monai-weekly 1.4.dev2428__tar.gz → 1.4.dev2430__tar.gz

{monai_weekly-1.4.dev2428/monai_weekly.egg-info → monai_weekly-1.4.dev2430}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.4.dev2428
+Version: 1.4.dev2430
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/__init__.py

@@ -93,4 +93,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "14b086b553693f5d344ff054f37d12ce6839da06"
+__commit_id__ = "2e53df78e580131046dc8db7f7638063db1f5045"

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-07-14T02:21:44+0000",
+ "date": "2024-07-28T02:19:22+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "2d242d8f1b2876133bcafbe7fa5d967728a74998",
- "version": "1.4.dev2428"
+ "full-revisionid": "9dd92b4a07706d4b80edace3d39fe008dc805d5a",
+ "version": "1.4.dev2430"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/apps/auto3dseg/hpo_gen.py

@@ -53,7 +53,7 @@ class HPOGen(AlgoGen):
         raise NotImplementedError
 
     @abstractmethod
-    def set_score(self):
+    def set_score(self, *args, **kwargs):
         """Report the evaluated results to HPO."""
         raise NotImplementedError
 

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/apps/detection/utils/anchor_utils.py

@@ -189,7 +189,7 @@ class AnchorGenerator(nn.Module):
             w_ratios = 1 / area_scale
             h_ratios = area_scale
         # if 3d, w:h:d = 1:aspect_ratios[:,0]:aspect_ratios[:,1]
-        elif self.spatial_dims == 3:
+        else:
             area_scale = torch.pow(aspect_ratios_t[:, 0] * aspect_ratios_t[:, 1], 1 / 3.0)
             w_ratios = 1 / area_scale
             h_ratios = aspect_ratios_t[:, 0] / area_scale
@@ -199,7 +199,7 @@ class AnchorGenerator(nn.Module):
         hs = (h_ratios[:, None] * scales_t[None, :]).view(-1)
         if self.spatial_dims == 2:
             base_anchors = torch.stack([-ws, -hs, ws, hs], dim=1) / 2.0
-        elif self.spatial_dims == 3:
+        else:  # elif self.spatial_dims == 3:
             ds = (d_ratios[:, None] * scales_t[None, :]).view(-1)
             base_anchors = torch.stack([-ws, -hs, -ds, ws, hs, ds], dim=1) / 2.0
 

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/apps/pathology/transforms/post/array.py

@@ -28,7 +28,7 @@ from monai.transforms import (
     SobelGradients,
 )
 from monai.transforms.transform import Transform
-from monai.transforms.utils_pytorch_numpy_unification import max, maximum, min, sum, unique
+from monai.transforms.utils_pytorch_numpy_unification import max, maximum, min, sum, unique, where
 from monai.utils import TransformBackends, convert_to_numpy, optional_import
 from monai.utils.misc import ensure_tuple_rep
 from monai.utils.type_conversion import convert_to_dst_type, convert_to_tensor
@@ -162,7 +162,8 @@ class GenerateWatershedMask(Transform):
         pred = label(pred)[0]
         if self.remove_small_objects is not None:
             pred = self.remove_small_objects(pred)
-        pred[pred > 0] = 1
+        pred_indices = np.where(pred > 0)
+        pred[pred_indices] = 1
 
         return convert_to_dst_type(pred, prob_map, dtype=self.dtype)[0]
 
@@ -338,7 +339,8 @@ class GenerateWatershedMarkers(Transform):
         instance_border = instance_border >= self.threshold  # uncertain area
 
         marker = mask - convert_to_dst_type(instance_border, mask)[0]  # certain foreground
-        marker[marker < 0] = 0
+        marker_indices = where(marker < 0)
+        marker[marker_indices] = 0  # type: ignore[index]
         marker = self.postprocess_fn(marker)
         marker = convert_to_numpy(marker)
 
@@ -379,6 +381,7 @@ class GenerateSuccinctContour(Transform):
         """
 
         p_delta = (current[0] - previous[0], current[1] - previous[1])
+        row, col = -1, -1
 
         if p_delta in ((0.0, 1.0), (0.5, 0.5), (1.0, 0.0)):
             row = int(current[0] + 0.5)
@@ -634,7 +637,7 @@ class GenerateInstanceType(Transform):
 
         seg_map_crop = convert_to_dst_type(seg_map_crop == instance_id, type_map_crop, dtype=bool)[0]
 
