support GPU tensor for GridPatch and GridPatchDataset

monai/data/grid_dataset.py

@@ -11,17 +11,18 @@
 
 from __future__ import annotations
 
-from collections.abc import Callable, Hashable, Iterable, Mapping, Sequence
+from collections.abc import Generator, Callable, Hashable, Iterable, Mapping, Sequence
 from copy import deepcopy
 
 import numpy as np
 
 from monai.config import KeysCollection
+from monai.config.type_definitions import NdarrayTensor
 from monai.data.dataset import Dataset
 from monai.data.iterable_dataset import IterableDataset
 from monai.data.utils import iter_patch
 from monai.transforms import apply_transform
-from monai.utils import NumpyPadMode, ensure_tuple, first, look_up_option
+from monai.utils import NumpyPadMode, ensure_tuple, first
 
 __all__ = ["PatchDataset", "GridPatchDataset", "PatchIter", "PatchIterd"]
 
@@ -34,17 +35,25 @@ class PatchIter:
     """
 
     def __init__(
-        self, patch_size: Sequence[int], start_pos: Sequence[int] = (), mode: str = NumpyPadMode.WRAP, **pad_opts: dict
+        self,
+        patch_size: Sequence[int],
+        start_pos: Sequence[int] = (),
+        mode: str | None = NumpyPadMode.WRAP,
+        **pad_opts: dict,
     ):
         """
 
         Args:
             patch_size: size of patches to generate slices for, 0/None selects whole dimension
             start_pos: starting position in the array, default is 0 for each dimension
-            mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
-                ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
-                One of the listed string values or a user supplied function. Defaults to ``"wrap"``.
-                See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
+            mode: available modes: (Numpy) {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``,
+                ``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
+                (PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}.
+                One of the listed string values or a user supplied function.
+                If None, no wrapping is performed. Defaults to ``"wrap"``.
+                See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html
+                https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
+                requires pytorch >= 1.10 for best compatibility.
             pad_opts: other arguments for the `np.pad` function.
                 note that `np.pad` treats channel dimension as the first dimension.
 
@@ -58,10 +67,10 @@ def __init__(
         """
         self.patch_size = (None,) + tuple(patch_size)  # expand to have the channel dim
         self.start_pos = ensure_tuple(start_pos)
-        self.mode: NumpyPadMode = look_up_option(mode, NumpyPadMode)
+        self.mode = mode
         self.pad_opts = pad_opts
 
-    def __call__(self, array: np.ndarray):
+    def __call__(self, array: NdarrayTensor) -> Generator[tuple[NdarrayTensor, np.ndarray], None, None]:
         """
         Args:
             array: the image to generate patches from.
@@ -89,10 +98,14 @@ class PatchIterd:
         keys: keys of the corresponding items to iterate patches.
         patch_size: size of patches to generate slices for, 0/None selects whole dimension
         start_pos: starting position in the array, default is 0 for each dimension
-        mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
-            ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
-            One of the listed string values or a user supplied function. Defaults to ``"wrap"``.
-            See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
+        mode: available modes: (Numpy) {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``,
+            ``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
+            (PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}.
+            One of the listed string values or a user supplied function.
+            If None, no wrapping is performed. Defaults to ``"wrap"``.
+            See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html
+            https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
+            requires pytorch >= 1.10 for best compatibility.
         pad_opts: other arguments for the `np.pad` function.
             note that `np.pad` treats channel dimension as the first dimension.
 
@@ -107,13 +120,13 @@ def __init__(
         keys: KeysCollection,
         patch_size: Sequence[int],
         start_pos: Sequence[int] = (),
-        mode: str = NumpyPadMode.WRAP,
+        mode: str | None = NumpyPadMode.WRAP,
         **pad_opts,
     ):
         self.keys = ensure_tuple(keys)
         self.patch_iter = PatchIter(patch_size=patch_size, start_pos=start_pos, mode=mode, **pad_opts)
 
-    def __call__(self, data: Mapping[Hashable, np.ndarray]):
+    def __call__(self, data: Mapping[Hashable, NdarrayTensor]) -> Generator[tuple[Mapping[Hashable, NdarrayTensor], np.ndarray], None, None]:
         d = dict(data)
         original_spatial_shape = d[first(self.keys)].shape[1:]
 

