rename concrete array types

Project.toml

@@ -1,7 +1,7 @@
 name = "IndividualDisplacements"
 uuid = "b92f0c32-5b7e-11e9-1d7b-238b2da8b0e6"
 authors = ["gaelforget <[email protected]>"]
-version = "0.4.8"
+version = "0.5.0"
 
 [deps]
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"

examples/worldwide/ECCO_FlowFields.jl

@@ -90,7 +90,7 @@ function setup_FlowFields(k::Int,Γ::NamedTuple,func::Function,pth::String)
 end
 
 """
-    update_FlowFields!(𝑃::F_MeshArray2D,D::NamedTuple,t::Float64)
+    update_FlowFields!(𝑃::uvMeshArrays,D::NamedTuple,t::Float64)
 
 Update flow field arrays (in 𝑃), 𝑃.T, and ancillary variables (in D) 
 according to the chosen time `t` (in `seconds`). 
@@ -99,7 +99,7 @@ _Note: for now, it is assumed that (1) the time interval `dt` between
 consecutive records is diff(𝑃.T), (2) monthly climatologies are used 
 with a periodicity of 12 months, (3) vertical 𝑃.k is selected_
 """
-function update_FlowFields!(𝑃::F_MeshArray2D,D::NamedTuple,t::AbstractFloat)
+function update_FlowFields!(𝑃::uvMeshArrays,D::NamedTuple,t::AbstractFloat)
     dt=𝑃.T[2]-𝑃.T[1]
 
     m0=Int(floor((t+dt/2.0)/dt))
@@ -133,7 +133,7 @@ function update_FlowFields!(𝑃::F_MeshArray2D,D::NamedTuple,t::AbstractFloat)
 end
 
 """
-    update_FlowFields!(𝑃::F_MeshArray3D,D::NamedTuple,t::Float64)
+    update_FlowFields!(𝑃::uvwMeshArrays,D::NamedTuple,t::Float64)
 
 Update flow field arrays (in 𝑃), 𝑃.T, and ancillary variables (in D) 
 according to the chosen time `t` (in `seconds`). 
@@ -142,7 +142,7 @@ _Note: for now, it is assumed that (1) the time interval `dt` between
 consecutive records is diff(𝑃.T), (2) monthly climatologies are used 
 with a periodicity of 12 months, (3) vertical 𝑃.k is selected_
 """
-function update_FlowFields!(𝑃::F_MeshArray3D,D::NamedTuple,t::Float64)
+function update_FlowFields!(𝑃::uvwMeshArrays,D::NamedTuple,t::Float64)
     dt=𝑃.T[2]-𝑃.T[1]
 
     m0=Int(floor((t+dt/2.0)/dt))

examples/worldwide/OCCA_FlowFields.jl

@@ -125,7 +125,7 @@ custom🔴 = DataFrame(ID=Int[], fid=Int[], x=Float64[], y=Float64[],
    lon=Float64[], lat=Float64[], dlon=Float64[], dlat=Float64[], 
    year=Float64[], col=Symbol[])
 
-function custom🔧(sol,𝑃::F_MeshArray3D,D::NamedTuple;id=missing,T=missing)
+function custom🔧(sol,𝑃::uvwMeshArrays,D::NamedTuple;id=missing,T=missing)
    df=postprocess_MeshArray(sol,𝑃,D,id=id,T=T)
    add_lonlat!(df,D.XC,D.YC)
    df.dlon=0*df.lon

src/API.jl

@@ -16,10 +16,10 @@ Also by convention, velocity fields are expected to have been normalized to grid
 before sending them to one of the supported `FlowFields` constructors (using either `Array` or `MeshArray`):
 
 ```
-F_Array2D(u0,u1,v0,v1,T)
-F_Array3D(u0,u1,v0,v1,w0,w1,T)
-F_MeshArray2D(u0,u1,v0,v1,T,update_location!)
-F_MeshArray3D(u0,u1,v0,v1,w0,w1,T,update_location!)
+uvArrays(u0,u1,v0,v1,T)
+uvwArrays(u0,u1,v0,v1,w0,w1,T)
+uvMeshArrays(u0,u1,v0,v1,T,update_location!)
+uvwMeshArrays(u0,u1,v0,v1,w0,w1,T,update_location!)
 ```
 
 Using the `FlowFields` constructor which gets selected by the type of `u0` etc. For example :
@@ -34,7 +34,7 @@ as shown in the online documentation examples.
 """
 abstract type FlowFields end
 