-        inst_type = type_map_crop[seg_map_crop]
+        inst_type = type_map_crop[seg_map_crop]  # type: ignore[index]
         type_list, type_pixels = unique(inst_type, return_counts=True)
         type_list = list(zip(type_list, type_pixels))
         type_list = sorted(type_list, key=lambda x: x[1], reverse=True)

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/auto3dseg/analyzer.py

@@ -470,7 +470,7 @@ class LabelStats(Analyzer):
 
         unique_label = unique(ndas_label)
         if isinstance(ndas_label, (MetaTensor, torch.Tensor)):
-            unique_label = unique_label.data.cpu().numpy()
+            unique_label = unique_label.data.cpu().numpy()  # type: ignore[assignment]
 
         unique_label = unique_label.astype(np.int16).tolist()
 

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/bundle/scripts.py

@@ -16,6 +16,7 @@ import json
 import os
 import re
 import warnings
+import zipfile
 from collections.abc import Mapping, Sequence
 from pathlib import Path
 from pydoc import locate
@@ -26,7 +27,7 @@ from typing import Any, Callable
 import torch
 from torch.cuda import is_available
 
-from monai.apps.mmars.mmars import _get_all_ngc_models
+from monai._version import get_versions
 from monai.apps.utils import _basename, download_url, extractall, get_logger
 from monai.bundle.config_item import ConfigComponent
 from monai.bundle.config_parser import ConfigParser
@@ -66,6 +67,9 @@ logger = get_logger(module_name=__name__)
 DEFAULT_DOWNLOAD_SOURCE = os.environ.get("BUNDLE_DOWNLOAD_SRC", "monaihosting")
 PPRINT_CONFIG_N = 5
 
+MONAI_HOSTING_BASE_URL = "https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting"
+NGC_BASE_URL = "https://api.ngc.nvidia.com/v2/models/nvidia/monaitoolkit"
+
 
 def update_kwargs(args: str | dict | None = None, ignore_none: bool = True, **kwargs: Any) -> dict:
     """
@@ -168,12 +172,19 @@ def _get_git_release_url(repo_owner: str, repo_name: str, tag_name: str, filenam
 
 
 def _get_ngc_bundle_url(model_name: str, version: str) -> str:
-    return f"https://api.ngc.nvidia.com/v2/models/nvidia/monaitoolkit/{model_name.lower()}/versions/{version}/zip"
+    return f"{NGC_BASE_URL}/{model_name.lower()}/versions/{version}/zip"
+
+
+def _get_ngc_private_base_url(repo: str) -> str:
+    return f"https://api.ngc.nvidia.com/v2/{repo}/models"
+
+
+def _get_ngc_private_bundle_url(model_name: str, version: str, repo: str) -> str:
+    return f"{_get_ngc_private_base_url(repo)}/{model_name.lower()}/versions/{version}/zip"
 
 
 def _get_monaihosting_bundle_url(model_name: str, version: str) -> str:
-    monaihosting_root_path = "https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting"
-    return f"{monaihosting_root_path}/{model_name.lower()}/versions/{version}/files/{model_name}_v{version}.zip"
+    return f"{MONAI_HOSTING_BASE_URL}/{model_name.lower()}/versions/{version}/files/{model_name}_v{version}.zip"
 
 
 def _download_from_github(repo: str, download_path: Path, filename: str, progress: bool = True) -> None:
@@ -219,29 +230,168 @@ def _download_from_ngc(
     extractall(filepath=filepath, output_dir=extract_path, has_base=True)
 
