R/retrieve.R
In dankelley/oceanglider: Analysis of Oceanographic Glider Data
#' Retrieve Part of a glider Object
#'
#' Retrieve something contained in a glider object, or something that can
#' be computed from what is contained there.
#'
#' First, a check is done to see if the object's metadata contains an item
#' with name given by `i`. If this is true, then that value is returned.
#'
#' Otherwise, the item is sought somewhere within the `data` slot.
#' This may be done within `data` directly for Slocum
#' data or within `data$payload` or a similar name for SeaExplorer
#' data. Note that `[[` can retrieve not just the actual stored
#' information, but also information that can be derived from that information.
#' For example, gliders do not store Absolute Salinity or Conservative
#' Temperature, but they can be retrieved with `g[["SA"]]` and `g[["CT"]]`
#' respectively, where `g` is a glider object (see Example 1). Use e.g. `g[["?"]]` on
#' a given glider object, to find out what items `[[` can retrieve
#' (see Example 2).
#'
#' @param x a glider object, i.e. one inheriting from [glider-class].
#'
#' @param i a character value that names the item to be retrieved.
#'
#' @param j an optional character value specifying the data-stream to be used.
#'
#' @param ... optional additional information (ignored).
#'
#' @author Dan Kelley
#'
#' @examples
#' library(oceglider)
#' directory <- system.file("extdata/sea_explorer/delayed_raw", package = "oceglider")
#' g <- read.glider.seaexplorer.raw(directory, pattern = "pld1.raw")
#'
#' # Example 1: look up Absolute Salinity
#' summary(g[["SA"]])
#'
#' # Example 2: discover what can be retrieved from this object
#' # (FIXME: not all of these work)
#' g[["?"]]
#'
#' @importFrom oce swSigmaTheta swSigma0 swSigma1 swSigma2 swSigma3 swSpice swZ
#' @importFrom gsw gsw_CT_from_t gsw_SA_from_SP gsw_sound_speed gsw_spiciness0
#'
#' @export
#'
#' @md
setMethod(
f = "[[",
signature(x = "glider", i = "ANY", j = "ANY"),
definition = function(x, i, j, ...) {
dots <- list(...)
debug <- if (is.null(dots$debug)) getOption("gliderDebug", default = 0L) else dots$debug
# . message("in [[, i='", i, "'")
# debug <- getOption("gliderDebug", default = 0L)
if (missing(i)) {
stop("Must name a glider item to retrieve, e.g. '[[\"temperature\"]]'", call. = FALSE)
}
if (length(i) > 1L) {
stop("can only access one item at a time", call. = FALSE)
}
if (!is.character(i)) {
stop("glider item must be specified by name", call. = FALSE)
}
gliderDebug(debug, "glider[[i=\"", i, "\", j=\"",
if (missing(j)) "(missing)" else j, ", ...]] START\n",
sep = "", unindent = 1
)
if (i == "filename") {
return(x@metadata$filename)
} else if (i == "data") {
return(x@data)
} else if (i == "metadata") {
return(x@metadata)
} else if (i == "yo" && !missing(j)) { # NOTE: not 'yoNumber'
lines <- which(x@data$yoNumber == j)
x@data <- x@data[lines, ]
for (f in names(x@metadata$flags$payload1)) {
x@metadata$flags[[f]] <- x@metadata$flags[[f]][lines]
}
return(x)
}
type <- x@metadata$type
if (is.null(type)) {
stop("'type' is NULL")
}
dataAreStreamed <- x@metadata$dataAreStreamed
gliderDebug(debug, "dataAreStreamed: ", dataAreStreamed, "\n")
defaultStream <- "payload1"
if (grepl("Flag$", i)) {
# message("DAN")
flags <- x@metadata$flags
if (is.null(flags)) {
return(NULL)
}
# returns a list
if (dataAreStreamed) {
flags <- x@metadata$flags[["payload1"]]
}
return(flags[[gsub("Flag$", "", i)]])
