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

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

## -----------------------------------------------------------------------------
head(lampreydata)

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(frame %in% c(10, 20)) |> 
  mutate(frame = factor(frame)) |> 
  ggplot(aes(x = mxmm, mymm, color = frame, group = frame)) +
  geom_path() +
  coord_fixed()

## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  group_by(frame) |>
  mutate(arclen0 = arclength(mxmm, mymm)) 

## -----------------------------------------------------------------------------
lampreydata |> 
  ungroup() |> 
  filter(point %in% c(5, 10, 18)) |> 
  ggplot(aes(x = t, y = arclen0, color = point)) +
  geom_point()

## -----------------------------------------------------------------------------
lampreydata <- lampreydata |> 
  interpolate_points_df(arclen0, mxmm, mymm, spar = 0.2,
                        tailmethod = 'extrapolate',
                        .out = c(arclen='arclen', xs='mxmm_s', ys='mymm_s'))

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(frame %in% c(10, 20)) |> 
  mutate(frame = factor(frame)) |> 
  ggplot(aes(x = mxmm, mymm, color = frame, group = frame)) +
  geom_point(shape = 10) +
  geom_path() +
  geom_point(aes(x = mxmm_s, y = mymm_s), shape = 5) +
  coord_fixed()

## -----------------------------------------------------------------------------
fishwidth

## -----------------------------------------------------------------------------
fishwidth |> 
  ggplot(aes(x = s, y = ammowidth)) +
  geom_path() +
  labs(x = 'Arc length (BL)', y = 'Width (BL)')

## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  group_by(frame) |> 
  mutate(width = interpolate_width(fishwidth$s, fishwidth$ammowidth, arclen))

## -----------------------------------------------------------------------------
lampreydata |> 
  dplyr::filter(frame == 10)

## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  ungroup() |> 
  get_midline_center_df(arclen, mxmm_s,mymm_s, width=width)

lampreydata |> 
  filter(frame %in% c(10, 20, 30, 40, 50)) |> 
  ggplot(aes(x = mxmm_s, y = mymm_s, color = frame)) +
  geom_path(aes(group = frame)) +
  geom_point(data = ~filter(.x, point == 1), aes(x = xcom, y = ycom)) +
  coord_fixed()

## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  group_by(frame) |> 
  mutate(curve_ang = curvature(arclen0, mxmm_s, mymm_s),
         curve_xy = curvature(arclen0, mxmm_s, mymm_s, method="xy"))

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(frame %in% c(10, 20)) |> 
  mutate(frame = factor(frame)) |> 
  ggplot(aes(x = arclen0, color = frame, group = frame)) +
  geom_path(aes(y = curve_ang), linetype='solid') +
  geom_path(aes(y = curve_xy), linetype='dashed')

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(point %in% c(10, 18)) |>
  mutate(point = factor(point)) |> 
  ggplot(aes(x = t, y = curve_ang, color = point)) +
  geom_path()

## -----------------------------------------------------------------------------
lampreydata <- lampreydata |> 
  ungroup() |> 
  mutate(mxmm_ctr = mxmm_s - xcom,
         mymm_ctr = mymm_s - ycom) |> 
  get_primary_swimming_axis_df(t, mxmm_ctr, mymm_ctr, .frame=frame)

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

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(point %in% c(10, 18)) |>
  mutate(point = factor(point)) |> 
  ggplot(aes(x = t, y = exc, color = point)) +
  geom_path()

## -----------------------------------------------------------------------------
sampfreq <-
  lampreydata |> 
  filter(frame %in% c(1, 2)) |> 
  group_by(frame) |> 
  summarize(t = first(t)) |> 
  ungroup() |> 
  summarize(sampfreq = 1 / (t[2] - t[1])) |> 
  pull(sampfreq)

sampfreq

## -----------------------------------------------------------------------------
filt <- build_filter(0.5, 15, sampfreq = sampfreq)

## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  arrange(point, t) |> 
  group_by(point) |> 
  mutate(exc_s = apply_filter(filt, exc),
         curve_ang_s = apply_filter(filt, curve_ang))

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(point %in% c(10, 18)) |>
  mutate(point = factor(point)) |> 
  ggplot(aes(x = t, color = point)) +
  geom_path(aes(y = exc)) +
  geom_path(aes(y = exc_s), linetype = 'dashed')

## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  arrange(frame, desc(point)) |> 
  group_by(point) |> 
  mutate(ph_c = hilbert_phase(curve_ang_s),
         ph_e = hilbert_phase(exc_s),
         ph_p = peak_phase(exc_s))

## -----------------------------------------------------------------------------
lampreydata |> 
  ungroup() |> 
  filter(point %in% c(3, 8, 15, 18)) |> 
  mutate(point = factor(point)) |> 
  pivot_longer(cols = c(ph_c, ph_e, ph_p), names_to = "method", values_to = "phase") |> 
  ggplot(aes(x = t, y = phase, color = point, linetype = method)) +
  geom_path() + 
  facet_wrap(~point)

## -----------------------------------------------------------------------------
examplet <- 1.2
colors <- c("#1f78b4", "black")

p1 <- lampreydata |> 
  ungroup() |> 
  filter(point %in% c(13, 15)) |> 
  mutate(point = factor(point)) |> 
  ggplot(aes(x = t, y = exc, color = point, linetype = point)) +
  geom_path(aes(group = point)) +
  geom_vline(xintercept = examplet) +
  scale_color_manual(values = colors) +
  theme_minimal() +
  xlim(c(1,1.5)) +
  labs(x = "Time (s)", y = "Excursion (mm)") +
  theme(legend.position="none",
        panel.grid.minor.x = element_blank(),
        panel.grid.minor.y = element_blank())

p2 <- lampreydata |> 
  ungroup() |> 
  filter(point %in% c(13, 15)) |> 
  mutate(point = factor(point),
         ph_e = (ph_e %% (2*pi)) / (2*pi)) |> 
  ggplot(aes(x = t, y = ph_e, color = point, linetype = point)) +
  geom_path(aes(group = point)) +
  geom_vline(xintercept = examplet) +
  scale_color_manual(values = colors) +
  xlim(c(1,1.5)) +
  ylim(0,1) +
  theme_minimal() +
  labs(x = "Time (s)", y = "Phase") +
  theme(legend.position="none",
        panel.grid.minor.x = element_blank(),
        panel.grid.minor.y = element_blank())

p3 <- lampreydata |> 
  ungroup() |> 
  mutate(point = factor(point)) |> 
  filter(near(t, examplet, tol = 0.001)) |> 
  ggplot(aes(y = exc, x = exc_x)) +
  geom_path() +
  geom_point(data = ~ filter(.x, point %in% c(13, 15)),
             aes(color = point, shape = point)) +
  scale_color_manual(values = colors) +
  scale_shape_manual(values = c(19, 5)) +
  coord_fixed() +
  theme_minimal() +
  theme(legend.position="none")

p4 <- lampreydata |> 
  ungroup() |> 
  mutate(point = factor(point)) |> 
  filter(near(t, examplet, tol = 0.001)) |> 
  mutate(ph_eu = (gsignal::unwrap(ph_e) / (2*pi)) %% 1) |> 
  ggplot(aes(y = ph_eu, x = arclen)) +
  geom_path() + #color = "#1b9e77") +
  geom_point(data = ~ filter(.x, point %in% c(13, 15)),
             aes(color = point, shape = point)) +
  scale_color_manual(values = colors) +
  scale_shape_manual(values = c(19, 5)) +
  ylim(0,1) +
  theme_minimal() +
  labs(x = "Arc length (mm)", y = "Phase") +
  theme(legend.position="none",
        panel.grid.minor.x = element_blank(),
        panel.grid.minor.y = element_blank())
  # scale_y_continuous(transform = "reverse") 

p1 + p3 + p2 + p4 +
  plot_layout(nrow = 2, heights = c(1,2))

## -----------------------------------------------------------------------------
lampreydata |> 
  group_by(point) |> 
  mutate(freq_c = get_frequency(t, ph_c, method='deriv'),
         freq_e = get_frequency(t, ph_e, method='deriv'),
         freq_p = get_frequency(t, ph_p, method='deriv')) |> 
  pivot_longer(cols = c(freq_c, freq_e, freq_p), names_to = "method", values_to = "freq") |> 
  filter(point %in% c(3, 15, 18)) |> 
  mutate(point = factor(point)) |> 
  ggplot(aes(x = t, y = freq, color = point, shape = method)) +
  scale_shape_manual(values = c(1, 17, 22)) +
  geom_point() +
  facet_wrap(~point)

