Index

A

AbstractLoss (class in tardis_em.utils.losses) activate() (tardis_em.utils.losses.AbstractLoss method) adaptive_threshold() (in module tardis_em.utils.normalization) AdaptiveDiceLoss (class in tardis_em.utils.losses) analyse_filaments() (in module tardis_em.analysis.analysis) analyse_filaments_list() (in module tardis_em.analysis.analysis) analyse_mt_classes() (in module tardis_em.analysis.analysis) angle_between_vectors() (in module tardis_em.analysis.geometry_metrics) AP() (in module tardis_em.utils.metrics) AP_instance() (in module tardis_em.utils.metrics)

area_scaling() (in module tardis_em.cnn.data_processing.scaling) assign_filaments_to_poles() (in module tardis_em.analysis.filament_structure) (in module tardis_em.analysis.mt_classification.utils) assign_mt_with_crossing() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) assign_to_bridge_mt() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) assign_to_int_mt() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) assign_to_kmts() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) assign_to_mid_mt() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) AUC() (in module tardis_em.utils.metrics) aws_check_pkg_with_temp() (in module tardis_em.utils.aws) aws_check_with_temp() (in module tardis_em.utils.aws)

B

BasicCNN (class in tardis_em.cnn.utils.build_cnn) BasicDataset (class in tardis_em.dist_pytorch.datasets.dataloader) BasicDIST (class in tardis_em.dist_pytorch.dist) BasicTrainer (class in tardis_em.utils.trainer) BCEDiceLoss (class in tardis_em.utils.losses) BCEGraphWiseLoss (class in tardis_em.utils.losses) BCELoss (class in tardis_em.utils.losses) BCEMSELoss (class in tardis_em.utils.losses) boundary_box() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet method) build_cnn_model() (tardis_em.cnn.utils.build_cnn.BasicCNN method) (tardis_em.cnn.utils.build_cnn.FNet method) build_cnn_network() (in module tardis_em.cnn.cnn)

build_dataset() (in module tardis_em.dist_pytorch.datasets.dataloader) build_decoder() (in module tardis_em.cnn.model.decoder_blocks) build_dist_network() (in module tardis_em.dist_pytorch.dist) build_encoder() (in module tardis_em.cnn.model.encoder_blocks) build_new_dir() (in module tardis_em.utils.setup_envir) build_NN() (tardis_em.utils.predictor.GeneralPredictor method) build_point_cloud() (tardis_em.dist_pytorch.utils.build_point_cloud.BuildPointCloud method) build_temp_dir() (in module tardis_em.utils.setup_envir) build_test_dataset() (in module tardis_em.utils.dataset) build_train_dataset() (in module tardis_em.cnn.datasets.build_dataset) BuildGraph (class in tardis_em.dist_pytorch.datasets.augmentation) BuildPointCloud (class in tardis_em.dist_pytorch.utils.build_point_cloud)

C

calculate_f1() (in module tardis_em.utils.metrics) CDIST (class in tardis_em.dist_pytorch.dist) CDistTrainer (class in tardis_em.dist_pytorch.trainer) cell_width() (tardis_em.utils.logo.TardisLogo method) CELoss (class in tardis_em.utils.losses) center_patch() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet static method) CenterCrop (class in tardis_em.cnn.datasets.augmentation) check_3d() (tardis_em.utils.export_data.NumpyToAmira method) check_data() (tardis_em.dist_pytorch.utils.build_point_cloud.BuildPointCloud static method) check_dir() (in module tardis_em.utils.setup_envir) check_model_dict() (in module tardis_em.cnn.utils.utils) (in module tardis_em.dist_pytorch.utils.utils) check_uint8() (in module tardis_em.utils.utils) classified_MTs() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) ClBCELoss (class in tardis_em.utils.losses) ClDiceLoss (class in tardis_em.utils.losses) clean_up() (in module tardis_em.utils.setup_envir) clear_output() (tardis_em.utils.logo.TardisLogo static method) CNNDataset (class in tardis_em.cnn.datasets.dataloader)

