├── .dockerignore ├── .github └── workflows │ ├── pre-commit.yml │ └── unit-test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .pylintrc ├── LICENSE ├── MELBA_Symposium_2024.pdf ├── Makefile ├── README.md ├── docker ├── Dockerfile ├── Dockerfile.tpu ├── environment.yml ├── environment_mac_m1.yml ├── environment_tpu.yml └── requirements.txt ├── examples └── segmentation │ ├── BB_anon_348_1.png │ ├── BB_anon_348_1_mask.png │ ├── config.yaml │ ├── files │ └── ckpt │ │ └── checkpoint_1900 │ │ └── checkpoint │ └── inference.ipynb ├── images ├── diffusion_class_diagram.png ├── diffusion_training_strategy_diagram.png └── melba_graphic_abstract.png ├── imgx ├── __init__.py ├── conf │ ├── __init__.py │ ├── config.yaml │ ├── data │ │ ├── amos_ct.yaml │ │ ├── brats2021_mr.yaml │ │ ├── male_pelvic_mr.yaml │ │ └── muscle_us.yaml │ └── task │ │ ├── gaussian_diff_seg.yaml │ │ └── seg.yaml ├── config.py ├── data │ ├── __init__.py │ ├── augmentation │ │ ├── __init__.py │ │ ├── affine.py │ │ ├── affine_test.py │ │ ├── flip.py │ │ ├── flip_test.py │ │ ├── intensity.py │ │ ├── intensity_test.py │ │ ├── patch.py │ │ └── patch_test.py │ ├── iterator.py │ ├── iterator_test.py │ ├── util.py │ ├── util_test.py │ ├── warp.py │ └── warp_test.py ├── datasets │ ├── README.md │ ├── __init__.py │ ├── amos_ct │ │ ├── __init__.py │ │ └── amos_ct_dataset_builder.py │ ├── brats2021_mr │ │ ├── __init__.py │ │ └── brats2021_mr_dataset_builder.py │ ├── constant.py │ ├── dataset_info.py │ ├── male_pelvic_mr │ │ ├── __init__.py │ │ └── male_pelvic_mr_dataset_builder.py │ ├── muscle_us │ │ ├── __init__.py │ │ └── muscle_us_dataset_builder.py │ ├── preprocess.py │ ├── preprocess_test.py │ ├── save.py │ ├── tests │ │ ├── conftest.py │ │ ├── fixtures │ │ │ ├── BB_anon_1789_3_mask_pred.png │ │ │ ├── BB_anon_1789_3_mask_pred_postprocessed_0.5.png │ │ │ ├── BB_anon_1789_3_mask_pred_postprocessed_0.75.png │ │ │ ├── BB_anon_425_2_mask_pred.png │ │ │ ├── BB_anon_425_2_mask_pred_postprocessed.png │ │ │ ├── GM_anon_780_3_mask_pred.png │ │ │ └── GM_anon_780_3_mask_pred_postprocessed.png │ │ └── test_muscle_us.py │ ├── util.py │ └── util_test.py ├── device.py ├── diffusion │ ├── README.md │ ├── __init__.py │ ├── diffusion.py │ ├── gaussian │ │ ├── __init__.py │ │ ├── gaussian_diffusion.py │ │ ├── gaussian_diffusion_test.py │ │ ├── sampler.py │ │ ├── variance_schedule.py │ │ └── variance_schedule_test.py │ ├── time_sampler.py │ ├── time_sampler_test.py │ ├── util.py │ └── util_test.py ├── experiment.py ├── integration_test.py ├── loss │ ├── __init__.py │ ├── cross_entropy.py │ ├── cross_entropy_test.py │ ├── deformation.py │ ├── deformation_test.py │ ├── dice.py │ ├── dice_test.py │ ├── segmentation.py │ ├── segmentation_test.py │ └── similarity.py ├── metric │ ├── __init__.py │ ├── area.py │ ├── area_test.py │ ├── centroid.py │ ├── centroid_test.py │ ├── deformation.py │ ├── deformation_test.py │ ├── dice.py │ ├── dice_test.py │ ├── distribution.py │ ├── segmentation.py │ ├── segmentation_test.py │ ├── similarity.py │ ├── similarity_test.py │ ├── smoothing.py │ ├── smoothing_test.py │ ├── surface_distance.py │ ├── surface_distance_test.py │ └── util.py ├── model │ ├── __init__.py │ ├── attention │ │ ├── __init__.py │ │ ├── efficient_attention.py │ │ ├── efficient_attention_test.py │ │ ├── transformer.py │ │ └── transformer_test.py │ ├── basic.py │ ├── basic_test.py │ ├── conv.py │ ├── conv_test.py │ ├── slice.py │ ├── slice_test.py │ └── unet │ │ ├── __init__.py │ │ ├── bottom_encoder.py │ │ ├── bottom_encoder_test.py │ │ ├── downsample_encoder.py │ │ ├── unet.py │ │ ├── unet_test.py │ │ └── upsample_decoder.py ├── run_test.py ├── run_train.py ├── run_valid.py ├── task │ ├── __init__.py │ ├── diffusion_segmentation │ │ ├── __init__.py │ │ ├── diffusion.py │ │ ├── diffusion_step.py │ │ ├── experiment.py │ │ ├── gaussian_diffusion.py │ │ ├── gaussian_diffusion_test.py │ │ ├── recycling_step.py │ │ ├── save.py │ │ ├── self_conditioning_step.py │ │ └── train_state.py │ ├── segmentation │ │ ├── __init__.py │ │ ├── experiment.py │ │ └── save.py │ └── util.py └── train_state.py └── pyproject.toml /.dockerignore: -------------------------------------------------------------------------------- 1 | wandb/ 2 | outputs/ 3 | tensorflow_datasets/ 4 | *.zip 5 | -------------------------------------------------------------------------------- /.github/workflows/pre-commit.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mathpluscode/ImgX-DiffSeg/HEAD/.github/workflows/pre-commit.yml -------------------------------------------------------------------------------- /.github/workflows/unit-test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mathpluscode/ImgX-DiffSeg/HEAD/.github/workflows/unit-test.yml -------------------------------------------------------------------------------- /.gitignore: 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