├── LICENSE ├── README.md ├── figs ├── framework_v1.png ├── iterative_results.png ├── iterative_results_supp.png └── qualitative_results.png ├── requirements.txt ├── splits ├── README.md ├── colon │ └── split.pkl ├── kits │ └── split.pkl ├── lits │ └── split.pkl └── pancreas │ └── split.pkl └── src ├── config ├── __pycache__ │ ├── config_args.cpython-39.pyc │ └── config_setup.cpython-39.pyc ├── config_args.py └── config_setup.py ├── dataset ├── __pycache__ │ ├── __init__.cpython-39.pyc │ ├── base_dataset_distance_map.cpython-39.pyc │ ├── dataloader.cpython-39.pyc │ └── datasets_distance_map.cpython-39.pyc └── dataloader.py ├── implementation ├── colon │ └── readme.log ├── kits │ └── readme.log ├── lits │ └── readme.log └── pancreas │ └── readme.log ├── models ├── __pycache__ │ ├── build_sam3D.cpython-39.pyc │ ├── image_encoder.cpython-39.pyc │ ├── mask_decoder.cpython-39.pyc │ ├── prompt_encoder.cpython-39.pyc │ ├── sam3D.cpython-39.pyc │ ├── transformer.cpython-39.pyc │ └── unet.cpython-39.pyc ├── build_sam3D.py ├── image_encoder.py ├── mask_decoder.py ├── prompt_encoder.py ├── sam3D.py ├── transformer.py └── unet.py ├── processor ├── __pycache__ │ ├── tester.cpython-39.pyc │ ├── trainer.cpython-39.pyc │ ├── trainer_basic.cpython-39.pyc │ ├── trainer_new.cpython-39.pyc │ └── validater.cpython-39.pyc ├── tester.py ├── trainer.py ├── trainer_basic.py └── validater.py ├── test.py ├── train.py ├── utils ├── __pycache__ │ ├── boundary_selection.cpython-39.pyc │ ├── scribble.cpython-39.pyc │ └── util.cpython-39.pyc ├── boundary_selection.py ├── plot.py ├── scribble.py └── util.py └── voxynth ├── __init__.py ├── __pycache__ ├── __init__.cpython-39.pyc ├── augment.cpython-39.pyc ├── filter.cpython-39.pyc ├── noise.cpython-39.pyc ├── synth.cpython-39.pyc ├── transform.cpython-39.pyc └── utility.cpython-39.pyc ├── augment.py ├── filter.py ├── noise.py ├── synth.py ├── transform.py └── utility.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/README.md -------------------------------------------------------------------------------- /figs/framework_v1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/figs/framework_v1.png -------------------------------------------------------------------------------- /figs/iterative_results.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/figs/iterative_results.png -------------------------------------------------------------------------------- /figs/iterative_results_supp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/figs/iterative_results_supp.png -------------------------------------------------------------------------------- /figs/qualitative_results.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/figs/qualitative_results.png -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/requirements.txt -------------------------------------------------------------------------------- /splits/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/splits/README.md -------------------------------------------------------------------------------- /splits/colon/split.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/splits/colon/split.pkl -------------------------------------------------------------------------------- /splits/kits/split.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/splits/kits/split.pkl -------------------------------------------------------------------------------- /splits/lits/split.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/splits/lits/split.pkl -------------------------------------------------------------------------------- /splits/pancreas/split.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/splits/pancreas/split.pkl -------------------------------------------------------------------------------- /src/config/__pycache__/config_args.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/config/__pycache__/config_args.cpython-39.pyc -------------------------------------------------------------------------------- /src/config/__pycache__/config_setup.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/config/__pycache__/config_setup.cpython-39.pyc -------------------------------------------------------------------------------- /src/config/config_args.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/config/config_args.py -------------------------------------------------------------------------------- /src/config/config_setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/config/config_setup.py -------------------------------------------------------------------------------- /src/dataset/__pycache__/__init__.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/dataset/__pycache__/__init__.cpython-39.pyc -------------------------------------------------------------------------------- /src/dataset/__pycache__/base_dataset_distance_map.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/dataset/__pycache__/base_dataset_distance_map.cpython-39.pyc -------------------------------------------------------------------------------- /src/dataset/__pycache__/dataloader.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/dataset/__pycache__/dataloader.cpython-39.pyc -------------------------------------------------------------------------------- /src/dataset/__pycache__/datasets_distance_map.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/dataset/__pycache__/datasets_distance_map.cpython-39.pyc -------------------------------------------------------------------------------- /src/dataset/dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/dataset/dataloader.py -------------------------------------------------------------------------------- /src/implementation/colon/readme.log: -------------------------------------------------------------------------------- 1 | put pretrained prism in this directory 2 | -------------------------------------------------------------------------------- /src/implementation/kits/readme.log: -------------------------------------------------------------------------------- 1 | put pretrained prism in this directory 2 | -------------------------------------------------------------------------------- /src/implementation/lits/readme.log: -------------------------------------------------------------------------------- 1 | put pretrained prism in this directory 2 | -------------------------------------------------------------------------------- /src/implementation/pancreas/readme.log: -------------------------------------------------------------------------------- 1 | put pretrained prism in this directory 2 | -------------------------------------------------------------------------------- /src/models/__pycache__/build_sam3D.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/build_sam3D.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/__pycache__/image_encoder.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/image_encoder.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/__pycache__/mask_decoder.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/mask_decoder.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/__pycache__/prompt_encoder.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/prompt_encoder.