monai-weekly 1.5.dev2442__py3-none-any.whl → 1.5.dev2444__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.
- monai/__init__.py +3 -3
- monai/_version.py +3 -3
- monai/apps/detection/networks/retinanet_network.py +2 -2
- monai/apps/detection/transforms/array.py +2 -1
- monai/apps/generation/maisi/networks/autoencoderkl_maisi.py +1 -1
- monai/apps/generation/maisi/networks/controlnet_maisi.py +1 -1
- monai/apps/pathology/engines/utils.py +2 -1
- monai/apps/pathology/inferers/inferer.py +2 -1
- monai/apps/pathology/metrics/lesion_froc.py +2 -1
- monai/apps/pathology/transforms/post/array.py +2 -1
- monai/apps/tcia/utils.py +1 -1
- monai/apps/utils.py +1 -4
- monai/apps/vista3d/transforms.py +1 -1
- monai/bundle/reference_resolver.py +2 -2
- monai/bundle/scripts.py +1 -2
- monai/bundle/workflows.py +3 -2
- monai/config/type_definitions.py +2 -1
- monai/data/dataset.py +9 -2
- monai/data/meta_obj.py +2 -1
- monai/data/meta_tensor.py +2 -1
- monai/engines/evaluator.py +2 -1
- monai/engines/trainer.py +2 -1
- monai/engines/utils.py +2 -2
- monai/handlers/clearml_handlers.py +2 -1
- monai/handlers/mlflow_handler.py +4 -2
- monai/handlers/stats_handler.py +3 -4
- monai/inferers/utils.py +2 -2
- monai/losses/hausdorff_loss.py +1 -1
- monai/metrics/fid.py +1 -1
- monai/metrics/utils.py +2 -1
- monai/networks/blocks/spatialattention.py +3 -20
- monai/networks/nets/segresnet_ds.py +3 -1
- monai/networks/nets/swin_unetr.py +1 -1
- monai/networks/nets/vista3d.py +3 -5
- monai/networks/trt_compiler.py +3 -3
- monai/networks/utils.py +5 -6
- monai/transforms/intensity/dictionary.py +2 -1
- monai/transforms/lazy/functional.py +2 -1
- monai/transforms/spatial/array.py +3 -3
- monai/transforms/utility/dictionary.py +2 -2
- monai/transforms/utils_morphological_ops.py +1 -1
- monai/transforms/utils_pytorch_numpy_unification.py +1 -1
- monai/utils/__init__.py +1 -0
- monai/utils/component_store.py +2 -1
- monai/utils/decorators.py +2 -1
- monai/utils/dist.py +1 -6
- monai/utils/misc.py +14 -1
- monai/utils/module.py +2 -2
- monai/utils/state_cacher.py +2 -1
- {monai_weekly-1.5.dev2442.dist-info → monai_weekly-1.5.dev2444.dist-info}/METADATA +1 -1
- {monai_weekly-1.5.dev2442.dist-info → monai_weekly-1.5.dev2444.dist-info}/RECORD +54 -54
- {monai_weekly-1.5.dev2442.dist-info → monai_weekly-1.5.dev2444.dist-info}/WHEEL +1 -1
- {monai_weekly-1.5.dev2442.dist-info → monai_weekly-1.5.dev2444.dist-info}/LICENSE +0 -0
- {monai_weekly-1.5.dev2442.dist-info → monai_weekly-1.5.dev2444.dist-info}/top_level.txt +0 -0
monai/__init__.py
CHANGED
@@ -11,12 +11,12 @@
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from __future__ import annotations
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import logging
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import os
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import sys
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import logging
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import warnings
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from ._version import get_versions
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from ._version import get_versions
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old_showwarning = warnings.showwarning
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@@ -136,4 +136,4 @@ except BaseException:
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if MONAIEnvVars.debug():
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raise
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__commit_id__ = "
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__commit_id__ = "c1ceea3d4cbb0781eae4e209b80fe651a776fed2"
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monai/_version.py
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version_json = '''
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{
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"date": "2024-
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"date": "2024-11-03T02:29:11+0000",
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"dirty": false,
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"error": null,
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"full-revisionid": "
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"version": "1.5.
