monai-weekly 1.5.dev2519__tar.gz → 1.5.dev2521__tar.gz

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.5.dev2519
+Version: 1.5.dev2521
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/__init__.py

@@ -136,4 +136,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "f97a0e9bc7787df261284db2cdeffa2e8d631512"
+__commit_id__ = "222d5094ac6ce07f68ce8b07100b0a517fd2506e"

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-05-11T02:34:08+0000",
+ "date": "2025-05-25T02:37:26+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "552815d9e48a40cf72c7c718034df7984f5d14dd",
- "version": "1.5.dev2519"
+ "full-revisionid": "b82b3ff93efc25aff2eee158e3acaab717973590",
+ "version": "1.5.dev2521"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/apps/auto3dseg/auto_runner.py

@@ -570,7 +570,7 @@ class AutoRunner:
             self.device_setting["CUDA_VISIBLE_DEVICES"] = ",".join([str(x) for x in cuda_visible_devices])
             self.device_setting["n_devices"] = len(cuda_visible_devices)
         else:
-            logger.warn(f"Wrong format of cuda_visible_devices {cuda_visible_devices}, devices not set")
+            logger.warning(f"Wrong format of cuda_visible_devices {cuda_visible_devices}, devices not set")
 
         if num_nodes is None:
             num_nodes = int(os.environ.get("NUM_NODES", 1))

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/bundle/scripts.py

@@ -702,8 +702,6 @@ def load(
         3. If `load_ts_module` is `True`, return a triple that include a TorchScript module,
             the corresponding metadata dict, and extra files dict.
             please check `monai.data.load_net_with_metadata` for more details.
-        4. If `return_state_dict` is True, return model weights, only used for compatibility
-            when `model` and `net_name` are all `None`.
 
     """
     bundle_dir_ = _process_bundle_dir(bundle_dir)

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/bundle/workflows.py

@@ -226,7 +226,7 @@ class BundleWorkflow(ABC):
         if self.properties is None:
             self.properties = {}
         if name in self.properties:
-            logger.warn(f"property '{name}' already exists in the properties list, overriding it.")
+            logger.warning(f"property '{name}' already exists in the properties list, overriding it.")
         self.properties[name] = {BundleProperty.DESC: desc, BundleProperty.REQUIRED: required}
 
     def check_properties(self) -> list[str] | None:
@@ -421,7 +421,7 @@ class ConfigWorkflow(BundleWorkflow):
             for _config_file in _config_files:
                 _config_file = Path(_config_file)
                 if _config_file.parent != config_root_path:
-                    logger.warn(
+                    logger.warning(
                         f"Not all config files are in {config_root_path}. If logging_file and meta_file are"
                         f"not specified, {config_root_path} will be used as the default config root directory."
                     )
@@ -434,11 +434,11 @@ class ConfigWorkflow(BundleWorkflow):
         self.config_root_path = config_root_path
         logging_file = str(self.config_root_path / "logging.conf") if logging_file is None else logging_file
         if logging_file is False:
-            logger.warn(f"Logging file is set to {logging_file}, skipping logging.")
+            logger.warning(f"Logging file is set to {logging_file}, skipping logging.")
         else:
             if not os.path.isfile(logging_file):
                 if logging_file == str(self.config_root_path / "logging.conf"):
-                    logger.warn(f"Default logging file in {logging_file} does not exist, skipping logging.")
+                    logger.warning(f"Default logging file in {logging_file} does not exist, skipping logging.")
                 else:
                     raise FileNotFoundError(f"Cannot find the logging config file: {logging_file}.")
             else:
@@ -503,17 +503,17 @@ class ConfigWorkflow(BundleWorkflow):
         """
         ret = super().check_properties()
         if self.properties is None:
-            logger.warn("No available properties had been set, skipping check.")
+            logger.warning("No available properties had been set, skipping check.")
             return None
         if ret:
-            logger.warn(f"Loaded bundle does not contain the following required properties: {ret}")
+            logger.warning(f"Loaded bundle does not contain the following required properties: {ret}")
         # also check whether the optional properties use correct ID name if existing
         wrong_props = []
         for n, p in self.properties.items():
             if not p.get(BundleProperty.REQUIRED, False) and not self._check_optional_id(name=n, property=p):
                 wrong_props.append(n)
         if wrong_props:
-            logger.warn(f"Loaded bundle defines the following optional properties with wrong ID: {wrong_props}")
+            logger.warning(f"Loaded bundle defines the following optional properties with wrong ID: {wrong_props}")
         if ret is not None:
             ret.extend(wrong_props)
         return ret

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/networks/nets/autoencoderkl.py

