removed commented out sections in GUI.jl and made ObserverBlox not sh…

…ow up in GUI
Neuroblox · Jan 12, 2024 · b428247 · b428247
1 parent 75ead7b
commit b428247
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diff --git a/src/Neuroblox.jl b/src/Neuroblox.jl
@@ -52,7 +52,7 @@ abstract type AbstractNeuronBlox <: AbstractBlox end
 abstract type NeuralMassBlox <: AbstractBlox end
 abstract type CompositeBlox <: AbstractBlox end
 abstract type StimulusBlox <: AbstractBlox end
-abstract type ObserverBlox <: AbstractBlox end
+abstract type ObserverBlox end # not AbstractBlox since it should not show up in the GUI
 
 # we define these in neural_mass.jl
 # abstract type HarmonicOscillatorBlox <: NeuralMassBlox end

diff --git a/src/gui/GUI.jl b/src/gui/GUI.jl
@@ -61,21 +61,6 @@ const MENU = "menu"
 const NODE = "node"
 const LINK = "link"
 
-# function arguments(::Type{Neuroblox.Merger})
-#   OrderedDict(
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.LinHemo})
-#   OrderedDict(
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.Hemodynamics})
-#   OrderedDict(
-#   )
-# end
-
 function arguments(::Type{Neuroblox.ImageStimulus})
   OrderedDict(
     :height => NCAD(15, INTEGER, 1, 100,[], false),
@@ -110,44 +95,6 @@ function outputs(::Type{Neuroblox.WinnerTakeAllBlox})
   ["out1","out2","out3","out4","out5"]
 end
 
-# function arguments(::Type{Neuroblox.LinearNeuralMassBlox})
-#   OrderedDict(
-#     :τ => NCAD(0.01, NUMBER, 1.0, 10.0,[]),
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.LinearNeuralMass})
-#   OrderedDict(
-#     :τ => NCAD(0.01, NUMBER, 1.0, 10.0,[]),
-#   )
-# end
-
-#TODO: create connector compatible stochastic blox
-# function arguments(::Type{Neuroblox.OUBlox})
-#   OrderedDict(
-#     :μ => NCAD(0.0, NUMBER, -100.0, 100.0,[]),
-#     :τ => NCAD(1.0, NUMBER, 0.00001,10,[]),
-#     :σ => NCAD(1.0, NUMBER, 0.00001,10,[])
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.OUCouplingBlox})
-#   OrderedDict(
-#     :μ => NCAD(0.0, NUMBER, -100.0, 100.0,[]),
-#     :τ => NCAD(1.0, NUMBER, 0.00001,10,[]),
-#     :σ => NCAD(1.0, NUMBER, 0.00001,10,[])
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.HarmonicOscillatorBlox})
-#   OrderedDict(
-#     :ω => NCAD(25*(2*pi), NUMBER, (2*pi), 150*(2*pi),[]),
-#     :ζ => NCAD(1.0, NUMBER, -1.0, 1.0,[]),
-#     :k => NCAD(625*(2*pi), NUMBER, (2*pi), 22500*(2*pi),[]),
-#     :h => NCAD(35.0, NUMBER, 0.01, 90.0,[])
-#   )
-# end
-
 function arguments(::Type{Neuroblox.HarmonicOscillator})
   OrderedDict(
     #:measurement => NCAD("Measurement", MENU, 1 , 4 ,["none","fMRI", "EEG", "LFP"]),
@@ -163,24 +110,6 @@ function plotdetail(::Type{Neuroblox.HarmonicOscillator})
   OrderedDict(:detail => ["x","y"], :nodetail => ["x"])
 end
 
-# function arguments(::Type{Neuroblox.JansenRitCBlox})
-#   OrderedDict(
-#     :τ => NCAD(0.001, NUMBER, 0.001, 2.0,[]),
-#     :H => NCAD(20.0, NUMBER, 0.0, 500.0,[]),
-#     :λ => NCAD(5.0, NUMBER, 1.0, 25.0,[]),
-#     :r => NCAD(0.15, NUMBER, 0.1, 5.0,[])
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.JansenRitSCBlox})
-#   OrderedDict(
-#     :τ => NCAD(0.014, NUMBER, 0.001, 0.1,[]),
-#     :H => NCAD(20.0, NUMBER, 0.0, 500.0,[]),
-#     :λ => NCAD(400.0, NUMBER, 20.0, 500.0,[]),
-#     :r => NCAD(0.1, NUMBER, 0.1, 5.0,[])
-#   )
-# end
-
 function arguments(::Type{Neuroblox.JansenRit})
   OrderedDict(
     :τ => NCAD(0.014, NUMBER, 0.001, 0.1,[],true),
@@ -194,22 +123,6 @@ function plotdetail(::Type{Neuroblox.JansenRit})
   OrderedDict(:detail => ["x","y"], :nodetail => ["x"])
 end
 
