MANIFEST.in
README.md
pyproject.toml
src/vesuvius/__init__.py
src/vesuvius/_version.py
src/vesuvius/vesuvius.py
src/vesuvius.egg-info/PKG-INFO
src/vesuvius.egg-info/SOURCES.txt
src/vesuvius.egg-info/dependency_links.txt
src/vesuvius.egg-info/entry_points.txt
src/vesuvius.egg-info/requires.txt
src/vesuvius.egg-info/top_level.txt
src/vesuvius/data/__init__.py
src/vesuvius/data/utils.py
src/vesuvius/data/vc_dataset.py
src/vesuvius/data/volume.py
src/vesuvius/data/paths/__init__.py
src/vesuvius/data/paths/fetcher.py
src/vesuvius/data/paths/local.py
src/vesuvius/data/paths/parser.py
src/vesuvius/examples/__init__.py
src/vesuvius/image_proc/__init__.py
src/vesuvius/image_proc/distance.py
src/vesuvius/image_proc/helpers.py
src/vesuvius/image_proc/resampling.py
src/vesuvius/image_proc/blur/__init__.py
src/vesuvius/image_proc/blur/gaussian.py
src/vesuvius/image_proc/features/__init__.py
src/vesuvius/image_proc/features/curvature.py
src/vesuvius/image_proc/features/ridges_vessels.py
src/vesuvius/image_proc/features/skeletonization.py
src/vesuvius/image_proc/geometry/__init__.py
src/vesuvius/image_proc/geometry/alpha_wrap.py
src/vesuvius/image_proc/geometry/structure_tensor.py
src/vesuvius/image_proc/geometry/diffusion/__init__.py
src/vesuvius/image_proc/geometry/diffusion/coherence_enhancing_diffusion.py
src/vesuvius/image_proc/intensity/__init__.py
src/vesuvius/image_proc/intensity/normalization.py
src/vesuvius/image_proc/mesh/__init__.py
src/vesuvius/image_proc/mesh/affine.py
src/vesuvius/image_proc/run/__init__.py
src/vesuvius/image_proc/run/add_or_remove_suffix.py
src/vesuvius/image_proc/run/add_segmentation_layer.py
src/vesuvius/image_proc/run/alpha_wrap_labels.py
src/vesuvius/image_proc/run/apply_affine.py
src/vesuvius/image_proc/run/apply_masks.py
src/vesuvius/image_proc/run/binarize_tifs.py
src/vesuvius/image_proc/run/build_mesh_manifest.py
src/vesuvius/image_proc/run/ced.py
src/vesuvius/image_proc/run/copy_matching_files.py
src/vesuvius/image_proc/run/edt_frangi_label.py
src/vesuvius/image_proc/run/eval_offline.py
src/vesuvius/image_proc/run/filter_branching_labels.py
src/vesuvius/image_proc/run/flatten_volume_from_surface_frames.py
src/vesuvius/image_proc/run/generate_mutex_graph.py
src/vesuvius/image_proc/run/move_ignore_only_patches.py
src/vesuvius/image_proc/run/prediction_grid.py
src/vesuvius/image_proc/run/remap_values.py
src/vesuvius/image_proc/run/resize_volumes.py
src/vesuvius/image_proc/run/scale_tif_volumes.py
src/vesuvius/image_proc/run/stack_composite_tifs.py
src/vesuvius/image_proc/run/uniform_rescale_tifs.py
src/vesuvius/image_proc/run/voxelize_objs.py
src/vesuvius/image_proc/run/workflow.py
src/vesuvius/image_proc/run/zarr_tasks.py
src/vesuvius/install/__init__.py
src/vesuvius/install/accept_terms.py
src/vesuvius/install/custom_install.py
src/vesuvius/install/configs/cubes.yaml
src/vesuvius/install/configs/scrolls.yaml
src/vesuvius/models/__init__.py
src/vesuvius/models/utils.py
src/vesuvius/models/augmentation/__init__.py
src/vesuvius/models/augmentation/dataloading/__init__.py
src/vesuvius/models/augmentation/helpers/__init__.py
src/vesuvius/models/augmentation/helpers/scalar_type.py
src/vesuvius/models/augmentation/transforms/__init__.py
src/vesuvius/models/augmentation/transforms/base/__init__.py
src/vesuvius/models/augmentation/transforms/base/basic_transform.py
src/vesuvius/models/augmentation/transforms/intensity/__init__.py
src/vesuvius/models/augmentation/transforms/intensity/brightness.py
src/vesuvius/models/augmentation/transforms/intensity/contrast.py
src/vesuvius/models/augmentation/transforms/intensity/gamma.py
src/vesuvius/models/augmentation/transforms/intensity/gaussian_noise.py
src/vesuvius/models/augmentation/transforms/intensity/illumination.py
src/vesuvius/models/augmentation/transforms/nnunet/__init__.py
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src/vesuvius/models/augmentation/transforms/noise/extranoisetransforms.py