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"full-revisionid": "c70fbd8ff919cabaacfabcbdbf28aa435ae622f9",
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"version": "1.5.dev2444"
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}
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''' # END VERSION_JSON
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import math
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import warnings
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from collections.abc import Callable, Sequence
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from typing import Any
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from typing import Any
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import torch
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from torch import Tensor, nn
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features = self.feature_extractor(images)
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if isinstance(features, Tensor):
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feature_maps = [features]
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elif torch.jit.isinstance(features,
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elif torch.jit.isinstance(features, dict[str, Tensor]):
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feature_maps = list(features.values())
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else:
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feature_maps = list(features)
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monai/apps/tcia/utils.py
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monai/apps/utils.py
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return True
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actual_hash_func = look_up_option(hash_type.lower(), SUPPORTED_HASH_TYPES)
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actual_hash = actual_hash_func(usedforsecurity=False) # allows checks on FIPS enabled machines
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else:
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actual_hash = actual_hash_func()
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actual_hash = actual_hash_func(usedforsecurity=False) # allows checks on FIPS enabled machines
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try:
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with open(filepath, "rb") as f:
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monai/apps/vista3d/transforms.py
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import re
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import warnings
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from collections.abc import Sequence
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from typing import Any
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from collections.abc import Iterator, Sequence
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from typing import Any
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from monai.bundle.config_item import ConfigComponent, ConfigExpression, ConfigItem
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from monai.bundle.utils import DEPRECATED_ID_MAPPING, ID_REF_KEY, ID_SEP_KEY
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monai/bundle/scripts.py
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"""
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_args = update_kwargs(args=args_file, workflow_name=workflow_name, config_file=config_file, **kwargs)
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_log_input_summary(tag="run", args=_args)
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(workflow_name, config_file) = _pop_args(
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_args, workflow_name=ConfigWorkflow, config_file=None
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) # the default workflow name is "ConfigWorkflow"
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workflow_ = workflow_class(**_args)
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workflow_.initialize()
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_log_input_summary(tag="run", args=_args)
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return workflow_
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monai/bundle/workflows.py
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import sys
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import time
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from abc import ABC, abstractmethod
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from collections.abc import Sequence
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from copy import copy
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from logging.config import fileConfig
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from pathlib import Path
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from typing import Any
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from typing import Any
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from monai.apps.utils import get_logger
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from monai.bundle.config_parser import ConfigParser
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else:
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raise FileNotFoundError(f"Cannot find the logging config file: {logging_file}.")
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else:
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logger.info(f"Setting logging properties based on config: {logging_file}.")
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fileConfig(str(logging_file), disable_existing_loggers=False)
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logger.info(f"Setting logging properties based on config: {logging_file}.")
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self.parser = ConfigParser()
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self.parser.read_config(f=config_file)
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monai/config/type_definitions.py
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from __future__ import annotations
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import os
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from
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from collections.abc import Collection, Hashable, Iterable, Sequence
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from typing import TypeVar, Union
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import numpy as np
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import torch
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monai/data/dataset.py
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import warnings
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from collections.abc import Callable, Sequence
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from copy import copy, deepcopy
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from inspect import signature
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from multiprocessing.managers import ListProxy
