kaiko-eva 0.0.1__py3-none-any.whl → 0.1.0__py3-none-any.whl

eva/vision/data/datasets/segmentation/total_segmentator.py

@@ -1,212 +0,0 @@
-"""TotalSegmentator 2D segmentation dataset class."""
-
-import functools
-import os
-from glob import glob
-from typing import Callable, Dict, List, Literal, Tuple
-
-import numpy as np
-from torchvision.datasets import utils
-from typing_extensions import override
-
-from eva.vision.data.datasets import _utils, _validators, structs
-from eva.vision.data.datasets.segmentation import base
-from eva.vision.utils import io
-
-
-class TotalSegmentator2D(base.ImageSegmentation):
-    """TotalSegmentator 2D segmentation dataset."""
-
-    _train_index_ranges: List[Tuple[int, int]] = [(0, 83)]
-    """Train range indices."""
-
-    _val_index_ranges: List[Tuple[int, int]] = [(83, 103)]
-    """Validation range indices."""
-
-    _n_slices_per_image: int = 20
-    """The amount of slices to sample per 3D CT scan image."""
-
-    _resources_full: List[structs.DownloadResource] = [
-        structs.DownloadResource(
-            filename="Totalsegmentator_dataset_v201.zip",
-            url="https://zenodo.org/records/10047292/files/Totalsegmentator_dataset_v201.zip",
-            md5="fe250e5718e0a3b5df4c4ea9d58a62fe",
-        ),
-    ]
-    """Resources for the full dataset version."""
-
-    _resources_small: List[structs.DownloadResource] = [
-        structs.DownloadResource(
-            filename="Totalsegmentator_dataset_small_v201.zip",
-            url="https://zenodo.org/records/10047263/files/Totalsegmentator_dataset_small_v201.zip",
-            md5="6b5524af4b15e6ba06ef2d700c0c73e0",
-        ),
-    ]
-    """Resources for the small dataset version."""
-
-    def __init__(
-        self,
-        root: str,
-        split: Literal["train", "val"] | None,
-        version: Literal["small", "full"] = "small",
-        download: bool = False,
-        image_transforms: Callable | None = None,
-        target_transforms: Callable | None = None,
-        image_target_transforms: Callable | None = None,
-    ) -> None:
-        """Initialize dataset.
-
-        Args:
-            root: Path to the root directory of the dataset. The dataset will
-                be downloaded and extracted here, if it does not already exist.
-            split: Dataset split to use. If `None`, the entire dataset is used.
-            version: The version of the dataset to initialize.
-            download: Whether to download the data for the specified split.
-                Note that the download will be executed only by additionally
-                calling the :meth:`prepare_data` method and if the data does not
-                exist yet on disk.
-            image_transforms: A function/transform that takes in an image
-                and returns a transformed version.
-            target_transforms: A function/transform that takes in the target
-                and transforms it.
-            image_target_transforms: A function/transforms that takes in an
-                image and a label and returns the transformed versions of both.
-                This transform happens after the `image_transforms` and
-                `target_transforms`.
-        """
-        super().__init__(
-            image_transforms=image_transforms,
-            target_transforms=target_transforms,
-            image_target_transforms=image_target_transforms,
-        )
-
-        self._root = root
-        self._split = split
-        self._version = version
-        self._download = download
-
-        self._samples_dirs: List[str] = []
-        self._indices: List[int] = []
-
-    @functools.cached_property
-    @override
-    def classes(self) -> List[str]:
-        def get_filename(path: str) -> str:
-            """Returns the filename from the full path."""
-            return os.path.basename(path).split(".")[0]
-
-        first_sample_labels = os.path.join(
-            self._root, self._samples_dirs[0], "segmentations", "*.nii.gz"
-        )
-        return sorted(map(get_filename, glob(first_sample_labels)))
-
-    @property
-    @override
-    def class_to_idx(self) -> Dict[str, int]:
-        return {label: index for index, label in enumerate(self.classes)}
-
-    @override
-    def filename(self, index: int) -> str:
-        sample_dir = self._samples_dirs[self._indices[index]]
-        return os.path.join(sample_dir, "ct.nii.gz")
-
-    @override
-    def prepare_data(self) -> None:
-        if self._download:
-            self._download_dataset()
-
-    @override
-    def configure(self) -> None:
-        self._samples_dirs = self._fetch_samples_dirs()
-        self._indices = self._create_indices()
-
-    @override
-    def validate(self) -> None:
-        _validators.check_dataset_integrity(
-            self,
-            length=1660 if self._split == "train" else 400,
-            n_classes=117,
-            first_and_last_labels=("adrenal_gland_left", "vertebrae_T9"),
-        )
-
-    @override
-    def __len__(self) -> int:
-        return len(self._indices) * self._n_slices_per_image
-
-    @override
-    def load_image(self, index: int) -> np.ndarray:
-        image_path = self._get_image_path(index)
-        slice_index = self._get_sample_slice_index(index)
-        image_array = io.read_nifti_slice(image_path, slice_index)
-        return image_array.repeat(3, axis=2)
-
-    @override
-    def load_mask(self, index: int) -> np.ndarray:
-        masks_dir = self._get_masks_dir(index)
-        slice_index = self._get_sample_slice_index(index)
-        mask_paths = (os.path.join(masks_dir, label + ".nii.gz") for label in self.classes)
-        masks = [io.read_nifti_slice(path, slice_index) for path in mask_paths]
-        return np.concatenate(masks, axis=-1)
-
-    def _get_masks_dir(self, index: int) -> str:
-        """Returns the directory of the corresponding masks."""
-        sample_dir = self._get_sample_dir(index)
-        return os.path.join(self._root, sample_dir, "segmentations")
-
-    def _get_image_path(self, index: int) -> str:
-        """Returns the corresponding image path."""
-        sample_dir = self._get_sample_dir(index)
-        return os.path.join(self._root, sample_dir, "ct.nii.gz")
-
-    def _get_sample_dir(self, index: int) -> str:
-        """Returns the corresponding sample directory."""
-        sample_index = self._indices[index // self._n_slices_per_image]
-        return self._samples_dirs[sample_index]
-
-    def _get_sample_slice_index(self, index: int) -> int:
-        """Returns the corresponding slice index."""
-        image_path = self._get_image_path(index)
-        total_slices = io.fetch_total_nifti_slices(image_path)
-        slice_indices = np.linspace(0, total_slices - 1, num=self._n_slices_per_image, dtype=int)
-        return slice_indices[index % self._n_slices_per_image]
-
-    def _fetch_samples_dirs(self) -> List[str]:
-        """Returns the name of all the samples of all the splits of the dataset."""
-        sample_filenames = [
-            filename
-            for filename in os.listdir(self._root)
-            if os.path.isdir(os.path.join(self._root, filename))
-        ]
-        return sorted(sample_filenames)
-
-    def _create_indices(self) -> List[int]:
-        """Builds the dataset indices for the specified split."""
-        split_index_ranges = {
-            "train": self._train_index_ranges,
-            "val": self._val_index_ranges,
-            None: [(0, 103)],
-        }
-        index_ranges = split_index_ranges.get(self._split)
-        if index_ranges is None:
-            raise ValueError("Invalid data split. Use 'train', 'val' or `None`.")
-
-        return _utils.ranges_to_indices(index_ranges)
-
-    def _download_dataset(self) -> None:
-        """Downloads the dataset."""
-        dataset_resources = {
-            "small": self._resources_small,
-            "full": self._resources_full,
-            None: (0, 103),
-        }
-        resources = dataset_resources.get(self._version)
-        if resources is None:
-            raise ValueError("Invalid data version. Use 'small' or 'full'.")
-
-        for resource in resources:
-            utils.download_and_extract_archive(
-                resource.url,
-                download_root=self._root,
-                filename=resource.filename,
-                remove_finished=True,
-            )

