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Fix kernel to be symetric and properly spheroid#609

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matham wants to merge 1 commit intobrainglobe:mainfrom
matham:kernel
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Fix kernel to be symetric and properly spheroid#609
matham wants to merge 1 commit intobrainglobe:mainfrom
matham:kernel

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@matham matham commented Mar 26, 2026

Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?

I noticed a bit of wonkiness in the kernel of the ball filter. I'm not sure how much of this intentional, so this PR edits it to how I would naively think the kernel should look so we can see if/what needs to change.

Primarily the issues I noticed is

  1. When the kernel size is odd, things look okay. But when it's even it's not symmetric and further it's a bit offset from where the center (centre 😉) should be between voxels. So the filtered data gets a bit shifted.
  2. This seems more of a bug, but the radius of the sphere is mostly the xy radius. So if the z radius is larger, it's essentially clipped to the xy radius instead of being a spheroid.

Following I printed out the kernel values so you can get a sense of what it's doing:

def print_kernel(ball_xy_size, ball_z_size):
    d = np.moveaxis(get_kernel(ball_xy_size, ball_z_size), 2, 0)
    for z in range(d.shape[0]):
        for y in range(d.shape[1]):
            print("\t".join([f"{v:0.2f}" for v in np.round(d[z, y], 2).tolist()]))
        print()

for xy in range(1, 5):
    for z in range(1, 5):
        print(f"Kernel: xy={xy}, z={z}")
        print_kernel(xy, z)

This gives for main:

Kernel: xy=1, z=1
0.52

Kernel: xy=1, z=2
0.21

0.31

Kernel: xy=1, z=3
0.00

0.52

0.00

Kernel: xy=1, z=4
0.00

0.21

0.31

0.00

Kernel: xy=1, z=5
0.00

0.00

0.52

0.00

0.00

Kernel: xy=2, z=1
0.59	0.71
0.71	0.85

Kernel: xy=2, z=2
0.37	0.46
0.46	0.57

0.46	0.57
0.57	0.69

Kernel: xy=2, z=3
0.12	0.15
0.15	0.20

0.59	0.71
0.71	0.85

0.12	0.15
0.15	0.20

Kernel: xy=2, z=4
0.00	0.00
0.00	0.00

0.37	0.46
0.46	0.57

0.46	0.57
0.57	0.69

0.00	0.00
0.00	0.00

Kernel: xy=2, z=5
0.00	0.00
0.00	0.00

0.12	0.15
0.15	0.20

0.59	0.71
0.71	0.85

0.12	0.15
0.15	0.20

0.00	0.00
0.00	0.00

Kernel: xy=3, z=1
0.52	0.97	0.52
0.97	1.00	0.97
0.52	0.97	0.52

Kernel: xy=3, z=2
0.39	0.83	0.39
0.83	1.00	0.83
0.39	0.83	0.39

0.44	0.90	0.44
0.90	1.00	0.90
0.44	0.90	0.44

Kernel: xy=3, z=3
0.17	0.52	0.17
0.52	0.97	0.52
0.17	0.52	0.17

0.52	0.97	0.52
0.97	1.00	0.97
0.52	0.97	0.52

0.17	0.52	0.17
0.52	0.97	0.52
0.17	0.52	0.17

Kernel: xy=3, z=4
0.01	0.10	0.01
0.10	0.39	0.10
0.01	0.10	0.01

0.39	0.83	0.39
0.83	1.00	0.83
0.39	0.83	0.39

0.44	0.90	0.44
0.90	1.00	0.90
0.44	0.90	0.44

0.03	0.18	0.03
0.18	0.54	0.18
0.03	0.18	0.03

Kernel: xy=3, z=5
0.00	0.00	0.00
0.00	0.00	0.00
0.00	0.00	0.00

0.17	0.52	0.17
0.52	0.97	0.52
0.17	0.52	0.17

0.52	0.97	0.52
0.97	1.00	0.97
0.52	0.97	0.52

0.17	0.52	0.17
0.52	0.97	0.52
0.17	0.52	0.17

0.00	0.00	0.00
0.00	0.00	0.00
0.00	0.00	0.00

Kernel: xy=4, z=1
0.20	0.79	0.83	0.29
0.79	1.00	1.00	0.94
0.83	1.00	1.00	0.97
0.29	0.94	0.97	0.41