 
+def _download_from_ngc_private(
+    download_path: Path, filename: str, version: str, remove_prefix: str | None, repo: str, headers: dict | None = None
+) -> None:
+    # ensure prefix is contained
+    filename = _add_ngc_prefix(filename)
+    request_url = _get_ngc_private_bundle_url(model_name=filename, version=version, repo=repo)
+    if has_requests:
+        headers = {} if headers is None else headers
+        response = requests_get(request_url, headers=headers)
+        response.raise_for_status()
+    else:
+        raise ValueError("NGC API requires requests package. Please install it.")
+
+    zip_path = download_path / f"{filename}_v{version}.zip"
+    with open(zip_path, "wb") as f:
+        f.write(response.content)
+    logger.info(f"Downloading: {zip_path}.")
+    if remove_prefix:
+        filename = _remove_ngc_prefix(filename, prefix=remove_prefix)
+    extract_path = download_path / f"{filename}"
+    with zipfile.ZipFile(zip_path, "r") as z:
+        z.extractall(extract_path)
+        logger.info(f"Writing into directory: {extract_path}.")
+
+
+def _get_ngc_token(api_key, retry=0):
+    """Try to connect to NGC."""
+    url = "https://authn.nvidia.com/token?service=ngc"
+    headers = {"Accept": "application/json", "Authorization": "ApiKey " + api_key}
+    if has_requests:
+        response = requests_get(url, headers=headers)
+        if not response.ok:
+            # retry 3 times, if failed, raise an error.
+            if retry < 3:
+                logger.info(f"Retrying {retry} time(s) to GET {url}.")
+                return _get_ngc_token(url, retry + 1)
+            raise RuntimeError("NGC API response is not ok. Failed to get token.")
+        else:
+            token = response.json()["token"]
+        return token
+
+
 def _get_latest_bundle_version_monaihosting(name):
-    url = "https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting"
-    full_url = f"{url}/{name.lower()}"
+    full_url = f"{MONAI_HOSTING_BASE_URL}/{name.lower()}"
     requests_get, has_requests = optional_import("requests", name="get")
     if has_requests:
         resp = requests_get(full_url)
         resp.raise_for_status()
     else:
-        raise ValueError("NGC API requires requests package.  Please install it.")
+        raise ValueError("NGC API requires requests package. Please install it.")
     model_info = json.loads(resp.text)
     return model_info["model"]["latestVersionIdStr"]
 
 
-def _get_latest_bundle_version(source: str, name: str, repo: str) -> dict[str, list[str] | str] | Any | None:
+def _examine_monai_version(monai_version: str) -> tuple[bool, str]:
+    """Examine if the package version is compatible with the MONAI version in the metadata."""
+    version_dict = get_versions()
+    package_version = version_dict.get("version", "0+unknown")
+    if package_version == "0+unknown":
+        return False, "Package version is not available. Skipping version check."
+    if monai_version == "0+unknown":
+        return False, "MONAI version is not specified in the bundle. Skipping version check."
+    # treat rc versions as the same as the release version
+    package_version = re.sub(r"rc\d.*", "", package_version)
+    monai_version = re.sub(r"rc\d.*", "", monai_version)
+    if package_version < monai_version:
+        return (
+            False,
+            f"Your MONAI version is {package_version}, but the bundle is built on MONAI version {monai_version}.",
+        )
+    return True, ""
+
+
+def _check_monai_version(bundle_dir: PathLike, name: str) -> None:
+    """Get the `monai_version` from the metadata.json and compare if it is smaller than the installed `monai` package version"""
+    metadata_file = Path(bundle_dir) / name / "configs" / "metadata.json"
+    if not metadata_file.exists():
+        logger.warning(f"metadata file not found in {metadata_file}.")
+        return
+    with open(metadata_file) as f:
+        metadata = json.load(f)
+    is_compatible, msg = _examine_monai_version(metadata.get("monai_version", "0+unknown"))
+    if not is_compatible:
+        logger.warning(msg)
+
+
+def _list_latest_versions(data: dict, max_versions: int = 3) -> list[str]:
+    """
+    Extract the latest versions from the data dictionary.
+
+    Args:
+        data: the data dictionary.
+        max_versions: the maximum number of versions to return.
+
+    Returns:
+        versions of the latest models in the reverse order of creation date, e.g. ['1.0.0', '0.9.0', '0.8.0'].
+    """
+    # Check if the data is a dictionary and it has the key 'modelVersions'
+    if not isinstance(data, dict) or "modelVersions" not in data:
+        raise ValueError("The data is not a dictionary or it does not have the key 'modelVersions'.")
+
+    # Extract the list of model versions
+    model_versions = data["modelVersions"]
+
+    if (
+        not isinstance(model_versions, list)
+        or len(model_versions) == 0
+        or "createdDate" not in model_versions[0]
+        or "versionId" not in model_versions[0]
+    ):
+        raise ValueError(
+            "The model versions are not a list or it is empty or it does not have the keys 'createdDate' and 'versionId'."
+        )
+
+    # Sort the versions by the 'createdDate' in descending order
+    sorted_versions = sorted(model_versions, key=lambda x: x["createdDate"], reverse=True)
+    return [v["versionId"] for v in sorted_versions[:max_versions]]
+
+
+def _get_latest_bundle_version_ngc(name: str, repo: str | None = None, headers: dict | None = None) -> str:
+    base_url = _get_ngc_private_base_url(repo) if repo else NGC_BASE_URL
+    version_endpoint = base_url + f"/{name.lower()}/versions/"
+
+    if not has_requests:
+        raise ValueError("requests package is required, please install it.")
+
+    version_header = {"Accept-Encoding": "gzip, deflate"}  # Excluding 'zstd' to fit NGC requirements
+    if headers:
+        version_header.update(headers)
+    resp = requests_get(version_endpoint, headers=version_header)
+    resp.raise_for_status()
+    model_info = json.loads(resp.text)
+    latest_versions = _list_latest_versions(model_info)
+
+    for version in latest_versions:
+        file_endpoint = base_url + f"/{name.lower()}/versions/{version}/files/configs/metadata.json"
+        resp = requests_get(file_endpoint, headers=headers)
+        metadata = json.loads(resp.text)
+        resp.raise_for_status()
+        # if the package version is not available or the model is compatible with the package version
+        is_compatible, _ = _examine_monai_version(metadata["monai_version"])
+        if is_compatible:
+            if version != latest_versions[0]:
+                logger.info(f"Latest version is {latest_versions[0]}, but the compatible version is {version}.")
+            return version
+
+    # if no compatible version is found, return the latest version
+    return latest_versions[0]
+
+
+def _get_latest_bundle_version(
+    source: str, name: str, repo: str, **kwargs: Any
+) -> dict[str, list[str] | str] | Any | None:
     if source == "ngc":
         name = _add_ngc_prefix(name)
-        model_dict = _get_all_ngc_models(name)
-        for v in model_dict.values():
-            if v["name"] == name:
-                return v["latest"]
-        return None
+        return _get_latest_bundle_version_ngc(name)
     elif source == "monaihosting":
         return _get_latest_bundle_version_monaihosting(name)
+    elif source == "ngc_private":
+        headers = kwargs.pop("headers", {})
+        name = _add_ngc_prefix(name)
+        return _get_latest_bundle_version_ngc(name, repo=repo, headers=headers)
     elif source == "github":
         repo_owner, repo_name, tag_name = repo.split("/")
         return get_bundle_versions(name, repo=f"{repo_owner}/{repo_name}", tag=tag_name)["latest_version"]
@@ -308,6 +458,9 @@ def download(
         # Execute this module as a CLI entry, and download bundle via URL:
         python -m monai.bundle download --name <bundle_name> --url <url>
 
