3d detection algo

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_64_quench.jl

@@ -0,0 +1,43 @@
+using FourierGPE
+using VortexDistributions
+using GraphMakie
+using GLMakie
+
+
+## Load sim
+@load "sim64.jld2" sim
+@load "sol64.jld2" sol
+
+## params
+t_idx = 27
+psi = sol[t_idx]
+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];
+
+## Isosurface
+density = abs2.(psi)
+pmax = maximum(density)
+density = density/pmax
+xlims = (X[1][1], X[1][end])
+ylims = (X[1][1], X[1][end])
+zlims = (X[1][1], X[1][end])
+volume(xlims, ylims, zlims, density, algorithm = :iso, transparency=true, alpha=0.2)
+
+## Detection
+
+
+@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

@@ -10,20 +10,15 @@ using SparseArrays
 using FFTW
 using FileIO
 using ProgressMeter
-using LightGraphs
+# using LightGraphs
 using SimpleWeightedGraphs
 
 # 3d deps
-# using GLMakie
-using ScikitLearn
-using NearestNeighbors
-using Distances
-using FLoops
+using FLoops, Graphs, Interpolations
+using LinearAlgebra, Distributions, DSP # ccma
 
-# using Colors
-
-
-# import Plots:stroke,scatter!,plot,plot!
+# plots
+using GLMakie, GraphPlot, GraphMakie, Colors
 
 const Λ = 0.8249
 
@@ -53,9 +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, 
@@ -69,6 +66,11 @@ 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")
 # include("seed_clusters.jl")
@@ -84,9 +86,6 @@ include("creation.jl")
 # utils
 include("utils.jl")
 
-# 3d utils
-include("utils_3d.jl")
-
 @load joinpath(@__DIR__,"cores.jld2") ψi ψa
 
 end