Replace glob with native Julia

henry2004y · Feb 2, 2024 · 3719b92 · 3719b92
1 parent 571dfe0
commit 3719b92
Show file tree

Hide file tree

Showing 25 changed files with 56 additions and 51 deletions.
diff --git a/docs/examples/postprocess/demo_convert2vti.md b/docs/examples/postprocess/demo_convert2vti.md
@@ -9,9 +9,9 @@
 
 To convert VLSV time series files to VTK image files using multithreads,
 ```julia
-using Vlasiator, Glob
+using Vlasiator
 
-files = glob("*.vlsv")
+files = filter(endswith(".vlsv"), readdir())
 
 Threads.@threads for file in files
    @info file, Threads.threadid()

diff --git a/docs/examples/postprocess/demo_em_extract_slice.md b/docs/examples/postprocess/demo_em_extract_slice.md
@@ -9,7 +9,7 @@
 
 To save Epar, Eperp, B in a selected slice region from 3D VLSV outputs,
 ```julia
-using Vlasiator, Glob
+using Vlasiator
 using JLD2: jldsave
 using StaticArrays
 using LinearAlgebra: norm
@@ -66,7 +66,7 @@ function main()
    outdir = "EM/"
    outfile = "EM.jld2"
 
-   files = glob("bulk1.*vlsv", directory)
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir(directory))
    # Only orthogonal slices are supported
    normal = :y # (:x, :y, :z)
    origin = 0.0

diff --git a/docs/examples/postprocess/demo_lineextracting_mt.md b/docs/examples/postprocess/demo_lineextracting_mt.md
@@ -9,11 +9,11 @@
 
 To extract variables along a line across multiple frames using multithreads,
 ```julia
-using Vlasiator, Glob
+using Vlasiator
 using JLD2: jldsave
 
 function main()
-   files = glob("bulk*.vlsv", ".")
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
    nfile = length(files)
    # Define end points of the line in Earth radius
    x1, x2 = 6.0, 20.0

diff --git a/docs/examples/postprocess/demo_magnetopause_2d_mt.md b/docs/examples/postprocess/demo_magnetopause_2d_mt.md
@@ -19,7 +19,7 @@ JULIA_NUM_THREADS=4 julia demo_magnetopause_2d_mt.jl
 ```
 
 ```julia
-using Vlasiator, Glob
+using Vlasiator
 using Vlasiator: RE # Earth radius, [m]
 using JLD2: jldsave
 
@@ -79,7 +79,7 @@ end
 
 ######
 
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 @time z,x,v,ey = extract_magnetopause_var(files)
 

diff --git a/docs/examples/postprocess/demo_pointextracting.md b/docs/examples/postprocess/demo_pointextracting.md
@@ -19,7 +19,7 @@ JULIA_NUM_THREADS=nthreads julia demo_virtual_satellite.jl
 ```
 
 ```julia
-using Glob, DelimitedFiles, Vlasiator, DataFrames
+using DelimitedFiles, Vlasiator, DataFrames
 using Vlasiator: RE # Earth radius [m]
 
 function extract_vars(files, loc)
@@ -54,7 +54,7 @@ end
 
 #####
 
-files = glob("bulk*.vlsv", "./")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 # virtual satellite location
 const loc = Float64[12, 0, 0] .* RE

diff --git a/docs/examples/postprocess/demo_pointsextracting.md b/docs/examples/postprocess/demo_pointsextracting.md
@@ -11,16 +11,19 @@ This demo shows how to extract data for virtual satellites at multiple locations
 Outputs are stored in binary format for sharing within Julia.
 
 Usage:
+
 ```shell
 julia -t nthreads demo_pointsextracting.jl
 ```
+
 or
+
 ```shell
 JULIA_NUM_THREADS=nthreads julia demo_pointsextracting.jl
 ```
 
 ```julia
-using Glob, Vlasiator
+using Vlasiator
 using Vlasiator: RE # Earth radius, [m]
 using JLD2: jldsave
 
