monai-weekly 1.4.dev2429__tar.gz → 1.4.dev2430__tar.gz

{monai_weekly-1.4.dev2429/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.dev2429
+Version: 1.4.dev2430
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/__init__.py

@@ -93,4 +93,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "d020facccbd3afe979fce68c24703dcda47234f6"
+__commit_id__ = "2e53df78e580131046dc8db7f7638063db1f5045"

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-07-21T02:18:43+0000",
+ "date": "2024-07-28T02:19:22+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "023827f344ab6236402ad609f0e938c308f68ca0",
- "version": "1.4.dev2429"
+ "full-revisionid": "9dd92b4a07706d4b80edace3d39fe008dc805d5a",
+ "version": "1.4.dev2430"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.4.dev2429 → 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.dev2429 → 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)
 
@@ -635,7 +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.dev2429 → 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.dev2429 → monai_weekly-1.4.dev2430}/monai/bundle/scripts.py

@@ -27,7 +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
@@ -67,6 +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:
     """
@@ -169,16 +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"https://api.ngc.nvidia.com/v2/{repo}/models/{model_name.lower()}/versions/{version}/zip"
+    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:
@@ -267,8 +273,7 @@ def _get_ngc_token(api_key, retry=0):
 
 
 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)
@@ -279,18 +284,100 @@ def _get_latest_bundle_version_monaihosting(name):
     return model_info["model"]["latestVersionIdStr"]
 
 
-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.")
+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)
-    return model_info["model"]["latestVersionIdStr"]
+    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(
@@ -298,17 +385,13 @@ def _get_latest_bundle_version(
 ) -> 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_private_registry(name, repo, headers)
+        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"]
@@ -470,9 +553,8 @@ def download(
         if version_ is None:
             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":
@@ -501,6 +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.dev2429 → 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.dev2429 → 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.dev2429 → monai_weekly-1.4.dev2430}/monai/metrics/cumulative_average.py

@@ -65,6 +65,7 @@ class CumulativeAverage:
         if self.val is None:
             return 0
 
+        val: NdarrayOrTensor
         val = self.val.clone()
         val[~torch.isfinite(val)] = 0
 
@@ -96,6 +97,7 @@ class CumulativeAverage:
             dist.all_reduce(sum)
             dist.all_reduce(count)
 
+        val: NdarrayOrTensor
         val = torch.where(count > 0, sum / count, sum)
 
         if to_numpy:

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/metrics/panoptic_quality.py

@@ -274,7 +274,7 @@ def _get_paired_iou(
 
         return paired_iou, paired_true, paired_pred
 
-    pairwise_iou = pairwise_iou.cpu().numpy()
+    pairwise_iou = pairwise_iou.cpu().numpy()  # type: ignore[assignment]
     paired_true, paired_pred = linear_sum_assignment(-pairwise_iou)
     paired_iou = pairwise_iou[paired_true, paired_pred]
     paired_true = torch.as_tensor(list(paired_true[paired_iou > match_iou_threshold] + 1), device=device)

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/metrics/rocauc.py

@@ -88,8 +88,8 @@ def _calculate(y_pred: torch.Tensor, y: torch.Tensor) -> float:
 
     n = len(y)
     indices = y_pred.argsort()
-    y = y[indices].cpu().numpy()
-    y_pred = y_pred[indices].cpu().numpy()
+    y = y[indices].cpu().numpy()  # type: ignore[assignment]
+    y_pred = y_pred[indices].cpu().numpy()  # type: ignore[assignment]
     nneg = auc = tmp_pos = tmp_neg = 0.0
 
     for i in range(n):

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/networks/blocks/crossattention.py

@@ -109,6 +109,8 @@ class CrossAttentionBlock(nn.Module):
                 torch.tril(torch.ones(sequence_length, sequence_length)).view(1, 1, sequence_length, sequence_length),
             )
             self.causal_mask: torch.Tensor
+        else:
+            self.causal_mask = torch.Tensor()
 
         self.att_mat = torch.Tensor()
         self.rel_positional_embedding = (
@@ -118,7 +120,7 @@ class CrossAttentionBlock(nn.Module):
         )
         self.input_size = input_size
 
