refactor files.

francoisbonneau · francoisbonneau · commit e5824706bbb9 · 2025-09-09T11:38:17.000+02:00
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -36,7 +36,7 @@ find_package(OpenGeode REQUIRED CONFIG)
 add_subdirectory(src/geode/stochastic)
 
 #------------------------------------------------------------------------------------------------
-# Optional modules configuration
+# Optional modules object_set
 if(OPENGEODE_STOCHASTIC_WITH_TESTS)
     # Enable testing with CTest
     enable_testing()
diff --git a/include/geode/stochastic/sampling/direct/object_set_sampler/object_set_sampler.hpp b/include/geode/stochastic/sampling/direct/object_set_sampler/object_set_sampler.hpp
@@ -23,8 +23,8 @@
 
 #pragma once
 
-#include <geode/stochastic/configuration/configuration.hpp>
 #include <geode/stochastic/sampling/random_engine.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 namespace geode
 {
diff --git a/include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp b/include/geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp
@@ -26,7 +26,7 @@
 #include <geode/geometry/basic_objects/sphere.hpp>
 #include <geode/geometry/point.hpp>
 
-#include <geode/stochastic/sampling/direct/configuration_sampler/configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/object_set_sampler.hpp>
 #include <geode/stochastic/sampling/direct/point_uniform_sampler.hpp>
 
 namespace geode
diff --git a/include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp b/include/geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp
@@ -60,7 +60,7 @@ namespace geode
                 proposal_kernel_ != nullptr, "[MH] null proposal kernel" );
         }
 
-        ObjectSet< Type > initialize_configuration_with_sampling(
+        ObjectSet< Type > initialize_object_set_with_sampling(
             RandomEngine& engine,
             const std::unordered_map< uuid, index_t >& group_targets ) const
         {
diff --git a/include/geode/stochastic/sampling/mcmc/models/components/energy_term.hpp b/include/geode/stochastic/sampling/mcmc/models/components/energy_term.hpp
@@ -23,7 +23,7 @@
 #pragma once
 
 #include <geode/stochastic/common.hpp>
-#include <geode/stochastic/configuration/configuration.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 #include <optional>
 
 namespace
@@ -77,6 +77,16 @@ namespace geode
 
         virtual ~EnergyTerm() = default;
 
+        geode::uuid id() const
+        {
+            return id_;
+        }
+
+        const std::string& name() const
+        {
+            return name_;
+        }
+
         double parameter() const
         {
             return neg_log_parameter_.param();
@@ -99,5 +109,9 @@ namespace geode
 
     protected:
         NegLogParam neg_log_parameter_;
+
+    private:
+        geode::uuid id_;
+        std::string name_;
     };
 } // namespace geode
diff --git a/include/geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp b/include/geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp
@@ -22,7 +22,7 @@
  */
 #pragma once
 
-#include <geode/stochastic/configuration/configuration.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 #include <geode/stochastic/sampling/mcmc/models/components/energy_term.hpp>
 
diff --git a/include/geode/stochastic/sampling/mcmc/models/components/pairwise_term.hpp b/include/geode/stochastic/sampling/mcmc/models/components/pairwise_term.hpp
@@ -23,7 +23,7 @@
 #pragma once
 
 #include <geode/basic/range.hpp>
-#include <geode/stochastic/configuration/configuration.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 #include <geode/stochastic/sampling/mcmc/models/components/energy_term.hpp>
 
diff --git a/include/geode/stochastic/sampling/mcmc/models/gibbs_energy.hpp b/include/geode/stochastic/sampling/mcmc/models/gibbs_energy.hpp
@@ -22,8 +22,8 @@
  */
 #pragma once
 
-#include <geode/stochastic/configuration/configuration.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/energy_term.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 namespace geode
 {
diff --git a/include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp b/include/geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp
@@ -25,7 +25,7 @@
 #pragma once
 
