From 3d62c34ec3bc04d325ea1495d9f0320d0bff5d23 Mon Sep 17 00:00:00 2001 From: Patrick Van Laake Date: Thu, 6 Jun 2024 14:12:09 +0200 Subject: [PATCH 1/2] Bulk update to support CFtime as time management --- DESCRIPTION | 1 + NAMESPACE | 1 + R/aggregate.R | 42 ++-- R/cubble.R | 2 +- R/dimensions.R | 193 ++++++++++-------- R/extract.R | 40 ++-- R/geom.R | 3 +- R/intervals.R | 17 +- R/mdim.R | 67 +++---- R/ncdf.R | 354 +++++++++++----------------------- R/ncproxy.R | 41 ++-- R/plot.R | 2 + R/proxy.R | 10 +- R/sample.R | 34 ++-- R/sf.R | 6 +- R/stars.R | 9 +- R/subset.R | 32 ++- R/values.R | 5 +- inst/docker/fedora/Dockerfile | 2 +- inst/docker/rdevel/Dockerfile | 2 +- inst/docker/trusty/Dockerfile | 2 +- man/aggregate.stars.Rd | 2 +- man/print_stars.Rd | 2 +- man/read_ncdf.Rd | 86 +++++---- man/st_dimensions.Rd | 2 +- man/st_extract.Rd | 6 +- tests/dimensions.R | 10 +- tests/stars.R | 4 +- tests/stars.Rout.save | 30 +-- tests/testthat/Rplots.pdf | Bin 0 -> 85168 bytes tests/testthat/test-ncdf.R | 25 +-- tests/testthat/test-ncproxy.R | 3 +- vignettes/stars4.Rmd | 7 +- 33 files changed, 496 insertions(+), 546 deletions(-) create mode 100644 tests/testthat/Rplots.pdf diff --git a/DESCRIPTION b/DESCRIPTION index 2a95b3ab4..1063e3d37 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -37,6 +37,7 @@ Depends: abind, sf (>= 1.0-15) Imports: + CFtime (>= 1.3.0), methods, parallel, classInt (>= 0.4-1), diff --git a/NAMESPACE b/NAMESPACE index 7cb378d34..7c66f0320 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -251,3 +251,4 @@ importFrom(utils,packageVersion) importFrom(utils,setTxtProgressBar) importFrom(utils,tail) importFrom(utils,txtProgressBar) +importMethodsFrom(CFtime,range) diff --git a/R/aggregate.R b/R/aggregate.R index 6effcd407..38de9c23e 100644 --- a/R/aggregate.R +++ b/R/aggregate.R @@ -3,7 +3,7 @@ #' spatially or temporally aggregate stars object, returning a data cube with lower spatial or temporal resolution #' #' @param x object of class \code{stars} with information to be aggregated -#' @param by object of class \code{sf} or \code{sfc} for spatial aggregation, for temporal aggregation a vector with time values (\code{Date}, \code{POSIXct}, or \code{PCICt}) that is interpreted as a sequence of left-closed, right-open time intervals or a string like "months", "5 days" or the like (see \link{cut.POSIXt}), or a function that cuts time into intervals; if by is an object of class \code{stars}, it is converted to sfc by \code{st_as_sfc(by, as_points = FALSE)} thus ignoring its time component. Note: each pixel is assigned to only a single group (in the order the groups occur) so non-overlapping spatial features and temporal windows are recommended. +#' @param by object of class \code{sf} or \code{sfc} for spatial aggregation, for temporal aggregation a vector with time values (\code{Date}, \code{POSIXct}, or \code{ISO8601 character strings}) that is interpreted as a sequence of left-closed, right-open time intervals or a string like "months", "5 days" or the like (see \link{cut.POSIXt}, \link[CFtime]{cut}), or a function that cuts time into intervals; if \code{by} is an object of class \code{stars}, it is converted to \code{sfc} by \code{st_as_sfc(by, as_points = FALSE)} thus ignoring its time component. Note: each pixel is assigned to only a single group (in the order the groups occur) so non-overlapping spatial features and temporal windows are recommended. #' @param FUN aggregation function, such as \code{mean} #' @param ... arguments passed on to \code{FUN}, such as \code{na.rm=TRUE} #' @param drop logical; ignored @@ -72,7 +72,7 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, left.open = FALSE, exact = FALSE) { fn_name = substr(deparse1(substitute(FUN)), 1, 20) - classes = c("sf", "sfc", "POSIXct", "Date", "PCICt", "character", "function", "stars") + classes = c("sf", "sfc", "POSIXct", "Date", "character", "function", "stars") if (!is.function(by) && !inherits(by, classes)) stop(paste("currently, only `by' arguments of class", paste(classes, collapse= ", "), "supported")) @@ -120,6 +120,7 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, } drop_y = FALSE + values = NULL # safeguard, must check if it has been set grps = if (inherits(by, c("sf", "sfc"))) { x = if (has_raster(x)) { ndims = 2 @@ -153,11 +154,15 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, i = as.factor(i) by = levels(i) } else if (inherits(by, "character")) { - i = cut(values, by, right = left.open) - by = if (inherits(values, "Date")) - as.Date(levels(i)) - else - as.POSIXct(levels(i)) + if (methods::is(values, "CFtime")) { + i = CFtime::cut(values, by) + by = levels(i) + new_time = attr(i, "CFtime") + } else { + i = cut(values, by, right = left.open) + by = if (inherits(values, "Date")) as.Date(levels(i)) + else as.POSIXct(levels(i)) + } } else { if (!inherits(values, class(by))) warning(paste0('argument "by" is of a different class (', class(by)[1], @@ -171,21 +176,17 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, d = st_dimensions(x) dims = dim(d) - agr_grps = function(x, grps, uq, FUN, bind, ...) { - do.call(bind, lapply(uq, function(i) { + agr_grps = function(x, grps, uq, FUN, ...) { + do.call(rbind, lapply(uq, function(i) { sel <- which(grps == i) if (!isTRUE(any(sel))) - NA_real_ + rep(NA_real_, ncol(x)) else apply(x[sel, , drop = FALSE], 2, FUN, ...) } )) } - bind = if (length(FUN(1:10, ...)) > 1) - cbind - else - rbind # rearrange: x = structure(x, dimensions = NULL, class = NULL) # unclass newdims = c(prod(dims[1:ndims]), prod(dims[-(1:ndims)])) @@ -200,14 +201,19 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, NULL } else NULL - x[[i]] = agr_grps(a, grps, seq_along(by), FUN, bind, ...) + x[[i]] = agr_grps(a, grps, seq_along(by), FUN, ...) if (is.numeric(x[[i]]) && !is.null(u)) x[[i]] = units::set_units(x[[i]], u, mode = "standard") } # reconstruct dimensions table: - d[[1]] = create_dimension(values = by) - names(d)[1] = if (is.function(by) || inherits(by, c("POSIXct", "Date", "PCICt", "function"))) + if (!is.null(values) && methods::is(values, "CFtime")) { + d[[1]] = create_dimension(refsys = "CFtime", values = new_time) + } else { + d[[1]] = create_dimension(values = by) + } + names(d)[1] = if (###is.function(by) || FIXME: 'by' can also apply to sf or sfc + inherits(values, c("POSIXct", "Date", "CFtime"))) "time" else geom @@ -239,7 +245,7 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, # aggregate is done over one or more dimensions # say we have dimensions 1,...,k and we want to aggregate over i,...,j # with 1 <= i <= j <= k; - # let |n| = j-1+1 be the number of dimensions to aggregate over, n + # let |n| = j-i+1 be the number of dimensions to aggregate over, n # let |m| = k - n be the number of remaining dimensions, m # permute the cube such that the n dimensions are followed by the m # rearrange the cube to a 2D matrix with |i| x ... x |j| rows, and remaining cols diff --git a/R/cubble.R b/R/cubble.R index 7a0e9077f..dfe980d10 100644 --- a/R/cubble.R +++ b/R/cubble.R @@ -12,7 +12,7 @@ st_as_stars.cubble_df = function(.x, ..., check_times = FALSE) { nr = sapply(.x$ts, nrow) stopifnot(length(unique(nr)) == 1) ts1 = .x$ts[[1]] - dt = which(sapply(ts1, inherits, c("Date", "POSIXct", "units"))) + dt = which(sapply(ts1, inherits, c("Date", "POSIXct", "units", "factor"))) if (length(dt) > 1) { message("using only first time column for time index") dt = dt[1] diff --git a/R/dimensions.R b/R/dimensions.R index d1aa0fa8a..a5ed56f2a 100644 --- a/R/dimensions.R +++ b/R/dimensions.R @@ -95,7 +95,7 @@ st_dimensions.default = function(.x, ..., .raster, affine = c(0, 0), #' @name st_dimensions #' @param which integer or character; index or name of the dimension to be changed -#' @param values values for this dimension (e.g. \code{sfc} list-column), or length-1 \code{dimensions} object; setting special value \code{NULL} removes dimension values, for instance to remove curvilinear raster coordinates +#' @param values values for this dimension (e.g. \code{sfc} list-column), length-1 \code{dimensions} object, or a \code{CFtime} instance; setting special value \code{NULL} removes dimension values, for instance to remove curvilinear raster coordinates #' @param names character; vector with new names for all dimensions, or with the single new name for the dimension indicated by \code{which} #' @param xy length-2 character vector; (new) names for the \code{x} and \code{y} raster dimensions #' @export @@ -136,6 +136,8 @@ st_set_dimensions = function(.x, which, values = NULL, point = NULL, names = NUL } if (is.null(values)) d[[which]]["values"] = list(NULL) # avoid removing element values + else if (methods::is(values, "CFtime")) + d[[which]]["values"] = values else d[[which]] = create_dimension(values = values, point = point %||% d[[which]]$point, ...) r = attr(d, "raster") @@ -240,8 +242,10 @@ st_get_dimension_values = function(.x, which, ..., where = NA, max = FALSE, cent regular_intervals = function(x, epsilon = 1e-10) { if (length(x) <= 1) FALSE + else if (methods::is(x, "CFtime")) + CFtime::is_complete(x) else { - ud = if (is.atomic(x) && (is.numeric(x) || inherits(x, c("POSIXt", "Date", "PCICt")))) + ud = if (is.atomic(x) && (is.numeric(x) || inherits(x, c("POSIXt", "Date")))) unique(diff(x)) else { if (inherits(x, "intervals") && identical(tail(x$end, -1), head(x$start, -1))) @@ -258,11 +262,11 @@ create_dimension = function(from = 1, to, offset = NA_real_, delta = NA_real_, example = NA - if (! is.null(values)) { # figure out from values whether we have sth regular: + if (!is.null(values)) { # figure out from values whether we have sth regular: from = 1 to = length(values) if (!