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3313 Add affine arg to the dict transform #3326

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Merged
merged 9 commits into from
Nov 12, 2021
Merged

3313 Add affine arg to the dict transform #3326

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42a45e0
Merge pull request #19 from Project-MONAI/master
Nic-Ma Feb 1, 2021
cd16a13
Merge pull request #32 from Project-MONAI/master
Nic-Ma Feb 24, 2021
6f87afd
Merge pull request #180 from Project-MONAI/dev
Nic-Ma Jul 22, 2021
f398298
Merge pull request #214 from Project-MONAI/dev
Nic-Ma Sep 8, 2021
93c7a26
Merge pull request #282 from Project-MONAI/dev
Nic-Ma Nov 12, 2021
8c25e0c
[DLMED] add affine to dict transform
Nic-Ma Nov 12, 2021
ae9c5fa
Merge branch 'dev' into 3313-add-arg-dict
Nic-Ma Nov 12, 2021
03fd0e2
Merge branch 'dev' into 3313-add-arg-dict
Nic-Ma Nov 12, 2021
1f18eec
[DLMED] add unit tests
Nic-Ma Nov 12, 2021
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5 changes: 5 additions & 0 deletions monai/transforms/spatial/dictionary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -605,6 +605,7 @@ def __init__(
shear_params: Optional[Union[Sequence[float], float]] = None,
translate_params: Optional[Union[Sequence[float], float]] = None,
scale_params: Optional[Union[Sequence[float], float]] = None,
affine: Optional[NdarrayOrTensor] = None,
spatial_size: Optional[Union[Sequence[int], int]] = None,
mode: GridSampleModeSequence = GridSampleMode.BILINEAR,
padding_mode: GridSamplePadModeSequence = GridSamplePadMode.REFLECTION,
Expand All @@ -631,6 +632,9 @@ def __init__(
pixel/voxel relative to the center of the input image. Defaults to no translation.
scale_params: scale factor for every spatial dims. a tuple of 2 floats for 2D,
a tuple of 3 floats for 3D. Defaults to `1.0`.
affine: if applied, ignore the params (`rotate_params`, etc.) and use the
supplied matrix. Should be square with each side = num of image spatial
dimensions + 1.
spatial_size: output image spatial size.
if `spatial_size` and `self.spatial_size` are not defined, or smaller than 1,
the transform will use the spatial size of `img`.
Expand Down Expand Up @@ -662,6 +666,7 @@ def __init__(
shear_params=shear_params,
translate_params=translate_params,
scale_params=scale_params,
affine=affine,
spatial_size=spatial_size,
device=device,
)
Expand Down
11 changes: 11 additions & 0 deletions tests/test_affine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,17 @@
p(np.array([[[0.0, 0.0, 0.0, 0.0], [0.0, 2.0, 0.0, 0.0], [0.0, 3.0, 1.0, 0.0], [0.0, 0.0, 0.0, 0.0]]])),
]
)
TESTS.append(
[
dict(
affine=p(torch.tensor([[0.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]])),
padding_mode="zeros",
device=device,
),
{"img": p(np.arange(4).reshape((1, 2, 2))), "spatial_size": (4, 4)},
p(np.array([[[0.0, 0.0, 0.0, 0.0], [0.0, 2.0, 0.0, 0.0], [0.0, 3.0, 1.0, 0.0], [0.0, 0.0, 0.0, 0.0]]])),
]
)
TESTS.append(
[
dict(padding_mode="zeros", device=device),
Expand Down
30 changes: 30 additions & 0 deletions tests/test_affine_grid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,35 @@
),
]
)
TESTS.append(
[
{
"affine": p(
torch.tensor(
[[-10.8060, -8.4147, 0.0000], [-16.8294, 5.4030, 0.0000], [0.0000, 0.0000, 1.0000]]
)
)
},
{"grid": p(torch.ones((3, 3, 3)))},
p(
torch.tensor(
[
[
[-19.2208, -19.2208, -19.2208],
[-19.2208, -19.2208, -19.2208],
[-19.2208, -19.2208, -19.2208],
],
[
[-11.4264, -11.4264, -11.4264],
[-11.4264, -11.4264, -11.4264],
[-11.4264, -11.4264, -11.4264],
],
[[1.0, 1.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
]
)
),
]
)
TESTS.append(
[
{"rotate_params": (1.0, 1.0, 1.0), "scale_params": (-20, 10), "device": device},
Expand Down Expand Up @@ -99,6 +128,7 @@
]
)


_rtol = 5e-2 if is_tf32_env() else 1e-4


Expand Down
13 changes: 13 additions & 0 deletions tests/test_affined.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,19 @@
p(np.array([[[0.0, 0.0, 0.0, 0.0], [0.0, 2.0, 0.0, 0.0], [0.0, 3.0, 1.0, 0.0], [0.0, 0.0, 0.0, 0.0]]])),
]
)
TESTS.append(
[
dict(
keys="img",
affine=p(torch.tensor([[0.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]])),
padding_mode="zeros",
spatial_size=(4, 4),
device=device,
),
{"img": p(np.arange(4).reshape((1, 2, 2)))},
p(np.array([[[0.0, 0.0, 0.0, 0.0], [0.0, 2.0, 0.0, 0.0], [0.0, 3.0, 1.0, 0.0], [0.0, 0.0, 0.0, 0.0]]])),
]
)
TESTS.append(
[
dict(keys="img", padding_mode="zeros", spatial_size=(-1, 0, 0), device=device),
Expand Down