Merge pull request #116 from JuliaRobotics/feature/3Q19/sortDFG

alias for sort dfg symbol lists

Author: GearsAD

Project.toml

@@ -7,6 +7,7 @@ Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JSON2 = "2535ab7d-5cd8-5a07-80ac-9b1792aadce3"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"

docs/src/func_ref.md

@@ -58,8 +58,9 @@ getSubgraphAroundNode
 getSubgraph
 ```
 
-### Visualization
+### Visualization and Plotting
 ```@docs
 toDot
 toDotFile
+dfgplot
 ```

src/Common.jl

@@ -1,4 +1,5 @@
-export sortVarNested
+
+export sortVarNested, sortDFG
 export isPrior, lsfPriors
 export getVariableType, getSofttype
 export getFactorType, getfnctype
@@ -88,6 +89,24 @@ function sortVarNested(vars::Vector{Symbol})::Vector{Symbol}
 	return retvars
 end
 
+"""
+    $SIGNATURES
+
+Sort variable (factor) lists in a meaningful way, for example `[:april;:x1_3;:x1_6;]`
+
+Notes
+- Not fool proof, but does better than native sort.
+
+Example
+
+`sortDFG(ls(dfg))`
+
+Related
+
+ls, lsf
+"""
+sortDFG(vars::Vector{Symbol})::Vector{Symbol} = sortVarNested(vars)
+
 """
     $SIGNATURES
 

src/DFGPlots/DFGPlots.jl

@@ -4,6 +4,7 @@ using Colors
 using LightGraphs
 using MetaGraphs
 using GraphPlot
+using DocStringExtensions
 import GraphPlot: gplot
 
 using ...DistributedFactorGraphs
@@ -28,6 +29,26 @@ DFGPlotProps() = DFGPlotProps(  (var=colorant"seagreen", fac=colorant"cyan3"),
                                 true)
 
 
+
+"""
+    $(SIGNATURES)
+Plots the structure of the factor graph. GraphPlot must be imported before DistributedFactoGraphs for these functions to be available.
+Returns the plot context.
+
+E.g.
+```
+using GraphPlot
+using DistributedFactorGraphs, DistributedFactorGraphs.DFGPlots
+# ... Make graph...
+# Using GraphViz plotting
+dfgplot(fg)
+# Save to PDFG
+using Compose
+draw(PDF("/tmp/graph.pdf", 16cm, 16cm), dfgplot(fg))
+```
+
+More information at [GraphPlot.jl](https://github.com/JuliaGraphs/GraphPlot.jl)
+"""
 function dfgplot(dfg::LightDFG, p::DFGPlotProps = DFGPlotProps())
 
     nodetypes = [haskey(dfg.g.variables, s) for s in dfg.g.labels]
@@ -46,6 +67,25 @@ function dfgplot(dfg::LightDFG, p::DFGPlotProps = DFGPlotProps())
 
 end
 
+"""
+    $(SIGNATURES)
+Plots the structure of the factor graph. GraphPlot must be imported before DistributedFactoGraphs for these functions to be available.
+Returns the plot context.
+
+E.g.
+```
+using GraphPlot
+using DistributedFactorGraphs, DistributedFactorGraphs.DFGPlots
+# ... Make graph...
+# Using GraphViz plotting
+dfgplot(fg)
+# Save to PDFG
+using Compose
+draw(PDF("/tmp/graph.pdf", 16cm, 16cm), dfgplot(fg))
+```
+
+More information at [GraphPlot.jl](https://github.com/JuliaGraphs/GraphPlot.jl)
+"""
 function dfgplot(dfg::MetaGraphsDFG, p::DFGPlotProps = DFGPlotProps())
 
     nodesize = [has_prop(dfg.g,i,:factor) ?  p.nodesize.fac : p.nodesize.var for i=vertices(dfg.g)]
@@ -60,14 +100,32 @@ function dfgplot(dfg::MetaGraphsDFG, p::DFGPlotProps = DFGPlotProps())
 
 end
 
+"""
+    $(SIGNATURES)
+Plots the structure of the factor graph. GraphPlot must be imported before DistributedFactoGraphs for these functions to be available.
+Returns the plot context.
+
+E.g.
+```
+using GraphPlot