CNNTrainer (class in tardis_em.cnn.trainer) combined_smoothness() (tardis_em.analysis.spatial_graph_utils.ComputeConfidenceScore method) compare_dict_metrics() (in module tardis_em.utils.metrics) compare_splines_probability() (in module tardis_em.analysis.spatial_graph_utils) ComparisonLayer (class in tardis_em.dist_pytorch.model.modules) ComposeRandomTransformation (class in tardis_em.cnn.datasets.augmentation) compute_laplacian() (tardis_em.utils.losses.LaplacianEigenmapsLoss static method) ComputeConfidenceScore (class in tardis_em.analysis.spatial_graph_utils) confusion_matrix() (in module tardis_em.utils.metrics) ContextFilter (class in tardis_em.utils.logo) convolution() (in module tardis_em.cnn.model.convolution) correct_data() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) count_true_groups() (in module tardis_em.analysis.mt_classification.utils) create_headers() (tardis_em.utils.predictor.GeneralPredictor method) create_simulated_dataset() (in module tardis_em.dist_pytorch.utils.build_point_cloud) Crop2D3D (class in tardis_em.dist_pytorch.datasets.augmentation) curvature() (in module tardis_em.analysis.geometry_metrics) curvature_list() (in module tardis_em.analysis.geometry_metrics) cut_150_degree() (in module tardis_em.analysis.filament_utils) cut_desc() (tardis_em.utils.errors.TardisError method)

D

decoder (tardis_em.cnn.utils.build_cnn.UNet3Plus attribute) DecoderBlockCNN (class in tardis_em.cnn.model.decoder_blocks) DecoderBlockRCNN (class in tardis_em.cnn.model.decoder_blocks) DecoderBlockUnet3Plus (class in tardis_em.cnn.model.decoder_blocks) deconv (tardis_em.cnn.model.decoder_blocks.DecoderBlockUnet3Plus attribute) deconv_module (tardis_em.cnn.model.decoder_blocks.DecoderBlockCNN attribute) deconv_res_module (tardis_em.cnn.model.decoder_blocks.DecoderBlockRCNN attribute) device_is_str() (in module tardis_em.utils.device) DiceLoss (class in tardis_em.utils.losses) DIST (class in tardis_em.dist_pytorch.dist) distance_to_the_pole() (in module tardis_em.analysis.mt_classification.utils) distances_of_ends_to_surface() (in module tardis_em.analysis.mt_classification.utils) DistLayer (class in tardis_em.dist_pytorch.model.layers) DistStack (class in tardis_em.dist_pytorch.model.layers) DistTrainer (class in tardis_em.dist_pytorch.trainer) divide_into_sequences() (in module tardis_em.analysis.mt_classification.utils) dot_product() (tardis_em.cnn.utils.build_cnn.UNet3Plus static method)

DoubleConvolution (class in tardis_em.cnn.model.convolution) DownSampling (class in tardis_em.dist_pytorch.utils.utils) draw_circle() (in module tardis_em.cnn.data_processing.draw_mask) (in module tardis_em.dist_pytorch.utils.build_point_cloud) draw_curved_line() (in module tardis_em.dist_pytorch.utils.build_point_cloud) draw_instances() (in module tardis_em.cnn.data_processing.draw_mask) draw_instances_membrane() (in module tardis_em.cnn.data_processing.draw_mask) draw_line() (in module tardis_em.dist_pytorch.utils.build_point_cloud) draw_mask() (in module tardis_em.cnn.data_processing.draw_mask) draw_semantic_membrane() (in module tardis_em.cnn.data_processing.draw_mask) draw_sheet() (in module tardis_em.dist_pytorch.utils.build_point_cloud) draw_sphere() (in module tardis_em.cnn.data_processing.draw_mask) (in module tardis_em.dist_pytorch.utils.build_point_cloud) dropout (tardis_em.cnn.model.decoder_blocks.DecoderBlockCNN attribute) (tardis_em.cnn.model.decoder_blocks.DecoderBlockRCNN attribute) (tardis_em.cnn.model.decoder_blocks.DecoderBlockUnet3Plus attribute) (tardis_em.cnn.model.encoder_blocks.EncoderBlock attribute)

