Merge branch 'dev' into temp-fix-windows-test

Author: wyli

monai/transforms/utils_pytorch_numpy_unification.py

@@ -82,7 +82,9 @@ def clip(a: NdarrayOrTensor, a_min, a_max) -> NdarrayOrTensor:
     return result
 
 
-def percentile(x: NdarrayOrTensor, q, dim: Optional[int] = None) -> Union[NdarrayOrTensor, float, int]:
+def percentile(
+    x: NdarrayOrTensor, q, dim: Optional[int] = None, keepdim: bool = False, **kwargs
+) -> Union[NdarrayOrTensor, float, int]:
     """`np.percentile` with equivalent implementation for torch.
 
     Pytorch uses `quantile`, but this functionality is only available from v1.7.
@@ -97,6 +99,9 @@ def percentile(x: NdarrayOrTensor, q, dim: Optional[int] = None) -> Union[Ndarra
         q: percentile to compute (should in range 0 <= q <= 100)
         dim: the dim along which the percentiles are computed. default is to compute the percentile
             along a flattened version of the array. only work for numpy array or Tensor with PyTorch >= 1.7.0.
+        keepdim: whether the output data has dim retained or not.
+        kwargs: if `x` is numpy array, additional args for `np.percentile`, more details:
+            https://numpy.org/doc/stable/reference/generated/numpy.percentile.html.
 
     Returns:
         Resulting value (scalar)
@@ -108,11 +113,11 @@ def percentile(x: NdarrayOrTensor, q, dim: Optional[int] = None) -> Union[Ndarra
         raise ValueError
     result: Union[NdarrayOrTensor, float, int]
     if isinstance(x, np.ndarray):
-        result = np.percentile(x, q, axis=dim)
+        result = np.percentile(x, q, axis=dim, keepdims=keepdim, **kwargs)
     else:
         q = torch.tensor(q, device=x.device)
         if hasattr(torch, "quantile"):  # `quantile` is new in torch 1.7.0
-            result = torch.quantile(x, q / 100.0, dim=dim)
+            result = torch.quantile(x, q / 100.0, dim=dim, keepdim=keepdim)
         else:
             # Note that ``kthvalue()`` works one-based, i.e., the first sorted value
             # corresponds to k=1, not k=0. Thus, we need the `1 +`.
@@ -282,13 +287,23 @@ def concatenate(to_cat: Sequence[NdarrayOrTensor], axis: int = 0, out=None) -> N
     return torch.cat(to_cat, dim=axis, out=out)  # type: ignore
 
 
-def cumsum(a: NdarrayOrTensor, axis=None):
-    """`np.cumsum` with equivalent implementation for torch."""
+def cumsum(a: NdarrayOrTensor, axis=None, **kwargs):
+    """
+    `np.cumsum` with equivalent implementation for torch.
+
+    Args:
+        a: input data to compute cumsum.
+        axis: expected axis to compute cumsum.
+        kwargs: if `a` is PyTorch Tensor, additional args for `torch.cumsum`, more details:
+            https://pytorch.org/docs/stable/generated/torch.cumsum.html.
+
+    """
+
     if isinstance(a, np.ndarray):
         return np.cumsum(a, axis)
     if axis is None:
-        return torch.cumsum(a[:], 0)
-    return torch.cumsum(a, dim=axis)
+        return torch.cumsum(a[:], 0, **kwargs)
+    return torch.cumsum(a, dim=axis, **kwargs)
 
 
 def isfinite(x):
@@ -298,18 +313,40 @@ def isfinite(x):
     return torch.isfinite(x)
 
 
-def searchsorted(a: NdarrayOrTensor, v: NdarrayOrTensor, right=False, sorter=None):
+def searchsorted(a: NdarrayOrTensor, v: NdarrayOrTensor, right=False, sorter=None, **kwargs):
+    """
+    `np.searchsorted` with equivalent implementation for torch.
+
+    Args:
+        a: numpy array or tensor, containing monotonically increasing sequence on the innermost dimension.
+        v: containing the search values.
+        right: if False, return the first suitable location that is found, if True, return the last such index.
+        sorter: if `a` is numpy array, optional array of integer indices that sort array `a` into ascending order.
+        kwargs: if `a` is PyTorch Tensor, additional args for `torch.searchsorted`, more details:
+            https://pytorch.org/docs/stable/generated/torch.searchsorted.html.
+
+    """
     side = "right" if right else "left"
     if isinstance(a, np.ndarray):
         return np.searchsorted(a, v, side, sorter)  # type: ignore
-    return torch.searchsorted(a, v, right=right)  # type: ignore
+    return torch.searchsorted(a, v, right=right, **kwargs)  # type: ignore
+
 
+def repeat(a: NdarrayOrTensor, repeats: int, axis: Optional[int] = None, **kwargs):
+    """
+    `np.repeat` with equivalent implementation for torch (`repeat_interleave`).
+
+    Args:
+        a: input data to repeat.
+        repeats: number of repetitions for each element, repeats is broadcasted to fit the shape of the given axis.
+        axis: axis along which to repeat values.
+        kwargs: if `a` is PyTorch Tensor, additional args for `torch.repeat_interleave`, more details:
+            https://pytorch.org/docs/stable/generated/torch.repeat_interleave.html.
 
-def repeat(a: NdarrayOrTensor, repeats: int, axis: Optional[int] = None):
-    """`np.repeat` with equivalent implementation for torch (`repeat_interleave`)."""
+    """
     if isinstance(a, np.ndarray):
         return np.repeat(a, repeats, axis)
-    return torch.repeat_interleave(a, repeats, dim=axis)
+    return torch.repeat_interleave(a, repeats, dim=axis, **kwargs)
 
 
 def isnan(x: NdarrayOrTensor):
@@ -330,7 +367,7 @@ def ascontiguousarray(x: NdarrayOrTensor, **kwargs):
     Args:
         x: array/tensor
         kwargs: if `x` is PyTorch Tensor, additional args for `torch.contiguous`, more details:
-            https://pytorch.org/docs/stable/generated/torch.Tensor.contiguous.html#torch.Tensor.contiguous.
+            https://pytorch.org/docs/stable/generated/torch.Tensor.contiguous.html.
 
     """
     if isinstance(x, np.ndarray):