monai-weekly 1.4.dev2437__py3-none-any.whl → 1.4.dev2439__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (57) hide show
  1. monai/__init__.py +2 -1
  2. monai/_version.py +3 -3
  3. monai/bundle/scripts.py +2 -1
  4. monai/bundle/workflows.py +3 -4
  5. monai/config/__init__.py +0 -1
  6. monai/config/deviceconfig.py +0 -10
  7. monai/data/image_reader.py +1 -1
  8. monai/engines/evaluator.py +2 -2
  9. monai/engines/trainer.py +1 -2
  10. monai/engines/utils.py +1 -2
  11. monai/engines/workflow.py +1 -2
  12. monai/handlers/__init__.py +1 -1
  13. monai/handlers/checkpoint_loader.py +1 -2
  14. monai/handlers/checkpoint_saver.py +1 -2
  15. monai/handlers/classification_saver.py +1 -1
  16. monai/handlers/decollate_batch.py +2 -2
  17. monai/handlers/earlystop_handler.py +1 -2
  18. monai/handlers/garbage_collector.py +1 -2
  19. monai/handlers/ignite_metric.py +1 -24
  20. monai/handlers/logfile_handler.py +1 -2
  21. monai/handlers/lr_schedule_handler.py +1 -2
  22. monai/handlers/metric_logger.py +1 -2
  23. monai/handlers/metrics_saver.py +1 -1
  24. monai/handlers/mlflow_handler.py +1 -2
  25. monai/handlers/nvtx_handlers.py +1 -2
  26. monai/handlers/parameter_scheduler.py +1 -2
  27. monai/handlers/postprocessing.py +1 -2
  28. monai/handlers/probability_maps.py +2 -2
  29. monai/handlers/smartcache_handler.py +1 -2
  30. monai/handlers/stats_handler.py +1 -2
  31. monai/handlers/tensorboard_handlers.py +1 -2
  32. monai/handlers/trt_handler.py +1 -2
  33. monai/handlers/utils.py +2 -2
  34. monai/handlers/validation_handler.py +1 -2
  35. monai/losses/dice.py +1 -16
  36. monai/networks/blocks/patchembedding.py +1 -7
  37. monai/networks/nets/hovernet.py +1 -2
  38. monai/networks/nets/unet.py +0 -3
  39. monai/networks/nets/unetr.py +1 -8
  40. monai/networks/nets/vit.py +0 -8
  41. monai/networks/nets/vitautoenc.py +1 -8
  42. monai/networks/nets/voxelmorph.py +0 -5
  43. monai/transforms/adaptors.py +0 -5
  44. monai/transforms/intensity/array.py +1 -1
  45. monai/transforms/utils.py +2 -1
  46. monai/utils/__init__.py +3 -3
  47. monai/utils/dist.py +1 -1
  48. monai/utils/enums.py +30 -34
  49. monai/utils/jupyter_utils.py +1 -1
  50. monai/utils/misc.py +1 -1
  51. monai/utils/module.py +0 -24
  52. {monai_weekly-1.4.dev2437.dist-info → monai_weekly-1.4.dev2439.dist-info}/METADATA +1 -1
  53. {monai_weekly-1.4.dev2437.dist-info → monai_weekly-1.4.dev2439.dist-info}/RECORD +56 -57
  54. {monai_weekly-1.4.dev2437.dist-info → monai_weekly-1.4.dev2439.dist-info}/WHEEL +1 -1
  55. monai/utils/aliases.py +0 -103
  56. {monai_weekly-1.4.dev2437.dist-info → monai_weekly-1.4.dev2439.dist-info}/LICENSE +0 -0
  57. {monai_weekly-1.4.dev2437.dist-info → monai_weekly-1.4.dev2439.dist-info}/top_level.txt +0 -0
monai/__init__.py CHANGED
@@ -79,6 +79,7 @@ if sys.version_info.major != PY_REQUIRED_MAJOR or sys.version_info.minor < PY_RE
79
79
  category=RuntimeWarning,
80
80
  )
81
81
 
82
+
82
83
  from .utils.module import load_submodules # noqa: E402
83
84
 
84
85
  # handlers_* have some external decorators the users may not have installed
@@ -135,4 +136,4 @@ except BaseException:
135
136
 
