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First local build of the docs
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‎docs/Project.toml‎

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[deps]
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"

‎docs/make.jl‎

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using Documenter, PartialRejectionSampling
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using DocumenterCitations
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bib = CitationBibliography(joinpath(@__DIR__, "src", "prs.bib"))
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# DocMeta.setdocmeta!(PartialRejectionSampling, :DocTestSetup, :(using PartialRejectionSampling); recursive=true)
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makedocs(
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sitename="My Documentation",
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bib,
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sitename="PartialRejectionSampling.jl",
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modules = [PartialRejectionSampling],
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pages=[
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"Home" => "index.md",
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"Sampling methods" => "sampling.md",
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"Graph point processes" => "graph.md",
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"Spatial point processes" => "spatial.md",
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"Misc" => "pattern_free_string.md",
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"References" => "references.md"
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]
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# doctest=:fix # = false to skip doctests
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)

‎docs/pedagogy.jl‎

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using Plots
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using GraphPlot, Colors
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using LazySets
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const LS = LazySets
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# Pedagogy
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function pedagogy_generate_sample_prs(
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hc::HardCorePointProcess{T};
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win::Union{Nothing,AbstractWindow}=nothing,
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path="",
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rng=-1
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)::Vector{T} where {T}
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rng = getRNG(rng)
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window_ = win === nothing ? window(hc) : win
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n = rand(rng, Distributions.Poisson(hc.β * volume(window_)))
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points = Matrix{Float64}(undef, dimension(hc), n)
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for x in eachcol(points)
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x .= rand(window_; rng=rng)
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end
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i = 0
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while true
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p = pedagogy_plot(points, true, 0.0, "white", hc.window)
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Plots.savefig(p, "$(path)/hard_core_$(i)_0.pdf")
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p = pedagogy_plot(points, true, hc.r/2, "white", hc.window)
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Plots.savefig(p, "$(path)/hard_core_$(i)_1.pdf")
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bad = vec(any(pairwise_distances(points) .< hc.r, dims=2))
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!any(bad) && break
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pedagogy_plot!(p, points[:, bad], false, hc.r/2, "red", hc.window)
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Plots.savefig(p, "$(path)/hard_core_$(i)_1bad_region.pdf")
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pedagogy_plot!(p, points[:, bad], false, hc.r, "orange", hc.window)
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Plots.savefig(p, "$(path)/hard_core_$(i)_2resample_region.pdf")
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p = pedagogy_plot(points[:, .!bad], true, 0.0, "white", hc.window)
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pedagogy_plot!(p, points[:, bad], false, hc.r, "orange", hc.window)
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Plots.savefig(p, "$(path)/hard_core_$(i)_3resample_region.pdf")
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resampled = generate_sample_poisson_union_balls(hc.β, points[:, bad], hc.r; win=window_, rng=rng)
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pedagogy_plot!(p, resampled, true, 0, "blue", hc.window)
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Plots.savefig(p, "$(path)/hard_core_$(i)_4resampled_points.pdf")
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points = hcat(points[:, .!bad], resampled)
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i += 1
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end
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return [points[:, i] for i in 1:size(points, 2)]
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end
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function pedagogy_plot!(
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p,
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points,
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show_center=true,
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radius=0.0,
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color="white",
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window=SquareWindow(zeros(2), 1.0)
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)
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for x in (points isa Matrix ? eachcol(points) : points)
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if show_center
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Plots.scatter!(p, [x[1]], [x[2]], markersize=2, color=color)
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end
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if radius > 0
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Plots.plot!(p, LS.Ball2(vec(x), radius), color=color)
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end
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end
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Plots.xlims!(window.c[1], window.c[1] + window.w)
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Plots.ylims!(window.c[2], window.c[2] + window.w)
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return p
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end
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function pedagogy_plot(
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points,
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show_center=true,
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radius=0.0,
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color="white",
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window=SquareWindow(zeros(2), 1.0)
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)
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p = Plots.plot([0], [0],
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label="", legend=false,
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color="white",
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linewidth=0.0,
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aspect_ratio=:equal,
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grid=:none,
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title="")
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pedagogy_plot!(p, points, show_center, radius, color, window)
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return p
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end
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function plot(
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pp::AbstractSpatialPointProcess,
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points;
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title=""
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)
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p = Plots.plot([0], [0],
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label="", legend=false,
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color="white",
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linewidth=0.0,
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aspect_ratio=:equal,
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grid=:none,
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title=title)
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θ = collect(range(0, 2π, length=15))
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rad = pp.r / 2 # radius = interaction range / 2
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circ_x, circ_y = rad .* cos.(θ), rad .* sin.(θ)
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for x in points
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Plots.plot!(x[1] .+ circ_x,
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x[2] .+ circ_y,
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color="black",
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linewidth=0.5)
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end
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win = pp.window
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Plots.xlims!(win.c[1], win.c[1] + win.w[1])
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Plots.ylims!(win.c[2], win.c[2] + (win.w isa Number ? win.w[1] : win.w[2]))
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return p
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end
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function plot(
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ising::Ising,
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state,
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width::Int=0,
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height::Int=0
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)
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if width == 0 || height == 0
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p = GraphPlot.gplot(ising.graph,
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nodelabel=LG.vertices(ising.graph),
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nodefillc=col_nodes
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)
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return p
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else
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pos = collect(Iterators.product(1:height, 1:width))[:]
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locs_x, locs_y = map(x->x[1], pos), map(x->x[2], pos)
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col_nodes = ifelse.(
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state .== 1,
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Colors.colorant"gray",
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Colors.colorant"white")
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p = GraphPlot.gplot(
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ising.graph,
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locs_x,
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reverse(locs_y),
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nodefillc=col_nodes)
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return p
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end
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end
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function plot(
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hcg::HardCoreGraph,
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state,
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width::Int=0,
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height::Int=0
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)
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col_nodes = [Colors.colorant"turquoise" for _ in 1:LG.nv(hcg.graph)]
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col_nodes[state] .= Colors.colorant"red"
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if width == 0 || height == 0
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p = GraphPlot.gplot(hcg.graph,
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nodelabel=LG.vertices(hcg.graph),
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nodefillc=col_nodes
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)
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return p
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else
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pos = collect(Iterators.product(1:height, 1:width))[:]
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locs_x, locs_y = map(x->x[1], pos), map(x->x[2], pos)
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p = GraphPlot.gplot(hcg.graph,
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locs_x,
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reverse(locs_y),
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nodelabel=LG.vertices(hcg.graph),
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nodefillc=col_nodes
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)
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return p
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end
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end
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function plot(
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rsf::RootedSpanningForest,
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sample,
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width::Int=0,
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height::Int=0
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)
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col_nodes, col_edges = color_cycles(sample)
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col_nodes[collect(rsf.roots)] .= Colors.colorant"orange"
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if width == 0 || height == 0
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p = GraphPlot.gplot(sample,
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nodelabel=LG.vertices(sample),
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nodefillc=col_nodes,
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edgestrokec=col_edges,
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arrowlengthfrac=0.05,
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)
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return p
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else
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pos = collect(Iterators.product(1:height, 1:width))[:]
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locs_x, locs_y = map(x->x[1], pos), map(x->x[2], pos)
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p = GraphPlot.gplot(sample,
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locs_x,
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reverse(locs_y),
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nodelabel=LG.vertices(sample),
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nodefillc=col_nodes,
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edgestrokec=col_edges,
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arrowlengthfrac=0.05,
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)
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return p
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end
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end
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function color_cycles(
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graph::LG.SimpleDiGraph{T}
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) where {T}
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edge_map = edgemap(graph)
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edge_idx = T[]
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nodes = Set{T}()
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for cycle in LG.simplecycles(graph)
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union!(nodes, cycle)
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for (x, y) in zip(cycle, circshift(cycle, -1))
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push!(edge_idx, edge_map[LG.Edge(x, y)])
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end
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end
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col_nodes = [colorant"turquoise" for _ in 1:LG.nv(graph)]
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col_nodes[collect(nodes)] .= colorant"red"
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col_edges = [colorant"lightgray" for _ in 1:LG.ne(graph)]
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col_edges[edge_idx] .= colorant"red"
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return col_nodes, col_edges
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end
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function plot(
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sfg::SinkFreeGraph,
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sample,
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width::Int=0,
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height::Int=0
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)
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col_nodes = [LG.outdegree(sample, v) == 0 ? colorant"red" : colorant"turquoise"
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for v in LG.vertices(sample)]
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if width == 0 || height == 0
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p = GraphPlot.gplot(sample,
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nodelabel=LG.vertices(sample),
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nodefillc=col_nodes,
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arrowlengthfrac=0.05,
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)
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return p
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else
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pos = collect(Iterators.product(1:height, 1:width))[:]
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locs_x, locs_y = map(x->x[1], pos), map(x->x[2], pos)
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p = GraphPlot.gplot(sample,
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locs_x,
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reverse(locs_y),
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nodelabel=LG.vertices(sample),
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nodefillc=col_nodes,
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arrowlengthfrac=0.05,
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)
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return p
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end
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end
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function color_sinks(
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graph::LG.SimpleDiGraph{T}
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) where {T}
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nodes = T[]
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edge_idx = T[]
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edge_map = edgemap(graph)
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for v in sink_nodes(graph)
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push!(nodes, v)
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for w in LG.inneighbors(graph, v)
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push!(edge_idx, edge_map[LG.Edge(w, v)])
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end
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end
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col_nodes = [Colors.colorant"turquoise" for _ in 1:LG.nv(graph)]
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col_nodes[nodes] .= Colors.colorant"red"
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col_edges = [Colors.colorant"lightgray" for _ in 1:LG.ne(graph)]
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col_edges[edge_idx] .= Colors.colorant"red"
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return col_nodes, col_edges
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end

