example_scripts/vis_percept_reviews.R
In vbaliga/pathviewR: Wrangle, Analyze, and Visualize Animal Movement Data
## work space for addressing visual perception functions reviews
## change argument for vertex_angle to mean the actual angle of the V in the
## V-shaped tunnel. Build into insert_treatments() a calculation that makes it
## work with calc_min_dist functions
## insert_treatments()
## use tunnel_length argument so that front/back wall distances can be calculated
insert_treatments <- function(obj_name,
tunnel_config = "box",
perch_2_vertex = NULL,
vertex_angle = NULL, # actual angle of vertex
tunnel_width = NULL,
tunnel_length = NULL,
stim_param_lat_pos = NULL,
stim_param_lat_neg = NULL,
stim_param_end_pos = NULL,
stim_param_end_neg = NULL,
treatment = NULL){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_full_trajectories has been run prior to use
if (!any(attr(obj_name, "pathviewr_steps") == "full_trajectories")){
stop("Run get_full_trajectories() prior to use")
}
## Translate arguments into variables at beginning of data frame
if (tunnel_config == "v"){
## Check that relevant numerical arguments have positive values
if (perch_2_vertex < 0){
stop("perch_2_vertex must have a positive value.")
} else if (vertex_angle < 0){
stop("vertex_angle must have a positive value")
} else if (tunnel_length < 0){
stop("tunnel_length must have a positive value")
} else if (stim_param_lat_pos < 0){
stop("stim_param_lat_pos must have a positive value")
} else if (stim_param_lat_neg < 0){
stop("stim_param_lat_neg must have a positive value")
} else if (stim_param_end_pos < 0){
stop("stim_param_end_pos must have a positive value")
} else if (stim_param_end_neg < 0){
stop("stim_param_end_neg must have a positive value")
}
obj_name <- tibble::add_column(obj_name, .before = "frame",
tunnel_config = tunnel_config,
perch_2_vertex = perch_2_vertex,
vertex_angle = deg_2_rad(vertex_angle/2),
tunnel_length = tunnel_length,
stim_param_lat_pos = stim_param_lat_pos,
stim_param_lat_neg = stim_param_lat_neg,
stim_param_end_pos = stim_param_end_pos,
stim_param_end_neg = stim_param_end_neg,
treatment = treatment)
} else if (tunnel_config == "box"){
## Check that relevant numerical arguments have positive values
if (tunnel_width < 0){
stop("tunnel_width must have a positive value")
} else if (tunnel_length < 0){
stop("tunnel_length must have a positive value")
} else if (stim_param_lat_pos < 0){
stop("stim_param_lat_pos must have a positive value")
} else if (stim_param_lat_neg < 0){
stop("stim_param_lat_neg must have a positive value")
} else if (stim_param_end_pos < 0){
stop("stim_param_end_pos must have a positive value")
} else if (stim_param_end_neg < 0){
stop("stim_param_end_neg must have a positive value")
}
obj_name <- tibble::add_column(obj_name, .before = "frame",
tunnel_config = tunnel_config,
tunnel_width = tunnel_width,
tunnel_length= tunnel_length,
stim_param_lat_pos = stim_param_lat_pos,
stim_param_lat_neg = stim_param_lat_neg,
stim_param_end_pos = stim_param_end_pos,
stim_param_end_neg = stim_param_end_neg,
treatment = treatment)
}
## Add arguments into metadata......surewhynot
if (tunnel_config == "v"){
attr(obj_name, "tunnel_config") <- tunnel_config
attr(obj_name, "perch_2_vertex") <- perch_2_vertex
attr(obj_name, "vertex_angle") <- vertex_angle
attr(obj_name, "tunnel_width") <- tunnel_width
attr(obj_name, "tunnel_length") <- tunnel_length
attr(obj_name, "stim_param_lat_pos") <- stim_param_lat_pos
attr(obj_name, "stim_param_lat_neg") <- stim_param_lat_neg
attr(obj_name, "stim_param_end_pos") <- stim_param_end_pos
attr(obj_name, "stim_param_end_neg") <- stim_param_end_neg
attr(obj_name, "treatment") <- treatment
} else if (tunnel_config == "box"){
attr(obj_name, "tunnel_config") <- tunnel_config
attr(obj_name, "tunnel_width") <- tunnel_width
attr(obj_name, "tunnel_length") <- tunnel_length
attr(obj_name, "stim_param_lat_pos") <- stim_param_lat_pos
attr(obj_name, "stim_param_lat_neg") <- stim_param_lat_neg
attr(obj_name, "stim_param_end_pos") <- stim_param_end_pos
attr(obj_name, "stim_param_end_neg") <- stim_param_end_neg
attr(obj_name, "treatment") <- treatment
}
## Leave note that treatments were added
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"treatments_added")
return(obj_name)
}
# min_dist function for V-shaped tunnel
# get min_dist for front/back wall by using direction of bird flight to
# determine the distance to the opposite wall. Then can use this distance to
# get vis_angle, sf, tf, image vel, and image expansion from the front of the
# tunnel
calc_min_dist_v <- function(obj_name,
simplify = TRUE){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that insert_treatments() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "treatments_added")){
stop("Please run insert_treatments() prior to use")
}
## duplicate object for simplify = TRUE
obj_simplify <- obj_name
## For distance to lateral walls ##
## Introduce variables for vertical_2_vertex and vertical_2_screen
## vertical_2_vertex and vertical_2_screen refer to the vertical distance
## between the subject's position and the the vertex of the tunnel and screen
## below them, respectively.
obj_name$vertical_2_vertex <-
abs(obj_name$perch_2_vertex) + obj_name$position_height
obj_name$vertical_2_screen <-
obj_name$vertical_2_vertex -
(abs(obj_name$position_width) / tan(obj_name$vertex_angle))
