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Merged
gaelforget merged 3 commits into from
Dec 8, 2025
Merged

nemoarray as new concrete type of AbstractMeshArray #204

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9ce1089
extend methods to work w AbstractMeshArray instead of just gcmarray
gaelforget Dec 8, 2025
183e758
preliminary def of nemoarray struct
gaelforget Dec 8, 2025
80df15f
consolidate nemoarray, more AbstractMeshArray type annotations
gaelforget Dec 8, 2025
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36 changes: 18 additions & 18 deletions ext/MeshArraysMakieExt.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -46,15 +46,15 @@ end
##

"""
scatter(XC::MeshArray,YC::MeshArray;color=:black,colorrange=[],colorbar=true,title="",kwargs...)
scatter(XC::AbstractMeshArray,YC::AbstractMeshArray;color=:black,colorrange=[],colorbar=true,title="",kwargs...)

```
scatter(Γ.XC,Γ.YC,color=:black)
MS=log10.(Γ.RAC)*μ
scatter(Γ.XC,Γ.YC,color=MS)
```
"""
function scatter(XC::MeshArray,YC::MeshArray;
function scatter(XC::AbstractMeshArray,YC::AbstractMeshArray;
color=:black,colorrange=[],colorbar=true,title="",kwargs...)

if isa(color,MeshArray)
Expand All @@ -68,22 +68,22 @@ function scatter(XC::MeshArray,YC::MeshArray;

fig = Figure(size = (900,600), backgroundcolor = :grey95)
ax = Axis(fig[1,1],xlabel="longitude",ylabel="latitude",title=title)
scatter!(ax,XC::MeshArray,YC::MeshArray;
scatter!(ax,XC::AbstractMeshArray,YC::AbstractMeshArray;
color=color, colorrange=colorrange, colorbar=colorbar, kwargs...)

fig
end

"""
scatter!(ax,XC::MeshArray,YC::MeshArray;color=:black,colorrange=[],colormap=:viridis)
scatter!(ax,XC::AbstractMeshArray,YC::AbstractMeshArray;color=:black,colorrange=[],colormap=:viridis)

```
fig=heatmap(Γ.Depth,interpolation=λ)
scatter!(current_axis(),Γ.XC,Γ.YC,color=:red)
fig
```
"""
function scatter!(ax,XC::MeshArray,YC::MeshArray;
function scatter!(ax,XC::AbstractMeshArray,YC::AbstractMeshArray;
color=:black,colorrange=[],colorbar=true,colormap=:veridis,kwargs...)

if isa(color,MeshArray)&&isempty(colorrange)
Expand Down Expand Up @@ -111,7 +111,7 @@ function scatter!(ax,XC::MeshArray,YC::MeshArray;
end

"""
heatmap(MS::MeshArray; interpolation=nothing,globalmap=false,x=nothing,y=nothing,colorbar=true,title="",kwargs...)
heatmap(MS::AbstractMeshArray; interpolation=nothing,globalmap=false,x=nothing,y=nothing,colorbar=true,title="",kwargs...)

Represent a `MeshArray` as a `heatmap`, or several, depending on keyword parameter choices.

