############################################################################################################################
############################ FUNCTIONS TO HANDLE FireMIP FILES ###########################################################
############################################################################################################################
#' Open a JSBACH FireMIP output file
#'
#' Opens a .nc file from the JSBACH FireMIP output and sorts out the meta-data and dimensions and all that messy stuff.
#' Returns a data.table, because it is intended to be called by getField(), but of course the data.table could be used directly if you wish
#'
#'
#' @param run A Source object to define the run we want to open.
#' @param quantity A Quantity object to define which variable we want to look up
#' @param first.year The first year we want to read (numeric)
#' @param last.year The last year we want to read (numeric)
#' @param spatial.extent The spatial extent we want to read (as defined by as raster::extent or an object that can be cast to a raster::extent)
#' @param verbose Logical, if TRUE spew forth a lot of info.
#' @import data.table
#' @import DGVMTools
#' @import ncdf4
#' @importFrom stats na.omit
#'
#' @keywords internal
#'
#' @return A list containaing a data.table and an STAInfo object
#'
#' @author Matthew Forrest \email{matthew.forrest@@senckenberg.de}
#'
#' @export
openFireMIPOutputFile_JSBACH <- function(run, quantity, sta.info, file.name, verbose = TRUE) {
first.year = sta.info@first.year
last.year = sta.info@last.year
Year = Lon = landmask = NULL
# get the name of the model
print(run@format@id)
# open the data file and the gridl file
file.string <- file.path(run@dir, paste0(run@id, "_", quantity@id, ".nc"))
print(file.string)
this.nc <- nc_open(file.string, readunlim=FALSE, verbose=verbose, suppress_dimvals=FALSE )
grid.file <- system.file("gridfiles", "JSBACH_grid.nc", package = "FireMIPTools")
grid.nc <- nc_open(grid.file, readunlim=FALSE, verbose=verbose, suppress_dimvals=FALSE )
# get and print the dimensions and variables present
dims.present <- names(this.nc$dim)
print(paste("Dimensions present: ", paste(dims.present, collapse = " ")))
vars.present <- names(this.nc$var)
print(paste("Variables present: ", paste(vars.present , collapse = " ")))
# PFTs - hard coded
this.pfts <- c("TrE", "TrD", "ExtE", "ExtD", "Rg_Shb", "De_Shb", "C3G", "C4G", "C3G_pas", "C4G_pas", "Crop")
# get dimensions
this.lat <- getDimension(this.nc, "lat", verbose)
if(is.null(this.lat)) this.lat <- getDimension(grid.nc, "lat", verbose)
this.lon <- getDimension(this.nc, "lon", verbose)
if(is.null(this.lon)) this.lon <- getDimension(grid.nc, "lon", verbose)
this.time <- getDimension(this.nc, "time", verbose)
# get the land mask
this.landmask <- ncvar_get(grid.nc, "masks", start = c(1,1), count = c(-1,-1))
dimnames(this.landmask) <- list(this.lon, this.lat)
this.landmask.dt <- as.data.table(melt(this.landmask))
setnames(this.landmask.dt, c("Lon", "Lat", "landmask"))
this.landmask.dt <- this.landmask.dt[landmask > 0,]
this.landmask.dt[, landmask:=NULL]
# attempt to automagically determine time axis
is.monthly <- FALSE
# monthly starting in 1861 -- CTEM
if(length(this.time) == 1836) {
is.monthly <- TRUE
all.years <- 1861:2013
}
# annual starting in 1950 -- CTEM
else if(length(this.time) == 64) {
all.years <- 1950:2013
}
# annual starting in 1950 -- CTEM
else if(length(this.time) == 156) {
all.years <- 1860:2013
}
# monthly starting in 1950 -- CTEM
else if(length(this.time) == 768) {
is.monthly <- TRUE
all.years <- 1950:2013
}
# monthly starting in 1700 -- JSBACH
else if(length(this.time) == 3768) {
is.monthly <- TRUE
all.years <- 1700:2013
}
# monthly starting in 1700 -- JSBACH
else if(length(this.time) == 3756) {
is.monthly <- TRUE
all.years <- 1701:2013
}
# monthly starting in 1700 -- JSBACH
else if(length(this.time) == 314) {
all.years <- 1700:2013
}
# monthly starting in 1700 -- JSBACH
else if(length(this.time) == 313) {
all.years <- 1700:2012
}
else {
stop(paste("Guess time axis for time dimensions length", length(this.time)))
}
# also determine if it is perPFT
is.perPFT <- FALSE
if(length(vars.present) > 3 || length(dims.present) > 3) {
