feat(Object Neihbor): find neighbor with Rtree

Author: francoisbonneau

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

@@ -266,10 +266,12 @@ namespace geode
                 "[MH] Change proposal has no new_object" );
             OPENGEODE_ASSERT( proposal.old_object_id.has_value(),
                 "[MH] Change proposal has no index" );
-            const auto delta_log_energy = energy_.delta_log_energy_change(
-                state, proposal.old_object_id.value(),
+            geode::ObjectRef< Type > new_object{
                 proposal.new_object.value().first,
-                proposal.new_object.value().second );
+                proposal.new_object.value().second
+            };
+            const auto delta_log_energy = energy_.delta_log_energy_change(
+                state, proposal.old_object_id.value(), new_object );
             // should we test that objects are in the same group?
             // should be ensured by the dynamic
             return accept_or_reject( proposal, state, engine, delta_log_energy,

include/geode/stochastic/sampling/mcmc/models/components/energy_term.hpp

@@ -127,13 +127,12 @@ namespace geode
         virtual double delta_log_add( const ObjectSet< Type >& state,
             const ObjectRef< Type >& new_object ) const = 0;
 
-        virtual double delta_log_remove(
-            const ObjectSet< Type >& state, ObjectId object_id ) const = 0;
+        virtual double delta_log_remove( const ObjectSet< Type >& state,
+            const ObjectId& object_id ) const = 0;
 
         virtual double delta_log_change( const ObjectSet< Type >& state,
-            ObjectId old_object_id,
-            const Type& new_object,
-            const uuid& new_object_subset_id ) const = 0;
+            const ObjectId& old_object_id,
+            const ObjectRef< Type >& new_object ) const = 0;
 
         virtual double statistic( const ObjectSet< Type >& state ) const = 0;
 

include/geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp

@@ -61,7 +61,7 @@ namespace geode
         }
 
         double delta_log_remove( const ObjectSet< Type >& /*state*/,
-            ObjectId object_id ) const override
+            const ObjectId& object_id ) const override
         {
             if( !this->is_targeted_subset( object_id.subset ) )
             {
@@ -71,9 +71,8 @@ namespace geode
         }
 
         double delta_log_change( const ObjectSet< Type >& /*state*/,
-            ObjectId /*old_object_id*/,
-            const Type& /*new_object*/,
-            const uuid& /*new_object_subset_id*/ ) const override
+            const ObjectId& /*old_object_id*/,
+            const ObjectRef< Type >& /*new_object*/ ) const override
         {
             return 0.0;
         }

include/geode/stochastic/sampling/mcmc/models/components/pairwise_term.hpp

@@ -79,8 +79,8 @@ namespace geode
             return this->contribution( delta );
         }
 
-        double delta_log_remove(
-            const ObjectSet< Type >& state, ObjectId object_id ) const override
+        double delta_log_remove( const ObjectSet< Type >& state,
+            const ObjectId& object_id ) const override
         {
             if( !this->is_targeted_subset( object_id.subset ) )
             {
@@ -102,12 +102,11 @@ namespace geode
         }
 
         double delta_log_change( const ObjectSet< Type >& state,
-            ObjectId old_object_id,
-            const Type& new_object,
-            const uuid& new_object_subset_id ) const override
+            const ObjectId& old_object_id,
+            const ObjectRef< Type >& new_object ) const override
         {
             if( !this->is_targeted_subset( old_object_id.subset )
-                || !this->is_targeted_subset( new_object_subset_id ) )
+                || !this->is_targeted_subset( new_object.subset ) )
             {
                 return 0.0;
             }
@@ -128,9 +127,8 @@ namespace geode
             }
 
