├── .env.example ├── .github ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── code-quality-main.yaml │ ├── code-quality-pr.yaml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── Makefile ├── README.md ├── ascent ├── __init__.py ├── configs │ ├── __init__.py │ ├── callbacks │ │ ├── default.yaml │ │ ├── early_stopping.yaml │ │ ├── latest_checkpoint.yaml │ │ ├── learning_rate_monitor.yaml │ │ ├── model_checkpoint.yaml │ │ ├── model_summary.yaml │ │ ├── nnunet.yaml │ │ ├── none.yaml │ │ └── rich_progress_bar.yaml │ ├── datamodule │ │ ├── a3c_2d.yaml │ │ ├── a3c_3d.yaml │ │ ├── augmentation │ │ │ ├── aliasing │ │ │ │ └── rand_artificial_aliasing.yaml │ │ │ ├── dealias_2d.yaml │ │ │ ├── default_2d.yaml │ │ │ ├── default_3d.yaml │ │ │ ├── flip │ │ │ │ ├── rand_flip_x.yaml │ │ │ │ ├── rand_flip_y.yaml │ │ │ │ └── rand_flip_z.yaml │ │ │ ├── intensity │ │ │ │ ├── rand_adjust_contrast.yaml │ │ │ │ └── rand_scale_intensity.yaml │ │ │ ├── noise │ │ │ │ ├── rand_gaussian_noise.yaml │ │ │ │ └── rand_gaussian_smooth.yaml │ │ │ ├── rotation │ │ │ │ └── rand_rotate.yaml │ │ │ └── zoom │ │ │ │ └── rand_zoom.yaml │ │ ├── camus_challenge_2d.yaml │ │ ├── cardinal+ted_3d.yaml │ │ ├── cardinal_2d.yaml │ │ ├── cardinal_3d.yaml │ │ ├── dealias_2d.yaml │ │ ├── dealiasc_2d.yaml │ │ ├── dealiasm_2d.yaml │ │ ├── dealiasreg_2d.yaml │ │ ├── dealiasv_2d.yaml │ │ ├── loading │ │ │ ├── crop │ │ │ │ ├── rand_posneg_crop.yaml │ │ │ │ └── rand_spatial_crop.yaml │ │ │ ├── data_loading │ │ │ │ ├── loadimage.yaml │ │ │ │ ├── loadnpy.yaml │ │ │ │ └── unfolded_loadnpy.yaml │ │ │ ├── default_test.yaml │ │ │ ├── default_train.yaml │ │ │ ├── pad │ │ │ │ └── spatial_pad.yaml │ │ │ └── utility │ │ │ │ ├── channel_first.yaml │ │ │ │ └── maybe_squeeze.yaml │ │ ├── mnist.yaml │ │ ├── myosaiq+emidec_2d.yaml │ │ ├── myosaiq+emidec_3d.yaml │ │ ├── myosaiq_2d.yaml │ │ ├── myosaiq_3d.yaml │ │ ├── nnunet.yaml │ │ ├── nnunet_reg.yaml │ │ ├── ted256_3d.yaml │ │ ├── ted_3d.yaml │ │ └── unwrap_2d.yaml │ ├── debug │ │ ├── default.yaml │ │ ├── fdr.yaml │ │ ├── limit.yaml │ │ ├── overfit.yaml │ │ └── profiler.yaml │ ├── eval.yaml │ ├── experiment │ │ ├── a3c_2d.yaml │ │ ├── a3c_3d.yaml │ │ ├── camus_challenge_2d.yaml │ │ ├── cardinal+ted_3d.yaml │ │ ├── cardinal_2d.yaml │ │ ├── cardinal_3d.yaml │ │ ├── dealias_2d.yaml │ │ ├── dealiasc_2d.yaml │ │ ├── dealiasm_2d.yaml │ │ ├── dealiasreg_2d.yaml │ │ ├── example.yaml │ │ ├── myosaiq+emidec_2d.yaml │ │ ├── myosaiq+emidec_3d.yaml │ │ ├── myosaiq_2d.yaml │ │ ├── myosaiq_3d.yaml │ │ ├── pdnet_2d.yaml │ │ ├── pdnet_reg_2d.yaml │ │ ├── pdunet_2d.yaml │ │ ├── pdunet_reg_2d.yaml │ │ ├── ted256_3d.yaml │ │ ├── ted_3d.yaml │ │ └── unwrap_2d.yaml │ ├── extras │ │ └── default.yaml │ ├── hparams_search │ │ └── mnist_optuna.yaml │ ├── hydra │ │ ├── default.yaml │ │ ├── launcher │ │ │ ├── alliancecan.yaml │ │ │ ├── beluga.yaml │ │ │ ├── cedar.yaml │ │ │ └── narval.yaml │ │ └── nnunet.yaml │ ├── launcher │ │ ├── alliancecan.yaml │ │ ├── beluga.yaml │ │ ├── cedar.yaml │ │ └── narval.yaml │ ├── local │ │ └── .gitkeep │ ├── logger │ │ ├── comet.yaml │ │ ├── csv.yaml │ │ ├── many_loggers.yaml │ │ ├── mlflow.yaml │ │ ├── neptune.yaml │ │ ├── tensorboard.yaml │ │ └── wandb.yaml │ ├── model │ │ ├── a3c_2d.yaml │ │ ├── a3c_3d.yaml │ │ ├── camus_challenge_2d.yaml │ │ ├── cardinal+ted_3d.yaml │ │ ├── cardinal_2d.yaml │ │ ├── cardinal_3d.yaml │ │ ├── cardinal_convnext_3d.yaml │ │ ├── dealias_2d.yaml │ │ ├── dealiasc_2d.yaml │ │ ├── dealiasm_2d.yaml │ │ ├── dealiasreg_2d.yaml │ │ ├── loss │ │ │ ├── dice_ce.yaml │ │ │ ├── l1.yaml │ │ │ ├── mse.yaml │ │ │ └── smooth_l1.yaml │ │ ├── mnist.yaml │ │ ├── myosaiq+emidec_2d.yaml │ │ ├── myosaiq+emidec_3d.yaml │ │ ├── myosaiq_2d.yaml │ │ ├── myosaiq_3d.yaml │ │ ├── myosaiq_convnext_3d.yaml │ │ ├── net │ │ │ ├── convnext.yaml │ │ │ ├── decoder │ │ │ │ └── unet_decoder.yaml │ │ │ ├── encoder │ │ │ │ ├── convnext.yaml │ │ │ │ └── unet_encoder.yaml │ │ │ ├── oripdnet.yaml │ │ │ ├── pdnet.yaml │ │ │ ├── pdunet.yaml │ │ │ ├── spyrit_net.yaml │ │ │ └── unet.yaml │ │ ├── nnunet.yaml │ │ ├── optimizer │ │ │ ├── adam.yaml │ │ │ ├── adamw.yaml │ │ │ └── sgd.yaml │ │ ├── pdnet_2d.yaml │ │ ├── pdnet_reg_2d.yaml │ │ ├── pdunet_2d.yaml │ │ ├── pdunet_reg_2d.yaml │ │ ├── scheduler │ │ │ ├── coslr.yaml │ │ │ ├── none.yaml │ │ │ └── polylr.yaml │ │ ├── scheduler_config │ │ │ └── default.yaml │ │ ├── ted256_3d.yaml │ │ ├── ted_3d.yaml │ │ └── unwrap_2d.yaml │ ├── onnx.yaml │ ├── paths │ │ ├── custom.yaml │ │ └── default.yaml │ ├── planner │ │ ├── nnunet2d.yaml │ │ └── nnunet3d.yaml │ ├── predict.yaml │ ├── preprocess_and_plan.yaml │ ├── preprocessor │ │ ├── dealias_du.yaml │ │ ├── regression.yaml │ │ └── segmentation.yaml │ ├── torchscript.yaml │ ├── train.yaml │ └── trainer │ │ ├── cpu.yaml │ │ ├── ddp.yaml │ │ ├── ddp_sim.yaml │ │ ├── default.yaml │ │ ├── gpu.yaml │ │ ├── mps.yaml │ │ └── nnunet.yaml ├── convert_onnx.py ├── convert_torchscript.py ├── datamodules │ ├── __init__.py │ ├── mnist_datamodule.py │ ├── nnunet_datamodule.py │ └── nnunet_dealias_datamodule.py ├── dataset_conversion │ ├── __init__.py │ ├── a3c.py │ ├── acdc.py │ ├── camus.py │ ├── cardinal.py │ ├── dealias_deep_unfolding.py │ ├── dealias_segmentation.py │ ├── myosaiq.py │ ├── ted.py │ └── utils.py ├── eval.py ├── models │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ ├── decoders │ │ │ ├── __init__.py │ │ │ └── unet_decoder.py │ │ ├── encoders │ │ │ ├── __init__.py │ │ │ ├── convnext.py │ │ │ └── unet_encoder.py │ │ ├── pdnet.py │ │ ├── simple_dense_net.py │ │ ├── spyrit_net.py │ │ ├── spyrit_related │ │ │ ├── __init__.py │ │ │ └── unwrap.py │ │ ├── unet.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── blocks.py │ │ │ ├── drop.py │ │ │ ├── initialization.py │ │ │ ├── layers.py │ │ │ └── normalization.py │ ├── mnist_module.py │ ├── nnunet_dealias_module.py │ ├── nnunet_module.py │ └── nnunet_reg_module.py ├── predict.py ├── preprocess_and_plan.py ├── preprocessing │ ├── __init__.py │ ├── experiment_planner_2DUNet.py │ ├── experiment_planner_3DUNet.py │ ├── preprocessing.py │ └── utils.py ├── train.py └── utils │ ├── __init__.py │ ├── data_loading.py │ ├── dataset.py │ ├── decorators.py │ ├── dict_utils.py │ ├── file_and_folder_operations.py │ ├── format │ ├── __init__.py │ └── torch.py │ ├── inferers.py │ ├── instantiators.py │ ├── logging_utils.py │ ├── loss_functions │ ├── __init__.py │ ├── crossentropy.py │ └── dice_loss.py │ ├── pylogger.py │ ├── rich_utils.py │ ├── scheduler │ ├── __init__.py │ └── poly_lr.py │ ├── softmax.py │ ├── tensor_utils.py │ ├── transforms.py │ ├── utils.py │ └── visualization.py ├── data └── .gitkeep ├── documentations └── hydra_config │ └── overriding_datamodule.md ├── hydra_plugins ├── README.md └── ascent │ ├── __init__.py │ ├── resolvers.py │ └── searchpath.py ├── logs └── .gitkeep ├── notebooks ├── .gitkeep └── acdc.ipynb ├── pyproject.toml ├── scripts ├── __init__.py ├── results │ ├── __init__.py │ └── pdnet │ 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