From c4c761671b64fa25cffb6f1691e8f1866b1e4a33 Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Sat, 16 Jan 2021 00:33:06 +0100
Subject: [PATCH] change about save of results of abc algorithm
---
algorithms/abc_smc.jl | 82 +++++++++++++++++++++++++++----------------
1 file changed, 51 insertions(+), 31 deletions(-)
diff --git a/algorithms/abc_smc.jl b/algorithms/abc_smc.jl
index 6790988..2667bce 100644
--- a/algorithms/abc_smc.jl
+++ b/algorithms/abc_smc.jl
@@ -27,23 +27,25 @@ struct ResultAbc
end
function automaton_abc(pm::ParametricModel; nbr_particles::Int = 100, alpha::Float64 = 0.75, kernel_type = "mvnormal",
- NT::Float64 = nbr_particles/2, duration_time::Float64 = Inf,
+ NT::Float64 = nbr_particles/2, duration_time::Float64 = Inf, dir_results::Union{Nothing,String} = nothing,
bound_sim::Int = typemax(Int), sym_var_aut::VariableAutomaton = :d, verbose::Int = 0)
@assert typeof(pm.m) <: SynchronizedModel
@assert 0 < nbr_particles
@assert 0.0 < alpha < 1.0
@assert kernel_type in ["mvnormal", "knn_mvnormal"]
- dir_res = create_results_dir()
- file_cfg = open(dir_res * "cfg_abc_pmc.txt", "w")
- write(file_cfg, "ParametricModel : $(pm) \n")
- write(file_cfg, "Number of particles : $(nbr_particles) \n")
- write(file_cfg, "alpha : $(alpha) \n")
- write(file_cfg, "kernel type : $(kernel_type) \n")
- close(file_cfg)
+ if dir_results != nothing
+ dir_results = basename(dir_results) != "" ? dir_results * "/" : dir_results
+ file_cfg = open(dir_results * "results.out", "w")
+ write(file_cfg, "ParametricModel : $(pm) \n")
+ write(file_cfg, "Number of particles : $(nbr_particles) \n")
+ write(file_cfg, "alpha : $(alpha) \n")
+ write(file_cfg, "kernel type : $(kernel_type) \n")
+ close(file_cfg)
+ end
if nprocs() == 1
- return _abc_smc(pm, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_res, sym_var_aut)
+ return _abc_smc(pm, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_results, sym_var_aut)
end
- return _distributed_abc_smc(pm, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_res, sym_var_aut)
+ return _distributed_abc_smc(pm, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_results, sym_var_aut)
end
"""
@@ -65,31 +67,34 @@ If pm is defined on a ContinuousTimeModel, then `T1` should verify `T1 <: Trajec
"""
function abc_smc(pm::ParametricModel, l_obs::AbstractVector, func_dist::Function;
nbr_particles::Int = 100, alpha::Float64 = 0.75, kernel_type = "mvnormal",
- NT::Float64 = nbr_particles/2, duration_time::Float64 = Inf,
+ NT::Float64 = nbr_particles/2, duration_time::Float64 = Inf, dir_results::Union{Nothing,String} = nothing,
bound_sim::Int = typemax(Int), sym_var_aut::VariableAutomaton = :d, verbose::Int = 0)
@assert 0 < nbr_particles
@assert 0.0 < alpha < 1.0
@assert kernel_type in ["mvnormal", "knn_mvnormal"]
- dir_res = create_results_dir()
- file_cfg = open(dir_res * "cfg_abc_pmc.txt", "w")
- write(file_cfg, "ParametricModel : $(pm) \n")
- write(file_cfg, "Number of particles : $(nbr_particles) \n")
- write(file_cfg, "alpha : $(alpha) \n")
- write(file_cfg, "kernel type : $(kernel_type) \n")
- close(file_cfg)
+ if dir_results != nothing
+ dir_results = basename(dir_results) != "" ? dir_results * "/" : dir_results
+ file_cfg = open(dir_results * "results.out", "w")
+ write(file_cfg, "Configuration of ABC algorithm\n")
+ write(file_cfg, "ParametricModel : $(pm) \n")
+ write(file_cfg, "Number of particles : $(nbr_particles) \n")
+ write(file_cfg, "alpha : $(alpha) \n")
+ write(file_cfg, "kernel type : $(kernel_type) \n")
+ close(file_cfg)
+ end
if nprocs() == 1
- return _abc_smc(pm, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_res, sym_var_aut; l_obs = l_obs, func_dist = func_dist)
+ return _abc_smc(pm, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_results, sym_var_aut; l_obs = l_obs, func_dist = func_dist)
end
- return _distributed_abc_smc(pm, l_obs, dist, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_res, sym_var_aut; l_obs = l_obs, func_dist = func_dist)
+ return _distributed_abc_smc(pm, l_obs, dist, nbr_particles, alpha, kernel_type, NT, duration_time, bound_sim, dir_results, sym_var_aut; l_obs = l_obs, func_dist = func_dist)
end
# To code:
-#Â Pkg related: draw!, prior_density!, create_results_dir
+#Â Pkg related: draw!, prior_density!
