as_viewr |
Convert data from another format into a viewr object |
bind_viewr_objects |
Bind viewr objects |
calc_min_dist_box |
Calculate minimum distance to lateral and end walls in a box-shaped experimental tunnel |
calc_min_dist_v |
Calculate minimum distance to lateral and end walls in a V-shaped experimental tunnel |
clean_by_span |
Remove file_sub_traj entries that do not span the full region of interest |
clean_viewr |
All-in-one function to clean imported objects |
clean_viewr_batch |
Batch clean viewr files |
deg_2_rad |
Convert degrees to radians |
exclude_by_velocity |
Remove trajectories entirely, based on velocity thresholds |
fill_traj_gaps |
Interpolate gaps within trajectories |
find_curve_elbow |
Find the "elbow" of a curve. |
gather_tunnel_data |
Gather data columns into key-value pairs |
get_2d_angle |
Compute an angle in 2D space |
get_3d_angle |
Compute an angle in 3D space |
get_3d_cross_prod |
Compute the cross product of two 3D vectors |
get_dist_point_line |
Compute distance between a point and a line |
get_full_trajectories |
Retain trajectories that span a selected region of interest |
get_header_viewr |
Extract header info from imported viewr object |
get_sf |
Estimate the spatial frequency of visual stimuli from the subject's perspective in an experimental tunnel. |
get_traj_velocities |
Recompute trajectory-specific velocities |
get_velocity |
Get instantaneous velocity for subjects |
get_vis_angle |
Estimate visual angles from a subject's perspective in an experimental tunnel |
import_and_clean_batch |
Batch import and clean files |
import_and_clean_viewr |
Import + clean_viewr() |
import_batch |
Batch import of files for either Motive or Flydra (but not a mix of both) |
insert_treatments |
Inserts treatment and experiment information |
plot_by_subject |
Plot trajectories and density plots of position by subject |
plot_viewr_trajectories |
Plot each trajectory within a viewr object |
quick_separate_trajectories |
Quick version of separate_trajectories() |
rad_2_deg |
Convert radians to degrees |
read_flydra_mat |
Import data from a MAT file exported from Flydra software |
read_motive_csv |
Import data from a CSV exported from Optitrack's Motive software |
redefine_tunnel_center |
"Center" the tunnel data, i.e. translation but no rotation |
relabel_viewr_axes |
Relabel the dimensions as length, width, and height |
remove_duplicate_frames |
Remove any duplicates or aliased frames within trajectories |
remove_vel_anomalies |
Remove any rows which show sharp shifts in velocity that are likely due to tracking errors |
rename_viewr_characters |
Rename subjects in the data via pattern detection |
rescale_tunnel_data |
Rescale position data within a 'viewr' object |
rm_by_trajnum |
Remove subjects by trajectory number |
rotate_tunnel |
Rotate a tunnel so that perches are approximately aligned |
section_tunnel_by |
Bin data along a specified axis |
select_x_percent |
Select a region of interest within the tunnel |
separate_trajectories |
Separate rows of data into separately labeled trajectories. |
set_traj_frametime |
Redefine frames and time stamps on a per-trajectory basis |
standardize_tunnel |
Rotate and center a tunnel based on landmarks |
trim_tunnel_outliers |
Trim out artifacts and other outliers from the extremes of the tunnel |
visualize_frame_gap_choice |
Visualize the consequence of using various max_frame_gap values |