@@ -153,9 +153,9 @@ class Encoder(nn.Module):
         channels: sequence of block output channels.
         out_channels: number of channels in the bottom layer (latent space) of the autoencoder.
         num_res_blocks: number of residual blocks (see _ResBlock) per level.
-        norm_num_groups: number of groups for the GroupNorm layers, num_channels must be divisible by this number.
+        norm_num_groups: number of groups for the GroupNorm layers, channels must be divisible by this number.
         norm_eps: epsilon for the normalization.
-        attention_levels: indicate which level from num_channels contain an attention block.
+        attention_levels: indicate which level from channels contain an attention block.
         with_nonlocal_attn: if True use non-local attention block.
         include_fc: whether to include the final linear layer. Default to True.
         use_combined_linear: whether to use a single linear layer for qkv projection, default to False.
@@ -299,9 +299,9 @@ class Decoder(nn.Module):
         in_channels: number of channels in the bottom layer (latent space) of the autoencoder.
         out_channels: number of output channels.
         num_res_blocks: number of residual blocks (see _ResBlock) per level.
-        norm_num_groups: number of groups for the GroupNorm layers, num_channels must be divisible by this number.
+        norm_num_groups: number of groups for the GroupNorm layers, channels must be divisible by this number.
         norm_eps: epsilon for the normalization.
-        attention_levels: indicate which level from num_channels contain an attention block.
+        attention_levels: indicate which level from channels contain an attention block.
         with_nonlocal_attn: if True use non-local attention block.
         use_convtranspose: if True, use ConvTranspose to upsample feature maps in decoder.
         include_fc: whether to include the final linear layer. Default to True.
@@ -483,7 +483,7 @@ class AutoencoderKL(nn.Module):
         channels: number of output channels for each block.
         attention_levels: sequence of levels to add attention.
         latent_channels: latent embedding dimension.
-        norm_num_groups: number of groups for the GroupNorm layers, num_channels must be divisible by this number.
+        norm_num_groups: number of groups for the GroupNorm layers, channels must be divisible by this number.
         norm_eps: epsilon for the normalization.
         with_encoder_nonlocal_attn: if True use non-local attention block in the encoder.
         with_decoder_nonlocal_attn: if True use non-local attention block in the decoder.
@@ -518,10 +518,10 @@ class AutoencoderKL(nn.Module):
 
         # All number of channels should be multiple of num_groups
         if any((out_channel % norm_num_groups) != 0 for out_channel in channels):
-            raise ValueError("AutoencoderKL expects all num_channels being multiple of norm_num_groups")
+            raise ValueError("AutoencoderKL expects all channels being multiple of norm_num_groups")
 
         if len(channels) != len(attention_levels):
-            raise ValueError("AutoencoderKL expects num_channels being same size of attention_levels")
+            raise ValueError("AutoencoderKL expects channels being same size of attention_levels")
 
         if isinstance(num_res_blocks, int):
             num_res_blocks = ensure_tuple_rep(num_res_blocks, len(channels))
@@ -529,7 +529,7 @@ class AutoencoderKL(nn.Module):
         if len(num_res_blocks) != len(channels):
             raise ValueError(
                 "`num_res_blocks` should be a single integer or a tuple of integers with the same length as "
-                "`num_channels`."
+                "`channels`."
             )
 
         self.encoder: nn.Module = Encoder(

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai/visualize/occlusion_sensitivity.py

@@ -80,7 +80,7 @@ class OcclusionSensitivity:
         n_batch: int = 16,
         verbose: bool = True,
         mode: str | float | Callable = "gaussian",
-        overlap: float = 0.25,
+        overlap: float = 0.6,
         activate: bool | Callable = True,
     ) -> None:
         """

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/monai_weekly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.5.dev2519
+Version: 1.5.dev2521
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.5.dev2519 → monai_weekly-1.5.dev2521}/tests/bundle/test_bundle_download.py

@@ -268,11 +268,10 @@ class TestLoad(unittest.TestCase):
     @skip_if_quick
     def test_load_weights(self, bundle_files, bundle_name, repo, device, model_file):
         with skip_if_downloading_fails():
-            # download bundle, and load weights from the downloaded path
             with tempfile.TemporaryDirectory() as tempdir:
                 bundle_root = os.path.join(tempdir, bundle_name)
                 # load weights
-                weights = load(
+                model_1 = load(
                     name=bundle_name,
                     model_file=model_file,
                     bundle_dir=tempdir,
@@ -280,7 +279,6 @@ class TestLoad(unittest.TestCase):
                     source="github",
                     progress=False,
                     device=device,
-                    return_state_dict=True,
                 )
                 # prepare network
                 with open(os.path.join(bundle_root, bundle_files[2])) as f:
@@ -289,7 +287,7 @@ class TestLoad(unittest.TestCase):
                 del net_args["_target_"]
                 model = getattr(nets, model_name)(**net_args)
                 model.to(device)
-                model.load_state_dict(weights)
+                model.load_state_dict(model_1)
                 model.eval()
 
                 # prepare data and test
@@ -313,13 +311,11 @@ class TestLoad(unittest.TestCase):
                     progress=False,
                     device=device,
                     source="github",
-                    return_state_dict=False,
                 )
                 model_2.eval()
                 output_2 = model_2.forward(input_tensor)
                 assert_allclose(output_2, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
 
-                # test compatibility with return_state_dict=True.
                 model_3 = load(
                     name=bundle_name,
                     model_file=model_file,
@@ -328,7 +324,6 @@ class TestLoad(unittest.TestCase):
                     device=device,
                     net_name=model_name,
                     source="github",
-                    return_state_dict=False,
                     **net_args,
                 )
                 model_3.eval()
@@ -343,14 +338,7 @@ class TestLoad(unittest.TestCase):
             # download bundle, and load weights from the downloaded path
             with tempfile.TemporaryDirectory() as tempdir:
                 # load weights
-                model = load(
-                    name=bundle_name,
-                    bundle_dir=tempdir,
-                    source="monaihosting",
-                    progress=False,
-                    device=device,
-                    return_state_dict=False,
-                )
+                model = load(name=bundle_name, bundle_dir=tempdir, source="monaihosting", progress=False, device=device)
 
                 # prepare data and test
                 input_tensor = torch.rand(1, 1, 96, 96, 96).to(device)
@@ -371,7 +359,6 @@ class TestLoad(unittest.TestCase):
                     source="monaihosting",
                     progress=False,
                     device=device,
-                    return_state_dict=False,
                     net_override=net_override,
                 )