136
137
  if MONAIEnvVars.debug():
137
138
  raise
138
- __commit_id__ = "64eee8cb9cfad9ef5bd3eaf597fef0fbe85144b4"
139
+ __commit_id__ = "8546be098daaf6841c39a2748412bbda83929c92"
monai/_version.py CHANGED
@@ -8,11 +8,11 @@ import json
8
8
 
9
9
  version_json = '''
10
10
  {
11
- "date": "2024-09-15T02:27:58+0000",
11
+ "date": "2024-09-29T02:29:04+0000",
12
12
  "dirty": false,
13
13
  "error": null,
14
- "full-revisionid": "1d72a6bbc4db84d507147fb422f9f54a939640b5",
15
- "version": "1.4.dev2437"
14
+ "full-revisionid": "1bac3a18df3d8aac051ac832fc0d7d3d3c50e350",
15
+ "version": "1.4.dev2439"
16
16
  }
17
17
  ''' # END VERSION_JSON
18
18
 
monai/bundle/scripts.py CHANGED
@@ -34,7 +34,7 @@ from monai.bundle.config_item import ConfigComponent
34
34
  from monai.bundle.config_parser import ConfigParser
35
35
  from monai.bundle.utils import DEFAULT_INFERENCE, DEFAULT_METADATA, merge_kv
36
36
  from monai.bundle.workflows import BundleWorkflow, ConfigWorkflow
37
- from monai.config import IgniteInfo, PathLike
37
+ from monai.config import PathLike
38
38
  from monai.data import load_net_with_metadata, save_net_with_metadata
39
39
  from monai.networks import (
40
40
  convert_to_onnx,
@@ -45,6 +45,7 @@ from monai.networks import (
45
45
  save_state,
46
46
  )
47
47
  from monai.utils import (
48
+ IgniteInfo,
48
49
  check_parent_dir,
49
50
  deprecated_arg,
50
51
  ensure_tuple,
monai/bundle/workflows.py CHANGED
@@ -26,7 +26,7 @@ from monai.bundle.config_parser import ConfigParser
26
26
  from monai.bundle.properties import InferProperties, MetaProperties, TrainProperties
27
27
  from monai.bundle.utils import DEFAULT_EXP_MGMT_SETTINGS, EXPR_KEY, ID_REF_KEY, ID_SEP_KEY
28
28
  from monai.config import PathLike
29
- from monai.utils import BundleProperty, BundlePropertyConfig, deprecated_arg, deprecated_arg_default, ensure_tuple
29
+ from monai.utils import BundleProperty, BundlePropertyConfig, deprecated_arg, ensure_tuple
30
30
 
31
31
  __all__ = ["BundleWorkflow", "ConfigWorkflow"]
32
32
 
@@ -43,7 +43,7 @@ class BundleWorkflow(ABC):
43
43
  workflow_type: specifies the workflow type: "train" or "training" for a training workflow,
44
44
  or "infer", "inference", "eval", "evaluation" for a inference workflow,
45
45
  other unsupported string will raise a ValueError.
46
- default to `None` for common workflow.
46
+ default to `train` for train workflow.
47
47
  workflow: specifies the workflow type: "train" or "training" for a training workflow,
48
48
  or "infer", "inference", "eval", "evaluation" for a inference workflow,
49
49
  other unsupported string will raise a ValueError.
@@ -274,7 +274,6 @@ class ConfigWorkflow(BundleWorkflow):
274
274
  new_name="workflow_type",
275
275
  msg_suffix="please use `workflow_type` instead.",
276
276
  )
277
- @deprecated_arg_default("workflow_type", None, "train", since="1.2", replaced="1.4")
278
277
  def __init__(
279
278
  self,
280
279
  config_file: str | Sequence[str],
@@ -284,7 +283,7 @@ class ConfigWorkflow(BundleWorkflow):
284
283
  run_id: str = "run",
285
284
  final_id: str = "finalize",
286
285
  tracking: str | dict | None = None,
287
- workflow_type: str | None = None,
286
+ workflow_type: str | None = "train",
288
287
  workflow: str | None = None,
289
288
  properties_path: PathLike | None = None,
290
289
  **override: Any,
monai/config/__init__.py CHANGED
@@ -14,7 +14,6 @@ from __future__ import annotations
14
14
  from .deviceconfig import (
15
15
  USE_COMPILED,
16
16
  USE_META_DICT,
17
- IgniteInfo,
18
17
  get_config_values,
19
18
  get_gpu_info,
20
19
  get_optional_config_values,
@@ -45,7 +45,6 @@ __all__ = [
45
45
  "print_debug_info",
46
46
  "USE_COMPILED",
47
47
  "USE_META_DICT",
48
- "IgniteInfo",
49
48
  ]
50
49
 
