6676 port generative engines

.github/workflows/chatops.yml

@@ -10,7 +10,7 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - name: dispatch
- uses: peter-evans/slash-command-dispatch@v3.0.1
+ uses: peter-evans/slash-command-dispatch@v3.0.2
  with:
  token: ${{ secrets.PR_MAINTAIN }}
  reaction-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
  # Initializes the CodeQL tools for scanning.
  - name: Initialize CodeQL
- uses: github/codeql-action/init@v2
+ uses: github/codeql-action/init@v3
  with:
  languages: ${{ matrix.language }}
  # If you wish to specify custom queries, you can do so here or in a config file.
@@ -72,4 +72,4 @@ jobs:
  BUILD_MONAI=1 ./runtests.sh --build
 
  - name: Perform CodeQL Analysis
- uses: github/codeql-action/analyze@v2
+ uses: github/codeql-action/analyze@v3

.github/workflows/cron-ngc-bundle.yml

@@ -19,7 +19,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: cache weekly timestamp

.github/workflows/docker.yml

@@ -26,7 +26,7 @@ jobs:
  ref: dev
  fetch-depth: 0
  - name: Set up Python 3.9
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.9'
  - shell: bash
@@ -36,7 +36,7 @@ jobs:
  python setup.py build
  cat build/lib/monai/_version.py
  - name: Upload version
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
  with:
  name: _version.py
  path: build/lib/monai/_version.py
@@ -56,7 +56,7 @@ jobs:
  with:
  ref: dev
  - name: Download version
- uses: actions/download-artifact@v3
+ uses: actions/download-artifact@v4
  with:
  name: _version.py
  - name: docker_build

.github/workflows/pythonapp-min.yml

@@ -30,7 +30,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: Prepare pip wheel
@@ -76,7 +76,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: Prepare pip wheel
@@ -121,7 +121,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: Prepare pip wheel

.github/workflows/pythonapp.yml

@@ -28,7 +28,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: cache weekly timestamp
@@ -69,7 +69,7 @@ jobs:
  disk-root: "D:"
  - uses: actions/checkout@v4
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: Prepare pip wheel
@@ -128,7 +128,7 @@ jobs:
  with:
  fetch-depth: 0
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: cache weekly timestamp
@@ -209,7 +209,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: cache weekly timestamp

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
  with:
  fetch-depth: 0
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install setuptools
@@ -66,7 +66,7 @@ jobs:
 
  - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
  name: Upload artifacts
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
  with:
  name: dist
  path: dist/
@@ -97,7 +97,7 @@ jobs:
  with:
  fetch-depth: 0
  - name: Set up Python 3.9
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.9'
  - shell: bash
@@ -108,7 +108,7 @@ jobs:
  python setup.py build
  cat build/lib/monai/_version.py
  - name: Upload version
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
  with:
  name: _version.py
  path: build/lib/monai/_version.py
@@ -125,7 +125,7 @@ jobs:
  steps:
  - uses: actions/checkout@v4
  - name: Download version
- uses: actions/download-artifact@v3
+ uses: actions/download-artifact@v4
  with:
  name: _version.py
  - name: Set tag

.github/workflows/setupapp.yml

@@ -83,7 +83,7 @@ jobs:
  with:
  fetch-depth: 0
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: cache weekly timestamp
@@ -120,7 +120,7 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - name: Set up Python 3.8
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.8'
  - name: cache weekly timestamp

.github/workflows/weekly-preview.yml

@@ -14,7 +14,7 @@ jobs:
  ref: dev
  fetch-depth: 0
  - name: Set up Python 3.9
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: '3.9'
  - name: Install setuptools

docs/requirements.txt

@@ -21,7 +21,7 @@ sphinxcontrib-serializinghtml
 sphinx-autodoc-typehints==1.11.1
 pandas
 einops
-transformers<4.22 # https://github.com/Project-MONAI/MONAI/issues/5157
+transformers<4.22; python_version <= '3.10' # https://github.com/Project-MONAI/MONAI/issues/5157
 mlflow>=1.28.0
 clearml>=1.10.0rc0
 tensorboardX

docs/source/engines.rst

@@ -30,6 +30,11 @@ Workflows
 .. autoclass:: GanTrainer
  :members:
 
