Merge pull request #8 from AtilaSaraiva/somesmallfixes

several small formating and functionality corrections

src/Recipes/SeisAmplitudeRecipe.jl

@@ -28,7 +28,7 @@ julia> amp = seisamplitude!(ax, d)
 """
 @recipe(SeisAmplitude, d) do scene
     Attributes(
-        fmax=100, 
+        fmax=100,
         dy=0.004,
 
         normalize=false,
@@ -39,7 +39,7 @@ julia> amp = seisamplitude!(ax, d)
 end
 
 function Makie.plot!(amp::SeisAmplitude{<:Tuple{AbstractMatrix{<:Real}}})
-    
+
     nx = size(amp.d[], 2)
     df = 1/amp.dy[]/size(amp.d[], 1)
     FMAX = df*size(amp.d[], 1)/2

src/Recipes/SeisFKRecipe.jl

@@ -36,14 +36,14 @@ julia> fk = seisfk!(ax, d)
 """
 @recipe(SeisFK, d) do scene
     Attributes(
-        dx=1, 
-        dy=1, 
+        dx=1,
+        dy=1,
         fmax=100,
 
-        pclip=99.9, 
-        vmin=nothing, 
-        vmax=nothing, 
-        
+        pclip=99.9,
+        vmin=nothing,
+        vmax=nothing,
+
         cmap=:PuOr
     )
 end
@@ -62,7 +62,7 @@ function Makie.plot!(fk::SeisFK{<:Tuple{AbstractMatrix{<:Real}}})
     nf = convert(Int32, floor((size(fk.d[], 1)/2)*fk.fmax[]/FMAX))
     D = abs.(fftshift(fft(fk.d[])))
     D = D[round(Int,end/2):round(Int,end/2)+nf, :]
-    
+
     if (isnothing(fk.vmin[]) || isnothing(fk.vmax[]))
         a = 0.
         if (fk.pclip[] <= 100)
@@ -76,5 +76,5 @@ function Makie.plot!(fk::SeisFK{<:Tuple{AbstractMatrix{<:Real}}})
     end
 
     image!(fk, (kmin, kmax), (0.0, fk.fmax[]), D', colorrange=(a, b), colormap=fk.cmap[])
-    
+
 end

src/Recipes/SeisImageRecipe.jl

@@ -32,7 +32,7 @@ julia> img = seisimage!(ax, d)
 @recipe(SeisImage, d) do scene
     Attributes(
         ox = 0,
-        dx = 1, 
+        dx = 1,
         oy = 0,
         dy = 1,
 
@@ -45,23 +45,23 @@ julia> img = seisimage!(ax, d)
 end
 
 function Makie.plot!(img::SeisImage{<:Tuple{AbstractMatrix{<:Real}}})
-    
+
     if (isnothing(img.vmin[]) || isnothing(img.vmax))
         if (img.pclip[]<=100)
             a = -quantile(abs.(img.d[][:]), (img.pclip[]/100))
         else
             a = -quantile(abs.(img.d[][:]), 1)*img.pclip[]/100
         end
-            b = -a
+        b = -a
     else
         a = img.vmin[]
         b = img.vmax[]
     end
-    
-    x = (img.ox[]-img.dx[], img.ox[]+size(img.d[],2)*img.dx[])
+
+    x = (img.ox[], img.ox[]+size(img.d[],2)*img.dx[])
     y = (img.oy[], img.oy[]+size(img.d[],1)*img.dy[])
 
     image!(img, x, y, img.d[]', colorrange=(a, b), colormap=img.cmap[])
-    
+
     img
-end
+end

src/Recipes/SeisOverlayRecipe.jl

@@ -38,21 +38,21 @@ julia> ov = seisoverlay!(ax, d)
     Attributes(
         trace_color = :black,
         trace_width = 0.7,
-    
+
         ox = 0,
         dx = 1,
-    
+
         oy = 0,
         dy = 1,
 
         xcur = 1,
         wiggle_trace_increment = 1,
-    
+
         pclip = 98,
         vmin = nothing,
         vmax = nothing,
-    
-        x = (1, 500), 
+
+        x = (1, 500),
         y = (1, 100),
 
         cmap = :seismic
@@ -61,11 +61,19 @@ end
 
 function Makie.plot!(overlay::SeisOverlay{<:Tuple{AbstractMatrix{<:Real}}})
 
-    seisimage!(overlay, overlay.d[], ox=overlay.ox[], dx=overlay.dx[], oy=overlay.oy[], dy=overlay.dy[], colormap=overlay.cmap[],
-                    vmin=overlay.vmin[], vmax=overlay.vmax[], pclip=overlay.pclip[])
-    seiswiggle!(overlay, overlay.d[], ox=overlay.ox[],  dx=overlay.dx[], oy=overlay.oy[], dy=overlay.dy[],
-            xcur=overlay.xcur[], wiggle_trace_increment=overlay.wiggle_trace_increment[], trace_color=overlay.trace_color[], 
-            trace_width=overlay.trace_width[], fillbands=false)
+    seisimage!(overlay, overlay.d[], ox=overlay.ox[], dx=overlay.dx[], oy=overlay.oy[],
+               dy=overlay.dy[],
+               colormap=overlay.cmap[],
+               vmin=overlay.vmin[],
+               vmax=overlay.vmax[],
+               pclip=overlay.pclip[])
+    seiswiggle!(overlay, overlay.d[], ox=overlay.ox[],  dx=overlay.dx[], oy=overlay.oy[],
+                dy=overlay.dy[],
+                xcur=overlay.xcur[],
+                wiggle_trace_increment=overlay.wiggle_trace_increment[],
+                trace_color=overlay.trace_color[],
+                trace_width=overlay.trace_width[],
+                fillbands=false)
 