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src/vesuvius/models/augmentation/transforms/spatial/__init__.py
src/vesuvius/models/augmentation/transforms/spatial/low_resolution.py
src/vesuvius/models/augmentation/transforms/spatial/mirroring.py
src/vesuvius/models/augmentation/transforms/spatial/spatial.py
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src/vesuvius/models/augmentation/transforms/utils/compose.py
src/vesuvius/models/augmentation/transforms/utils/cropping.py
src/vesuvius/models/augmentation/transforms/utils/deep_supervision_downsampling.py
src/vesuvius/models/augmentation/transforms/utils/morphological_closing.py
src/vesuvius/models/augmentation/transforms/utils/nnunet_masking.py
src/vesuvius/models/augmentation/transforms/utils/oneoftransform.py
src/vesuvius/models/augmentation/transforms/utils/pseudo2d.py
src/vesuvius/models/augmentation/transforms/utils/random.py
src/vesuvius/models/augmentation/transforms/utils/remove_label.py
src/vesuvius/models/augmentation/transforms/utils/seg_to_regions.py
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src/vesuvius/models/build/__init__.py
src/vesuvius/models/build/activations.py
src/vesuvius/models/build/build_network_from_config.py
src/vesuvius/models/build/decoder.py
src/vesuvius/models/build/encoder.py
src/vesuvius/models/build/primus_wrapper.py
src/vesuvius/models/build/resblocks.py
src/vesuvius/models/build/simple_conv_blocks.py
src/vesuvius/models/build/transformers/__init__.py
src/vesuvius/models/build/transformers/abstract_arch.py
src/vesuvius/models/build/transformers/eva.py
src/vesuvius/models/build/transformers/patch_encode_decode.py
src/vesuvius/models/build/transformers/primus.py
src/vesuvius/models/configuration/__init__.py
src/vesuvius/models/configuration/config_manager.py
src/vesuvius/models/configuration/config_utils.py
src/vesuvius/models/datasets/__init__.py
src/vesuvius/models/datasets/base_dataset.py
src/vesuvius/models/datasets/find_valid_patches.py
src/vesuvius/models/datasets/intensity_properties.py
src/vesuvius/models/datasets/intensity_sampling.py
src/vesuvius/models/datasets/mutex_affinity_dataset.py
src/vesuvius/models/datasets/orchestrator.py
src/vesuvius/models/datasets/save_valid_patches.py
src/vesuvius/models/datasets/adapters/__init__.py
src/vesuvius/models/datasets/adapters/base_io.py
src/vesuvius/models/datasets/adapters/image_io.py
src/vesuvius/models/datasets/adapters/napari_io.py
src/vesuvius/models/datasets/adapters/zarr_io.py
src/vesuvius/models/datasets/mesh/__init__.py
src/vesuvius/models/datasets/mesh/base.py
src/vesuvius/models/datasets/mesh/filesystem.py
src/vesuvius/models/datasets/mesh/handles.py
src/vesuvius/models/datasets/mesh/types.py
src/vesuvius/models/datasets/mesh/voxelize.py
src/vesuvius/models/datasets/slicers/__init__.py
src/vesuvius/models/datasets/slicers/chunk.py
src/vesuvius/models/datasets/slicers/plane.py
src/vesuvius/models/evaluation/__init__.py
src/vesuvius/models/evaluation/affinity_metrics.py
src/vesuvius/models/evaluation/base_metric.py
src/vesuvius/models/evaluation/connected_components.py
src/vesuvius/models/evaluation/critical_components.py
src/vesuvius/models/evaluation/hausdorff.py
src/vesuvius/models/evaluation/iou_dice.py
src/vesuvius/models/evaluation/mean_average_precision.py
src/vesuvius/models/evaluation/precision_recall_f1.py
src/vesuvius/models/evaluation/skeleton_branch_points.py
src/vesuvius/models/run/__init__.py
src/vesuvius/models/run/blending.py
src/vesuvius/models/run/finalize_outputs.py
src/vesuvius/models/run/inference.py
src/vesuvius/models/run/tta.py
src/vesuvius/models/run/vesuvius_pipeline.py
src/vesuvius/models/training/__init__.py
src/vesuvius/models/training/lr_schedulers.py
src/vesuvius/models/training/normalization.py
src/vesuvius/models/training/optimizers.py
src/vesuvius/models/training/save_checkpoint.py
src/vesuvius/models/training/train.py
src/vesuvius/models/training/wandb_logging.py
src/vesuvius/models/training/auxiliary_tasks/__init__.py
