kaiko-eva 0.0.0.dev6__py3-none-any.whl

eva/vision/utils/io/nifti.py

@@ -0,0 +1,50 @@
+"""NIfTI I/O related functions."""
+
+from typing import Any
+
+import nibabel as nib
+import numpy.typing as npt
+
+from eva.vision.utils.io import _utils
+
+
+def read_nifti_slice(path: str, slice_index: int) -> npt.NDArray[Any]:
+    """Reads and loads a NIfTI image from a file path as `uint8`.
+
+    Args:
+        path: The path to the NIfTI file.
+        slice_index: The image slice index to return. If `None`, it will
+            return the full 3D image.
+
+    Returns:
+        The image as a numpy array.
+
+    Raises:
+        FileExistsError: If the path does not exist or it is unreachable.
+        ValueError: If the input channel is invalid for the image.
+    """
+    _utils.check_file(path)
+    image_data = nib.load(path)  # type: ignore
+    dtype = image_data.get_data_dtype()  # type: ignore
+    image_slice = image_data.slicer[:, :, slice_index : slice_index + 1]  # type: ignore
+    image_array = image_slice.get_fdata()
+    return image_array.astype(dtype)
+
+
+def fetch_total_nifti_slices(path: str) -> int:
+    """Fetches the total slides of a NIfTI image file.
+
+    Args:
+        path: The path to the NIfTI file.
+
+    Returns:
+        The number of the total available slides.
+
+    Raises:
+        FileExistsError: If the path does not exist or it is unreachable.
+        ValueError: If the input channel is invalid for the image.
+    """
+    _utils.check_file(path)
+    image = nib.load(path)  # type: ignore
+    image_shape = image.header.get_data_shape()  # type: ignore
+    return image_shape[-1]

eva/vision/utils/io/text.py

@@ -0,0 +1,18 @@
+"""Text I/O related functions."""
+
+import csv
+from typing import Dict, List
+
+
+def read_csv(path: str) -> List[Dict[str, str]]:
+    """Reads a CSV file and returns its contents as a list of dictionaries.
+
+    Args:
+        path: The path to the CSV file.
+
+    Returns:
+        A list of dictionaries representing the data in the CSV file.
+    """
+    with open(path, newline="") as file:
+        data = csv.DictReader(file, skipinitialspace=True)
+        return list(data)

