Fix bug with metadata set too late

Author: franzpoeschel

include/openPMD/Iteration.hpp

@@ -291,6 +291,11 @@ class Iteration
         particles.visitHierarchy(v);
     }
 
+    // TODO: make this available on every class that inherits from
+    // scientificdefaults for this, somehow make visitHierarchy a non-template,
+    // so we can use it as a virtual function of attributable
+    void populateDefaultMetadata();
+
     Container<Mesh> meshes{};
     Container<ParticleSpecies> particles{}; // particleSpecies?
 
@@ -370,8 +375,6 @@ class Iteration
     void readMeshes(std::string const &meshesPath);
     void readParticles(std::string const &particlesPath);
 
-    void setDefaultAttributes();
-
     /**
      * Status after beginning an IO step. Currently includes:
      * * The advance status (OK, OVER, RANDOMACCESS)

src/Iteration.cpp

@@ -127,7 +127,7 @@ Iteration &Iteration::close(bool _flush)
 
     if (access::write(IOHandler()->m_frontendAccess))
     {
-        setDefaultAttributes();
+        populateDefaultMetadata();
     }
 
     if (_flush)
@@ -161,40 +161,6 @@ Iteration &Iteration::close(bool _flush)
     return *this;
 }
 
-void Iteration::setDefaultAttributes()
-{
-    auto standard = IOHandler()->m_standard;
-    visitHierarchy([standard](auto &component) {
-        using ComponentType = std::remove_reference_t<decltype(component)>;
-        if constexpr (auxiliary::IsTemplateBaseOf_v<BaseRecord, ComponentType>)
-        {
-            if (component.empty() && !component.datasetDefined())
-            {
-                std::cerr
-                    << "Cannot flush Record without any contained components: '"
-                    << component.myPath().openPMDPath() << "'. Will ignore.";
-                if (component.written())
-                {
-                    std::cerr
-                        << "\n(Note: The Record seems to have been written "
-                           "previously?)";
-                }
-                std::cerr << std::endl;
-                return;
-            }
-        }
-
-        if constexpr (
-            !std::is_same_v<ComponentType, Container<Mesh>> &&
-            !std::is_same_v<ComponentType, Container<Record>> &&
-            !std::is_same_v<ComponentType, Container<PatchRecord>> &&
-            !std::is_same_v<ComponentType, Container<ParticleSpecies>>)
-        {
-            component.writeDefaults(standard);
-        }
-    });
-}
-
 Iteration &Iteration::open()
 {
     Series s = retrieveSeries();
@@ -278,6 +244,40 @@ bool Iteration::closedByWriter() const
     }
 }
 
+void Iteration::populateDefaultMetadata()
+{
+    auto standard = IOHandler()->m_standard;
+    visitHierarchy([standard](auto &component) {
+        using ComponentType = std::remove_reference_t<decltype(component)>;
+        if constexpr (auxiliary::IsTemplateBaseOf_v<BaseRecord, ComponentType>)
+        {
+            if (component.empty() && !component.datasetDefined())
+            {
+                std::cerr
+                    << "Cannot flush Record without any contained components: '"
+                    << component.myPath().openPMDPath() << "'. Will ignore.";
+                if (component.written())
+                {
+                    std::cerr
+                        << "\n(Note: The Record seems to have been written "
+                           "previously?)";
+                }
+                std::cerr << std::endl;
+                return;
+            }
+        }
+
+        if constexpr (
+            !std::is_same_v<ComponentType, Container<Mesh>> &&
+            !std::is_same_v<ComponentType, Container<Record>> &&
+            !std::is_same_v<ComponentType, Container<PatchRecord>> &&
+            !std::is_same_v<ComponentType, Container<ParticleSpecies>>)
+        {
+            component.writeDefaults(standard);
+        }
+    });
+}
+
 void Iteration::flushFileBased(
     std::string const &filename,
     IterationIndex_t i,

src/binding/python/Iteration.cpp

@@ -93,6 +93,7 @@ void init_Iteration(py::module &m)
         .def("set_time", &Iteration::setTime<double>)
         .def("set_dt", &Iteration::setDt<double>)
         .def("set_time_unit_SI", &Iteration::setTimeUnitSI)
+        .def("populate_default_metadata", &Iteration::populateDefaultMetadata)
 
         .def_property_readonly(
             "meshes",

test/python/unittest/API/APITest.py

@@ -2383,6 +2383,7 @@ def get_component_only():
             mesh.axis_labels = ["x", "y"]
             component.reset_dataset(io.Dataset(np.dtype("float"), [10, 10]))
 
+            iteration.populate_default_metadata()
             del iteration
             del mesh
             del series
@@ -2430,6 +2431,7 @@ def get_component_only():
             position.reset_dataset(
                 io.Dataset(np.dtype("float"), [num_particles]))
 
+            iteration.populate_default_metadata()
             del iteration
             del particles
             del series
@@ -2481,6 +2483,7 @@ def get_component_only():
             num_particles_comp.store(0, np.uint64(10))
             num_particles_comp.store(1, np.uint64(20))
 
+            iteration.populate_default_metadata()
             del iteration
             del particles
             del series