+        # Execute this module as a CLI entry, and download bundle from ngc_private with latest version:
+        python -m monai.bundle download --name <bundle_name> --source "ngc_private" --bundle_dir "./" --repo "org/org_name"
+
         # Set default args of `run` in a JSON / YAML file, help to record and simplify the command line.
         # Other args still can override the default args at runtime.
         # The content of the JSON / YAML file is a dictionary. For example:
@@ -328,10 +481,13 @@ def download(
             Default is `bundle` subfolder under `torch.hub.get_dir()`.
         source: storage location name. This argument is used when `url` is `None`.
             In default, the value is achieved from the environment variable BUNDLE_DOWNLOAD_SRC, and
-            it should be "ngc", "monaihosting", "github", or "huggingface_hub".
+            it should be "ngc", "monaihosting", "github", "ngc_private", or "huggingface_hub".
+            If source is "ngc_private", you need specify the NGC_API_KEY in the environment variable.
         repo: repo name. This argument is used when `url` is `None` and `source` is "github" or "huggingface_hub".
             If `source` is "github", it should be in the form of "repo_owner/repo_name/release_tag".
             If `source` is "huggingface_hub", it should be in the form of "repo_owner/repo_name".
+            If `source` is "ngc_private", it should be in the form of "org/org_name" or "org/org_name/team/team_name",
+            or you can specify the environment variable NGC_ORG and NGC_TEAM.
         url: url to download the data. If not `None`, data will be downloaded directly
             and `source` will not be checked.
             If `name` is `None`, filename is determined by `monai.apps.utils._basename(url)`.
@@ -363,11 +519,18 @@ def download(
 
