5782 Flexible interp modes in regunet (#5807)

Signed-off-by: Wenqi Li <[email protected]>

Fixes #5782

### Description
- adds 'mode' and 'align_corners' options to the blocks and nets
- fixes a few typos

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>

Author: wyli

.github/workflows/conda.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, ubuntu-latest]
+        os: [ubuntu-latest]
         python-version: ["3.9"]
     runs-on: ${{ matrix.os }}
     env:

monai/networks/blocks/localnet_block.py

@@ -166,7 +166,7 @@ def forward(self, x) -> Tuple[torch.Tensor, torch.Tensor]:
 
 class LocalNetUpSampleBlock(nn.Module):
     """
-    A up-sample module that can be used for LocalNet, based on:
+    An up-sample module that can be used for LocalNet, based on:
     `Weakly-supervised convolutional neural networks for multimodal image registration
     <https://doi.org/10.1016/j.media.2018.07.002>`_.
     `Label-driven weakly-supervised learning for multimodal deformable image registration
@@ -176,12 +176,21 @@ class LocalNetUpSampleBlock(nn.Module):
         DeepReg (https://github.com/DeepRegNet/DeepReg)
     """
 
-    def __init__(self, spatial_dims: int, in_channels: int, out_channels: int) -> None:
+    def __init__(
+        self,
+        spatial_dims: int,
+        in_channels: int,
+        out_channels: int,
+        mode: str = "nearest",
+        align_corners: Optional[bool] = None,
+    ) -> None:
         """
         Args:
             spatial_dims: number of spatial dimensions.
             in_channels: number of input channels.
             out_channels: number of output channels.
+            mode: interpolation mode of the additive upsampling, default to 'nearest'.
+            align_corners: whether to align corners for the additive upsampling, default to None.
         Raises:
             ValueError: when ``in_channels != 2 * out_channels``
         """
@@ -199,9 +208,11 @@ def __init__(self, spatial_dims: int, in_channels: int, out_channels: int) -> No
                 f"got in_channels={in_channels}, out_channels={out_channels}"
             )
         self.out_channels = out_channels
+        self.mode = mode
+        self.align_corners = align_corners
 
-    def addictive_upsampling(self, x, mid) -> torch.Tensor:
-        x = F.interpolate(x, mid.shape[2:])
+    def additive_upsampling(self, x, mid) -> torch.Tensor:
+        x = F.interpolate(x, mid.shape[2:], mode=self.mode, align_corners=self.align_corners)
         # [(batch, out_channels, ...), (batch, out_channels, ...)]
         x = x.split(split_size=int(self.out_channels), dim=1)
         # (batch, out_channels, ...)
@@ -226,7 +237,7 @@ def forward(self, x, mid) -> torch.Tensor:
                     "expecting mid spatial dimensions be exactly the double of x spatial dimensions, "
                     f"got x of shape {x.shape}, mid of shape {mid.shape}"
                 )
-        h0 = self.deconv_block(x) + self.addictive_upsampling(x, mid)
+        h0 = self.deconv_block(x) + self.additive_upsampling(x, mid)
         r1 = h0 + mid
         r2 = self.conv_block(h0)
         out: torch.Tensor = self.residual_block(r2, r1)

monai/networks/blocks/regunet_block.py

@@ -200,6 +200,8 @@ def __init__(
         out_channels: int,
         kernel_initializer: Optional[str] = "kaiming_uniform",
         activation: Optional[str] = None,
+        mode: str = "nearest",
+        align_corners: Optional[bool] = None,
     ):
         """
 
@@ -211,6 +213,8 @@ def __init__(
             out_channels: number of output channels
             kernel_initializer: kernel initializer
             activation: kernel activation function
+            mode: feature map interpolation mode, default to "nearest".
+            align_corners: whether to align corners for feature map interpolation.
         """
         super().__init__()
         self.extract_levels = extract_levels
@@ -228,6 +232,8 @@ def __init__(
                 for d in extract_levels
             ]
         )
+        self.mode = mode
+        self.align_corners = align_corners
 
     def forward(self, x: List[torch.Tensor], image_size: List[int]) -> torch.Tensor:
         """
@@ -240,7 +246,9 @@ def forward(self, x: List[torch.Tensor], image_size: List[int]) -> torch.Tensor:
             Tensor of shape (batch, `out_channels`, size1, size2, size3), where (size1, size2, size3) = ``image_size``
         """
         feature_list = [
-            F.interpolate(layer(x[self.max_level - level]), size=image_size)
+            F.interpolate(
+                layer(x[self.max_level - level]), size=image_size, mode=self.mode, align_corners=self.align_corners
+            )
             for layer, level in zip(self.layers, self.extract_levels)
         ]
         out: torch.Tensor = torch.mean(torch.stack(feature_list, dim=0), dim=0)

