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Default Composition Diagrams #52

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4 changes: 2 additions & 2 deletions src/DiagrammaticEquations.jl
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@ recursive_delete_parents, spacename, varname, unicode!, vec_to_dec!,
## collages
Collage, collate,
## composition
oapply, unique_by, unique_by!, OpenSummationDecapodeOb, OpenSummationDecapode, Open,
oapply, unique_by, unique_by!, OpenSummationDecapodeOb, OpenSummationDecapode, Open, default_composition_diagram,
## acset
SchDecapode, SchNamedDecapode, AbstractDecapode, AbstractNamedDecapode, NamedDecapode, SummationDecapode,
contract_operators!, contract_operators, add_constant!, add_parameter, fill_names!, dot_rename!, expand_operators, infer_state_names, recognize_types,
contract_operators!, contract_operators, add_constant!, add_parameter, fill_names!, dot_rename!, expand_operators, infer_state_names, infer_terminal_names, recognize_types,
resolve_overloads!, replace_names!,
apply_inference_rule_op1!, apply_inference_rule_op2!,
transfer_parents!, transfer_children!,
Expand Down
26 changes: 23 additions & 3 deletions src/acset.jl
Original file line number Diff line number Diff line change
Expand Up @@ -202,10 +202,10 @@ end
""" function infer_states(d::SummationDecapode)

Find variables which have a time derivative or are not the source of a computation.
See also: [`infer_state_names`](@ref).
See also: [`infer_terminals`](@ref).
"""
function infer_states(d::SummationDecapode)
childless = filter(parts(d, :Var)) do v
parentless = filter(parts(d, :Var)) do v
length(incident(d, v, :tgt)) == 0 &&
length(incident(d, v, :res)) == 0 &&
length(incident(d, v, :sum)) == 0 &&
Expand All @@ -214,7 +214,7 @@ function infer_states(d::SummationDecapode)
parents_of_tvars =
union(d[incident(d,:∂ₜ, :op1), :src],
d[incident(d,:dt, :op1), :src])
union(childless, parents_of_tvars)
union(parentless, parents_of_tvars)
end

""" function infer_state_names(d)
Expand All @@ -224,6 +224,26 @@ See also: [`infer_states`](@ref).
"""
infer_state_names(d) = d[infer_states(d), :name]

""" function infer_terminals(d::SummationDecapode)
Find variables which have no children.
See also: [`infer_states`](@ref).
"""
function infer_terminals(d::SummationDecapode)
filter(parts(d, :Var)) do v
length(incident(d, v, :src)) == 0 &&
length(incident(d, v, :proj1)) == 0 &&
length(incident(d, v, :proj2)) == 0 &&
length(incident(d, v, :summand)) == 0
end
end

""" function infer_terminal_names(d)

Find names of variables which have no children.
See also: [`infer_terminals`](@ref).
"""
infer_terminal_names(d) = d[infer_terminals(d), :name]

""" function expand_operators(d::SummationDecapode)

Find operations that are compositions, and expand them with intermediate variables.
Expand Down
92 changes: 72 additions & 20 deletions src/composition.jl
Original file line number Diff line number Diff line change
@@ -1,26 +1,8 @@
## TODO: Decapodey

import Catlab.CategoricalAlgebra: apex, feet, legs
import Catlab.WiringDiagrams: oapply

OpenSummationDecapodeOb, OpenSummationDecapode = OpenACSetTypes(SummationDecapode, :Var)

#FIXME: why can't we just add a constructor for OpenSummationDecapode
""" Open(d::SummationDecapode{T,U,V}, names::AbstractVector{Symbol}) where {T,U,V}

creates an OpenSummationDecapode based on named variables rather than variable indices.
See AlgebraicPetri.jl's Open for the analogous verion for LabelledReactionNetworks.
"""
function Open(d::SummationDecapode{T,U,V}, names::AbstractVector{Symbol}) where {T,U,V}
legs = map(names) do name
FinFunction(incident(d, name, :name), nparts(d, :Var))
end
OpenSummationDecapode{T,U,V}(d, legs...)
end

apex(Decapode::OpenSummationDecapode) = apex(Decapode.cospan)
legs(Decapode::OpenSummationDecapode) = legs(Decapode.cospan)
feet(Decapode::OpenSummationDecapode) = Decapode.feet
# ACSet manipulation helper functions
# -----------------------------------

""" function unique_by!(acset, column_names::Vector{Symbol})

Expand Down Expand Up @@ -67,6 +49,28 @@
unique_by!(acset_copy, table, columns)
end

# Operadic composition
# --------------------

OpenSummationDecapodeOb, OpenSummationDecapode = OpenACSetTypes(SummationDecapode, :Var)

