STYLE: Rename Mesh class to PointSet

Mesh class is renamed to PointSet since
the word 'mesh' implies that connectivity
information is part of the class which is
not the case

Base/Collision/CollisionDetection/imstkCollisionDetection.cpp

@@ -24,11 +24,11 @@
 #include "imstkUnidirectionalPlaneToSphereCD.h"
 #include "imstkBidirectionalPlaneToSphereCD.h"
 #include "imstkSphereToSphereCD.h"
-#include "imstkMeshToSphereCD.h"
-#include "imstkMeshToPlaneCD.h"
+#include "imstkPointSetToSphereCD.h"
+#include "imstkPointSetToPlaneCD.h"
 #include "imstkMeshToMeshCD.h"
 #include "imstkSphereCylinderCD.h"
-#include "imstkMeshToSpherePickingCD.h"
+#include "imstkPointSetToSpherePickingCD.h"
 
 #include "imstkCollidingObject.h"
 #include "imstkPlane.h"
@@ -107,9 +107,9 @@ CollisionDetection::make_collision_detection(const Type& type,
         return std::make_shared<SphereCylinderCD>(sphere, cylinder, colData);
     }
     break;
-    case Type::MeshToSphere:
+    case Type::PointSetToSphere:
     {
-        auto mesh = std::dynamic_pointer_cast<Mesh>(objA->getCollidingGeometry());
+        auto mesh = std::dynamic_pointer_cast<PointSet>(objA->getCollidingGeometry());
         auto sphere = std::dynamic_pointer_cast<Sphere>(objB->getCollidingGeometry());
 
         // Geometries check
@@ -119,12 +119,12 @@ CollisionDetection::make_collision_detection(const Type& type,
                          << "invalid object geometries for SphereToSphere collision detection.";
             return nullptr;
         }
-        return std::make_shared<MeshToSphereCD>(mesh, sphere, colData);
+        return std::make_shared<PointSetToSphereCD>(mesh, sphere, colData);
     }
     break;
-    case Type::MeshToPlane:
+    case Type::PointSetToPlane:
     {
-        auto mesh = std::dynamic_pointer_cast<Mesh>(objA->getCollidingGeometry());
+        auto mesh = std::dynamic_pointer_cast<PointSet>(objA->getCollidingGeometry());
         auto plane = std::dynamic_pointer_cast<Plane>(objB->getCollidingGeometry());
 
         // Geometries check
@@ -134,7 +134,7 @@ CollisionDetection::make_collision_detection(const Type& type,
                          << "invalid object geometries for SphereToSphere collision detection.";
             return nullptr;
         }
-        return std::make_shared<MeshToPlaneCD>(mesh, plane, colData);
+        return std::make_shared<PointSetToPlaneCD>(mesh, plane, colData);
     }
     break;
     case Type::MeshToMesh:
@@ -152,9 +152,9 @@ CollisionDetection::make_collision_detection(const Type& type,
         return std::make_shared<MeshToMeshCD>(meshA, meshB, colData);
     }
     break;
-    case Type::MeshToSpherePicking:
+    case Type::PointSetToSpherePicking:
     {
-        auto mesh = std::dynamic_pointer_cast<Mesh>(objA->getCollidingGeometry());
+        auto mesh = std::dynamic_pointer_cast<PointSet>(objA->getCollidingGeometry());
         auto sphere = std::dynamic_pointer_cast<Sphere>(objB->getCollidingGeometry());
 
         // Geometries check
@@ -164,7 +164,7 @@ CollisionDetection::make_collision_detection(const Type& type,
                          << "invalid object geometries for SphereToSphere collision detection.";
             return nullptr;
         }
-        return std::make_shared<MeshToSpherePickingCD>(mesh, sphere, colData);
+        return std::make_shared<PointSetToSpherePickingCD>(mesh, sphere, colData);
     }
     break;
     default:

Base/Collision/CollisionDetection/imstkCollisionDetection.h

@@ -47,11 +47,11 @@ public:
         BidirectionalPlaneToSphere,
         SphereToCylinder,
         SphereToSphere,
-        MeshToSphere,
-        MeshToPlane,
+        PointSetToSphere,
+        PointSetToPlane,
         MeshToMesh,
-        MeshToCapsule,
-        MeshToSpherePicking
+        PointSetToCapsule,
+        PointSetToSpherePicking
     };
 
