From 2a9d3b72075e476d4a57d684049b59f92e632a3e Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Sun, 22 Nov 2020 12:08:26 +0100
Subject: [PATCH] Add of a function in models that creates new model objects +
tests.
Add of a major test based on Cosmos: tests/cosmos/distance_F/ER_1D.jl
The LHA distance F of this package is tested with Cosmos.
For several parameters in R1, R2, R3 experiments (see Bentriou,
Ballarini, Cournede 2018), Cosmos is called to
compute an average distance. Then we collect the number of simulations
and the estimated value computed by Cosmos.
We compute an average distance by the package methods with the same
number of simulations done by Cosmos
Then the two average distances are compared to each others with
regard to the width of the confidence interval set in Cosmos.
Test passed.
---
core/MarkovProcesses.jl | 2 +-
core/utils.jl | 14 ++++++
models/ER.jl | 10 +++-
models/SIR.jl | 10 +++-
tests/cosmos/distance_F/ER.gspn | 45 +++++++++++++++++
tests/cosmos/distance_F/ER_1D.jl | 71 +++++++++++++++++++++++++++
tests/cosmos/distance_F/dist_F_ER.lha | 40 +++++++++++++++
tests/run_all.jl | 1 +
tests/run_cosmos.jl | 7 +++
tests/run_unit.jl | 1 +
tests/unit/create_models.jl | 26 ++++++++++
11 files changed, 224 insertions(+), 3 deletions(-)
create mode 100644 tests/cosmos/distance_F/ER.gspn
create mode 100644 tests/cosmos/distance_F/ER_1D.jl
create mode 100644 tests/cosmos/distance_F/dist_F_ER.lha
create mode 100644 tests/run_cosmos.jl
create mode 100644 tests/unit/create_models.jl
diff --git a/core/MarkovProcesses.jl b/core/MarkovProcesses.jl
index 4ae10bb..946d155 100644
--- a/core/MarkovProcesses.jl
+++ b/core/MarkovProcesses.jl
@@ -26,7 +26,7 @@ export isbounded, isaccepted, check_consistency
export load_model, get_module_path
# Utils
-export get_module_path
+export get_module_path, cosmos_get_values
include("common.jl")
diff --git a/core/utils.jl b/core/utils.jl
index 4128525..5b46b3b 100644
--- a/core/utils.jl
+++ b/core/utils.jl
@@ -1,3 +1,17 @@
get_module_path() = dirname(dirname(pathof(@__MODULE__)))
+function cosmos_get_values(name_file::String)
+ output_file = open(name_file)
+ dict_values = Dict{String}{Float64}()
+ while !eof(output_file)
+ line = readline(output_file)
+ splitted_line = split(line, ':')
+ if (length(splitted_line) > 1) && tryparse(Float64, splitted_line[2]) !== nothing
+ dict_values[splitted_line[1]] = parse(Float64, splitted_line[2])
+ end
+ end
+ close(output_file)
+ return dict_values
+end
+
diff --git a/models/ER.jl b/models/ER.jl
index deace15..3c4a3c4 100644
--- a/models/ER.jl
+++ b/models/ER.jl
@@ -46,5 +46,13 @@ isabsorbing_ER(p::Vector{Float64},xn::SubArray{Int,1}) =
g_ER = ["P"]
ER = ContinuousTimeModel(d,k,dict_var,dict_p,l_tr_ER,p_ER,x0_ER,t0_ER,ER_f!,isabsorbing_ER; g=g_ER)
-export ER
+
+function create_ER(new_p::Vector{Float64})
+ ER_new = deepcopy(ER)
+ @assert length(ER_new.p) == length(new_p)
+ set_param!(ER_new, new_p)
+ return ER_new
+end
+
+export ER, create_ER
diff --git a/models/SIR.jl b/models/SIR.jl
index 37990bc..c9033d4 100644
--- a/models/SIR.jl
+++ b/models/SIR.jl
