In raphidoc/sear: Data Management and Processing for Ocean Optics

knitr::opts_chunk$set(echo = TRUE)

golem::document_and_reload()

library(dplyr)
library(lubridate)
library(plotly)
library(readr)
library(sear)
library(tidyr)

Calibration data

SeaOWLCalFile <- sear:::app_sys("cal", "seaowl", "0144.cal")

SeaOWLCal <- sear:::read_seaowl_cal()

Load data

Station <- interval(ymd_hms("2022-07-05 12:23:13"), ymd_hms("2022-07-05 12:23:15"))

DataFile <- sear:::app_sys("extdata", "DATA_20220705_105732.txt")

MTELog <- sear:::read_mtelog(DataFile)

MTELog <- MTELog %>% filter(date_time %within% Station)

SeaOWLData <- sear:::read_seaowl(MTELog)

Calibrate data

cal_seaowl <- function(SeaOWLData, SeaOWLCal) {
  # Test that calibration and data have the same serial number
  if (!all(SeaOWLCal$SERIALNO == stringr::str_extract(SeaOWLData$sn, "(?<=-).*"))) {
    stop("Calibration and SeaOWL have different serial number")
  }

  SeaOWLData %>%
    mutate(
      vsf_700 = SeaOWLCal$vsf_scale_factor * (vsf_700_channel - SeaOWLCal$vsf_dark_count),
      chl = SeaOWLCal$chl_scale_factor * (chl_channel - SeaOWLCal$chl_dark_count),
      fdom = SeaOWLCal$fdom_scale_factor * (fdom_output - SeaOWLCal$fdom_dark_count),
      .after = sn
    ) %>%
    select(date_time, sn, vsf_700, chl, fdom)
}

seaowl_l1b <- cal_seaowl(SeaOWLData, SeaOWLCal) %>%
  mutate(
    id = seq_along(rownames(SeaOWLData)),
    qc = "1"
  )

Plot data

L1b

SeaOWLL1bNest <- seaowl_l1b %>%
  select(!any_of(c("sn"))) %>%
  pivot_longer(
    cols = any_of(c("vsf_700", "chl", "fdom")),
    names_to = "parameter",
    values_to = "value"
  ) %>%
  group_by(parameter) %>%
  nest()

PlyFont <- list(family = "times New Roman", size = 18)
BlackSquare <- list(
  type = "rect",
  fillcolor = "transparent",
  line = list(width = 0.5),
  xref = "paper",
  yref = "paper",
  x0 = 0,
  x1 = 1,
  y0 = 0,
  y1 = 1
)


SeaOWLL1bNest <- SeaOWLL1bNest %>%
  mutate(
    Plot = purrr::map2(.x = data, .y = parameter, ~
      plot_ly(.x, text = ~id) %>%
        add_markers(x = ~date_time, y = ~value) %>%
        layout(
          shapes = BlackSquare,
          yaxis = list(title = list(text = .y))
        ))
  )


# format(SBE19nest[[2]][[1]]$date_time, "%Y-%m-%d %H:%M:%OS3")

subplot(SeaOWLL1bNest$Plot, nrows = nrow(SeaOWLL1bNest), shareX = TRUE, titleY = TRUE)