Index

_

_allowed_filetypes (core.triangulation_calibration_module.Triangulation attribute)

A

add_errors_between_computed_and_ground_truth_angles() (in module core.angles_and_distances) add_errors_between_computed_and_ground_truth_distances_for_different_references() (in module core.angles_and_distances) add_ground_truth_config() (core.triangulation_calibration_module.CalibrationValidation method), [1] add_motif_template() (core.video_synchronization.MultiMotifTemplate method), [1] add_recording_config() (core.filename_checker.FilenameCheckerInterface method), [1] (core.meta.MetaInterface method), [1] add_recording_manually() (core.filename_checker.FilenameCheckerInterface method) (core.meta.MetaInterface method) add_reprojection_errors_of_all_calibration_validation_markers() (in module core.angles_and_distances) add_triangulated_csv_to_database() (core.meta.MetaInterface method) adjust_template_timeseries_to_fps() (core.video_synchronization.MotifTemplate method) (core.video_synchronization.MultiMotifTemplate method) (core.video_synchronization.TimeseriesTemplate method)

AlignmentPlotCrossvalidation (class in core.plotting) AlignmentPlotIndividual (class in core.plotting) all_cameras (core.triangulation_calibration_module.Triangulation attribute) allowed_num_diverging_frames (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) analyze_objects() (core.marker_detection.DeeplabcutInterface method) (core.marker_detection.ManualAnnotation method) (core.marker_detection.MarkerDetection method) anipose_io (core.triangulation_calibration_module.Triangulation attribute)

C

calibrate() (core.meta.MetaInterface method) calibrate_optimal() (core.triangulation_calibration_module.Calibration method), [1] Calibration (class in core.triangulation_calibration_module) calibration (core.video_metadata.VideoMetadata.self attribute) calibration_index (core.checker_objects.CheckCalibration attribute) (core.checker_objects.CheckCalibrationValidation attribute) (core.checker_objects.CheckRecording attribute) (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) calibration_tag (core.triangulation_calibration_module.Calibration attribute) calibration_validation_tag (core.triangulation_calibration_module.Triangulation attribute) CalibrationValidation (class in core.triangulation_calibration_module) CalibrationValidationPlot (class in core.plotting) calvin (core.video_metadata.VideoMetadata.self attribute) cam_id (core.video_metadata.VideoMetadata.self attribute) camera_group (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation.self attribute) camera_objects (core.triangulation_calibration_module.Calibration attribute) cams_to_exclude (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) CharucoVideoSynchronizer (class in core.video_synchronization) check_keys() (in module core.utils) CheckCalibration (class in core.checker_objects) CheckCalibrationValidation (class in core.checker_objects) checkerboard_rows_and_columns (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) (core.camera_intrinsics.IntrinsicCameraCalibrator property) CheckRecording (class in core.checker_objects) construct_dlc_output_style_df_from_dictionary() (in module core.utils) construct_template_motif() (in module core.video_synchronization) convert_to_path() (in module core.utils) Coordinates (class in core.utils) core module core.angles_and_distances module core.camera_intrinsics module

core.checker_objects module core.filename_checker module core.marker_detection module core.meta module core.plotting module core.triangulation_calibration_module module core.user_specific_rules module core.utils module core.video_interface module core.video_metadata module core.video_synchronization module create_calibration_key() (in module core.utils) create_calibrations() (core.filename_checker.FilenameCheckerInterface method) (core.meta.MetaInterface method) create_plot() (core.plotting.AlignmentPlotCrossvalidation method) (core.plotting.AlignmentPlotIndividual method) (core.plotting.CalibrationValidationPlot method) (core.plotting.Intrinsics method) (core.plotting.LEDMarkerPlot method) (core.plotting.PredictionsPlot method) (core.plotting.RotationVisualization method) (core.plotting.TriangulationVisualization method) create_recordings() (core.filename_checker.FilenameCheckerInterface method) (core.meta.MetaInterface method) create_triangulated_video() (core.triangulation_calibration_module.TriangulationRecordings method) csv_output_filepath (core.triangulation_calibration_module.Triangulation attribute)

D

d (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) (core.camera_intrinsics.IntrinsicCameraCalibrator property)

DeeplabcutInterface (class in core.marker_detection)

E

evaluate_triangulation_of_calibration_validation_markers() (core.triangulation_calibration_module.CalibrationValidation method), [1] exclude_markers() (core.meta.MetaInterface method) (core.triangulation_calibration_module.Triangulation method)

exclusion_state (core.video_metadata.VideoMetadata.self attribute) export_for_aniposelib() (core.video_interface.VideoInterface method) export_meta_to_yaml() (core.meta.MetaInterface method)