‎docs/src/graph.md‎

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# Graph point processes
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```@docs
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PRS.AbstractGraphPointProcess
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PRS.GraphNode
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```
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## Hard core graph
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```@autodocs
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Modules = [PartialRejectionSampling]
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Pages = ["graph/hard_core.jl"]
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Private = true
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Order = [:module, :constant, :type, :function, :macro]
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```
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## Rooted spanning forests
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```@autodocs
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Modules = [PartialRejectionSampling]
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Pages = ["graph/rooted_spanning_forest.jl"]
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Private = true
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Order = [:module, :constant, :type, :function, :macro]
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```
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## Sink free graph
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```@autodocs
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Modules = [PartialRejectionSampling]
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Pages = ["graph/sink_free_graph.jl"]
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Private = true
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Order = [:module, :constant, :type, :function, :macro]
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```
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## Ising model
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```@autodocs
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Modules = [PartialRejectionSampling]
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Pages = ["graph/window.jl",
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"graph/ising.jl",
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"graph/ising_sampling_gibbs_perfect.jl",
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"graph/ising_sampling_grid_prs"]
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Private = true
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Order = [:module, :constant, :type, :function, :macro]
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```

‎docs/src/index.md‎

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# PartialRejectionSampling.jl Documentation
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```@contents
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```
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## Functions
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83
## Index
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```@index

‎docs/src/pattern_free_string.md‎

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## Pattern Free String
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```@autodocs
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Modules = [PartialRejectionSampling]
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Pages = ["misc/pattern_free_string.jl"]
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Private = true
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Order = [:module, :constant, :type, :function, :macro]
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```

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