deepof package

Submodules

• deepof.data module
  • deepof.data
  • deepof.data.load_project
    • load_project()
  • deepof.data.Coordinates
    • Coordinates
      • Coordinates.__init__()
      • Coordinates.__init__()
  • deepof.data.Project
    • Project
      • Project.__init__()
      • Project.__init__()
  • deepof.data.TableDict
    • TableDict
      • TableDict.__init__()
      • TableDict.__init__()
• deepof.deepof_train_embeddings module
• deepof.hypermodels module
  • deepof.hypermodels
• deepof.models module
  • deepof.models
  • deepof.models.get_TCN_decoder
    • get_TCN_decoder()
  • deepof.models.get_TCN_encoder
    • get_TCN_encoder()
  • deepof.models.get_recurrent_decoder
    • get_recurrent_decoder()
  • deepof.models.get_recurrent_encoder
    • get_recurrent_encoder()
  • deepof.models.get_transformer_decoder
    • get_transformer_decoder()
  • deepof.models.get_transformer_encoder
    • get_transformer_encoder()
  • deepof.models.get_vade
    • get_vade()
  • deepof.models.get_vqvae
    • get_vqvae()
  • deepof.models.Classifier
    • Classifier
      • Classifier.__init__()
      • Classifier.__init__()
  • deepof.models.Contrastive
    • Contrastive
      • Contrastive.__init__()
      • Contrastive.__init__()
  • deepof.models.GaussianMixtureLatent
    • GaussianMixtureLatent
      • GaussianMixtureLatent.__init__()
      • GaussianMixtureLatent.__init__()
  • deepof.models.VQVAE
    • VQVAE
      • VQVAE.__init__()
      • VQVAE.__init__()
  • deepof.models.VaDE
    • VaDE
      • VaDE.__init__()
      • VaDE.__init__()
  • deepof.models.VectorQuantizer
    • VectorQuantizer
      • VectorQuantizer.__init__()
      • VectorQuantizer.__init__()
• deepof.post_hoc module
  • deepof.post_hoc
  • deepof.post_hoc.recluster
    • recluster()
  • deepof.post_hoc.get_time_on_cluster
    • get_time_on_cluster()
  • deepof.post_hoc.get_aggregated_embedding
    • get_aggregated_embedding()
  • deepof.post_hoc.select_time_bin
    • select_time_bin()
  • deepof.post_hoc.condition_distance_binning
    • condition_distance_binning()
  • deepof.post_hoc.separation_between_conditions
    • separation_between_conditions()
  • deepof.post_hoc.fit_normative_global_model
    • fit_normative_global_model()
  • deepof.post_hoc.enrichment_across_conditions
    • enrichment_across_conditions()
  • deepof.post_hoc.get_transitions
    • get_transitions()
  • deepof.post_hoc.compute_transition_matrix_per_condition
    • compute_transition_matrix_per_condition()
  • deepof.post_hoc.compute_steady_state
    • compute_steady_state()
  • deepof.post_hoc.compute_UMAP
    • compute_UMAP()
  • deepof.post_hoc.align_deepof_kinematics_with_unsupervised_labels
    • align_deepof_kinematics_with_unsupervised_labels()
  • deepof.post_hoc.chunk_summary_statistics
    • chunk_summary_statistics()
  • deepof.post_hoc.annotate_time_chunks
    • annotate_time_chunks()
  • deepof.post_hoc.chunk_cv_splitter
    • chunk_cv_splitter()
  • deepof.post_hoc.train_supervised_cluster_detectors
    • train_supervised_cluster_detectors()
  • deepof.post_hoc.explain_clusters
    • explain_clusters()
• deepof.annotation_utils module
  • deepof.annotation_utils
  • deepof.annotation_utils.climb_wall
    • climb_wall()
  • deepof.annotation_utils.close_double_contact
    • close_double_contact()
  • deepof.annotation_utils.close_single_contact
    • close_single_contact()
  • deepof.annotation_utils.following_path
    • following_path()
  • deepof.annotation_utils.frame_corners
    • frame_corners()
  • deepof.annotation_utils.get_hparameters
    • get_hparameters()
  • deepof.annotation_utils.huddle
    • huddle()