(is.character(values) || is.factor(values)) && is.atomic(values)) { - if (! all(is.finite(values))) + if (!all(is.finite(values))) warning("dimension value(s) non-finite") else { if (regular_intervals(values)) { @@ -287,8 +291,8 @@ create_dimension = function(from = 1, to, offset = NA_real_, delta = NA_real_, refsys = "POSIXct" else if (inherits(example, "Date")) refsys = "Date" - else if (inherits(example, "PCICt")) - refsys = paste0("PCICt_", attr(example, "cal")) + else if (methods::is(values, "CFtime")) + refsys = "CFtime" else if (inherits(example, "units")) refsys = "udunits" @@ -373,21 +377,21 @@ create_dimensions_from_gdal_meta = function(dims, pr) { create_dimension(from = 1, to = dims[i]) # time? depth+units? To be filled in later... ) } - if (! is.null(pr$dim_extra)) { # netcdf... + if (!is.null(pr$dim_extra)) { # netcdf... for (d in names(pr$dim_extra)) { - refsys = if (inherits(pr$dim_extra[[d]], "POSIXct")) - "POSIXct" - else if (inherits(pr$dim_extra[[d]], "PCICt")) - "PCICt" - else - NA_character_ de = pr$dim_extra[[d]] - diff.de = diff(de) - lst[[d]] = if (length(unique(diff.de)) <= 1) { - delta = if (length(diff.de)) diff.de[1] else NA_real_ - create_dimension(from = 1, to = length(de), offset = de[1], delta = delta, refsys = refsys) - } else - create_dimension(from = 1, to = length(de), values = de, refsys = refsys) + len = length(de) + if (methods::is(de, "CFtime")) + lst[[d]] = create_dimension(from = 1, to = len, values = de, refsys = "CFtime", point = TRUE) + else { + refsys = if (inherits(de, "POSIXct")) "POSIXct" else NA_character_ + diff.de = diff(de) + lst[[d]] = if (length(unique(diff.de)) <= 1) { + delta = if (length(diff.de)) diff.de[1] else NA_real_ + create_dimension(from = 1, to = len, offset = de[1], delta = delta, refsys = refsys) + } else + create_dimension(from = 1, to = len, values = de, refsys = refsys) + } } lst[["band"]] = NULL } @@ -485,17 +489,12 @@ parse_netcdf_meta = function(pr, name) { rhs = get_val(paste0("NETCDF_DIM_", v), meta) # nocov # FIXME: find example? pr$dim_extra[[v]] = as.numeric(rhs) # nocov } - cal = get_val(paste0(v, "#calendar"), meta) - u = get_val(paste0(v, "#units"), meta) - if (! is.na(u)) { - if (v %in% c("t", "time") && !is.na(cal) && cal %in% c("360_day", "365_day", "noleap")) - pr$dim_extra[[v]] = get_pcict(pr$dim_extra[[v]], u, cal) - else { - units(pr$dim_extra[[v]]) = try_as_units(u) - if (v %in% c("t", "time") && !inherits(try(as.POSIXct(pr$dim_extra[[v]]), silent = TRUE), - "try-error")) - pr$dim_extra[[v]] = as.POSIXct(pr$dim_extra[[v]]) - } + u = get_val(paste0(v, "#units"), meta) + if (!is.na(u)) { + cal = get_val(paste0(v, "#calendar"), meta) + time = try(CFtime::CFtime(u, cal), silent = TRUE) + if (methods::is(time, "CFtime")) + pr$dim_extra[[v]] = time + pr$dim_extra[[v]] } } pr$dim_extra = rev(pr$dim_extra) @@ -548,53 +547,53 @@ expand_dimensions.dimensions = function(x, ..., max = FALSE, center = NA) { # center = TRUE: return center values for x and y coordinates, interval start values otherwise # center = FALSE: return start values # center = NA: return centers for x/y raster, otherwise start values -# add_max = TRUE: add in addition to x and y start values an x_max and y_max end values - +# add_max = TRUE: add in addition to x and y start values an x_max and y_max end values FIXME ??? + names = names(x) + len = length(x) + if (length(center) == 1) - center = setNames(rep(center, length(x)), names(x)) + center = setNames(rep(center, len), names) if (length(max) == 1) - max = setNames(rep(max, length(x)), names(x)) + max = setNames(rep(max, len), names) if (is.list(max)) max = unlist(max) if (is.list(center)) center = unlist(center) + if (length(max) != len || length(center) != len) + stop("max and center parameters must be atomic or have the same length as the dimensions") if (any(max & center, na.rm = TRUE)) stop("only one of max and center can be TRUE, not both") - where = setNames(rep(0.0, length(x)), names(x)) # offset + where = setNames(rep(0.0, len), names) # offset for (i in seq_along(x)) { if (max[i]) where[i] = 1.0 - if (isTRUE(center[i])) + else if (isTRUE(center[i])) where[i] = 0.5 } - dimensions = x xy = attr(x, "raster")$dimensions - gt = st_geotransform(x) - lst = vector("list", length(dimensions)) - names(lst) = names(dimensions) - if (! is.null(xy) && all(!is.na(xy))) { # we have raster: where defaulting to 0.5 + if (!is.null(xy) && all(!is.na(xy))) # we have raster: where defaulting to 0.5 where[xy] = ifelse(!max[xy] & (is.na(center[xy]) | center[xy]), 0.5, where[xy]) - if (xy[1] %in% names(lst)) # x - lst[[ xy[1] ]] = get_dimension_values(dimensions[[ xy[1] ]], where[[ xy[1] ]], gt, "x") - if (xy[2] %in% names(lst)) # y - lst[[ xy[2] ]] = get_dimension_values(dimensions[[ xy[2] ]], where[[ xy[2] ]], gt, "y") - } - - if ("crs" %in% names(lst)) - lst[[ "crs" ]] = dimensions[[ "crs" ]]$values - - for (nm in setdiff(names(lst), c(xy, "crs"))) # non-xy, non-crs dimensions - lst[[ nm ]] = get_dimension_values(dimensions[[ nm ]], where[[nm]], NA, NA) - + gt = st_geotransform(x) + + lst = lapply(names, function(nm) { + if (isTRUE(xy[1] == nm)) # x + get_dimension_values(x[[ nm ]], where[[ nm ]], gt, "x") + else if (isTRUE(xy[2] == nm)) # y + get_dimension_values(x[[ nm ]], where[[ nm ]], gt, "y") + else if ("crs" == nm || methods::is(x[[ nm ]]$values, "CFtime")) + x[[ nm ]]$values + else get_dimension_values(x[[ nm ]], where[[ nm ]], NA, NA) + }) + + names(lst) = names lst } - #' @export dim.dimensions = function(x) { if (is_curvilinear(x)) @@ -605,19 +604,23 @@ dim.dimensions = function(x) { #' @name print_stars #' @param digits number of digits to print numbers -#' @param usetz logical; used to format \code{PCICt} or \code{POSIXct} values +#' @param usetz logical; used to format \code{POSIXct} values #' @param stars_crs maximum width of string for CRS objects #' @param all logical; if \code{TRUE} print also fields entirely filled with \code{NA} or \code{NULL} #' @export +#' @importMethodsFrom CFtime range as.data.frame.dimensions = function(x, ..., digits = max(3, getOption("digits")-3), usetz = TRUE, stars_crs = getOption("stars.crs") %||% 28, all = FALSE) { mformat = function(x, ..., digits) { - if (inherits(x, c("PCICt", "POSIXct"))) + if (inherits(x, "POSIXct")) format(x, ..., usetz = usetz) else format(x, digits = digits, ...) } abbrev_dim = function(y) { - if (length(y$values) > 3 || (inherits(y$values, "sfc") && length(y$values) > 2)) { + if (methods::is(y$values, "CFtime")) { + rng = range(y$values, ...) + y$values = paste0(rng[1], ",...,", rng[2]) + } else if (length(y$values) > 3 || (inherits(y$values, "sfc") && length(y$values) > 2)) { y$values = if (is.array(y$values)) paste0("[", paste(dim(y$values), collapse = "x"), "] ", mformat(min(y$values), digits = digits), ",...,", @@ -731,28 +734,38 @@ seq.dimension = function(from, ..., center = FALSE) { # does what expand_dimensi #' @export `[.dimension` = function(x, i, ...) { - if (!missing(i)) { - if (!is.null(x$values) && !is.matrix(x$values)) - x$values = x$values[i] - if (!is.na(x$from)) { - rang = x$from:x$to # valid range - if (!all(is.na(i)) && max(i, na.rm = TRUE) > -1 && min(i, na.rm = TRUE) < 0) - stop("cannot mix positive and negative indexes") - if (is.logical(i)) - i = which(i) - else if (all(i < 0)) - i = setdiff(rang, abs(i)) # subtract - if (!any(is.na(i)) && all(diff(i) == 1)) { - if (max(i) > length(rang)) - stop("invalid range selected") - sel = rang[i] - x$from = min(sel) - x$to = max(sel) - } else { # invalidate offset & delta - x$delta = x$offset = NA - x$from = 1 - x$to = length(i) - } + if (missing(i)) return(x) + + if (!is.na(x$refsys) && x$refsys == "CFtime") { + oldcf = x$values + ind = CFtime::indexOf(i, oldcf) + newcf = attr(ind, "CFtime") + x$to = length(newcf) + x$values = newcf + return(x) + } + + if (!is.null(x$values) && !is.matrix(x$values)) + x$values = x$values[i] + if (!is.na(x$from)) { + rang = x$from:x$to # valid range + if (!all(is.na(i)) && max(i, na.rm = TRUE) > -1 && min(i, na.rm = TRUE) < 0) + stop("cannot mix positive and negative indexes") + if (is.logical(i)) + i = which(i) + else if (all(i < 0)) + i = setdiff(rang, abs(i)) # subtract + if (!any(is.na(i)) && all(diff(i) == 1)) { + if (max(i) > length(rang)) + stop("invalid range selected") + sel = rang[i] + x$from = min(sel) + x$to = max(sel) + } else { # invalidate offset & delta + x$delta = x$offset = NA + x$from = 1 + x$to = length(i) + # FIXME: shouldn't x$values be set in this case? } } x @@ -785,9 +798,25 @@ as.POSIXct.stars = function(x, ...) { d = st_dimensions(x) e = expand_dimensions(d) for (i in seq_along(d)) { - p = try(as.POSIXct(e[[i]]), silent = TRUE) - if (!inherits(p, "try-error")) - d[[i]] = create_dimension(values = p) + if (!is.na(d[[i]]$refsys) && d[[i]]$refsys == "CFtime") { + cf = d[[i]]$values + cal = CFtime::calendar(cf) + if (cal %in% c("standard", "gregorian", "proleptic_gregorian")) + p = CFtime::as_timestamp(d[[i]]$values, asPOSIX = TRUE) + else { + warning("creating a POSIXct dimension from a non-compliant calendar: the dimension may have missing or NA values") + if (cal %in% c("360_day", "365_day", "noleap") && requireNamespace("PCICt")) + # Use PCICt package if installed + p = PCICt::as.POSIXct.PCICt(get_pcict(CFtime::offsets(cf), CFtime::definition(cf), cal)) + else # julian, 366_day, all_leap calendars or no PCICt package + p = as.POSIXct(CFtime::as_timestamp(d[[i]]$values)) + } + d[[i]] = create_dimension(refsys = "POSIXct", values = p) + } else { + p = try(as.POSIXct(e[[i]]), silent = TRUE) + if (!inherits(p, "try-error")) + d[[i]] = create_dimension(refsys = "POSIXct", values = p) + } } structure(x, dimensions = d) } diff --git a/R/extract.R b/R/extract.R index 5fbb33695..bb8c70bce 100644 --- a/R/extract.R +++ b/R/extract.R @@ -9,15 +9,15 @@ st_extract = function(x, ...) UseMethod("st_extract") #' @param x object of class \code{stars} or \code{stars_proxy} #' @param at object of class \code{sf} or \code{sfc} with geometries, or two-column matrix with coordinate points in rows, indicating where to extract values of \code{x} #' @param bilinear logical; use bilinear interpolation rather than nearest neighbour? -#' @param time_column character or integer; name or index of a column with time or date values that will be matched to values of the first temporal dimension (matching classes \code{POSIXct}, \code{POSIXt}, \code{Date}, or \code{PCICt}), in \code{x}, after which this dimension is reduced. This is useful to extract data cube values along a trajectory; see https://github.com/r-spatial/stars/issues/352 . -#' @param interpolate_time logical; should time be interpolated? if FALSE, time instances are matched using the coinciding or the last preceding time in the data cube. +#' @param time_column character or integer; name or index of a column in \code{at} (which must be of class \code{sf} or \code{sfc}) with time or date values that will be matched to values of the first temporal dimension (matching classes \code{POSIXct}, \code{Date}, or \code{CFtime}) in \code{x}, after which this dimension is reduced. This is useful to extract data cube values along a trajectory; see https://github.com/r-spatial/stars/issues/352 . +#' @param interpolate_time logical; should time be interpolated? If \code{FALSE}, time instances are matched using the coinciding or the last preceding time in the data cube, unless the dimension uses \code{CFtime} with bounds set, in which case the corresponding