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from multiprocessing.pool import ThreadPool
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from pathlib import Path
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if hashfile is not None and hashfile.is_file(): # cache hit
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try:
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if "weights_only" in signature(torch.load).parameters:
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return torch.load(hashfile, weights_only=False)
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else:
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return torch.load(hashfile)
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except PermissionError as e:
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raise e
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monai/data/meta_obj.py
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monai/data/meta_tensor.py
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monai/engines/evaluator.py
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monai/engines/trainer.py
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monai/engines/utils.py
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from collections.abc import Callable, Mapping, Sequence
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monai/handlers/mlflow_handler.py
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from monai.utils import CommonKeys, IgniteInfo, ensure_tuple, min_version, optional_import
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from monai.utils import CommonKeys, IgniteInfo, ensure_tuple, flatten_dict, min_version, optional_import
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]
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def _parse_artifacts(self):
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monai/handlers/stats_handler.py
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name: str | None = "monai.handlers.StatsHandler",
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monai/inferers/utils.py
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monai/losses/hausdorff_loss.py
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monai/metrics/fid.py
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monai/metrics/utils.py
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h, w, d = x.shape[2], x.shape[3], x.shape[4]
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rearrange_input = Rearrange("b c h w d -> b (h w d) c")
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rearrange_output = Rearrange("b (h w d) c -> b c h w d", h=h, w=w, d=d)
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shape = x.shape
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x = x.reshape(*shape[:2], -1).transpose(1, 2) # "b c h w d -> b (h w d) c"
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x =
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x_ = x
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x_ = x
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if with_label:
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import torch
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CHANGED
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-
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-
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mask = class_embedding @ src[[i]].view(1, c, h * w * d)
|
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masks.append(mask.view(-1, 1, h, w, d))
|
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+
masks_embedding = class_embedding.squeeze() @ src.view(b, c, h * w * d)
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masks_embedding = masks_embedding.view(b, -1, h, w, d).transpose(0, 1)
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return
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return masks_embedding, class_embedding
|
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class TwoWayTransformer(nn.Module):
|
monai/networks/trt_compiler.py
CHANGED
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"""
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|
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self.logger = logger or get_logger("
|
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+
self.logger = logger or get_logger("monai.networks.trt_compiler")
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|
@@ -563,7 +563,7 @@ def trt_compile(
|
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563
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else:
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wrap(model, base_path)
|
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565
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else:
|
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logger = logger or get_logger("
|
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+
logger = logger or get_logger("monai.networks.trt_compiler")
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logger.warning("TensorRT and/or polygraphy packages are not available! trt_compile() has no effect.")
|
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return model
|
monai/networks/utils.py
CHANGED
@@ -16,6 +16,7 @@ from __future__ import annotations
|
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import io
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18
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import re
|
19
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+
import tempfile
|
19
20
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import warnings
|
20
21
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from collections import OrderedDict
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21
22
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from collections.abc import Callable, Mapping, Sequence
|
@@ -688,9 +689,10 @@ def convert_to_onnx(
|
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688
689
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onnx_inputs = (inputs,)
|
689
690
|
else:
|
690
691
|
onnx_inputs = tuple(inputs)
|
691
|
-
|
692
|
+
temp_file = None
|
692
693
|
if filename is None:
|
693
|
-
|
694
|
+
temp_file = tempfile.NamedTemporaryFile()
|
695
|
+
f = temp_file.name
|
694
696
|
else:
|
695
697
|
f = filename
|
696
698
|
|
@@ -705,10 +707,7 @@ def convert_to_onnx(
|
|
705
707
|
do_constant_folding=do_constant_folding,
|
706
708
|
**torch_versioned_kwargs,
|
707
709
|
)
|
708
|
-
|
709
|
-
onnx_model = onnx.load_model_from_string(f.getvalue())
|
710
|
-
else:
|
711
|
-
onnx_model = onnx.load(filename)
|
710
|
+
onnx_model = onnx.load(f)
|
712
711
|
|
713
712
|
if do_constant_folding and polygraphy_imported:
|
714
713
|
from polygraphy.backend.onnx.loader import fold_constants
|
@@ -17,7 +17,8 @@ Class names are ended with 'd' to denote dictionary-based transforms.
|
|
17
17
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18
18
|
from __future__ import annotations
|
19
19
|
|
20
|
-
from
|
20
|
+
from collections.abc import Hashable, Mapping, Sequence
|
21
|
+
from typing import Callable
|
21
22
|
|
22
23
|
import numpy as np
|
23
24
|
|
@@ -15,10 +15,10 @@ A collection of "vanilla" transforms for spatial operations.
