Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __call__() (atommic.core.classes.common.typecheck method) __init__() (atommic.collections.common.losses.AggregatorLoss method) (atommic.collections.common.losses.SinkhornDistance method) (atommic.collections.common.metrics.global_average_loss_metric.GlobalAverageLossMetric method) (atommic.collections.common.parts.coil_sensitivity_maps.EspiritCalibration method) (atommic.collections.common.parts.coil_sensitivity_maps.MaximumEigenvaluePowerMethod method) (atommic.collections.common.parts.transforms.Composer method) (atommic.collections.common.parts.transforms.Cropper method) (atommic.collections.common.parts.transforms.EstimateCoilSensitivityMaps method) (atommic.collections.common.parts.transforms.GeometricDecompositionCoilCompression method) (atommic.collections.common.parts.transforms.MRIDataTransforms method) (atommic.collections.common.parts.transforms.N2R method) (atommic.collections.common.parts.transforms.NoisePreWhitening method) (atommic.collections.common.parts.transforms.Normalizer method) (atommic.collections.common.parts.transforms.SNREstimator method) (atommic.collections.common.parts.transforms.SSDU method) (atommic.collections.common.parts.transforms.ZeroFillingPadding method) (atommic.collections.motioncorrection.parts.motionsimulation.MotionSimulation method) (atommic.collections.multitask.rs.parts.transforms.RSMRIDataTransforms method) (atommic.collections.reconstruction.losses.SSIMLoss method) (atommic.collections.segmentation.losses.CrossEntropyLoss method) (atommic.collections.segmentation.losses.Dice method) A add_coil_dim_if_singlecoil() (in module atommic.collections.common.parts.utils) AggregatorLoss (class in atommic.collections.common.losses) AHEADqMRIDataset (class in atommic.collections.quantitative.data.qmri_loader) align_compressed_coils() (atommic.collections.common.parts.transforms.GeometricDecompositionCoilCompression method) apply_mask() (in module atommic.collections.common.parts.utils) ave() (atommic.collections.common.losses.SinkhornDistance static method) AxisType (class in atommic.core.neural_types.axes) B batched_mask_center() (in module atommic.collections.common.parts.utils) BraTS2023AdultGliomaSegmentationMRIDataset (class in atommic.collections.segmentation.data.mri_segmentation_loader) C calculate_acs_mask() (atommic.collections.common.parts.transforms.EstimateCoilSensitivityMaps method) calculate_gcc() (atommic.collections.common.parts.transforms.GeometricDecompositionCoilCompression method) calculate_sensitivity_map() (atommic.collections.common.parts.coil_sensitivity_maps.EspiritCalibration method) CC359ReconstructionMRIDataset (class in atommic.collections.reconstruction.data.mri_reconstruction_loader) center_crop() (in module atommic.collections.common.parts.utils) center_crop_to_smallest() (in module atommic.collections.common.parts.utils) centered_circle() (atommic.collections.common.data.subsample.Poisson2DMaskFunc method) cfg (atommic.core.classes.modelPT.ModelPT property) check_stacked_complex() (in module atommic.collections.common.parts.utils) checkpoint_callback_params (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] choose_acceleration() (atommic.collections.common.data.subsample.MaskFunc method) coil_combination_method() (in module atommic.collections.common.parts.utils) compare() (atommic.core.neural_types.elements.ElementType method) (atommic.core.neural_types.neural_type.NeuralType method) compare_and_raise_error() (atommic.core.neural_types.neural_type.NeuralType method) complex_abs() (in module atommic.collections.common.parts.utils) complex_abs_sq() (in module atommic.collections.common.parts.utils) complex_center_crop() (in module atommic.collections.common.parts.utils) complex_conj() (in module atommic.collections.common.parts.utils) complex_mul() (in module atommic.collections.common.parts.utils) Composer (class in atommic.collections.common.parts.transforms) compute() (atommic.collections.common.metrics.global_average_loss_metric.GlobalAverageLossMetric method) configure_optimizers() (atommic.core.classes.modelPT.ModelPT