From 987f9441d3b7bc97896bacc07184c65f75b27e13 Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Thu, 26 Nov 2020 01:32:07 +0100
Subject: [PATCH] Add of plots of trajectory + observe_all! + tests
---
core/MarkovProcesses.jl | 4 ++--
core/model.jl | 17 ++++++++++---
core/plots.jl | 46 ++++++++++++++++++++++++++++++++++++
core/utils.jl | 2 ++
tests/simulation/plot_pkg.jl | 9 +++++++
tests/unit/observe_all.jl | 11 +++++++++
6 files changed, 84 insertions(+), 5 deletions(-)
create mode 100644 core/plots.jl
create mode 100644 tests/simulation/plot_pkg.jl
create mode 100644 tests/unit/observe_all.jl
diff --git a/core/MarkovProcesses.jl b/core/MarkovProcesses.jl
index 11c2b2d..e547640 100644
--- a/core/MarkovProcesses.jl
+++ b/core/MarkovProcesses.jl
@@ -24,13 +24,13 @@ export init_state, next_state!, read_trajectory
export load_automaton, get_index, get_value, length_var, isaccepted
# Model related methods
-export simulate, set_param!, get_param, set_observed_var!
+export simulate, set_param!, get_param, set_observed_var!, observe_all!
export set_time_bound!, getproperty, draw!
export isbounded, isaccepted, check_consistency
export load_model, get_module_path
# Utils
-export get_module_path, cosmos_get_values
+export get_module_path, cosmos_get_values, load_plots
include("common.jl")
diff --git a/core/model.jl b/core/model.jl
index 3e363ca..0a305c3 100644
--- a/core/model.jl
+++ b/core/model.jl
@@ -227,10 +227,10 @@ end
function simulate(m::ContinuousTimeModel, n::Int)
end
-function set_observed_var!(m::Model,g::Vector{String})
+function set_observed_var!(m::Model, g::Vector{String})
dobs = length(g)
- _map_obs_var_idx = Dict()
- _g_idx = Vector{Int}(undef, dobs)
+ _map_obs_var_idx = Dict{String}{Int}()
+ _g_idx = zeros(Int, dobs)
for i = 1:dobs
_g_idx[i] = m.map_var_idx[g[i]] # = ( (g[i] = i-th obs var)::String => idx in state space )
_map_obs_var_idx[g[i]] = i
@@ -240,6 +240,17 @@ function set_observed_var!(m::Model,g::Vector{String})
m._map_obs_var_idx = _map_obs_var_idx
end
+function observe_all!(m::Model)
+ g = Vector{String}(undef, m.d)
+ _g_idx = collect(1:m.d)
+ for var in keys(m.map_var_idx)
+ g[m.map_var_idx[var]] = var
+ end
+ m.g = g
+ m._g_idx = _g_idx
+ m._map_obs_var_idx = m.map_var_idx
+end
+
isbounded(m::ContinuousTimeModel) = m.time_bound < Inf
function check_consistency(m::ContinuousTimeModel)
@assert m.d == length(m.map_var_idx)
diff --git a/core/plots.jl b/core/plots.jl
new file mode 100644
index 0000000..b2092ef
--- /dev/null
+++ b/core/plots.jl
@@ -0,0 +1,46 @@
+
+import Plots: plot, plot!, scatter!
+import Plots: palette, display, png, close
+
+function plot(σ::AbstractTrajectory, vars::String...; filename::String = "", plot_transitions = false)
+ # Setup
+ palette_tr = palette(:default)
+ l_tr = unique(transitions(σ))
+ map_tr_color(tr) = palette_tr[findfirst(x->x==tr, l_tr)]
+ to_plot = vars
+ if length(vars) == 0
+ to_plot = get_obs_var(σ)
+ end
+
+ # Plots
+ p = plot(title = "Trajectory", palette = :lightrainbow)
+ for var in to_plot
+ @assert var in get_obs_var(σ)
+ plot!(p, times(σ), σ[var],
+ xlabel = "Time", ylabel = "Number of species",
+ label = var,
+ linetype=:steppost)
+ end
+ if plot_transitions
+ for (i, var) in enumerate(to_plot)
+ for tr in l_tr
+ idx_tr = findall(x->x==tr, transitions(σ))
+ label = (tr == nothing ||Â i > 1) ? "" : tr
+ alpha = (tr == nothing) ? 0.0 : 0.5
+ scatter!(p, times(σ)[idx_tr], σ[var][idx_tr], label=label,
+ markershape=:cross, markeralpha=alpha,
+ markersize = 2,
+ markercolor=palette_tr[findfirst(x->x==tr, l_tr)])
+ end
+ end
+ end
+ if filename == ""
+ display(p)
+ else
+ png(p, filename)
+ close(p)
+ end
+end
+
+export plot
+
diff --git a/core/utils.jl b/core/utils.jl
index 5b46b3b..c403635 100644
--- a/core/utils.jl
+++ b/core/utils.jl
@@ -15,3 +15,5 @@ function cosmos_get_values(name_file::String)
return dict_values
end
+load_plots() = include(get_module_path() * "/core/plots.jl")
+
diff --git a/tests/simulation/plot_pkg.jl b/tests/simulation/plot_pkg.jl
new file mode 100644
index 0000000..9ebbdd9
--- /dev/null
+++ b/tests/simulation/plot_pkg.jl
@@ -0,0 +1,9 @@
+
+using MarkovProcesses
+
+load_model("SIR")
+σ = simulate(SIR)
+
+load_plots()
+plot(σ; plot_transitions = true)
+
diff --git a/tests/unit/observe_all.jl b/tests/unit/observe_all.jl
new file mode 100644
index 0000000..3608bfc
--- /dev/null
+++ b/tests/unit/observe_all.jl
@@ -0,0 +1,11 @@
+
+using MarkovProcesses
+
+load_model("ER")
+load_model("SIR")
+
+observe_all!(ER)
+observe_all!(SIR)
+
+return ER.g == ["E", "S", "ER", "P"] && SIR.g == ["S", "I", "R"]
+
--
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