NCD updates

experiments/AMIP/modular/user_io/ncep_visualizer.jl

@@ -87,16 +87,16 @@ function download_read_nc(data_source::NCEPMonthlyDataSource, https::String, nce
     local_file = joinpath(data_source.tmp_dir, ncep_vname * ".nc")
     Downloads.download(https, local_file)
     NCDataset(local_file) do ds
-        t_i = findall(x -> Dates.yearmonth(x) == Dates.yearmonth(data_source.month_date[1]), ds["time"][:]) # time index of month in file
-        d_i = length(size(ds[ncep_vname][:])) # index of time in the dimension list
-        lev = "level" in keys(ds) ? ds["level"][:] : [Float64(-999)]
-        data = dropdims(selectdim(ds[ncep_vname][:], d_i, t_i), dims = d_i)
+        t_i = findall(x -> Dates.yearmonth(x) == Dates.yearmonth(data_source.month_date[1]), Array(ds["time"])) # time index of month in file
+        d_i = length(size(Array(ds[ncep_vname]))) # index of time in the dimension list
+        lev = "level" in keys(ds) ? Array(ds["level"]) : [Float64(-999)]
+        data = dropdims(selectdim(Array(ds[ncep_vname]), d_i, t_i), dims = d_i)
         if length(size(data)) == 3
             data .= data[:, end:-1:1, end:-1:1]
         else
             data .= data[:, end:-1:1]
         end
-        coords = (; lon = ds["lon"][:], lat = ds["lat"][:][end:-1:1], lev = lev[end:-1:1])
+        coords = (; lon = Array(ds["lon"]), lat = Array(ds["lat"])[end:-1:1], lev = lev[end:-1:1])
         (Array(data), coords)
     end
 end

src/Regridder.jl

@@ -263,7 +263,7 @@ determined by the space type.
 """
 function get_coords(ds, ::Spaces.ExtrudedFiniteDifferenceSpace)
     data_dates = get_time(ds)
-    z = ds["z"][:]
+    z = Array(ds["z"])
     return (data_dates, z)
 end
 function get_coords(ds, ::Spaces.SpectralElementSpace2D)
@@ -278,9 +278,9 @@ Extracts the time information from a NetCDF file `ds`.
 """
 function get_time(ds)
     if "time" in ds
-        data_dates = Dates.DateTime.(ds["time"][:])
+        data_dates = Dates.DateTime.(Array(ds["time"]))
     elseif "date" in ds
-        data_dates = TimeManager.strdate_to_datetime.(string.(Int.(ds["date"][:])))
+        data_dates = TimeManager.strdate_to_datetime.(string.(Int.(Array(ds["date"]))))
     else
         @warn "No dates available in input data file"
         data_dates = [Dates.DateTime(0)]
@@ -585,10 +585,10 @@ Extract data and coordinates from `datafile_latlon`.
 """
 function read_remapped_field(name::Symbol, datafile_latlon::String, lev_name = "z")
     out = NCDataset(datafile_latlon, "r") do nc
-        lon = nc["lon"][:]
-        lat = nc["lat"][:]
-        lev = lev_name in keys(nc) ? nc[lev_name][:] : Float64(-999)
-        var = nc[name][:]
+        lon = Array(nc["lon"])
+        lat = Array(nc["lat"])
+        lev = lev_name in keys(nc) ? Array(nc[lev_name]) : Float64(-999)
+        var = Array(nc[name])
         coords = (; lon = lon, lat = lat, lev = lev)
 
         (var, coords)

test/TestHelper.jl

@@ -13,7 +13,7 @@ using NCDatasets
 export create_space, gen_ncdata
 
 """
-    create_space(FT; comms_ctx = ClimaComms.SingletonCommsContext(), 
+    create_space(FT; comms_ctx = ClimaComms.SingletonCommsContext(),
         R = FT(6371e3), ne = 4, polynomial_degree = 3, nz = 1)
 
 Initialize a space on a sphere with the given parameters.

test/regridder_tests.jl

@@ -294,7 +294,7 @@ for FT in (Float32, Float64)
             T_rll, _ = Regridder.cgll2latlonz(T_cgll)
 
             # check consistency across z-levels
-            @test T_rll[:, :, 1] == T_rll[:, :, 2]
+            @test Array(T_rll)[:, :, 1] == Array(T_rll)[:, :, 2]
 
             # check consistency of CGLL remapped data with original data
             @test all(isapprox.(extrema(data), extrema(parent(T_cgll)), atol = 1e-2))
@@ -304,7 +304,7 @@ for FT in (Float32, Float64)
 
             # visual inspection
             # Plots.plot(T_cgll) # using ClimaCorePlots
-            # Plots.contourf(T_rll[:,:,1])
+            # Plots.contourf(Array(T_rll)[:,1])
 
             # Delete testing directory and files
             rm(REGRID_DIR; recursive = true, force = true)