}
# FIXME (DK) recognize "Unit$" as done in oce.
if (i == "type") {
return(type)
}
if (i == "sigmaTheta") {
return(swSigmaTheta(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma0") {
return(swSigma0(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma1") {
return(swSigma1(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma2") {
return(swSigma2(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma3") {
return(swSigma3(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "SA") {
return(gsw_SA_from_SP(
SP = x[["salinity"]], p = x[["pressure"]],
longitude = x[["longitude"]], latitude = x[["latitude"]]
))
}
if (i == "z") {
return(swZ(x[["pressure"]], latitude = mean(x[["latitude"]], na.rm = TRUE)))
}
if (i == "CT") {
t <- x[["temperature"]]
SP <- x[["salinity"]] # stored as practical salinity
p <- x[["pressure"]]
SA <- gsw_SA_from_SP(SP = SP, p = p, longitude = x[["longitude"]], latitude = x[["latitude"]])
return(gsw_CT_from_t(SA, t, p))
}
if (i == "sound speed") {
t <- x[["temperature"]]
SP <- x[["salinity"]] # stored as practical salinity
p <- x[["pressure"]]
SA <- gsw_SA_from_SP(SP = SP, p = p, longitude = x[["longitude"]], latitude = x[["latitude"]])
CT <- gsw_CT_from_t(SA, t, p)
return(gsw_sound_speed(SA, CT, p))
}
if (i == "spiciness0") {
t <- x[["temperature"]]
SP <- x[["salinity"]] # stored as practical salinity
p <- x[["pressure"]]
# SA <- gsw::gsw_SA_from_SP(SP, p, x[["longitude"]], x[["latitude"]])
# CT <- gsw::gsw_CT_from_t(SA, t, p)
# return(gsw::gsw_spiciness0(SA=SA, CT=CT))
SA <- gsw_SA_from_SP(SP, p, x[["longitude"]], x[["latitude"]])
CT <- gsw_CT_from_t(SA, t, p)
return(gsw_spiciness0(SA = SA, CT = CT))
}
if (i == "oxygen") {
if (identical(x@metadata$type, "seaexplorer")) {
dataNames <- names(x@data)
# get payload name
w <- grep("payload", dataNames)
if (length(w) == 0L) {
stop("sea-explorer object has no payload")
}
if (length(w) > 1L) {
stop("sea-explorer object has more than one \"payload\"-type element")
}
payloadName <- dataNames[w]
dataNames <- names(x@data[[payloadName]])
# message("dataNames--")
# print(dataNames)
if ("oxygen" %in% dataNames) {
gliderDebug(debug, " accessing \"oxygen\" directly in seaexplorer object\n")
return(x@data[payloadName]$oxygen)
} else if ("oxygenFrequency" %in% dataNames) {
gliderDebug(debug, " computing \"oxygen\" from \"oxygenFrequency\" in seaexplorer object\n")
if (!"oxycalib" %in% names(x@metadata)) {
warning(
"cannot compute oxygen, because metadata lacks an",
" oxycalib item, with which to compute oxygen using data$payload1$oxygenFrequency"
)
return(NULL)
