inst/R.par/pncdf4_open_class_object.R
In snoweye/pbdNCDF4: Interface to Parallel Unidata NetCDF4 Format Data Files
nc_open_class_object <- function(filename, rv, write, readunlim, verbose){
#-------------------------------------------------
# Now we make our elaborate ncdf class object
#-------------------------------------------------
nc <- list( filename=filename, writable=write, id=rv$id )
attr(nc,"class") <- "ncdf4"
#-------------------------------------------------------------
# See what format this file is. Possible (string) values are:
# 'NC_FORMAT_CLASSIC', 'NC_FORMAT_64BIT', 'NC_FORMAT_NETCDF4',
# and 'NC_FORMAT_NETCDF4_CLASSIC'
#-------------------------------------------------------------
nc$format = ncdf4_format( nc$id )
if( verbose )
print(paste("file", filename, "is format", nc$format ))
#-----------------------------------------------------
# Get all the groups in the file. Later we have to
# remember that dims and vars can live in groups other
# than the root group.
#-----------------------------------------------------
groups <- list()
groups[[1]] <- nc_get_grp_info( nc$id, "", nc$format ) # sets $name, $fqgn, $id, $nvars, $ndims, $natts, $ngrps, etc
if( nc$format == 'NC_FORMAT_NETCDF4' ) {
gg <- nc_groups_below( groups[[1]], nc$format )
for( i in nc4_loop(1,length(gg)))
groups[[1+i]] <- gg[[i]]
}
nc$groups <- groups
if( verbose ) {
print("Group info:")
for( ig in 1:length(groups)) {
print(paste("Group", ig, ": ",
"name=", groups[[ig]]$name,
"id=", groups[[ig]]$id,
"fqgn= \"", groups[[ig]]$fqgn, "\"",
"nvars=", groups[[ig]]$nvars,
"ndims=", groups[[ig]]$ndims,
"dimid="))
print( groups[[ig]]$dimid )
}
}
#---------------------------------------------------------------------------
# Get general information about the file. ndims and natts is the sum across
# all groups in the file. nvars is set below to only include non-dimvars,
# but otherwise is also the sum across all groups.
#---------------------------------------------------------------------------
nc$ndims <- 0
nc$natts <- 0
tot_nvars_inc_dimvars <- 0 # total number of vars INCLUDING dimvars; regular nc$nvars excludes dimvars
for( ig in 1:length(groups)) {
nc$ndims <- nc$ndims + nc$groups[[ig]]$ndims
nc$natts <- nc$natts + nc$groups[[ig]]$natts
tot_nvars_inc_dimvars <- tot_nvars_inc_dimvars + nc$groups[[ig]]$nvars
}
#--------------------------------------------
# Get all the dimensions that this file has.
# Get their values as well (for caching).
#--------------------------------------------
nc$dim <- list()
nc$unlimdimid <- -1 # Will be set to the FIRST encountered unlim dim ID
dimnames <- character()
global_dim_counter <- 0 # counter of dims across ALL groups
for( ig in 1:length(groups)) {
for( idim in nc4_loop(1,groups[[ig]]$ndims)) {
#-----------------------------------------------
# New in v4: dimids don't go from 0..ndims, they
# can be arbitrary
#-----------------------------------------------
dimid2use <- groups[[ig]]$dimid[idim]
if( is.na(dimid2use)) {
print(paste("Error, got a NA as a dimid2use ... group=",
groups[[ig]]$name," which has ndims=",
groups[[ig]]$ndims ))
print("Here are the dimids from the ncgroup object:")
print( groups[[ig]]$dimid )
stop("Error, cannot have NAs as dimids!")
}
if( verbose )
print(paste("nc_open: getting dim info for dim number",idim,"in group \"",
groups[[ig]]$name, "\" dim ID=", dimid2use))
#-----------------------------------------------------------
# As a general note, the function ncdim_inq does NOT return
# a full-fledged "ncdim" object. It returns only a subset of
# fields that directly correspond to a low-level, netCDF
# dimension in a file. We now fill in the rest of the fields
# to make it into a real ncdim object.
#-----------------------------------------------------------
d <- ncdim_inq(groups[[ig]]$id,dimid2use) # sets dim$name, $len, $unlim
#---------------------------------------------------------------------
# Routine ncdim_inq sets only the simple name, not the fully qualified
# dim name. Fix that now
#---------------------------------------------------------------------
if( groups[[ig]]$name != "" ) # this comparison is FALSE if this is the root group
d$name <- paste( groups[[ig]]$name, "/", d$name, sep='' ) # example: "model1/run1/longitude". NO leading slash!
