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Merge pull request #165 from pascal-sauer/master
ncdf4-based nc writing (+ extend helper)
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| ValidationKey: '121045680' | ||
| ValidationKey: '121449200' | ||
| AcceptedWarnings: | ||
| - 'Warning: package ''.*'' was built under R version' | ||
| - 'Warning: namespace ''.*'' is not available and has been replaced' | ||
| - is.na\(\) applied to non-\(list or vector\) of type 'closure' | ||
| AcceptedNotes: unable to verify current time | ||
| AutocreateReadme: yes | ||
| allowLinterWarnings: no | ||
| enforceVersionUpdate: no |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,59 @@ | ||
| #' extend | ||
| #' | ||
| #' Extend a magpie object to a dense grid based on the given xRange, yRange and resolution. | ||
| #' This is e.g. required when writing netCDF files. Extending a sparse magpie object to a dense grid | ||
| #' requires much more memory, so use with caution. | ||
| #' | ||
| #' @param x A magpie object | ||
| #' @param xRange Range of x coordinates, in ascending order when writing to netCDF | ||
| #' @param yRange Range of y coordinates, in descending order when writing to netCDF | ||
| #' @param res Resolution of the data, if not provided it will be guessed | ||
| #' @return An extended magpie object with the same data as x and gaps filled with NA | ||
| #' @author Pascal Sauer | ||
| #' @export | ||
| extend <- function(x, | ||
| xRange = c(-179.75, 179.75), | ||
| yRange = c(89.75, -89.75), | ||
| res = NULL) { | ||
| stopifnot(length(xRange) == 2, length(yRange) == 2) | ||
| if (is.null(res)) { | ||
| res <- guessResolution(x) | ||
| } | ||
| coords <- expand.grid(x = seq(xRange[1], xRange[2], if (xRange[1] < xRange[2]) res else -res), | ||
| y = seq(yRange[1], yRange[2], if (yRange[1] < yRange[2]) res else -res)) | ||
| coords <- paste0(coords$x, "|", coords$y) | ||
| coords <- gsub("\\.", "p", coords) | ||
| coords <- sub("\\|", ".", coords) | ||
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| sparseCoords <- paste0(getItems(x, "x", full = TRUE), | ||
| ".", | ||
| getItems(x, "y", full = TRUE)) | ||
| if (!all(sparseCoords %in% coords)) { | ||
| stop("The coordinates of the input object are not a subset of the extended coordinates. ", | ||
| "Try changing res, xRange or yRange.") | ||
| } | ||
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| subdims1 <- getSets(x)[grep("^d1\\.", names(getSets(x)))] | ||
| notCoords <- subdims1[!subdims1 %in% c("x", "y")] | ||
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| dim1 <- paste0(coords, paste(rep(".NA", length(notCoords)), collapse = "")) | ||
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| extended <- new.magpie(dim1, getItems(x, 2), getItems(x, 3)) | ||
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| # dimOrder subdims x and y to where they are in x | ||
| perm <- match(getSets(x), c("x", "y"))[seq_along(subdims1)] | ||
| perm[is.na(perm)] <- seq_along(notCoords) + 2 | ||
| extended <- dimOrder(extended, perm, dim = 1) | ||
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| getSets(extended) <- getSets(x) | ||
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| posInCoords <- match(sparseCoords, coords) | ||
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| # fill subdims for dim 1 other than x and y (e.g. country code) if they were set in x | ||
| dimnames(extended)[[1]][posInCoords] <- getItems(x, 1) | ||
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| # fill extended with data from x where available | ||
| extended[posInCoords, , ] <- x | ||
|
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| return(extended) | ||
| } |
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| #' guessResolution | ||
| #' | ||
