of grid.
21 bounds
22 Sampling bounds in the x, y, and z directions.
23 resolution
24 Distance between samples (um).
25 scale_xy
26 Resolution scaling in x/y (um/pixel).
27 scale_z
28 Resolution scaling in z (um/pixel).
30 Returns
31 -------
32 :
33 List of sample indices.
34 """
36 if grid == "rect":
37 return get_rect_sample_indices(bounds, resolution, scale_xy, scale_z)
39 if grid == "hex":
40 return get_hex_sample_indices(bounds, resolution, scale_xy, scale_z)
42 raise ValueError(f"invalid grid type {grid}")
45def get_rect_sample_indices(
46 bounds: tuple[int, int, int],
47 resolution: float,
48 scale_xy: float,
49 scale_z: float,
50) -> list:
51 """
52 Get list of (x, y, z) sample indices for rect grid.
54 Parameters
55 ----------
56 bounds
57 Sampling bounds in the x, y, and z directions.
58 resolution
59 Distance between samples (um).
60 scale_xy
61 Resolution scaling in x/y.
62 scale_z
63 Resolution scaling in z.
65 Returns
66 -------
67 :
68 List of sample indices.
69 """
71 increment_z = round(resolution / scale_z)
72 increment_xy = round(resolution / scale_xy)
74 sample_coordinates = make_rect_grid_coordinates(bounds, increment_xy, increment_z)
75 sample_indices = [(round(x), round(y), z) for x, y, z in sample_coordinates]
77 return sample_indices
80def get_hex_sample_indices(
81 bounds: tuple[int, int, int],
82 resolution: float,
83 scale_xy: float,
84 scale_z: float,
85) -> list:
86 """
87 Get list of (x, y, z) sample indices for hex grid.
89 Sample indices are offset in sets of three z slices to form a
90 face-centered cubic (FCC) packing.
92 Parameters
93 ----------
94 bounds
95 Sampling bounds in the x, y, and z directions.
96 resolution
97 Distance between samples (um).
98 scale_xy
99 Resolution scaling in x/y.
100 scale_z
101 Resolution scaling in z.
103 Returns
104 -------
105 :
106 List of sample indices.
107 """
109 increment_z = round(resolution / scale_z)
110 increment_xy = round(resolution / scale_xy)
112 sample_coordinates = make_hex_grid_coordinates(bounds, increment_xy, increment_z)
113 sample_indices = [(round(x), round(y), z) for x, y, z in sample_coordinates]
115 return sample_indices