51
50
 
@@ -261,14 +260,5 @@ def print_debug_info(file: TextIO = sys.stdout) -> None:
261
260
  print_gpu_info(file)
262
261
 
263
262
 
264
- class IgniteInfo:
265
- """
266
- Config information of the PyTorch ignite package.
267
-
268
- """
269
-
270
- OPT_IMPORT_VERSION = "0.4.4"
271
-
272
-
273
263
  if __name__ == "__main__":
274
264
  print_debug_info()
@@ -1359,7 +1359,7 @@ class NrrdReader(ImageReader):
1359
1359
  x, y = direction.shape
1360
1360
  affine_diam = min(x, y) + 1
1361
1361
  affine: np.ndarray = np.eye(affine_diam)
1362
- affine[:x, :y] = direction
1362
+ affine[:x, :y] = direction.T
1363
1363
  affine[: (affine_diam - 1), -1] = origin # len origin is always affine_diam - 1
1364
1364
  return affine
1365
1365
 
@@ -17,14 +17,14 @@ from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence
17
17
  import torch
18
18
  from torch.utils.data import DataLoader
19
19
 
20
- from monai.config import IgniteInfo, KeysCollection
20
+ from monai.config import KeysCollection
21
21
  from monai.data import MetaTensor
22
22
  from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch
23
23
  from monai.engines.workflow import Workflow
24
24
  from monai.inferers import Inferer, SimpleInferer
25
25
  from monai.networks.utils import eval_mode, train_mode
26
26
  from monai.transforms import Transform
27
- from monai.utils import ForwardMode, ensure_tuple, min_version, optional_import
27
+ from monai.utils import ForwardMode, IgniteInfo, ensure_tuple, min_version, optional_import
28
28
  from monai.utils.enums import CommonKeys as Keys
29
29
  from monai.utils.enums import EngineStatsKeys as ESKeys
30
30
  from monai.utils.module import look_up_option, pytorch_after
monai/engines/trainer.py CHANGED
@@ -18,13 +18,12 @@ import torch
18
18
  from torch.optim.optimizer import Optimizer
19
19
  from torch.utils.data import DataLoader
20
20
 
21
- from monai.config import IgniteInfo
22
21
  from monai.data import MetaTensor
23
22
  from monai.engines.utils import IterationEvents, default_make_latent, default_metric_cmp_fn, default_prepare_batch
24
23
  from monai.engines.workflow import Workflow
25
24
  from monai.inferers import Inferer, SimpleInferer
26
25
  from monai.transforms import Transform
27
- from monai.utils import AdversarialIterationEvents, AdversarialKeys, GanKeys, min_version, optional_import
26
+ from monai.utils import AdversarialIterationEvents, AdversarialKeys, GanKeys, IgniteInfo, min_version, optional_import
28
27
  from monai.utils.enums import CommonKeys as Keys
29
28
  from monai.utils.enums import EngineStatsKeys as ESKeys
30
29
  from monai.utils.module import pytorch_after
monai/engines/utils.py CHANGED
@@ -18,9 +18,8 @@ from typing import TYPE_CHECKING, Any, Mapping, cast
18
18
  import torch
19
19
  import torch.nn as nn
20
20
 
21
- from monai.config import IgniteInfo
22
21
  from monai.transforms import apply_transform
23
- from monai.utils import ensure_tuple, min_version, optional_import
22
+ from monai.utils import IgniteInfo, ensure_tuple, min_version, optional_import
24
23
  from monai.utils.enums import CommonKeys, GanKeys
25
24
 
