Merge pull request #272 from Neuroblox/parameter_scope

PR to enable shared parameters

src/Neuroblox.jl

@@ -61,6 +61,7 @@ include("utilities/learning_tools.jl")
 include("control/controlerror.jl")
 include("measurementmodels/fmri.jl")
 include("datafitting/spectralDCM.jl")
+include("blox/blox_utilities.jl")
 include("blox/neural_mass.jl")
 include("blox/cortical_blox.jl")
 include("blox/canonicalmicrocircuit.jl")

src/blox/blox_utilities.jl

@@ -0,0 +1,11 @@
+function scope_dict(para_dict::Dict{Symbol, Union{Real,Num}})
+    para_dict_copy = copy(para_dict)
+    for (n,v) in para_dict_copy
+        if typeof(v) == Num
+            para_dict_copy[n] = ParentScope(v)
+        else
+            para_dict_copy[n] = (@parameters $n=v)[1]
+        end
+    end
+    return para_dict_copy
+end

src/blox/neural_mass.jl

@@ -54,11 +54,15 @@ mutable struct JansenRitCBlox <: NeuralMassBlox
     initial::Dict{Num, Tuple{Float64, Float64}}
     odesystem::ODESystem
     function JansenRitCBlox(;name, τ=0.001, H=20.0, λ=5.0, r=0.15)
-        params = @parameters τ=τ H=H λ=λ r=r
+        para_dict = scope_dict(Dict{Symbol,Union{Real,Num}}(:τ => τ,:H => H,:λ => λ,:r => r))
+        τ=para_dict[:τ]
+        H=para_dict[:H]
+        λ=para_dict[:λ]
+        r=para_dict[:r]
         sts    = @variables x(t)=1.0 y(t)=1.0 jcn(t)=0.0
         eqs    = [D(x) ~ y - ((2/τ)*x),
                 D(y) ~ -x/(τ*τ) + (H/τ)*((2*λ)/(1 + exp(-r*(jcn))) - λ)]
-        odesys = ODESystem(eqs, t, sts, params; name=name)
+        odesys = ODESystem(eqs, t, sts, values(para_dict); name=name)
         new(τ, H, λ, r, odesys.x,[odesys.x],[odesys.x,odesys.y],
             Dict(odesys.x => (-1.0,1.0), odesys.y => (-1.0,1.0)),
             odesys)
@@ -78,11 +82,15 @@ mutable struct  JansenRitSCBlox <: NeuralMassBlox
     initial::Dict{Num, Tuple{Float64, Float64}}
     odesystem::ODESystem
     function JansenRitSCBlox(;name, τ=0.014, H=20.0, λ=400.0, r=0.1)
-        params = @parameters τ=τ H=H λ=λ r=r
+        para_dict = scope_dict(Dict{Symbol,Union{Real,Num}}(:τ => τ,:H => H,:λ => λ,:r => r))
+        τ=para_dict[:τ]
+        H=para_dict[:H]
+        λ=para_dict[:λ]
+        r=para_dict[:r]
         sts    = @variables x(t)=1.0 y(t)=1.0 jcn(t)=0.0
         eqs    = [D(x) ~ y - ((2/τ)*x),
                   D(y) ~ -x/(τ*τ) + (H/τ)*((2*λ)/(1 + exp(-r*(jcn))) - λ)]
-        odesys = ODESystem(eqs, t, sts, params; name=name)
+        odesys = ODESystem(eqs, t, sts, values(para_dict); name=name)
         new(τ, H, λ, r, odesys.x,[odesys.x],[odesys.x,odesys.y],
             Dict(odesys.x => (-1.0,1.0), odesys.y => (-1.0,1.0)),
             odesys)

test/components.jl

@@ -127,11 +127,11 @@ Components Test for Cortical-Subcortical Jansen-Rit blox
 """
 
 # Create Regions
-@named GPe       = jansen_ritC(τ=0.04, H=20, λ=400, r=0.1)
-@named STN       = jansen_ritC(τ=0.01, H=20, λ=500, r=0.1)
-@named GPi       = jansen_ritC(τ=0.014, H=20, λ=400, r=0.1)
-@named Thalamus  = jansen_ritSC(τ=0.002, H=10, λ=20, r=5)
-@named PFC       = jansen_ritSC(τ=0.001, H=20, λ=5, r=0.15)
+@named GPe       = JansenRitCBlox(τ=0.04, H=20, λ=400, r=0.1)
+@named STN       = JansenRitCBlox(τ=0.01, H=20, λ=500, r=0.1)
+@named GPi       = JansenRitCBlox(τ=0.014, H=20, λ=400, r=0.1)
+@named Thalamus  = JansenRitSCBlox(τ=0.002, H=10, λ=20, r=5)
+@named PFC       = JansenRitSCBlox(τ=0.001, H=20, λ=5, r=0.15)
 
 # Connect Regions through Adjacency Matrix
 blox = [GPe, STN, GPi, Thalamus, PFC]

test/ode_from_graph.jl

@@ -1,7 +1,7 @@
 using Neuroblox, Test, SparseArrays, Graphs, MetaGraphs
 
-@named GPe = harmonic_oscillator(ω=4*2*π, ζ=1, k=(4*2*π)^2, h=0.1)
-@named STN = harmonic_oscillator(ω=4*2*π, ζ=1, k=(4*2*π)^2, h=1)
+@named GPe = HarmonicOscillatorBlox()
+@named STN = HarmonicOscillatorBlox()
 @named BP = BandPassFilterBlox()
 
 # Connect Regions through Adjacency Matrix
@@ -77,4 +77,19 @@ add_edge!(gg,3,1,:weight,.2)
 # add your test to see whether you get the same ODESystem
 @test typeof(neuron_net) == ODESystem
 @test typeof(neuron_net_graph) == ODESystem
-@test equations(neuron_net) == equations(neuron_net_graph)
+@test equations(neuron_net) == equations(neuron_net_graph)
+
+# parameter sharing test
+@parameters λ=400.0
+@named jr1 = JansenRitSCBlox(τ=0.014, H=20.0, λ=λ, r=0.1)
+@named jr2 = JansenRitSCBlox(τ=0.014, H=20.0, λ=λ, r=0.1)
+jg = MetaDiGraph()
+add_blox!(jg,jr1)
+add_blox!(jg,jr2)
+add_edge!(jg,1,2,:weight,1.0)
+add_edge!(jg,2,1,:weight,2.0)
+add_edge!(jg,1,1,:weight,-1.0)
+add_edge!(jg,2,2,:weight,-2.0)
+@named jg_graph = ODEfromGraph(jg)
+jg_graph_s = structural_simplify(jg_graph)
+@test length(parameters(jg_graph_s))==7