Merge branch 'feature/meshgraph-io' into 'master'

Separate MeshGraph input/output functions into a new class

See merge request nektar/nektar!1778

library/SpatialDomains/Python/MeshGraph.cpp

@@ -34,8 +34,7 @@
 
 #include <LibUtilities/Python/NekPyConfig.hpp>
 #include <SpatialDomains/MeshGraph.h>
-#include <SpatialDomains/MeshGraphXml.h>
-#include <SpatialDomains/MeshGraphXmlCompressed.h>
+#include <SpatialDomains/MeshGraphIO.h>
 #include <SpatialDomains/Movement/Movement.h>
 #include <boost/python/suite/indexing/map_indexing_suite.hpp>
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
@@ -43,16 +42,6 @@
 using namespace Nektar;
 using namespace Nektar::SpatialDomains;
 
-/*
- * @brief Lightweight wrapper around MeshGraph::Read to avoid wrapping
- * DomainRange struct.
- */
-MeshGraphSharedPtr MeshGraph_Read(
-    const LibUtilities::SessionReaderSharedPtr &session)
-{
-    return MeshGraph::Read(session);
-}
-
 /*
  * @brief Simple wrapper to build Composite objects from lists of
  * Geometry objects.
@@ -69,29 +58,6 @@ CompositeSharedPtr Composite_Init(py::list geometries)
     return composite;
 }
 
-/*
- * @brief Wrapper to construct MeshGraphXml object, initialising mesh
- * and spatial dimensions.
- */
-std::shared_ptr<MeshGraph> MeshGraphXml_Init(int meshDim, int spatialDim)
-{
-    auto result = MeshGraphXml::create();
-    result->Empty(meshDim, spatialDim);
-    return result;
-}
-
-/*
- * @brief Wrapper to construct MeshGraphXmlCompressed object, initialising mesh
- * and spatial dimensions.
- */
-std::shared_ptr<MeshGraph> MeshGraphXmlCompressed_Init(int meshDim,
-                                                       int spatialDim)
-{
-    auto result = MeshGraphXmlCompressed::create();
-    result->Empty(meshDim, spatialDim);
-    return result;
-}
-
 /**
  * @brief MeshGraph exports.
  */
@@ -130,17 +96,16 @@ void export_MeshGraph()
         .def(py::map_indexing_suite<std::map<int, CompositeMap>, true>());
 
     py::class_<MeshGraph, std::shared_ptr<MeshGraph>, boost::noncopyable>(
-        "MeshGraph", py::no_init)
+        "MeshGraph", py::init<>())
 
-        .def("Read", MeshGraph_Read)
-        .staticmethod("Read")
-
-        .def("Write", &MeshGraph::WriteGeometry, py::default_call_policies(),
-             (py::arg("outfile"), py::arg("defaultExp") = false,
-              py::arg("metadata") = LibUtilities::NullFieldMetaDataMap))
+        .def("Empty", &MeshGraph::Empty)
 
         .def("GetMeshDimension", &MeshGraph::GetMeshDimension)
         .def("GetSpaceDimension", &MeshGraph::GetSpaceDimension)
+
+        .def("SetMeshDimension", &MeshGraph::SetMeshDimension)
+        .def("SetSpaceDimension", &MeshGraph::SetSpaceDimension)
+
         .def("GetAllPointGeoms", &MeshGraph::GetAllPointGeoms,
              py::return_internal_reference<>())
         .def("GetAllSegGeoms", &MeshGraph::GetAllSegGeoms,
@@ -178,14 +143,4 @@ void export_MeshGraph()
              &MeshGraph::SetExpansionInfoToNumModes)
         .def("SetExpansionInfosToPointOrder",
              &MeshGraph::SetExpansionInfoToPointOrder);
-
-    py::class_<MeshGraphXml, py::bases<MeshGraph>,
-               std::shared_ptr<MeshGraphXml>, boost::noncopyable>(
-        "MeshGraphXml", py::no_init)
-        .def("__init__", py::make_constructor(&MeshGraphXml_Init));
-
-    py::class_<MeshGraphXmlCompressed, py::bases<MeshGraphXml>,
-               std::shared_ptr<MeshGraphXmlCompressed>, boost::noncopyable>(
-        "MeshGraphXmlCompressed", py::no_init)
-        .def("__init__", py::make_constructor(&MeshGraphXmlCompressed_Init));
 }