Expand All @@ -124,11 +124,11 @@ heatmap(MS,interpolation=λ,title="ocean depth") #same but w title
heatmap(MS,x=lon,y=lat) #only for simple domains; will show MS[1]
```
"""
heatmap(MS::MeshArray;interpolation=nothing,globalmap=false,x=nothing,y=nothing,colorbar=true,title="",kwargs...)=begin
heatmap(MS::AbstractMeshArray;interpolation=nothing,globalmap=false,x=nothing,y=nothing,colorbar=true,title="",kwargs...)=begin
if (!isnothing(interpolation))||globalmap||(!isnothing(x))
f=Figure()
ax=Axis(f[1,1],title=title)
hm1=heatmap!(ax,MS::MeshArray;
hm1=heatmap!(ax,MS::AbstractMeshArray;
interpolation=interpolation,globalmap=globalmap,x=x,y=y,
kwargs...)
colorbar ? Colorbar(f[1,2], hm1, height = Relative(0.65)) : nothing
Expand All @@ -138,7 +138,7 @@ heatmap(MS::MeshArray;interpolation=nothing,globalmap=false,x=nothing,y=nothing,
end
end

function heatmap!(ax::Axis,MS::MeshArray;interpolation=nothing,globalmap=false,x=nothing,y=nothing,kwargs...)
function heatmap!(ax::Axis,MS::AbstractMeshArray;interpolation=nothing,globalmap=false,x=nothing,y=nothing,kwargs...)
if !isnothing(interpolation)
heatmap_interpolation!(ax,MS,interpolation;kwargs...)
elseif globalmap
Expand All @@ -150,47 +150,47 @@ function heatmap!(ax::Axis,MS::MeshArray;interpolation=nothing,globalmap=false,x
end
end

function heatmap_globalmap!(ax,MS::MeshArray;kwargs...)
function heatmap_globalmap!(ax,MS::AbstractMeshArray;kwargs...)
γ=MS.grid
DD=γ.write(MS)
# !isempty(colorrange) ? cr=colorrange : cr=(nanmin(DD),nanmax(DD))
hm1=heatmap!(ax,DD;kwargs...)
end

function heatmap_globalmap(MS::MeshArray;title="",colorbar=true,kwargs...)
function heatmap_globalmap(MS::AbstractMeshArray;title="",colorbar=true,kwargs...)
fig = Figure(size = (900,900), backgroundcolor = :grey95)
ax = Axis(fig[1,1],xlabel="i index",ylabel="j index",title=title)
hm1=heatmap_globalmap!(ax,MS;kwargs...)
colorbar ? Colorbar(fig[1,2], hm1, height = Relative(0.65)) : nothing
fig
end

heatmap_xy!(ax,MS::MeshArray,x::Union{UnitRange,Array},y::Union{UnitRange,Array};kwargs...) = heatmap!(ax,x,y,MS[1];kwargs...)
#heatmap_xy!(ax,MS::MeshArray,x::Union{UnitRange,Array},y::Union{UnitRange,Array};kwargs...) = surface!(ax,x,y,0*x;color=MS[1],shading=NoShading, kwargs...)
heatmap_xy!(ax,MS::AbstractMeshArray,x::Union{UnitRange,Array},y::Union{UnitRange,Array};kwargs...) = heatmap!(ax,x,y,MS[1];kwargs...)
#heatmap_xy!(ax,MS::AbstractMeshArray,x::Union{UnitRange,Array},y::Union{UnitRange,Array};kwargs...) = surface!(ax,x,y,0*x;color=MS[1],shading=NoShading, kwargs...)

function heatmap_xy(MS::MeshArray,x::Union{UnitRange,Array},y::Union{UnitRange,Array};title="",colorbar=true,kwargs...)
function heatmap_xy(MS::AbstractMeshArray,x::Union{UnitRange,Array},y::Union{UnitRange,Array};title="",colorbar=true,kwargs...)
fig = Figure(size = (900,400), backgroundcolor = :grey95)
ax = Axis(fig[1,1],xlabel="longitude",ylabel="latitude",title=title)
hm1=heatmap_xy!(ax,MS,x,y;kwargs...)
colorbar ? Colorbar(fig[1,2], hm1, height = Relative(0.65)) : nothing
fig
end

function heatmap_interpolation!(ax,MS::MeshArray,λ::NamedTuple;kwargs...)
function heatmap_interpolation!(ax,MS::AbstractMeshArray,λ::NamedTuple;kwargs...)
DD=Interpolate(MS,λ.f,λ.i,λ.j,λ.w)
DD=reshape(DD,size(λ.lon))
hm1=heatmap!(ax,λ.lon[:,1],λ.lat[1,:],DD;kwargs...)
end

function heatmap_interpolation(MS::MeshArray,λ::NamedTuple;title="",colorbar=true,kwargs...)
function heatmap_interpolation(MS::AbstractMeshArray,λ::NamedTuple;title="",colorbar=true,kwargs...)
fig = Figure(size = (900,400), backgroundcolor = :grey95)
ax = Axis(fig[1,1],xlabel="longitude",ylabel="latitude",title=title)
hm1=heatmap_interpolation!(ax,MS,λ;kwargs...)
colorbar ? Colorbar(fig[1,2], hm1, height = Relative(0.65)) : nothing
fig
end

function heatmap_tiled(MS::MeshArray;title="",
function heatmap_tiled(MS::AbstractMeshArray;title="",
colorbar=true,colorrange=[],colormap=:viridis,kwargs...)