-    def forward(self, x: torch.Tensor, context: torch.Tensor | None = None):
+    def forward(self, x: torch.Tensor, context: Optional[torch.Tensor] = None):
         """
         Args:
             x (torch.Tensor): input tensor. B x (s_dim_1 * ... * s_dim_n) x C

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/networks/blocks/selfattention.py

@@ -105,6 +105,8 @@ class SABlock(nn.Module):
                 torch.tril(torch.ones(sequence_length, sequence_length)).view(1, 1, sequence_length, sequence_length),
             )
             self.causal_mask: torch.Tensor
+        else:
+            self.causal_mask = torch.Tensor()
 
         self.rel_positional_embedding = (
             get_rel_pos_embedding_layer(rel_pos_embedding, input_size, self.dim_head, self.num_heads)

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/networks/blocks/transformerblock.py

@@ -11,6 +11,8 @@
 
 from __future__ import annotations
 
+from typing import Optional
+
 import torch
 import torch.nn as nn
 
@@ -68,13 +70,12 @@ class TransformerBlock(nn.Module):
         self.norm2 = nn.LayerNorm(hidden_size)
         self.with_cross_attention = with_cross_attention
 
-        if self.with_cross_attention:
-            self.norm_cross_attn = nn.LayerNorm(hidden_size)
-            self.cross_attn = CrossAttentionBlock(
-                hidden_size=hidden_size, num_heads=num_heads, dropout_rate=dropout_rate, qkv_bias=qkv_bias, causal=False
-            )
+        self.norm_cross_attn = nn.LayerNorm(hidden_size)
+        self.cross_attn = CrossAttentionBlock(
+            hidden_size=hidden_size, num_heads=num_heads, dropout_rate=dropout_rate, qkv_bias=qkv_bias, causal=False
+        )
 
-    def forward(self, x: torch.Tensor, context: torch.Tensor | None = None) -> torch.Tensor:
+    def forward(self, x: torch.Tensor, context: Optional[torch.Tensor] = None) -> torch.Tensor:
         x = x + self.attn(self.norm1(x))
         if self.with_cross_attention:
             x = x + self.cross_attn(self.norm_cross_attn(x), context=context)

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/networks/layers/simplelayers.py

@@ -452,7 +452,7 @@ def get_binary_kernel(window_size: Sequence[int], dtype=torch.float, device=None
 
 def median_filter(
     in_tensor: torch.Tensor,
-    kernel_size: Sequence[int] = (3, 3, 3),
+    kernel_size: Sequence[int] | int = (3, 3, 3),
     spatial_dims: int = 3,
     kernel: torch.Tensor | None = None,
     **kwargs,

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/networks/nets/quicknat.py

@@ -42,7 +42,7 @@ class SkipConnectionWithIdx(SkipConnection):
     Inherits from SkipConnection but provides the indizes with each forward pass.
     """
 
-    def forward(self, input, indices):
+    def forward(self, input, indices):  # type: ignore[override]
         return super().forward(input), indices
 
 
@@ -57,7 +57,7 @@ class SequentialWithIdx(nn.Sequential):
     def __init__(self, *args):
         super().__init__(*args)
 
-    def forward(self, input, indices):
+    def forward(self, input, indices):  # type: ignore[override]
         for module in self:
             input, indices = module(input, indices)
         return input, indices
@@ -165,7 +165,7 @@ class ConvConcatDenseBlock(ConvDenseBlock):
         )
         return nn.Sequential(conv.get_submodule("adn"), conv.get_submodule("conv"))
 
-    def forward(self, input, _):
+    def forward(self, input, _):  # type: ignore[override]
         i = 0
         result = input
         result1 = input  # this will not stay this value, needed here for pylint/mypy
@@ -215,7 +215,7 @@ class Encoder(ConvConcatDenseBlock):
         super().__init__(in_channels, se_layer, dropout, kernel_size, num_filters)
         self.max_pool = max_pool
 