E

EarlyStopping (class in tardis_em.utils.utils) EdgeEmbedding (class in tardis_em.dist_pytorch.model.embedding) embed_input() (tardis_em.dist_pytorch.dist.BasicDIST method) encoder (tardis_em.cnn.utils.build_cnn.UNet3Plus attribute)

EncoderBlock (class in tardis_em.cnn.model.encoder_blocks) error_log_build_data() (in module tardis_em.cnn.datasets.build_dataset) eval_graph_f1() (in module tardis_em.utils.metrics) export_amira() (tardis_em.utils.export_data.NumpyToAmira method)

F

FFTNormalize (class in tardis_em.utils.normalization) FilamentDataset (class in tardis_em.dist_pytorch.datasets.dataloader) fill_gaps() (in module tardis_em.analysis.mt_classification.utils) filter() (tardis_em.utils.logo.ContextFilter method) FilterConnectedNearSegments (class in tardis_em.analysis.spatial_graph_utils) FilterSpatialGraph (class in tardis_em.analysis.spatial_graph_utils) find_filtered_files() (in module tardis_em.utils.dataset) FNet (class in tardis_em.cnn.utils.build_cnn) forward() (tardis_em.cnn.model.convolution.GeLU method) (tardis_em.cnn.model.convolution.RecurrentDoubleConvolution method) (tardis_em.cnn.model.decoder_blocks.DecoderBlockCNN method) (tardis_em.cnn.model.decoder_blocks.DecoderBlockRCNN method) (tardis_em.cnn.model.decoder_blocks.DecoderBlockUnet3Plus method) (tardis_em.cnn.model.encoder_blocks.EncoderBlock method) (tardis_em.cnn.utils.build_cnn.FNet method) (tardis_em.cnn.utils.build_cnn.ResUNet method) (tardis_em.cnn.utils.build_cnn.UNet method) (tardis_em.cnn.utils.build_cnn.UNet3Plus method) (tardis_em.dist_pytorch.dist.BasicDIST method) (tardis_em.dist_pytorch.model.embedding.EdgeEmbedding method) (tardis_em.dist_pytorch.model.embedding.NodeEmbedding method) (tardis_em.dist_pytorch.model.layers.DistLayer method) (tardis_em.dist_pytorch.model.layers.DistStack method) (tardis_em.dist_pytorch.model.modules.ComparisonLayer method) (tardis_em.dist_pytorch.model.modules.GeluFeedForward method) (tardis_em.dist_pytorch.model.modules.MultiHeadAttention method) (tardis_em.dist_pytorch.model.modules.PairBiasSelfAttention method) (tardis_em.dist_pytorch.model.modules.QuadraticEdgeUpdate method) (tardis_em.dist_pytorch.model.modules.SelfAttention2D method) (tardis_em.dist_pytorch.model.modules.TriangularEdgeUpdate method) (tardis_em.utils.losses.AbstractLoss method) (tardis_em.utils.losses.AdaptiveDiceLoss method) (tardis_em.utils.losses.BCEDiceLoss method) (tardis_em.utils.losses.BCEGraphWiseLoss method) (tardis_em.utils.losses.BCELoss method) (tardis_em.utils.losses.BCEMSELoss method) (tardis_em.utils.losses.CELoss method) (tardis_em.utils.losses.ClBCELoss method) (tardis_em.utils.losses.ClDiceLoss method) (tardis_em.utils.losses.DiceLoss method) (tardis_em.utils.losses.LaplacianEigenmapsLoss method) (tardis_em.utils.losses.SigmoidFocalLoss method) (tardis_em.utils.losses.SoftSkeletonization method) (tardis_em.utils.losses.WBCELoss method)

fourier_scaling() (in module tardis_em.cnn.data_processing.scaling)

