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francoisbonneaufrancoisbonneau
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feat(Helpers): add poisson and strauss helpers
1 parent 700f135 commit 6da78cf

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Lines changed: 980 additions & 677 deletions

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‎include/geode/stochastic/applications/poisson_process.hpp‎

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#pragma once
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#include <geode/stochastic/inference/target_statistics.hpp>
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#include <geode/stochastic/sampling/mcmc/helpers/simulation_context.hpp>
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namespace geode
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{
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template < typename ObjectType >
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struct PoissonSetDescription
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{
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std::string set_name;
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ObjectSamplerConfig< ObjectType > sampler;
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std::string density_name;
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double lambda;
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std::optional< double > expected_nb_objects;
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double birth_ratio{ 1.0 };
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double death_ratio{ 1.0 };
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double change_ratio{ 1.0 };
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};
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template < typename ObjectType >
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struct PoissonProcessDescription
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{
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SpatialDomainConfig< ObjectType::dim > domain;
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std::vector< PoissonSetDescription< ObjectType > > sets;
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PoissonSetDescription< ObjectType >& add_set(
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absl::string_view set_name, absl::string_view density_name )
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{
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auto& set = sets.emplace_back();
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set.set_name = set_name;
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set.density_name = density_name;
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return set;
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}
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};
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template < typename ObjectType >
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SimulationContext< ObjectType > build_poisson_process(
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const PoissonProcessDescription< ObjectType >& description );
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template < typename ObjectType >
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std::vector< geode::TargetStatisticConfig > build_poisson_targeted_stat(
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const PoissonProcessDescription< ObjectType >& description );
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} // namespace geode

‎include/geode/stochastic/applications/strauss_process.hpp‎

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#pragma once
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#include <geode/stochastic/applications/poisson_process.hpp>
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#include <geode/stochastic/inference/target_statistics.hpp>
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#include <geode/stochastic/sampling/mcmc/helpers/simulation_context.hpp>
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namespace geode
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{
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template < typename ObjectType >
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struct StraussInteractionDescription
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{
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std::string interaction_name;
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std::vector< std::string > set_names;
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double gamma;
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double distance;
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bool include_intra_set{ true };
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bool include_inter_set{ false };
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std::optional< double > expected_nb_interactions;
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};
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template < typename ObjectType >
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struct StraussProcessDescription
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{
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SpatialDomainConfig< ObjectType::dim > domain;
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std::vector< PoissonSetDescription< ObjectType > > sets;
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std::vector< StraussInteractionDescription< ObjectType > > interactions;
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PoissonSetDescription< ObjectType >& add_set(
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absl::string_view set_name, absl::string_view density_name )
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{
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auto& set = sets.emplace_back();
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set.set_name = set_name;
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set.density_name = density_name;
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return set;
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}
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StraussInteractionDescription< ObjectType >& add_interaction(
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absl::string_view interaction_name )
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{
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auto& interaction = interactions.emplace_back();
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interaction.interaction_name = interaction_name;
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return interaction;
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}
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};
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template < typename ObjectType >
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SimulationContext< ObjectType > build_strauss_process(
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const StraussProcessDescription< ObjectType >& description );
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template < typename ObjectType >
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std::vector< geode::TargetStatisticConfig > build_strauss_targeted_stat(
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const StraussProcessDescription< ObjectType >& description );
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} // namespace geode

‎include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp‎

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@@ -70,6 +70,7 @@ namespace geode
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constexpr index_t max_try{ 100 };
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for( const auto try_id : geode::Range{ max_try } )
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{
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geode_unused( try_id );
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if( domain_.extended_contains( new_point ) )
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{
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return new_point;
@@ -107,11 +108,11 @@ namespace geode
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};
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109110
template < index_t dimension >
110-
std::unique_ptr< ObjectSetSampler< Point2D > > build_objectset_sampler(
111-
const SpatialDomain< 2 >& domain,
112-
const ObjectSamplerConfig< Point< dimension > >& config )
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std::unique_ptr< ObjectSetSampler< Point< dimension > > >
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build_objectset_sampler( const SpatialDomain< dimension >& domain,
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const ObjectSamplerConfig< Point< dimension > >& config )
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{
114-
return std::make_unique< UniformPointSetSampler< 2 > >(
115+
return std::make_unique< UniformPointSetSampler< dimension > >(
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domain, config );
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}
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‎include/geode/stochastic/sampling/mcmc/helpers/simulation_context.hpp‎

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@@ -82,6 +82,13 @@ namespace geode
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template < typename ObjectType >
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struct SimulationContextConfig
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{
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ObjectSetDefinition< ObjectType >& add_set( absl::string_view name )
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{
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auto& set = sets.emplace_back();
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set.name = name;
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return set;
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}
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SpatialDomainConfig< ObjectType::dim > domain;
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8794
std::vector< ObjectSetDefinition< ObjectType > > sets;
@@ -127,7 +134,7 @@ namespace geode
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// MH sampler
128135
// -------------------------
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context.mh_sampler =
130-
std::make_unique< geode::MetropolisHastings< geode::Point2D > >(
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std::make_unique< geode::MetropolisHastings< ObjectType > >(
131138
*context.model, std::move( proposal_kernel ) );
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return context;