-struct F_Array2D{Ty} <: FlowFields
+struct uvArrays{Ty} <: FlowFields
     u0::Array{Ty,2}
     u1::Array{Ty,2}
     v0::Array{Ty,2}
@@ -50,10 +50,10 @@ function FlowFields(u0::Array{Ty,2},u1::Array{Ty,2},
     tst=prod([(size(u0)==size(tmp)) for tmp in (u1,v0,v1)])
     !tst ? error("inconsistent array sizes") : nothing
     #call constructor
-    F_Array2D(u0,u1,v0,v1,T)
+    uvArrays(u0,u1,v0,v1,T)
 end
 
-struct F_Array3D{Ty} <: FlowFields
+struct uvwArrays{Ty} <: FlowFields
     u0::Array{Ty,3}
     u1::Array{Ty,3}
     v0::Array{Ty,3}
@@ -127,10 +127,10 @@ function FlowFields(u0::Array{Ty,3},u1::Array{Ty,3},v0::Array{Ty,3},v1::Array{Ty
     tst=tst*prod([(size(u0)==size(tmp).-(0,0,1)) for tmp in (w0,w1)])
     !tst ? error("inconsistent array sizes") : nothing
     #call constructor
-    F_Array3D(u0,u1,v0,v1,w0,w1,T)
+    uvwArrays(u0,u1,v0,v1,w0,w1,T)
 end
 
-struct F_MeshArray2D{Ty} <: FlowFields
+struct uvMeshArrays{Ty} <: FlowFields
     u0::AbstractMeshArray{Ty,1}
     u1::AbstractMeshArray{Ty,1}
     v0::AbstractMeshArray{Ty,1}
@@ -148,10 +148,10 @@ function FlowFields(u0::AbstractMeshArray{Ty,1},u1::AbstractMeshArray{Ty,1},
     tst=prod([(size(u0)==size(tmp))*(u0.fSize==tmp.fSize) for tmp in (u1,v0,v1)])
     !tst ? error("inconsistent array sizes") : nothing
     #call constructor
-    F_MeshArray2D(u0,u1,v0,v1,T,update_location!)
+    uvMeshArrays(u0,u1,v0,v1,T,update_location!)
 end
 
-struct F_MeshArray3D{Ty} <: FlowFields
+struct uvwMeshArrays{Ty} <: FlowFields
     u0::AbstractMeshArray{Ty,2}
     u1::AbstractMeshArray{Ty,2}
     v0::AbstractMeshArray{Ty,2}
@@ -173,7 +173,7 @@ function FlowFields(u0::AbstractMeshArray{Ty,2},u1::AbstractMeshArray{Ty,2},
     tst=tst*prod([(size(u0)==size(tmp).-(0,1))*(u0.fSize==tmp.fSize) for tmp in (w0,w1)])
     !tst ? error("inconsistent array sizes") : nothing
     #call constructor
-    F_MeshArray3D(u0,u1,v0,v1,w0,w1,T,update_location!)
+    uvwMeshArrays(u0,u1,v0,v1,w0,w1,T,update_location!)
 end
 
 """
@@ -191,7 +191,7 @@ function ensemble_solver(prob;solver=Tsit5(),reltol=1e-8,abstol=1e-8,safetycopy=
 end
 
 a=fill(0.0,1,1)
-default_flowfields = F_Array2D{Float64}(a,a,a,a,[0. 1.])
+default_flowfields = uvArrays{Float64}(a,a,a,a,[0. 1.])
 default_recorder = DataFrame(ID=Int[], x=Float64[], y=Float64[], t=Float64[])
 default_postproc = (x->x)
 
@@ -216,10 +216,10 @@ Unicode cheatsheet:
 
 Simple constructors that use `FlowFields` to choose adequate defaults:
 
-- Individuals(F::F_Array2D,x,y)
-- Individuals(F::F_Array3D,x,y,z)
-- Individuals(F::F_MeshArray2D,x,y,fid)
-- Individuals(F::F_MeshArray3D,x,y,z,fid)
+- Individuals(F::uvArrays,x,y)
+- Individuals(F::uvwArrays,x,y,z)
+- Individuals(F::uvMeshArrays,x,y,fid)
+- Individuals(F::uvwMeshArrays,x,y,z,fid)
 
 Further customization is achievable via keyword constructors:
 
@@ -266,7 +266,7 @@ function Individuals(NT::NamedTuple)
     Individuals{T,ndims(📌)}(📌=📌,🔴=🔴,🆔=🆔,🚄=🚄,∫=∫,🔧=🔧,P=P,D=D,M=M)    
 end
 
-function Individuals(F::F_Array2D,x,y, NT::NamedTuple = NamedTuple())
+function Individuals(F::uvArrays,x,y, NT::NamedTuple = NamedTuple())
     📌=permutedims([[x[i];y[i]] for i in eachindex(x)])
     if length(📌)==1
         📌=📌[1]
@@ -293,7 +293,7 @@ function Individuals(F::F_Array2D,x,y, NT::NamedTuple = NamedTuple())
     Individuals{T,ndims(📌)}(P=F,📌=📌,🔴=🔴,🆔=🆔,🚄=dxdt!,∫=∫,🔧=🔧,D=D)
 end
 