## Introduce variables for horizontal_2_screen on positive and negative sides
## of the tunnel.
## horizontal_2_screen refers to the horizontal distance between the bird and
## either screen.
obj_name$horizontal_2_screen_pos <-
ifelse(obj_name$position_width >= 0, # if in positive side of tunnel
obj_name$vertical_2_screen * tan(obj_name$vertex_angle), # TRUE
(obj_name$vertical_2_screen * tan(obj_name$vertex_angle)) +
(2 * abs(obj_name$position_width))) # FALSE
obj_name$horizontal_2_screen_neg <-
ifelse(obj_name$position_width < 0, # if in negative side of tunnel
obj_name$vertical_2_screen * tan(obj_name$vertex_angle), # TRUE
(obj_name$vertical_2_screen * tan(obj_name$vertex_angle)) +
(2 * abs(obj_name$position_width))) # FALSE
## Introduce variable min_dist on positive and negative sides of the
## tunnel. min_dist refers to the minimum distance between the bird and either
## screen (axis of gaze is orthogonal to plane of each screen)
obj_name$min_dist_pos <-
obj_name$horizontal_2_screen_pos * sin(pi/2 - obj_name$vertex_angle)
# min_dist to positive screen
obj_name$min_dist_neg <-
obj_name$horizontal_2_screen_neg * sin(pi/2 - obj_name$vertex_angle)
# min_dist to negative screen
## When the subject is outside the boundaries created by orthogonal planes to
## each wall, erroneous visual angles are calculated.
## Therefore we must adjust min_dist values according to position_width
## Create variable holding the boundary values for each observation
obj_name$bound_pos <-
obj_name$vertical_2_vertex * tan(pi/2 - obj_name$vertex_angle)
obj_name$bound_neg <-
obj_name$vertical_2_vertex * -tan(pi/2 - obj_name$vertex_angle)
obj_name$min_dist_pos <- # overwrite min_dist_pos
ifelse(obj_name$position_width <= 0 &
obj_name$position_width <= obj_name$bound_neg,
# if position_width is positive and greater than the boundary value
sqrt(obj_name$vertical_2_vertex^2 + obj_name$position_width^2),
# return distance to vertex
obj_name$min_dist_pos)
# return original min_dist_pos calculation
obj_name$min_dist_neg <-
ifelse(obj_name$position_width >= 0 &
obj_name$position_width >= obj_name$bound_pos,
# if position_width is negative and smaller than the boundary value
sqrt(obj_name$vertical_2_vertex^2 + obj_name$position_width^2),
# return distance to vertex
obj_name$min_dist_neg)
# return original min_dist_neg calculation
## For minimum distances to end walls (assuming animal locomotes forward)
obj_name$min_dist_end <-
ifelse(obj_name$end_length_sign == 1,
obj_name$tunnel_length/2 - obj_name$position_length,
obj_name$tunnel_length/2 + obj_name$position_length)
## for simplify = TRUE
obj_simplify$min_dist_pos <- obj_name$min_dist_pos
obj_simplify$min_dist_neg <- obj_name$min_dist_neg
obj_simplify$min_dist_end <- obj_name$min_dist_end
## return object and add note that minimum distaces were calculated
if(simplify == TRUE){
attr(obj_simplify, "pathviewr_steps") <-
c(attr(obj_name, "pathviewr_steps"), "min_dist_calculated")
return(obj_simplify)
} else {
attr(obj_name, "pathviewr_steps") <-
c(attr(obj_name, "pathviewr_steps"), "min_dist_calculated")
return(obj_name)
}
}
## min_dist function for box shaped chamber
calc_min_dist_box <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")) {
stop("This doesn't seem to be a viewr object")
}
## Check that insert_treatments() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "treatments_added")){
stop("Please run insert_treatments() prior to use")
}
## Calculate minimum distance to each wall from positive or negative sides of
## tunnel
obj_name$min_dist_pos <- obj_name$tunnel_width/2 - obj_name$position_width
obj_name$min_dist_neg <- obj_name$tunnel_width/2 + obj_name$position_width
## For minimum distances to end walls (assuming animal locomotes forward)
obj_name$min_dist_end <-
ifelse(obj_name$end_length_sign == 1,
obj_name$tunnel_length/2 - obj_name$position_length,
obj_name$tunnel_length/2 + obj_name$position_length)
## Leave note that minimum distances were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"min_dist_calculated")
return(obj_name)
}
## get_vis_angle
## include vis_angle for end wall
get_vis_angle <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that calc_min_dist() has been run
if (!any(attr(obj_name, "pathviewr_steps") == "min_dist_calculated")){
stop("Please run calc_min_dist_v() or calc_min_dist_box() prior to use")
}
## Calculate visual angles (radians and degrees) using distance to
## positive and negative screens. Add these variables into the dataframe.
# visual angle to positive wall
obj_name$vis_angle_pos_rad <-
2*atan(obj_name$stim_param_lat_pos/(2*obj_name$min_dist_pos))
# visual angle to negative wall
obj_name$vis_angle_neg_rad <-
2*atan(obj_name$stim_param_lat_neg/(2*obj_name$min_dist_neg))
# visual angle to end wall (depending on direction of locomotion)
obj_name$vis_angle_end_rad <-
ifelse(obj_name$end_length_sign == 1,
2*atan(obj_name$stim_param_end_pos/(2*obj_name$min_dist_end)),
2*atan(obj_name$stim_param_end_neg/(2*obj_name$min_dist_end)))
# convert to degrees
obj_name$vis_angle_pos_deg <- rad_2_deg(obj_name$vis_angle_pos_rad)
obj_name$vis_angle_neg_deg <- rad_2_deg(obj_name$vis_angle_neg_rad)
obj_name$vis_angle_end_deg <- rad_2_deg(obj_name$vis_angle_end_rad)
## Leave a note that visual angles were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"vis_angles_calculated")
return(obj_name)
