Use FieldTimeSeries in tilted BBL example (with NetCDF output) (#5273)

Author: tomchor

examples/tilted_bottom_boundary_layer.jl

@@ -214,15 +214,9 @@ run!(simulation)
 
 using CairoMakie
 
-xb, yb, zb = nodes(B)
-xω, yω, zω = nodes(ωy)
-xv, yv, zv = nodes(V)
-
 # Read in the simulation's `output_writer` for the two-dimensional fields and then create an
 # animation showing the ``y``-component of vorticity.
 
-ds = NCDataset(simulation.output_writers[:fields].filepath, "r")
-
 fig = Figure(size = (800, 600))
 
 axis_kwargs = (xlabel = "Across-slope distance (m)",
@@ -234,21 +228,22 @@ ax_v = Axis(fig[3, 1]; title = "Along-slope velocity (v)", axis_kwargs...)
 
 n = Observable(1)
 
-ωy = @lift ds["ωy"][:, :, $n]
-B = @lift ds["B"][:, :, $n]
-ωlim = 0.015
-hm_ω = heatmap!(ax_ω, xω, zω, ωy, colorrange = (-ωlim, +ωlim), colormap = :balance)
-Colorbar(fig[2, 2], hm_ω; label = "s⁻¹")
-ct_b = contour!(ax_ω, xb, zb, B, levels=-1e-3:5e-5:1e-3, color=:black)
+ωy_timeseries = FieldTimeSeries(simulation.output_writers[:fields].filepath, "ωy")
+B_timeseries = FieldTimeSeries(simulation.output_writers[:fields].filepath, "B")
+V_timeseries = FieldTimeSeries(simulation.output_writers[:fields].filepath, "V")
 
-V = @lift ds["V"][:, :, $n]
-V_max = @lift maximum(abs, ds["V"][:, :, $n])
+ωy = @lift ωy_timeseries[$n]
+B = @lift B_timeseries[$n]
+hm_ω = heatmap!(ax_ω, ωy, colorrange = (-0.015, +0.015), colormap = :balance)
+Colorbar(fig[2, 2], hm_ω; label = "s⁻¹")
+ct_b = contour!(ax_ω, B, levels=-1e-3:5e-5:1e-3, color=:black)
 
-hm_v = heatmap!(ax_v, xv, zv, V, colorrange = (-V∞, +V∞), colormap = :balance)
+V = @lift V_timeseries[$n]
+hm_v = heatmap!(ax_v, V, colorrange = (-V∞, +V∞), colormap = :balance)
 Colorbar(fig[3, 2], hm_v; label = "m s⁻¹")
-ct_b = contour!(ax_v, xb, zb, B, levels=-1e-3:5e-5:1e-3, color=:black)
+ct_b = contour!(ax_v, B, levels=-1e-3:5e-5:1e-3, color=:black)
 
-times = collect(ds["time"])
+times = ωy_timeseries.times
 title = @lift "t = " * string(prettytime(times[$n]))
 fig[1, :] = Label(fig, title, fontsize=20, tellwidth=false)
 
@@ -265,7 +260,3 @@ end
 nothing #hide
 
 # ![](tilted_bottom_boundary_layer.mp4)
-
-# Don't forget to close the NetCDF file!
-
-close(ds)

ext/OceananigansNCDatasetsExt/dimensions.jl

@@ -258,15 +258,15 @@ function default_dimension_attributes(grid::RectilinearGrid, dim_name_generator)
     Δyᵃᶠᵃ_name = dim_name_generator("Δy", grid, nothing, f, nothing, Val(:y))
     Δyᵃᶜᵃ_name = dim_name_generator("Δy", grid, nothing, c, nothing, Val(:y))
 
