Rename UNeXt2 (#84)

* rename file

* rename the architecture

* fix merge

viscy/data/hcs.py

@@ -263,7 +263,7 @@ class HCSDataModule(LightningDataModule):
         by default 0.8
     :param int batch_size: batch size, defaults to 16
     :param int num_workers: number of data-loading workers, defaults to 8
-    :param Literal["2D", "2.1D", "2.2D", "2.5D", "3D"] architecture: U-Net architecture,
+    :param Literal["2D", "UNeXt2", "2.5D", "3D"] architecture: U-Net architecture,
         defaults to "2.5D"
     :param tuple[int, int] yx_patch_size: patch size in (Y, X),
         defaults to (256, 256)
@@ -288,7 +288,7 @@ def __init__(
         split_ratio: float = 0.8,
         batch_size: int = 16,
         num_workers: int = 8,
-        architecture: Literal["2D", "2.1D", "2.2D", "2.5D", "3D", "fcmae"] = "2.5D",
+        architecture: Literal["2D", "UNeXt2", "2.5D", "3D", "fcmae"] = "2.5D",
         yx_patch_size: tuple[int, int] = (256, 256),
         normalizations: list[MapTransform] = [],
         augmentations: list[MapTransform] = [],
@@ -301,7 +301,7 @@ def __init__(
         self.target_channel = _ensure_channel_list(target_channel)
         self.batch_size = batch_size
         self.num_workers = num_workers
-        self.target_2d = False if architecture in ["2.2D", "3D", "fcmae"] else True
+        self.target_2d = False if architecture in ["UNeXt2", "3D", "fcmae"] else True
         self.z_window_size = z_window_size
         self.split_ratio = split_ratio
         self.yx_patch_size = yx_patch_size

viscy/light/engine.py

@@ -29,8 +29,8 @@
 from viscy.evaluation.evaluation_metrics import mean_average_precision, ms_ssim_25d
 from viscy.unet.networks.fcmae import FullyConvolutionalMAE
 from viscy.unet.networks.Unet2D import Unet2d
-from viscy.unet.networks.Unet22D import Unet22d
 from viscy.unet.networks.Unet25D import Unet25d
+from viscy.unet.networks.unext2 import UNeXt2
 
 try:
     from cellpose.models import CellposeModel
@@ -40,7 +40,7 @@
 
 _UNET_ARCHITECTURE = {
     "2D": Unet2d,
-    "2.2D": Unet22d,
+    "UNeXt2": UNeXt2,
     "2.5D": Unet25d,
     "fcmae": FullyConvolutionalMAE,
 }
@@ -117,7 +117,7 @@ class VSUNet(LightningModule):
 
     def __init__(
         self,
-        architecture: Literal["2D", "2.1D", "2.2D", "2.5D", "3D", "fcmae"],
+        architecture: Literal["2D", "UNeXt2", "2.5D", "3D", "fcmae"],
         model_config: dict = {},
         loss_function: Union[nn.Module, MixedLoss] = None,
         lr: float = 1e-3,

viscy/scripts/count_flops.py

@@ -6,7 +6,7 @@
 
 # %%
 model = VSUNet(
-    architecture="2.2D",
+    architecture="UNeXt2",
     model_config={
         "in_channels": 1,
         "out_channels": 2,

viscy/scripts/network_diagram.py

@@ -46,7 +46,7 @@
 # %%
 # 3D->2D
 model = VSUNet(
-    architecture="2.2D",
+    architecture="UNext2",
     model_config={
         "in_channels": 2,
         "out_channels": 3,
@@ -61,17 +61,17 @@
 model_graph = draw_graph(
     model,
     model.example_input_array,
-    graph_name="2.2D UNet",
+    graph_name="UNext2",
     roll=True,
     depth=3,
 )
 
 model_graph.visual_graph
 
 # %%
-# 2.1D UNet with upsampling in Z.
+# 3D->3D
 model = VSUNet(
-    architecture="2.2D",
+    architecture="UNext2",
     model_config={
         "in_channels": 1,
         "out_channels": 2,
@@ -85,13 +85,12 @@
 model_graph = draw_graph(
     model,
     model.example_input_array,
-    graph_name="2.2D UNet",
+    graph_name="UNext2",
     roll=True,
     depth=3,
 )
 
