From 2a4b878fd5da23553fa8f953b71ee3f81885532f Mon Sep 17 00:00:00 2001
From: spelufo <santiagopelufo@gmail.com>
Date: Mon, 30 Oct 2023 19:41:17 -0300
Subject: [PATCH 01/12] Try to output normals with a consitent orientation for
 convex meshes.

---
 .../include/vc/meshing/CalculateNormals.hpp   |  2 +
 meshing/src/CalculateNormals.cpp              | 45 ++++++++++++++++++-
 2 files changed, 46 insertions(+), 1 deletion(-)

diff --git a/meshing/include/vc/meshing/CalculateNormals.hpp b/meshing/include/vc/meshing/CalculateNormals.hpp
index 644318418..c5c419eb2 100644
--- a/meshing/include/vc/meshing/CalculateNormals.hpp
+++ b/meshing/include/vc/meshing/CalculateNormals.hpp
@@ -84,5 +84,7 @@ class CalculateNormals
 
     /** Storage for summed normals, organized by vertex ID */
     std::vector<cv::Vec3d> vertexNormals_;
+
+    bool flippedNormals_;
 };
 }  // namespace volcart::meshing
diff --git a/meshing/src/CalculateNormals.cpp b/meshing/src/CalculateNormals.cpp
index 915bcf2ca..1ca4f1381 100644
--- a/meshing/src/CalculateNormals.cpp
+++ b/meshing/src/CalculateNormals.cpp
@@ -22,6 +22,28 @@ void CalculateNormals::compute_normals_()
 {
     vertexNormals_ = std::vector<cv::Vec3d>(output_->GetNumberOfPoints(), 0);
 
+    // Compute the average mesh coordinates, to use as reference when choosing
+    // an orientation for the mesh normals. Should produce consistent result on
+    // convex-ish meshes.
+    unsigned int pointCount = 0;
+    ITKPoint pointAverage;
+    pointAverage.Fill(0.0);
+    for (auto it = input_->GetPoints()->Begin(); it != input_->GetPoints()->End(); ++it) {
+        auto point = it.Value();
+        pointAverage[0] += point[0];
+        pointAverage[1] += point[1];
+        pointAverage[2] += point[2];
+        pointCount++;
+    }
+    if (pointCount > 0) {
+        pointAverage[0] /= pointCount;
+        pointAverage[1] /= pointCount;
+        pointAverage[2] /= pointCount;
+    }
+
+    unsigned int outwardNormalsCount = 0;
+    unsigned int inwardNormalsCount = 0;
+
     for (auto cellIt = input_->GetCells()->Begin();
          cellIt != input_->GetCells()->End(); ++cellIt) {
 
@@ -38,21 +60,29 @@ void CalculateNormals::compute_normals_()
 
         // To-Do: #185
 
+        ITKPoint facePoint;
+        facePoint.Fill(0.0);
+
         // Collect the vertex info for each point
         vert = input_->GetPoint(pointIds[0]);
         v0(0) = vert[0];
         v0(1) = vert[1];
         v0(2) = vert[2];
+        facePoint += vert;
 
         vert = input_->GetPoint(pointIds[1]);
         v1(0) = vert[0];
         v1(1) = vert[1];
         v1(2) = vert[2];
+        facePoint += vert;
 
         vert = input_->GetPoint(pointIds[2]);
         v2(0) = vert[0];
         v2(1) = vert[1];
         v2(2) = vert[2];
+        facePoint += vert;
+
+        facePoint /= 3.0;
 
         // Get the edge vectors
         e0 = v2 - v0;
@@ -62,11 +92,20 @@ void CalculateNormals::compute_normals_()
         cv::Vec3d normals;
         normals = e1.cross(e0);
 
+        // Accumulate the relative direction of the normals for this face.
+        if (normals.dot(facePoint - pointAverage) > 0) {
+            outwardNormalsCount++;
+        } else {
+            inwardNormalsCount++;
+        }
+
         // Add the norm for this face to the running sum for each vertex
         vertexNormals_[pointIds[0]] += normals;
         vertexNormals_[pointIds[1]] += normals;
         vertexNormals_[pointIds[2]] += normals;
     }
+
+    flippedNormals_ = outwardNormalsCount > inwardNormalsCount;
 }
 
 void CalculateNormals::assign_to_mesh_()
@@ -76,6 +115,10 @@ void CalculateNormals::assign_to_mesh_()
         cv::Vec3d norm = vertexNormals_[point.Index()];
         cv::normalize(norm, norm);
 
-        output_->SetPointData(point.Index(), norm.val);
+        auto val = norm.val;
+        if (flippedNormals_) {
+            val = -val;
+        }
+        output_->SetPointData(point.Index(), val);
     }
 }

From e338234472751fdd5b1ebf039e6ccc2df96af34d Mon Sep 17 00:00:00 2001
From: spelufo <santiagopelufo@gmail.com>
Date: Mon, 30 Oct 2023 20:15:56 -0300
Subject: [PATCH 02/12] Get it to compile.

---
 meshing/src/CalculateNormals.cpp | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/meshing/src/CalculateNormals.cpp b/meshing/src/CalculateNormals.cpp
index 1ca4f1381..ddbfdf1cc 100644
--- a/meshing/src/CalculateNormals.cpp
+++ b/meshing/src/CalculateNormals.cpp
@@ -68,21 +68,29 @@ void CalculateNormals::compute_normals_()
         v0(0) = vert[0];
         v0(1) = vert[1];
         v0(2) = vert[2];
-        facePoint += vert;
+        facePoint[0] += vert[0];
+        facePoint[1] += vert[1];
+        facePoint[2] += vert[2];
 
         vert = input_->GetPoint(pointIds[1]);
         v1(0) = vert[0];
         v1(1) = vert[1];
         v1(2) = vert[2];
-        facePoint += vert;
+        facePoint[0] += vert[0];
+        facePoint[1] += vert[1];
+        facePoint[2] += vert[2];
 
         vert = input_->GetPoint(pointIds[2]);
         v2(0) = vert[0];
         v2(1) = vert[1];
         v2(2) = vert[2];
-        facePoint += vert;
+        facePoint[0] += vert[0];
+        facePoint[1] += vert[1];
+        facePoint[2] += vert[2];
 
-        facePoint /= 3.0;
+        facePoint[0] /= 3.0;
+        facePoint[1] /= 3.0;
+        facePoint[2] /= 3.0;
 
         // Get the edge vectors
         e0 = v2 - v0;
@@ -93,7 +101,8 @@ void CalculateNormals::compute_normals_()
         normals = e1.cross(e0);
 
         // Accumulate the relative direction of the normals for this face.
-        if (normals.dot(facePoint - pointAverage) > 0) {
+        cv::Vec3d itkVecToCvVec(facePoint[0] - pointAverage[0], facePoint[1] - pointAverage[1], facePoint[2] - pointAverage[2]);
+        if (normals.dot(itkVecToCvVec) > 0) {
             outwardNormalsCount++;
         } else {
             inwardNormalsCount++;
@@ -115,10 +124,9 @@ void CalculateNormals::assign_to_mesh_()
         cv::Vec3d norm = vertexNormals_[point.Index()];
         cv::normalize(norm, norm);
 
-        auto val = norm.val;
         if (flippedNormals_) {
-            val = -val;
+            norm = -norm;
         }
-        output_->SetPointData(point.Index(), val);
+        output_->SetPointData(point.Index(), norm.val);
     }
 }

From c6714f2a727348292eb4671c40ef76677c97c880 Mon Sep 17 00:00:00 2001
From: spelufo <santiagopelufo@gmail.com>
Date: Wed, 1 Nov 2023 06:51:59 -0300
Subject: [PATCH 03/12] Mesh normals orientation PR changes.

---
 .../include/vc/meshing/CalculateNormals.hpp   | 14 ++++
 meshing/src/CalculateNormals.cpp              | 82 +++++++------------
 2 files changed, 45 insertions(+), 51 deletions(-)

diff --git a/meshing/include/vc/meshing/CalculateNormals.hpp b/meshing/include/vc/meshing/CalculateNormals.hpp
index c5c419eb2..e504aa8d9 100644
--- a/meshing/include/vc/meshing/CalculateNormals.hpp
+++ b/meshing/include/vc/meshing/CalculateNormals.hpp
@@ -59,6 +59,15 @@ class CalculateNormals
      */
     ITKMesh::Pointer compute();
 
+    /**
+     * @brief Flag specifying if we should reorient normals.
+     * 
+     * If this flag is set and most of the mesh's normals are facing outwards
+     * relative to the mesh's centroid, then they're considered flipped, and
+     * will be reversed to face inwards, the conventionally positive direction.
+     */
+    bool shouldOrientNormals = true;
+
 private:
     /**
      * @brief Compute normals for each vertex.
@@ -76,6 +85,11 @@ class CalculateNormals
      */
     void assign_to_mesh_();
 
+    /**
+     * @brief Compute the mesh's centroid, the arithmetic mean of its vertices.
+     */
+    cv::Vec3d compute_mesh_centroid_();
+
     /** Mesh for which normals will be calculated. */
     ITKMesh::Pointer input_;
 
diff --git a/meshing/src/CalculateNormals.cpp b/meshing/src/CalculateNormals.cpp
index ddbfdf1cc..f2d6aed58 100644
--- a/meshing/src/CalculateNormals.cpp
+++ b/meshing/src/CalculateNormals.cpp
@@ -22,34 +22,16 @@ void CalculateNormals::compute_normals_()
 {
     vertexNormals_ = std::vector<cv::Vec3d>(output_->GetNumberOfPoints(), 0);
 
-    // Compute the average mesh coordinates, to use as reference when choosing
-    // an orientation for the mesh normals. Should produce consistent result on
-    // convex-ish meshes.
-    unsigned int pointCount = 0;
-    ITKPoint pointAverage;
-    pointAverage.Fill(0.0);
-    for (auto it = input_->GetPoints()->Begin(); it != input_->GetPoints()->End(); ++it) {
-        auto point = it.Value();
-        pointAverage[0] += point[0];
-        pointAverage[1] += point[1];
-        pointAverage[2] += point[2];
-        pointCount++;
-    }
-    if (pointCount > 0) {
-        pointAverage[0] /= pointCount;
-        pointAverage[1] /= pointCount;
-        pointAverage[2] /= pointCount;
-    }
+    // Compute the mesh centroid to use as reference when deciding if the mesh
+    // normals are flipped. Should produce consistent result on convex meshes.
+    cv::Vec3d meshCentroid = compute_mesh_centroid_();
 
-    unsigned int outwardNormalsCount = 0;
-    unsigned int inwardNormalsCount = 0;
+    std::size_t outwardNormalsCount = 0;
+    std::size_t inwardNormalsCount = 0;
 
     for (auto cellIt = input_->GetCells()->Begin();
          cellIt != input_->GetCells()->End(); ++cellIt) {
 
-        // Empty vectors for the vertex and edge info
-        cv::Vec3d v0, v1, v2, e0, e1;
-
         // Collect the point id's for this cell
         std::vector<uint64_t> pointIds;
         ITKPoint vert;
@@ -60,49 +42,34 @@ void CalculateNormals::compute_normals_()
 
         // To-Do: #185
 
-        ITKPoint facePoint;
-        facePoint.Fill(0.0);
+        cv::Vec3d faceCentroid(0.0, 0.0, 0.0);
 