fig = Figure(size = (900,900), backgroundcolor = :grey95)
nf=length(MS.fSize)
Expand Down Expand Up @@ -717,7 +717,7 @@ function scatter!(pr_ax::PrAxis,lon,lat,kargs...; kwargs...)
scatter!(pr_ax.ax,x,y,kargs...; kwargs...)
end

plot(x::MeshArray; kwargs...) = begin
plot(x::AbstractMeshArray; kwargs...) = begin
if ndims(x) == 1
heatmap(x; kwargs...)
else
Expand Down
26 changes: 13 additions & 13 deletions src/Exchanges.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -5,27 +5,27 @@
## User Front Ends

"""
exchange(fld::MeshArray)
exchange(fld::AbstractMeshArray)
Exchange / transfer data between neighboring arrays. Other methods are
exchange(fld::MeshArray,N::Integer)
exchange(u::MeshArray,v::MeshArray)
exchange(u::MeshArray,v::MeshArray,N::Integer)
exchange(fld::AbstractMeshArray,N::Integer)
exchange(u::AbstractMeshArray,v::AbstractMeshArray)
exchange(u::AbstractMeshArray,v::AbstractMeshArray,N::Integer)
"""
function exchange(fld::MeshArray)
function exchange(fld::AbstractMeshArray)
MeshArray_wh(exch_T_N(fld,1),1)
end

function exchange(fld::MeshArray,N::Integer)
function exchange(fld::AbstractMeshArray,N::Integer)
MeshArray_wh(exch_T_N(fld,N),N)
end

function exchange(u::MeshArray,v::MeshArray)
function exchange(u::AbstractMeshArray,v::AbstractMeshArray)
MeshArray_wh.(exch_UV_N(u,v,1),1)
end

function exchange(u::MeshArray,v::MeshArray,N::Integer)
function exchange(u::AbstractMeshArray,v::AbstractMeshArray,N::Integer)
MeshArray_wh.(exch_UV_N(u,v,N),N)
end

Expand Down Expand Up @@ -89,7 +89,7 @@ end

## Grid-specific implementations: PeriodicDomain case

function exch_T_N_dpdo(fld::MeshArray,N::Integer)
function exch_T_N_dpdo(fld::AbstractMeshArray,N::Integer)

fillval=0.0

Expand Down Expand Up @@ -189,7 +189,7 @@ end

## Grid-specific implementations: PeriodicChannel case

function exch_T_N_ll(fld::MeshArray,N::Integer)
function exch_T_N_ll(fld::AbstractMeshArray,N::Integer)

fillval=0.0

Expand Down Expand Up @@ -253,7 +253,7 @@ end

#note: the "CubeSphere" implementation covers both cs and llc

function exch_T_N_cs(fld::MeshArray,N::Integer)
function exch_T_N_cs(fld::AbstractMeshArray,N::Integer)

fillval=0.0

Expand Down Expand Up @@ -301,7 +301,7 @@ end

##

function exch_UV_N_cs(fldU::MeshArray,fldV::MeshArray,N::Integer)
function exch_UV_N_cs(fldU::AbstractMeshArray,fldV::AbstractMeshArray,N::Integer)

fillval=0.0

Expand Down Expand Up @@ -355,7 +355,7 @@ end

##

function exch_UV_cs(fldU::MeshArray,fldV::MeshArray)
function exch_UV_cs(fldU::AbstractMeshArray,fldV::AbstractMeshArray)

fillval=0.0

Expand Down
4 changes: 2 additions & 2 deletions src/Integration.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ module Integration
using Distributed, SharedArrays, Glob
import MeshArrays: read_jld2, write_jld2
import MeshArrays: GridLoad, GridLoadVar, GridSpec
import MeshArrays: demo, MeshArray, gridmask
import MeshArrays: demo, AbstractMeshArray, MeshArray, gridmask

##

Expand Down Expand Up @@ -244,7 +244,7 @@ function streamlined_loop(mask::gridmask; files=String[], var=:THETA, rd=read)
Array(BA)
end

function one_comp(mask::gridmask, tmp::MeshArray)
function one_comp(mask::gridmask, tmp::AbstractMeshArray)
nh=length(mask.names)
nv=length(mask.depths)
BA=zeros(nh,nv)
Expand Down
14 changes: 7 additions & 7 deletions src/Interpolation.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ using NearestNeighbors
import NearestNeighbors: knn

"""
knn(xgrid,ygrid::MeshArray,x,y::Array{T,1},k::Int)
knn(xgrid,ygrid::AbstractMeshArray,x,y::Array{T,1},k::Int)

Find k nearest neighbors to each point in x,y on xgrid,ygrid

Expand All @@ -12,7 +12,7 @@ lon=collect(0.1:0.5:2.1); lat=collect(0.1:0.5:2.1);
(f,i,j,c)=knn(Γ.XC,Γ.YC,lon,lat)
```
"""
function knn(xgrid::MeshArray,ygrid::MeshArray,
function knn(xgrid::AbstractMeshArray,ygrid::AbstractMeshArray,
xvec::Array{T,1},yvec::Array{T,1},k=1::Int) where {T}