-# function arguments(::Type{Neuroblox.WilsonCowanBlox})
-#   OrderedDict(
-#     :τ_E => NCAD(1.0, NUMBER, 1.0, 100.0,[]),
-#     :τ_I => NCAD(1.0, NUMBER, 1.0, 100.0,[]),
-#     :a_E => NCAD(1.2, NUMBER, 1.0, 100.0,[]),
-#     :a_I => NCAD(2.0, NUMBER, 1.0, 100.0,[]),
-#     :c_EE => NCAD(5.0, NUMBER, 1.0, 100.0,[]),
-#     :c_EI => NCAD(10.0, NUMBER, 1.0, 100.0,[]),
-#     :c_IE => NCAD(6.0, NUMBER, 1.0, 100.0,[]),
-#     :c_II => NCAD(1.0, NUMBER, 1.0, 100.0,[]),
-#     :θ_E => NCAD(2.0, NUMBER, 1.0, 100.0,[]),
-#     :θ_I => NCAD(3.5, NUMBER, 1.0, 100.0,[]),
-#     :η => NCAD(1.0, NUMBER, 1.0, 100.0,[])
-#   )
-# end
-
 function arguments(::Type{Neuroblox.WilsonCowan})
   OrderedDict(
     :τ_E => NCAD(1.0, NUMBER, 1.0, 100.0,[],true),
@@ -230,39 +143,6 @@ function plotdetail(::Type{Neuroblox.WilsonCowan})
   OrderedDict(:detail => ["E","I"], :nodetail => ["E"])
 end
 
-# function arguments(::Type{Neuroblox.LarterBreakspearBlox})
-#   OrderedDict(
-#     :C => NCAD(0.35, NUMBER, 0.0, 1.0,[]),
-#     :δ_VZ => NCAD(0.61, NUMBER, 0.1, 2.0,[]),
-#     :T_Ca => NCAD(-0.01, NUMBER, 0.02, -0.04,[]),
-#     :δ_Ca => NCAD(0.15, NUMBER, 0.1, 0.2,[]),
-#     :g_Ca => NCAD(1.0, NUMBER, 0.96, 1.01,[]), #tested in Jolien's work/similar to V_Ca in Anthony's paper
-#     :V_Ca => NCAD(1.0, NUMBER, 0.96, 1.01,[]), #limits established by bifurcation
-#     :T_K => NCAD(0.0, NUMBER, -0.05, 0.05,[]),
-#     :δ_K => NCAD(0.3, NUMBER,0.25, 0.35,[]),
-#     :g_K => NCAD(2.0, NUMBER, 1.95, 2.05,[]),  #tested in Jolien's work
-#     :V_K => NCAD(-0.7, NUMBER, -0.8, -0.6,[]),  #limits established by bifurcation
-#     :T_Na => NCAD(0.3, NUMBER, 0.25, 0.35,[]),
-#     :δ_Na => NCAD(0.15, NUMBER, 0.1, 0.2,[]),
-#     :g_Na => NCAD(6.7, NUMBER, 6.6, 6.8,[]),   #tested in Botond and Jolien's work
-#     :V_Na => NCAD(0.53, NUMBER, 0.41, 0.59,[]), #limits established by bifurcation
-#     :V_L => NCAD(-0.5, NUMBER, -0.6, -0.4,[]),
-#     :g_L => NCAD(0.5, NUMBER, 0.4, 0.6,[]),
-#     :V_T => NCAD(0.0, NUMBER, -0.05, 0.05,[]),
-#     :Z_T => NCAD(0.0, NUMBER, -0.05, 0.05,[]),
-#     :IS => NCAD(0.3, NUMBER, 0.0, 1.0,[]),
-#     :a_ee => NCAD(0.36, NUMBER, 0.33, 0.39,[]), #tested in Botond and Jolien's work
-#     :a_ei => NCAD(2.0, NUMBER, 1.95, 2.05,[]), #tested in Botond and Jolien's work
-#     :a_ie => NCAD(2.0, NUMBER, 1.95, 2.05,[]), #testing in Jolien's work
-#     :a_ne => NCAD(1.0, NUMBER, 0.95, 1.05,[]),
-#     :a_ni => NCAD(0.4, NUMBER, 0.3, 0.5,[]),
-#     :b => NCAD(0.1, NUMBER, 0.05, 0.15,[]),
-#     :τ_K => NCAD(1.0, NUMBER, 0.8, 1.2,[]), #shouldn't be varied, but useful in bifurcations to "harshen" the potassium landscape
-#     :ϕ => NCAD(0.7, NUMBER, 0.6, 0.8,[]),
-#     :r_NMDA => NCAD( 0.25, NUMBER, 0.2, 0.3,[]) #tested in Botond's work
-#   )
-# end
-
 function arguments(::Type{Neuroblox.LarterBreakspear})
   OrderedDict(
     :C => NCAD(0.35, NUMBER, 0.0, 1.0,[],true),
@@ -300,17 +180,6 @@ function plotdetail(::Type{Neuroblox.LarterBreakspear})
   OrderedDict(:detail => ["V","Z","W"], :nodetail => ["V"])
 end
 
