Merge branch 'dev' into 8369-ci-pipeline-setup

Author: KumoLiu

docs/source/transforms.rst

@@ -37,6 +37,11 @@ Generic Interfaces
 .. autoclass:: MultiSampleTrait
     :members:
 
+`ReduceTrait`
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: ReduceTrait
+    :members:
+
 `Randomizable`
 ^^^^^^^^^^^^^^
 .. autoclass:: Randomizable
@@ -1252,6 +1257,12 @@ Utility
     :members:
     :special-members: __call__
 
+`FlattenSequence`
+""""""""""""""""""""""""
+.. autoclass:: FlattenSequence
+    :members:
+    :special-members: __call__
+
 Dictionary Transforms
 ---------------------
 
@@ -2337,6 +2348,12 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
+`FlattenSequenced`
+"""""""""""""""""""""""""
+.. autoclass:: FlattenSequenced
+    :members:
+    :special-members: __call__
+
 
 MetaTensor
 ^^^^^^^^^^

monai/transforms/__init__.py

@@ -506,7 +506,7 @@
     ZoomDict,
 )
 from .spatial.functional import spatial_resample
-from .traits import LazyTrait, MultiSampleTrait, RandomizableTrait, ThreadUnsafe
+from .traits import LazyTrait, MultiSampleTrait, RandomizableTrait, ReduceTrait, ThreadUnsafe
 from .transform import LazyTransform, MapTransform, Randomizable, RandomizableTransform, Transform, apply_transform
 from .utility.array import (
     AddCoordinateChannels,
@@ -521,6 +521,7 @@
     EnsureChannelFirst,
     EnsureType,
     FgBgToIndices,
+    FlattenSequence,
     Identity,
     ImageFilter,
     IntensityStats,
@@ -593,6 +594,9 @@
     FgBgToIndicesd,
     FgBgToIndicesD,
     FgBgToIndicesDict,
+    FlattenSequenced,
+    FlattenSequenceD,
+    FlattenSequenceDict,
     FlattenSubKeysd,
     FlattenSubKeysD,
     FlattenSubKeysDict,

monai/transforms/traits.py

@@ -14,7 +14,7 @@
 
 from __future__ import annotations
 
-__all__ = ["LazyTrait", "InvertibleTrait", "RandomizableTrait", "MultiSampleTrait", "ThreadUnsafe"]
+__all__ = ["LazyTrait", "InvertibleTrait", "RandomizableTrait", "MultiSampleTrait", "ThreadUnsafe", "ReduceTrait"]
 
 from typing import Any
 
@@ -99,3 +99,14 @@ class ThreadUnsafe:
     """
 
     pass
+
+
+class ReduceTrait:
+    """
+    An interface to indicate that the transform has the capability to reduce multiple samples
+    into a single sample.
+    This interface can be extended from by people adapting transforms to the MONAI framework as well
+    as by implementors of MONAI transforms.
+    """
+
+    pass

monai/transforms/transform.py

@@ -25,7 +25,7 @@
 from monai import config, transforms
 from monai.config import KeysCollection
 from monai.data.meta_tensor import MetaTensor
-from monai.transforms.traits import LazyTrait, RandomizableTrait, ThreadUnsafe
+from monai.transforms.traits import LazyTrait, RandomizableTrait, ReduceTrait, ThreadUnsafe
 from monai.utils import MAX_SEED, ensure_tuple, first
 from monai.utils.enums import TransformBackends
 from monai.utils.misc import MONAIEnvVars
@@ -142,7 +142,7 @@ def apply_transform(
     """
     try:
         map_items_ = int(map_items) if isinstance(map_items, bool) else map_items
-        if isinstance(data, (list, tuple)) and map_items_ > 0:
+        if isinstance(data, (list, tuple)) and map_items_ > 0 and not isinstance(transform, ReduceTrait):
             return [
                 apply_transform(transform, item, map_items_ - 1, unpack_items, log_stats, lazy, overrides)
                 for item in data
@@ -482,8 +482,7 @@ def key_iterator(self, data: Mapping[Hashable, Any], *extra_iterables: Iterable
                 yield (key,) + tuple(_ex_iters) if extra_iterables else key
             elif not self.allow_missing_keys:
                 raise KeyError(
-                    f"Key `{key}` of transform `{self.__class__.__name__}` was missing in the data"
-                    " and allow_missing_keys==False."
+                    f"Key `{key}` of transform `{self.__class__.__name__}` was missing in the data and allow_missing_keys==False."
                 )
 
     def first_key(self, data: dict[Hashable, Any]):

monai/transforms/utility/array.py

@@ -43,7 +43,7 @@
     median_filter,
 )
 from monai.transforms.inverse import InvertibleTransform, TraceableTransform
-from monai.transforms.traits import MultiSampleTrait
+from monai.transforms.traits import MultiSampleTrait, ReduceTrait
 from monai.transforms.transform import Randomizable, RandomizableTrait, RandomizableTransform, Transform
 from monai.transforms.utils import (
     apply_affine_to_points,
@@ -110,6 +110,7 @@
     "ImageFilter",
     "RandImageFilter",
     "ApplyTransformToPoints",
+    "FlattenSequence",
 ]
 
