#' Makes a logical subset of a System4 GeoGrid
#'
#' Makes a logical subset of a System4 GeoGrid using the parameters specified by the user,
#' applying the java methods makeSubset and readDataSlice. Subroutine of loadSeasonalForecast.S4
#'
#' @param grid An input java GeoGrid
#' @param latLon A list of geolocation parameters, as returned by getLatLonDomainForecast
#' @param runTimePars A list of run time definition parameters, as returned by getRunTimeDomain.ECOMS
#' @param memberRangeList A list of ensemble java ranges as returned by getMemberDomain.S4
#' @param foreTimePars A list of forecast time definition parameters, as returned by getForecastTimeDomain.S4
#' @param verticalPars A list with vertical level definition, as returned by \code{getVerticalLevelPars.ECOMS}. Only the last element (the kava index position) is used
#' @return A list containing a n-dimensional array and the (possibly) modified foreTimePars object with the
#' corrected dates in case of time aggregations. Dimensions are labelled by the \dQuote{dimnames} attribute.
#' @details Dimensions of length one are dropped and the \dQuote{dimnames} attribute is consequently modified.
#' In the current version the Z dimension is ignored (and dropped), as it is not planned to include multi-level variables
#' in the ECOMS-UDG by the moment.
#'
#' @references \url{http://www.unidata.ucar.edu/software/thredds/v4.3/netcdf-java/v4.3/javadocAll/ucar/nc2/dt/grid/GeoGrid.html}
#' @author J Bedia and A. Cofi\~no
makeSubset.S4 <- function(grid, latLon, runTimePars, memberRangeList, foreTimePars, verticalPars) {
message("[", Sys.time(), "] Retrieving data subset ..." )
gcs <- grid$getCoordinateSystem()
dimNames <- rev(names(scanVarDimensions(grid))) # reversed!
z <- verticalPars$zRange
aux.foreDatesList <- rep(list(foreTimePars$forecastDates), length(memberRangeList))
foreTimePars$forecastDates <- NULL
aux.list <- rep(list(bquote()), length(memberRangeList))
for (i in 1:length(memberRangeList)) {
ens <- memberRangeList[[i]]
aux.list1 <- rep(list(bquote()), length(runTimePars$runTimeRanges))
for (j in 1:length(runTimePars$runTimeRanges)) {
rt <- runTimePars$runTimeRanges[[j]]
ft <- foreTimePars$ForeTimeRangesList[[j]]
aux.list2 <- rep(list(bquote()), length(latLon$llRanges))
# dateline crossing
for (k in 1:length(latLon$llRanges)) {
subSet <- grid$makeSubset(rt, ens, ft, z, latLon$llRanges[[k]]$get(0L), latLon$llRanges[[k]]$get(1L))
shapeArray <- rev(subSet$getShape())
dimNamesRef <- dimNames
if (latLon$pointXYindex[1] >= 0) {
rm.dim <- grep(gcs$getXHorizAxis()$getDimensionsString(), dimNamesRef, fixed = TRUE)
shapeArray <- shapeArray[-rm.dim]
dimNamesRef <- dimNamesRef[-rm.dim]
}
if (latLon$pointXYindex[2] >= 0) {
rm.dim <- grep(gcs$getYHorizAxis()$getDimensionsString(), dimNamesRef, fixed = TRUE)
shapeArray <- shapeArray[-rm.dim]
dimNamesRef <- dimNamesRef[-rm.dim]
}
aux.list2[[k]] <- array(subSet$readDataSlice(-1L, -1L, -1L, -1L, latLon$pointXYindex[2], latLon$pointXYindex[1])$copyTo1DJavaArray(), dim = shapeArray)
