Index

_

__call__() (lightning_pose.data.dali.PrepareDALI method) (lightning_pose.data.utils.DataExtractor method) (lightning_pose.losses.factory.LossFactory method) (lightning_pose.losses.helpers.EmpiricalEpsilon method) (lightning_pose.losses.losses.HeatmapLoss method) (lightning_pose.losses.losses.Loss method) (lightning_pose.losses.losses.PCALoss method) (lightning_pose.losses.losses.RegressionMSELoss method) (lightning_pose.losses.losses.TemporalHeatmapLoss method) (lightning_pose.losses.losses.TemporalLoss method) (lightning_pose.losses.losses.UnimodalLoss method) (lightning_pose.utils.fiftyone.dfConverter method) (lightning_pose.utils.pca.ComponentChooser method) (lightning_pose.utils.pca.KeypointPCA method) (lightning_pose.utils.predictions.PredictionHandler method)

A

add_split_indices_to_df() (lightning_pose.utils.predictions.PredictionHandler method)

AnnealWeight (class in lightning_pose.callbacks)

B

BaseDataModule (class in lightning_pose.data.datamodules) BaseFeatureExtractor (class in lightning_pose.models.base) BaseLabeledBatchDict (class in lightning_pose.data.utils) BaseLabeledExampleDict (class in lightning_pose.data.utils)

BaseSupervisedTracker (class in lightning_pose.models.base) BaseTrackingDataset (class in lightning_pose.data.datasets) build_backbone() (in module lightning_pose.models.backbones.torchvision) (in module lightning_pose.models.backbones.vits) build_single_frame_keypoints() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method)

C

calculate_train_batches() (in module lightning_pose.utils.scripts) check_dataset() (in module lightning_pose.utils.fiftyone) check_if_semi_supervised() (in module lightning_pose.utils.io) check_lists_equal() (in module lightning_pose.utils.fiftyone) check_video_paths() (in module lightning_pose.utils.io) ckpt_path_from_base_path() (in module lightning_pose.utils.io) clean_any_nans() (in module lightning_pose.data.utils) ComponentChooser (class in lightning_pose.utils.pca) compute_loss() (lightning_pose.losses.losses.HeatmapJSLoss method) (lightning_pose.losses.losses.HeatmapKLLoss method) (lightning_pose.losses.losses.HeatmapLoss method) (lightning_pose.losses.losses.HeatmapMSELoss method) (lightning_pose.losses.losses.Loss method) (lightning_pose.losses.losses.PCALoss method) (lightning_pose.losses.losses.RegressionMSELoss method) (lightning_pose.losses.losses.RegressionRMSELoss method) (lightning_pose.losses.losses.TemporalHeatmapLoss method) (lightning_pose.losses.losses.TemporalLoss method) (lightning_pose.losses.losses.UnimodalLoss method)

compute_metrics() (in module lightning_pose.utils.scripts) compute_num_train_frames() (in module lightning_pose.data.utils) compute_reprojection_error() (lightning_pose.utils.pca.KeypointPCA method) configure_optimizers() (lightning_pose.models.base.BaseFeatureExtractor method) convert_dict_values_to_tensors() (in module lightning_pose.losses.helpers) count_frames() (in module lightning_pose.data.utils) create_dataset() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) create_double_upsampling_layer() (lightning_pose.models.heatmap_tracker.HeatmapTracker static method) create_labeled_video() (in module lightning_pose.utils.predictions) cumsum_explained_variance (lightning_pose.utils.pca.ComponentChooser attribute)

D

DataExtractor (class in lightning_pose.data.utils) dataset_info_print() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) dataset_length (lightning_pose.data.utils.DataExtractor attribute)

dfConverter (class in lightning_pose.utils.fiftyone) dict_per_bp() (lightning_pose.utils.fiftyone.dfConverter method) do_context (lightning_pose.utils.predictions.PredictionHandler attribute)

E

EmpiricalEpsilon (class in lightning_pose.losses.helpers) evaluate_heatmaps_at_location() (in module lightning_pose.data.utils)

evaluate_labeled() (lightning_pose.models.base.BaseSupervisedTracker method) evaluate_unlabeled() (lightning_pose.models.base.SemiSupervisedTrackerMixin method) export_predictions_and_labeled_video() (in module lightning_pose.utils.scripts)