method) create_checkpoint_callback (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] create_early_stopping_callback (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] create_masker() (in module atommic.collections.common.data.subsample) create_preemption_callback (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] create_rand_partition() (in module atommic.collections.motioncorrection.parts.motionsimulation) create_rotation_matrix_3d() (in module atommic.collections.motioncorrection.parts.motionsimulation) create_tensorboard_logger (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] create_wandb_logger (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] crop() (atommic.collections.common.parts.transforms.GeometricDecompositionCoilCompression method) crop_to_acs() (in module atommic.collections.common.parts.utils) Cropper (class in atommic.collections.common.parts.transforms) CrossEntropyLoss (class in atommic.collections.segmentation.losses) cuda() (atommic.core.classes.modelPT.ModelPT method) D Dice (class in atommic.collections.segmentation.losses) DIM_INCOMPATIBLE (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) disable_checks() (atommic.core.classes.common.typecheck static method) disable_validation_on_resume (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] disabled_deployment_input_names (atommic.core.classes.export.Exportable property) disabled_deployment_output_names (atommic.core.classes.export.Exportable property) done() (atommic.collections.common.parts.coil_sensitivity_maps.MaximumEigenvaluePowerMethod method) E early_stopping_callback_params (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] ElementType (class in atommic.core.neural_types.elements) ema (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] Equispaced1DMaskFunc (class in atommic.collections.common.data.subsample) Equispaced2DMaskFunc (class in atommic.collections.common.data.subsample) EspiritCalibration (class in atommic.collections.common.parts.coil_sensitivity_maps) estimate_acs_image() (atommic.collections.common.parts.transforms.EstimateCoilSensitivityMaps method) EstimateCoilSensitivityMaps (class in atommic.collections.common.parts.transforms) exp_dir (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] exp_manager (class in atommic.utils.exp_manager) expand_op() (in module atommic.collections.common.parts.utils) explicit_log_dir (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] ExpManagerConfig (class in atommic.utils.exp_manager), [1] export() (atommic.core.classes.export.Exportable method) Exportable (class in atommic.core.classes.export) extract_state_dict_from() (atommic.core.classes.modelPT.ModelPT class method) (atommic.core.connectors.save_restore_connector.SaveRestoreConnector method) F fft2() (in module atommic.collections.common.parts.fft) fftshift() (in module atommic.collections.common.parts.fft) fields (atommic.core.neural_types.elements.ElementType property) files_to_copy (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] find_optimal_patch_size() (atommic.collections.common.parts.transforms.NoisePreWhitening static method) fit() (atommic.collections.common.parts.coil_sensitivity_maps.MaximumEigenvaluePowerMethod method) forward() (atommic.collections.common.losses.AggregatorLoss method) (atommic.collections.common.losses.SinkhornDistance method) (atommic.collections.common.parts.coil_sensitivity_maps.EspiritCalibration method) (atommic.collections.common.parts.transforms.Cropper method) (atommic.collections.common.parts.transforms.EstimateCoilSensitivityMaps method) (atommic.collections.common.parts.transforms.GeometricDecompositionCoilCompression method) (atommic.collections.common.parts.transforms.N2R method) (atommic.collections.common.parts.transforms.NoisePreWhitening method) (atommic.collections.common.parts.transforms.Normalizer method) (atommic.collections.common.parts.transforms.SSDU method) (atommic.collections.common.parts.transforms.ZeroFillingPadding method) (atommic.collections.motioncorrection.parts.motionsimulation.MotionSimulation method) (atommic.collections.reconstruction.losses.NoiseAwareLoss