Pass on plots

Author: guilgautier

docs/plots/hard_core_graph.jl

@@ -1,16 +1,16 @@
-# const PRS = PartialRejectionSampling, Plots, GraphPlot, Colors, LS = LazySets, LG = LightGraphs
-includet("docs/plots/pedagogy_graph.jl")
+include(joinpath(@__DIR__, "pedagogy_graph.jl"))
+using Random
 
 dims = [5, 5]
 g = LG.grid(dims)
 β = 1.0
 
 hcg = PRS.HardCoreGraph(g, β)
 
-using Random
 rng = Random.MersenneTwister(123)
 @time sample = PRS.generate_sample_prs(rng, hcg)
 
-p = plot(hcg, sample, dims, "docs/plots/output/hard_core_graph.pdf")
+path = joinpath(@__DIR__, "output", "hard_core_graph", "hard_core_graph.pdf")
+p = plot(hcg, sample, dims, path)
 
-@time sample = PRS.generate_sample_prs(hcg)
+# @time sample = PRS.generate_sample_prs(hcg)

docs/plots/hard_core_graph_pedagogy.jl

@@ -1,67 +1,11 @@
-# const PRS = PartialRejectionSampling, Plots, GraphPlot, Colors, LS = LazySets, LG = LightGraphs
-includet("docs/plots/pedagogy_graph.jl")
+include(joinpath(@__DIR__, "pedagogy_graph.jl"))
 using Random
 
 dims = [5, 5]
 g = LG.grid(dims)
 β = 0.5
 
 pp = PRS.HardCoreGraph(g, β)
-
 rng = Random.MersenneTwister(123)
 
-path(i) = joinpath("docs/plots/output/hard_core_graph", join([lpad(i, 3, "0"), ".pdf"]))
-
-c_node_normal = Colors.colorant"turquoise";
-
-c_node_unccupied = Colors.colorant"white";
-c_node_occupied = Colors.colorant"gray";
-
-c_node_update = Colors.colorant"orange";
-c_node_bad = Colors.colorant"red";
-
-i = 0
-c_nodes = fill(c_node_normal, LG.nv(pp.graph))
-plot(pp.graph, dims, path(i); nodefillc=c_nodes)
-
-proba = pp.β / (one(pp.β) + pp.β)
-
-adj = LG.adjacency_matrix(pp.graph)
-occupied = Random.randsubseq(rng, LG.vertices(pp.graph), proba)
-
-while true
-
-    i += 1
-    c_nodes = fill(c_node_unccupied, LG.nv(pp.graph))
-    c_nodes[occupied] .= c_node_occupied
-    plot(pp.graph, dims, path(i); nodefillc=c_nodes)
-
-    # Check if occupied vertices form an independent set
-    sub_graph = LG.SimpleGraph(adj[occupied, occupied])
-    LG.ne(sub_graph) == 0 && break
-
-    bad = []
-    independent, resample = [], Set()
-    for cc in LG.connected_components(sub_graph)
-        if length(cc) == 1  # Identify current independent vertices
-            append!(independent, occupied[cc])
-        else  # Construct the resampling set of vertices
-            union!(resample, occupied[cc])
-            union!(bad, occupied[cc])
-            for v in cc
-                union!(resample, LG.neighbors(pp.graph, occupied[v]))
-            end
-        end
-    end
-
-    i += 1
-    c_nodes[bad] .= c_node_bad
-    plot(pp.graph, dims, path(i); nodefillc=c_nodes)
-
-    Random.randsubseq!(rng, occupied, collect(resample), proba)
-    append!(occupied, independent)
-
-    i += 1
-    c_nodes[collect(resample)] .= c_node_update;
-    plot(pp.graph, dims, path(i); nodefillc=c_nodes)
-end
+hard_core_graph_pedagogy(pp, dims, rng)

docs/plots/hard_core_spatial.jl

@@ -1,5 +1,5 @@
-# const PRS = PartialRejectionSampling, Plots, GraphPlot, Colors, LS = LazySets, LG = LightGraphs
-includet("docs/plots/pedagogy_spatial.jl")
+include(joinpath(@__DIR__, "pedagogy_spatial.jl"))
+using Random
 
