├── .env.example ├── .github ├── CODEOWNERS └── workflows │ ├── manage-pr.yml │ └── pre-commit.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── config ├── da_default.yaml ├── data │ └── camus.yaml ├── default.yaml ├── exp │ ├── camus │ │ ├── lv-crisp-samples.yaml │ │ ├── test-camus-confidnet.yaml │ │ ├── test-camus-crisp.yaml │ │ ├── test-camus-entropy.yaml │ │ ├── test-camus-lce.yaml │ │ ├── test-camus-mc.yaml │ │ ├── test-camus-morph.yaml │ │ ├── train-camus-baseline.yaml │ │ ├── train-camus-confidnet.yaml │ │ ├── train-camus-crisp.yaml │ │ ├── train-camus-lce.yaml │ │ └── train-camus-mc.yaml │ ├── default.yaml │ ├── hmc-qu │ │ ├── hmcqu-crisp-samples.yaml │ │ ├── test-hmcqu-confidnet.yaml │ │ ├── test-hmcqu-crisp.yaml │ │ ├── test-hmcqu-entropy.yaml │ │ ├── test-hmcqu-lce.yaml │ │ ├── test-hmcqu-mc.yaml │ │ └── test-hmcqu-morph.yaml │ ├── lung │ │ ├── lung-crisp-samples.yaml │ │ ├── test-lung-confidnet.yaml │ │ ├── test-lung-crisp.yaml │ │ ├── test-lung-entropy.yaml │ │ ├── test-lung-lce.yaml │ │ ├── test-lung-mc.yaml │ │ ├── test-lung-morph.yaml │ │ ├── train-lung-baseline.yaml │ │ ├── train-lung-confidnet.yaml │ │ ├── train-lung-crisp.yaml │ │ ├── train-lung-lce.yaml │ │ └── train-lung-mc.yaml │ └── lung_default.yaml └── system │ ├── aleatoric.yaml │ ├── confidnet.yaml │ ├── crisp.yaml │ ├── crisp │ ├── eval.yaml │ └── train.yaml │ ├── evalensemble.yaml │ ├── learnconf.yaml │ ├── mcdropout.yaml │ ├── module │ ├── confidenet.yaml │ ├── confidunet.yaml │ ├── enet.yaml │ └── unet.yaml │ ├── morph.yaml │ ├── softmax.yaml │ ├── trainensemble.yaml │ └── uncertainty.yaml ├── crisp_uncertainty ├── __init__.py ├── evaluation │ ├── __init__.py │ ├── data_struct.py │ ├── datasetevaluator.py │ ├── evaluator.py │ ├── patientevaluator.py │ ├── segmentation │ │ ├── __init__.py │ │ └── metrics.py │ └── uncertainty │ │ ├── __init__.py │ │ ├── calibration.py │ │ ├── correlation.py │ │ ├── distribution.py │ │ ├── mutual_information.py │ │ ├── overlap.py │ │ ├── stats.py │ │ ├── successerrorhistogram.py │ │ └── vis.py ├── modules │ ├── __init__.py │ ├── enet.py │ └── unet.py ├── system │ ├── __init__.py │ ├── aleatoric.py │ ├── confidnet.py │ ├── crisp │ │ ├── __init__.py │ │ ├── crisp.py │ │ ├── eval.py │ │ └── train.py │ ├── ensemble.py │ ├── learnconf.py │ ├── mcdropout.py │ ├── morphology.py │ ├── softmax.py │ └── uncertainty.py └── utils │ ├── __init__.py │ ├── mcdropout.py │ ├── metrics.py │ ├── numpy.py │ └── reductions.py ├── generate_figures.py ├── generate_tables.py ├── miccai2022 ├── camus.sh ├── hmc-qu.sh ├── lung.sh └── lv.sh ├── pyproject.toml ├── requirements ├── dev.txt ├── environment.yml ├── requirements.txt └── test-requirements.txt ├── runner.py ├── setup.cfg ├── setup.py └── vital ├── .github ├── CODEOWNERS └── workflows │ ├── code-format.yml │ └── manage-pr.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── hydra_plugins ├── README.md ├── searchpath │ ├── __init__.py │ └── vital.py └── sweeper │ ├── __init__.py │ └── configsweeper.py ├── pyproject.toml ├── requirements ├── dev.txt └── requirements.txt ├── scripts ├── comet_grouped_plots.py ├── config │ └── table1.yaml └── resubmit_slurm_job.py ├── setup.cfg ├── setup.py └── vital ├── .env.example ├── __init__.py ├── config ├── __init__.py ├── callbacks │ ├── early_stopping.yaml │ └── model_checkpoint.yaml ├── data │ ├── acdc.yaml │ ├── camus.yaml │ ├── data.yaml │ ├── hmc_qu.yaml │ ├── lung.yaml │ ├── mnist.yaml │ └── transform │ │ ├── compose.yaml │ │ ├── normalize.yaml │ │ └── normalizesample.yaml ├── exp │ ├── acdc-unet.yaml │ ├── camus-enet.yaml │ └── mnist-mlp.yaml ├── experiment │ ├── acdc-unet.yaml │ └── mnist-mlp.yaml ├── logger │ ├── comet │ │ ├── offline.yaml │ │ └── online.yaml │ └── tensorboard.yaml ├── system │ ├── classification.yaml │ ├── module │ │ ├── enet.yaml │ │ ├── mlp.yaml │ │ ├── module.yaml │ │ └── unet.yaml │ ├── segmentation.yaml │ └── system.yaml ├── trainer │ └── default.yaml └── vital_default.yaml ├── config_example ├── default.yaml └── mnist-sweep.yaml ├── data ├── HMC_QU │ ├── __init__.py │ ├── config.py │ ├── data_module.py │ ├── dataset.py │ ├── dataset_generator.py │ └── hmc_qu.png ├── __init__.py ├── acdc │ ├── README.md │ ├── __init__.py │ ├── config.py │ ├── data_module.py │ ├── data_struct.py │ ├── dataset.py │ ├── dataset_generator.py │ └── utils │ │ ├── __init__.py │ │ └── register.py ├── camus │ ├── README.md │ ├── __init__.py │ ├── camus.png │ ├── config.py │ ├── data_module.py │ ├── data_struct.py │ ├── dataset.py │ ├── dataset_generator.py │ └── utils │ │ ├── __init__.py │ │ ├── measure.py │ │ └── register.py ├── config.py ├── data_module.py ├── lung_xray │ ├── __init__.py │ ├── config.py │ ├── data_module.py │ ├── dataset.py │ ├── dataset_generator.py │ ├── jstr.png │ ├── jstr_generator.py │ └── shenzen.png ├── mixins.py ├── mnist │ ├── __init__.py │ ├── data_module.py │ └── mnist.py └── transforms.py ├── metrics ├── __init__.py ├── camus │ ├── __init__.py │ ├── anatomical │ │ ├── __init__.py │ │ ├── atrium_metrics.py │ │ ├── config.py │ │ ├── epi_metrics.py │ │ ├── frontier_metrics.py │ │ ├── lv_metrics.py │ │ ├── myo_metrics.py │ │ ├── size_metrics.py │ │ └── utils.py │ └── clinical │ │ ├── __init__.py │ │ └── utils.py ├── evaluate │ ├── __init__.py │ ├── anatomical_structure.py │ ├── clinical │ │ ├── __init__.py │ │ └── heart_us.py │ └── segmentation.py └── train │ ├── __init__.py │ ├── functional.py │ └── metric.py ├── modules ├── __init__.py ├── classification │ ├── __init__.py │ └── mlp.py ├── generative │ ├── __init__.py │ ├── autoencoder.py │ ├── decoder.py │ └── encoder.py ├── layers.py └── segmentation │ ├── __init__.py │ ├── camus_unet.py │ ├── deeplabv3.py │ ├── enet.py │ ├── localization_net.py │ └── unet.py ├── runner.py ├── systems ├── __init__.py ├── classification.py ├── computation.py ├── segmentation.py └── system.py └── utils ├── __init__.py ├── config.py ├── decorators.py ├── format ├── __init__.py ├── native.py └── numpy.py ├── image ├── __init__.py ├── io.py ├── measure.py ├── process.py ├── register │ ├── __init__.py │ └── affine.py └── transform.py ├── itertools.py ├── jobs ├── __init__.py ├── job.py ├── local.py └── slurm.py ├── logging.py ├── parsing.py ├── sampling ├── __init__.py ├── rejection_sampling.py └── tests │ ├── __init__.py │ └── rejection_sampling_test.py ├── serialization.py └── vcs.py /.env.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ThierryJudge/CRISP-uncertainty/HEAD/.env.example -------------------------------------------------------------------------------- /.github/CODEOWNERS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ThierryJudge/CRISP-uncertainty/HEAD/.github/CODEOWNERS -------------------------------------------------------------------------------- /.github/workflows/manage-pr.yml: 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