Apply collages to intermediate variables

src/collages.jl

@@ -7,24 +7,20 @@ end
 
 collate(c::Collage) = collate(c.src, c.tgt, c.uwd, c.symbols)
 
+# TODO: This is assuming only "restriction"-type morphisms.
+# TODO: Throw an error if the user tries to use a boundary value differential
+# form that is of a different type of the thing that we are applying the bound
+# to. i.e. Form1 but target is a Form0.
 """    function collate(equations, boundaries, uwd, symbols)
 
 Create a collage of two Decapodes that simulates with boundary conditions.
 ```
 """
 function collate(equations, boundaries, uwd, symbols)
-  # TODO: This is assuming only "restriction"-type morphisms.
-
   f = SummationDecapode{Any, Any, Symbol}()
-  # TODO: Double-check
   copy_parts!(f, equations, (:Var, :TVar, :Op1, :Op2, :Σ, :Summand))
-
-  # TODO: Throw an error if the user tries to use a boundary value differential
-  # form that is of a different type of the thing that we are applying the bound
-  # to. i.e. Form1 but target is a Form0.
-
-  # TODO: This sets restrictions as Op1s. They are actually Op2s. i.e. Use `bv`.
   for b in boxes(uwd)
+    # Set up pointers.
     ps = incident(uwd, b, :box)
     ev = first(ps)
     bv = last(ps)
@@ -33,15 +29,22 @@ function collate(equations, boundaries, uwd, symbols)
     en = symbols[en_key]
     bn = symbols[bn_key]
     var = only(incident(f, en, :name))
-    b_var = add_part!(f, :Var, type=f[var, :type], name=f[var, :name])
-    f[var, :name] = Symbol("r$(b)_" * string(f[var, :name]))
+    # Add a new variable and transfer the children of the original variable to it.
+    b_var = add_part!(f, :Var, type=f[var, :type], name=Symbol("r$(b)_" * string(f[var, :name])))
+    transfer_children!(f, var, b_var)
+    # Transfer ∂ₜ morphisms back, if any.
+    tangent_op1s = filter(x -> f[x, :op1]==:∂ₜ, incident(f, b_var, :src))
+    if !isempty(tangent_op1s)
+      f[only(tangent_op1s), :src] = var
+    end
+    # Transfer ∂ₜ morphisms forward, if any.
+    tangent_op1s = filter(x -> f[x, :op1]==:∂ₜ, incident(f, var, :tgt))
+    if !isempty(tangent_op1s)
+      f[tangent_op1s, :tgt] = b_var
+    end
+    # Insert the "masking" operation.
     s_var = add_part!(f, :Var, type=boundaries[only(incident(boundaries, bn, :name)), :type], name=bn)
-    add_part!(f, :Op2, proj1=b_var, proj2=s_var, res=var, op2=uwd[b, :name])
-
-    # Update tangent variable pointers, if any.
-    tangent_op1s = filter(x -> f[x, :op1]==:∂ₜ, incident(f, var, :src))
-    isempty(tangent_op1s) && continue
-    f[only(tangent_op1s), :src] = b_var
+    add_part!(f, :Op2, proj1=var, proj2=s_var, res=b_var, op2=uwd[b, :name])
   end
 
   f

test/collages.jl

@@ -12,6 +12,17 @@ using Catlab
 
 # TODO: Add test with empty boundary Decapode.
 
+# Note: Since the order does not matter in which rb1 and rb2 are applied, it
+# seems informal to state that one goes before the other.
+# It might be better to provide a semantics for incident edges a la:
+#Diffusion = @Decapode begin
+#  C::Form0
+#  ∂ₜ(C) == rb3(∘(d,⋆,d,⋆)(rb1(C)))
+#  ∂ₜ(C) == rb3(∘(d,⋆,d,⋆)(rb2(C)))
+#end
+# Such a technique would preserve the technical definition of "collage".
+
+
 # Test simple boundary masks.
 DiffusionDynamics = @decapode begin
   K::Form0
@@ -20,20 +31,17 @@ end
 DiffusionBoundaries = @decapode begin
   (Kb1, Kb2, Null)::Form0
 end
-
 DiffusionMorphism = @relation () begin