         // Collect the vertex info for each point
         vert = input_->GetPoint(pointIds[0]);
-        v0(0) = vert[0];
-        v0(1) = vert[1];
-        v0(2) = vert[2];
-        facePoint[0] += vert[0];
-        facePoint[1] += vert[1];
-        facePoint[2] += vert[2];
+        cv::Vec3d v0(vert[0], vert[1], vert[2]);
+        faceCentroid += v0;
 
         vert = input_->GetPoint(pointIds[1]);
-        v1(0) = vert[0];
-        v1(1) = vert[1];
-        v1(2) = vert[2];
-        facePoint[0] += vert[0];
-        facePoint[1] += vert[1];
-        facePoint[2] += vert[2];
+        cv::Vec3d v1(vert[0], vert[1], vert[2]);
+        faceCentroid += v1;
 
         vert = input_->GetPoint(pointIds[2]);
-        v2(0) = vert[0];
-        v2(1) = vert[1];
-        v2(2) = vert[2];
-        facePoint[0] += vert[0];
-        facePoint[1] += vert[1];
-        facePoint[2] += vert[2];
+        cv::Vec3d v2(vert[0], vert[1], vert[2]);
+        faceCentroid += v2;
 
-        facePoint[0] /= 3.0;
-        facePoint[1] /= 3.0;
-        facePoint[2] /= 3.0;
+        // Centroid is the average of the three points of the face.
+        faceCentroid /= 3.;
 
         // Get the edge vectors
-        e0 = v2 - v0;
-        e1 = v1 - v0;
+        cv::Vec3d e0 = v2 - v0;
+        cv::Vec3d e1 = v1 - v0;
 
         // Take the cross-product
         cv::Vec3d normals;
         normals = e1.cross(e0);
 
         // Accumulate the relative direction of the normals for this face.
-        cv::Vec3d itkVecToCvVec(facePoint[0] - pointAverage[0], facePoint[1] - pointAverage[1], facePoint[2] - pointAverage[2]);
-        if (normals.dot(itkVecToCvVec) > 0) {
+        if (normals.dot(faceCentroid - meshCentroid) > 0) {
             outwardNormalsCount++;
         } else {
             inwardNormalsCount++;
@@ -114,6 +81,7 @@ void CalculateNormals::compute_normals_()
         vertexNormals_[pointIds[2]] += normals;
     }
 
+    // If more face normals were facing outwards than inwards, they are flipped.
     flippedNormals_ = outwardNormalsCount > inwardNormalsCount;
 }
 
@@ -124,9 +92,21 @@ void CalculateNormals::assign_to_mesh_()
         cv::Vec3d norm = vertexNormals_[point.Index()];
         cv::normalize(norm, norm);
 
-        if (flippedNormals_) {
+        if (shouldOrientNormals && flippedNormals_) {
             norm = -norm;
         }
         output_->SetPointData(point.Index(), norm.val);
     }
 }
+
+cv::Vec3d CalculateNormals::compute_mesh_centroid_() {
+    cv::Vec3d meshCentroid(0.0, 0.0, 0.0);
+    double pointCount = 1.0;
+    for (auto it = input_->GetPoints()->Begin(); it != input_->GetPoints()->End(); ++it) {
+        auto vert = it.Value();
+        cv::Vec3d point(vert[0], vert[1], vert[2]);
+        meshCentroid = meshCentroid + (point - meshCentroid)/pointCount;
+        pointCount += 1.0;
+    }
+    return meshCentroid;
+}

From 9d00574063b8089cb3ae4516c67c3b49e6b72084 Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Wed, 1 Nov 2023 15:10:01 -0400
Subject: [PATCH 04/12] Move normal orientation code to a new class

---
 meshing/CMakeLists.txt                        |  1 +
 .../include/vc/meshing/CalculateNormals.hpp   | 16 ----
 meshing/include/vc/meshing/OrientNormals.hpp  | 32 ++++++++
 meshing/src/CalculateNormals.cpp              | 59 ++++---------
 meshing/src/OrientNormals.cpp                 | 82 +++++++++++++++++++
 5 files changed, 129 insertions(+), 61 deletions(-)
 create mode 100644 meshing/include/vc/meshing/OrientNormals.hpp
 create mode 100644 meshing/src/OrientNormals.cpp

diff --git a/meshing/CMakeLists.txt b/meshing/CMakeLists.txt
index e92c6bbe0..813681bb9 100644
--- a/meshing/CMakeLists.txt
+++ b/meshing/CMakeLists.txt
@@ -9,6 +9,7 @@ set(srcs
     src/SmoothNormals.cpp
     src/OrderedResampling.cpp
     src/OrderedPointSetMesher.cpp
+    src/OrientNormals.cpp
     src/UVMapToITKMesh.cpp
     src/LaplacianSmooth.cpp
 )
diff --git a/meshing/include/vc/meshing/CalculateNormals.hpp b/meshing/include/vc/meshing/CalculateNormals.hpp
index e504aa8d9..644318418 100644
--- a/meshing/include/vc/meshing/CalculateNormals.hpp
+++ b/meshing/include/vc/meshing/CalculateNormals.hpp
@@ -59,15 +59,6 @@ class CalculateNormals
      */
     ITKMesh::Pointer compute();
 
-    /**
-     * @brief Flag specifying if we should reorient normals.
-     * 
-     * If this flag is set and most of the mesh's normals are facing outwards
-     * relative to the mesh's centroid, then they're considered flipped, and
-     * will be reversed to face inwards, the conventionally positive direction.
-     */
-    bool shouldOrientNormals = true;
-
 private:
     /**
      * @brief Compute normals for each vertex.
@@ -85,11 +76,6 @@ class CalculateNormals
      */
     void assign_to_mesh_();
 
-    /**
-     * @brief Compute the mesh's centroid, the arithmetic mean of its vertices.
-     */
-    cv::Vec3d compute_mesh_centroid_();
-
     /** Mesh for which normals will be calculated. */
     ITKMesh::Pointer input_;
 
@@ -98,7 +84,5 @@ class CalculateNormals
 
     /** Storage for summed normals, organized by vertex ID */
     std::vector<cv::Vec3d> vertexNormals_;
-
-    bool flippedNormals_;
 };
 }  // namespace volcart::meshing
diff --git a/meshing/include/vc/meshing/OrientNormals.hpp b/meshing/include/vc/meshing/OrientNormals.hpp
new file mode 100644
index 000000000..6b809d19e
--- /dev/null
+++ b/meshing/include/vc/meshing/OrientNormals.hpp
@@ -0,0 +1,32 @@
+#pragma once
+
+#include "vc/core/types/ITKMesh.hpp"
+
+namespace volcart::meshing
+{
+class OrientNormals
+{
+public:
+    OrientNormals() = default;
+
+    /**
+     * @brief Set the input mesh.
+     * @param mesh The mesh for which normals will be calculated
+     */
+    void setMesh(const ITKMesh::Pointer& mesh);
+
+    /**
+     * @brief Get the output mesh with computed normals
+     */
+    [[nodiscard]] auto getMesh() const -> ITKMesh::Pointer;
+
+    /**
+     * @brief Compute vertex normals for the mesh.
+     */
+    auto compute() -> ITKMesh::Pointer;
+
+private:
+    ITKMesh::Pointer input_;
+    ITKMesh::Pointer output_;
+};
+}  // namespace volcart::meshing
diff --git a/meshing/src/CalculateNormals.cpp b/meshing/src/CalculateNormals.cpp
index f2d6aed58..915bcf2ca 100644
--- a/meshing/src/CalculateNormals.cpp
+++ b/meshing/src/CalculateNormals.cpp
@@ -22,16 +22,12 @@ void CalculateNormals::compute_normals_()
 {
     vertexNormals_ = std::vector<cv::Vec3d>(output_->GetNumberOfPoints(), 0);
 
-    // Compute the mesh centroid to use as reference when deciding if the mesh
-    // normals are flipped. Should produce consistent result on convex meshes.
-    cv::Vec3d meshCentroid = compute_mesh_centroid_();
-
-    std::size_t outwardNormalsCount = 0;
-    std::size_t inwardNormalsCount = 0;
-
     for (auto cellIt = input_->GetCells()->Begin();
          cellIt != input_->GetCells()->End(); ++cellIt) {
 
+        // Empty vectors for the vertex and edge info
+        cv::Vec3d v0, v1, v2, e0, e1;
+
         // Collect the point id's for this cell
         std::vector<uint64_t> pointIds;
         ITKPoint vert;
@@ -42,47 +38,35 @@ void CalculateNormals::compute_normals_()
 
         // To-Do: #185
 
-        cv::Vec3d faceCentroid(0.0, 0.0, 0.0);
-
         // Collect the vertex info for each point
         vert = input_->GetPoint(pointIds[0]);
-        cv::Vec3d v0(vert[0], vert[1], vert[2]);
-        faceCentroid += v0;
+        v0(0) = vert[0];
+        v0(1) = vert[1];
+        v0(2) = vert[2];
 
         vert = input_->GetPoint(pointIds[1]);
-        cv::Vec3d v1(vert[0], vert[1], vert[2]);
-        faceCentroid += v1;
+        v1(0) = vert[0];
+        v1(1) = vert[1];
+        v1(2) = vert[2];
 
         vert = input_->GetPoint(pointIds[2]);
-        cv::Vec3d v2(vert[0], vert[1], vert[2]);
-        faceCentroid += v2;
-
-        // Centroid is the average of the three points of the face.
-        faceCentroid /= 3.;
+        v2(0) = vert[0];
+        v2(1) = vert[1];
+        v2(2) = vert[2];
 
         // Get the edge vectors
-        cv::Vec3d e0 = v2 - v0;
-        cv::Vec3d e1 = v1 - v0;
+        e0 = v2 - v0;
+        e1 = v1 - v0;
 
         // Take the cross-product
         cv::Vec3d normals;
         normals = e1.cross(e0);
 
-        // Accumulate the relative direction of the normals for this face.
-        if (normals.dot(faceCentroid - meshCentroid) > 0) {
-            outwardNormalsCount++;
-        } else {
-            inwardNormalsCount++;
-        }
-
         // Add the norm for this face to the running sum for each vertex
         vertexNormals_[pointIds[0]] += normals;
         vertexNormals_[pointIds[1]] += normals;
         vertexNormals_[pointIds[2]] += normals;
     }
-
-    // If more face normals were facing outwards than inwards, they are flipped.
-    flippedNormals_ = outwardNormalsCount > inwardNormalsCount;
 }
 
 void CalculateNormals::assign_to_mesh_()
@@ -92,21 +76,6 @@ void CalculateNormals::assign_to_mesh_()
         cv::Vec3d norm = vertexNormals_[point.Index()];
         cv::normalize(norm, norm);
 