26
25
  if TYPE_CHECKING:
monai/engines/workflow.py CHANGED
@@ -20,10 +20,9 @@ import torch.distributed as dist
20
20
  from torch.utils.data import DataLoader
21
21
  from torch.utils.data.distributed import DistributedSampler
22
22
 
23
- from monai.config import IgniteInfo
24
23
  from monai.engines.utils import IterationEvents, default_metric_cmp_fn, default_prepare_batch
25
24
  from monai.transforms import Decollated
26
- from monai.utils import ensure_tuple, is_scalar, min_version, optional_import
25
+ from monai.utils import IgniteInfo, ensure_tuple, is_scalar, min_version, optional_import
27
26
 
28
27
  from .utils import engine_apply_transform
29
28
 
@@ -20,7 +20,7 @@ from .decollate_batch import DecollateBatch
20
20
  from .earlystop_handler import EarlyStopHandler
21
21
  from .garbage_collector import GarbageCollector
22
22
  from .hausdorff_distance import HausdorffDistance
23
- from .ignite_metric import IgniteMetric, IgniteMetricHandler
23
+ from .ignite_metric import IgniteMetricHandler
24
24
  from .logfile_handler import LogfileHandler
25
25
  from .lr_schedule_handler import LrScheduleHandler
26
26
  from .mean_dice import MeanDice
@@ -17,9 +17,8 @@ from typing import TYPE_CHECKING
17
17
 
18
18
  import torch
19
19
 
20
- from monai.config import IgniteInfo
21
20
  from monai.networks.utils import copy_model_state
22
- from monai.utils import min_version, optional_import
21
+ from monai.utils import IgniteInfo, min_version, optional_import
23
22
 
24
23
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
25
24
  Checkpoint, _ = optional_import("ignite.handlers", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Checkpoint")
@@ -17,8 +17,7 @@ import warnings
17
17
  from collections.abc import Mapping
18
18
  from typing import TYPE_CHECKING, Any
19
19
 
20
- from monai.config import IgniteInfo
21
- from monai.utils import is_scalar, min_version, optional_import
20
+ from monai.utils import IgniteInfo, is_scalar, min_version, optional_import
22
21
 
23
22
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
24
23
 
@@ -18,8 +18,8 @@ from typing import TYPE_CHECKING
18
18
 
19
19
  import torch
20
20
 
21
- from monai.config import IgniteInfo
22
21
  from monai.data import CSVSaver, decollate_batch
22
+ from monai.utils import IgniteInfo
23
23
  from monai.utils import ImageMetaKey as Key
24
24
  from monai.utils import evenly_divisible_all_gather, min_version, optional_import, string_list_all_gather
25
25
 
@@ -13,10 +13,10 @@ from __future__ import annotations
13
13
 
14
14
  from typing import TYPE_CHECKING
15
15
 
16
- from monai.config import IgniteInfo, KeysCollection
16
+ from monai.config import KeysCollection
17
17
  from monai.engines.utils import IterationEvents
18
18
  from monai.transforms import Decollated
19
- from monai.utils import min_version, optional_import
19
+ from monai.utils import IgniteInfo, min_version, optional_import
20
20
 
21
21
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
22
22
  if TYPE_CHECKING:
@@ -14,8 +14,7 @@ from __future__ import annotations
14
14
  from collections.abc import Callable
15
15
  from typing import TYPE_CHECKING
16
16
 
17
- from monai.config import IgniteInfo
18
- from monai.utils import min_version, optional_import
17
+ from monai.utils import IgniteInfo, min_version, optional_import
19
18
 
20
19
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
21
20
  EarlyStopping, _ = optional_import("ignite.handlers", IgniteInfo.OPT_IMPORT_VERSION, min_version, "EarlyStopping")
@@ -14,8 +14,7 @@ from __future__ import annotations
14
14
  import gc
15
15
  from typing import TYPE_CHECKING
16
16
 
17
- from monai.config import IgniteInfo
18
- from monai.utils import min_version, optional_import
17
+ from monai.utils import IgniteInfo, min_version, optional_import
19
18
 
20
19
  if TYPE_CHECKING:
21
20
  from ignite.engine import Engine, Events
@@ -18,9 +18,8 @@ from typing import TYPE_CHECKING, Any, cast
18
18
  import torch
19
19
  from torch.nn.modules.loss import _Loss
20
20
 
