Added SMC Presentation visualization

src/visualization.jl

@@ -1,3 +1,4 @@
+using Catlab.Present
 using Catlab.Graphics.Graphviz
 import Catlab.Graphics.Graphviz: Graph, Edge
 import Base.Iterators: flatten
@@ -35,4 +36,31 @@ end
 
 function Graph(op::Union{OpenPetriNet, OpenLabelledPetriNetUntyped, OpenReactionNet, OpenLabelledReactionNetUntyped})
  Graph(apex(op))
+end
+
+function Graph(p::Presentation)
+ ob_names = Symbol.(generators(p, :Ob))
+ hom_names = Symbol.(generators(p, :Hom))
+ hom_dict = Dict{Symbol, Tuple}()
+
+ for hom in generators(p, :Hom)
+ # Evaluate Dom
+ dom_v = if eltype(dom(hom).args) <: GATExpr
+ Tuple(Symbol.(dom(hom).args))
+ else
+ Symbol(dom(hom))
+ end
+
+ # Operate on Codom
+ codom_v = if eltype(codom(hom).args) <: GATExpr
+ Tuple(Symbol.(codom(hom).args))
+ else
+ Symbol(codom(hom))
+ end
+
+ hom_dict[Symbol(hom)] = (dom_v, codom_v)
+ end
+
+ schema_ap = LabelledPetriNet(ob_names, hom_dict...)
+ return Graph(schema_ap)
 end

test/runtests.jl

@@ -5,6 +5,7 @@ using LabelledArrays
 using AlgebraicPetri
 using AlgebraicPetri.Epidemiology
 using Catlab.Theories
+using Catlab.Present
 using Catlab.CategoricalAlgebra
 using Catlab.CategoricalAlgebra.FinSets
 
@@ -16,6 +17,10 @@ end
  include("types.jl")
 end
 
+@testset "Visualization" begin
+ include("visualization.jl")
+end
+
 @testset "Petri" begin
  include("petri.jl")
 end

test/types.jl

@@ -13,13 +13,6 @@ sir_tpetri= PetriNet(TransitionMatrices(sir_petri))
 @test Petri.Model(sir_petri) == Petri.Model(sir_rxn)
 @test Petri.Model(sir_lpetri) == Petri.Model(sir_lrxn)
 
-@test typeof(Graph(sir_petri)) == Graph
-@test typeof(Graph(sir_lpetri)) == Graph
-@test typeof(Graph(sir_rxn)) == Graph
-@test typeof(Graph(open_sir_rxn)) == Graph
-@test typeof(Graph(sir_lrxn)) == Graph
-@test typeof(Graph(open_sir_lrxn)) == Graph
-
 @test inputs(sir_petri, 1) == [1,2]
 @test outputs(sir_petri, 1) == [2,2]
 @test concentration(sir_rxn, 1) == 990

test/visualization.jl

@@ -0,0 +1,49 @@
+@testset "PetriNet Visualization" begin
+ sir_petri = PetriNet(3, ((1, 2), (2, 2)), (2, 3))
+ sir_lpetri = LabelledPetriNet([:S, :I, :R], :inf=>((:S, :I), (:I, :I)), :rec=>(:I, :R))
+ β(u,t) = 1 / sum(u)
+ γ = .25
+ sir_rxn = ReactionNet{Function, Int}([990, 10, 0], (β)=>((1, 2)=>(2,2)), (t->γ)=>(2=>3))
+ open_sir_rxn = Open([1,2], sir_rxn, [3])
+ sir_lrxn = LabelledReactionNet{Number, Int}((:S=>990, :I=>10, :R=>0), (:inf, .001)=>((:S, :I)=>(:I,:I)), (:rec, .25)=>(:I=>:R))
+ open_sir_lrxn = Open([:S,:I], sir_lrxn, [:R])
+
+ sir_tpetri= PetriNet(TransitionMatrices(sir_petri))
+
+ @test typeof(Graph(sir_petri)) == Graph
+ @test typeof(Graph(sir_lpetri)) == Graph
+ @test typeof(Graph(sir_rxn)) == Graph
+ @test typeof(Graph(open_sir_rxn)) == Graph
+ @test typeof(Graph(sir_lrxn)) == Graph
+ @test typeof(Graph(open_sir_lrxn)) == Graph
+end
+
+@testset "Presentation Visualization" begin
+ @present TheoryPetriNet(FreeSymmetricMonoidalCategory) begin
+ T::Ob
+ S::Ob
+ I::Ob
+ O::Ob
+
+ it::Hom(I,T)
+ is::Hom(I,S)
+ ot::Hom(O,T)
+ os::Hom(O,S)
+ end
+
+ @present TheoryMLSchema(FreeSymmetricMonoidalCategory) begin
+ Files::Ob
+ Images::Ob
+ NeuralNet::Ob
+ Accuracy::Ob
+ Metadata::Ob
+
+ extract::Hom(Files, Images)
+ split::Hom(Images, Images⊗Images)
+ train::Hom(NeuralNet⊗Images, NeuralNet⊗Metadata)
+ evaluate::Hom(NeuralNet⊗Images, Accuracy⊗Metadata)
+ end
+
+ @test typeof(Graph(TheoryPetriNet)) == Graph
+ @test typeof(Graph(TheoryMLSchema)) == Graph
+end