monai-weekly 1.5.dev2505__tar.gz → 1.5.dev2507__tar.gz

monai_weekly-1.5.dev2507/PKG-INFO

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+Metadata-Version: 2.2
+Name: monai-weekly
+Version: 1.5.dev2507
+Summary: AI Toolkit for Healthcare Imaging
+Home-page: https://monai.io/
+Author: MONAI Consortium
+Author-email: monai.contact@gmail.com
+License: Apache License 2.0
+Project-URL: Documentation, https://docs.monai.io/
+Project-URL: Bug Tracker, https://github.com/Project-MONAI/MONAI/issues
+Project-URL: Source Code, https://github.com/Project-MONAI/MONAI
+Platform: OS Independent
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown; charset=UTF-8
+License-File: LICENSE
+Requires-Dist: torch>=1.13.1
+Requires-Dist: numpy<2.0,>=1.24
+Provides-Extra: all
+Requires-Dist: nibabel; extra == "all"
+Requires-Dist: ninja; extra == "all"
+Requires-Dist: scikit-image>=0.14.2; extra == "all"
+Requires-Dist: scipy>=1.12.0; python_version >= "3.9" and extra == "all"
+Requires-Dist: pillow; extra == "all"
+Requires-Dist: tensorboard; extra == "all"
+Requires-Dist: gdown>=4.7.3; extra == "all"
+Requires-Dist: pytorch-ignite==0.4.11; extra == "all"
+Requires-Dist: torchio; extra == "all"
+Requires-Dist: torchvision; extra == "all"
+Requires-Dist: itk>=5.2; extra == "all"
+Requires-Dist: tqdm>=4.47.0; extra == "all"
+Requires-Dist: lmdb; extra == "all"
+Requires-Dist: psutil; extra == "all"
+Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "all"
+Requires-Dist: openslide-python; extra == "all"
+Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
+Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
+Requires-Dist: pandas; extra == "all"
+Requires-Dist: einops; extra == "all"
+Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "all"
+Requires-Dist: mlflow>=2.12.2; extra == "all"
+Requires-Dist: clearml>=1.10.0rc0; extra == "all"
+Requires-Dist: matplotlib>=3.6.3; extra == "all"
+Requires-Dist: tensorboardX; extra == "all"
+Requires-Dist: pyyaml; extra == "all"
+Requires-Dist: fire; extra == "all"
+Requires-Dist: jsonschema; extra == "all"
+Requires-Dist: pynrrd; extra == "all"
+Requires-Dist: pydicom; extra == "all"
+Requires-Dist: h5py; extra == "all"
+Requires-Dist: nni; (platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine) and extra == "all"
+Requires-Dist: optuna; extra == "all"
+Requires-Dist: onnx>=1.13.0; extra == "all"
+Requires-Dist: onnxruntime; python_version <= "3.10" and extra == "all"
+Requires-Dist: zarr; extra == "all"
+Requires-Dist: lpips==0.1.4; extra == "all"
+Requires-Dist: nvidia-ml-py; extra == "all"
+Requires-Dist: huggingface_hub; extra == "all"
+Requires-Dist: pyamg>=5.0.0; extra == "all"
+Provides-Extra: nibabel
+Requires-Dist: nibabel; extra == "nibabel"
+Provides-Extra: ninja
+Requires-Dist: ninja; extra == "ninja"
+Provides-Extra: skimage
+Requires-Dist: scikit-image>=0.14.2; extra == "skimage"
+Provides-Extra: scipy
+Requires-Dist: scipy>=1.12.0; python_version >= "3.9" and extra == "scipy"
+Provides-Extra: pillow
+Requires-Dist: pillow!=8.3.0; extra == "pillow"
+Provides-Extra: tensorboard
+Requires-Dist: tensorboard; extra == "tensorboard"
+Provides-Extra: gdown
+Requires-Dist: gdown>=4.7.3; extra == "gdown"
+Provides-Extra: ignite
+Requires-Dist: pytorch-ignite==0.4.11; extra == "ignite"
+Provides-Extra: torchio
+Requires-Dist: torchio; extra == "torchio"
+Provides-Extra: torchvision