if("vegtype" %in% vars.present || "vegtype" %in% dims.present){
is.perPFT <- TRUE
this.vegtype <- ncvar_get(this.nc,"vegtype",verbose=verbose)
#if(length(this.vegtype) == 9) this.pfts <- c("NDL-EVG", "NDL-DCD", "BDL-EVG", "BDL-DCD-COLD", "BDL-DCD-DRY", "C3-CROP", "C4-CROP", "C3-GRASS", "C4-GRASS")
#else if(length(this.vegtype) == 10) this.pfts <- c("NDL-EVG", "NDL-DCD", "BDL-EVG", "BDL-DCD-COLD", "BDL-DCD-DRY", "C3-CROP", "C4-CROP", "C3-GRASS", "C4-GRASS", "Bare")
}
}
first.year.output <- all.years[1]
last.year.output <- all.years[length(all.years)]
# choose range of years (if specifed, else take the whole range)
if(is.null(first.year) || length(first.year) == 0) first.year <- first.year.output
if(is.null(last.year) || length(last.year) == 0) last.year <- last.year.output
# What we do now depend on how we want the output to be
full.dt <- data.table()
# get each year and make it into a data.table
if(is.monthly && is.perPFT) {
print("per month and per PFT")
t1 <- Sys.time()
for(counter in first.year:last.year) {
year.counter <- counter - first.year.output
# diagnostics
#this.slice <- ncvar_get(this.nc, start = c(1,1,1,1), count = c(-1,-1,-1, -1))
#print(dim(this.slice))
this.slice <- ncvar_get(this.nc, start = c(1,1,1,(year.counter*12)+1), count = c(-1,-1,-1, 12))
dimnames(this.slice) <- list(this.lon, this.lat, this.pfts, 1:12)
# melt to a data.table, via data.frame
this.slice.dt <- as.data.table(melt(this.slice))
# set names, chuck out the water and set NAs to 0
setnames(this.slice.dt, c("Lon", "Lat", "PFT", "Month", quantity@id))
# use land mask
this.slice.dt <- selectGridcells(this.slice.dt, this.landmask.dt)
# set any remaining NAs to zero
for (j in seq_len(ncol(this.slice.dt))[4:ncol(this.slice.dt)]) set(this.slice.dt,which(is.na(this.slice.dt[[j]])),j,0)
# add Year dcast back to a column for every PFT
this.slice.dt[, Year := counter]
new.order <- c("Lon", "Lat", "Year", "Month", quantity@id)
setcolorder(this.slice.dt, new.order)
this.slice.dt <- dcast(this.slice.dt, Lon + Lat + Year + Month ~ PFT, value.var = quantity@id, fill = 0)
# add it on to the full data.table
full.dt <- rbind(full.dt, this.slice.dt)
rm(this.slice, this.slice.dt)
}
t2 <- Sys.time()
print(t2-t1)
} # END ANNUAL PER-PFT CASE
# get each year and make it into a data.table
else if(is.perPFT) {
print("per PFT")
t1 <- Sys.time()
year.start.index <- first.year - first.year.output +1
count.index <- last.year - first.year +1
# diagnostics
# this.slice <- ncvar_get(this.nc, start = c(1,1,1,1), count = c(-1,-1,-1, -1))
# print(dim(this.slice))
this.slice <- ncvar_get(this.nc, start = c(1,1,1,year.start.index), count = c(-1,-1,-1,count.index))
dimnames(this.slice) <- list(this.lon, this.lat, this.pfts, first.year:last.year)
# melt to a data.table, via data.frame
this.slice.dt <- as.data.table(melt(this.slice))
# set names, chuck out the water and set NAs to 0
setnames(this.slice.dt, c("Lon", "Lat", "PFT", "Year", quantity@id))
this.slice.dt <- selectGridcells(this.slice.dt, this.landmask.dt)
for (j in seq_len(ncol(this.slice.dt))[5:ncol(this.slice.dt)]) set(this.slice.dt,which(is.na(this.slice.dt[[j]])),j,0)
# dcast back to a column for every PFT
this.slice.dt <- dcast(this.slice.dt, Lon + Lat + Year ~ PFT, value.var = quantity@id)
# add it on to the full data.table
full.dt <- rbind(full.dt, this.slice.dt)
rm(this.slice, this.slice.dt)
t2 <- Sys.time()
print(t2-t1)
} # END ANNUAL PER-PFT CASE
else if(is.monthly) {
print("per month")
# get each year and make it into a data.table
t1 <- Sys.time()
for(counter in first.year:last.year) {
# get the slice
year.counter <- counter - first.year.output
# diagnostics
#this.slice <- ncvar_get(this.nc, start = c(1,1,1,1), count = c(-1,-1,-1, -1))
#print(dim(this.slice))
#stop()
this.slice <- ncvar_get(this.nc, start = c(1,1,(year.counter*12)+1), count = c(-1,-1,12))
dimnames(this.slice) <- list(this.lon, this.lat, paste(1:12))
# if necessary multiply data by a constant
# this.slice <- (1/0.00001157407407) * this.slice
# melt to a data.table, via data.frame
this.slice.dt <- as.data.table(melt(this.slice))
# set names, chuck out the water and set NAs to 0
setnames(this.slice.dt, c("Lon", "Lat", "Month", quantity@id))
#setcolorder(this.slice.dt, c("Lon", "Lat","Month", quantity@id))