|
|
15
15
|
from __future__ import annotations
|
16
16
|
|
17
17
|
import warnings
|
18
|
-
from collections.abc import Callable
|
18
|
+
from collections.abc import Callable, Sequence
|
19
19
|
from copy import deepcopy
|
20
20
|
from itertools import zip_longest
|
21
|
-
from typing import Any, Optional,
|
21
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+
from typing import Any, Optional, Union, cast
|
22
22
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|
23
23
|
import numpy as np
|
24
24
|
import torch
|
@@ -116,7 +116,7 @@ __all__ = [
|
|
116
116
|
"RandSimulateLowResolution",
|
117
117
|
]
|
118
118
|
|
119
|
-
RandRange = Optional[Union[Sequence[Union[
|
119
|
+
RandRange = Optional[Union[Sequence[Union[tuple[float, float], float]], float]]
|
120
120
|
|
121
121
|
|
122
122
|
class SpatialResample(InvertibleTransform, LazyTransform):
|
@@ -18,9 +18,9 @@ Class names are ended with 'd' to denote dictionary-based transforms.
|
|
18
18
|
from __future__ import annotations
|
19
19
|
|
20
20
|
import re
|
21
|
-
from collections.abc import Callable, Hashable, Mapping
|
21
|
+
from collections.abc import Callable, Hashable, Mapping, Sequence
|
22
22
|
from copy import deepcopy
|
23
|
-
from typing import Any,
|
23
|
+
from typing import Any, cast
|
24
24
|
|
25
25
|
import numpy as np
|
26
26
|
import torch
|
@@ -88,7 +88,7 @@ def moveaxis(x: NdarrayOrTensor, src: int | Sequence[int], dst: int | Sequence[i
|
|
88
88
|
def in1d(x, y):
|
89
89
|
"""`np.in1d` with equivalent implementation for torch."""
|
90
90
|
if isinstance(x, np.ndarray):
|
91
|
-
return np.
|
91
|
+
return np.isin(x, y)
|
92
92
|
return (x[..., None] == torch.tensor(y, device=x.device)).any(-1).view(-1)
|
93
93
|
|
94
94
|
|
monai/utils/__init__.py
CHANGED
monai/utils/component_store.py
CHANGED
@@ -12,9 +12,10 @@
|
|
12
12
|
from __future__ import annotations
|
13
13
|
|
14
14
|
from collections import namedtuple
|
15
|
+
from collections.abc import Iterable
|
15
16
|
from keyword import iskeyword
|
16
17
|
from textwrap import dedent, indent
|
17
|
-
from typing import Any, Callable,
|
18
|
+
from typing import Any, Callable, TypeVar
|
18
19
|
|
19
20
|
T = TypeVar("T")
|
20
21
|
|
monai/utils/decorators.py
CHANGED
monai/utils/dist.py
CHANGED
@@ -11,15 +11,10 @@
|
|
11
11
|
|
12
12
|
from __future__ import annotations
|
13
13
|
|
14
|
-
import sys
|
15
14
|
import warnings
|
16
15
|
from collections.abc import Callable
|
17
16
|
from logging import Filter
|
18
|
-
|
19
|
-
if sys.version_info >= (3, 8):
|
20
|
-
from typing import Literal
|
21
|
-
|
22
|
-
from typing import overload
|
17
|
+
from typing import Literal, overload
|
23
18
|
|
24
19
|
import torch
|
25
20
|
import torch.distributed as dist
|
monai/utils/misc.py
CHANGED
@@ -887,7 +887,7 @@ def run_cmd(cmd_list: list[str], **kwargs: Any) -> subprocess.CompletedProcess:
|
|
887
887
|
if kwargs.pop("run_cmd_verbose", False):
|
888
888
|
import monai
|
889
889
|
|
890
|
-
monai.apps.utils.get_logger("run_cmd").info(f"{cmd_list}") # type: ignore[attr-defined]
|
890
|
+
monai.apps.utils.get_logger("monai.utils.run_cmd").info(f"{cmd_list}") # type: ignore[attr-defined]
|
891
891
|
try:
|
892
892
|
return subprocess.run(cmd_list, **kwargs)
|
893
893
|
except subprocess.CalledProcessError as e:
|
@@ -916,3 +916,16 @@ def unsqueeze_right(arr: NT, ndim: int) -> NT:
|
|
916
916
|
def unsqueeze_left(arr: NT, ndim: int) -> NT:
|
917
917
|
"""Prepend 1-sized dimensions to `arr` to create a result with `ndim` dimensions."""