-    xᶠᵃᵃ_attrs = Dict("long_name" => "Cell face locations in the x-direction.",   "units" => "m")
-    xᶜᵃᵃ_attrs = Dict("long_name" => "Cell center locations in the x-direction.", "units" => "m")
-    yᵃᶠᵃ_attrs = Dict("long_name" => "Cell face locations in the y-direction.",   "units" => "m")
-    yᵃᶜᵃ_attrs = Dict("long_name" => "Cell center locations in the y-direction.", "units" => "m")
-
-    Δxᶠᵃᵃ_attrs = Dict("long_name" => "Spacings between cell centers (located at the cell faces) in the x-direction.", "units" => "m")
-    Δxᶜᵃᵃ_attrs = Dict("long_name" => "Spacings between cell faces (located at the cell centers) in the x-direction.", "units" => "m")
-    Δyᵃᶠᵃ_attrs = Dict("long_name" => "Spacings between cell centers (located at cell faces) in the y-direction.", "units" => "m")
-    Δyᵃᶜᵃ_attrs = Dict("long_name" => "Spacings between cell faces (located at cell centers) in the y-direction.", "units" => "m")
+    xᶠᵃᵃ_attrs = Dict("long_name" => "Cell face locations in the x-direction.",   "units" => "m", "location" => "Face")
+    xᶜᵃᵃ_attrs = Dict("long_name" => "Cell center locations in the x-direction.", "units" => "m", "location" => "Center")
+    yᵃᶠᵃ_attrs = Dict("long_name" => "Cell face locations in the y-direction.",   "units" => "m", "location" => "Face")
+    yᵃᶜᵃ_attrs = Dict("long_name" => "Cell center locations in the y-direction.", "units" => "m", "location" => "Center")
+
+    Δxᶠᵃᵃ_attrs = Dict("long_name" => "Spacings between cell centers (located at the cell faces) in the x-direction.", "units" => "m", "location" => "Face")
+    Δxᶜᵃᵃ_attrs = Dict("long_name" => "Spacings between cell faces (located at the cell centers) in the x-direction.", "units" => "m", "location" => "Center")
+    Δyᵃᶠᵃ_attrs = Dict("long_name" => "Spacings between cell centers (located at cell faces) in the y-direction.",     "units" => "m", "location" => "Face")
+    Δyᵃᶜᵃ_attrs = Dict("long_name" => "Spacings between cell faces (located at cell centers) in the y-direction.",     "units" => "m", "location" => "Center")
 
     horizontal_dimension_attributes = Dict(xᶠᵃᵃ_name  => xᶠᵃᵃ_attrs,
                                            xᶜᵃᵃ_name  => xᶜᵃᵃ_attrs,

ext/OceananigansNCDatasetsExt/netcdf_writer.jl

@@ -28,12 +28,10 @@ function defVar(ds::AbstractDataset, field_name, fd::AbstractField;
     effective_dim_names = create_field_dimensions!(ds, fd, dimension_name_generator; time_dependent, with_halos, array_type, dimension_type)
 
     # Add location to attributes
-    loc = location(fd) |> convert_for_netcdf
-    loc_attrib = Dict("location" => loc)
     if :attrib ∈ keys(kwargs)
-        attrib = merge(loc_attrib, kwargs[:attrib])
+        attrib = add_location_attribute!(kwargs[:attrib], fd)
     else
-        attrib = loc_attrib
+        attrib = add_location_attribute!(Dict(), fd)
     end
 
     # Add indices to attributes
@@ -55,6 +53,12 @@ end
 
 defVar(ds::AbstractDataset, field_name::Union{AbstractString, Symbol}, data::Array{Bool}, dim_names; kwargs...) = defVar(ds, field_name, Int8.(data), dim_names; kwargs...)
 
+function add_location_attribute!(attrib, fd::AbstractField)
+    loc = location(fd) |> convert_for_netcdf
+    loc_attrib = Dict("location" => loc)
+    return merge(loc_attrib, attrib)
+end
+
 #####
 ##### Variable attributes
 #####
@@ -495,7 +499,6 @@ function write_output!(ow::NetCDFWriter, model::AbstractModel)
     update_file_splitting_schedule!(ow.file_splitting, ow.filepath)
 
     ow.dataset = open(ow)
-
     ds, verbose, filepath = ow.dataset, ow.verbose, ow.filepath
 
     time_index = length(ds["time"]) + 1

src/OutputWriters/netcdf_writer.jl

@@ -236,7 +236,7 @@ NetCDFWriter scheduled on TimeInterval(1 minute):
 ├── 2 outputs: (c, u)
 ├── array_type: Array{Float32}
 ├── file_splitting: NoFileSplitting
-└── file size: 32.6 KiB
+└── file size: 32.7 KiB
 ```
 
 ```jldoctest netcdf1
@@ -269,7 +269,7 @@ NetCDFWriter scheduled on TimeInterval(1 minute):
 ├── 2 outputs: (c, u) averaged on AveragedTimeInterval(window=20 seconds, stride=1, interval=1 minute)
 ├── array_type: Array{Float32}
 ├── file_splitting: NoFileSplitting
-└── file size: 33.8 KiB
+└── file size: 33.9 KiB
 ```
 
 `NetCDFWriter` also accepts output functions that write scalars and arrays to disk,
@@ -320,7 +320,7 @@ NetCDFWriter scheduled on IterationInterval(1):
 ├── 3 outputs: (profile, slice, scalar)
 ├── array_type: Array{Float32}
 ├── file_splitting: NoFileSplitting
-└── file size: 34.0 KiB
+└── file size: 34.1 KiB
 ```
 
 `NetCDFWriter` can also be configured for `outputs` that are interpolated or regridded