d$group_index <- ig
d$group_id <- groups[[ig]]$id
d$id <- dimid2use # note: dim$id is the raw C-style integer ID to use WITHIN THE CORRECT GROUP
#------------------
# Handle the dimvar
#------------------
tt <- ncvar_id(groups[[ig]]$id, nc4_basename(d$name)) # note: dimvarid must be used with correct group. This is -1 if there is no dimvar
d$dimvarid = ncdf4_make_id( id=tt, group_index=ig, group_id=groups[[ig]]$id, list_index=-1, isdimvar=TRUE ) # NOTE: dimvars are not on the global var list, so list_index == -1
if( verbose )
print(paste(".....dim name is",d$name," id=", d$id, " len=",d$len," dimvarid=",d$dimvarid$id))
if( d$dimvarid$id == -1 ) { # No dimvar for this dim
d$vals <- 1:d$len
d$units <- ""
d$create_dimvar <- FALSE # in case this dim is passed to nc_create()
}
else {
# This dim has a dimvar -- get its properties
if( verbose )
print(paste("nc_open: getting dimvar info for dim ",d$name))
attv <- ncatt_get_inner( d$dimvarid$group_id, d$dimvarid$id, "units" )
if( attv$hasatt )
d$units <- attv$value
else
d$units <- ""
attv <- ncatt_get_inner( d$dimvarid$group_id, d$dimvarid$id, "calendar" )
if( attv$hasatt )
d$calendar <- attv$value
#else
# since nothing else is defined here, is.null(d$calendar) will return TRUE
if( d$unlim && (! readunlim)) # Is unlimited, don't read vals, too slow
d$vals <- rep(NA,d$len)
else # Otherwise, read vals
d$vals <- ncvar_get_inner( d$dimvarid$group_id, d$dimvarid$id, default_missval_ncdf4(),
verbose=verbose )
d$create_dimvar <- TRUE # in case this dim is passed to nc_create()
}
attr(d,"class") <- "ncdim4" # Is a complete ncdim object now
global_dim_counter <- global_dim_counter + 1 # global is for ALL groups
if( verbose )
{
print("------------------------------")
print("Here is new dim:")
print(paste("Global index=", global_dim_counter,
"name=",d$name,"len=",d$len,"unlim=",d$unlim,
"id=",d$id,"dimvarid=",d$dimvarid$id,"units=",d$units))
print("------------------------------")
}
if( d$unlim && (nc$unlimdimid == -1))
nc$unlimdimid = global_dim_counter # NOTE: technically, this is not an ID, it's an index into the nc$dim[[]] list
nc$dim[[global_dim_counter]] <- d # NOTE: nc$dim[[]] list is across ALL dims in file, regardless of group
dimnames[global_dim_counter] <- d$name # NOTE: in ncdf4, dim[[]] is indexed by FULLY QUALIFIED dim name
if( verbose )
print(paste(".......nc_open: done processing dim ",d$name))
}
}
attr(nc$dim,"names") <- dimnames
if(verbose) {
print("nc_open: setting dim$<names> to:")
print(dimnames)
}
#-------------------------------------------
# Get all the vars that this file has. Note
# that dimvars are NOT included in the count
# of vars!!
#-------------------------------------------
if( verbose )
print(paste("nc_open: getting var info. Number of vars (INCLUDING dimvars)=",tot_nvars_inc_dimvars))
nc$nvars <- 0 # NOTE this is a GLOBAL list, i.e., it includes vars from ALL groups
nc$var <- list()
varnames <- character()
have_warned_noncompliant <- FALSE
for( ig in 1:length(groups)) {
for( ivar in nc4_loop(1,groups[[ig]]$nvars)) {
#-----------------------------------------------------------------
# Note this is the 'simple' name, NOT the fully qualified var name
#-----------------------------------------------------------------
name <- ncvar_name( groups[[ig]]$id, ivar-1 ) # ivar-1 because ncvar_name takes input in C standard, which starts at 0
if( verbose ) print(paste("Working on group",ig,"(of",length(groups),"), var", ivar, "(of", groups[[ig]]$nvars,"), name=", name))
