From a94525a52e1b85c13c5ad58dcbbd5ce8eaeb5062 Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Tue, 2 Feb 2021 14:49:31 +0100
Subject: [PATCH] Now pictures are saved in svg. All tests passed.
---
core/plots.jl | 10 +++++-----
examples/scripts/doping_3way_oscillator.jl | 6 +++---
examples/scripts/enzym_1d.jl | 4 ++--
examples/scripts/enzym_2d.jl | 6 +++---
tests/automaton_abc/R1.jl | 2 +-
tests/automaton_abc/R2.jl | 2 +-
tests/automaton_abc/R3.jl | 2 +-
tests/automaton_abc/R6.jl | 16 ++++++++++++++++
tests/automaton_abc/distributed_R1.jl | 2 +-
tests/simulation/sim_er_row_buffer_bounded.jl | 2 +-
tests/simulation/sim_pm_er.jl | 2 +-
tests/simulation/sim_pm_sync_er.jl | 2 +-
tests/simulation/sim_poisson.jl | 2 +-
tests/simulation/sim_sir.jl | 2 +-
tests/simulation/sim_sir_bounded.jl | 2 +-
tests/simulation/sim_sir_col_buffer_bounded.jl | 2 +-
tests/simulation/sim_sir_row_buffer_bounded.jl | 2 +-
tests/simulation/sim_sir_tauleap.jl | 2 +-
18 files changed, 42 insertions(+), 26 deletions(-)
create mode 100644 tests/automaton_abc/R6.jl
diff --git a/core/plots.jl b/core/plots.jl
index caf17e7..2f260ff 100644
--- a/core/plots.jl
+++ b/core/plots.jl
@@ -1,6 +1,6 @@
import Plots: plot, plot!, scatter!, hline!, Shape, text
-import Plots: current, palette, display, png, close
+import Plots: current, palette, display, png, close, savefig
"""
`plot(σ, var...; plot_transitions=false)`
@@ -27,14 +27,14 @@ function plot(σ::AbstractTrajectory, vars::VariableModel...; plot_transitions::
@assert var in get_obs_var(σ) "Variable $var is not observed."
plot!(p, times(σ), σ[var],
xlabel = "Time", ylabel = "Number of species",
- label = var,
+ label = "$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
+ label = (tr == nothing ||Â i > 1) ? "" : "$tr"
alpha = (tr == nothing) ? 0.0 : 0.5
scatter!(p, times(σ)[idx_tr], σ[var][idx_tr], label=label,
markershape=:cross, markeralpha=alpha,
@@ -49,7 +49,7 @@ function plot(σ::AbstractTrajectory, vars::VariableModel...; plot_transitions::
if filename == ""
display(p)
else
- png(p, filename)
+ savefig(p, filename)
end
end
@@ -124,7 +124,7 @@ function plot_periodic_trajectory(A::LHA, σ::SynchronizedTrajectory, sym_obs::S
if filename == ""
display(p)
else
- png(p, filename)
+ savefig(p, filename)
end
end
diff --git a/examples/scripts/doping_3way_oscillator.jl b/examples/scripts/doping_3way_oscillator.jl
index cbfba14..bfd1167 100644
--- a/examples/scripts/doping_3way_oscillator.jl
+++ b/examples/scripts/doping_3way_oscillator.jl
@@ -10,7 +10,7 @@ sync_doping = doping_3way_oscillator * A_per
set_time_bound!(sync_doping, 0.1)
set_x0!(doping_3way_oscillator, [:A, :B, :C, :DA, :DB, :DC], [333, 333, 333, 10, 10, 10])
σ = simulate(sync_doping)
-plot(σ; A = A_per, filename = "traj_full.png")
-plot(σ, :A; A = A_per, filename = "traj_A.png")
-plot_periodic_trajectory(A_per, σ, :A, filename = "traj_automaton.png")
+plot(σ; A = A_per, filename = "traj_full.svg")
+plot(σ, :A; A = A_per, filename = "traj_A.svg")
+plot_periodic_trajectory(A_per, σ, :A, filename = "traj_automaton.svg")
diff --git a/examples/scripts/enzym_1d.jl b/examples/scripts/enzym_1d.jl
index 6e38558..bc6196e 100644
--- a/examples/scripts/enzym_1d.jl
+++ b/examples/scripts/enzym_1d.jl
@@ -45,7 +45,7 @@ samples_weights = r.weights
# Histogram
histogram(samples_abc_post, weights = r.weights, normalize = :density)
-png(path_results * "histogram.png")
+savefig(path_results * "histogram.svg")
## Satisfaction function
@@ -92,5 +92,5 @@ y_MC = readdlm("/home/moud/plot_R1-3/estim_MC/$(exp)/satisfaction_func.csv", ','
inf_x, sup_x = 0.0, 100.0
x_MC = inf_x:((sup_x-inf_x)/(length(y_MC)-1)):sup_x
plot!(x_MC, y_MC, label = "MC spf")
-png(path_results * "satisfaction_prob_function.png")
+savefig(path_results * "satisfaction_prob_function.svg")
diff --git a/examples/scripts/enzym_2d.jl b/examples/scripts/enzym_2d.jl
index dc74706..1ebb12d 100644
--- a/examples/scripts/enzym_2d.jl
+++ b/examples/scripts/enzym_2d.jl