@@ -45,5 +45,13 @@ isabsorbing_SIR(p::Vector{Float64}, xn::SubArray{Int,1}) = (p[1]*xn[1]*xn[2] + p
g_SIR = ["I"]
SIR = ContinuousTimeModel(d,k,dict_var,dict_p,l_tr_SIR,p_SIR,x0_SIR,t0_SIR,SIR_f!,isabsorbing_SIR; g=g_SIR)
-export SIR
+
+function create_SIR(new_p::Vector{Float64})
+ SIR_new = deepcopy(SIR)
+ @assert length(SIR_new.p) == length(new_p)
+ set_param!(SIR_new, new_p)
+ return SIR_new
+end
+
+export SIR, create_SIR
diff --git a/tests/cosmos/distance_F/ER.gspn b/tests/cosmos/distance_F/ER.gspn
new file mode 100644
index 0000000..bd6462e
--- /dev/null
+++ b/tests/cosmos/distance_F/ER.gspn
@@ -0,0 +1,45 @@
+const int E_init=100;
+const int S_init=100;
+const int ES_init=0;
+const int P_init=0;
+
+const double k_1=1.0;
+const double k_2=1.0;
+const double k_3=1.0;
+
+
+NbPlaces = 4;
+NbTransitions = 3;
+
+PlacesList = {
+E,S, ES, P
+} ;
+
+TransitionsList = {
+TR1, TR2, TR3
+} ;
+
+Marking={
+(E , E_init); (S , S_init); (ES , ES_init);
+(P , P_init);
+};
+
+Transitions={
+(TR1,EXPONENTIAL(k_1*E*S),1,1, SINGLE);
+(TR2,EXPONENTIAL(k_2*ES),1,1, SINGLE);
+(TR3,EXPONENTIAL(k_3*ES),1,1, SINGLE);
+};
+
+InArcs={
+(E, TR1,1); (S, TR1,1);
+(ES, TR2,1); (ES, TR3,1);
+};
+
+OutArcs={
+(TR1, ES,1);
+(TR2, E,1);
+(TR2, S,1);
+(TR3, E,1);
+(TR3, P,1);
+};
+
diff --git a/tests/cosmos/distance_F/ER_1D.jl b/tests/cosmos/distance_F/ER_1D.jl
new file mode 100644
index 0000000..4c7a502
--- /dev/null
+++ b/tests/cosmos/distance_F/ER_1D.jl
@@ -0,0 +1,71 @@
+
+
+using MarkovProcesses
+absolute_path = get_module_path() * "/tests/cosmos/"
+
+# Remarque: la valeur estimée par Cosmos varie plus que de 0.01
+
+# Values x1, x2 t1, t2
+dict_exp = Dict(
+ "R1" => [50, 75, 0.025, 0.05],
+ "R2" => [50, 75, 0.05, 0.075],
+ "R3" => [25, 50, 0.05, 0.075]
+ )
+
+str_model = "ER"
+if str_model == "ER"
+ load_model(str_model)
+ model = ER
+end
+load_automaton("automaton_F")
+
+test_all = true
+width = 0.1
+level = 0.95
+l_exp = ["R1", "R2", "R3"]
+#l_exp = ["R2"]
+for exp in l_exp
+ if !(exp in keys(dict_exp))
+ println("Unrecognized experiment: <<$exp>>")
+ continue
+ end
+ val_exp = dict_exp[exp]
+ x1, x2, t1, t2 = val_exp[1], val_exp[2], val_exp[3], val_exp[4]
+ A_F = create_automaton_F(model, x1, x2, t1, t2, "P")
+ l_k3 = 0:10:100
+ nb_param = length(l_k3)
+ l_dist_cosmos = zeros(nb_param)
+ l_dist_pkg = zeros(nb_param)
+ for i in 1:nb_param
+ # Cosmos estimation
+ k3 = l_k3[i]
+ command = `Cosmos $(absolute_path * "distance_F/" * str_model * ".gspn")
+ $(absolute_path * "distance_F/dist_F_" * str_model * ".lha") --njob $(ENV["JULIA_NUM_THREADS"])
+ --const k_3=$(k3),x1=$x1,x2=$x2,t1=$t1,t2=$t2
+ --level $(level) --width $(width)
+ --verbose 0`
+ run(pipeline(command, stderr=devnull))
+ dict_values = cosmos_get_values("Result_dist_F_$(str_model).res")
+ l_dist_cosmos[i] = dict_values["Estimated value"]
+ nb_sim = dict_values["Total paths"]
+ nb_accepted = dict_values["Accepted paths"]
+ nb_sim = convert(Int, nb_sim)
+ # MarkovProcesses estimation
+ set_param!(ER, "k3", convert(Float64, k3))
+ sync_ER = ER*A_F
+ l_dist_i_threads = zeros(Threads.nthreads())
+ Threads.@threads for j = 1:nb_sim
+ σ = simulate(sync_ER)
