Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/utility_functions.R
The rotation is applied about the height axis and affects tunnel length and width only, i.e. no rotation of height.
1 2 3 4 5 6 7 8 9 10 11 12 13 14  rotate_tunnel(
obj_name,
all_heights_min = 0.11,
all_heights_max = 0.3,
perch1_len_min = 0.06,
perch1_len_max = 0.06,
perch2_len_min = 2.48,
perch2_len_max = 2.6,
perch1_wid_min = 0.09,
perch1_wid_max = 0.31,
perch2_wid_min = 0.13,
perch2_wid_max = 0.35,
...
)

obj_name 
The input viewr object; a tibble or data.frame with attribute

all_heights_min 
Minimum perch height 
all_heights_max 
Maximum perch height 
perch1_len_min 
Minimum length value of perch 1 
perch1_len_max 
Maximum length value of perch 1 
perch2_len_min 
Minimum length value of perch 2 
perch2_len_max 
Maximum length value of perch 2 
perch1_wid_min 
Minimum width value of perch 1 
perch1_wid_max 
Maximum width value of perch 1 
perch2_wid_min 
Minimum width value of perch 2 
perch2_wid_max 
Maximum width value of perch 2 
... 
Additional arguments passed to/from other pathviewr functions 
The user first estimates the locations of the perches by specifying bounds for where each perch is located. The function then computes the center of each bounding box and estimates that to be the midpoint of each perch. Then the center point of the tunnel (center between the perch midpoints) is estimated. The angle between perch1_center, tunnel_center_point, and arbitrary point along the length axis (tunnel_center_point  1 on length) is estimated. That angle is then used to rotate the data, again only in the length and width dimensions. Height is standardized by (approximate) perch height; values greater than 0 are above the perch and values less than 0 are below the perch level.
A viewr object (tibble or data.frame with attribute
pathviewr_steps
that includes "viewr"
) in which data have
been rotated according to user specifications.
Vikram B. Baliga
Other data cleaning functions:
gather_tunnel_data()
,
get_full_trajectories()
,
quick_separate_trajectories()
,
redefine_tunnel_center()
,
relabel_viewr_axes()
,
rename_viewr_characters()
,
select_x_percent()
,
separate_trajectories()
,
standardize_tunnel()
,
trim_tunnel_outliers()
,
visualize_frame_gap_choice()
Other tunnel standardization functions:
redefine_tunnel_center()
,
standardize_tunnel()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27  ## Import the example Motive data included in the package
motive_data <
read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
package = 'pathviewr'))
## Clean the file. It is generally recommended to clean up to the
## "trimmed" step before running rotate_tunnel().
motive_trimmed <
motive_data %>%
relabel_viewr_axes() %>%
gather_tunnel_data() %>%
trim_tunnel_outliers()
## Now rotate the tunnel using default values
motive_rotated <
motive_trimmed %>%
rotate_tunnel()
## The following attributes store information about
## how rotation & translation was applied
attr(motive_rotated, "rotation_degrees")
attr(motive_rotated, "rotation_radians")
attr(motive_rotated, "perch1_midpoint_original")
attr(motive_rotated, "perch1_midpoint_current")
attr(motive_rotated, "tunnel_centerpoint_original")
attr(motive_rotated, "perch2_midpoint_original")
attr(motive_rotated, "perch2_midpoint_current")

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