Merge branch 'dev' into dev

Author: ericspod

.github/workflows/pythonapp-min.yml

@@ -124,7 +124,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: ['2.4.1', '2.5.1', '2.6.0', '2.7.1']
+        pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4

.github/workflows/pythonapp.yml

@@ -94,7 +94,7 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==2.4.1 torchvision==0.19.1+cpu --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
@@ -103,7 +103,7 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
-        python -m pip install torch==2.4.1 torchvision==0.19.1
+        python -m pip install torch==2.5.1 torchvision==0.20.1
         cat "requirements-dev.txt"
         python -m pip install -r requirements-dev.txt
         python -m pip list
@@ -155,7 +155,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.4.1 torchvision
+        python -m pip install torch>=2.5.1 torchvision
     - name: Check packages
       run: |
         pip uninstall monai

monai/apps/detection/metrics/coco.py

@@ -457,7 +457,7 @@ def _compute_statistics(self, results_list: list[dict[int, dict[str, np.ndarray]
                 dt_ignores = np.concatenate([r["dtIgnore"][:, 0:max_det] for r in results], axis=1)[:, inds]
                 self.check_number_of_iou(dt_matches, dt_ignores)
                 gt_ignore = np.concatenate([r["gtIgnore"] for r in results])
-                num_gt = np.count_nonzero(gt_ignore == 0)  # number of ground truth boxes (non ignored)
+                num_gt = int(np.count_nonzero(gt_ignore == 0))  # number of ground truth boxes (non ignored)
                 if num_gt == 0:
                     logger.warning(f"WARNING, no gt found for coco metric for class {cls_i}")
                     continue
@@ -523,13 +523,12 @@ def _compute_stats_single_threshold(
         recall = 0
 
     # array where precision values nearest to given recall th are saved
-    precision = np.zeros((num_recall_th,))
+    precision = [0.0] * num_recall_th
     # save scores for corresponding recall value in here
     th_scores = np.zeros((num_recall_th,))
     # numpy is slow without cython optimization for accessing elements
     # use python array gets significant speed improvement
     pr = pr.tolist()
-    precision = precision.tolist()
 
     # smooth precision curve (create box shape)
     for i in range(len(tp) - 1, 0, -1):

monai/apps/detection/utils/box_coder.py

@@ -210,7 +210,10 @@ def decode_single(self, rel_codes: Tensor, reference_boxes: Tensor) -> Tensor:
         offset = reference_boxes.shape[-1]
 
         pred_boxes = []
-        boxes_cccwhd = convert_box_mode(reference_boxes, src_mode=StandardMode, dst_mode=CenterSizeMode)
+        boxes_cccwhd: torch.Tensor = convert_box_mode(
+            reference_boxes, src_mode=StandardMode, dst_mode=CenterSizeMode
+        )  # type: ignore[assignment]
+
         for axis in range(self.spatial_dims):
             whd_axis = boxes_cccwhd[:, axis + self.spatial_dims]
             ctr_xyz_axis = boxes_cccwhd[:, axis]

monai/apps/generation/maisi/networks/diffusion_model_unet_maisi.py

@@ -358,8 +358,9 @@ def _apply_down_blocks(self, h, emb, context, down_block_additional_residuals):
 
     def _apply_up_blocks(self, h, emb, context, down_block_res_samples):
         for upsample_block in self.up_blocks:
-            res_samples = down_block_res_samples[-len(upsample_block.resnets) :]
-            down_block_res_samples = down_block_res_samples[: -len(upsample_block.resnets)]
+            idx: int = -len(upsample_block.resnets)  # type: ignore
+            res_samples = down_block_res_samples[idx:]
+            down_block_res_samples = down_block_res_samples[:idx]
             h = upsample_block(hidden_states=h, res_hidden_states_list=res_samples, temb=emb, context=context)
 
         return h

monai/data/box_utils.py

@@ -811,9 +811,9 @@ def _box_inter_union(
 
     # compute size for the intersection region for the NxM combinations
     wh = (rb - lt + TO_REMOVE).clamp(min=0)  # (N,M,spatial_dims)
-    inter = torch.prod(wh, dim=-1, keepdim=False)  # (N,M)
+    inter: torch.Tensor = torch.prod(wh, dim=-1, keepdim=False)  # (N,M)
 
-    union = area1[:, None] + area2 - inter
+    union: torch.Tensor = area1[:, None] + area2 - inter  # type: ignore
     return inter, union
 