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(frame %in% c(60, 80)) |> 
  group_by(frame) |> 
  mutate(phbody = ph_p) |>
  ggplot(aes(x = arclen, y = phbody, color = frame)) +
  geom_path(aes(group = frame))

## -----------------------------------------------------------------------------
lampreydata |> 
  filter(frame %in% c(50, 60)) |> 
  group_by(frame) |> 
  mutate(phbody = gsignal::unwrap(ph_e)) |>
  ggplot(aes(x = arclen, y = phbody, color = frame)) +
  geom_path(aes(group = frame))

## -----------------------------------------------------------------------------
w <-
  lampreydata |> 
  arrange(frame, arclen) |> 
  filter(frame %in% c(40)) |> 
  group_by(frame) |> 
  mutate(ph2 = gsignal::unwrap(ph_e),
         wavelen_deriv = get_wavelength(arclen, ph2, method="deriv",
                                   ignore_arclen_vals = \(s) s < 30),
         wavelen_slope = get_wavelength(arclen, ph2, method="slope",
                                   ignore_arclen_vals = \(s) s < 30),
         wavelen_cycle = get_wavelength(arclen, ph2, method="cycle",
                                   ignore_arclen_vals = \(s) s < 30,
                                   sort_arclen = FALSE),
         wavelen_halfcycle = get_wavelength(arclen, ph2, method="halfcycle",
                                   ignore_arclen_vals = \(s) s < 30,
                                   sort_arclen = TRUE))
w |> 
  pivot_longer(cols = contains("wavelen"), names_to = "method", values_to = "wavelen") |> 
  ggplot(aes(x = arclen, y = wavelen, color = method, shape = method)) +
  geom_point()

## -----------------------------------------------------------------------------
lampreydata |> 
  arrange(frame, arclen) |> 
  group_by(frame) |> 
  mutate(phbody_e = gsignal::unwrap(ph_e),
         phbody_c = gsignal::unwrap(ph_c),
         wavelen_exc = get_wavelength(arclen, phbody_e, method="halfcycle",
                                    ignore_arclen_vals = \(s) s < 30),
         wavelen_curve = get_wavelength(arclen, phbody_c, method="halfcycle",
                                    ignore_arclen_vals = \(s) s < 30)) |> 
  pivot_longer(cols = contains("wavelen"), names_to = "method", values_to = "wavelen") |> 
  ggplot(aes(x = t)) +
  geom_point(aes(y = wavelen, color = arclen, shape=method)) +
  scale_shape_manual(values = c(15, 4))


## -----------------------------------------------------------------------------
lampreydata |> 
  arrange(frame, arclen) |> 
  group_by(frame) |> 
  mutate(phbody_e = gsignal::unwrap(ph_e),
         phbody_c = gsignal::unwrap(ph_c),
         wavelen_exc = get_wavelength(arclen, phbody_e, method="halfcycle",
                                    ignore_arclen_vals = \(s) s < 30),
         wavelen_curve = get_wavelength(arclen, phbody_c, method="halfcycle",
                                    ignore_arclen_vals = \(s) s < 30)) |> 
  pivot_longer(cols = contains("wavelen"), names_to = "method", values_to = "wavelen") |> 
  ggplot(aes(x = arclen)) +
  geom_point(aes(y = wavelen, color = arclen, shape=method)) +
  scale_shape_manual(values = c(15, 4)) +
  facet_wrap(~method)


## -----------------------------------------------------------------------------
lampreydata <-
  lampreydata |> 
  get_body_cycle_numbers_df(ph_p, 20) |> 
  arrange(t, point)

lampreydata

## -----------------------------------------------------------------------------
lampreydata |> 
  group_by(point, cycle) |> 
  summarize(amp = (max(exc) - min(exc)) / 2,
            arclen = mean(arclen)) |> 
  ggplot(aes(x = arclen, y = amp, color = cycle)) +
  geom_path(aes(group = cycle))