kaiko_eva-0.0.0.dev6.dist-info/METADATA

@@ -0,0 +1,393 @@
+Metadata-Version: 2.1
+Name: kaiko-eva
+Version: 0.0.0.dev6
+Summary: Evaluation Framework for oncology foundation models.
+Keywords: machine-learning evaluation-framework oncology foundation-models
+Author-Email: Ioannis Gatopoulos <ioannis@kaiko.ai>, Nicolas Känzig <nicolas@kaiko.ai>, Roman Moser <roman@kaiko.ai>
+Maintainer-Email: Ioannis Gatopoulos <ioannis@kaiko.ai>, Nicolas Känzig <nicolas@kaiko.ai>, Roman Moser <roman@kaiko.ai>
+License:                                  Apache License
+                                   Version 2.0, January 2004
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+        
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+           Copyright 2024 kaiko.ai
+        
+           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
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+Classifier: Topic :: Software Development :: Build Tools
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Project-URL: Homepage, https://kaiko-ai.github.io/eva/dev/
+Project-URL: Repository, https://github.com/kaiko-ai/eva
+Project-URL: Documentation, https://kaiko-ai.github.io/eva/dev/
+Requires-Python: >=3.10
+Requires-Dist: lightning>=2.2.1
+Requires-Dist: jsonargparse[omegaconf]>=4.27.4
+Requires-Dist: tensorboard>=2.16.2
+Requires-Dist: loguru>=0.7.2
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: transformers>=4.38.2
+Requires-Dist: onnxruntime>=1.17.1
+Requires-Dist: onnx>=1.15.0
+Requires-Dist: toolz>=0.12.1
+Requires-Dist: h5py>=3.10.0; extra == "vision"
+Requires-Dist: nibabel>=5.2.0; extra == "vision"
+Requires-Dist: opencv-python-headless>=4.9.0.80; extra == "vision"
+Requires-Dist: timm>=0.9.12; extra == "vision"
+Requires-Dist: torchvision>=0.17.0; extra == "vision"
+Requires-Dist: h5py>=3.10.0; extra == "all"
+Requires-Dist: nibabel>=5.2.0; extra == "all"
+Requires-Dist: opencv-python-headless>=4.9.0.80; extra == "all"
+Requires-Dist: timm>=0.9.12; extra == "all"
+Requires-Dist: torchvision>=0.17.0; extra == "all"
+Provides-Extra: vision
+Provides-Extra: all
+Description-Content-Type: text/markdown
+
+<div align="center">
+
+<img src="./docs/images/eva-logo.png" width="400">
+
+<br />
+
+_Oncology FM Evaluation Framework by kaiko.ai_
+
+[![PyPI](https://img.shields.io/pypi/v/kaiko-eva.svg?logo=python)](https://pypi.python.org/pypi/kaiko-eva)
+[![CI](https://github.com/kaiko-ai/eva/workflows/CI/badge.svg)](https://github.com/kaiko-ai/eva/actions?query=workflow%3ACI)
+[![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg?labelColor=gray)](https://github.com/kaiko-ai/eva#license)
+
+<p align="center">
+  <a href="#installation">Installation</a> •
+  <a href="#how-to-use">How To Use</a> •
+  <a href="https://kaiko-ai.github.io/eva/">Documentation</a> •
+  <a href="https://kaiko-ai.github.io/eva/dev/datasets/">Datasets</a> •
+  <a href="#benchmarks">Benchmarks</a> <br>
+  <a href="#contributing">Contribute</a> •
+  <a href="#acknowledgements">Acknowledgements</a>
+</p>
+
+</div>
+
+### Introduction
+
+_`eva`_ is an evaluation framework for oncology foundation models (FMs) by [kaiko.ai](https://kaiko.ai/). Check out the [documentation](https://kaiko-ai.github.io/eva/) for more information.
+
+<div align="center">
+
+<img src="./docs/images/eva-process.gif" width="800">
+
+</div>
+
+### Highlights:
+- Easy and reliable benchmark of Oncology FMs
+- Automatic embedding inference and evaluation of a downstream task
+- Native support of popular medical [datasets](https://kaiko-ai.github.io/eva/dev/datasets/) and models
+- Produce statistics over multiple evaluation fits and multiple metrics
+
+## Installation
+
+Simple installation from PyPI:
+```sh
+# to install the core version only
+pip install kaiko-eva
+
+# to install the expanded `vision` version
+pip install 'kaiko-eva[vision]'
+
+# to install everything
+pip install 'kaiko-eva[all]'
+```
+
+To install the latest version of the `main` branch:
+```sh
+pip install "kaiko-eva[vision] @ git+https://github.com/kaiko-ai/eva.git"
+```
+
+You can verify that the installation was successful by executing:
+```sh
+eva --version
+```
+
+## How To Use
+
+_eva_ can be used directly from the terminal as a CLI tool as follows:
+```sh
+eva {fit,predict,predict_fit} --config url/or/path/to/the/config.yaml 
+```
+