-function Individuals(F::F_Array3D,x,y,z, NT::NamedTuple = NamedTuple())
+function Individuals(F::uvwArrays,x,y,z, NT::NamedTuple = NamedTuple())
     📌=permutedims([[x[i];y[i];z[i]] for i in eachindex(x)])
     if length(📌)==1
         📌=📌[1]
@@ -306,7 +306,7 @@ function Individuals(F::F_Array3D,x,y,z, NT::NamedTuple = NamedTuple())
     🔴 = DataFrame(ID=Int[], x=Float64[], y=Float64[], z=Float64[], t=Float64[])
     haskey(NT,:🔴) ? 🔴=NT.🔴 : nothing
 
-    function 🔧(sol,F::F_Array3D,D::NamedTuple;id=missing,T=missing)
+    function 🔧(sol,F::uvwArrays,D::NamedTuple;id=missing,T=missing)
         df=postprocess_xy(sol,F,D,id=id,T=T)
         if isa(sol,EnsembleSolution)
             np=length(sol)
@@ -330,7 +330,7 @@ function Individuals(F::F_Array3D,x,y,z, NT::NamedTuple = NamedTuple())
     Individuals{T,ndims(📌)}(P=F,📌=📌,🔴=🔴,🆔=🆔,🚄=dxdt!,∫=∫,🔧=🔧,D=D)
 end
 
-function Individuals(F::F_MeshArray2D,x,y,fid, NT::NamedTuple = NamedTuple())
+function Individuals(F::uvMeshArrays,x,y,fid, NT::NamedTuple = NamedTuple())
     📌=permutedims([[x[i];y[i];fid[i]] for i in eachindex(x)])
     if length(📌)==1
         📌=📌[1]
@@ -357,7 +357,7 @@ function Individuals(F::F_MeshArray2D,x,y,fid, NT::NamedTuple = NamedTuple())
     Individuals{T,ndims(📌)}(P=F,📌=📌,🔴=🔴,🆔=🆔,🚄=dxdt!,∫=∫,🔧=🔧,D=D)
 end
 
-function Individuals(F::F_MeshArray3D,x,y,z,fid, NT::NamedTuple = NamedTuple())
+function Individuals(F::uvwMeshArrays,x,y,z,fid, NT::NamedTuple = NamedTuple())
     📌=permutedims([[x[i];y[i];z[i];fid[i]] for i in eachindex(x)])
     if length(📌)==1
         📌=📌[1]
@@ -370,7 +370,7 @@ function Individuals(F::F_MeshArray3D,x,y,z,fid, NT::NamedTuple = NamedTuple())
     🔴 = DataFrame(ID=Int[], x=Float64[], y=Float64[], z=Float64[], fid=Int64[], t=Float64[])
     haskey(NT,:🔴) ? 🔴=NT.🔴 : nothing
 
-    function 🔧(sol,F::F_MeshArray3D,D::NamedTuple;id=missing,T=missing)
+    function 🔧(sol,F::uvwMeshArrays,D::NamedTuple;id=missing,T=missing)
         df=postprocess_MeshArray(sol,F,D,id=id,T=T)
         if isa(sol,EnsembleSolution)
             np=length(sol)
@@ -417,7 +417,7 @@ function ∫!(I::Individuals,T::Tuple)
     if isa(sol,EnsembleSolution)
         np=length(sol)
         📌[:] = deepcopy([sol[i].u[end] for i in 1:np])
-        if isa(P,F_MeshArray3D)||isa(P,F_MeshArray2D)
+        if isa(P,uvwMeshArrays)||isa(P,uvMeshArrays)
             [update_location!(i,P) for i in I.📌]
         end
     else

src/IndividualDisplacements.jl

@@ -15,7 +15,7 @@ DataFrames.DataFrame(I::Individuals) = I.🔴
 
 export Individuals, ∫!, solve!, DataFrame, groupby
 export FlowFields, convert_to_FlowFields
-export F_Array3D, F_Array2D, F_MeshArray3D, F_MeshArray2D
+export uvwArrays, uvArrays, uvwMeshArrays, uvMeshArrays
 export dxdt!, dxy_dt_CyclicArray, dxy_dt_replay
 export postprocess_MeshArray, add_lonlat!, postprocess_xy, interp_to_xy
 export nearest_to_xy, randn_lonlat, interp_to_lonlat

src/compute.jl

@@ -12,7 +12,7 @@ fview(f::Array{Array{Float32,2},2},i::Int,j::Int) = view(f[i,j],:,:)
 fview(f::Array{Array{Float64,2},2},i::Int,j::Int) = view(f[i,j],:,:)
 