     overlay
 end
@@ -75,4 +83,4 @@ function Makie.extract_colormap(pl::Plot{seisoverlay, Tuple{Matrix{Float64}}})
     #   -  typeof(pl.plots[1]) = Plot{SeisMakie.seisimage, Tuple{Matrix{<:Real}}}
     #   -  typeof(pl.plots[1].plots[1]) = Image{Tuple{ClosedInterval{Float32}, ClosedInterval{Float32}, Matrix{Float32}}}
     return Makie.extract_colormap(pl.plots[1].plots[1])
-end
+end

src/Recipes/SeisWiggleRecipe.jl

@@ -53,7 +53,7 @@ julia> wp = seiswiggle!(ax, d)
 end
 
 function Makie.plot!(wp::SeisWiggle{<:Tuple{AbstractMatrix{<:Real}}})
-    
+
     d = wp.d
     gx = wp.gx
 
@@ -62,23 +62,23 @@ function Makie.plot!(wp::SeisWiggle{<:Tuple{AbstractMatrix{<:Real}}})
 
     oy = wp.oy[]
     dy = wp.dy[]
-    
+
     xcur = wp.xcur[]
     wiggle_trace_increment = wp.wiggle_trace_increment[]
 
     if isnothing(gx[])
-        gx[] = [ox+(i-1)*dx for i in 1:size(d[], 2)]        
+        gx[] = [ox+(i-1)*dx for i in 1:size(d[], 2)]
     end
-    
+
     traces = Observable(Vector{Point2f}[])
     positive_traces = Observable(Vector{Point2f}[])
     zero_lines = Observable(Vector{Point2f}[])
 
-    function update_plot(d, gx)                        
+    function update_plot(d, gx)
         empty!(traces[])
         empty!(positive_traces[])
         empty!(zero_lines[])
-                             
+
         dgx = minimum([gx[i]-gx[i-1] for i in 2:length(gx)])
         max_perturb = maximum(abs, d)
         times = oy:dy:(dy*(size(d, 1)-1)+oy)
@@ -90,7 +90,7 @@ function Makie.plot!(wp::SeisWiggle{<:Tuple{AbstractMatrix{<:Real}}})
             while gx[i] >= st+wiggle_trace_increment*dgx
                 st += wiggle_trace_increment*dgx
             end
-            
+
             if gx[i] >= st && gx[i] < st+wiggle_trace_increment*dgx
                 trace = Point2.(gx[i] .+ (scale .* d[:, i]), times)
                 pos_trace = Point2.(gx[i] .+ max.(scale .* d[:, i], 0), times)
@@ -101,7 +101,7 @@ function Makie.plot!(wp::SeisWiggle{<:Tuple{AbstractMatrix{<:Real}}})
                 st += wiggle_trace_increment*dgx
             end
         end
-    end 
+    end
 
     Makie.Observables.onany(update_plot, d, gx)
 

src/SeisDifference.jl

@@ -37,13 +37,13 @@ Return the figure and 3 axes corresponding to d1, d2, d1-d2.
 
 # Example
 ```julia
-julia> d1 = SeisLinearEvents(); d2 = SeisLinearEvents(); 
+julia> d1 = SeisLinearEvents(); d2 = SeisLinearEvents();
 julia> f, ax1, ax2, ax_diff = SeisDifference(d1, d2);
 ```
 """
 function SeisDifference(d1, d2;
                         fig=nothing, ox=0, dx=1, oy=0, dy=1,  gx=nothing,
-                        pclip=98, vmin=nothing, vmax=nothing, wiggle_line_color=:black, 
+                        pclip=98, vmin=nothing, vmax=nothing, wiggle_line_color=:black,
                         wiggle_fill_color=:black, trace_width=0.7, cmap=:viridis, style="overlay", horizontal=true)
 
     if isnothing(fig)
@@ -68,9 +68,12 @@ function SeisDifference(d1, d2;
 
     for (i, ax) in enumerate(axes)
         xlims!(ax, low=ox-dx, high=ox+size(d1,2)*dx)
-        push!(plots, plotfunc(ax, data[i], ox=ox, dx=dx, oy=oy, dy=dy, gx=gx, pclip=pclip, vmin=vmin, vmax=vmax,
-                    wiggle_line_color=wiggle_line_color, wiggle_fill_color=wiggle_fill_color,
-                    trace_width=trace_width, cmap=cmap))
+        push!(plots, plotfunc(ax, data[i], ox=ox, dx=dx, oy=oy, dy=dy, gx=gx, pclip=pclip,
+                              vmin=vmin, vmax=vmax,
+                              wiggle_line_color=wiggle_line_color,
+                              wiggle_fill_color=wiggle_fill_color,
+                              trace_width=trace_width,
+                              cmap=cmap))
     end
 