-        if (shouldOrientNormals && flippedNormals_) {
-            norm = -norm;
-        }
         output_->SetPointData(point.Index(), norm.val);
     }
 }
-
-cv::Vec3d CalculateNormals::compute_mesh_centroid_() {
-    cv::Vec3d meshCentroid(0.0, 0.0, 0.0);
-    double pointCount = 1.0;
-    for (auto it = input_->GetPoints()->Begin(); it != input_->GetPoints()->End(); ++it) {
-        auto vert = it.Value();
-        cv::Vec3d point(vert[0], vert[1], vert[2]);
-        meshCentroid = meshCentroid + (point - meshCentroid)/pointCount;
-        pointCount += 1.0;
-    }
-    return meshCentroid;
-}
diff --git a/meshing/src/OrientNormals.cpp b/meshing/src/OrientNormals.cpp
new file mode 100644
index 000000000..b9edb34fe
--- /dev/null
+++ b/meshing/src/OrientNormals.cpp
@@ -0,0 +1,82 @@
+#include "vc/meshing/OrientNormals.hpp"
+
+#include <opencv2/core.hpp>
+
+#include "vc/meshing/DeepCopy.hpp"
+
+using namespace volcart;
+using namespace volcart::meshing;
+
+namespace
+{
+auto ComputeMeshCentroid(const ITKMesh::Pointer& mesh) -> cv::Vec3d
+{
+    cv::Vec3d centroid{0, 0, 0};
+    double cnt = 1.;
+    for (auto it = mesh->GetPoints()->Begin(); it != mesh->GetPoints()->End();
+         ++it) {
+        auto vert = it.Value();
+        const cv::Vec3d point{vert[0], vert[1], vert[2]};
+        centroid = centroid + (point - centroid) / cnt;
+        cnt += 1.;
+    }
+    return centroid;
+}
+}  // namespace
+
+void OrientNormals::setMesh(const ITKMesh::Pointer& mesh) { input_ = mesh; }
+
+auto OrientNormals::getMesh() const -> ITKMesh::Pointer { return output_; }
+
+auto OrientNormals::compute() -> ITKMesh::Pointer
+{
+    // Compute the mesh refPt
+    auto refPt = ::ComputeMeshCentroid(input_);
+
+    // Get a count of the vectors which points towards and away from the
+    // reference point
+    std::size_t coDir{0};
+    std::size_t antiDir{0};
+
+    for (auto it = input_->GetPoints()->Begin();
+         it != input_->GetPoints()->End(); ++it) {
+        // Temp variables
+        ITKPoint vert;
+        ITKPixel normal;
+
+        // Convert point data to cv::Vec3d
+        vert = it->Value();
+        input_->GetPointData(it.Index(), &normal);
+        cv::Vec3d pt{vert[0], vert[1], vert[2]};
+        cv::Vec3d n{normal[0], normal[1], normal[2]};
+        n = cv::normalize(n);
+
+        // Accumulate the relative direction of the normals for this face.
+        if (n.dot(cv::normalize(refPt - pt)) > 0) {
+            coDir++;
+        } else {
+            antiDir++;
+        }
+    }
+
+    // If more face normals were facing outwards than inwards, they are flipped.
+    auto flip = antiDir > coDir;
+
+    // Setup output mesh
+    output_ = ITKMesh::New();
+    DeepCopy(input_, output_);
+
+    // Flip the normals as required
+    if (flip) {
+        for (auto it = input_->GetPoints()->Begin();
+             it != input_->GetPoints()->End(); ++it) {
+            // Convert point data to cv::Vec3d
+            ITKPixel normal;
+            input_->GetPointData(it.Index(), &normal);
+            normal *= -1;
+            input_->SetPointData(it.Index(), normal);
+        }
+    }
+
+    return output_;
+}

From 457dc3d5588a3631db1345ccbd303580878ed436 Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 10:25:03 -0400
Subject: [PATCH 05/12] Fill out the interface to support manual reference
 point

---
 meshing/include/vc/meshing/OrientNormals.hpp | 46 +++++++++++++++++---
 meshing/src/OrientNormals.cpp                | 24 ++++++++--
 2 files changed, 59 insertions(+), 11 deletions(-)

diff --git a/meshing/include/vc/meshing/OrientNormals.hpp b/meshing/include/vc/meshing/OrientNormals.hpp
index 6b809d19e..bf32902f7 100644
--- a/meshing/include/vc/meshing/OrientNormals.hpp
+++ b/meshing/include/vc/meshing/OrientNormals.hpp
@@ -1,32 +1,64 @@
 #pragma once
 
+/** @file */
+
+#include <opencv2/core.hpp>
+
 #include "vc/core/types/ITKMesh.hpp"
 
 namespace volcart::meshing
 {
+
+/**
+ * @class OrientNormals
+ *
+ * @brief Orient vertex normals towards a reference point.
+ */
 class OrientNormals
 {
 public:
+    /** @brief Reference point mode */
+    enum class ReferenceMode {
+        Centroid, /** Mesh centroid reference point for convex meshes. */
+        Manual    /** Point provided by setReferencePoint(). */
+    };
+
+    /** @brief Default constructor */
     OrientNormals() = default;
 
-    /**
-     * @brief Set the input mesh.
-     * @param mesh The mesh for which normals will be calculated
-     */
+    /** @brief Set the input mesh */
     void setMesh(const ITKMesh::Pointer& mesh);
 
+    /** @brief Get the output mesh with updated normals */
+    [[nodiscard]] auto getMesh() const -> ITKMesh::Pointer;
+
     /**
-     * @brief Get the output mesh with computed normals
+     * @brief Set reference point mode
+     *
+     * Determines which automatically calculated reference point to use. See
+     * ReferenceMode for more details.
      */
-    [[nodiscard]] auto getMesh() const -> ITKMesh::Pointer;
+    void setReferenceMode(ReferenceMode mode);
 
     /**
-     * @brief Compute vertex normals for the mesh.
+     * @brief Set manual reference point
+     *
+     * If provided, automatically sets the reference mode to
+     * ReferenceMode::Manual.
      */
+    void setReferencePoint(const cv::Vec3d& point);
+
+    /** @brief Compute vertex normal reorientation */
     auto compute() -> ITKMesh::Pointer;
 
 private:
+    /** Input mesh */
     ITKMesh::Pointer input_;
+    /** Reference point mode */
+    ReferenceMode mode_{ReferenceMode::Centroid};
+    /** User-defined reference point */
+    cv::Vec3d refPt_;
+    /** Output mesh */
     ITKMesh::Pointer output_;
 };
 }  // namespace volcart::meshing
diff --git a/meshing/src/OrientNormals.cpp b/meshing/src/OrientNormals.cpp
index b9edb34fe..810b48c8e 100644
--- a/meshing/src/OrientNormals.cpp
+++ b/meshing/src/OrientNormals.cpp
@@ -1,7 +1,5 @@
 #include "vc/meshing/OrientNormals.hpp"
 
-#include <opencv2/core.hpp>
-
 #include "vc/meshing/DeepCopy.hpp"
 
 using namespace volcart;
@@ -28,10 +26,28 @@ void OrientNormals::setMesh(const ITKMesh::Pointer& mesh) { input_ = mesh; }
 
 auto OrientNormals::getMesh() const -> ITKMesh::Pointer { return output_; }
 
+void OrientNormals::setReferenceMode(OrientNormals::ReferenceMode mode)
+{
+    mode_ = mode;
+}
+
+void OrientNormals::setReferencePoint(const cv::Vec3d& point)
+{
+    mode_ = ReferenceMode::Manual;
+    refPt_ = point;
+}
+
 auto OrientNormals::compute() -> ITKMesh::Pointer
 {
-    // Compute the mesh refPt
-    auto refPt = ::ComputeMeshCentroid(input_);
+    // Get the reference point based on the reference mode
+    cv::Vec3d refPt;
+    if (mode_ == ReferenceMode::Centroid) {
+        refPt = ::ComputeMeshCentroid(input_);
+    } else if (mode_ == ReferenceMode::Manual) {
+        refPt = refPt_;
+    } else {
+        refPt = ::ComputeMeshCentroid(input_);
+    }
 
     // Get a count of the vectors which points towards and away from the
     // reference point

From 6e9f78a81862ad88c0e665456a3919b114cb008d Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 11:28:13 -0400
Subject: [PATCH 06/12] (graph) Add OrientNormalsNode

---
 core/CMakeLists.txt                          |  1 +
 core/include/vc/core/types/Metadata.hpp      | 24 +-------
 core/include/vc/core/util/Json.hpp           | 46 ++++++++++++++
 graph/include/vc/graph.hpp                   |  4 +-
 graph/include/vc/graph/meshing.hpp           | 43 +++++++++++++
 graph/src/graph.cpp                          |  3 +-
 graph/src/meshing.cpp                        | 65 +++++++++++++++++---
 meshing/include/vc/meshing/OrientNormals.hpp |  6 ++
 meshing/src/OrientNormals.cpp                |  7 +++
 9 files changed, 167 insertions(+), 32 deletions(-)
 create mode 100644 core/include/vc/core/util/Json.hpp

diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
index 1f211f9e5..5f49a83ae 100644
--- a/core/CMakeLists.txt
+++ b/core/CMakeLists.txt
@@ -61,6 +61,7 @@ set(util_srcs
 
 set(logging_srcs
     src/Logging.cpp
+        include/vc/core/util/Json.hpp
 )
 
 configure_file(src/Version.cpp.in Version.cpp)
diff --git a/core/include/vc/core/types/Metadata.hpp b/core/include/vc/core/types/Metadata.hpp
index 395bce9ce..51bce2ae0 100644
--- a/core/include/vc/core/types/Metadata.hpp
+++ b/core/include/vc/core/types/Metadata.hpp
@@ -9,6 +9,7 @@
 #include <opencv2/core.hpp>
 
 #include "vc/core/filesystem.hpp"
+#include "vc/core/util/Json.hpp"
 
 namespace volcart
 {
@@ -104,26 +105,3 @@ class Metadata
     volcart::filesystem::path path_;
 };
 }  // namespace volcart
-
-/** JSON Serializer for cv::Vec */
-namespace nlohmann
-{
-template <typename T, int Cn>
-struct adl_serializer<cv::Vec<T, Cn>> {
-    // NOLINTNEXTLINE(readability-identifier-naming): Must be exact signature
-    static void to_json(nlohmann::json& j, const cv::Vec<T, Cn>& v)
-    {
-        for (int i = 0; i < Cn; i++) {
-            j.push_back(v[i]);
-        }
-    }
-
-    // NOLINTNEXTLINE(readability-identifier-naming): Must be exact signature
-    static void from_json(const nlohmann::json& j, cv::Vec<T, Cn>& v)
-    {
-        for (int i = 0; i < Cn; i++) {
-            v[i] = j.at(i).get<T>();
-        }
-    }
-};
-}  // namespace nlohmann
diff --git a/core/include/vc/core/util/Json.hpp b/core/include/vc/core/util/Json.hpp
new file mode 100644
index 000000000..6094a82a3
--- /dev/null
+++ b/core/include/vc/core/util/Json.hpp
@@ -0,0 +1,46 @@
+#pragma once
+
+/**
+ * @file Json.hpp
+ * JSON serialization/deserialization type specializations.
+ */
+
+#include <nlohmann/json.hpp>
+
+/** cv::Vec */
+NLOHMANN_JSON_NAMESPACE_BEGIN
+template <typename T, int Cn>
+struct adl_serializer<cv::Vec<T, Cn>> {
+    // NOLINTNEXTLINE(readability-identifier-naming): Must be exact signature
+    static void to_json(json& j, const cv::Vec<T, Cn>& v)
+    {
+        for (int i = 0; i < Cn; i++) {
+            j.push_back(v[i]);
+        }
+    }
+
+    // NOLINTNEXTLINE(readability-identifier-naming): Must be exact signature
+    static void from_json(const json& j, cv::Vec<T, Cn>& v)
+    {
+        for (int i = 0; i < Cn; i++) {
+            v[i] = j.at(i).get<T>();
+        }
+    }
+
+    // NOLINTNEXTLINE(readability-identifier-naming): Must be exact signature
+    static void to_json(ordered_json& j, const cv::Vec<T, Cn>& v)
+    {
+        for (int i = 0; i < Cn; i++) {
+            j.push_back(v[i]);
+        }
+    }
+
+    // NOLINTNEXTLINE(readability-identifier-naming): Must be exact signature
+    static void from_json(const ordered_json& j, cv::Vec<T, Cn>& v)
+    {
+        for (int i = 0; i < Cn; i++) {
+            v[i] = j.at(i).get<T>();
+        }
+    }
+};
+NLOHMANN_JSON_NAMESPACE_END
\ No newline at end of file
diff --git a/graph/include/vc/graph.hpp b/graph/include/vc/graph.hpp
index eba8fccd4..aac799b18 100644
--- a/graph/include/vc/graph.hpp
+++ b/graph/include/vc/graph.hpp
@@ -2,6 +2,8 @@
 