@@ -47,7 +47,7 @@ samples_weights = r.weights
# Histogram
histogram2d(samples_abc_post[1,:], samples_abc_post[2,:], weights = samples_weights, normalize = :density)
-png(path_results * "histogram.png")
+savefig(path_results * "histogram.svg")
=#
## Satisfaction function
@@ -88,11 +88,11 @@ xaxis = 0:0.1:1.5
yaxis = 0:1.0:100.0
p = plot(title = "Multivariate KDE", dpi = 480, background_color_legend = :transparent)
plot!(p, xaxis, yaxis, prob_func, st = :surface, c = :coolwarm, camera = (30, 45))
-png(path_results * "estim_abc_satisfaction_prob_function.png")
+savefig(path_results * "estim_abc_satisfaction_prob_function.svg")
x_MC = readdlm("/home/moud/results_last_automata/estim_satisfaction_func_MC/$(exp)/grid_X.csv", ',')
y_MC = readdlm("/home/moud/results_last_automata/estim_satisfaction_func_MC/$(exp)/grid_Y.csv", ',')
z_MC = readdlm("/home/moud/results_last_automata/estim_satisfaction_func_MC/$(exp)/satisfaction_func.csv", ',')
p = plot(title = "ABC MC", dpi = 480, background_color_legend = :transparent)
plot!(p, [x_MC...], [y_MC...], [z_MC...], st = :surface, c = :coolwarm, camera = (30, 45), label = "MC spf")
-png(path_results * "estim_MC_satisfaction_prob_function.png")
+savefig(path_results * "estim_MC_satisfaction_prob_function.svg")
diff --git a/tests/automaton_abc/R1.jl b/tests/automaton_abc/R1.jl
index cde4a9f..ee76c2e 100644
--- a/tests/automaton_abc/R1.jl
+++ b/tests/automaton_abc/R1.jl
@@ -20,5 +20,5 @@ return test
#using Plots
#histogram(r.mat_p_end', weights = r.weights, normalize = :density)
-#png("R1_hist.png")
+#savefig("R1_hist.svg")
diff --git a/tests/automaton_abc/R2.jl b/tests/automaton_abc/R2.jl
index ac624b3..369050f 100644
--- a/tests/automaton_abc/R2.jl
+++ b/tests/automaton_abc/R2.jl
@@ -13,5 +13,5 @@ pm_sync_ER = ParametricModel(sync_ER, (:k3, Uniform(0.0, 100.0)))
@show r.nbr_sim
histogram(r.mat_p_end', bins = :sqrt, weights = r.weights, normalize = :density, xlims = (0.0, 100.0))
-png("R2_hist.png")
+savefig("R2_hist.svg")
diff --git a/tests/automaton_abc/R3.jl b/tests/automaton_abc/R3.jl
index bc41c68..b263f94 100644
--- a/tests/automaton_abc/R3.jl
+++ b/tests/automaton_abc/R3.jl
@@ -11,5 +11,5 @@ pm_sync_ER = ParametricModel(sync_ER, (:k3, Uniform(0.0, 100.0)))
r = automaton_abc(pm_sync_ER; nbr_particles = 1000)
histogram(r.mat_p_end', weights = r.weights, normalize = :density, xlims = (0.0, 100.0))
-png("R3_hist.png")
+savefig("R3_hist.svg")
diff --git a/tests/automaton_abc/R6.jl b/tests/automaton_abc/R6.jl
new file mode 100644
index 0000000..b8c8cef
--- /dev/null
+++ b/tests/automaton_abc/R6.jl
@@ -0,0 +1,16 @@
+
+using MarkovProcesses
+
+load_model("ER")
+observe_all!(ER)
+load_automaton("automaton_G_and_F")
+A_G_F_R6 = create_automaton_G_and_F(ER, 50.0, 100.0, 0.0, 0.8, :E, 30.0, 100.0, 0.8, 0.9, :P)
+sync_ER = A_G_F_R6 * ER
+pm_sync_ER = ParametricModel(sync_ER, (:k1, Uniform(0.0,100.0)), (:k2, Uniform(0.0,100.0)))
+
+r = automaton_abc(pm_sync_ER; alpha=0.2)
+
+using Plots
+histogram2d(r.mat_p_end[1,:], r.mat_p_end[2,:], bins=50)
+savefig("R6_hist.svg")
+
diff --git a/tests/automaton_abc/distributed_R1.jl b/tests/automaton_abc/distributed_R1.jl
index f10b7af..5fda0e8 100644
--- a/tests/automaton_abc/distributed_R1.jl
+++ b/tests/automaton_abc/distributed_R1.jl
@@ -34,5 +34,5 @@ test = size(r.mat_p_end)[1] == pm_sync_ER.df &&
return test
#histogram(r.mat_p_end', weights = r.weights, normalize = :density)
-#png("R1_hist.png")
+#savefig("R1_hist.svg")
diff --git a/tests/simulation/sim_er_row_buffer_bounded.jl b/tests/simulation/sim_er_row_buffer_bounded.jl
index 940fdce..c92dd9e 100644
--- a/tests/simulation/sim_er_row_buffer_bounded.jl
+++ b/tests/simulation/sim_er_row_buffer_bounded.jl
@@ -9,7 +9,7 @@ ER_row_buffer.time_bound = 10.0
σ = _simulate_row_buffer(ER_row_buffer)
plt.figure()
plt.step(times(σ), _get_values_row(σ,:P), "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_er_row_buffer_bounded.png")
+plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_er_row_buffer_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_pm_er.jl b/tests/simulation/sim_pm_er.jl
index b5e3e5a..492d464 100644
--- a/tests/simulation/sim_pm_er.jl
+++ b/tests/simulation/sim_pm_er.jl
@@ -9,7 +9,7 @@ pm_ER = ParametricModel(ER, (:k1, Uniform(0.0,100.0)), (:k2, Uniform(0.0,100.0))
prior_p = [0.2, 40.0]
σ = simulate(pm_ER, prior_p)
-MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_pm_er_long.png")
+MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_pm_er_long.svg")
return true
diff --git a/tests/simulation/sim_pm_sync_er.jl b/tests/simulation/sim_pm_sync_er.jl
index 56e92b6..19559d7 100644
--- a/tests/simulation/sim_pm_sync_er.jl
+++ b/tests/simulation/sim_pm_sync_er.jl
@@ -11,7 +11,7 @@ pm_sync_ER = ParametricModel(ER*A_F, (:k1, Uniform(0.0,100.0)), (:k2, Uniform(0.
prior_p = [0.2, 40.0]
σ = simulate(pm_sync_ER, prior_p)
-MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_pm_sync_er_long.png")
+MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_pm_sync_er_long.svg")
return true
diff --git a/tests/simulation/sim_poisson.jl b/tests/simulation/sim_poisson.jl
index 40aa61d..ca050a5 100644
--- a/tests/simulation/sim_poisson.jl
+++ b/tests/simulation/sim_poisson.jl
@@ -4,7 +4,7 @@ load_plots()
load_model("poisson")
σ = simulate(poisson)
-MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_poisson.png")
+MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_poisson.svg")
return true
diff --git a/tests/simulation/sim_sir.jl b/tests/simulation/sim_sir.jl
index 9ee9755..fe2740a 100644
--- a/tests/simulation/sim_sir.jl
+++ b/tests/simulation/sim_sir.jl
@@ -7,7 +7,7 @@ load_model("SIR")
σ = simulate(SIR)
plt.figure()
plt.step(times(σ), σ[:I], "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir.png")
+plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_bounded.jl b/tests/simulation/sim_sir_bounded.jl
index 19a3a12..fe3dcc7 100644
--- a/tests/simulation/sim_sir_bounded.jl
+++ b/tests/simulation/sim_sir_bounded.jl
@@ -8,7 +8,7 @@ SIR.time_bound = 100.0
σ = simulate(SIR)
plt.figure()
plt.step(times(σ), σ[:I], "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_bounded.png")
+plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_col_buffer_bounded.jl b/tests/simulation/sim_sir_col_buffer_bounded.jl
index 472195d..d68f990 100644
--- a/tests/simulation/sim_sir_col_buffer_bounded.jl
+++ b/tests/simulation/sim_sir_col_buffer_bounded.jl
@@ -9,7 +9,7 @@ SIR_col_buffer.time_bound = 100.0
σ = _simulate_col_buffer(SIR_col_buffer)
plt.figure()
plt.step(times(σ), _get_values_col(σ,:I), "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_col_buffer_bounded.png")
+plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_col_buffer_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_row_buffer_bounded.jl b/tests/simulation/sim_sir_row_buffer_bounded.jl
index 034862d..d10633d 100644
--- a/tests/simulation/sim_sir_row_buffer_bounded.jl
+++ b/tests/simulation/sim_sir_row_buffer_bounded.jl
@@ -9,7 +9,7 @@ SIR_row_buffer.time_bound = 100.0
σ = _simulate_row_buffer(SIR_row_buffer)
plt.figure()
plt.step(times(σ), _get_values_row(σ,:I), "ro--", marker="x", where="post", linewidth=1.0)
-plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_row_buffer_bounded.png")
+plt.savefig(get_module_path() * "/tests/simulation/res_pics/sim_sir_row_buffer_bounded.svg")
plt.close()
return true
diff --git a/tests/simulation/sim_sir_tauleap.jl b/tests/simulation/sim_sir_tauleap.jl
index a1fa7cf..3b22d6d 100644
--- a/tests/simulation/sim_sir_tauleap.jl
+++ b/tests/simulation/sim_sir_tauleap.jl
@@ -4,7 +4,7 @@ load_plots()
load_model("SIR_tauleap")
σ = simulate(SIR_tauleap)
-MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_sir_tauleap.png")
+MarkovProcesses.plot(σ; filename = get_module_path() * "/tests/simulation/res_pics/sim_sir_tauleap.svg")
return true
--
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