Merge branch 'dev' into h3rrr-patch-1

Author: ericspod

monai/networks/blocks/fcn.py

@@ -123,7 +123,9 @@ def __init__(
         self.upsample_mode = upsample_mode
         self.conv2d_type = conv2d_type
         self.out_channels = out_channels
-        resnet = models.resnet50(pretrained=pretrained, progress=progress)
+        resnet = models.resnet50(
+            progress=progress, weights=models.ResNet50_Weights.IMAGENET1K_V1 if pretrained else None
+        )
 
         self.conv1 = resnet.conv1
         self.bn0 = resnet.bn1

monai/networks/nets/milmodel.py

@@ -16,7 +16,7 @@
 import torch
 import torch.nn as nn
 
-from monai.utils.module import optional_import
+from monai.utils import optional_import
 
 models, _ = optional_import("torchvision.models")
 
@@ -48,7 +48,6 @@ class MILModel(nn.Module):
             Defaults to ``None`` (necessary only when using a custom backbone)
         trans_blocks: number of the blocks in `TransformEncoder` layer.
         trans_dropout: dropout rate in `TransformEncoder` layer.
-
     """
 
     def __init__(
@@ -74,7 +73,7 @@ def __init__(
         self.transformer: nn.Module | None = None
 
         if backbone is None:
-            net = models.resnet50(pretrained=pretrained)
+            net = models.resnet50(weights=models.ResNet50_Weights.IMAGENET1K_V1 if pretrained else None)
             nfc = net.fc.in_features  # save the number of final features
             net.fc = torch.nn.Identity()  # remove final linear layer
 
@@ -99,7 +98,7 @@ def hook(module, input, output):
             torch_model = getattr(models, backbone, None)
             if torch_model is None:
                 raise ValueError("Unknown torch vision model" + str(backbone))
-            net = torch_model(pretrained=pretrained)
+            net = torch_model(weights="DEFAULT" if pretrained else None)
 
             if getattr(net, "fc", None) is not None:
                 nfc = net.fc.in_features  # save the number of final features

monai/networks/nets/torchvision_fc.py

@@ -112,12 +112,11 @@ def __init__(
         weights=None,
         **kwargs,
     ):
-        if weights is not None:
-            model = getattr(models, model_name)(weights=weights, **kwargs)
-        elif pretrained:
-            model = getattr(models, model_name)(weights="DEFAULT", **kwargs)
-        else:
-            model = getattr(models, model_name)(weights=None, **kwargs)
+        # if pretrained is False, weights is a weight tensor or None for no pretrained loading
+        if pretrained and weights is None:
+            weights = "DEFAULT"
+
+        model = getattr(models, model_name)(weights=weights, **kwargs)
 
         super().__init__(
             model=model,

monai/transforms/io/array.py

@@ -43,9 +43,9 @@
 from monai.data.utils import is_no_channel
 from monai.transforms.transform import Transform
 from monai.transforms.utility.array import EnsureChannelFirst
-from monai.utils import GridSamplePadMode
-from monai.utils import ImageMetaKey as Key
 from monai.utils import (
+    GridSamplePadMode,
+    ImageMetaKey,
     MetaKeys,
     OptionalImportError,
     convert_to_dst_type,
@@ -293,7 +293,8 @@ def __call__(self, filename: Sequence[PathLike] | PathLike, reader: ImageReader
         # make sure all elements in metadata are little endian
         meta_data = switch_endianness(meta_data, "<")
 
-        meta_data[Key.FILENAME_OR_OBJ] = f"{ensure_tuple(filename)[0]}"  # Path obj should be strings for data loader
+        # Path obj should be strings for data loader
+        meta_data[ImageMetaKey.FILENAME_OR_OBJ] = f"{ensure_tuple(filename)[0]}"
         img = MetaTensor.ensure_torch_and_prune_meta(
             img_array, meta_data, self.simple_keys, pattern=self.pattern, sep=self.sep
         )
@@ -548,7 +549,7 @@ def __call__(self, img: NdarrayOrTensor):
                 "Missing 'saved_to' key in metadata. Check SaveImage argument 'savepath_in_metadict' is True."
             )
 
-        input_path = meta_data[Key.FILENAME_OR_OBJ]
+        input_path = meta_data[ImageMetaKey.FILENAME_OR_OBJ]
         output_path = meta_data[MetaKeys.SAVED_TO]
         log_data = {"input": input_path, "output": output_path}
 

requirements-dev.txt

@@ -18,7 +18,7 @@ pep8-naming
 pycodestyle
 pyflakes
 black>=25.1.0
-isort>=5.1, <6.0
+isort>=5.1, !=6.0.0
 ruff
 pytype>=2020.6.1, <=2024.4.11; platform_system != "Windows"
 types-setuptools

tests/networks/nets/test_densenet.py

@@ -96,7 +96,7 @@ def test_pretrain_consistency(self, model, input_param, input_shape):
             net = model(**input_param).to(device)
         with eval_mode(net):
             result = net.features.forward(example)
-        torchvision_net = torchvision.models.densenet121(pretrained=True).to(device)
+        torchvision_net = torchvision.models.densenet121(weights="DEFAULT").to(device)
         with eval_mode(torchvision_net):
             expected_result = torchvision_net.features.forward(example)
         self.assertTrue(torch.all(result == expected_result))

tests/networks/nets/test_milmodel.py

@@ -44,13 +44,13 @@
     TEST_CASE_MILMODEL.append(test_case)
 
 # torchvision backbone
-TEST_CASE_MILMODEL.append(
-    [{"num_classes": 5, "backbone": "resnet18", "pretrained": False}, (2, 2, 3, 512, 512), (2, 5)]
-)
-TEST_CASE_MILMODEL.append([{"num_classes": 5, "backbone": "resnet18", "pretrained": True}, (2, 2, 3, 512, 512), (2, 5)])
+for pretrained in [True, False]:
+    TEST_CASE_MILMODEL.append(
+        [{"num_classes": 5, "backbone": "resnet18", "pretrained": pretrained}, (2, 2, 3, 512, 512), (2, 5)]
+    )
 
 # custom backbone
-backbone = models.densenet121(pretrained=False)
+backbone = models.densenet121()
 backbone_nfeatures = backbone.classifier.in_features
 backbone.classifier = torch.nn.Identity()
 TEST_CASE_MILMODEL.append(