21
- from monai.config import IgniteInfo
22
21
  from monai.metrics import CumulativeIterationMetric, LossMetric
23
- from monai.utils import MetricReduction, deprecated, min_version, optional_import
22
+ from monai.utils import IgniteInfo, MetricReduction, min_version, optional_import
24
23
 
25
24
  idist, _ = optional_import("ignite", IgniteInfo.OPT_IMPORT_VERSION, min_version, "distributed")
26
25
 
@@ -153,25 +152,3 @@ class IgniteMetricHandler(Metric):
153
152
  self._name = name
154
153
  if self.save_details and not hasattr(engine.state, "metric_details"):
155
154
  engine.state.metric_details = {} # type: ignore
156
-
157
-
158
- @deprecated(since="1.2", removed="1.4", msg_suffix="Use IgniteMetricHandler instead of IgniteMetric.")
159
- class IgniteMetric(IgniteMetricHandler):
160
-
161
- def __init__(
162
- self,
163
- metric_fn: CumulativeIterationMetric | None = None,
164
- loss_fn: _Loss | None = None,
165
- output_transform: Callable = lambda x: x,
166
- save_details: bool = True,
167
- reduction: MetricReduction | str = MetricReduction.MEAN,
168
- get_not_nans: bool = False,
169
- ) -> None:
170
- super().__init__(
171
- metric_fn=metric_fn,
172
- loss_fn=loss_fn,
173
- output_transform=output_transform,
174
- save_details=save_details,
175
- reduction=reduction,
176
- get_not_nans=get_not_nans,
177
- )
@@ -15,8 +15,7 @@ import logging
15
15
  import os
16
16
  from typing import TYPE_CHECKING
17
17
 
18
- from monai.config import IgniteInfo
19
- from monai.utils import min_version, optional_import
18
+ from monai.utils import IgniteInfo, min_version, optional_import
20
19
 
21
20
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
22
21
  if TYPE_CHECKING:
@@ -17,8 +17,7 @@ from typing import TYPE_CHECKING, Any
17
17
 
18
18
  from torch.optim.lr_scheduler import ReduceLROnPlateau, _LRScheduler
19
19
 
20
- from monai.config import IgniteInfo
21
- from monai.utils import ensure_tuple, min_version, optional_import
20
+ from monai.utils import IgniteInfo, ensure_tuple, min_version, optional_import
22
21
 
23
22
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
24
23
  if TYPE_CHECKING:
@@ -17,8 +17,7 @@ from enum import Enum
17
17
  from threading import RLock
18
18
  from typing import TYPE_CHECKING, Any
19
19
 
20
- from monai.config import IgniteInfo
21
- from monai.utils import min_version, optional_import
20
+ from monai.utils import IgniteInfo, min_version, optional_import
22
21
  from monai.utils.enums import CommonKeys
23
22
 
24
23
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
@@ -14,9 +14,9 @@ from __future__ import annotations
14
14
  from collections.abc import Callable, Sequence
15
15
  from typing import TYPE_CHECKING
16
16
 
17
- from monai.config import IgniteInfo
18
17
  from monai.data import decollate_batch
19
18
  from monai.handlers.utils import write_metrics_reports
19
+ from monai.utils import IgniteInfo
20
20
  from monai.utils import ImageMetaKey as Key
21
21
  from monai.utils import ensure_tuple, min_version, optional_import, string_list_all_gather
22
22
 
@@ -22,8 +22,7 @@ import torch
22
22
  from torch.utils.data import Dataset
23
23
 
24
24
  from monai.apps.utils import get_logger
25
- from monai.config import IgniteInfo
26
- from monai.utils import CommonKeys, ensure_tuple, min_version, optional_import
25
+ from monai.utils import CommonKeys, IgniteInfo, ensure_tuple, min_version, optional_import
27
26
 
28
27
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
29
28
  mlflow, _ = optional_import("mlflow", descriptor="Please install mlflow before using MLFlowHandler.")
@@ -16,8 +16,7 @@ from __future__ import annotations
16
16
 