‎include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp‎

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@@ -150,8 +150,8 @@ namespace geode
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}
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private:
153-
const double compute_log_accept( const double deltaU,
154-
const ProposalProbabilities& proposal_probas ) const
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double compute_log_accept(
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double deltaU, const ProposalProbabilities& proposal_probas ) const
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{
156156
return -beta_ * deltaU + proposal_probas.transition_probability();
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}
@@ -189,10 +189,11 @@ namespace geode
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const auto delta_log_energy =
190190
model_.energy().delta_log_add( state, new_object );
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return accept_or_reject( proposal, state, engine, delta_log_energy,
192-
[]( auto& state, auto& proposal ) {
193-
state.add_object(
194-
std::move( proposal.proposed_move.new_object.value() ),
195-
proposal.set_id, false );
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[]( auto& cur_state, auto& accepted_proposal ) {
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cur_state.add_object(
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std::move( accepted_proposal.proposed_move.new_object
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.value() ),
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accepted_proposal.set_id, false );
196197
} );
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};
198199

@@ -204,8 +205,9 @@ namespace geode
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const auto delta_log_energy =
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model_.energy().delta_log_remove( state, old_object_id );
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return accept_or_reject( proposal, state, engine, delta_log_energy,
207-
[]( auto& state, auto& proposal ) {
208-
state.remove_free_object( proposal.old_object_id() );
208+
[]( auto& cur_state, auto& accepted_proposal ) {
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cur_state.remove_free_object(
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accepted_proposal.old_object_id() );
209211
} );
210212
};
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@@ -218,10 +220,11 @@ namespace geode
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const auto delta_log_energy = model_.energy().delta_log_change(
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state, old_object_id, new_object );
220222
return accept_or_reject( proposal, state, engine, delta_log_energy,
221-
[]( auto& state, auto& proposal ) {
222-
state.update_free_object( proposal.old_object_id(),
223-
std::move(
224-
proposal.proposed_move.new_object.value() ) );
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[]( auto& cur_state, auto& accepted_proposal ) {
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cur_state.update_free_object(
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accepted_proposal.old_object_id(),
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std::move( accepted_proposal.proposed_move.new_object
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.value() ) );
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} );
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};
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‎include/geode/stochastic/spatial/single_object_features/segment_length_feature.hpp‎

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* USE OR OTHER DEALINGS IN THE SOFTWARE.
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*
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*/
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#pragma once
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2526
#include <geode/stochastic/spatial/single_object_features/single_object_feature.hpp>
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‎src/geode/stochastic/CMakeLists.txt‎

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@@ -22,6 +22,8 @@ add_geode_library(
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NAME stochastic
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FOLDER "geode/stochastic"
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SOURCES
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"applications/poisson_process.cpp"
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"applications/strauss_process.cpp"
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"spatial/object_set.cpp"
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"spatial/object_sets.cpp"
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"spatial/object_neighborhood.cpp"
@@ -37,6 +39,8 @@ add_geode_library(
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"sampling/random_engine.cpp"
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"common.cpp"
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PUBLIC_HEADERS
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"applications/poisson_process.hpp"
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"applications/strauss_process.hpp"
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#"inference/abc_shadow.hpp"
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"inference/statistics_tools.hpp"
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"inference/statistics_tracker.hpp"

‎src/geode/stochastic/applications/poisson_process.cpp‎

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#pragma once
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#include <geode/stochastic/applications/poisson_process.hpp>
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namespace geode
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{
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using PoissonDensityDescription = geode::SingleObjectTermConfig;
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template < typename ObjectType >
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SimulationContext< ObjectType > build_poisson_process(
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const PoissonProcessDescription< ObjectType >& desc )
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{
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SimulationContextConfig< ObjectType > config;
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config.domain = desc.domain;
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for( const auto& set_desc : desc.sets )
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{
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auto& set = config.add_set( set_desc.set_name );
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set.sampler = set_desc.sampler;
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set.dynamics.birth_ratio = set_desc.birth_ratio;
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set.dynamics.death_ratio = set_desc.death_ratio;
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set.dynamics.change_ratio = set_desc.change_ratio;
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27+
PoissonDensityDescription density;
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29+
density.term_name = set_desc.density_name;
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density.object_set_names = { set_desc.set_name };
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density.lambda = set_desc.lambda;
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density.object_feature = ObjectInDomainFeatureConfig{};
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config.model.terms.emplace_back( std::move( density ) );
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}
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37+
return build_simulation_context( config );
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}
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40+
template opengeode_stochastic_stochastic_api SimulationContext< Point2D >
41+
build_poisson_process< Point2D >(
42+
const PoissonProcessDescription< Point2D >& );
43+
template opengeode_stochastic_stochastic_api SimulationContext< Point3D >
44+
build_poisson_process< Point3D >(
45+
const PoissonProcessDescription< Point3D >& );
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47+
template < typename ObjectType >
48+
std::vector< geode::TargetStatisticConfig > build_poisson_targeted_stat(
49+
const PoissonProcessDescription< ObjectType >& description )
50+
{
51+
std::vector< geode::TargetStatisticConfig > targets;
52+
53+
for( const auto& set_desc : description.sets )
54+
{
55+
if( !set_desc.expected_nb_objects )
56+
{
57+
continue;
58+
}
59+
60+
targets.push_back( geode::TargetStatisticConfig{
61+
set_desc.density_name, *set_desc.expected_nb_objects, 0.1 } );
62+
}
63+
64+
return targets;
65+
}
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67+
template opengeode_stochastic_stochastic_api
68+
std::vector< geode::TargetStatisticConfig >
69+
build_poisson_targeted_stat< Point2D >(
70+
const PoissonProcessDescription< Point2D >& );
71+
template opengeode_stochastic_stochastic_api
72+
std::vector< geode::TargetStatisticConfig >
73+
build_poisson_targeted_stat< Point3D >(
74+
const PoissonProcessDescription< Point3D >& );
75+
} // namespace geode

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