-# function arguments(::Type{Neuroblox.NextGenerationBlox})
-#   OrderedDict(
-#     :C => NCAD(30.0, NUMBER, 1.0, 50.0,[]),
-#     :Δ => NCAD(1.0, NUMBER, 0.01, 100.0,[]),
-#     :η_0 => NCAD(5.0, NUMBER, 0.01, 20.0,[]),
-#     :v_syn => NCAD(-10.0, NUMBER, -20.0, 0.0,[]),
-#     :alpha_inv => NCAD(35.0, NUMBER, 0.01, 10.0,[]),
-#     :k => NCAD(0.105, NUMBER, 0.01, 2.0,[])
-#   )
-# end
-
 function arguments(::Type{Neuroblox.NextGenerationEIBlox})
   OrderedDict(
     :Cₑ => NCAD(52.0, NUMBER, 1.0, 50.0,[],true),
@@ -366,28 +235,6 @@ function info_link(::Type{Neuroblox.HebbianPlasticity})
   Dict(:link => "https://www.neuroblox.org")
 end
 
-#TODO: create connector compatible CMC
-# function arguments(::Type{Neuroblox.CanonicalMicroCircuitBlox})
-#   OrderedDict(
-#     :τ_ss => NCAD(0.002, NUMBER, 0.0001, 0.1,[]),
-#     :τ_sp => NCAD(0.002, NUMBER, 0.0001, 0.1,[]),
-#     :τ_ii => NCAD(0.016, NUMBER, 0.0001, 0.1,[]),
-#     :τ_dp => NCAD(0.028, NUMBER, 0.0001, 0.1,[]),
-#     :r_ss => NCAD(2.0/3.0, NUMBER, 0.1, 5.0,[]),
-#     :r_sp => NCAD(2.0/3.0, NUMBER, 0.1, 5.0,[]),
-#     :r_ii => NCAD(2.0/3.0, NUMBER, 0.1, 5.0,[]),
-#     :r_dp => NCAD(2.0/3.0, NUMBER, 0.1, 5.0,[])
-#   )
-# end
-
-# function inputs(::Type{Neuroblox.CanonicalMicroCircuitBlox})
-#   ["in_ss","in_sp","in_ii","in_sp"]
-# end
-
-# function outputs(::Type{Neuroblox.CanonicalMicroCircuitBlox})
-#   ["out_ss","out_sp","out_ii","out_sp"]
-# end
-
 function arguments(::Type{Neuroblox.Thalamus})
   OrderedDict(
     :N_exci => NCAD(25, INTEGER, 1, 100,[],true),
@@ -467,38 +314,6 @@ function arguments(::Type{Neuroblox.GreedyPolicy})
   )
 end
 
-#TODO: create connector compatible CMC
-# function arguments(::Type{Neuroblox.IFNeuronBlox}) #TODO: add correct settings for the arguments
-#   OrderedDict(
-#     :C => NCAD(30.0, NUMBER, 1.0, 50.0,[]),
-#     :E_syn => NCAD(1.0, NUMBER, 0.01, 100.0,[]),
-#     :G_syn => NCAD(5.0, NUMBER, 0.01, 20.0,[]),
-# 	  :I_in => NCAD(-10.0, NUMBER, -20.0, 0.0,[]),
-# 	  :freq => NCAD(35.0, NUMBER, 0.01, 10.0,[]),
-# 	  :phase => NCAD(0.105, NUMBER, 0.01, 2.0,[]),
-# 	  :τ => NCAD(0.105, NUMBER, 0.01, 2.0,[])
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.QIFNeuronBlox}) #TODO: add correct settings for the arguments
-#   OrderedDict(
-#     :E_syn => NCAD(1.0, NUMBER, 0.01, 100.0,[]),
-#     :G_syn => NCAD(5.0, NUMBER, 0.01, 20.0,[]),
-# 	  :w => NCAD(-10.0, NUMBER, -20.0, 0.0,[]),
-# 	  :τ => NCAD(0.105, NUMBER, 0.01, 2.0,[])
-#   )
-# end
-
-# function arguments(::Type{Neuroblox.LIFNeuronBlox}) #TODO: add correct settings for the arguments
-#   OrderedDict(
-#     :I_in => NCAD(0.0, NUMBER, -5.0, 5.0,[]),
-#     :V_L => NCAD(-70.0, NUMBER, -90, -10,[]),
-#     :τ => NCAD(10.0, NUMBER, 0.01, 100.0,[]),
-#     :R => NCAD(100.0, NUMBER, 0.01, 200.0,[]),
-#     :θ => NCAD(-10.0, NUMBER, -20, 20.0,[]),
-#   )
-# end
-
 function arguments(::Type{Neuroblox.HHNeuronExciBlox}) #TODO: add correct settings for the arguments
   OrderedDict(
     :t_spike_window => NCAD(90.0, NUMBER, 0.1, 100.0,[],true),