-    def forward(self, input, indices=None):
+    def forward(self, input, indices=None):  # type: ignore[override]
         input, indices = self.max_pool(input)
 
         out_block, _ = super().forward(input, None)
@@ -243,7 +243,7 @@ class Decoder(ConvConcatDenseBlock):
         super().__init__(in_channels, se_layer, dropout, kernel_size, num_filters)
         self.un_pool = un_pool
 
-    def forward(self, input, indices):
+    def forward(self, input, indices):  # type: ignore[override]
         out_block, _ = super().forward(input, None)
         out_block = self.un_pool(out_block, indices)
         return out_block, None
@@ -270,7 +270,7 @@ class Bottleneck(ConvConcatDenseBlock):
         self.max_pool = max_pool
         self.un_pool = un_pool
 
-    def forward(self, input, indices):
+    def forward(self, input, indices):  # type: ignore[override]
         out_block, indices = self.max_pool(input)
         out_block, _ = super().forward(out_block, None)
         out_block = self.un_pool(out_block, indices)

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/transforms/croppad/array.py

@@ -362,10 +362,10 @@ class Crop(InvertibleTransform, LazyTransform):
 
     @staticmethod
     def compute_slices(
-        roi_center: Sequence[int] | NdarrayOrTensor | None = None,
-        roi_size: Sequence[int] | NdarrayOrTensor | None = None,
-        roi_start: Sequence[int] | NdarrayOrTensor | None = None,
-        roi_end: Sequence[int] | NdarrayOrTensor | None = None,
+        roi_center: Sequence[int] | int | NdarrayOrTensor | None = None,
+        roi_size: Sequence[int] | int | NdarrayOrTensor | None = None,
+        roi_start: Sequence[int] | int | NdarrayOrTensor | None = None,
+        roi_end: Sequence[int] | int | NdarrayOrTensor | None = None,
         roi_slices: Sequence[slice] | None = None,
     ) -> tuple[slice]:
         """
@@ -459,10 +459,10 @@ class SpatialCrop(Crop):
 
     def __init__(
         self,
-        roi_center: Sequence[int] | NdarrayOrTensor | None = None,
-        roi_size: Sequence[int] | NdarrayOrTensor | None = None,
-        roi_start: Sequence[int] | NdarrayOrTensor | None = None,
-        roi_end: Sequence[int] | NdarrayOrTensor | None = None,
+        roi_center: Sequence[int] | int | NdarrayOrTensor | None = None,
+        roi_size: Sequence[int] | int | NdarrayOrTensor | None = None,
+        roi_start: Sequence[int] | int | NdarrayOrTensor | None = None,
+        roi_end: Sequence[int] | int | NdarrayOrTensor | None = None,
         roi_slices: Sequence[slice] | None = None,
         lazy: bool = False,
     ) -> None:

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/transforms/croppad/dictionary.py

@@ -438,10 +438,10 @@ class SpatialCropd(Cropd):
     def __init__(
         self,
         keys: KeysCollection,
-        roi_center: Sequence[int] | None = None,
-        roi_size: Sequence[int] | None = None,
-        roi_start: Sequence[int] | None = None,
-        roi_end: Sequence[int] | None = None,
+        roi_center: Sequence[int] | int | None = None,
+        roi_size: Sequence[int] | int | None = None,
+        roi_start: Sequence[int] | int | None = None,
+        roi_end: Sequence[int] | int | None = None,
         roi_slices: Sequence[slice] | None = None,
         allow_missing_keys: bool = False,
         lazy: bool = False,

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/transforms/croppad/functional.py

@@ -48,7 +48,7 @@ def _np_pad(img: NdarrayTensor, pad_width: list[tuple[int, int]], mode: str, **k
             warnings.warn(f"Padding: moving img {img.shape} from cuda to cpu for dtype={img.dtype} mode={mode}.")
         img_np = img.detach().cpu().numpy()
     else:
-        img_np = img
+        img_np = np.asarray(img)
     mode = convert_pad_mode(dst=img_np, mode=mode).value
     if mode == "constant" and "value" in kwargs:
         kwargs["constant_values"] = kwargs.pop("value")

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/transforms/spatial/array.py

