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getAdjacencyMatrixSparse integration (#86)
* getAdjacencyMatrixSparse - LigthDFG - LightGraphsDFG - SymbolDFG - GraphsDFG
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11 files changed

+80
-46
lines changed

11 files changed

+80
-46
lines changed

‎Project.toml

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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name = "DistributedFactorGraphs"
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uuid = "b5cc3c7e-6572-11e9-2517-99fb8daf2f04"
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version = "0.3.2"
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version = "0.4.0"
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[deps]
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -15,6 +15,7 @@ MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
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Neo4j = "d2adbeaf-5838-5367-8a2f-e46d570981db"
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Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
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Requires = "ae029012-a4dd-5104-9daa-d747884805df"
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SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
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[compat]
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Distributions = "≥ 0.18"

‎src/DistributedFactorGraphs.jl

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@@ -8,6 +8,7 @@ using Distributions
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using Reexport
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using JSON2
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using LinearAlgebra
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using SparseArrays
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# Entities
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include("entities/AbstractTypes.jl")
@@ -38,6 +39,10 @@ export pack, unpack
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include("services/AbstractDFG.jl")
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include("services/DFGVariable.jl")
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#TODO @sam I'm just doing it like this at the moment because I don't know a better way.
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include("services/interfaces.jl")
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export getAdjacencyMatrixSparse
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# Include the Graphs.jl API.
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include("GraphsDFG/GraphsDFG.jl")
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‎src/GraphsDFG/services/GraphsDFG.jl

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Original file line numberDiff line numberDiff line change
@@ -484,6 +484,21 @@ function getAdjacencyMatrix(dfg::GraphsDFG)::Matrix{Union{Nothing, Symbol}}
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return adjMat
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end
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function getAdjacencyMatrixSparse(dfg::GraphsDFG)::Tuple{LightGraphs.SparseMatrixCSC, Vector{Symbol}, Vector{Symbol}}
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varLabels = map(v->v.label, getVariables(dfg))
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factLabels = map(f->f.label, getFactors(dfg))
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vDict = Dict(varLabels .=> [1:length(varLabels)...])
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adjMat = spzeros(Int, length(factLabels), length(varLabels))
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for (fIndex, factLabel) in enumerate(factLabels)
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factVars = getNeighbors(dfg, getFactor(dfg, factLabel))
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map(vLabel -> adjMat[fIndex,vDict[vLabel]] = 1, factVars)
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end
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return adjMat, varLabels, factLabels
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end
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487502
"""
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$(SIGNATURES)
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Produces a dot-format of the graph for visualization.

‎src/LightDFG/LightDFG.jl

Lines changed: 2 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,8 @@ import ...DistributedFactorGraphs: setSolverParams,
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getNeighbors,
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getSubgraphAroundNode,
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getSubgraph,
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getAdjacencyMatrix
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getAdjacencyMatrix,
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getAdjacencyMatrixSparse
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include("FactorGraphs/FactorGraphs.jl")
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using .FactorGraphs
@@ -46,21 +47,5 @@ include("services/LightDFG.jl")
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# Exports
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export LightDFG
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49-
export exists
50-
export getLabelDict, getDescription, setDescription, getInnerGraph, getAddHistory, getSolverParams, setSolverParams
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#
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export getAddHistory, getDescription, getLabelDict
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export addVariable!, addFactor!
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export ls, lsf, getVariables, getFactors, getVariableIds, getFactorIds
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export getVariable, getFactor
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export updateVariable!, updateFactor!
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export deleteVariable!, deleteFactor!
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export getAdjacencyMatrix
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export getAdjacencyMatrixDataFrame
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export getNeighbors
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export getSubgraphAroundNode
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export getSubgraph
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export isFullyConnected, hasOrphans
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export toDot, toDotFile
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end

‎src/LightDFG/services/LightDFG.jl

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Original file line numberDiff line numberDiff line change
@@ -466,6 +466,18 @@ function getAdjacencyMatrix(dfg::LightDFG)::Matrix{Union{Nothing, Symbol}}
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return adjMat
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end
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function getAdjacencyMatrixSparse(dfg::LightDFG)::Tuple{LightGraphs.SparseMatrixCSC, Vector{Symbol}, Vector{Symbol}}
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varLabels = collect(keys(dfg.g.variables))
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factLabels = collect(keys(dfg.g.factors))
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varIndex = [dfg.g.labels[s] for s in varLabels]
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factIndex = [dfg.g.labels[s] for s in factLabels]
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475+
adj = adjacency_matrix(dfg.g)
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477+
adjvf = adj[factIndex, varIndex]
478+
return adjvf, varLabels, factLabels
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end
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#=
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"""
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$(SIGNATURES)

‎src/LightGraphsDFG/services/LightGraphsDFG.jl

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@@ -510,8 +510,8 @@ Rows are all factors, columns are all variables, and each cell contains either n
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The first row and first column are factor and variable headings respectively.
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"""
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function getAdjacencyMatrix(dfg::LightGraphsDFG)::Matrix{Union{Nothing, Symbol}}
513-
varLabels = sort(map(v->v.label, getVariables(dfg)))
514-
factLabels = sort(map(f->f.label, getFactors(dfg)))
513+
varLabels = map(v->v.label, getVariables(dfg))
514+
factLabels = map(f->f.label, getFactors(dfg))
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vDict = Dict(varLabels .=> [1:length(varLabels)...].+1)
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517517
adjMat = Matrix{Union{Nothing, Symbol}}(nothing, length(factLabels)+1, length(varLabels)+1)
@@ -525,7 +525,7 @@ function getAdjacencyMatrix(dfg::LightGraphsDFG)::Matrix{Union{Nothing, Symbol}}
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return adjMat
526526
end
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528-
function getAdjacencyMatrixSparse(dfg::LightGraphsDFG)
528+
function getAdjacencyMatrixSparse(dfg::LightGraphsDFG)::Tuple{LightGraphs.SparseMatrixCSC, Vector{Symbol}, Vector{Symbol}}
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adj = LightGraphs.adjacency_matrix(dfg.g)
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v_labels = getVariableIds(dfg)
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f_labels = getFactorIds(dfg)