|
918
918
|
return arr[(None,) * (ndim - arr.ndim)]
|
919
|
+
|
920
|
+
|
921
|
+
def flatten_dict(metrics: dict[str, Any]) -> dict[str, Any]:
|
922
|
+
"""
|
923
|
+
Flatten the nested dictionary to a flat dictionary.
|
924
|
+
"""
|
925
|
+
result = {}
|
926
|
+
for key, value in metrics.items():
|
927
|
+
if isinstance(value, dict):
|
928
|
+
result.update(flatten_dict(value))
|
929
|
+
else:
|
930
|
+
result[key] = value
|
931
|
+
return result
|
monai/utils/module.py
CHANGED
@@ -18,14 +18,14 @@ import pdb
|
|
18
18
|
import re
|
19
19
|
import sys
|
20
20
|
import warnings
|
21
|
-
from collections.abc import Callable, Collection, Hashable, Mapping
|
21
|
+
from collections.abc import Callable, Collection, Hashable, Iterable, Mapping
|
22
22
|
from functools import partial, wraps
|
23
23
|
from importlib import import_module
|
24
24
|
from pkgutil import walk_packages
|
25
25
|
from pydoc import locate
|
26
26
|
from re import match
|
27
27
|
from types import FunctionType, ModuleType
|
28
|
-
from typing import Any,
|
28
|
+
from typing import Any, cast
|
29
29
|
|
30
30
|
import torch
|
31
31
|
|
monai/utils/state_cacher.py
CHANGED
@@ -15,8 +15,9 @@ import copy
|
|
15
15
|
import os
|
16
16
|
import pickle
|
17
17
|
import tempfile
|
18
|
+
from collections.abc import Hashable
|
18
19
|
from types import ModuleType
|
19
|
-
from typing import Any
|
20
|
+
from typing import Any
|
20
21
|
|
21
22
|
import torch
|
22
23
|
from torch.serialization import DEFAULT_PROTOCOL
|
@@ -1,5 +1,5 @@
|
|
1
|
-
monai/__init__.py,sha256=
|
2
|
-
monai/_version.py,sha256=
|
1
|
+
monai/__init__.py,sha256=ysop022HrpjMOa3OOXOxu9wMEzBaWZ-pmyPSSp1xhGA,4095
|
2
|
+
monai/_version.py,sha256=HNl2ruiDvEKUYXx2U5fo82JGZpufk97ds-8BJeV011g,503
|
3
3
|
monai/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
4
4
|
monai/_extensions/__init__.py,sha256=NEBPreRhQ8H9gVvgrLr_y52_TmqB96u_u4VQmeNT93I,642
|
5
5
|
monai/_extensions/loader.py,sha256=7SiKw36q-nOzH8CRbBurFrz7GM40GCu7rc93Tm8XpnI,3643
|
@@ -10,7 +10,7 @@ monai/_extensions/gmm/gmm_cuda.cu,sha256=egWZBIpNYfOfxn0TKX82y-S2M6jg9NCzWwRcTLN
|
|
10
10
|
monai/_extensions/gmm/gmm_cuda_linalg.cuh,sha256=Glqg2oAcUFUXg-DVfpROkiv-DdXvvVdM1nyiFm8qlHY,3520
|
11
11
|
monai/apps/__init__.py,sha256=VDIc3HB_uFbqKL1TS-OeRvryEMDfzm22KJRzwpkXsGo,908
|
12
12
|
monai/apps/datasets.py,sha256=msT58BoHlQFQpD4Tx-CThwAkkaUowoNZOgcH0THg0u0,35085
|
13
|
-
monai/apps/utils.py,sha256=
|
13
|
+
monai/apps/utils.py,sha256=Gellkseuv3XKs-A6XcgbtqktQayv9NVIhX9tTQGM10I,14362
|
14
14
|
monai/apps/auto3dseg/__init__.py,sha256=DhUB2Ol0-iNAk1ZNmD1RkTODUOhdiibv8h9MgcLuF6s,1016
|
15
15
|
monai/apps/auto3dseg/__main__.py,sha256=fCDhD8uhmJQKkKBxLO6hMJhEvZJRIsjTc1Ad3bYmNIY,1411
|
16
16
|
