updated readme again

README.md

@@ -1,12 +1,10 @@
 # SCJ_Projekt
 
-# SCJ Projekt
-
-## Installation
+## Setup
 
 1. **Aktiviere das Projekt**:
    
-   Wechsel in den **Package Manager** von Julia und aktiviere das Projekt:
+   Im **Package Manager** von Julia muss zuerst das Projekt aktiviert werden:
 
     ```julia
     ] activate .
@@ -16,9 +14,10 @@
     ] instantiate
     ```
 
-
-es steht erstmal nur so ein möglicher Projekt Dateiaufbau
-
 ## Nutzung
 
-Wenn ihr `scripts/run_simulation.jl` ausführt, sollte sich mit **Makie** eine GUI öffnen, die einen **Slider** hat, mit dem man ein paar generierte Frames angucken kann.
+```bash
+include("scripts/main.jl")
+```
+
+Wenn der obige Befehl in der REPL ausgeführt wird, öffnet sich mit **Makie** eine GUI, wo unser Produkt zu finden ist!

scripts/main.jl

@@ -6,7 +6,7 @@ using GLMakie
 
 using .Visualization
 
-# GSParams AND FHNParams
+# CombinedPDEParams
 N = 128
 dx = 1.0
 params = (
@@ -22,6 +22,8 @@ params = (
 )
 
 params_obs = Observable{CombinedPDEParams}(CombinedPDEParams(N, dx, params.Du[], params.Dv[], params.F[], params.k[], params.ϵ[], params.a[], params.b[]))
+
+# needed so params in param_boxes are updated
 lift(params.N, params.dx, params.Du, params.Dv, params.F, params.k, params.ϵ, params.a, params.b) do N, dx, Du, Dv, F, k, ϵ, a, b
     params_obs[] = CombinedPDEParams(N, dx, Du, Dv, F, k, ϵ, a, b)
 end

src/fhn_solver.jl

@@ -8,6 +8,18 @@ using Observables
 
 using .Laplacian
 
+"""
+    step_fhn!(U, V, params_obs::Observable; dx=1, dt=0.01)
+
+    calculation of new "matrix" for each iteration (step) with FitzHugh-Nagumo
+
+    # Arguments:
+    `U`: activator matrix
+    `V`: inhibitor matrix
+    `param_obs`: used parameters from CombinedPDEParams
+    `dx`: dx
+    `dt`: dt
+"""
 function step_fhn!(U, V, params_obs::Observable; dx=1, dt=0.01)
     p = params_obs[]
 

src/gray_scott_solver.jl

@@ -6,6 +6,17 @@ using Observables
 
 using .Laplacian
 
+"""
+    step_fhn!(U, V, params_obs::Observable; dx=1, dt=0.01)
+
+    calculation of new "matrix" for each iteration (step) with GrayScott
+
+    # Arguments:
+    `U`: activator matrix
+    `V`: inhibitor matrix
+    `param_obs`: used parameters from CombinedPDEParams
+    `dx`: dx
+"""
 function step_gray_scott!(U, V, params_obs::Observable; dx=1)
     # Extract parameters
     p = params_obs[]

src/utils/constants.jl

@@ -1,28 +1,5 @@
-
-
-abstract type PDEParams end
-
-struct FHNParams <: PDEParams
-    N::Int
-    dx::Float64 # grid spacing
-    Du::Float64
-    Dv::Float64
-    ϵ::Float64
-    a::Float64
-    b::Float64
-end
-
-struct GSParams <: PDEParams
-    N::Int       # grid size
-    dx::Float64  # grid spacing
-    Du::Float64  # diffusion rate U
-    Dv::Float64  # diffusion rate V
-    F::Float64   # feed rate
-    k::Float64   # kill rate
-
-end
-
-struct CombinedPDEParams <: PDEParams
+# This struct includes all parameters needed for FHN and GrayScott
+struct CombinedPDEParams
     N::Int
     dx::Float64
     Du::Float64

src/utils/laplacian.jl

@@ -1,5 +1,14 @@
 module Laplacian
 
+"""
+    laplacian(U::AbstractMatrix{<:Real}, dx::Real)
+
+    laplacian operator implemented in code
+
+    # Arguments:
+    - `U`: activator or inhibitor matrix
+    - `dx`: dx
+"""
 function laplacian(U::AbstractMatrix{<:Real}, dx::Real)
     h2 = dx^2
     center = U[2:end-1, 2:end-1]

src/utils/templates.jl

@@ -3,6 +3,7 @@
 
 module Templates
 
+# square in the center
 function blocks_ic(N)
     u = fill(1.0, N, N)
     v = fill(0.0, N, N)
@@ -21,6 +22,7 @@ function blocks_ic(N)
     return u, v
 end
 
+# column that fills center of matrix. column as wide a 1 / col_width of the matrix
 function column_ic(N)
     u = fill(0.01, N, N)
     v = fill(0.99, N, N)
@@ -36,17 +38,8 @@ function column_ic(N)
     return u, v
 end
 
-function stripe_ic(N)
-    u = zeros(N, N)
-    v = zeros(N, N)
-    for i in 1:N
-        for j in 1:N
-            u[i, j] = 0.1 + 0.05 * sin(2π * j / 10) + 0.01 * randn()
-        end
-    end
-    return u, v
-end
 
+# two rows that are equally distant from both edges
 function two_rows_edge_distance_ic(N)
     row_width = 8
     distance_from_edge = 50
@@ -83,20 +76,7 @@ function two_rows_edge_distance_ic(N)
     return u, v
 end
 