 #include <geode/stochastic/common.hpp>
-#include <geode/stochastic/sampling/direct/configuration_sampler/configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/object_set_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp>
 
 namespace geode
diff --git a/include/geode/stochastic/sampling/mcmc/proposal/moves.hpp b/include/geode/stochastic/sampling/mcmc/proposal/moves.hpp
@@ -22,8 +22,8 @@
  */
 
 #pragma once
-#include <geode/stochastic/configuration/configuration.hpp>
-#include <geode/stochastic/sampling/direct/configuration_sampler/configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/object_set_sampler.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 namespace geode
 {
diff --git a/include/geode/stochastic/spatial/kneighbors_object_ids.hpp b/include/geode/stochastic/spatial/kneighbors_object_ids.hpp
@@ -22,7 +22,7 @@
  */
 
 #pragma once
-#include <geode/stochastic/configuration/r_tree.hpp>
+#include <geode/stochastic/object_set/r_tree.hpp>
 
 namespace geode
 {
diff --git a/include/geode/stochastic/spatial/kr_tree.hpp b/include/geode/stochastic/spatial/kr_tree.hpp
diff --git a/include/geode/stochastic/spatial/object_helpers.hpp b/include/geode/stochastic/spatial/object_helpers.hpp
diff --git a/include/geode/stochastic/spatial/object_set.hpp b/include/geode/stochastic/spatial/object_set.hpp
@@ -30,7 +30,7 @@
 #include <geode/geometry/bounding_box.hpp>
 #include <geode/geometry/point.hpp>
 
-// #include <geode/stochastic/configuration/neighbors_object_ids.hpp>
+// #include <geode/stochastic/object_set/neighbors_object_ids.hpp>
 namespace geode
 {
     struct SubSetDescriptor
@@ -78,7 +78,7 @@ namespace geode
         std::vector< ObjectId > neighbors(
             const ObjectId& object_id, double searching_distance ) const;
         // Object neighbor search by arbitrary object (return self if in the
-        // configuration)
+        // object_set)
         std::vector< ObjectId > neighbors(
             const Type& object, double searching_distance ) const;
 
diff --git a/include/geode/stochastic/spatial/pairwise_interactions.hpp b/include/geode/stochastic/spatial/pairwise_interactions.hpp
@@ -26,7 +26,7 @@
 #include <geode/geometry/distance.hpp>
 #include <geode/geometry/point.hpp>
 
-#include <geode/stochastic/configuration/object_helpers.hpp>
+#include <geode/stochastic/spatial/object_helpers.hpp>
 
 namespace geode
 {
diff --git a/src/geode/stochastic/CMakeLists.txt b/src/geode/stochastic/CMakeLists.txt
@@ -22,8 +22,8 @@ add_geode_library(
     NAME stochastic
     FOLDER "geode/stochastic"
     SOURCES
-        "configuration/configuration.cpp"
-        #"configuration/neighbors_object_ids.cpp"
+        "spatial/object_set.cpp"
+        #"spatial/neighbors_object_ids.cpp"
         "sampling/direct/ball_sampler.cpp"
         "sampling/direct/bounding_box_sampler.cpp"
         "sampling/direct/double_sampler.cpp"
@@ -34,13 +34,13 @@ add_geode_library(
         "common.cpp"
         "hello_world.cpp"
     PUBLIC_HEADERS
-        "configuration/configuration.hpp"
-        #"configuration/neighbors_object_ids.hpp"
-        "configuration/object_helpers.hpp"
-        "configuration/pairwise_interactions.hpp"
-        #"configuration/r_tree.hpp"
-        "sampling/direct/configuration_sampler/configuration_sampler.hpp"
-        "sampling/direct/configuration_sampler/point_configuration_sampler.hpp"
+        "spatial/object_set.hpp"
+        #"spatial/neighbors_object_ids.hpp"
+        "spatial/object_helpers.hpp"
+        "spatial/pairwise_interactions.hpp"
+        #"spatial/r_tree.hpp"
+        "sampling/direct/object_set_sampler/object_set_sampler.hpp"
+        "sampling/direct/object_set_sampler/point_set_sampler.hpp"
         "sampling/direct/ball_sampler.hpp"
         "sampling/direct/bounding_box_sampler.hpp"
         "sampling/direct/double_sampler.hpp"
diff --git a/src/geode/stochastic/spatial/neighbors_object_ids.cpp b/src/geode/stochastic/spatial/neighbors_object_ids.cpp
@@ -21,7 +21,7 @@
  *
  */
 
