Index

_

__indice_pairs (fish_corr.utility.Movie attribute)

__labels (fish_corr.utility.Movie attribute)

A

a2r_cost() (in module fish_corr.static) accept_buddy() (fish_gui.epipolar.StereoImageItem method) ActiveLinker (class in fish_track.linking) add() (fish_corr.utility.Movie method) add_neighbour() (fish_gui.measure_line.StereoImageItem method) add_new_measure() (fish_gui.measure_line.Model method)

add_shadow() (in module fish_track.kernel) alias (fish_gui.tplight.LB130 property) align_sub_image() (in module fish_track.shape) apply_network_link() (in module fish_track.linking) apply_network_merge() (in module fish_track.linking) AverageAnalyser (class in fish_corr.dynamic)

B

back (fish_gui.roi.Model property) (fish_gui.threshold.Model property) back() (fish_gui.shape_gallery.Model method) (fish_gui.shape_gallery.Viewer method) (fish_gui.threshold.Viewer method) biased_discrete_nd() (in module fish_corr.utility) bisection_search() (in module fish_corr.tower_sample)

box_count_polar_image() (in module fish_3d.utility) box_count_polar_video() (in module fish_3d.utility) box_density_polar() (in module fish_corr.static) break_into_two() (fish_track.linking.Trajectory method) brightness (fish_gui.tplight.LB130 property) brightness() (fish_gui.brightness.Controller method) build_dist_matrix_sparse() (in module fish_track.linking) build_tower() (in module fish_corr.tower_sample)

C

cache (fish_corr.dynamic.AverageAnalyser attribute) calib_mult_ext() (in module fish_3d.camera) calibrate() (fish_3d.camera.Camera method) calibrate_ext() (fish_3d.camera.Camera method) calibrate_int() (fish_3d.camera.Camera method) Camera (class in fish_3d.camera) check_order() (in module fish_gui.calib_order) choose_network() (in module fish_track.linking) color_rendering_index (fish_gui.tplight.LB130 attribute) Configure (class in fish_track.utility)

Controller (class in fish_gui.brightness) convert_traj_format() (in module fish_3d.utility) cost_conic() (in module fish_3d.ellipse) cost_conic_triple() (in module fish_3d.ellipse) cost_dist() (in module fish_track.linking) cost_merge() (in module fish_track.linking) cost_snell() (in module fish_3d.ray_trace) cost_xu() (in module fish_track.linking) Critic (class in fish_corr.dynamic) cursor (fish_gui.shape_gallery.Model property) curvilinear_2_cylindar() (fish_corr.static.Tank method)

D

decorrelated_scan_2() (fish_corr.dynamic.AverageAnalyser method) decorrelated_scan_3() (fish_corr.dynamic.AverageAnalyser method) decrypt() (in module fish_gui.decrypt) delete() (fish_gui.measure_line.Viewer method) depth (fish_gui.epipolar.Model property) (fish_gui.measure_line.Model property) detect_chessboard() (in module fish_3d.camera) detect_circle() (in module fish_track.utility) device_id (fish_gui.tplight.LB130 attribute)

distance() (fish_track.linking.Trajectory method) dragEnterEvent() (fish_gui.calib_order.Viewer method) (fish_gui.shape_gallery.Viewer method) draw() (in module fish_3d.camera) draw_2d() (in module fish_track.utility) draw_ellipse() (in module fish_3d.ellipse) draw_fish() (in module fish_3d.utility) dropEvent() (fish_gui.calib_order.Viewer method) (fish_gui.shape_gallery.Viewer method)

E

encrypt() (in module fish_gui.decrypt) encryption_key (fish_gui.tplight.LB130 attribute) epipolar_app() (in module fish_gui.epipolar) epipolar_draw() (in module fish_3d.ray_trace) epipolar_la() (in module fish_3d.ray_trace) epipolar_la_draw() (in module fish_3d.ray_trace)

epipolar_refractive() (in module fish_3d.ray_trace) export() (fish_gui.measure_line.Viewer method) export_json() (fish_gui.measure_line.Model method) export_xyz() (fish_corr.utility.SimMovie method) ext (fish_3d.camera.Camera.self attribute) extra_three_view_cluster_match() (in module fish_3d.stereolink)