monai/apps/auto3dseg/auto_runner.py,sha256=a4Ry93TkK0aTb68bwle8HoG4SzUbUf0IbDrY33jTReg,40106
|
@@ -33,9 +33,9 @@ monai/apps/detection/metrics/coco.py,sha256=bpF6hAAMKsBNLfat-Fzh0CR-0swDsAAVcwTa
|
|
33
33
|
monai/apps/detection/metrics/matching.py,sha256=GF4wgH5Let7GwW1SGwzfzz5BRnCVEhDe7_KR7zpLr44,17161
|
34
34
|
monai/apps/detection/networks/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
|
35
35
|
monai/apps/detection/networks/retinanet_detector.py,sha256=-EcGvDJK13o7qqx6bUHtxEniIdCXriIzwty1o5pmG90,53640
|
36
|
-
monai/apps/detection/networks/retinanet_network.py,sha256=
|
36
|
+
monai/apps/detection/networks/retinanet_network.py,sha256=Xbx1WeGWHkQC7VJUAgYD3GjGizehF8_wWntjdFYySD4,19038
|
37
37
|
monai/apps/detection/transforms/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
|
38
|
-
monai/apps/detection/transforms/array.py,sha256=
|
38
|
+
monai/apps/detection/transforms/array.py,sha256=CHc-zl7IPlKYPBVR88zVT6_eBFElPihtkfO9oo2Bsak,24546
|
39
39
|
monai/apps/detection/transforms/box_ops.py,sha256=3RFK8zNH8ufpHT_aB5xFR2wXrQauBQEWQyxNojl1mSY,18035
|
40
40
|
monai/apps/detection/transforms/dictionary.py,sha256=OGEYrq2F8gFjYRYv7ZdlWFM6yYRs_24yYn7J2GYlgJc,69282
|
41
41
|
monai/apps/detection/utils/ATSS_matcher.py,sha256=aajY2UJ-Ot9L5KDwORFOCuMsTQEU02BZ9-tNMfIYH98,13532
|
@@ -49,8 +49,8 @@ monai/apps/detection/utils/predict_utils.py,sha256=6j7U-7pLtbmgE6SXKR_MVImc67-M8
|
|
49
49
|
monai/apps/generation/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
|
50
50
|
monai/apps/generation/maisi/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
|
51
51
|
monai/apps/generation/maisi/networks/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
|
52
|
-
monai/apps/generation/maisi/networks/autoencoderkl_maisi.py,sha256=
|
53
|
-
monai/apps/generation/maisi/networks/controlnet_maisi.py,sha256=
|
52
|
+
monai/apps/generation/maisi/networks/autoencoderkl_maisi.py,sha256=FxHsB7W1I11Npdyg4gN1k3QIc0tcq3FMLI0TDjI4mgg,36704
|
53
|
+
monai/apps/generation/maisi/networks/controlnet_maisi.py,sha256=0K2uyMfvc1-2cFCoNDngeMbzcPpvFR1JZ0fqF9pj8r4,7707
|
54
54
|
monai/apps/generation/maisi/networks/diffusion_model_unet_maisi.py,sha256=XFOiy6GngXC_OKM1dUiel_gp71yUFWgPErYdgrVLQAU,19072
|
55
55
|
monai/apps/mmars/__init__.py,sha256=BolpgEi9jNBgrOQd3Kwp-9QQLeWQwQtlN_MJkK1eu5s,726
|
56
56
|
monai/apps/mmars/mmars.py,sha256=AYsx5FDmJ0dT0hAkWGYhM470aPIG23PYloHihDZfOKE,13115
|
@@ -64,18 +64,18 @@ monai/apps/nuclick/transforms.py,sha256=kf2xOb1iBx-OWc7wngsRWvdNV8KpX6xeTMFuYZqZ
|
|
64
64
|
monai/apps/pathology/__init__.py,sha256=SRBbxgPzZdtC22TpY1m0-Z3SSBfMig6xYVSdgOClgXg,1030
|
65
65
|
monai/apps/pathology/utils.py,sha256=ulgDy43tSSmJwwBf-51NC0D0_Kf0BeymxEK7p136VFI,2838
|
66
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