F

FiftyOneImagePlotter (class in lightning_pose.utils.fiftyone) fix_context_preds_confs() (lightning_pose.utils.predictions.PredictionHandler method) format_multiview_data_for_pca() (in module lightning_pose.utils.pca) forward() (lightning_pose.models.base.BaseFeatureExtractor method) (lightning_pose.models.heatmap_tracker.HeatmapTracker method) (lightning_pose.models.heatmap_tracker_mhcrnn.HeatmapTrackerMHCRNN method) (lightning_pose.models.heatmap_tracker_mhcrnn.UpsamplingCRNN method) (lightning_pose.models.regression_tracker.RegressionTracker method)

frame_count (lightning_pose.utils.predictions.PredictionHandler attribute) full_labeled_dataloader() (lightning_pose.data.datamodules.BaseDataModule method)

G

generate_heatmaps() (in module lightning_pose.data.utils) get_callbacks() (in module lightning_pose.utils.scripts) get_cfg_file() (in module lightning_pose.utils.predictions) get_context_from_sequence() (in module lightning_pose.models.base) get_data_module() (in module lightning_pose.utils.scripts) get_dataset() (in module lightning_pose.utils.scripts) get_gt_keypoints_list() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) get_image_tags() (in module lightning_pose.utils.fiftyone) get_imgaug_transform() (in module lightning_pose.utils.scripts) get_keypoint_names() (in module lightning_pose.utils.io) get_keypoints_per_image() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) get_loader() (lightning_pose.data.utils.DataExtractor method) get_loss_classes() (in module lightning_pose.losses.losses) get_loss_factories() (in module lightning_pose.utils.scripts) get_loss_inputs_labeled() (lightning_pose.models.base.BaseSupervisedTracker method) (lightning_pose.models.heatmap_tracker.HeatmapTracker method) (lightning_pose.models.heatmap_tracker_mhcrnn.HeatmapTrackerMHCRNN method) (lightning_pose.models.regression_tracker.RegressionTracker method)

get_loss_inputs_unlabeled() (lightning_pose.models.base.SemiSupervisedTrackerMixin method) (lightning_pose.models.heatmap_tracker.SemiSupervisedHeatmapTracker method) (lightning_pose.models.heatmap_tracker_mhcrnn.SemiSupervisedHeatmapTrackerMHCRNN method) (lightning_pose.models.regression_tracker.SemiSupervisedRegressionTracker method) get_model() (in module lightning_pose.utils.scripts) get_model_abs_paths() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) get_model_class() (in module lightning_pose.utils.predictions) get_parameters() (lightning_pose.models.base.BaseFeatureExtractor method) (lightning_pose.models.base.BaseSupervisedTracker method) (lightning_pose.models.base.SemiSupervisedTrackerMixin method) (lightning_pose.models.heatmap_tracker_mhcrnn.HeatmapTrackerMHCRNN method) (lightning_pose.models.heatmap_tracker_mhcrnn.SemiSupervisedHeatmapTrackerMHCRNN method) get_pred_keypoints_dict() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) get_representations() (lightning_pose.models.base.BaseFeatureExtractor method) get_scheduler() (lightning_pose.models.base.BaseFeatureExtractor method) get_videos_in_dir() (in module lightning_pose.utils.io) grab_layers_sequential() (in module lightning_pose.models.backbones.torchvision)

H

HeatmapDataset (class in lightning_pose.data.datasets) HeatmapJSLoss (class in lightning_pose.losses.losses) HeatmapKLLoss (class in lightning_pose.losses.losses) HeatmapLabeledBatchDict (class in lightning_pose.data.utils) HeatmapLabeledExampleDict (class in lightning_pose.data.utils)

HeatmapLoss (class in lightning_pose.losses.losses) HeatmapMSELoss (class in lightning_pose.losses.losses) heatmaps_from_representations() (lightning_pose.models.heatmap_tracker.HeatmapTracker method) (lightning_pose.models.heatmap_tracker_mhcrnn.HeatmapTrackerMHCRNN method) HeatmapTracker (class in lightning_pose.models.heatmap_tracker) HeatmapTrackerMHCRNN (class in lightning_pose.models.heatmap_tracker_mhcrnn)