eva/vision/models/networks/postprocesses/__init__.py

@@ -1,5 +0,0 @@
-"""Model post-process transforms."""
-
-from eva.vision.models.networks.postprocesses.cls import ExtractCLSFeatures
-
-__all__ = ["ExtractCLSFeatures"]

eva/vision/models/networks/postprocesses/cls.py

@@ -1,25 +0,0 @@
-"""Transforms for extracting the CLS output from a model output."""
-
-import torch
-from transformers import modeling_outputs
-
-
-class ExtractCLSFeatures:
-    """Extracts the CLS token from a ViT model output."""
-
-    def __call__(
-        self, tensor: torch.Tensor | modeling_outputs.BaseModelOutputWithPooling
-    ) -> torch.Tensor:
-        """Call method for the transformation.
-
-        Args:
-            tensor: The tensor representing the model output.
-        """
-        if isinstance(tensor, torch.Tensor):
-            transformed_tensor = tensor[:, 0, :]
-        elif isinstance(tensor, modeling_outputs.BaseModelOutputWithPooling):
-            transformed_tensor = tensor.last_hidden_state[:, 0, :]
-        else:
-            raise ValueError(f"Unsupported type {type(tensor)}")
-
-        return transformed_tensor

kaiko_eva-0.0.1.dist-info/METADATA

@@ -1,405 +0,0 @@
-Metadata-Version: 2.1
-Name: kaiko-eva
-Version: 0.0.1
-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
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-Classifier: Programming Language :: Python :: 3
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-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="https://github.com/kaiko-ai/eva/blob/main/docs/images/eva-logo.png?raw=true" 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="https://github.com/kaiko-ai/eva#installation">Installation</a> •
-  <a href="https://github.com/kaiko-ai/eva#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="https://github.com/kaiko-ai/eva#benchmarks">Benchmarks</a> <br>
-  <a href="https://github.com/kaiko-ai/eva#contributing">Contribute</a> •
-  <a href="https://github.com/kaiko-ai/eva#acknowledgements">Acknowledgements</a>
-</p>
-
-</div>
-
-<br />
-
-_`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.
-
-### 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[all] @ 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 
-```
-
-When used as a CLI tool, `_eva_` supports configuration files (`.yaml`) as an argument to define its functionality.
-Native supported configs can be found at the [configs](https://github.com/kaiko-ai/eva/tree/main/configs) directory
-of the repo. Apart from cloning the repo, you can download the latest config folder as `.zip` from your browser from
-[here](https://download-directory.github.io/?url=https://github.com/kaiko-ai/eva/tree/main/configs). Alternatively,
-from a specific release the configs can be downloaded from the terminal as follows:
-```sh
-curl -LO https://github.com/kaiko-ai/eva/releases/download/0.0.1/configs.zip | unzip configs.zip
-```
-
-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
-# from a locally stored config file
-eva predict_fit --config ./configs/vision/dino_vit/offline/bach.yaml
-
-# from a remote stored config file
-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>              | 0.710 | 0.939 | 0.814 | 0.870    | 0.856     |
-| DINO<sub>(p=16)</sub> <sup>[2]</sup>             | 0.801 | 0.934 | 0.768 | 0.889    | 0.895     |
-| 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 Pathology Foundation Models: from TCGA to Hospital Scale”_
-
-## 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="https://github.com/kaiko-ai/eva/blob/main/docs/images/kaiko-logo.png?raw=true" width="200">
-</div>