-graph22d = model_graph.visual_graph
-graph22d
+model_graph.visual_graph
 # %% If you want to save the graphs as SVG files:
 # model_graph.visual_graph.render(format="svg")
 

viscy/scripts/visualize_features.py

@@ -38,7 +38,7 @@
 # load model
 model = VSUNet.load_from_checkpoint(
     "model.ckpt",
-    architecture="2.2D",
+    architecture="UNeXt2",
     model_config={
         "in_channels": 1,
         "out_channels": 2,

viscy/unet/networks/fcmae.py

@@ -20,7 +20,7 @@
 )
 from torch import BoolTensor, Size, Tensor, nn
 
-from viscy.unet.networks.Unet22D import PixelToVoxelHead, Unet2dDecoder
+from viscy.unet.networks.unext2 import PixelToVoxelHead, UNeXt2Decoder
 
 
 def _init_weights(module: nn.Module) -> None:
@@ -430,7 +430,7 @@ def __init__(
             decoder_channels[-1] = (
                 out_channels * in_stack_depth * stem_kernel_size[-1] ** 2
             )
-        self.decoder = Unet2dDecoder(
+        self.decoder = UNeXt2Decoder(
             decoder_channels,
             norm_name="instance",
             mode="pixelshuffle",

viscy/unet/networks/Unet22D.py → viscy/unet/networks/unext2.py

@@ -64,8 +64,8 @@ def _get_convnext_stage(
     return stage
 
 
-class Conv22dStem(nn.Module):
-    """Stem for 2.1D networks."""
+class UNeXt2Stem(nn.Module):
+    """Stem for UNeXt2 networks."""
 
     def __init__(
         self,
@@ -91,7 +91,7 @@ def forward(self, x: Tensor):
         return x.reshape(b, c * d, h, w)
 
 
-class Unet2dUpStage(nn.Module):
+class UNeXt2UpStage(nn.Module):
     def __init__(
         self,
         in_channels: int,
@@ -214,7 +214,7 @@ def forward(self, x: Tensor) -> Tensor:
         return x
 
 
-class Unet2dDecoder(nn.Module):
+class UNeXt2Decoder(nn.Module):
     def __init__(
         self,
         num_channels: list[int],
@@ -228,7 +228,7 @@ def __init__(
         self.decoder_stages = nn.ModuleList([])
         stages = len(num_channels) - 1
         for i in range(stages):
-            stage = Unet2dUpStage(
+            stage = UNeXt2UpStage(
                 in_channels=num_channels[i],
                 skip_channels=num_channels[i] // 2,
                 out_channels=num_channels[i + 1],
@@ -249,7 +249,7 @@ def forward(self, features: Sequence[Tensor]) -> Tensor:
         return feat
 
 
-class Unet22d(nn.Module):
+class UNeXt2(nn.Module):
     def __init__(
         self,
         in_channels: int = 1,
@@ -285,15 +285,15 @@ def __init__(
         # replace first convolution layer with a projection tokenizer
         multi_scale_encoder.stem_0 = nn.Identity()
         self.encoder_stages = multi_scale_encoder
-        self.stem = Conv22dStem(
+        self.stem = UNeXt2Stem(
             in_channels, num_channels[0], stem_kernel_size, in_stack_depth
         )
         decoder_channels = num_channels
         decoder_channels.reverse()
         decoder_channels[-1] = (
             (out_stack_depth + 2) * out_channels * 2**2 * head_expansion_ratio
         )
-        self.decoder = Unet2dDecoder(
+        self.decoder = UNeXt2Decoder(
             decoder_channels,
             norm_name=decoder_norm_layer,
             mode=decoder_mode,