I

image_paths (lightning_pose.utils.fiftyone.FiftyOneImagePlotter attribute) img_height (lightning_pose.utils.fiftyone.FiftyOneImagePlotter attribute) img_width (lightning_pose.utils.fiftyone.FiftyOneImagePlotter attribute)

imgaug_transform() (in module lightning_pose.data.augmentations) initialize_layers() (lightning_pose.models.heatmap_tracker_mhcrnn.UpsamplingCRNN method) initialize_upsampling_layers() (lightning_pose.models.heatmap_tracker.HeatmapTracker method) iterate_over_dataloader() (lightning_pose.data.utils.DataExtractor method)

K

keypoint_names (lightning_pose.utils.predictions.PredictionHandler attribute)

KeypointPCA (class in lightning_pose.utils.pca)

L

lightning_pose.callbacks module lightning_pose.data.augmentations module lightning_pose.data.dali module lightning_pose.data.datamodules module lightning_pose.data.datasets module lightning_pose.data.utils module lightning_pose.losses.factory module lightning_pose.losses.helpers module lightning_pose.losses.losses module lightning_pose.metrics module lightning_pose.models.backbones.torchvision module lightning_pose.models.backbones.vit_img_encoder module lightning_pose.models.backbones.vits module

lightning_pose.models.base module lightning_pose.models.heatmap_tracker module lightning_pose.models.heatmap_tracker_mhcrnn module lightning_pose.models.regression_tracker module lightning_pose.utils.fiftyone module lightning_pose.utils.io module lightning_pose.utils.pca module lightning_pose.utils.predictions module lightning_pose.utils.scripts module lightning_pose.utils.tests module LitDaliWrapper (class in lightning_pose.data.dali) load_label_csv_from_cfg() (in module lightning_pose.utils.io) load_model_from_checkpoint() (in module lightning_pose.utils.predictions) load_model_predictions() (lightning_pose.utils.fiftyone.FiftyOneImagePlotter method) log_loss() (lightning_pose.losses.losses.Loss method) Loss (class in lightning_pose.losses.losses) LossFactory (class in lightning_pose.losses.factory)

M

make_cmap() (in module lightning_pose.utils.predictions) make_dlc_pandas_index() (in module lightning_pose.utils.predictions) (lightning_pose.utils.predictions.PredictionHandler method) make_pred_arr_undo_resize() (lightning_pose.utils.predictions.PredictionHandler method) make_upsampling_layers() (lightning_pose.models.heatmap_tracker.HeatmapTracker method) model_names (lightning_pose.utils.fiftyone.FiftyOneImagePlotter attribute) module lightning_pose.callbacks lightning_pose.data.augmentations lightning_pose.data.dali lightning_pose.data.datamodules lightning_pose.data.datasets lightning_pose.data.utils lightning_pose.losses.factory lightning_pose.losses.helpers lightning_pose.losses.losses lightning_pose.metrics lightning_pose.models.backbones.torchvision lightning_pose.models.backbones.vit_img_encoder lightning_pose.models.backbones.vits lightning_pose.models.base lightning_pose.models.heatmap_tracker lightning_pose.models.heatmap_tracker_mhcrnn lightning_pose.models.regression_tracker lightning_pose.utils.fiftyone lightning_pose.utils.io lightning_pose.utils.pca lightning_pose.utils.predictions lightning_pose.utils.scripts lightning_pose.utils.tests

N

num_filters_for_upsampling (lightning_pose.models.heatmap_tracker.HeatmapTracker attribute)

num_iters (lightning_pose.data.dali.PrepareDALI attribute) num_keypoints (lightning_pose.utils.fiftyone.FiftyOneImagePlotter attribute)

O

on_train_epoch_start() (lightning_pose.callbacks.AnnealWeight method)

on_train_start() (lightning_pose.callbacks.AnnealWeight method)

