kaiko-eva 0.0.2__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-0.0.2.dist-info → kaiko_eva-0.1.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: pdm-backend (2.3.0)
+Generator: pdm-backend (2.4.1)
 Root-Is-Purelib: true
 Tag: py3-none-any

{kaiko_eva-0.0.2.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/data/datasets/embeddings/__init__.py

@@ -1,13 +0,0 @@
-"""Datasets API."""
-
-from eva.core.data.datasets.embeddings.base import EmbeddingsDataset
-from eva.core.data.datasets.embeddings.classification import (
-    EmbeddingsClassificationDataset,
-    MultiEmbeddingsClassificationDataset,
-)
-
-__all__ = [
-    "EmbeddingsDataset",
-    "EmbeddingsClassificationDataset",
-    "MultiEmbeddingsClassificationDataset",
-]

eva/core/data/datasets/embeddings/classification/__init__.py

@@ -1,10 +0,0 @@
-"""Embedding cllassification datasets API."""
-
-from eva.core.data.datasets.embeddings.classification.embeddings import (
-    EmbeddingsClassificationDataset,
-)
-from eva.core.data.datasets.embeddings.classification.multi_embeddings import (
-    MultiEmbeddingsClassificationDataset,
-)
-
-__all__ = ["EmbeddingsClassificationDataset", "MultiEmbeddingsClassificationDataset"]

eva/core/data/datasets/embeddings/classification/embeddings.py

@@ -1,66 +0,0 @@
-"""Embeddings classification dataset."""
-
-import os
-from typing import Callable, Dict, Literal
-
-import numpy as np
-import torch
-from typing_extensions import override
-
-from eva.core.data.datasets.embeddings import base
-
-
-class EmbeddingsClassificationDataset(base.EmbeddingsDataset):
-    """Embeddings dataset class for classification tasks."""
-
-    def __init__(
-        self,
-        root: str,
-        manifest_file: str,
-        split: Literal["train", "val", "test"] | None = None,
-        column_mapping: Dict[str, str] = base.default_column_mapping,
-        embeddings_transforms: Callable | None = None,
-        target_transforms: Callable | None = None,
-    ) -> None:
-        """Initialize dataset.
-
-        Expects a manifest file listing the paths of .pt files that contain
-        tensor embeddings of shape [embedding_dim] or [1, embedding_dim].
-
-        Args:
-            root: Root directory of the dataset.
-            manifest_file: The path to the manifest file, which is relative to
-                the `root` argument.
-            split: The dataset split to use. The `split` column of the manifest
-                file will be splitted based on this value.
-            column_mapping: Defines the map between the variables and the manifest
-                columns. It will overwrite the `default_column_mapping` with
-                the provided values, so that `column_mapping` can contain only the
-                values which are altered or missing.
-            embeddings_transforms: A function/transform that transforms the embedding.
-            target_transforms: A function/transform that transforms the target.
-        """
-        super().__init__(
-            root=root,
-            manifest_file=manifest_file,
-            split=split,
-            column_mapping=column_mapping,
-            embeddings_transforms=embeddings_transforms,
-            target_transforms=target_transforms,
-        )
-
-    @override
-    def _load_embeddings(self, index: int) -> torch.Tensor:
-        filename = self.filename(index)
-        embeddings_path = os.path.join(self._root, filename)
-        tensor = torch.load(embeddings_path, map_location="cpu")
-        return tensor.squeeze(0)
-
-    @override
-    def _load_target(self, index: int) -> np.ndarray:
-        target = self._data.at[index, self._column_mapping["target"]]
-        return np.asarray(target, dtype=np.int64)
-
-    @override
-    def __len__(self) -> int:
-        return len(self._data)

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/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