if( ncdim_id( groups[[ig]]$id, name ) == -1 ) { # Only process if NOT a dimvar
#--------------------------------------
# No dim with same name as this var, so
# this var must NOT be a dimvar.
#--------------------------------------
if( verbose )
print(paste("nc_open var loop: will process with group id=", groups[[ig]]$id, " varid=",ivar," var name=",name))
#---------------------------------------------------------------------------------------------------
# ncvar_inq sets the following:
# $id: an object of class 'ncid', with $id, $group_id, $group_index(==-1), and list_index(==-1)
# $name
# $ndims
# $natts
# $size
# $dimids: raw integer C-style (0-based counting) dimids but in R order
# $prec: one of "short', "int", "float", "double", "byte"
# $units: units string, or ""
# $longname: longname attribute, or ""
#---------------------------------------------------------------------------------------------------
v <- ncvar_inq( groups[[ig]]$id, ivar-1 ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
attr(v,"class") <- "ncvar4"
nc$nvars <- nc$nvars + 1
v$group_index = ig
v$id$list_index = nc$nvars
#--------------------------------------------------------------------------------
# Routine ncvar_inq sets the var's name to the SIMPLE (not-fully qualified) name.
# Fix that now.
#--------------------------------------------------------------------------------
if( groups[[ig]]$name != "" ) # this comparison is FALSE if this is the root group
v$name <- paste( groups[[ig]]$name, "/", v$name, sep='' ) # example: "model1/run1/Temperature". NO leading slash!
#---------------------------------------------------
# Get netcdf-4 specific information for the variable
#---------------------------------------------------
if( nc$format == 'NC_FORMAT_NETCDF4' ) {
#-----------------------
# Inquire about chunking
#-----------------------
chunkrv = ncvar_inq_chunking( groups[[ig]]$id, ivar-1, v$ndims ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
v$chunksizes = chunkrv$chunksizes
v$storage = chunkrv$storage # 1 for NC_CONTIGUOUS and 2 for NC_CHUNKED
#--------------------------
# Inquire about compression
#--------------------------
comprv = ncvar_inq_deflate( groups[[ig]]$id, ivar-1 ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
v$shuffle = comprv$shuffle
if( comprv$deflate == 0 )
v$compression = NA
else
v$compression = as.integer( comprv$deflate_level )
}
else
{
v$chunksizes = NA
v$storage = 1 # 1 for NC_CONTIGUOUS and 2 for NC_CHUNKED
v$shuffle = FALSE
v$compression = NA
}
#-----------------------------------------------------------------------------------
# Get this var's dims. Special netcdf-4 note: it seems that the way the netcdf-4
# library works is that variables are numbered starting at 0 for each group, but
# that dims are numbered consecutively across all groups. I guess this is mandated
# by the way that a var's dims can be in either the var's group or ANY PARENT GROUP,
# which implies that dimids cannot ever be repeated in a file, even if the file has
# multiple groups.
#-----------------------------------------------------------------------------------
v$dims <- list()
varunlim <- FALSE
if( v$ndims > 0 ) {
for( j in 1:v$ndims ) {
dimid2find = v$dimids[j]
matchidx = -1
for( iidim in 1:nc$ndims ) {
if( nc$dim[[iidim]]$id == dimid2find ) {
matchidx = iidim
break
}
}
if( matchidx == -1 )
stop(paste("internal error, did not find dim with id=",dimid2find,"in dim list!"))