     bundle_dir_ = _process_bundle_dir(bundle_dir_)
     if repo_ is None:
-        repo_ = "Project-MONAI/model-zoo/hosting_storage_v1"
-    if len(repo_.split("/")) != 3 and source_ != "huggingface_hub":
-        raise ValueError("repo should be in the form of `repo_owner/repo_name/release_tag`.")
+        org_ = os.getenv("NGC_ORG", None)
+        team_ = os.getenv("NGC_TEAM", None)
+        if org_ is not None and source_ == "ngc_private":
+            repo_ = f"org/{org_}/team/{team_}" if team_ is not None else f"org/{org_}"
+        else:
+            repo_ = "Project-MONAI/model-zoo/hosting_storage_v1"
+    if len(repo_.split("/")) not in (2, 4) and source_ == "ngc_private":
+        raise ValueError(f"repo should be in the form of `org/org_name/team/team_name` or `org/org_name`, got {repo_}.")
+    if len(repo_.split("/")) != 3 and source_ == "github":
+        raise ValueError(f"repo should be in the form of `repo_owner/repo_name/release_tag`, got {repo_}.")
     elif len(repo_.split("/")) != 2 and source_ == "huggingface_hub":
-        raise ValueError("Hugging Face Hub repo should be in the form of `repo_owner/repo_name`")
+        raise ValueError(f"Hugging Face Hub repo should be in the form of `repo_owner/repo_name`, got {repo_}.")
     if url_ is not None:
         if name_ is not None:
             filepath = bundle_dir_ / f"{name_}.zip"
@@ -376,14 +539,22 @@ def download(
         download_url(url=url_, filepath=filepath, hash_val=None, progress=progress_)
         extractall(filepath=filepath, output_dir=bundle_dir_, has_base=True)
     else:
+        headers = {}
         if name_ is None:
             raise ValueError(f"To download from source: {source_}, `name` must be provided.")
+        if source == "ngc_private":
+            api_key = os.getenv("NGC_API_KEY", None)
+            if api_key is None:
+                raise ValueError("API key is required for ngc_private source.")
+            else:
+                token = _get_ngc_token(api_key)
+                headers = {"Authorization": f"Bearer {token}"}
+
         if version_ is None:
-            version_ = _get_latest_bundle_version(source=source_, name=name_, repo=repo_)
+            version_ = _get_latest_bundle_version(source=source_, name=name_, repo=repo_, headers=headers)
         if source_ == "github":
-            if version_ is not None:
-                name_ = "_v".join([name_, version_])
-            _download_from_github(repo=repo_, download_path=bundle_dir_, filename=name_, progress=progress_)
+            name_ver = "_v".join([name_, version_]) if version_ is not None else name_
+            _download_from_github(repo=repo_, download_path=bundle_dir_, filename=name_ver, progress=progress_)
         elif source_ == "monaihosting":
             _download_from_monaihosting(download_path=bundle_dir_, filename=name_, version=version_, progress=progress_)
         elif source_ == "ngc":
@@ -394,6 +565,15 @@ def download(
                 remove_prefix=remove_prefix_,
                 progress=progress_,
             )
+        elif source_ == "ngc_private":
+            _download_from_ngc_private(
+                download_path=bundle_dir_,
+                filename=name_,
+                version=version_,
+                remove_prefix=remove_prefix_,
+                repo=repo_,
+                headers=headers,
+            )
         elif source_ == "huggingface_hub":
             extract_path = os.path.join(bundle_dir_, name_)
             huggingface_hub.snapshot_download(repo_id=repo_, revision=version_, local_dir=extract_path)
@@ -403,6 +583,8 @@ def download(
                 f"got source: {source_}."
             )
 
+    _check_monai_version(bundle_dir_, name_)
+
 
 @deprecated_arg("net_name", since="1.2", removed="1.5", msg_suffix="please use ``model`` instead.")
 @deprecated_arg("net_kwargs", since="1.2", removed="1.5", msg_suffix="please use ``model`` instead.")

