Regularization

.gitignore

@@ -0,0 +1 @@
+build

ChangeLog.md

@@ -68,6 +68,9 @@
      (Bertrand Kerautret, [#285](https://github.com/DGtal-team/DGtalTools/pull/285))
     - tangentBC: add an option to read sdp points as input.
      (Bertrand Kerautret, [#285](https://github.com/DGtal-team/DGtalTools/pull/288))
+    - volSurfaceRegularization: a tool to compute a regularized quadrangulation from
+     from a digital surface.
+     (Pierre Gueth, David Coeurjolly, [#306](https://github.com/DGtal-team/DGtalTools/pull/306))
 
 
 # DGtalTools 0.9.2

doc/estimators.dox

@@ -1,6 +1,6 @@
 /**
  * @file estimators.dox
- * @author Bertrand Kerautret 
+ * @author Bertrand Kerautret
  * LORIA (CNRS, UMR 7503), University of Lorraine, France
  *
  * @date 2016/05/12
@@ -20,38 +20,39 @@
 
 
   - @ref Doc2dLocalEstimators : compares local estimators on implicit shapes using DGtal Library.
-  - @ref Doc3dCurveTangentEstimator : estimates the tangent vector to a set of 3D integer points.  
+  - @ref Doc3dCurveTangentEstimator : estimates the tangent vector to a set of 3D integer points.
   - @ref curvatureBC : estimates curvature using a binomial convolver.
   - @ref curvatureMCMS : estimates curvature using length of most centered segment computers.
   - @ref curvatureScaleSpaceBCC : generates the Curvature Scale Space image using a binomial convolver based estimator.
-  - @ref eulerCharacteristic : computes the Euleur Characteristic of  a vol to a 8-bit raw file.  
+  - @ref eulerCharacteristic : computes the Euleur Characteristic of  a vol to a 8-bit raw file.
   - @ref generic3dNormalEstimators : computes a normal vector field over a digitized 3D implicit surface for several estimators.
   - @ref lengthEstimators : generates multigrid length estimations of paramteric shapes using DGtal library.
   - @ref statisticsEstimators : computes satistics (L1, L2, Loo) from results of two estimators.
   - @ref tangentBC : estimates tangent using a binomial convolver.
   - @ref vol2normalField : generates normal vector field from a vol file using DGtal library.
+  - @ref volSurfaceRegularization : regularizes a digital surface into a smooth cubical complex.
+
 
-
 <center>
 <table>
   <tr>
         <td> <img height=200px src="res2dLocalEstimators.png"> </td>
         <td><img height=200px src="res3dCurveTangentEstimator.png"></td>
-        <td><table> <tr><td><img height=50px src="resCurvatureBCcontour.png"></td><td><img height=200px src="resCurvatureBCcurvature.png"></td></tr></table></td>        
+        <td><table> <tr><td><img height=50px src="resCurvatureBCcontour.png"></td><td><img height=200px src="resCurvatureBCcurvature.png"></td></tr></table></td>
 </tr>
 <tr>
         <td align = center>@ref Doc2dLocalEstimators </td>
-        <td align = center>@ref Doc3dCurveTangentEstimator </td>   
+        <td align = center>@ref Doc3dCurveTangentEstimator </td>
         <td align = center>@ref curvatureBC</td>
 </tr>
   <tr>
         <td> <img height=200px src="resVol2normalField.png"> </td>
         <td><img height=200px src="resGeneric3dNormalEstimatorsVCM.png"></td>
-        <td><img height=100px src="resCurvatureScaleSpaceBCC.png"></td>        
+        <td><img height=100px src="resCurvatureScaleSpaceBCC.png"></td>
 </tr>
 <tr>
         <td align = center>@ref vol2normalField </td>
-        <td align = center>@ref generic3dNormalEstimators </td>   
+        <td align = center>@ref generic3dNormalEstimators </td>
         <td align = center>@ref curvatureScaleSpaceBCC</td>
 </tr>
 
@@ -60,4 +61,4 @@
 </center>
 
 
-*/
+*/

estimators/CMakeLists.txt

@@ -11,6 +11,11 @@ SET(DGTAL_TOOLS_SRC
   eulerCharacteristic
 )
 