 /** @file */
 
+#include <opencv2/core.hpp>
+
 #include "vc/graph/core.hpp"
 #include "vc/graph/meshing.hpp"
 #include "vc/graph/texturing.hpp"
@@ -12,4 +14,4 @@ namespace volcart
 /** @brief Register all VC provided nodes with the Smeagol library */
 void RegisterNodes();
 
-}  // namespace volcart
+}  // namespace volcart
\ No newline at end of file
diff --git a/graph/include/vc/graph/meshing.hpp b/graph/include/vc/graph/meshing.hpp
index f4c4f18ca..9fe009a45 100644
--- a/graph/include/vc/graph/meshing.hpp
+++ b/graph/include/vc/graph/meshing.hpp
@@ -11,6 +11,7 @@
 #include "vc/meshing/ACVD.hpp"
 #include "vc/meshing/LaplacianSmooth.hpp"
 #include "vc/meshing/OrderedPointSetMesher.hpp"
+#include "vc/meshing/OrientNormals.hpp"
 #include "vc/meshing/UVMapToITKMesh.hpp"
 
 namespace volcart
@@ -261,4 +262,46 @@ class UVMapToMeshNode : public smgl::Node
         const smgl::Metadata& meta, const filesystem::path& cacheDir) override;
 };
 
+/**
+ * @copybrief meshing::OrientNormals
+ *
+ * @see meshing::OrientNormals
+ * @ingroup Graph
+ */
+class OrientNormalsNode : public smgl::Node
+{
+private:
+    /** Orient Normals class type */
+    using OrientNormals = meshing::OrientNormals;
+    /** Orient normals compute */
+    OrientNormals orientNormals_{};
+    /** Output mesh */
+    ITKMesh::Pointer output_{nullptr};
+
+public:
+    /** @copydoc OrientNormals::ReferenceMode */
+    using ReferenceMode = OrientNormals::ReferenceMode;
+
+    /** @brief Input mesh */
+    smgl::InputPort<ITKMesh::Pointer> input;
+    /** @copydoc OrientNormals::setReferenceMode(ReferenceMode) */
+    smgl::InputPort<ReferenceMode> referenceMode;
+    /** @copydoc OrientNormals::setReferencePoint() */
+    smgl::InputPort<cv::Vec3d> referencePoint;
+    /** @brief Output mesh */
+    smgl::OutputPort<ITKMesh::Pointer> output;
+
+    /** Constructor */
+    OrientNormalsNode();
+
+private:
+    /** Smeagol custom serialization */
+    auto serialize_(bool useCache, const filesystem::path& cacheDir)
+        -> smgl::Metadata override;
+
+    /** Smeagol custom deserialization */
+    void deserialize_(
+        const smgl::Metadata& meta, const filesystem::path& cacheDir) override;
+};
+
 }  // namespace volcart
\ No newline at end of file
diff --git a/graph/src/graph.cpp b/graph/src/graph.cpp
index df55e0aaf..ac7e55a2e 100644
--- a/graph/src/graph.cpp
+++ b/graph/src/graph.cpp
@@ -38,7 +38,8 @@ static auto RegisterNodesImpl() -> bool
         CalculateNumVertsNode,
         LaplacianSmoothMeshNode,
         ResampleMeshNode,
-        UVMapToMeshNode
+        UVMapToMeshNode,
+        OrientNormalsNode
     >();
 
     // Texturing
diff --git a/graph/src/meshing.cpp b/graph/src/meshing.cpp
index 21a8a1d63..063b59a6d 100644
--- a/graph/src/meshing.cpp
+++ b/graph/src/meshing.cpp
@@ -3,6 +3,7 @@
 #include <nlohmann/json.hpp>
 
 #include "vc/core/io/MeshIO.hpp"
+#include "vc/core/util/Json.hpp"
 #include "vc/meshing/ScaleMesh.hpp"
 
 using namespace volcart;
@@ -16,7 +17,13 @@ namespace volcart::meshing
 using ResampleMode = ResampleMeshNode::Mode;
 NLOHMANN_JSON_SERIALIZE_ENUM(ResampleMode, {
     {ResampleMode::Isotropic, "isotropic"},
-    {ResampleMode::Anisotropic, "Anisotropic"}
+    {ResampleMode::Anisotropic, "anisotropic"}
+})
+
+using ReferenceMode = OrientNormalsNode::ReferenceMode;
+NLOHMANN_JSON_SERIALIZE_ENUM(ReferenceMode , {
+    {ReferenceMode::Centroid, "centroid"},
+    {ReferenceMode::Manual, "manual"}
 })
 // clang-format on
 }  // namespace volcart::meshing
@@ -26,7 +33,7 @@ MeshingNode::MeshingNode()
 {
     registerInputPort("points", points);
     registerOutputPort("mesh", mesh);
-    compute = [=]() { mesh_ = mesher_.compute(); };
+    compute = [this]() { mesh_ = mesher_.compute(); };
 }
 
 auto MeshingNode::serialize_(bool useCache, const fs::path& cacheDir)
@@ -56,7 +63,7 @@ ScaleMeshNode::ScaleMeshNode()
     registerInputPort("scaleFactor", scaleFactor);
     registerOutputPort("output", output);
 
-    compute = [=]() {
+    compute = [this]() {
         if (input_) {
             output_ = ScaleMesh(input_, scaleFactor_);
         }
@@ -95,7 +102,7 @@ CalculateNumVertsNode::CalculateNumVertsNode()
     registerInputPort("density", density);
     registerOutputPort("numVerts", numVerts);
 
-    compute = [=]() {
+    compute = [this]() {
         using meshmath::SurfaceArea;
         static constexpr double UM_TO_MM{0.000001};
         static constexpr std::size_t MIN_NUM{100};
@@ -127,7 +134,7 @@ LaplacianSmoothMeshNode::LaplacianSmoothMeshNode()
 {
     registerInputPort("input", input);
     registerOutputPort("output", output);
-    compute = [=]() { mesh_ = smoother_.compute(); };
+    compute = [this]() { mesh_ = smoother_.compute(); };
 }
 
 auto LaplacianSmoothMeshNode::serialize_(
@@ -180,7 +187,7 @@ ResampleMeshNode::ResampleMeshNode()
     registerInputPort("subsampleThreshold", subsampleThreshold);
     registerInputPort("quadricsOptimizationLevel", quadricsOptimizationLevel);
     registerOutputPort("output", output);
-    compute = [=]() { mesh_ = acvd_.compute(); };
+    compute = [this]() { mesh_ = acvd_.compute(); };
 }
 
 auto ResampleMeshNode::serialize_(bool useCache, const fs::path& cacheDir)
@@ -227,7 +234,7 @@ UVMapToMeshNode::UVMapToMeshNode()
     registerInputPort("scaleToUVDimensions", scaleToUVDimensions);
     registerOutputPort("outputMesh", outputMesh);
 
-    compute = [=]() {
+    compute = [this]() {
         mesher_.setScaleToUVDimensions(scaleDims_);
         output_ = mesher_.compute();
     };
@@ -253,3 +260,47 @@ void UVMapToMeshNode::deserialize_(
         output_ = ReadMesh(cacheDir / file).mesh;
     }
 }
+
+OrientNormalsNode::OrientNormalsNode()
+    : Node{true}
+    , input{&orientNormals_, &OrientNormals::setMesh}
+    , referenceMode{&orientNormals_, &OrientNormals::setReferenceMode}
+    , referencePoint{&orientNormals_, &OrientNormals::setReferencePoint}
+    , output{&output_}
+{
+    registerInputPort("input", input);
+    registerInputPort("referenceMode", referenceMode);
+    registerInputPort("referencePoint", referencePoint);
+    registerOutputPort("output", output);
+    compute = [this]() { output_ = orientNormals_.compute(); };
+}
+
+auto OrientNormalsNode::serialize_(bool useCache, const fs::path& cacheDir)
+    -> smgl::Metadata
+{
+    smgl::Metadata meta{{"referenceMode", orientNormals_.referenceMode()}};
+    if (orientNormals_.referenceMode() == ReferenceMode::Manual) {
+        meta["referencePoint"] = orientNormals_.referencePoint();
+    }
+    if (useCache and output_) {
+        WriteMesh(cacheDir / "orient_normals.obj", output_);
+        meta["mesh"] = "orient_normals.obj";
+    }
+    return meta;
+}
+
+void OrientNormalsNode::deserialize_(
+    const smgl::Metadata& meta, const fs::path& cacheDir)
+{
+    auto refMode = meta["referenceMode"].get<ReferenceMode>();
+    orientNormals_.setReferenceMode(refMode);
+    if (refMode == ReferenceMode::Manual) {
+        orientNormals_.setReferencePoint(
+            meta["referencePoint"].get<cv::Vec3d>());
+    }
+
+    if (meta.contains("mesh")) {
+        auto meshFile = meta["mesh"].get<std::string>();
+        output_ = ReadMesh(cacheDir / meshFile).mesh;
+    }
+}
\ No newline at end of file
diff --git a/meshing/include/vc/meshing/OrientNormals.hpp b/meshing/include/vc/meshing/OrientNormals.hpp
index bf32902f7..add06200b 100644
--- a/meshing/include/vc/meshing/OrientNormals.hpp
+++ b/meshing/include/vc/meshing/OrientNormals.hpp
@@ -40,6 +40,9 @@ class OrientNormals
      */
     void setReferenceMode(ReferenceMode mode);
 
+    /** @brief Get the current reference mode */
+    [[nodiscard]] auto referenceMode() const -> ReferenceMode;
+
     /**
      * @brief Set manual reference point
      *
@@ -48,6 +51,9 @@ class OrientNormals
      */
     void setReferencePoint(const cv::Vec3d& point);
 
+    /** @brief Get the manually defined reference point */
+    [[nodiscard]] auto referencePoint() const -> cv::Vec3d;
+
     /** @brief Compute vertex normal reorientation */
     auto compute() -> ITKMesh::Pointer;
 
diff --git a/meshing/src/OrientNormals.cpp b/meshing/src/OrientNormals.cpp
index 810b48c8e..2da44a1fc 100644
--- a/meshing/src/OrientNormals.cpp
+++ b/meshing/src/OrientNormals.cpp
@@ -31,12 +31,19 @@ void OrientNormals::setReferenceMode(OrientNormals::ReferenceMode mode)
     mode_ = mode;
 }
 
+auto OrientNormals::referenceMode() const -> OrientNormals::ReferenceMode
+{
+    return mode_;
+}
+
 void OrientNormals::setReferencePoint(const cv::Vec3d& point)
 {
     mode_ = ReferenceMode::Manual;
     refPt_ = point;
 }
 
+auto OrientNormals::referencePoint() const -> cv::Vec3d { return refPt_; }
+
 auto OrientNormals::compute() -> ITKMesh::Pointer
 {
     // Get the reference point based on the reference mode

From a70e3b71d7dabacc7cb3522ec8a824a0f18fee95 Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 11:51:04 -0400
Subject: [PATCH 07/12] (apps) Add orient-normals option

---
 apps/src/GeneratePPM.cpp   |  20 ++++-
 apps/src/Mesher.cpp        |  19 ++++-
 apps/src/Render.cpp        |  13 ++-
 apps/src/RenderMeshing.cpp | 171 -------------------------------------
 4 files changed, 42 insertions(+), 181 deletions(-)
 delete mode 100644 apps/src/RenderMeshing.cpp

diff --git a/apps/src/GeneratePPM.cpp b/apps/src/GeneratePPM.cpp
index b79726104..393ff4059 100644
--- a/apps/src/GeneratePPM.cpp
+++ b/apps/src/GeneratePPM.cpp
@@ -7,12 +7,15 @@
 #include "vc/core/util/Logging.hpp"
 #include "vc/texturing/AngleBasedFlattening.hpp"
 #include "vc/texturing/PPMGenerator.hpp"
+#include "vc/meshing/OrientNormals.hpp"
 
 namespace vc = volcart;
+namespace vcm = volcart::meshing;
+namespace vct = volcart::texturing;
 namespace fs = volcart::filesystem;
 namespace po = boost::program_options;
 
-int main(int argc, char* argv[])
+auto main(int argc, char* argv[]) -> int
 {
     // clang-format off
     po::options_description all("Usage");
@@ -23,7 +26,8 @@ int main(int argc, char* argv[])
         ("output-ppm,o", po::value<std::string>()->required(),
             "Path for the output ppm")
         ("uv-reuse", "If input-mesh is specified, attempt to use its existing "
-            "UV map instead of generating a new one.");
+            "UV map instead of generating a new one.")
+        ("orient-normals", "Auto-orient surface normals towards the mesh centroid");
     // clang-format on
 
     // parsed will hold the values of all parsed options as a Map
@@ -54,11 +58,19 @@ int main(int argc, char* argv[])
     auto mesh = meshFile.mesh;
     auto uvMap = meshFile.uv;
 
+    // Reorient the surface normals
+    if (parsed.count("orient-normals") > 0) {
+        vcm::OrientNormals orient;
+        orient.setReferenceMode(vcm::OrientNormals::ReferenceMode::Centroid);
+        orient.setMesh(mesh);
+        mesh = orient.compute();
+    }
+
     // Generate UV map
     auto genUV = parsed.count("uv-reuse") == 0;
     if (genUV or not uvMap) {
         // ABF
-        vc::texturing::AngleBasedFlattening abf;
+        vct::AngleBasedFlattening abf;
         abf.setMesh(mesh);
         abf.compute();
 
@@ -71,7 +83,7 @@ int main(int argc, char* argv[])
 
     // PPM
     vc::Logger()->info("Generating per-pixel map");
-    vc::texturing::PPMGenerator p;
+    vct::PPMGenerator p;
     p.setDimensions(height, width);
     p.setMesh(mesh);
     p.setUVMap(uvMap);
diff --git a/apps/src/Mesher.cpp b/apps/src/Mesher.cpp
index 803c5a8ae..06fa88178 100644
--- a/apps/src/Mesher.cpp
+++ b/apps/src/Mesher.cpp
@@ -6,20 +6,21 @@
 #include "vc/core/filesystem.hpp"
 #include "vc/core/io/MeshIO.hpp"
 #include "vc/core/io/PointSetIO.hpp"
-#include "vc/core/types/OrderedPointSet.hpp"
 #include "vc/core/util/Logging.hpp"
 #include "vc/meshing/OrderedPointSetMesher.hpp"
+#include "vc/meshing/OrientNormals.hpp"
 
 namespace fs = volcart::filesystem;
 namespace po = boost::program_options;
 namespace vc = volcart;
+namespace vcm = volcart::meshing;
 
 using psio = vc::PointSetIO<cv::Vec3d>;
 
 auto main(int argc, char* argv[]) -> int
 {
     ///// Parse the command line options /////
-    // All command line options
+    // clang-format off
     po::options_description all("Usage");
     all.add_options()
         ("help,h", "Show this message")
@@ -29,7 +30,9 @@ auto main(int argc, char* argv[]) -> int
             "Path for the output mesh")
         ("mode,m", po::value<int>()->default_value(1),
             "Reading mode: 0 = ASCII, 1 = Binary")
-        ("disable-triangulation", "Disable vertex triangulation");
+        ("disable-triangulation", "Disable vertex triangulation")
+        ("orient-normals", "Auto-orient surface normals towards the mesh centroid");
+    // clang-format on
 
     // parsed will hold the values of all parsed options as a Map
     po::variables_map parsed;
@@ -59,10 +62,18 @@ auto main(int argc, char* argv[]) -> int
 
     // Convert to a mesh
     vc::Logger()->info("Generating mesh...");
-    vc::meshing::OrderedPointSetMesher mesher(inputCloud);
+    vcm::OrderedPointSetMesher mesher(inputCloud);
     mesher.setComputeTriangulation(parsed.count("disable-triangulation") == 0);
     auto output = mesher.compute();
 
+    // Reorient the surface normals
+    if (parsed.count("orient-normals") > 0) {
+        vcm::OrientNormals orient;
+        orient.setReferenceMode(vcm::OrientNormals::ReferenceMode::Centroid);
+        orient.setMesh(output);
+        output = orient.compute();
+    }
+
     // Write the mesh
     vc::Logger()->info("Writing mesh...");
     vc::WriteMesh(outputPath, output);
diff --git a/apps/src/Render.cpp b/apps/src/Render.cpp
index 363fc3ba9..0be602a07 100644
--- a/apps/src/Render.cpp
+++ b/apps/src/Render.cpp
@@ -103,7 +103,8 @@ static auto GetMeshingOpts() -> po::options_description
             "  3 = Both before and after mesh resampling")
         ("intermediate-mesh", po::value<std::string>(),"Output file path for the "
             "intermediate (i.e. scale + resampled) mesh. File is saved prior "
-            "to flattening. Useful for testing meshing parameters.");
+            "to flattening. Useful for testing meshing parameters.")
+        ("orient-normals", "Auto-orient surface normals towards the mesh centroid");
     // clang-format on
 
     return opts;
@@ -331,7 +332,7 @@ auto main(int argc, char* argv[]) -> int
     };
     // clang-format on
     graph->setProjectMetadata(projectInfo);
-    // Setup a map to keep a reference to important output ports
+    // Set up a map to keep a reference to important output ports
     std::unordered_map<std::string, smgl::Output*> results;
 
     //// Load the segmentation/mesh ////
@@ -489,6 +490,14 @@ auto main(int argc, char* argv[]) -> int
         }
     }
 
+    ///// Reorient the mesh normals /////
+    if (parsed.count("orient-normals") > 0) {
+        auto orient = graph->insertNode<OrientNormalsNode>();
+        orient->input = *results["mesh"];
+        orient->referenceMode = OrientNormalsNode::ReferenceMode::Centroid;
+        results["mesh"] = &orient->output;
+    }
+
     ///// Flattening /////
     if (needResample and results.count("uvMap") > 0) {
         Logger()->warn(
diff --git a/apps/src/RenderMeshing.cpp b/apps/src/RenderMeshing.cpp
deleted file mode 100644
index 269b7d7bc..000000000
--- a/apps/src/RenderMeshing.cpp
+++ /dev/null
@@ -1,171 +0,0 @@
-#include "vc/apps/render/RenderMeshing.hpp"
-
-#include <vtkCleanPolyData.h>
-#include <vtkSmoothPolyDataFilter.h>
-
-#include "vc/core/filesystem.hpp"
-#include "vc/core/io/FileExtensionFilter.hpp"
-#include "vc/core/io/OBJWriter.hpp"
-#include "vc/core/io/PLYWriter.hpp"
-#include "vc/core/types/Volume.hpp"
-#include "vc/core/util/Logging.hpp"
-#include "vc/core/util/MeshMath.hpp"
-#include "vc/meshing/ACVD.hpp"
-#include "vc/meshing/CalculateNormals.hpp"
-#include "vc/meshing/ITK2VTK.hpp"
-
-namespace fs = volcart::filesystem;
-namespace po = boost::program_options;
-namespace vc = volcart;
-namespace vcm = volcart::meshing;
-
-extern po::variables_map parsed_;
-extern vc::Volume::Pointer volume_;
-
-// Square Micron to square millimeter conversion factor
-static constexpr double UM_TO_MM = 0.000001;
-// Min. number of points required to do flattening
-static constexpr size_t CLEANER_MIN_REQ_POINTS = 100;
-// Default resampling factor
-static constexpr size_t DEFAULT_RESAMPLE_FACTOR = 50;
-
-po::options_description GetMeshingOpts()
-{
-    // clang-format off
-    po::options_description opts("Meshing Options");
-    opts.add_options()
-        ("scale-mesh", po::value<double>(), "Scale the mesh by a linear scale "
-            "factor")
-        ("enable-mesh-resampling", "Enable ACVD mesh resampling. Automatically "
-            "enabled if the input is a Segmentation")
-        ("mesh-resample-factor", po::value<double>()->default_value(DEFAULT_RESAMPLE_FACTOR),
-         "Roughly, the number of vertices per square millimeter in the "
-            "output mesh")
-        ("mesh-resample-vcount", po::value<size_t>(), "The target number of vertices "
-            "in the resampled mesh. If specified, overrides both the mesh-resample-factor "
-            "and mesh-resample-keep-vcount options.")
-        ("mesh-resample-keep-vcount", "If enabled, mesh resampling will "
-            "attempt to maintain the number of vertices in the input mesh. "
-            "Overrides the value set by --mesh-resample-factor.")
-        ("mesh-resample-anisotropic", "Enable the anisotropic extension "
-            "of the mesh resampler.")
-        ("mesh-resample-gradation", po::value<double>()->default_value(0),
-            "Set the resampling gradation constraint.")
-        ("mesh-resample-quadrics-level", po::value<size_t>()->default_value(1),
-            "Set the mesh resampling quadrics optimization level.")
-        ("mesh-resample-smoothing", po::value<int>()->default_value(0),
-            "Smoothing Options:\n"
-         "  0 = Off\n"
-         "  1 = Before mesh resampling\n"
-         "  2 = After mesh resampling\n"
-         "  3 = Both before and after mesh resampling")
-        ("intermediate-mesh", po::value<std::string>(),"Output file path for the "
-            "intermediate (i.e. scale + resampled) mesh. File is saved prior "
-            "to flattening. Useful for testing meshing parameters.");
-    // clang-format on
-
-    return opts;
-}
-
-vc::ITKMesh::Pointer ResampleMesh(const vc::ITKMesh::Pointer& m)
-{
-    auto smooth =
-        static_cast<SmoothOpt>(parsed_["mesh-resample-smoothing"].as<int>());
-
-    ///// Resample the segmentation /////
-    // Calculate sampling density
-    size_t vertCount{0};
-    auto voxelToMicron = volume_->voxelSize() * volume_->voxelSize();
-    auto area = vc::meshmath::SurfaceArea(m) * voxelToMicron * UM_TO_MM;
-    auto currentDensityFactor = m->GetNumberOfPoints() / area;
-    double newDensityFactor{50};
-    if (parsed_.count("mesh-resample-vcount")) {
-        vertCount = parsed_["mesh-resample-vcount"].as<size_t>();
-        newDensityFactor = vertCount / area;
-    } else if (parsed_.count("mesh-resample-keep-vcount")) {
-        newDensityFactor = currentDensityFactor;
-        vertCount = static_cast<size_t>(m->GetNumberOfPoints());
-    } else {
-        newDensityFactor = parsed_["mesh-resample-factor"].as<double>();
-        vertCount = static_cast<size_t>(newDensityFactor * area);
-    }
-
-    vertCount = (vertCount < CLEANER_MIN_REQ_POINTS) ? CLEANER_MIN_REQ_POINTS
-                                                     : vertCount;
-    // Copy the pointer to the input mesh
-    auto workingMesh = m;
-
-    // Pre-Smooth
-    if (smooth == SmoothOpt::Both || smooth == SmoothOpt::Before) {
-        // Convert to polydata
-        auto vtkMesh = vtkSmartPointer<vtkPolyData>::New();
-        vcm::ITK2VTK(workingMesh, vtkMesh);
-        // Smoother
-        vc::Logger()->info("Smoothing mesh");
-        auto vtkSmoother = vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
-        vtkSmoother->SetInputData(vtkMesh);
-        vtkSmoother->Update();
-        vtkMesh = vtkSmoother->GetOutput();
-        // Convert back to ITK
-        workingMesh = vc::ITKMesh::New();
-        vcm::VTK2ITK(vtkMesh, workingMesh);
-    }
-
-    // Decimate using ACVD
-    vc::Logger()->info(
-        "Resampling mesh (Density: {:.3g} -> {:.3g})", currentDensityFactor,
-        newDensityFactor);
-
-    vcm::ACVD resampler;
-    resampler.setInputMesh(workingMesh);
-    resampler.setNumberOfClusters(vertCount);
-    resampler.setGradation(parsed_["mesh-resample-gradation"].as<double>());
-    resampler.setQuadricsOptimizationLevel(
-        parsed_["mesh-resample-quadrics-level"].as<size_t>());
-    if (parsed_.count("mesh-resample-anisotropic")) {
-        resampler.setMode(vcm::ACVD::Mode::Anisotropic);
-    }
-    workingMesh = resampler.compute();
-
-    // Post-Smooth
-    if (smooth == SmoothOpt::Both || smooth == SmoothOpt::After) {
-        // Convert to polydata
-        auto vtkMesh = vtkSmartPointer<vtkPolyData>::New();
-        vcm::ITK2VTK(workingMesh, vtkMesh);
-        // Smoother
-        vc::Logger()->info("Smoothing mesh");
-        auto vtkSmoother = vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
-        vtkSmoother->SetInputData(vtkMesh);
-        vtkSmoother->Update();
-        vtkMesh = vtkSmoother->GetOutput();
-        // Convert back to ITK
-        workingMesh = vc::ITKMesh::New();
-        vcm::VTK2ITK(vtkMesh, workingMesh);
-    }
-
-    // Make sure the normals are up-to-date if we've smoothed
-    if (smooth != SmoothOpt::Off) {
-        vcm::CalculateNormals normals;
-        normals.setMesh(workingMesh);
-        workingMesh = normals.compute();
-    }
-
-    // Save the intermediate mesh
-    if (parsed_.count("intermediate-mesh")) {
-        vc::Logger()->info("Writing intermediate mesh");
-        fs::path meshPath = parsed_["intermediate-mesh"].as<std::string>();
-        if (vc::io::FileExtensionFilter(meshPath, {"ply"})) {
-            vc::io::PLYWriter writer;
-            writer.setMesh(workingMesh);
-            writer.setPath(meshPath);
-            writer.write();
-        } else if (vc::io::FileExtensionFilter(meshPath, {"obj"})) {
-            vc::io::OBJWriter writer;
-            writer.setMesh(workingMesh);
-            writer.setPath(meshPath);
-            writer.write();
-        }
-    }
-
-    return workingMesh;
-}

