Incorporating DimensionalData

Project.toml

@@ -4,6 +4,7 @@ authors = ["Hongyang Zhou <hyzhou@umich.edu>"]
 version = "0.7.3"
 
 [deps]
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 FortranFiles = "c58ffaec-ab22-586d-bfc5-781a99fd0b10"
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
@@ -28,6 +29,7 @@ Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 BatsrusMakieExt = "Makie"
 
 [compat]
+DimensionalData = "0.29"
 FortranFiles = "0.6"
 Glob = "1.3"
 HDF5 = "0.17"

benchmark/benchmarks.jl

@@ -19,11 +19,11 @@ SUITE["read"]["ASCII"] = @benchmarkable load($file)
 
 file = joinpath(directory, files[2])
 bd = load(file)
-SUITE["read"]["Binary structured"] = @benchmarkable load($file)
+SUITE["read"]["Load binary structured"] = @benchmarkable load($file)
 SUITE["read"]["Extract density"] = @benchmarkable Batsrus.getvar($bd, "Rho")
-SUITE["read"]["Extract B"] = @benchmarkable Batsrus.getvar($bd, "B")
+SUITE["read"]["Extract Bmag"] = @benchmarkable get_magnitude($bd, :B)
 SUITE["read"]["Interp2d"] = @benchmarkable Batsrus.interp2d($bd, "rho")
 
 file = joinpath(directory, files[3])
 bd = load(file)
-SUITE["read"]["Anisotropy"] = @benchmarkable bd["Anisotropy1"]
+SUITE["read"]["Anisotropy"] = @benchmarkable get_anisotropy($bd, 1)

docs/examples/visualization/demo_animate_2d.md

@@ -190,8 +190,8 @@ function get_vector(bd, var, plotrange, plotinterval)
    X, Y = eachslice(x, dims=3)
    X, Y = vec(X), vec(Y)
    varstream = split(var, ";")
-   var1_ = findfirst(x->lowercase(x)==lowercase(varstream[1]), bd.head.wnames)
-   var2_ = findfirst(x->lowercase(x)==lowercase(varstream[2]), bd.head.wnames)
+   var1_ = findfirst(x->lowercase(x)==lowercase(varstream[1]), bd.head.wname)
+   var2_ = findfirst(x->lowercase(x)==lowercase(varstream[2]), bd.head.wname)
    # Create grid values first.
    xi = range(Float64(plotrange[1]), stop=Float64(plotrange[2]), step=plotinterval)
    yi = range(Float64(plotrange[3]), stop=Float64(plotrange[4]), step=plotinterval)

docs/src/man/manual.md

@@ -57,26 +57,24 @@ w = interp1d(bd, "rho", point1, point2)
 
 - Derived variables
 
+We provide utility methods `get_magnitude`, `get_magnitude2`, and `fill_vector_from_scalars` for vector processing:
+
 ```julia
-Bmag = bd["Bmag"]
+Bmag = get_magnitude(bd, :B)
+B2 = get_magnitude2(bd, :B)
+Bvec = Batsrus.fill_vector_from_scalars(bd, :B)
+paniso0 = get_anisotropy(bd, 0)
 ```
 
-Here is a full list of predefined derived quantities:
+These are built upon `get_vectors`. Here is a full list of predefined derived quantities in `get_vectors`:
 
 | Derived variable name | Meaning                          | Required variable |
 |-----------------------|----------------------------------|-------------------|
-| B2                    | Magnetic field magnitude squared | Bx, By, Bz        |
-| E2                    | Electric field magnitude squared | Ex, Ey, Ez        |
-| U2                    | Velocity magnitude squared       | Ux, Uy, Uz        |
-| Bmag                  | Magnetic field magnitude         | Bx, By, Bz        |
-| Emag                  | Electric field magnitude         | Ex, Ey, Ez        |
-| Umag                  | Velocity magnitude               | Ux, Uy, Uz        |
-| Uemag                 | Electron Velocity magnitude      | UxS0, UyS0, UzS0  |
-| Uimag                 | Ion Velocity magnitude           | UxS1, UyS1, UzS1  |
-| B                     | Magnetic field vector            | Bx, By, Bz        |
-| E                     | Electric field vector            | Ex, Ey, Ez        |
-| U                     | Velocity vector                  | Ux, Uy, Uz        |
-| Anisotropy[0-1]       | Pressure/Temperature anisotropy  | B, P tensor       |
+| :B                    | Magnetic field vector            | Bx, By, Bz        |
+| :E                    | Electric field vector            | Ex, Ey, Ez        |
+| :U                    | Velocity vector                  | Ux, Uy, Uz        |
+| :U0                   | Electron velocity vector         | UxS0, UyS0, UzS0  |
+| :U1                   | Proton velocity vector           | UxS1, UyS1, UzS1  |
 
