kaiko-eva 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- eva/core/data/datasets/base.py +7 -2
- eva/core/models/modules/head.py +4 -2
- eva/core/models/modules/typings.py +2 -2
- eva/core/models/transforms/__init__.py +2 -1
- eva/core/models/transforms/as_discrete.py +57 -0
- eva/core/models/wrappers/_utils.py +121 -1
- eva/core/utils/suppress_logs.py +28 -0
- eva/vision/data/__init__.py +2 -2
- eva/vision/data/dataloaders/__init__.py +5 -0
- eva/vision/data/dataloaders/collate_fn/__init__.py +5 -0
- eva/vision/data/dataloaders/collate_fn/collection.py +22 -0
- eva/vision/data/datasets/__init__.py +2 -2
- eva/vision/data/datasets/classification/bach.py +3 -4
- eva/vision/data/datasets/classification/bracs.py +3 -4
- eva/vision/data/datasets/classification/breakhis.py +3 -4
- eva/vision/data/datasets/classification/camelyon16.py +4 -5
- eva/vision/data/datasets/classification/crc.py +3 -4
- eva/vision/data/datasets/classification/gleason_arvaniti.py +3 -4
- eva/vision/data/datasets/classification/mhist.py +3 -4
- eva/vision/data/datasets/classification/panda.py +4 -5
- eva/vision/data/datasets/classification/patch_camelyon.py +3 -4
- eva/vision/data/datasets/classification/unitopatho.py +3 -4
- eva/vision/data/datasets/classification/wsi.py +6 -5
- eva/vision/data/datasets/segmentation/__init__.py +2 -2
- eva/vision/data/datasets/segmentation/_utils.py +47 -0
- eva/vision/data/datasets/segmentation/bcss.py +7 -8
- eva/vision/data/datasets/segmentation/btcv.py +236 -0
- eva/vision/data/datasets/segmentation/consep.py +6 -7
- eva/vision/data/datasets/segmentation/lits.py +9 -8
- eva/vision/data/datasets/segmentation/lits_balanced.py +2 -1
- eva/vision/data/datasets/segmentation/monusac.py +4 -5
- eva/vision/data/datasets/segmentation/total_segmentator_2d.py +12 -10
- eva/vision/data/datasets/vision.py +95 -4
- eva/vision/data/datasets/wsi.py +5 -5
- eva/vision/data/transforms/__init__.py +22 -3
- eva/vision/data/transforms/common/__init__.py +1 -2
- eva/vision/data/transforms/croppad/__init__.py +11 -0
- eva/vision/data/transforms/croppad/crop_foreground.py +110 -0
- eva/vision/data/transforms/croppad/rand_crop_by_pos_neg_label.py +109 -0
- eva/vision/data/transforms/croppad/spatial_pad.py +67 -0
- eva/vision/data/transforms/intensity/__init__.py +11 -0
- eva/vision/data/transforms/intensity/rand_scale_intensity.py +59 -0
- eva/vision/data/transforms/intensity/rand_shift_intensity.py +55 -0
- eva/vision/data/transforms/intensity/scale_intensity_ranged.py +56 -0
- eva/vision/data/transforms/spatial/__init__.py +7 -0
- eva/vision/data/transforms/spatial/flip.py +72 -0
- eva/vision/data/transforms/spatial/rotate.py +53 -0
- eva/vision/data/transforms/spatial/spacing.py +69 -0
- eva/vision/data/transforms/utility/__init__.py +5 -0
- eva/vision/data/transforms/utility/ensure_channel_first.py +51 -0
- eva/vision/data/tv_tensors/__init__.py +5 -0
- eva/vision/data/tv_tensors/volume.py +61 -0
- eva/vision/metrics/segmentation/monai_dice.py +9 -2
- eva/vision/models/modules/semantic_segmentation.py +28 -20
- eva/vision/models/networks/backbones/__init__.py +9 -2
- eva/vision/models/networks/backbones/pathology/__init__.py +11 -2
- eva/vision/models/networks/backbones/pathology/bioptimus.py +47 -1
- eva/vision/models/networks/backbones/pathology/hkust.py +69 -0
- eva/vision/models/networks/backbones/pathology/kaiko.py +18 -0
- eva/vision/models/networks/backbones/radiology/__init__.py +11 -0
- eva/vision/models/networks/backbones/radiology/swin_unetr.py +231 -0
- eva/vision/models/networks/backbones/radiology/voco.py +75 -0
- eva/vision/models/networks/decoders/segmentation/__init__.py +6 -2
- eva/vision/models/networks/decoders/segmentation/linear.py +5 -10
- eva/vision/models/networks/decoders/segmentation/semantic/__init__.py +8 -1
- eva/vision/models/networks/decoders/segmentation/semantic/swin_unetr.py +104 -0
- eva/vision/utils/io/__init__.py +2 -0
- eva/vision/utils/io/nifti.py +91 -11
- {kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.1.dist-info}/METADATA +3 -1
- {kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.1.dist-info}/RECORD +73 -57
- {kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.1.dist-info}/WHEEL +1 -1
- eva/vision/data/datasets/classification/base.py +0 -96
- eva/vision/data/datasets/segmentation/base.py +0 -96
- eva/vision/data/transforms/common/resize_and_clamp.py +0 -51
- eva/vision/data/transforms/normalization/__init__.py +0 -6
- eva/vision/data/transforms/normalization/clamp.py +0 -43
- eva/vision/data/transforms/normalization/functional/__init__.py +0 -5
- eva/vision/data/transforms/normalization/functional/rescale_intensity.py +0 -28
- eva/vision/data/transforms/normalization/rescale_intensity.py +0 -53