From c61c7ed2f991183d39dc7418e2ececa40b3da395 Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 15:01:11 -0400
Subject: [PATCH 08/12] (core) Fix Cube shape primitive winding order and all
 related tests

---
 core/include/vc/core/shapes/Cube.hpp          |  21 +-
 core/src/ShapePrimitive.cpp                   |   8 +-
 meshing/test/ITK2VTKTest.cpp                  |   2 +-
 .../res/ArchResamplePointCloudExample.pcd     | 109 ----------
 meshing/test/res/ArchWithSmoothedNormals.obj  | 200 +++++++++---------
 meshing/test/res/Cone.obj                     |   8 +-
 .../res/ConeResamplePointCloudExample.pcd     |  29 ---
 meshing/test/res/ConeWithSmoothedNormals.obj  |   8 +-
 .../res/CubeResamplePointCloudExample.pcd     |  18 --
 meshing/test/res/CubeWithSmoothedNormals.obj  |  36 ++--
 .../test/res/ITKArchMeshConvertedToVTK.ply    | 198 ++++++++---------
 .../test/res/ITKConeMeshConvertedToVTK.ply    |   8 +-
 .../test/res/ITKCubeMeshConvertedToVTK.ply    |  36 ++--
 .../test/res/ITKSphereMeshConvertedToVTK.ply  |  80 +++----
 .../res/PlaneResamplePointCloudExample.pcd    |  36 ----
 meshing/test/res/ScaledArchMesh.obj           | 198 ++++++++---------
 meshing/test/res/ScaledConeMesh.obj           |   8 +-
 meshing/test/res/ScaledCubeMesh.obj           |  36 ++--
 meshing/test/res/ScaledSphereMesh.obj         |  80 +++----
 .../res/SphereResamplePointCloudExample.pcd   |  27 ---
 .../test/res/SphereWithSmoothedNormals.obj    |  84 ++++----
 .../test/res/VTKArchMeshConvertedToITK.obj    | 198 ++++++++---------
 .../test/res/VTKConeMeshConvertedToITK.obj    |   8 +-
 .../test/res/VTKCubeMeshConvertedToITK.obj    |  36 ++--
 .../test/res/VTKSphereMeshConvertedToITK.obj  |  80 +++----
 25 files changed, 666 insertions(+), 886 deletions(-)
 delete mode 100644 meshing/test/res/ArchResamplePointCloudExample.pcd
 delete mode 100644 meshing/test/res/ConeResamplePointCloudExample.pcd
 delete mode 100644 meshing/test/res/CubeResamplePointCloudExample.pcd
 delete mode 100644 meshing/test/res/PlaneResamplePointCloudExample.pcd
 delete mode 100644 meshing/test/res/SphereResamplePointCloudExample.pcd

diff --git a/core/include/vc/core/shapes/Cube.hpp b/core/include/vc/core/shapes/Cube.hpp
index 22894ed17..14c2863db 100644
--- a/core/include/vc/core/shapes/Cube.hpp
+++ b/core/include/vc/core/shapes/Cube.hpp
@@ -41,18 +41,17 @@ class Cube : public ShapePrimitive
 
         // generate the 12 cells for faces
         addCell_(0, 1, 2);
-        addCell_(0, 1, 5);
         addCell_(0, 2, 3);
-        addCell_(0, 3, 4);
-        addCell_(0, 4, 5);
-        addCell_(1, 2, 6);
-        addCell_(1, 5, 6);
-        addCell_(2, 3, 7);
-        addCell_(2, 6, 7);
-        addCell_(3, 4, 7);
-        addCell_(4, 5, 7);
-        addCell_(5, 6, 7);
-
+        addCell_(3, 2, 6);
+        addCell_(3,6,7);
+        addCell_(7, 6, 5);
+        addCell_(7, 5, 4);
+        addCell_(4, 5, 1);
+        addCell_(4, 1, 0);
+        addCell_(0, 3, 7);
+        addCell_(0, 7, 4);
+        addCell_(5, 6, 2);
+        addCell_(5, 2, 1);
     }  // Constructor
 
 };  // Cube
diff --git a/core/src/ShapePrimitive.cpp b/core/src/ShapePrimitive.cpp
index 56c2ffd6c..8bc729515 100644
--- a/core/src/ShapePrimitive.cpp
+++ b/core/src/ShapePrimitive.cpp
@@ -161,7 +161,7 @@ void ShapePrimitive::addVertex_(double x, double y, double z)
     v.nx = 0;
     v.ny = 0;
     v.nz = 0;
-    v.faceCount = 0;
+    v.faceCount = 1;
     points_.push_back(v);
 }
 
@@ -209,9 +209,9 @@ void ShapePrimitive::updateNormal_(int vertID, double nx, double ny, double nz)
 {
     // recalculate average (unaverage, add new component, recalculate average)
     SimpleMesh::Vertex v = points_[vertID];
-    v.nx = (v.nx * v.faceCount + nx) / (v.faceCount + 1);
-    v.ny = (v.ny * v.faceCount + ny) / (v.faceCount + 1);
-    v.nz = (v.nz * v.faceCount + nz) / (v.faceCount + 1);
+    v.nx = v.nx + (nx - v.nx) / v.faceCount;
+    v.ny = v.ny + (ny - v.ny) / v.faceCount;
+    v.nz = v.nz + (nz - v.nz) / v.faceCount;
     v.faceCount++;
     points_[vertID] = v;
 }
diff --git a/meshing/test/ITK2VTKTest.cpp b/meshing/test/ITK2VTKTest.cpp
index 0d33e1765..85dc542d8 100644
--- a/meshing/test/ITK2VTKTest.cpp
+++ b/meshing/test/ITK2VTKTest.cpp
@@ -15,7 +15,7 @@ using namespace volcart;
 /*
  * The following five fixture build test inputs for the ITK2VTK tests
  *
- * Comments are included in the Plane Fixture only...the remainder of the fixure
+ * Comments are included in the Plane Fixture only...the remainder of the fixture
  * copy the same ideas
  */
 