   rb1_leftwall(C, Cb1)
   rb2_rightwall(C, Cb2)
   rb3(Ċ, Zero)
 end
-
 DiffusionSymbols = Dict(
   :C => :K,
   :Ċ => :K̇,
   :Cb1 => :Kb1,
   :Cb2 => :Kb2,
   :Zero => :Null)
-
 DiffusionCollage = DiagrammaticEquations.collate(
   DiffusionDynamics,
   DiffusionBoundaries,
@@ -45,30 +53,91 @@ DiffusionCollage = DiagrammaticEquations.collate(
   TVar = 1
   Op1 = 2
   Op2 = 3
-  src  = [5, 1]
-  tgt  = [2, 2]
-  proj1  = [3, 5, 7]
-  proj2  = [4, 6, 8]
-  res  = [1, 3, 2]
-  incl  = [2]
-  op1  = Any[:∂ₜ, [:d, :⋆, :d, :⋆]]
-  op2  = [:rb1_leftwall, :rb2_rightwall, :rb3]
-  type  = [:Form0, :infer, :Form0, :Form0, :Form0, :Form0, :infer, :Form0]
-  name  = [:r1_K, :r3_K̇, :r2_K, :Kb1, :K, :Kb2, :K̇, :Null]
+  src = [1, 3]
+  tgt = [7, 2]
+  proj1 = [5, 1, 2]
+  proj2 = [4, 6, 8]
+  res = [3, 5, 7]
+  incl = [2]
+  op1 = Any[:∂ₜ, [:d, :⋆, :d, :⋆]]
+  op2 = [:rb1_leftwall, :rb2_rightwall, :rb3]
+  type = [:Form0, :infer, :Form0, :Form0, :Form0, :Form0, :infer, :Form0]
+  name = [:K, :K̇, :r1_K, :Kb1, :r2_K, :Kb2, :r3_K̇, :Null]
 end
 
-# Note: Since the order does not matter in which rb1 and rb2 are applied, it
-# seems informal to state that one goes before the other.
-# It might be better to provide a semantics for incident edges a la:
-#Diffusion = @Decapode begin
-#  C::Form0
-#  ∂ₜ(C) == rb3(∘(d,⋆,d,⋆)(rb1(C)))
-#  ∂ₜ(C) == rb3(∘(d,⋆,d,⋆)(rb2(C)))
-#end
-# Such a technique would preserve the technical definition of "collage".
+# Test boundary condition applications on intermediate variables.
+IntermediateDynamics = @decapode begin
+  K::Form0
+  J == Δ(K)
+  ∂ₜ(K) == Δ(J)
+end
+IntermediateBoundaries = @decapode begin
+  (Jb1)::Form0
+end
+IntermediateMorphism = @relation () begin
+  rb1_leftwall(C, Cb1)
+end
+IntermediateSymbols = Dict(
+  :C => :J,
+  :Cb1 => :Jb1)
+IntermediateCollage = DiagrammaticEquations.collate(
+  IntermediateDynamics,
+  IntermediateBoundaries,
+  IntermediateMorphism,
+  IntermediateSymbols)
+@test IntermediateCollage == @acset SummationDecapode{Any, Any, Symbol} begin
+  Var = 5
+  TVar = 1
+  Op1 = 3
+  Op2 = 1
+  src = [1, 1, 4]
+  tgt = [2, 3, 3]
+  proj1 = [2]
+  proj2 = [5]
+  res = [4]
+  incl = [3]
+  op1 = [:Δ, :∂ₜ, :Δ]
+  op2 = [:rb1_leftwall]
+  type = [:Form0, :infer, :infer, :infer, :Form0]
+  name = [:K, :J, :K̇, :r1_J, :Jb1]
+end
 
-# Test gensim on a collage.
-c = Collage(DiffusionDynamics, DiffusionBoundaries,
-  DiffusionMorphism, DiffusionSymbols)
+# Test twice-applied boundary condition applications on intermediate variables.
+TwiceDynamics = @decapode begin
+  K::Form0
+  J == Δ(K)
+  ∂ₜ(K) == Δ(J)
+end
+TwiceBoundaries = @decapode begin
+  (Jb1, Jb2)::Form0
+end
+TwiceMorphism = @relation () begin
+  rb1_leftwall(C, Cb1)
+  rb2_rightwall(C, Cb2)
+end
+TwiceSymbols = Dict(
+  :C => :J,
+  :Cb1 => :Jb1,
+  :Cb2 => :Jb2)
+TwiceCollage = DiagrammaticEquations.collate(
+  TwiceDynamics,
+  TwiceBoundaries,
+  TwiceMorphism,
+  TwiceSymbols)
+@test TwiceCollage == @acset SummationDecapode{Any, Any, Symbol} begin
+  Var = 7
+  TVar = 1
+  Op1 = 3
+  Op2 = 2
+  src = [1, 1, 4]
+  tgt = [2, 3, 3]
+  proj1 = [6, 2]
+  proj2 = [5, 7]
+  res = [4, 6]
+  incl  = [3]
+  op1 = [:Δ, :∂ₜ, :Δ]
+  op2 = [:rb1_leftwall, :rb2_rightwall]
+  type = [:Form0, :infer, :infer, :infer, :Form0, :infer, :Form0]
+  name = [:K, :J, :K̇, :r1_J, :Jb1, :r2_J, :Jb2]
+end
 
-# @test gensim(c) == gensim(DiffusionCollage)