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/bundle/utils.py

@@ -221,6 +221,7 @@ def load_bundle_config(bundle_path: str, *config_names: str, **load_kw_args: Any
                 raise ValueError(f"Cannot find config file '{full_cname}'")
 
             ardata = archive.read(full_cname)
+            cdata = {}
 
             if full_cname.lower().endswith("json"):
                 cdata = json.loads(ardata, **load_kw_args)

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/data/dataset_summary.py

@@ -84,6 +84,7 @@ class DatasetSummary:
         """
 
         for data in self.data_loader:
+            meta_dict = {}
             if isinstance(data[self.image_key], MetaTensor):
                 meta_dict = data[self.image_key].meta
             elif self.meta_key in data:

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/data/meta_tensor.py

@@ -505,7 +505,7 @@ class MetaTensor(MetaObj, torch.Tensor):
         a = self.pending_operations[-1].get(LazyAttr.AFFINE, None) if self.pending_operations else self.affine
         return 1 if a is None else int(max(1, len(a) - 1))
 
-    def new_empty(self, size, dtype=None, device=None, requires_grad=False):
+    def new_empty(self, size, dtype=None, device=None, requires_grad=False):  # type: ignore[override]
         """
         must be defined for deepcopy to work
 
@@ -580,7 +580,7 @@ class MetaTensor(MetaObj, torch.Tensor):
             img.affine = MetaTensor.get_default_affine()
         return img
 
-    def __repr__(self):
+    def __repr__(self):  # type: ignore[override]
         """
         Prints a representation of the tensor.
         Prepends "meta" to ``torch.Tensor.__repr__``.

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/data/test_time_augmentation.py

@@ -106,6 +106,8 @@ class TestTimeAugmentation:
             mode, mean, std, vvc = tt_aug(test_data)
     """
 
+    __test__ = False  # indicate to pytest that this class is not intended for collection
+
     def __init__(
         self,
         transform: InvertibleTransform,

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/data/utils.py

@@ -53,10 +53,6 @@ from monai.utils import (
     pytorch_after,
 )
 
-if pytorch_after(1, 13):
-    # import private code for reuse purposes, comment in case things break in the future
-    from torch.utils.data._utils.collate import collate_tensor_fn, default_collate_fn_map
-
 pd, _ = optional_import("pandas")
 DataFrame, _ = optional_import("pandas", name="DataFrame")
 nib, _ = optional_import("nibabel")
@@ -454,8 +450,13 @@ def collate_meta_tensor_fn(batch, *, collate_fn_map=None):
     Collate a sequence of meta tensor into a single batched metatensor. This is called by `collage_meta_tensor`
     and so should not be used as a collate function directly in dataloaders.
     """
-    collate_fn = collate_tensor_fn if pytorch_after(1, 13) else default_collate
-    collated = collate_fn(batch)  # type: ignore
+    if pytorch_after(1, 13):
+        from torch.utils.data._utils.collate import collate_tensor_fn  # imported here for pylint/mypy issues
+
+        collated = collate_tensor_fn(batch)
+    else:
+        collated = default_collate(batch)
+
     meta_dicts = [i.meta or TraceKeys.NONE for i in batch]
     common_ = set.intersection(*[set(d.keys()) for d in meta_dicts if isinstance(d, dict)])
     if common_:
@@ -496,6 +497,8 @@ def list_data_collate(batch: Sequence):
 
     if pytorch_after(1, 13):
         # needs to go here to avoid circular import
+        from torch.utils.data._utils.collate import default_collate_fn_map
+
         from monai.data.meta_tensor import MetaTensor
 
         default_collate_fn_map.update({MetaTensor: collate_meta_tensor_fn})

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/data/wsi_reader.py

@@ -1097,8 +1097,8 @@ class TiffFileWSIReader(BaseWSIReader):
         ):
             unit = wsi.pages[level].tags.get("ResolutionUnit")
             if unit is not None:
-                unit = str(unit.value)[8:]
-            else:
+                unit = str(unit.value.name)
+            if unit is None or len(unit) == 0:
                 warnings.warn("The resolution unit is missing. `micrometer` will be used as default.")
                 unit = "micrometer"
 

{monai_weekly-1.4.dev2428 → monai_weekly-1.4.dev2430}/monai/engines/__init__.py

@@ -12,12 +12,14 @@
 from __future__ import annotations
 
 from .evaluator import EnsembleEvaluator, Evaluator, SupervisedEvaluator
-from .trainer import GanTrainer, SupervisedTrainer, Trainer
+from .trainer import AdversarialTrainer, GanTrainer, SupervisedTrainer, Trainer
 from .utils import (
+    DiffusionPrepareBatch,
     IterationEvents,
     PrepareBatch,
     PrepareBatchDefault,
     PrepareBatchExtraInput,
+    VPredictionPrepareBatch,
     default_make_latent,
     default_metric_cmp_fn,
     default_prepare_batch,