More UI fixes & improvements for IAP course (#513)

* don't hide y axis in firing rate plot

* add `SPikeSource` abstract type alias and export relevant functions for custom sources

* generalize `generate_discrete_callbacks` for any spike source

* dispatch `system` separately for composite and non-composite bloxs to account for namespacing

* switch QIF spiking to discrete callback

* add `ContantInput` source

* revert back to continuous event for QIF spiking

ext/MakieExtension.jl

@@ -241,8 +241,6 @@ function Makie.plot!(p::FRPlot)
     ax.xlabel = p.xlabel[]
     ax.ylabel = p.ylabel[]
     ax.title = p.title[]
-
-    hideydecorations!(ax)
 
     fr = firing_rate(blox, sol; win_size = p.win_size[], overlap = p.overlap[], transient = p.transient[], threshold = p.threshold[])
 

src/Neuroblox.jl

@@ -67,8 +67,6 @@ abstract type StimulusBlox <: AbstractBlox end
 abstract type ObserverBlox end # not AbstractBlox since it should not show up in the GUI
 abstract type AbstractPINGNeuron <: AbstractNeuronBlox end
 
-const Neuron = AbstractNeuronBlox
-
 # we define these in neural_mass.jl
 # abstract type HarmonicOscillatorBlox <: NeuralMassBlox end
 # abstract type JansenRitCBlox <: NeuralMassBlox end
@@ -124,6 +122,9 @@ include("GraphDynamicsInterop/GraphDynamicsInterop.jl")
 include("Neurographs.jl")
 include("adjacency.jl")
 
+const Neuron = AbstractNeuronBlox
+const SpikeSource = AbstractSpikeSource
+
 function simulate(sys::ODESystem, u0, timespan, p, solver = AutoVern7(Rodas4()); kwargs...)
     prob = ODEProblem(sys, u0, timespan, p)
     sol = solve(prob, solver; kwargs...) #pass keyword arguments to solver
@@ -233,7 +234,8 @@ export Matrisome, Striosome, Striatum, GPi, GPe, Thalamus, STN, TAN, SNc
 export HebbianPlasticity, HebbianModulationPlasticity
 export Agent, ClassificationEnvironment, GreedyPolicy, reset!
 export LearningBlox
-export CosineSource, CosineBlox, NoisyCosineBlox, PhaseBlox, ImageStimulus, ExternalInput, PoissonSpikeTrain, DBS, ProtocolDBS, detect_transitions, compute_transition_times, compute_transition_values, get_protocol_duration
+export CosineSource, CosineBlox, NoisyCosineBlox, PhaseBlox, ImageStimulus, ConstantInput, ExternalInput, SpikeSource, PoissonSpikeTrain, generate_spike_times
+export DBS, ProtocolDBS, detect_transitions, compute_transition_times, compute_transition_values, get_protocol_duration
 export BandPassFilterBlox
 export OUBlox, OUCouplingBlox
 export phase_inter, phase_sin_blox, phase_cos_blox

src/Neurographs.jl

@@ -127,10 +127,10 @@ end
 
 generate_discrete_callbacks(blox, ::Connector; t_block = missing) = []
 
-function generate_discrete_callbacks(blox::PoissonSpikeTrain, bc::Connector; t_block = missing)
+function generate_discrete_callbacks(blox::AbstractSpikeSource, bc::Connector; t_block = missing)
     sa = spike_affects(bc)
     name_blox = namespaced_nameof(blox)
-
+  
     if haskey(sa, name_blox)
         eqs = sa[name_blox]
 
@@ -143,7 +143,7 @@ function generate_discrete_callbacks(blox::PoissonSpikeTrain, bc::Connector; t_b
             t_spikes = generate_spike_times(blox)
             t_spikes => to_vector(eq)
         end
-
+        
         return cb
     end
 end

src/blox/blox_utilities.jl

@@ -92,9 +92,9 @@ end
 
 get_system(blox) = blox.system
 get_system(sys::AbstractODESystem) = sys
-get_system(stim::PoissonSpikeTrain) = System(Equation[], t, [], []; name=stim.name)
+get_system(stim::AbstractSpikeSource) = System(Equation[], t, [], []; name=stim.name)
 
-function system(blox::AbstractBlox; simplify=true)
+function system(blox::CompositeBlox; simplify=true)
     sys = get_system(blox)
     eqs = get_input_equations(blox; namespaced=false)
 
@@ -103,6 +103,15 @@ function system(blox::AbstractBlox; simplify=true)
     return simplify ? structural_simplify(csys) : csys
 end
 
+
+function system(blox::AbstractBlox; simplify=true, kwargs...)
+    sys = get_system(blox)
+    eqs = get_input_equations(blox; namespaced=true)
+    csys =  compose(System(eqs, t, [], []; name=namespaced_nameof(blox), kwargs...), sys)
+
+    return simplify ? structural_simplify(csys) : csys
+end
+
 function get_namespaced_sys(blox)
     sys = get_system(blox)
 
@@ -457,7 +466,7 @@ replace_refractory!(V, blox, sol::SciMLBase.AbstractSolution) = V
 function find_spikes(x::AbstractVector{T}; threshold=zero(T)) where {T}    
     spike_idxs = argmaxima(x)
     peakheights!(spike_idxs, x[spike_idxs]; minheight = threshold)
-
+    
     spikes = sparsevec(spike_idxs, ones(length(spike_idxs)), length(x))
 
     return spikes
@@ -486,7 +495,6 @@ function detect_spikes(
     end
 
     V = voltage_timeseries(blox, sol; ts)
-
     spikes = find_spikes(V; threshold = thrs_value - tolerance)
 
     return spikes

src/blox/neuron_models.jl

@@ -795,7 +795,8 @@ struct QIFNeuron <: AbstractNeuronBlox
 		 		D(G)~(-1/τ₂)*G + z,
 	        	D(z)~(-1/τ₁)*z
 	    	  ]
-   		ev = [V~θ] => [V~Vᵣₑₛ,z~G_syn]
+
+		ev = [V~θ] => [V~Vᵣₑₛ,z~G_syn]
 		sys = ODESystem(eqs, t, sts, p, continuous_events=[ev]; name=name)
 
 		new(p, sys, namespace)

src/blox/sources.jl

@@ -1,3 +1,19 @@
+abstract type AbstractSpikeSource <: StimulusBlox end
+
+struct ConstantInput <: StimulusBlox
+    namespace
+    system
+
+    function ConstantInput(; name, namespace=nothing, I=1)
+        @variables u(t) [output=true, description="ext_input"]
+        @parameters I=I
+        eqs = [u ~ I]
+        sys = System(eqs, t, [u], [I]; name=name)
+
+        new(namespace, sys)
+    end
+end
+
 # Simple input blox
 mutable struct ExternalInput <: StimulusBlox
     namespace
@@ -156,7 +172,7 @@ end
 
 increment_pixel!(stim::ImageStimulus) = stim.current_pixel = mod(stim.current_pixel, stim.N_pixels) + 1
 
-struct PoissonSpikeTrain{N} <: StimulusBlox
+struct PoissonSpikeTrain{N} <: AbstractSpikeSource
     name
     namespace
     N_trains