}
## get_sf
## include sf for front wall?
get_sf <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## spatial frequency (cycles/rad) is the inverse of visual angle (rad/cycle)
obj_name$sf_pos <- 1/obj_name$vis_angle_pos_deg
obj_name$sf_neg <- 1/obj_name$vis_angle_neg_deg
obj_name$sf_end <- 1/obj_name$vis_angle_end_deg
## Leave a note that visual angles were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"sf_calculated")
return(obj_name)
}
## get_tf
get_tf <- function(obj_name,
dimensionality = NULL){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## Check that get_velocity() has been run
if (!any(attr(obj_name, "pathviewr_steps") == "velocity_computed")){
stop("Please run get_velocity() prior to use")
}
## Temporal frequency (cycles/second)instantaneous velocity of the subject and
## the arc length of the cycle from the subject's perspective
## For box-shaped tunnel
if (attr(obj_name, "tunnel_config") == "box"){
## Lateral wall 1D (axial) temporal frequencies
# tf of positive wall from forward movement
obj_name$tf_forward_pos <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# tf of negative wall from forward movement
obj_name$tf_forward_neg <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
# tf of positive wall from vertical movement
obj_name$tf_vertical_pos <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# tf of negative wall from vertical movement
obj_name$tf_vertical_neg <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
# tf of end wall from horizontal movement
## End wall 1D (axial) temporal frequencies
# tf of end wall from horizontal movement
obj_name$tf_horizontal_end <-
abs(obj_name$width_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
# tf of end wall from vertical movement
obj_name$tf_vertical_end <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
## Lateral wall 2D (planar) temporal frequencies
# relevant locomotion
obj_name$lat_planar_inst_vel <-
sqrt(obj_name$length_inst_vel^2 + obj_name$height_inst_vel^2)
# planar tf from positive wall
obj_name$tf_planar_pos <-
abs(obj_name$lat_planar_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# planar tf from negative wall
obj_name$tf_planar_neg <-
abs(obj_name$lat_planar_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
## End wall 2d (planar) temporal frequency
# relevant locomotion
obj_name$end_planar_inst_vel <-
sqrt(obj_name$width_inst_vel^2 + obj_name$height_inst_vel^2)
# planar tf from end wall
obj_name$tf_planar_end <-
abs(obj_name$end_planar_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
## for v-shaped tunnel
} else if (attr(obj_name, "tunnel_config") == "v"){
## Lateral wall 1D (axial) temporal frequencies
# tf of positive wall from forward movement
obj_name$tf_forward_pos <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# tf of negative wall from forward movement
obj_name$tf_forward_neg <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
## End wall 1D (axial) temporal frequencies
# tf of end wall from horizontal movement
obj_name$tf_horizontal_end <-
abs(obj_name$width_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
# tf of end wall from vertical movement
obj_name$tf_vertical_end <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
## End wall 2d (planar) temporal frequency
# relevant locomotion
obj_name$end_planar_inst_vel <-
sqrt(obj_name$width_inst_vel^2 + obj_name$height_inst_vel^2)
# planar tf from end wall
obj_name$tf_planar_end <-
abs(obj_name$end_planar_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
}
### analysis of how multi-dimensional motion affects temporal frequency is in
### development for V-shaped tunnel configurations
## Leave a note that temporal frequencies were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"tf_calculated")
return(obj_name)
}
## get_pattern_velocity
## include pattern velocity for end wall
get_pattern_vel <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## Check that get_sf() and get_tf() have been run
if (!any(attr(obj_name, "pathviewr_steps") == "sf_calculated")){
stop("Please run get_sf() prior to use")
} else if (!any(attr(obj_name, "pathviewr_steps") == "tf_calculated")){
stop("Please run get_tf() prior to use")
}
## For box-shaped tunnel configuration
if (attr(obj_name, "tunnel_config") == "box"){
## Lateral wall 1D (axial) pattern velocities
# forward pattern velocity from positive wall
obj_name$forward_pattern_vel_pos <-
obj_name$tf_forward_pos/obj_name$sf_pos
# forward pattern velocity from negative wall
obj_name$forward_pattern_vel_neg <-
obj_name$tf_forward_neg/obj_name$sf_neg
# vertical pattern velocity from positive wall
obj_name$vertical_pattern_vel_pos <-
obj_name$tf_vertical_pos/obj_name$sf_pos
# vertical pattern velocity from negative wall
obj_name$vertical_pattern_vel_neg <-
obj_name$tf_vertical_neg/obj_name$sf_neg
## End wall 1D (axial) pattern velocities
# horizontal pattern velocity from end wall
obj_name$horizontal_pattern_vel_end <-
obj_name$tf_horizontal_end/obj_name$sf_end
# vertical pattern velocity from end wall
obj_name$vertical_pattern_vel_end <-
obj_name$tf_vertical_end/obj_name$sf_end
## Lateral wall 2D (planar) pattern velocities
# planar pattern velocity from positive wall
obj_name$planar_pattern_vel_pos <- o
bj_name$tf_planar_pos/obj_name$sf_pos
# planar pattern velocity from negative wall
obj_name$planar_pattern_vel_neg <-
obj_name$tf_planar_neg/obj_name$sf_neg
## End wall 2D (planar) pattern velocity
# planar pattern velocity from positive wall
obj_name$planar_pattern_vel_end <-
obj_name$tf_planar_end/obj_name$sf_end
## For v-shaped tunnel configuration
} else if (attr(obj_name, "tunnel_config") == "v"){