+ l_dist_i_threads[Threads.threadid()] += (σ.S)["d"]
+ end
+ l_dist_pkg[i] = sum(l_dist_i_threads) / nb_sim
+ global test_all = test_all && isapprox(l_dist_cosmos[i], l_dist_pkg[i]; atol = width)
+ end
+
+end
+
+rm("Result_dist_F_$(str_model).res")
+rm("Result.res")
+
+return test_all
+
diff --git a/tests/cosmos/distance_F/dist_F_ER.lha b/tests/cosmos/distance_F/dist_F_ER.lha
new file mode 100644
index 0000000..baa9f54
--- /dev/null
+++ b/tests/cosmos/distance_F/dist_F_ER.lha
@@ -0,0 +1,40 @@
+NbVariables = 3;
+NbLocations = 4;
+
+const int x1 = 50;
+const int x2 = 75;
+
+const double t1 = 0.025;
+const double t2 = 0.05;
+
+VariablesList = {t,d,n};
+
+LocationsList = {l0, l1, l2, l3};
+
+AVG(Last(d));
+
+InitialLocations={l0};
+FinalLocations={l2};
+
+Locations={
+(l0, TRUE , (t:1));
+(l1, TRUE , (t:1));
+(l2, TRUE , (t:1));
+(l3, TRUE , (t:1));
+};
+
+Edges={
+((l0,l1), #, t>=0, {n=P});
+((l1,l3), #, t<=t1 & n<=x1-1, {d=min(((t-t1)^2+(n-x2)^2)^0.5,((t-t1)^2+(n-x1)^2)^0.5)});
+((l1,l3), #, t<=t1 & n>=x2+1, {d=min(((t-t1)^2+(n-x2)^2)^0.5,((t-t1)^2+(n-x1)^2)^0.5)});
+((l1,l3), #, n>=x1 & n<=x2, {d=0});
+((l1,l3), #, n<=x1-1 & t >= t1 & t<=t2, {d=min(d ,min( ((n-x1)^2)^0.5, ((n-x2)^2)^0.5 ) )});
+((l1,l3), #, n>=x2+1 & t >= t1 & t<=t2, {d=min(d,min( ((n-x1)^2)^0.5, ((n-x2)^2)^0.5 ) ) });
+((l3,l1), ALL, t>=0, {n=P});
+
+((l3,l2), #, t>=t2 ,#);
+
+((l1,l2),#, n>=x1 & n<=x2 & t>=t1 & t<=t2 ,{d=0});
+((l1,l2),#, t>=t2 , #);
+((l1,l2),#, d=0 & t>=t1, #);
+};
diff --git a/tests/run_all.jl b/tests/run_all.jl
index 5ed6f29..67ed817 100644
--- a/tests/run_all.jl
+++ b/tests/run_all.jl
@@ -3,4 +3,5 @@ include("run_unit.jl")
include("run_simulation.jl")
include("run_dist_lp.jl")
include("run_automata.jl")
+include("run_cosmos.jl")
diff --git a/tests/run_cosmos.jl b/tests/run_cosmos.jl
new file mode 100644
index 0000000..096a7f5
--- /dev/null
+++ b/tests/run_cosmos.jl
@@ -0,0 +1,7 @@
+
+using Test
+
+@testset "Cosmos tests" begin
+ @test include("cosmos/distance_F/ER_1D.jl")
+end
+
diff --git a/tests/run_unit.jl b/tests/run_unit.jl
index 49dfe1f..ea30b82 100644
--- a/tests/run_unit.jl
+++ b/tests/run_unit.jl
@@ -20,5 +20,6 @@ using Test
@test include("unit/check_model_consistency.jl")
@test include("unit/set_param.jl")
@test include("unit/side_effects_1.jl")
+ @test include("unit/create_models.jl")
end
diff --git a/tests/unit/create_models.jl b/tests/unit/create_models.jl
new file mode 100644
index 0000000..1d2df65
--- /dev/null
+++ b/tests/unit/create_models.jl
@@ -0,0 +1,26 @@
+
+using MarkovProcesses
+
+load_model("SIR")
+load_model("ER")
+
+test_all = true
+
+new_p = [0.01, 0.2]
+new_SIR = create_SIR(new_p)
+test_all = test_all && new_SIR.p == new_p && new_SIR !== SIR
+
+p_SIR = [0.0012, 0.05]
+new_SIR = create_SIR(p_SIR)
+test_all = test_all && new_SIR.p == p_SIR && new_SIR !== SIR
+
+new_p = [0.01, 0.2, 20.0]
+new_ER = create_ER(new_p)
+test_all = test_all && new_ER.p == new_p && new_ER !== ER
+
+p_ER = [1.0, 1.0, 1.0]
+new_ER = create_ER(p_ER)
+test_all = test_all && new_ER.p == p_ER && new_ER !== ER
+
+return true
+
--
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