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#' Read '.csv' File Saved by Avantes' Software for AvaSpec.
#'
#' Reads and parses the header of a processed data file as output by the
#' program Avaspec and then imports wavelength and spectral irradiance
#' values. The file header has little useful metadata information.
#'
#' @param file character string
#' @param date a \code{POSIXct} object to use to set the \code{"when.measured"}
#' attribute. If \code{NULL}, the default, the date is extracted from the
#' file header.
#' @param geocode A data frame with columns \code{lon} and \code{lat} used to
#' set attribute \code{"where.measured"}.
#' @param label character string, but if \code{NULL} the value of \code{file} is
#' used, and if \code{NA} the "what.measured" attribute is not set.
#' @param tz character Time zone used for interpreting times saved in the
#' file header.
#' @param locale The locale controls defaults that vary from place to place. The
#' default locale is US-centric (like R), but you can use
#' \code{\link[readr]{locale}} to create your own locale that controls things
#' like the default time zone, encoding, decimal mark, big mark, and day/month
#' names.
#'
#' @return A source_spct object.
#' @export
#' @references \url{https://www.avantes.com/}
#' @keywords misc
#'
#' @examples
#'
#' file.name <-
#' system.file("extdata", "spectrum-avaspec.csv",
#' package = "photobiologyInOut", mustWork = TRUE)
#'
#' avaspec.spct <- read_avaspec_csv(file = file.name)
#'
#' avaspec.spct
#' getWhatMeasured(avaspec.spct)
#' cat(comment(avaspec.spct))
#'
read_avaspec_csv <- function(file,
date = NULL,
geocode = NULL,
label = NULL,
tz = NULL,
locale = readr::default_locale()) {
if (is.null(tz)) {
tz <- locale$tz
}
label.file <- paste("File: ", basename(file), sep = "")
if (is.null(label)) {
label <- label.file
} else if (!is.na(label)) {
label <- paste(label.file, label, sep = "\n")
}
file_header <- scan(file = file, nlines = 6, skip = 0,
what = "character", quiet = TRUE)
# watt / cm ?
if (length(grep("Watt/cm", file_header[2], fixed = TRUE))) {
mult <- 10e-4
} else {
mult <- NA
}
z <- readr::read_csv(file = file,
col_names = c("w.length", "s.e.irrad"),
skip = 6,
col_types = readr::cols(),
progress = FALSE,
locale = locale)
z[ , "s.e.irrad"] <- z[ , "s.e.irrad"] * mult
old.opts <- options("photobiology.strict.range" = NA_integer_)
z <- photobiology::as.source_spct(z, time.unit = "second")
options(old.opts)
comment(z) <-
paste(paste("Avantes AvaSpec irradiance file '", basename(file), "' imported on ",
lubridate::now(tzone = "UTC"), " UTC", sep = ""),
paste(file_header, collapse = "\n"),
sep = "\n")
photobiology::setWhenMeasured(z, date)
photobiology::setWhereMeasured(z, geocode)
photobiology::setWhatMeasured(z, label)
how <- "Measured with an array spectrometer."
photobiology::setHowMeasured(z, how)
attr(z, "file.header") <- file_header
z
}
#' @rdname read_avaspec_csv
#'
#' @param path Path to the xls/xlsx file
#'
#' @export
#'
read_avaspec_xls <- function(path,
date = NULL,
geocode = NULL,
label = NULL,
tz = NULL,
locale = readr::default_locale()) {
if (is.null(tz)) {
tz <- locale$tz
}
label.file <- paste("File: ", basename(file), sep = "")
if (is.null(label)) {
label <- label.file
} else if (!is.na(label)) {
label <- paste(label.file, label, sep = "\n")
}
file_header <- readxl::read_excel(path, skip = 0, col_names = FALSE)[1:4, 1]
column_names <- readxl::read_excel(path, skip = 4, col_names = FALSE)[1, ]
column_names <- as.vector(as.matrix(column_names))
column_names <- gsub("Wave.*", "w.length", column_names)
column_names <- gsub("Absolute Irradiance.*", "s.e.irrad", column_names)
column_names <- gsub("Photon Count.*", "s.q.irrad", column_names)
z <- readxl::read_excel(path,
col_names = column_names,
progress = FALSE,
skip = 6)
z <- z[!is.na(z["w.length"]),
names(z) %in% c("w.length", "s.e.irrad", "s.q.irrad")]
z["s.e.irrad"] <- z["s.e.irrad"] * 1e-2 # 1e4 * 1e-6
z["s.q.irrad"] <- z["s.q.irrad"] * 1e-6
old.opts <- options("photobiology.strict.range" = NA_integer_)
z <- photobiology::as.source_spct(z, time.unit = "second")
options(old.opts)
comment(z) <-
paste(paste("Avantes AvaSpec irradiance file (Excel)'", basename(path), "' imported on ",
lubridate::now(tzone = "UTC"), " UTC", sep = ""),
paste(file_header, collapse = "\n"),
sep = "\n")
photobiology::setWhenMeasured(z, date)
photobiology::setWhereMeasured(z, geocode)
photobiology::setWhatMeasured(z, label)
how <- "Measured with an array spectrometer."
photobiology::setHowMeasured(z, how)
attr(z, "file.header") <- file_header
z
}
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