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

kaiko_eva-0.1.0.dist-info/RECORD

@@ -0,0 +1,205 @@
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+kaiko_eva-0.1.0.dist-info/RECORD,,

{kaiko_eva-0.0.1.dist-info → kaiko_eva-0.1.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: pdm-backend (2.1.8)
+Generator: pdm-backend (2.4.1)
 Root-Is-Purelib: true
 Tag: py3-none-any

{kaiko_eva-0.0.1.dist-info → kaiko_eva-0.1.0.dist-info}/entry_points.txt

@@ -2,3 +2,5 @@
 eva = eva.__main__:main
 kaiko-eva = eva.__main__:main
 
+[gui_scripts]
+

eva/core/callbacks/writers/embeddings.py

@@ -1,169 +0,0 @@
-"""Embeddings writer."""
-
-import csv
-import io
-import os
-from typing import Any, Dict, Sequence
-
-import lightning.pytorch as pl
-import torch
-from lightning.pytorch import callbacks
-from loguru import logger
-from torch import multiprocessing, nn
-from typing_extensions import override
-
-from eva.core.callbacks.writers.typings import QUEUE_ITEM
-from eva.core.models.modules.typings import INPUT_BATCH
-from eva.core.utils import multiprocessing as eva_multiprocessing
-
-
-class EmbeddingsWriter(callbacks.BasePredictionWriter):
-    """Callback for writing generated embeddings to disk."""
-
-    def __init__(
-        self,
-        output_dir: str,
-        backbone: nn.Module | None = None,
-        dataloader_idx_map: Dict[int, str] | None = None,
-        group_key: str | None = None,
-        overwrite: bool = True,
-    ) -> None:
-        """Initializes a new EmbeddingsWriter instance.
-
-        This callback writes the embedding files in a separate process to avoid blocking the
-        main process where the model forward pass is executed.
-
-        Args:
-            output_dir: The directory where the embeddings will be saved.
-            backbone: A model to be used as feature extractor. If `None`,
-                it will be expected that the input batch returns the features directly.
-            dataloader_idx_map: A dictionary mapping dataloader indices to their respective
-                names (e.g. train, val, test).
-            group_key: The metadata key to group the embeddings by. If specified, the
-                embedding files will be saved in subdirectories named after the group_key.
-                If specified, the key must be present in the metadata of the input batch.
-            overwrite: Whether to overwrite the output directory. Defaults to True.
-        """
-        super().__init__(write_interval="batch")
-
-        self._output_dir = output_dir
-        self._backbone = backbone
-        self._dataloader_idx_map = dataloader_idx_map or {}
-        self._group_key = group_key
-        self._overwrite = overwrite
-
-        self._write_queue: multiprocessing.Queue
-        self._write_process: eva_multiprocessing.Process
-
-    @override
-    def on_predict_start(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None:
-        os.makedirs(self._output_dir, exist_ok=self._overwrite)
-        self._initialize_write_process()
-        self._write_process.start()
-
-        if self._backbone is not None:
-            self._backbone = self._backbone.to(pl_module.device)
-            self._backbone.eval()
-
-    @override
-    def write_on_batch_end(
-        self,
-        trainer: pl.Trainer,
-        pl_module: pl.LightningModule,
-        prediction: Any,
-        batch_indices: Sequence[int],
-        batch: INPUT_BATCH,
-        batch_idx: int,
-        dataloader_idx: int,
-    ) -> None:
-        dataset = trainer.predict_dataloaders[dataloader_idx].dataset  # type: ignore
-        _, targets, metadata = INPUT_BATCH(*batch)
-        split = self._dataloader_idx_map.get(dataloader_idx)
-
-        embeddings = self._get_embeddings(prediction)
-        for local_idx, global_idx in enumerate(batch_indices[: len(embeddings)]):
-            input_name, save_name = self._construct_save_name(
-                dataset.filename(global_idx), metadata, local_idx
-            )
-            embeddings_buffer, target_buffer = io.BytesIO(), io.BytesIO()
-            torch.save(embeddings[local_idx].clone(), embeddings_buffer)
-            torch.save(targets[local_idx], target_buffer)  # type: ignore
-            item = QUEUE_ITEM(embeddings_buffer, target_buffer, input_name, save_name, split)
-            self._write_queue.put(item)
-
-        self._write_process.check_exceptions()
-
-    @override
-    def on_predict_end(self, trainer: pl.Trainer, pl_module: pl.LightningModule) -> None:
-        self._write_queue.put(None)
-        self._write_process.join()
-        logger.info(f"Predictions and manifest saved to {self._output_dir}")
-
-    def _initialize_write_process(self) -> None:
-        self._write_queue = multiprocessing.Queue()
-        self._write_process = eva_multiprocessing.Process(
-            target=_process_write_queue, args=(self._write_queue, self._output_dir, self._overwrite)
-        )
-
-    def _get_embeddings(self, prediction: torch.Tensor) -> torch.Tensor:
-        """Returns the embeddings from predictions."""
-        if self._backbone is None:
-            return prediction
-
-        with torch.no_grad():
-            return self._backbone(prediction)
-
-    def _construct_save_name(self, input_name, metadata, local_idx):
-        group_name = metadata[self._group_key][local_idx] if self._group_key else None
-        save_name = os.path.splitext(input_name)[0] + ".pt"
-        if group_name:
-            save_name = os.path.join(group_name, save_name)
-        return input_name, save_name
-
-
-def _process_write_queue(
-    write_queue: multiprocessing.Queue, output_dir: str, overwrite: bool = False
-) -> None:
-    manifest_file, manifest_writer = _init_manifest(output_dir, overwrite)
-    while True:
-        item = write_queue.get()
-        if item is None:
-            break
-
-        prediction_buffer, target_buffer, input_name, save_name, split = QUEUE_ITEM(*item)
-        _save_prediction(prediction_buffer, save_name, output_dir)
-        _update_manifest(target_buffer, input_name, save_name, split, manifest_writer)
-
-    manifest_file.close()
-
-
-def _save_prediction(prediction_buffer: io.BytesIO, save_name: str, output_dir: str) -> None:
-    save_path = os.path.join(output_dir, save_name)
-    prediction = torch.load(io.BytesIO(prediction_buffer.getbuffer()), map_location="cpu")
-    os.makedirs(os.path.dirname(save_path), exist_ok=True)
-    torch.save(prediction, save_path)
-
-
-def _init_manifest(output_dir: str, overwrite: bool = False) -> tuple[io.TextIOWrapper, Any]:
-    manifest_path = os.path.join(output_dir, "manifest.csv")
-    if os.path.exists(manifest_path) and not overwrite:
-        raise FileExistsError(
-            f"Manifest file already exists at {manifest_path}. This likely means that the "
-            "embeddings have been computed before. Consider using `eva fit` instead "
-            "of `eva predict_fit` or `eva predict`."
-        )
-    manifest_file = open(manifest_path, "w", newline="")
-    manifest_writer = csv.writer(manifest_file)
-    manifest_writer.writerow(["origin", "embeddings", "target", "split"])
-    return manifest_file, manifest_writer
-
-
-def _update_manifest(
-    target_buffer: io.BytesIO,
-    input_name: str,
-    save_name: str,
-    split: str | None,
-    manifest_writer,
-) -> None:
-    target = torch.load(io.BytesIO(target_buffer.getbuffer()), map_location="cpu")
-    manifest_writer.writerow([input_name, save_name, target.item(), split])