-#include <geode/stochastic/configuration/neighbors_object_ids.hpp>
+#include <geode/stochastic/object_set/neighbors_object_ids.hpp>
 
 namespace
 {
diff --git a/src/geode/stochastic/spatial/object_set.cpp b/src/geode/stochastic/spatial/object_set.cpp
@@ -1,6 +1,6 @@
 
-#include <geode/stochastic/configuration/configuration.hpp>
-#include <geode/stochastic/configuration/object_helpers.hpp>
+#include <geode/stochastic/spatial/object_helpers.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 #include <geode/geometry/basic_objects/segment.hpp>
 #include <geode/geometry/point.hpp>
diff --git a/tests/stochastic/CMakeLists.txt b/tests/stochastic/CMakeLists.txt
@@ -19,7 +19,7 @@
 # SOFTWARE.
 
 add_geode_test(
-    SOURCE "configuration/test-pairwise-interactions.cpp"
+    SOURCE "spatial/test-pairwise-interactions.cpp"
     DEPENDENCIES
         OpenGeode::basic
         OpenGeode::geometry
diff --git a/tests/stochastic/sampling/mcmc/models/components/test-intensity-term.cpp b/tests/stochastic/sampling/mcmc/models/components/test-intensity-term.cpp
@@ -23,9 +23,9 @@
 #include <geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp>
 
 #include <geode/geometry/point.hpp>
-#include <geode/stochastic/configuration/configuration.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
-geode::ObjectSet< geode::Point2D > create_configuration(
+geode::ObjectSet< geode::Point2D > create_object_set(
     const geode::uuid &subset_id )
 {
     geode::Point2D p1{ { 0., 0. } };
@@ -101,7 +101,7 @@ int main()
         geode::StochasticLibrary::initialize();
         geode::uuid subset_id;
 
-        auto pattern = create_configuration( subset_id );
+        auto pattern = create_object_set( subset_id );
 
         test_normal_positive_intensity( 0.5, pattern, subset_id );
         test_normal_positive_intensity(
diff --git a/tests/stochastic/sampling/mcmc/models/components/test-pairwise-term.cpp b/tests/stochastic/sampling/mcmc/models/components/test-pairwise-term.cpp
@@ -25,9 +25,9 @@
 #include <geode/stochastic/sampling/mcmc/models/components/pairwise_term.hpp>
 
 #include <geode/geometry/point.hpp>
-#include <geode/stochastic/configuration/configuration.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
-geode::ObjectSet< geode::Point2D > create_pairwise_configuration(
+geode::ObjectSet< geode::Point2D > create_pairwise_object_set(
     const geode::uuid& subset_id )
 {
     geode::Point2D p1{ { 0., 0. } };
@@ -125,7 +125,7 @@ int main()
         geode::StochasticLibrary::initialize();
 
         geode::uuid subset_id;
-        auto pattern = create_pairwise_configuration( subset_id );
+        auto pattern = create_pairwise_object_set( subset_id );
 
         test_normal_positive_pairwise( 0.5, pattern, subset_id );
         test_normal_positive_pairwise(
diff --git a/tests/stochastic/sampling/mcmc/models/test-gibbs-energy.cpp b/tests/stochastic/sampling/mcmc/models/test-gibbs-energy.cpp
@@ -25,14 +25,14 @@
 
