feat(PVDInput): load time series through ExternalTimeSeriesHelpers

include/geode/io/time_series/internal/brep_time_attributes_transfer.hpp → include/geode/io/time_series/internal/pvd_attributes_transfer.hpp

@@ -28,70 +28,66 @@
 #include <string>
 #include <string_view>
 
+#include <vector>
+
 #include <absl/container/flat_hash_set.h>
-#include <absl/functional/function_ref.h>
 #include <absl/types/span.h>
 
 #include <geode/io/time_series/common.hpp>
-#include <geode/io/time_series/internal/brep_blocks_matcher.hpp>
+#include <geode/io/time_series/internal/pvd_point_sets.hpp>
 
 namespace geode
 {
     FORWARD_DECLARATION_DIMENSION_CLASS( SolidMesh );
     ALIAS_3D( SolidMesh );
     class AttributeManager;
-    class BRep;
 } // namespace geode
 
 namespace geode::internal
 {
-    class BRepTimeAttributesTransfer
+    // Writes the attributes of the .pvd datasets on the PVDPointSets
+    class PVDAttributesTransfer
     {
-        // Elements of one dataset of a time step and their mappings to
-        // the Block elements
+        // Elements of one dataset of a time step, the point set vertices they
+        // fill and the mapping to them
         struct DatasetElements
         {
             AttributeManager& manager;
-            const absl::flat_hash_map< uuid, GenericMapping< index_t > >&
-                block_mappings;
+            AttributeManager& target;
+            const GenericMapping< index_t >& mapping;
         };
 
     public:
-        BRepTimeAttributesTransfer( BRep& brep,
+        explicit PVDAttributesTransfer(
             absl::Span< const std::string_view > ignored_attributes );
 
         /*!
          * Write the attributes of all the datasets of a time step (e.g. one
          * per GEOS region and per MPI rank) as time step attributes of the
-         * Block meshes.
+         * time series point sets (unique vertices and cell barycenters).
          * Attributes sharing a name across the datasets are merged into a
-         * single time step attribute per Block.
+         * single time step attribute.
          * @warning The attributes of the given meshes are modified: those
          * sharing a name are given the same id.
          */
         void write_step( double time,
             absl::Span< const std::unique_ptr< SolidMesh3D > > meshes,
-            absl::Span< const SolidToBlocksMappings > mappings );
+            const PVDPointSets& point_sets );
 
     private:
-        void write_elements_step( double time,
-            absl::Span< const DatasetElements > datasets,
-            absl::FunctionRef< AttributeManager&( const SolidMesh3D& ) >
-                block_manager );
+        void write_elements_step(
+            double time, absl::Span< const DatasetElements > datasets );
 
         [[nodiscard]] absl::flat_hash_set< std::string > unify_attribute_ids(
             absl::Span< const DatasetElements > datasets );
 
         [[nodiscard]] std::optional< std::string > transferred_name(
             const AttributeManager& manager, const uuid& attribute_id ) const;
 
-        void write_block_step( double time,
-            const AttributeManager& manager,
-            AttributeManager& block_manager,
-            const GenericMapping< index_t >& mesh2block );
+        void write_dataset_step(
+            double time, const DatasetElements& dataset ) const;
 
     private:
-        BRep& brep_;
         absl::flat_hash_set< std::string > ignored_attributes_;
     };
 } // namespace geode::internal

include/geode/io/time_series/internal/brep_blocks_matcher.hpp → include/geode/io/time_series/internal/pvd_point_sets.hpp

@@ -23,61 +23,48 @@
 
 #pragma once
 
+#include <memory>
 #include <vector>
 
-#include <absl/container/flat_hash_map.h>
 #include <absl/types/span.h>
 
 #include <geode/basic/mapping.hpp>
-#include <geode/basic/uuid.hpp>
 
-#include <geode/geometry/nn_search.hpp>
+#include <geode/mesh/core/point_set.hpp>
 
 #include <geode/io/time_series/common.hpp>
 
 namespace geode
 {
     FORWARD_DECLARATION_DIMENSION_CLASS( SolidMesh );
     ALIAS_3D( SolidMesh );
-    class BRep;
 } // namespace geode
 
 namespace geode::internal
 {
-    // Solid elements to Block elements, per Block id
-    struct SolidToBlocksMappings
+    // Vertices of a .pvd dataset to unique vertices, its polyhedra to cell
+    // barycenters
+    struct PVDDatasetMappings
     {
-        absl::flat_hash_map< uuid, GenericMapping< index_t > > polyhedra;
-        absl::flat_hash_map< uuid, GenericMapping< index_t > > vertices;
+        GenericMapping< index_t > vertices;
+        GenericMapping< index_t > polyhedra;
     };
 
-    class BRepBlocksMatcher
+    // Point sets of a .pvd time series, given to the ExternalTimeSeries
+    // once all the time steps are written
+    struct PVDPointSets
     {
-        struct BlockElement
-        {
-            uuid block_id;
-            index_t element;
-        };
-
-    public:
-        explicit BRepBlocksMatcher( const BRep& brep );
-
-        [[nodiscard]] SolidToBlocksMappings mappings(
-            const SolidMesh3D& solid ) const;
-
-    private:
-        [[nodiscard]] std::vector< Point3D > compute_barycenters();
-
-        [[nodiscard]] std::vector< index_t > match_polyhedra(
-            const SolidMesh3D& solid ) const;
-
-        [[nodiscard]] SolidToBlocksMappings build_mappings(
-            const SolidMesh3D& solid,
-            absl::Span< const index_t > matched_ids ) const;
-
-    private:
-        const BRep& brep_;
-        std::vector< BlockElement > polyhedra_;
-        NNSearch3D barycenters_;
+        std::unique_ptr< PointSet3D > unique_vertices;
+        std::unique_ptr< PointSet3D > cell_barycenters;
+        std::vector< PVDDatasetMappings > mappings;
     };
+
+    /*!
+     * Create the .pvd point sets from the datasets of a time step
+     * (e.g. one per GEOS region and per MPI rank): the dataset vertices,
+     * colocated ones merged, and the dataset polyhedron barycenters, with
+     * the mappings of each dataset to them.
+     */
+    [[nodiscard]] PVDPointSets create_pvd_point_sets(
+        absl::Span< const std::unique_ptr< SolidMesh3D > > meshes );
 } // namespace geode::internal

src/geode/io/time_series/CMakeLists.txt

@@ -22,16 +22,16 @@ add_geode_library(
     NAME time_series
     FOLDER "geode/io/time_series"
     SOURCES
-        "brep_blocks_matcher.cpp"
         "common.cpp"
         "pvd_input.cpp"
-        "brep_time_attributes_transfer.cpp"
+        "pvd_attributes_transfer.cpp"
+        "pvd_point_sets.cpp"
     PUBLIC_HEADERS
         "common.hpp"
     INTERNAL_HEADERS
-        "internal/brep_blocks_matcher.hpp"
         "internal/pvd_input.hpp"
-        "internal/brep_time_attributes_transfer.hpp"
+        "internal/pvd_attributes_transfer.hpp"
+        "internal/pvd_point_sets.hpp"
     PRIVATE_DEPENDENCIES
         OpenGeode::basic
         OpenGeode::geometry