## Lateral wall 1D (axial) pattern velocities
# forward pattern velocity for positive wall
obj_name$forward_pattern_vel_pos <-
obj_name$tf_forward_pos/obj_name$sf_pos
# forward pattern velocity for negative wall
obj_name$forward_pattern_vel_neg <-
obj_name$tf_forward_neg/obj_name$sf_neg
## End wall 1D (axial) pattern velocities
# horizontal pattern velocity from end wall
obj_name$horizontal_pattern_vel_end <-
obj_name$tf_horizontal_end/obj_name$sf_end
# vertical pattern velocity from end wall
obj_name$vertical_pattern_vel_end <-
obj_name$tf_vertical_end/obj_name$sf_end
## End wall 2D (planar) pattern velocity
# planar pattern velocity from positive wall
obj_name$planar_pattern_vel_end <-
obj_name$tf_planar_end/obj_name$sf_end
}
## Leave a note that pattern velocities were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"pattern_vel_calculated")
return(obj_name)
}
## get image expansion
get_image_expansion <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## Convert obj_name to data.frame for diff functions
obj_name <- as.data.frame(obj_name)
## Get relevant frame-by-frame differences
time_diff <- c(NA, diff(obj_name[,"time_sec"]))
pos_angle_diff <- c(NA, diff(obj_name[,"vis_angle_pos_deg"]))
neg_angle_diff <- c(NA, diff(obj_name[,"vis_angle_neg_deg"]))
end_angle_diff <- c(NA, diff(obj_name[,"vis_angle_end_deg"]))
obj_name$expansion_pos <- pos_angle_diff/time_diff
obj_name$expansion_neg <- neg_angle_diff/time_diff
obj_name$expansion_end <- end_angle_diff/time_diff
obj_name$time_diff <- time_diff
## Leave note that image expansion was calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"image_expansion_calculated")
return(as_tibble(obj_name))
}
# get pattern velocity direction
# All functions, including this one assume the bird is looking straight ahead
# (i.e. a "rightwards" flight means the bird is always facing "rightwards" etc.)
# Once head orientation is included, this function will include an offset equal
# to the head orientation for each observation
get_pattern_vel_direction <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_velocity() has been run
if (!any(attr(obj_name, "pathviewr_steps") == "velocity_computed")){
stop("Please run get_velocity() prior to use")
}
## For lateral walls, forward pattern velocity is 0 degree/360 degree and intermediate
## angles fill the circle counter-clockwise.
## The direction of pattern velocity depends on the end wall to which the
## subject is facing and whether it's moving forward or backward.
## for box-shaped tunnel configurations
if (attr(obj_name, "tunnel_config") == "box"){
obj_name$lat_pattern_direction <-
ifelse(obj_name$end_length_sign == 1,
# when facing positive end of tunnel
ifelse(obj_name$length_inst_vel >= 0,
# when moving forward
180 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)),
# when moving backward
(360 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)))) %% 360,
# when facing negative end of tunnel
ifelse(obj_name$length_inst_vel < 0,
# when moving forward
180 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)),
# when moving backward
(360 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)))) %% 360
)
## For end wall, rightward pattern velocity is 0 degree or 360 degree and intermediate
## angles fill the circle counter-clockwise.
## The direction of pattern velocity depends on the end wall to which the
## subject is facing and whether it's moving towards the positive or negative
## lateral walls.
obj_name$end_pattern_direction <-
ifelse(obj_name$end_length_sign == 1,
# when facing positive end of tunnel
ifelse(obj_name$width_inst_vel >= 0,
# when moving rightwards
180 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)))) %% 360,
# when facing negative end of tunnel
ifelse(obj_name$width_inst_vel < 0,
# when moving rightwards
180 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 - (rad_2_deg(atan(
obj_name$width_inst_vel/
obj_name$length_inst_vel))))) %% 360
)} else if (
## For v-shaped tunnel configurations
attr(obj_name, "tunnel_config") == "v"){
## For end wall, rightward pattern velocity is 0 degree or 360 degree and intermediate
## angles fill the circle counter-clockwise.
## The direction of pattern velocity depends on the end wall to which the
## subject is facing and whether it's moving towards the positive or negative
## lateral walls.
obj_name$end_pattern_direction <-
ifelse(obj_name$end_length_sign == 1,
# when facing positive end of tunnel
ifelse(obj_name$width_inst_vel >= 0,
# when moving rightwards
180 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)))) %% 360,
# when facing negative end of tunnel
ifelse(obj_name$width_inst_vel < 0,
# when moving rightwards
180 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 - (rad_2_deg(atan(
obj_name$width_inst_vel/
obj_name$length_inst_vel))))) %% 360
)
}
## Leave a note that pattern velocity direction was calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"pattern_vel_direction_calculated")
return(obj_name)
}
## all in one function for visual perceptions
get_vis_percepts <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name, "pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Run appropriate calc_min_dist based on tunnel configuration
if (any(names(obj_name) == "vertex_angle")){
calc_min_dist_v(obj_name)
} else if (any(names(obj_name)) == "pos_wall"){
calc_min_dist_box(obj_name)
} else {
print("Please check arguments for insert_treatments()")
}
## Get visual angles, spatial frequency, temporal frequency, pattern velocity,
## and image expansion
get_vis_angle(obj_name)
get_sf(obj_name)
get_tf(obj_name) # need to get instantaneous velocity first
get_pattern_vel(obj_name)
get_image_expansion(obj_name)
}
vbaliga/pathviewR documentation built on March 16, 2023, 4:13 p.m.