}
cal <- x@metadata$oxycalib
oxygenFrequency <- x@data[[payloadName]]$oxygenFrequency
# cat(oce::vectorShow(oxygenFrequency))
salinity <- x@data[[payloadName]]$salinity
# cat(oce::vectorShow(salinity))
temperature <- x@data[[payloadName]]$temperature
# cat(oce::vectorShow(temperature))
pressure <- x@data[[payloadName]]$pressure
# cat(oce::vectorShow(pressure))
cc <- cal$calibrationCoefficients
# This Kelvin temperature is as used in swSatOw. Note the
# non-standard offset and the non-unity factor
# Tk <- 273.15 + temperature * 1.00024
# _ # NOTE: the calibration formula I have for
# _ # sea-explorer datasets also has something called
# _ # Tau20, but I don't see that below. For details
# _ # on the formula, see
# _ # https://github.com/DFOglider/pilotingApp/blob/glimpseFtp/oxygenCalibrationCoefficients.R
# _ # and emails from Chantelle Layton and Clark
# _ # Richards.
# _ res <- cc$Soc * (oxygenFrequency + cc$Foffset) *
# _ (1.0 + cc$A * temperature + cc$B * temperature^2 + cc$C * temperature^3) *
# _ swSatO2(temperature = temperature, salinity = salinity) *
# _ exp(cc$Enom * pressure / Tk)
# _ res <- 44.6591 * res # the factor converts to umol/kg
return(swOxygenFrequencyToSaturation(
temperature = temperature, salinity = salinity,
pressure = pressure, frequency = oxygenFrequency, cal = cc, unit = "umol/kg"
))
} else {
return(NULL)
}
} else if (identical(x@metadata$type, "slocum")) {
gliderDebug(debug, " analysing \"slocum\" object\n", sep = "")
message("FIXME: get oxygen from slocum")
dataNames <- names(x@data)
# I don't know whether oxygen-frequency can be in such data,
# and I don't have docs on calibration formulae, so I return
# NULL in such a case; the user will need to do that work.
for (nickname in c("oxygen", "oxygenConcentration", "O2")) {
if (nickname %in% dataNames) {
return(x@data[[nickname]])
}
}
return(NULL)
} else {
stop("glider type must be either \"seaexplorer\" or \"slocum\"")
}
}
if (i == "?") {
dataNames <- names(x@data)
w <- grep("payload", dataNames)
if (length(w) > 1L) {
stop("cannot handle files with multiple 'payloadN' items")
} else if (length(w) == 1L) {
dataNames <- names(x@data[[dataNames[w]]])
}
# the next is patterned on oce:computableWaterProperties, which I
# will update to handle names as a parameter, but I don't want to
# make oceglider depend on a non-CRAN version of oce.
if (all(c("salinity", "temperature", "pressure") %in% dataNames)) {
dataNames <- c(dataNames, c(
"theta", paste("potential", "temperature"), "z",
"depth", "spice", "Rrho", "RrhoSF", "sigmaTheta", "SP",
"density", "N2", paste("sound", "speed")
))
}
if (all(c("longitude", "latitude") %in% dataNames)) {
dataNames <- c(
dataNames, "SR", "Sstar",
paste0("sigma", 0:4),
"SA", paste("Absolute", "Salinity"),
"CT", paste("Conservative", "Temperature"),
paste0("spiciness", 0:2)
)
}
# It is possible to compute nitrate from NO2+NO3 and nitrite, if
# it's not stored in the object already. This occurs in data(section).
# I also added a similar scheme for nitrite, although I don't know
# whether that condition ever happens, in practice.
if (!("nitrate" %in% dataNames) && ("NO2+NO3" %in% dataNames) && ("nitrite" %in% dataNames)) {
dataNames <- c(dataNames, "nitrate")
}
if (!("nitrite" %in% dataNames) && ("NO2+NO3" %in% dataNames) && ("nitrate" %in% dataNames)) {
dataNames <- c(dataNames, "nitrite")
}
return(sort(unique(dataNames)))
}
# . message("it is a seaexplorer")
if (i == "glider") {
return(x@data$glider)
}
if (missing(j)) {
# . message("j is missing")
if (i %in% names(x@metadata)) {
gliderDebug(debug, " returning item from @metadata\n")
return(x@metadata[[i]])
} else if (i %in% names(x@data)) {
gliderDebug(debug, " returning item from @data\n")
return(x@data[[i]])
} else {
if (dataAreStreamed) { # FIXME: handle original names here also
return(x@data[[defaultStream]][[i]])
}
# message("DAN FIXME 1")
# cat(str(x@metadata$dataNamesOriginal$payload1))
# message("DAN FIXME 2")
if (i %in% names(x@data)) {
gliderDebug(debug, " result in @data\n")
return(x@data[[i]])
} else if (i %in% x@metadata$dataNamesOriginal) {
gliderDebug(debug, " result in @data inferred from original name\n")
w <- which(x@metadata$dataNamesOriginal == i)
# print(w)
names <- names(x@metadata$dataNamesOriginal)
# print(names)
gliderDebug(debug, " returning ", names[w], "\n")
return(x@data[[names[w]]])
} else if (i %in% names(x@metadata$dataNamesOriginal)) {
gliderDebug(debug, " result in @data$glider inferred from original name\n")
iname <- names(which(x@metadata$dataNamesOriginal == i))[2]
return(x@data$glider[[iname]])
}
gliderDebug(debug, " cannot find what to return\n")
return(NULL)
}
}
warning("[[", i, ",", j, "]] not understood, so returning NULL", sep = "")
return(NULL)
}
)
dankelley/oceanglider documentation built on June 8, 2025, 4:20 a.m.