}
aux.list1[[j]] <- do.call("abind", c(aux.list2, along = 1))
aux.list2 <- NULL
# Deaccumulator
if (foreTimePars$deaccum) {
mar <- c(1:length(dim(aux.list1[[j]])))[-grep("^time", dimNamesRef)]
aux.list1[[j]] <- apply(aux.list1[[j]], mar, diff) #deaccumulate, foreTimePars$deaccumFromFirst)
dimNamesRef <- c("time", dimNamesRef[grep("^time$", dimNamesRef, invert = TRUE)])
}
# Daily aggregator
if (foreTimePars$aggr.d != "none") {
aux.string <- paste((aux.foreDatesList[[i]][[j]])$mon, (aux.foreDatesList[[i]][[j]])$mday, sep = "-")
aux.factor <- factor(aux.string, levels = unique(aux.string), ordered = TRUE)
mar <- grep("^time", dimNamesRef, invert = TRUE)
aux.list1[[j]] <- apply(aux.list1[[j]], mar, function(x) {
tapply(x, INDEX = aux.factor, FUN = foreTimePars$aggr.d, na.rm = TRUE)
})
dimNamesRef <- c("time", dimNamesRef[mar])
# Convert dates to daily:
nhours <- length(aux.factor) / nlevels(aux.factor)
aux.foreDatesList[[i]][[j]] <- aux.foreDatesList[[i]][[j]][seq(1, by = nhours, length.out = nlevels(aux.factor))]
}
# Monthly aggregator
if (foreTimePars$aggr.m != "none") {
mes <- (aux.foreDatesList[[i]][[j]])$mon
day <- (aux.foreDatesList[[i]][[j]])$mday
mes <- factor(mes, levels = unique(mes), ordered = TRUE)
mar <- grep("^time", dimNamesRef, invert = TRUE)
aux.list1[[j]] <- apply(aux.list1[[j]], MARGIN = mar, FUN = function(x) {
tapply(x, INDEX = mes, FUN = foreTimePars$aggr.m)
})
dimNamesRef <- if (length(unique(mes)) > 1) {
c("time", dimNamesRef[mar])
} else {
dimNamesRef[mar]
}
aux.foreDatesList[[i]][[j]] <- if (aux.foreDatesList[[i]][[j]][1]$mday == 2) { # case of lm0 precip
append(aux.foreDatesList[[i]][[j]][1], aux.foreDatesList[[i]][[j]][which(day == 1)])
} else {
aux.foreDatesList[[i]][[j]][which(day == 1)]
}
}
}
if (foreTimePars$aggr.m != "none") {
if (length(unique(mes)) > 1) {
aux.list[[i]] <- do.call("abind", c(aux.list1, along = grep("^time", dimNamesRef)))
} else {
aux.list[[i]] <- do.call("abind", c(aux.list1, along = -1L))
dimNamesRef <- c("time", dimNamesRef)
}
} else {
aux.list[[i]] <- do.call("abind", c(aux.list1, along = grep("^time", dimNamesRef)))
}
aux.list1 <- NULL
}
along <- tryCatch(expr = grep(gcs$getEnsembleAxis()$getDimensionsString(), dimNamesRef, fixed = TRUE),
error = function(err) 1L) ## Static grids lack EnsembleAxis and yield error
mdArray <- do.call("abind", c(aux.list, along = along))
aux.list <- NULL
if (any(dim(mdArray) == 1)) {
dimNames <- dimNamesRef[-which(dim(mdArray) == 1)]
mdArray <- drop(mdArray)
} else {
dimNames <- dimNamesRef
}
dimNames <- gsub("^time.*", "time", dimNames)
mdArray <- unname(mdArray)
attr(mdArray, "dimensions") <- dimNames
# Date adjustment
foreTimePars$forecastDates <- aux.foreDatesList
if (!is.null(aux.foreDatesList[[1]][[1]])) { ## Otherwise static
foreTimePars$forecastDates <- adjustDates.forecast(foreTimePars)
}
return(list("mdArray" = mdArray, "foreTimePars" = foreTimePars))
}
# End
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