  • deepof.annotation_utils.look_around
    • look_around()
  • deepof.annotation_utils.max_behaviour
    • max_behaviour()
  • deepof.annotation_utils.outside_ellipse
    • outside_ellipse()
  • deepof.annotation_utils.rotate
    • rotate()
  • deepof.annotation_utils.sniff_object
    • sniff_object()
  • deepof.annotation_utils.supervised_tagging
    • supervised_tagging()
  • deepof.annotation_utils.tagged_video_output
    • tagged_video_output()
• deepof.model_utils module
  • deepof.model_utils
  • deepof.model_utils.cluster_frequencies_regularizer
    • cluster_frequencies_regularizer()
  • deepof.model_utils.compute_kmeans_loss
    • compute_kmeans_loss()
  • deepof.model_utils.compute_shannon_entropy
    • compute_shannon_entropy()
  • deepof.model_utils.create_look_ahead_mask
    • create_look_ahead_mask()
  • deepof.model_utils.create_masks
    • create_masks()
  • deepof.model_utils.create_padding_mask
    • create_padding_mask()
  • deepof.model_utils.dcl_loss
    • dcl_loss()
  • deepof.model_utils.embedding_model_fitting
    • embedding_model_fitting()
  • deepof.model_utils.embedding_per_video
    • embedding_per_video()
  • deepof.model_utils.fc_loss
    • fc_loss()
  • deepof.model_utils.find_learning_rate
    • find_learning_rate()
  • deepof.model_utils.get_angles
    • get_angles()
  • deepof.model_utils.get_callbacks
    • get_callbacks()
  • deepof.model_utils.get_hard_counts
    • get_hard_counts()
  • deepof.model_utils.get_k_nearest_neighbors
    • get_k_nearest_neighbors()
  • deepof.model_utils.get_recurrent_block
    • get_recurrent_block()
  • deepof.model_utils.hard_loss
    • hard_loss()
  • deepof.model_utils.log_hyperparameters
    • log_hyperparameters()
  • deepof.model_utils.nce_loss
    • nce_loss()
  • deepof.model_utils.plot_lr_vs_loss
    • plot_lr_vs_loss()
  • deepof.model_utils.positional_encoding
    • positional_encoding()
  • deepof.model_utils.select_contrastive_loss
    • select_contrastive_loss()
  • deepof.model_utils.tune_search
    • tune_search()
  • deepof.model_utils.ClusterControl
    • ClusterControl
      • ClusterControl.__init__()
      • ClusterControl.__init__()
  • deepof.model_utils.CustomStopper
    • CustomStopper
      • CustomStopper.__init__()
      • CustomStopper.__init__()
  • deepof.model_utils.ExponentialLearningRate
    • ExponentialLearningRate
      • ExponentialLearningRate.__init__()
      • ExponentialLearningRate.__init__()
  • deepof.model_utils.ProbabilisticDecoder
    • ProbabilisticDecoder
      • ProbabilisticDecoder.__init__()
      • ProbabilisticDecoder.__init__()
  • deepof.model_utils.TransformerDecoder
    • TransformerDecoder
      • TransformerDecoder.__init__()
      • TransformerDecoder.__init__()
  • deepof.model_utils.TransformerDecoderLayer
    • TransformerDecoderLayer
      • TransformerDecoderLayer.__init__()
      • TransformerDecoderLayer.__init__()
  • deepof.model_utils.TransformerEncoder
    • TransformerEncoder
      • TransformerEncoder.__init__()
      • TransformerEncoder.__init__()
  • deepof.model_utils.TransformerEncoderLayer
    • TransformerEncoderLayer
      • TransformerEncoderLayer.__init__()
      • TransformerEncoderLayer.__init__()
• deepof.utils module
  • deepof.utils
  • deepof.utils.align_trajectories
    • align_trajectories()
  • deepof.utils.angle
    • angle()
  • deepof.utils.arena_parameter_extraction
    • arena_parameter_extraction()
  • deepof.utils.automatically_recognize_arena
    • automatically_recognize_arena()
  • deepof.utils.bp2polar
    • bp2polar()
  • deepof.utils.bpart_distance
    • bpart_distance()
  • deepof.utils.closest_side