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#' Retrieve Part of a glider Object
#'
#' Retrieve something contained in a glider object, or something that can
#' be computed from what is contained there.
#'
#' First, a check is done to see if the object's metadata contains an item
#' with name given by `i`. If this is true, then that value is returned.
#'
#' Otherwise, the item is sought somewhere within the `data` slot.
#' This may be done within `data` directly for Slocum
#' data or within `data$payload` or a similar name for SeaExplorer
#' data. Note that `[[` can retrieve not just the actual stored
#' information, but also information that can be derived from that information.
#' For example, gliders do not store Absolute Salinity or Conservative
#' Temperature, but they can be retrieved with `g[["SA"]]` and `g[["CT"]]`
#' respectively, where `g` is a glider object (see Example 1). Use e.g. `g[["?"]]` on
#' a given glider object, to find out what items `[[` can retrieve
#' (see Example 2).
#'
#' @param x a glider object, i.e. one inheriting from [glider-class].
#'
#' @param i a character value that names the item to be retrieved.
#'
#' @param j an optional character value specifying the data-stream to be used.
#'
#' @param ... optional additional information (ignored).
#'
#' @author Dan Kelley
#'
#' @examples
#' library(oceglider)
#' directory <- system.file("extdata/sea_explorer/delayed_raw", package = "oceglider")
#' g <- read.glider.seaexplorer.raw(directory, pattern = "pld1.raw")
#'
#' # Example 1: look up Absolute Salinity
#' summary(g[["SA"]])
#'
#' # Example 2: discover what can be retrieved from this object
#' # (FIXME: not all of these work)
#' g[["?"]]
#'
#' @importFrom oce swSigmaTheta swSigma0 swSigma1 swSigma2 swSigma3 swSpice swZ
#' @importFrom gsw gsw_CT_from_t gsw_SA_from_SP gsw_sound_speed gsw_spiciness0
#'
#' @export
#'
#' @md
setMethod(
f = "[[",
signature(x = "glider", i = "ANY", j = "ANY"),
definition = function(x, i, j, ...) {
dots <- list(...)
debug <- if (is.null(dots$debug)) getOption("gliderDebug", default = 0L) else dots$debug
# . message("in [[, i='", i, "'")
# debug <- getOption("gliderDebug", default = 0L)
if (missing(i)) {
stop("Must name a glider item to retrieve, e.g. '[[\"temperature\"]]'", call. = FALSE)
}
if (length(i) > 1L) {
stop("can only access one item at a time", call. = FALSE)
}
if (!is.character(i)) {
stop("glider item must be specified by name", call. = FALSE)
}
gliderDebug(debug, "glider[[i=\"", i, "\", j=\"",
if (missing(j)) "(missing)" else j, ", ...]] START\n",
sep = "", unindent = 1
)
if (i == "filename") {
return(x@metadata$filename)
} else if (i == "data") {
return(x@data)
} else if (i == "metadata") {
return(x@metadata)
} else if (i == "yo" && !missing(j)) { # NOTE: not 'yoNumber'
lines <- which(x@data$yoNumber == j)
x@data <- x@data[lines, ]
for (f in names(x@metadata$flags$payload1)) {
x@metadata$flags[[f]] <- x@metadata$flags[[f]][lines]
}
return(x)
}
type <- x@metadata$type
if (is.null(type)) {
stop("'type' is NULL")
}
dataAreStreamed <- x@metadata$dataAreStreamed
gliderDebug(debug, "dataAreStreamed: ", dataAreStreamed, "\n")
defaultStream <- "payload1"
if (grepl("Flag$", i)) {
# message("DAN")
flags <- x@metadata$flags
if (is.null(flags)) {
return(NULL)
}
# returns a list
if (dataAreStreamed) {
flags <- x@metadata$flags[["payload1"]]
}
return(flags[[gsub("Flag$", "", i)]])
