ENH: Implement ismtkVegaMeshReader

Base/Geometry/Reader/imstkMeshReader.cpp

@@ -22,6 +22,7 @@
 #include "imstkMeshReader.h"
 
 #include "imstkVTKMeshReader.h"
+#include "imstkVegaMeshReader.h"
 
 #include "g3log/g3log.hpp"
 
@@ -46,8 +47,7 @@ MeshReader::read(const std::string& filePath)
         return VTKMeshReader::read(filePath, meshType);
         break;
     case FileType::VEG :
-        LOG(WARNING) << "MeshReader::read error: vega reader not yet implemented.";
-        return nullptr;
+        return VegaMeshReader::read(filePath, meshType);
         break;
     }
 

Base/Geometry/Reader/imstkVegaMeshReader.cpp

+/*=========================================================================
+
+   Library: iMSTK
+
+   Copyright (c) Kitware, Inc. & Center for Modeling, Simulation,
+   & Imaging in Medicine, Rensselaer Polytechnic Institute.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0.txt
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+   =========================================================================*/
+
+#include "imstkVegaMeshReader.h"
+
+#include "imstkMeshReader.h"
+#include "imstkTetrahedralMesh.h"
+#include "imstkHexahedralMesh.h"
+
+// Vega
+#include "volumetricMeshLoader.h"
+#include "volumetricMesh.h"
+
+#include "g3log/g3log.hpp"
+
+namespace imstk{
+std::shared_ptr<VolumetricMesh>
+VegaMeshReader::read(const std::string& filePath, MeshReader::FileType meshType)
+{
+    if (meshType != MeshReader::FileType::VEG)
+    {
+        LOG(WARNING) << "VegaMeshReader::read error: file type not supported";
+        return nullptr;
+    }
+
+    // Vega VolumetricMesh (not imstk::)
+    auto fileName = const_cast<char*>(filePath.c_str());
+    std::shared_ptr<vega::VolumetricMesh> vegaMesh(vega::VolumetricMeshLoader::load(fileName));
+
+    // Copy vertices
+    std::vector<Vec3d> vertices;
+    for(size_t i = 0; i < vegaMesh->getNumVertices(); ++i)
+    {
+        auto pos = *vegaMesh->getVertex(i);
+        vertices.emplace_back(pos[0], pos[1], pos[2]);
+    }
+
+    // Check
+    auto cellType = vegaMesh->getElementType();
+    if(cellType == vega::VolumetricMesh::TET)
+    {
+        std::vector<TetrahedralMesh::TetraArray> cells;
+        TetrahedralMesh::TetraArray cell;
+        for(size_t cellId = 0; cellId < vegaMesh->getNumElements(); ++cellId)
+        {
+            for (size_t i = 0; i < vegaMesh->getNumElementVertices(); ++i)
+            {
+                cell[i] = vegaMesh->getVertexIndex(cellId,i);
+            }
+            cells.emplace_back(cell);
+        }
+
+        auto mesh = std::make_shared<TetrahedralMesh>();
+        mesh->initialize(vertices, cells, false);
+        return mesh;
+    }
+    else if(cellType == vega::VolumetricMesh::CUBIC)
+    {
+        std::vector<HexahedralMesh::HexaArray> cells;
+        HexahedralMesh::HexaArray cell;
+        for(size_t cellId = 0; cellId < vegaMesh->getNumElements(); ++cellId)
+        {
+            for (size_t i = 0; i < vegaMesh->getNumElementVertices(); ++i)
+            {
+                cell[i] = vegaMesh->getVertexIndex(cellId,i);
+            }
+            cells.emplace_back(cell);
+        }
+
+        auto mesh = std::make_shared<HexahedralMesh>();
+        mesh->initialize(vertices, cells, false);
+        return mesh;
+    }
+    else
+    {
+        vegaMesh.reset();
+        LOG(WARNING) << "VegaMeshReader::read error: invalid cell type.";
+        return nullptr;
+    }
+}
+}

Base/Geometry/Reader/imstkVegaMeshReader.h

+/*=========================================================================
+
+   Library: iMSTK
+
+   Copyright (c) Kitware, Inc. & Center for Modeling, Simulation,
+   & Imaging in Medicine, Rensselaer Polytechnic Institute.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0.txt
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+   =========================================================================*/
+
+#ifndef imstkVegaMeshReader_h
+#define imstkVegaMeshReader_h
+
+#include <memory>
+
+#include "imstkMeshReader.h"
+#include "imstkVolumetricMesh.h"
+
+namespace imstk {
+
+///
+/// \class VegaMeshReader
+///
+/// \brief
+///
+class VegaMeshReader
+{
+public:
+
+    VegaMeshReader() = default;
+    ~VegaMeshReader() = default;
+
+    ///
+    /// \brief
+    ///
+    static std::shared_ptr<VolumetricMesh> read(const std::string& filePath, MeshReader::FileType meshType);
+};
+}
+
+#endif // ifndef imstkVegaMeshReader_h

Examples/Sandbox/main.cpp

@@ -62,24 +62,24 @@ void testReadMesh()
     scene->setLoopDelay(1000);
 
     // Read surface mesh
-    /*
     auto objMesh = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/asianDragon/asianDragon.obj");
     auto plyMesh = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/Cube/models/cube.ply");
     auto stlMesh = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/Cube/models/cube.stl");
     auto vtkMesh = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/Cube/models/cube.vtk");
     auto vtpMesh = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/Cube/models/cube.vtp");
-    */
 
     // Read volumetricMesh
-    auto mesh = imstk::MeshReader::read("nidus10KTet.vtk");
-    auto volumeMesh = std::dynamic_pointer_cast<imstk::VolumetricMesh>(mesh);
+    auto vtkMesh2 = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/AVM/nidus-model/nidus10KTet.vtk");
+    auto vegaMesh = imstk::MeshReader::read("/home/virtualfls/Projects/IMSTK/resources/asianDragon/asianDragon.veg");
 
+    // Extract surface mesh
+    auto volumeMesh = std::dynamic_pointer_cast<imstk::VolumetricMesh>(vegaMesh); // change to any volumetric mesh above
     volumeMesh->computeAttachedSurfaceMesh();
     auto surfaceMesh = volumeMesh->getAttachedSurfaceMesh();
 
     // Create object and add to scene
     auto object = std::make_shared<imstk::VisualObject>("meshObject");
-    object->setVisualGeometry(surfaceMesh);
+    object->setVisualGeometry(surfaceMesh); // change to any mesh created above
     scene->addSceneObject(object);
 
     // Run