17
17
  from typing import TYPE_CHECKING
18
18
 
19
- from monai.config import IgniteInfo
20
- from monai.utils import ensure_tuple, min_version, optional_import
19
+ from monai.utils import IgniteInfo, ensure_tuple, min_version, optional_import
21
20
 
22
21
  _nvtx, _ = optional_import("torch._C._nvtx", descriptor="NVTX is not installed. Are you sure you have a CUDA build?")
23
22
  if TYPE_CHECKING:
@@ -16,8 +16,7 @@ from bisect import bisect_right
16
16
  from collections.abc import Callable
17
17
  from typing import TYPE_CHECKING
18
18
 
19
- from monai.config import IgniteInfo
20
- from monai.utils import min_version, optional_import
19
+ from monai.utils import IgniteInfo, min_version, optional_import
21
20
 
22
21
  if TYPE_CHECKING:
23
22
  from ignite.engine import Engine, Events
@@ -14,9 +14,8 @@ from __future__ import annotations
14
14
  from collections.abc import Callable
15
15
  from typing import TYPE_CHECKING
16
16
 
17
- from monai.config import IgniteInfo
18
17
  from monai.engines.utils import IterationEvents, engine_apply_transform
19
- from monai.utils import min_version, optional_import
18
+ from monai.utils import IgniteInfo, min_version, optional_import
20
19
 
21
20
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
22
21
  if TYPE_CHECKING:
@@ -17,10 +17,10 @@ from typing import TYPE_CHECKING
17
17
 
18
18
  import numpy as np
19
19
 
20
- from monai.config import DtypeLike, IgniteInfo
20
+ from monai.config import DtypeLike
21
21
  from monai.data.folder_layout import FolderLayout
22
22
  from monai.utils import ProbMapKeys, min_version, optional_import
23
- from monai.utils.enums import CommonKeys
23
+ from monai.utils.enums import CommonKeys, IgniteInfo
24
24
 
25
25
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
26
26
  if TYPE_CHECKING:
@@ -13,9 +13,8 @@ from __future__ import annotations
13
13
 
14
14
  from typing import TYPE_CHECKING
15
15
 
16
- from monai.config import IgniteInfo
17
16
  from monai.data import SmartCacheDataset
18
- from monai.utils import min_version, optional_import
17
+ from monai.utils import IgniteInfo, min_version, optional_import
19
18
 
20
19
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
21
20
  if TYPE_CHECKING:
@@ -19,8 +19,7 @@ from typing import TYPE_CHECKING, Any
19
19
  import torch
20
20
 
21
21
  from monai.apps import get_logger
22
- from monai.config import IgniteInfo
23
- from monai.utils import is_scalar, min_version, optional_import
22
+ from monai.utils import IgniteInfo, is_scalar, min_version, optional_import
24
23
 
25
24
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
26
25
  if TYPE_CHECKING:
@@ -18,8 +18,7 @@ from typing import TYPE_CHECKING, Any
18
18
  import numpy as np
19
19
  import torch
20
20
 
21
- from monai.config import IgniteInfo
22
- from monai.utils import is_scalar, min_version, optional_import
21
+ from monai.utils import IgniteInfo, is_scalar, min_version, optional_import
23
22
  from monai.visualize import plot_2d_or_3d_image
24
23
 
25
24
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
@@ -13,9 +13,8 @@ from __future__ import annotations
13
13
 
14
14
  from typing import TYPE_CHECKING
15
15
 
16
- from monai.config import IgniteInfo
17
16
  from monai.networks import trt_compile
18
- from monai.utils import min_version, optional_import
17
+ from monai.utils import IgniteInfo, min_version, optional_import
19
18
 
20
19
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
21
20
  if TYPE_CHECKING:
monai/handlers/utils.py CHANGED
@@ -19,8 +19,8 @@ from typing import TYPE_CHECKING, Any
19
19
  import numpy as np
20
20
  import torch
21
21
 
22
- from monai.config import IgniteInfo, KeysCollection, PathLike
23
- from monai.utils import ensure_tuple, look_up_option, min_version, optional_import
22
+ from monai.config import KeysCollection, PathLike
23
+ from monai.utils import IgniteInfo, ensure_tuple, look_up_option, min_version, optional_import
24
24
 
