Merge branch 'master' into 2346-landmarks-zoom

Author: akenmorris

ExternalLibs/robin_hood/robin_hood.h

@@ -192,13 +192,7 @@ static Counts& counts() {
 #    define ROBIN_HOOD_PRIVATE_DEFINITION_HAS_NATIVE_WCHART() 1
 #endif
 
-// workaround missing "is_trivially_copyable" in g++ < 5.0
-// See https://stackoverflow.com/a/31798726/48181
-#if defined(__GNUC__) && __GNUC__ < 5
-#    define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) __has_trivial_copy(__VA_ARGS__)
-#else
-#    define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) std::is_trivially_copyable<__VA_ARGS__>::value
-#endif
+#define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) std::is_trivially_copyable<__VA_ARGS__>::value
 
 // helpers for C++ versions, see https://gcc.gnu.org/onlinedocs/cpp/Standard-Predefined-Macros.html
 #define ROBIN_HOOD_PRIVATE_DEFINITION_CXX() __cplusplus

Libs/Analyze/Analyze.cpp

@@ -75,7 +75,7 @@ static void write_good_bad_angles(json& json_object, ProjectHandle project, Anal
   std::vector<json> good_bad_angles;
 
   for (int d = 0; d < project->get_number_of_domains_per_subject(); d++) {
-    std::vector<std::shared_ptr<MeshWrapper>> meshes;
+    std::vector<std::shared_ptr<Surface>> meshes;
     for (auto& shape : analyze.get_shapes()) {
       meshes.push_back(shape->get_groomed_mesh_wrappers()[d]);
     }

Libs/Analyze/Shape.cpp

@@ -16,7 +16,7 @@
 #include <vtkKdTreePointLocator.h>
 #include <vtkPointData.h>
 
-#include "Libs/Optimize/Domain/MeshWrapper.h"
+#include "Libs/Optimize/Domain/Surface.h"
 
 using ReaderType = itk::ImageFileReader<ImageType>;
 
@@ -931,14 +931,14 @@ bool Shape::has_planes() {
 }
 
 //---------------------------------------------------------------------------
-std::vector<std::shared_ptr<MeshWrapper>> Shape::get_groomed_mesh_wrappers() {
+std::vector<std::shared_ptr<Surface>> Shape::get_groomed_mesh_wrappers() {
   if (!groomed_mesh_wrappers_.empty()) {
     return groomed_mesh_wrappers_;
   }
 
   auto group = get_groomed_meshes(true /* wait */);
   for (auto& mesh : group.meshes()) {
-    auto wrapper = std::make_shared<MeshWrapper>(mesh->get_poly_data());
+    auto wrapper = std::make_shared<Surface>(mesh->get_poly_data());
     groomed_mesh_wrappers_.push_back(wrapper);
   }
   return groomed_mesh_wrappers_;

Libs/Analyze/Shape.h

@@ -22,7 +22,7 @@ namespace shapeworks {
 class Shape;
 using ShapeHandle = std::shared_ptr<Shape>;
 using ShapeList = std::vector<ShapeHandle>;
-class MeshWrapper;
+class Surface;
 
 //! Representation of a single shape/patient/subject.
 class Shape {
@@ -187,7 +187,7 @@ class Shape {
 
   bool has_planes();
 
-  std::vector<std::shared_ptr<MeshWrapper>> get_groomed_mesh_wrappers();
+  std::vector<std::shared_ptr<Surface>> get_groomed_mesh_wrappers();
 
   void recompute_original_surface();
 
@@ -208,7 +208,7 @@ class Shape {
   MeshGroup original_meshes_;
   MeshGroup groomed_meshes_;
   MeshGroup reconstructed_meshes_;
-  std::vector<std::shared_ptr<MeshWrapper>> groomed_mesh_wrappers_;
+  std::vector<std::shared_ptr<Surface>> groomed_mesh_wrappers_;
 
   std::string override_feature_;
 

Libs/Mesh/Mesh.cpp

@@ -60,7 +60,7 @@
 
 #include "FEFixMesh.h"
 #include "Image.h"
-#include "Libs/Optimize/Domain/MeshWrapper.h"
+#include "Libs/Optimize/Domain/Surface.h"
 #include "Logging.h"
 #include "MeshComputeThickness.h"
 #include "MeshUtils.h"
@@ -785,8 +785,8 @@ double Mesh::geodesicDistance(int source, int target) const {
     throw std::invalid_argument("requested point ids outside range of points available in mesh");
   }
 
-  MeshWrapper wrap(this->poly_data_, true);
-  return wrap.ComputeDistance(getPoint(source), -1, getPoint(target), -1);
+  Surface surface(this->poly_data_, true);
+  return surface.compute_distance(getPoint(source), -1, getPoint(target), -1);
 }
 
 Field Mesh::geodesicDistance(const Point3 landmark) const {
@@ -795,10 +795,10 @@ Field Mesh::geodesicDistance(const Point3 landmark) const {
   distance->SetNumberOfTuples(numPoints());
   distance->SetName("GeodesicDistanceToLandmark");
 
-  MeshWrapper wrap(this->poly_data_, true);
+  Surface surface(this->poly_data_, true);
 
   for (int i = 0; i < numPoints(); i++) {
-    distance->SetValue(i, wrap.ComputeDistance(landmark, -1, getPoint(i), -1));
+    distance->SetValue(i, surface.compute_distance(landmark, -1, getPoint(i), -1));
   }
 
   return distance;
@@ -1767,7 +1767,7 @@ Eigen::Vector3d Mesh::getFFCGradient(Eigen::Vector3d query) const {
   return grad;
 }
 
-// WARNING: Copied directly from Meshwrapper. TODO: When refactoring, take this into account.
+// WARNING: Copied directly from Surface. TODO: When refactoring, take this into account.
 vtkSmartPointer<vtkPoints> Mesh::getIGLMesh(Eigen::MatrixXd& V, Eigen::MatrixXi& F) const {
   const int n_verts = this->poly_data_->GetNumberOfPoints();
   const int n_faces = this->poly_data_->GetNumberOfCells();

Libs/Mesh/Mesh.h

@@ -277,8 +277,8 @@ class Mesh {
 
   //! Formats mesh into an IGL format
   vtkSmartPointer<vtkPoints> getIGLMesh(Eigen::MatrixXd& V, Eigen::MatrixXi& F)
-      const;  // Copied directly from MeshWrapper. this->poly_data_ becomes this->mesh. // WARNING: Copied directly
-              // from Meshwrapper. TODO: When refactoring, take this into account.
+      const;  // Copied directly from Surface. this->poly_data_ becomes this->mesh. // WARNING: Copied directly
+              // from Surface. TODO: When refactoring, take this into account.
 
   //! Clips the mesh according to a field value
   vtkSmartPointer<vtkPolyData> clipByField(const std::string& name, double value);
@@ -293,7 +293,7 @@ class Mesh {
 
   /// Computes baricentric coordinates given a query point and a face number
   Eigen::Vector3d computeBarycentricCoordinates(const Eigen::Vector3d& pt, int face)
-      const;  // // WARNING: Copied directly from Meshwrapper. TODO: When refactoring, take this into account.
+      const;  // // WARNING: Copied directly from Surface. TODO: When refactoring, take this into account.
 
   //! Interpolates scalar values at points (e.g. correspondence points) to the mesh, assign/create a field with the
   //! given name