+Requires-Dist: torchvision; extra == "torchvision"
+Provides-Extra: itk
+Requires-Dist: itk>=5.2; extra == "itk"
+Provides-Extra: tqdm
+Requires-Dist: tqdm>=4.47.0; extra == "tqdm"
+Provides-Extra: lmdb
+Requires-Dist: lmdb; extra == "lmdb"
+Provides-Extra: psutil
+Requires-Dist: psutil; extra == "psutil"
+Provides-Extra: cucim
+Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "cucim"
+Provides-Extra: openslide
+Requires-Dist: openslide-python; extra == "openslide"
+Provides-Extra: tifffile
+Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "tifffile"
+Provides-Extra: imagecodecs
+Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "Darwin") and extra == "imagecodecs"
+Provides-Extra: pandas
+Requires-Dist: pandas; extra == "pandas"
+Provides-Extra: einops
+Requires-Dist: einops; extra == "einops"
+Provides-Extra: transformers
+Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "transformers"
+Provides-Extra: mlflow
+Requires-Dist: mlflow>=2.12.2; extra == "mlflow"
+Provides-Extra: matplotlib
+Requires-Dist: matplotlib>=3.6.3; extra == "matplotlib"
+Provides-Extra: clearml
+Requires-Dist: clearml; extra == "clearml"
+Provides-Extra: tensorboardx
+Requires-Dist: tensorboardX; extra == "tensorboardx"
+Provides-Extra: pyyaml
+Requires-Dist: pyyaml; extra == "pyyaml"
+Provides-Extra: fire
+Requires-Dist: fire; extra == "fire"
+Provides-Extra: packaging
+Requires-Dist: packaging; extra == "packaging"
+Provides-Extra: jsonschema
+Requires-Dist: jsonschema; extra == "jsonschema"
+Provides-Extra: pynrrd
+Requires-Dist: pynrrd; extra == "pynrrd"
+Provides-Extra: pydicom
+Requires-Dist: pydicom; extra == "pydicom"
+Provides-Extra: h5py
+Requires-Dist: h5py; extra == "h5py"
+Provides-Extra: nni
+Requires-Dist: nni; (platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine) and extra == "nni"
+Provides-Extra: optuna
+Requires-Dist: optuna; extra == "optuna"
+Provides-Extra: onnx
+Requires-Dist: onnx>=1.13.0; extra == "onnx"
+Requires-Dist: onnxruntime; python_version <= "3.10" and extra == "onnx"
+Provides-Extra: zarr
+Requires-Dist: zarr; extra == "zarr"
+Provides-Extra: lpips
+Requires-Dist: lpips==0.1.4; extra == "lpips"
+Provides-Extra: pynvml
+Requires-Dist: nvidia-ml-py; extra == "pynvml"
+Provides-Extra: polygraphy
+Requires-Dist: polygraphy; extra == "polygraphy"
+Provides-Extra: huggingface-hub
+Requires-Dist: huggingface_hub; extra == "huggingface-hub"
+Provides-Extra: pyamg
+Requires-Dist: pyamg>=5.0.0; extra == "pyamg"
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png" width="50%" alt='project-monai'>
+</p>
+
+**M**edical **O**pen **N**etwork for **AI**
+
+![Supported Python versions](https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/python.svg)
+[![License](https://img.shields.io/badge/license-Apache%202.0-green.svg)](https://opensource.org/licenses/Apache-2.0)
+[![PyPI version](https://badge.fury.io/py/monai.svg)](https://badge.fury.io/py/monai)
+[![docker](https://img.shields.io/badge/docker-pull-green.svg?logo=docker&logoColor=white)](https://hub.docker.com/r/projectmonai/monai)
+[![conda](https://img.shields.io/conda/vn/conda-forge/monai?color=green)](https://anaconda.org/conda-forge/monai)
+
+[![premerge](https://github.com/Project-MONAI/MONAI/actions/workflows/pythonapp.yml/badge.svg?branch=dev)](https://github.com/Project-MONAI/MONAI/actions/workflows/pythonapp.yml)
+[![postmerge](https://img.shields.io/github/checks-status/project-monai/monai/dev?label=postmerge)](https://github.com/Project-MONAI/MONAI/actions?query=branch%3Adev)
+[![Documentation Status](https://readthedocs.org/projects/monai/badge/?version=latest)](https://docs.monai.io/en/latest/)
+[![codecov](https://codecov.io/gh/Project-MONAI/MONAI/branch/dev/graph/badge.svg?token=6FTC7U1JJ4)](https://codecov.io/gh/Project-MONAI/MONAI)
+[![monai Downloads Last Month](https://assets.piptrends.com/get-last-month-downloads-badge/monai.svg 'monai Downloads Last Month by pip Trends')](https://piptrends.com/package/monai)
+
+MONAI is a [PyTorch](https://pytorch.org/)-based, [open-source](https://github.com/Project-MONAI/MONAI/blob/dev/LICENSE) framework for deep learning in healthcare imaging, part of the [PyTorch Ecosystem](https://pytorch.org/ecosystem/).
+Its ambitions are as follows:
+- Developing a community of academic, industrial and clinical researchers collaborating on a common foundation;
+- Creating state-of-the-art, end-to-end training workflows for healthcare imaging;
+- Providing researchers with the optimized and standardized way to create and evaluate deep learning models.
+
+
+## Features
+> _Please see [the technical highlights](https://docs.monai.io/en/latest/highlights.html) and [What's New](https://docs.monai.io/en/latest/whatsnew.html) of the milestone releases._
+
+- flexible pre-processing for multi-dimensional medical imaging data;
+- compositional & portable APIs for ease of integration in existing workflows;
+- domain-specific implementations for networks, losses, evaluation metrics and more;
+- customizable design for varying user expertise;
+- multi-GPU multi-node data parallelism support.
+
+
+## Installation
+
+To install [the current release](https://pypi.org/project/monai/), you can simply run:
+
+```bash
+pip install monai
+```
+
+Please refer to [the installation guide](https://docs.monai.io/en/latest/installation.html) for other installation options.
+
+## Getting Started
+
+[MedNIST demo](https://colab.research.google.com/drive/1wy8XUSnNWlhDNazFdvGBHLfdkGvOHBKe) and [MONAI for PyTorch Users](https://colab.research.google.com/drive/1boqy7ENpKrqaJoxFlbHIBnIODAs1Ih1T) are available on Colab.
+
+Examples and notebook tutorials are located at [Project-MONAI/tutorials](https://github.com/Project-MONAI/tutorials).
+
+Technical documentation is available at [docs.monai.io](https://docs.monai.io).
+
+## Citation
+
+If you have used MONAI in your research, please cite us! The citation can be exported from: https://arxiv.org/abs/2211.02701.
+
+## Model Zoo
+[The MONAI Model Zoo](https://github.com/Project-MONAI/model-zoo) is a place for researchers and data scientists to share the latest and great models from the community.
+Utilizing [the MONAI Bundle format](https://docs.monai.io/en/latest/bundle_intro.html) makes it easy to [get started](https://github.com/Project-MONAI/tutorials/tree/main/model_zoo) building workflows with MONAI.
+
+## Contributing
+For guidance on making a contribution to MONAI, see the [contributing guidelines](https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md).
+
+## Community
+Join the conversation on Twitter/X [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
+
+Ask and answer questions over on [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions).