monai/data/utils.py

@@ -247,14 +247,14 @@ def iter_patch_position(
 
 
 def iter_patch(
-    arr: np.ndarray,
+    arr: NdarrayTensor,
     patch_size: Sequence[int] | int = 0,
     start_pos: Sequence[int] = (),
     overlap: Sequence[float] | float = 0.0,
     copy_back: bool = True,
     mode: str | None = NumpyPadMode.WRAP,
     **pad_opts: dict,
-):
+) -> Generator[tuple[NdarrayTensor, np.ndarray], None, None]:
     """
     Yield successive patches from `arr` of size `patch_size`. The iteration can start from position `start_pos` in `arr`
     but drawing from a padded array extended by the `patch_size` in each dimension (so these coordinates can be negative
@@ -268,9 +268,16 @@ def iter_patch(
         overlap: the amount of overlap of neighboring patches in each dimension (a value between 0.0 and 1.0).
             If only one float number is given, it will be applied to all dimensions. Defaults to 0.0.
         copy_back: if True data from the yielded patches is copied back to `arr` once the generator completes
-        mode: One of the listed string values in ``monai.utils.NumpyPadMode`` or ``monai.utils.PytorchPadMode``,
-            or a user supplied function. If None, no wrapping is performed. Defaults to ``"wrap"``.
-        pad_opts: padding options, see `numpy.pad`
+        mode: available modes: (Numpy) {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``,
+            ``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
+            (PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}.
+            One of the listed string values or a user supplied function.
+            If None, no wrapping is performed. Defaults to ``"wrap"``.
+            See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html
+            https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
+            requires pytorch >= 1.10 for best compatibility.
+        pad_opts: other arguments for the `np.pad` or `torch.pad` function.
+            note that `np.pad` treats channel dimension as the first dimension.
 
     Yields:
         Patches of array data from `arr` which are views into a padded array which can be modified, if `copy_back` is
@@ -285,6 +292,9 @@ def iter_patch(
              Nth_dim_start, Nth_dim_end]]
 
     """
+
+    from monai.transforms.croppad.functional import pad_nd # needs to be here to avoid circular import
+
     # ensure patchSize and startPos are the right length
     patch_size_ = get_valid_patch_size(arr.shape, patch_size)
     start_pos = ensure_tuple_size(start_pos, arr.ndim)
@@ -296,7 +306,7 @@ def iter_patch(
     _overlap = [op if v else 0.0 for op, v in zip(ensure_tuple_rep(overlap, arr.ndim), is_v)]  # overlap if v else 0.0
     # pad image by maximum values needed to ensure patches are taken from inside an image
     if padded:
-        arrpad = np.pad(arr, tuple((p, p) for p in _pad_size), look_up_option(mode, NumpyPadMode).value, **pad_opts)
+        arrpad = pad_nd(arr, to_pad=tuple((p, p) for p in _pad_size), mode=mode, **pad_opts)
         # choose a start position in the padded image
         start_pos_padded = tuple(s + p for s, p in zip(start_pos, _pad_size))
 

monai/transforms/croppad/array.py

@@ -150,7 +150,7 @@ def __call__(  # type: ignore[override]
         kwargs_.update(kwargs)
 
         img_t = convert_to_tensor(data=img, track_meta=get_track_meta())
-        return pad_func(img_t, to_pad_, mode_, self.get_transform_info(), kwargs_)
+        return pad_func(img_t, to_pad_, self.get_transform_info(), mode_, **kwargs_)
 
     def inverse(self, data: MetaTensor) -> MetaTensor:
         transform = self.pop_transform(data)

monai/transforms/croppad/functional.py

@@ -21,6 +21,7 @@
 import torch
 from torch.nn.functional import pad as pad_pt
 
+from monai.config.type_definitions import NdarrayTensor
 from monai.data.meta_obj import get_track_meta
 from monai.data.meta_tensor import MetaTensor
 from monai.data.utils import to_affine_nd
@@ -49,7 +50,7 @@ def _convert_pt_pad_mode(padding_mode):
     return PytorchPadMode.REPLICATE  # "nearest", "border", and others
 
 
-def _np_pad(img: torch.Tensor, pad_width: list[tuple[int, int]], mode: str, **kwargs) -> torch.Tensor:
+def _np_pad(img: NdarrayTensor, pad_width: list[tuple[int, int]], mode: str, **kwargs) -> NdarrayTensor:
     if isinstance(img, torch.Tensor):
         if img.is_cuda:
             warnings.warn(f"Padding: moving img {img.shape} from cuda to cpu for dtype={img.dtype} mode={mode}.")
@@ -59,28 +60,30 @@ def _np_pad(img: torch.Tensor, pad_width: list[tuple[int, int]], mode: str, **kw
     mode = convert_pad_mode(dst=img_np, mode=mode).value
     if mode == "constant" and "value" in kwargs:
         kwargs["constant_values"] = kwargs.pop("value")
-    out = torch.as_tensor(np.pad(img, pad_width, mode=mode, **kwargs))  # type: ignore
-    if isinstance(img, MetaTensor):
-        out = convert_to_dst_type(out, dst=img)[0]
-    return out
+    img_np = np.pad(img_np, pad_width, mode=mode, **kwargs)
+    return convert_to_dst_type(img_np, dst=img)[0]
 