}
# FIXME (DK) recognize "Unit$" as done in oce.
if (i == "type") {
return(type)
}
if (i == "sigmaTheta") {
return(swSigmaTheta(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma0") {
return(swSigma0(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma1") {
return(swSigma1(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma2") {
return(swSigma2(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "sigma3") {
return(swSigma3(
salinity = x[["salinity"]],
temperature = x[["temperature"]],
pressure = x[["pressure"]],
longitude = x[["longitude"]],
latitude = x[["latitude"]]
))
}
if (i == "SA") {
return(gsw_SA_from_SP(
SP = x[["salinity"]], p = x[["pressure"]],
longitude = x[["longitude"]], latitude = x[["latitude"]]
))
}
if (i == "z") {
return(swZ(x[["pressure"]], latitude = mean(x[["latitude"]], na.rm = TRUE)))
}
if (i == "CT") {
t <- x[["temperature"]]
SP <- x[["salinity"]] # stored as practical salinity
p <- x[["pressure"]]
SA <- gsw_SA_from_SP(SP = SP, p = p, longitude = x[["longitude"]], latitude = x[["latitude"]])
return(gsw_CT_from_t(SA, t, p))
}
if (i == "sound speed") {
t <- x[["temperature"]]
SP <- x[["salinity"]] # stored as practical salinity
p <- x[["pressure"]]
SA <- gsw_SA_from_SP(SP = SP, p = p, longitude = x[["longitude"]], latitude = x[["latitude"]])
CT <- gsw_CT_from_t(SA, t, p)
return(gsw_sound_speed(SA, CT, p))
}
if (i == "spiciness0") {
t <- x[["temperature"]]
SP <- x[["salinity"]] # stored as practical salinity
p <- x[["pressure"]]
# SA <- gsw::gsw_SA_from_SP(SP, p, x[["longitude"]], x[["latitude"]])
# CT <- gsw::gsw_CT_from_t(SA, t, p)
# return(gsw::gsw_spiciness0(SA=SA, CT=CT))
SA <- gsw_SA_from_SP(SP, p, x[["longitude"]], x[["latitude"]])
CT <- gsw_CT_from_t(SA, t, p)
return(gsw_spiciness0(SA = SA, CT = CT))
}
if (i == "oxygen") {
if (identical(x@metadata$type, "seaexplorer")) {
dataNames <- names(x@data)
# get payload name
w <- grep("payload", dataNames)
if (length(w) == 0L) {
stop("sea-explorer object has no payload")
}
if (length(w) > 1L) {
stop("sea-explorer object has more than one \"payload\"-type element")
}
payloadName <- dataNames[w]
dataNames <- names(x@data[[payloadName]])
# message("dataNames--")
# print(dataNames)
if ("oxygen" %in% dataNames) {
gliderDebug(debug, " accessing \"oxygen\" directly in seaexplorer object\n")
return(x@data[payloadName]$oxygen)
} else if ("oxygenFrequency" %in% dataNames) {
gliderDebug(debug, " computing \"oxygen\" from \"oxygenFrequency\" in seaexplorer object\n")
if (!"oxycalib" %in% names(x@metadata)) {
warning(
"cannot compute oxygen, because metadata lacks an",
" oxycalib item, with which to compute oxygen using data$payload1$oxygenFrequency"
)
return(NULL)