     ///

Base/Collision/CollisionDetection/imstkMeshToCapsuleCD.cpp → Base/Collision/CollisionDetection/imstkPointSetToCapsuleCD.cpp

@@ -19,11 +19,11 @@
 
 =========================================================================*/
 
-#include "imstkMeshToCapsuleCD.h"
+#include "imstkPointSetToCapsuleCD.h"
 
 #include "imstkCollisionData.h"
 #include "imstkCapsule.h"
-#include "imstkMesh.h"
+#include "imstkPointSet.h"
 #include "imstkMath.h"
 
 #include <g3log/g3log.hpp>
@@ -31,7 +31,7 @@
 namespace imstk
 {
 void
-MeshToCapsuleCD::computeCollisionData()
+PointSetToCapsuleCD::computeCollisionData()
 {
     // Clear collisionData
     m_colData.clearAll();
@@ -50,7 +50,7 @@ MeshToCapsuleCD::computeCollisionData()
     auto pDotp0 = p.dot(p0);
 
     size_t nodeId = 0;
-    for (const auto& q : m_mesh->getVertexPositions())
+    for (const auto& q : m_pointSet->getVertexPositions())
     {
         // First, check collision with bounding sphere
         if ((mid - q).norm() > (radius + length*0.5))

Base/Collision/CollisionDetection/imstkMeshToCapsuleCD.h → Base/Collision/CollisionDetection/imstkPointSetToCapsuleCD.h

@@ -19,8 +19,8 @@
 
 =========================================================================*/
 
-#ifndef imstkMeshToCapsuleCD_h
-#define imstkMeshToCapsuleCD_h
+#ifndef imstkPointSetToCapsuleCD_h
+#define imstkPointSetToCapsuleCD_h
 
 #include <memory>
 
@@ -28,34 +28,34 @@
 
 namespace imstk
 {
-class Mesh;
+class PointSet;
 class Capsule;
 class CollisionData;
 
 ///
-/// \class MeshToCapsuleCD
+/// \class PointSetToCapsuleCD
 ///
-/// \brief Mesh to Capsule collision detection
+/// \brief PointSet to Capsule collision detection
 ///
-class MeshToCapsuleCD : public CollisionDetection
+class PointSetToCapsuleCD : public CollisionDetection
 {
 public:
 
     ///
     /// \brief Constructor
     ///
-    MeshToCapsuleCD(std::shared_ptr<Mesh> mesh,
-                    std::shared_ptr<Capsule> capsule,
-                    CollisionData& colData) :
-        CollisionDetection(CollisionDetection::Type::MeshToCapsule,
+    PointSetToCapsuleCD(std::shared_ptr<PointSet> pointSet,
+                        std::shared_ptr<Capsule> capsule,
+                        CollisionData& colData) :
+        CollisionDetection(CollisionDetection::Type::PointSetToCapsule,
                            colData),
-        m_mesh(mesh),
+        m_pointSet(pointSet),
         m_capsule(capsule){}
 
     ///
     /// \brief Destructor
     ///
-    ~MeshToCapsuleCD() = default;
+    ~PointSetToCapsuleCD() = default;
 
     ///
     /// \brief Detect collision and compute collision data
@@ -64,9 +64,9 @@ public:
 
 private:
 
-    std::shared_ptr<Mesh> m_mesh;       ///> Mesh
-    std::shared_ptr<Capsule> m_capsule; ///> Capsule
+    std::shared_ptr<PointSet> m_pointSet;       ///> PointSet
+    std::shared_ptr<Capsule> m_capsule;         ///> Capsule
 };
 }
 
-#endif // ifndef imstkMeshToCapsuleCD_h
\ No newline at end of file
+#endif // ifndef imstkPointSetToCapsuleCD_h
\ No newline at end of file

Base/Collision/CollisionDetection/imstkMeshToPlaneCD.cpp → Base/Collision/CollisionDetection/imstkPointSetToPlaneCD.cpp