 ## Output format conversion
 
@@ -280,7 +278,7 @@ For 3D outputs, we may use `cutplot` for visualizing on a sliced plane, or `stre
 To get the index of a certain quantity, e.g. electron number density
 
 ```julia
-ρe_= findfirst(x->x=="rhoS0", bd.head.wnames)
+ρe_= findfirst(x->x=="rhoS0", bd.head.wname)
 ```
 
 #### Get variable range

examples/beta.jl

@@ -31,7 +31,7 @@ PBcut = hypot.(Bx, By, Bz)
 c = ax.contourf(cut1, cut2, Pcut./PBcut)
 fig.colorbar(c; ax)
 ax.axis("scaled")
-title(data.head[:wnames][p_])
+title(data.head.wname[p_])
 
 xlabel("x"); ylabel("z")
 

examples/vdf.jl

@@ -52,16 +52,16 @@ function dist_select(fnameParticle, xC=-1.90, yC=0.0, zC=-0.1, xL=0.005, yL=0.2,
 
    x, y, z = eachslice(data.x, dims=4)
 
-   ux_ = findfirst(x->x=="ux", data.head.wnames)
-   uy_ = findfirst(x->x=="uy", data.head.wnames)
-   uz_ = findfirst(x->x=="uz", data.head.wnames)
+   ux_ = findfirst(x->x=="ux", data.head.wname)
+   uy_ = findfirst(x->x=="uy", data.head.wname)
+   uz_ = findfirst(x->x=="uz", data.head.wname)
 
    ux = @view data.w[:,:,:,ux_]
    uy = @view data.w[:,:,:,uy_]
    uz = @view data.w[:,:,:,uz_]
 
    for ip in eachindex(x)
-      for iR = 1:nBox
+      for iR in 1:nBox
          if region[1,iR] < x[ip] < region[2,iR] &&
             region[3,iR] < y[ip] < region[4,iR] &&
             region[5,iR] < z[ip] < region[6,iR]
@@ -182,9 +182,9 @@ function GetMeanField(filefield, limits; dir=".")
    y = data.x[:,:,:,2]
    z = data.x[:,:,:,3]
 
-   bx_ = findfirst(x->x=="Bx", data.head.wnames)
-   by_ = findfirst(x->x=="By", data.head.wnames)
-   bz_ = findfirst(x->x=="Bz", data.head.wnames)
+   bx_ = findfirst(x->x=="Bx", data.head.wname)
+   by_ = findfirst(x->x=="By", data.head.wname)
+   bz_ = findfirst(x->x=="Bz", data.head.wname)
 
    Bx = @view data.w[:,:,:,bx_]
    By = @view data.w[:,:,:,by_]
@@ -211,8 +211,8 @@ function plotExCut(filefield::String, region, xC, yC, zC, xL, yL, zL;
    # Sample region plot over contour
    data = load(joinpath(dir, filefield))
 
-   bx_ = findfirst(x->x=="Bx", data.head.wnames)
-   bz_ = findfirst(x->x=="Bz", data.head.wnames)
+   bx_ = findfirst(x->x=="Bx", data.head.wname)
+   bz_ = findfirst(x->x=="Bz", data.head.wname)
 
    Bx = @view data.w[:,:,:,bx_]
    Bz = @view data.w[:,:,:,bz_]
@@ -280,9 +280,9 @@ function dist_plot(pType='e')
       y = @view data.x[:,:,:,2]
       z = @view data.x[:,:,:,3]
 
-      ux_ = findfirst(x->x=="ux", data.head.wnames)
-      uy_ = findfirst(x->x=="uy", data.head.wnames)
-      uz_ = findfirst(x->x=="uz", data.head.wnames)
+      ux_ = findfirst(x->x=="ux", data.head.wname)
+      uy_ = findfirst(x->x=="uy", data.head.wname)
+      uz_ = findfirst(x->x=="uz", data.head.wname)
 
       ux = @view data.w[:,:,:,ux_]
       uy = @view data.w[:,:,:,uy_]
@@ -319,9 +319,9 @@ function dist_plot(pType='e')
       y = @view data.x[:,:,:,2]
       z = @view data.x[:,:,:,3]
 
-      ux_ = findfirst(x->x=="ux", data.head.wnames)
-      uy_ = findfirst(x->x=="uy", data.head.wnames)
-      uz_ = findfirst(x->x=="uz", data.head.wnames)
+      ux_ = findfirst(x->x=="ux", data.head.wname)
+      uy_ = findfirst(x->x=="uy", data.head.wname)
+      uz_ = findfirst(x->x=="uz", data.head.wname)
 
       ux = @view data.w[:,:,:,ux_]
       uy = @view data.w[:,:,:,uy_]
@@ -587,9 +587,9 @@ function HF_velocity()
    y = data.x[:,:,:,2]
    z = data.x[:,:,:,3]
 