Kernel: xy=4, z=2
0.14	0.71	0.75	0.22
0.71	1.00	1.00	0.85
0.75	1.00	1.00	0.90
0.22	0.85	0.90	0.31

0.16	0.75	0.79	0.24
0.75	1.00	1.00	0.90
0.79	1.00	1.00	0.93
0.24	0.90	0.93	0.35

Kernel: xy=4, z=3
0.06	0.50	0.55	0.10
0.50	1.00	1.00	0.64
0.55	1.00	1.00	0.69
0.10	0.64	0.69	0.17

0.20	0.79	0.83	0.29
0.79	1.00	1.00	0.94
0.83	1.00	1.00	0.97
0.29	0.94	0.97	0.41

0.06	0.50	0.55	0.10
0.50	1.00	1.00	0.64
0.55	1.00	1.00	0.69
0.10	0.64	0.69	0.17

Kernel: xy=4, z=4
0.00	0.14	0.16	0.01
0.14	0.71	0.75	0.22
0.16	0.75	0.79	0.24
0.01	0.22	0.24	0.03

0.14	0.71	0.75	0.22
0.71	1.00	1.00	0.85
0.75	1.00	1.00	0.90
0.22	0.85	0.90	0.31

0.16	0.75	0.79	0.24
0.75	1.00	1.00	0.90
0.79	1.00	1.00	0.93
0.24	0.90	0.93	0.35

0.01	0.22	0.24	0.03
0.22	0.85	0.90	0.31
0.24	0.90	0.93	0.35
0.03	0.31	0.35	0.05

Kernel: xy=4, z=5
0.00	0.01	0.01	0.00
0.01	0.29	0.32	0.03
0.01	0.32	0.36	0.03
0.00	0.03	0.03	0.00

0.06	0.50	0.55	0.10
0.50	1.00	1.00	0.64
0.55	1.00	1.00	0.69
0.10	0.64	0.69	0.17

0.20	0.79	0.83	0.29
0.79	1.00	1.00	0.94
0.83	1.00	1.00	0.97
0.29	0.94	0.97	0.41

0.06	0.50	0.55	0.10
0.50	1.00	1.00	0.64
0.55	1.00	1.00	0.69
0.10	0.64	0.69	0.17

0.00	0.01	0.01	0.00
0.01	0.29	0.32	0.03
0.01	0.32	0.36	0.03
0.00	0.03	0.03	0.00

Kernel: xy=5, z=1
0.12	0.76	0.99	0.76	0.12
0.76	1.00	1.00	1.00	0.76
0.99	1.00	1.00	1.00	0.99
0.76	1.00	1.00	1.00	0.76
0.12	0.76	0.99	0.76	0.12

Kernel: xy=5, z=2
0.09	0.68	0.91	0.68	0.09
0.68	1.00	1.00	1.00	0.68
0.91	1.00	1.00	1.00	0.91
0.68	1.00	1.00	1.00	0.68
0.09	0.68	0.91	0.68	0.09

0.10	0.71	0.94	0.71	0.10
0.71	1.00	1.00	1.00	0.71
0.94	1.00	1.00	1.00	0.94
0.71	1.00	1.00	1.00	0.71
0.10	0.71	0.94	0.71	0.10

Kernel: xy=5, z=3
0.04	0.51	0.76	0.51	0.04
0.51	1.00	1.00	1.00	0.51
0.76	1.00	1.00	1.00	0.76
0.51	1.00	1.00	1.00	0.51
0.04	0.51	0.76	0.51	0.04

0.12	0.76	0.99	0.76	0.12
0.76	1.00	1.00	1.00	0.76
0.99	1.00	1.00	1.00	0.99
0.76	1.00	1.00	1.00	0.76
0.12	0.76	0.99	0.76	0.12

0.04	0.51	0.76	0.51	0.04
0.51	1.00	1.00	1.00	0.51
0.76	1.00	1.00	1.00	0.76
0.51	1.00	1.00	1.00	0.51
0.04	0.51	0.76	0.51	0.04