@@ -3441,7 +3441,7 @@ class RandGridPatch(GridPatch, RandomizableTransform, MultiSampleTrait):
             idx = self.R.permutation(image_np.shape[0])
             idx = idx[: self.num_patches]
             idx_np = convert_data_type(idx, np.ndarray)[0]
-            image_np = image_np[idx]
+            image_np = image_np[idx]  # type: ignore[index]
             locations = locations[idx_np]
             return image_np, locations
         elif self.sort_fn not in (None, GridPatchSort.MIN, GridPatchSort.MAX):

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/visualize/class_activation_maps.py

@@ -290,7 +290,7 @@ class CAM(CAMBase):
         )
         self.fc_layers = fc_layers
 
-    def compute_map(self, x, class_idx=None, layer_idx=-1, **kwargs):
+    def compute_map(self, x, class_idx=None, layer_idx=-1, **kwargs):  # type: ignore[override]
         logits, acti, _ = self.nn_module(x, **kwargs)
         acti = acti[layer_idx]
         if class_idx is None:
@@ -302,7 +302,7 @@ class CAM(CAMBase):
         output = torch.stack([output[i, b : b + 1] for i, b in enumerate(class_idx)], dim=0)
         return output.reshape(b, 1, *spatial)  # resume the spatial dims on the selected class
 
-    def __call__(self, x, class_idx=None, layer_idx=-1, **kwargs):
+    def __call__(self, x, class_idx=None, layer_idx=-1, **kwargs):  # type: ignore[override]
         """
         Compute the activation map with upsampling and postprocessing.
 
@@ -361,7 +361,7 @@ class GradCAM(CAMBase):
 
     """
 
-    def compute_map(self, x, class_idx=None, retain_graph=False, layer_idx=-1, **kwargs):
+    def compute_map(self, x, class_idx=None, retain_graph=False, layer_idx=-1, **kwargs):  # type: ignore[override]
         _, acti, grad = self.nn_module(x, class_idx=class_idx, retain_graph=retain_graph, **kwargs)
         acti, grad = acti[layer_idx], grad[layer_idx]
         b, c, *spatial = grad.shape
@@ -369,7 +369,7 @@ class GradCAM(CAMBase):
         acti_map = (weights * acti).sum(1, keepdim=True)
         return F.relu(acti_map)
 
-    def __call__(self, x, class_idx=None, layer_idx=-1, retain_graph=False, **kwargs):
+    def __call__(self, x, class_idx=None, layer_idx=-1, retain_graph=False, **kwargs):  # type: ignore[override]
         """
         Compute the activation map with upsampling and postprocessing.
 
@@ -401,7 +401,7 @@ class GradCAMpp(GradCAM):
 
     """
 
-    def compute_map(self, x, class_idx=None, retain_graph=False, layer_idx=-1, **kwargs):
+    def compute_map(self, x, class_idx=None, retain_graph=False, layer_idx=-1, **kwargs):  # type: ignore[override]
         _, acti, grad = self.nn_module(x, class_idx=class_idx, retain_graph=retain_graph, **kwargs)
         acti, grad = acti[layer_idx], grad[layer_idx]
         b, c, *spatial = grad.shape

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/monai/visualize/img2tensorboard.py

@@ -176,7 +176,9 @@ def plot_2d_or_3d_image(
     # as the `d` data has no batch dim, reduce the spatial dim index if positive
     frame_dim = frame_dim - 1 if frame_dim > 0 else frame_dim
 
-    d: np.ndarray = data_index.detach().cpu().numpy() if isinstance(data_index, torch.Tensor) else data_index
+    d: np.ndarray = (
+        data_index.detach().cpu().numpy() if isinstance(data_index, torch.Tensor) else np.asarray(data_index)
+    )
 
     if d.ndim == 2:
         d = rescale_array(d, 0, 1)  # type: ignore

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430/monai_weekly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.4.dev2429
+Version: 1.4.dev2430
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.4.dev2429 → monai_weekly-1.4.dev2430}/tests/test_arraydataset.py

@@ -40,6 +40,7 @@ TEST_CASE_2 = [
 
 
 class TestCompose(Compose):
+    __test__ = False  # indicate to pytest that this class is not intended for collection
 
     def __call__(self, input_, lazy=False):
         img = self.transforms[0](input_)