Adding normal adjacency, cleaning up tests

Author: GearsAD

REQUIRE

@@ -4,3 +4,4 @@ LightGraphs 1.2.0
 MetaGraphs 0.6.1
 Requires 0.5.2
 DataFrames
+JSON2

src/services/GraphsDFG.jl

@@ -20,6 +20,7 @@ export addFactor!
 export ls, lsf, getVariables, getFactors
 export getVariable, getFactor
 export updateVariable, updateFactor
+export getAdjacencyMatrix
 export getAdjacencyMatrixDataFrame
 export getNeighbors
 export getSubgraphAroundNode
@@ -270,8 +271,22 @@ function getSubGraph(dfg::GraphsDFG, variableFactorLabels::Vector{Symbol}, inclu
     _copyIntoGraph!(dfg, addToDFG, variableFactorLabels, includeOrphanFactors)
     return addToDFG
 end
-#
 
+function getAdjacencyMatrix(dfg::GraphsDFG)::Matrix{Union{Nothing, Symbol}}
+    varLabels = sort(map(v->v.label, getVariables(dfg)))
+    factLabels = sort(map(f->f.label, getFactors(dfg)))
+    vDict = Dict(varLabels .=> [1:length(varLabels)...].+1)
+
+    adjMat = Matrix{Union{Nothing, Symbol}}(nothing, length(factLabels)+1, length(varLabels)+1)
+    # Set row/col headings
+    adjMat[2:end, 1] = factLabels
+    adjMat[1, 2:end] = varLabels
+    for (fIndex, factLabel) in enumerate(factLabels)
+        factVars = getNeighbors(dfg, getFactor(dfg, factLabel))
+        map(vLabel -> adjMat[fIndex+1,vDict[vLabel]] = factLabel, factVars)
+    end
+    return adjMat
+end
 
 function __init__()
     @require DataFrames="a93c6f00-e57d-5684-b7b6-d8193f3e46c0" begin

test/runtests.jl

@@ -6,51 +6,68 @@ using DistributedFactorGraphs.GraphsJlAPI
 dfg = GraphsDFG()
 v1 = DFGVariable(:a)
 v2 = DFGVariable(:b)
-addVariable!(dfg, v1)
-@test_throws Exception addVariable!(dfg, v1)
-addVariable!(dfg, v2)
 f1 = DFGFactor(:f1)
-addFactor!(dfg, f1, [v1, v2])
-@test_throws Exception addFactor!(dfg, DFGFactor("f2"), [v1, DFGVariable("Nope")])
+@testset "Creating Graphs" begin
+    global dfg,v1,v2,f1
+    addVariable!(dfg, v1)
+    @test_throws Exception addVariable!(dfg, v1)
+    addVariable!(dfg, v2)
+    addFactor!(dfg, f1, [v1, v2])
+    @test_throws Exception addFactor!(dfg, DFGFactor("f2"), [v1, DFGVariable("Nope")])
+end
 
-@test length(ls(dfg)) == 2
-@test length(lsf(dfg)) == 1
-# Regexes
-@test ls(dfg, r"a") == [v1]
-@test lsf(dfg, r"f*") == [f1]
+@testset "Listing Nodes" begin
+    global dfg,v1,v2,f1
+    @test length(ls(dfg)) == 2
+    @test length(lsf(dfg)) == 1
+    # Regexes
+    @test ls(dfg, r"a") == [v1]
+    @test lsf(dfg, r"f*") == [f1]
+end
 
 # Gets
-@test getVariable(dfg, v1.label) == v1
-@test getFactor(dfg, f1.label) == f1
-@test_throws Exception getVariable(dfg, :nope)
-@test_throws Exception getVariable(dfg, "nope")
-@test_throws Exception getFactor(dfg, :nope)
-@test_throws Exception getFactor(dfg, "nope")
+@testset "Gets and Sets" begin
+    global dfg,v1,v2,f1
+    @test getVariable(dfg, v1.label) == v1
+    @test getFactor(dfg, f1.label) == f1
+    @test_throws Exception getVariable(dfg, :nope)
+    @test_throws Exception getVariable(dfg, "nope")
+    @test_throws Exception getFactor(dfg, :nope)
+    @test_throws Exception getFactor(dfg, "nope")
 
-# Sets
-v1Prime = deepcopy(v1)
-@test updateVariable(dfg, v1Prime) != v1
-f1Prime = deepcopy(f1)
-@test updateFactor(dfg, f1Prime) != f1
+    # Sets
+    v1Prime = deepcopy(v1)
+    @test updateVariable(dfg, v1Prime) != v1
+    f1Prime = deepcopy(f1)
+    @test updateFactor(dfg, f1Prime) != f1
+end
 
 # Deletions
 # Not supported at present
-@warn "Deletions with Graph.jl is not supported at present"
+@testset "Deletions" begin
+    @warn "Deletions with Graph.jl is not supported at present"
+end
 
 # Connectivity test
-@test isFullyConnected(dfg) == true
-addVariable!(dfg, DFGVariable(:orphan))
-@test isFullyConnected(dfg) == false
+@testset "Connectivity Test" begin
+    global dfg,v1,v2,f1
+    @test isFullyConnected(dfg) == true
+    addVariable!(dfg, DFGVariable(:orphan))
+    @test isFullyConnected(dfg) == false
+end
 