@@ -59,7 +62,7 @@ end
 
 #####
 
-files = glob("bulk*.vlsv", "./")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 # virtual satellite locations
 const locations = [[7RE, 0, 0], [9RE, 0, 0], [11RE, 0, 0], [12RE, 0, 0],

diff --git a/docs/examples/postprocess/demo_pointsextracting_2d_uniform.md b/docs/examples/postprocess/demo_pointsextracting_2d_uniform.md
@@ -11,7 +11,7 @@ This demo shows how to extract data for virtual satellites at uniformly sampled
 Outputs are stored in binary format for sharing within Julia.
 
 ```julia
-using Glob, Vlasiator
+using Vlasiator
 using JLD2: jldsave
 
 "Select cells in 2D `meta` with uniform distance `dx`."
@@ -74,7 +74,7 @@ end
 
 #####
 
-files = glob("bulk*.vlsv", "./")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 const dx = 5RE # uniform sampling distance [m]
 

diff --git a/docs/examples/postprocess/demo_wave_satellite_mt.md b/docs/examples/postprocess/demo_wave_satellite_mt.md
@@ -21,7 +21,7 @@ JULIA_NUM_THREADS=4 julia demo_wave_satellite_mt.jl
 ```julia
 using Statistics: mean
 using LinearAlgebra: ⋅, normalize!, norm
-using DSP, PyPlot, Glob
+using DSP, PyPlot
 using Vlasiator
 using Vlasiator: μ₀, mᵢ, RE
 using Polyester
@@ -114,7 +114,7 @@ function align_yaxis(ax1, ax2)
 end
 
 function main()
-   files = glob("bulk*.vlsv", ".")
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
    # virtual satellite location
    loc = [12Vlasiator.RE, 0, 0]

diff --git a/docs/examples/postprocess/demo_wave_search_mt.md b/docs/examples/postprocess/demo_wave_search_mt.md
@@ -32,7 +32,7 @@ JULIA_NUM_THREADS=4 julia demo_wave_search_mt.jl
 ```
 
 ```julia
-using Glob, Vlasiator, PyPlot, LaTeXStrings
+using Vlasiator, PyPlot, LaTeXStrings
 
 "Extract time series variable"
 function extract_var(files, ncells, varname, component=0)
@@ -147,7 +147,8 @@ function plot_dist(files, varnames, varnames_print, components, Δt, nboxlength;
    for i in eachindex(varnames)
       outdir = "../out/$(lowercase(varnames_print[i]))"
       !isdir(outdir) && mkdir(outdir)
-      length(glob("spatial*.png", outdir)) == length(files) - nboxlength + 1 && continue
+      length(filter(contains(r"^spatial.*\.png$"), readdir(outdir))) ==
+         length(files) - nboxlength + 1 && continue
 
       # Obtain time series data
       var = extract_var(files, ncells, varnames[i], components[i])
@@ -181,7 +182,7 @@ function main()
    nplotstride = 50                   # plot intervals in frames
    dir = "./" # data directory
 
-   files = glob("bulk*.vlsv", dir)
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir(dir))
 
    println("Total number of snapshots: $(length(files))")
    println("Running with $(Threads.nthreads()) threads...")

diff --git a/docs/examples/postprocess/demo_wave_tracing_mt.md b/docs/examples/postprocess/demo_wave_tracing_mt.md
@@ -25,7 +25,7 @@ JULIA_NUM_THREADS=4 julia demo_wave_tracing_mt.jl
 ```julia
 using Vlasiator, VlasiatorPyPlot
 using Vlasiator: qᵢ, μ₀, c, mᵢ, ϵ₀, RE
-using Glob, DSP, FFTW, ImageFiltering, Interpolations
+using DSP, FFTW, ImageFiltering, Interpolations
 using Statistics: mean
 using LinearAlgebra
 
@@ -397,7 +397,7 @@ function main()
    components = [0, 3, 1, 0] # 0 for scalar, 1-3 for vector components
 
    dir = "../run_rho2_bz-5_timevarying_startfrom300s"
-   files = glob("bulk.*.vlsv", dir)
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir(dir))
 
    vars = Variables(varnames, varnames_print, components)
 

diff --git a/docs/examples/postprocess/demo_x_points_extracting.md b/docs/examples/postprocess/demo_x_points_extracting.md
@@ -12,10 +12,10 @@ save the coordinates as well as extracted reconnection rate Ey from multiple out
 Here we assume a X-Z plane.
 ```julia
 using JLD2: jldsave
-using Vlasiator, Glob, ProgressMeter
+using Vlasiator, ProgressMeter
 