library/SpatialDomains/Python/MeshGraphIO.cpp

+////////////////////////////////////////////////////////////////////////////////
+//
+//  File: MeshGraphIO.cpp
+//
+//  For more information, please see: http://www.nektar.info/
+//
+//  The MIT License
+//
+//  Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
+//  Department of Aeronautics, Imperial College London (UK), and Scientific
+//  Computing and Imaging Institute, University of Utah (USA).
+//
+//  Permission is hereby granted, free of charge, to any person obtaining a
+//  copy of this software and associated documentation files (the "Software"),
+//  to deal in the Software without restriction, including without limitation
+//  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+//  and/or sell copies of the Software, and to permit persons to whom the
+//  Software is furnished to do so, subject to the following conditions:
+//
+//  The above copyright notice and this permission notice shall be included
+//  in all copies or substantial portions of the Software.
+//
+//  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+//  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+//  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+//  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+//  DEALINGS IN THE SOFTWARE.
+//
+//  Description: Python wrapper for MeshGraphIO.
+//
+////////////////////////////////////////////////////////////////////////////////
+
+#include <LibUtilities/Python/NekPyConfig.hpp>
+
+#include <SpatialDomains/MeshGraphIO.h>
+
+using namespace Nektar;
+using namespace Nektar::SpatialDomains;
+
+/*
+ * @brief Lightweight wrapper around MeshGraph::Read to avoid wrapping
+ * DomainRange struct.
+ */
+MeshGraphSharedPtr MeshGraphIO_Read(
+    const LibUtilities::SessionReaderSharedPtr &session)
+{
+    return MeshGraphIO::Read(session);
+}
+
+MeshGraphIOSharedPtr MeshGraphIO_Create(std::string ioType)
+{
+    return GetMeshGraphIOFactory().CreateInstance(ioType);
+}
+
+void export_MeshGraphIO()
+{
+    py::class_<MeshGraphIO, std::shared_ptr<MeshGraphIO>, boost::noncopyable>(
+        "MeshGraphIO", py::no_init)
+
+        .def("Write", &MeshGraphIO::WriteGeometry, py::default_call_policies(),
+             (py::arg("outfile"), py::arg("defaultExp") = false,
+              py::arg("metadata") = LibUtilities::NullFieldMetaDataMap))
+
+        .def("SetMeshGraph", &MeshGraphIO::SetMeshGraph)
+
+        .def("Read", MeshGraphIO_Read)
+        .staticmethod("Read")
+
+        .def("Create", MeshGraphIO_Create)
+        .staticmethod("Create");
+}

library/SpatialDomains/Python/SpatialDomains.cpp

@@ -37,6 +37,7 @@
 void export_Geometry();
 void export_Curve();
 void export_MeshGraph();
+void export_MeshGraphIO();
 void export_GeomElements();
 void export_Zones();
 void export_Interfaces();
@@ -49,6 +50,7 @@ BOOST_PYTHON_MODULE(_SpatialDomains)
     export_Geometry();
     export_Curve();
     export_MeshGraph();
+    export_MeshGraphIO();
     export_GeomElements();
     export_Zones();
     export_Interfaces();

library/UnitTests/MultiRegions/TestVarcoeffHashing.cpp

@@ -36,6 +36,7 @@
 
 #include <MultiRegions/ContField.h>
 #include <MultiRegions/MultiRegions.hpp>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <boost/test/unit_test.hpp>
 
@@ -204,7 +205,7 @@ void setupContFieldSolve(fs::path &ph,
     // Read Session, MeshGraph and create ContField
     Session = LibUtilities::SessionReader::CreateInstance(argc, argv);
     SpatialDomains::MeshGraphSharedPtr Graph =
-        SpatialDomains::MeshGraph::Read(Session);
+        SpatialDomains::MeshGraphIO::Read(Session);
     Exp = MemoryManager<MultiRegions::ContField>::AllocateSharedPtr(
         Session, Graph, Session->GetVariable(0));
     Fce = MemoryManager<MultiRegions::ContField>::AllocateSharedPtr(*Exp);

solvers/ADRSolver/ADRSolver.cpp

@@ -36,6 +36,7 @@
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <LibUtilities/BasicUtils/Timer.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -59,7 +60,7 @@ int main(int argc, char *argv[])
         LIKWID_MARKER_REGISTER("IProductWRTDerivBase_coll");
 
         // Create MeshGraph
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/AcousticSolver/AcousticSolver.cpp

@@ -34,6 +34,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -52,7 +53,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/CardiacEPSolver/CardiacEPSolver.cpp

@@ -34,6 +34,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -52,7 +53,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/CompressibleFlowSolver/CompressibleFlowSolver.cpp

@@ -35,6 +35,7 @@
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
 #include <SolverUtils/EquationSystem.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <LibUtilities/BasicUtils/Timer.h>
 
@@ -55,7 +56,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/CompressibleFlowSolver/Utilities/CompressibleBL.cpp

@@ -57,7 +57,7 @@
 #include <LibUtilities/BasicUtils/SharedArray.hpp>
 #include <LibUtilities/Memory/NekMemoryManager.hpp>
 
-#include <SpatialDomains/MeshGraph.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <SolverUtils/SolverUtilsDeclspec.h>
 
@@ -361,7 +361,7 @@ int main(int argc, char *argv[])
 