Kernel: xy=5, z=4
0.00	0.20	0.39	0.20	0.00
0.20	0.89	1.00	0.89	0.20
0.39	1.00	1.00	1.00	0.39
0.20	0.89	1.00	0.89	0.20
0.00	0.20	0.39	0.20	0.00

0.09	0.68	0.91	0.68	0.09
0.68	1.00	1.00	1.00	0.68
0.91	1.00	1.00	1.00	0.91
0.68	1.00	1.00	1.00	0.68
0.09	0.68	0.91	0.68	0.09

0.10	0.71	0.94	0.71	0.10
0.71	1.00	1.00	1.00	0.71
0.94	1.00	1.00	1.00	0.94
0.71	1.00	1.00	1.00	0.71
0.10	0.71	0.94	0.71	0.10

0.01	0.27	0.50	0.27	0.01
0.27	0.95	1.00	0.95	0.27
0.50	1.00	1.00	1.00	0.50
0.27	0.95	1.00	0.95	0.27
0.01	0.27	0.50	0.27	0.01

Kernel: xy=5, z=5
0.00	0.04	0.12	0.04	0.00
0.04	0.51	0.76	0.51	0.04
0.12	0.76	0.99	0.76	0.12
0.04	0.51	0.76	0.51	0.04
0.00	0.04	0.12	0.04	0.00

0.04	0.51	0.76	0.51	0.04
0.51	1.00	1.00	1.00	0.51
0.76	1.00	1.00	1.00	0.76
0.51	1.00	1.00	1.00	0.51
0.04	0.51	0.76	0.51	0.04

0.12	0.76	0.99	0.76	0.12
0.76	1.00	1.00	1.00	0.76
0.99	1.00	1.00	1.00	0.99
0.76	1.00	1.00	1.00	0.76
0.12	0.76	0.99	0.76	0.12

0.04	0.51	0.76	0.51	0.04
0.51	1.00	1.00	1.00	0.51
0.76	1.00	1.00	1.00	0.76
0.51	1.00	1.00	1.00	0.51
0.04	0.51	0.76	0.51	0.04

0.00	0.04	0.12	0.04	0.00
0.04	0.51	0.76	0.51	0.04
0.12	0.76	0.99	0.76	0.12
0.04	0.51	0.76	0.51	0.04
0.00	0.04	0.12	0.04	0.00

You can see how skewed the kernel gets in either direction when xy is significantly different than z.

What does this PR do?

I changed the sphere shape to be properly spheroid and to be centered between voxels when the kernel is even.

With this PR, the printout is instead:

Kernel: xy=1, z=1
0.52

Kernel: xy=1, z=2
0.52

0.52

Kernel: xy=1, z=3
0.43

0.76

0.43

Kernel: xy=1, z=4
0.31

0.73

0.73

0.31

Kernel: xy=1, z=5
0.28

0.67

0.76

0.67

0.28

Kernel: xy=2, z=1
0.56	0.56
0.56	0.56

Kernel: xy=2, z=2
0.54	0.54
0.54	0.54

0.54	0.54
0.54	0.54

Kernel: xy=2, z=3
0.42	0.42
0.42	0.42

0.77	0.77
0.77	0.77

0.42	0.42
0.42	0.42

Kernel: xy=2, z=4
0.33	0.33
0.33	0.33

0.72	0.72
0.72	0.72

0.72	0.72
0.72	0.72

0.33	0.33
0.33	0.33

Kernel: xy=2, z=5
0.27	0.27
0.27	0.27

0.66	0.66
0.66	0.66

0.77	0.77
0.77	0.77

0.66	0.66
0.66	0.66

0.27	0.27
0.27	0.27

Kernel: xy=3, z=1
0.29	0.68	0.29
0.68	1.00	0.68
0.29	0.68	0.29

Kernel: xy=3, z=2
0.28	0.65	0.28
0.65	0.99	0.65
0.28	0.65	0.28

0.28	0.65	0.28
0.65	0.99	0.65
0.28	0.65	0.28

Kernel: xy=3, z=3
0.17	0.52	0.17
0.52	0.97	0.52
0.17	0.52	0.17

0.52	0.97	0.52
0.97	1.00	0.97
0.52	0.97	0.52

0.17	0.52	0.17
0.52	0.97	0.52
0.17	0.52	0.17

Kernel: xy=3, z=4
0.10	0.40	0.10
0.40	0.92	0.40
0.10	0.40	0.10

0.47	0.91	0.47
0.91	1.00	0.91
0.47	0.91	0.47

0.47	0.91	0.47
0.91	1.00	0.91
0.47	0.91	0.47

0.10	0.40	0.10
0.40	0.92	0.40
0.10	0.40	0.10

Kernel: xy=3, z=5
0.06	0.33	0.06
0.33	0.92	0.33
0.06	0.33	0.06

0.39	0.84	0.39
0.84	1.00	0.84
0.39	0.84	0.39

0.53	0.98	0.53
0.98	1.00	0.98
0.53	0.98	0.53

0.39	0.84	0.39
0.84	1.00	0.84
0.39	0.84	0.39

0.06	0.33	0.06
0.33	0.92	0.33
0.06	0.33	0.06

Kernel: xy=4, z=1
0.12	0.51	0.51	0.12
0.51	0.95	0.95	0.51
0.51	0.95	0.95	0.51
0.12	0.51	0.51	0.12

Kernel: xy=4, z=2
0.13	0.54	0.54	0.13
0.54	0.92	0.92	0.54
0.54	0.92	0.92	0.54
0.13	0.54	0.54	0.13

0.13	0.54	0.54	0.13
0.54	0.92	0.92	0.54
0.54	0.92	0.92	0.54
0.13	0.54	0.54	0.13

Kernel: xy=4, z=3
0.06	0.34	0.34	0.06
0.34	0.87	0.87	0.34
0.34	0.87	0.87	0.34
0.06	0.34	0.34	0.06

0.28	0.88	0.88	0.28
0.88	1.00	1.00	0.88
0.88	1.00	1.00	0.88
0.28	0.88	0.88	0.28

0.06	0.34	0.34	0.06
0.34	0.87	0.87	0.34
0.34	0.87	0.87	0.34
0.06	0.34	0.34	0.06

Kernel: xy=4, z=4
0.01	0.24	0.24	0.01
0.24	0.83	0.83	0.24
0.24	0.83	0.83	0.24
0.01	0.24	0.24	0.01

0.24	0.83	0.83	0.24
0.83	1.00	1.00	0.83
0.83	1.00	1.00	0.83
0.24	0.83	0.83	0.24

0.24	0.83	0.83	0.24
0.83	1.00	1.00	0.83
0.83	1.00	1.00	0.83
0.24	0.83	0.83	0.24

0.01	0.24	0.24	0.01
0.24	0.83	0.83	0.24
0.24	0.83	0.83	0.24
0.01	0.24	0.24	0.01

Kernel: xy=4, z=5
0.00	0.15	0.15	0.00
0.15	0.78	0.78	0.15
0.15	0.78	0.78	0.15
0.00	0.15	0.15	0.00

0.15	0.71	0.71	0.15
0.71	1.00	1.00	0.71
0.71	1.00	1.00	0.71
0.15	0.71	0.71	0.15

0.31	0.91	0.91	0.31
0.91	1.00	1.00	0.91
0.91	1.00	1.00	0.91
0.31	0.91	0.91	0.31

0.15	0.71	0.71	0.15
0.71	1.00	1.00	0.71
0.71	1.00	1.00	0.71
0.15	0.71	0.71	0.15

0.00	0.15	0.15	0.00
0.15	0.78	0.78	0.15
0.15	0.78	0.78	0.15
0.00	0.15	0.15	0.00

Kernel: xy=5, z=1
0.03	0.38	0.55	0.38	0.03
0.38	0.80	0.92	0.80	0.38
0.55	0.92	1.00	0.92	0.55
0.38	0.80	0.92	0.80	0.38
0.03	0.38	0.55	0.38	0.03

