Merge genaidev Into Dev (Project-MONAI#7886)

Fixes Project-MONAI#6676 . ### Description This merges the Generative Models code into dev. Everything has been checked by the generative team, tests all pass, and the changes that have been done recently are integrated. This is ready to merge. ### 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. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Mark Graham <[email protected]> Signed-off-by: KumoLiu <[email protected]> Signed-off-by: YunLiu <[email protected]> Signed-off-by: Mark Graham <[email protected]> Signed-off-by: vgrau98 <[email protected]> Signed-off-by: vgrau98 <[email protected]> Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: dongy <[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: Ishan Dutta <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: heyufan1995 <[email protected]> Signed-off-by: binliu <[email protected]> Signed-off-by: axel.vlaminck <[email protected]> Signed-off-by: Ibrahim Hadzic <[email protected]> Signed-off-by: Behrooz <[email protected]> Signed-off-by: Timothy Baker <[email protected]> Signed-off-by: Mathijs de Boer <[email protected]> Signed-off-by: Fabian Klopfer <[email protected]> Signed-off-by: Lucas Robinet <[email protected]> Signed-off-by: Lucas Robinet <[email protected]> Signed-off-by: chaoliu <[email protected]> Signed-off-by: cxlcl <[email protected]> Signed-off-by: chaoliu <[email protected]> Signed-off-by: Suraj Pai <[email protected]> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <[email protected]> Signed-off-by: John Zielke <[email protected]> Signed-off-by: Mingxin Zheng <[email protected]> Signed-off-by: Vladimir Chernyi <[email protected]> Signed-off-by: Yiheng Wang <[email protected]> Signed-off-by: Szabolcs Botond Lorincz Molnar <[email protected]> Signed-off-by: Lucas Robinet <[email protected]> Signed-off-by: Mingxin <[email protected]> Signed-off-by: Han Wang <[email protected]> Signed-off-by: Konstantin Sukharev <[email protected]> Signed-off-by: Ben Murray <[email protected]> Signed-off-by: Matthew Vine <[email protected]> Signed-off-by: Peter Kaplinsky <[email protected]> Signed-off-by: Simon Jensen <[email protected]> Signed-off-by: NabJa <[email protected]> Signed-off-by: virginiafdez <[email protected]> Signed-off-by: Eric Kerfoot <[email protected]> Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: Mark Graham <[email protected]> Co-authored-by: YunLiu <[email protected]> Co-authored-by: KumoLiu <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: vgrau98 <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Dong Yang <[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: Ishan Dutta <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kaibo Tang <[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]> Co-authored-by: Mingxin Zheng <[email protected]> Co-authored-by: Ibrahim Hadzic <[email protected]> Co-authored-by: Dr. Behrooz Hashemian <[email protected]> Co-authored-by: Timothy J. Baker <[email protected]> Co-authored-by: Mathijs de Boer <[email protected]> Co-authored-by: Mathijs de Boer <[email protected]> Co-authored-by: Fabian Klopfer <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Lucas Robinet <[email protected]> Co-authored-by: Lucas Robinet <[email protected]> Co-authored-by: cxlcl <[email protected]> Co-authored-by: Suraj Pai <[email protected]> Co-authored-by: Juampa <[email protected]> Co-authored-by: johnzielke <[email protected]> Co-authored-by: Vladimir Chernyi <[email protected]> Co-authored-by: Lőrincz-Molnár Szabolcs-Botond <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Lucas Robinet <[email protected]> Co-authored-by: Han Wang <[email protected]> Co-authored-by: Konstantin Sukharev <[email protected]> Co-authored-by: Matthew Vine <[email protected]> Co-authored-by: Pkaps25 <[email protected]> Co-authored-by: Peter Kaplinsky <[email protected]> Co-authored-by: Simon Jensen <[email protected]> Co-authored-by: NabJa <[email protected]> Co-authored-by: Virginia Fernandez <[email protected]> Co-authored-by: virginiafdez <[email protected]> Co-authored-by: Yu <[email protected]>
dongyang0122 · Jul 19, 2024 · d020fac · d020fac
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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/inferers.rst b/docs/source/inferers.rst
@@ -49,6 +49,29 @@ Inferers
     :members:
     :special-members: __call__
 
+`DiffusionInferer`
+~~~~~~~~~~~~~~~~~~
+.. autoclass:: DiffusionInferer
+    :members:
+    :special-members: __call__
+
+`LatentDiffusionInferer`
+~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: LatentDiffusionInferer
+    :members:
+    :special-members: __call__
+
+`ControlNetDiffusionInferer`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: ControlNetDiffusionInferer
+    :members:
+    :special-members: __call__
+
+`ControlNetLatentDiffusionInferer`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: ControlNetLatentDiffusionInferer
+    :members:
+    :special-members: __call__
 
 Splitters
 ---------

diff --git a/docs/source/utils.rst b/docs/source/utils.rst
@@ -81,3 +81,8 @@ Component store
 ---------------
 .. autoclass:: monai.utils.component_store.ComponentStore
   :members:
+
+Ordering
+--------
+.. automodule:: monai.utils.ordering
+  :members:
diff --git a/monai/apps/detection/utils/anchor_utils.py b/monai/apps/detection/utils/anchor_utils.py
@@ -189,7 +189,7 @@ def generate_anchors(
             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 @@ def generate_anchors(
         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
 

diff --git a/monai/apps/pathology/transforms/post/array.py b/monai/apps/pathology/transforms/post/array.py
@@ -379,6 +379,7 @@ def _generate_contour_coord(self, current: np.ndarray, previous: np.ndarray) ->
         """
 
         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)

diff --git a/monai/bundle/utils.py b/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)

diff --git a/monai/data/dataset_summary.py b/monai/data/dataset_summary.py
@@ -84,6 +84,7 @@ def collect_meta_data(self):
         """
 
         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:

diff --git a/monai/data/utils.py b/monai/data/utils.py
@@ -53,10 +53,6 @@
     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})

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,