G

GeLU (class in tardis_em.cnn.model.convolution) GeluFeedForward (class in tardis_em.dist_pytorch.model.modules) GeneralPredictor (class in tardis_em.utils.predictor) generate_grid() (in module tardis_em.cnn.data_processing.stitch) get_all_version_aws() (in module tardis_em.utils.aws) get_benchmark_aws() (in module tardis_em.utils.aws) get_classified_fibers() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_classified_indices() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_device() (in module tardis_em.utils.device) get_filament_endpoints() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_filament_file() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier static method) get_filaments() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_file_list() (tardis_em.utils.predictor.GeneralPredictor method) get_image() (tardis_em.utils.load_data.ImportDataFromAmira method) get_labels() (tardis_em.utils.load_data.ImportDataFromAmira method)

get_lr_scale() (tardis_em.utils.trainer.ISR_LR method) get_model_aws() (in module tardis_em.utils.aws) get_n_params() (in module tardis_em.utils.utils) get_pixel_size() (tardis_em.utils.load_data.ImportDataFromAmira method) get_points() (tardis_em.utils.load_data.ImportDataFromAmira method) get_poles() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_poles_file() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier static method) get_segmented_points() (tardis_em.utils.load_data.ImportDataFromAmira method) get_surface() (tardis_em.utils.load_data.ImportDataFromAmira method) get_vertex() (tardis_em.utils.load_data.ImportDataFromAmira method) get_vertices() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_vertices_file() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method) get_weights_aws() (in module tardis_em.utils.aws) get_xyz_position() (tardis_em.dist_pytorch.datasets.augmentation.Crop2D3D static method) gmm_fit() (tardis_em.utils.normalization.FFTNormalize static method)

H

hostname (tardis_em.utils.logo.ContextFilter attribute)

I

ignor_diagonal() (tardis_em.utils.losses.AbstractLoss method) ImportDataFromAmira (class in tardis_em.utils.load_data) init_check() (tardis_em.utils.predictor.GeneralPredictor method) init_weights() (in module tardis_em.cnn.model.init_weights) initialize_tensors() (tardis_em.utils.losses.AbstractLoss method) instance_header (tardis_em.utils.predictor.GeneralPredictor attribute)

intensity() (in module tardis_em.analysis.geometry_metrics) intensity_list() (in module tardis_em.analysis.geometry_metrics) interpolate_generator() (in module tardis_em.cnn.data_processing.interpolation) interpolation() (in module tardis_em.cnn.data_processing.interpolation) IoU() (in module tardis_em.utils.metrics) is_interactive() (in module tardis_em.utils.logo) ISR_LR (class in tardis_em.utils.trainer)

K

kmts_inside_outside() (tardis_em.analysis.mt_classification.mt_classes.MicrotubuleClassifier method)

L

LaplacianEigenmapsLoss (class in tardis_em.utils.losses) length_list() (in module tardis_em.analysis.geometry_metrics) linear_scaling() (in module tardis_em.cnn.data_processing.scaling) list_to_tensor() (tardis_em.dist_pytorch.datasets.dataloader.BasicDataset static method) load_am() (in module tardis_em.utils.load_data) load_am_surf() (in module tardis_em.utils.load_data) load_data() (tardis_em.utils.predictor.GeneralPredictor method) load_image() (in module tardis_em.utils.load_data) load_img_mask_data() (in module tardis_em.cnn.datasets.build_dataset) load_mrc_file() (in module tardis_em.utils.load_data)

load_nd2_file() (in module tardis_em.utils.load_data) load_ply_partnet() (in module tardis_em.utils.load_data) load_ply_scannet() (in module tardis_em.utils.load_data) load_s3dis_scene() (in module tardis_em.utils.load_data) load_state_dict() (tardis_em.utils.trainer.ISR_LR method) load_temp() (tardis_em.dist_pytorch.datasets.dataloader.BasicDataset method) load_tiff() (in module tardis_em.utils.load_data) load_txt_s3dis() (in module tardis_em.utils.load_data) log_prediction (tardis_em.utils.predictor.GeneralPredictor attribute) log_tardis() (tardis_em.utils.predictor.GeneralPredictor method)