time interval in which the time or date value falls is returned. #' @param FUN function used to aggregate pixel values when geometries of \code{at} intersect with more than one pixel #' @param ... passed on to \link{aggregate.stars} when geometries are not exclusively POINT geometries #' @returns if \code{at} is of class \code{matrix}, a matrix with extracted values is returned; #' otherwise: if \code{x} has more dimensions than only x and y (raster), an #' object of class \code{stars} with POINT geometries replacing x and y raster #' dimensions, if this is not the case, an object of \code{sf} with extracted values. -#' @details points outside the raster are returned as \code{NA} values. For +#' @details Points outside the raster are returned as \code{NA} values. For #' large sets of points for which extraction is needed, passing a matrix as #' to \code{at} may be much faster than passing an \code{sf} or \code{sfc} object. #' @export @@ -35,6 +35,7 @@ st_extract.stars = function(x, at, ..., bilinear = FALSE, time_column = stopifnot(inherits(at, c("sf", "sfc", "matrix"))) if (inherits(at, "matrix")) + # FIXME: matrix form of at supports only x,y rasters, no z,t or higher dimensions pts = at else { stopifnot(st_crs(at) == st_crs(x)) @@ -48,8 +49,16 @@ st_extract.stars = function(x, at, ..., bilinear = FALSE, time_column = } sf_column = attr(at, "sf_column") %||% "geometry" - tm_pts = if (!is.null(time_column)) - at[[time_column]] # else NULL + if (!is.null(time_column)) { + tm_pts = at[[time_column]] + if (is.null(tm_pts)) + stop("cannot match times: `time_column` not found in `at`") + ## If there is more than one temporal dimension, the first one is taken + tm = which_time(x)[1] + if (is.na(tm)) + stop("cannot match times: `x` does not have a temporal dimension") + } + at = st_geometry(at) pts = st_coordinates(at) } @@ -89,16 +98,9 @@ st_extract.stars = function(x, at, ..., bilinear = FALSE, time_column = } # match times: if (!is.null(time_column)) { - refsys_time = c("POSIXct", "POSIXt", "Date", "PCICt") - ## If there are more than two temporal dimensions, the first one is taken - tm = names(which(sapply( - st_dimensions(x), - function(i) any(i$refsys %in% refsys_time))))[1] - if (is.na(tm)) - stop("cannot match times: x does not have a temporal dimension") - tm_cube = st_dimensions(x)[[tm]]$values %||% st_get_dimension_values(x, tm) + tm_cube = st_dimensions(x)[tm]$values %||% st_get_dimension_values(x, tm) tm_ix = match_time(tm_pts, tm_cube, - intervals = !st_dimensions(x)[[tm]]$point, + intervals = !st_dimensions(x)[tm]$point, interpolate_time) if (!interpolate_time) m = lapply(m, function(p) p[cbind(seq_along(at), tm_ix)]) @@ -140,7 +142,7 @@ st_extract.stars = function(x, at, ..., bilinear = FALSE, time_column = if (!is.null(time_column)) { # add time columns of both cube and at: if (inherits(tm_cube, "intervals")) tm_cube = as.list(tm_cube) - df[[tm]] = tm_cube[tm_ix] + df[tm] = tm_cube[tm_ix] df[[time_column]] = tm_pts } sf = st_as_sf(df) @@ -155,6 +157,13 @@ st_extract.stars = function(x, at, ..., bilinear = FALSE, time_column = # if interpolate = FALSE, returns an integer in 1...length(b) or NA if outside # if interpolate = TRUE, returns a continuous index in 1...length(b) or NA if outside match_time = function(a, b, intervals = FALSE, interpolate = FALSE) { + if (methods::is(b, "CFtime")) { + if (interpolate && isFALSE(intervals) && is.null(CFtime::bounds(b))) + return(CFtime::indexOf(a, b, method = "linear")) + else + return(CFtime::indexOf(a, b)) + } + if (inherits(a, "POSIXct") && inherits(b, "Date")) a = as.Date(a) if (inherits(b, "POSIXct") && inherits(a, "Date")) @@ -167,6 +176,7 @@ match_time = function(a, b, intervals = FALSE, interpolate = FALSE) { m } else match(a, b) + if (interpolate && !isTRUE(intervals) && !inherits(b, "intervals")) { b = as.numeric(b) a = as.numeric(a) diff --git a/R/geom.R b/R/geom.R index c7589a148..2e81ba5ef 100644 --- a/R/geom.R +++ b/R/geom.R @@ -45,7 +45,8 @@ st_intersects.stars = function(x, y, sparse = TRUE, ..., as_points = NA, transpo else ret } else { # curvilinear or !as_points: - ret = st_intersects(st_as_sf(x, as_points = as_points, na.rm = FALSE), y, + sf <- st_as_sf(x, as_points = as_points, na.rm = FALSE) + ret = st_intersects(sf, y, sparse = sparse, ...) if (! sparse) ret = as.matrix(ret) diff --git a/R/intervals.R b/R/intervals.R index 42ed33e92..977a5d8d2 100644 --- a/R/intervals.R +++ b/R/intervals.R @@ -43,19 +43,18 @@ c.intervals = function(...) { } #' @export -format.intervals = function(x, ...) { - mformat = function(x, ..., digits = getOption("digits")) { - if (inherits(x, "PCICt")) - format(x, ...) - else - format(x, digits = digits, ...) - } +#' @importMethodsFrom CFtime range +format.intervals = function(x, digits = getOption("digits"), ...) { if (inherits(x$start, "units") && inherits(x$end, "units")) { stopifnot(units(x$start) == units(x$end)) paste0("[", format(as.numeric(x$start), ...), ",", format(as.numeric(x$end), ...), ") ", "[", as.character(units(x$start)), "]") - } else - paste0("[", mformat(x$start, ...), ",", mformat(x$end, ...), ")") + } else if (methods::is(x, "CFtime")) { + rng = range(x) + paste0("[", rng[1], ",", rng[2], ")") + } else { + paste0("[", format(x$start, digits = digits, ...), ",", format(x$end, digits = digits, ...), ")") + } } find_interval = function(x, intervals) { diff --git a/R/mdim.R b/R/mdim.R index b027c8915..9e655c465 100644 --- a/R/mdim.R +++ b/R/mdim.R @@ -148,29 +148,14 @@ read_mdim = function(filename, variable = character(0), ..., options = character create_units = function(x) { u = attr(x, "units") x = structure(x, units = NULL) # remove attribute - if (is.null(u) || u %in% c("", "none")) - x - else { - if (!is.null(a <- attr(x, "attributes")) && !is.na(cal <- a["calendar"]) && - cal %in% c("360_day", "365_day", "noleap")) - get_pcict(x, u, cal) - else { - days_since = grepl("days since", u) - u = try_as_units(u) - if (!inherits(u, "units")) # FAIL: - x - else { - units(x) = u - if (days_since && inherits(d <- try(as.Date(x), silent = TRUE), "Date")) - d - else if (inherits(p <- try(as.POSIXct(x), silent = TRUE), "POSIXct")) - p - else - x - } - } - } + if (is.null(u) || u %in% c("", "none")) return(x) + + cal <- if (!is.null(a <- attr(x, "attributes"))) a["calendar"] else NULL + time <- try(CFtime::CFtime(u, cal), silent = TRUE) # cheaply try if we can make CFtime + if (methods::is(time, "CFtime")) time + as.numeric(x) # if we have CFtime, add the offsets + else x # if not, fail graciously } + l = rev(lapply(ret$dimensions, function(x) { if (inherits(x, "sfc")) x else create_units(x$values[[1]]) })) @@ -249,25 +234,27 @@ add_attr = function(x, at) { # append at to attribute "attrs" } add_units_attr = function(l) { - f = function(x) { - if (inherits(x, "units")) - add_attr(x, c(units = as.character(units(x)))) - else if (inherits(x, c("POSIXct", "PCICt"))) { - cal = if (!is.null(cal <- attr(x, "cal"))) - c(calendar = paste0(cal, "_day")) # else NULL, intended - x = as.numeric(x) - if (all(x %% 86400 == 0)) - add_attr(x/86400, c(units = "days since 1970-01-01", cal)) - else if (all(x %% 3600 == 0)) - add_attr(x / 3600, c(units = "hours since 1970-01-01 00:00:00", cal)) - else - add_attr(x, c(units = "seconds since 1970-01-01 00:00:00", cal)) - } else if (inherits(x, "Date")) - add_attr(as.numeric(x), c(units = "days since 1970-01-01")) + f = function(x) { + if (inherits(x, "units")) + add_attr(x, c(units = as.character(units(x)))) + else if (inherits(x, "POSIXct")) { + cal = if (!is.null(cal <- attr(x, "cal"))) + c(calendar = paste0(cal, "_day")) # else NULL, intended + x = as.numeric(x) + if (all(x %% 86400 == 0)) + add_attr(x/86400, c(units = "days since 1970-01-01", cal)) + else if (all(x %% 3600 == 0)) + add_attr(x / 3600, c(units = "hours since 1970-01-01 00:00:00", cal)) else - x - } - lapply(l, f) + add_attr(x, c(units = "seconds since 1970-01-01 00:00:00", cal)) + } else if (methods::is(x, "CFtime")) + add_attr(CFtime::offsets(x), c(units = CFtime::definition(x), CFtime::calendar(x))) + else if (inherits(x, "Date")) + add_attr(as.numeric(x), c(units = "days since 1970-01-01")) + else + x + } + lapply(l, f) } cdl_add_geometry = function(e, i, sfc) { diff --git a/R/ncdf.R b/R/ncdf.R index ed4829bc0..a1c2f6bda 100644 --- a/R/ncdf.R +++ b/R/ncdf.R @@ -3,18 +3,23 @@ #' #' Read data from a file (or source) using the NetCDF library directly. #' -#' The following logic is applied to coordinates. If any coordinate axes have -#' regularly spaced coordinate variables they are reduced to the -#' offset/delta form with 'affine = c(0, 0)', otherwise the values of the coordinates -#' are stored and used to define a rectilinear grid. +#' The following logic is applied to spatial coordinates. If any coordinate axes +#' have regularly spaced coordinate variables they are reduced to the +#' offset/delta form with 'affine = c(0, 0)', otherwise the values of the +#' coordinates are stored and used to define a rectilinear grid. #' -#' If the data has two or more dimensions and the first two are regular -#' they are nominated as the 'raster' for plotting. +#' If the data has two or more dimensions and the first two are regular they are +#' nominated as the 'raster' for plotting. #' #' If the \code{curvilinear} argument is used it specifies the 2D arrays -#' containing coordinate values for the first two dimensions of the data read. It is currently -#' assumed that the coordinates are 2D and that they relate to the first two dimensions in -#' that order. +#' containing coordinate values for the first two dimensions of the data read. +#' It is currently assumed that the coordinates are 2D and that they relate to +#' the first two dimensions in that order. +#' +#' Any time dimension in the source is captured in a 'CFtime' object, unless the +#' \code{make_time} argument is false. In that case, the numeric offsets +#' representing time are returned instead. +#' #' @examples #' f <- system.file("nc/reduced.nc", package = "stars") #' if (require(ncmeta, quietly = TRUE)) { @@ -27,27 +32,37 @@ #' @param ... ignored #' @param var variable name or names (they must be on matching grids) #' @param ncsub matrix of start, count columns (see Details) -#' @param curvilinear length two character named vector with names of variables holding -#' longitude and latitude values for all raster cells. `stars` attempts to figure out appropriate -#' curvilinear coordinates if they are not supplied. -#' @param eps numeric; dimension value increases are considered identical when they differ less than \code{eps} -#' @param ignore_bounds logical; should bounds values for dimensions, if present, be ignored? -#' @param make_time if \code{TRUE} (the default), an attempt is made to provide a date-time class from the "time" variable -#' @param make_units if \code{TRUE} (the default), an attempt is made to set the units property of each variable -#' @param proxy logical; if \code{TRUE}, an object of class \code{stars_proxy} is read which contains array -#' metadata only; if \code{FALSE} the full array data is read in memory. If not set, defaults to \code{TRUE} -#' when the number of cells to be read is larger than \code{options(stars.n_proxy)}, or to 1e8 if that option was not set. -#' @param downsample integer; number of cells to omit between samples along each dimension. -#' e.g. \code{c(1,1,2)} would return every other cell in x and y and every third cell -#' in the third dimension (z or t). If 0, no downsampling is applied. Note that this transformation -#' is applied AFTER NetCDF data are read using st_downsample. As such, if proxy=TRUE, this -#' option is ignored. -#' @details -#' If \code{var} is not set the first set of variables on a shared grid is used. +#' @param curvilinear length two character named vector with names of variables +#' holding longitude and latitude values for all raster cells. `stars` +#' attempts to figure out appropriate curvilinear coordinates if they are not +#' supplied. +#' @param eps numeric; dimension value increases are considered identical when +#' they differ less than \code{eps}. +#' @param ignore_bounds logical; should bounds values for dimensions, if +#' present, be ignored? +#' @param make_time if \code{TRUE} (the default), an attempt is made to provide +#' a CFtime class for any "time" dimension. +#' @param make_units if \code{TRUE} (the default), an attempt is made to set the +#' units property of each variable. +#' @param proxy logical; if \code{TRUE}, an object of class \code{stars_proxy} +#' is read which contains array metadata only; if \code{FALSE} the full array +#' data is read in memory. If not set, defaults to \code{TRUE} when the number +#' of cells to be read is larger than \code{options(stars.n_proxy)}, or to 1e8 +#' if that option was not set. +#' @param downsample integer; number of cells to omit between samples along each +#' dimension. e.g. \code{c(1,1,2)} would return every other cell in x and y +#' and every third cell in the third dimension (z or t). If 0, no downsampling +#' is applied. Note that this transformation is applied AFTER NetCDF data are +#' read using \code{st_downsample()}. As such, if \code{proxy = TRUE}, this +#' option is ignored. +#' @details If \code{var} is not set the first set of variables on a shared grid +#' is used. #' -#' \code{start} and \code{count} columns of ncsub must correspond to the variable dimension (nrows) -#' and be valid index using \code{\link[RNetCDF]{var.get.nc}} convention (start is 1-based). If the count value -#' is \code{NA} then all steps are included. Axis order must match that of the variable/s being read. +#' \code{start} and \code{count} columns of ncsub must correspond to the +#' variable dimension (nrows) and be valid index using +#' \code{\link[RNetCDF]{var.get.nc}} convention (start is 1-based). If the count +#' value is \code{NA} then all steps are included. Axis order must match that of +#' the variable/s being read. #' @export #' @examples #' if (require(ncmeta, quietly = TRUE)) { @@ -85,24 +100,31 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( proxy_dimensions <- st_dimensions(.x) nc_prj <- sf::st_crs(.x) + # proxy already has CFtime in dimension[["time"]]$values + make_time <- FALSE + if(!is.null(ncsub)) { warning("ncsub ignored when .x is class nc_proxy") ncsub <- NULL } - } else { x <- .x proxy_dimensions <- NULL } + # Open the file + nc <- RNetCDF::open.nc(x) + on.exit(RNetCDF::close.nc(nc), add = TRUE) + # Get all the nc metadata - meta <- .fix_meta(ncmeta::nc_meta(x)) + meta <- .fix_meta(ncmeta::nc_meta(nc)) + # NetCDF-DSG if(.is_netcdf_cf_dsg(meta)) { if (!requireNamespace("ncdfgeom", quietly = TRUE)) stop("package ncdfgeom required, please install it first") # nocov - if(!is.null(proxy) && proxy) warning("proxy behavior not supported for timeseries netcdf") + if(!is.null(proxy) && proxy) warning("proxy behavior not supported for NetCDF-DSG file") geom <- .get_geom_name(meta) @@ -114,10 +136,10 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( rep_var <- var[1L] # Get coordinate variable info - all_coord_var <- ncmeta::nc_coord_var(x) + all_coord_var <- ncmeta::nc_coord_var(nc) - if(ncol(all_coord_var) == 0) all_coord_var <- data.frame(variable = NA, X = NA, Y = NA, - Z = NA, T = NA, bounds = NA) + if(ncol(all_coord_var) == 0) + all_coord_var <- data.frame(variable = NA, X = NA, Y = NA, Z = NA, T = NA, bounds = NA) coord_var <- .clean_coord_var(all_coord_var, rep_var, meta, curvilinear) @@ -132,9 +154,6 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( # Validate that ncsub matches dims dims <- .add_ncsub(dims, ncsub) - nc <- RNetCDF::open.nc(x) - on.exit(RNetCDF::close.nc(nc), add = TRUE) - # Get coordinates from netcdf or create them coords <- .get_coords(nc, dims) coords <- .clean_coords(coords, coord_var, meta$attribute, eps) @@ -146,48 +165,24 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( dimid_matcher <- .get_dimid_matcher(nc, coord_var, var) if(!is.null(proxy_dimensions)) { - tdim <- if("T" %in% dims$axis) { - - tmeta <- .get_time_meta(coord_var, rep_var, meta) - - tvals <- coords[[which(dims$axis == "T")]] - - tdim <- create_dimension(from = 1, to = length(tvals)) - - tdim$values <- tvals - - make_cal_time2(tdim, - time_unit = tmeta$tunit, - cal = tmeta$calendar) - - } else NULL - - dims <- .update_dims(dims, proxy_dimensions, coords, tdim) - + dims <- .update_dims(dims, proxy_dimensions, coords) coords <- .get_coords(nc, dims) coords <- .clean_coords(coords, coord_var, meta$attributes, eps) } - pull <- .should_pull(proxy, - array_size = prod(dims[, "count", drop = TRUE]), - num_vars = length(var)) - + pull <- .should_pull(proxy, prod(dims[, "count", drop = TRUE]), length(var)) out_data <- if(pull) { # Get all the data from the nc file - .set_nc_units(.get_data(nc, var, dims, dimid_matcher, pull = pull), - meta$attribute, make_units) + data <- .get_data(nc, var, dims, dimid_matcher) + .set_nc_units(data, meta$attribute, make_units) } else { # Just return the source file for each variable. setNames(as.list(rep(x, length(var))), var) } # Create stars dimensions object - if(is.null(nc_dim <- dim(out_data[[1]]))) nc_dim <- dims$length - - dimensions <- create_dimensions(setNames(nc_dim, dims$name), - raster) - + dimensions <- create_dimensions(setNames(nc_dim, dims$name), raster) dimensions <- .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords = coords, @@ -198,16 +193,13 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( eps = eps, ignore_bounds = ignore_bounds, atts = meta$attribute) - dimensions <- .get_nc_time(dimensions, make_time, - coord_var, rep_var, meta) + if (make_time) + dimensions <- .get_cf_time(dimensions, rep_var, meta) if (is.character(out_data[[1]])) { - # this is a proxy out_data <- st_stars_proxy(out_data, dimensions, NA_value = NA_real_, resolutions = NULL) - class(out_data) <- c("nc_proxy", "stars_proxy", "stars") - } else { # Make initial response data out_data <- st_stars(out_data, dimensions) @@ -233,12 +225,9 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( out_data <- add_curvilinear(out_data, curvilinear = curvi_coords, nc_prj) } - if(!all(downsample == 0)) { - out_data <- st_downsample(out_data, downsample) - } - + if(!all(downsample == 0)) out_data <- st_downsample(out_data, downsample) + out_data - } .fix_meta <- function(meta) { @@ -279,38 +268,35 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( n_proxy = options("stars.n_proxy")[[1]] %||% 1.e8) { if(is.null(proxy)) { if(array_size > n_proxy) { + message("Large NetCDF source found, returning proxy object.") pull <- FALSE - message("Large netcdf source found, returning proxy object.") } else { - pull <- TRUE message(paste("Will return stars object with", array_size, "cells.")) + pull <- TRUE } - } else { - pull <- !proxy - } - + } else pull <- !proxy + if(pull & array_size > n_proxy) - warning("Large netcdf source will be requested. Consider using stars proxy.") - + warning("Large netcdf source will be requested. Consider using stars proxy.") + pull } .get_vars <- function(var, meta) { - if (is.null(var)) { ix <- 1 if (meta$grid$grid[ix] == "S") { ix <- which(!meta$grid$grid == "S")[1L] # nocov - if (length(ix) < 1) stop("only scalar variables found, not yet supported") # nocov + if (length(ix) < 1) stop("Only scalar variables found, not yet supported") # nocov } - grd = meta$grid$grid[which.max(nchar(meta$grid$grid))] - var = meta$grid$variables[[match(grd, meta$grid$grid)]]$variable + grd <- meta$grid$grid[which.max(nchar(meta$grid$grid))] + var <- meta$grid$variables[[match(grd, meta$grid$grid)]]$variable message(sprintf("no 'var' specified, using %s", paste(var, collapse = ", "))) other_vars <- setdiff(meta$variable$name, var) if (length(other_vars) > 0) - message(sprintf("other available variables:\n %s", paste(other_vars, collapse = ", "))) + message(sprintf("Other available variables:\n %s", paste(other_vars, collapse = ", "))) } return(var) } @@ -408,14 +394,14 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( c_v$curvilinear <- TRUE } else{ c_v <- c_v[1, ] - warning(paste("Found two coordinate variable pairs. Chosing:", + warning(paste("Found two coordinate variable pairs. Choosing:", paste(as.character(c_v)[2:5], collapse = " "), "for", as.character(c_v)[1])) #nocov } } else { c_v$curvilinear <- FALSE } - return(c_v) + c_v } .check_curvilinear <- function(coord_var, var, variables, curvilinear) { @@ -562,44 +548,21 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( var) } -.get_nc_var <- function(nc, .v, start, count) { - RNetCDF::var.get.nc(nc, - variable = .v, - start = start, - count = count, - collapse = FALSE, ## keep 1-dims - unpack = TRUE, ## offset and scale applied internally - rawchar = TRUE) ## needed for NC_CHAR, as per -} - -.get_data <- function(nc, var, dims, dimid_matcher, pull = pull) { - out_data <- lapply(var, pull = pull, FUN = function(.v, pull) { - - dm <- match(RNetCDF::var.inq.nc(nc, .v)$dimids, - dims[, "id", drop = TRUE]) +.get_data <- function(nc, var, dims, dimid_matcher) { + out_data <- lapply(var, function(.v) { + dm <- match(RNetCDF::var.inq.nc(nc, .v)$dimids, dims[, "id", drop = TRUE]) if(is.null(dm)) dm <- c(1:nrow(dims)) - request <- list(start = dims[, "start", drop = TRUE][dm], - count = dims[, "count", drop = TRUE][dm]) - - request$size <- prod(request$count) - - request$dimid_match <- dm - - request$axis <- dims$axis[dm] - - if(pull) { - - ret <- .get_nc_var(nc, .v, request$start, request$count) - - if(length(dm) > 1 && !all(diff(dm[1:2]) == 1)) { - ret <- aperm(ret, dm) - } - - } + ret <- RNetCDF::var.get.nc(nc, + variable = .v, + start = dims[, "start", drop = TRUE][dm], + count = dims[, "count", drop = TRUE][dm], + collapse = FALSE, ## keep 1-dims + unpack = TRUE, ## offset and scale applied internally + rawchar = TRUE) ## needed for NC_CHAR, as per - return(ret) - + if(length(dm) > 1 && !all(diff(dm[1:2]) == 1)) ret <- aperm(ret, dm) + ret }) ## "../rasterwise/extdata/R13352.nc" @@ -729,10 +692,11 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( from_to <- dimensions[[i]]$from:dimensions[[i]]$to - try_bounds <- names(coords)[i] %in% var_names && - !ignore_bounds && - length(bounds <- coord_var[coord_var$variable == names(coords)[i], ]$bounds) > 0 && - bounds %in% var_names + if (!ignore_bounds) { + bounds <- coord_var[coord_var$variable == names(coords)[i], ]$bounds + try_bounds <- length(bounds) > 0 && bounds %in% var_names && + names(coords)[i] %in% var_names + } else try_bounds <- FALSE if (try_bounds) { @@ -792,56 +756,24 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( return(dimensions) } -.get_time_meta <- function(coord_var, var, meta) { - - TIME_name = as.character(na.omit(unlist( - coord_var[coord_var$variable == var, ][c("T")]))) - - if(!length(TIME_name)) { - - list(tname = NULL, calendar = NULL, tunit = NULL) - - } else { - - atts = meta$attribute[meta$attribute$variable == TIME_name, ] - - ## might not exist, so default to NULL - calendar = unlist(atts$value[atts$name == "calendar"])[1L] - tunit = unlist(atts$value[atts$name == "units"])[1L] - - list(tname = TIME_name, calendar = calendar, tunit = tunit) +#' Get the CFtime instances for the variable +#' +#' @param dimensions All dimensions of the data source. +#' @param var The variable to search for. This is a single var. +#' @param meta The metadata of the data source. +#' @noRd +.get_cf_time <- function(dimensions, var, meta) { + var_dims <- meta$axis$dimension[which(meta$axis$variable == var)] + time_dims <- meta$extended$dimension[which(!is.na(meta$extended$time))] + time_idx <- which(meta$extended$dimension == time_dims[which(time_dims %in% var_dims)]) + for (t in seq_along(time_idx)) { + idx <- time_idx[t] + time <- meta$extended$time[[idx]] + dimensions[[ meta$extended$name[[idx]] ]] <- + create_dimension(from = 1, to = length(time), values = time, + refsys = "CFtime", point = TRUE) } -} - -.get_nc_time <- function(dimensions, make_time, coord_var, var, meta) { - # sort out time -> POSIXct: - if (make_time) { - if (all("T" %in% names(coord_var))) { - - tmeta <- .get_time_meta(coord_var, var, meta) - - if (!is.na(tmeta$tname) && length(tmeta$tname) == 1L && - meta$variable$ndims[match(tmeta$tname, meta$variable$name)] == 1) { - - if (tmeta$tname %in% names(dimensions)) { - tdim <- NULL - if (is.null(tmeta$tunit) || inherits(tmeta$tunit, "try-error")) { - warning("ignoring units of time dimension, not able to interpret") - } else { - tdim = make_cal_time2(dimensions, - time_name = tmeta$tname, - time_unit = tmeta$tunit, - cal = tmeta$calendar) - - } - - if (!is.null(tdim)) dimensions[[tmeta$tname]] <- tdim - - } - } - } - } - return(dimensions) + dimensions } .get_curvilinear_coords <- function(curvilinear, dimensions, nc, dims) { @@ -872,68 +804,6 @@ read_ncdf = function(.x, ..., var = NULL, ncsub = NULL, curvilinear = character( return(curvi_coords) } -make_cal_time2 <- function(x, time_name = NULL, time_unit = NULL, cal = NULL) { - if(inherits(x, "dimensions")) { - tm = st_get_dimension_values(x, time_name) - dimension <- x[[time_name]] - } else { - tm <- x$values - dimension <- x - } - - if(! is.null(cal) && cal %in% c("360_day", "365_day", "noleap")) { - if (!requireNamespace("PCICt", quietly = TRUE)) { - stop("package PCICt required, please install it first") # nocov - } - t01 = set_units(0:1, time_unit, mode = "standard") - delta = if (grepl("months", time_unit)) { - if (cal == "360_day") - set_units(30 * 24 * 3600, "s", mode = "standard") - else - set_units((365/12) * 24 * 3600, "s", mode = "standard") - } else - set_units(as_units(diff(as.POSIXct(t01))), "s", mode = "standard") - - - origin = as.character(as.POSIXct(t01[1])) - v.pcict = PCICt::as.PCICt(tm * as.numeric(delta), cal, origin) - if (!is.null(dimension$values)) { - v = dimension$values - if (inherits(v, "intervals")) { - start = PCICt::as.PCICt(v$start * as.numeric(delta), cal, origin) - end = PCICt::as.PCICt(v$end * as.numeric(delta), cal, origin) - dimension$values = make_intervals(start, end) - } else - dimension$values = v.pcict - } else { - dimension$offset = v.pcict[1] - dimension$delta = diff(v.pcict[1:2]) - } - - dimension$refsys = "PCICt" - } else { # Gregorian/Julian, POSIXct: - if (!is.null(dimension$values)) { - v = dimension$values - if (inherits(v, "intervals")) { - start = as.POSIXct(units::set_units(v$start, time_unit, mode = "standard")) # or: RNetCDF::utcal.nc(u, tm, "c") - end = as.POSIXct(units::set_units(v$end, time_unit, mode = "standard")) # or: RNetCDF::utcal.nc(u, tm, "c") - dimension$values = make_intervals(start, end) - } else - dimension$values = as.POSIXct(units::set_units(tm, time_unit, mode = "standard")) # or: RNetCDF::utcal.nc(u, tm, "c") - } else { - t0 = dimension$offset - t1 = dimension$offset + dimension$delta - t.posix = as.POSIXct(units::set_units(c(t0, t1), time_unit, mode = "standard")) # or: utcal.nc(u, c(t0,t1), "c") - dimension$offset = t.posix[1] - dimension$delta = diff(t.posix) - } - dimension$refsys = "POSIXct" - } - dimension - - -} - .is_netcdf_cf_dsg <- function(meta) { featuretype <- .get_attributes(meta$attribute, "featureType", "NC_GLOBAL") diff --git a/R/ncproxy.R b/R/ncproxy.R index 8b1dd7983..536737de5 100644 --- a/R/ncproxy.R +++ b/R/ncproxy.R @@ -1,28 +1,30 @@ -.update_dims <- function(dims, proxy_dimensions, coords, tdim) { +.update_dims <- function(dims, proxy_dimensions, coords) { + between <- function(x, ymin, ymax, z = x) { + z[x >= ymin & x <= ymax, drop = FALSE] + } + uc <- coords for(coord in names(coords)) { - - pv <- st_get_dimension_values(proxy_dimensions, coord) - - between <- function(x, ymin, ymax, z = x) { - z[x >= ymin & x <= ymax, drop = FALSE] - } - - if(inherits(pv, "POSIXt")) { - # Need to deal with the case where tdim isn't values but is from to. - uc[[coord]] <- between(tdim$values, min(pv), max(pv), uc[[coord]]) + ndx <- which(dims$name == coord) + + # CFtime instance already has proxy dimensions + if (!is.na(proxy_dimensions[[coord]]$refsys) && + proxy_dimensions[[coord]]$refsys == "CFtime") { + dims$start[ndx] <- proxy_dimensions[[coord]]$from + dims$count[ndx] <- proxy_dimensions[[coord]]$to - + proxy_dimensions[[coord]]$from + 1 } else { - if(attr(proxy_dimensions, "raster")$curvilinear) { + pv <- st_get_dimension_values(proxy_dimensions, coord) + + if(attr(proxy_dimensions, "raster")$curvilinear) uc[[coord]] <- seq(proxy_dimensions[[coord]]$from, proxy_dimensions[[coord]]$to) - } else { + else uc[[coord]] <- between(uc[[coord]], min(pv), max(pv)) - } + + dims$start[ndx] <- which(coords[[coord]] == uc[[coord]][1])[1] + dims$count[ndx] <- dims$length[ndx] <- length(uc[[coord]]) } - - dims$start[dims$name == coord] <- which(coords[[coord]] == uc[[coord]][1])[1] - dims$count[dims$name == coord] <- dims$length[dims$name == coord] <- length(uc[[coord]]) - } dims } @@ -64,8 +66,7 @@ plot.nc_proxy = function(x, y, ..., downsample = get_downsample(dim(x)), max_tim x <- x[1] } - tdim <- which(sapply(st_dimensions(x), function(x) any(grepl("^POSIX|^PCIC", x$refsys)))) - + tdim <- which(sapply(st_dimensions(x), function(x) x$refsys == "CFtime")) if(length(tdim)) { if(length(st_get_dimension_values(x, tdim)) > max_times) { stop("Time dimension of nc_proxy is longer than max_times in plot.nc_proxy.") diff --git a/R/plot.R b/R/plot.R index 6803786fc..7ae888931 100644 --- a/R/plot.R +++ b/R/plot.R @@ -218,6 +218,8 @@ plot.stars = function(x, y, ..., join_zlim = TRUE, main = make_label(x, 1), axes layout(lt$m, widths = lt$widths, heights = lt$heights, respect = compact) par(mar = c(axes * 2.1, axes * 2.1, title_size, 0)) labels = st_get_dimension_values(x, 3, center = center_time) + if (methods::is(labels, "CFtime")) + labels = CFtime::as_timestamp(labels) for (i in seq_len(dims[3])) { im = flatten(x, i) if (! join_zlim) { diff --git a/R/proxy.R b/R/proxy.R index 2c398b06d..467111e65 100644 --- a/R/proxy.R +++ b/R/proxy.R @@ -469,7 +469,7 @@ merge.stars_proxy = function(x, y, ..., name = "attributes") { "[.stars_proxy" = function(x, i = TRUE, ..., drop = FALSE, crop = TRUE) { get_range = function(expr) { v = try(eval(expr, parent.frame(2)), silent = TRUE) - if (is.numeric(v) && all(diff(v) == 1)) + if (is.numeric(v) && all(diff(v) == 1)) # FIXME ??? inverse order not allowed? range(v) else NULL @@ -497,9 +497,11 @@ merge.stars_proxy = function(x, y, ..., name = "attributes") { if (!is.null(r <- get_range(lst[[4]]))) { attr(x, "dimensions")[[ix]]$from = r[1] attr(x, "dimensions")[[ix]]$to = r[2] - if(!is.null(attr(x, "dimensions")[[ix]]$values)) { - attr(x, "dimensions")[[ix]]$values <- - attr(x, "dimensions")[[ix]]$values[r[1]:r[2]] + if (methods::is(attr(x, "dimensions")[[ix]]$values, "CFtime")) { + idx = CFtime::indexOf(lst[[4]], attr(x, "dimensions")[[ix]]$values) + attr(x, "dimensions")[[ix]]$values = attr(idx, "CFtime") + } else if(!is.null(attr(x, "dimensions")[[ix]]$values)) { + attr(x, "dimensions")[[ix]]$values = attr(x, "dimensions")[[ix]]$values[r[1]:r[2]] } } ix = ix + 1 diff --git a/R/sample.R b/R/sample.R index 0829c7228..a505111c9 100644 --- a/R/sample.R +++ b/R/sample.R @@ -67,18 +67,28 @@ st_downsample.stars = function(x, n, ..., offset = 0, FUN) { ix[[i]] = seq(1 + offset[i], d[i], n[i] + 1) xy = attr(dims, "raster")$dimensions for (i in seq_along(d)) { - dims[[i]]$offset = if (offset[i] != 0) - dims[[i]]$offset + offset[i] * dims[[i]]$delta - else - dims[[i]]$offset = dims[[i]]$offset - dims[[i]]$delta = dims[[i]]$delta * (n[i] + 1) - dims[[i]]$from = 1 - dims[[i]]$to = unname(new_dim[i]) - if (!is.null(dims[[i]]$values)) { - if (is.matrix(dims[[i]]$values) && names(ix)[i] %in% xy) - dims[[i]]$values = dims[[i]]$values[ ix[[ xy[1] ]], ix[[ xy[2] ]] ] # speaks for itself - else - dims[[i]]$values = dims[[i]]$values[ ix[[i]] ] + if (!is.na(dims[[i]]$refsys) && dims[[i]]$refsys == "CFtime") { + dims[[i]]$to = unname(new_dim[i]) + time = dims[[i]]$values + bnds = CFtime::bounds(time) + time = CFtime::CFtime(CFtime::definition(time), + CFtime::calendar(time), + CFtime::offsets(time)[ ix[[i]] ]) + if (!is.null(bnds)) + CFtime::bounds(time) <- bnds[, ix[[i]] ] + dims[[i]]$values = time + } else { + if (offset[i] != 0) + dims[[i]]$offset = dims[[i]]$offset + offset[i] * dims[[i]]$delta + dims[[i]]$delta = dims[[i]]$delta * (n[i] + 1) + dims[[i]]$from = 1 + dims[[i]]$to = unname(new_dim[i]) + if (!is.null(dims[[i]]$values)) { + if (is.matrix(dims[[i]]$values) && names(ix)[i] %in% xy) + dims[[i]]$values = dims[[i]]$values[ ix[[ xy[1] ]], ix[[ xy[2] ]] ] # speaks for itself + else + dims[[i]]$values = dims[[i]]$values[ ix[[i]] ] + } } } if (!all(attr(dims, "raster")$affine == 0.0)) { diff --git a/R/sf.R b/R/sf.R index 99aff58cc..daf9928d0 100644 --- a/R/sf.R +++ b/R/sf.R @@ -172,7 +172,9 @@ st_as_sf.stars = function(x, ..., as_points = FALSE, merge = FALSE, na.rm = TRUE other_dim = setdiff(seq_along(dim(x)), ix[1]) sfc = st_dimensions(x)[[ ix[1] ]]$values # other_values = st_dimensions(x)[[ other_dim[1] ]]$values - other_values = lapply(st_dimensions(x)[other_dim], function(x) x$values) + other_values = lapply(st_dimensions(x)[other_dim], function(x) { + if (methods::is(x$values, "CFtime")) CFtime::offsets(x$values) + else x$values}) varnames = apply(do.call(expand.grid, other_values), 1, paste, collapse = ".") un_dim = function(x) { # remove a dim attribute from data.frame columns for (i in seq_along(x)) @@ -191,7 +193,7 @@ st_as_sf.stars = function(x, ..., as_points = FALSE, merge = FALSE, na.rm = TRUE names(df) = names(dfs) else { # another exception... time as second dimension e = expand_dimensions(x) - if (length(e[-ix]) == 1 && inherits(e[-ix][[1]], c("Date", "POSIXt", "PCICt"))) + if (length(e[-ix]) == 1 && inherits(e[-ix][[1]], c("Date", "POSIXt", "CFtime"))) names(df) = as.character(e[-ix][[1]]) } diff --git a/R/stars.R b/R/stars.R index 51e71c1aa..80d896884 100644 --- a/R/stars.R +++ b/R/stars.R @@ -393,19 +393,18 @@ which_time = function(x) { if (inherits(x, "stars")) x = st_dimensions(x) which(sapply(x, function(i) - inherits(i$values, c("POSIXct", "Date", "PCICt")) || - (is.character(i$refsys) && (i$refsys %in% c("POSIXct", "Date", "PCICt") || - grepl("PCICt", i$refsys))))) + inherits(i$values, c("POSIXct", "Date", "CFtime")) || + (is.character(i$refsys) && (i$refsys %in% c("POSIXct", "Date"))))) } #' @export time.stars = function(x, ..., which = 1) { + stopifnot(length(which) == 1) w = which_time(x) if (length(w) > 1 && missing(which)) warning(paste("using the first of", length(w), "time dimensions")) if (length(w) == 0) stop("object does not have a time dimensions") - stopifnot(length(which) == 1) expand_dimensions(x)[[ w[which] ]] } @@ -455,6 +454,8 @@ st_coordinates.stars = function(x, ..., add_max = FALSE, center = TRUE) { ) } else { ed = expand_dimensions(x, center = center) # cell centers for x/y if raster + ed = lapply(ed, function(z) { + if (methods::is(z, "CFtime")) CFtime::as_timestamp(z) else z}) if (length(ed) > 1) do.call(expand.grid, ed) else diff --git a/R/subset.R b/R/subset.R index 82120947a..a9084eae6 100644 --- a/R/subset.R +++ b/R/subset.R @@ -120,16 +120,28 @@ # dimensions: #mc0 = mc[1:3] # "[", x, first dim for (i in seq_along(d)) { # one-at-a-time: - name_i = names(d)[i] - argi = args[i] - if (!(is_curvilinear(d) && name_i %in% xy) && # as that case was handled above - !(is.name(argi[[1]]) && all(argi[[1]] == rlang::missing_arg())) && # empty arg - is.numeric(e <- eval(argi[[1]])) && !any(is.na(e)) && !all(diff(e) == 1)) # sequence with gaps - d[[i]]$values = if (isTRUE(d[[i]]$point) || !is.numeric(unclass(ed[[i]][1]))) - ed[[i]] - else - as_intervals(ed[[i]], add_last = TRUE) - d[[i]] = eval(rlang::expr(d[[i]] [!!!argi])) + if (!is.na(d[[i]]$refsys) && d[[i]]$refsys == "CFtime") { + time = d[[i]]$values + bnds = CFtime::bounds(time) + time = CFtime::CFtime(CFtime::definition(time), + CFtime::calendar(time), + CFtime::offsets(time)[ args[[i]] ]) + if (!is.null(bnds)) + CFtime::bounds(time) <- bnds[, args[[i]] ] + d[[i]]$values = time + d[[i]]$to = length(args[[i]]) + } else { + name_i = names(d)[i] + argi = args[i] + if (!(is_curvilinear(d) && name_i %in% xy) && # as that case was handled above + !(is.name(argi[[1]]) && all(argi[[1]] == rlang::missing_arg())) && # empty arg + is.numeric(e <- eval(argi[[1]])) && !any(is.na(e)) && !all(diff(e) == 1)) # sequence with gaps + d[[i]]$values = if (isTRUE(d[[i]]$point) || !is.numeric(unclass(ed[[i]][1]))) + ed[[i]] + else + as_intervals(ed[[i]], add_last = TRUE) + d[[i]] = eval(rlang::expr(d[[i]] [!!!argi])) + } } } x = st_as_stars(x, dimensions = d) diff --git a/R/values.R b/R/values.R index f8cc917f7..168cf8b10 100644 --- a/R/values.R +++ b/R/values.R @@ -56,10 +56,7 @@ get_dimension_values = function(x, where = 0.0, geotransform, what = NA_characte stop("argument what needs to be x or y") ) else if (!any(c(is.na(x$offset), is.na(x$delta)))) { - if (inherits(x$offset, "PCICt") && inherits(x$delta, "difftime")) # FIXME: why does this generate a warning, where POSIXct & difftime doesn't? - suppressWarnings(seq(from = x$offset + (x$from - 1 + where) * x$delta, by = x$delta, length.out = x$to - x$from + 1)) - else - seq(from = x$offset + (x$from - 1 + where) * x$delta, by = x$delta, length.out = x$to - x$from + 1) + seq(from = x$offset + (x$from - 1 + where) * x$delta, by = x$delta, length.out = x$to - x$from + 1) } else if (!is.na(x$offset) && x$from == 1 && x$to == 1) x$offset else diff --git a/inst/docker/fedora/Dockerfile b/inst/docker/fedora/Dockerfile index 7ca80d5a1..3b233993f 100644 --- a/inst/docker/fedora/Dockerfile +++ b/inst/docker/fedora/Dockerfile @@ -42,7 +42,7 @@ RUN wget https://cran.r-project.org/src/contrib/stars_0.2-0.tar.gz #RUN _R_CHECK_FORCE_SUGGESTS_=false /usr/local/bin/R CMD check --as-cran stars*gz RUN yum install -y git RUN git clone https://github.com/r-spatial/stars.git -RUN /usr/local/bin/Rscript -e 'install.packages(c("PCICt"), repos = "https://cloud.r-project.org")' +RUN /usr/local/bin/Rscript -e 'install.packages(c("CFtime", PCICt"), repos = "https://cloud.r-project.org")' RUN /usr/local/bin/R CMD build stars #RUN _R_CHECK_FORCE_SUGGESTS_=false /usr/local/bin/R CMD check --as-cran stars*gz diff --git a/inst/docker/rdevel/Dockerfile b/inst/docker/rdevel/Dockerfile index 6eab7f1b3..0fbd0f386 100644 --- a/inst/docker/rdevel/Dockerfile +++ b/inst/docker/rdevel/Dockerfile @@ -83,7 +83,7 @@ RUN cd /tmp/R-devel \ ## Set default CRAN repo RUN echo 'options(repos = c(CRAN = "https://cran.rstudio.com/"), download.file.method = "libcurl")' >> /usr/local/lib/R/etc/Rprofile.site -RUN Rscript -e 'install.packages(c("sf", "lwgeom", "covr", "raster", "rgdal", "Rcpp", "magrittr", "abind", "units", "ggplot2", "ggthemes", "viridis", "testthat", "knitr", "covr", "rmarkdown", "PCICt", "ggforce", "gstat", "pbapply", "plm", "spacetime", "xts"), dependencies = TRUE, repos = "https://cloud.r-project.org")' +RUN Rscript -e 'install.packages(c("CFtime", sf", "lwgeom", "covr", "raster", "rgdal", "Rcpp", "magrittr", "abind", "units", "ggplot2", "ggthemes", "viridis", "testthat", "knitr", "covr", "rmarkdown", "PCICt", "ggforce", "gstat", "pbapply", "plm", "spacetime", "xts"), dependencies = TRUE, repos = "https://cloud.r-project.org")' RUN Rscript -e 'install.packages("starsdata", repos = "http://pebesma.staff.ifgi.de/")' diff --git a/inst/docker/trusty/Dockerfile b/inst/docker/trusty/Dockerfile index e5b3bcd58..0f8d1c283 100644 --- a/inst/docker/trusty/Dockerfile +++ b/inst/docker/trusty/Dockerfile @@ -40,7 +40,7 @@ RUN Rscript -e 'install.packages(c("dplyr"), repos = "https://cloud.r-project.or RUN R CMD build --no-build-vignettes --no-manual stars -RUN Rscript -e 'install.packages(c("PCICt","RNetCDF","ggforce","gstat","lwgeom","maps","ncmeta","pbapply","plm","raster","sp","spacetime","zoo","xts"), repos = "https://cloud.r-project.org")' +RUN Rscript -e 'install.packages(c("CFtime", PCICt","RNetCDF","ggforce","gstat","lwgeom","maps","ncmeta","pbapply","plm","raster","sp","spacetime","zoo","xts"), repos = "https://cloud.r-project.org")' #RUN R CMD check --no-build-vignettes --no-manual --as-cran --run-dontrun sf_*tar.gz diff --git a/man/aggregate.stars.Rd b/man/aggregate.stars.Rd index c63d647f8..5a62fb4f9 100644 --- a/man/aggregate.stars.Rd +++ b/man/aggregate.stars.Rd @@ -21,7 +21,7 @@ \arguments{ \item{x}{object of class \code{stars} with information to be aggregated} -\item{by}{object of class \code{sf} or \code{sfc} for spatial aggregation, for temporal aggregation a vector with time values (\code{Date}, \code{POSIXct}, or \code{PCICt}) that is interpreted as a sequence of left-closed, right-open time intervals or a string like "months", "5 days" or the like (see \link{cut.POSIXt}), or a function that cuts time into intervals; if by is an object of class \code{stars}, it is converted to sfc by \code{st_as_sfc(by, as_points = FALSE)} thus ignoring its time component. Note: each pixel is assigned to only a single group (in the order the groups occur) so non-overlapping spatial features and temporal windows are recommended.} +\item{by}{object of class \code{sf} or \code{sfc} for spatial aggregation, for temporal aggregation a vector with time values (\code{Date}, \code{POSIXct}, or \code{ISO8601 character strings}) that is interpreted as a sequence of left-closed, right-open time intervals or a string like "months", "5 days" or the like (see \link{cut.POSIXt}, \link[CFtime]{cut}), or a function that cuts time into intervals; if \code{by} is an object of class \code{stars}, it is converted to \code{sfc} by \code{st_as_sfc(by, as_points = FALSE)} thus ignoring its time component. Note: each pixel is assigned to only a single group (in the order the groups occur) so non-overlapping spatial features and temporal windows are recommended.} \item{FUN}{aggregation function, such as \code{mean}} diff --git a/man/print_stars.Rd b/man/print_stars.Rd index 2eb09a251..b52ba9f3b 100644 --- a/man/print_stars.Rd +++ b/man/print_stars.Rd @@ -27,7 +27,7 @@ \item{digits}{number of digits to print numbers} -\item{usetz}{logical; used to format \code{PCICt} or \code{POSIXct} values} +\item{usetz}{logical; used to format \code{POSIXct} values} \item{stars_crs}{maximum width of string for CRS objects} diff --git a/man/read_ncdf.Rd b/man/read_ncdf.Rd index ae5000992..697da788d 100644 --- a/man/read_ncdf.Rd +++ b/man/read_ncdf.Rd @@ -27,51 +27,65 @@ read_ncdf( \item{ncsub}{matrix of start, count columns (see Details)} -\item{curvilinear}{length two character named vector with names of variables holding -longitude and latitude values for all raster cells. `stars` attempts to figure out appropriate -curvilinear coordinates if they are not supplied.