-function center_band_ic(N)
-    u = fill(0.0, N, N)
-    v = fill(0.0, N, N)
-
-    band_width = div(N, 8)
-    row_start = div(N, 2) - div(band_width, 2)
-    row_end = div(N, 2) + div(band_width, 2)
-
-    u[row_start:row_end, :] .= 0.1 .+ 0.01 .* randn(band_width + 1, N)
-    v[row_start:row_end, :] .= 0.1 .+ 0.01 .* randn(band_width + 1, N)
-
-    return u, v
-end
-
+# circle in the center of matrix
 function circle_ic(N)
     u = fill(0.01, N, N)
     v = fill(0.99, N, N)
@@ -112,6 +92,7 @@ function circle_ic(N)
     return u, v
 end
 
+# place three circles at random places of matrix
 function three_circles_random_ic(N)
     u = fill(0.01, N, N)
     v = fill(0.99, N, N)
@@ -125,7 +106,7 @@ function three_circles_random_ic(N)
         error("Matrix size N is too small to place circles of this radius without overlap or going out of bounds.")
     end
 
-    for _ in 1:5 # Place 3 circles
+    for _ in 1:3 # Place # of circles
         # Generate random center coordinates
         cx = rand(min_coord:max_coord)
         cy = rand(min_coord:max_coord)
@@ -141,6 +122,7 @@ function three_circles_random_ic(N)
     return u, v
 end
 
+# like column_ic() but with a squiggle in the middle
 function squiggle_ic(N, Lx=400.0, Ly=400.0)
     uplus = 0.01
     vplus = 0.99
@@ -168,6 +150,7 @@ function squiggle_ic(N, Lx=400.0, Ly=400.0)
     return u, v
 end
 
+# places patches for coral pattern
 function coral_ic(N)
     u = ones(N, N)
     v = zeros(N, N)
@@ -180,6 +163,6 @@ function coral_ic(N)
     return u, v
 end
 
-export blocks_ic, column_ic, squiggle_ic, three_circles_random_ic, circle_ic, center_band_ic, two_rows_edge_distance_ic, coral_ic, stripe_ic
+export blocks_ic, column_ic, two_rows_edge_distance_ic, circle_ic, three_circles_random_ic, squiggle_ic, coral_ic
 
 end

src/visualization.jl

@@ -45,6 +45,19 @@ function reset!(U, V, heat_obs)
     heat_obs[] = copy(U)
 end
 
+
+"""
+    param_box!(grid, row, labeltxt, observable; col)
+
+    Creates a param box
+
+    # Arguments
+    - `grid`: which grid this parameter box is placed in
+    - `row`: row inside the grid
+    - `labeltext`: labeltext in front of param box
+    - `observable`: observable that contains the value for the param
+    - `col`: column inside the grid. Param box uses up 2 columns
+"""
 function param_box!(grid, row, labeltxt, observable::Observable; col=1)
     label_cell = 2 * col - 1
     textbox_cell = 2 * col
@@ -63,23 +76,54 @@ function param_box!(grid, row, labeltxt, observable::Observable; col=1)
     end
 end
 
+"""
+    multi_step!(state, n_steps, heat_obs::Observable, params_obs::Observable; step_method=step_gray_scott!, dx=1)
+
+    returns a new matrix for the heatmap for n steps of computing with the corresponding step_method.
+    The step_methods have different names because switching models via multi-dispatching is too complex.
+
+    # Arguments:
+    - `state`: activator and inhibitor matrices
+    - `n_steps`: # of steps
+    - `param_obs`: observable of the params
+    - `step_method`: step_gray_scott! or step_fhn! method
+    - `dx`: dx
+
+"""
 function multi_step!(state, n_steps, heat_obs::Observable, params_obs::Observable; step_method=step_gray_scott!, dx=1)
     for _ in 1:n_steps
         heat_obs[] = step_method(state[1], state[2], params_obs; dx=1)
     end
 end
 
+"""
+    build_ui(U, V, param_obs_map:, params_obs, heat_obs)
+
+    building the whole ui
+
+    # Arguments:
+    - `U`: activator matrix
+    - `V`: inhibitor matrix
+    - `param_obs_map`: values of the observable
+    - `param_obs`: observable of params
+    - `heat_obs`: used matrix in the heatmap
+
+"""
 function build_ui(U, V, param_obs_map::NamedTuple, params_obs, heat_obs)
 
     reset!(U, V, heat_obs)
-    fig = Figure(size=(1300, 950))
+    fig = Figure(size=(1500, 950))
 
     gh = GridLayout(fig[1, 1])
     dropdown = Menu(fig, options=collect(zip(["Gray-Scott", "FHN"], [:gray_scott, :fhn])))
     gh[1, 1] = dropdown
-    ax = Axis(gh[2, 1])
+    plotgrid = GridLayout()
+    gh[2, 1] = plotgrid
+
+    ax = Axis(plotgrid[1, 1])
+    hm = heatmap!(ax, heat_obs, colormap=:viridis)
+    plotgrid[1, 2] = Colorbar(fig, hm, label="Inhibitor ⇒ Activator")
 
-    hm = Makie.heatmap!(ax, heat_obs, colormap=:viridis)
     deactivate_interaction!(ax, :rectanglezoom)
     ax.aspect = DataAspect()
 
@@ -182,7 +226,6 @@ function build_ui(U, V, param_obs_map::NamedTuple, params_obs, heat_obs)
         heat_obs[] = copy(U)
     end
 
-    # Template Control
     on(btn_cow.clicks) do _
         # fill matrix with random noise
         U = 0.05 .* (2 .* rand(params_obs[].N, params_obs[].N) .- 1)  # noise in [-0.05, 0.05]