Works in JSON and HDF5 now too

openPMD · Feb 22, 2024 · 9987204 · 9987204
1 parent 36ae6ec
commit 9987204
Show file tree

Hide file tree

Showing 4 changed files with 40 additions and 9 deletions.
diff --git a/include/openPMD/backend/Attributable.hpp b/include/openPMD/backend/Attributable.hpp
@@ -74,7 +74,6 @@ namespace internal
          */
         Writable m_writable;
 
-    private:
         /**
          * The attributes defined by this Attributable.
          */

diff --git a/src/Series.cpp b/src/Series.cpp
@@ -1987,6 +1987,12 @@ void Series::readBase()
                 "string, found " +
                     datatypeToString(Attribute(*aRead.resource).dtype) + ")");
     }
+    else
+    {
+        // Make sure that the meshesPath does not leak from one iteration into
+        // the other in file-based iteration encoding
+        get().m_attributes.erase("meshesPath");
+    }
 
     if (std::count(
             aList.attributes->begin(),
@@ -2017,6 +2023,11 @@ void Series::readBase()
                 "string, found " +
                     datatypeToString(Attribute(*aRead.resource).dtype) + ")");
     }
+    {
+        // Make sure that the particlesPath does not leak from one iteration
+        // into the other in file-based iteration encoding
+        get().m_attributes.erase("particlesPath");
+    }
 }
 
 std::string Series::iterationFilename(IterationIndex_t i)

diff --git a/src/snapshots/StatefulIterator.cpp b/src/snapshots/StatefulIterator.cpp
@@ -471,7 +471,6 @@ StatefulIterator::StatefulIterator(
 
     switch (series.iterationEncoding())
     {
-
     case IterationEncoding::fileBased: {
         initIteratorFilebased();
         break;
@@ -646,14 +645,28 @@ std::optional<StatefulIterator *> StatefulIterator::loopBody(Seek const &seek)
        */
         auto maybe_current_iteration = data.currentStep.get_iteration_index();
         if (maybe_current_iteration.has_value() &&
+            // don't deactivate the iteration if it's the one that's currently
+            // active anyway
+            std::visit(
+                auxiliary::overloaded{
+                    [&](detail::seek_types::Next_t const &) { return true; },
+                    [&](detail::seek_types::Seek_Iteration_t const
+                            &go_to_iteration) {
+                        return go_to_iteration.iteration_idx !=
+                            **maybe_current_iteration;
+                    }},
+                seek) &&
             iterations.contains(**maybe_current_iteration))
         {
             auto &currentIteration = iterations.at(**maybe_current_iteration);
             if (!currentIteration.closed())
             {
                 currentIteration.close();
             }
-            if (series.IOHandler()->m_frontendAccess == Access::READ_LINEAR)
+            // sic! only erase if the Iteration was explicitly closed, don't
+            // implicitly sweep the iteration away from under the user
+            else if (
+                series.IOHandler()->m_frontendAccess == Access::READ_LINEAR)
             {
                 data.series.iterations.container().erase(
                     **maybe_current_iteration);

diff --git a/test/Files_SerialIO/close_iteration_test.cpp b/test/Files_SerialIO/close_iteration_test.cpp
@@ -201,9 +201,9 @@ auto run_test_groupbased(
         it.close();
 
         it.open();
-        auto e_position_x = it.particles["e"]["position"]["x"];
-        e_position_x.resetDataset({Datatype::INT, {5}});
-        e_position_x.storeChunk(data, {0}, {5});
+        auto E_y = it.meshes["E"]["y"];
+        E_y.resetDataset({Datatype::INT, {5}});
+        E_y.storeChunk(data, {0}, {5});
         it.close();
     }
     {
@@ -257,8 +257,7 @@ auto run_test_groupbased(
         {
             auto it = read.snapshots()[1].open();
             std::vector<int> data(5);
-            it.particles["e"]["position"]["x"].loadChunkRaw(
-                data.data(), {0}, {5});
+            it.meshes["E"]["y"].loadChunkRaw(data.data(), {0}, {5});
             it.close();
             REQUIRE((data == std::vector<int>{0, 1, 2, 3, 4}));
         }
@@ -270,7 +269,10 @@ auto close_and_reopen_test() -> void
     run_test_filebased([](Series &s) { return s.iterations; }, "bp");
     run_test_filebased([](Series &s) { return s.writeIterations(); }, "bp");
     run_test_filebased([](Series &s) { return s.snapshots(); }, "bp");
-    // run_test_filebased([](Series &s) { return s.snapshots(); }, "json");
+    run_test_filebased([](Series &s) { return s.snapshots(); }, "json");
+#if openPMD_HAVE_HDF5
+    run_test_filebased([](Series &s) { return s.snapshots(); }, "h5");
+#endif
 
     run_test_groupbased(
         [](Series &s) { return s.iterations; },
@@ -291,6 +293,12 @@ auto close_and_reopen_test() -> void
         [](Series &s) { return s.snapshots(); },
         "json",
         {Access::READ_RANDOM_ACCESS, Access::READ_LINEAR});
+#if openPMD_HAVE_HDF5
+    run_test_groupbased(
+        [](Series &s) { return s.snapshots(); },
+        "h5",
+        {Access::READ_RANDOM_ACCESS, Access::READ_LINEAR});
+#endif
 }
 #else
 auto close_and_reopen_test() -> void