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updated attributes code to RNetCDF
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@aestears
aestears committed May 22, 2024
1 parent fbf0b03 commit 1e50a5d
Showing 1 changed file with 193 additions and 69 deletions.
262 changes: 193 additions & 69 deletions functions/netcdf_functions_HPC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1110,6 +1110,58 @@ var_defs <- var_names
)

var_defs <- c(var_defs, xy_attributes[["name"]][1], xy_attributes[["name"]][2])
} else {
# define x and y variables if gridded
# x var
RNetCDF::var.def.nc(
nc,
varname = xy_attributes[["name"]][1],
vartype = "NC_DOUBLE",
dimensions = "lon",
deflate = nc_deflate,
shuffle = nc_shuffle,
chunksizes = c( n_xvals)
)
# y var
RNetCDF::var.def.nc(
nc,
varname = xy_attributes[["name"]][2],
vartype = "NC_DOUBLE",
dimensions = "lat",
deflate = nc_deflate,
shuffle = nc_shuffle,
chunksizes = c(n_yvals)
)
if (has_Z_verticalAxis != "none") {

RNetCDF::var.def.nc(
nc,
varname = "vertical",
vartype = "NC_DOUBLE",
dimensions = c("vertical"),
deflate = nc_deflate,
shuffle = nc_shuffle,
chunksizes = c(n_vertical)
)


nc_dimvars <- c(nc_dimvars, "vertical_bnds")
}

if (has_T_timeAxis != "none") {
RNetCDF::var.def.nc(
nc,
varname = "time",
vartype = "NC_DOUBLE",
dimensions = c("time"),
deflate = nc_deflate,
shuffle = nc_shuffle,
chunksizes = if (time_unlim) c(1L) else c( n_time)
)


nc_dimvars <- c(nc_dimvars, varid_timebnds)
}
}


Expand Down Expand Up @@ -1251,110 +1303,174 @@ var_defs <- var_names
)
}

#AES stopped here
#------ Write attributes ------

#--- add standard_name attribute of x/y variables
if ("standard_name" %in% names(xy_attributes)) {
for (k in seq_len(2)) {
ncdf4::ncatt_put(
nc,
varid = xy_attributes[["name"]][k],
attname = "standard_name",
attval = xy_attributes[["standard_name"]][k]
RNetCDF::att.put.nc(
nc,
variable = xy_attributes[["name"]][k],
name = "standard_name",
value = xy_attributes[["standard_name"]][k],
type = "NC_CHAR"
)
}
}

#--- add dimension attributes
if (is_gridded) {
ncdf4::ncatt_put(nc, xy_attributes[["name"]][1], "axis", "X")
ncdf4::ncatt_put(nc, xy_attributes[["name"]][1], "bounds", bnds_name[1])
ncdf4::ncatt_put(nc, xy_attributes[["name"]][2], "axis", "Y")
ncdf4::ncatt_put(nc, xy_attributes[["name"]][2], "bounds", bnds_name[2])
RNetCDF::att.put.nc(
nc,
variable = xy_attributes[["name"]][1],
name = "axis",
value = "X",
type = "NC_CHAR"
)
RNetCDF::att.put.nc(
nc,
variable = xy_attributes[["name"]][1],
name = "bounds",
value = bnds_name[1],
type = "NC_CHAR"
)
RNetCDF::att.put.nc(
nc,
variable = xy_attributes[["name"]][2],
name = "axis",
value = "Y",
type = "NC_CHAR"
)
RNetCDF::att.put.nc(
nc,
variable = xy_attributes[["name"]][2],
name = "bounds",
value = bnds_name[2],
type = "NC_CHAR"
)
}

if (has_Z_verticalAxis != "none") {
ncdf4::ncatt_put(nc, "vertical", "axis", "Z")
ncdf4::ncatt_put(nc, "vertical", "bounds", "vertical_bnds")

RNetCDF::att.put.nc(
nc,
variable = "vertical",
name = "axis",
value = "Z",
type = "NC_CHAR"
)
RNetCDF::att.put.nc(
nc,
variable = "vertical",
name = "bounds",
value = "vertical_bnds",
type = "NC_CHAR"
)

for (natt in ns_att_vert) {
ncdf4::ncatt_put(
nc,
varid = "vertical",
attname = natt,
attval = vertical_attributes[[natt]]
RNetCDF::att.put.nc(
nc,
variable = "variable",
name = natt,
value = vertical_attributes[[natt]],
type = "NC_CHAR"
)
}
}

if (has_T_timeAxis != "none") {
ncdf4::ncatt_put(nc, "time", "axis", "T")
ncdf4::ncatt_put(nc, "time", att_timebnds, varid_timebnds)