+`AdversarialTrainer`
+~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: AdversarialTrainer
+ :members:
+
 `Evaluator`
 ~~~~~~~~~~~
 .. autoclass:: Evaluator

docs/source/losses.rst

@@ -96,6 +96,11 @@ Registration Losses
 .. autoclass:: BendingEnergyLoss
  :members:
 
+`DiffusionLoss`
+~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionLoss
+ :members:
+
 `LocalNormalizedCrossCorrelationLoss`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: LocalNormalizedCrossCorrelationLoss

monai/apps/auto3dseg/data_analyzer.py

@@ -28,7 +28,7 @@
 from monai.data import DataLoader, Dataset, partition_dataset
 from monai.data.utils import no_collation
 from monai.transforms import Compose, EnsureTyped, LoadImaged, Orientationd
-from monai.utils import StrEnum, min_version, optional_import
+from monai.utils import ImageMetaKey, StrEnum, min_version, optional_import
 from monai.utils.enums import DataStatsKeys, ImageStatsKeys
 
 
@@ -343,19 +343,25 @@ def _get_all_case_stats(
  d = summarizer(batch_data)
  except BaseException as err:
  if "image_meta_dict" in batch_data.keys():
- filename = batch_data["image_meta_dict"]["filename_or_obj"]
+ filename = batch_data["image_meta_dict"][ImageMetaKey.FILENAME_OR_OBJ]
  else:
- filename = batch_data[self.image_key].meta["filename_or_obj"]
+ filename = batch_data[self.image_key].meta[ImageMetaKey.FILENAME_OR_OBJ]
  logger.info(f"Unable to process data {filename} on {device}. {err}")
  if self.device.type == "cuda":
  logger.info("DataAnalyzer `device` set to GPU execution hit an exception. Falling back to `cpu`.")
- batch_data[self.image_key] = batch_data[self.image_key].to("cpu")
- if self.label_key is not None:
- label = batch_data[self.label_key]
- if not _label_argmax:
- label = torch.argmax(label, dim=0) if label.shape[0] > 1 else label[0]
- batch_data[self.label_key] = label.to("cpu")
- d = summarizer(batch_data)
+ try:
+ batch_data[self.image_key] = batch_data[self.image_key].to("cpu")
+ if self.label_key is not None:
+ label = batch_data[self.label_key]
+ if not _label_argmax:
+ label = torch.argmax(label, dim=0) if label.shape[0] > 1 else label[0]
+ batch_data[self.label_key] = label.to("cpu")
+ d = summarizer(batch_data)
+ except BaseException as err:
+ logger.info(f"Unable to process data {filename} on {device}. {err}")
+ continue
+ else:
+ continue
 
  stats_by_cases = {
  DataStatsKeys.BY_CASE_IMAGE_PATH: d[DataStatsKeys.BY_CASE_IMAGE_PATH],

monai/apps/detection/utils/anchor_utils.py

@@ -369,8 +369,12 @@ class AnchorGeneratorWithAnchorShape(AnchorGenerator):
  def __init__(
  self,
  feature_map_scales: Sequence[int] | Sequence[float] = (1, 2, 4, 8),
- base_anchor_shapes: Sequence[Sequence[int]]
- | Sequence[Sequence[float]] = ((32, 32, 32), (48, 20, 20), (20, 48, 20), (20, 20, 48)),
+ base_anchor_shapes: Sequence[Sequence[int]] | Sequence[Sequence[float]] = (
+ (32, 32, 32),
+ (48, 20, 20),
+ (20, 48, 20),
+ (20, 20, 48),
+ ),
  indexing: str = "ij",
  ) -> None:
  nn.Module.__init__(self)

monai/apps/utils.py

@@ -30,7 +30,7 @@
 from monai.config.type_definitions import PathLike
 from monai.utils import look_up_option, min_version, optional_import
 
-gdown, has_gdown = optional_import("gdown", "4.4")
+gdown, has_gdown = optional_import("gdown", "4.6.3")
 
 if TYPE_CHECKING:
  from tqdm import tqdm

monai/auto3dseg/analyzer.py

@@ -256,7 +256,7 @@ def __call__(self, data):
  )
 
