Read stuff back again

Author: franzpoeschel

src/Iteration.cpp

@@ -288,8 +288,10 @@ Iteration::flush()
         if( !meshes.empty() || s->containsAttribute("meshesPath") )
         {
             if( !s->containsAttribute("meshesPath") )
+            {
                 s->setMeshesPath("meshes/");
-            s->flushMeshesPath();
+                s->flushMeshesPath();
+            }
             meshes.flush(s->meshesPath());
             for( auto& m : meshes )
                 m.second.flush(m.first);
@@ -298,8 +300,10 @@ Iteration::flush()
         if( !particles.empty() || s->containsAttribute("particlesPath") )
         {
             if( !s->containsAttribute("particlesPath") )
+            {
                 s->setParticlesPath("particles/");
-            s->flushParticlesPath();
+                s->flushParticlesPath();
+            }
             particles.flush(s->particlesPath());
             for( auto& species : particles )
                 species.second.flush(species.first);

src/Series.cpp

@@ -824,6 +824,15 @@ Series::readFileBased( )
                                 << "time series with fileBased iteration "
                                     "encoding. Loaded file is groupBased.\n";
                 }
+                else if( encoding == "stepBased" )
+                {
+                    // @todo should we throw? test this path
+                    *m_iterationEncoding = IterationEncoding::stepBased;
+                    std::cerr << "Series constructor called with iteration "
+                                    "regex '%T' suggests loading a "
+                                << "time series with fileBased iteration "
+                                    "encoding. Loaded file is stepBased.\n";
+                }
                 else
                     throw std::runtime_error(
                         "Unknown iterationEncoding: " + encoding );
@@ -901,6 +910,8 @@ Series::readGroupBased( bool do_init )
             std::string encoding = Attribute(*aRead.resource).get< std::string >();
             if( encoding == "groupBased" )
                 *m_iterationEncoding = IterationEncoding::groupBased;
+            else if( encoding == "stepBased" )
+                *m_iterationEncoding = IterationEncoding::stepBased;
             else if( encoding == "fileBased" )
             {
                 *m_iterationEncoding = IterationEncoding::fileBased;
@@ -1018,22 +1029,43 @@ Series::read()
     readAttributes();
     iterations.readAttributes();
 
-    // @todo change this for stepBased
     /* obtain all paths inside the basepath (i.e. all iterations) */
-    Parameter< Operation::LIST_PATHS > pList;
-    IOHandler->enqueue(IOTask(&iterations, pList));
-    IOHandler->flush();
-
-    for( auto const& it : *pList.paths )
+    switch(*m_iterationEncoding)
     {
-        Iteration& i = iterations[std::stoull(it)];
-        if ( i.closedByWriter( ) )
+        using IE = IterationEncoding;
+        case IE::groupBased:
+        case IE::fileBased:
         {
-            continue;
+            Parameter< Operation::LIST_PATHS > pList;
+            IOHandler->enqueue(IOTask(&iterations, pList));
+            IOHandler->flush();
+
+            for( auto const& it : *pList.paths )
+            {
+                Iteration& i = iterations[std::stoull(it)];
+                if ( i.closedByWriter( ) )
+                {
+                    continue;
+                }
+                pOpen.path = it;
+                IOHandler->enqueue(IOTask(&i, pOpen));
+                i.read();
+            }
+        }
+        break;
+        case IE::stepBased:
+        {
+            Parameter< Operation::READ_ATT > aRead;
+            aRead.name = "iterationIndex";
+            IOHandler->enqueue( IOTask( &iterations, aRead ) );
+            IOHandler->flush();
+            uint64_t index = Attribute( *aRead.resource ).get< uint64_t >();
+            Iteration & i = iterations[ index ];
+            pOpen.path = "currentIteration";
+            IOHandler->enqueue( IOTask( &i, pOpen ) );
+            i.read();
         }
-        pOpen.path = it;
-        IOHandler->enqueue(IOTask(&i, pOpen));
-        i.read();
+        break;
     }
 }
 
@@ -1438,7 +1470,7 @@ WriteIterations::operator[]( key_type && key )
         res.beginStep();
         res.setStepStatus( StepStatus::DuringStep );
     }
-    res.setAttribute( "iterationIndex", key );
+    shared->iterations.setAttribute( "iterationIndex", key );
     return res;
 }
 } // namespace openPMD

test/SerialIOTest.cpp

@@ -3173,8 +3173,7 @@ stepBasedSeries( std::string const & file )
         }
     }
 
-#if 0
-    Series readSeries( file, Access::READ_ONLY );
+    Series readSeries( file, Access::READ_ONLY, config );
 
     size_t last_iteration_index = 0;
     for( auto iteration : readSeries.readIterations() )
@@ -3191,7 +3190,6 @@ stepBasedSeries( std::string const & file )
         last_iteration_index = iteration.iterationIndex;
     }
     REQUIRE( last_iteration_index == 9 );
-#endif
 }
 
 TEST_CASE( "stepBasedSeries", "[serial][adios2]" )