 #include <geode/geometry/point.hpp>
 
-#include <geode/stochastic/configuration/configuration.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/pairwise_term.hpp>
 #include <geode/stochastic/sampling/mcmc/models/gibbs_energy.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 namespace
 {
-    geode::ObjectSet< geode::Point2D > create_configuration(
+    geode::ObjectSet< geode::Point2D > create_object_set(
         const geode::uuid& subset_id )
     {
         geode::Point2D p1{ { 0., 0. } };
@@ -69,7 +69,7 @@ void test_gibbs_energy( const geode::uuid& subset_id )
     OPENGEODE_EXCEPTION( gibbs_energy.number_of_energy_terms() == 2,
         "[test gibbs] Wrong number of components after adding terms." );
 
-    auto pattern = create_configuration( subset_id );
+    auto pattern = create_object_set( subset_id );
 
     // Check total log-energy is finite
     double total_energy = gibbs_energy.total_log_energy( pattern );
diff --git a/tests/stochastic/sampling/mcmc/proposal/test-proposal-kernel.cpp b/tests/stochastic/sampling/mcmc/proposal/test-proposal-kernel.cpp
@@ -24,16 +24,16 @@
 
 #include <geode/basic/assert.hpp>
 #include <geode/geometry/point.hpp>
-#include <geode/stochastic/configuration/configuration.hpp>
-#include <geode/stochastic/sampling/direct/configuration_sampler/point_configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp>
 #include <geode/stochastic/sampling/mcmc/proposal/moves.hpp>
 #include <geode/stochastic/sampling/mcmc/proposal/proposal_kernel.hpp>
 #include <geode/stochastic/sampling/random_engine.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 
 namespace
 {
-    geode::ObjectSet< geode::Point2D > create_configuration(
+    geode::ObjectSet< geode::Point2D > create_object_set(
         const geode::uuid& subset_id )
     {
         geode::Point2D p1{ { 0., 0. } };
@@ -50,7 +50,7 @@ namespace
     void test_proposal_kernel()
     {
         geode::uuid subset_id;
-        auto config = create_configuration( subset_id );
+        auto config = create_object_set( subset_id );
 
         geode::Point2D min_point{ { 0., 0. } };
         geode::Point2D max_point{ { 10., 100. } };
@@ -144,7 +144,7 @@ namespace
         OPENGEODE_EXCEPTION( saw_birth && saw_death && saw_change,
             "[test proposal] Kernel did not produce all move types." );
 
-        // --- Edge case: empty configuration ---
+        // --- Edge case: empty object_set ---
         geode::ObjectSet< geode::Point2D > empty_config;
         empty_config.add_subset( subset_id );
 
diff --git a/tests/stochastic/sampling/mcmc/test-metropolis-hasting-sampler.cpp b/tests/stochastic/sampling/mcmc/test-metropolis-hasting-sampler.cpp
@@ -21,7 +21,7 @@
  *
  */
 #include <geode/geometry/point.hpp>
-#include <geode/stochastic/sampling/direct/configuration_sampler/point_configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp>
 #include <geode/stochastic/sampling/mcmc/models/gibbs_energy.hpp>
@@ -80,7 +80,7 @@ namespace
             { subset_id, 20 }
         };
         geode::ObjectSet< geode::Point2D > state =
-            mh.initialize_configuration_with_sampling( engine, targets );
+            mh.initialize_object_set_with_sampling( engine, targets );
 
         geode::index_t stat_sum{ 0 };
         constexpr geode::index_t N{ 100000 };
diff --git a/tests/stochastic/sampling/mcmc/test-mh-poisson-statistics-and-convergence.cpp b/tests/stochastic/sampling/mcmc/test-mh-poisson-statistics-and-convergence.cpp
@@ -21,12 +21,12 @@
  *
  */
 #include <geode/geometry/point.hpp>
-#include <geode/stochastic/configuration/configuration.hpp>
-#include <geode/stochastic/sampling/direct/configuration_sampler/point_configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp>
 #include <geode/stochastic/sampling/mcmc/models/gibbs_energy.hpp>
 #include <geode/stochastic/sampling/mcmc/proposal/classical_proposals.hpp>
+#include <geode/stochastic/spatial/object_set.hpp>
 namespace
 {
 