 function main()
-   files = glob("bulk*.vlsv", ".")
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
    nG = 2 # number of ghost cells
 

diff --git a/docs/examples/visualization/demo_1d2d_mp_pyplot.md b/docs/examples/visualization/demo_1d2d_mp_pyplot.md
@@ -14,7 +14,7 @@ julia -p $ncores demo_1d2d_mp_pyplot.jl
 ```
 
 ```julia
-using Distributed, Glob
+using Distributed
 @everywhere using Vlasiator, VlasiatorPyPlot, Printf, LaTeXStrings
 
 @assert matplotlib.__version__ ≥ "3.4" "Require Matplotlib version 3.4+ to use subfigure!"
@@ -225,7 +225,7 @@ end
 end
 
 ################################################################################
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 nfile = length(files)
 # Set output directory

diff --git a/docs/examples/visualization/demo_1d2d_pyplot.md b/docs/examples/visualization/demo_1d2d_pyplot.md
@@ -9,7 +9,7 @@
 
 To generate combined 1D/2D plots across multiple frames,
 ```julia
-using Vlasiator, VlasiatorPyPlot, Glob, Printf, LaTeXStrings
+using Vlasiator, VlasiatorPyPlot, Printf, LaTeXStrings
 using Vlasiator: set_args, prep2d
 
 @assert VERSION ≥ v"1.7.0" "Compatible with Julia v1.7+!"
@@ -207,7 +207,7 @@ end
 
 ####### Main
 
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 nfile = length(files)
 # Set output directory
 const outdir = "out/"

diff --git a/docs/examples/visualization/demo_1d_animation_pyplot.md b/docs/examples/visualization/demo_1d_animation_pyplot.md
@@ -9,11 +9,11 @@
 
 This example demonstrates 1D plot animation. `ffmpeg` is required to be installed for saving into mp4.
 ```julia
-using Vlasiator, Glob, VlasiatorPyPlot, Printf
+using Vlasiator, VlasiatorPyPlot, Printf
 using PyCall
 @pyimport matplotlib.animation as anim
 
-files = glob("bulk.*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 # Choose plotting variable
 const var = "proton/vg_rho"
 const comp = 0 # component of vector, if used

diff --git a/docs/examples/visualization/demo_2d_animation_pyplot.md b/docs/examples/visualization/demo_2d_animation_pyplot.md
@@ -10,11 +10,11 @@
 This example shows how to plot 2D colored contours with `pcolormesh`.
 `ffmpeg` is required to be installed for saving into mp4.
 ```julia
-using Vlasiator, Glob, VlasiatorPyPlot, Printf
+using Vlasiator, VlasiatorPyPlot, Printf
 using PyCall
 @pyimport matplotlib.animation as anim
 
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 const var = "proton/vg_rho"
 const comp = 0 # vector component for plotting (if applicable)
 

diff --git a/docs/examples/visualization/demo_2d_mp_pyplot.md b/docs/examples/visualization/demo_2d_mp_pyplot.md
@@ -14,7 +14,7 @@ julia -p $ncores demo_2d_mp_pyplot.jl
 ```
 
 ```julia
-using Distributed, ParallelDataTransfer, Glob
+using Distributed, ParallelDataTransfer
 @everywhere using Vlasiator, VlasiatorPyPlot, Printf, LaTeXStrings
 
 @everywhere function init_figure(cmaps, norms, ticks, pArgs1, extent)
@@ -135,7 +135,7 @@ end
 end
 
 ################################################################################
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 nfile = length(files)
 # Set output directory

diff --git a/docs/examples/visualization/demo_2dcontourseries_pyplot.md b/docs/examples/visualization/demo_2dcontourseries_pyplot.md
@@ -10,9 +10,9 @@
 This script creates contours from a series of input files with a fixed color range.
 Combined with `ffmpeg`, we can easily make animations from data.
 ```julia
-using Vlasiator, Glob, VlasiatorPyPlot, Printf
+using Vlasiator, VlasiatorPyPlot, Printf
 