    • closest_side()
  • deepof.utils.cluster_transition_matrix
    • cluster_transition_matrix()
  • deepof.utils.compute_animal_presence_mask
    • compute_animal_presence_mask()
  • deepof.utils.compute_areas
    • compute_areas()
  • deepof.utils.compute_dist
    • compute_dist()
  • deepof.utils.connect_mouse
    • connect_mouse()
  • deepof.utils.edges_to_weighted_adj
    • edges_to_weighted_adj()
  • deepof.utils.enumerate_all_bridges
    • enumerate_all_bridges()
  • deepof.utils.extract_polygonal_arena_coordinates
    • extract_polygonal_arena_coordinates()
  • deepof.utils.filter_columns
    • filter_columns()
  • deepof.utils.filter_short_bouts
    • filter_short_bouts()
  • deepof.utils.fit_ellipse_to_polygon
    • fit_ellipse_to_polygon()
  • deepof.utils.full_outlier_mask
    • full_outlier_mask()
  • deepof.utils.get_arenas
    • get_arenas()
  • deepof.utils.gmm_compute
    • gmm_compute()
  • deepof.utils.gmm_model_selection
    • gmm_model_selection()
  • deepof.utils.interpolate_outliers
    • interpolate_outliers()
  • deepof.utils.iterative_imputation
    • iterative_imputation()
  • deepof.utils.kleinberg
    • kleinberg()
  • deepof.utils.load_segmentation_model
    • load_segmentation_model()
  • deepof.utils.load_table
    • load_table()
  • deepof.utils.mask_outliers
    • mask_outliers()
  • deepof.utils.moving_average
    • moving_average()
  • deepof.utils.rename_track_bps
    • rename_track_bps()
  • deepof.utils.retrieve_corners_from_image
    • retrieve_corners_from_image()
  • deepof.utils.rolling_speed
    • rolling_speed()
  • deepof.utils.rolling_window
    • rolling_window()
  • deepof.utils.rotate
    • rotate()
  • deepof.utils.rupture_per_experiment
    • rupture_per_experiment()
  • deepof.utils.scale_animal
    • scale_animal()
  • deepof.utils.scale_table
    • scale_table()
  • deepof.utils.set_missing_animals
    • set_missing_animals()
  • deepof.utils.simplify_polygon
    • simplify_polygon()
  • deepof.utils.smooth_boolean_array
    • smooth_boolean_array()
  • deepof.utils.smooth_mult_trajectory
    • smooth_mult_trajectory()
  • deepof.utils.split_with_breakpoints
    • split_with_breakpoints()
  • deepof.utils.str2bool
    • str2bool()
  • deepof.utils.tab2polar
    • tab2polar()
• deepof.visuals module
  • deepof.visuals
  • deepof.visuals.plot_arena
    • plot_arena()
  • deepof.visuals.heatmap
    • heatmap()
  • deepof.visuals.plot_heatmaps
    • plot_heatmaps()
  • deepof.visuals.plot_gantt
    • plot_gantt()
  • deepof.visuals.plot_enrichment
    • plot_enrichment()
  • deepof.visuals.plot_transitions
    • plot_transitions()
  • deepof.visuals.plot_stationary_entropy
    • plot_stationary_entropy()
  • deepof.visuals.plot_normative_log_likelihood
    • plot_normative_log_likelihood()
  • deepof.visuals.plot_embeddings
    • plot_embeddings()
  • deepof.visuals.animate_skeleton
    • animate_skeleton()
  • deepof.visuals.plot_cluster_detection_performance
    • plot_cluster_detection_performance()
  • deepof.visuals.plot_shap_swarm_per_cluster
    • plot_shap_swarm_per_cluster()
  • deepof.visuals.output_cluster_video
    • output_cluster_video()
  • deepof.visuals.output_videos_per_cluster
    • output_videos_per_cluster()
  • deepof.visuals.output_unsupervised_annotated_video
    • output_unsupervised_annotated_video()
  • deepof.visuals.export_annotated_video
    • export_annotated_video()
  • deepof.visuals.plot_distance_between_conditions
    • plot_distance_between_conditions()
  • deepof.visuals.tag_annotated_frames
    • tag_annotated_frames()
  • deepof.visuals.annotate_video
    • annotate_video()

Module contents