radius_graph

Author: YichengDWu

src/GNNGraphs/GNNGraphs.jl

@@ -60,7 +60,8 @@ export add_nodes,
 
 include("generate.jl")
 export rand_graph, 
-       knn_graph
+       knn_graph,
+       radius_graph
 
 include("sampling.jl")
 export sample_neighbors

src/GNNGraphs/generate.jl

@@ -127,3 +127,78 @@ function knn_graph(points::AbstractMatrix, k::Int;
     end
     return g
 end
+
+"""
+    radius_graph(points::AbstractMatrix, 
+              r::AbstractFloat; 
+              graph_indicator = nothing,
+              self_loops = false, 
+              dir = :in, 
+              kws...)
+
+Create a graph where each node is linked 
+to its neighbors within a given distance `r`.  
+
+# Arguments
+
+- `points`: A num_features × num_nodes matrix storing the Euclidean positions of the nodes.
+- `r`: The radius.
+- `graph_indicator`: Either nothing or a vector containing the graph assigment of each node, 
+                     in which case the returned graph will be a batch of graphs. 
+- `self_loops`: If `true`, consider the node itself among its `k` nearest neighbors, in which
+                case the graph will contain self-loops. 
+- `dir`: The direction of the edges. If `dir=:in` edges go from the `k` 
+         neighbors to the central node. If `dir=:out` we have the opposite
+         direction.
+- `kws`: Further keyword arguments will be passed to the [`GNNGraph ](@ref) constructor.
+
+# Examples
+
+```juliarepl
+julia> n, r = 10, 0.75;
+
+julia> x = rand(3, n);
+
+julia> g = radius_graph(x, r)
+GNNGraph:
+    num_nodes = 10
+    num_edges = 46
+
+julia> graph_indicator = [1,1,1,1,1,2,2,2,2,2];
+
+julia> g = radius_graph(x, r; graph_indicator)
+GNNGraph:
+    num_nodes = 10
+    num_edges = 20
+    num_graphs = 2
+
+```
+"""
+function radius_graph(points::AbstractMatrix, r::AbstractFloat; 
+        graph_indicator = nothing,
+        self_loops = false, 
+        dir = :in, 
+        kws...)
+
+    if graph_indicator !== nothing
+        d, n = size(points)
+        @assert graph_indicator isa AbstractVector{<:Integer}
+        @assert length(graph_indicator) == n
+        
+        # Make sure that the distance between points in different graphs
+        # is always larger than r.
+        dummy_feature = 2r .* reshape(graph_indicator, 1, n)
+        points = vcat(points, dummy_feature)
+    end
+
+    balltree = NearestNeighbors.BallTree(points)
+
+    sortres = false
+    idxs = NearestNeighbors.inrange(balltree, points, r, sortres)
+    
+    g = GNNGraph(idxs; dir, graph_indicator, kws...)
+    if !self_loops
+        g = remove_self_loops(g)
+    end
+    return g
+end

test/GNNGraphs/generate.jl

@@ -50,4 +50,22 @@
         @test all(6 .<= s[ne+1:end] .<= 10)
         @test all(6 .<= t[ne+1:end] .<= 10)     
     end
+
+    @testset "radius_graph" begin
+        n, r = 10, 0.5
+        x = rand(3, n)
+        g = radius_graph(x, r; graph_type=GRAPH_T)
+        @test g.num_nodes == 10
+        @test has_self_loops(g) == false 
+
+        g = radius_graph(x, r; dir=:out, self_loops=true, graph_type=GRAPH_T)
+        @test g.num_nodes == 10
+        @test has_self_loops(g) == true 
+
+        graph_indicator = [1,1,1,1,1,2,2,2,2,2]
+        g = radius_graph(x, r; graph_indicator, graph_type=GRAPH_T)
+        @test g.num_graphs == 2
+        s, t = edge_index(g)
+        @test (s.>5) == (t.>5)  
+    end
 end