PetriNets and Wiring Diagrams #195
Assignees
Labels
enhancement
New feature or request
Comments
|
@mehalter take a look at https://eprints.soton.ac.uk/261951/1/strong-conf.pdf |
|
What should the return value of run! be? The network, the final marking, or some kind of return code like struct ReturnCode
iterations::Int # number of iterations
changes::Int # number of state changes,
infite::Bool # a flag for infinite loop detected
end |
|
@ewdavis, @rrwright, @cl4yton i think this is the new code for the PetriNet (AMIDOL flavor) based simulation of the SIR system. function main(β, γ, μ)
@grounding begin
S => Noun(Susceptible, ontology=Snowmed)
I => Noun(Infectious, ontology=ICD9)
R => Noun(Recovered, ontology=ICD9)
λ₁ => Verb(infection)
λ₂ => Verb(recovery)
λ₃ => Verb(loss_of_immunity)
end
@reaction begin
λ₁, S + I -> 2I
λ₂, I -> R
λ₃, R -> S
end, λ₁, λ₂, λ₃
# β, 1S + 1I -> 0S + 2I
# γ, 0R + 1I -> 0I + 1R
# μ, 1R + 0S -> 1S + 0R
Δ = [
(S,I) -> (S-1, I+1),
(I,R) -> (I-1, R+1),
(R,S) -> (R-1, S+1),
]
ϕ = [
(S, I) -> x > 0 && I > 0,
(I) -> x > 0,
(R) -> x > 0,
]
Λ = [
λ₁(S,I) = begin n = +(S,I,R); β*S*I/n end,
λ₂(I) = begin γ*I end,
λ₃(R) = begin μ*R end
]
m = Petri.Model(g, Δ, ϕ, Λ)
d = convert(ODEProblem, m)
soln = solve(m) #discrete
soln = solve(d) #continuos
endthe |
|
The corresponding AST dumped without line numbers is julia> MacroTools.postwalk(ast) do x
rmlines(x)
end |> x->dump(IOContext(stdout, :limit => true), x, maxdepth=100)
Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol function
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((4,))
1: Symbol main
2: Symbol β
3: Symbol γ
4: Symbol μ
2: Expr
head: Symbol block
args: Array{Any}((9,))
1: Expr
head: Symbol macrocall
args: Array{Any}((3,))
1: Symbol @grounding
2: Nothing nothing
3: Expr
head: Symbol block
args: Array{Any}((6,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol =>
2: Symbol S
3: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol Noun
2: Symbol Susceptible
3: Expr
head: Symbol kw
args: Array{Any}((2,))
1: Symbol ontology
2: Symbol Snowmed
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol =>
2: Symbol I
3: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol Noun
2: Symbol Infectious
3: Expr
head: Symbol kw
args: Array{Any}((2,))
1: Symbol ontology
2: Symbol ICD9
3: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol =>
2: Symbol R
3: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol Noun
2: Symbol Recovered
3: Expr
head: Symbol kw
args: Array{Any}((2,))
1: Symbol ontology
2: Symbol ICD9
4: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol =>
2: Symbol λ₁
3: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol Verb
2: Symbol infection
5: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol =>
2: Symbol λ₂
3: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol Verb
2: Symbol recovery
6: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol =>
2: Symbol λ₃
3: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol Verb
2: Symbol loss_of_immunity
2: Expr
head: Symbol macrocall
args: Array{Any}((3,))
1: Symbol @reaction
2: Nothing nothing
3: Expr
head: Symbol tuple
args: Array{Any}((4,))
1: Expr
head: Symbol block
args: Array{Any}((3,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol λ₁
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol +
2: Symbol S
3: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol *
2: Int64 2
3: Symbol I
2: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol λ₂
2: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Symbol R
3: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol λ₃
2: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Symbol R
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Symbol S
2: Symbol λ₁
3: Symbol λ₂
4: Symbol λ₃
3: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol Δ
2: Expr
head: Symbol vect
args: Array{Any}((3,))
1: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol S
2: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol -
2: Symbol S
3: Int64 1
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol +
2: Symbol I
3: Int64 1
2: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol I
2: Symbol R
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol -
2: Symbol I
3: Int64 1
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol +
2: Symbol R
3: Int64 1
3: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol R
2: Symbol S
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol -
2: Symbol R
3: Int64 1
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol +
2: Symbol S
3: Int64 1
4: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol ϕ
2: Expr
head: Symbol vect
args: Array{Any}((3,))
1: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Expr
head: Symbol tuple
args: Array{Any}((2,))
1: Symbol S
2: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol &&
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol >
2: Symbol x
3: Int64 0
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol >
2: Symbol I
3: Int64 0
2: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol >
2: Symbol x
3: Int64 0
3: Expr
head: Symbol ->
args: Array{Any}((2,))
1: Symbol R
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol >
2: Symbol x
3: Int64 0
5: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol Λ
2: Expr
head: Symbol vect
args: Array{Any}((3,))
1: Expr
head: Symbol =
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol λ₁
2: Symbol S
3: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((2,))
1: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol n
2: Expr
head: Symbol call
args: Array{Any}((4,))
1: Symbol +
2: Symbol S
3: Symbol I
4: Symbol R
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol /
2: Expr
head: Symbol call
args: Array{Any}((4,))
1: Symbol *
2: Symbol β
3: Symbol S
4: Symbol I
3: Symbol n
2: Expr
head: Symbol =
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol λ₂
2: Symbol I
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol *
2: Symbol γ
3: Symbol I
3: Expr
head: Symbol =
args: Array{Any}((2,))
1: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol λ₃
2: Symbol R
2: Expr
head: Symbol block
args: Array{Any}((1,))
1: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol *
2: Symbol μ
3: Symbol R
6: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol m
2: Expr
head: Symbol call
args: Array{Any}((5,))
1: Expr
head: Symbol .
