to and from meta tensor

Signed-off-by: Richard Brown <[email protected]>

monai/data/meta_tensor.py

@@ -12,6 +12,7 @@
 from __future__ import annotations
 
 import warnings
+from copy import deepcopy
 from typing import Callable
 
 import torch
@@ -54,10 +55,10 @@ class MetaTensor(MetaObj, torch.Tensor):
 
     Notes:
         - Older versions of pytorch (<=1.8), `torch.jit.trace(net, im)` may
-          not work if `im` is of type `MetaTensor`. This can be resolved with
-          `torch.jit.trace(net, im.as_tensor())`.
+            not work if `im` is of type `MetaTensor`. This can be resolved with
+            `torch.jit.trace(net, im.as_tensor())`.
         - A warning will be raised if in the constructor `affine` is not `None` and
-          `meta` already contains the key `affine`.
+            `meta` already contains the key `affine`.
     """
 
     @staticmethod
@@ -89,6 +90,11 @@ def __new__(cls, x, affine: torch.Tensor | None = None, meta: dict | None = None
             out.affine = out.get_default_affine()
         out.affine = out.affine.to(out.device)
 
+        # if we are creating a new MetaTensor, then deep copy attributes
+        if isinstance(x, torch.Tensor) and not isinstance(x, MetaTensor):
+            out.meta = deepcopy(out.meta)
+        out.affine = out.affine.to(out.device)
+
         return out
 
     def _copy_attr(self, attribute: str, input_objs: list[MetaObj], default_fn: Callable, deep_copy: bool) -> None:

monai/transforms/__init__.py

@@ -206,6 +206,14 @@
 from .inverse_batch_transform import BatchInverseTransform, Decollated, DecollateD, DecollateDict
 from .io.array import SUPPORTED_READERS, LoadImage, SaveImage
 from .io.dictionary import LoadImaged, LoadImageD, LoadImageDict, SaveImaged, SaveImageD, SaveImageDict
+from .meta_utility.dictionary import (
+    FromMetaTensord,
+    FromMetaTensorD,
+    FromMetaTensorDict,
+    ToMetaTensord,
+    ToMetaTensorD,
+    ToMetaTensorDict,
+)
 from .nvtx import (
     Mark,
     Markd,

monai/transforms/meta_utility/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

monai/transforms/meta_utility/dictionary.py

@@ -0,0 +1,102 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+A collection of dictionary-based wrappers for moving between MetaTensor types and dictionaries of data.
+These can be used to make backwards compatible code.
+
+Class names are ended with 'd' to denote dictionary-based transforms.
+"""
+
+from copy import deepcopy
+from typing import Dict, Hashable, Mapping
+
+from monai.config.type_definitions import NdarrayOrTensor
+from monai.data.meta_tensor import MetaTensor
+from monai.transforms.inverse import InvertibleTransform
+from monai.transforms.transform import MapTransform
+from monai.utils.enums import PostFix, TransformBackends
+
+__all__ = [
+    "FromMetaTensord",
+    "FromMetaTensorD",
+    "FromMetaTensorDict",
+    "ToMetaTensord",
+    "ToMetaTensorD",
+    "ToMetaTensorDict",
+]
+
+
+class FromMetaTensord(MapTransform, InvertibleTransform):
+    """
+    Dictionary-based transform to convert MetaTensor to a dictionary.
+
+    If input is `{"a": MetaTensor, "b": MetaTensor}`, then output will
+    have the form `{"a": torch.Tensor, "a_meta_dict": dict, "b": ...}`.
+    """
+
+    backend = [TransformBackends.TORCH, TransformBackends.NUMPY]
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, NdarrayOrTensor]:
+        d = dict(data)
+        for key in self.key_iterator(d):
+            self.push_transform(d, key)
+            im: MetaTensor = d[key]  # type: ignore
+            d.update(im.as_dict(key))
+        return d
+
+    def inverse(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, NdarrayOrTensor]:
+        d = deepcopy(dict(data))
+        for key in self.key_iterator(d):
+            # check transform
+            _ = self.get_most_recent_transform(d, key)
+            # do the inverse
+            im, meta = d[key], d.pop(PostFix.meta(key), None)
+            im = MetaTensor(im, meta=meta)  # type: ignore
+            d[key] = im
+            # Remove the applied transform
+            self.pop_transform(d, key)
+        return d
+
+
+class ToMetaTensord(MapTransform, InvertibleTransform):
+    """
+    Dictionary-based transform to convert a dictionary to MetaTensor.
+
+    If input is `{"a": torch.Tensor, "a_meta_dict": dict, "b": ...}`, then output will
+    have the form `{"a": MetaTensor, "b": MetaTensor}`.
+    """
+
+    backend = [TransformBackends.TORCH, TransformBackends.NUMPY]
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, NdarrayOrTensor]:
+        d = dict(data)
+        for key in self.key_iterator(d):
+            self.push_transform(d, key)
+            im, meta = d[key], d.pop(PostFix.meta(key), None)
+            im = MetaTensor(im, meta=meta)  # type: ignore
+            d[key] = im
+        return d
+
+    def inverse(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, NdarrayOrTensor]:
+        d = deepcopy(dict(data))
+        for key in self.key_iterator(d):
+            # check transform
+            _ = self.get_most_recent_transform(d, key)
+            # do the inverse
+            im: MetaTensor = d[key]  # type: ignore
+            d.update(im.as_dict(key))
+            # Remove the applied transform
+            self.pop_transform(d, key)
+        return d
+
+
+FromMetaTensorD = FromMetaTensorDict = FromMetaTensord
+ToMetaTensorD = ToMetaTensorDict = ToMetaTensord