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## work space for addressing visual perception functions reviews
## change argument for vertex_angle to mean the actual angle of the V in the
## V-shaped tunnel. Build into insert_treatments() a calculation that makes it
## work with calc_min_dist functions
## insert_treatments()
## use tunnel_length argument so that front/back wall distances can be calculated
insert_treatments <- function(obj_name,
tunnel_config = "box",
perch_2_vertex = NULL,
vertex_angle = NULL, # actual angle of vertex
tunnel_width = NULL,
tunnel_length = NULL,
stim_param_lat_pos = NULL,
stim_param_lat_neg = NULL,
stim_param_end_pos = NULL,
stim_param_end_neg = NULL,
treatment = NULL){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_full_trajectories has been run prior to use
if (!any(attr(obj_name, "pathviewr_steps") == "full_trajectories")){
stop("Run get_full_trajectories() prior to use")
}
## Translate arguments into variables at beginning of data frame
if (tunnel_config == "v"){
## Check that relevant numerical arguments have positive values
if (perch_2_vertex < 0){
stop("perch_2_vertex must have a positive value.")
} else if (vertex_angle < 0){
stop("vertex_angle must have a positive value")
} else if (tunnel_length < 0){
stop("tunnel_length must have a positive value")
} else if (stim_param_lat_pos < 0){
stop("stim_param_lat_pos must have a positive value")
} else if (stim_param_lat_neg < 0){
stop("stim_param_lat_neg must have a positive value")
} else if (stim_param_end_pos < 0){
stop("stim_param_end_pos must have a positive value")
} else if (stim_param_end_neg < 0){
stop("stim_param_end_neg must have a positive value")
}
obj_name <- tibble::add_column(obj_name, .before = "frame",
tunnel_config = tunnel_config,
perch_2_vertex = perch_2_vertex,
vertex_angle = deg_2_rad(vertex_angle/2),
tunnel_length = tunnel_length,
stim_param_lat_pos = stim_param_lat_pos,
stim_param_lat_neg = stim_param_lat_neg,
stim_param_end_pos = stim_param_end_pos,
stim_param_end_neg = stim_param_end_neg,
treatment = treatment)
} else if (tunnel_config == "box"){
## Check that relevant numerical arguments have positive values
if (tunnel_width < 0){
stop("tunnel_width must have a positive value")
} else if (tunnel_length < 0){
stop("tunnel_length must have a positive value")
} else if (stim_param_lat_pos < 0){
stop("stim_param_lat_pos must have a positive value")
} else if (stim_param_lat_neg < 0){
stop("stim_param_lat_neg must have a positive value")
} else if (stim_param_end_pos < 0){
stop("stim_param_end_pos must have a positive value")
} else if (stim_param_end_neg < 0){
stop("stim_param_end_neg must have a positive value")
}
obj_name <- tibble::add_column(obj_name, .before = "frame",
tunnel_config = tunnel_config,
tunnel_width = tunnel_width,
tunnel_length= tunnel_length,
stim_param_lat_pos = stim_param_lat_pos,
stim_param_lat_neg = stim_param_lat_neg,
stim_param_end_pos = stim_param_end_pos,
stim_param_end_neg = stim_param_end_neg,
treatment = treatment)
}
## Add arguments into metadata......surewhynot
if (tunnel_config == "v"){
attr(obj_name, "tunnel_config") <- tunnel_config
attr(obj_name, "perch_2_vertex") <- perch_2_vertex
attr(obj_name, "vertex_angle") <- vertex_angle
attr(obj_name, "tunnel_width") <- tunnel_width
attr(obj_name, "tunnel_length") <- tunnel_length
attr(obj_name, "stim_param_lat_pos") <- stim_param_lat_pos
attr(obj_name, "stim_param_lat_neg") <- stim_param_lat_neg
attr(obj_name, "stim_param_end_pos") <- stim_param_end_pos
attr(obj_name, "stim_param_end_neg") <- stim_param_end_neg
attr(obj_name, "treatment") <- treatment
} else if (tunnel_config == "box"){
attr(obj_name, "tunnel_config") <- tunnel_config
attr(obj_name, "tunnel_width") <- tunnel_width
attr(obj_name, "tunnel_length") <- tunnel_length
attr(obj_name, "stim_param_lat_pos") <- stim_param_lat_pos
attr(obj_name, "stim_param_lat_neg") <- stim_param_lat_neg
attr(obj_name, "stim_param_end_pos") <- stim_param_end_pos
attr(obj_name, "stim_param_end_neg") <- stim_param_end_neg
attr(obj_name, "treatment") <- treatment
}
## Leave note that treatments were added
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"treatments_added")
return(obj_name)
}
# min_dist function for V-shaped tunnel
# get min_dist for front/back wall by using direction of bird flight to
# determine the distance to the opposite wall. Then can use this distance to
# get vis_angle, sf, tf, image vel, and image expansion from the front of the
# tunnel
calc_min_dist_v <- function(obj_name,
simplify = TRUE){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that insert_treatments() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "treatments_added")){
stop("Please run insert_treatments() prior to use")
}
## duplicate object for simplify = TRUE
obj_simplify <- obj_name
## For distance to lateral walls ##
## Introduce variables for vertical_2_vertex and vertical_2_screen
## vertical_2_vertex and vertical_2_screen refer to the vertical distance
## between the subject's position and the the vertex of the tunnel and screen
## below them, respectively.
obj_name$vertical_2_vertex <-
abs(obj_name$perch_2_vertex) + obj_name$position_height
obj_name$vertical_2_screen <-
obj_name$vertical_2_vertex -
(abs(obj_name$position_width) / tan(obj_name$vertex_angle))