args: Array{Any}((2,))
1: Symbol Petri
2: QuoteNode
value: Symbol Model
2: Symbol g
3: Symbol Δ
4: Symbol ϕ
5: Symbol Λ
7: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol d
2: Expr
head: Symbol call
args: Array{Any}((3,))
1: Symbol convert
2: Symbol ODEProblem
3: Symbol m
8: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol soln
2: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol solve
2: Symbol m
9: Expr
head: Symbol =
args: Array{Any}((2,))
1: Symbol soln
2: Expr
head: Symbol call
args: Array{Any}((2,))
1: Symbol solve
2: Symbol d |
|
A more compact, and easier to parse version of the AST can be given by something about the parentheses is very appealing... julia> MacroTools.postwalk(ast) do x
rmlines(x)
end |> x->Base.Meta.show_sexpr(stdout, x)
(:block,
(:function, (:call, :main, :β, :γ, :μ), (:block,
(:macrocall, Symbol("@grounding"), nothing, (:block,
(:call, :(=>), :S, (:call, :Noun, :Susceptible, (:kw, :ontology, :Snowmed))),
(:call, :(=>), :I, (:call, :Noun, :Infectious, (:kw, :ontology, :ICD9))),
(:call, :(=>), :R, (:call, :Noun, :Recovered, (:kw, :ontology, :ICD9))),
(:call, :(=>), :λ₁, (:call, :Verb, :infection)),
(:call, :(=>), :λ₂, (:call, :Verb, :recovery)),
(:call, :(=>), :λ₃, (:call, :Verb, :loss_of_immunity))
)),
(:macrocall, Symbol("@reaction"), nothing, (:tuple, (:block,
(:tuple, :λ₁, (:call, :+, :S, (:->, :I, (:block,
(:call, :*, 2, :I)
)))),
(:tuple, :λ₂, (:->, :I, (:block,
:R
))),
(:tuple, :λ₃, (:->, :R, (:block,
:S
)))
), :λ₁, :λ₂, :λ₃)),
(:(=), :Δ, (:vect, (:->, (:tuple, :S, :I), (:block,
(:tuple, (:call, :-, :S, 1), (:call, :+, :I, 1))
)), (:->, (:tuple, :I, :R), (:block,
(:tuple, (:call, :-, :I, 1), (:call, :+, :R, 1))
)), (:->, (:tuple, :R, :S), (:block,
(:tuple, (:call, :-, :R, 1), (:call, :+, :S, 1))
)))),
(:(=), :ϕ, (:vect, (:->, (:tuple, :S, :I), (:block,
(:&&, (:call, :>, :x, 0), (:call, :>, :I, 0))
)), (:->, :I, (:block,
(:call, :>, :x, 0)
)), (:->, :R, (:block,
(:call, :>, :x, 0)
)))),
(:(=), :Λ, (:vect, (:(=), (:call, :λ₁, :S, :I), (:block,
(:(=), :n, (:call, :+, :S, :I, :R)),
(:call, :/, (:call, :*, :β, :S, :I), :n)
)), (:(=), (:call, :λ₂, :I), (:block,
(:call, :*, :γ, :I)
)), (:(=), (:call, :λ₃, :R), (:block,
(:call, :*, :μ, :R)
)))),
(:(=), :m, (:call, (:., :Petri, (:quote, #QuoteNode
:Model
)), :g, :Δ, :ϕ, :Λ)),
(:(=), :d, (:call, :convert, :ODEProblem, :m)),
(:(=), :soln, (:call, :solve, :m)),
(:(=), :soln, (:call, :solve, :d))
))
) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
The catlab branch has some code in
src/petri.jlthat implements petrinets as a modeling framework and then some code to convert them to wiring diagrams, I don't think that code is right, but I'm not sure how to fix it.We should be able to model a Petri Nets as a category P and represent each Petri Net as a functor from the category of P to Set like a P-Instance or something like that.
The text was updated successfully, but these errors were encountered: