Redesign load

README.md

@@ -43,16 +43,16 @@ With JuliaCall:
 ```python
 from juliacall import Main as jl
 jl.seval("using Batsrus")
-file = 'example.out'
-data = Batsrus.load(file, dir='test')
+file = 'test/example.out'
+data = Batsrus.load(file)
 ```
 
 With PyJulia:
 
 ```python
 from julia import Batsrus
-file = 'example.out'
-data = Batsrus.load(file, dir='test')
+file = 'test/example.out'
+data = Batsrus.load(file)
 ```
 
 ## Benchmark

docs/src/index.md

@@ -75,17 +75,16 @@ With JuliaCall:
 ```python
 from juliacall import Main as jl
 jl.seval("using Batsrus")
-file = 'example.out'
-data = Batsrus.load(file, dir='test')
+file = 'test/example.out'
+data = Batsrus.load(file)
 ```
 
 With PyJulia:
 
 ```python
 from julia import Batsrus
-dir = 'test'
-file = '1d__raw_2_t25.60000_n00000258.out'
-data = Batsrus.load(file, dir=dir)
+file = 'test/1d__raw_2_t25.60000_n00000258.out'
+data = Batsrus.load(file)
 ```
 
 !!! warning "Python dependency"

docs/src/man/examples.md

@@ -9,7 +9,6 @@ file = "1d_bin.out";
 data = load(file);
 data = load(file, verbose=true);
 data = load(file, npict=1);
-data = load(file, dir=".");
 ```
 
 - 3D structured spherical coordinates
@@ -287,8 +286,8 @@ An example of tracing in a 2D cut and plot the field lines over contour:
 ```julia
 using Batsrus, PyPlot
 
-file = "y=0_var_1_t00000000_n00000000.out"
-data = load(file, dir="test")
+file = "test/y=0_var_1_t00000000_n00000000.out"
+data = load(file)
 
 bx = data.w[:,:,5]
 bz = data.w[:,:,7]

examples/pic.jl

@@ -12,10 +12,9 @@ inset_axes = inset_locator.inset_axes
 DN = matplotlib.colors.DivergingNorm
 
 dir = "."
-fnameField = "3d_var_region0_0_t00001640_n00020369.out"
-#fnameField = "3d_var_region0_0_t00001520_n00004093.out"
+file = "3d_var_region0_0_t00001640_n00020369.out"
 
-data = load(fnameField, dir=dir)
+data = load(joinpath(dir, file))
 
 me = data.head.eqpar[1]
 qe = data.head.eqpar[2]
@@ -32,7 +31,6 @@ const J₀ = 4.0*vAlfven # Actual normalization unit: q*4.0*vAlfven
 const T₀ = 0.2/4 # Pe/n₀
 
 plotrange = [-2.05, -1.75, -0.5, 0.5]
-#plotrange = [-2.12, -1.75, -0.65, 0.6]
 #plotrange=[-Inf, Inf, -Inf, Inf]
 cI = 129 # plane cut index
 

examples/plot_batch.jl

@@ -19,7 +19,7 @@ nfiles = length(filenames)
 fig, ax = subplots(figsize=(10,7.5))
 
 @info "1 / $nfiles, $(basename(filenames[1]))"
-data = load(basename(filenames[1]); dir)
+data = load(filenames[1])
 varIndex_ = Batsrus.findindex(data, var)
 cnorm, cticks = @views Batsrus.set_colorbar(colorscale, vmin, vmax, data.w[:,:,varIndex_])
 
@@ -37,9 +37,9 @@ plt.cla()
 
 if nfiles > 1
    for i in 2:nfiles
-      f = filenames[i] |> basename
+      f = filenames[i]
       @info "$i / $nfiles, $f"
-      local data = load(f; dir)
+      local data = load(f)
 
       contourf(data, var, levels; ax, plotrange, plotinterval, innermask=true, norm=cnorm)
 

examples/vdf.jl

@@ -30,7 +30,7 @@ function dist_select(fnameParticle, xC=-1.90, yC=0.0, zC=-0.1, xL=0.005, yL=0.2,
       !occursin("region0_1", fnameParticle) && @error "Check filename!"
    end
 
-   fnameField = "3d_var_region0_0_"*fnameParticle[end-22:end]
+   filefield = "3d_var_region0_0_"*fnameParticle[end-22:end]
 
    nBox = 9 # number of box regions
 
@@ -48,7 +48,7 @@ function dist_select(fnameParticle, xC=-1.90, yC=0.0, zC=-0.1, xL=0.005, yL=0.2,
 
    particle = [Array{Float32}(undef, 3, 0) for _ in 1:nBox]
 