+
+## Links
+- Website: https://monai.io/
+- API documentation (milestone): https://docs.monai.io/
+- API documentation (latest dev): https://docs.monai.io/en/latest/
+- Code: https://github.com/Project-MONAI/MONAI
+- Project tracker: https://github.com/Project-MONAI/MONAI/projects
+- Issue tracker: https://github.com/Project-MONAI/MONAI/issues
+- Wiki: https://github.com/Project-MONAI/MONAI/wiki
+- Test status: https://github.com/Project-MONAI/MONAI/actions
+- PyPI package: https://pypi.org/project/monai/
+- conda-forge: https://anaconda.org/conda-forge/monai
+- Weekly previews: https://pypi.org/project/monai-weekly/
+- Docker Hub: https://hub.docker.com/r/projectmonai/monai

monai_weekly-1.5.dev2507/monai/__init__.py

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+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import logging
+import os
+import sys
+import warnings
+
+from ._version import get_versions
+
+old_showwarning = warnings.showwarning
+
+
+def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
+    ignore_files = ["ignite/handlers/checkpoint", "modelopt/torch/quantization/tensor_quant"]
+    if any(ignore in filename for ignore in ignore_files):
+        return
+    old_showwarning(message, category, filename, lineno, file, line)
+
+
+class DeprecatedTypesWarningFilter(logging.Filter):
+    def filter(self, record):
+        message_bodies_to_ignore = [
+            "np.bool8",
+            "np.object0",
+            "np.int0",
+            "np.uint0",
+            "np.void0",
+            "np.str0",
+            "np.bytes0",
+            "@validator",
+            "@root_validator",
+            "class-based `config`",
+            "pkg_resources",
+            "Implicitly cleaning up",
+        ]
+        for message in message_bodies_to_ignore:
+            if message in record.getMessage():
+                return False
+        return True
+
+
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
+# TODO: remove this workaround after upstream fixed the warning
+# Set the custom warning handler to filter warning
+warnings.showwarning = custom_warning_handler
+# Get the logger for warnings and add the filter to the logger
+logging.getLogger("py.warnings").addFilter(DeprecatedTypesWarningFilter())
+
+
+PY_REQUIRED_MAJOR = 3
+PY_REQUIRED_MINOR = 9
+
+version_dict = get_versions()
+__version__: str = version_dict.get("version", "0+unknown")
+__revision_id__: str = version_dict.get("full-revisionid")
+del get_versions, version_dict
+
+__copyright__ = "(c) MONAI Consortium"
+
+__basedir__ = os.path.dirname(__file__)
+
+if sys.version_info.major != PY_REQUIRED_MAJOR or sys.version_info.minor < PY_REQUIRED_MINOR:
+    import warnings
+
+    warnings.warn(
+        f"MONAI requires Python {PY_REQUIRED_MAJOR}.{PY_REQUIRED_MINOR} or higher. "
+        f"But the current Python is: {sys.version}",
+        category=RuntimeWarning,
+    )
+
+
+from .utils.module import load_submodules  # noqa: E402
+
+# handlers_* have some external decorators the users may not have installed
+# *.so files and folder "_C" may not exist when the cpp extensions are not compiled
+excludes = "|".join(
+    [
+        "(^(monai.handlers))",
+        "(^(monai.bundle))",
+        "(^(monai.fl))",
+        "((\\.so)$)",
+        "(^(monai._C))",
+        "(.*(__main__)$)",
+        "(.*(video_dataset)$)",
+        "(.*(nnunet).*$)",
+    ]
+)
+
+# load directory modules only, skip loading individual files
+load_submodules(sys.modules[__name__], False, exclude_pattern=excludes)
+
+# load all modules, this will trigger all export decorations
+load_submodules(sys.modules[__name__], True, exclude_pattern=excludes)
+
+__all__ = [
+    "apps",
+    "auto3dseg",
+    "bundle",
+    "config",
+    "data",
+    "engines",
+    "fl",
+    "handlers",
+    "inferers",
+    "losses",
+    "metrics",
+    "networks",
+    "optimizers",
+    "transforms",
+    "utils",
+    "visualize",
+]
+
+try:
+    from .utils.tf32 import detect_default_tf32
+
+    detect_default_tf32()
+    import torch
+
+    # workaround related to https://github.com/Project-MONAI/MONAI/issues/7575