             // Add new object's interactions
-            ObjectRef< Type > object_to_add{ new_object, new_object_subset_id };
-            const auto new_neighbors = state.neighbors(
-                new_object, interaction_->neighborhood_searching_distance() );
+            const auto new_neighbors = state.neighbors( new_object.object,
+                interaction_->neighborhood_searching_distance() );
             for( auto neigh_id : new_neighbors )
             {
                 if( old_object_id == neigh_id )
@@ -139,7 +137,7 @@ namespace geode
                 }
                 ObjectRef< Type > neigh_object{ state.get_object( neigh_id ),
                     neigh_id.subset };
-                delta += interaction_->evaluate( object_to_add, neigh_object );
+                delta += interaction_->evaluate( new_object, neigh_object );
             }
 
             return this->contribution( delta );

include/geode/stochastic/sampling/mcmc/models/gibbs_energy.hpp

@@ -104,15 +104,14 @@ namespace geode
 
         double delta_log_energy_change( const ObjectSet< Type >& state,
             ObjectId old_object_id,
-            const Type& new_object,
-            const uuid& new_object_subset_id ) const
+            const ObjectRef< Type >& new_object ) const
         {
             double log_energy{ 0.0 };
             for( const auto& [id, term] : energy_terms_ )
             {
                 geode_unused( id );
-                log_energy += term->delta_log_change(
-                    state, old_object_id, new_object, new_object_subset_id );
+                log_energy +=
+                    term->delta_log_change( state, old_object_id, new_object );
             }
             return log_energy;
         }

tests/stochastic/sampling/mcmc/models/components/test-intensity-term.cpp

@@ -62,9 +62,7 @@ void test_normal_positive_intensity( double lambda,
 
     OPENGEODE_EXCEPTION( delta_remove == neg_log_lambda * -1.,
         "[test intensity]- delta_log_remove wrong value." );
-
-    double delta_change =
-        term.delta_log_change( pattern, obj_id, p3, subset_id );
+    double delta_change = term.delta_log_change( pattern, obj_id, p_ref );
     OPENGEODE_EXCEPTION(
         delta_change == 0., "[test intensity]- delta_log_change wrong value." );
 }
@@ -91,9 +89,7 @@ void test_normal_zero_intensity( double lambda,
     double delta_remove = term.delta_log_remove( pattern, obj_id );
     OPENGEODE_EXCEPTION( delta_remove == 0.,
         "[test zero intensity]- delta_log_remove wrong value." );
-
-    double delta_change =
-        term.delta_log_change( pattern, obj_id, p3, subset_id );
+    double delta_change = term.delta_log_change( pattern, obj_id, p_ref );
     OPENGEODE_EXCEPTION( delta_change == 0.,
         "[test zero intensity]- delta_log_change wrong value." );
 }

tests/stochastic/sampling/mcmc/models/components/test-pairwise-term.cpp

@@ -74,7 +74,7 @@ void test_normal_positive_pairwise( double gamma,
     OPENGEODE_EXCEPTION( delta_remove == neg_log_gamma * -1.,
         "[test pairwise] - delta_log_remove wrong value." );
 
-    auto delta_change = term.delta_log_change( pattern, obj_id, p3, subset_id );
+    auto delta_change = term.delta_log_change( pattern, obj_id, p_ref );
     // Replacing p1 with p3 changes interactions: p3 interacts with p2 → 1 pair
     // Old p1 interacted with p2 → 1 pair → no net change
     OPENGEODE_EXCEPTION(
@@ -106,7 +106,7 @@ void test_zero_pairwise( double gamma,
     OPENGEODE_EXCEPTION( delta_remove == 0.,
         "[test zero pairwise] - delta_log_remove wrong value." );
 
-    auto delta_change = term.delta_log_change( pattern, obj_id, p3, subset_id );
+    auto delta_change = term.delta_log_change( pattern, obj_id, p_ref );
     OPENGEODE_EXCEPTION( delta_change == 0.,
         "[test zero pairwise] - delta_log_change wrong value." );
 }

tests/stochastic/sampling/mcmc/models/test-gibbs-energy.cpp

@@ -90,7 +90,7 @@ void test_gibbs_energy( const geode::uuid& subset_id )
 
     // Change point test
     double delta_change =
-        gibbs_energy.delta_log_energy_change( pattern, obj_id, p3, subset_id );
+        gibbs_energy.delta_log_energy_change( pattern, obj_id, p_ref );
     OPENGEODE_EXCEPTION( std::isfinite( delta_change ),
         "[test gibbs] Delta change should be finite." );