rnz R NetCDF Zarr
rnz wraps the pizzarr and
RNetCDF package providing very similar set of functions to
the RNetCDF package. The intent is to allow access to
NetCDF and zarr in essentially the same way as is done with NetCDF such
that packages with a NetCDF backend can easily implement an equivalent
ZARR back end using base R.
This vignette shows the most basic operation of the package using a core demo dataset derived from: https://gdo-dcp.ucllnl.org/downscaled_cmip_projections/
A NetCDF and Zarr copy of the dataset are included.
# these files are in `z_demo()` as a file store
# and via "https://raw.githubusercontent.com/DOI-USGS/rnz/main/inst/extdata/bcsd.zarr/" as an http store.
gsub(normalizePath(dirname(rnz::z_demo())), "",
list.files(rnz::z_demo(), recursive = TRUE, all.files = TRUE),
fixed = TRUE)
#> [1] ".zattrs" ".zgroup" ".zmetadata"
#> [4] "latitude/.zarray" "latitude/.zattrs" "latitude/0"
#> [7] "longitude/.zarray" "longitude/.zattrs" "longitude/0"
#> [10] "pr/.zarray" "pr/.zattrs" "pr/0.0.0"
#> [13] "tas/.zarray" "tas/.zattrs" "tas/0.0.0"
#> [16] "time/.zarray" "time/.zattrs" "time/0"
(z <- rnz::open_nz(rnz::z_demo()))
#> <ZarrGroup>
#> Public:
#> clone: function (deep = FALSE)
#> contains_item: function (item)
#> create_dataset: function (name, data = NA, ...)
#> create_group: function (name, overwrite = FALSE)
#> get_attrs: function ()
#> get_chunk_store: function ()
#> get_item: function (item)
#> get_meta: function ()
#> get_name: function ()
#> get_path: function ()
#> get_read_only: function ()
#> get_store: function ()
#> get_synchronizer: function ()
#> initialize: function (store, path = NA, read_only = FALSE, chunk_store = NA,
#> Private:
#> attrs: Attributes, R6
#> cache_attrs: NULL
#> chunk_store: NA
#> create_dataset_nosync: function (name, data = NA, ...)
#> create_group_nosync: function (name, overwrite = FALSE)
#> item_path: function (item)
#> key_prefix:
#> meta: list
#> path:
#> read_only: TRUE
#> store: DirectoryStore, Store, R6
#> synchronizer: NULL
cat(c(capture.output(rnz::nzdump(rnz::z_demo()))[1:25], "..."), sep = "\n")
#> zarr {
#> dimensions:
#> latitude = 33 ;
#> longitude = 81 ;
#> time = 12 ;
#> variables:
#> <f4 latitude(latitude) ;
#> latitude:_CoordinateAxisType = Lat ;
#> latitude:axis = Y ;
#> latitude:bounds = latitude_bnds ;
#> latitude:long_name = Latitude ;
#> latitude:standard_name = latitude ;
#> latitude:units = degrees_north ;
#> <f4 longitude(longitude) ;
#> longitude:_CoordinateAxisType = Lon ;
#> longitude:axis = X ;
#> longitude:bounds = longitude_bnds ;
#> longitude:long_name = Longitude ;
#> longitude:standard_name = longitude ;
#> longitude:units = degrees_east ;
#> <f4 pr(time, latitude, longitude) ;
#> pr:coordinates = time latitude longitude ;
#> pr:long_name = monthly_sum_pr ;
#> pr:name = pr ;
#> pr:units = mm/m ;
#> ...
nc_file <- rnz::z_demo(format = "netcdf")
(nc <- RNetCDF::open.nc(nc_file))
#> [1] 65536
#> attr(,"handle_ptr")
#> <pointer: 0x0000013bd98cc5e0>
#> attr(,"class")
#> [1] "NetCDF"
cat(c(capture.output(RNetCDF::print.nc(nc))[1:25], "..."), sep = "\n")
#> netcdf classic {
#> dimensions:
#> latitude = 33 ;
#> longitude = 81 ;
#> time = UNLIMITED ; // (12 currently)
#> variables:
#> NC_FLOAT latitude(latitude) ;
#> NC_CHAR latitude:standard_name = "latitude" ;
#> NC_CHAR latitude:long_name = "Latitude" ;
#> NC_CHAR latitude:units = "degrees_north" ;
#> NC_CHAR latitude:axis = "Y" ;
#> NC_CHAR latitude:bounds = "latitude_bnds" ;
#> NC_CHAR latitude:_CoordinateAxisType = "Lat" ;
#> NC_FLOAT longitude(longitude) ;
#> NC_CHAR longitude:standard_name = "longitude" ;
#> NC_CHAR longitude:long_name = "Longitude" ;
#> NC_CHAR longitude:units = "degrees_east" ;
#> NC_CHAR longitude:axis = "X" ;
#> NC_CHAR longitude:bounds = "longitude_bnds" ;
#> NC_CHAR longitude:_CoordinateAxisType = "Lon" ;
#> NC_FLOAT pr(longitude, latitude, time) ;
#> NC_CHAR pr:long_name = "monthly_sum_pr" ;
#> NC_CHAR pr:units = "mm/m" ;
#> NC_FLOAT pr:_FillValue = 100000002004087734272 ;
#> NC_CHAR pr:name = "pr" ;
#> ...“Inquire” about elements of a Zarr store
We can do all the normal inquire stuff using 0-indexed ids or names.