+For example, to perform a downstream evaluation of DINO ViT-S/16 on the BACH dataset with linear probing by first inferring the embeddings and performing 5 sequential fits, execute:
+```sh
+eva predict_fit --config https://raw.githubusercontent.com/kaiko-ai/eva/main/configs/vision/dino_vit/offline/bach.yaml
+```
+
+> [!NOTE] 
+> All the datasets that support automatic download in the repo have by default the option to automatically download set to false. For automatic download you have to manually set download=true.
+
+
+To view all the possibles, execute:
+```sh
+eva --help
+```
+
+For more information, please refer to the [documentation](https://kaiko-ai.github.io/eva/dev/user-guide/tutorials/offline_vs_online/) and [tutorials](https://kaiko-ai.github.io/eva/dev/user-guide/advanced/replicate_evaluations/).
+
+## Benchmarks
+
+In this section you will find model benchmarks which were generated with _eva_.
+
+### Table I: WSI patch-level benchmark
+
+<br />
+
+<div align="center">
+
+| Model                                            | BACH  | CRC   | MHIST | PCam/val | PCam/test |
+|--------------------------------------------------|-------|-------|-------|----------|-----------|
+| ViT-S/16 _(random)_	<sup>[1]</sup>               | 0.410 | 0.617 | 0.501 | 0.753    | 0.728     |
+| ViT-S/16 _(ImageNet)_ <sup>[1]</sup>             | 0.695 | 0.935 | 0.831 | 0.864    | 0.849     |
+| ViT-B/8 _(ImageNet)_ <sup>[1]</sup>              | 0.797 | 0.943 | 0.828 | 0.903    | 0.893     |
+| DINO<sub>(p=16)</sub> <sup>[2]</sup>             | 0.710 | 0.935 | 0.814 | 0.870    | 0.856     |
+| Phikon <sup>[3]</sup>                            | 0.725 | 0.935 | 0.777 | 0.912    | 0.915     |
+| ViT-S/16 _(kaiko.ai)_ <sup>[4]</sup>             | 0.797 | 0.943 | 0.828 | 0.903    | 0.893     |
+| ViT-S/8 _(kaiko.ai)_ <sup>[4]</sup>              | 0.834 | 0.946 | 0.832 | 0.897    | 0.887     |
+| ViT-B/16 _(kaiko.ai)_	<sup>[4]</sup>             | 0.810 | 0.960 | 0.826 | 0.900    | 0.898     |
+| ViT-B/8 _(kaiko.ai)_ <sup>[4]</sup>              | 0.865 | 0.956 | 0.809 | 0.913    | 0.921     |
+| ViT-L/14 _(kaiko.ai)_ <sup>[4]</sup>             | 0.870 | 0.930 | 0.809 | 0.908    | 0.898     |
+
+_Table I: Linear probing evaluation of FMs on patch-level downstream datasets.<br> We report averaged balanced accuracy
+over 5 runs_, with an average standard deviation of ±0.003.
+
+</div>
+
+<br />
+
+_References_:
+1. _"Emerging properties in self-supervised vision transformers”_
+2. _"Benchmarking self-supervised learning on diverse pathology datasets”_
+3. _"Scaling self-supervised learning for histopathology with masked image modeling”_
+4. _"Towards training Large-Scale Medical Foundation Models: from TCGA to hospital-scale pathology FMs”_
+
+## Contributing
+
+_eva_ is an open source project and welcomes contributions of all kinds. Please checkout the [developer](./docs/DEVELOPER_GUIDE.md) and [contributing guide](./docs/CONTRIBUTING.md) for help on how to do so.
+
+All contributors must follow the [code of conduct](./docs/CODE_OF_CONDUCT.md).
+
+
+## Acknowledgements
+
+Our codebase is built using multiple opensource contributions
+
+<div align="center">
+
+[![python](https://img.shields.io/badge/-Python-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![pytorch](https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white)](https://pytorch.org/get-started/locally/)
+[![lightning](https://img.shields.io/badge/-⚡️_Lightning-792ee5?logo=pytorchlightning&logoColor=white)](https://pytorchlightning.ai/)<br>
+[![black](https://img.shields.io/badge/Code%20Style-Black-black.svg?labelColor=gray)](https://black.readthedocs.io/en/stable/)
+[![isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)<br>
+[![pdm-managed](https://img.shields.io/badge/pdm-managed-blueviolet)](https://pdm-project.org)
+[![Nox](https://img.shields.io/badge/%F0%9F%A6%8A-Nox-D85E00.svg)](https://github.com/wntrblm/nox)
+[![Built with Material for MkDocs](https://img.shields.io/badge/Material_for_MkDocs-526CFE?logo=MaterialForMkDocs&logoColor=white)](https://squidfunk.github.io/mkdocs-material/)
+
+</div>
+
+---
+<div align="center">
+  <img src="./docs/images/kaiko-logo.png" width="200">
+</div>

kaiko_eva-0.0.0.dev6.dist-info/RECORD

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kaiko_eva-0.0.0.dev6.dist-info/WHEEL

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kaiko_eva-0.0.0.dev6.dist-info/entry_points.txt

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