M

main() (in module tardis_em.utils.ota_update) marge_splines() (tardis_em.analysis.spatial_graph_utils.FilterConnectedNearSegments method) max_number_of_conv_layer() (in module tardis_em.cnn.utils.utils) mcov() (in module tardis_em.utils.metrics) MeanStdNormalize (class in tardis_em.utils.normalization) MicrotubuleClassifier (class in tardis_em.analysis.mt_classification.mt_classes) MinMaxNormalize (class in tardis_em.utils.normalization) module tardis_em.analysis.analysis tardis_em.analysis.filament_structure tardis_em.analysis.filament_utils tardis_em.analysis.geometry_metrics tardis_em.analysis.mt_classification.mt_classes tardis_em.analysis.mt_classification.utils tardis_em.analysis.spatial_graph_utils tardis_em.cnn.cnn tardis_em.cnn.data_processing.draw_mask tardis_em.cnn.data_processing.interpolation tardis_em.cnn.data_processing.scaling tardis_em.cnn.data_processing.stitch tardis_em.cnn.data_processing.trim tardis_em.cnn.datasets.augmentation tardis_em.cnn.datasets.build_dataset tardis_em.cnn.datasets.dataloader tardis_em.cnn.model.convolution tardis_em.cnn.model.decoder_blocks tardis_em.cnn.model.encoder_blocks tardis_em.cnn.model.init_weights tardis_em.cnn.train tardis_em.cnn.trainer tardis_em.cnn.utils.build_cnn tardis_em.cnn.utils.utils tardis_em.dist_pytorch.datasets.augmentation tardis_em.dist_pytorch.datasets.patches tardis_em.dist_pytorch.dist tardis_em.dist_pytorch.model.embedding tardis_em.dist_pytorch.model.layers tardis_em.dist_pytorch.model.modules tardis_em.dist_pytorch.train tardis_em.dist_pytorch.trainer tardis_em.dist_pytorch.utils.build_point_cloud tardis_em.dist_pytorch.utils.segment_point_cloud tardis_em.dist_pytorch.utils.utils tardis_em.tardis_helper.helper_func tardis_em.utils.aws tardis_em.utils.dataset tardis_em.utils.device tardis_em.utils.errors tardis_em.utils.export_data tardis_em.utils.load_data tardis_em.utils.logo tardis_em.utils.losses tardis_em.utils.metrics tardis_em.utils.normalization tardis_em.utils.ota_update tardis_em.utils.predictor tardis_em.utils.setup_envir tardis_em.utils.trainer tardis_em.utils.utils

move_train_dataset() (in module tardis_em.utils.dataset) mrc_mode() (in module tardis_em.utils.load_data) mrc_read_header() (in module tardis_em.utils.load_data) mrc_write_header() (in module tardis_em.utils.load_data) MultiHeadAttention (class in tardis_em.dist_pytorch.model.modules)

N

nn_scaling() (in module tardis_em.cnn.data_processing.scaling) NodeEmbedding (class in tardis_em.dist_pytorch.model.embedding) norm_fit() (tardis_em.utils.normalization.FFTNormalize method) normalize_idx() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet static method)

normalize_image() (in module tardis_em.cnn.utils.utils) (in module tardis_em.utils.metrics) normalized_length() (tardis_em.analysis.spatial_graph_utils.ComputeConfidenceScore static method) number_of_features_per_level() (in module tardis_em.cnn.utils.utils) NumpyToAmira (class in tardis_em.utils.export_data)

O

omit_format (tardis_em.utils.predictor.GeneralPredictor attribute) optimal_patches() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet method)

ota_update() (in module tardis_em.utils.ota_update) output_format() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet method)

P

PairBiasSelfAttention (class in tardis_em.dist_pytorch.model.modules) PartnetDataset (class in tardis_em.dist_pytorch.datasets.dataloader) patch_to_segment() (tardis_em.dist_pytorch.utils.segment_point_cloud.PropGreedyGraphCut method) PatchDataSet (class in tardis_em.dist_pytorch.datasets.patches) patched_dataset() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet method) pc_down_sample() (tardis_em.dist_pytorch.utils.utils.DownSampling static method) (tardis_em.dist_pytorch.utils.utils.RandomDownSampling static method) (tardis_em.dist_pytorch.utils.utils.VoxelDownSampling method) pc_median_dist() (in module tardis_em.dist_pytorch.utils.utils) pick_pole_to_surfaces() (in module tardis_em.analysis.mt_classification.utils) pixel_intensity() (in module tardis_em.analysis.geometry_metrics) point_in_bb() (in module tardis_em.dist_pytorch.utils.utils) points_in_patch() (tardis_em.dist_pytorch.datasets.patches.PatchDataSet method) points_on_mesh_knn() (in module tardis_em.analysis.mt_classification.utils)