     if !(style == "wiggles" || style == "wiggle")
@@ -82,4 +85,4 @@ function SeisDifference(d1, d2;
     end
 
     return fig, axes[1], axes[2], axes[3]
-end
+end

src/SeisMakie.jl

@@ -1,7 +1,5 @@
-
 module SeisMakie
 
-    # Write your package code here.
     using Makie
     using Statistics
     using FFTW
@@ -19,14 +17,14 @@ module SeisMakie
     include("SeisPlotAmplitude.jl")
 
     include("Util.jl")
-  
+
     export seisamplitude
     export seisamplitude!
     export seisfk
     export seisfk!
     export seisimage
     export seisimage!
-    export seisoverlay 
+    export seisoverlay
     export seisoverlay!
     export seiswiggle
     export seiswiggle!

src/SeisPlotAmplitude.jl

@@ -20,14 +20,14 @@ Plot amplitude-frequency 2D seismic data `d`
 
 # Example
 ```julia
-julia> d = SeisLinearEvents(); 
+julia> d = SeisLinearEvents();
 julia> f, ax = SeisPlotAmplitude(d,100,0.004);
 ```
 """
 function SeisPlotAmplitude(d::Array{<:Real, 2}; fig=nothing, ax=nothing, fmax=100, dy=0.004,
                            normalize=false, color=:black, label="")
 
-    if isnothing(fig) 
+    if isnothing(fig)
         fig = Figure()
     end
 
@@ -42,4 +42,4 @@ function SeisPlotAmplitude(d::Array{<:Real, 2}; fig=nothing, ax=nothing, fmax=10
     seisamplitude!(ax, d, fmax=fmax, dy=dy, normalize=normalize, color=color, label=label)
 
     return fig, ax
-end
+end

src/SeisPlotTX.jl

@@ -34,38 +34,43 @@ Return the figure and axis corresponding to d.
 
 # Example
 ```julia
-julia> d = SeisLinearEvents(); 
+julia> d = SeisLinearEvents();
 julia> f, ax = SeisPlotTX(d);
 ```
 """
-function SeisPlotTX(d; 
+function SeisPlotTX(d;
                     fig=nothing, gx=nothing, ox=0, dx=1, oy=0, dy=1, xcur=1.2, wiggle_trace_increment=1,
-                    pclip=98, vmin=nothing, vmax=nothing, 
-                    wiggle_line_color=:black, wiggle_fill_color=:black,trace_width=0.7, 
+                    pclip=98, vmin=nothing, vmax=nothing,
+                    wiggle_line_color=:black, wiggle_fill_color=:black,trace_width=0.7,
                     cmap=:seismic, style="image")
 
     if isnothing(fig)
         fig = Figure()
     end
 
     ax = __create_axis(fig[1,1])
-    
+
     if style == "overlay"
-        overlay = seisoverlay!(ax, d; ox=ox, dx=dx, oy=oy, dy=dy, pclip=pclip, vmin=vmin, vmax=vmax, xcur=xcur,
-                                      wiggle_trace_increment=wiggle_trace_increment, wiggle_line_color=wiggle_line_color,
-                                      wiggle_fill_color=wiggle_fill_color, trace_width=trace_width, cmap=cmap)
-
+        overlay = seisoverlay!(ax, d;
+                               ox=ox, dx=dx, oy=oy, dy=dy, pclip=pclip, vmin=vmin, vmax=vmax, xcur=xcur,
+                               wiggle_trace_increment=wiggle_trace_increment,
+                               wiggle_line_color=wiggle_line_color,
+                               wiggle_fill_color=wiggle_fill_color,
+                               trace_width=trace_width, cmap=cmap)
+
         Colorbar(fig[1, 2], overlay)
     elseif style == "wiggles" || style == "wiggle"
         if !isnothing(gx)
             ox = gx[1]
             dx = wiggle_trace_increment*minimum([gx[i]-gx[i-1] for i = 2:length(gx)])
         end
 
-        seiswiggle!(ax, d; gx=gx, ox=ox, dx=dx, oy=oy, dy=dy, xcur=xcur, wiggle_trace_increment=wiggle_trace_increment, 
-                           wiggle_line_color=wiggle_line_color, wiggle_fill_color=wiggle_fill_color,
-                           trace_width=trace_width)    
-    else        
+        seiswiggle!(ax, d; gx=gx, ox=ox, dx=dx, oy=oy, dy=dy, xcur=xcur,
+                    wiggle_trace_increment=wiggle_trace_increment,
+                    wiggle_line_color=wiggle_line_color,
+                    wiggle_fill_color=wiggle_fill_color,
+                    trace_width=trace_width)
+    else
         img = seisimage!(ax, d; ox=ox, dx=dx, oy=oy, dy=dy, pclip=pclip, vmin=vmin, vmax=vmax, cmap=cmap)
         Colorbar(fig[1,2], img)
     end