├── GenerateMasks.py ├── compute_stats.py ├── config.py ├── convert_chkpt_tf2pytorch.py ├── convert_format.py ├── convert_json_xml.py ├── dataloader ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── augs.cpython-37.pyc │ ├── infer_loader.cpython-37.pyc │ └── train_loader.cpython-37.pyc ├── augs.py ├── infer_loader.py └── train_loader.py ├── dataset.py ├── environment.yml ├── extract_patches.py ├── infer ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── base.cpython-37.pyc │ ├── tile.cpython-37.pyc │ └── wsi.cpython-37.pyc ├── base.py ├── tile.py └── wsi.py ├── metrics ├── README.md ├── __init__.py └── stats_utils.py ├── misc ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── patch_extractor.cpython-37.pyc │ ├── utils.cpython-37.pyc │ ├── viz_utils.cpython-37.pyc │ └── wsi_handler.cpython-37.pyc ├── patch_extractor.py ├── utils.py ├── viz_utils.py ├── wsi_handler.py └── wsi_handler_valid.py ├── models ├── __init__.py ├── __pycache__ │ └── __init__.cpython-37.pyc └── hovernet │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── net_desc.cpython-37.pyc │ ├── net_utils.cpython-37.pyc │ ├── opt.cpython-37.pyc │ ├── post_proc.cpython-37.pyc │ ├── run_desc.cpython-37.pyc │ ├── targets.cpython-37.pyc │ └── utils.cpython-37.pyc │ ├── net_desc.py │ ├── net_utils.py │ ├── opt-bk.py │ ├── opt.py │ ├── post_proc.py │ ├── run_desc.py │ ├── targets.py │ └── utils.py ├── plot_heat_map.py ├── proc_kumar.py ├── readme.md ├── run_infer.py ├── run_tile.sh ├── run_train.py ├── run_utils ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── engine.cpython-37.pyc │ └── utils.cpython-37.pyc ├── callbacks │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── base.cpython-37.pyc │ │ ├── logging.cpython-37.pyc │ │ └── serialize.cpython-37.pyc │ ├── base.py │ ├── logging.py │ └── serialize.py ├── engine.py └── utils.py └── run_wsi.sh /GenerateMasks.py: 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