TadPose
0.1

Contents

  • Overview
    • What problem does TadPose address?
    • The pipeline
    • What the method recovers
    • Provenance
  • Installation
    • Environment
    • Dependencies
    • Configure machine-specific paths (required first step)
  • Usage
    • Command-line interface
    • Choosing the number of clusters
    • Using the library
    • High-performance computing
  • Ring CNN — well-geometry detector
    • What it predicts
    • Architecture
    • Training data
    • Loss and optimisation
    • The background projection — the decisive design choice
    • Inference and deployment
    • Reproducing
  • API reference
    • Configuration
      • PathConfigError
      • active_profile()
      • active_profile_name()
      • configured_path()
      • data_root()
      • export_lines()
      • get()
      • get_path()
      • main()
      • profile()
      • main()
    • Acquisition and pose estimation
      • WellDetector
      • main()
      • split_plate_video()
      • VideoInfoExtractor
      • main()
    • Feature extraction
      • align_posture()
      • compute_com()
      • compute_frons()
      • compute_posture_dynamics()
      • compute_velocity()
      • compute_yaw()
      • correct_eye_positions()
      • extract_features()
      • interpolate_low_confidence()
      • main()
      • px_per_frame_to_mm_per_s()
      • clean_features()
      • clean_features_from_array()
      • plot_feature_histograms()
      • compute_and_save_mu_sigma()
      • compute_mu_sigma()
      • de_z_score()
      • load_mu_sigma()
      • save_mu_sigma()
      • z_score()
    • Clustering
      • calinski_harabasz()
      • leave_out()
      • main()
      • make_output_paths()
      • meta_path()
      • run_kmeans()
      • ClusterMetaAnalysis
      • ClusterPlotter
      • main()
      • write_results_to_jsonFile()
      • CentroidProcessor
    • Cluster validation (choosing k)
      • compute_inertia()
      • compute_instability()
      • compute_silhouette_stratified()
      • gather_meta_metrics()
      • locate_elbow_kneedle()
      • main()
      • parse_columns()
      • plot_selection()
      • plot_selection_metrics()
      • recompute_inertia_for_meta_dir()
      • selection_summary()
    • Post-clustering analysis
      • analyse_proportions()
      • assign_groups()
      • compute_trial_proportions()
      • group_summary()
      • proportions_long()
      • compare_cluster_proportions()
      • compare_groups()
      • permutation_test_proportions()
      • ClusterInfo
      • ClusterMap
      • identity_map()
      • map_from_dict()
      • thesis_k36_map()
      • TadpoleMarkovChain
      • main()
      • plot_above_transitions()
      • plot_threshold_transitions()
      • plot_transition_matrix()
      • TadpoleMarkovChain
      • TadpoleMarkovChainGroupAnalysis
      • main()
      • plot_above_transitions()
      • plot_threshold_transitions()
      • plot_transition_matrix()
      • assign_clusters_from_numpy()
      • assign_new_data_to_clustering()
      • main()
      • nearest_centroid()
      • normalise_and_assign()
      • add_clustering_labels()
      • main()
    • Visualisation
      • apply_tadpose_style()
      • kinematic_label()
      • make_results_tree()
      • pm_category()
      • pm_label()
      • save_figure()
      • sig_letter()
      • sig_stars()
      • plot_centroid()
      • plot_centroid_grid()
      • plot_kinematics_cross()
      • plot_posture()
      • proportion_bars()
      • raincloud()
      • raincloud_grid()
      • raincloud_with_stats()
    • Database and experiment management
      • Base
      • BodyPart
      • Clustering
      • ClusteringFeatureStat
      • ClusteringRun
      • ClusteringRunTrial
      • ClusteringType
      • DatabaseHandler
      • ExperimentSeries
      • ExperimentType
      • ExperimentTypeAttribute
      • FrameCluster
      • FrameClusterProportion
      • Frog
      • Investigator
      • Posture
      • TadpoleGroup
      • TimeSeries
      • Trajectory
      • Trial
      • Velocity
      • Video
      • WellGeometry
      • WellType
      • WellTypeAttribute
      • FileManager
      • PlateManager
      • ExperimentManager
      • PresetManager
      • ResultManager
      • main()
      • SlurmJobManager
      • TadpoleFrameExtractor
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