monai/networks/nets/regunet.py

@@ -337,14 +337,23 @@ def build_output_block(self):
 
 
 class AdditiveUpSampleBlock(nn.Module):
-    def __init__(self, spatial_dims: int, in_channels: int, out_channels: int):
+    def __init__(
+        self,
+        spatial_dims: int,
+        in_channels: int,
+        out_channels: int,
+        mode: str = "nearest",
+        align_corners: Optional[bool] = None,
+    ):
         super().__init__()
         self.deconv = get_deconv_block(spatial_dims=spatial_dims, in_channels=in_channels, out_channels=out_channels)
+        self.mode = mode
+        self.align_corners = align_corners
 
     def forward(self, x: torch.Tensor) -> torch.Tensor:
         output_size = [size * 2 for size in x.shape[2:]]
         deconved = self.deconv(x)
-        resized = F.interpolate(x, output_size)
+        resized = F.interpolate(x, output_size, mode=self.mode, align_corners=self.align_corners)
         resized = torch.sum(torch.stack(resized.split(split_size=resized.shape[1] // 2, dim=1), dim=-1), dim=-1)
         out: torch.Tensor = deconved + resized
         return out
@@ -372,8 +381,10 @@ def __init__(
         out_activation: Optional[str] = None,
         out_channels: int = 3,
         pooling: bool = True,
-        use_addictive_sampling: bool = True,
+        use_additive_sampling: bool = True,
         concat_skip: bool = False,
+        mode: str = "nearest",
+        align_corners: Optional[bool] = None,
     ):
         """
         Args:
@@ -385,10 +396,14 @@ def __init__(
             out_channels: number of channels for the output
             extract_levels: list, which levels from net to extract. The maximum level must equal to ``depth``
             pooling: for down-sampling, use non-parameterized pooling if true, otherwise use conv3d
-            use_addictive_sampling: whether use additive up-sampling layer for decoding.
+            use_additive_sampling: whether use additive up-sampling layer for decoding.
             concat_skip: when up-sampling, concatenate skipped tensor if true, otherwise use addition
+            mode: mode for interpolation when use_additive_sampling, default is "nearest".
+            align_corners: align_corners for interpolation when use_additive_sampling, default is None.
         """
-        self.use_additive_upsampling = use_addictive_sampling
+        self.use_additive_upsampling = use_additive_sampling
+        self.mode = mode
+        self.align_corners = align_corners
         super().__init__(
             spatial_dims=spatial_dims,
             in_channels=in_channels,
@@ -412,7 +427,11 @@ def build_bottom_block(self, in_channels: int, out_channels: int):
     def build_up_sampling_block(self, in_channels: int, out_channels: int) -> nn.Module:
         if self.use_additive_upsampling:
             return AdditiveUpSampleBlock(
-                spatial_dims=self.spatial_dims, in_channels=in_channels, out_channels=out_channels
+                spatial_dims=self.spatial_dims,
+                in_channels=in_channels,
+                out_channels=out_channels,
+                mode=self.mode,
+                align_corners=self.align_corners,
             )
 
         return get_deconv_block(spatial_dims=self.spatial_dims, in_channels=in_channels, out_channels=out_channels)

tests/test_localnet.py

@@ -32,6 +32,8 @@
             "extract_levels": (0, 1),
             "pooling": False,
             "concat_skip": True,
+            "mode": "bilinear",
+            "align_corners": True,
         },
         (1, 2, 16, 16),
         (1, 2, 16, 16),

tests/test_localnet_block.py

@@ -25,7 +25,17 @@
     [{"spatial_dims": spatial_dims, "in_channels": 2, "out_channels": 4, "kernel_size": 3}] for spatial_dims in [2, 3]
 ]
 
-TEST_CASE_UP_SAMPLE = [[{"spatial_dims": spatial_dims, "in_channels": 4, "out_channels": 2}] for spatial_dims in [2, 3]]
+TEST_CASE_UP_SAMPLE = [
+    [
+        {
+            "spatial_dims": spatial_dims,
+            "in_channels": 4,
+            "out_channels": 2,
+            "mode": "bilinear" if spatial_dims == 2 else "trilinear",
+        }
+    ]
+    for spatial_dims in [2, 3]
+]
 
 TEST_CASE_EXTRACT = [
     [{"spatial_dims": spatial_dims, "in_channels": 2, "out_channels": 3, "act": act, "initializer": initializer}]

tests/test_regunet_block.py

@@ -53,6 +53,7 @@
             "out_channels": 1,
             "kernel_initializer": "zeros",
             "activation": "sigmoid",
+            "mode": "trilinear",
         },
         [(1, 3, 2, 2, 2), (1, 2, 4, 4, 4), (1, 1, 8, 8, 8)],
         (3, 3, 3),