+if (WITH_EIGEN)
+    add_executable(volSurfaceRegularization volSurfaceRegularization.cpp volSurfaceRegularization-details/surface_approx.cpp)
+    target_link_libraries(volSurfaceRegularization ${DGTAL_LIBRARIES} ${DGtalToolsLibDependencies})
+endif()
+
 if ( WITH_VISU3D_QGLVIEWER )
   SET(VISU3D_TESTS_SRC
       3dCurveTangentEstimator
@@ -23,7 +28,7 @@ endif ( WITH_VISU3D_QGLVIEWER )
 
 if (  WITH_CGAL )
   SET(CGAL_TESTS_SRC
-#    3dLocalEstimators 
+#    3dLocalEstimators
      )
   FOREACH(FILE ${CGAL_TESTS_SRC})
     add_executable(${FILE} ${FILE})

estimators/volSurfaceRegularization-details/shape.h

@@ -0,0 +1,141 @@
+#pragma once
+
+#include <DGtal/base/Common.h>
+#include <DGtal/math/linalg/EigenSupport.h>
+
+struct RoundedCubeShape
+{
+    typedef DGtal::Z3i::Point Point;
+    typedef Eigen::Vector3d Vector;
+    typedef Eigen::Matrix3d Matrix;
+
+    RoundedCubeShape(const Matrix& transform_, const double& size_, const double& radius_) : transform(transform_), size(size_), radius(radius_)
+    {
+        ASSERT( radius < size );
+    }
+
+    bool operator()(const Point& point) const
+    {
+        const Vector vector_(point[0], point[1], point[2]);
+        Vector vector = transform*vector_;
+        vector = vector.cwiseAbs();
+        if (vector.maxCoeff() <= size-radius) return true;
+        Vector projected = vector;
+        for (int kk=0; kk<projected.size(); kk++)
+            if (projected[kk] > size-radius)
+                projected[kk] = size-radius;
+        return (vector-projected).norm() <= radius;
+    }
+
+    Matrix transform;
+    double size;
+    double radius;
+};
+
+struct TorusShape
+{
+    typedef DGtal::Z3i::Point Point;
+    typedef Eigen::Vector3d Vector;
+    typedef Eigen::Matrix3d Matrix;
+
+    TorusShape(const Matrix& transform_, const double& radius_large_, const double& radius_small_) : transform(transform_), radius_large(radius_large_), radius_small(radius_small_)
+    {
+        ASSERT( radius_small < radius_large );
+    }
+
+    bool operator()(const Point& point) const
+    {
+        const Vector vector_(point[0], point[1], point[2]);
+        const Vector vector = transform*vector_;
+        Vector projected = vector;
+        projected[1] = 0;
+        if (projected.norm() == 0) return false;
+        projected *= radius_large/projected.norm();
+        return (vector-projected).norm() <= radius_small;
+    }
+
+    Matrix transform;
+    double radius_large;
+    double radius_small;
+};
+
+struct SphereShape
+{
+    typedef DGtal::Z3i::Point Point;
+    typedef DGtal::Z3i::RealPoint RealPoint;
+
+    SphereShape(const double& radius_, const RealPoint& center_) : radius(radius_), center(center_)
+    {
+    }
+
+    bool operator()(const Point& point) const
+    {
+        return (point-center).norm() <= radius;
+    }
+
+    double radius;
+    RealPoint center;
+};
+
+struct CapsuleShape
+{
+    typedef DGtal::Z3i::Point Point;
+    typedef DGtal::Z3i::RealPoint RealPoint;
+
+    CapsuleShape(const double& radius_, const double& length_, const RealPoint& direction_) : radius(radius_), length(length_), direction(direction_)
+    {
+        if (direction.norm() > 0) direction /= direction.norm();
+    }
+
+    bool operator()(const Point& point) const
+    {
+        double alpha = direction.dot(point);
+        if (alpha > length/2) alpha = length/2;
+        if (alpha < -length/2) alpha = -length/2;
+        return (point-alpha*direction).norm() <= radius;
+    }
+
+    double radius;
+    double length;
+    RealPoint direction;
+};
+
+template <typename ImageType>
+struct ImageShape
+{
+    typedef typename ImageType::Point Point;
+    typedef Eigen::Vector3d Vector;
+    typedef Eigen::Matrix3d Matrix;
+
+    ImageShape(const ImageType* image_, const Point& shift_) : image(image_), shift(shift_)
+    {
+        ASSERT( image );
+    }
+
+    bool operator()(const Point& point_) const
+    {
+        const Point point = point_+shift;
+        if (!image->domain().isInside(point)) return false;
+        return (*image)(point) > 0;
+    }
+
+    const ImageType* image;
+    Point shift;
+};
+
+struct PlaneShape
+{
+    typedef DGtal::Z3i::Point Point;
+    typedef DGtal::Z3i::RealPoint RealPoint;
+
+    PlaneShape(const RealPoint& normal_) : normal(normal_)
+    {
+    }
+
+    bool operator()(const Point& point) const
+    {
+        return normal.dot(point) <= 0;
+    }
+
+    RealPoint normal;
+};