25
25
  idist, _ = optional_import("ignite", IgniteInfo.OPT_IMPORT_VERSION, min_version, "distributed")
26
26
  if TYPE_CHECKING:
@@ -13,9 +13,8 @@ from __future__ import annotations
13
13
 
14
14
  from typing import TYPE_CHECKING
15
15
 
16
- from monai.config import IgniteInfo
17
16
  from monai.engines.evaluator import Evaluator
18
- from monai.utils import min_version, optional_import
17
+ from monai.utils import IgniteInfo, min_version, optional_import
19
18
 
20
19
  Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
21
20
  if TYPE_CHECKING:
monai/losses/dice.py CHANGED
@@ -24,7 +24,7 @@ from torch.nn.modules.loss import _Loss
24
24
  from monai.losses.focal_loss import FocalLoss
25
25
  from monai.losses.spatial_mask import MaskedLoss
26
26
  from monai.networks import one_hot
27
- from monai.utils import DiceCEReduction, LossReduction, Weight, deprecated_arg, look_up_option, pytorch_after
27
+ from monai.utils import DiceCEReduction, LossReduction, Weight, look_up_option, pytorch_after
28
28
 
29
29
 
30
30
  class DiceLoss(_Loss):
@@ -646,9 +646,6 @@ class DiceCELoss(_Loss):
646
646
 
647
647
  """
648
648
 
649
- @deprecated_arg(
650
- "ce_weight", since="1.2", removed="1.4", new_name="weight", msg_suffix="please use `weight` instead."
651
- )
652
649
  def __init__(
653
650
  self,
654
651
  include_background: bool = True,
@@ -662,7 +659,6 @@ class DiceCELoss(_Loss):
662
659
  smooth_nr: float = 1e-5,
663
660
  smooth_dr: float = 1e-5,
664
661
  batch: bool = False,
665
- ce_weight: torch.Tensor | None = None,
666
662
  weight: torch.Tensor | None = None,
667
663
  lambda_dice: float = 1.0,
668
664
  lambda_ce: float = 1.0,
@@ -712,7 +708,6 @@ class DiceCELoss(_Loss):
712
708
  """
713
709
  super().__init__()
714
710
  reduction = look_up_option(reduction, DiceCEReduction).value
715
- weight = ce_weight if ce_weight is not None else weight
716
711
  dice_weight: torch.Tensor | None
717
712
  if weight is not None and not include_background:
718
713
  dice_weight = weight[1:]
@@ -825,9 +820,6 @@ class DiceFocalLoss(_Loss):
825
820
 
826
821
  """
827
822
 
828
- @deprecated_arg(
829
- "focal_weight", since="1.2", removed="1.4", new_name="weight", msg_suffix="please use `weight` instead."
830
- )
831
823
  def __init__(
832
824
  self,
833
825
  include_background: bool = True,
@@ -842,7 +834,6 @@ class DiceFocalLoss(_Loss):
842
834
  smooth_dr: float = 1e-5,
843
835
  batch: bool = False,
844
836
  gamma: float = 2.0,
845
- focal_weight: Sequence[float] | float | int | torch.Tensor | None = None,
846
837
  weight: Sequence[float] | float | int | torch.Tensor | None = None,
847
838
  lambda_dice: float = 1.0,
848
839
  lambda_focal: float = 1.0,
@@ -885,7 +876,6 @@ class DiceFocalLoss(_Loss):
885
876
  [0, 1]. Defaults to None.
886
877
  """
887
878
  super().__init__()
888
- weight = focal_weight if focal_weight is not None else weight
889
879
  self.dice = DiceLoss(
890
880
  include_background=include_background,
891
881
  to_onehot_y=False,
@@ -994,9 +984,6 @@ class GeneralizedDiceFocalLoss(_Loss):
994
984
  ValueError: if either `lambda_gdl` or `lambda_focal` is less than 0.
995
985
  """
996
986
 
