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

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

## -----------------------------------------------------------------------------
library(cli)
options(cli.progress_show_after = 0)
options(cli.progress_clear = FALSE)

## ----eval=FALSE---------------------------------------------------------------
# library(here)
# 
# sleapfiles <- c(
#   here("data-raw","2024-11-14_labels2.000_fish_01-030RPM-ortho-2024-11-14T044441.analysis.csv"),
#   here("data-raw","2024-11-14_labels2.001_fish_01-040RPM-ortho-2024-11-14T044525.analysis.csv"),
#   here("data-raw", "2024-11-14_labels2.002_fish_01-050RPM-ortho-2024-11-14T045204.analysis.csv"),
#   here("data-raw","2024-11-14_labels2.003_fish_01-060RPM-ortho-2024-11-14T044754.analysis.csv"),
#   here("data-raw","2024-11-14_labels2.004_fish_01-070RPM-ortho-2024-11-14T044858.analysis.csv")
# )
# 
# parse_file_name <- function(fn)
# {
#   d <- stringr::str_match(fn,
#                  "_(?<id>\\w+_\\d+)-(?<speed>\\d+)RPM.+(?<datetime>\\d{4}-\\d{2}-\\d{2}T\\d{6})")
# 
#   tibble::as_tibble_row(d[1, 2:4], .name_repair = "minimal")
# }
# 
# zfishdata <- purrr::map(sleapfiles, \(fn) readr::read_csv(fn, id = "fn",
#                                          show_col_types = FALSE)) |>
#   bind_rows() |>
#   mutate(dd = purrr::map(fn, parse_file_name)) |>
#   unnest(dd) |>
#   mutate(fn = basename(fn),
#          speed = as.numeric(speed))
# 
# zfish_goodframes <- readr::read_csv(here("data-raw", "zfish_goodframes.csv"))

## -----------------------------------------------------------------------------
head(zfishdata)
head(zfish_goodframes)

## -----------------------------------------------------------------------------
fps <- 50

## -----------------------------------------------------------------------------
pointnames <- c("snout", "eye_ctr", "left_eye", "right_eye", "hyoid",   
                "pec_fin_ctr", "left_pec_fin_base", "left_pec_fin_tip", 
                "right_pec_fin_base", "right_pec_fin_tip", "pelvic_fin_base",
                "anus", "peduncle", "ventral_caudal", "dorsal_caudal")

## -----------------------------------------------------------------------------
zfdata_ctr <-
  zfishdata |>  
  mutate(eye_ctr.x = (left_eye.x + right_eye.x)/2,
         eye_ctr.y = (left_eye.y + right_eye.y)/2,
         eye_ctr.score = NA,
         pec_fin_ctr.x = (left_pec_fin_base.x + right_pec_fin_base.x)/2,
         pec_fin_ctr.y = (left_pec_fin_base.y + right_pec_fin_base.y)/2,
         pec_fin_ctr.score = NA
         )

## -----------------------------------------------------------------------------
zfdata_ctr <- zfdata_ctr |> 
  relocate(id, speed, datetime) |> 
  pivot_kinematics_longer(pointnames = pointnames)

## -----------------------------------------------------------------------------
head(zfdata_ctr)

## -----------------------------------------------------------------------------
zfdata_good <- list()
for (i in seq(1, nrow(zfish_goodframes))) {
  good1 <- zfdata_ctr |> 
    filter(fn == zfish_goodframes$File[[i]],
           between(frame_idx, zfish_goodframes$Start[[i]], zfish_goodframes$End[[i]])) |> 
    mutate(block = zfish_goodframes$Block[[i]])
  zfdata_good[[i]] <- good1
}
zfdata_good <- bind_rows(zfdata_good)

## -----------------------------------------------------------------------------
zfdata_good |> 
  arrange(speed, frame_idx, point) |> 
  filter(speed == 30,
         between(frame_idx, 120, 140)) |> 
  filter(point %in% c("snout", "hyoid", "eye_ctr", "pec_fin_ctr", 
                      "pelvic_fin_base", "anus", "peduncle", "ventral_caudal")) |> 
  ggplot(aes(x = x, y = y, color = point)) +
  geom_point() +
  geom_path(aes(group = frame_idx)) +
  coord_fixed()

## -----------------------------------------------------------------------------
zfdata_good |> 
  arrange(speed, frame_idx, point) |> 
  filter(speed == 40,
         between(frame_idx, 120, 250)) |> 
  filter(point %in% c("snout", "peduncle", "ventral_caudal")) |> 
  ggplot(aes(x = frame_idx, y = y, color = point)) +
  geom_point() +
  geom_path()

## -----------------------------------------------------------------------------
zfdata_sm <-
  zfdata_good |> 
  arrange(speed, frame_idx, point) |> 
  filter(point %in% c("snout", "hyoid", "eye_ctr", "pec_fin_ctr", 
                      "pelvic_fin_base", "anus", "peduncle", "ventral_caudal")) |> 
  group_by(fn, frame_idx) |>
  # calculate the arc length
  mutate(arclen0 = arclength(x, y, na.skip = TRUE)) |> 
  # smooth and fill gaps
  interpolate_points_df(arclen0, x, y, spar = 0.2,
                        tailmethod = 'extrapolate',
                        fill_gaps = 1,
                        .frame = frame_idx,
                        .out = c(arclen='arclen', xs='xs', ys='ys')) |> 
  ungroup()
  