P

pca_multiview_reprojection_error() (in module lightning_pose.metrics) pca_prints() (lightning_pose.utils.pca.KeypointPCA method) pca_singleview_reprojection_error() (in module lightning_pose.metrics) PCALoss (class in lightning_pose.losses.losses) pixel_error() (in module lightning_pose.metrics) predict_dataset() (in module lightning_pose.utils.predictions)

predict_single_video() (in module lightning_pose.utils.predictions) predict_step() (lightning_pose.models.heatmap_tracker.HeatmapTracker method) (lightning_pose.models.heatmap_tracker_mhcrnn.HeatmapTrackerMHCRNN method) (lightning_pose.models.regression_tracker.RegressionTracker method) PredictionHandler (class in lightning_pose.utils.predictions) PrepareDALI (class in lightning_pose.data.dali)

R

rectify_epsilon() (lightning_pose.losses.losses.Loss method) (lightning_pose.losses.losses.TemporalHeatmapLoss method) (lightning_pose.losses.losses.TemporalLoss method) reduce_loss() (lightning_pose.losses.losses.Loss method) RegressionMSELoss (class in lightning_pose.losses.losses) RegressionRMSELoss (class in lightning_pose.losses.losses) RegressionTracker (class in lightning_pose.models.regression_tracker) remove_nans() (lightning_pose.losses.losses.HeatmapLoss method) (lightning_pose.losses.losses.Loss method) (lightning_pose.losses.losses.PCALoss method) (lightning_pose.losses.losses.RegressionMSELoss method) (lightning_pose.losses.losses.TemporalHeatmapLoss method) (lightning_pose.losses.losses.TemporalLoss method) (lightning_pose.losses.losses.UnimodalLoss method)

remove_string_w_substring_from_list() (in module lightning_pose.utils.fiftyone) reproject() (lightning_pose.utils.pca.KeypointPCA method) resample_abs_pos_embed_nhwc() (in module lightning_pose.models.backbones.vit_img_encoder) return_absolute_data_paths() (in module lightning_pose.utils.io) return_absolute_path() (in module lightning_pose.utils.io) run_hard_argmax() (lightning_pose.models.heatmap_tracker.HeatmapTracker method) run_subpixelmaxima() (lightning_pose.models.heatmap_tracker.HeatmapTracker method)

S

SemiSupervisedBatchDict (class in lightning_pose.data.utils) SemiSupervisedDataLoaderDict (class in lightning_pose.data.utils) SemiSupervisedHeatmapBatchDict (class in lightning_pose.data.utils) SemiSupervisedHeatmapTracker (class in lightning_pose.models.heatmap_tracker) SemiSupervisedHeatmapTrackerMHCRNN (class in lightning_pose.models.heatmap_tracker_mhcrnn)

SemiSupervisedRegressionTracker (class in lightning_pose.models.regression_tracker) SemiSupervisedTrackerMixin (class in lightning_pose.models.base) setup() (lightning_pose.data.datamodules.BaseDataModule method) setup_unlabeled() (lightning_pose.data.datamodules.UnlabeledDataModule method) split_sizes_from_probabilities() (in module lightning_pose.data.utils)

T

temporal_norm() (in module lightning_pose.metrics) TemporalHeatmapLoss (class in lightning_pose.losses.losses) TemporalLoss (class in lightning_pose.losses.losses) test_dataloader() (lightning_pose.data.datamodules.BaseDataModule method)

test_step() (lightning_pose.models.base.BaseSupervisedTracker method) train_dataloader() (lightning_pose.data.datamodules.BaseDataModule method) (lightning_pose.data.datamodules.UnlabeledDataModule method) training_step() (lightning_pose.models.base.BaseSupervisedTracker method) (lightning_pose.models.base.SemiSupervisedTrackerMixin method)

U

undo_affine_transform() (in module lightning_pose.data.utils) UnimodalLoss (class in lightning_pose.losses.losses) UnlabeledBatchDict (class in lightning_pose.data.utils)

UnlabeledDataModule (class in lightning_pose.data.datamodules) unpack_preds() (lightning_pose.utils.predictions.PredictionHandler method) upsample() (in module lightning_pose.models.heatmap_tracker) UpsamplingCRNN (class in lightning_pose.models.heatmap_tracker_mhcrnn)

V

val_dataloader() (lightning_pose.data.datamodules.BaseDataModule method) validation_step() (lightning_pose.models.base.BaseSupervisedTracker method)

verify_labeled_loader() (lightning_pose.data.utils.DataExtractor static method) video_pipe() (in module lightning_pose.data.dali)

W

weight (lightning_pose.losses.losses.Loss attribute)