ENH: Adds geometry maps

Adds geometry map base class and isometriMap

Signed-off-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>

Base/Core/imstkMath.h

@@ -48,16 +48,41 @@ using Quatf = Eigen::Quaternionf;
 using Quatd = Eigen::Quaterniond;
 
 // 3x3 Matrix
-using Mat3f = Eigen::Matrix<float, 3, 3>;
-using Mat3d = Eigen::Matrix<double, 3, 3>;
-
-#define UP Vec3d(0.0, 1.0, 0.0)
-#define DOWN Vec3d(0, -1, 0)
-#define RIGHT Vec3d(1, 0, 0)
-#define LEFT Vec3d(-1, 0, 0)
-#define FORWARD Vec3d(0, 0, -1)
-#define BACKWARD Vec3d(0, 0, 1)
+using Mat3f = Eigen::Matrix3f;
+using Mat3d = Eigen::Matrix3d;
+
+// Rigid transform (translation and rotation)
+using RigidTransform3f = Eigen::Isometry3f;
+using RigidTransform3d = Eigen::Isometry3d;
+
+// Affine transform (translation, rotation, scaling and shearing)
+using AffineTransform3f = Eigen::Affine3f;
+using AffineTransform3d = Eigen::Affine3d;
+
+// Handy cartesian vectors in 3d
+#define UP_VECTOR Vec3d(0.0, 1.0, 0.0)
+#define DOWN_VECTOR Vec3d(0, -1, 0)
+#define RIGHT_VECTOR Vec3d(1, 0, 0)
+#define LEFT_VECTOR Vec3d(-1, 0, 0)
+#define FORWARD_VECTOR Vec3d(0, 0, -1)
+#define BACKWARD_VECTOR Vec3d(0, 0, 1)
 #define WORLD_ORIGIN Vec3d::Zero()
+
+// Some commonly used math constants
+const double iMSTK_PI = 3.14159265358979323846;
+const double iMSTK_PI_2 = 1.57079632679489661923;
+const double iMSTK_PI_4 = 0.785398163397448309616;
+const double iMSTK_1_PI = 0.318309886183790671538;
+const double iMSTK_2_PI = 0.636619772367581343076;
+const double iMSTK_2_SQRTPI = 1.12837916709551257390;
+const double iMSTK_SQRT2 = 1.41421356237309504880;
+const double iMSTK_SQRT1_2 = 0.707106781186547524401;
+const double iMSTK_E = 2.71828182845904523536;
+const double iMSTK_LOG2E = 1.44269504088896340736;
+const double iMSTK_LOG10E = 0.434294481903251827651;
+const double iMSTK_LN2 = 0.693147180559945309417;
+const double iMSTK_LN10 = 2.30258509299404568402;
+
 }
 
 #endif // ifndef imstkMath_h

Base/Geometry/CMakeLists.txt

@@ -13,6 +13,8 @@ imstk_add_library( Geometry
     imstkVolumetricMesh.h
     imstkTetrahedralMesh.h
     imstkHexahedralMesh.h
+	imstkGeometryMap.h
+	imstkIsometricMap.h
   CPP_FILES
     imstkGeometry.cpp
     imstkPlane.cpp
@@ -23,6 +25,8 @@ imstk_add_library( Geometry
     imstkVolumetricMesh.cpp
     imstkTetrahedralMesh.cpp
     imstkHexahedralMesh.cpp
+	imstkGeometryMap.cpp
+	imstkIsometricMap.cpp
   LIBRARIES
     Core
     VegaFEM::volumetricMesh

Base/Geometry/imstkGeometry.cpp

@@ -60,6 +60,13 @@ Geometry::scale(const double& scaling)
     m_scaling *= scaling;
 }
 
+void
+Geometry::transform(const RigidTransform3d& transform)
+{
+    this->rotate(transform.rotation());
+    this->translate(transform.translation());
+}
+
 const Vec3d&
 Geometry::getPosition() const
 {

Base/Geometry/imstkGeometry.h

@@ -51,6 +51,9 @@ public:
                         const double& angle);
     void         scale(const double& scaling);
 
+    void        transform(const RigidTransform3d& transform);
+
+    // Accessors
     const Vec3d& getPosition() const;
     void         setPosition(const Vec3d& position);
     void         setPosition(const double& x,

