Merge pull request #10 from firasalchalabi/animations

Animations, Tests, README, Author

Project.toml

@@ -12,7 +12,9 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 julia = "1"
 
 [extras]
+SeisProcessing = "3ac90d68-5a11-50c7-932e-af3f40d97fdc"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [targets]
-test = ["Test"]
+test = ["Test", "SeisProcessing", "Random"]

README.md

@@ -3,3 +3,76 @@
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://seismicjulia.github.io/SeisMakie.jl/stable/)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://seismicjulia.github.io/SeisMakie.jl/dev/)
 [![Build Status](https://github.com/SeismicJulia/SeisMakie.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/SeismicJulia/SeisMakie.jl/actions/workflows/CI.yml?query=branch%3Amain)
+
+SeisMakie.jl is a package intended for plotting seismic data. Some examples are wiggle, image, overlay and frequency-wavenumber plots.
+
+## Examples
+
+### Wiggle Plot
+
+```julia
+using CairoMakie, SeisProcessing
+
+# Seismic data consisting of linear events
+d = SeisLinearEvents()
+f, ax = SeisPlotTX(d, style="wiggle")
+save("./images/wiggle.png", f)
+f
+```
+
+<img src="./images/wiggle.png" width="600">
+
+
+### Image Plot
+
+```julia
+using CairoMakie, SeisProcessing
+
+# Seismic data consisting of linear events
+d = SeisLinearEvents()
+f, ax = SeisPlotTX(d, style="image")
+save("./images/image.png", f)
+f
+```
+
+<img src="./images/image.png" width="600">
+
+
+### Overlay Plot
+
+```julia
+using CairoMakie, SeisProcessing
+
+# Seismic data consisting of linear events
+d = SeisLinearEvents()
+f = Figure()
+_, ax = SeisPlotTX(d, fig=f, style="overlay")  # If you would like to plot on an existing figure
+save("./images/overlay.png", f)
+f
+```
+
+<img src="./images/overlay.png" width="600">
+
+
+### Frequency-Wavenumber Plot
+
+```julia
+using CairoMakie, SeisProcessing
+
+# Seismic data consisting of linear events
+d = SeisLinearEvents()
+f, ax = SeisPlotFK(d)
+save("./images/fk.png", f)
+f
+```
+
+<img src="./images/fk.png" width="600">
+</br>
+</br>
+
+---------------------------
+
+</br>
+For more information about the different functions, view the docs. For more examples,
+check out the Pluto notebook under examples/.
+

src/Recipes/SeisAmplitudeRecipe.jl

@@ -25,6 +25,10 @@ julia> f, ax, amp = seisamplitude(d)
 julia> d = SeisLinearEvents(); f = Figure(); ax = Axis(f)
 julia> amp = seisamplitude!(ax, d)
 ```
+
+Author: Firas Al Chalabi (2024)
+Credits: Aaron Stanton (2015)
+- Most of the code in this file is taken from SeisPlot.jl written by Aaron Stanton.
 """
 @recipe(SeisAmplitude, d) do scene
     Attributes(

src/Recipes/SeisFKRecipe.jl

@@ -2,8 +2,7 @@
     seisfk(d; <keyword arguments>)
     seisfk!(ax, d; <keyword arguments>)
 
-Plot time-space, frequency-wavenumber or amplitude-frequency 2D seismic data `d`
-with color, wiggles or overlay.
+Plot frequency-wavenumber 2D seismic data `d`.
 
 # Arguments
 - `d::Matrix{<:AbstractFloat}`: 2D data to plot.
@@ -20,7 +19,7 @@ with color, wiggles or overlay.
 - `dx=1`: increment of x-axis.
 - `dy=1`: increment of y-axis.
 
-- `cmap=:PuOr`: colormap for  `"color"` or `"overlay"` style.
+- `cmap=:PuOr`: colormap
 
 Return the figure and axis corresponding to d.
 
@@ -33,6 +32,10 @@ julia> f, ax, fk = seisfk(d)
 julia> d = SeisLinearEvents(); f = Figure(); ax = Axis(f)
 julia> fk = seisfk!(ax, d)
 ```
+
+Author: Firas Al Chalabi (2024)
+Credits: Aaron Stanton (2015)
+- Most of the code in this file is taken from SeisPlot.jl written by Aaron Stanton.
 """
 @recipe(SeisFK, d) do scene
     Attributes(