 # Adjacency matrices
-adjMat = getAdjacencyMatrixDataFrame(dfg)
-@test size(adjMat) == (4,4)
-
-# Testing
-using Test
-using DataFrames
-using DistributedFactorGraphs
-using DistributedFactorGraphs.GraphsJlAPI
+@testset "Adjacency Matrices" begin
+    global dfg,v1,v2,f1
+    # Normal
+    adjMat = getAdjacencyMatrix(dfg)
+    @test size(adjMat) == (2,4)
+    @test adjMat[1, :] == [nothing, :a, :b, :orphan]
+    @test adjMat[2, :] == [:f1, :f1, :f1, nothing]
+    # Dataframe
+    adjDf = getAdjacencyMatrixDataFrame(dfg)
+    @test size(adjDf) == (1,4)
+end
 
 # Now make a complex graph for connectivity tests
 numNodes = 10
@@ -59,37 +76,27 @@ verts = map(n -> DFGVariable(Symbol("x$n")), 1:numNodes)
 map(v -> addVariable!(dfg, v), verts)
 map(n -> addFactor!(dfg, DFGFactor(Symbol("x$(n)x$(n+1)f1")), [verts[n], verts[n+1]]), 1:(numNodes-1))
 # map(n -> addFactor!(dfg, [verts[n], verts[n+2]], DFGFactor(Symbol("x$(n)x$(n+2)f2"))), 1:2:(numNodes-2))
-adjMat = getAdjacencyMatrixDataFrame(dfg)
 
-# Get neighbors tests
-@test getNeighbors(dfg, verts[1]) == [:x1x2f1]
-neighbors = getNeighbors(dfg, getFactor(dfg, :x1x2f1))
-@test all([v in [:x1, :x2] for v in neighbors])
-# Testing aliases
-@test getNeighbors(dfg, getFactor(dfg, :x1x2f1)) == ls(dfg, getFactor(dfg, :x1x2f1))
-@test getNeighbors(dfg, :x1x2f1) == ls(dfg, :x1x2f1)
-
-# Subgraphs
-dfgSubgraph = getSubgraphAroundNode(dfg, verts[1], 2)
-# Only returns x1 and x2
-@test all([v in [:x1, :x1x2f1, :x2] for v in map(n -> n.label, [ls(dfgSubgraph)..., lsf(dfgSubgraph)...])])
-# Test include orphan factorsVoid
-dfgSubgraph = getSubgraphAroundNode(dfg, verts[1], 1, true)
-@test all([v in [:x1, :x1x2f1] for v in map(n -> n.label, [ls(dfgSubgraph)..., lsf(dfgSubgraph)...])])
-# Test adding to the dfg
-dfgSubgraph = getSubgraphAroundNode(dfg, verts[1], 2, true, dfgSubgraph)
-@test all([v in [:x1, :x1x2f1, :x2] for v in map(n -> n.label, [ls(dfgSubgraph)..., lsf(dfgSubgraph)...])])
-
-# Adjacency matrix
-varLabels = sort(map(v->v.label, getVariables(dfg)))
-factLabels = sort(map(f->f.label, getFactors(dfg)))
-adjDf = DataFrame(:Factor => Union{Missing, Symbol}[])
-for varLabel in varLabels
-    adjDf[varLabel] = Union{Missing, Symbol}[]
+@testset "Getting Neighbors" begin
+    global dfg,verts
+    # Get neighbors tests
+    @test getNeighbors(dfg, verts[1]) == [:x1x2f1]
+    neighbors = getNeighbors(dfg, getFactor(dfg, :x1x2f1))
+    @test all([v in [:x1, :x2] for v in neighbors])
+    # Testing aliases
+    @test getNeighbors(dfg, getFactor(dfg, :x1x2f1)) == ls(dfg, getFactor(dfg, :x1x2f1))
+    @test getNeighbors(dfg, :x1x2f1) == ls(dfg, :x1x2f1)
 end
-for (i, factLabel) in enumerate(factLabels)
-    global adjDf
-    push!(adjDf, [factLabel, missings(length(varLabels))...])
-    factVars = getNeighbors(dfg, getFactor(dfg, factLabel))
-    map(vLabel -> adjDf[vLabel][i] = factLabel, factVars)
+
+@testset "Getting Subgraphs" begin
+    # Subgraphs
+    dfgSubgraph = getSubgraphAroundNode(dfg, verts[1], 2)
+    # Only returns x1 and x2
+    @test all([v in [:x1, :x1x2f1, :x2] for v in map(n -> n.label, [ls(dfgSubgraph)..., lsf(dfgSubgraph)...])])
+    # Test include orphan factorsVoid
+    dfgSubgraph = getSubgraphAroundNode(dfg, verts[1], 1, true)
+    @test all([v in [:x1, :x1x2f1] for v in map(n -> n.label, [ls(dfgSubgraph)..., lsf(dfgSubgraph)...])])
+    # Test adding to the dfg
+    dfgSubgraph = getSubgraphAroundNode(dfg, verts[1], 2, true, dfgSubgraph)
+    @test all([v in [:x1, :x1x2f1, :x2] for v in map(n -> n.label, [ls(dfgSubgraph)..., lsf(dfgSubgraph)...])])
 end