 
-def _pt_pad(img: torch.Tensor, pad_width: list[tuple[int, int]], mode: str, **kwargs) -> torch.Tensor:
-    mode = convert_pad_mode(dst=img, mode=mode).value
+def _pt_pad(img: NdarrayTensor, pad_width: list[tuple[int, int]], mode: str, **kwargs) -> NdarrayTensor:
+    img_pt = torch.as_tensor(img)
+    mode = convert_pad_mode(dst=img_pt, mode=mode).value
     if mode == "constant" and "constant_values" in kwargs:
         _kwargs = kwargs.copy()
         _kwargs["value"] = _kwargs.pop("constant_values")
     else:
         _kwargs = kwargs
     pt_pad_width = [val for sublist in pad_width[1:] for val in sublist[::-1]][::-1]
     # torch.pad expects `[B, C, H, W, [D]]` shape
-    return pad_pt(img.unsqueeze(0), pt_pad_width, mode=mode, **_kwargs).squeeze(0)
+    img_pt = pad_pt(img_pt.unsqueeze(0), pt_pad_width, mode=mode, **_kwargs).squeeze(0)
+    return convert_to_dst_type(img_pt, dst=img)[0]
 
 
-def pad_nd(img: torch.Tensor, to_pad: list[tuple[int, int]], mode: str, **kwargs):
+def pad_nd(img: NdarrayTensor, to_pad: list[tuple[int, int]], mode: str=PytorchPadMode.CONSTANT, **kwargs) -> NdarrayTensor:
     """
-    PyTorch/Numpy pad ``img`` with integers ``to_pad`` amounts. Depending on the ``mode`` and input dtype,
-    a suitable backend will be used automatically.
+    Pad `img` for a given an amount of padding in each dimension.
+
+    `torch.nn.functional.pad` is used unless the mode or kwargs are not available in torch,
+    in which case `np.pad` will be used.
 
     Args:
         img: data to be transformed, assuming `img` is channel-first and padding doesn't apply to the channel dim.
@@ -90,20 +93,18 @@ def pad_nd(img: torch.Tensor, to_pad: list[tuple[int, int]], mode: str, **kwargs
             ``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
             (PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}.
             One of the listed string values or a user supplied function. Defaults to ``"constant"``.
-            See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
+            See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html
             https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
         kwargs: other arguments for the `np.pad` or `torch.pad` function.
             note that `np.pad` treats channel dimension as the first dimension.
     """
     if mode in {"linear_ramp", "maximum", "mean", "median", "minimum", "symmetric", "empty"}:
         return _np_pad(img, pad_width=to_pad, mode=mode, **kwargs)
-    mode = convert_pad_mode(dst=img, mode=mode).value
     try:
-        _pad = (
-            _np_pad
-            if mode in {"reflect", "replicate"} and img.dtype in {torch.int16, torch.int64, torch.bool, torch.uint8}
-            else _pt_pad
-        )
+        _pad = _np_pad
+        if (mode in {"constant", "reflect", "edge", "replicate", "wrap", "circular"} and
+            img.dtype not in {torch.int16, torch.int64, torch.bool, torch.uint8}):
+            _pad = _pt_pad
         return _pad(img, pad_width=to_pad, mode=mode, **kwargs)
     except (ValueError, TypeError, RuntimeError) as err:
         if isinstance(err, NotImplementedError) or any(
@@ -148,23 +149,26 @@ def crop_or_pad_nd(img: torch.Tensor, translation_mat, spatial_size: tuple[int,
 
 
 def pad_func(
-    img: torch.Tensor, to_pad: tuple[tuple[int, int]], mode: str, transform_info: dict, kwargs
+    img: torch.Tensor, to_pad: tuple[tuple[int, int]], transform_info: dict, mode: str=PytorchPadMode.CONSTANT, **kwargs
 ) -> torch.Tensor:
     """
     Functional implementation of padding a MetaTensor. This function operates eagerly or lazily according
     to ``transform_info[TraceKeys.LAZY_EVALUATION]`` (default ``False``).
 
+    `torch.nn.functional.pad` is used unless the mode or kwargs are not available in torch,
+    in which case `np.pad` will be used.
+
     Args:
         img: data to be transformed, assuming `img` is channel-first and padding doesn't apply to the channel dim.
         to_pad: the amount to be padded in each dimension [(low_H, high_H), (low_W, high_W), ...].
             note that it including channel dimension.
+        transform_info: a dictionary with the relevant information pertaining to an applied transform.
         mode: available modes: (Numpy) {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``,
             ``"mean"``, ``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
             (PyTorch) {``"constant"``, ``"reflect"``, ``"replicate"``, ``"circular"``}.
             One of the listed string values or a user supplied function. Defaults to ``"constant"``.
-            See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
+            See also: https://numpy.org/doc/stable/reference/generated/numpy.pad.html
             https://pytorch.org/docs/stable/generated/torch.nn.functional.pad.html
-        transform_info: a dictionary with the relevant information pertaining to an applied transform.
         kwargs: other arguments for the `np.pad` or `torch.pad` function.
             note that `np.pad` treats channel dimension as the first dimension.
     """