## Introduce variables for horizontal_2_screen on positive and negative sides
## of the tunnel.
## horizontal_2_screen refers to the horizontal distance between the bird and
## either screen.
obj_name$horizontal_2_screen_pos <-
ifelse(obj_name$position_width >= 0, # if in positive side of tunnel
obj_name$vertical_2_screen * tan(obj_name$vertex_angle), # TRUE
(obj_name$vertical_2_screen * tan(obj_name$vertex_angle)) +
(2 * abs(obj_name$position_width))) # FALSE
obj_name$horizontal_2_screen_neg <-
ifelse(obj_name$position_width < 0, # if in negative side of tunnel
obj_name$vertical_2_screen * tan(obj_name$vertex_angle), # TRUE
(obj_name$vertical_2_screen * tan(obj_name$vertex_angle)) +
(2 * abs(obj_name$position_width))) # FALSE
## Introduce variable min_dist on positive and negative sides of the
## tunnel. min_dist refers to the minimum distance between the bird and either
## screen (axis of gaze is orthogonal to plane of each screen)
obj_name$min_dist_pos <-
obj_name$horizontal_2_screen_pos * sin(pi/2 - obj_name$vertex_angle)
# min_dist to positive screen
obj_name$min_dist_neg <-
obj_name$horizontal_2_screen_neg * sin(pi/2 - obj_name$vertex_angle)
# min_dist to negative screen
## When the subject is outside the boundaries created by orthogonal planes to
## each wall, erroneous visual angles are calculated.
## Therefore we must adjust min_dist values according to position_width
## Create variable holding the boundary values for each observation
obj_name$bound_pos <-
obj_name$vertical_2_vertex * tan(pi/2 - obj_name$vertex_angle)
obj_name$bound_neg <-
obj_name$vertical_2_vertex * -tan(pi/2 - obj_name$vertex_angle)
obj_name$min_dist_pos <- # overwrite min_dist_pos
ifelse(obj_name$position_width <= 0 &
obj_name$position_width <= obj_name$bound_neg,
# if position_width is positive and greater than the boundary value
sqrt(obj_name$vertical_2_vertex^2 + obj_name$position_width^2),
# return distance to vertex
obj_name$min_dist_pos)
# return original min_dist_pos calculation
obj_name$min_dist_neg <-
ifelse(obj_name$position_width >= 0 &
obj_name$position_width >= obj_name$bound_pos,
# if position_width is negative and smaller than the boundary value
sqrt(obj_name$vertical_2_vertex^2 + obj_name$position_width^2),
# return distance to vertex
obj_name$min_dist_neg)
# return original min_dist_neg calculation
## For minimum distances to end walls (assuming animal locomotes forward)
obj_name$min_dist_end <-
ifelse(obj_name$end_length_sign == 1,
obj_name$tunnel_length/2 - obj_name$position_length,
obj_name$tunnel_length/2 + obj_name$position_length)
## for simplify = TRUE
obj_simplify$min_dist_pos <- obj_name$min_dist_pos
obj_simplify$min_dist_neg <- obj_name$min_dist_neg
obj_simplify$min_dist_end <- obj_name$min_dist_end
## return object and add note that minimum distaces were calculated
if(simplify == TRUE){
attr(obj_simplify, "pathviewr_steps") <-
c(attr(obj_name, "pathviewr_steps"), "min_dist_calculated")
return(obj_simplify)
} else {
attr(obj_name, "pathviewr_steps") <-
c(attr(obj_name, "pathviewr_steps"), "min_dist_calculated")
return(obj_name)
}
}
## min_dist function for box shaped chamber
calc_min_dist_box <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")) {
stop("This doesn't seem to be a viewr object")
}
## Check that insert_treatments() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "treatments_added")){
stop("Please run insert_treatments() prior to use")
}
## Calculate minimum distance to each wall from positive or negative sides of
## tunnel
obj_name$min_dist_pos <- obj_name$tunnel_width/2 - obj_name$position_width
obj_name$min_dist_neg <- obj_name$tunnel_width/2 + obj_name$position_width
## For minimum distances to end walls (assuming animal locomotes forward)
obj_name$min_dist_end <-
ifelse(obj_name$end_length_sign == 1,
obj_name$tunnel_length/2 - obj_name$position_length,
obj_name$tunnel_length/2 + obj_name$position_length)
## Leave note that minimum distances were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"min_dist_calculated")
return(obj_name)
}
## get_vis_angle
## include vis_angle for end wall
get_vis_angle <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that calc_min_dist() has been run
if (!any(attr(obj_name, "pathviewr_steps") == "min_dist_calculated")){
stop("Please run calc_min_dist_v() or calc_min_dist_box() prior to use")
}
## Calculate visual angles (radians and degrees) using distance to
## positive and negative screens. Add these variables into the dataframe.
# visual angle to positive wall
obj_name$vis_angle_pos_rad <-
2*atan(obj_name$stim_param_lat_pos/(2*obj_name$min_dist_pos))
# visual angle to negative wall
obj_name$vis_angle_neg_rad <-
2*atan(obj_name$stim_param_lat_neg/(2*obj_name$min_dist_neg))
# visual angle to end wall (depending on direction of locomotion)
obj_name$vis_angle_end_rad <-
ifelse(obj_name$end_length_sign == 1,
2*atan(obj_name$stim_param_end_pos/(2*obj_name$min_dist_end)),
2*atan(obj_name$stim_param_end_neg/(2*obj_name$min_dist_end)))
# convert to degrees
obj_name$vis_angle_pos_deg <- rad_2_deg(obj_name$vis_angle_pos_rad)
obj_name$vis_angle_neg_deg <- rad_2_deg(obj_name$vis_angle_neg_rad)
obj_name$vis_angle_end_deg <- rad_2_deg(obj_name$vis_angle_end_rad)
## Leave a note that visual angles were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"vis_angles_calculated")
return(obj_name)