@@ -40,7 +40,7 @@ namespace
         const geode::GibbsEnergy< geode::Point2D >& energy )
     {
         geode::ObjectSet< geode::Point2D > state =
-            mh.initialize_configuration_with_sampling( engine, group_targets );
+            mh.initialize_object_set_with_sampling( engine, group_targets );
 
         constexpr geode::index_t N{ 1000000 };
 
diff --git a/tests/stochastic/sampling/mcmc/test-mh-strauss-statistics-and-convergence.cpp b/tests/stochastic/sampling/mcmc/test-mh-strauss-statistics-and-convergence.cpp
@@ -21,7 +21,7 @@
  *
  */
 #include <geode/geometry/point.hpp>
-#include <geode/stochastic/sampling/direct/configuration_sampler/point_configuration_sampler.hpp>
+#include <geode/stochastic/sampling/direct/object_set_sampler/point_set_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/metropolis_hasting_sampler.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/intensity_term.hpp>
 #include <geode/stochastic/sampling/mcmc/models/components/pairwise_term.hpp>
@@ -78,7 +78,7 @@ namespace
             { subset_id, 0 }
         };
         geode::ObjectSet< geode::Point2D > state =
-            mh.initialize_configuration_with_sampling( engine, targets );
+            mh.initialize_object_set_with_sampling( engine, targets );
 
         constexpr geode::index_t N{ 100000 };
 
diff --git a/tests/stochastic/spatial/test-pairwise-interactions.cpp b/tests/stochastic/spatial/test-pairwise-interactions.cpp
@@ -24,7 +24,7 @@
 #include <geode/geometry/distance.hpp>
 #include <geode/geometry/point.hpp>
 
-#include <geode/stochastic/configuration/pairwise_interactions.hpp>
+#include <geode/stochastic/spatial/pairwise_interactions.hpp>
 namespace
 {
     void test_interaction()

Original file line number	Diff line number	Diff line change
`@@ -23,8 +23,8 @@`
`23`	`23`
`24`	`24`	`#pragma once`
`25`	`25`
`26`		`-#include <geode/stochastic/configuration/configuration.hpp>`
`27`	`26`	`#include <geode/stochastic/sampling/random_engine.hpp>`
	`27`	`+#include <geode/stochastic/spatial/object_set.hpp>`
`28`	`28`
`29`	`29`	`namespace geode`
`30`	`30`	`{`
Original file line number	Diff line number	Diff line change
`@@ -60,7 +60,7 @@ namespace geode`
`60`	`60`	`proposal_kernel_ != nullptr, "[MH] null proposal kernel" );`
`61`	`61`	`}`
`62`	`62`
`63`		`- ObjectSet< Type > initialize_configuration_with_sampling(`
	`63`	`+ ObjectSet< Type > initialize_object_set_with_sampling(`
`64`	`64`	`RandomEngine& engine,`
`65`	`65`	`const std::unordered_map< uuid, index_t >& group_targets ) const`
`66`	`66`	`{`
Original file line number	Diff line number	Diff line change
`@@ -22,8 +22,8 @@`
`22`	`22`	`*/`
`23`	`23`	`#pragma once`
`24`	`24`
`25`		`-#include <geode/stochastic/configuration/configuration.hpp>`
`26`	`25`	`#include <geode/stochastic/sampling/mcmc/models/components/energy_term.hpp>`
	`26`	`+#include <geode/stochastic/spatial/object_set.hpp>`
`27`	`27`
`28`	`28`	`namespace geode`
`29`	`29`	`{`