-   data = load(fnameParticle; dir)
+   data = load(joinpath(dir, fnameParticle))
 
    x = @view data.x[:,:,:,1]
    y = @view data.x[:,:,:,2]
@@ -83,7 +83,7 @@ Velocity distribution plot in 9 box regions.
 `plottype`: 1: uy-ux; 2: ux-uz; 3:uy-uz; 4:u⟂O-u⟂I; 5:u⟂I-u∥; 5:u⟂O-u∥
 """
 function dist_scan(region, particle, ParticleType='i', plottype=1; dir=".",
-   fnameField::AbstractString, nbin=60, fs=10)
+   filefield::AbstractString, nbin=60, fs=10)
 
    if ParticleType == 'i'
       binRange = [[-3.,3.], [-3.,3.]]
@@ -99,7 +99,7 @@ function dist_scan(region, particle, ParticleType='i', plottype=1; dir=".",
          uy = particle[iB][2,:] ./ cAlfven
          uz = particle[iB][3,:] ./ cAlfven
       else
-         dBx, dBy, dBz = GetMeanField(fnameField, region[:,iB]; dir)
+         dBx, dBy, dBz = GetMeanField(filefield, region[:,iB]; dir)
 
          dPar = [dBx; dBy; dBz] # Parallel direction
          dPerpI = cross([0; -1; 0], dPar) # Perpendicular direction in-plane
@@ -173,14 +173,12 @@ function dist_scan(region, particle, ParticleType='i', plottype=1; dir=".",
 end
 
 """
-    GetMeanField(fnameField, limits; dir=".")
+    GetMeanField(filefield, limits; dir=".")
 
-Get the average field direction in region `limits`.
+Get the average field direction in a box region specified by `limits`.
 """
-function GetMeanField(fnameField, limits; dir=".")
-
-   # Get the average field direction in limited region
-   data = load(fnameField; dir)
+function GetMeanField(filefield, limits; dir=".")
+   data = load(joinpath(dir, filefield))
 
    x = data.x[:,:,:,1]
    y = data.x[:,:,:,2]
@@ -208,12 +206,12 @@ end
 
 
 
-function plotExCut(fnameField::String, region, xC, yC, zC, xL, yL, zL;
+function plotExCut(filefield::String, region, xC, yC, zC, xL, yL, zL;
    dir=".", fs=16, sequence=129)
 
    plotrange = [xC-xL*16, xC+xL*16, zC-zL*5, zC+zL*5]
    # Sample region plot over contour
-   data = load(fnameField, dir=dir)
+   data = load(joinpath(dir, filefield))
 
    bx_ = findfirst(x->x=="Bx", data.head.wnames)
    bz_ = findfirst(x->x=="Bz", data.head.wnames)
@@ -256,7 +254,7 @@ function dist_plot(pType='e')
    fnameE = "cut_particles0_region0_1_t00001640_n00020369.out"
    fnameI = "cut_particles1_region0_2_t00001640_n00020369.out"
 
-   fnameField = "3d_var_region0_0_"*fnameE[end-22:end]
+   filefield = "3d_var_region0_0_"*fnameE[end-22:end]
 
    binRangeI = [[-3.,3.], [-3.,3.]]
    binRangeE = [[-7.,13.], [-10.,10.]]
@@ -278,7 +276,7 @@ function dist_plot(pType='e')
       region[:,3] = [-1.930, -1.925, -0.08, 0.08, -0.10, -0.06]
       region[:,4] = [-1.930, -1.925, -0.08, 0.08,  0.00,  0.04]
 
-      data = load(fnameE, dir=dir)
+      data = load(joinpath(dir, fnameE))
 
       x = @view data.x[:,:,:,1]
       y = @view data.x[:,:,:,2]
@@ -317,7 +315,7 @@ function dist_plot(pType='e')
       region[:,3] = [-1.930, -1.920, -0.08, 0.08, -0.10, -0.06]
       region[:,4] = [-1.930, -1.920, -0.08, 0.08,  0.00,  0.04]
 
-      data = load(fnameI, dir=dir)
+      data = load(joinpath(dir, fnameI))
 
       x = @view data.x[:,:,:,1]
       y = @view data.x[:,:,:,2]
@@ -368,7 +366,7 @@ function dist_plot(pType='e')
          uy = particle[iB][2,:] ./ cAlfven
          uz = particle[iB][3,:] ./ cAlfven
       else
-         dBx, dBy, dBz = GetMeanField(fnameField, region[:,iB]; dir=dir)
+         dBx, dBy, dBz = GetMeanField(filefield, region[:,iB]; dir=dir)
 
          dPar   = [dBx; dBy; dBz]         # Parallel direction
          dPerpI = cross([0; -1; 0], dPar) # Perpendicular direction in-plane
@@ -477,13 +475,13 @@ function show_box_region()
    fnameE = "cut_particles0_region0_1_t00001640_n00020369.out"
    fnameI = "cut_particles1_region0_2_t00001640_n00020369.out"
 