Inquire about a store
rnz::inq_nz_source(nc)
#> $ndims
#> [1] 3
#>
#> $nvars
#> [1] 5
#>
#> $ngatts
#> [1] 30
#>
#> $unlimdimid
#> [1] 2
#>
#> $format
#> [1] "classic"
#>
#> $libvers
#> [1] "4.9.2 of Mar 7 2024 22:39:28 $"
rnz::inq_nz_source(z)
#> $ndims
#> [1] 3
#>
#> $nvars
#> [1] 5
#>
#> $ngatts
#> [1] 30
#>
#> $format
#> [1] "DirectoryStore"Inquire about a group
TODO: get rnz working with more than root groups?
rnz::inq_grp(nc)
#> $self
#> [1] 65536
#> attr(,"handle_ptr")
#> <pointer: 0x0000013bd98cc5e0>
#> attr(,"class")
#> [1] "NetCDF"
#>
#> $grps
#> list()
#>
#> $name
#> [1] "/"
#>
#> $fullname
#> [1] "/"
#>
#> $dimids
#> [1] 0 1 2
#>
#> $unlimids
#> [1] 2
#>
#> $varids
#> [1] 0 1 2 3 4
#>
#> $typeids
#> integer(0)
#>
#> $ngatts
#> [1] 30
rnz::inq_grp(z)
#> $grps
#> list()
#>
#> $name
#> [1] "/"
#>
#> $fullname
#> [1] "/"
#>
#> $dimids
#> [1] 0 1 2
#>
#> $varids
#> [1] 0 1 2 3 4
#>
#> $ngatts
#> [1] 30Inquire about a dimension
rnz::inq_dim(nc, 2)
#> $id
#> [1] 2
#>
#> $name
#> [1] "time"
#>
#> $length
#> [1] 12
#>
#> $unlim
#> [1] TRUE
rnz::inq_dim(z, 2)
#> $id
#> [1] 2
#>
#> $name
#> [1] "time"
#>
#> $length
#> [1] 12
rnz::inq_dim(nc, "time")
#> $id
#> [1] 2
#>
#> $name
#> [1] "time"
#>
#> $length
#> [1] 12
#>
#> $unlim
#> [1] TRUE
rnz::inq_dim(z, "time")
#> $id
#> [1] 2
#>
#> $name
#> [1] "time"
#>
#> $length
#> [1] 12Inquire about a variable
rnz::inq_var(nc, 4)
#> $id
#> [1] 4
#>
#> $name
#> [1] "time"
#>
#> $type
#> [1] "NC_DOUBLE"
#>
#> $ndims
#> [1] 1
#>
#> $dimids
#> [1] 2
#>
#> $natts
#> [1] 4
rnz::inq_var(z, 4)
#> $id
#> [1] 4
#>
#> $name
#> [1] "time"
#>
#> $type
#> [1] "<f8"
#>
#> $ndims
#> [1] 1
#>
#> $dimids
#> [1] 2
#>
#> $natts
#> [1] 4
rnz::inq_var(nc, "time")
#> $id
#> [1] 4
#>
#> $name
#> [1] "time"
#>
#> $type
#> [1] "NC_DOUBLE"
#>
#> $ndims
#> [1] 1
#>
#> $dimids
#> [1] 2
#>
#> $natts
#> [1] 4
rnz::inq_var(z, "time")
#> $id
#> [1] 4
#>
#> $name
#> [1] "time"
#>
#> $type
#> [1] "<f8"
#>
#> $ndims
#> [1] 1
#>
#> $dimids
#> [1] 2
#>
#> $natts
#> [1] 4Inquire about an attribute
rnz::inq_att(nc, "time", "units")
#> $id
#> [1] 1
#>
#> $name
#> [1] "units"
#>
#> $type
#> [1] "NC_CHAR"
#>
#> $length
#> [1] 30
rnz::inq_att(z, "time", "units")
#> $id
#> [1] 3
#>
#> $name
#> [1] "units"
#>
#> $type
#> [1] "character"
#>
#> $length
#> [1] 1
rnz::inq_att(nc, 4, 3)
#> $id
#> [1] 3
#>
#> $name
#> [1] "_CoordinateAxisType"
#>
#> $type
#> [1] "NC_CHAR"
#>
#> $length
#> [1] 4
rnz::inq_att(z, 4, 3)
#> $id
#> [1] 3
#>
#> $name
#> [1] "units"
#>
#> $type
#> [1] "character"
#>
#> $length
#> [1] 1Get a variable
rnz::get_var(nc, "time")
#> [1] 17927 17955 17986 18016 18047 18077 18108 18139 18169 18200 18230 18261
rnz::get_var(z, "time")
#> [1] 17927 17955 17986 18016 18047 18077 18108 18139 18169 18200 18230 18261
rnz::get_var(nc, var = "pr",
start = c(1,1,5), count = c(3,3,1))
#> , , 1
#>
#> [,1] [,2] [,3]
#> [1,] 69.27 69.59 69.51
#> [2,] 60.19 65.76 68.04
#> [3,] 49.68 55.63 55.45
rnz::get_var(z, var = "pr",
start = c(1,1,5), count = c(3,3,1))
#> , , 1
#>
#> [,1] [,2] [,3]
#> [1,] 134.90 137.65 149.01
#> [2,] 59.46 73.97 79.23
#> [3,] 101.86 101.06 96.12
# TODO: figure out why aperm #3
pr <- rnz::get_var(z, "pr") |>
aperm(c(3,2,1))
# TODO: figure out NA handling
pr[pr > 1000] <- NA
image(pr[,,1], col = hcl.colors(12, "PuBuGn", rev = TRUE),
useRaster = TRUE, axes = FALSE)
pr <- rnz::get_var(nc, "pr")
image(pr[,,1], col = hcl.colors(12, "PuBuGn", rev = TRUE),
useRaster = TRUE, axes = FALSE)