Nothing
runx_wrapper <- function(op, var, nts, infile, outfile, nc34, overwrite, verbose, nc = NULL) {
calc_time_start <- Sys.time()
gc()
check_variable(var)
if (is.null(nc)) check_infile(infile)
check_outfile(outfile)
outfile <- correct_filename(outfile)
check_overwrite(outfile, overwrite)
check_nc_version(nc34)
##### extract data from file #####
file_data <- read_file(infile, var, nc = nc)
if(nts <= length(file_data$dimension_data$t))
{
if (op > 2) {
file_data$variable$prec <- "float"
}
date_time <- get_date_time(file_data$dimension_data$t, file_data$time_info$units)
# Use placeholder for result so that it can be calculated later without the
# need to have all input data in memory concurrently.
length.dimension.x <- length(file_data$dimension_data$x)
length.dimension.y <- length(file_data$dimension_data$y)
length.dimension.t <- (length(file_data$dimension_data$t)-(nts-1))
# data_placeholder <- array(
# file_data$variable$attributes$missing_value,
# dim = c(length.dimension.x,
# length.dimension.y,
# length.dimension.t)
# )
time_bnds <- get_time_bounds_run(file_data$dimension_data$t, nts)
vars_data <- list(time_bounds = time_bnds)
nc_format <- get_nc_version(nc34)
cmsaf_info <- switch(
op,
paste0("cmsafops::runmin for variable ", file_data$variable$name),
paste0("cmsafops::runmax for variable ", file_data$variable$name),
paste0("cmsafops::runrange for variable ", file_data$variable$name),
paste0("cmsafops::runsum for variable ", file_data$variable$name),
paste0("cmsafops::runmean for variable ", file_data$variable$name),
paste0("cmsafops::runsd for variable ", file_data$variable$name),
)
time_data <- time_bnds[1, ]
##### prepare output #####
global_att_list <- names(file_data$global_att)
global_att_list <- global_att_list[toupper(global_att_list) %in% toupper(GLOBAL_ATT_DEFAULT)]
global_attributes <- file_data$global_att[global_att_list]
dims <- define_dims(file_data$grid$is_regular,
file_data$dimension_data$x,
file_data$dimension_data$y,
time_data,
NB2,
file_data$time_info$units)
vars <- define_vars(file_data$variable, dims, nc_format$compression)
write_output_file(
outfile,
nc_format$force_v4,
vars,
vars_data,
file_data$variable$name,
file_data$grid$vars, file_data$grid$vars_data,
cmsaf_info,
file_data$time_info$calendar,
file_data$variable$attributes,
global_attributes,
write_result = FALSE # avoid vector memory exhaustion, Can be adjust
)
##### calculate and write result #####
nc_out <- nc_open(outfile, write = TRUE)
if (!is.null(nc)) nc_in <- nc
else nc_in <- nc_open(infile)
# limit <- 2601 * 2601 * 31 # limit to avoid vector memory exhaustion, Can be adjust
# dimensionality <- as.double(length.dimension.x) *
# as.double(length.dimension.y) * as.double(length.dimension.t)
#
# if(limit < dimensionality){
# for (i in 1:length.dimension.t) {
# data <- data_placeholder[,,i]
# ncvar_put(nc_out, vars[[1]], data, start = c(1, 1, i), count = c(-1, -1, 1))
# }
# }else{
# ncvar_put(nc_out, vars[[1]], data_placeholder)
# }
# rm(data_placeholder)
startt <- 1
countt <- nts
# length of running time steps
length_time <- length(file_data$dimension_data$t)-(nts-1)
for (i in 1:length_time) {
# read data from infile
dum_dat <- ncvar_get(
nc_in,
file_data$variable$name,
start = c(1, 1, startt),
count = c(-1, -1, countt),
collapse_degen = FALSE
)
startt <- startt + 1
switch(op,
{
if (verbose) message(paste0("apply running minimum ", i," of ", length_time))
data <- do.call(pmin, c(na.rm = TRUE, lapply(seq_len(dim(dum_dat)[3]), function(i) dum_dat[, , i])))
},
{
if (verbose) message(paste0("apply running maximum ", i," of ", length_time))
data <- do.call(pmax, c(na.rm = TRUE, lapply(seq_len(dim(dum_dat)[3]), function(i) dum_dat[, , i])))
},
{
if (verbose) message(paste0("apply running range ", i," of ", length_time))
data.max <- do.call(pmax, c(na.rm = TRUE, lapply(seq_len(dim(dum_dat)[3]), function(i) dum_dat[, , i])))
data.min <- do.call(pmin, c(na.rm = TRUE, lapply(seq_len(dim(dum_dat)[3]), function(i) dum_dat[, , i])))
data <- data.max - data.min
},
{
if (verbose) message(paste0("apply running sum ", i," of ", length_time))
data <- rowSums(dum_dat, dims = 2, na.rm = TRUE) * ifelse(rowSums(is.na(dum_dat), dims = 2) == dim(dum_dat)[3], NA, 1)
},
{
if (verbose) message(paste0("apply running mean ", i," of ", length_time))
data <- rowMeans(dum_dat, dims = 2, na.rm = TRUE)
},
{
if (verbose) message(paste0("apply running standard deviation ", i," of ", length_time))
data <- apply(dum_dat, c(1, 2), stats::sd, na.rm = TRUE)
}
)
data[is.na(data)] <- file_data$variable$attributes$missing_value
ncvar_put(nc_out, vars[[1]], data, start = c(1, 1, i), count = c(-1, -1, 1))
}
if (is.null(nc)) nc_close(nc_in)
nc_close(nc_out)
}
else{
stop("The input of the time steps must not be greater than the number of time steps from the input file")
}
calc_time_end <- Sys.time()
if (verbose) message(get_processing_time_string(calc_time_start, calc_time_end))
}
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