Base/Geometry/imstkGeometryMap.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 "imstkGeometryMap.h"
+
+namespace imstk {
+    void GeometryMap::muteMap()
+    {
+        m_isActive = false;
+    }
+
+    void GeometryMap::activateMap()
+    {
+        m_isActive = true;
+    }
+
+    const GeometryMapType& GeometryMap::getType() const
+    {
+        return m_type;
+    }
+
+    void GeometryMap::setMaster(std::shared_ptr<Geometry> master)
+    {
+        m_master = master;
+    }
+
+    std::shared_ptr<Geometry> GeometryMap::getMaster() const
+    {
+        return m_master;
+    }
+
+    void GeometryMap::setSlave(std::shared_ptr<Geometry> slave)
+    {
+        m_slave = slave;
+    }
+
+    std::shared_ptr<Geometry> GeometryMap::getSlave() const
+    {
+        return m_slave;
+    }
+
+    bool GeometryMap::isActive() const
+    {
+        return m_isActive;
+    }
+}
\ No newline at end of file

Base/Geometry/imstkGeometryMap.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 imstkGeometryMap_h
+#define imstkGeometryMap_h
+
+#include <memory>
+
+#include "imstkGeometry.h"
+
+namespace imstk {
+
+enum class GeometryMapType
+{
+    Isometric,
+    TetraTriangle,
+    HexaTriangle,
+    TetraTetra
+};
+
+class GeometryMap
+{
+public:
+
+    ~GeometryMap() = default;
+
+    ///
+    /// \brief Compute the map
+    ///
+    virtual void computeMap() = 0;
+
+    ///
+    /// \brief Apply the map
+    ///
+    virtual void applyMap() = 0;
+
+    ///
+    /// \brief Deactivate the map
+    ///
+    void muteMap();
+
+    ///
+    /// \brief Activate the map
+    ///
+    void activateMap();
+
+    // Accessors
+
+    const GeometryMapType& getType() const;
+
+    void setMaster(std::shared_ptr<Geometry> master);
+    std::shared_ptr<Geometry> getMaster() const;
+
+    void setSlave(std::shared_ptr<Geometry> slave);
+    std::shared_ptr<Geometry> getSlave() const;
+
+    ///
+    /// \brief Returns true if the map is actively applied at runtime, else false.
+    ///
+    bool isActive() const;
+
+protected:
+
+    GeometryMap(GeometryMapType type) : m_isActive(true) {}
+
+    GeometryMapType m_type; ///> type of the map
+
+    bool m_isActive; ///> true if the map us active at runtime
+
+    std::shared_ptr<Geometry> m_master; ///> the geometry which dictates the configuration
+    std::shared_ptr<Geometry> m_slave; ///> the geometry which follows the master
+
+};
+}
+
+#endif // imstkGeometryMap_h

Base/Geometry/imstkIsometricMap.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 "imstkIsometricMap.h"
+namespace imstk {
+    void IsometricMap::setTransform(const RigidTransform3d& affineTransform)
+    {
+        m_rigidTransform = affineTransform;
+    }
+
+    const imstk::RigidTransform3d& IsometricMap::getTransform() const
+    {
+        return m_rigidTransform;
+    }
+
+    void IsometricMap::applyMap()
+    {
+        if (m_isActive)
+        {
+            // First set the follower mesh configuration to that of master
+            m_slave->setPosition(m_master->getPosition());
+            m_slave->setOrientation(m_master->getOrientation());
+
+            // Now, apply the offset transform
+            m_slave->transform(m_rigidTransform);
+        }
+    }
+}
\ No newline at end of file

Base/Geometry/imstkIsometricMap.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 imstkAffineMap_h
+#define imstkAffineMap_h
+
+#include "imstkGeometryMap.h"
+
+namespace imstk {
+
+class IsometricMap : public GeometryMap
+{
+public:
+
+    ~IsometricMap() = default;
+
+    IsometricMap() : GeometryMap(GeometryMapType::Isometric), m_rigidTransform(RigidTransform3d::Identity()){}
+
+    void applyMap();
+
+    // Accessors
+    void setTransform(const RigidTransform3d& affineTransform);
+    const RigidTransform3d& getTransform() const;
+
+protected:
+    RigidTransform3d m_rigidTransform;
+};
+}
+
+#endif // imstkGeometryMap_h

Base/Geometry/imstkMesh.h

@@ -45,7 +45,7 @@ protected:
     Mesh(GeometryType type) : Geometry(type, WORLD_ORIGIN, Quatd()) {}
 