v$dim[[j]] = nc$dim[[matchidx]]
if( v$dim[[j]]$unlim )
varunlim <- TRUE
v$varsize <- append(v$varsize, v$dim[[j]]$len)
}
}
v$unlim <- varunlim
#------------------------------------------------------------
# Fix for classic files that are unlimited -- they are stored
# in chunked format, as far as I know
#------------------------------------------------------------
if( (nc$format != 'NC_FORMAT_NETCDF4') && varunlim)
v$storage = 2 # 1 for NC_CONTIGUOUS and 2 for NC_CHUNKED
#----------------------------------------
# Get this var's missing value, or set to
# a default value if it does not have one
#----------------------------------------
found_mv <- FALSE
v$make_missing_value <- FALSE
mv <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "missing_value" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( mv$hasatt ) {
found_mv <- TRUE
v$missval <- mv$value
v$make_missing_value <- TRUE
}
else
{
mv <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "_FillValue" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( mv$hasatt ) {
found_mv <- TRUE
v$missval <- mv$value
v$make_missing_value <- TRUE
}
}
if( ! found_mv ) {
if( (v$prec=="float") || (v$prec=="double"))
v$missval <- default_missval_ncdf4()
else
v$missval <- NA
}
#--------------------------------------------
# Special check for noncompliant netCDF files
#--------------------------------------------
if( (v$prec=="float") || (v$prec=="double")) {
if( storage.mode(v$missval) == "character" ) {
v$missval <- as.double( v$missval )
if(! have_warned_noncompliant ) {
print(paste("WARNING file",filename,"is not compliant netCDF; variable",name," is numeric but has a character-type missing value! This is an error! Compensating, but you should fix the file!"))
have_warned_noncompliant <- TRUE
}
}
}
#-------------------------------------------
# Get add_offset and scale_factor attributes
#-------------------------------------------
ao <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "add_offset" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( ao$hasatt ) {
v$hasAddOffset <- TRUE
v$addOffset <- ao$value
}
else
v$hasAddOffset <- FALSE
sf <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "scale_factor" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( sf$hasatt ) {
v$hasScaleFact <- TRUE
v$scaleFact <- sf$value
}
else
v$hasScaleFact <- FALSE
nc$var[[nc$nvars]] <- v
varnames <- append(varnames,v$name) # NOTE: fully qualified var name, not simple name
if( verbose ) {
print("-----------------------")
print("Here is new var:")
print(paste("name=",v$name," group_id=",v$id$group_id, " id=",v$id$id," ndims=",v$ndims," prec=",v$prec))
print("size=")
print(v$size)
print("dimids=")
print(v$dimids)
}
} # end of "if NOT dimvar" clause
} # end of loop over vars in this group
} # end of loop over all groups
attr(nc$var,"names") <- varnames
if( verbose )
print(paste("nc_open: leaving for ncid=",nc$id))
return(nc)
} # End of nc_open_class_object().
snoweye/pbdNCDF4 documentation built on July 15, 2019, 2:01 p.m.
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nc_open_class_object <- function(filename, rv, write, readunlim, verbose){
#-------------------------------------------------
# Now we make our elaborate ncdf class object
#-------------------------------------------------
nc <- list( filename=filename, writable=write, id=rv$id )
attr(nc,"class") <- "ncdf4"
#-------------------------------------------------------------
# See what format this file is. Possible (string) values are:
# 'NC_FORMAT_CLASSIC', 'NC_FORMAT_64BIT', 'NC_FORMAT_NETCDF4',
# and 'NC_FORMAT_NETCDF4_CLASSIC'
#-------------------------------------------------------------
nc$format = ncdf4_format( nc$id )
if( verbose )
print(paste("file", filename, "is format", nc$format ))
#-----------------------------------------------------
# Get all the groups in the file. Later we have to
# remember that dims and vars can live in groups other
# than the root group.
#-----------------------------------------------------
groups <- list()
groups[[1]] <- nc_get_grp_info( nc$id, "", nc$format ) # sets $name, $fqgn, $id, $nvars, $ndims, $natts, $ngrps, etc
if( nc$format == 'NC_FORMAT_NETCDF4' ) {
gg <- nc_groups_below( groups[[1]], nc$format )
for( i in nc4_loop(1,length(gg)))
groups[[1+i]] <- gg[[i]]
}
nc$groups <- groups
if( verbose ) {
print("Group info:")
for( ig in 1:length(groups)) {
print(paste("Group", ig, ": ",
"name=", groups[[ig]]$name,
"id=", groups[[ig]]$id,
"fqgn= \"", groups[[ig]]$fqgn, "\"",
"nvars=", groups[[ig]]$nvars,
"ndims=", groups[[ig]]$ndims,
"dimid="))
print( groups[[ig]]$dimid )