this.slice.dt <- selectGridcells(this.slice.dt, this.landmask.dt)
for (j in seq_len(ncol(this.slice.dt))[3:ncol(this.slice.dt)]) set(this.slice.dt,which(is.na(this.slice.dt[[j]])),j,0)
this.slice.dt <- na.omit(this.slice.dt)
# add a column for "Year"
this.slice.dt[, Year := counter]
# reorder columns so that "Year" follows after "Lon" and "Lat"
new.order <- c("Lon", "Lat", "Year", "Month", quantity@id)
setcolorder(this.slice.dt, new.order)
# add it on to the full data.table
full.dt <- rbind(full.dt, this.slice.dt)
rm(this.slice, this.slice.dt)
}
t2 <- Sys.time()
print(t2-t1)
}
# get each year and make it into a data.table
else {
print("simple annual")
t1 <- Sys.time()
# diagnostics
#this.slice <- ncvar_get(this.nc, start = c(1,1,1), count = c(-1,-1,-1))
#print(dim(this.slice))
year.start.index <- first.year - first.year.output +1
count.index <- last.year - first.year +1
this.slice <- ncvar_get(this.nc, start = c(1,1,year.start.index), count = c(-1, -1, count.index))
dimnames(this.slice) <- list(this.lon, this.lat, first.year:last.year)
# melt to a data.table, via data.frame
this.slice.dt <- as.data.table(melt(this.slice))
# set names, chuck out the water and set NAs to 0
setnames(this.slice.dt, c("Lon", "Lat", "Year", quantity@id))
this.slice.dt <- selectGridcells(this.slice.dt, this.landmask.dt)
for (j in seq_len(ncol(this.slice.dt))[4:ncol(this.slice.dt)]) set(this.slice.dt,which(is.na(this.slice.dt[[j]])),j,0)
# add it on to the full data.table
full.dt <- rbind(full.dt, this.slice.dt)
rm(this.slice, this.slice.dt)
t2 <- Sys.time()
print(t2-t1)
} # END ANNUAL PER-PFT CASE
# Tidy stuff and unit hacks
full.dt <- stats::na.omit(full.dt)
# convert burntArea to percent
if(quantity@id == "burntArea") {
layer.names <- names(full.dt)
layer.names <- layer.names[!layer.names %in% getDimInfo(full.dt)]
# full.dt[, (layer.names) := .SD * 100, .SDcols = layer.names]
}
# if london.centre is requested, make sure all negative longitudes are shifted to positive
if(run@london.centre){ full.dt[, Lon := vapply(full.dt[,Lon], 1, FUN = LondonCentre)] }
all.years <- sort(unique(full.dt[["Year"]]))
if(is.monthly) subannual <- "Month"
else subannual <- "Annual"
sta.info = new("STAInfo",
first.year = min(all.years),
last.year = max(all.years),
subannual.resolution = subannual,
subannual.original = subannual,
spatial.extent = extent(full.dt),
spatial.extent.id = "Full")
# close the file
nc_close(this.nc)
nc_close(grid.nc)
gc()
this.Field <- new("Field",
id = makeFieldID(source = run, var.string = quantity@id, sta.info = sta.info),
source = run,
quant = quantity,
data = full.dt,
sta.info)
return(this.Field)
}
#' List all quantities available for a FireMIP Source
#'
#' Simply lists all LPJ-GUESS output variables (stored as .out files) available in a directory.
#' Also ignores some common red herrings like "guess.out" and "*.out"
#'
#' @param source A path to a directory on the file system containing some .out files
#' @return A list of all the .out files present, with the ".out" removed.
#'
#' @keywords internal
#' @author Matthew Forrest \email{matthew.forrest@@senckenberg.de}
availableQuantities_JSBACH_FireMIP <- function(source, names){
# First get the list of *.out files present
files.present <- list.files(source@dir, "*.nc")
quantities.present <- list()
for(file in files.present) {
# remove the.nc
var.str <- gsub(".nc", "", file)
split.thing <- unlist(strsplit(var.str, "_"))
var.str <- split.thing[length(split.thing)]
if(var.str == "Frst") var.str <- NULL # not standard
else if(var.str == "depth") var.str <- "snow_depth"
else if(var.str == "dlai") var.str <- NULL # daily LAI not supported
else if(var.str == "v2") var.str <- NULL # nbp_v2?
else if(var.str == "tsl") var.str <- NULL # ignore temperature of soil
if(!is.null(var.str)) {
if(names) quantities.present <- append(quantities.present, var.str)
else quantities.present <- append(quantities.present, lookupQuantity(var.str, source@format@quantities))
}
}
return(quantities.present)
}
########################################################
########### FireMIP Coarse PFTS ########################
########################################################
#' @format An S4 class object with the slots as defined below.
