Merge branch 'dev' into signal_type_fix

Author: KumoLiu

monai/transforms/spatial/array.py

@@ -64,6 +64,7 @@
     GridSamplePadMode,
     InterpolateMode,
     NumpyPadMode,
+    SpaceKeys,
     convert_to_cupy,
     convert_to_dst_type,
     convert_to_numpy,
@@ -75,6 +76,7 @@
     issequenceiterable,
     optional_import,
 )
+from monai.utils.deprecate_utils import deprecated_arg_default
 from monai.utils.enums import GridPatchSort, PatchKeys, TraceKeys, TransformBackends
 from monai.utils.misc import ImageMetaKey as Key
 from monai.utils.module import look_up_option
@@ -556,11 +558,20 @@ class Orientation(InvertibleTransform, LazyTransform):
 
     backend = [TransformBackends.NUMPY, TransformBackends.TORCH]
 
+    @deprecated_arg_default(
+        name="labels",
+        old_default=(("L", "R"), ("P", "A"), ("I", "S")),
+        new_default=None,
+        msg_suffix=(
+            "Default value changed to None meaning that the transform now uses the 'space' of a "
+            "meta-tensor, if applicable, to determine appropriate axis labels."
+        ),
+    )
     def __init__(
         self,
         axcodes: str | None = None,
         as_closest_canonical: bool = False,
-        labels: Sequence[tuple[str, str]] | None = (("L", "R"), ("P", "A"), ("I", "S")),
+        labels: Sequence[tuple[str, str]] | None = None,
         lazy: bool = False,
     ) -> None:
         """
@@ -573,7 +584,14 @@ def __init__(
             as_closest_canonical: if True, load the image as closest to canonical axis format.
             labels: optional, None or sequence of (2,) sequences
                 (2,) sequences are labels for (beginning, end) of output axis.
-                Defaults to ``(('L', 'R'), ('P', 'A'), ('I', 'S'))``.
+                If ``None``, an appropriate value is chosen depending on the
+                value of the ``"space"`` metadata item of a metatensor: if
+                ``"space"`` is ``"LPS"``, the value used is ``(('R', 'L'),
+                ('A', 'P'), ('I', 'S'))``, if ``"space"`` is ``"RPS"`` or the
+                input is not a meta-tensor or has no ``"space"`` item, the
+                value ``(('L', 'R'), ('P', 'A'), ('I', 'S'))`` is used. If not
+                ``None``, the provided value is always used and the ``"space"``
+                metadata item (if any) of the input is ignored.
             lazy: a flag to indicate whether this transform should execute lazily or not.
                 Defaults to False
 
@@ -619,9 +637,19 @@ def __call__(self, data_array: torch.Tensor, lazy: bool | None = None) -> torch.
             raise ValueError(f"data_array must have at least one spatial dimension, got {spatial_shape}.")
         affine_: np.ndarray
         affine_np: np.ndarray
+        labels = self.labels
         if isinstance(data_array, MetaTensor):
             affine_np, *_ = convert_data_type(data_array.peek_pending_affine(), np.ndarray)
             affine_ = to_affine_nd(sr, affine_np)
+
+            # Set up "labels" such that LPS tensors are handled correctly by default
+            if (
+                self.labels is None
+                and "space" in data_array.meta
+                and SpaceKeys(data_array.meta["space"]) == SpaceKeys.LPS
+            ):
+                labels = (("R", "L"), ("A", "P"), ("I", "S"))  # value for LPS
+
         else:
             warnings.warn("`data_array` is not of type `MetaTensor, assuming affine to be identity.")
             # default to identity
@@ -640,7 +668,7 @@ def __call__(self, data_array: torch.Tensor, lazy: bool | None = None) -> torch.
                     f"{self.__class__.__name__}: spatial shape = {spatial_shape}, channels = {data_array.shape[0]},"
                     "please make sure the input is in the channel-first format."
                 )
-            dst = nib.orientations.axcodes2ornt(self.axcodes[:sr], labels=self.labels)
+            dst = nib.orientations.axcodes2ornt(self.axcodes[:sr], labels=labels)
             if len(dst) < sr:
                 raise ValueError(
                     f"axcodes must match data_array spatially, got axcodes={len(self.axcodes)}D data_array={sr}D"
@@ -653,8 +681,19 @@ def inverse(self, data: torch.Tensor) -> torch.Tensor:
         transform = self.pop_transform(data)
         # Create inverse transform
         orig_affine = transform[TraceKeys.EXTRA_INFO]["original_affine"]
-        orig_axcodes = nib.orientations.aff2axcodes(orig_affine)
-        inverse_transform = Orientation(axcodes=orig_axcodes, as_closest_canonical=False, labels=self.labels)
+        labels = self.labels
+
+        # Set up "labels" such that LPS tensors are handled correctly by default
+        if (
+            isinstance(data, MetaTensor)
+            and self.labels is None
+            and "space" in data.meta
+            and SpaceKeys(data.meta["space"]) == SpaceKeys.LPS
+        ):
+            labels = (("R", "L"), ("A", "P"), ("I", "S"))  # value for LPS
+
+        orig_axcodes = nib.orientations.aff2axcodes(orig_affine, labels=labels)
+        inverse_transform = Orientation(axcodes=orig_axcodes, as_closest_canonical=False, labels=labels)
         # Apply inverse
         with inverse_transform.trace_transform(False):
             data = inverse_transform(data)