@@ -19,19 +19,19 @@
 
 =========================================================================*/
 
-#include "imstkMeshToPlaneCD.h"
+#include "imstkPointSetToPlaneCD.h"
 
 #include "imstkCollidingObject.h"
 #include "imstkCollisionData.h"
 #include "imstkPlane.h"
-#include "imstkMesh.h"
+#include "imstkPointSet.h"
 
 #include <g3log/g3log.hpp>
 
 namespace imstk
 {
 void
-MeshToPlaneCD::computeCollisionData()
+PointSetToPlaneCD::computeCollisionData()
 {
     // Clear collisionData
     m_colData.clearAll();
@@ -43,7 +43,7 @@ MeshToPlaneCD::computeCollisionData()
     auto planeNormal = m_plane->getNormal();
 
     size_t nodeId = 0;
-    for (const auto& p : m_mesh->getVertexPositions())
+    for (const auto& p : m_pointSet->getVertexPositions())
     {
         auto peneDistance = (planePos - p).dot(planeNormal);
         if (peneDistance <= 0.0)

Base/Collision/CollisionDetection/imstkMeshToPlaneCD.h → Base/Collision/CollisionDetection/imstkPointSetToPlaneCD.h

@@ -19,8 +19,8 @@
 
 =========================================================================*/
 
-#ifndef imstkMeshToPlaneCD_h
-#define imstkMeshToPlaneCD_h
+#ifndef imstkPointSetToPlaneCD_h
+#define imstkPointSetToPlaneCD_h
 
 #include <memory>
 
@@ -28,34 +28,34 @@
 
 namespace imstk
 {
-class Mesh;
+class PointSet;
 class Plane;
 class CollisionData;
 
 ///
-/// \class MeshToPlaneCD
+/// \class PointSetToPlaneCD
 ///
-/// \brief Mesh to plane collision detection
+/// \brief PointSet to plane collision detection
 ///
-class MeshToPlaneCD : public CollisionDetection
+class PointSetToPlaneCD : public CollisionDetection
 {
 public:
 
     ///
     /// \brief Constructor
     ///
-    MeshToPlaneCD(std::shared_ptr<Mesh> mesh,
-                  std::shared_ptr<Plane> plane,
-                  CollisionData& colData) :
-        CollisionDetection(CollisionDetection::Type::MeshToSphere,
+    PointSetToPlaneCD(std::shared_ptr<PointSet> pointSet,
+                      std::shared_ptr<Plane> plane,
+                      CollisionData& colData) :
+        CollisionDetection(CollisionDetection::Type::PointSetToSphere,
                            colData),
-        m_mesh(mesh),
+        m_pointSet(pointSet),
         m_plane(plane){}
 
     ///
     /// \brief Destructor
     ///
-    ~MeshToPlaneCD() = default;
+    ~PointSetToPlaneCD() = default;
 
     ///
     /// \brief Detect collision and compute collision data
@@ -64,9 +64,9 @@ public:
 
 private:
 
-    std::shared_ptr<Mesh> m_mesh;      ///> Mesh
-    std::shared_ptr<Plane> m_plane;    ///> Plane
+    std::shared_ptr<PointSet> m_pointSet;      ///> PointSet
+    std::shared_ptr<Plane> m_plane;            ///> Plane
 };
 }
 
-#endif // ifndef imstkMeshToPlaneCD_h
+#endif // ifndef imstkPointSetToPlaneCD_h

Base/Collision/CollisionDetection/imstkMeshToSphereCD.cpp → Base/Collision/CollisionDetection/imstkPointSetToSphereCD.cpp

@@ -19,19 +19,19 @@
 
 =========================================================================*/
 
-#include "imstkMeshToSphereCD.h"
+#include "imstkPointSetToSphereCD.h"
 
 #include "imstkCollidingObject.h"
 #include "imstkCollisionData.h"
 #include "imstkSphere.h"
-#include "imstkMesh.h"
+#include "imstkPointSet.h"
 
