Forgot the file core/utils.jl in previous commit

Add of several useful functions for access values of model, lha and
trajectory objects.

core/MarkovProcesses.jl

@@ -22,14 +22,18 @@ export load_automaton, get_index, get_value, length_var
 
 # Model related methods
 export simulate, set_param!, get_param, set_observed_var!
-export is_bounded
+export is_bounded, check_consistency
 export load_model, get_module_path
 
+# Utils
+export get_module_path
+
 include("common.jl")
 
 include("trajectory.jl")
 include("lha.jl")
 include("model.jl")
+include("utils.jl")
 
 end
 

core/common.jl

@@ -88,4 +88,6 @@ end
 LHA(A::LHA, map_var::Dict{String,Int}) = LHA(A.l_transitions, A.l_loc, A.Λ, 
                                              A.l_loc_init, A.l_loc_final, A.map_var_automaton_idx, A.l_flow,
                                              A.map_edges, A.l_ctes, map_var)
+Base.:*(m::ContinuousTimeModel, A::LHA) = SynchronizedModel(m, A)
+Base.:*(A::LHA, m::ContinuousTimeModel) = SynchronizedModel(m, A)
 

core/lha.jl

@@ -19,6 +19,8 @@ function Base.show(io::IO, S::StateLHA)
     end
 end
 
+isaccepted(S::StateLHA) = S.loc in (S.A).l_loc_final
+
 # Methods for synchronize / read the trajectory
 function init_state(A::LHA, x0::SubArray{Int,1}, t0::Float64)
     S0 = StateLHA(A, "", zeros(length_var(A)), t0)

core/model.jl

 
+load_model(name_model::String) = include(get_module_path() * "/models/" * name_model * ".jl")
+
 # Simulation
 function simulate(m::ContinuousTimeModel)
     # trajectory fields
@@ -120,14 +122,18 @@ function set_observed_var!(m::Model,g::Vector{String})
     m._map_obs_var_idx = _map_obs_var_idx
 end
 
-is_bounded(m::Model) = m.time_bound < Inf
-function check_consistency(m::Model) end
-function simulate(m::Model, n::Int; bound::Float64 = Inf)::AbstractObservations end
-function set_param!(m::Model, p::Vector{Float64})::Nothing end
-function get_param(m::Model)::Vector{Float64} end
-
-get_module_path() = dirname(dirname(pathof(@__MODULE__)))
-function load_model(name_model::String)
-    include(get_module_path() * "/models/" * name_model * ".jl")
+is_bounded(m::ContinuousTimeModel) = m.time_bound < Inf
+function check_consistency(m::ContinuousTimeModel) 
+    @assert m.d == length(m.map_var_idx) 
+    @assert m.k == length(m.map_param_idx)
+    @assert m.k == length(m.p)
+    @assert length(m.g) <= m.d
+    @assert length(m._g_idx) == length(m.g)
+    @assert m.buffer_size >= 0
+    @assert typeof(m.is_absorbing(m.p, view(reshape(m.x0, 1, m.d), 1, :))) == Bool
+    return true
 end
+set_param!(m::ContinuousTimeModel, p::Vector{Float64}) = (m.p = p)
+set_param!(m::ContinuousTimeModel, name_p::String, p_i::Float64) = (m.p[m.map_param_idx[name_p]] = p_i)
+get_param(m::ContinuousTimeModel) = m.p
 

core/utils.jl

+
+get_module_path() = dirname(dirname(pathof(@__MODULE__)))
+

models/ER.jl

@@ -5,10 +5,10 @@ d=4
 k=3
 dict_var = Dict("E" => 1, "S" => 2, "ES" => 3, "P" => 4)
 dict_p = Dict("k1" => 1, "k2" => 2, "k3" => 3)
-l_tr = ["R1","R2","R3"]
-p = [1.0, 1.0, 1.0]
-x0 = [100, 100, 0, 0]
-t0 = 0.0
+l_tr_ER = ["R1","R2","R3"]
+p_ER = [1.0, 1.0, 1.0]
+x0_ER = [100, 100, 0, 0]
+t0_ER = 0.0
 function ER_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{String}, idx::Int,
                xn::SubArray{Int,1}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
@@ -43,8 +43,8 @@ function ER_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{String}, i
 end
 is_absorbing_ER(p::Vector{Float64},xn::SubArray{Int,1}) = 
     (p[1]*xn[1]*xn[2] + (p[2]+p[3])*xn[3]) === 0.0
-g = ["P"]
+g_ER = ["P"]
 
