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Fix output channel calculation in PixelShuffle2DUpBlock #40

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Fix output channel calculation in PixelShuffle2DUpBlock #40

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fc50d79
Fix output channel calculation in PixelShuffle2DUpBlock to account fo…
wli51 Aug 19, 2026
44d1c1f
Add preserve_channels option to PixelShuffle2DUpBlock to support both…
wli51 Aug 19, 2026
62e01aa
Add _pixel_shuffle_preserve_channels attribute to ConvNeXtUNet for im…
wli51 Aug 21, 2026
a7c0dd6
Fix potential bug with out_h and out_w methods in Stage class where o…
wli51 Aug 21, 2026
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3 changes: 3 additions & 0 deletions src/virtual_stain_flow/models/blocks/up_down_blocks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -287,6 +287,7 @@ def __init__(
self,
in_channels: int,
out_channels: Optional[int] = None,
preserve_channels: bool = False,
**kwargs
):
"""
Expand All @@ -304,6 +305,8 @@ def __init__(
# as the pixel shuffle operation merely rearranges the channels
# to the spatial dimensions
out_channels = in_channels
if not preserve_channels:
out_channels = out_channels // (scale_factor ** spatial_dims)

Comment on lines 307 to 310

@MikeLippincott MikeLippincott Aug 22, 2026

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consider not overwriting here and replacing the out_channels with in_channels in the if block?

super().__init__(
in_channels=in_channels,
Expand Down
8 changes: 3 additions & 5 deletions src/virtual_stain_flow/models/stages.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,15 +176,13 @@ def out_channels(self) -> int:
def out_h(self, in_h: int) -> int:
_out_h = in_h
for block in [self.in_block, self.comp_block]:
if isinstance(block, Conv2DDownBlock):
_out_h = block.out_h(_out_h)
_out_h = block.out_h(_out_h)
return _out_h

def out_w(self, in_w: int) -> int:
_out_w = in_w
for block in [self.in_block, self.comp_block]:
if isinstance(block, Conv2DDownBlock):
_out_w = block.out_w(_out_w)
_out_w = block.out_w(_out_w)
return _out_w

"""
Expand Down
12 changes: 10 additions & 2 deletions src/virtual_stain_flow/models/unext.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,8 @@ def __init__(
decoder_up_block: Literal['pixelshuffle', 'convt'] = 'pixelshuffle',
decoder_compute_block: Literal['convnext', 'conv2d'] = 'convnext',
act_type: ActivationType = 'sigmoid',
_num_units: Union[List[int], int] = 2
_num_units: Union[List[int], int] = 2,
_pixel_shuffle_preserve_channels: bool = False,
):
"""
Initializes the ConvNeXtUNet model.
Expand Down Expand Up @@ -98,13 +99,16 @@ def __init__(

if decoder_up_block == 'pixelshuffle':
in_block_handles = [PixelShuffle2DUpBlock] * (depth - 1)
in_block_kwargs = [{'preserve_channels': _pixel_shuffle_preserve_channels}] * (depth - 1)
elif decoder_up_block == 'convt':
in_block_handles = [ConvTrans2DUpBlock] * (depth - 1)
in_block_kwargs = [{'norm_type': 'layer'}] * (depth - 1)
else:
raise ValueError(
f"Unsupported decoder_up_block: {decoder_up_block!r}. "
"Expected 'pixelshuffle' or 'convt'."
)
self._pixel_shuffle_preserve_channels = _pixel_shuffle_preserve_channels
self._decoder_up_block = decoder_up_block

if decoder_compute_block == 'convnext':
Expand Down Expand Up @@ -138,7 +142,7 @@ def __init__(
encoder_feature_map_channels=convnextv2_model.feature_info.channels(),
# use convolutional up-sampling blocks
in_block_handles=in_block_handles,
in_block_kwargs=[{'norm_type': 'layer'}] * (depth - 1),
in_block_kwargs=in_block_kwargs,
comp_block_handles=comp_block_handles,
comp_block_kwargs=comp_block_kwargs,
)
Expand Down Expand Up @@ -194,6 +198,7 @@ def to_config(self) -> Dict[str, Any]:
"decoder_compute_block": self._decoder_compute_block,
"act_type": self._act_type,
"_num_units": self._num_units_cfg,
"_pixel_shuffle_preserve_channels": self._pixel_shuffle_preserve_channels,
},
}

Expand All @@ -205,5 +210,8 @@ def from_config(cls, config: Dict[str, Any]) -> "ConvNeXtUNet":
"""

init_cfg = config.get("init", config)
if "_pixel_shuffle_preserve_channels" not in init_cfg:
# For backward compatibility with configs that don't have this key
init_cfg["_pixel_shuffle_preserve_channels"] = False

return cls(**init_cfg)
6 changes: 4 additions & 2 deletions tests/models/test_up_down_blocks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,10 @@ class TestUpDownBlocks:
(MaxPool2DDownBlock, {"out_channels": 8}, 3, 3, 0.5),
(ConvTrans2DUpBlock, {}, 4, 2, 2),
(ConvTrans2DUpBlock, {"out_channels": 3}, 4, 3, 2),
(PixelShuffle2DUpBlock, {}, 4, 4, 2),
(PixelShuffle2DUpBlock, {"out_channels": 8}, 4, 4, 2),
(PixelShuffle2DUpBlock, {}, 4, 1, 2),
(PixelShuffle2DUpBlock, {"out_channels": 8}, 4, 1, 2),
(PixelShuffle2DUpBlock, {"preserve_channels": True}, 4, 4, 2),
(PixelShuffle2DUpBlock, {"preserve_channels": True, "out_channels": 8}, 4, 4, 2),
(Bilinear2DUpsampleBlock, {}, 3, 3, 2),
(Bilinear2DUpsampleBlock, {"out_channels": 8}, 3, 3, 2),
],
Expand Down
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