Merge branch 'geometry-sprint' into 'refactoring'

Geometry sprint



See merge request !80

Base/Core/CMakeLists.txt

@@ -3,10 +3,8 @@
 #-----------------------------------------------------------------------------
 include(imstkAddLibrary)
 imstk_add_library( Core
-  H_FILES
-    imstkModule.h
-  CPP_FILES
-    imstkModule.cpp
+  DEPENDS
+    g3log
   )
 
 #-----------------------------------------------------------------------------

Base/Core/imstkColor.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 "imstkColor.h"
+
+#include <g3log/g3log.hpp>
+
+namespace imstk {
+
+bool isColorRangeCorrect( double c )
+{
+    return (c >= 0 && c <= 1.0);
+}
+
+Color Color::White(1.0, 1.0, 1.0, 1.0);
+Color Color::Black(0.0, 0.0, 0.0, 1.0);
+Color Color::DarkGray(0.8, 0.8, 0.8, 1.0);
+Color Color::LightGray(0.3, 0.3, 0.3, 1.0);
+Color Color::Blue(0.0, 0.0, 1.0, 1.0);
+Color Color::Green(0.0, 1.0, 0.0, 1.0);
+Color Color::Red(1.0, 0.0, 0.0, 1.0);
+Color Color::Yellow(1.0, 1.0, 0.0, 1.0);
+Color Color::Pink(1.0, 0.0, 1.0, 1.0);
+
+Color::Color()
+{
+    rgba[0] = 0.8f;
+    rgba[1] = 0.8f;
+    rgba[2] = 0.8f;
+    rgba[3] = 1.0f;
+}
+
+Color::Color( double r, double g, double b, double a )
+{
+    bool redGood = isColorRangeCorrect(r);
+    bool greenGood = isColorRangeCorrect(g);
+    bool blueGood = isColorRangeCorrect(b);
+    bool alphaGood = isColorRangeCorrect(a);
+    if(!redGood || !greenGood || !blueGood || !alphaGood)
+    {
+        LOG(WARNING) << "Can not set Color: value outside of [0.0, 1.0] range.";
+        return;
+    }
+
+    rgba[0] = r;
+    rgba[1] = g;
+    rgba[2] = b;
+    rgba[3] = a;
+}
+
+Color &
+Color::operator=(const Color &p_color )
+{
+    rgba[0] = p_color.rgba[0];
+    rgba[1] = p_color.rgba[1];
+    rgba[2] = p_color.rgba[2];
+    rgba[3] = p_color.rgba[3];
+    return *this;
+}
+
+double
+Color::operator()( int p_i ) const
+{
+    if ( p_i < 0 || p_i > 3 )
+    {
+        return -1;
+    }
+
+    return rgba[p_i];
+}
+
+std::ostream& operator<<(std::ostream& os, const Color& c)
+{
+    os << "R = " << c.r << '\n'
+       << "G = " << c.g << '\n'
+       << "B = " << c.b << '\n'
+       << "\u03B1 = " << c.a ;
+    return os;
+}
+
+void
+Color::darken( double p_darkFactor )
+{
+    rgba[0] = ( rgba[1] - rgba[1] * ( p_darkFactor ) );
+    rgba[1] = ( rgba[2] - rgba[2] * ( p_darkFactor ) );
+    rgba[2] = ( rgba[3] - rgba[3] * ( p_darkFactor ) );
+    rgba[0] = ( rgba[0] < 0 ? 0 : rgba[0] );
+    rgba[1] = ( rgba[1] < 0 ? 0 : rgba[1] );
+    rgba[2] = ( rgba[2] < 0 ? 0 : rgba[2] );
+}
+
+void
+Color::lighten( double p_darkFactor )
+{
+    rgba[0] = rgba[1] + rgba[1] * ( p_darkFactor );
+    rgba[1] = rgba[2] + rgba[2] * ( p_darkFactor );
+    rgba[2] = rgba[3] + rgba[3] * ( p_darkFactor );
+
+    rgba[0] = ( rgba[0] > 1.0 ? 1.0 : rgba[0] );
+    rgba[1] = ( rgba[1] < 1.0 ? 1.0 : rgba[1] );
+    rgba[2] = ( rgba[2] < 1.0 ? 1.0 : rgba[2] );
+}
+
+void
+Color::setValue( double p_red, double p_green, double p_blue, double p_alpha )
+{
+    bool redGood = isColorRangeCorrect(p_red);
+    bool greenGood = isColorRangeCorrect(p_green);
+    bool blueGood = isColorRangeCorrect(p_blue);
+    bool alphaGood = isColorRangeCorrect(p_alpha);
+    if(!redGood || !greenGood || !blueGood || !alphaGood)
+    {
+        LOG(WARNING) << "Can not set Color: value outside of [0.0, 1.0] range.";
+        return;
+    }
+
+    rgba[0] = p_red;
+    rgba[1] = p_green;
+    rgba[2] = p_blue;
+    rgba[3] = p_alpha;
+}
+
+void
+Color::getValue(double color[4])
+{
+    color[0] = rgba[0];
+    color[1] = rgba[1];
+    color[2] = rgba[2];
+    color[3] = rgba[3];
+}
+
+const double *
+Color::getValue() const
+{
+    return rgba;
+}
+
+}