monai/utils/enums.py

@@ -227,13 +227,13 @@ class ForwardMode(Enum):
 class TraceKeys:
     """Extra meta data keys used for traceable transforms."""
 
-    CLASS_NAME = "class"
-    ID = "id"
-    ORIG_SIZE = "orig_size"
-    EXTRA_INFO = "extra_info"
-    DO_TRANSFORM = "do_transforms"
-    KEY_SUFFIX = "_transforms"
-    NONE = "none"
+    CLASS_NAME: str = "class"
+    ID: str = "id"
+    ORIG_SIZE: str = "orig_size"
+    EXTRA_INFO: str = "extra_info"
+    DO_TRANSFORM: str = "do_transforms"
+    KEY_SUFFIX: str = "_transforms"
+    NONE: str = "none"
 
 
 @deprecated(since="0.8.0", msg_suffix="use monai.utils.enums.TraceKeys instead.")
@@ -287,6 +287,10 @@ def meta(key: Optional[str] = None):
     def orig_meta(key: Optional[str] = None):
         return PostFix._get_str(key, "orig_meta_dict")
 
+    @staticmethod
+    def transforms(key: Optional[str] = None):
+        return PostFix._get_str(key, TraceKeys.KEY_SUFFIX[1:])
+
 
 class TransformBackends(Enum):
     """

tests/test_module_list.py

@@ -40,6 +40,7 @@ def test_transform_api(self):
         to_exclude = {"MapTransform"}  # except for these transforms
         to_exclude_docs = {"Decollate", "Ensemble", "Invert", "SaveClassification", "RandTorchVision"}
         to_exclude_docs.update({"DeleteItems", "SelectItems", "CopyItems", "ConcatItems"})
+        to_exclude_docs.update({"ToMetaTensor", "FromMetaTensor"})
         xforms = {
             name: obj
             for name, obj in monai.transforms.__dict__.items()