}
cal <- x@metadata$oxycalib
oxygenFrequency <- x@data[[payloadName]]$oxygenFrequency
# cat(oce::vectorShow(oxygenFrequency))
salinity <- x@data[[payloadName]]$salinity
# cat(oce::vectorShow(salinity))
temperature <- x@data[[payloadName]]$temperature
# cat(oce::vectorShow(temperature))
pressure <- x@data[[payloadName]]$pressure
# cat(oce::vectorShow(pressure))
cc <- cal$calibrationCoefficients
# This Kelvin temperature is as used in swSatOw. Note the
# non-standard offset and the non-unity factor
# Tk <- 273.15 + temperature * 1.00024
# _ # NOTE: the calibration formula I have for
# _ # sea-explorer datasets also has something called
# _ # Tau20, but I don't see that below. For details
# _ # on the formula, see
# _ # https://github.com/DFOglider/pilotingApp/blob/glimpseFtp/oxygenCalibrationCoefficients.R
# _ # and emails from Chantelle Layton and Clark
# _ # Richards.
# _ res <- cc$Soc * (oxygenFrequency + cc$Foffset) *
# _ (1.0 + cc$A * temperature + cc$B * temperature^2 + cc$C * temperature^3) *
# _ swSatO2(temperature = temperature, salinity = salinity) *
# _ exp(cc$Enom * pressure / Tk)
# _ res <- 44.6591 * res # the factor converts to umol/kg
return(swOxygenFrequencyToSaturation(
temperature = temperature, salinity = salinity,
pressure = pressure, frequency = oxygenFrequency, cal = cc, unit = "umol/kg"
))
} else {
return(NULL)
}
} else if (identical(x@metadata$type, "slocum")) {
gliderDebug(debug, " analysing \"slocum\" object\n", sep = "")
message("FIXME: get oxygen from slocum")
dataNames <- names(x@data)
# I don't know whether oxygen-frequency can be in such data,
# and I don't have docs on calibration formulae, so I return
# NULL in such a case; the user will need to do that work.
for (nickname in c("oxygen", "oxygenConcentration", "O2")) {
if (nickname %in% dataNames) {
return(x@data[[nickname]])
}
}
return(NULL)
} else {
stop("glider type must be either \"seaexplorer\" or \"slocum\"")
}
}
if (i == "?") {
dataNames <- names(x@data)
w <- grep("payload", dataNames)
if (length(w) > 1L) {
stop("cannot handle files with multiple 'payloadN' items")
} else if (length(w) == 1L) {
dataNames <- names(x@data[[dataNames[w]]])
}
# the next is patterned on oce:computableWaterProperties, which I
# will update to handle names as a parameter, but I don't want to
# make oceglider depend on a non-CRAN version of oce.
if (all(c("salinity", "temperature", "pressure") %in% dataNames)) {
dataNames <- c(dataNames, c(
"theta", paste("potential", "temperature"), "z",
"depth", "spice", "Rrho", "RrhoSF", "sigmaTheta", "SP",
"density", "N2", paste("sound", "speed")
))
}
if (all(c("longitude", "latitude") %in% dataNames)) {
dataNames <- c(
dataNames, "SR", "Sstar",
paste0("sigma", 0:4),
"SA", paste("Absolute", "Salinity"),
"CT", paste("Conservative", "Temperature"),
paste0("spiciness", 0:2)
)
}
# It is possible to compute nitrate from NO2+NO3 and nitrite, if
# it's not stored in the object already. This occurs in data(section).
# I also added a similar scheme for nitrite, although I don't know
# whether that condition ever happens, in practice.
if (!("nitrate" %in% dataNames) && ("NO2+NO3" %in% dataNames) && ("nitrite" %in% dataNames)) {
dataNames <- c(dataNames, "nitrate")
}
if (!("nitrite" %in% dataNames) && ("NO2+NO3" %in% dataNames) && ("nitrate" %in% dataNames)) {
dataNames <- c(dataNames, "nitrite")
}
return(sort(unique(dataNames)))
}
# . message("it is a seaexplorer")
if (i == "glider") {
return(x@data$glider)
}
if (missing(j)) {
# . message("j is missing")
if (i %in% names(x@metadata)) {
gliderDebug(debug, " returning item from @metadata\n")
return(x@metadata[[i]])
} else if (i %in% names(x@data)) {
gliderDebug(debug, " returning item from @data\n")
return(x@data[[i]])
} else {
if (dataAreStreamed) { # FIXME: handle original names here also
return(x@data[[defaultStream]][[i]])
}
# message("DAN FIXME 1")
# cat(str(x@metadata$dataNamesOriginal$payload1))
# message("DAN FIXME 2")
if (i %in% names(x@data)) {
gliderDebug(debug, " result in @data\n")
return(x@data[[i]])
} else if (i %in% x@metadata$dataNamesOriginal) {
gliderDebug(debug, " result in @data inferred from original name\n")
w <- which(x@metadata$dataNamesOriginal == i)
# print(w)
names <- names(x@metadata$dataNamesOriginal)
# print(names)
gliderDebug(debug, " returning ", names[w], "\n")
return(x@data[[names[w]]])
} else if (i %in% names(x@metadata$dataNamesOriginal)) {
gliderDebug(debug, " result in @data$glider inferred from original name\n")
iname <- names(which(x@metadata$dataNamesOriginal == i))[2]
return(x@data$glider[[iname]])
}
gliderDebug(debug, " cannot find what to return\n")
return(NULL)
}
}
warning("[[", i, ",", j, "]] not understood, so returning NULL", sep = "")
return(NULL)
}
)
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