postprocess_CNN() (tardis_em.utils.predictor.GeneralPredictor method) postprocess_DIST() (tardis_em.utils.predictor.GeneralPredictor method) predict() (tardis_em.utils.predictor.Predictor method) predict_cnn() (tardis_em.utils.predictor.GeneralPredictor method) predict_cnn_napari() (tardis_em.utils.predictor.GeneralPredictor method) predict_DIST() (tardis_em.utils.predictor.GeneralPredictor method) PredictionDataset (class in tardis_em.cnn.datasets.dataloader) Predictor (class in tardis_em.utils.predictor) preprocess() (in module tardis_em.cnn.datasets.augmentation) preprocess_connections() (tardis_em.dist_pytorch.utils.segment_point_cloud.PropGreedyGraphCut method) preprocess_data() (in module tardis_em.dist_pytorch.datasets.augmentation) preprocess_DIST() (tardis_em.utils.predictor.GeneralPredictor method) print_progress_bar() (in module tardis_em.utils.logo) PropGreedyGraphCut (class in tardis_em.dist_pytorch.utils.segment_point_cloud) put_benchmark_aws() (in module tardis_em.utils.aws)

Q

quadratic_bezier() (in module tardis_em.dist_pytorch.utils.build_point_cloud)

QuadraticEdgeUpdate (class in tardis_em.dist_pytorch.model.modules)

R

RandomDownSampling (class in tardis_em.dist_pytorch.utils.utils) RandomFlip (class in tardis_em.cnn.datasets.augmentation) RandomRotation (class in tardis_em.cnn.datasets.augmentation) RecurrentDoubleConvolution (class in tardis_em.cnn.model.convolution) reorder_segments_id() (in module tardis_em.analysis.filament_utils)

resample_filament() (in module tardis_em.analysis.filament_utils) RescaleNormalize (class in tardis_em.utils.normalization) reset_parameters() (tardis_em.dist_pytorch.model.modules.MultiHeadAttention method) ResUNet (class in tardis_em.cnn.utils.build_cnn) run_trainer() (tardis_em.utils.trainer.BasicTrainer method)

S

save_analysis() (in module tardis_em.analysis.analysis) save_instance_PC() (tardis_em.utils.predictor.GeneralPredictor method) save_semantic_mask() (tardis_em.utils.predictor.GeneralPredictor method) save_temp() (tardis_em.dist_pytorch.datasets.dataloader.BasicDataset method) scale_image() (in module tardis_em.cnn.data_processing.scaling) ScannetColorDataset (class in tardis_em.dist_pytorch.datasets.dataloader) ScannetDataset (class in tardis_em.dist_pytorch.datasets.dataloader) select_mt_ids_within_bb() (in module tardis_em.analysis.mt_classification.utils) SelfAttention2D (class in tardis_em.dist_pytorch.model.modules) semantic_header (tardis_em.utils.predictor.GeneralPredictor attribute) SigmoidFocalLoss (class in tardis_em.utils.losses) SimpleNormalize (class in tardis_em.utils.normalization) SingleConvolution (class in tardis_em.cnn.model.convolution)

smooth_spline() (in module tardis_em.analysis.filament_utils) soft_skel() (tardis_em.utils.losses.SoftSkeletonization method) SoftSkeletonization (class in tardis_em.utils.losses) sort_by_length() (in module tardis_em.analysis.filament_utils) sort_segment() (in module tardis_em.analysis.filament_utils) sort_segments() (in module tardis_em.analysis.filament_utils) SparseDistTrainer (class in tardis_em.dist_pytorch.trainer) SpatialGraphCompare (class in tardis_em.analysis.spatial_graph_utils) splines_direction() (tardis_em.analysis.spatial_graph_utils.FilterConnectedNearSegments method) standard_error_id() (in module tardis_em.utils.errors) Stanford3DDataset (class in tardis_em.dist_pytorch.datasets.dataloader) state_dict() (tardis_em.utils.trainer.ISR_LR method) step() (tardis_em.utils.trainer.ISR_LR method) StitchImages (class in tardis_em.cnn.data_processing.stitch)