 
@@ -981,7 +981,7 @@ def box_pair_giou(boxes1: NdarrayOrTensor, boxes2: NdarrayOrTensor) -> NdarrayOr
     wh = (rb - lt + TO_REMOVE).clamp(min=0)  # (N,spatial_dims)
     enclosure = torch.prod(wh, dim=-1, keepdim=False)  # (N,)
 
-    giou_t = iou - (enclosure - union) / (enclosure + torch.finfo(COMPUTE_DTYPE).eps)
+    giou_t: torch.Tensor = iou - (enclosure - union) / (enclosure + torch.finfo(COMPUTE_DTYPE).eps)  # type: ignore
     giou_t = giou_t.to(dtype=box_dtype)  # (N,spatial_dims)
     if torch.isnan(giou_t).any() or torch.isinf(giou_t).any():
         raise ValueError("Box GIoU is NaN or Inf.")

monai/data/dataset.py

@@ -1353,7 +1353,7 @@ def __len__(self) -> int:
         return len(self.dataset)
 
     def randomize(self, data: Any | None = None) -> None:
-        self._seed = self.R.randint(MAX_SEED, dtype="uint32")
+        self._seed = int(self.R.randint(MAX_SEED, dtype="uint32"))
 
     def __getitem__(self, index: int):
         self.randomize()

monai/data/image_dataset.py

@@ -97,7 +97,7 @@ def __len__(self) -> int:
         return len(self.image_files)
 
     def randomize(self, data: Any | None = None) -> None:
-        self._seed = self.R.randint(MAX_SEED, dtype="uint32")
+        self._seed = int(self.R.randint(MAX_SEED, dtype="uint32"))
 
     def __getitem__(self, index: int):
         self.randomize()

monai/data/image_reader.py

@@ -580,7 +580,7 @@ def _combine_dicom_series(self, data: Iterable, filenames: Sequence[PathLike]):
         shape = first_array.shape
         spacing = getattr(first_slice, "PixelSpacing", [1.0] * len(shape))
         prev_pos = getattr(first_slice, "ImagePositionPatient", (0.0, 0.0, 0.0))[2]
-        stack_array = [first_array]
+        stack_array_list: list = [first_array]
         for idx in range(1, len(slices)):
             slc_array = self._get_array_data(slices[idx][0], slices[idx][1])
             slc_shape = slc_array.shape
@@ -592,22 +592,24 @@ def _combine_dicom_series(self, data: Iterable, filenames: Sequence[PathLike]):
                 warnings.warn(f"the list contains slices that have different shapes {shape} and {slc_shape}.")
             average_distance += abs(prev_pos - slc_pos)
             prev_pos = slc_pos
-            stack_array.append(slc_array)
+            stack_array_list.append(slc_array)
 
         if len(slices) > 1:
             average_distance /= len(slices) - 1
             spacing.append(average_distance)
             if self.to_gpu:
-                stack_array = cp.stack(stack_array, axis=-1)
+                stack_array = cp.stack(stack_array_list, axis=-1)
             else:
-                stack_array = np.stack(stack_array, axis=-1)
+                stack_array = np.stack(stack_array_list, axis=-1)
+
+            del stack_array_list[:]
             stack_metadata = self._get_meta_dict(first_slice)
             stack_metadata["spacing"] = np.asarray(spacing)
             if hasattr(slices[-1][0], "ImagePositionPatient"):
                 stack_metadata["lastImagePositionPatient"] = np.asarray(slices[-1][0].ImagePositionPatient)
             stack_metadata[MetaKeys.SPATIAL_SHAPE] = shape + (len(slices),)
         else:
-            stack_array = stack_array[0]
+            stack_array = stack_array_list[0]
             stack_metadata = self._get_meta_dict(first_slice)
             stack_metadata["spacing"] = np.asarray(spacing)
             stack_metadata[MetaKeys.SPATIAL_SHAPE] = shape

monai/networks/nets/diffusion_model_unet.py

@@ -1795,8 +1795,9 @@ def forward(
 
         # 6. up
         for upsample_block in self.up_blocks:
-            res_samples = down_block_res_samples[-len(upsample_block.resnets) :]
-            down_block_res_samples = down_block_res_samples[: -len(upsample_block.resnets)]
+            idx: int = -len(upsample_block.resnets)  # type: ignore
+            res_samples = down_block_res_samples[idx:]
+            down_block_res_samples = down_block_res_samples[:idx]
             h = upsample_block(hidden_states=h, res_hidden_states_list=res_samples, temb=emb, context=context)
 
         # 7. output block