monai-weekly 1.4.dev2427__py3-none-any.whl → 1.4.dev2429__py3-none-any.whl

monai/__init__.py

@@ -17,7 +17,7 @@ import sys
 from ._version import get_versions
 
 PY_REQUIRED_MAJOR = 3
-PY_REQUIRED_MINOR = 8
+PY_REQUIRED_MINOR = 9
 
 version_dict = get_versions()
 __version__: str = version_dict.get("version", "0+unknown")
@@ -93,4 +93,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "64ea76d83a92b7cf7f13c8f93498d50037c3324c"
+__commit_id__ = "d020facccbd3afe979fce68c24703dcda47234f6"

monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-07-07T02:18:37+0000",
+ "date": "2024-07-21T02:18:43+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "cbf90d0ddb27dc96a91385e4dd2f4eb239dea976",
- "version": "1.4.dev2427"
+ "full-revisionid": "023827f344ab6236402ad609f0e938c308f68ca0",
+ "version": "1.4.dev2429"
 }
 '''  # END VERSION_JSON
 

monai/apps/auto3dseg/auto_runner.py

@@ -551,7 +551,7 @@ class AutoRunner:
             cmd_prefix: command line prefix for subprocess running in BundleAlgo and EnsembleRunner.
                 Default using env "CMD_PREFIX" or None, examples are:
 
-                    - single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.8 ",
+                    - single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.9 ",
                     - single node multi-GPU running "torchrun --nnodes=1 --nproc_per_node=2 "
 
                 If user define this prefix, please make sure --nproc_per_node matches cuda_visible_device or

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/apps/generation/maisi/networks/autoencoderkl_maisi.py

@@ -27,13 +27,11 @@ AttentionBlock, has_attentionblock = optional_import("generative.networks.nets.a
 AutoencoderKL, has_autoencoderkl = optional_import("generative.networks.nets.autoencoderkl", name="AutoencoderKL")
 ResBlock, has_resblock = optional_import("generative.networks.nets.autoencoderkl", name="ResBlock")
 
-
 if TYPE_CHECKING:
     from generative.networks.nets.autoencoderkl import AutoencoderKL as AutoencoderKLType
 else:
     AutoencoderKLType = cast(type, AutoencoderKL)
 
-
 # Set up logging configuration
 logger = logging.getLogger(__name__)
 

monai/apps/pathology/transforms/post/array.py

@@ -379,6 +379,7 @@ 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)

monai/auto3dseg/utils.py

@@ -407,7 +407,7 @@ def _prepare_cmd_default(cmd: str, cmd_prefix: str | None = None, **kwargs: Any)
 
     Args:
         cmd: the command or script to run in the distributed job.
-        cmd_prefix: the command prefix to run the script, e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.8 ".
+        cmd_prefix: the command prefix to run the script, e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.9 ".
         kwargs: the keyword arguments to be passed to the script.
 
     Returns:

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
@@ -171,6 +172,10 @@ 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"
 
 
+def _get_ngc_private_bundle_url(model_name: str, version: str, repo: str) -> str:
+    return f"https://api.ngc.nvidia.com/v2/{repo}/models/{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"
@@ -219,6 +224,48 @@ 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()}"
@@ -227,12 +274,28 @@ def _get_latest_bundle_version_monaihosting(name):
         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 _get_latest_bundle_version_private_registry(name, repo, headers=None):
+    url = f"https://api.ngc.nvidia.com/v2/{repo}/models"
+    full_url = f"{url}/{name.lower()}"
+    requests_get, has_requests = optional_import("requests", name="get")
+    if has_requests:
+        headers = {} if headers is None else headers
+        resp = requests_get(full_url, headers=headers)
+        resp.raise_for_status()
+    else:
+        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, **kwargs: Any
+) -> dict[str, list[str] | str] | Any | None:
     if source == "ngc":
         name = _add_ngc_prefix(name)
         model_dict = _get_all_ngc_models(name)
@@ -242,6 +305,10 @@ def _get_latest_bundle_version(source: str, name: str, repo: str) -> dict[str, l
         return None
     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_private_registry(name, repo, 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 +375,9 @@ 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 +398,13 @@ 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 +436,18 @@ 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"
@@ -376,10 +456,19 @@ 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_])
@@ -394,6 +483,15 @@ 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)

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/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/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/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/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,