From 1e04fe0dc334cfa9ce4593cf41ef5abeabcb8735 Mon Sep 17 00:00:00 2001
From: Hongyang Zhou <hyzhou@umich.edu>
Date: Tue, 9 Jul 2024 07:26:54 +0800
Subject: [PATCH] Clean up docs

---
 src/plot/pyplot.jl  | 20 ++++++++++----------
 src/plot/utility.jl | 12 +++++++-----
 2 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/plot/pyplot.jl b/src/plot/pyplot.jl
index 3bbbdcd..6a02b2e 100644
--- a/src/plot/pyplot.jl
+++ b/src/plot/pyplot.jl
@@ -55,15 +55,16 @@ end
 
 
 """
-    plotdata(data, func, args, kwargs...)
+    plotdata(bd, func, args, kwargs...)
 
 Plot the variable from SWMF output.
 
-`plotdata(data, "p", plotmode="contbar")`
+# Examples
+`plotdata(bd, "p", plotmode="contbar")`
 
-`plotdata(data, "p", plotmode="grid")`
+`plotdata(bd, "p", plotmode="grid")`
 
-`plotdata(data, func, plotmode="trimesh", plotrange=[-1.0, 1.0, -1.0, 1.0], plotinterval=0.2)`
+`plotdata(bd, func, plotmode="trimesh", plotrange=[-1.0, 1.0, -1.0, 1.0], plotinterval=0.2)`
 
 # Arguments
 - `bd::BATLData`: BATSRUS data.
@@ -317,13 +318,12 @@ end
 
 
 """
-    cutplot(data, var, ax=nothing; plotrange=[-Inf,Inf,-Inf,Inf], dir="x", sequence=1,
-       levels=20)
+    cutplot(data, var, ax=nothing; plotrange=[-Inf,Inf,-Inf,Inf], dir="x", sequence=1)
 
-2D plane cut contourf of 3D box data.
+2D plane cut pcolormesh of 3D box data. `sequence` is the index along `dir`.
 """
 function cutplot(bd::BATLData, var::AbstractString, ax=nothing;
-   plotrange=[-Inf,Inf,-Inf,Inf], dir="x", sequence=1, levels::Int=20)
+   plotrange=[-Inf,Inf,-Inf,Inf], dir="x", sequence=1)
    x, w = bd.x, bd.w
    varIndex_ = findindex(bd, var)
 
@@ -349,7 +349,7 @@ function cutplot(bd::BATLData, var::AbstractString, ax=nothing;
       cut1, cut2, W = subsurface(cut1, cut2, W, plotrange)
    end
    if isnothing(ax) ax = plt.gca() end
-   c = ax.contourf(cut1, cut2, W, levels)
+   c = ax.pcolormesh(cut1, cut2, W)
 
    title(bd.head.wnames[varIndex_])
 
@@ -473,7 +473,7 @@ end
     contourf(data, var, ax=nothing; levels=0, plotrange=[-Inf,Inf,-Inf,Inf],
        plotinterval=0.1, innermask=false, kwargs...)
 
-Wrapper over `contourf` in matplotlib.
+Wrapper over `contourf` in matplotlib. See [`getdata2d`](@ref) for some related keywords.
 """
 function PyPlot.contourf(bd::BATLData, var::AbstractString, ax=nothing; levels::Int=0,
    plotrange=[-Inf,Inf,-Inf,Inf], plotinterval=0.1, innermask=false, kwargs...)
diff --git a/src/plot/utility.jl b/src/plot/utility.jl
index 225b5cf..780977b 100644
--- a/src/plot/utility.jl
+++ b/src/plot/utility.jl
@@ -2,13 +2,15 @@
 
 """
     getdata2d(bd::BATLData, var::AbstractString, plotrange=[-Inf, Inf, -Inf, Inf],
-       plotinterval=Inf; innermask=false, rbody=1.0)
+       plotinterval=Inf; kwargs...)
 
 Return 2D slices of data `var` from `bd`. If `plotrange` is not set, output data resolution
-is the same as the original. If `innermask==true`, then the inner boundary cells are set to
-NaN. If `innermask == true` but the rbody parameter is not found in the header, we use the
-keyword `rbody` as the inner radius. If `useMatplotlib==false`, a native Julia scattered
-interpolation is used (but is somehow slower than Matplotlib).
+is the same as the original.
+
+# Keyword Arguments 
+- `innermask=false`: Whether to mask the inner boundary with NaN.
+- `rbody=1.0`: Radius of the inner mask. Used when the rbody parameter is not found in the header.
+- `useMatplotlib=true`: Whether to Matplotlib (somehow faster) or NaturalNeighbours for scattered interpolation.
 """
 function getdata2d(bd::BATLData, var::AbstractString,
    plotrange::Vector=[-Inf, Inf, -Inf, Inf], plotinterval::Real=Inf;