F

fill_hole_1d() (in module fish_3d.utility) find_pairs() (in module fish_3d.camera) find_projection() (in module fish_3d.ellipse) find_u() (in module fish_3d.ray_trace) fish_3d module fish_3d.camera module fish_3d.cgreta module fish_3d.cray_trace module fish_3d.cstereo module fish_3d.ctemporal module fish_3d.cutility module fish_3d.ellipse module fish_3d.ray_trace module fish_3d.stereolink module fish_3d.utility module fish_corr module fish_corr.dynamic module fish_corr.static module fish_corr.tower_sample module fish_corr.utility module fish_corr.voro module

fish_gui module fish_gui.brightness module fish_gui.calib_order module fish_gui.decrypt module fish_gui.epipolar module fish_gui.measure_line module fish_gui.roi module fish_gui.shape_gallery module fish_gui.threshold module fish_gui.tplight module fish_track module fish_track.kernel module fish_track.linking module fish_track.nrook module, [1] fish_track.oishi module fish_track.read module fish_track.shape module fish_track.utility module fit_acf_exp() (in module fish_corr.utility) fit_maxwell_boltzmann() (in module fish_corr.utility) fit_rot_acf() (in module fish_corr.utility)

G

GCE (class in fish_corr.utility) get_ABCD() (in module fish_3d.utility) get_acf() (in module fish_corr.utility) get_acf_fft() (in module fish_corr.utility) get_affinity() (in module fish_3d.utility) get_align_diff() (in module fish_track.oishi) get_align_map() (in module fish_track.oishi) get_average_euclidean_transform() (in module fish_3d.utility) get_background() (fish_gui.threshold.Viewer method) (in module fish_track.read) get_background_movie() (in module fish_track.read) get_best_dilatation_rotation() (in module fish_corr.utility) get_best_rotation() (in module fish_corr.utility) get_biased_gr() (in module fish_corr.utility) get_biased_gr_randomly() (in module fish_corr.utility) get_box_for_kernel() (in module fish_track.oishi) get_brcs() (in module fish_3d.utility) get_cameras_with_averaged_euclidean_transform() (in module fish_3d.utility) get_centre() (in module fish_corr.utility) get_centre_move() (in module fish_corr.utility) get_centres() (in module fish_corr.utility) get_clusters() (in module fish_3d.utility) (in module fish_track.oishi) get_clusters_from_image() (in module fish_track.oishi) get_clusters_with_roi() (in module fish_track.oishi) get_conic_coef() (in module fish_3d.ellipse) get_conic_matrix() (in module fish_3d.ellipse) get_convex_hull_from_trajs() (in module fish_corr.utility) get_corners() (in module fish_3d.utility) get_corr_flctn() (fish_corr.dynamic.Critic method) get_curvilinear() (fish_corr.static.Tank method) get_cylinder() (fish_corr.static.Tank method) get_ep12() (fish_gui.epipolar.Model method) get_ep21() (fish_gui.epipolar.Model method) get_error() (in module fish_3d.cstereo) get_fg_color() (in module fish_gui.threshold) get_foreground_movie() (in module fish_track.read) get_frame() (in module fish_track.read) get_frame_number() (in module fish_track.read) get_frames_from_xyz() (in module fish_track.read) get_fundamental() (in module fish_3d.camera) get_fundamental_from_projections() (in module fish_3d.stereolink) get_geometric_coef() (in module fish_3d.ellipse) get_gr() (in module fish_corr.utility) get_gr_pbc() (in module fish_corr.utility) get_homography() (in module fish_3d.utility) get_homography_image() (in module fish_3d.utility) get_indices() (in module fish_3d.utility) get_indices_with_voro_volumes_select() (in module fish_corr.voro) get_intersect_multiple() (in module fish_3d.cray_trace) get_intersect_of_lines() (in module fish_3d.cray_trace) (in module fish_3d.ray_trace) get_intersect_of_lines_slow() (in module fish_3d.ray_trace) get_intersect_single() (in module fish_3d.cray_trace) get_intersection() (in module fish_3d.ellipse) get_isometry() (fish_corr.dynamic.Critic method) get_kernels() (in module fish_track.kernel) get_max() (fish_gui.roi.Viewer method) get_maxima() (in module fish_track.shape) get_mean_spd() (in module fish_corr.utility) get_min() (fish_gui.roi.Viewer method)