-   ux_ = findfirst(x->lowercase(x)=="uxs1", data.head.wnames)
-   uy_ = findfirst(x->lowercase(x)=="uys1", data.head.wnames)
-   uz_ = findfirst(x->lowercase(x)=="uzs1", data.head.wnames)
+   ux_ = findfirst(x->lowercase(x)=="uxs1", data.head.wname)
+   uy_ = findfirst(x->lowercase(x)=="uys1", data.head.wname)
+   uz_ = findfirst(x->lowercase(x)=="uzs1", data.head.wname)
 
    Ux = @view data.w[:,:,:,ux_]
    Uy = @view data.w[:,:,:,uy_]

ext/BatsrusMakieExt/typerecipe.jl

@@ -4,7 +4,7 @@
 function Makie.convert_arguments(P::Makie.PointBased, bd::BATS, var::String)
    var_ = findindex(bd, var)
    if hasunit(bd)
-      unitx = getunit(bd, bd.head.variables[1])
+      unitx = getunit(bd, bd.head.wname[1])
       unitw = getunit(bd, var)
       x = bd.x .* unitx
       y = bd.w[:,var_] .* unitw
@@ -21,8 +21,8 @@
    plotrange=[-Inf,Inf,-Inf,Inf], plotinterval=0.1)
    x, y, w = interp2d(bd, var, plotrange, plotinterval)
 
-   unitx = getunit(bd, bd.head.variables[1])
-   unity = getunit(bd, bd.head.variables[2])
+   unitx = getunit(bd, bd.head.wname[1])
+   unity = getunit(bd, bd.head.wname[2])
    unitw = getunit(bd, var)
 
    if unitx isa UnitfulBatsrus.Unitlike

src/Batsrus.jl

@@ -9,10 +9,11 @@ using Parsers
 using Interpolations: cubic_spline_interpolation, BSpline, Linear, scale, interpolate
 import NaturalNeighbours as NN
 using StaticArrays: SVector, @SMatrix, SA
+using DimensionalData
 
 export BATS,
    load, readlogdata, readtecdata, showhead, # io
-   getvar, cutdata, subvolume, subsurface, get_convection_E, get_hall_E, 
+   getvar, getderivedvar, cutdata, subvolume, subsurface, get_convection_E, get_hall_E, 
    get_anisotropy, get_vectors, get_magnitude, get_magnitude2,
    fill_vector_from_scalars, # select
    Batl, convertTECtoVTU, convertIDLtoVTK, readhead, readtree, getConnectivity, # vtk

src/io.jl

@@ -47,13 +47,13 @@ function readlogdata(file::AbstractString)
    nLine = countlines(f) - 2
    seekstart(f)
    headline  = readline(f)
-   variables = split(readline(f))
+   variable = split(readline(f))
    ndim      = 1
    it        = 0
    t         = 0.0
    gencoord  = false
    nx        = 1
-   nw        = length(variables)
+   nw        = length(variable)
 
    data = zeros(nw, nLine)
    @inbounds for i in 1:nLine
@@ -64,7 +64,7 @@ function readlogdata(file::AbstractString)
    close(f)
 
    head = (ndim=ndim, headline=headline, it=it, time=t, gencoord=gencoord,
-      nw=nw, nx=nx, variables=variables)
+      nw=nw, nx=nx, variable=variable)
 
    head, data
 end
@@ -97,7 +97,7 @@ function readtecdata(file::AbstractString; verbose::Bool=false)
    ln = readline(f) |> strip
    if startswith(ln, "VARIABLES")
       # Read until another keyword appears
-      varline = split(ln,'=')[2]
+      varline = split(ln, '=')[2]
 
       ln = readline(f) |> strip
       while !startswith(ln, "ZONE")
@@ -122,12 +122,12 @@ function readtecdata(file::AbstractString; verbose::Bool=false)
          name = uppercase(name)
          if name == "T" # ZONE title
             T = value
-         elseif name in ("NODES","N")
+         elseif name in ("NODES", "N")
             nNode = Parsers.parse(Int32, value)
-         elseif name in ("ELEMENTS","E")
+         elseif name in ("ELEMENTS", "E")
             nCell = Parsers.parse(Int32, value)
-         elseif name in ("ET","ZONETYPE")
-            if uppercase(value) in ("BRICK","FEBRICK")
+         elseif name in ("ET", "ZONETYPE")
+            if uppercase(value) in ("BRICK", "FEBRICK")
                nDim = 3
             elseif uppercase(value) in ("QUADRILATERAL", "FEQUADRILATERAL")
                nDim = 2
@@ -146,7 +146,7 @@ function readtecdata(file::AbstractString; verbose::Bool=false)
       name, value = split(ln,'"', keepempty=false)
       name = string(name[9:end-1])
       str = string(strip(value))
-      if name in ("ITER","NPROC")
+      if name in ("ITER", "NPROC")
          str = Parsers.parse(Int32, value)
       elseif name == "TIMESIM"
          sec = split(str, "=")
@@ -199,7 +199,7 @@ function readtecdata(file::AbstractString; verbose::Bool=false)
 
    close(f)
 