| #' Guess the resolution of the given magpie object/coordinates by looking at the minimum | ||
| #' difference between unique sorted values. Fall back to 0.5 if guess is infinite. | ||
| #' | ||
| #' @param x A magpie object or the coordinates of a magpie object (the result | ||
| #' of \code{\link{getCoords}}) | ||
| #' @return The guessed resolution of the data | ||
| #' @author Jan Philipp Dietrich, Pascal Sauer | ||
| #' @export | ||
| guessResolution <- function(x) { | ||
| if (is.magpie(x)) { | ||
| xy <- getCoords(x) | ||
| } else { | ||
| xy <- x | ||
| } | ||
| .tmp <- function(x) { | ||
| return(min(diff(sort(unique(x))))) | ||
| } | ||
| guess <- min(.tmp(xy[[1]]), .tmp(xy[[2]])) | ||
| # use 0.5deg as guess if it cannot be determined otherwise as this is | ||
| # the default spatial resolution in the magpie universe. | ||
| if (is.infinite(guess)) guess <- 0.5 | ||
| return(guess) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| #' Write a magpie object to a netCDF file | ||
| #' | ||
| #' @param x A magpie object | ||
| #' @param filename Name of the netCDF file to write | ||
| #' @param unit Unit of the data, to omit pass "" (empty string) | ||
| #' @param ... For future expansion. | ||
| #' @param compression Level of compression to use (1-9), NA for no compression | ||
| #' @param missval The value that encodes NA in the resulting netCDF file | ||
| #' @param res Resolution of the data, if not provided it will be guessed | ||
| #' @param zname Name of the z dimension in the netCDF file | ||
| #' @author Pascal Sauer | ||
| writeNC <- function(x, filename, unit, ..., compression = 2, missval = NA, | ||
| res = NULL, zname = "time") { | ||
| if (!requireNamespace("ncdf4", quietly = TRUE)) { | ||
| stop("The ncdf4 package is required to write netCDF files, please install it.") | ||
| } | ||
| # fail immediately if arguments are not set | ||
| stopifnot(is.character(filename), is.character(unit)) | ||
| if (!(...length() == 0 || all(...names() == "verbose"))) { | ||
| stop("Unknown argument passed to writeNC: ", paste(...names(), collapse = ", ")) | ||
| } | ||
|
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| # magclass objects are sparse, fill gaps with NA | ||
| coords <- getCoords(x) | ||
| x <- extend(x, xRange = c(min(coords$x), max(coords$x)), yRange = c(max(coords$y), min(coords$y)), res = res) | ||
| coords <- getCoords(x) | ||
|
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| if (zname != "time") { | ||
| message("terra will not recognize zname != 'time' as time dimension") | ||
| } | ||
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| if (is.null(getItems(x, 3))) { | ||
| getItems(x, 3) <- sub("\\.nc$", "", basename(filename)) | ||
| } | ||
|
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| # create netCDF file | ||
| dimVars <- list(ncdf4::ncdim_def("lon", "degrees_east", unique(coords$x)), | ||
| ncdf4::ncdim_def("lat", "degrees_north", unique(coords$y))) | ||
| if (!is.null(getItems(x, 2))) { | ||
| dimVars <- c(dimVars, list(ncdf4::ncdim_def(zname, "years since 0", getYears(x, as.integer = TRUE), unlim = TRUE))) | ||
| } | ||
| vars <- lapply(getItems(x, 3), function(vname) { | ||
| return(ncdf4::ncvar_def(vname, units = unit, dim = dimVars, | ||
| missval = missval, compression = compression)) | ||
| }) | ||
|
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| nc <- ncdf4::nc_create(filename, vars = vars) | ||
| withr::defer(ncdf4::nc_close(nc)) | ||
|
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| if (!is.null(getItems(x, 2)) && zname == "time") { | ||
| ncdf4::ncatt_put(nc, "time", "axis", "T") | ||
| } | ||
|
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| for (vname in getItems(x, 3)) { | ||
| ncdf4::ncvar_put(nc, vname, x[, , vname]) | ||
| } | ||
| } |
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