pathviewr (version 1.1.8)

redefine_tunnel_center: "Center" the tunnel data, i.e. translation but no rotation

Description

Redefine the center (0, 0, 0,) of the tunnel data via translating positions along axes.

Usage

redefine_tunnel_center(
  obj_name,
  axes = c("position_length", "position_width", "position_height"),
  length_method = c("original", "middle", "median", "user-defined"),
  width_method = c("original", "middle", "median", "user-defined"),
  height_method = c("original", "middle", "median", "user-defined"),
  length_zero = NA,
  width_zero = NA,
  height_zero = NA,
  ...
)

Value

A viewr object (tibble or data.frame with attribute pathviewr_steps that includes "viewr") in which data have been translated according to the user's inputs, generally with (0, 0, 0,) being relocated to the center of the tunnel.

Arguments

obj_name

The input viewr object; a tibble or data.frame with attribute pathviewr_steps that includes "viewr"

axes

Names of axes to be centered

length_method

Method for length

width_method

Method for width

height_method

Method for height

length_zero

User-defined value

width_zero

User-defined value

height_zero

User-defined value

...

Additional arguments passed to/from other pathviewr functions

Author

Vikram B. Baliga

Details

For each _method argument, there are four choices of how centering is handled: 1) "original" keeps axis as is -- this is how width and (possibly) height should be handled for flydra data; 2) "middle" is the middle of the range of data: (min + max) / 2; 3) "median" is the median value of data on that axis. Probably not recommended; and 4) "user-defined" lets the user customize where the (0, 0, 0) point in the tunnel will end up. Each _zero argument is subtracted from its corresponding axis' data.

See Also

Other data cleaning functions: gather_tunnel_data(), get_full_trajectories(), quick_separate_trajectories(), relabel_viewr_axes(), rename_viewr_characters(), rotate_tunnel(), select_x_percent(), separate_trajectories(), standardize_tunnel(), trim_tunnel_outliers(), visualize_frame_gap_choice()

Other tunnel standardization functions: rotate_tunnel(), standardize_tunnel()

Examples

## Import the Flydra example data included in
## the package
flydra_data <-
  read_flydra_mat(
    system.file("extdata",
                "pathviewr_flydra_example_data.mat",
                package = 'pathviewr'),
    subject_name = "birdie_wooster"
  )

## Re-center the Flydra data set.
## Width will be untouched
## Length will use the "middle" definition
## And height will be user-defined to be
## zeroed at 1.44 on the original axis
flydra_centered <-
  flydra_data %>%
  redefine_tunnel_center(length_method = "middle",
                         height_method = "user-defined",
                         height_zero = 1.44)