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/__pycache__/sam3D.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/sam3D.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/__pycache__/transformer.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/transformer.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/__pycache__/unet.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/__pycache__/unet.cpython-39.pyc -------------------------------------------------------------------------------- /src/models/build_sam3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/build_sam3D.py -------------------------------------------------------------------------------- /src/models/image_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/image_encoder.py -------------------------------------------------------------------------------- /src/models/mask_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/mask_decoder.py -------------------------------------------------------------------------------- /src/models/prompt_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/prompt_encoder.py -------------------------------------------------------------------------------- /src/models/sam3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/sam3D.py -------------------------------------------------------------------------------- /src/models/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/transformer.py -------------------------------------------------------------------------------- /src/models/unet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/models/unet.py -------------------------------------------------------------------------------- /src/processor/__pycache__/tester.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/__pycache__/tester.cpython-39.pyc -------------------------------------------------------------------------------- /src/processor/__pycache__/trainer.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/__pycache__/trainer.cpython-39.pyc -------------------------------------------------------------------------------- /src/processor/__pycache__/trainer_basic.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/__pycache__/trainer_basic.cpython-39.pyc -------------------------------------------------------------------------------- /src/processor/__pycache__/trainer_new.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/__pycache__/trainer_new.cpython-39.pyc -------------------------------------------------------------------------------- /src/processor/__pycache__/validater.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/__pycache__/validater.cpython-39.pyc -------------------------------------------------------------------------------- /src/processor/tester.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/tester.py -------------------------------------------------------------------------------- /src/processor/trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/trainer.py -------------------------------------------------------------------------------- /src/processor/trainer_basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/trainer_basic.py -------------------------------------------------------------------------------- /src/processor/validater.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/processor/validater.py -------------------------------------------------------------------------------- /src/test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/test.py -------------------------------------------------------------------------------- /src/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/train.py -------------------------------------------------------------------------------- /src/utils/__pycache__/boundary_selection.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/__pycache__/boundary_selection.cpython-39.pyc -------------------------------------------------------------------------------- /src/utils/__pycache__/scribble.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/__pycache__/scribble.cpython-39.pyc -------------------------------------------------------------------------------- /src/utils/__pycache__/util.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/__pycache__/util.cpython-39.pyc -------------------------------------------------------------------------------- /src/utils/boundary_selection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/boundary_selection.py -------------------------------------------------------------------------------- /src/utils/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/plot.py -------------------------------------------------------------------------------- /src/utils/scribble.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/scribble.py -------------------------------------------------------------------------------- /src/utils/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/utils/util.py -------------------------------------------------------------------------------- /src/voxynth/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__init__.py -------------------------------------------------------------------------------- /src/voxynth/__pycache__/__init__.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/__init__.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/__pycache__/augment.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/augment.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/__pycache__/filter.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/filter.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/__pycache__/noise.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/noise.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/__pycache__/synth.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/synth.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/__pycache__/transform.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/transform.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/__pycache__/utility.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/__pycache__/utility.cpython-39.pyc -------------------------------------------------------------------------------- /src/voxynth/augment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/augment.py -------------------------------------------------------------------------------- /src/voxynth/filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/filter.py -------------------------------------------------------------------------------- /src/voxynth/noise.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/noise.py -------------------------------------------------------------------------------- /src/voxynth/synth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/synth.py -------------------------------------------------------------------------------- /src/voxynth/transform.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/transform.py -------------------------------------------------------------------------------- /src/voxynth/utility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedICL-VU/PRISM/HEAD/src/voxynth/utility.py --------------------------------------------------------------------------------