tests/test_to_from_meta_tensord.py

@@ -0,0 +1,182 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import random
+import string
+import unittest
+from copy import deepcopy
+from typing import Optional, Union
+
+import torch
+from parameterized import parameterized
+
+from monai.data.meta_tensor import MetaTensor
+from monai.transforms import FromMetaTensord, ToMetaTensord
+from monai.utils.enums import PostFix
+from monai.utils.module import get_torch_version_tuple
+from tests.utils import TEST_DEVICES, assert_allclose
+
+PT_VER_MAJ, PT_VER_MIN = get_torch_version_tuple()
+
+DTYPES = [[torch.float32], [torch.float64], [torch.float16], [torch.int64], [torch.int32]]
+TESTS = []
+for _device in TEST_DEVICES:
+    for _dtype in DTYPES:
+        TESTS.append((*_device, *_dtype))
+
+
+def rand_string(min_len=5, max_len=10):
+    str_size = random.randint(min_len, max_len)
+    chars = string.ascii_letters + string.punctuation
+    return "".join(random.choice(chars) for _ in range(str_size))
+
+
+class TestToFromMetaTensord(unittest.TestCase):
+    @staticmethod
+    def get_im(shape=None, dtype=None, device=None):
+        if shape is None:
+            shape = shape = (1, 10, 8)
+        affine = torch.randint(0, 10, (4, 4))
+        meta = {"fname": rand_string()}
+        t = torch.rand(shape)
+        if dtype is not None:
+            t = t.to(dtype)
+        if device is not None:
+            t = t.to(device)
+        m = MetaTensor(t.clone(), affine, meta)
+        return m
+
+    def check_ids(self, a, b, should_match):
+        comp = self.assertEqual if should_match else self.assertNotEqual
+        comp(id(a), id(b))
+
+    def check(
+        self,
+        out: torch.Tensor,
+        orig: torch.Tensor,
+        *,
+        shape: bool = True,
+        vals: bool = True,
+        ids: bool = True,
+        device: Optional[Union[str, torch.device]] = None,
+        meta: bool = True,
+        check_ids: bool = True,
+        **kwargs,
+    ):
+        if device is None:
+            device = orig.device
+
+        # check the image
+        self.assertIsInstance(out, type(orig))
+        if shape:
+            assert_allclose(torch.as_tensor(out.shape), torch.as_tensor(orig.shape))
+        if vals:
+            assert_allclose(out, orig, **kwargs)
+        if check_ids:
+            self.check_ids(out, orig, ids)
+        self.assertTrue(str(device) in str(out.device))
+
+        # check meta and affine are equal and affine is on correct device
+        if isinstance(orig, MetaTensor) and isinstance(out, MetaTensor) and meta:
+            orig_meta_no_affine = deepcopy(orig.meta)
+            del orig_meta_no_affine["affine"]
+            out_meta_no_affine = deepcopy(out.meta)
+            del out_meta_no_affine["affine"]
+            self.assertEqual(orig_meta_no_affine, out_meta_no_affine)
+            assert_allclose(out.affine, orig.affine)
+            self.assertTrue(str(device) in str(out.affine.device))
+            if check_ids:
+                self.check_ids(out.affine, orig.affine, ids)
+                self.check_ids(out.meta, orig.meta, ids)
+
+    @parameterized.expand(TESTS)
+    def test_from_to_meta_tensord(self, device, dtype):
+        m1 = self.get_im(device=device, dtype=dtype)
+        m2 = self.get_im(device=device, dtype=dtype)
+        m3 = self.get_im(device=device, dtype=dtype)
+        d_metas = {"m1": m1, "m2": m2, "m3": m3}
+        m1_meta = {k: v for k, v in m1.meta.items() if k != "affine"}
+        m1_aff = m1.affine
+
+        # FROM -> forward
+        t_from_meta = FromMetaTensord(["m1", "m2"])
+        d_dict = t_from_meta(d_metas)
+
+        self.assertEqual(
+            sorted(d_dict.keys()),
+            [
+                "m1",
+                PostFix.meta("m1"),
+                PostFix.transforms("m1"),
+                "m2",
+                PostFix.meta("m2"),
+                PostFix.transforms("m2"),
+                "m3",
+            ],
+        )
+        self.check(d_dict["m3"], m3, ids=True)  # unchanged
+        self.check(d_dict["m1"], m1.as_tensor(), ids=False)
+        meta_out = {k: v for k, v in d_dict["m1_meta_dict"].items() if k != "affine"}
+        aff_out = d_dict["m1_meta_dict"]["affine"]
+        self.check(aff_out, m1_aff, ids=True)
+        self.assertEqual(meta_out, m1_meta)
+
+        # FROM -> inverse
+        d_meta_dict_meta = t_from_meta.inverse(d_dict)
+        self.assertEqual(
+            sorted(d_meta_dict_meta.keys()), ["m1", PostFix.transforms("m1"), "m2", PostFix.transforms("m2"), "m3"]
+        )
+        self.check(d_meta_dict_meta["m3"], m3, ids=False)  # unchanged (except deep copy in inverse)
+        self.check(d_meta_dict_meta["m1"], m1, ids=False)
+        meta_out = {k: v for k, v in d_meta_dict_meta["m1"].meta.items() if k != "affine"}
+        aff_out = d_meta_dict_meta["m1"].affine
+        self.check(aff_out, m1_aff, ids=False)
+        self.assertEqual(meta_out, m1_meta)
+
+        # TO -> Forward
+        t_to_meta = ToMetaTensord(["m1", "m2"])
+        del d_dict["m1_transforms"]
+        del d_dict["m2_transforms"]
+        d_dict_meta = t_to_meta(d_dict)
+        self.assertEqual(
+            sorted(d_dict_meta.keys()), ["m1", PostFix.transforms("m1"), "m2", PostFix.transforms("m2"), "m3"]
+        )
+        self.check(d_dict_meta["m3"], m3, ids=True)  # unchanged (except deep copy in inverse)
+        self.check(d_dict_meta["m1"], m1, ids=False)
+        meta_out = {k: v for k, v in d_dict_meta["m1"].meta.items() if k != "affine"}
+        aff_out = d_dict_meta["m1"].meta["affine"]
+        self.check(aff_out, m1_aff, ids=False)
+        self.assertEqual(meta_out, m1_meta)
+
+        # TO -> Inverse
+        d_dict_meta_dict = t_to_meta.inverse(d_dict_meta)
+        self.assertEqual(
+            sorted(d_dict_meta_dict.keys()),
+            [
+                "m1",
+                PostFix.meta("m1"),
+                PostFix.transforms("m1"),
+                "m2",
+                PostFix.meta("m2"),
+                PostFix.transforms("m2"),
+                "m3",
+            ],
+        )
+        self.check(d_dict_meta_dict["m3"], m3.as_tensor(), ids=False)  # unchanged (except deep copy in inverse)
+        self.check(d_dict_meta_dict["m1"], m1.as_tensor(), ids=False)
+        meta_out = {k: v for k, v in d_dict_meta_dict["m1_meta_dict"].items() if k != "affine"}
+        aff_out = d_dict_meta_dict["m1_meta_dict"]["affine"]
+        self.check(aff_out, m1_aff, ids=False)
+        self.assertEqual(meta_out, m1_meta)
+
+
+if __name__ == "__main__":
+    unittest.main()