 #include <g3log/g3log.hpp>
 
 namespace imstk
 {
 void
-MeshToSphereCD::computeCollisionData()
+PointSetToSphereCD::computeCollisionData()
 {
     // Clear collisionData
     m_colData.clearAll();
@@ -41,7 +41,7 @@ MeshToSphereCD::computeCollisionData()
     auto radius = m_sphere->getRadius();
 
     size_t nodeId = 0;
-    for (const auto& p : m_mesh->getVertexPositions())
+    for (const auto& p : m_pointSet->getVertexPositions())
     {
         auto dist = (spherePos - p).norm();
         if (dist <= radius)

Base/Collision/CollisionDetection/imstkMeshToSphereCD.h → Base/Collision/CollisionDetection/imstkPointSetToSphereCD.h

@@ -19,8 +19,8 @@
 
 =========================================================================*/
 
-#ifndef imstkMeshToSphereCD_h
-#define imstkMeshToSphereCD_h
+#ifndef imstkPointSetToSphereCD_h
+#define imstkPointSetToSphereCD_h
 
 #include <memory>
 
@@ -28,34 +28,34 @@
 
 namespace imstk
 {
-class Mesh;
+class PointSet;
 class Sphere;
 class CollisionData;
 
 ///
-/// \class MeshToSphereCD
+/// \class PointSetToSphereCD
 ///
-/// \brief Mesh to sphere collision detection
+/// \brief PointSet to sphere collision detection
 ///
-class MeshToSphereCD : public CollisionDetection
+class PointSetToSphereCD : public CollisionDetection
 {
 public:
 
     ///
     /// \brief Constructor
     ///
-    MeshToSphereCD(std::shared_ptr<Mesh> mesh,
-                   std::shared_ptr<Sphere> sphere,
-                   CollisionData& colData) :
-        CollisionDetection(CollisionDetection::Type::MeshToSphere,
+    PointSetToSphereCD(std::shared_ptr<PointSet> pointSet,
+                       std::shared_ptr<Sphere> sphere,
+                       CollisionData& colData) :
+        CollisionDetection(CollisionDetection::Type::PointSetToSphere,
                            colData),
-        m_mesh(mesh),
+        m_pointSet(pointSet),
         m_sphere(sphere){}
 
     ///
     /// \brief Destructor
     ///
-    ~MeshToSphereCD() = default;
+    ~PointSetToSphereCD() = default;
 
     ///
     /// \brief Detect collision and compute collision data
@@ -64,9 +64,9 @@ public:
 
 private:
 
-    std::shared_ptr<Mesh> m_mesh;       ///> Mesh
-    std::shared_ptr<Sphere> m_sphere;  ///> Sphere
+    std::shared_ptr<PointSet> m_pointSet;       ///> PointSet
+    std::shared_ptr<Sphere> m_sphere;           ///> Sphere
 };
 }
 
-#endif // ifndef imstkMeshToSphereCD_h
+#endif // ifndef imstkPointSetToSphereCD_h

Base/Collision/CollisionDetection/imstkMeshToSpherePickingCD.cpp → Base/Collision/CollisionDetection/imstkPointSetToSpherePickingCD.cpp

@@ -19,15 +19,15 @@ limitations under the License.
 
 =========================================================================*/
 
-#include "imstkMeshToSpherePickingCD.h"
+#include "imstkPointSetToSpherePickingCD.h"
 #include "imstkCollisionData.h"
-#include "imstkMesh.h"
+#include "imstkPointSet.h"
 #include "imstkSphere.h"
 
 namespace imstk
 {
 void
-MeshToSpherePickingCD::computeCollisionData()
+PointSetToSpherePickingCD::computeCollisionData()
 {
     // Clear collisionData
     m_colData.clearAll();
@@ -42,7 +42,7 @@ MeshToSpherePickingCD::computeCollisionData()
     auto radius = m_sphere->getRadius()*m_sphere->getScaling();
 
     size_t nodeId = 0;
-    for (const auto& p : m_mesh->getVertexPositions())
+    for (const auto& p : m_pointSet->getVertexPositions())
     {
         auto dist = (spherePos - p).norm();
         if (dist <= radius)

Base/Collision/CollisionDetection/imstkMeshToSpherePickingCD.h → Base/Collision/CollisionDetection/imstkPointSetToSpherePickingCD.h