get_msd() (in module fish_corr.utility) get_nn() (in module fish_corr.static) get_nn_iter() (in module fish_corr.static) get_nn_iter_pbc() (in module fish_corr.static) get_nn_movie() (in module fish_corr.dynamic) get_nn_pbc() (in module fish_corr.static) get_nn_with_velocity() (in module fish_corr.static) get_nn_with_velocity_2d() (in module fish_corr.static) get_nn_with_velocity_pbc() (in module fish_corr.static) get_oishi_features() (in module fish_track.oishi) get_oishi_kernels() (in module fish_track.oishi) get_optimised_camera_c2c() (in module fish_3d.utility) get_optimised_camera_triplet_c2c() (in module fish_3d.utility) get_order_movie() (in module fish_corr.dynamic) get_orders() (fish_corr.dynamic.Critic method) get_orient_line() (in module fish_3d.utility) get_overlap_pairs() (in module fish_3d.utility) get_partial_cluster() (in module fish_3d.stereolink) get_poda() (in module fish_corr.static) get_poda_pbc() (in module fish_corr.static) get_poi() (in module fish_3d.ray_trace) get_poi_cluster() (in module fish_3d.ray_trace) get_points_from_order() (in module fish_3d.camera) get_polar_chop_spatial() (in module fish_3d.utility) get_position_pair() (fish_corr.dynamic.Critic method) get_projection() (fish_corr.static.Tank method) get_reproj_err() (in module fish_3d.ray_trace) get_reproject_error() (in module fish_3d.camera) get_rg_tensor() (in module fish_corr.utility) get_rot_mat() (in module fish_corr.static) get_rot_mat_2d() (in module fish_corr.static) get_shapes() (in module fish_track.shape) get_short_trajs() (in module fish_3d.utility) get_similarity() (fish_corr.dynamic.Critic method) (in module fish_3d.utility) get_spd_movie() (in module fish_corr.dynamic) get_std_spd() (in module fish_corr.utility) get_sub_image() (in module fish_track.oishi) get_sub_image_box() (in module fish_track.shape) get_sub_images() (in module fish_track.shape) get_temporal_overlapped_pairs() (in module fish_3d.utility) get_threshold() (in module fish_gui.threshold) get_trajectories() (in module fish_3d.ctemporal) get_trajectories_xyz() (in module fish_track.read) get_trajectory() (in module fish_track.linking) get_trajectory_batches() (in module fish_3d.utility) get_trajs_3d() (in module fish_3d.cgreta) get_trajs_3d_t1t2() (in module fish_3d.cgreta) get_trajs_3d_t1t2t3() (in module fish_3d.cgreta) get_trans_vec() (in module fish_3d.ray_trace) get_trans_vecs() (in module fish_3d.ray_trace) get_trimmed_trajs() (fish_corr.utility.Movie method) get_trimmed_velocities() (fish_corr.dynamic.AverageAnalyser method) get_u() (in module fish_3d.ray_trace) get_updated_camera() (in module fish_3d.utility) get_valid_ctraj() (in module fish_3d.utility) get_vanilla_gr() (in module fish_corr.utility) get_vicsek_order() (in module fish_corr.utility) get_voro_volumes() (in module fish_corr.voro) get_voro_volumes_select() (in module fish_corr.voro) get_xyz() (fish_corr.static.Tank method) greedy_match() (in module fish_3d.stereolink)

H

hsb (fish_gui.tplight.LB130 property)

hue (fish_gui.tplight.LB130 property)

I

incandescent_equivalent (fish_gui.tplight.LB130 attribute) index (fish_gui.measure_line.StereoImageItem attribute) index_map (fish_gui.measure_line.Model property) indice_pair() (fish_corr.utility.Movie method) (fish_corr.utility.SimMovie method) interpolate() (fish_corr.utility.Trajectory method) (fish_track.linking.Trajectory method) interpolate_nan() (in module fish_3d.utility)

is_inside() (in module fish_track.shape) is_inside_image() (in module fish_3d.ray_trace) is_pbc (fish_corr.dynamic.Critic attribute) is_simulation (fish_corr.dynamic.Critic attribute) is_valid (fish_gui.epipolar.Model property) (fish_gui.measure_line.Model property) iter_image_sequence() (in module fish_track.read) iter_video() (in module fish_gui.roi) (in module fish_track.read)