monai/transforms/spatial/dictionary.py

@@ -71,6 +71,7 @@
     ensure_tuple_rep,
     fall_back_tuple,
 )
+from monai.utils.deprecate_utils import deprecated_arg_default
 from monai.utils.enums import TraceKeys
 from monai.utils.module import optional_import
 
@@ -545,12 +546,21 @@ class Orientationd(MapTransform, InvertibleTransform, LazyTransform):
 
     backend = Orientation.backend
 
+    @deprecated_arg_default(
+        name="labels",
+        old_default=(("L", "R"), ("P", "A"), ("I", "S")),
+        new_default=None,
+        msg_suffix=(
+            "Default value changed to None meaning that the transform now uses the 'space' of a "
+            "meta-tensor, if applicable, to determine appropriate axis labels."
+        ),
+    )
     def __init__(
         self,
         keys: KeysCollection,
         axcodes: str | None = None,
         as_closest_canonical: bool = False,
-        labels: Sequence[tuple[str, str]] | None = (("L", "R"), ("P", "A"), ("I", "S")),
+        labels: Sequence[tuple[str, str]] | None = None,
         allow_missing_keys: bool = False,
         lazy: bool = False,
     ) -> None:
@@ -564,7 +574,14 @@ def __init__(
             as_closest_canonical: if True, load the image as closest to canonical axis format.
             labels: optional, None or sequence of (2,) sequences
                 (2,) sequences are labels for (beginning, end) of output axis.
-                Defaults to ``(('L', 'R'), ('P', 'A'), ('I', 'S'))``.
+                If ``None``, an appropriate value is chosen depending on the
+                value of the ``"space"`` metadata item of a metatensor: if
+                ``"space"`` is ``"LPS"``, the value used is ``(('R', 'L'),
+                ('A', 'P'), ('I', 'S'))``, if ``"space"`` is ``"RPS"`` or the
+                input is not a meta-tensor or has no ``"space"`` item, the
+                value ``(('L', 'R'), ('P', 'A'), ('I', 'S'))`` is used. If not
+                ``None``, the provided value is always used and the ``"space"``
+                metadata item (if any) of the input is ignored.
             allow_missing_keys: don't raise exception if key is missing.
             lazy: a flag to indicate whether this transform should execute lazily or not.
                 Defaults to False

tests/transforms/test_orientation.py

@@ -12,6 +12,7 @@
 from __future__ import annotations
 
 import unittest
+from typing import cast
 
 import nibabel as nib
 import numpy as np
@@ -21,6 +22,7 @@
 from monai.data.meta_obj import set_track_meta
 from monai.data.meta_tensor import MetaTensor
 from monai.transforms import Orientation, create_rotate, create_translate
+from monai.utils import SpaceKeys
 from tests.lazy_transforms_utils import test_resampler_lazy
 from tests.test_utils import TEST_DEVICES, assert_allclose
 