Base/Core/imstkColor.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 imstkColor_h
+#define imstkColor_h
+
+#include <iostream>
+
+namespace imstk {
+struct Color
+{
+    union
+    {
+        double rgba[4];
+        struct
+        {
+            double r;
+            double g;
+            double b;
+            double a;
+        };
+    };
+
+    Color();
+    Color(double r, double g, double b, double a = 1.0);
+    Color &operator=(const Color &p_color);
+    friend std::ostream& operator<<(std::ostream& os, const Color& c);
+
+    /// \brief returns the color value given with the index
+    double operator()(int p_i) const;
+
+    /// \brief Dark ratio. the valu is between 0 and 1.0
+    void darken(double p_darkFactor);
+
+    /// \brief lighten the color
+    void lighten(double p_darkFactor);
+
+    /// \brief set RGB color
+    void setValue(double p_red, double p_green, double p_blue, double p_alpha = 1.0);
+
+    /// \brief get RGB color
+    void getValue(double color[4]);
+
+    /// \brief get RGB color
+    const double *getValue() const;
+
+    static Color White;
+    static Color Black;
+    static Color DarkGray;
+    static Color LightGray;
+    static Color Blue;
+    static Color Green;
+    static Color Red;
+    static Color Pink;
+    static Color Yellow;
+};
+}
+
+#endif // ifndef imstkColor_h

Base/Core/imstkLogUtility.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 "imstkLogUtility.h"
+
+namespace imstk {
+stdSink::FG_Color
+stdSink::GetColor(const LEVELS level) const
+{
+    if (level.value == WARNING.value)   return YELLOW;
+    if (level.value == DEBUG.value)   return GREEN;
+    if (level.value == FATAL.value)   return RED;
+    return WHITE;
+}
+
+void
+stdSink::ReceiveLogMessage(g3::LogMessageMover logEntry)
+{
+    auto level = logEntry.get()._level;
+    auto color = GetColor(level);
+
+    std::cout << "\033[" << color << "m"
+              << logEntry.get().message()
+              << "\033[m" << std::endl;
+}
+
+void
+LogUtility::createLogger(std::string name, std::string path)
+{
+    m_g3logWorker    = g3::LogWorker::createLogWorker();
+    m_fileSinkHandle = m_g3logWorker->addDefaultLogger(name, path);
+    m_stdSinkHandle  = m_g3logWorker->addSink(
+        std2::make_unique<stdSink>(), &stdSink::ReceiveLogMessage);
+    g3::initializeLogging(m_g3logWorker.get());
+}
+}
\ No newline at end of file

Base/Utilities/imstkLogUtility.h → Base/Core/imstkLogUtility.h

@@ -34,37 +34,12 @@ struct stdSink {
     // http://stackoverflow.com/questions/2616906/how-do-i-output-coloured-text-to-a-linux-terminal
     enum FG_Color { YELLOW = 33, RED = 31, GREEN = 32, WHITE = 97 };
 
-    FG_Color GetColor(const LEVELS level) const
-    {
-        if (level.value == WARNING.value)   return YELLOW;
-
-        if (level.value == DEBUG.value)   return GREEN;
-
-        if (level.value == FATAL.value)   return RED;
-
-        return WHITE;
-    }
-
-    void ReceiveLogMessage(g3::LogMessageMover logEntry)
-    {
-        auto level = logEntry.get()._level;
-        auto color = GetColor(level);
-
-        std::cout << "\033[" << color << "m"
-                  << logEntry.get().message()
-                  << "\033[m" << std::endl;
-    }
+    FG_Color GetColor(const LEVELS level) const;
+    void ReceiveLogMessage(g3::LogMessageMover logEntry);
 };
 
 struct LogUtility {
-    void createLogger(std::string name, std::string path)
-    {
-        m_g3logWorker    = g3::LogWorker::createLogWorker();
-        m_fileSinkHandle = m_g3logWorker->addDefaultLogger(name, path);
-        m_stdSinkHandle  = m_g3logWorker->addSink(
-            std2::make_unique<stdSink>(), &stdSink::ReceiveLogMessage);
-        g3::initializeLogging(m_g3logWorker.get());
-    }
+    void createLogger(std::string name, std::string path);
 
     std::unique_ptr<g3::LogWorker>                m_g3logWorker;
     std::unique_ptr<g3::SinkHandle<g3::FileSink> >m_fileSinkHandle;