997
- @deprecated_arg(
998
- "focal_weight", since="1.2", removed="1.4", new_name="weight", msg_suffix="please use `weight` instead."
999
- )
1000
987
  def __init__(
1001
988
  self,
1002
989
  include_background: bool = True,
@@ -1010,7 +997,6 @@ class GeneralizedDiceFocalLoss(_Loss):
1010
997
  smooth_dr: float = 1e-5,
1011
998
  batch: bool = False,
1012
999
  gamma: float = 2.0,
1013
- focal_weight: Sequence[float] | float | int | torch.Tensor | None = None,
1014
1000
  weight: Sequence[float] | float | int | torch.Tensor | None = None,
1015
1001
  lambda_gdl: float = 1.0,
1016
1002
  lambda_focal: float = 1.0,
@@ -1028,7 +1014,6 @@ class GeneralizedDiceFocalLoss(_Loss):
1028
1014
  smooth_dr=smooth_dr,
1029
1015
  batch=batch,
1030
1016
  )
1031
- weight = focal_weight if focal_weight is not None else weight
1032
1017
  self.focal = FocalLoss(
1033
1018
  include_background=include_background,
1034
1019
  to_onehot_y=to_onehot_y,
@@ -21,7 +21,7 @@ from torch.nn import LayerNorm
21
21
 
22
22
  from monai.networks.blocks.pos_embed_utils import build_sincos_position_embedding
23
23
  from monai.networks.layers import Conv, trunc_normal_
24
- from monai.utils import deprecated_arg, ensure_tuple_rep, optional_import
24
+ from monai.utils import ensure_tuple_rep, optional_import
25
25
  from monai.utils.module import look_up_option
26
26
 
27
27
  Rearrange, _ = optional_import("einops.layers.torch", name="Rearrange")
@@ -42,9 +42,6 @@ class PatchEmbeddingBlock(nn.Module):
42
42
 
43
43
  """
44
44
 
45
- @deprecated_arg(
46
- name="pos_embed", since="1.2", removed="1.4", new_name="proj_type", msg_suffix="please use `proj_type` instead."
47
- )
48
45
  def __init__(
49
46
  self,
50
47
  in_channels: int,
@@ -52,7 +49,6 @@ class PatchEmbeddingBlock(nn.Module):
52
49
  patch_size: Sequence[int] | int,
53
50
  hidden_size: int,
54
51
  num_heads: int,
55
- pos_embed: str = "conv",
56
52
  proj_type: str = "conv",
57
53
  pos_embed_type: str = "learnable",
58
54
  dropout_rate: float = 0.0,
@@ -69,8 +65,6 @@ class PatchEmbeddingBlock(nn.Module):
69
65
  pos_embed_type: position embedding layer type.
70
66
  dropout_rate: fraction of the input units to drop.
71
67
  spatial_dims: number of spatial dimensions.
72
- .. deprecated:: 1.4
73
- ``pos_embed`` is deprecated in favor of ``proj_type``.
74
68
  """
75
69
 
76
70
  super().__init__()
@@ -43,7 +43,7 @@ from monai.networks.blocks import UpSample
43
43
  from monai.networks.layers.factories import Conv, Dropout
44
44
  from monai.networks.layers.utils import get_act_layer, get_norm_layer
45
45
  from monai.utils.enums import HoVerNetBranch, HoVerNetMode, InterpolateMode, UpsampleMode
46
- from monai.utils.module import export, look_up_option
46
+ from monai.utils.module import look_up_option
47
47
 
48
48
  __all__ = ["HoVerNet", "Hovernet", "HoVernet", "HoVerNet"]
49
49
 
@@ -409,7 +409,6 @@ class _DecoderBranch(nn.ModuleList):
409
409
  return x
410
410
 
411
411
 
412
- @export("monai.networks.nets")
413
412
  class HoVerNet(nn.Module):
414
413
  """HoVerNet model
415
414
 
@@ -20,13 +20,10 @@ import torch.nn as nn
20
20
  from monai.networks.blocks.convolutions import Convolution, ResidualUnit
21
21
  from monai.networks.layers.factories import Act, Norm
22
22
  from monai.networks.layers.simplelayers import SkipConnection
23
- from monai.utils import alias, export
24
23
 
25
24
  __all__ = ["UNet", "Unet"]
26
25
 
27
26
 
28
- @export("monai.networks.nets")
29
- @alias("Unet")
30
27
  class UNet(nn.Module):
31
28
  """
32
29
  Enhanced version of UNet which has residual units implemented with the ResidualUnit class.