Detection functions, minimum working example, some plotting functions

Project.toml

@@ -4,14 +4,21 @@ authors = ["Ashton Bradley <[email protected]>"]
 version = "0.3.6"
 
 [deps]
+Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
+DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 FLoops = "cc61a311-1640-44b5-9fba-1b764f453329"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+FourierGPE = "f013a474-557c-11e9-3596-438edcad9d97"
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
+GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
@@ -31,7 +38,6 @@ FLoops = "~0.2"
 FileIO = "1, 1.8, 1.9"
 Interpolations = "~0.15"
 JLD2 = "~0.4"
-LightGraphs = "1, 1.3"
 NearestNeighbors = "~0.4"
 Parameters = "~0.12"
 ProgressMeter = "1, 1.5, 1.6, 1.7"

examples/3d_detection/periodic_128_quench.jl

@@ -0,0 +1,39 @@
+using FourierGPE
+using VortexDistributions
+using GraphMakie
+
+
+## Load sim
+@load "sim64.jld2" sim
+@load "sol64.jld2" sol
+
+## Isosurface plot of the solution
+
+t_idx = 25
+
+psi = sol[t_idx]
+density = abs2.(psi)
+pmax = maximum(density)
+density = density/pmax
+
+# volume(density, algorithm = :iso)
+
+## Get params for detection
+X = sim.X;
+x = X[1]; y = X[2]; z = X[3];
+x = round.(x, digits=3); y = round.(y, digits=3); z = round.(z, digits=3);
+dx = x[2] - x[1]; dy = y[2] - y[1]; dz = z[2] - z[1];
+
+@time g, vort_lines, vort_loops, vort_rings, vorts_coords = full_algorithm(psi, x, y, z, n_itp = 4);
+graphplot(g, layout = (adj) -> vorts_coords, markersize=0.02, edge_width=1, node_size=5)
+
+## Smoothing
+
+vort_lines_coords = [reduce(vcat, transpose.(vorts_coords[v_line])) for v_line in vort_lines];
+vort_loops_coords = [reduce(vcat, transpose.(vorts_coords[v_loop])) for v_loop in vort_loops];
+vort_rings_coords = [reduce(vcat, transpose.(vorts_coords[v_ring])) for v_ring in vort_rings];
+
+@time vort_lines_ccma_j, vort_loops_ccma_j, vort_rings_ccma_j = vortex_ccma_j(vort_lines_coords, vort_loops_coords, vort_rings_coords, w_ma = 6, w_cc = 3, distrib = "hanning");
+
+graphplot(g, layout = (adj) -> vorts_coords, markersize=0.02, edge_width=0, node_size=5)
+plot_unconnected_vorts_mat(vort_lines_ccma_j, vort_loops_ccma_j, vort_rings_ccma_j, linewidth=5)

examples/3d_detection/periodic_64_quench_sim.jl

@@ -0,0 +1,34 @@
+using FourierGPE
+using VortexDistributions
+
+## Creating a 3D simulation
+
+L=(16.,16.,16.);
+N=(64,64,64);
+sim = Sim(L,N);
+@unpack_Sim sim;
+
+μ = 25.0;
+γ = 0.05;
+tf = 4/γ;
+Nt = 50;
+t = LinRange(0.,tf,Nt);
+
+## Run sim
+x,y,z = X;
+ψi = randn(N)+im*randn(N);
+ϕi = kspace(ψi,sim);
+
+@pack_Sim! sim;
+
+## Evolve in k-space
+# import FourierGPE
+@time sol = runsim(sim); # will take a few minutes to run.
+
+# Mutate the solution to xspace before saving to jld2
+for i in eachindex(sol)
+    sol[i] = xspace(sol[i], sim)
+end
+
+@save "sol64.jld2" sol
+@save "sim64.jld2" sim

src/VortexDistributions.jl

@@ -10,13 +10,15 @@ using SparseArrays
 using FFTW
 using FileIO
 using ProgressMeter
-using LightGraphs
+# using LightGraphs
 using SimpleWeightedGraphs
 
 # 3d deps
+using FLoops, Graphs, Interpolations
+using LinearAlgebra, Distributions, DSP # ccma
 
-using FLoops
-
+# plots
+using GLMakie, GraphPlot, GraphMakie, Colors
 
 const Λ = 0.8249
 
@@ -46,9 +48,11 @@ charge, xpos, ypos, pos,
 
 # 3d functions
 
-find_vortex_points_3d, connect_vortex_points_3d, sort_classified_vorts_3d 
-# , vortInBounds, vortInBounds2, vortInBounds3
-# plot_iso, scatterVortsOnIso, plot_line, scatterClassifiedVortices, periodicPlotting, euclid, vorts3DMatri
+full_algorithm, vortex_ccma_j,
+
+# plotting
+plot_unconnected_vorts_mat
+
 
 # RCA
 # distances, periodic_distances, sparse_distances, 
@@ -62,6 +66,10 @@ include("pointvortex.jl")
 include("detection.jl")
 include("creation.jl")
 