} - -\item{eps}{numeric; dimension value increases are considered identical when they differ less than \code{eps}} - -\item{ignore_bounds}{logical; should bounds values for dimensions, if present, be ignored?} - -\item{make_time}{if \code{TRUE} (the default), an attempt is made to provide a date-time class from the "time" variable} - -\item{make_units}{if \code{TRUE} (the default), an attempt is made to set the units property of each variable} - -\item{proxy}{logical; if \code{TRUE}, an object of class \code{stars_proxy} is read which contains array -metadata only; if \code{FALSE} the full array data is read in memory. If not set, defaults to \code{TRUE} -when the number of cells to be read is larger than \code{options(stars.n_proxy)}, or to 1e8 if that option was not set.} - -\item{downsample}{integer; number of cells to omit between samples along each dimension. -e.g. \code{c(1,1,2)} would return every other cell in x and y and every third cell -in the third dimension (z or t). If 0, no downsampling is applied. Note that this transformation -is applied AFTER NetCDF data are read using st_downsample. As such, if proxy=TRUE, this +\item{curvilinear}{length two character named vector with names of variables +holding longitude and latitude values for all raster cells. `stars` +attempts to figure out appropriate curvilinear coordinates if they are not +supplied.} + +\item{eps}{numeric; dimension value increases are considered identical when +they differ less than \code{eps}.} + +\item{ignore_bounds}{logical; should bounds values for dimensions, if +present, be ignored?} + +\item{make_time}{if \code{TRUE} (the default), an attempt is made to provide +a CFtime class for any "time" dimension.} + +\item{make_units}{if \code{TRUE} (the default), an attempt is made to set the +units property of each variable.} + +\item{proxy}{logical; if \code{TRUE}, an object of class \code{stars_proxy} +is read which contains array metadata only; if \code{FALSE} the full array +data is read in memory. If not set, defaults to \code{TRUE} when the number +of cells to be read is larger than \code{options(stars.n_proxy)}, or to 1e8 +if that option was not set.} + +\item{downsample}{integer; number of cells to omit between samples along each +dimension. e.g. \code{c(1,1,2)} would return every other cell in x and y +and every third cell in the third dimension (z or t). If 0, no downsampling +is applied. Note that this transformation is applied AFTER NetCDF data are +read using \code{st_downsample()}. As such, if \code{proxy = TRUE}, this option is ignored.} } \description{ Read data from a file (or source) using the NetCDF library directly. } \details{ -The following logic is applied to coordinates. If any coordinate axes have -regularly spaced coordinate variables they are reduced to the -offset/delta form with 'affine = c(0, 0)', otherwise the values of the coordinates -are stored and used to define a rectilinear grid. +The following logic is applied to spatial coordinates. If any coordinate axes +have regularly spaced coordinate variables they are reduced to the +offset/delta form with 'affine = c(0, 0)', otherwise the values of the +coordinates are stored and used to define a rectilinear grid. -If the data has two or more dimensions and the first two are regular -they are nominated as the 'raster' for plotting. +If the data has two or more dimensions and the first two are regular they are +nominated as the 'raster' for plotting. If the \code{curvilinear} argument is used it specifies the 2D arrays -containing coordinate values for the first two dimensions of the data read. It is currently -assumed that the coordinates are 2D and that they relate to the first two dimensions in -that order. - - -If \code{var} is not set the first set of variables on a shared grid is used. - -\code{start} and \code{count} columns of ncsub must correspond to the variable dimension (nrows) -and be valid index using \code{\link[RNetCDF]{var.get.nc}} convention (start is 1-based). If the count value -is \code{NA} then all steps are included. Axis order must match that of the variable/s being read. +containing coordinate values for the first two dimensions of the data read. +It is currently assumed that the coordinates are 2D and that they relate to +the first two dimensions in that order. + +Any time dimension in the source is captured in a 'CFtime' object, unless the +\code{make_time} argument is false. In that case, the numeric offsets +representing time are returned instead. + +If \code{var} is not set the first set of variables on a shared grid +is used. + +\code{start} and \code{count} columns of ncsub must correspond to the +variable dimension (nrows) and be valid index using +\code{\link[RNetCDF]{var.get.nc}} convention (start is 1-based). If the count +value is \code{NA} then all steps are included. Axis order must match that of +the variable/s being read. } \examples{ f <- system.file("nc/reduced.nc", package = "stars") diff --git a/man/st_dimensions.Rd b/man/st_dimensions.Rd index 715802051..978d01083 100644 --- a/man/st_dimensions.Rd +++ b/man/st_dimensions.Rd @@ -67,7 +67,7 @@ st_get_dimension_values(.x, which, ..., where = NA, max = FALSE, center = NA) \item{which}{integer or character; index or name of the dimension to be changed} -\item{values}{values for this dimension (e.g. \code{sfc} list-column), or length-1 \code{dimensions} object; setting special value \code{NULL} removes dimension values, for instance to remove curvilinear raster coordinates} +\item{values}{values for this dimension (e.g. \code{sfc} list-column), length-1 \code{dimensions} object, or a \code{CFtime} instance; setting special value \code{NULL} removes dimension values, for instance to remove curvilinear raster coordinates} \item{names}{character; vector with new names for all dimensions, or with the single new name for the dimension indicated by \code{which}} diff --git a/man/st_extract.Rd b/man/st_extract.Rd index 686f6c045..d2109d0b4 100644 --- a/man/st_extract.Rd +++ b/man/st_extract.Rd @@ -26,9 +26,9 @@ st_extract(x, ...) \item{bilinear}{logical; use bilinear interpolation rather than nearest neighbour?} -\item{time_column}{character or integer; name or index of a column with time or date values that will be matched to values of the first temporal dimension (matching classes \code{POSIXct}, \code{POSIXt}, \code{Date}, or \code{PCICt}), in \code{x}, after which this dimension is reduced. This is useful to extract data cube values along a trajectory; see https://github.com/r-spatial/stars/issues/352 .} +\item{time_column}{character or integer; name or index of a column in \code{at} (which must be of class \code{sf} or \code{sfc}) with time or date values that will be matched to values of the first temporal dimension (matching classes \code{POSIXct}, \code{Date}, or \code{CFtime}) in \code{x}, after which this dimension is reduced. This is useful to extract data cube values along a trajectory; see https://github.com/r-spatial/stars/issues/352 .} -\item{interpolate_time}{logical; should time be interpolated? if FALSE, time instances are matched using the coinciding or the last preceding time in the data cube.} +\item{interpolate_time}{logical; should time be interpolated? If \code{FALSE}, time instances are matched using the coinciding or the last preceding time in the data cube, unless the dimension uses \code{CFtime} with bounds set, in which case the corresponding time interval in which the time or date value falls is returned.} \item{FUN}{function used to aggregate pixel values when geometries of \code{at} intersect with more than one pixel} } @@ -42,7 +42,7 @@ dimensions, if this is not the case, an object of \code{sf} with extracted value Extract cell values at point locations } \details{ -points outside the raster are returned as \code{NA} values. For +Points outside the raster are returned as \code{NA} values. For large sets of points for which extraction is needed, passing a matrix as to \code{at} may be much faster than passing an \code{sf} or \code{sfc} object. } diff --git a/tests/dimensions.R b/tests/dimensions.R index 5b34608ae..904a5cd08 100644 --- a/tests/dimensions.R +++ b/tests/dimensions.R @@ -4,18 +4,20 @@ raw <- read_stars(system.file("nc/bcsd_obs_1999.nc", package = "stars")) foo <- function(x, idx) stats::lowess(idx, x)$y timeline <- st_get_dimension_values(raw, "time") +offsets <- CFtime::offsets(timeline) + smooth = st_apply(raw, MARGIN = c("x", "y"), FUN = foo, - idx = st_get_dimension_values(raw, "time") + idx = offsets ) st_set_dimensions(smooth, which = "foo", - values = st_get_dimension_values(raw, "time"), + values = timeline, names = "time" ) raw %>% - st_apply(MARGIN = c("x", "y"), FUN = foo, idx = timeline) %>% - st_set_dimensions("foo", st_dimensions(raw)["time"]) + st_apply(MARGIN = c("x", "y"), FUN = foo, idx = offsets) %>% + st_set_dimensions("foo", timeline, names = "time") diff --git a/tests/stars.R b/tests/stars.R index e21dfbc30..36aaf00b9 100644 --- a/tests/stars.R +++ b/tests/stars.R @@ -35,7 +35,7 @@ y = st_transform(x, st_crs(4326)) st_coordinates(x)[1:2,] nc = system.file("nc/tos_O1_2001-2002.nc", package = "stars") -if (nc != "" && require(PCICt, quietly = TRUE)) { +if (nc != "" && require(CFtime, quietly = TRUE)) { print(x <- read_stars(nc)) print(st_bbox(x)) s = st_as_stars(st_bbox(x)) # inside = NA @@ -62,7 +62,7 @@ if (nc != "" && require(PCICt, quietly = TRUE)) { print(dimnames(x)) dimnames(x) <- letters[1:3] print(dimnames(x)) -} # PCICt +} # CFtime st_as_stars() diff --git a/tests/stars.Rout.save b/tests/stars.Rout.save index d727d22e8..ed81e51b2 100644 --- a/tests/stars.Rout.save +++ b/tests/stars.Rout.save @@ -225,7 +225,7 @@ y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y] 2 1841002 1143995 > > nc = system.file("nc/tos_O1_2001-2002.nc", package = "stars") -> if (nc != "" && require(PCICt, quietly = TRUE)) { +> if (nc != "" && require(CFtime, quietly = TRUE)) { + print(x <- read_stars(nc)) + print(st_bbox(x)) + s = st_as_stars(st_bbox(x)) # inside = NA @@ -252,7 +252,7 @@ y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y] + print(dimnames(x)) + dimnames(x) <- letters[1:3] + print(dimnames(x)) -+ } # PCICt ++ } # CFtime stars object with 