diff --git a/meshing/test/res/ArchResamplePointCloudExample.pcd b/meshing/test/res/ArchResamplePointCloudExample.pcd
deleted file mode 100644
index 53b170bef..000000000
--- a/meshing/test/res/ArchResamplePointCloudExample.pcd
+++ /dev/null
@@ -1,109 +0,0 @@
-# .PCD v0.7 - Point Cloud Data file format
-VERSION 0.7
-FIELDS x y z normal_x normal_y normal_z curvature
-SIZE 4 4 4 4 4 4 4
-TYPE F F F F F F F
-COUNT 1 1 1 1 1 1 1
-WIDTH 98
-HEIGHT 1
-VIEWPOINT 0 0 0 1 0 0 0
-POINTS 98
-DATA ascii
--4.7196779 1.1439068 4.4404564 0.83873248 -0.54454106 0.0017029543 0.08540491
--4.7155428 2.023772 -0.48824656 0.87195528 -0.47281954 -0.12702645 0.087087363
--4.7333698 1.7040005 0.65563709 0.85817075 -0.49672848 -0.12962942 0.08540491
--4.7422323 1.4192768 1.7949101 0.85174459 -0.51287144 -0.10721022 0.08540491
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--4.7519822 1.1060221 3.9481392 0.84449285 -0.53497583 -0.025152318 0.08540491
--4.7519026 1.1085943 4.9468808 0.84083432 -0.54025793 0.03345155 0.08540491
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--4.7682142 1.5845191 7.2032332 0.82183278 -0.52725375 0.21585727 0.08540491
--4.7801232 2.2019179 8.3903828 0.79615974 -0.50541949 0.33268717 0.08540491
--4.7850137 3.0447936 9.4672403 0.76078528 -0.47985253 0.43697515 0.08540491
--4.7842879 4.0681076 10.455836 0.72023678 -0.45901343 0.5201593 0.08540491
--4.7797756 5.2130904 11.384918 0.68060941 -0.45086306 0.57748884 0.08540491
--4.7735963 6.4116178 12.287808 0.64651847 -0.4625417 0.60668689 0.08540491
--4.7680826 7.5887628 13.201158 0.62001961 -0.50061995 0.60411531 0.08540491
--4.7657046 8.6651621 14.163786 0.59974802 -0.57092899 0.56066251 0.08540491
--3.7831573 3.1044343 0.43806735 0.7277993 -0.6506272 -0.21677735 0.08540491
--3.7947135 2.733155 1.6196791 0.71640438 -0.6736756 -0.18145509 0.08540491
--3.803179 2.4611731 2.7527194 0.70756 -0.69453776 -0.13029274 0.08540491
--3.8081048 2.302923 3.8301277 0.69927365 -0.71208715 -0.062835477 0.08540491
--3.8092215 2.2670436 4.8476782 0.6889587 -0.72451001 0.020522613 0.08540491
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--3.7997503 2.5713327 6.6988349 0.65078545 -0.72545105 0.22405156 0.08540491
--3.7893729 2.9047387 7.5357485 0.61881816 -0.71152163 0.33286795 0.08540491
--3.7755768 3.3479836 8.3189344 0.57821757 -0.68940353 0.43633386 0.08540491
--3.7587583 3.8883238 9.0546265 0.53242379 -0.66221249 0.52725661 0.08540491
--1.6436236 3.5873718 3.2452316 0.22631618 -0.95130843 -0.20926832 0.08540491
--1.6817131 3.363632 4.8438258 0.19842951 -0.97929955 -0.039977085 0.08540491
--1.7102406 3.4471021 6.2921476 0.16208379 -0.97290522 0.16487671 0.08540491
--1.72987 3.816452 7.6006312 0.11670578 -0.92157692 0.37023747 0.08540491
--1.741799 4.4331932 8.7881031 0.067176409 -0.84142369 0.53618419 0.08540491
--1.7476571 5.2449856 9.8801651 0.018600699 -0.76357591 0.64545012 0.08540491
--1.7494094 6.1886873 10.907703 -0.028003018 -0.71158946 0.70203722 0.08540491
--1.7492695 7.1931844 11.905503 -0.075004995 -0.69645214 0.7136727 0.08540491
--1.7496173 8.1820059 12.910972 -0.12590623 -0.72170693 0.68065172 0.08540491
--1.7529246 9.0757513 13.962946 -0.1829327 -0.78481883 0.59211063 0.08540491
--0.75826031 4.904325 0.046799578 0.12478372 -0.89634496 -0.4254348 0.08540491
--0.77567524 4.3448186 1.320483 0.10784497 -0.92391509 -0.36708358 0.08540491
--0.78901029 3.9163902 2.5300493 0.092047483 -0.95255154 -0.29012561 0.08540491
--0.7980054 3.6273944 3.671412 0.076539278 -0.97834975 -0.19228488 0.08540491
--0.80256641 3.4808598 4.7430897 0.060611188 -0.99546355 -0.07333865 0.08540491
--0.80274725 3.4750483 5.7459326 0.043848705 -0.99707264 0.062637761 0.08540491
--0.79873395 3.6039886 6.6828609 0.026300073 -0.97820622 0.20596337 0.08540491
--0.79082829 3.8579807 7.5586205 0.0084498236 -0.9392193 0.34321386 0.08540491
--0.77943337 4.2240767 8.3795443 -0.009115871 -0.88675445 0.46215087 0.08540491
--0.76503909 4.6865373 9.1533308 -0.026127398 -0.83082843 0.55591506 0.08540491
-1.3562229 3.5824411 3.2476435 -0.20785515 -0.95066124 -0.23030284 0.08540491
-1.3176597 3.3434854 4.8536806 -0.18045916 -0.98202235 -0.055376951 0.08540491
-1.288854 3.4180133 6.3063765 -0.14132528 -0.9779802 0.15356395 0.08540491
-1.2689382 3.7781575 7.6193628 -0.094294146 -0.92856395 0.35899529 0.08540491
-1.2565353 4.3796778 8.8142796 -0.04889081 -0.8522886 0.52078187 0.08540491
-1.2498642 5.1653504 9.9191189 -0.01302101 -0.78149426 0.62377656 0.08540491
-1.2468374 6.0681038 10.966687 0.010440452 -0.73935598 0.67323381 0.08540491
-1.2451509 7.0139217 11.99319 0.02116972 -0.73638374 0.67623281 0.08540491
-1.2423687 7.9245338 13.036915 0.018525615 -0.77555013 0.63101411 0.08540491
-1.2359998 8.7199135 14.137005 0.00056802173 -0.85161948 0.52416021 0.08540491
-2.2650237 4.6523948 -0.31911984 -0.39923376 -0.81977999 -0.41057661 0.08540491
-2.2467132 4.0641112 0.96863991 -0.38838485 -0.84951633 -0.35704228 0.08540491
-2.2326095 3.6109872 2.1902862 -0.3755751 -0.88163704 -0.28576124 0.08540491
-2.2229793 3.3015928 3.3416269 -0.35839629 -0.91318953 -0.19400254 0.08540491
-2.2179182 3.1389904 4.421164 -0.33405685 -0.93910784 -0.080513895 0.08540491
-2.2173681 3.1213162 5.4298096 -0.30005911 -0.95249486 0.052134838 0.08540491
-2.2211349 3.2423358 6.3706126 -0.25555527 -0.94683099 0.19545491 0.08540491
-2.228905 3.4919703 7.2485032 -0.20262446 -0.91988724 0.33578387 0.08540491
-2.2402604 3.8567972 8.0700474 -0.14599974 -0.87629473 0.45912048 0.08540491
-2.2546942 4.3205261 8.843214 -0.090992011 -0.8257609 0.55663222 0.08540491
-3.3265817 2.6301281 3.713469 -0.59261936 -0.79925781 -0.099946477 0.08540491
-3.2948318 2.6100652 5.2124343 -0.53890038 -0.83955783 0.068767913 0.08540491
-3.2723196 2.8867962 6.5662222 -0.45165223 -0.85081321 0.26856494 0.08540491
-3.258065 3.4288218 7.7902412 -0.33415818 -0.82220232 0.46078375 0.08540491
-3.2506347 4.1901021 8.907011 -0.20798898 -0.76783508 0.60594547 0.08540491
-3.2480135 5.1058884 9.948205 -0.096043691 -0.71739447 0.69001508 0.08540491
-3.2481773 6.1111488 10.945631 -0.0064452155 -0.69294393 0.72096264 0.08540491
-3.2487109 7.1282959 11.937243 0.06086091 -0.70584172 0.70575029 0.08540491
-3.2471313 8.0775471 12.962068 0.10747338 -0.75977349 0.64124388 0.08540491
-3.2409189 8.8779535 14.059699 0.13132679 -0.84880584 0.51213467 0.08540491
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diff --git a/meshing/test/res/ArchWithSmoothedNormals.obj b/meshing/test/res/ArchWithSmoothedNormals.obj
index 3a549434d..e6102569f 100644
--- a/meshing/test/res/ArchWithSmoothedNormals.obj
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 # Faces: 162
 f 12//12 11//11 1//1 
 f 12//12 1//1 2//2 
diff --git a/meshing/test/res/Cone.obj b/meshing/test/res/Cone.obj
index 2cb9d0013..96e5352ce 100644
--- a/meshing/test/res/Cone.obj
+++ b/meshing/test/res/Cone.obj
@@ -2,11 +2,11 @@
 # VC OBJ Exporter v1.0
 # Vertices: 50
 v 0 0 0
-vn -8.46545e-16 -3.46366e-16 -0.370705
+vn -8.39606e-16 -2.35922e-16 -0.370705
 v 0 0 5
 vn 0 0 1
 v 2 0 5
-vn 0.463381 -4.56232e-16 0.314648
+vn 0.463381 -4.55365e-16 0.314648
 v 1.98289 0.261052 5
 vn 0.459417 0.0604834 0.314648
 v 1.93185 0.517638 5
@@ -54,7 +54,7 @@ vn -0.447592 0.119932 0.314648
 v -1.98289 0.261052 5
 vn -0.459417 0.0604834 0.314648
 v -2 2.02129e-15 5
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 v -1.98289 -0.261052 5
 vn -0.459417 -0.0604834 0.314648
 v -1.93185 -0.517638 5
@@ -78,7 +78,7 @@ vn -0.119932 -0.447592 0.314648
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 v 0.261052 -1.98289 5
 vn 0.0604834 -0.459417 0.314648
 v 0.517638 -1.93185 5
diff --git a/meshing/test/res/ConeResamplePointCloudExample.pcd b/meshing/test/res/ConeResamplePointCloudExample.pcd
deleted file mode 100644
index 2e53e5d59..000000000
--- a/meshing/test/res/ConeResamplePointCloudExample.pcd
+++ /dev/null
@@ -1,29 +0,0 @@
-# .PCD v0.7 - Point Cloud Data file format
-VERSION 0.7
-FIELDS x y z normal_x normal_y normal_z curvature
-SIZE 4 4 4 4 4 4 4
-TYPE F F F F F F F
-COUNT 1 1 1 1 1 1 1
-WIDTH 18
-HEIGHT 1
-VIEWPOINT 0 0 0 1 0 0 0
-POINTS 18
-DATA ascii
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--2 -0.61763817 4.6055732 2.4483653e-17 -0.67944962 0.73372221 0.030049849
--2 -0.079289913 5.1041002 2.4483653e-17 -0.67944962 0.73372221 0.030049849
--2 0.45905831 5.6026278 -4.1721316e-17 -0.67944962 0.73372221 0.030049849
--2 4.5667396 9.4064684 -6.6548176e-17 -0.67944962 0.73372221 0.030049849
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--1 4.5667396 9.4064684 -1.1399478e-16 -0.67944962 0.73372221 0.030049849
-0 -1.1559864 4.1070457 -2.0084897e-18 -0.67944962 0.73372221 0.030049849
--1.5922603e-18 -0.61763817 4.6055732 2.9619603e-18 -0.67944962 0.73372221 0.030049849
-0 0.45905834 5.6026278 -2.0084897e-18 -0.67944962 0.73372221 0.030049849
-3.9294863e-18 4.5667396 9.4064684 -4.8576132e-18 -0.67944962 0.73372221 0.030049849
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-2 4.5667396 9.4064684 9.7885772e-19 -0.67944962 0.73372221 0.030049849
diff --git a/meshing/test/res/ConeWithSmoothedNormals.obj b/meshing/test/res/ConeWithSmoothedNormals.obj
index 4c2309cf7..5f297e5a9 100644
--- a/meshing/test/res/ConeWithSmoothedNormals.obj
+++ b/meshing/test/res/ConeWithSmoothedNormals.obj
