├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ ├── method_development.md │ └── old_templates │ │ └── bug_report.yaml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── workflow.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE.md ├── README.md ├── assets ├── anno_auto.png ├── anno_hand.png ├── anno_multiclass.png ├── graph_pred.png ├── graph_true.png ├── logo_trans.png ├── logo_white.png ├── napari_anno.png ├── napari_demo.mov ├── optimiser_dummy.png ├── triangles.png └── workflow_steps.png ├── environment-napari-free.yaml ├── environment-with-napari.yaml ├── examples ├── show_cbox.py ├── show_data.py └── show_starfile.py ├── grace ├── __init__.py ├── base.py ├── evaluation │ ├── README.md │ ├── __init__.py │ ├── inference.py │ ├── manifold.py │ ├── metrics_classifier.py │ ├── metrics_objects.py │ └── process.py ├── io │ ├── __init__.py │ ├── core.py │ ├── image_dataset.py │ ├── schema.py │ ├── starfile.py │ ├── store_edge_properties.py │ └── store_node_features.py ├── models │ ├── README.md │ ├── __init__.py │ ├── classifier.py │ ├── datasets.py │ ├── feature_extractor.py │ ├── graph_laplacian.py │ ├── optimiser.py │ └── property_cruncher.py ├── napari.yaml ├── napari │ ├── __init__.py │ ├── core.py │ ├── logo.png │ ├── utils.py │ └── widgets.py ├── run.py ├── simulator │ ├── README.md │ ├── __init__.py │ ├── simulate_dataset.py │ ├── simulate_graph.py │ └── simulate_image.py ├── styling.py ├── training │ ├── README.md │ ├── archiver.py │ ├── assess.py │ ├── config.py │ ├── config.yaml │ └── train.py ├── utils │ ├── __init__.py │ ├── augment_graph.py │ ├── augment_image.py │ └── transforms.py └── visualisation │ ├── __init__.py │ ├── animation.py │ ├── annotation.py │ ├── plotting.py │ ├── subgraph.py │ └── utils.py ├── notebooks ├── edge_properties.ipynb ├── infer_predictions.ipynb ├── measure_metrics.ipynb ├── opt.ipynb ├── read_grace.ipynb ├── run.ipynb └── train_and_infer.ipynb ├── pyproject.toml ├── requirements.txt ├── setup.cfg └── tests ├── conftest.py ├── test_augmentation.py ├── test_classifier.py ├── test_config.py ├── test_dataset.py ├── test_dummy.py ├── test_extractor.py ├── test_grace.py ├── test_optimiser.py ├── test_run.py ├── test_subgraphs.py └── test_train.py /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alan-turing-institute/grace/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alan-turing-institute/grace/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/method_development.md: 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