Index

A

adjoint_data_step_size() (LION.reconstructors.diffusion.data_consistency.AdjointDataConsistency method) adjoint_project() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method)

AdjointDataConsistency (class in LION.reconstructors.diffusion.data_consistency) AnnealedLangevin (class in LION.reconstructors.diffusion.langevin) apply_adjoint_correction() (LION.reconstructors.diffusion.data_consistency.AdjointDataConsistency method)

B

build_position_grid() (in module LION.losses.PaDIS)

C

check_complete() (LION.optimizers.LIONsolver.LIONsolver method) check_training_ready() (LION.optimizers.LIONsolver.LIONsolver method) cite() (in module LION.classical_algorithms.fdk) (in module LION.classical_algorithms.tv_min) (LION.reconstructors.diffusion.padis.citations.PaDISCitations static method) (LION.reconstructors.PnP.PnP static method)

clean_checkpoints() (LION.optimizers.LIONsolver.LIONsolver method) clinicalCTRecon (class in LION.experiments.ct_experiments) compute_clean_sinogram() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method)

D

data_consistency_normalizer() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method) default_geo() (LION.CTtools.ct_geometry.Geometry method) default_parameters() (LION.CTtools.ct_geometry.Geometry static method) (LION.data_loaders.LIDC_IDRI.LIDC_IDRI static method) (LION.models.diffusion.NCSNpp.NCSNpp static method) (LION.optimizers.PaDISSolver.PaDISSolver static method) (LION.reconstructors.diffusion.padis.parameters.PaDISParameters static method)

denoise_fixed_overlap_patches() (LION.reconstructors.diffusion.padis.prior.PaDISPrior method) denoise_patches() (LION.reconstructors.diffusion.padis.prior.PaDISPrior method) denoise_prior() (LION.reconstructors.diffusion.padis.prior.PaDISPrior method) denoise_whole_image() (LION.reconstructors.diffusion.padis.prior.PaDISPrior method) dps_data_gradient() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method) dps_langevin() (LION.reconstructors.diffusion.dps_langevin.DPSLangevin method) DPSLangevin (class in LION.reconstructors.diffusion.dps_langevin)

E

edm_denoise_batch() (LION.reconstructors.diffusion.PaDIS.PaDIS method) epoch_step() (LION.optimizers.LIONsolver.LIONsolver method)

Experiment (class in LION.experiments.ct_experiments) ExtremeLowDoseCTRecon (class in LION.experiments.ct_experiments)

F

fdk() (in module LION.classical_algorithms.fdk) fixed_overlap_patch_layout() (LION.reconstructors.diffusion.padis.prior.PaDISPrior method) forward() (LION.losses.PaDIS.PaDISDenoisingLoss method) (LION.models.diffusion.NCSNpp.NCSNpp method) forward_backward_splitting() (LION.reconstructors.PnP.PnP method)

forward_project() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method) forward_projection() (in module LION.CTtools.ct_utils) from_HU_to_material_id() (in module LION.CTtools.ct_utils) from_HU_to_mu() (in module LION.CTtools.ct_utils) from_HU_to_normal() (in module LION.CTtools.ct_utils) from_normal_to_HU() (in module LION.CTtools.ct_utils)

G

generate_naive_patch_sample() (LION.reconstructors.diffusion.padis.generation.PaDISGeneration method) generate_naive_patch_samples() (LION.reconstructors.diffusion.PaDIS.PaDIS method) generate_sample() (LION.reconstructors.diffusion.padis.generation.PaDISGeneration method) generate_samples() (LION.reconstructors.diffusion.PaDIS.PaDIS method) Geometry (class in LION.CTtools.ct_geometry) get_dataset_parameters() (LION.experiments.ct_experiments.Experiment static method) get_mask_tensor() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method)

get_model() (LION.optimizers.LIONsolver.LIONsolver method) get_patient_id_to_first_index_dict() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method) get_reconstruction_tensor() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method) get_slice_index_to_patient_id_list() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method) get_slices_to_load() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method) get_testing_dataset() (LION.experiments.ct_experiments.Experiment method) get_training_dataset() (LION.experiments.ct_experiments.Experiment method) get_validation_dataset() (LION.experiments.ct_experiments.Experiment method)

H

hqs_algorithm() (LION.reconstructors.PnP.PnP method)

I

init_from_parameter() (LION.CTtools.ct_geometry.Geometry class method)

initial_padded_state() (LION.reconstructors.diffusion.PaDIS.PaDIS method) initial_reconstruction() (LION.reconstructors.diffusion.PaDIS.PaDIS method)