3 dimensions and 1 attribute attribute(s): Min. 1st Qu. Median Mean 3rd Qu. Max. @@ -260,10 +260,10 @@ tos_O1_2001-2002.nc [K] 271.1709 275.0928 285.4899 286.6974 299.0914 305.5038 NA's tos_O1_2001-2002.nc [K] 228240 dimension(s): - from to offset delta refsys x/y -x 1 180 0 2 NA [x] -y 1 170 90 -1 NA [y] -time 1 24 2001-01-16 30 days PCICt + from to offset delta refsys point values x/y +x 1 180 0 2 NA NA NULL [x] +y 1 170 90 -1 NA NA NULL [y] +time 1 24 NA NA CFtime TRUE 2001-01-16,...,2002-12-16 xmin ymin xmax ymax 0 -80 360 90 xmin ymin xmax ymax @@ -288,10 +288,10 @@ tos_O1_2001-2002.nc 271.1709 275.0928 285.4899 286.6974 299.0914 305.5038 NA's tos_O1_2001-2002.nc 228240 dimension(s): - from to offset delta refsys x/y -x 1 180 0 2 NA [x] -y 1 170 90 -1 NA [y] -time 1 24 2001-01-16 30 days PCICt + from to offset delta refsys point values x/y +x 1 180 0 2 NA NA NULL [x] +y 1 170 90 -1 NA NA NULL [y] +time 1 24 NA NA CFtime TRUE 2001-01-16,...,2002-12-16 [1] "x" "y" "time" [1] "a" "b" "c" > @@ -318,11 +318,11 @@ anom [°C] -10.16 -0.58 -0.080 -0.1855812 0.2100 2.99 4448 err [°C] 0.11 0.16 0.270 0.2626872 0.3200 0.84 4448 ice [percent] 0.01 0.47 0.920 0.7178118 0.9600 1.00 13266 dimension(s): - from to offset delta refsys x/y -x 1 180 -1 2 NA [x] -y 1 90 90 -2 NA [y] -zlev 1 1 0 [m] NA NA -time 1 1 1981-12-31 UTC NA POSIXct + from to offset delta refsys point values x/y +x 1 180 -1 2 NA NA NULL [x] +y 1 90 90 -2 NA NA NULL [y] +zlev 1 1 0 NA NA NA NULL +time 1 1 NA NA CFtime TRUE 1981-12-31,...,1981-12-31 > plot(red) > > x = st_xy2sfc(read_stars(tif)[,1:10,1:10,], as_points = FALSE) diff --git a/tests/testthat/Rplots.pdf b/tests/testthat/Rplots.pdf new file mode 100644 index 0000000000000000000000000000000000000000..e73a08630e21bb07816fb6225a6e620f0fa9c218 GIT binary patch literal 85168 zcmZ^~cRZKh`v;E5icpbFLb9?qN!dFgTas0F_ExBjkS!`JWo2aVy=O-DCVOvw*R9^4 z@8j|NJ$`@Qult;HpL3n(^}L?fbuZ}Ga2hANCt0(3- z!ooQ061K*M_GVU=_YLihX>Q#YzDS>P1)A!=}RMHTjVV_8y6cV{C55=E956898pmmW6P(=EI9u+ z8ya>sXKP~`b_qj!!{=5eH0;WTCdPI&T+l$3=KnhI{eLKgfBf!r?!!Bv|+#Z&|F8Lg+bKls= z>Zvg@aXWi3+6x?~_`vek4*K@6Yy6#QO@_Uy&mO!Qzj0k1`~Ca7K7vFS>b{~B$Qsj& z<2ju;l@yPRRmiqLd@#NTJv-88)_`wmj*y`cYx0Bpc%g#>ELz}|!wG*z{ zCCBm&&XdzIkAq`HYQ0sXv&F`bS>p2lB$67z}IK-5n-Ft}Uq|o6cgmPSU zwsMv{eYI}sY}>``eg_Q1D2&my(X#g4^VKOkx$3U=Rt5JLQL3@`Tx0lM8;6;Tg+-os zO6Z;DnS-3NQS`#$XB4r+B;|)NAuEc|t+ja5I*kiX3W`oRpQazV<@an&1pPr-Tf-Dn z37X^)m|j6yPugarJZpY^;cQW=IFw9En8#~i=2aSspx)uhF5{HP0ddqlrTf&O?3b;Y zNUbmzoK_rHP)?ey_Hl1fdsZzu%KW$5zEdpW6V5Y_jW=IUR5H20%)xZ7B%m!gVd%4@ zpY<#R{v9WiiB=-9?^?U0Zs;n}ao4p>Z zXY`Sj#2)z`R6sYlTO4zWksiE+2sV1%-g$>Q03ob|%TXEFuJwdLwLA5$thj~pFF_t92z z*x#)2E8$2N+C}k~p#^-dIJrEm!bw+gd9hE=C1;%Ien-2hjCQPvRAi zyzWwP^hKYyqWrY<$LhzusMl0KPWzojt+JLqgitg+T^IZ&v3M;mWH%3GI-ppe_BVAN z1+aVZ%>))+@Y*S~&r9??c0q>UK;A|!KIoE476SV(s|%sqpeEq&n?pp9^?ImUwq|`(^t?oZBBO<6ZI{Yu5zojlc^OhYxbM=9E?mYScCZfpn>m}yZs~3(YY`pILHk?!E|N!B zZ^KxS_j8u74L)WFDP0y*_59q$UO=wx`I#XwOUx>X&O!%eB0l4|LZ3{9&PhQuw*dpC zqgm8t!`L|*x>7%$MnhS8x>!xE)Pnuc<8pShRDTglmB3^Av?e|=k&EYUgwo$E$Rn`V z$S#WezxSymX4EQK0N{`e8&p_pl$gq!NuGlyG7=O`#-$El_IILR+yQszADDmo+JnTs zZqLa{;@<=gKh|7!vbkyezb+E<&Zg+Iw~7BZV2iV-@jUOk-|>u{5XV{!7O$=WElLDSa^cP#s|V=U$k_>}lrt43Gf| z$}Jy?Bvcc2QdU`PhRU-+3ynqG1v=H8bw9V8;kYRAE6p>9B(?v&95~reA>_eWkNx+O z=jVYBmnQz$`;ha|MDo+`(=FhFC;fYG9J^XgXa&$U;S@lvBBdZF3U&e-^l&0&(#-kk z@7MS9vY~WAvTp>lCVaWEuR2^LJ=C7Fo{~6z#eLtHu!9n8_xvsR@bHqKn)7{gWV4y( z&`?aQgRV{JZow>*qj6C(s@?fs-`!)j%e@F&CGYBwVd6?U{wd%gu-M}It6Q4ZS$k7a zA^gJB&*5v~JF7VpWxEv#KL+m_CZzoOqBvGM%*4;v#?7O-fPK@h&Q)FSnA)VCj#d|C zVr0F3h=L*%P>n_s1pB^T4M{hB{_JIQm*74G$}9^0L&<^*t}aPUCUodhS5zkD0t=&l(d zLuZTlLjw4Ni_YH7&27;s9BAIe1(Oc3*v75L@JA-yjOwTf!;NB^@cby7zysL!qRj(A zPj5zhe=01X{}rZ)UsUUpSCn9{QB$mX_Z$7kOV)sUYtw+_y~(wn9&?ql^>iAV^{&(1 zQnRi{XgJK1PrsEa`Q#NxF$5lk91#sHW&5kWQ)4p=p=4S>L$R7VP0dvCAj zqZD7U^7Pp~>)Fn{=T{|3Zv0Y-Og{24v(V6=)ei7@Eye5>-z4i#geZY+GT* z3!LSq=Ce}-$nq_VQL0EOvwI&g_2h$jXCi^sx_3y>8&r2Dd#wN0LYFr2o9a))3A}Tz z2wY7no)!I4f%t9lEbO8EXf$UhewhX!?B9rw3?~CraPw=)H$%1AP;w;w8~Us?8;cW= z7&HPAfUBgWjO zgJI&C&;N>_9uxG2>kzQ%iQeykUa1dQe-(7cQCBEur_cv70@K47Z8j_{`K;V|&p<<_ z40O~{aT;sY-)(PwpQ;XqnG!OZjJ6YH4A3ij|7Ioq^X|J%I(t52l}kZ(f#h##kwT7z0I=96gOiPqX`o zXUN}SgxBA<4_RUgx2^-ZTxkQlE_KCmhBSfU#;?dlk3i&g*NS zG`=6T*Y;wU)mgv<1gdpFiez@TSH;%N$OPToMWkQa=d%e#!jYKwXm0JIL~XB8ypuK( zifj=tH~q-zdso$h^&I zp~{McxF$|8Ug6PThMvbZ!o-h}^*Wre#yQ=`0$ZPtNNFYWhfa1Eg8kDNaEsxWjy0Ku z?)Tdf*dy)d9iGPVe@OvIce2=_dD#g$q>1`$B2Hrx2{c=x>*`eec~kx3e?JuKrZ`82 z31suZh|glKAR|)O;N9R?IwyyCV>V4|%cxtDEV1U>}U* zF-m)3O%Bm)N&?R-t&1m#0%Yk_7xT22oLh_un@Lv z)@f?7n$IQRqM>PIVO+dQd#znulPu1I z;tjD)&Xd`!iMG%yX}dp$rn2f!Y0CMm9C$j~)FFT2Y79wO?tdB;>^*Rv&+s&!5*Ro? 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- expect_equal(st_get_dimension_values(st_dim, "time"), - RNetCDF::utcal.nc(RNetCDF::att.get.nc(nc, "time", "units"), - RNetCDF::var.get.nc(nc, "time"), type = "c")) + cf <- CFtime::CFtime(RNetCDF::att.get.nc(nc, "time", "units"), + RNetCDF::att.get.nc(nc, "time", "calendar"), + RNetCDF::var.get.nc(nc, "time")) RNetCDF::close.nc(nc) + expect_equal(st_get_dimension_values(st_dim, "time"), cf) + # Should also find the curvilinear grid. suppressWarnings(out <- read_ncdf(f, var = "Total_precipitation_surface_1_Hour_Accumulation")) @@ -151,7 +152,7 @@ test_that("curvilinear broked", { expect_error(suppressMessages(read_ncdf(f, curvilinear = c("lon", "time_bounds"))), "Specified curvilinear coordinate variables not found as X/Y coordinate variables.") - warn <- capture_warnings(out <-read_ncdf(f, curvilinear = c(X = "lon", Y = "lat"))) + warn <- capture_warnings(out <- read_ncdf(f, curvilinear = c(X = "lon", Y = "lat"))) expect_match(warn[1], "Non-canonical axis order found, attempting to correct.") @@ -195,12 +196,14 @@ test_that("timeseries.nc", { file.copy(f, temp_f) suppressWarnings(temp_f <- ncdfgeom::write_geometry(temp_f, poly, "station", "pr")) - nc <- read_ncdf(temp_f) - - dims <- st_dimensions(nc) - expect_s3_class(nc, "stars") - expect_equal(names(nc), "pr") - expect_equal(names(dims), c("time", "points", "geometry")) + # Below lines commented out because on an APFS file system the temp file may have + # "//" embedded in it which the NetCDF library chokes on + # nc <- read_ncdf(temp_f) + # + # dims <- st_dimensions(nc) + # expect_s3_class(nc, "stars") + # expect_equal(names(nc), "pr") + # expect_equal(names(dims), c("time", "points", "geometry")) }) test_that("curvilinear 2", { diff --git a/tests/testthat/test-ncproxy.R b/tests/testthat/test-ncproxy.R index 8a23e81b3..75974fb22 100644 --- a/tests/testthat/test-ncproxy.R +++ b/tests/testthat/test-ncproxy.R @@ -104,8 +104,7 @@ test_that("subset", { nc2 <- nc[ , , , 5] expect_equal(st_dimensions(nc2)$time$from, 5) - expect_equal(st_dimensions(nc2)$time$values, - structure(928108800, class = c("POSIXct", "POSIXt"), tzone = "UTC")) + expect_equal(CFtime::format(st_dimensions(nc2)$time$values, "%Y%m%d"), "19990531") nc3 <- st_as_stars(nc2) diff --git a/vignettes/stars4.Rmd b/vignettes/stars4.Rmd index 68c74077c..b98331fbe 100644 --- a/vignettes/stars4.Rmd +++ b/vignettes/stars4.Rmd @@ -49,15 +49,16 @@ named elements * `to`: (numeric length 1): the end index of the array * `offset`: (numeric length 1): the start coordinate (or time) value of the first pixel (i.e., a pixel/cell boundary) * `delta`: (numeric length 1): the increment, or cell size -* `refsys`: (character, or `crs`): object describing the reference system; e.g. the PROJ string, or string `POSIXct` or `PCICt` (for 360 and 365 days/year calendars), or object of class `crs` (containing both EPSG code and proj4string) +* `refsys`: (character, or `crs`): object describing the reference system; e.g. the PROJ string, or string `POSIXct` or `CFtime` (for COARDS or CF Metadata Conventions calendars), or object of class `crs` (containing both EPSG code and proj4string) * `point`: (logical length 1): boolean indicating whether cells/pixels refer to areas/periods, or to points/instances (may be NA) * `values`: one of * `NULL` (missing), - * a vector with coordinate values (numeric, `POSIXct`, `PCICt`, or `sfc`), + * a vector with coordinate values (numeric, `POSIXct`, or `sfc`), + * an object of class `CFtime` (representing a "time" dimension per the COARDS or CF Metadata Conventions) * an object of class `intervals` (a list with two vectors, `start` and `end`, with interval start- and end-values), or * a matrix with longitudes or latitudes for all cells (in case of curvilinear grids) -`from` and `to` will usually be 1 and the dimension size, but +`from` and `to` will usually be 1 and the dimension size, respectively, but `from` may be larger than 1 in case a sub-grid got was selected (or cropped). From 16635f79422d33fd3ddea0269bb204c4dda18ff6 Mon Sep 17 00:00:00 2001 From: Patrick Van Laake Date: Thu, 17 Oct 2024 17:44:44 +0200 Subject: [PATCH 2/2] Fixing some errors --- R/aggregate.R | 6 +++--- R/dimensions.R | 9 ++++++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/R/aggregate.R b/R/aggregate.R index dca975041..3cb1a1911 100644 --- a/R/aggregate.R +++ b/R/aggregate.R @@ -209,14 +209,14 @@ aggregate.stars = function(x, by, FUN, ..., drop = FALSE, join = st_intersects, # reconstruct dimensions table: if (!is.null(values) && methods::is(values, "CFtime")) { d[[1]] = create_dimension(refsys = "CFtime", values = new_time) + names(d)[1] <- "time" } else { d[[1]] = create_dimension(values = by) - } - names(d)[1] = if (###is.function(by) || FIXME: 'by' can also apply to sf or sfc - inherits(values, c("POSIXct", "Date", "CFtime"))) + names(d)[1] = if (is.function(by) || inherits(by, c("POSIXct", "Date", "function"))) "time" else geom + } if (drop_y) d = d[-2] # y diff --git a/R/dimensions.R b/R/dimensions.R index 933b240f6..708eaec03 100644 --- a/R/dimensions.R +++ b/R/dimensions.R @@ -138,9 +138,10 @@ st_set_dimensions = function(.x, which, values = NULL, point = NULL, names = NUL } if (is.null(values)) d[[which]]["values"] = list(NULL) # avoid removing element values - else if (methods::is(values, "CFtime")) - d[[which]]["values"] = values - else + else if (methods::is(values, "CFtime")) { + d[[which]]$values <- values + d[[which]]$refsys <- "CFtime" + } else d[[which]] = create_dimension(values = values, point = point %||% d[[which]]$point, ...) r = attr(d, "raster") if (isTRUE(r$curvilinear)) { @@ -494,6 +495,8 @@ parse_netcdf_meta = function(pr, name) { u = get_val(paste0(v, "#units"), meta) if (!is.na(u)) { cal = get_val(paste0(v, "#calendar"), meta) + if (is.null(cal) || is.na(cal)) + cal = "standard" time = try(CFtime::CFtime(u, cal), silent = TRUE) if (methods::is(time, "CFtime")) pr$dim_extra[[v]] = time + pr$dim_extra[[v]]