src/Recipes/SeisImageRecipe.jl

@@ -28,6 +28,10 @@ julia> f, ax, img = seisimage(d)
 julia> d = SeisLinearEvents(); f = Figure(); ax = Axis(f)
 julia> img = seisimage!(ax, d)
 ```
+
+Author: Firas Al Chalabi (2024)
+Credits: Aaron Stanton (2015)
+- Most of the code in this file is taken from SeisPlot.jl written by Aaron Stanton.
 """
 @recipe(SeisImage, d) do scene
     Attributes(
@@ -46,22 +50,57 @@ 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))
+    transposed_d = Observable{Any}()
+
+    x = Observable{Any}()
+    y = Observable{Any}()
+
+    colorrange = Observable{Any}()
+
+
+    function update_plot(d, ox, oy, dx, dy, pclip, vmin, vmax)
+        transposed_d[] = d'
+
+        x[] = (ox, ox + size(d,2)*dx)
+        y[] = (oy, oy + size(d,2)*dy)
+
+        if (isnothing(vmin) || isnothing(vmax))
+            if (img.pclip[]<=100)
+                a = -quantile(abs.(d[:]), (pclip/100))
+            else
+                a = -quantile(abs.(d[:]), 1)*pclip/100
+            end
+            b = -a
         else
-            a = -quantile(abs.(img.d[][:]), 1)*img.pclip[]/100
+            a = vmin
+            b = vmax
         end
-        b = -a
-    else
-        a = img.vmin[]
-        b = img.vmax[]
+
+        colorrange[] = (a, b)
+
     end
 
-    x = (img.ox[], img.ox[]+size(img.d[],2)*img.dx[])
-    y = (img.oy[], img.oy[]+size(img.d[],1)*img.dy[])
+    Makie.Observables.onany(update_plot, img.d, img.ox, img.oy, img.dx, img.dy, img.pclip, img.vmin, img.vmax)
+
+    update_plot(img.d[], img.ox[], img.oy[], img.dx[], img.dy[], img.pclip[], img.vmin[], img.vmax[])
+
+
+    # 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
+    # else
+    #     a = img.vmin[]
+    #     b = img.vmax[]
+    # end
+
+    # 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[])
+    image!(img, x, y, transposed_d, colorrange=colorrange, colormap=img.cmap)
 
     img
 end

src/Recipes/SeisWiggleRecipe.jl

@@ -30,6 +30,10 @@ julia> f, ax, wp = seiswiggle(d)
 julia> d = SeisLinearEvents(); f = Figure(); ax = Axis(f)
 julia> wp = seiswiggle!(ax, d)
 ```
+
+Author: Firas Al Chalabi (2024)
+Credits: Aaron Stanton (2015) 
+- The code in this file was inspired by some of Aaron Stanton's in SeisPlot.jl.
 """
 @recipe(SeisWiggle, d) do scene
     Attributes(

src/SeisDifference.jl

@@ -40,6 +40,8 @@ Return the figure and 3 axes corresponding to d1, d2, d1-d2.
 julia> d1 = SeisLinearEvents(); d2 = SeisLinearEvents();
 julia> f, ax1, ax2, ax_diff = SeisDifference(d1, d2);
 ```
+
+Author: Firas Al Chalabi (2024)
 """
 function SeisDifference(d1, d2;
                         fig=nothing, ox=0, dx=1, oy=0, dy=1,  gx=nothing,

src/SeisPlotAmplitude.jl

@@ -23,6 +23,8 @@ Plot amplitude-frequency 2D seismic data `d`
 julia> d = SeisLinearEvents();
 julia> f, ax = SeisPlotAmplitude(d,100,0.004);
 ```
+
+Author: Firas Al Chalabi (2024)
 """
 function SeisPlotAmplitude(d::Array{<:Real, 2}; fig=nothing, ax=nothing, fmax=100, dy=0.004,
                            normalize=false, color=:black, label="")

src/SeisPlotFK.jl

@@ -1,8 +1,7 @@
 """
     SeisPlotFK(d; <keyword arguments>)
 
-Plot time-space, frequency-wavenumber or amplitude-frequency 2D seismic data `d`
-with color, wiggles or overlay.
+Plot frequency-wavenumber 2D seismic data `d`.
 
 # Arguments
 - `d::Matrix{<:AbstractFloat}`: 2D data to plot.
@@ -19,7 +18,7 @@ with color, wiggles or overlay.
 - `dx=1`: increment of x-axis.
 - `dy=1`: increment of y-axis.
 