}
}
#---------------------------------------------------------------------------
# Get general information about the file. ndims and natts is the sum across
# all groups in the file. nvars is set below to only include non-dimvars,
# but otherwise is also the sum across all groups.
#---------------------------------------------------------------------------
nc$ndims <- 0
nc$natts <- 0
tot_nvars_inc_dimvars <- 0 # total number of vars INCLUDING dimvars; regular nc$nvars excludes dimvars
for( ig in 1:length(groups)) {
nc$ndims <- nc$ndims + nc$groups[[ig]]$ndims
nc$natts <- nc$natts + nc$groups[[ig]]$natts
tot_nvars_inc_dimvars <- tot_nvars_inc_dimvars + nc$groups[[ig]]$nvars
}
#--------------------------------------------
# Get all the dimensions that this file has.
# Get their values as well (for caching).
#--------------------------------------------
nc$dim <- list()
nc$unlimdimid <- -1 # Will be set to the FIRST encountered unlim dim ID
dimnames <- character()
global_dim_counter <- 0 # counter of dims across ALL groups
for( ig in 1:length(groups)) {
for( idim in nc4_loop(1,groups[[ig]]$ndims)) {
#-----------------------------------------------
# New in v4: dimids don't go from 0..ndims, they
# can be arbitrary
#-----------------------------------------------
dimid2use <- groups[[ig]]$dimid[idim]
if( is.na(dimid2use)) {
print(paste("Error, got a NA as a dimid2use ... group=",
groups[[ig]]$name," which has ndims=",
groups[[ig]]$ndims ))
print("Here are the dimids from the ncgroup object:")
print( groups[[ig]]$dimid )
stop("Error, cannot have NAs as dimids!")
}
if( verbose )
print(paste("nc_open: getting dim info for dim number",idim,"in group \"",
groups[[ig]]$name, "\" dim ID=", dimid2use))
#-----------------------------------------------------------
# As a general note, the function ncdim_inq does NOT return
# a full-fledged "ncdim" object. It returns only a subset of
# fields that directly correspond to a low-level, netCDF
# dimension in a file. We now fill in the rest of the fields
# to make it into a real ncdim object.
#-----------------------------------------------------------
d <- ncdim_inq(groups[[ig]]$id,dimid2use) # sets dim$name, $len, $unlim
#---------------------------------------------------------------------
# Routine ncdim_inq sets only the simple name, not the fully qualified
# dim name. Fix that now
#---------------------------------------------------------------------
if( groups[[ig]]$name != "" ) # this comparison is FALSE if this is the root group
d$name <- paste( groups[[ig]]$name, "/", d$name, sep='' ) # example: "model1/run1/longitude". NO leading slash!
d$group_index <- ig
d$group_id <- groups[[ig]]$id
d$id <- dimid2use # note: dim$id is the raw C-style integer ID to use WITHIN THE CORRECT GROUP
#------------------
# Handle the dimvar
#------------------
tt <- ncvar_id(groups[[ig]]$id, nc4_basename(d$name)) # note: dimvarid must be used with correct group. This is -1 if there is no dimvar
d$dimvarid = ncdf4_make_id( id=tt, group_index=ig, group_id=groups[[ig]]$id, list_index=-1, isdimvar=TRUE ) # NOTE: dimvars are not on the global var list, so list_index == -1
if( verbose )
print(paste(".....dim name is",d$name," id=", d$id, " len=",d$len," dimvarid=",d$dimvarid$id))
if( d$dimvarid$id == -1 ) { # No dimvar for this dim
d$vals <- 1:d$len
d$units <- ""
d$create_dimvar <- FALSE # in case this dim is passed to nc_create()
}
else {
# This dim has a dimvar -- get its properties
if( verbose )
print(paste("nc_open: getting dimvar info for dim ",d$name))
attv <- ncatt_get_inner( d$dimvarid$group_id, d$dimvarid$id, "units" )
if( attv$hasatt )
d$units <- attv$value
else
d$units <- ""
attv <- ncatt_get_inner( d$dimvarid$group_id, d$dimvarid$id, "calendar" )
if( attv$hasatt )
d$calendar <- attv$value
#else
# since nothing else is defined here, is.null(d$calendar) will return TRUE
if( d$unlim && (! readunlim)) # Is unlimited, don't read vals, too slow
d$vals <- rep(NA,d$len)
else # Otherwise, read vals
d$vals <- ncvar_get_inner( d$dimvarid$group_id, d$dimvarid$id, default_missval_ncdf4(),
verbose=verbose )
d$create_dimvar <- TRUE # in case this dim is passed to nc_create()
}
attr(d,"class") <- "ncdim4" # Is a complete ncdim object now
global_dim_counter <- global_dim_counter + 1 # global is for ALL groups
if( verbose )
{
print("------------------------------")
print("Here is new dim:")
print(paste("Global index=", global_dim_counter,
"name=",d$name,"len=",d$len,"unlim=",d$unlim,
"id=",d$id,"dimvarid=",d$dimvarid$id,"units=",d$units))
print("------------------------------")
}
if( d$unlim && (nc$unlimdimid == -1))
nc$unlimdimid = global_dim_counter # NOTE: technically, this is not an ID, it's an index into the nc$dim[[]] list
nc$dim[[global_dim_counter]] <- d # NOTE: nc$dim[[]] list is across ALL dims in file, regardless of group
dimnames[global_dim_counter] <- d$name # NOTE: in ncdf4, dim[[]] is indexed by FULLY QUALIFIED dim name
if( verbose )
print(paste(".......nc_open: done processing dim ",d$name))
}
}
attr(nc$dim,"names") <- dimnames
if(verbose) {
print("nc_open: setting dim$<names> to:")
print(dimnames)