+    if hasattr(torch.cuda.device_count, "cache_clear"):
+        torch.cuda.device_count.cache_clear()
+except BaseException:
+    from .utils.misc import MONAIEnvVars
+
+    if MONAIEnvVars.debug():
+        raise
+__commit_id__ = "44add8d134f0cf0df6e4b0f5ffdd710474d211e5"

monai_weekly-1.5.dev2507/monai/_version.py

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+
+# This file was generated by 'versioneer.py' (0.23) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2025-02-16T02:27:59+0000",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "bbd080bb9d263c06a0884a871b645a434e3d4cdd",
+ "version": "1.5.dev2507"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

monai_weekly-1.5.dev2507/monai/apps/auto3dseg/transforms.py

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+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import warnings
+from collections.abc import Hashable, Mapping
+
+import numpy as np
+import torch
+
+from monai.config import KeysCollection
+from monai.transforms import MapTransform
+from monai.utils.misc import ImageMetaKey
+
+
+class EnsureSameShaped(MapTransform):
+    """
+    Checks if segmentation label images (in keys) have the same spatial shape as the main image (in source_key),
+    and raise an error if the shapes are significantly different.
+    If the shapes are only slightly different (within an allowed_shape_difference in each dim), then resize the label using
+    nearest interpolation. This transform is designed to correct datasets with slight label shape mismatches.
+    Generally image and segmentation label must have the same spatial shape, however some public datasets are having slight
+    shape mismatches, which will cause potential crashes when calculating loss or metric functions.
+    """
+
+    def __init__(
+        self,
+        keys: KeysCollection = "label",
+        allow_missing_keys: bool = False,
+        source_key: str = "image",
+        allowed_shape_difference: int = 5,
+        warn: bool = True,
+    ) -> None:
+        """
+        Args:
+            keys: keys of the corresponding items to be compared to the source_key item shape.
+            allow_missing_keys: do not raise exception if key is missing.
+            source_key: key of the item with the reference shape.
+            allowed_shape_difference: raises error if shapes are different more than this value in any dimension,
+                otherwise corrects for the shape mismatch using nearest interpolation.
+            warn: if `True` prints a warning if the label image is resized
+
+
+        """
+        super().__init__(keys=keys, allow_missing_keys=allow_missing_keys)
+        self.source_key = source_key
+        self.allowed_shape_difference = allowed_shape_difference
+        self.warn = warn
+
+    def __call__(self, data: Mapping[Hashable, torch.Tensor]) -> dict[Hashable, torch.Tensor]:
+        d = dict(data)
+        image_shape = d[self.source_key].shape[1:]
+        for key in self.key_iterator(d):
+            label_shape = d[key].shape[1:]
+            if label_shape != image_shape:
+                filename = ""
+                if hasattr(d[key], "meta") and isinstance(d[key].meta, Mapping):  # type: ignore[attr-defined]
+                    filename = d[key].meta.get(ImageMetaKey.FILENAME_OR_OBJ)  # type: ignore[attr-defined]
+
+                if np.allclose(list(label_shape), list(image_shape), atol=self.allowed_shape_difference):
+                    if self.warn:
+                        warnings.warn(
+                            f"The {key} with shape {label_shape} was resized to match the source shape {image_shape}"
+                            f", the metadata was not updated {filename}."
+                        )
+                    d[key] = torch.nn.functional.interpolate(
+                        input=d[key].unsqueeze(0), size=image_shape, mode="nearest-exact"
+                    ).squeeze(0)
+                else:
+                    raise ValueError(
+                        f"The {key} shape {label_shape} is different from the source shape {image_shape} {filename}."
+                    )
+        return d