@@ -19,8 +19,8 @@
 
    =========================================================================*/
 
-#ifndef imstkMeshToSpherePickingCD_h
-#define imstkMeshToSpherePickingCD_h
+#ifndef imstkPointSetToSpherePickingCD_h
+#define imstkPointSetToSpherePickingCD_h
 
 #include <memory>
 
@@ -29,34 +29,34 @@
 
 namespace imstk
 {
-class Mesh;
+class PointSet;
 class Sphere;
 class CollisionData;
 
 ///
-/// \class MeshToSpherePickingCD
+/// \class PointSetToSpherePickingCD
 ///
-/// \brief Mesh to sphere collision detection while picking
+/// \brief PointSet to sphere collision detection while picking
 ///
-class MeshToSpherePickingCD : public CollisionDetection
+class PointSetToSpherePickingCD : public CollisionDetection
 {
 public:
 
     ///
     /// \brief Constructor
     ///
-    MeshToSpherePickingCD(std::shared_ptr<Mesh> mesh,
-                          std::shared_ptr<Sphere> sphere,
-                          CollisionData& colData) :
-        CollisionDetection(CollisionDetection::Type::MeshToSphere,
+    PointSetToSpherePickingCD(std::shared_ptr<PointSet> pointSet,
+                              std::shared_ptr<Sphere> sphere,
+                              CollisionData& colData) :
+        CollisionDetection(CollisionDetection::Type::PointSetToSphere,
                            colData),
-        m_mesh(mesh),
+        m_pointSet(pointSet),
         m_sphere(sphere){}
 
     ///
     /// \brief Destructor
     ///
-    ~MeshToSpherePickingCD() = default;
+    ~PointSetToSpherePickingCD() = default;
 
     ///
     /// \brief Detect collision and compute collision data
@@ -70,12 +70,12 @@ public:
                                    const unsigned int buttonId = 0){ m_deviceTracker = devTracker; }
 private:
 
-    std::shared_ptr<Mesh> m_mesh;      ///> Mesh
-    std::shared_ptr<Sphere> m_sphere;  ///> Sphere
+    std::shared_ptr<PointSet> m_pointSet;  ///> PointSet
+    std::shared_ptr<Sphere> m_sphere;      ///> Sphere
 
     std::shared_ptr<imstk::DeviceTracker> m_deviceTracker;  ///> Device tracker to get the button status
-    unsigned int m_buttonId = 0; ///> button id
+    unsigned int m_buttonId = 0;                            ///> button id
 };
 }
 
-#endif // ifndef imstkMeshToSphereCD_h
+#endif // ifndef imstkPointSetToSphereCD_h

Base/Collision/CollisionHandling/imstkPickingCH.cpp

@@ -58,7 +58,7 @@ PickingCH::addPickConstraints(std::shared_ptr<DeformableObject> deformableObj)
     const auto& Uprev = deformableObj->getDisplacements();
     const auto& Vprev = deformableObj->getVelocities();
 
-    auto PhysTetMesh = std::dynamic_pointer_cast<Mesh>(deformableObj->getPhysicsGeometry());
+    auto PhysTetMesh = std::dynamic_pointer_cast<PointSet>(deformableObj->getPhysicsGeometry());
     auto dT = std::dynamic_pointer_cast<FEMDeformableBodyModel>(m_object->getDynamicalModel())->getTimeIntegrator()->getTimestepSize();
 
     // If collision data, append LPC constraints

Base/Collision/imstkPbdInteractionPair.cpp

@@ -32,8 +32,8 @@ PbdInteractionPair::doBroadPhaseCollision()
 {
     auto g1 = first->getCollidingGeometry();
     auto g2 = second->getCollidingGeometry();
-    auto mesh1 = std::static_pointer_cast<Mesh>(g1);
-    auto mesh2 = std::static_pointer_cast<Mesh>(g2);
+    auto mesh1 = std::static_pointer_cast<PointSet>(g1);
+    auto mesh2 = std::static_pointer_cast<PointSet>(g2);
 