#FIXME: why can't we just add a constructor for OpenSummationDecapode
""" Open(d::SummationDecapode{T,U,V}, names::AbstractVector{Symbol}) where {T,U,V}

creates an OpenSummationDecapode based on named variables rather than variable indices.
See AlgebraicPetri.jl's Open for the analogous verion for LabelledReactionNetworks.
"""
function Open(d::SummationDecapode{T,U,V}, names::AbstractVector{Symbol}) where {T,U,V}
legs = map(names) do name
FinFunction(incident(d, name, :name), nparts(d, :Var))
end
OpenSummationDecapode{T,U,V}(d, legs...)
end

apex(Decapode::OpenSummationDecapode) = apex(Decapode.cospan)
legs(Decapode::OpenSummationDecapode) = legs(Decapode.cospan)
feet(Decapode::OpenSummationDecapode) = Decapode.feet

""" function type_check_Decapodes_composition(relation::RelationDiagram, decs::Vector{OpenSummationDecapode})

Check that the types of all Vars connected by the same junction match.
Expand Down Expand Up @@ -212,3 +216,51 @@
# oapply(r, OpenPode(Heat, [:H]))

oapply(r::RelationDiagram, pode::OpenSummationDecapode) = oapply(r, [pode])

# Default composition
# -------------------

# This helper function finds elements which appear in an array more than once.
function find_duplicates(vs::Vector{T}) where T
once, twice = Set{T}(), Set{T}()
foreach(v -> v ∈ once ? push!(twice,v) : push!(once,v), vs)
twice

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src/composition.jl#L224-L227

Added lines #L224 - L227 were not covered by tests
end

# TODO: Upstream this to Catlab?
function construct_relation_diagram(boxes::Vector{Symbol}, junctions::Vector{Vector{Symbol}})
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tables = map(boxes, junctions) do b, j
Expr(:call, b, j...)
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end
quote @relation () begin $(tables...) end end |> eval
end

# TODO: Add a macro which provides names for boxes via the Symbol of the Decapode.
""" function default_composition_diagram(podes::Vector{D}, names::Vector{Symbol}) where {D<:SummationDecapode}

Given a list of Decapodes and their names, return a composition diagram which assumes that variables sharing the same name ought to be composed.

No Literals are exposed. Use [`unique_lits!`](@ref) after composing.

Throw an error if any individual Decapode already contains a repeated name (except for Literals).

If `only_states_terminals` is `true`, only expose state and terminal variables. Defaults to `false`.

Note that composing immediately with [`oapply`](@ref) will fail if types do not match (e.g. (:infer, :Form0) or (:Form0, :Form1)).
"""
function default_composition_diagram(podes::Vector{D}, names::Vector{Symbol}, only_states_terminals=false) where {D<:SummationDecapode}
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non_lit_names = map(podes) do pode
pode[findall(!=(:Literal), pode[:type]), :name]
end
for (nln, name) in zip(non_lit_names, names)
allunique(nln) || error("Decapode $name contains repeated variable names: $(find_duplicates(nln)).")
end
if only_states_terminals
foreach(non_lit_names, podes) do nln, pode
outers = infer_state_names(pode) ∪ infer_terminal_names(pode)
filter!(x -> x ∈ outers, nln)
end
end
construct_relation_diagram(names, non_lit_names)
end

56 changes: 56 additions & 0 deletions test/composition.jl
Original file line number Diff line number Diff line change
Expand Up @@ -195,4 +195,60 @@ end
# Test none of the decapodes were mutated
@test isequal(adv_adv, deep_copies)

@testset "Default Composition Diagrams" begin
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# Compose Diffusion, Advection, and Superposition.
# Observe that we have pre-named ϕ to ϕ₁ or ϕ₂.
# Note that only one Decapode contains TVars.
Diffusion = @decapode begin
C::Form0
ϕ₁::Form1
ϕ₁ == ∘(k, d₀)(C)
end
Advection = @decapode begin
C::Form0
(V, ϕ₂)::Form1
ϕ₂ == ∧₀₁(C,V)
end
Superposition = @decapode begin
(C, Ċ)::Form0
(ϕ, ϕ₁, ϕ₂)::Form1
ϕ == ϕ₁ + ϕ₂
Ċ == ∘(⋆₀⁻¹, dual_d₁, ⋆₁)(ϕ)
∂ₜ(C) == Ċ
end
expected =
@relation () begin
Diffusion(C,ϕ₁)
Advection(C,V,ϕ₂)
Superposition(C,ϕ₁,ϕ₂,Ċ,ϕ)
end
@test is_isomorphic(expected, default_composition_diagram(
[Diffusion, Advection, Superposition],
[:Diffusion, :Advection, :Superposition]))
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# Compose Halfar's equation with Glen's law.
GlensLaw = @decapode begin
Γ::Form1
(A,ρ,g,n)::Constant

Γ == (2/(n+2))*A*(ρ*g)^n
end
HalfarsEquation = @decapode begin
h::Form0
Γ::Form1
n::Constant

∂ₜ(h) == ∘(⋆, d, ⋆)(Γ * d(h) ∧ (mag(♯(d(h)))^(n-1)) ∧ (h^(n+2)))
end
expected =
@relation () begin
GlensLaw(Γ,A,ρ,g,n)
HalfarsEquation(h,Γ,n,ḣ)
end
@test is_isomorphic(expected, default_composition_diagram(
[GlensLaw, HalfarsEquation],
[:GlensLaw, :HalfarsEquation],
true))
end

# end
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