L

langevin() (LION.reconstructors.diffusion.langevin.AnnealedLangevin method) LIDC_IDRI (class in LION.data_loaders.LIDC_IDRI) LimitedAngleCTRecon (class in LION.experiments.ct_experiments) LimitedAngleExtremeLowDoseCTRecon (class in LION.experiments.ct_experiments) LimitedAngleLowDoseCTRecon (class in LION.experiments.ct_experiments) LION.classical_algorithms.fdk module LION.classical_algorithms.spgl1_torch module LION.classical_algorithms.tv_min module LION.CTtools.ct_geometry module LION.CTtools.ct_utils module LION.data_loaders.LIDC_IDRI module LION.experiments.ct_experiments module LION.losses.PaDIS module LION.models.diffusion.NCSNpp module LION.models.LIONmodel module LION.optimizers.LIONsolver module LION.optimizers.PaDISSolver module LION.reconstructors.diffusion.data_consistency module LION.reconstructors.diffusion.dps_langevin module

LION.reconstructors.diffusion.langevin module LION.reconstructors.diffusion.PaDIS module LION.reconstructors.diffusion.padis.citations module LION.reconstructors.diffusion.padis.generation module LION.reconstructors.diffusion.padis.parameters module LION.reconstructors.diffusion.padis.physics module LION.reconstructors.diffusion.padis.prior module LION.reconstructors.diffusion.padis.sampling module LION.reconstructors.diffusion.predictor_corrector module LION.reconstructors.LIONreconstructor module LION.reconstructors.PnP module LION.utils.paths module lion_physics_ct_parameters() (LION.reconstructors.diffusion.padis.parameters.PaDISParameters static method) lion_quality_ct_parameters() (LION.reconstructors.diffusion.padis.parameters.PaDISParameters static method) LIONmodel (class in LION.models.LIONmodel) LIONReconstructor (class in LION.reconstructors.LIONreconstructor) LIONsolver (class in LION.optimizers.LIONsolver) load() (LION.models.LIONmodel.LIONmodel class method) load_checkpoint() (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method) LowDoseCTRecon (class in LION.experiments.ct_experiments)

M

make_fdk_filter() (in module LION.classical_algorithms.fdk) make_operator() (in module LION.CTtools.ct_utils) measurement_gradient() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method) mini_batch_step() (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method) ModelInputType (class in LION.models.LIONmodel) module LION.classical_algorithms.fdk LION.classical_algorithms.spgl1_torch LION.classical_algorithms.tv_min LION.CTtools.ct_geometry LION.CTtools.ct_utils LION.data_loaders.LIDC_IDRI LION.experiments.ct_experiments LION.losses.PaDIS LION.models.diffusion.NCSNpp LION.models.LIONmodel LION.optimizers.LIONsolver LION.optimizers.PaDISSolver LION.reconstructors.diffusion.data_consistency LION.reconstructors.diffusion.dps_langevin LION.reconstructors.diffusion.langevin LION.reconstructors.diffusion.PaDIS LION.reconstructors.diffusion.padis.citations LION.reconstructors.diffusion.padis.generation LION.reconstructors.diffusion.padis.parameters LION.reconstructors.diffusion.padis.physics LION.reconstructors.diffusion.padis.prior LION.reconstructors.diffusion.padis.sampling LION.reconstructors.diffusion.predictor_corrector LION.reconstructors.LIONreconstructor LION.reconstructors.PnP LION.utils.paths

N

NCSNpp (class in LION.models.diffusion.NCSNpp)

noise_schedule() (LION.reconstructors.diffusion.PaDIS.PaDIS method) normalise_data_gradient() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method)

O

operator_norm() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method)

P

PaDIS (class in LION.reconstructors.diffusion.PaDIS) padis_fan_beam_parameters() (LION.CTtools.ct_geometry.Geometry static method) padis_repo_ct_parameters() (LION.reconstructors.diffusion.padis.parameters.PaDISParameters static method) PaDISCitations (class in LION.reconstructors.diffusion.padis.citations) PaDISDenoisingLoss (class in LION.losses.PaDIS) PaDISFanBeam120LimitedCTRecon (class in LION.experiments.ct_experiments) PaDISFanBeam180CTRecon (class in LION.experiments.ct_experiments) PaDISFanBeam20CTRecon (class in LION.experiments.ct_experiments) PaDISFanBeam60CTRecon (class in LION.experiments.ct_experiments) PaDISFanBeam8CTRecon (class in LION.experiments.ct_experiments) PaDISGeneration (class in LION.reconstructors.diffusion.padis.generation) PaDISParameters (class in LION.reconstructors.diffusion.padis.parameters) PaDISPhysics (class in LION.reconstructors.diffusion.padis.physics) PaDISPrior (class in LION.reconstructors.diffusion.padis.prior)