-ER = ContinuousTimeModel(d,k,dict_var,dict_p,l_tr,p,x0,t0,ER_f!,is_absorbing_ER; g=g)
+ER = ContinuousTimeModel(d,k,dict_var,dict_p,l_tr_ER,p_ER,x0_ER,t0_ER,ER_f!,is_absorbing_ER; g=g_ER)
 export ER
 

models/SIR.jl

@@ -5,10 +5,10 @@ d=3
 k=2
 dict_var = Dict("S" => 1, "I" => 2, "R" => 3)
 dict_p = Dict("ki" => 1, "kr" => 2)
-l_tr = ["R1","R2"]
-p = [0.0012, 0.05]
-x0 = [95, 5, 0]
-t0 = 0.0
+l_tr_SIR = ["R1","R2"]
+p_SIR = [0.0012, 0.05]
+x0_SIR = [95, 5, 0]
+t0_SIR = 0.0
 function SIR_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{String}, idx::Int,
            xn::SubArray{Int,1}, tn::Float64, p::Vector{Float64})
     a1 = p[1] * xn[1] * xn[2]
@@ -42,8 +42,8 @@ function SIR_f!(mat_x::Matrix{Int}, l_t::Vector{Float64}, l_tr::Vector{String},
     l_tr[idx] = "R$(reaction)"
 end
 is_absorbing_SIR(p::Vector{Float64}, xn::SubArray{Int,1}) = (p[1]*xn[1]*xn[2] + p[2]*xn[2]) === 0.0
-g = ["I"]
+g_SIR = ["I"]
 
-SIR = ContinuousTimeModel(d,k,dict_var,dict_p,l_tr,p,x0,t0,SIR_f!,is_absorbing_SIR; g=g)
+SIR = ContinuousTimeModel(d,k,dict_var,dict_p,l_tr_SIR,p_SIR,x0_SIR,t0_SIR,SIR_f!,is_absorbing_SIR; g=g_SIR)
 export SIR
 

tests/automata/read_trajectory_last_state_F.jl

@@ -11,7 +11,7 @@ A_F = create_automaton_F(SIR, x1, x2, t1, t2, "I") # <: LHA
 function test_last_state(A::LHA, m::ContinuousTimeModel)
     σ = simulate(m)
     Send = read_trajectory(A, σ)
-    test = (get_state_from_time(σ, Send.time)[1] == Send["n"]) & (Send["d"] == 0)
+    test = (get_state_from_time(σ, Send.time)[1] == Send["n"]) && (Send["d"] == 0)
     #=
     if !test
         @show Send
@@ -25,7 +25,7 @@ test_all = true
 nbr_sim = 10000
 for i = 1:nbr_sim
     test = test_last_state(A_F, SIR)
-    global test_all = test_all & test
+    global test_all = test_all && test
 end
 
 return test_all

tests/run_unit.jl

@@ -17,5 +17,8 @@ using Test
     @test include("unit/dist_lp.jl")
     @test include("unit/l_dist_lp.jl")
     @test include("unit/check_trajectory_consistency.jl")
+    @test include("unit/check_model_consistency.jl")
+    @test include("unit/set_param.jl")
+    @test include("unit/side_effects_1.jl")
 end
 

tests/unit/check_model_consistency.jl

+
+using MarkovProcesses
+
+load_model("SIR")
+load_model("ER")
+
+return check_consistency(ER) && check_consistency(SIR)
+

tests/unit/set_param.jl

+
+using MarkovProcesses
+
+load_model("SIR") # p = 0.0012, 0.05 
+load_model("ER") # p = 1; 1; 1 
+
+test_all = true
+
+new_param_ER = [1.0, 2.0, 1.5]
+set_param!(ER, new_param_ER)
+test_all = test_all && (ER.p == new_param_ER)
+
+k2 = 4.0
+set_param!(ER, "k2", k2)
+test_all = test_all && (ER.p == [1.0, 4.0, 1.5])
+
+k1 = 0.5
+set_param!(ER, "k1", k1)
+test_all = test_all && (ER.p == [0.5, 4.0, 1.5])
+
+k3 = 10.0
+set_param!(ER, "k3", 10.0)
+test_all = test_all && (ER.p == [0.5, 4.0, 10.0])
+
+new_param_SIR = [0.0013, 0.08]
+set_param!(SIR, new_param_SIR)
+test_all = test_all && (SIR.p == new_param_SIR)
+
+kr = 0.06
+set_param!(SIR, "kr", kr)
+test_all = test_all && (SIR.p == [0.0013, 0.06])
+
+ki = 0.011
+set_param!(SIR, "ki", ki)
+test_all = test_all && (SIR.p == [0.011, 0.06])
+
+return test_all
+

tests/unit/side_effects_1.jl

+
+using MarkovProcesses
+
+load_model("SIR")
+load_model("ER")
+
+test = SIR.map_var_idx !== ER.map_var_idx &&
+       SIR.map_param_idx !== ER.map_var_idx &&
+       SIR.l_transitions !== ER.l_transitions &&
+       SIR.g !== ER.g &&
+       SIR._g_idx !== ER._g_idx &&
+       SIR.f! != ER.f! &&
+       SIR.is_absorbing != ER.is_absorbing
+
+return test
+