@@ -33,6 +35,18 @@
             torch.eye(4),
             torch.arange(12).reshape((2, 1, 2, 3)),
             "RAS",
+            False,
+            *device,
+        ]
+    )
+    TESTS.append(
+        [
+            {"axcodes": "LPS"},
+            torch.arange(12).reshape((2, 1, 2, 3)),
+            torch.eye(4),
+            torch.arange(12).reshape((2, 1, 2, 3)),
+            "LPS",
+            True,
             *device,
         ]
     )
@@ -43,6 +57,18 @@
             torch.as_tensor(np.diag([-1, -1, 1, 1])),
             torch.tensor([[[[3, 4, 5]], [[0, 1, 2]]], [[[9, 10, 11]], [[6, 7, 8]]]]),
             "ALS",
+            False,
+            *device,
+        ]
+    )
+    TESTS.append(
+        [
+            {"axcodes": "PRS"},
+            torch.arange(12).reshape((2, 1, 2, 3)),
+            torch.as_tensor(np.diag([-1, -1, 1, 1])),
+            torch.tensor([[[[3, 4, 5]], [[0, 1, 2]]], [[[9, 10, 11]], [[6, 7, 8]]]]),
+            "PRS",
+            True,
             *device,
         ]
     )
@@ -53,6 +79,18 @@
             torch.as_tensor(np.diag([-1, -1, 1, 1])),
             torch.tensor([[[[3, 4, 5], [0, 1, 2]]], [[[9, 10, 11], [6, 7, 8]]]]),
             "RAS",
+            False,
+            *device,
+        ]
+    )
+    TESTS.append(
+        [
+            {"axcodes": "LPS"},
+            torch.arange(12).reshape((2, 1, 2, 3)),
+            torch.as_tensor(np.diag([-1, -1, 1, 1])),
+            torch.tensor([[[[3, 4, 5], [0, 1, 2]]], [[[9, 10, 11], [6, 7, 8]]]]),
+            "LPS",
+            True,
             *device,
         ]
     )
@@ -63,6 +101,18 @@
             torch.eye(3),
             torch.tensor([[[0], [1], [2]], [[3], [4], [5]]]),
             "AL",
+            False,
+            *device,
+        ]
+    )
+    TESTS.append(
+        [
+            {"axcodes": "PR"},
+            torch.arange(6).reshape((2, 1, 3)),
+            torch.eye(3),
+            torch.tensor([[[0], [1], [2]], [[3], [4], [5]]]),
+            "PR",
+            True,
             *device,
         ]
     )
@@ -73,6 +123,18 @@
             torch.eye(2),
             torch.tensor([[2, 1, 0], [5, 4, 3]]),
             "L",
+            False,
+            *device,
+        ]
+    )
+    TESTS.append(
+        [
+            {"axcodes": "R"},
+            torch.arange(6).reshape((2, 3)),
+            torch.eye(2),
+            torch.tensor([[2, 1, 0], [5, 4, 3]]),
+            "R",
+            True,
             *device,
         ]
     )
@@ -83,6 +145,7 @@
             torch.eye(2),
             torch.tensor([[2, 1, 0], [5, 4, 3]]),
             "L",
+            False,
             *device,
         ]
     )
@@ -93,6 +156,7 @@
             torch.as_tensor(np.diag([-1, 1])),
             torch.arange(6).reshape((2, 3)),
             "L",
+            False,
             *device,
         ]
     )
@@ -107,6 +171,7 @@
             ),
             torch.tensor([[[[2, 5]], [[1, 4]], [[0, 3]]], [[[8, 11]], [[7, 10]], [[6, 9]]]]),
             "LPS",
+            False,
             *device,
         ]
     )
@@ -121,6 +186,7 @@
             ),
             torch.tensor([[[[0, 3]], [[1, 4]], [[2, 5]]], [[[6, 9]], [[7, 10]], [[8, 11]]]]),
             "RAS",
+            False,
             *device,
         ]
     )
@@ -131,6 +197,7 @@
             torch.as_tensor(create_translate(2, (10, 20)) @ create_rotate(2, (np.pi / 3)) @ np.diag([-1, -0.2, 1])),
             torch.tensor([[[3, 0], [4, 1], [5, 2]]]),
             "RA",
+            False,
             *device,
         ]
     )
@@ -141,6 +208,7 @@
             torch.as_tensor(create_translate(2, (10, 20)) @ create_rotate(2, (np.pi / 3)) @ np.diag([-1, -0.2, 1])),
             torch.tensor([[[2, 5], [1, 4], [0, 3]]]),
             "LP",
+            False,
             *device,
         ]
     )
@@ -151,6 +219,7 @@
             torch.as_tensor(np.diag([-1, -0.2, -1, 1, 1])),
             torch.zeros((1, 2, 3, 4, 5)),
             "LPID",
+            False,
             *device,
         ]
     )
@@ -161,6 +230,7 @@
             torch.as_tensor(np.diag([-1, -0.2, -1, 1, 1])),
             torch.zeros((1, 2, 3, 4, 5)),
             "RASD",
+            False,
             *device,
         ]
     )
@@ -175,6 +245,11 @@
     [{"axcodes": "RA"}, torch.arange(12).reshape((2, 1, 2, 3)), torch.eye(4)]
 ]
 