+using DistributedFactorGraphs, DistributedFactorGraphs.DFGPlots
+# ... Make graph...
+# Using GraphViz plotting
+dfgplot(fg)
+# Save to PDFG
+using Compose
+draw(PDF("/tmp/graph.pdf", 16cm, 16cm), dfgplot(fg))
+```
+
+More information at [GraphPlot.jl](https://github.com/JuliaGraphs/GraphPlot.jl)
+"""
 function dfgplot(dfg::AbstractDFG, p::DFGPlotProps = DFGPlotProps())
     # TODO implement convert functions
     @warn "TODO Implement convert"
     ldfg = MetaGraphsDFG{AbstractParams}()
     DistributedFactorGraphs._copyIntoGraph!(dfg, ldfg, union(getVariableIds(dfg), getFactorIds(dfg)), true)
 
     dfgplot(ldfg, p)
-
 end
 
 function gplot(dfg::MetaGraphsDFG; keyargs...)

src/DistributedFactorGraphs.jl

@@ -42,6 +42,9 @@ export pack, unpack
 #Interfaces
 export getAdjacencyMatrixSparse
 
+# File import and export
+export saveDFG, loadDFG
+
 # Common includes
 include("services/AbstractDFG.jl")
 include("services/DFGVariable.jl")
@@ -61,8 +64,6 @@ include("SymbolDFG/SymbolDFG.jl")
 include("LightDFG/LightDFG.jl")
 @reexport using .LightDFGs
 
-export saveDFG, loadDFG
-
 function __init__()
     @require Neo4j="d2adbeaf-5838-5367-8a2f-e46d570981db" begin
         # Include the Cloudgraphs API

src/entities/DFGFactor.jl

@@ -1,4 +1,3 @@
-
 # Originally from IncrementalInference
 
 abstract type InferenceType end
@@ -48,18 +47,37 @@ mutable struct DFGFactor{T, S} <: DFGNode
 end
 
 label(f::F) where F <: DFGFactor = f.label
-data(f::F) where F <: DFGFactor = f.data
+"""
+    $SIGNATURES
+
+Retrieve solver data structure stored in a factor.
+"""
+function solverData(f::F) where F <: DFGFactor
+  return f.data
+end
+"""
+    $SIGNATURES
+
+Retrieve solver data structure stored in a factor.
+"""
+function data(f::DFGFactor)::GenericFunctionNodeData
+  @warn "data() is deprecated, please use solverData()"
+  return f.data
+end
+"""
+    $SIGNATURES
+
+Retrieve solver data structure stored in a factor.
+"""
+function getData(f::DFGFactor)::GenericFunctionNodeData
+  @warn "getData is deprecated, please use solverData()"
+  return f.data
+end
+
 internalId(f::F) where F <: DFGFactor = f._internalId
 
 # Simply for convenience - don't export
 const PackedFunctionNodeData{T} = GenericFunctionNodeData{T, <: AbstractString}
 PackedFunctionNodeData(x1, x2, x3, x4, x5::S, x6::T, x7::String="", x8::Vector{Int}=Int[]) where {T <: PackedInferenceType, S <: AbstractString} = GenericFunctionNodeData(x1, x2, x3, x4, x5, x6, x7, x8)
 const FunctionNodeData{T} = GenericFunctionNodeData{T, Symbol}
 FunctionNodeData(x1, x2, x3, x4, x5::Symbol, x6::T, x7::String="", x8::Vector{Int}=Int[]) where {T <: Union{FunctorInferenceType, ConvolutionObject}}= GenericFunctionNodeData{T, Symbol}(x1, x2, x3, x4, x5, x6, x7, x8)
-
-"""
-    $SIGNATURES
-
-Retrieve data structure stored in a node.
-"""
-getData(v::DFGFactor)::GenericFunctionNodeData = v.data

src/entities/DFGVariable.jl

@@ -104,8 +104,26 @@ timestamp(v::DFGVariable) = v.timestamp
 tags(v::DFGVariable) = v.tags
 estimates(v::DFGVariable) = v.estimateDict
 estimate(v::DFGVariable, key::Symbol=:default) = haskey(v.estimateDict, key) ? v.estimateDict[key] : nothing
+"""
+    $SIGNATURES
+