-   fnameField = "3d_var_region0_0_"*fnameE[end-22:end]
+   filefield = "3d_var_region0_0_"*fnameE[end-22:end]
 
    fs = 10
    plotrange = [-2.0, -1.8, -0.35, 0.35]
    sequence = 129 # cut plane index starting from -
 
-   data = load(fnameField; dir)
+   data = load(joinpath(dir, filefield())
 
    X, Z, Bx = cutdata(data, "Bx"; dir="y", sequence, plotrange)
    X, Z, Bz = cutdata(data, "Bz"; dir="y", sequence, plotrange)
@@ -583,9 +581,9 @@ function HF_velocity()
    fnameE = "cut_particles0_region0_1_t00001640_n00020369.out"
    fnameI = "cut_particles1_region0_2_t00001640_n00020369.out"
 
-   fnameField = "3d_var_region0_0_"*fnameE[end-22:end]
+   filefield = "3d_var_region0_0_"*fnameE[end-22:end]
 
-   data = load(fnameField; dir)
+   data = load(joinpath(dir, filefield))
 
    x = data.x[:,:,:,1]
    y = data.x[:,:,:,2]
@@ -612,7 +610,7 @@ end
 
 
 dir = "/Users/hyzhou/Documents/Computer/DeepBlue"
-fnameField = "3d_var_region0_0_t00001640_n00020369.out"
+filefield = "3d_var_region0_0_t00001640_n00020369.out"
 PType = 'e'
 plottype = 2
 
@@ -633,9 +631,9 @@ xL, yL, zL = 0.008, 0.2, 0.03 # box length in x,y,z
    fnameParticle, xC, yC, zC, xL, yL, zL,
    dir=dir, ParticleType=PType)
 
-@time dist_scan(region, particle, PType, plottype; dir, fnameField)
+@time dist_scan(region, particle, PType, plottype; dir, filefield)
 
-@time plotExCut(fnameField, region, xC,yC,zC,xL,yL,zL; dir)
+@time plotExCut(filefield, region, xC,yC,zC,xL,yL,zL; dir)
 
 
 #ax = dist_plot('i')

src/io.jl

@@ -7,7 +7,7 @@ const TAG = 4 # Fortran record tag size
 searchdir(path, key) = filter(x->occursin(key, x), readdir(path))
 
 """
-    load(filenameIn; dir=".", npict=1, verbose=false)
+    load(filename; npict=1, verbose=false)
 
 Read BATSRUS output files. Stores the `npict` snapshot from an ascii or binary data file
 into the arrays of coordinates `x` and data `w`. Filename can be provided with wildcards.
@@ -17,14 +17,14 @@ into the arrays of coordinates `x` and data `w`. Filename can be provided with w
 data = load("1d_raw*")
 ```
 """
-function load(filenameIn::AbstractString; dir::String=".", npict::Int=1,
-   verbose::Bool=false)
+function load(filenameIn::AbstractString; npict::Int=1, verbose::Bool=false)
    # Check the existence of files
-   file = searchdir(dir, Regex(replace(filenameIn, s"*" => s".*")))
+   dir, filename = splitdir(filenameIn)
+   file = searchdir(dir, Regex(replace(filename, s"*" => s".*")))
    if isempty(file)
       throw(ArgumentError("No matching filename was found for $(filenameIn)"))
    elseif length(file) > 1
-      throw(ArgumentError("Ambiguous filename $(filenameIn)!"))
+      throw(ArgumentError("Ambiguous filename $(filename)!"))
    end
 
    filelist, fileID, pictsize = getfiletype(file[1], dir)

src/vtk.jl

@@ -140,17 +140,16 @@ function convertTECtoVTU(head, data, connectivity, filename="out")
 end
 
 """
-    convertIDLtoVTK(filename; dir=".", gridType=1, verbose=false)
+    convertIDLtoVTK(filename; gridType=1, verbose=false)
 
 Convert 3D BATSRUS *.out to VTK. If `gridType==1`, it converts to the rectilinear grid; if
 `gridType==2`, it converts to the structured grid. If `filename` does not end with "out", it
 tries to find the ".info" and ".tree" file with the same name tag and generates 3D
 unstructured VTU file.
 """
-function convertIDLtoVTK(filename::AbstractString; dir::String=".", gridType::Int=1,
-   verbose::Bool=false)
+function convertIDLtoVTK(filename::AbstractString; gridType::Int=1, verbose::Bool=false)
    if endswith(filename, ".out")
-      data = load(filename, dir=dir)
+      data = load(filename)
 
       nVar = length(data.head.wnames)
 
@@ -202,7 +201,7 @@ function convertIDLtoVTK(filename::AbstractString; dir::String=".", gridType::In
 
    else
       # info, tree, and out files
-      data = load(filename*".out", dir=dir)
+      data = load(filename*".out")
       batl = Batl(readhead(filename*".info"), readtree(filename)...)
       connectivity = getConnectivity(batl)