J

join_pairs() (in module fish_3d.cutility) (in module fish_3d.stereolink) (in module fish_track.oishi) (in module fish_track.utility)

K

keyPressEvent() (fish_gui.shape_gallery.Viewer method)

L

label (fish_gui.shape_gallery.Photo property) (fish_gui.threshold.Model property) label() (fish_corr.utility.Movie method) (fish_corr.utility.SimMovie method) lamp_beam_angle (fish_gui.tplight.LB130 attribute) LB130 (class in fish_gui.tplight) light_details() (fish_gui.tplight.LB130 method) line (fish_gui.measure_line.StereoImageItem attribute) line2func() (in module fish_3d.stereolink)

line_measure_app() (in module fish_gui.measure_line) link() (fish_track.linking.ActiveLinker method) (fish_track.linking.TrackpyLinker method) load() (fish_corr.utility.Movie method) (fish_corr.utility.SimMovie method) (fish_gui.measure_line.Viewer method) (fish_gui.roi.Viewer method) load_json() (fish_3d.camera.Camera method) (fish_gui.measure_line.Model method) locate_v3() (in module fish_3d.cstereo)

M

main() (in module fish_gui.decrypt) make() (fish_corr.utility.Movie method) (fish_corr.utility.SimMovie method) make_difference_movie() (in module fish_track.read) mark() (fish_gui.shape_gallery.Model method) match_clusters() (in module fish_3d.stereolink) match_ellipse_sloopy() (in module fish_3d.ellipse) match_points_v3() (in module fish_3d.stereolink) match_v3() (in module fish_3d.cstereo) match_v3_verbose() (in module fish_3d.cstereo) max (fish_gui.roi.Model property) max_lumens (fish_gui.tplight.LB130 attribute) max_voltage (fish_gui.tplight.LB130 attribute) maxwell_boltzmann_nd() (in module fish_corr.utility) measure() (fish_gui.measure_line.Viewer method) measure_roi() (in module fish_gui.roi) measurements_2d (fish_gui.measure_line.Model attribute) measurements_3d (fish_gui.measure_line.Model attribute) merge_trajectories() (in module fish_track.linking) min (fish_gui.roi.Model property) min_voltage (fish_gui.tplight.LB130 attribute) Model (class in fish_gui.calib_order) (class in fish_gui.epipolar) (class in fish_gui.measure_line) (class in fish_gui.roi) (class in fish_gui.shape_gallery) (class in fish_gui.threshold) model (fish_gui.measure_line.StereoImageItem attribute) module fish_3d fish_3d.camera fish_3d.cgreta fish_3d.cray_trace fish_3d.cstereo fish_3d.ctemporal fish_3d.cutility fish_3d.ellipse fish_3d.ray_trace fish_3d.stereolink fish_3d.utility fish_corr fish_corr.dynamic fish_corr.static fish_corr.tower_sample fish_corr.utility fish_corr.voro fish_gui fish_gui.brightness fish_gui.calib_order fish_gui.decrypt fish_gui.epipolar fish_gui.measure_line fish_gui.roi fish_gui.shape_gallery fish_gui.threshold fish_gui.tplight fish_track fish_track.kernel fish_track.linking fish_track.nrook, [1] fish_track.oishi fish_track.read fish_track.shape fish_track.utility

mouseClickEvent() (fish_gui.epipolar.StereoImageItem method) (fish_gui.measure_line.StereoImageItem method) (fish_gui.shape_gallery.Photo method) Movie (class in fish_corr.utility) movie (fish_corr.dynamic.AverageAnalyser attribute) (fish_corr.dynamic.Critic attribute) (fish_corr.utility.Movie attribute) multi_view_link() (in module fish_3d.stereolink)

