6676 port generative engines (#7406)

Part of #6676 . ### Description A few sentences describing the changes proposed in this pull request. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Mark Graham <[email protected]> Signed-off-by: dongy <[email protected]> Signed-off-by: KumoLiu <[email protected]> Signed-off-by: myron <[email protected]> Signed-off-by: kaibo <[email protected]> Signed-off-by: monai-bot <[email protected]> Signed-off-by: elitap <[email protected]> Signed-off-by: Felix Schnabel <[email protected]> Signed-off-by: YanxuanLiu <[email protected]> Signed-off-by: ytl0623 <[email protected]> Signed-off-by: Dženan Zukić <[email protected]> Signed-off-by: YunLiu <[email protected]> Signed-off-by: Ishan Dutta <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: Mark Graham <[email protected]> Signed-off-by: vgrau98 <[email protected]> Signed-off-by: vgrau98 <[email protected]> Signed-off-by: heyufan1995 <[email protected]> Signed-off-by: binliu <[email protected]> Signed-off-by: axel.vlaminck <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: YunLiu <[email protected]> Co-authored-by: myron <[email protected]> Co-authored-by: Kaibo Tang <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: elitap <[email protected]> Co-authored-by: Felix Schnabel <[email protected]> Co-authored-by: YanxuanLiu <[email protected]> Co-authored-by: ytl0623 <[email protected]> Co-authored-by: Dženan Zukić <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ishan Dutta <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: KumoLiu <[email protected]> Co-authored-by: Kaibo Tang <[email protected]> Co-authored-by: vgrau98 <[email protected]> Co-authored-by: Yufan He <[email protected]> Co-authored-by: binliunls <[email protected]> Co-authored-by: Ben Murray <[email protected]> Co-authored-by: axel.vlaminck <[email protected]>
Project-MONAI · Feb 1, 2024 · f15a173 · f15a173
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diff --git a/.github/workflows/chatops.yml b/.github/workflows/chatops.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: dispatch
-        uses: peter-evans/[email protected].1
+        uses: peter-evans/[email protected].2
         with:
           token: ${{ secrets.PR_MAINTAIN }}
           reaction-token: ${{ secrets.GITHUB_TOKEN }}

diff --git a/.github/workflows/codeql-analysis.yml b/.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
diff --git a/.github/workflows/cron-ngc-bundle.yml b/.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

diff --git a/.github/workflows/docker.yml b/.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

diff --git a/.github/workflows/pythonapp-min.yml b/.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

diff --git a/.github/workflows/pythonapp.yml b/.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

diff --git a/.github/workflows/release.yml b/.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

diff --git a/.github/workflows/setupapp.yml b/.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

diff --git a/.github/workflows/weekly-preview.yml b/.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

diff --git a/docs/requirements.txt b/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

diff --git a/docs/source/engines.rst b/docs/source/engines.rst
@@ -30,6 +30,11 @@ Workflows
 .. autoclass:: GanTrainer
     :members:
 
+`AdversarialTrainer`
+~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: AdversarialTrainer
+    :members:
+
 `Evaluator`
 ~~~~~~~~~~~
 .. autoclass:: Evaluator

diff --git a/docs/source/losses.rst b/docs/source/losses.rst
@@ -96,6 +96,11 @@ Registration Losses
 .. autoclass:: BendingEnergyLoss
     :members:
 
+`DiffusionLoss`
+~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionLoss
+    :members:
+
 `LocalNormalizedCrossCorrelationLoss`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: LocalNormalizedCrossCorrelationLoss

diff --git a/monai/apps/auto3dseg/data_analyzer.py b/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],

diff --git a/monai/apps/detection/utils/anchor_utils.py b/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)

diff --git a/monai/apps/utils.py b/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

diff --git a/monai/auto3dseg/analyzer.py b/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}")

diff --git a/monai/data/decathlon_datalist.py b/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):

diff --git a/monai/data/image_reader.py b/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

diff --git a/monai/engines/__init__.py b/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,