     // Read in mesh from input file and create an object of class MeshGraph
     SpatialDomains::MeshGraphSharedPtr graphShPt =
-        SpatialDomains::MeshGraph::Read(vSession);
+        SpatialDomains::MeshGraphIO::Read(vSession);
 
     int expdim = graphShPt->GetMeshDimension();
 

solvers/CompressibleFlowSolver/Utilities/ExtractSurface2DCFS.cpp

@@ -56,7 +56,7 @@
 
 #include <LibUtilities/Memory/NekMemoryManager.hpp>
 #include <MultiRegions/ContField.h>
-#include <SpatialDomains/MeshGraph.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <SolverUtils/SolverUtilsDeclspec.h>
 
@@ -124,7 +124,7 @@ int main(int argc, char *argv[])
     LibUtilities::SessionReaderSharedPtr vSession =
         LibUtilities::SessionReader::CreateInstance(argc, argv);
     SpatialDomains::MeshGraphSharedPtr graphShPt =
-        SpatialDomains::MeshGraph::Read(vSession);
+        SpatialDomains::MeshGraphIO::Read(vSession);
 
     fname = vSession->GetSessionName() + ".cfs";
 

solvers/CompressibleFlowSolver/Utilities/ExtractSurface3DCFS.cpp

@@ -54,7 +54,7 @@
 
 #include <LibUtilities/Memory/NekMemoryManager.hpp>
 #include <MultiRegions/ContField.h>
-#include <SpatialDomains/MeshGraph.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <SolverUtils/SolverUtilsDeclspec.h>
 
@@ -99,7 +99,7 @@ int main(int argc, char *argv[])
     LibUtilities::SessionReaderSharedPtr vSession =
         LibUtilities::SessionReader::CreateInstance(3, argv);
     SpatialDomains::MeshGraphSharedPtr graphShPt =
-        SpatialDomains::MeshGraph::Read(vSession);
+        SpatialDomains::MeshGraphIO::Read(vSession);
 
     std::string m_ViscosityType;
 

solvers/DiffusionSolver/DiffusionSolver.cpp

@@ -35,7 +35,7 @@
 #include <LibUtilities/BasicUtils/FieldIO.h>
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <MultiRegions/ContField.h>
-#include <SpatialDomains/MeshGraph.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -55,7 +55,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Read the geometry and the expansion information
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create Field I/O object.
         fld = LibUtilities::FieldIO::CreateDefault(session);

solvers/DiffusionSolver/DiffusionSolverTimeInt.cpp

@@ -40,7 +40,7 @@
 #include <LibUtilities/TimeIntegration/TimeIntegrationSchemeOperators.h>
 
 #include <MultiRegions/ContField.h>
-#include <SpatialDomains/MeshGraph.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -85,7 +85,7 @@ Diffusion::Diffusion(int argc, char *argv[])
     session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
     // Read the geometry and the expansion information
-    graph = SpatialDomains::MeshGraph::Read(session);
+    graph = SpatialDomains::MeshGraphIO::Read(session);
 
     // Create Field I/O object.
     fld = LibUtilities::FieldIO::CreateDefault(session);

solvers/DiffusionSolver/EquationSystems/MMFDiffusion.cpp

@@ -41,6 +41,7 @@
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <MultiRegions/AssemblyMap/AssemblyMapDG.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <boost/math/special_functions/spherical_harmonic.hpp>
 using namespace std;
@@ -875,7 +876,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/DummySolver/DummySolver.cpp

@@ -35,6 +35,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -53,7 +54,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/ImageWarpingSolver/ImageWarpingSolver.cpp

@@ -34,6 +34,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 using namespace std;
 using namespace Nektar;
@@ -52,7 +53,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/IncNavierStokesSolver/IncNavierStokesSolver.cpp

@@ -34,6 +34,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <LibUtilities/BasicUtils/Timer.h>
 
@@ -54,7 +55,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/IncNavierStokesSolver/Utilities/Aliasing.cpp

@@ -37,6 +37,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <IncNavierStokesSolver/AdvectionTerms/NavierStokesAdvection.h>
 #include <IncNavierStokesSolver/EquationSystems/IncNavierStokes.h>
@@ -65,7 +66,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");

solvers/IncNavierStokesSolver/Utilities/CFLStep.cpp

@@ -37,6 +37,7 @@
 
 #include <LibUtilities/BasicUtils/SessionReader.h>
 #include <SolverUtils/Driver.h>
+#include <SpatialDomains/MeshGraphIO.h>
 
 #include <IncNavierStokesSolver/EquationSystems/IncNavierStokes.h>
 
@@ -65,7 +66,7 @@ int main(int argc, char *argv[])
         session = LibUtilities::SessionReader::CreateInstance(argc, argv);
 
         // Create MeshGraph.
-        graph = SpatialDomains::MeshGraph::Read(session);
+        graph = SpatialDomains::MeshGraphIO::Read(session);
 
         // Create driver
         session->LoadSolverInfo("Driver", vDriverModule, "Standard");