## -----------------------------------------------------------------------------
zfdata_sm |> 
  arrange(speed, frame_idx, point) |> 
  filter(speed == 40,
         between(frame_idx, 120, 250)) |> 
  filter(point %in% c("snout", "peduncle", "ventral_caudal")) |> 
  ggplot(aes(x = frame_idx, y = ys, color = point)) +
  geom_point() +
  geom_path()


## -----------------------------------------------------------------------------
zebrafish_shape |> 
  ggplot(aes(x = s)) +
  geom_path(aes(y = width)) +
  geom_path(aes(y = height), color = "blue")

## -----------------------------------------------------------------------------
zfdata_sm <- zfdata_sm |> 
  group_by(id, speed, datetime, frame_idx) |> 
  mutate(width = interpolate_width(zebrafish_shape$s,
                                   zebrafish_shape$width,
                                   arclen),
         height = interpolate_width(zebrafish_shape$s,
                                   zebrafish_shape$height,
                                   arclen)
         )

## -----------------------------------------------------------------------------
zfdata_sm |> 
  filter(speed ==30,
         frame_idx == 150)

## -----------------------------------------------------------------------------
zfdata_split <-
  zfdata_sm |> 
  group_by(id, speed, datetime, block) |> 
  group_split()

## -----------------------------------------------------------------------------
zfdata_ctr <- list()
for (i in seq(1, length(zfdata_split))) {
  zfdata_ctr[[i]] <-
    zfdata_split[[i]] |> 
    get_midline_center_df(arclen, xs, ys,
                          width = width, height = height,
                          .frame = frame_idx) |> 
    # center everything on the center of mass
    mutate(xctr = xs - xcom,
           yctr = ys - ycom,
           t = frame_idx / fps) |> 
    # find the main axis of the body
    get_primary_swimming_axis_df(t, xctr, yctr, 
                                 .frame = frame_idx)
}

## -----------------------------------------------------------------------------
zfdata_ctr[[2]] |> 
  ggplot(aes(x = exc_x, y = exc, color = point)) +
  geom_path(aes(group = frame_idx)) +
  geom_point()

## -----------------------------------------------------------------------------
zfdata_ctr[[2]] |> 
  filter(point %in% c("peduncle", "ventral_caudal")) |> 
  # filter(between(t, 1, 1.2)) |> 
  ggplot(aes(x = t, y = exc, color = point)) +
  geom_path()

## -----------------------------------------------------------------------------
zfdata_phase <- list()

for (i in seq(1, length(zfdata_ctr))) {
  zfdata_phase[[i]] <- 
  zfdata_ctr[[i]] |> 
  arrange(id, speed, datetime, frame_idx, desc(point)) |> 
  group_by(id, speed, datetime, point) |> 
  mutate(ph_p = peak_phase(exc))
}

## -----------------------------------------------------------------------------
zfdata_phase[[2]] |> 
  ungroup() |> 
  filter(point %in% c("snout", "peduncle", "ventral_caudal")) |> 
  mutate(point = factor(point)) |> 
  ggplot(aes(x = t, y = ph_p, color = point)) +
  geom_path() + 
  facet_wrap(~point)

## -----------------------------------------------------------------------------
zfdata_phase[[2]] |> 
  ungroup() |> 
  group_by(point) |> 
  mutate(freq_p = get_frequency(t, ph_p, method='deriv')) |> 
  filter(point %in% c("snout", "peduncle", "ventral_caudal")) |> 
  ggplot(aes(x = t, y = freq_p, color = point)) +
  scale_shape_manual(values = c(1, 17, 22)) +
  geom_point() +
  facet_wrap(~point)

## -----------------------------------------------------------------------------
zfdata_cyc <- list()

for (i in seq(1, length(zfdata_phase))) {
  zfdata_cyc[[i]] <- 
    zfdata_phase[[i]] |> 
    group_by(point) |> 
    mutate(freq = get_frequency(t, ph_p, method='deriv')) |>
    ungroup() |> 
    get_body_cycle_numbers_df(ph_p, pointval = "peduncle",
                              .frame = frame_idx) |> 
    arrange(id, speed, datetime, block, t, point)
}

## -----------------------------------------------------------------------------
zfdata_cyc[[1]] |> 
  ungroup() |> 
  group_by(speed, point, cycle) |> 
  summarize(amp = (max(exc) - min(exc)) / 2,
            arclen = mean(arclen)) |> 
  ggplot(aes(x = arclen, y = amp, color = speed)) +
  geom_path(aes(group = cycle))


## -----------------------------------------------------------------------------
zfdata_cyc <- bind_rows(zfdata_cyc)

## -----------------------------------------------------------------------------
zfsummary <-
  zfdata_cyc |> 
  group_by(id, datetime, speed, frame_idx) |> 
  mutate(meanfreq = mean(freq)) |> 
  filter(point == "ventral_caudal") |> 
  group_by(speed, cycle) |> 
  summarize(amp = (max(exc) - min(exc)) / 2,
            arclen = mean(arclen),
            meanfreq = mean(meanfreq)) |> 
  ungroup()

zfsummary |> 
  ggplot(aes(x = speed, y = meanfreq)) +
  geom_point(aes(group = factor(speed)))