T

tardis_em.analysis.analysis module tardis_em.analysis.filament_structure module tardis_em.analysis.filament_utils module tardis_em.analysis.geometry_metrics module tardis_em.analysis.mt_classification.mt_classes module tardis_em.analysis.mt_classification.utils module tardis_em.analysis.spatial_graph_utils module tardis_em.cnn.cnn module tardis_em.cnn.data_processing.draw_mask module tardis_em.cnn.data_processing.interpolation module tardis_em.cnn.data_processing.scaling module tardis_em.cnn.data_processing.stitch module tardis_em.cnn.data_processing.trim module tardis_em.cnn.datasets.augmentation module tardis_em.cnn.datasets.build_dataset module tardis_em.cnn.datasets.dataloader module tardis_em.cnn.model.convolution module tardis_em.cnn.model.decoder_blocks module tardis_em.cnn.model.encoder_blocks module tardis_em.cnn.model.init_weights module tardis_em.cnn.train module tardis_em.cnn.trainer module tardis_em.cnn.utils.build_cnn module tardis_em.cnn.utils.utils module tardis_em.dist_pytorch.datasets.augmentation module tardis_em.dist_pytorch.datasets.patches module tardis_em.dist_pytorch.dist module tardis_em.dist_pytorch.model.embedding module tardis_em.dist_pytorch.model.layers module

tardis_em.dist_pytorch.model.modules module tardis_em.dist_pytorch.train module tardis_em.dist_pytorch.trainer module tardis_em.dist_pytorch.utils.build_point_cloud module tardis_em.dist_pytorch.utils.segment_point_cloud module tardis_em.dist_pytorch.utils.utils module tardis_em.tardis_helper.helper_func module tardis_em.utils.aws module tardis_em.utils.dataset module tardis_em.utils.device module tardis_em.utils.errors module tardis_em.utils.export_data module tardis_em.utils.load_data module tardis_em.utils.logo module tardis_em.utils.losses module tardis_em.utils.metrics module tardis_em.utils.normalization module tardis_em.utils.ota_update module tardis_em.utils.predictor module tardis_em.utils.setup_envir module tardis_em.utils.trainer module tardis_em.utils.utils module tardis_helper() (in module tardis_em.tardis_helper.helper_func) TardisError TardisLogo (class in tardis_em.utils.logo) thicken_line_coordinates() (in module tardis_em.analysis.geometry_metrics) to_am() (in module tardis_em.utils.export_data) to_mrc() (in module tardis_em.utils.export_data) to_stl() (in module tardis_em.utils.export_data) tortuosity() (in module tardis_em.analysis.geometry_metrics) tortuosity_list() (in module tardis_em.analysis.geometry_metrics) total_length() (in module tardis_em.analysis.geometry_metrics) train_cnn() (in module tardis_em.cnn.train) train_dist() (in module tardis_em.dist_pytorch.train) TriangularEdgeUpdate (class in tardis_em.dist_pytorch.model.modules) trim_label_mask() (in module tardis_em.cnn.data_processing.trim) trim_with_stride() (in module tardis_em.cnn.data_processing.trim)

U

UNet (class in tardis_em.cnn.utils.build_cnn) UNet3Plus (class in tardis_em.cnn.utils.build_cnn) update_edges() (tardis_em.dist_pytorch.model.layers.DistLayer method)

update_nodes() (tardis_em.dist_pytorch.model.layers.DistLayer method) update_patch_size() (tardis_em.cnn.utils.build_cnn.BasicCNN method) (tardis_em.cnn.utils.build_cnn.FNet method) upsample_pc() (in module tardis_em.dist_pytorch.datasets.augmentation)

V

VoxelDownSampling (class in tardis_em.dist_pytorch.utils.utils)

W

WBCELoss (class in tardis_em.utils.losses)

weights_init_kaiming() (in module tardis_em.cnn.model.init_weights)

Z

zero_grad() (tardis_em.utils.trainer.ISR_LR method)