eva/core/callbacks/writers/typings.py

@@ -1,23 +0,0 @@
-"""Typing definitions for the writer callback functions."""
-
-import io
-from typing import NamedTuple
-
-
-class QUEUE_ITEM(NamedTuple):
-    """The default input batch data scheme."""
-
-    prediction_buffer: io.BytesIO
-    """IO buffer containing the prediction tensor"""
-
-    target_buffer: io.BytesIO
-    """IO buffer containing the target tensor"""
-
-    input_name: str
-    """Name of the original input file that was used to generate the embedding."""
-
-    save_name: str
-    """Name to store the generated embedding"""
-
-    split: str | None
-    """The dataset split the item belongs to (e.g. train, val, test)."""

eva/core/models/networks/transforms/__init__.py

@@ -1,5 +0,0 @@
-"""Model outputs transforms API."""
-
-from eva.core.models.networks.transforms.extract_cls_features import ExtractCLSFeatures
-
-__all__ = ["ExtractCLSFeatures"]

eva/core/models/networks/wrappers/__init__.py

@@ -1,8 +0,0 @@
-"""Model Wrappers API."""
-
-from eva.core.models.networks.wrappers.base import BaseModel
-from eva.core.models.networks.wrappers.from_function import ModelFromFunction
-from eva.core.models.networks.wrappers.huggingface import HuggingFaceModel
-from eva.core.models.networks.wrappers.onnx import ONNXModel
-
-__all__ = ["BaseModel", "ModelFromFunction", "HuggingFaceModel", "ONNXModel"]

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

@@ -1,213 +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.classification import base
-from eva.vision.utils import io
-
-
-class TotalSegmentatorClassification(base.ImageClassification):
-    """TotalSegmentator multi-label classification 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,
-    ) -> 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.
-        """
-        super().__init__(
-            image_transforms=image_transforms,
-            target_transforms=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()
-        _validators.check_dataset_exists(self._root, True)
-
-    @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_target(self, index: int) -> np.ndarray:
-        masks = self._load_masks(index)
-        targets = [1 in masks[..., mask_index] for mask_index in range(masks.shape[-1])]
-        return np.asarray(targets, dtype=np.int64)
-
-    def _load_masks(self, index: int) -> np.ndarray:
-        """Returns the `index`'th target mask sample."""
-        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,
-            )