method) (atommic.collections.reconstruction.losses.SSIMLoss method) (atommic.collections.segmentation.losses.CrossEntropyLoss method) (atommic.collections.segmentation.losses.Dice method) full_state_update (atommic.collections.common.metrics.global_average_loss_metric.GlobalAverageLossMetric attribute) G Gaussian1DMaskFunc (class in atommic.collections.common.data.subsample) Gaussian2DMaskFunc (class in atommic.collections.common.data.subsample) gaussian_coordinates() (atommic.collections.common.data.subsample.Gaussian1DMaskFunc method) (atommic.collections.common.data.subsample.Gaussian2DMaskFunc method) gaussian_kernel() (atommic.collections.common.data.subsample.Gaussian1DMaskFunc method) (atommic.collections.common.data.subsample.Gaussian2DMaskFunc method) gaussian_kspace() (atommic.collections.common.data.subsample.Gaussian1DMaskFunc method) (atommic.collections.common.data.subsample.Gaussian2DMaskFunc method) generate_poisson_mask() (atommic.collections.common.data.subsample.Poisson2DMaskFunc static method) GeometricDecompositionCoilCompression (class in atommic.collections.common.parts.transforms) get_center_rect() (in module atommic.collections.motioncorrection.parts.motionsimulation) get_consecutive_slices() (atommic.collections.common.data.mri_loader.MRIDataset method) (atommic.collections.reconstruction.data.mri_reconstruction_loader.CC359ReconstructionMRIDataset method) (atommic.collections.segmentation.data.mri_segmentation_loader.BraTS2023AdultGliomaSegmentationMRIDataset method) (atommic.collections.segmentation.data.mri_segmentation_loader.SKMTEASegmentationMRIDataset method) get_export_config() (atommic.core.classes.export.Exportable method) get_export_subnet() (atommic.core.classes.export.Exportable method) get_test_dataloader_prefix() (atommic.core.classes.modelPT.ModelPT method) get_validation_dataloader_prefix() (atommic.core.classes.modelPT.ModelPT method) GlobalAverageLossMetric (class in atommic.collections.common.metrics.global_average_loss_metric) GREATER (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) H has_artifacts() (atommic.core.classes.modelPT.ModelPT method) has_atommic_submodules() (atommic.core.classes.modelPT.ModelPT method) has_native_or_submodules_artifacts() (atommic.core.classes.modelPT.ModelPT method) I ifft2() (in module atommic.collections.common.parts.fft) ifftshift() (in module atommic.collections.common.parts.fft) INCOMPATIBLE (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) input_module (atommic.core.classes.export.Exportable property) input_names (atommic.core.classes.export.Exportable property) input_types (atommic.collections.common.losses.AggregatorLoss property) input_types_for_export (atommic.core.classes.export.Exportable property) is_none() (in module atommic.collections.common.parts.utils) ISLES2022SubAcuteStrokeSegmentationMRIDataset (class in atommic.collections.segmentation.data.mri_segmentation_loader) L LESS (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) list_export_subnets() (atommic.core.classes.export.Exportable static method) load_config_and_state_dict() (atommic.core.connectors.save_restore_connector.SaveRestoreConnector method) load_from_checkpoint() (atommic.core.classes.modelPT.ModelPT class method) load_instance_with_state_dict() (atommic.core.connectors.save_restore_connector.SaveRestoreConnector static method) load_part_of_state_dict() (atommic.core.classes.modelPT.ModelPT method) log_global_rank_0_only (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] log_local_rank_0_only (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] log_step_timing (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] M M() (atommic.collections.common.losses.SinkhornDistance method) mask_center() (in module atommic.collections.common.parts.utils) MaskFunc (class in atommic.collections.common.data.subsample) max_time_per_run (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] MaximumEigenvaluePowerMethod (class in atommic.collections.common.parts.coil_sensitivity_maps) maybe_init_from_pretrained_checkpoint() (atommic.core.classes.modelPT.ModelPT method) model_config_yaml (atommic.core.connectors.save_restore_connector.SaveRestoreConnector property) model_extracted_dir (atommic.core.connectors.save_restore_connector.SaveRestoreConnector property) model_weights_ckpt (atommic.core.connectors.save_restore_connector.SaveRestoreConnector property) ModelPT (class in atommic.core.classes.modelPT) MotionSimulation (class in atommic.collections.motioncorrection.parts.motionsimulation) MRIDataset (class in atommic.collections.common.data.mri_loader) MRIDataTransforms (class in atommic.collections.common.parts.transforms) multi_test_epoch_end() (atommic.core.classes.modelPT.ModelPT static method) multi_validation_epoch_end() (atommic.core.classes.modelPT.ModelPT static method) N N2R (class in atommic.collections.common.parts.transforms) name (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] named_atommic_modules() (atommic.core.classes.modelPT.ModelPT method) NeuralType (class in atommic.core.neural_types.neural_type) NeuralTypeComparisonResult (class in atommic.core.neural_types.comparison) NoiseAwareLoss (class in atommic.collections.reconstruction.losses) NoisePreWhitening (class in atommic.collections.common.parts.transforms) normalize_inplace() (in module atommic.collections.common.parts.utils) Normalizer (class in atommic.collections.common.parts.transforms) num_weights (atommic.core.classes.modelPT.ModelPT property) O on_test_epoch_end() (atommic.core.classes.modelPT.ModelPT method) on_train_batch_end() (atommic.core.classes.modelPT.ModelPT method) on_train_batch_start() (atommic.core.classes.modelPT.ModelPT method) on_train_end() (atommic.core.classes.modelPT.ModelPT method) on_train_start() (atommic.core.classes.modelPT.ModelPT method) on_validation_epoch_end() (atommic.core.classes.modelPT.ModelPT method) output_module (atommic.core.classes.export.Exportable property) output_names (atommic.core.classes.export.Exportable property) output_types (atommic.collections.common.losses.AggregatorLoss property) output_types_for_export (atommic.core.classes.export.Exportable property) P parse_list_and_keep_last() (in module atommic.collections.common.parts.utils) Poisson2DMaskFunc (class in atommic.collections.common.data.subsample) prepare_test() (atommic.core.classes.modelPT.ModelPT method) process_segmentation_labels() (atommic.collections.multitask.rs.data.mrirs_loader.RSMRIDataset method) (atommic.collections.segmentation.data.mri_segmentation_loader.SegmentationMRIDataset method) Q qMRIDataset (class in atommic.collections.quantitative.data.qmri_loader) R Random1DMaskFunc (class in atommic.collections.common.data.subsample) ReconstructionMRIDataset (class in atommic.collections.reconstruction.data.mri_reconstruction_loader) register_artifact() (atommic.core.classes.modelPT.ModelPT method) (atommic.core.connectors.save_restore_connector.SaveRestoreConnector static method) register_atommic_submodule() (atommic.core.classes.modelPT.ModelPT method) register_optimizer() (in module atommic.core.optim.optimizers) register_scheduler() (in module atommic.core.optim.lr_scheduler) reshape_fortran() (in module atommic.collections.common.parts.utils) restore_from() (atommic.core.classes.modelPT.ModelPT class method) (atommic.core.connectors.save_restore_connector.SaveRestoreConnector method) resume_from_checkpoint (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] resume_if_exists (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] resume_ignore_no_checkpoint (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] resume_past_end (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] rnn_weights_init() (in module atommic.collections.common.parts.utils) roll() (in module atommic.collections.common.parts.fft) roll_one_dim() (in module atommic.collections.common.parts.fft) rotate_and_compress() (atommic.collections.common.parts.transforms.GeometricDecompositionCoilCompression method) RSMRIDataset (class in atommic.collections.multitask.rs.data.mrirs_loader) RSMRIDataTransforms (class in atommic.collections.multitask.rs.parts.transforms) rss() (in module atommic.collections.common.parts.utils) rss_complex() (in module atommic.collections.common.parts.utils) S