N

neighbours (fish_gui.measure_line.StereoImageItem attribute) next (fish_gui.roi.Model property) (fish_gui.threshold.Model property) next() (fish_gui.shape_gallery.Model method) (fish_gui.shape_gallery.Viewer method) (fish_gui.threshold.Viewer method)

normal (fish_gui.epipolar.Model property) (fish_gui.measure_line.Model property)

O

o (fish_3d.camera.Camera.self attribute) o2v() (in module fish_track.oishi) off() (fish_gui.tplight.LB130 method) offset() (fish_corr.utility.Trajectory method) (fish_track.linking.Trajectory method)

on() (fish_gui.tplight.LB130 method) optimise_c2c() (in module fish_3d.utility) optimise_triplet_c2c() (in module fish_3d.utility)

P

p (fish_3d.camera.Camera.self attribute) parse_ellipses_imagej() (in module fish_3d.ellipse) pdist_pbc() (in module fish_corr.utility) Photo (class in fish_gui.shape_gallery) pl_dist() (in module fish_3d.ray_trace) pl_dist_batch() (in module fish_3d.ray_trace) pl_dist_faster() (in module fish_3d.ray_trace) plot (fish_gui.measure_line.StereoImageItem attribute) plot_cameras() (in module fish_3d.camera) (in module fish_3d.utility) plot_epl() (in module fish_3d.utility)

plot_pca() (in module fish_track.kernel) plot_reproject() (in module fish_3d.utility) plot_reproject_with_roi() (in module fish_3d.utility) plot_spatial_3d() (in module fish_corr.utility) polar_chop() (in module fish_3d.utility) post_process_ctraj() (in module fish_3d.utility) predict() (fish_corr.utility.Trajectory method) (fish_track.linking.Trajectory method) project() (fish_3d.camera.Camera method) project_refractive() (fish_3d.camera.Camera method) py_get_intersect_of_lines_batch() (in module fish_3d.ray_trace)

R

r (fish_3d.camera.Camera.self attribute) rand_max (fish_gui.roi.Model property) rand_min (fish_gui.roi.Model property) random() (fish_corr.static.Tank method) random_curvilinear() (fish_corr.static.Tank method) ray_trace_refractive() (in module fish_3d.ray_trace) ray_trace_refractive_cluster() (in module fish_3d.ray_trace) ray_trace_refractive_faster() (in module fish_3d.ray_trace) ray_trace_refractive_trajectory() (in module fish_3d.ray_trace) read_calibration() (fish_3d.camera.Camera method) read_int() (fish_3d.camera.Camera method) reboot() (fish_gui.tplight.LB130 method) redistort_points() (fish_3d.camera.Camera method) reduce_angle_gap() (in module fish_corr.static) reduce_network() (in module fish_track.linking)

refine_oishi_features() (in module fish_track.oishi) refine_trajectory() (in module fish_3d.utility) refractive_project() (in module fish_3d.cstereo) refractive_triangulate() (in module fish_3d.cstereo) relink() (in module fish_track.linking) relink_by_segments() (in module fish_track.linking) remove_conflict() (in module fish_3d.stereolink) remove_measure() (fish_gui.measure_line.Model method) remove_overlap() (in module fish_3d.stereolink) remove_spatial_overlap() (in module fish_3d.utility) reproject_refractive() (in module fish_3d.ray_trace) reproject_refractive_no_distort() (in module fish_3d.ray_trace) resolve_temporal_overlap() (in module fish_3d.utility) retrace() (fish_track.linking.Trajectory method) rotate_kernel() (in module fish_track.oishi)

S

same_direction() (in module fish_3d.ray_trace) saturation (fish_gui.tplight.LB130 property) save() (fish_3d.camera.Camera method) (fish_corr.utility.Movie method) (fish_corr.utility.SimMovie method) (fish_gui.measure_line.Viewer method) (fish_gui.roi.Viewer method) (fish_gui.shape_gallery.Viewer method) (fish_gui.threshold.Viewer method) save_cache() (fish_corr.dynamic.AverageAnalyser method) save_json() (fish_3d.camera.Camera method) save_xyz() (fish_corr.utility.Movie method) save_xyz_with_tank() (fish_corr.utility.Movie method) scan_array() (fish_corr.dynamic.AverageAnalyser method) scan_array_std() (fish_corr.dynamic.AverageAnalyser method) scan_biased_attraction() (fish_corr.dynamic.AverageAnalyser method) scan_biased_attraction_err() (fish_corr.dynamic.AverageAnalyser method) scan_biased_gr() (fish_corr.dynamic.AverageAnalyser method) scan_gr() (fish_corr.dynamic.AverageAnalyser method) scan_nn() (fish_corr.dynamic.AverageAnalyser method) scan_nn_pbc() (fish_corr.dynamic.AverageAnalyser method) scan_nn_pbc_std() (fish_corr.dynamic.AverageAnalyser method) scan_nn_std() (fish_corr.dynamic.AverageAnalyser method)