RNetCDF::att.put.nc(
nc,
variable = "time",
name = "axis",
value = "T",
type = "NC_CHAR"
)
RNetCDF::att.put.nc(
nc,
variable = "time",
name = att_timebnds,
value = varid_timebnds,
type = "NC_CHAR"
)

for (natt in ns_att_time) {
ncdf4::ncatt_put(
nc,
varid = "time",
attname = natt,
attval = time_attributes[[natt]]
RNetCDF::att.put.nc(
nc,
variable = "time",
name = natt,
value = time_attributes[[natt]],
type = "NC_CHAR"
)
}
}


#--- add variable attributes
for (k in seq_len(n_vars)) {
for (natt in ns_att_vars) {
ncdf4::ncatt_put(
nc,
varid = var_names[k],
attname = natt,
attval = var_attributes[[natt]][k]
RNetCDF::att.put.nc(
nc,
variable = var_names[k],
name = natt,
value = var_attributes[[natt]][k],
type = "NC_CHAR"
)
}
}

#--- add coordinate system attributes
for (natt in ns_att_crs) {
ncdf4::ncatt_put(
nc,
varid = "crs",
attname = natt,
attval = crs_attributes[[natt]]
crs_types <- c("NC_CHAR", "NC_DOUBLE", "NC_FLOAT", "NC_FLOAT")
for (i in 1:length(ns_att_crs)) {
RNetCDF::att.put.nc(
nc,
variable = "crs",
name = ns_att_crs[i],
value = crs_attributes[[ns_att_crs[i]]],
type = crs_types[i]
)
}

ncdf4::ncatt_put(nc, "crs", attname = "crs_wkt", attval = crs_wkt$Wkt)

RNetCDF::att.put.nc(
nc,
variable = "crs",
name = "crs_wkt",
value = crs_wkt$Wkt,
type = "NC_CHAR")

#--- add global attributes
ncdf4::ncatt_put(nc, varid = 0, attname = "Conventions", attval = "CF-1.8")
RNetCDF::att.put.nc(
nc,
variable = "NC_GLOBAL",
name = "Conventions",
value = "CF-1.8",
type = "NC_CHAR"
)

tmp_version_netcdf <- try(
system2("nc-config", "--version", stdout = TRUE, stderr = TRUE),
silent = TRUE
)

ncdf4::ncatt_put(
nc,
varid = 0,
attname = "created_by",
attval = paste0(
RNetCDF::att.put.nc(
nc,
variable = "NC_GLOBAL",
name = "created_by",
value = paste0(
R.version[["version.string"]],
", R package ",
"ncdf4 v", getNamespaceVersion("ncdf4"),
"RNetCDF v", getNamespaceVersion("RNetCDF"),
if (!inherits(tmp_version_netcdf, "try-error")) {
paste0(", and ", tmp_version_netcdf)
}
)
),
type = "NC_CHAR"
)

ncdf4::ncatt_put(
nc,
varid = 0,
attname = "creation_date",
attval = format(Sys.time(), "%Y-%m-%d %H:%M:%S")
RNetCDF::att.put.nc(
nc,
variable = "NC_GLOBAL",
name = "create_date",
value = format(Sys.time(), "%Y-%m-%d %H:%M:%S"),
type = "NC_CHAR"
)

if (!missing(global_attributes)) {
Expand All @@ -1375,34 +1491,42 @@ var_defs <- var_names
}

for (natt in ns_att_glob) {
ncdf4::ncatt_put(
nc,
varid = 0,
attname = natt,
attval = global_attributes[[natt]]
RNetCDF::att.put.nc(
nc,
variable = "NC_GLOBAL",
name = natt,
value = global_attributes[[natt]],
type = "NC_CHAR"
)
}
}

if (has_T_timeAxis == "none") {
ncdf4::ncatt_put(nc, varid = 0, attname = "time_label", attval = "None")
ncdf4::ncatt_put(
nc,
varid = 0,
attname = "time_title",
attval = "No temporal dimensions ... fixed field"
RNetCDF::att.put.nc(
nc,
variable = "NC_GLOBAL",
name = "time_label",
value = "None",
type = "NC_CHAR"
)
RNetCDF::att.put.nc(
nc,
variable = "NC_GLOBAL",
name = "time_title",
value = "No temporal dimensions ... fixed field",
type = "NC_CHAR"
)
}




#------ The end --------------------------------------------------------------
if (verbose) {
message(
"The netCDF has ", nc$nvars, " variables and ", nc$ndim, " dimensions"
)
}
# if (verbose) {
# message(
# "The netCDF has ", nc$nvars, " variables and ", nc$ndim, " dimensions"
# )
# }

return(nc)
invisible(TRUE)
Expand Down

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