 
@@ -1950,3 +1951,39 @@ def inverse(self, data: torch.Tensor) -> torch.Tensor:
             data = inverse_transform(data, transform[TraceKeys.EXTRA_INFO]["image_affine"])
 
         return data
+
+
+class FlattenSequence(Transform, ReduceTrait):
+    """
+    Flatten a nested sequence (list or tuple) by one level.
+    If the input is a sequence of sequences, it will flatten them into a single sequence.
+    Non-nested sequences and other data types are returned unchanged.
+
+    For example:
+
+    .. code-block:: python
+
+        flatten = FlattenSequence()
+        data = [[1, 2], [3, 4], [5, 6]]
+        print(flatten(data))
+        [1, 2, 3, 4, 5, 6]
+
+    """
+
+    def __init__(self):
+        super().__init__()
+
+    def __call__(self, data: list | tuple | Any) -> list | tuple | Any:
+        """
+        Flatten a nested sequence by one level.
+        Args:
+            data: Input data, can be a nested sequence.
+        Returns:
+            Flattened list if input is a nested sequence, otherwise returns data unchanged.
+        """
+        if isinstance(data, (list, tuple)):
+            if len(data) == 0:
+                return data
+            if all(isinstance(item, (list, tuple)) for item in data):
+                return [item for sublist in data for item in sublist]
+        return data

monai/transforms/utility/dictionary.py

@@ -30,7 +30,7 @@
 from monai.data.meta_tensor import MetaObj, MetaTensor
 from monai.data.utils import no_collation
 from monai.transforms.inverse import InvertibleTransform
-from monai.transforms.traits import MultiSampleTrait, RandomizableTrait
+from monai.transforms.traits import MultiSampleTrait, RandomizableTrait, ReduceTrait
 from monai.transforms.transform import MapTransform, Randomizable, RandomizableTransform
 from monai.transforms.utility.array import (
     AddCoordinateChannels,
@@ -45,6 +45,7 @@
     EnsureChannelFirst,
     EnsureType,
     FgBgToIndices,
+    FlattenSequence,
     Identity,
     ImageFilter,
     IntensityStats,
@@ -191,6 +192,9 @@
     "ApplyTransformToPointsd",
     "ApplyTransformToPointsD",
     "ApplyTransformToPointsDict",
+    "FlattenSequenced",
+    "FlattenSequenceD",
+    "FlattenSequenceDict",
 ]
 
 DEFAULT_POST_FIX = PostFix.meta()
@@ -1906,6 +1910,28 @@ def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch
         return d
 
 
+class FlattenSequenced(MapTransform, ReduceTrait):
+    """
+    Dictionary-based wrapper of :py:class:`monai.transforms.FlattenSequence`.
+
+    Args:
+        keys: keys of the corresponding items to be transformed.
+            See also: monai.transforms.MapTransform
+        allow_missing_keys:
+            Don't raise exception if key is missing.
+    """
+
+    def __init__(self, keys: KeysCollection, allow_missing_keys: bool = False, **kwargs) -> None:
+        super().__init__(keys, allow_missing_keys)
+        self.flatten_sequence = FlattenSequence(**kwargs)
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
+        d = dict(data)
+        for key in self.key_iterator(d):
+            d[key] = self.flatten_sequence(d[key])  # type: ignore[assignment]
+        return d
+
+
 RandImageFilterD = RandImageFilterDict = RandImageFilterd
 ImageFilterD = ImageFilterDict = ImageFilterd
 IdentityD = IdentityDict = Identityd
@@ -1949,3 +1975,4 @@ def inverse(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch
 AddCoordinateChannelsD = AddCoordinateChannelsDict = AddCoordinateChannelsd
 FlattenSubKeysD = FlattenSubKeysDict = FlattenSubKeysd
 ApplyTransformToPointsD = ApplyTransformToPointsDict = ApplyTransformToPointsd
+FlattenSequenceD = FlattenSequenceDict = FlattenSequenced

tests/transforms/compose/test_compose.py

@@ -282,6 +282,40 @@ def test_flatten_and_len(self):
     def test_backwards_compatible_imports(self):
         from monai.transforms.transform import MapTransform, RandomizableTransform, Transform  # noqa: F401
 
+    def test_list_extend_multi_sample_trait(self):
+        center_crop = mt.CenterSpatialCrop([128, 128])
+        multi_sample_transform = mt.RandSpatialCropSamples([64, 64], 1)
+        flatten_sequence_transform = mt.FlattenSequence()
+
+        img = torch.zeros([1, 512, 512])
+
+        self.assertEqual(execute_compose(img, [center_crop]).shape, torch.Size([1, 128, 128]))
+        single_multi_sample_trait_result = execute_compose(
+            img, [multi_sample_transform, center_crop, flatten_sequence_transform]
+        )
+        self.assertIsInstance(single_multi_sample_trait_result, list)
+        self.assertEqual(len(single_multi_sample_trait_result), 1)
+        self.assertEqual(single_multi_sample_trait_result[0].shape, torch.Size([1, 64, 64]))
+
+        double_multi_sample_trait_result = execute_compose(
+            img, [multi_sample_transform, multi_sample_transform, flatten_sequence_transform, center_crop]
+        )
+        self.assertIsInstance(double_multi_sample_trait_result, list)
+        self.assertEqual(len(double_multi_sample_trait_result), 1)
+        self.assertEqual(double_multi_sample_trait_result[0].shape, torch.Size([1, 64, 64]))
+
+    def test_multi_sample_trait_cardinality(self):
+        img = torch.zeros([1, 128, 128])
+        t2 = mt.RandSpatialCropSamples([32, 32], num_samples=2)
+        flatten_sequence_transform = mt.FlattenSequence()
+
+        # chaining should multiply counts: 2 x 2 = 4, flattened
+        res = execute_compose(img, [t2, t2, flatten_sequence_transform])
+        self.assertIsInstance(res, list)
+        self.assertEqual(len(res), 4)
+        for r in res:
+            self.assertEqual(r.shape, torch.Size([1, 32, 32]))
+
 
 TEST_COMPOSE_EXECUTE_TEST_CASES = [
     [None, tuple()],