  report[ImageStatsKeys.SIZEMM] = [
- int(a * b) for a, b in zip(report[ImageStatsKeys.SHAPE][0], report[ImageStatsKeys.SPACING])
+ a * b for a, b in zip(report[ImageStatsKeys.SHAPE][0], report[ImageStatsKeys.SPACING])
  ]
 
  report[ImageStatsKeys.INTENSITY] = [
@@ -460,7 +460,7 @@ def __call__(self, data: Mapping[Hashable, MetaTensor]) -> dict[Hashable, MetaTe
  torch.set_grad_enabled(False)
 
  ndas: list[MetaTensor] = [d[self.image_key][i] for i in range(d[self.image_key].shape[0])] # type: ignore
- ndas_label: MetaTensor = d[self.label_key] # (H,W,D)
+ ndas_label: MetaTensor = d[self.label_key].astype(torch.int8) # (H,W,D)
 
  if ndas_label.shape != ndas[0].shape:
  raise ValueError(f"Label shape {ndas_label.shape} is different from image shape {ndas[0].shape}")

monai/data/decathlon_datalist.py

@@ -24,13 +24,11 @@
 
 
 @overload
-def _compute_path(base_dir: PathLike, element: PathLike, check_path: bool = False) -> str:
- ...
+def _compute_path(base_dir: PathLike, element: PathLike, check_path: bool = False) -> str: ...
 
 
 @overload
-def _compute_path(base_dir: PathLike, element: list[PathLike], check_path: bool = False) -> list[str]:
- ...
+def _compute_path(base_dir: PathLike, element: list[PathLike], check_path: bool = False) -> list[str]: ...
 
 
 def _compute_path(base_dir, element, check_path=False):

monai/data/image_reader.py

@@ -168,8 +168,8 @@ class ITKReader(ImageReader):
  series_name: the name of the DICOM series if there are multiple ones.
  used when loading DICOM series.
  reverse_indexing: whether to use a reversed spatial indexing convention for the returned data array.
- If ``False``, the spatial indexing follows the numpy convention;
- otherwise, the spatial indexing convention is reversed to be compatible with ITK. Default is ``False``.
+ If ``False``, the spatial indexing convention is reversed to be compatible with ITK;
+ otherwise, the spatial indexing follows the numpy convention. Default is ``False``.
  This option does not affect the metadata.
  series_meta: whether to load the metadata of the DICOM series (using the metadata from the first slice).
  This flag is checked only when loading DICOM series. Default is ``False``.
@@ -1323,7 +1323,7 @@ def get_data(self, img: NrrdImage | list[NrrdImage]) -> tuple[np.ndarray, dict]:
  header = dict(i.header)
  if self.index_order == "C":
  header = self._convert_f_to_c_order(header)
- header[MetaKeys.ORIGINAL_AFFINE] = self._get_affine(i)
+ header[MetaKeys.ORIGINAL_AFFINE] = self._get_affine(header)
 
  if self.affine_lps_to_ras:
  header = self._switch_lps_ras(header)
@@ -1344,7 +1344,7 @@ def get_data(self, img: NrrdImage | list[NrrdImage]) -> tuple[np.ndarray, dict]:
 
  return _stack_images(img_array, compatible_meta), compatible_meta
 
- def _get_affine(self, img: NrrdImage) -> np.ndarray:
+ def _get_affine(self, header: dict) -> np.ndarray:
  """
  Get the affine matrix of the image, it can be used to correct
  spacing, orientation or execute spatial transforms.
@@ -1353,8 +1353,8 @@ def _get_affine(self, img: NrrdImage) -> np.ndarray:
  img: A `NrrdImage` loaded from image file
 
  """
- direction = img.header["space directions"]
- origin = img.header["space origin"]
+ direction = header["space directions"]
+ origin = header["space origin"]
 
  x, y = direction.shape
  affine_diam = min(x, y) + 1

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,