PaDISSampling (class in LION.reconstructors.diffusion.padis.sampling) PaDISSolver (class in LION.optimizers.PaDISSolver) paper_ct_parameters() (LION.reconstructors.diffusion.padis.parameters.PaDISParameters static method) parallel_default_parameters() (LION.CTtools.ct_geometry.Geometry static method) parallel_sparse_angle_parameters() (LION.CTtools.ct_geometry.Geometry method) parallel_sparse_view_parameters() (LION.CTtools.ct_geometry.Geometry static method) patch_layout() (LION.reconstructors.diffusion.padis.prior.PaDISPrior method) PatchLayout (class in LION.reconstructors.diffusion.padis.prior) pc_corrector_step_size() (LION.reconstructors.diffusion.predictor_corrector.PredictorCorrector static method) PnP (class in LION.reconstructors.PnP) predictor_corrector() (LION.reconstructors.diffusion.predictor_corrector.PredictorCorrector method) PredictorCorrector (class in LION.reconstructors.diffusion.predictor_corrector) prune_periodic_checkpoints() (LION.optimizers.PaDISSolver.PaDISSolver method) pseudoinverse_reconstruction() (LION.reconstructors.diffusion.PaDIS.PaDIS method)

R

reconstruct() (LION.reconstructors.LIONreconstructor.LIONReconstructor method)

reconstruct_sample() (LION.reconstructors.diffusion.PaDIS.PaDIS method) (LION.reconstructors.PnP.PnP method)

S

sample_image_patch() (in module LION.losses.PaDIS) sample_image_patch_with_position_channels() (in module LION.losses.PaDIS) sample_patch_pair() (in module LION.losses.PaDIS) sample_patch_size() (in module LION.losses.PaDIS) sample_sigma() (LION.losses.PaDIS.PaDISDenoisingLoss method) save() (LION.models.LIONmodel.LIONmodel method) save_checkpoint() (LION.models.LIONmodel.LIONmodel method) (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method) save_final_results() (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method) save_validation() (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method) scheduled_adjoint_data_consistency_scale() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method) scheduled_data_consistency_scale() (LION.reconstructors.diffusion.padis.physics.PaDISPhysics method) score_from_denoiser() (in module LION.losses.PaDIS) (in module LION.models.diffusion.NCSNpp)

set_checkpoint_retention() (LION.optimizers.PaDISSolver.PaDISSolver method) set_checkpointing() (LION.optimizers.LIONsolver.LIONsolver method) set_image_transform() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method) set_saving() (LION.optimizers.LIONsolver.LIONsolver method) set_sinogram_transform() (LION.data_loaders.LIDC_IDRI.LIDC_IDRI method) set_testing() (LION.optimizers.LIONsolver.LIONsolver method) set_training() (LION.optimizers.LIONsolver.LIONsolver method) set_validation() (LION.optimizers.LIONsolver.LIONsolver method) sinogram_add_noise() (in module LION.CTtools.ct_utils) SolverState (class in LION.optimizers.LIONsolver) sparse_angle_parameters() (LION.CTtools.ct_geometry.Geometry static method) sparse_view_parameters() (LION.CTtools.ct_geometry.Geometry static method) SparseAngleCTRecon (class in LION.experiments.ct_experiments) SparseAngleExtremeLowDoseCTRecon (class in LION.experiments.ct_experiments) SparseAngleLowDoseCTRecon (class in LION.experiments.ct_experiments) spgl1_torch() (in module LION.classical_algorithms.spgl1_torch)

T

train() (LION.optimizers.LIONsolver.LIONsolver method) train_for_patches() (LION.optimizers.PaDISSolver.PaDISSolver method)

train_step() (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method) tv_min() (in module LION.classical_algorithms.tv_min)

V

validate() (LION.optimizers.LIONsolver.LIONsolver method) (LION.optimizers.PaDISSolver.PaDISSolver method)

validate_patch_schedule() (in module LION.losses.PaDIS)

Z

zero_pad_images() (in module LION.losses.PaDIS)