+TESTS_INVERSE = []
+for device in TEST_DEVICES:
+    TESTS_INVERSE.append([True, *device])
+    TESTS_INVERSE.append([False, *device])
+
 
 class TestOrientationCase(unittest.TestCase):
     @parameterized.expand(TESTS)
@@ -185,17 +260,20 @@ def test_ornt_meta(
         affine: torch.Tensor,
         expected_data: torch.Tensor,
         expected_code: str,
+        lps_convention: bool,
         device,
     ):
-        img = MetaTensor(img, affine=affine).to(device)
+        meta = {"space": SpaceKeys.LPS} if lps_convention else None
+        img = MetaTensor(img, affine=affine, meta=meta).to(device)
         ornt = Orientation(**init_param)
         call_param = {"data_array": img}
         res = ornt(**call_param)  # type: ignore[arg-type]
         if img.ndim in (3, 4):
             test_resampler_lazy(ornt, res, init_param, call_param)
 
         assert_allclose(res, expected_data.to(device))
-        new_code = nib.orientations.aff2axcodes(res.affine.cpu(), labels=ornt.labels)  # type: ignore
+        labels = (("R", "L"), ("A", "P"), ("I", "S")) if lps_convention else ornt.labels
+        new_code = nib.orientations.aff2axcodes(res.affine.cpu(), labels=labels)  # type: ignore
         self.assertEqual("".join(new_code), expected_code)
 
     @parameterized.expand(TESTS_TORCH)
@@ -224,23 +302,23 @@ def test_bad_params(self, init_param, img: torch.Tensor, affine: torch.Tensor):
         with self.assertRaises(ValueError):
             Orientation(**init_param)(img)
 
-    @parameterized.expand(TEST_DEVICES)
-    def test_inverse(self, device):
+    @parameterized.expand(TESTS_INVERSE)
+    def test_inverse(self, lps_convention: bool, device):
         img_t = torch.rand((1, 10, 9, 8), dtype=torch.float32, device=device)
         affine = torch.tensor(
             [[0, 0, -1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]], dtype=torch.float32, device="cpu"
         )
-        meta = {"fname": "somewhere"}
+        meta = {"fname": "somewhere", "space": SpaceKeys.LPS if lps_convention else SpaceKeys.RAS}
         img = MetaTensor(img_t, affine=affine, meta=meta)
         tr = Orientation("LPS")
         # check that image and affine have changed
-        img = tr(img)
+        img = cast(MetaTensor, tr(img))
         self.assertNotEqual(img.shape, img_t.shape)
-        self.assertGreater((affine - img.affine).max(), 0.5)
+        self.assertGreater(float((affine - img.affine).max()), 0.5)
         # check that with inverse, image affine are back to how they were
-        img = tr.inverse(img)
+        img = cast(MetaTensor, tr.inverse(img))
         self.assertEqual(img.shape, img_t.shape)
-        self.assertLess((affine - img.affine).max(), 1e-2)
+        self.assertLess(float((affine - img.affine).max()), 1e-2)
 
 
 if __name__ == "__main__":