 β₀ = 0.1
 r = 0.05  # interaction range = 2*radius
@@ -10,7 +10,6 @@ win = PRS.SquareWindow(c, w)
 
 hc = PRS.HardCorePointProcess(b, r, win)
 
-using Random
 rng = Random.MersenneTwister(123)
 @time sample = PRS.generate_sample_prs(rng, hc)
 # @time sample = PRS.generate_sample_grid_prs(rng, hc)

docs/plots/hard_core_spatial_pedagogy.jl

@@ -1,5 +1,5 @@
-# const PRS = PartialRejectionSampling, Plots, GraphPlot, Colors, LS = LazySets, LG = LightGraphs
-includet("docs/plots/pedagogy_spatial.jl")
+include(joinpath(@__DIR__, "pedagogy_spatial.jl"))
+using Random
 
 β₀ = 0.3
 r = 0.1  # interaction range = 2*radius
@@ -10,6 +10,5 @@ win = PRS.SquareWindow(c, w)
 
 hc = PRS.HardCorePointProcess(b, r, win)
 
-using Random
 rng = Random.MersenneTwister(123)
-pedagogy_generate_sample_prs(hc; rng=rng)
+hard_core_spatial_pedagogy(hc; rng=rng)

docs/plots/ising_gibbs_perfect.jl

@@ -1,15 +1,14 @@
-# const PRS = PartialRejectionSampling, Plots, GraphPlot, Colors, LS = LazySets, LG = LightGraphs
-includet("docs/plots/pedagogy_graph.jl")
+include(joinpath(@__DIR__, "pedagogy_graph.jl"))
+using Random
 
 dims = [15, 15] # if > (14, 14) the display becomes all black, don't know why !
 periodic = false
 H, J = 0.0, 0.01
 
 ising = PRS.Ising(dims, J, H; periodic=periodic)
 
-using Random
 rng = Random.MersenneTwister(123)
 @time sample = PRS.generate_sample_gibbs_perfect(rng, ising)
 
-p = plot(ising, sample, dims, "docs/plots/output/ising_gibbs_perfect.pdf";
-         nodelabel=nothing)
+path = joinpath(@__DIR__, "output", "ising", "ising_gibbs_perfect.pdf")
+p = plot(ising, sample, dims, path; nodelabel=nothing)

docs/plots/ising_grid_prs.jl

@@ -1,5 +1,5 @@
-# const PRS = PartialRejectionSampling, Plots, GraphPlot, Colors, LS = LazySets, LG = LightGraphs
-includet("docs/plots/pedagogy_graph.jl")
+include(joinpath(@__DIR__, "pedagogy_graph.jl"))
+using Random
 
 dims = [5, 5] # if > (14, 14) the display becomes all black, don't know why !
 periodic = false
@@ -11,5 +11,5 @@ using Random
 rng = Random.MersenneTwister(123)
 @time sample = PRS.generate_sample_gibbs_perfect(rng, ising)
 
-p = plot(ising, sample, dims, "docs/plots/output/ising/ising_grid_prs.pdf";
-         nodelabel=nothing)
+path = joinpath(@__DIR__, "output", "ising", "ising_grid_prs.pdf")
+p = plot(ising, sample, dims, path; nodelabel=nothing)

docs/plots/pattern_free_string_prs.jl

@@ -1,8 +1,10 @@
+using PartialRejectionSampling
+using Random
+
 n = 100
-alph = ["A", "C", "G", "T"]
+alphabet = ["A", "C", "G", "T"]
 pattern = "ACAC"
-pfs = PRS.PatternFreeString(alph, pattern)
+pfs = PRS.PatternFreeString(pattern, alphabet)
 
-using Random
 rng = Random.MersenneTwister(123)
 @time PRS.generate_sample_prs(rng, pfs, n)