F

FilenameCheckerInterface (class in core.filename_checker)

filepath (core.video_metadata.VideoMetadata.self attribute) filepath_calibration_video (core.camera_intrinsics.IntrinsicCameraCalibrator attribute)

G

get_3D_array() (in module core.utils) get_3D_df_keys() (in module core.utils) get_marker_predictions() (core.triangulation_calibration_module.CalibrationValidation method), [1]

get_multi_index() (in module core.utils) get_xyz_distance_in_triangulation_space() (in module core.angles_and_distances) ground_truth_config (core.triangulation_calibration_module.Triangulation attribute)

I

imsize (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) (core.camera_intrinsics.IntrinsicCameraCalibrator property) initialize_meta_config() (core.filename_checker.FilenameCheckerInterface method) (core.meta.MetaInterface method) inspect_intrinsic_calibration() (core.video_interface.VideoInterface method) intrinsic_calibration (core.video_metadata.VideoMetadata.self attribute)

intrinsic_calibration_filepath (core.video_metadata.VideoMetadata.self attribute) IntrinsicCalibratorFisheyeCamera (class in core.camera_intrinsics) IntrinsicCalibratorRegularCameraCheckerboard (class in core.camera_intrinsics) IntrinsicCameraCalibrator (class in core.camera_intrinsics) IntrinsicCameraCalibratorCheckerboard (class in core.camera_intrinsics) Intrinsics (class in core.plotting)

K

k (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) (core.camera_intrinsics.IntrinsicCameraCalibrator property)

KEYS_TO_CHECK_CAMERA_RECORDING (in module core.utils) KEYS_TO_CHECK_PROJECT (in module core.utils) KEYS_TO_CHECK_RECORDING (in module core.utils)

L

led_box_size (core.video_synchronization.Synchronizer attribute) led_detection (core.video_synchronization.Synchronizer attribute) led_detection_individuals (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) led_on_time_in_ms (core.video_synchronization.MotifTemplate attribute) led_pattern (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute)

led_timeseries (core.video_synchronization.Synchronizer attribute) led_timeseries_for_cross_video_validation (core.video_synchronization.Synchronizer attribute) LEDMarkerPlot (class in core.plotting) load_distances_from_ground_truth() (in module core.angles_and_distances) load_image() (in module core.utils) load_single_frame_of_video() (in module core.utils)

M

ManualAnnotation (class in core.marker_detection) marker_detection_directory (core.marker_detection.MarkerDetection attribute) MarkerDetection (class in core.marker_detection) markers (core.triangulation_calibration_module.Triangulation attribute) markers_excluded_manually (core.triangulation_calibration_module.Triangulation attribute) max_calibration_frames (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) meta (core.filename_checker.FilenameCheckerInterface attribute) (core.meta.MetaInterface attribute) metadata_from_videos (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) MetaInterface (class in core.meta) module core core.angles_and_distances core.camera_intrinsics core.checker_objects core.filename_checker core.marker_detection core.meta core.plotting core.triangulation_calibration_module core.user_specific_rules core.utils core.video_interface core.video_metadata core.video_synchronization

motif_duration_in_ms (core.video_synchronization.MotifTemplate attribute) motif_templates (core.video_synchronization.MultiMotifTemplate attribute) MotifTemplate (class in core.video_synchronization) mouse_id (core.checker_objects.CheckRecording attribute) (core.triangulation_calibration_module.Triangulation attribute) (core.video_metadata.VideoMetadata.self attribute) mouse_line (core.video_metadata.VideoMetadata.self attribute) mouse_number (core.video_metadata.VideoMetadata.self attribute) multi_motif_template (core.video_synchronization.MultiMotifTemplate attribute) MultiMotifTemplate (class in core.video_synchronization)

N

normalised_dataframe (core.triangulation_calibration_module.Triangulation attribute)

normalize() (core.triangulation_calibration_module.TriangulationRecordings method) normalize_recordings() (core.meta.MetaInterface method)

O

object_to_analyse (core.marker_detection.MarkerDetection attribute) objects (core.filename_checker.FilenameCheckerInterface attribute) (core.meta.MetaInterface attribute) objp (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) (core.camera_intrinsics.IntrinsicCameraCalibrator property)

on_off_period_length_in_ms (core.video_synchronization.MotifTemplate attribute) output_directory (core.marker_detection.MarkerDetection attribute) (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) (core.video_synchronization.Synchronizer attribute)