- eva/vision/metrics/segmentation/BUILD +0 -1
- eva/vision/models/networks/backbones/torchhub/__init__.py +0 -5
- eva/vision/models/networks/backbones/torchhub/backbones.py +0 -61
- {kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.1.dist-info}/entry_points.txt +0 -0
- {kaiko_eva-0.2.0.dist-info → kaiko_eva-0.2.1.dist-info}/licenses/LICENSE +0 -0
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"""torch.hub backbones."""
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import functools
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from typing import Tuple
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import torch
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from loguru import logger
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from torch import nn
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from eva.core.models import wrappers
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from eva.vision.models.networks.backbones.registry import BackboneModelRegistry
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HUB_REPOS = ["facebookresearch/dinov2:main", "kaiko-ai/towards_large_pathology_fms"]
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"""List of torch.hub repositories for which to add the models to the registry."""
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def torch_hub_model(
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model_name: str,
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repo_or_dir: str,
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checkpoint_path: str | None = None,
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pretrained: bool = False,
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out_indices: int | Tuple[int, ...] | None = None,
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**kwargs,
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) -> nn.Module:
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"""Initializes any ViT model from torch.hub with weights from a specified checkpoint.
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Args:
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model_name: The name of the model to load.
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repo_or_dir: The torch.hub repository or local directory to load the model from.
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checkpoint_path: The path to the checkpoint file.
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pretrained: If set to `True`, load pretrained model weights if available.
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out_indices: Whether and which multi-level patch embeddings to return.
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**kwargs: Additional arguments to pass to the model
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Returns:
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The VIT model instance.
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"""
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logger.info(
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f"Loading torch.hub model {model_name} from {repo_or_dir}"
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+ (f"using checkpoint {checkpoint_path}" if checkpoint_path else "")
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)
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return wrappers.TorchHubModel(
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model_name=model_name,
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repo_or_dir=repo_or_dir,
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pretrained=pretrained,
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checkpoint_path=checkpoint_path or "",
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out_indices=out_indices,
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model_kwargs=kwargs,
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)
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BackboneModelRegistry._registry.update(
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{
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f"torchhub/{repo}:{model_name}": functools.partial(
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torch_hub_model, model_name=model_name, repo_or_dir=repo
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)
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for repo in HUB_REPOS
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for model_name in torch.hub.list(repo, verbose=False)
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}
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)
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