}
## get_sf
## include sf for front wall?
get_sf <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## spatial frequency (cycles/rad) is the inverse of visual angle (rad/cycle)
obj_name$sf_pos <- 1/obj_name$vis_angle_pos_deg
obj_name$sf_neg <- 1/obj_name$vis_angle_neg_deg
obj_name$sf_end <- 1/obj_name$vis_angle_end_deg
## Leave a note that visual angles were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"sf_calculated")
return(obj_name)
}
## get_tf
get_tf <- function(obj_name,
dimensionality = NULL){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## Check that get_velocity() has been run
if (!any(attr(obj_name, "pathviewr_steps") == "velocity_computed")){
stop("Please run get_velocity() prior to use")
}
## Temporal frequency (cycles/second)instantaneous velocity of the subject and
## the arc length of the cycle from the subject's perspective
## For box-shaped tunnel
if (attr(obj_name, "tunnel_config") == "box"){
## Lateral wall 1D (axial) temporal frequencies
# tf of positive wall from forward movement
obj_name$tf_forward_pos <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# tf of negative wall from forward movement
obj_name$tf_forward_neg <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
# tf of positive wall from vertical movement
obj_name$tf_vertical_pos <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# tf of negative wall from vertical movement
obj_name$tf_vertical_neg <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
# tf of end wall from horizontal movement
## End wall 1D (axial) temporal frequencies
# tf of end wall from horizontal movement
obj_name$tf_horizontal_end <-
abs(obj_name$width_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
# tf of end wall from vertical movement
obj_name$tf_vertical_end <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
## Lateral wall 2D (planar) temporal frequencies
# relevant locomotion
obj_name$lat_planar_inst_vel <-
sqrt(obj_name$length_inst_vel^2 + obj_name$height_inst_vel^2)
# planar tf from positive wall
obj_name$tf_planar_pos <-
abs(obj_name$lat_planar_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# planar tf from negative wall
obj_name$tf_planar_neg <-
abs(obj_name$lat_planar_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
## End wall 2d (planar) temporal frequency
# relevant locomotion
obj_name$end_planar_inst_vel <-
sqrt(obj_name$width_inst_vel^2 + obj_name$height_inst_vel^2)
# planar tf from end wall
obj_name$tf_planar_end <-
abs(obj_name$end_planar_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
## for v-shaped tunnel
} else if (attr(obj_name, "tunnel_config") == "v"){
## Lateral wall 1D (axial) temporal frequencies
# tf of positive wall from forward movement
obj_name$tf_forward_pos <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_pos * obj_name$vis_angle_pos_rad)
# tf of negative wall from forward movement
obj_name$tf_forward_neg <-
abs(obj_name$length_inst_vel)/
(obj_name$min_dist_neg * obj_name$vis_angle_neg_rad)
## End wall 1D (axial) temporal frequencies
# tf of end wall from horizontal movement
obj_name$tf_horizontal_end <-
abs(obj_name$width_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
# tf of end wall from vertical movement
obj_name$tf_vertical_end <-
abs(obj_name$height_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
## End wall 2d (planar) temporal frequency
# relevant locomotion
obj_name$end_planar_inst_vel <-
sqrt(obj_name$width_inst_vel^2 + obj_name$height_inst_vel^2)
# planar tf from end wall
obj_name$tf_planar_end <-
abs(obj_name$end_planar_inst_vel)/
(obj_name$min_dist_end * obj_name$vis_angle_end_rad)
}
### analysis of how multi-dimensional motion affects temporal frequency is in
### development for V-shaped tunnel configurations
## Leave a note that temporal frequencies were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"tf_calculated")
return(obj_name)
}
## get_pattern_velocity
## include pattern velocity for end wall
get_pattern_vel <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## Check that get_sf() and get_tf() have been run
if (!any(attr(obj_name, "pathviewr_steps") == "sf_calculated")){
stop("Please run get_sf() prior to use")
} else if (!any(attr(obj_name, "pathviewr_steps") == "tf_calculated")){
stop("Please run get_tf() prior to use")
}
## For box-shaped tunnel configuration
if (attr(obj_name, "tunnel_config") == "box"){
## Lateral wall 1D (axial) pattern velocities
# forward pattern velocity from positive wall
obj_name$forward_pattern_vel_pos <-
obj_name$tf_forward_pos/obj_name$sf_pos
# forward pattern velocity from negative wall
obj_name$forward_pattern_vel_neg <-
obj_name$tf_forward_neg/obj_name$sf_neg
# vertical pattern velocity from positive wall
obj_name$vertical_pattern_vel_pos <-
obj_name$tf_vertical_pos/obj_name$sf_pos
# vertical pattern velocity from negative wall
obj_name$vertical_pattern_vel_neg <-
obj_name$tf_vertical_neg/obj_name$sf_neg
## End wall 1D (axial) pattern velocities
# horizontal pattern velocity from end wall
obj_name$horizontal_pattern_vel_end <-
obj_name$tf_horizontal_end/obj_name$sf_end
# vertical pattern velocity from end wall
obj_name$vertical_pattern_vel_end <-
obj_name$tf_vertical_end/obj_name$sf_end
## Lateral wall 2D (planar) pattern velocities
# planar pattern velocity from positive wall
obj_name$planar_pattern_vel_pos <- o
bj_name$tf_planar_pos/obj_name$sf_pos
# planar pattern velocity from negative wall
obj_name$planar_pattern_vel_neg <-
obj_name$tf_planar_neg/obj_name$sf_neg
## End wall 2D (planar) pattern velocity
# planar pattern velocity from positive wall
obj_name$planar_pattern_vel_end <-
obj_name$tf_planar_end/obj_name$sf_end
## For v-shaped tunnel configuration
} else if (attr(obj_name, "tunnel_config") == "v"){
## Lateral wall 1D (axial) pattern velocities
# forward pattern velocity for positive wall
obj_name$forward_pattern_vel_pos <-
obj_name$tf_forward_pos/obj_name$sf_pos