P

paradigm (core.checker_objects.CheckRecording attribute) (core.triangulation_calibration_module.Triangulation attribute) (core.video_metadata.VideoMetadata.self attribute) paradigms (core.filename_checker.FilenameCheckerInterface attribute) (core.meta.MetaInterface attribute) plot_image() (in module core.utils)

plot_single_frame_of_video() (in module core.utils) PredictionsPlot (class in core.plotting) project_config_filepath (core.filename_checker.FilenameCheckerInterface attribute) (core.meta.MetaInterface attribute) (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) project_name (core.meta.MetaInterface attribute)

R

rapid_aligner_path (core.video_synchronization.Synchronizer attribute) read_config() (in module core.utils) recording (core.video_metadata.VideoMetadata.self attribute) recording_configs (core.filename_checker.FilenameCheckerInterface attribute) (core.meta.MetaInterface attribute) recording_date (core.checker_objects.CheckCalibration attribute) (core.checker_objects.CheckCalibrationValidation attribute) (core.checker_objects.CheckRecording attribute) (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) (core.video_metadata.VideoMetadata.self attribute) recording_dates (core.filename_checker.FilenameCheckerInterface attribute) (core.meta.MetaInterface attribute) RecordingVideoDownSynchronizer (class in core.video_synchronization) RecordingVideoSynchronizer (class in core.video_synchronization)

RecordingVideoUpSynchronizer (class in core.video_synchronization) remove_recordings() (core.filename_checker.FilenameCheckerInterface method) (core.meta.MetaInterface method) report_filepath (core.triangulation_calibration_module.Calibration attribute) reprojerr (core.triangulation_calibration_module.Calibration attribute) return_fig() (core.plotting.TriangulationVisualization method) rotated_filepath (core.triangulation_calibration_module.Triangulation attribute) RotationVisualization (class in core.plotting) run() (core.camera_intrinsics.IntrinsicCameraCalibrator method), [1] run_calibration() (core.triangulation_calibration_module.Calibration method), [1] run_synchronization() (core.triangulation_calibration_module.Calibration method), [1] (core.triangulation_calibration_module.TriangulationRecordings method) (core.video_synchronization.Synchronizer method), [1] run_synchronizer() (core.video_interface.VideoInterface method) run_triangulation() (core.triangulation_calibration_module.Triangulation method)

S

select_recording_configs() (core.filename_checker.FilenameCheckerInterface method) (core.meta.MetaInterface method) set_distances_and_angles_for_evaluation() (in module core.angles_and_distances) standard_yaml_filepath (core.meta.MetaInterface attribute) synchro_metadata (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) (core.video_synchronization.Synchronizer attribute)

synchronization_individuals (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) synchronize_calibrations() (core.meta.MetaInterface method) synchronize_recordings() (core.meta.MetaInterface method) synchronized_charuco_videofiles (core.triangulation_calibration_module.Calibration attribute) Synchronizer (class in core.video_synchronization)

T

target_fps (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) (core.video_synchronization.Synchronizer property) template_attribute_string (core.video_synchronization.MotifTemplate property) (core.video_synchronization.MultiMotifTemplate property) (core.video_synchronization.TimeseriesTemplate property) template_blinking_motif (core.video_synchronization.Synchronizer attribute)

template_timeseries (core.video_synchronization.MotifTemplate attribute) TimeseriesTemplate (class in core.video_synchronization) triangulate_recordings() (core.meta.MetaInterface method) Triangulation (class in core.triangulation_calibration_module) triangulation_dlc_cams_filepaths (core.triangulation_calibration_module.Triangulation attribute) triangulation_visualization (core.triangulation_calibration_module.Triangulation attribute) TriangulationRecordings (class in core.triangulation_calibration_module) TriangulationVisualization (class in core.plotting)

U

use_gpu (core.video_synchronization.Synchronizer attribute) use_rapid_aligner (core.video_synchronization.Synchronizer attribute)

user_specific_rules_on_triangulation_calibration_videos() (in module core.user_specific_rules) user_specific_rules_on_videometadata() (in module core.user_specific_rules)

V

valid_videos (core.triangulation_calibration_module.Calibration attribute) video_interfaces (core.triangulation_calibration_module.Calibration attribute) (core.triangulation_calibration_module.Triangulation attribute) video_metadata (core.video_synchronization.Synchronizer attribute) video_plotting_config (core.triangulation_calibration_module.Triangulation attribute)

video_reader (core.camera_intrinsics.IntrinsicCameraCalibrator attribute) video_start_s (core.triangulation_calibration_module.Triangulation attribute) VideoInterface (class in core.video_interface) VideoMetadata (class in core.video_metadata) VideoMetadataChecker (class in core.video_metadata)

X

x (core.utils.Coordinates attribute)

Z

z (core.utils.Coordinates attribute)