     //   Orientation * Scaling * initialVertexPositions
-    // + Position
+    // + Position (Initial translation)
     // + vertexDisplacements
     // = vertexPositions
     std::vector<Vec3d> m_initialVertexPositions;

Base/Geometry/imstkPlane.cpp

@@ -25,13 +25,13 @@ namespace imstk {
 Vec3d
 Plane::getNormal() const
 {
-    return m_orientation._transformVector(UP);
+    return m_orientation._transformVector(UP_VECTOR);
 }
 
 void
 Plane::setNormal(const Vec3d& normal)
 {
-    this->setOrientation(Quatd::FromTwoVectors(UP, normal));
+    this->setOrientation(Quatd::FromTwoVectors(UP_VECTOR, normal));
 }
 
 const double&

Base/Geometry/imstkPlane.h

@@ -30,11 +30,11 @@ class Plane : public Geometry
 public:
 
     Plane(const Vec3d & position = WORLD_ORIGIN,
-          const Vec3d & normal = UP,
+          const Vec3d & normal = UP_VECTOR,
           const double& width = 1) :
         Geometry(GeometryType::Plane,
                  position,
-                 Quatd::FromTwoVectors(UP, normal)),
+                 Quatd::FromTwoVectors(UP_VECTOR, normal)),
         m_width(width)
     {}
 

Base/Geometry/imstkSurfaceMesh.h

@@ -45,6 +45,7 @@ public:
     void                              computeVertexNormals();
     void                              computeVertexTangents();
 
+    // Accessors
     void                              setTriangleVertices(
         const std::vector<TriangleArray>& triangles);
 

Base/Geometry/imstkTetrahedralMesh.h

@@ -37,13 +37,14 @@ public:
 
     ~TetrahedralMesh() = default;
 
+    // Accessors
     const std::vector<TetraArray>& getTetrahedronVertices() const;
     void                           setTetrahedronVertices(
         const std::vector<TetraArray>& tetrahedrons);
 
 protected:
 
-    std::vector<TetraArray> m_tetrahedronVertices;
+    std::vector<TetraArray> m_tetrahedronVertices; ///< vertices of the tetrahedra
 };
 }
 

Base/Geometry/imstkVolumetricMesh.h

@@ -34,7 +34,9 @@ public:
 
     ~VolumetricMesh() = default;
 
+    // Accessors
     std::shared_ptr<SurfaceMesh>getAttachedSurfaceMesh();
+
     void                        setAttachedSurfaceMesh(std::shared_ptr<SurfaceMesh>surfaceMesh);
 
 protected:

Base/Rendering/imstkPlaneRenderDelegate.cpp

@@ -30,7 +30,7 @@ PlaneRenderDelegate::PlaneRenderDelegate(std::shared_ptr<Plane>plane) :
     auto source = vtkSmartPointer<vtkPlaneSource>::New();
 
     source->SetCenter(WORLD_ORIGIN[0], WORLD_ORIGIN[1], WORLD_ORIGIN[2]);
-    source->SetNormal(UP[0], UP[1], UP[2]);
+    source->SetNormal(UP_VECTOR[0], UP_VECTOR[1], UP_VECTOR[2]);
 
     this->setActorMapper(source->GetOutputPort());
     this->setActorTransform(m_geometry);

Base/Scene/imstkSceneObject.h

@@ -58,7 +58,7 @@ protected:
 
     SceneObjectType m_type = SceneObjectType::Visual;
     std::string     m_name;
-    std::shared_ptr<Geometry> m_visualGeometry;
+    std::shared_ptr<Geometry> m_visualGeometry; ///> Geometry for rendering
 };
 
 using VisualObject = SceneObject;

Examples/Sandbox/main.cpp

@@ -31,8 +31,8 @@ int main()
 
     auto cubeGeom = std::make_shared<imstk::Cube>();
     cubeGeom->scale(0.5);
-    cubeGeom->rotate(imstk::UP,    M_PI/4);
-    cubeGeom->rotate(imstk::RIGHT, M_PI/4);
+    cubeGeom->rotate(imstk::UP_VECTOR,    M_PI/4);
+    cubeGeom->rotate(imstk::RIGHT_VECTOR, M_PI / 4);
     cubeGeom->translate(2, 1, 0.5);
     auto cubeObj = std::make_shared<imstk::VisualObject>("VisualCube");
     cubeObj->setVisualGeometry(cubeGeom);