     Vec3d min1, max1;
     mesh1->computeBoundingBox(min1, max1);
@@ -168,7 +168,7 @@ PbdInteractionPair::doNarrowPhaseCollision()
     }
     else if (g1->getType() == Geometry::Type::PointSet)
     {
-        auto mesh1 = std::static_pointer_cast<Mesh>(g1);
+        auto mesh1 = std::static_pointer_cast<PointSet>(g1);
 
         // brute force, use BVH or spatial grid would be much better
         // point

Base/DynamicalModels/ObjectModels/imstkPbdModel.cpp

@@ -43,7 +43,7 @@ PbdModel::PbdModel() :
 }
 
 void
-PbdModel::setModelGeometry(std::shared_ptr<Mesh> m)
+PbdModel::setModelGeometry(std::shared_ptr<PointSet> m)
 {
     m_mesh = m;
 }

Base/DynamicalModels/ObjectModels/imstkPbdModel.h

@@ -59,8 +59,8 @@ public:
     ///
     /// \brief Set/Get the geometry (mesh in this case) used by the pbd model
     ///
-    void setModelGeometry(std::shared_ptr<Mesh> m);
-    std::shared_ptr<Mesh> getModelGeometry() const { return m_mesh; }
+    void setModelGeometry(std::shared_ptr<PointSet> m);
+    std::shared_ptr<PointSet> getModelGeometry() const { return m_mesh; }
 
     ///
     /// \brief setElasticModulus
@@ -211,7 +211,7 @@ public:
     void updateBodyStates(const Vectord& q, const stateUpdateType updateType = stateUpdateType::displacement) override {};
 
 protected:
-    std::shared_ptr<Mesh> m_mesh;   ///> Mesh on which the pbd model operates on
+    std::shared_ptr<PointSet> m_mesh;   ///> PointSet on which the pbd model operates on
     std::vector<std::shared_ptr<PbdConstraint>> m_constraints; ///> List of pbd constraints
 
     // Lame's constants

Base/DynamicalModels/ObjectStates/imstkPbdState.cpp

@@ -44,7 +44,7 @@ PbdState::initialize(const size_t numNodes, const bool(&options)[3])
 }
 
 void
-PbdState::initialize(const std::shared_ptr<Mesh>& m, const bool (&options)[3])
+PbdState::initialize(const std::shared_ptr<PointSet>& m, const bool (&options)[3])
 {
     this->initialize(m->getNumVertices(), options);
 }

Base/DynamicalModels/ObjectStates/imstkPbdState.h

@@ -25,7 +25,7 @@
 #include <Eigen/Dense>
 #include <vector>
 
-#include "imstkMesh.h"
+#include "imstkPointSet.h"
 #include "imstkMath.h"
 
 namespace imstk
@@ -48,7 +48,7 @@ public:
     /// \brief Initialize the pbd state
     ///
     void initialize(const size_t numNodes, const bool (&options)[3]);
-    void initialize(const std::shared_ptr<Mesh>& m, const bool(&options)[3]);
+    void initialize(const std::shared_ptr<PointSet>& m, const bool(&options)[3]);
 
     ///
     /// \brief Get/Set nodal position given the index

Base/Geometry/Map/imstkOneToOneMap.cpp

@@ -33,7 +33,7 @@ OneToOneMap::compute()
     }
 
     // returns the first matching vertex
-    auto findMatchingVertex = [](std::shared_ptr<Mesh> masterMesh, const Vec3d& p) -> size_t
+    auto findMatchingVertex = [](std::shared_ptr<PointSet> masterMesh, const Vec3d& p) -> size_t
                               {
                                   for (size_t nodeId = 0; nodeId < masterMesh->getNumVertices(); ++nodeId)
                                   {
@@ -45,8 +45,8 @@ OneToOneMap::compute()
                                   return -1;
                               };
 
-    auto meshMaster = std::dynamic_pointer_cast<Mesh>(m_master);
-    auto meshSlave = std::dynamic_pointer_cast<Mesh>(m_slave);
+    auto meshMaster = std::dynamic_pointer_cast<PointSet>(m_master);
+    auto meshSlave = std::dynamic_pointer_cast<PointSet>(m_slave);