SAME (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) SAME_TYPE_INCOMPATIBLE_PARAMS (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) save_predictions() (in module atommic.collections.common.parts.utils) save_to() (atommic.core.classes.modelPT.ModelPT method) (atommic.core.connectors.save_restore_connector.SaveRestoreConnector method) SaveRestoreConnector (class in atommic.core.connectors.save_restore_connector) seconds_to_sleep (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] segment_array_by_locs() (in module atommic.collections.motioncorrection.parts.motionsimulation) SegmentationMRIDataset (class in atommic.collections.segmentation.data.mri_segmentation_loader) segments_to_random_blocks() (in module atommic.collections.motioncorrection.parts.motionsimulation) segments_to_random_indices() (in module atommic.collections.motioncorrection.parts.motionsimulation) sense() (in module atommic.collections.common.parts.utils) set_export_config() (atommic.core.classes.export.Exportable method) set_trainer() (atommic.core.classes.modelPT.ModelPT method) set_typecheck_enabled() (atommic.core.classes.common.typecheck static method) set_world_size() (atommic.core.classes.modelPT.ModelPT method) setup() (atommic.core.classes.modelPT.ModelPT method) setup_multiple_test_data() (atommic.core.classes.modelPT.ModelPT method) setup_multiple_validation_data() (atommic.core.classes.modelPT.ModelPT method) setup_optimization() (atommic.core.classes.modelPT.ModelPT method) setup_optimizer_param_groups() (atommic.core.classes.modelPT.ModelPT method) setup_test_data() (atommic.core.classes.modelPT.ModelPT method) setup_training_data() (atommic.core.classes.modelPT.ModelPT method) setup_validation_data() (atommic.core.classes.modelPT.ModelPT method) SinkhornDistance (class in atommic.collections.common.losses) SKMTEAReconstructionMRIDataset (class in atommic.collections.reconstruction.data.mri_reconstruction_loader) SKMTEARSMRIDataset (class in atommic.collections.multitask.rs.data.mrirs_loader) SKMTEASegmentationMRIDataset (class in atommic.collections.segmentation.data.mri_segmentation_loader) SNREstimator (class in atommic.collections.common.parts.transforms) SSDU (class in atommic.collections.common.parts.transforms) SSIMLoss (class in atommic.collections.reconstruction.losses) StanfordKneesReconstructionMRIDataset (class in atommic.collections.reconstruction.data.mri_reconstruction_loader) step_timing_kwargs (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] summarize() (atommic.core.classes.modelPT.ModelPT method) summary_writer_kwargs (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] supported_export_formats (atommic.core.classes.export.Exportable property) T test_dataloader() (atommic.core.classes.modelPT.ModelPT method) to_tensor() (in module atommic.collections.common.parts.utils) train_dataloader() (atommic.core.classes.modelPT.ModelPT method) translate_kspace() (in module atommic.collections.motioncorrection.parts.motionsimulation) TRANSPOSE_SAME (atommic.core.neural_types.comparison.NeuralTypeComparisonResult attribute) type_parameters (atommic.core.neural_types.elements.ElementType property) typecheck (class in atommic.core.classes.common) typecheck.TypeState (class in atommic.core.classes.common) U UNINITIALIZED (atommic.core.classes.common.typecheck.TypeState attribute) unnormalize() (in module atommic.collections.common.parts.utils) update() (atommic.collections.common.metrics.global_average_loss_metric.GlobalAverageLossMetric method) (atommic.collections.common.parts.coil_sensitivity_maps.MaximumEigenvaluePowerMethod method) update_save_restore_connector() (atommic.core.classes.modelPT.ModelPT class method) use_datetime_version (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] V val_dataloader() (atommic.core.classes.modelPT.ModelPT method) version (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] W wandb_logger_kwargs (atommic.utils.exp_manager.ExpManagerConfig attribute), [1] Z zero_nan_inf() (in module atommic.collections.common.parts.utils) ZeroFillingPadding (class in atommic.collections.common.parts.transforms)