 """
-    dxdt!(du,u,p::F_MeshArray3D,tim)
+    dxdt!(du,u,p::uvwMeshArrays,tim)
 
 Interpolate velocity from gridded fields (3D; with halos) to position `u`
 (`x,y,z,fIndex`) to compute the derivative of position v time  `du_dt`.
@@ -34,7 +34,7 @@ prod(isapprox.(I.📌,ref,atol=1.0)) # hide
 true
 ```
 """
-function dxdt!(du::Array{T,1},u::Array{T,1},P::F_MeshArray3D,tim) where T
+function dxdt!(du::Array{T,1},u::Array{T,1},P::uvwMeshArrays,tim) where T
     dt=mydt(tim,P.T)
     g=P.u0.grid
     #
@@ -95,7 +95,7 @@ function dxdt!(du::Array{T,1},u::Array{T,1},P::F_MeshArray3D,tim) where T
 end
 
 """
-    dxdt!(du,u,p::F_MeshArray2D,tim)
+    dxdt!(du,u,p::uvMeshArrays,tim)
 
 Interpolate velocity from gridded fields (2D; with halos) to position `u`
 (`x,y,fIndex`) to compute the derivative of position v time  `du_dt`.
@@ -116,7 +116,7 @@ isa(I.📌,Vector)
 true
 ```
 """
-function dxdt!(du::Array{T,1},u::Array{T,1},P::F_MeshArray2D,tim) where T
+function dxdt!(du::Array{T,1},u::Array{T,1},P::uvMeshArrays,tim) where T
     #compute positions in index units
     dt=mydt(tim,P.T)
     g=P.u0.grid
@@ -157,7 +157,7 @@ function dxdt!(du::Array{T,1},u::Array{T,1},P::F_MeshArray2D,tim) where T
 end
 
 """
-    dxdt!(du,u,P::F_Array3D,tim)
+    dxdt!(du,u,P::uvwArrays,tim)
 
 Interpolate velocity from gridded fields (3D; NO halos) to position `u`
 (`x,y,z`) to compute the derivative of position v time  `du_dt`.
@@ -179,7 +179,7 @@ prod(isapprox.(I.📌,ref,atol=1.0)) # hide
 true
 ```
 """
-function dxdt!(du::Array{T,1},u::Array{T,1},P::F_Array3D,tim) where T
+function dxdt!(du::Array{T,1},u::Array{T,1},P::uvwArrays,tim) where T
     #compute positions in index units
     dt=mydt(tim,P.T)
     #
@@ -226,12 +226,12 @@ function dxdt!(du::Array{T,1},u::Array{T,1},P::F_Array3D,tim) where T
     return du
 end
 
-function dxdt!(du::Array{T,2},u::Array{T,2},P::F_Array3D,tim) where T
+function dxdt!(du::Array{T,2},u::Array{T,2},P::uvwArrays,tim) where T
     [dxdt!(du[i],u[i],P,tim) for i=1:size(u,2)]
 end
 
 """
-    dxdt!(du,u,P::F_Array2D,tim)
+    dxdt!(du,u,P::uvArrays,tim)
 
 Interpolate velocity from gridded fields (2D; NO halos) to position `u`
 (`x,y`) to compute the derivative of position v time  `du_dt`.
@@ -252,7 +252,7 @@ isa(I.📌,Vector)
 true
 ```
 """
-function dxdt!(du::Array{T,1},u::Array{T,1},P::F_Array2D,tim) where T
+function dxdt!(du::Array{T,1},u::Array{T,1},P::uvArrays,tim) where T
     dt=mydt(tim,P.T)
     #
     (nx,ny) = size(P.u0)

src/data_wrangling.jl

@@ -2,7 +2,7 @@
     convert_to_FlowFields(U::Array{T,2},V::Array{T,2},t1::T) where T
 
 Convert a pair of U,V arrays (staggered C-grid velocity field in 2D) to
-a `F_MeshArray2D` struct ready for integration of individual displacements
+a `uvMeshArrays` struct ready for integration of individual displacements
 from time `t0=0` to time `t1`.
 """
 function convert_to_FlowFields(U::Array{T,2},V::Array{T,2},t1::T) where T
@@ -15,7 +15,7 @@ function convert_to_FlowFields(U::Array{T,2},V::Array{T,2},t1::T) where T
     (u,v)=exchange(u,v,1)
     func=(u -> MeshArrays.update_location_dpdo!(u,g))
 
-    F_MeshArray2D{eltype(u)}(u,u,v,v,[0,t1],func)
+    uvMeshArrays{eltype(u)}(u,u,v,v,[0,t1],func)
 end
 
 """