+# 3d 
+include("detection_3d.jl")
+include("ccma.jl")
+include("plotting.jl")
 
 # RCA
 # include("get_dipoles.jl")
@@ -78,9 +86,6 @@ include("creation.jl")
 # utils
 include("utils.jl")
 
-# 3d utils
-include("utils_3d.jl")
-
 @load joinpath(@__DIR__,"cores.jld2") ψi ψa
 
 end

src/ccma.jl

@@ -1,5 +1,3 @@
-using LinearAlgebra, Distributions, DSP 
-
 # Auxiliary Functions
 function get_unit_vector(vec)
     vec_norm = norm(vec)

src/detection_3d.jl

@@ -1,5 +1,3 @@
-using FLoops, Graphs, Interpolations
-
 function link_graph_vorts(g; repeat_end_of_ring=true)
     g_temp = deepcopy(g)
     visited = Set()
@@ -170,6 +168,19 @@ function connect_vortex_ends(vorts, vort_lines, vort_loops, vort_rings, X)
     return connected_vorts
 end
 
+function findvortices_jumps_plane(phase)
+    # phase = angle.(ψ);
+
+    Δϕx, Δϕy = phase_jumps(phase,1),phase_jumps(phase,2)
+
+    circshift!(phase,Δϕx,(0,1))
+    Δϕx .-= phase; Δϕx .-= Δϕy
+    circshift!(phase,Δϕy,(1,0))
+    Δϕx .+= phase
+
+    return abs.(Δϕx)
+end
+
 function findvortices_planes_threaded(ψ; n_itr = 1)
 
     ϕ = angle.(ψ)

src/plotting.jl

@@ -0,0 +1,58 @@
+function plot_unconnected_vorts_mat(vort_lines, vort_loops, vort_rings; linewidth=5)
+    colors = distinguishable_colors(length(vort_lines) + length(vort_loops) + length(vort_rings));
+
+    all_vorts = []
+    all_colors = []
+
+    for i in eachindex(vort_lines)
+        for j in 1:size(vort_lines[i])[1]
+            v_sort = vort_lines[i][j, :]
+            push!(all_vorts, (v_sort[1], v_sort[2], v_sort[3]))
+            push!(all_colors, colors[i])
+        end
+        push!(all_vorts, (NaN, NaN, NaN))
+        push!(all_colors, colors[i])
+    end
+
+    # for i in eachindex(vort_loops)
+    #     for j in eachindex(vort_loops[i])
+    #         v_sort = vort_loops[i][j]
+    #         push!(all_vorts, (v_sort[1], v_sort[2], v_sort[3]))
+    #         push!(all_colors, colors[i + length(vort_lines)])
+    #     end
+    #     push!(all_vorts, (NaN, NaN, NaN))
+    #     push!(all_colors, colors[i + length(vort_lines)])
+    # end
+
+    for i in eachindex(vort_loops)
+        for j in 1:size(vort_loops[i])[1]
+            v_sort = vort_loops[i][j, :]
+            push!(all_vorts, (v_sort[1], v_sort[2], v_sort[3]))
+            push!(all_colors, colors[i + length(vort_lines)])
+        end
+        push!(all_vorts, (NaN, NaN, NaN))
+        push!(all_colors, colors[i + length(vort_lines)])
+    end
+
+    # for i in eachindex(vort_rings)
+    #     for j in eachindex(vort_rings[i])
+    #         v_sort = vort_rings[i][j]
+    #         push!(all_vorts, (v_sort[1], v_sort[2], v_sort[3]))
+    #         push!(all_colors, colors[i + length(vort_lines) + length(vort_loops)])
+    #     end
+    #     push!(all_vorts, (NaN, NaN, NaN))
+    #     push!(all_colors, colors[i + length(vort_lines) + length(vort_loops)])
+    # end
+
+    for i in eachindex(vort_rings)
+        for j in 1:size(vort_rings[i])[1]
+            v_sort = vort_rings[i][j, :]
+            push!(all_vorts, (v_sort[1], v_sort[2], v_sort[3]))
+            push!(all_colors, colors[i + length(vort_lines) + length(vort_loops)])
+        end
+        push!(all_vorts, (NaN, NaN, NaN))
+        push!(all_colors, colors[i + length(vort_lines) + length(vort_loops)])
+    end
+
+    lines!(all_vorts, color=all_colors, linewidth=linewidth)
+end

src/types.jl

@@ -75,6 +75,6 @@ end
 
 mutable struct Cluster <: VortexGroup
     vortices::Array{PointVortex,1}
-    tree::Array{LightGraphs.SimpleGraphs.SimpleEdge{Int64},1}
+    tree::Array{Graphs.SimpleGraphs.SimpleEdge{Int64},1}
 end
 Cluster(vort::Array{PointVortex,1}) = Cluster(vort,spanning_tree(xpos(vort),ypos(vort)))