├── .dockerignore ├── .gitignore ├── EXPERIMENT_LOG.md ├── Makefile ├── README.md ├── WRITEUP.md ├── cryoet ├── __init__.py ├── data │ ├── __init__.py │ ├── augmentations │ │ ├── __init__.py │ │ ├── copy_paste_merge.py │ │ └── functional.py │ ├── cross_validation.py │ ├── detection │ │ ├── __init__.py │ │ ├── data_module.py │ │ ├── detection_dataset.py │ │ ├── instance_crop_dataset.py │ │ ├── mixin.py │ │ ├── random_crop_dataset.py │ │ └── sliding_window_dataset.py │ ├── functional.py │ ├── heatmap │ │ ├── __init__.py │ │ ├── point_detection_crop_around_dataset.py │ │ ├── point_detection_data_module.py │ │ ├── point_detection_dataset.py │ │ ├── point_detection_random_crop_dataset.py │ │ └── point_detection_sliding_window_dataset.py │ └── parsers.py ├── ensembling.py ├── ensembling_eval.py ├── inference │ ├── dataset.py │ └── predict_volume.py ├── metric.py ├── modelling │ ├── __init__.py │ ├── ch_models │ │ ├── adaptors.py │ │ ├── mdl_ch_20d_ce2.py │ │ └── mdl_ch_20d_ce2c2.py │ ├── detection │ │ ├── __init__.py │ │ ├── convnext.py │ │ ├── detection_head.py │ │ ├── dynunet.py │ │ ├── functional.py │ │ ├── global_response_norm.py │ │ ├── layer_norm_3d.py │ │ ├── litehrnet.py │ │ ├── maxvit_unet25d.py │ │ ├── segresnet_object_detection_s1.py │ │ ├── segresnet_object_detection_v2.py │ │ ├── task_aligned_assigner.py │ │ ├── unet3d_detection.py │ │ └── unetr.py │ ├── point_detection_head.py │ └── segresnet_point_detection.py ├── schedulers │ ├── __init__.py │ └── cosine_with_warmup.py └── training │ ├── __init__.py │ ├── args.py │ ├── ema.py │ ├── ensemble_object_detection_module.py │ ├── ensemble_object_detection_module_v2.py │ ├── object_detection_module.py │ ├── od_accumulator.py │ ├── point_detection_module.py │ └── visualization.py ├── evaluate_ensemble.py ├── export_ensemble_onnx.py ├── playground ├── copy_paste.ipynb ├── iou_inspect.ipynb ├── random_erase.ipynb └── viz_tiling.py ├── pyproject.toml ├── requirements.txt ├── scripts ├── kaggle_convert_onnx_to_tensorrt.py ├── kaggle_inference_with_iobinding.py └── kaggle_inference_without_iobinding.py ├── summarize_checkpoints.py ├── tests ├── test_augmentations.py ├── test_data.py ├── test_loading_new_models.py ├── test_model.py ├── test_od.py ├── test_point_detection.py └── test_tiling.py ├── trace_model.py ├── train.sh └── train_od.py /.dockerignore: -------------------------------------------------------------------------------- 1 | data/ 2 | .idea/ -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BloodAxe/Kaggle-2024-CryoET/HEAD/.gitignore -------------------------------------------------------------------------------- /EXPERIMENT_LOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BloodAxe/Kaggle-2024-CryoET/HEAD/EXPERIMENT_LOG.md 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