‎src/SymbolDFG/SymbolDFG.jl

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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,10 @@
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module SymbolDFGs
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using LightGraphs
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using SparseArrays
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using DocStringExtensions
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import ...DistributedFactorGraphs: AbstractDFG, DFGNode, AbstractParams, NoSolverParams, DFGVariable, DFGFactor
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# import DFG functions to exstend
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import ...DistributedFactorGraphs: setSolverParams,
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getInnerGraph,
@@ -31,7 +33,8 @@ import ...DistributedFactorGraphs: setSolverParams,
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getNeighbors,
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getSubgraphAroundNode,
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getSubgraph,
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getAdjacencyMatrix
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getAdjacencyMatrix,
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getAdjacencyMatrixSparse
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include("SymbolFactorGraphs/SymbolFactorGraphs.jl")
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using .SymbolFactorGraphs
@@ -44,21 +47,5 @@ include("services/SymbolDFG.jl")
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# Exports
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export SymbolDFG
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47-
export exists
48-
export getLabelDict, getDescription, setDescription, getInnerGraph, getAddHistory, getSolverParams, setSolverParams
49-
#
50-
export getAddHistory, getDescription, getLabelDict
51-
export addVariable!, addFactor!
52-
export ls, lsf, getVariables, getFactors, getVariableIds, getFactorIds
53-
export getVariable, getFactor
54-
export updateVariable!, updateFactor!
55-
export deleteVariable!, deleteFactor!
56-
export getAdjacencyMatrix
57-
export getAdjacencyMatrixDataFrame
58-
export getNeighbors
59-
export getSubgraphAroundNode
60-
export getSubgraph
61-
export isFullyConnected, hasOrphans
62-
export toDot, toDotFile
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end

‎src/SymbolDFG/entities/SymbolDFG.jl

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@@ -1,7 +1,4 @@
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import ...DistributedFactorGraphs: AbstractDFG, DFGNode, AbstractParams, NoSolverParams, DFGVariable, DFGFactor
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4-
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mutable struct SymbolDFG{T <: AbstractParams, V <: DFGNode, F <:DFGNode} <: AbstractDFG
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g::SymbolFactorGraph{V,F}
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description::String

‎src/SymbolDFG/services/SymbolDFG.jl

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@@ -1,4 +1,3 @@
1-
import ...DistributedFactorGraphs: DFGVariable, DFGFactor
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# Accessors
43
getLabelDict(dfg::SymbolDFG) = dfg.labelDict
@@ -461,8 +460,8 @@ Rows are all factors, columns are all variables, and each cell contains either n
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The first row and first column are factor and variable headings respectively.
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"""
463462
function getAdjacencyMatrix(dfg::SymbolDFG)::Matrix{Union{Nothing, Symbol}}
464-
varLabels = sort(map(v->v.label, getVariables(dfg)))
465-
factLabels = sort(map(f->f.label, getFactors(dfg)))
463+
varLabels = map(v->v.label, getVariables(dfg))
464+
factLabels = map(f->f.label, getFactors(dfg))
466465
vDict = Dict(varLabels .=> [1:length(varLabels)...].+1)
467466

468467
adjMat = Matrix{Union{Nothing, Symbol}}(nothing, length(factLabels)+1, length(varLabels)+1)
@@ -476,6 +475,21 @@ function getAdjacencyMatrix(dfg::SymbolDFG)::Matrix{Union{Nothing, Symbol}}
476475
return adjMat
477476
end
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478+
479+
function getAdjacencyMatrixSparse(dfg::SymbolDFG)::Tuple{LightGraphs.SparseMatrixCSC, Vector{Symbol}, Vector{Symbol}}
480+
varLabels = collect(keys(dfg.g.variables))
481+
factLabels = collect(keys(dfg.g.factors))
482+
483+
vDict = Dict(varLabels .=> [1:length(varLabels)...])
484+
485+
adjMat = spzeros(Int, length(factLabels), length(varLabels))
486+
487+
for (fIndex, factLabel) in enumerate(factLabels)
488+
factVars = outneighbors(dfg.g, factLabel)
489+
map(vLabel -> adjMat[fIndex,vDict[vLabel]] = 1, factVars)
490+
end
491+
return adjMat, varLabels, factLabels
492+
end
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#=
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"""
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$(SIGNATURES)

‎src/services/interfaces.jl

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@@ -0,0 +1,8 @@
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"""
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$(SIGNATURES)
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Get an adjacency matrix for the DFG, returned as a tuple: adjmat::SparseMatrixCSC{Int}, var_labels::Vector{Symbol) fac_labels::Vector{Symbol).
6+
Rows are the factors, columns are the variables, with the corresponding labels in fac_labels,var_labels.
7+
"""
8+
getAdjacencyMatrixSparse(dfg::AbstractDFG) = error("getAdjacencyMatrixSparse not implemented for $(typeof(dfg))")

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