-files = glob("bulk*.vlsv")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 nfile = length(files)
 # Set output directory
 const outdir = "out/"

diff --git a/docs/examples/visualization/demo_B_fieldline_mp_pyplot.md b/docs/examples/visualization/demo_B_fieldline_mp_pyplot.md
@@ -14,7 +14,7 @@ julia -p $ncores demo_fieldline_mp_pyplot.jl
 ```
 
 ```julia
-using Distributed, ParallelDataTransfer, Glob
+using Distributed, ParallelDataTransfer
 @everywhere using Vlasiator, VlasiatorPyPlot, PyCall, Printf, LaTeXStrings, FieldTracer
 @everywhere using Vlasiator: RE
 
@@ -128,7 +128,7 @@ end
 end
 
 ################################################################################
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 nfile = length(files)
 # Set output directory

diff --git a/docs/examples/visualization/demo_bowshock_2d_mt.md b/docs/examples/visualization/demo_bowshock_2d_mt.md
@@ -18,7 +18,7 @@ JULIA_NUM_THREADS=$nthreads julia demo_bowshock_2d_mt.jl
 ```
 
 ```julia
-using Vlasiator, Glob
+using Vlasiator
 using Vlasiator: RE # Earth radius, [m]
 using JLD2: jldsave
 
@@ -63,7 +63,7 @@ function extract_bowshock_position(files; verbose=true)
 end
 
 #####
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
 @time x_crossing, y_crossing = extract_bowshock_position(files)
 

diff --git a/docs/examples/visualization/demo_lineextracting_mp_pyplot.md b/docs/examples/visualization/demo_lineextracting_mp_pyplot.md
@@ -17,7 +17,7 @@ julia -p $ncores demo_vars_extracting_mp.jl
 ```
 
 ```julia
-using Distributed, ParallelDataTransfer, Glob
+using Distributed, ParallelDataTransfer
 using Vlasiator: RE
 @everywhere using Vlasiator, PyPlot, Printf
 
@@ -116,7 +116,7 @@ end
 end
 
 ################################################################################
-files = glob("bulk*.vlsv", ".")
+files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 nfile = length(files)
 
 const x1, x2 = 8.0, 29.0

diff --git a/docs/examples/visualization/demo_lineextracting_pyplot.md b/docs/examples/visualization/demo_lineextracting_pyplot.md
@@ -9,11 +9,11 @@
 
 This demo shows how to plot variables along a line.
 ```julia
-using Vlasiator, PyPlot, Glob, Printf
+using Vlasiator, PyPlot, Printf
 using Vlasiator: RE # Earth radius [m]
 
 function main()
-   files = glob("bulk*.vlsv", ".")
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
    nfiles = length(files)
 
    x1, x2 = 8.0, 29.0

diff --git a/docs/examples/visualization/demo_lineextracting_pyplot_basic1.md b/docs/examples/visualization/demo_lineextracting_pyplot_basic1.md
@@ -12,11 +12,11 @@ This demo shows how to extract data alone a line across frames.
     This can be made faster by updating the data without deleting the lines.
 
 ```julia
-using Vlasiator, Glob, PyPlot, Printf
+using Vlasiator, PyPlot, Printf
 using Vlasiator: RE # Earth radius, [m]
 
 function main()
-   files = glob("run4/bulk*.vlsv")
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
 
    point1 = [0e8, 0, 0]
    point2 = [1.9e8, 0, 0]

diff --git a/docs/examples/visualization/demo_lineextracting_pyplot_basic2.md b/docs/examples/visualization/demo_lineextracting_pyplot_basic2.md
@@ -9,11 +9,11 @@
 
 This demo shows how to plot pressure along a line across multiple frames.
 ```julia
-using Vlasiator, PyPlot, Glob, Printf
+using Vlasiator, PyPlot, Printf
 using Vlasiator: RE # Earth radius [m]
 
 function main()
-   files = glob("bulk*.vlsv", ".")
+   files = filter(contains(r"^bulk.*\.vlsv$"), readdir())
    nfile = length(files)
 
    x1, x2 = 8.0, 29.0