-   head = (variables=VARS, nNode=nNode, nCell=nCell, nDim=nDim, ET=ET,
+   head = (variable=VARS, nNode=nNode, nCell=nCell, nDim=nDim, ET=ET,
 		title=title, auxdataname=auxdataname, auxdata=auxdata)
 
    head, data, connectivity
@@ -297,13 +297,14 @@ function getfilehead(fileID::IOStream, filelist::FileList)
       skip(fileID, TAG)
    end
 
-   # Obtain output array
-   variables = split(varname)
-	# Obtain variable names
-   wnames = @view variables[ndim+1:ndim+nw]
+   # Obtain output variable names
+   variable = lowercase.(split(varname))
+   coord = @view variable[1:ndim]
+   wname = @view variable[ndim+1:ndim+nw]
+   param = @view variable[ndim+nw+1:end]
 
-   head = BatsHead(ndim, headline, it, t, gencoord,
-      neqpar, nw, nx, eqpar, variables, wnames)
+   head = BatsHead(ndim, headline, it, t, gencoord, neqpar, nw, nx, eqpar,
+      coord, wname, param)
 end
 
 function skipline(s::IO)
@@ -481,12 +482,12 @@ Also calculate convenient constants ti0, cs0 ... for typical formulas.
 This function is currently not used anywhere!
 """
 function setunits(head, type; distance=1.0, mp=1.0, me=1.0)
-   ndim      = head.ndim
-   headline  = head.headline
-   neqpar    = head.neqpar
-   nw        = head.nw
-   eqpar     = head.eqpar
-   variables = head.variables
+   ndim     = head.ndim
+   headline = head.headline
+   neqpar   = head.neqpar
+   nw       = head.nw
+   eqpar    = head.eqpar
+   param    = head.param
 
    mu0SI = 4π*1e-7      # H/m
    cSI   = 2.9978e8       # speed of light, [m/s]
@@ -588,7 +589,7 @@ function setunits(head, type; distance=1.0, mp=1.0, me=1.0)
 
    # Overwrite values if given by eqpar
    for ieqpar in 1:neqpar
-      var = variables[ndim+nw+ieqpar]
+      var = param[ieqpar]
       if var == "xSI"
          xSI   = eqpar[ieqpar]
       elseif var == "tSI"
@@ -707,9 +708,9 @@ function showhead(file::FileList, head, io=stdout)
 
    if head.neqpar > 0
       println(io, "parameters : $(head.eqpar)")
-      println(io, "coord names: $(head.variables[1:head.ndim])")
-      println(io, "var   names: $(head.variables[head.ndim+1:head.ndim+head.nw])")
-      println(io, "param names: $(head.variables[head.ndim+head.nw+1:end])")
+      println(io, "coordinate names: $(head.coord)")
+      println(io, "variable   names: $(head.wname)")
+      println(io, "parameter  names: $(head.param)")
    end
 
    return

src/plot/plots.jl

@@ -3,11 +3,11 @@
 using RecipesBase
 
 # Build a recipe which acts on a custom type.
-@recipe function f(bd::BATS{1, 2, T}, var::AbstractString) where {T}
+@recipe function f(bd::BATS{1, TV, TX, TW}, var::AbstractString) where {TV, TX, TW}
    hasunits = hasunit(bd)
 
    if hasunits
-      unitx = getunit(bd, bd.head.variables[1])
+      unitx = getunit(bd, bd.head.wname[1])
       unitw = getunit(bd, var)
       x = bd.x .* unitx
       y = getview(bd, var) .* unitw
@@ -22,14 +22,14 @@
    end
 end
 
-@recipe function f(bd::BATS{2, 3, T}, var::AbstractString;
-   plotrange=[-Inf,Inf,-Inf,Inf], plotinterval=0.1) where {T}
+@recipe function f(bd::BATS{2, TV, TX, TW}, var::AbstractString;
+   plotrange=[-Inf,Inf,-Inf,Inf], plotinterval=0.1) where {TV, TX, TW}
    hasunits = hasunit(bd)
 
    x, y, w = interp2d(bd, var, plotrange, plotinterval)
    if hasunits
-      unitx = getunit(bd, bd.head.variables[1])
-      unity = getunit(bd, bd.head.variables[2])
+      unitx = getunit(bd, bd.head.wname[1])
+      unity = getunit(bd, bd.head.wname[2])
       unitw = getunit(bd, var)
 
       if unitx isa UnitfulBatsrus.Unitlike