consolidate nemoarray, more AbstractMeshArray type annotations

Author: gaelforget

ext/MeshArraysMakieExt.jl

@@ -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)
@@ -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)
@@ -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. 
 
@@ -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
@@ -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
@@ -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)
@@ -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

src/Exchanges.jl

@@ -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
 
@@ -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
 
@@ -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
 
@@ -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
 
@@ -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
 
@@ -355,7 +355,7 @@ end
 
 ##
 
-function exch_UV_cs(fldU::MeshArray,fldV::MeshArray)
+function exch_UV_cs(fldU::AbstractMeshArray,fldV::AbstractMeshArray)
 
 fillval=0.0
 

src/Integration.jl

@@ -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
 
 ##
 
@@ -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)

src/Interpolation.jl

@@ -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
 
@@ -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
@@ -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
@@ -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)
@@ -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
@@ -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