}
#-------------------------------------------
# Get all the vars that this file has. Note
# that dimvars are NOT included in the count
# of vars!!
#-------------------------------------------
if( verbose )
print(paste("nc_open: getting var info. Number of vars (INCLUDING dimvars)=",tot_nvars_inc_dimvars))
nc$nvars <- 0 # NOTE this is a GLOBAL list, i.e., it includes vars from ALL groups
nc$var <- list()
varnames <- character()
have_warned_noncompliant <- FALSE
for( ig in 1:length(groups)) {
for( ivar in nc4_loop(1,groups[[ig]]$nvars)) {
#-----------------------------------------------------------------
# Note this is the 'simple' name, NOT the fully qualified var name
#-----------------------------------------------------------------
name <- ncvar_name( groups[[ig]]$id, ivar-1 ) # ivar-1 because ncvar_name takes input in C standard, which starts at 0
if( verbose ) print(paste("Working on group",ig,"(of",length(groups),"), var", ivar, "(of", groups[[ig]]$nvars,"), name=", name))
if( ncdim_id( groups[[ig]]$id, name ) == -1 ) { # Only process if NOT a dimvar
#--------------------------------------
# No dim with same name as this var, so
# this var must NOT be a dimvar.
#--------------------------------------
if( verbose )
print(paste("nc_open var loop: will process with group id=", groups[[ig]]$id, " varid=",ivar," var name=",name))
#---------------------------------------------------------------------------------------------------
# ncvar_inq sets the following:
# $id: an object of class 'ncid', with $id, $group_id, $group_index(==-1), and list_index(==-1)
# $name
# $ndims
# $natts
# $size
# $dimids: raw integer C-style (0-based counting) dimids but in R order
# $prec: one of "short', "int", "float", "double", "byte"
# $units: units string, or ""
# $longname: longname attribute, or ""
#---------------------------------------------------------------------------------------------------
v <- ncvar_inq( groups[[ig]]$id, ivar-1 ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
attr(v,"class") <- "ncvar4"
nc$nvars <- nc$nvars + 1
v$group_index = ig
v$id$list_index = nc$nvars
#--------------------------------------------------------------------------------
# Routine ncvar_inq sets the var's name to the SIMPLE (not-fully qualified) name.
# Fix that now.
#--------------------------------------------------------------------------------
if( groups[[ig]]$name != "" ) # this comparison is FALSE if this is the root group
v$name <- paste( groups[[ig]]$name, "/", v$name, sep='' ) # example: "model1/run1/Temperature". NO leading slash!