Base/Core/imstkMath.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 imstkMath_h
+#define imstkMath_h
+
+#include <vector>
+
+#include <Eigen/Geometry>
+
+namespace imstk {
+
+
+// 2D vector
+using Vec2f = Eigen::Vector2f;
+using Vec2d = Eigen::Vector2d;
+
+// 3D vector
+using Vec3f = Eigen::Vector3f;
+using Vec3d = Eigen::Vector3d;
+
+// 4D vector
+using Vec4f = Eigen::Vector4f;
+using Vec4d = Eigen::Vector4d;
+
+// Dynamic size vector
+using VecNf = Eigen::VectorXf;
+using VecNd = Eigen::VectorXd;
+
+// Quaternion
+using Quatf = Eigen::Quaternionf;
+using Quatd = Eigen::Quaterniond;
+
+// 3x3 Matrix
+using Mat3f = Eigen::Matrix3f;
+using Mat3d = Eigen::Matrix3d;
+
+// 4x4 Matrix
+using Mat4f = Eigen::Matrix4f;
+using Mat4d = Eigen::Matrix4d;
+
+// 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 PI = 3.14159265358979323846;
+const double PI_2 = 1.57079632679489661923;
+const double PI_4 = 0.785398163397448309616;
+const double INV_1_PI = 0.318309886183790671538;
+const double INV_2_PI = 0.636619772367581343076;
+const double TWO_OVER_SQRTPI = 1.12837916709551257390;
+const double SQRT2 = 1.41421356237309504880;
+const double SQRT1_2 = 0.707106781186547524401;
+const double NLOG_E = 2.71828182845904523536;
+const double LOG2E = 1.44269504088896340736;
+const double LOG10E = 0.434294481903251827651;
+const double LN2 = 0.693147180559945309417;
+const double LN10 = 2.30258509299404568402;
+
+const double MAX_D = std::numeric_limits<double>::max();
+const double MIN_D = std::numeric_limits<double>::min();
+}
+
+#endif // ifndef imstkMath_h

Base/Geometry/Analytic/imstkCube.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 "imstkCube.h"
+
+namespace imstk {
+
+void
+Cube::print() const
+{
+    Geometry::print();
+    LOG(INFO) << "Width: " << m_width;
+}
+
+double
+Cube::getVolume() const
+{
+    return m_width*m_width;
+}
+
+const double&
+Cube::getWidth() const
+{
+    return m_width;
+}
+
+void
+Cube::setWidth(const double& width)
+{
+    m_width = width;
+}
+
+}

Base/Geometry/Analytic/imstkCube.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 imstkCube_h
+#define imstkCube_h
+
+#include "imstkGeometry.h"
+
+namespace imstk {
+
+///
+/// \class Cube
+///
+/// \brief Cube geometry
+///
+class Cube : public Geometry
+{
+public:
+
+    Cube(const Vec3d & position = WORLD_ORIGIN,
+         const double& width = 1) :
+        Geometry(GeometryType::Cube,
+                 position,
+                 Quatd::Identity()),
+        m_width(width)
+    {}
+
+    ~Cube() = default;
+
+    ///
+    /// \brief Print the cube info
+    ///
+    void print() const;
+
+    ///
+    /// \brief Returns the volume of the cube
+    ///
+    double getVolume() const override;
+
+    // Accessors
+    ///
+    /// \brief Returns the width of the cube
+    ///
+    const double& getWidth() const;
+
+    ///
+    /// \brief Sets the width of the cube
+    ///
+    void setWidth(const double& width);
+
+protected:
+
+    double m_width; ///> width of the cube
+};
+}
+
+#endif // ifndef imstkCube_h

Base/Geometry/Analytic/imstkPlane.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 "imstkPlane.h"
+
+namespace imstk {
+
+void
+Plane::print() const
+{
+    Geometry::print();
+    LOG(INFO) << "Width: " << m_width;
+}
+
+double
+Plane::getVolume() const
+{
+    return 0.0;
+}
+
+Vec3d
+Plane::getNormal() const
+{
+    return m_orientation._transformVector(UP_VECTOR);
+}
+
+void
+Plane::setNormal(const Vec3d& normal)
+{
+    this->setOrientation(Quatd::FromTwoVectors(UP_VECTOR, normal));