function _abc_smc(pm::ParametricModel, nbr_particles::Int, alpha::Float64,
kernel_type::String, NT::Float64, duration_time::Float64,
- bound_sim::Int, dir_res::String, sym_var_aut::VariableAutomaton;
+ bound_sim::Int, dir_results::Union{Nothing,String}, sym_var_aut::VariableAutomaton;
l_obs::Union{Nothing,AbstractVector} = nothing, func_dist::Union{Nothing,Function} = nothing)
@info "ABC PMC with $(nworkers()) processus and $(Threads.nthreads()) threads"
begin_time = time()
@@ -171,10 +176,17 @@ function _abc_smc(pm::ParametricModel, nbr_particles::Int, alpha::Float64,
mat_p = mat_p_old
mat_cov = cov(mat_p, ProbabilityWeights(wl_old), 2; corrected=false)
- save_mat_p_end = false
- if save_mat_p_end
- writedlm(dir_res * "weights_end.csv", wl_old, ',')
- writedlm(dir_res * "mat_p_end.csv", mat_p_old, ',')
+ if dir_results != nothing
+ writedlm(dir_results * "weights_end.csv", wl_old, ',')
+ writedlm(dir_results * "mat_p_end.csv", mat_p_old, ',')
+ file_cfg = open(dir_results * "results.out", "a")
+ write(file_cfg, "\n")
+ write(file_cfg, "About the results: \n")
+ write(file_cfg, "Total number of simulations: $nbr_tot_sim\n")
+ write(file_cfg, "Execution time: $(time() - begin_time)\n")
+ write(file_cfg, "Number of jobs: $(nprocs())\n")
+ write(file_cfg, "Number of threads: $(Threads.nthreads())\n")
+ close(file_cfg)
end
r = ResultAbc(mat_p, mat_cov, nbr_tot_sim, time() - begin_time, vec_dist, epsilon, wl_old, l_ess)
return r
@@ -182,7 +194,7 @@ end
function _distributed_abc_smc(pm::ParametricModel, nbr_particles::Int, alpha::Float64,
kernel_type::String, NT::Float64, duration_time::Float64, bound_sim::Int,
- dir_res::String, sym_var_aut::VariableAutomaton;
+ dir_results::Union{Nothing,String}, sym_var_aut::VariableAutomaton;
l_obs::Union{Nothing,AbstractVector} = nothing, func_dist::Union{Nothing,Function} = nothing)
@info "Distributed ABC PMC with $(nworkers()) processus and $(Threads.nthreads()) threads"
begin_time = time()
@@ -272,10 +284,18 @@ function _distributed_abc_smc(pm::ParametricModel, nbr_particles::Int, alpha::Fl
end
mat_cov = cov(mat_p, ProbabilityWeights(wl_old), 2; corrected=false)
- save_mat_p_end = false
- if save_mat_p_end
- writedlm(dir_res * "weights_end.csv", wl_current, ',')
- writedlm(dir_res * "mat_p_end.csv", mat_p, ',')
+ save_mat_p_end = true
+ if dir_results != nothing
+ writedlm(dir_results * "weights_end.csv", wl_current, ',')
+ writedlm(dir_results * "mat_p_end.csv", mat_p, ',')
+ file_cfg = open(dir_results * "results.out", "a")
+ write(file_cfg, "\n")
+ write(file_cfg, "About the results: \n")
+ write(file_cfg, "Total number of simulations: $nbr_tot_sim\n")
+ write(file_cfg, "Execution time: $(time() - begin_time)\n")
+ write(file_cfg, "Number of jobs: $(nprocs())\n")
+ write(file_cfg, "Number of threads: $(Threads.nthreads())\n")
+ close(file_cfg)
end
r = ResultAbc(mat_p, mat_cov, nbr_tot_sim, time() - begin_time, convert(Array, d_vec_dist), epsilon, wl_current, l_ess)
return r
--
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