#---------------------------------------------------
# Get netcdf-4 specific information for the variable
#---------------------------------------------------
if( nc$format == 'NC_FORMAT_NETCDF4' ) {
#-----------------------
# Inquire about chunking
#-----------------------
chunkrv = ncvar_inq_chunking( groups[[ig]]$id, ivar-1, v$ndims ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
v$chunksizes = chunkrv$chunksizes
v$storage = chunkrv$storage # 1 for NC_CONTIGUOUS and 2 for NC_CHUNKED
#--------------------------
# Inquire about compression
#--------------------------
comprv = ncvar_inq_deflate( groups[[ig]]$id, ivar-1 ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
v$shuffle = comprv$shuffle
if( comprv$deflate == 0 )
v$compression = NA
else
v$compression = as.integer( comprv$deflate_level )
}
else
{
v$chunksizes = NA
v$storage = 1 # 1 for NC_CONTIGUOUS and 2 for NC_CHUNKED
v$shuffle = FALSE
v$compression = NA
}
#-----------------------------------------------------------------------------------
# Get this var's dims. Special netcdf-4 note: it seems that the way the netcdf-4
# library works is that variables are numbered starting at 0 for each group, but
# that dims are numbered consecutively across all groups. I guess this is mandated
# by the way that a var's dims can be in either the var's group or ANY PARENT GROUP,
# which implies that dimids cannot ever be repeated in a file, even if the file has
# multiple groups.
#-----------------------------------------------------------------------------------
v$dims <- list()
varunlim <- FALSE
if( v$ndims > 0 ) {
for( j in 1:v$ndims ) {
dimid2find = v$dimids[j]
matchidx = -1
for( iidim in 1:nc$ndims ) {
if( nc$dim[[iidim]]$id == dimid2find ) {
matchidx = iidim
break
}
}
if( matchidx == -1 )
stop(paste("internal error, did not find dim with id=",dimid2find,"in dim list!"))
v$dim[[j]] = nc$dim[[matchidx]]
if( v$dim[[j]]$unlim )
varunlim <- TRUE
v$varsize <- append(v$varsize, v$dim[[j]]$len)
}
}
v$unlim <- varunlim
#------------------------------------------------------------
# Fix for classic files that are unlimited -- they are stored
# in chunked format, as far as I know
#------------------------------------------------------------
if( (nc$format != 'NC_FORMAT_NETCDF4') && varunlim)
v$storage = 2 # 1 for NC_CONTIGUOUS and 2 for NC_CHUNKED
#----------------------------------------
# Get this var's missing value, or set to
# a default value if it does not have one
#----------------------------------------
found_mv <- FALSE
v$make_missing_value <- FALSE
mv <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "missing_value" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( mv$hasatt ) {
found_mv <- TRUE
v$missval <- mv$value
v$make_missing_value <- TRUE
}
else
{
mv <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "_FillValue" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( mv$hasatt ) {
found_mv <- TRUE
v$missval <- mv$value
v$make_missing_value <- TRUE
}
}
if( ! found_mv ) {
if( (v$prec=="float") || (v$prec=="double"))
v$missval <- default_missval_ncdf4()
else
v$missval <- NA
}
#--------------------------------------------
# Special check for noncompliant netCDF files
#--------------------------------------------
if( (v$prec=="float") || (v$prec=="double")) {
if( storage.mode(v$missval) == "character" ) {
v$missval <- as.double( v$missval )
if(! have_warned_noncompliant ) {
print(paste("WARNING file",filename,"is not compliant netCDF; variable",name," is numeric but has a character-type missing value! This is an error! Compensating, but you should fix the file!"))
have_warned_noncompliant <- TRUE
}
}
}
#-------------------------------------------
# Get add_offset and scale_factor attributes
#-------------------------------------------
ao <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "add_offset" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( ao$hasatt ) {
v$hasAddOffset <- TRUE
v$addOffset <- ao$value
}
else
v$hasAddOffset <- FALSE
sf <- ncatt_get_inner( groups[[ig]]$id, ivar-1, "scale_factor" ) # ivar-1 because ncvar_inq takes input in C standard, which starts at 0
if( sf$hasatt ) {
v$hasScaleFact <- TRUE
v$scaleFact <- sf$value
}
else
v$hasScaleFact <- FALSE
nc$var[[nc$nvars]] <- v
varnames <- append(varnames,v$name) # NOTE: fully qualified var name, not simple name
if( verbose ) {
print("-----------------------")
print("Here is new var:")
print(paste("name=",v$name," group_id=",v$id$group_id, " id=",v$id$id," ndims=",v$ndims," prec=",v$prec))
print("size=")
print(v$size)
print("dimids=")
print(v$dimids)
}
} # end of "if NOT dimvar" clause
} # end of loop over vars in this group
} # end of loop over all groups
attr(nc$var,"names") <- varnames
if( verbose )
print(paste("nc_open: leaving for ncid=",nc$id))
return(nc)
} # End of nc_open_class_object().
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