#ancillary variables
Expand Down Expand Up @@ -49,10 +49,10 @@ function knn(xgrid::MeshArray,ygrid::MeshArray,
return a_f[kk[idxs]],a_i[kk[idxs]],a_j[kk[idxs]],kk[idxs]
end

knn(xgrid::MeshArray,ygrid::MeshArray,lon::Number,lat::Number) = knn(xgrid::MeshArray,ygrid::MeshArray,[lon],[lat])
knn(xgrid::AbstractMeshArray,ygrid::AbstractMeshArray,lon::Number,lat::Number) = knn(xgrid::AbstractMeshArray,ygrid::AbstractMeshArray,[lon],[lat])

"""
Interpolate(z_in::MeshArray,f,i,j,w)
Interpolate(z_in::AbstractMeshArray,f,i,j,w)

```
using MeshArrays
Expand All @@ -69,7 +69,7 @@ using CairoMakie
heatmap(vec(lon[:,1]),vec(lat[1,:]),DD,colorrange=(0.,6000.))
```
"""
function Interpolate(z_in::MeshArray,f,i,j,w)
function Interpolate(z_in::AbstractMeshArray,f,i,j,w)
z_out=NaN*similar(f[:,1])
for jj=1:size(f,1)
if (!isnan(sum(w[jj,:])))&&(sum(f[jj,:].==0)==0)
Expand All @@ -82,7 +82,7 @@ function Interpolate(z_in::MeshArray,f,i,j,w)
end

"""
Interpolate(z_in::MeshArray,f,i,j,w)
Interpolate(z_in::AbstractMeshArray,f,i,j,w)

```
using MeshArrays
Expand All @@ -105,7 +105,7 @@ or
heatmap(Γ.Depth,interpolation=L,colorrange=(0.,6000.))
```
"""
function Interpolate(z_in::MeshArray,λ::NamedTuple)
function Interpolate(z_in::AbstractMeshArray,λ::NamedTuple)
z=Interpolate(z_in,λ.f,λ.i,λ.j,λ.w)
z=reshape(z,size(λ.lon))
return λ.lon[:,1],λ.lat[1,:],z
Expand Down
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