#' @keywords datasets
JSBACH_FireMIP.PFTs <- list(
new("Layer",
id = "ExtE",
name = "Extratropical Evergreen Tree",
colour = "darkblue",
properties = list(type = "PFT",
growth.form = "Tree",
leaf.form = "Needleleaved",
phenology = "Evergreen",
climate.zone = "Extratropical",
shade.tolerance = "no")
),
new("Layer",
id = "ExtD",
name = "Extratropical Deciduous Tree",
colour = "cyan",
properties = list(type = "PFT",
growth.form = "Tree",
leaf.form = "Broadleaved",
phenology = "Summergreen",
climate.zone = "NA",
shade.tolerance = "no")
),
new("Layer",
id = "TrE",
name = "Tropical Evergreen Tree",
colour = "darkgreen",
properties = list(type = "PFT",
growth.form = "Tree",
leaf.form = "Broadleaved",
phenology = "Evergreen",
climate.zone = "Tropical",
shade.tolerance = "no")
),
new("Layer",
id = "TrD",
name = "Tropical Deciduous Tree",
colour = "maroon",
properties = list(type = "PFT",
growth.form = "Tree",
leaf.form = "Broadleaved",
phenology = "Deciduous",
climate.zone = "NA",
shade.tolerance = "no")
),
# GRASSES
new("Layer",
id = "C3G",
name = "Boreal/Temperate Grass",
colour = "lightgoldenrod1",
properties = list(type = "PFT",
growth.form = "Grass",
leaf.form = "Broadleaved",
phenology = "GrassPhenology",
climate.zone = "NA",
shade.tolerance = "no")
),
new("Layer",
id = "C3G_pas",
name = "C3 Pasture Grass",
colour = "lightgoldenrod4",
properties = list(type = "PFT",
growth.form = "Grass",
leaf.form = "Broadleaved",
phenology = "GrassPhenology",
climate.zone = "NA",
shade.tolerance = "no")
),
new("Layer",
id = "C4G",
name = "Tropical Grass",
colour = "sienna2",
properties = list(type = "PFT",
growth.form = "Grass",
leaf.form = "Broadleaved",
phenology = "GrassPhenology",
climate.zone = "NA",
shade.tolerance = "no")
),
new("Layer",
id = "C4G_pas",
name = "C4 Pasture Grass",
colour = "sienna",
properties = list(type = "PFT",
growth.form = "Grass",
leaf.form = "Broadleaved",
phenology = "GrassPhenology",
climate.zone = "NA",
shade.tolerance = "no")
),
# SHRUBS
new("Layer",
id = "Rg_Shb",
name = "Raingreen Shrub",
colour = "darkred",
properties = list(type = "PFT",
growth.form = "Shrub",
leaf.form = "NA",
phenology = "Evergreen",
climate.zone = "NA",
shade.tolerance = "no")
),
new("Layer",
id = "De_Shb",
name = "Deciduous Shrub",
colour = "palevioletred1",
properties = list(type = "PFT",
growth.form = "Shrub",
leaf.form = "NA",
phenology = "Deciduous",
climate.zone = "NA",
shade.tolerance = "no")
),
# CROPS
new("Layer",
id = "Crop",
name = "Agricultural",
colour = "palegreen",
properties = list(type = "PFT",
growth.form = "Agricultural",
leaf.form = "NA",
phenology = "NA",
climate.zone = "NA",
shade.tolerance = "no")
)
)
####################################################
########### JSBACH_FireMIP FORMAT ########################
####################################################
#' JSBACH-FireMIP Format objects
#'
#' @description \code{JSBACH_FireMIP} - a Format for reading JSBACH FireMIP model output
#'
#' @format A \code{Quantity} object is an S4 class.
#' @keywords datasets
#' @importClassesFrom DGVMTools Quantity Source Format Field Layer Period STAInfo
#' @import DGVMTools
#' @include PFTs.R
#' @export
#'
JSBACH_FireMIP<- new("Format",
# UNIQUE ID
id = "JSBACH-FireMIP",
# FUNCTION TO LIST ALL QUANTIES AVAILABLE IN A RUN
availableQuantities = availableQuantities_JSBACH_FireMIP,
# FUNCTION TO READ A FIELD
getField = openFireMIPOutputFile_JSBACH,
# DEFAULT LAYERS
predefined.layers = JSBACH_FireMIP.PFTs,
# QUANTITIES THAT CAN BE PULLED DIRECTLY FROM LPJ-GUESS RUNS
quantities = FireMIP.quantities
)
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