# forward pattern velocity for negative wall
obj_name$forward_pattern_vel_neg <-
obj_name$tf_forward_neg/obj_name$sf_neg
## End wall 1D (axial) pattern velocities
# horizontal pattern velocity from end wall
obj_name$horizontal_pattern_vel_end <-
obj_name$tf_horizontal_end/obj_name$sf_end
# vertical pattern velocity from end wall
obj_name$vertical_pattern_vel_end <-
obj_name$tf_vertical_end/obj_name$sf_end
## End wall 2D (planar) pattern velocity
# planar pattern velocity from positive wall
obj_name$planar_pattern_vel_end <-
obj_name$tf_planar_end/obj_name$sf_end
}
## Leave a note that pattern velocities were calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"pattern_vel_calculated")
return(obj_name)
}
## get image expansion
get_image_expansion <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_vis_angle() has been run
if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
stop("Please run get_vis_angle() prior to use")
}
## Convert obj_name to data.frame for diff functions
obj_name <- as.data.frame(obj_name)
## Get relevant frame-by-frame differences
time_diff <- c(NA, diff(obj_name[,"time_sec"]))
pos_angle_diff <- c(NA, diff(obj_name[,"vis_angle_pos_deg"]))
neg_angle_diff <- c(NA, diff(obj_name[,"vis_angle_neg_deg"]))
end_angle_diff <- c(NA, diff(obj_name[,"vis_angle_end_deg"]))
obj_name$expansion_pos <- pos_angle_diff/time_diff
obj_name$expansion_neg <- neg_angle_diff/time_diff
obj_name$expansion_end <- end_angle_diff/time_diff
obj_name$time_diff <- time_diff
## Leave note that image expansion was calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"image_expansion_calculated")
return(as_tibble(obj_name))
}
# get pattern velocity direction
# All functions, including this one assume the bird is looking straight ahead
# (i.e. a "rightwards" flight means the bird is always facing "rightwards" etc.)
# Once head orientation is included, this function will include an offset equal
# to the head orientation for each observation
get_pattern_vel_direction <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Check that get_velocity() has been run
if (!any(attr(obj_name, "pathviewr_steps") == "velocity_computed")){
stop("Please run get_velocity() prior to use")
}
## For lateral walls, forward pattern velocity is 0 degree/360 degree and intermediate
## angles fill the circle counter-clockwise.
## The direction of pattern velocity depends on the end wall to which the
## subject is facing and whether it's moving forward or backward.
## for box-shaped tunnel configurations
if (attr(obj_name, "tunnel_config") == "box"){
obj_name$lat_pattern_direction <-
ifelse(obj_name$end_length_sign == 1,
# when facing positive end of tunnel
ifelse(obj_name$length_inst_vel >= 0,
# when moving forward
180 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)),
# when moving backward
(360 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)))) %% 360,
# when facing negative end of tunnel
ifelse(obj_name$length_inst_vel < 0,
# when moving forward
180 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)),
# when moving backward
(360 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$length_inst_vel)))) %% 360
)
## For end wall, rightward pattern velocity is 0 degree or 360 degree and intermediate
## angles fill the circle counter-clockwise.
## The direction of pattern velocity depends on the end wall to which the
## subject is facing and whether it's moving towards the positive or negative
## lateral walls.
obj_name$end_pattern_direction <-
ifelse(obj_name$end_length_sign == 1,
# when facing positive end of tunnel
ifelse(obj_name$width_inst_vel >= 0,
# when moving rightwards
180 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)))) %% 360,
# when facing negative end of tunnel
ifelse(obj_name$width_inst_vel < 0,
# when moving rightwards
180 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 - (rad_2_deg(atan(
obj_name$width_inst_vel/
obj_name$length_inst_vel))))) %% 360
)} else if (
## For v-shaped tunnel configurations
attr(obj_name, "tunnel_config") == "v"){
## For end wall, rightward pattern velocity is 0 degree or 360 degree and intermediate
## angles fill the circle counter-clockwise.
## The direction of pattern velocity depends on the end wall to which the
## subject is facing and whether it's moving towards the positive or negative
## lateral walls.
obj_name$end_pattern_direction <-
ifelse(obj_name$end_length_sign == 1,
# when facing positive end of tunnel
ifelse(obj_name$width_inst_vel >= 0,
# when moving rightwards
180 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 + rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)))) %% 360,
# when facing negative end of tunnel
ifelse(obj_name$width_inst_vel < 0,
# when moving rightwards
180 - rad_2_deg(atan(
obj_name$height_inst_vel/
obj_name$width_inst_vel)),
# when moving leftwards
(360 - (rad_2_deg(atan(
obj_name$width_inst_vel/
obj_name$length_inst_vel))))) %% 360
)
}
## Leave a note that pattern velocity direction was calculated
attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
"pattern_vel_direction_calculated")
return(obj_name)
}
## all in one function for visual perceptions
get_vis_percepts <- function(obj_name){
## Check that it's a viewr object
if (!any(attr(obj_name, "pathviewr_steps") == "viewr")){
stop("This doesn't seem to be a viewr object")
}
## Run appropriate calc_min_dist based on tunnel configuration
if (any(names(obj_name) == "vertex_angle")){
calc_min_dist_v(obj_name)
} else if (any(names(obj_name)) == "pos_wall"){
calc_min_dist_box(obj_name)
} else {
print("Please check arguments for insert_treatments()")
}
## Get visual angles, spatial frequency, temporal frequency, pattern velocity,
## and image expansion
get_vis_angle(obj_name)
get_sf(obj_name)
get_tf(obj_name) # need to get instantaneous velocity first
get_pattern_vel(obj_name)
get_image_expansion(obj_name)
}
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