src/vesuvius/models/training/auxiliary_tasks/apply_aux_targets.py
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src/vesuvius/models/training/auxiliary_tasks/aux_inplane_direction.py
src/vesuvius/models/training/auxiliary_tasks/aux_nearest_component.py
src/vesuvius/models/training/auxiliary_tasks/aux_structure_tensor.py
src/vesuvius/models/training/auxiliary_tasks/aux_surface_normals.py
src/vesuvius/models/training/loss/__init__.py
src/vesuvius/models/training/loss/betti_losses.py
src/vesuvius/models/training/loss/ect_loss.py
src/vesuvius/models/training/loss/loss_helpers.py
src/vesuvius/models/training/loss/losses.py
src/vesuvius/models/training/loss/nnunet_losses.py
src/vesuvius/models/training/loss/robustcrossentropy.py
src/vesuvius/models/training/loss/skeleton_recall.py
src/vesuvius/models/training/loss/surface_frame.py
src/vesuvius/models/training/trainers/__init__.py
src/vesuvius/models/training/trainers/mutex_affinity_trainer.py
src/vesuvius/models/training/trainers/surface_frame_trainer.py
src/vesuvius/models/training/trainers/auxiliary/__init__.py
src/vesuvius/models/training/trainers/auxiliary/base_aux_trainer.py
src/vesuvius/models/training/trainers/auxiliary/distance_transform_trainer.py
src/vesuvius/models/training/trainers/auxiliary/inplane_direction_trainer.py
src/vesuvius/models/training/trainers/auxiliary/nearest_component_trainer.py
src/vesuvius/models/training/trainers/auxiliary/structure_tensor_trainer.py
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src/vesuvius/models/training/trainers/self_supervised/__init__.py
src/vesuvius/models/training/trainers/self_supervised/train_eva_mae.py
src/vesuvius/models/training/trainers/self_supervised/train_finetune_mae_unet.py
src/vesuvius/models/training/trainers/self_supervised/train_unet_mae.py
src/vesuvius/models/training/trainers/self_supervised/warmup_lr.py
src/vesuvius/models/training/trainers/semi_supervised/__init__.py
src/vesuvius/models/training/trainers/semi_supervised/ramps.py
src/vesuvius/models/training/trainers/semi_supervised/train_mean_teacher.py
src/vesuvius/models/training/trainers/semi_supervised/train_uncertainty_aware_mean_teacher.py
src/vesuvius/models/training/trainers/semi_supervised/two_stream_batch_sampler.py
src/vesuvius/models/utilities/__init__.py
src/vesuvius/models/utilities/cli_utils.py
src/vesuvius/models/utilities/compute_gradient_norm.py
src/vesuvius/models/utilities/data_format_utils.py
src/vesuvius/models/utilities/get_accelerator.py
src/vesuvius/models/utilities/load_checkpoint.py
src/vesuvius/models/utilities/s3_utils.py
src/vesuvius/models/utilities/utils.py
src/vesuvius/napari_trainer/__init__.py
src/vesuvius/napari_trainer/inference.py
src/vesuvius/napari_trainer/inference_widget.py
src/vesuvius/napari_trainer/main_window.py
src/vesuvius/rendering/__init__.py
src/vesuvius/rendering/finalize_mesh.py
src/vesuvius/rendering/large_mesh_to_surface.py
src/vesuvius/rendering/mesh_to_surface.py
src/vesuvius/rendering/slim_uv.py
src/vesuvius/rendering/rendering_utils/__init__.py
src/vesuvius/rendering/rendering_utils/interpolate_image_3d.py
src/vesuvius/structure_tensor/__init__.py
src/vesuvius/structure_tensor/_compile_utils.py
src/vesuvius/structure_tensor/compute_vf.py
src/vesuvius/structure_tensor/create_st.py
src/vesuvius/structure_tensor/create_vf.py
src/vesuvius/structure_tensor/run_create_st.py
src/vesuvius/structure_tensor/smooth_vf.py
src/vesuvius/structure_tensor/vf_format.py
src/vesuvius/structure_tensor/vf_io.py
src/vesuvius/utils/__init__.py
src/vesuvius/utils/build_betti.py
src/vesuvius/utils/catalog.py
src/vesuvius/utils/plotting.py
src/vesuvius/utils/type_conversion.py
src/vesuvius/utils/utils.py
src/vesuvius/utils/io/__init__.py
src/vesuvius/utils/io/patch_cache_utils.py
src/vesuvius/utils/io/zarr_utils.py
src/vesuvius/utils/models/__init__.py
src/vesuvius/utils/models/ddp_allgather.py
src/vesuvius/utils/models/helpers.py
src/vesuvius/utils/models/load_nnunet_model.py
tests/test_imports.py