Invoke mask_immersed_field! when converting args for Makie

docs/make.jl

@@ -219,6 +219,6 @@ if ci_build
     deploydocs(repo = "github.com/CliMA/OceananigansDocumentation.git",
                versions = ["stable" => "v^", "dev" => "dev", "v#.#.#"],
                forcepush = true,
-               push_preview = true,
+               push_preview = false,
                devbranch = "main")
 end

examples/internal_tide.jl

@@ -205,19 +205,11 @@ wmax = maximum(abs, w_t[end])
 times = u′_t.times
 nothing #hide
 
-# For visualization purposes, we mask the region below the bathymetry with NaNs.
-
-using Oceananigans.ImmersedBoundaries: mask_immersed_field!
-
-for φ_t in (u′_t, w_t, N²_t), n in 1:length(times)
-    mask_immersed_field!(φ_t[n], NaN)
-end
-
 # We retrieve each field's coordinates and convert from meters to kilometers.
 
-xu,  yu,  zu  = nodes(u′_t[1])
-xw,  yw,  zw  = nodes(w_t[1])
-xN², yN², zN² = nodes(N²_t[1])
+xu,  _, zu  = nodes(u′_t[1])
+xw,  _, zw  = nodes(w_t[1])
+xN², _, zN² = nodes(N²_t[1])
 
 xu  = xu  ./ 1e3
 xw  = xw  ./ 1e3
@@ -242,9 +234,9 @@ n = Observable(1)
 title = @lift @sprintf("t = %1.2f days = %1.2f T₂",
                        round(times[$n] / day, digits=2) , round(times[$n] / T₂, digits=2))
 
-u′ₙ = @lift interior(u′_t[$n], :, 1, :)
- wₙ = @lift interior( w_t[$n], :, 1, :)
-N²ₙ = @lift interior(N²_t[$n], :, 1, :)
+u′ₙ = @lift u′_t[$n]
+ wₙ = @lift  w_t[$n]
+N²ₙ = @lift N²_t[$n]
 
 axis_kwargs = (xlabel = "x [km]",
                ylabel = "z [km]",

ext/OceananigansMakieExt.jl

@@ -2,6 +2,7 @@ module OceananigansMakieExt
 
 using Oceananigans
 using Oceananigans.Architectures: on_architecture
+using Oceananigans.ImmersedBoundaries: mask_immersed_field!
 
 using MakieCore: AbstractPlot
 import MakieCore: convert_arguments, _create_plot
@@ -22,7 +23,20 @@ end
 convert_arguments(pl::Type{<:AbstractPlot}, f::Field) =
     convert_arguments(pl, convert_field_argument(f)...)
 
-function flattened_cpu_interior(f)
+"""
+    make_plottable_array(f)
+
+Convert a field `f` to an array that can be plotted with Makie by
+
+- masking immersed cells (for fields on immersed boundary
+grids) with NaNs;
+- dropping singleton dimensions, and
+- transferring data from GPU to CPU if necessary.
+"""
+function make_plottable_array(f)
+
+    mask_immersed_field!(f, NaN)
+
     Nx, Ny, Nz = size(f)
 
     ii = drop_singleton_indices(Nx)
@@ -37,8 +51,7 @@ end
 
 function convert_field_argument(f::Field)
 
-    # Drop singleton dimensions and convert to CPU if necessary
-    fi_cpu = flattened_cpu_interior(f)
+    fi_cpu = make_plottable_array(f)
 
     # Indices of the non-zero dimensions
     d1 = findfirst(n -> n > 1, size(f))
@@ -83,12 +96,12 @@ end
 #####
 
 function convert_arguments(pl::Type{<:AbstractPlot}, ξ1::AbstractArray, f::Field)
-    fi_cpu = flattened_cpu_interior(f)
+    fi_cpu = make_plottable_array(f)
     return convert_arguments(pl, ξ1, fi_cpu)
 end
 
 function convert_arguments(pl::Type{<:AbstractPlot}, ξ1::AbstractArray, ξ2::AbstractArray, f::Field)
-    fi_cpu = flattened_cpu_interior(f)
+    fi_cpu = make_plottable_array(f)
     return convert_arguments(pl, ξ1, ξ2, fi_cpu)
 end