+Retrieve solver data structure stored in a variable.
+"""
 solverData(v::DFGVariable, key::Symbol=:default) = haskey(v.solverDataDict, key) ? v.solverDataDict[key] : nothing
-getData(v::DFGVariable; solveKey::Symbol=:default)::VariableNodeData = v.solverDataDict[solveKey]
+"""
+    $SIGNATURES
+
+Retrieve data structure stored in a variable.
+"""
+function getData(v::DFGVariable; solveKey::Symbol=:default)::VariableNodeData
+  @warn "getData is deprecated, please use solverData()"
+  return v.solverDataDict[solveKey]
+end
+"""
+    $SIGNATURES
+
+Set solver data structure stored in a variable.
+"""
 setSolverData(v::DFGVariable, data::VariableNodeData, key::Symbol=:default) = v.solverDataDict[key] = data
 solverDataDict(v::DFGVariable) = v.solverDataDict
 internalId(v::DFGVariable) = v._internalId

test/interfaceTests.jl

@@ -47,7 +47,7 @@ end
     @test getFactorIds(dfg) == [:f1]
     #
     @test lsf(dfg, :a) == [f1.label]
-    #tags
+    # Tags
     @test ls(dfg, tags=[:POSE]) == [:a]
     @test symdiff(ls(dfg, tags=[:POSE, :LANDMARK]), ls(dfg, tags=[:VARIABLE])) == []
     # Regexes
@@ -61,6 +61,11 @@ end
     @test exists(dfg, :a) == true
     @test exists(dfg, v1) == true
     @test exists(dfg, :nope) == false
+    # Sorting of results
+    # TODO - this function needs to be cleaned up
+    unsorted = [:x1_3;:x1_6;:l1;:april1] #this will not work for :x1x2f1
+    @test sortDFG(unsorted) == sortVarNested(unsorted)
+    @test_skip sortDFG([:x1x2f1, :x1l1f1]) == [:x1l1f1, :x1x2f1]
 end
 
 # Gets
@@ -85,12 +90,17 @@ end
     @test estimates(v1) == v1.estimateDict
     @test estimate(v1, :notfound) == nothing
     @test solverData(v1) === v1.solverDataDict[:default]
+    @test getData(v1) === v1.solverDataDict[:default]
     @test solverData(v1, :default) === v1.solverDataDict[:default]
     @test solverDataDict(v1) == v1.solverDataDict
     @test internalId(v1) == v1._internalId
 
     @test label(f1) == f1.label
+    @test solverData(f1) == f1.data
+    # Deprecated functions
     @test data(f1) == f1.data
+    @test getData(f1) == f1.data
+    # Internal function
     @test internalId(f1) == f1._internalId
 
     @test getSolverParams(dfg) != nothing

test/plottingTest.jl

@@ -0,0 +1,22 @@
+# using GraphPlot
+using DistributedFactorGraphs
+using DistributedFactorGraphs.DFGPlots
+using Test
+
+# Now make a complex graph for connectivity tests
+numNodes = 10
+dfg = GraphsDFG{NoSolverParams}()
+verts = map(n -> DFGVariable(Symbol("x$n")), 1:numNodes)
+#change ready and backendset for x7,x8 for improved tests on x7x8f1
+verts[7].ready = 1
+verts[8].backendset = 1
+map(v -> addVariable!(dfg, v), verts)
+map(n -> addFactor!(dfg, [verts[n], verts[n+1]], DFGFactor{Int, :Symbol}(Symbol("x$(n)x$(n+1)f1"))), 1:(numNodes-1))
+
+# Using toDot
+dot = toDot(dfg)
+@test dot != nothing
+
+# Using GraphViz plotting
+plot = dfgplot(dfg)
+@test plot != nothing

test/runtests.jl

@@ -1,4 +1,5 @@
 using Test
+using GraphPlot # For plotting tests
 using DistributedFactorGraphs
 
 # Test each interface
@@ -9,3 +10,9 @@ for api in apis
         include("interfaceTests.jl")
     end
 end
+
+# Test special cases
+
+@testset "Plotting Tests" begin
+    include("plottingTest.jl")
+end