-- `cmap=:PuOr`: colormap for  `"color"` or `"overlay"` style.
+- `cmap=:PuOr`: colormap
 
 Return the figure and axis corresponding to d.
 
@@ -28,6 +27,8 @@ Return the figure and axis corresponding to d.
 julia> d = SeisLinearEvents(); 
 julia> f, ax = SeisPlotFK(d);
 ```
+
+Author: Firas Al Chalabi (2024)
 """
 function SeisPlotFK(d; fig=nothing, dx=1, dy=1, fmax=100,
                     pclip=99.9, vmin=nothing, vmax=nothing, cmap=:PuOr)

src/SeisPlotTX.jl

@@ -38,6 +38,8 @@ Return the figure and axis corresponding to d.
 julia> d = SeisLinearEvents();
 julia> f, ax = SeisPlotTX(d);
 ```
+
+Author: Firas Al Chalabi (2024)
 """
 function SeisPlotTX(d;
                     fig=nothing, gx=nothing, ox=0, dx=1, oy=0, dy=1, xcur=1.2, wiggle_trace_increment=1,

src/Util.jl

@@ -1,6 +1,4 @@
-"""
-    Creates an Axis object to be used by SeisColor, SeisOverlay, SeisWiggle.
-"""
+# Creates an Axis object to be used by SeisColor, SeisOverlay, SeisWiggle.
 function __create_axis(fig)
     return Axis(fig, yreversed=true, xautolimitmargin=(0,0), yautolimitmargin=(0,0))
 end

test/runtests.jl

@@ -1,6 +1,79 @@
 using SeisMakie
+using SeisProcessing
+using Random
 using Test
 
 @testset "SeisMakie.jl" begin
-    # Write your tests here
+
+    d = SeisLinearEvents()
+
+    dx = 10
+    dy = 0.004
+
+    @testset "SeisWiggleRecipe" begin
+        gx = [ dx*(i-1) for i=1:size(d,2) ]
+        # create a random permutation vector to sample gx and d
+        p = (randsubseq(gx, 0.85) .÷ dx) .+ 1
+        gx = gx[p]
+
+        f, ax, wp = seiswiggle(d[:, p], gx=gx, dy=dy, xcur=2, wiggle_trace_increment=4)
+
+        @test true
+    end
+
+    @testset "SeisImageRecipe" begin
+
+        f, ax, img = seisimage(d, dx=dx, dy=dy, pclip=97, cmap=:viridis)
+
+        @test true
+
+    end
+
+    @testset "SeisOverlayRecipe" begin
+
+        f, ax, ov = seisoverlay(d, dx=dx, dy=dy, xcur=2, wiggle_trace_increment=4, pclip=97, cmap=:viridis)
+
+        @test true
+
+    end
+
+    @testset "SeisFKRecipe" begin
+
+        f, ax, fk = seisfk(d, dx=dx, dy=dy, pclip=97, fmax=90)
+
+        @test true
+    end
+
+    @testset "SeisAmplitudeRecipe" begin
+
+        f, ax, amp = seisamplitude(d, dy=dy, fmax=90)
+
+        @test true
+    end
+
+    @testset "SeisPlotTX" begin
+        gx = [ dx*(i-1) for i=1:size(d,2) ]
+        # create a random permutation vector to sample gx and d
+        p = (randsubseq(gx, 0.85) .÷ dx) .+ 1
+        gx = gx[p]
+        f, ax = SeisPlotTX(d[:, p], gx=gx, dy=dy, xcur=2, wiggle_trace_increment=4, style="wiggle")
+        @test true
+        f, ax = SeisPlotTX(d, dx=dx, dy=dy, pclip=97, cmap=:viridis, style="image")
+        @test true
+        f, ax = SeisPlotTX(d, dx=dx, dy=dy, xcur=2, wiggle_trace_increment=4, pclip=97, cmap=:viridis, style="overlay")
+        @test true
+    end
+
+    @testset "SeisPlotFK" begin
+        f, ax = SeisPlotFK(d, dx=dx, dy=dy, pclip=97, fmax=90)
+
+        @test true
+    end
+
+    @testset "SeisAmplitude" begin
+        f, ax = SeisPlotAmplitude(d, dy=dy, fmax=90)
+
+        @test true
+    end
+
 end