## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(fishmechr)
library(ggplot2)
library(tidyr)
library(dplyr)

## -----------------------------------------------------------------------------
head(xmucosusdata)

## -----------------------------------------------------------------------------
pointnames <- c("Snout", "BP1", "BP2", "BP3", "BP4", "BP5", "BP6", "Tail")
xmucosusdata <- xmucosusdata |> 
  pivot_kinematics_longer(pointnames = pointnames,
                          point_to = "bodypart")

## -----------------------------------------------------------------------------
head(xmucosusdata)

## -----------------------------------------------------------------------------
xmucosusdata |> 
  filter(frame_idx %in% c(10, 20)) |> 
  mutate(frame_idx = factor(frame_idx)) |> 
  ggplot(aes(x = x, y = y, color = frame_idx, group = frame_idx)) +
  geom_path() +
  coord_fixed()

## -----------------------------------------------------------------------------
xmucosusdata <-
  xmucosusdata |> 
  group_by(frame_idx) |> 
  mutate(arclen0 = arclength(x, y))

## -----------------------------------------------------------------------------
xmucosusdata |> 
  ungroup() |> 
  filter(bodypart %in% c("BP2", "BP5", "Tail")) |> 
  ggplot(aes(x = frame_idx, y = arclen0, color = bodypart)) +
  geom_point()

## -----------------------------------------------------------------------------
xmucosusdata <- xmucosusdata |> 
  interpolate_points_df(arclen0, x, y, spar = 0.2,
                        tailmethod = 'extrapolate',
                        .frame = frame_idx,
                        .point = bodypart,
                        .out = c(arclen='arclen', xs='x_s', ys='y_s'))


## -----------------------------------------------------------------------------
xmucosusdata |> 
  filter(frame_idx %in% c(10, 20)) |> 
  mutate(frame_idx = factor(frame_idx)) |> 
  ggplot(aes(x = x, y, color = frame_idx, group = frame_idx)) +
  geom_point(shape = 10) +
  geom_path() +
  geom_point(aes(x = x_s, y = y_s), shape = 5) +
  coord_fixed()

## -----------------------------------------------------------------------------
xmucosusdata <-
  xmucosusdata |> 
  group_by(frame_idx) |> 
  mutate(width = interpolate_width(fishwidth$s, fishwidth$eelwidth, arclen))

## -----------------------------------------------------------------------------
xmucosusdata <-
  xmucosusdata |> 
  ungroup() |> 
  get_midline_center_df(arclen, x_s,y_s, width=width,
                        .frame = frame_idx)

## -----------------------------------------------------------------------------
xmucosusdata <-
  xmucosusdata |> 
  mutate(x_ctr = x_s - xcom,
         y_ctr = y_s - ycom,
         t = frame_idx / 60) |> 
  get_primary_swimming_axis_df(t, x_ctr,y_ctr,
                               .frame = frame_idx,
                               .point = bodypart)

## -----------------------------------------------------------------------------
xmucosusdata |> 
  filter(frame_idx %in% c(10, 20, 30)) |> 
  ggplot(aes(x = x, y = y, color = frame_idx)) +
  geom_path(aes(group = frame_idx)) +
  geom_segment(data = ~ filter(.x, bodypart == "Tail"), 
               aes(x = xcom, y = ycom, 
                   xend = xcom - 50*swimaxis_x, 
                   yend = ycom - 50*swimaxis_y)) +
  geom_point(data = ~ filter(.x, bodypart == "Tail"), 
               aes(x = xcom, y = ycom), color = 'red') +
  facet_grid(frame_idx ~ .) +
  coord_fixed()