scan_number() (fish_corr.dynamic.AverageAnalyser method) scan_orientation_acf() (fish_corr.dynamic.AverageAnalyser method) scan_rotation() (fish_corr.dynamic.AverageAnalyser method) scan_rotation_err() (fish_corr.dynamic.AverageAnalyser method) scan_speed() (fish_corr.dynamic.AverageAnalyser method) scan_speed_std() (fish_corr.dynamic.AverageAnalyser method) scan_vicsek_order() (fish_corr.dynamic.AverageAnalyser method) scan_vicsek_order_std() (fish_corr.dynamic.AverageAnalyser method) see_corners() (in module fish_3d.utility) segment_trajectories() (in module fish_track.linking) select() (fish_gui.measure_line.Viewer method) shape_gallery() (in module fish_gui.shape_gallery) SimMovie (class in fish_corr.utility) solve_nrook() (in module fish_track.nrook), [1] solve_nrook_dense() (in module fish_track.nrook), [1] solve_overlap_lp() (in module fish_3d.utility) solve_unique() (in module fish_track.linking) sort_trajectories() (in module fish_track.linking) squeeze_sparse() (in module fish_track.linking) status() (fish_gui.tplight.LB130 method) StereoImageItem (class in fish_gui.epipolar) (class in fish_gui.measure_line) SubProperty (class in fish_track.utility)

T

Tank (class in fish_corr.static) temperature (fish_gui.tplight.LB130 property) three_view_cluster_match() (in module fish_3d.stereolink) three_view_match() (in module fish_3d.stereolink) time (fish_gui.tplight.LB130 property) time_filter_link() (in module fish_track.linking) time_filter_merge() (in module fish_track.linking) timezone (fish_gui.tplight.LB130 property)

tower_sampling() (in module fish_corr.tower_sample) TrackpyLinker (class in fish_track.linking) Trajectory (class in fish_corr.utility) (class in fish_track.linking) trajs (fish_corr.dynamic.Critic attribute) (fish_corr.utility.Movie attribute) transition_period (fish_gui.tplight.LB130 property) triangulation_v3() (in module fish_3d.stereolink)

U

undistort() (fish_3d.camera.Camera method) undistort_image() (fish_3d.camera.Camera method) undistort_points() (fish_3d.camera.Camera method) unzip_essential() (fish_3d.camera.Camera method) update() (fish_3d.camera.Camera method) (fish_gui.shape_gallery.Viewer method) (fish_gui.threshold.Viewer method)

update_color() (fish_gui.shape_gallery.Photo method) update_orientation() (in module fish_3d.utility) update_text() (fish_gui.threshold.Viewer method) update_trajs() (fish_corr.utility.Movie method)

V

validate() (in module fish_track.utility) vanilla_pca() (in module fish_track.kernel) velocity() (fish_corr.utility.Movie method) (fish_corr.utility.SimMovie method) Viewer (class in fish_gui.calib_order) (class in fish_gui.epipolar) (class in fish_gui.measure_line) (class in fish_gui.roi) (class in fish_gui.shape_gallery) (class in fish_gui.threshold)

W

warn() (in module fish_gui.calib_order) (in module fish_gui.measure_line) (in module fish_gui.shape_gallery)

water_level (fish_gui.epipolar.Model property) (fish_gui.measure_line.Model property) wattage (fish_gui.tplight.LB130 attribute) write() (fish_track.utility.Configure method)

Z

z() (fish_corr.static.Tank method)

zip_essential() (fish_3d.camera.Camera method)