Kernel: xy=5, z=2
0.04	0.36	0.55	0.36	0.04
0.36	0.81	0.91	0.81	0.36
0.55	0.91	1.00	0.91	0.55
0.36	0.81	0.91	0.81	0.36
0.04	0.36	0.55	0.36	0.04

0.04	0.36	0.55	0.36	0.04
0.36	0.81	0.91	0.81	0.36
0.55	0.91	1.00	0.91	0.55
0.36	0.81	0.91	0.81	0.36
0.04	0.36	0.55	0.36	0.04

Kernel: xy=5, z=3
0.00	0.20	0.36	0.20	0.00
0.20	0.71	0.85	0.71	0.20
0.36	0.85	1.00	0.85	0.36
0.20	0.71	0.85	0.71	0.20
0.00	0.20	0.36	0.20	0.00

0.10	0.72	0.95	0.72	0.10
0.72	1.00	1.00	1.00	0.72
0.95	1.00	1.00	1.00	0.95
0.72	1.00	1.00	1.00	0.72
0.10	0.72	0.95	0.72	0.10

0.00	0.20	0.36	0.20	0.00
0.20	0.71	0.85	0.71	0.20
0.36	0.85	1.00	0.85	0.36
0.20	0.71	0.85	0.71	0.20
0.00	0.20	0.36	0.20	0.00

Kernel: xy=5, z=4
0.00	0.09	0.20	0.09	0.00
0.09	0.61	0.79	0.61	0.09
0.20	0.79	1.00	0.79	0.20
0.09	0.61	0.79	0.61	0.09
0.00	0.09	0.20	0.09	0.00

0.07	0.64	0.88	0.64	0.07
0.64	1.00	1.00	1.00	0.64
0.88	1.00	1.00	1.00	0.88
0.64	1.00	1.00	1.00	0.64
0.07	0.64	0.88	0.64	0.07

0.07	0.64	0.88	0.64	0.07
0.64	1.00	1.00	1.00	0.64
0.88	1.00	1.00	1.00	0.88
0.64	1.00	1.00	1.00	0.64
0.07	0.64	0.88	0.64	0.07

0.00	0.09	0.20	0.09	0.00
0.09	0.61	0.79	0.61	0.09
0.20	0.79	1.00	0.79	0.20
0.09	0.61	0.79	0.61	0.09
0.00	0.09	0.20	0.09	0.00

Kernel: xy=5, z=5
0.00	0.04	0.12	0.04	0.00
0.04	0.51	0.76	0.51	0.04
0.12	0.76	0.99	0.76	0.12
0.04	0.51	0.76	0.51	0.04
0.00	0.04	0.12	0.04	0.00

0.04	0.51	0.76	0.51	0.04
0.51	1.00	1.00	1.00	0.51
0.76	1.00	1.00	1.00	0.76
0.51	1.00	1.00	1.00	0.51
0.04	0.51	0.76	0.51	0.04

0.12	0.76	0.99	0.76	0.12
0.76	1.00	1.00	1.00	0.76
0.99	1.00	1.00	1.00	0.99
0.76	1.00	1.00	1.00	0.76
0.12	0.76	0.99	0.76	0.12

0.04	0.51	0.76	0.51	0.04
0.51	1.00	1.00	1.00	0.51
0.76	1.00	1.00	1.00	0.76
0.51	1.00	1.00	1.00	0.51
0.04	0.51	0.76	0.51	0.04

0.00	0.04	0.12	0.04	0.00
0.04	0.51	0.76	0.51	0.04
0.12	0.76	0.99	0.76	0.12
0.04	0.51	0.76	0.51	0.04
0.00	0.04	0.12	0.04	0.00

References

Please reference any existing issues/PRs that relate to this PR.

How has this PR been tested?

I added a test that checks for symmetry.

Is this a breaking change?

In a way it's a break, because the kernel size parameter would behave a bit differently for even kernels and when xy is different than z.

Does this PR require an update to the documentation?

No.

Checklist:

  • The code has been tested locally
  • Tests have been added to cover all new functionality (unit & integration)
  • The documentation has been updated to reflect any changes
  • The code has been formatted with pre-commit

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1 participant

@matham