@@ -2,9 +2,9 @@
 # VC OBJ Exporter v1.0
 # Vertices: 50
 v 0 0 0
-vn -8.46545e-16 -3.46366e-16 -0.370705
+vn -8.39606e-16 -2.35922e-16 -0.370705
 v 0 0 5
-vn -4.30767e-16 -1.03494e-16 0.342062
+vn -4.25215e-16 -1.02366e-16 0.342062
 v 2 0 5
 vn 0.365891 0.0222944 0.352723
 v 1.98289 0.261052 5
@@ -54,7 +54,7 @@ vn -0.346601 0.0928714 0.350719
 v -1.98289 0.261052 5
 vn -0.355758 0.0468364 0.350719
 v -2 2.02129e-15 5
-vn -0.358828 3.62283e-16 0.350719
+vn -0.358828 3.68127e-16 0.350719
 v -1.98289 -0.261052 5
 vn -0.355758 -0.0468364 0.350719
 v -1.93185 -0.517638 5
@@ -78,7 +78,7 @@ vn -0.0928714 -0.346601 0.350719
 v -0.261052 -1.98289 5
 vn -0.0468364 -0.355758 0.350719
 v -5.69646e-15 -2 5
-vn -1.03426e-15 -0.358828 0.350719
+vn -1.02842e-15 -0.358828 0.350719
 v 0.261052 -1.98289 5
 vn 0.0468364 -0.355758 0.350719
 v 0.517638 -1.93185 5
diff --git a/meshing/test/res/CubeResamplePointCloudExample.pcd b/meshing/test/res/CubeResamplePointCloudExample.pcd
deleted file mode 100644
index 08686c3af..000000000
--- a/meshing/test/res/CubeResamplePointCloudExample.pcd
+++ /dev/null
@@ -1,18 +0,0 @@
-# .PCD v0.7 - Point Cloud Data file format
-VERSION 0.7
-FIELDS x y z normal_x normal_y normal_z curvature
-SIZE 4 4 4 4 4 4 4
-TYPE F F F F F F F
-COUNT 1 1 1 1 1 1 1
-WIDTH 7
-HEIGHT 1
-VIEWPOINT 0 0 0 1 0 0 0
-POINTS 7
-DATA ascii
-2.165462 2.5337777 4.2007227 -0.63178128 -0.73923874 0.23319198 0.10373919
--0.90635568 3.9394855 0.33453804 -0.63178128 -0.73923874 0.23319198 0.10373919
--0.16972403 4.8014083 5.0626454 -0.63178128 -0.73923874 0.23319198 0.10373919
-0.56690758 5.663331 9.7907534 -0.63178128 -0.73923874 0.23319198 0.10373919
-4.4330926 -0.66333091 0.20924695 -0.63178128 -0.73923874 0.23319198 0.10373919
-5.169724 0.19859178 4.9373546 -0.63178128 -0.73923874 0.23319198 0.10373919
-3.5711696 3.328145 10.527385 -0.63178128 -0.73923874 0.23319198 0.10373919
diff --git a/meshing/test/res/CubeWithSmoothedNormals.obj b/meshing/test/res/CubeWithSmoothedNormals.obj
index 5a4d93bd9..ddd89a32e 100644
--- a/meshing/test/res/CubeWithSmoothedNormals.obj
+++ b/meshing/test/res/CubeWithSmoothedNormals.obj
@@ -2,31 +2,31 @@
 # VC OBJ Exporter v1.0
 # Vertices: 8
 v 0 0 0
-vn 0 -0.2 -0.4
+vn -0.2 -0.4 -0.4
 v 0 5 0
-vn 0.25 0 -0.25
+vn -0.5 0.25 -0.25
 v 5 5 0
-vn 0 -0.2 -0.4
+vn 0.2 0.4 -0.4
 v 5 0 0
-vn -0.25 0 -0.25
+vn 0.5 -0.25 -0.25
 v 0 0 5
-vn -0.25 0 -0.25
+vn -0.5 -0.25 0.25
 v 0 5 5
-vn 0 0.2 -0.4
+vn -0.2 0.4 0.4
 v 5 5 5
-vn 0.25 0 -0.25
+vn 0.5 0.25 0.25
 v 5 0 5
-vn 0 0.2 -0.4
+vn 0.2 -0.4 0.4
 # Faces: 12
 f 1//1 2//2 3//3 
-f 1//1 2//2 6//6 
 f 1//1 3//3 4//4 
-f 1//1 4//4 5//5 
-f 1//1 5//5 6//6 
-f 2//2 3//3 7//7 
-f 2//2 6//6 7//7 
-f 3//3 4//4 8//8 
-f 3//3 7//7 8//8 
-f 4//4 5//5 8//8 
-f 5//5 6//6 8//8 
-f 6//6 7//7 8//8 
+f 4//4 3//3 7//7 
+f 4//4 7//7 8//8 
+f 8//8 7//7 6//6 
+f 8//8 6//6 5//5 
+f 5//5 6//6 2//2 
+f 5//5 2//2 1//1 
+f 1//1 4//4 8//8 
+f 1//1 8//8 5//5 
+f 6//6 7//7 3//3 
+f 6//6 3//3 2//2 
diff --git a/meshing/test/res/ITKArchMeshConvertedToVTK.ply b/meshing/test/res/ITKArchMeshConvertedToVTK.ply
index b18e0c48c..2f87ad976 100644
--- a/meshing/test/res/ITKArchMeshConvertedToVTK.ply
+++ b/meshing/test/res/ITKArchMeshConvertedToVTK.ply
@@ -11,106 +11,106 @@ property float nz
 element face 162
 property list uchar int vertex_indices
 end_header
-5 0 0 0.987688 0.156434 0
-4.75528 1.54508 0 0.923234 0.354805 0
-4.04508 2.93893 0 0.768407 0.622735 0
-2.93893 4.04508 0 0.538363 0.829707 0
-1.54508 4.75528 0 0.25562 0.955461 0
-3.06162e-16 5 0 -0.0521448 0.987688 0
--1.54508 4.75528 0 -0.354805 0.923234 0
--2.93893 4.04508 0 -0.622735 0.768407 0
--4.04508 2.93893 0 -0.829707 0.538363 0
+5 0 0 0.987688 0.156434 -2.51658e-18
+4.75528 1.54508 0 0.923234 0.354805 -1.03699e-17
+4.04508 2.93893 0 0.768407 0.622735 1.71919e-17
+2.93893 4.04508 0 0.538363 0.829707 -4.24636e-19
+1.54508 4.75528 0 0.25562 0.955461 -1.67772e-18
+3.06162e-16 5 0 -0.0521448 0.987688 4.9736e-18
+-1.54508 4.75528 0 -0.354805 0.923234 7.75683e-18
+-2.93893 4.04508 0 -0.622735 0.768407 2.00762e-17
+-4.04508 2.93893 0 -0.829707 0.538363 -9.72117e-18
 -4.75528 1.54508 0 -0.891007 0.45399 0
-5 0 1 0.987688 0.156434 0
-4.75528 1.54508 1 0.939347 0.305212 0
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-2.93893 4.04508 1 0.580549 0.799057 0
-1.54508 4.75528 1 0.305212 0.939347 0
-3.06162e-16 5 1 2.91434e-16 0.987688 0
--1.54508 4.75528 1 -0.305212 0.939347 0
--2.93893 4.04508 1 -0.580549 0.799057 0
--4.04508 2.93893 1 -0.799057 0.580549 0
--4.75528 1.54508 1 -0.891007 0.45399 0
-5 0 2 0.987688 0.156434 0
-4.75528 1.54508 2 0.939347 0.305212 0
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-1.54508 4.75528 2 0.305212 0.939347 0
-3.06162e-16 5 2 2.91434e-16 0.987688 0
--1.54508 4.75528 2 -0.305212 0.939347 0
--2.93893 4.04508 2 -0.580549 0.799057 0
--4.04508 2.93893 2 -0.799057 0.580549 0
--4.75528 1.54508 2 -0.891007 0.45399 0
-5 0 3 0.987688 0.156434 0
-4.75528 1.54508 3 0.939347 0.305212 0
-4.04508 2.93893 3 0.799057 0.580549 0
-2.93893 4.04508 3 0.580549 0.799057 0
-1.54508 4.75528 3 0.305212 0.939347 0
-3.06162e-16 5 3 2.91434e-16 0.987688 0
--1.54508 4.75528 3 -0.305212 0.939347 0
--2.93893 4.04508 3 -0.580549 0.799057 0
--4.04508 2.93893 3 -0.799057 0.580549 0
--4.75528 1.54508 3 -0.891007 0.45399 0
-5 0 4 0.987688 0.156434 0
-4.75528 1.54508 4 0.939347 0.305212 0
-4.04508 2.93893 4 0.799057 0.580549 0
-2.93893 4.04508 4 0.580549 0.799057 0
-1.54508 4.75528 4 0.305212 0.939347 0
-3.06162e-16 5 4 2.91434e-16 0.987688 0
--1.54508 4.75528 4 -0.305212 0.939347 0
--2.93893 4.04508 4 -0.580549 0.799057 0
--4.04508 2.93893 4 -0.799057 0.580549 0
--4.75528 1.54508 4 -0.891007 0.45399 0
-5 0 5 0.987688 0.156434 0
-4.75528 1.54508 5 0.939347 0.305212 0
-4.04508 2.93893 5 0.799057 0.580549 0
-2.93893 4.04508 5 0.580549 0.799057 0
-1.54508 4.75528 5 0.305212 0.939347 0
-3.06162e-16 5 5 2.91434e-16 0.987688 0
--1.54508 4.75528 5 -0.305212 0.939347 0
--2.93893 4.04508 5 -0.580549 0.799057 0
--4.04508 2.93893 5 -0.799057 0.580549 0
--4.75528 1.54508 5 -0.891007 0.45399 0
-5 0 6 0.987688 0.156434 0
-4.75528 1.54508 6 0.939347 0.305212 0
-4.04508 2.93893 6 0.799057 0.580549 0
-2.93893 4.04508 6 0.580549 0.799057 0
-1.54508 4.75528 6 0.305212 0.939347 0
-3.06162e-16 5 6 2.91434e-16 0.987688 0
--1.54508 4.75528 6 -0.305212 0.939347 0
--2.93893 4.04508 6 -0.580549 0.799057 0
--4.04508 2.93893 6 -0.799057 0.580549 0
--4.75528 1.54508 6 -0.891007 0.45399 0
-5 0 7 0.987688 0.156434 0
-4.75528 1.54508 7 0.939347 0.305212 0
-4.04508 2.93893 7 0.799057 0.580549 0
-2.93893 4.04508 7 0.580549 0.799057 0
-1.54508 4.75528 7 0.305212 0.939347 0
-3.06162e-16 5 7 2.91434e-16 0.987688 0
--1.54508 4.75528 7 -0.305212 0.939347 0
--2.93893 4.04508 7 -0.580549 0.799057 0
--4.04508 2.93893 7 -0.799057 0.580549 0
--4.75528 1.54508 7 -0.891007 0.45399 0
-5 0 8 0.987688 0.156434 0
-4.75528 1.54508 8 0.939347 0.305212 0
-4.04508 2.93893 8 0.799057 0.580549 0
-2.93893 4.04508 8 0.580549 0.799057 0
-1.54508 4.75528 8 0.305212 0.939347 0
-3.06162e-16 5 8 2.91434e-16 0.987688 0
--1.54508 4.75528 8 -0.305212 0.939347 0
--2.93893 4.04508 8 -0.580549 0.799057 0
--4.04508 2.93893 8 -0.799057 0.580549 0
--4.75528 1.54508 8 -0.891007 0.45399 0
-5 0 9 0.987688 0.156434 0
-4.75528 1.54508 9 0.955461 0.25562 0
-4.04508 2.93893 9 0.829707 0.538363 0
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-1.54508 4.75528 9 0.354805 0.923234 0
-3.06162e-16 5 9 0.0521448 0.987688 0
--1.54508 4.75528 9 -0.25562 0.955461 0
--2.93893 4.04508 9 -0.538363 0.829707 0
--4.04508 2.93893 9 -0.768407 0.622735 0
--4.75528 1.54508 9 -0.891007 0.45399 0
+5 0 1 0.987688 0.156434 -3.35545e-18
+4.75528 1.54508 1 0.939347 0.305212 -1.12087e-17
+4.04508 2.93893 1 0.799057 0.580549 1.2007e-17
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+-1.54508 4.75528 1 -0.305212 0.939347 1.02436e-17
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+-4.75528 1.54508 1 -0.891007 0.45399 -9.72117e-18
+5 0 2 0.987688 0.156434 -3.35545e-18
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+-1.54508 4.75528 2 -0.305212 0.939347 1.02436e-17
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+-4.75528 1.54508 2 -0.891007 0.45399 -9.72117e-18
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+3.06162e-16 5 3 2.91434e-16 0.987688 4.13474e-18
+-1.54508 4.75528 3 -0.305212 0.939347 1.02436e-17
+-2.93893 4.04508 3 -0.580549 0.799057 2.39547e-17
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+3.06162e-16 5 4 2.91434e-16 0.987688 4.13474e-18
+-1.54508 4.75528 4 -0.305212 0.939347 1.02436e-17
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+-4.75528 1.54508 4 -0.891007 0.45399 -9.72117e-18
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+-4.04508 2.93893 8 -0.799057 0.580549 3.16945e-19
+-4.75528 1.54508 8 -0.891007 0.45399 -9.72117e-18
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+2.93893 4.04508 9 0.622735 0.768407 1.67673e-17
+1.54508 4.75528 9 0.354805 0.923234 -2.10236e-18
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+-1.54508 4.75528 9 -0.25562 0.955461 1.27304e-17
+-2.93893 4.04508 9 -0.538363 0.829707 2.78331e-17
+-4.04508 2.93893 9 -0.768407 0.622735 1.03551e-17
+-4.75528 1.54508 9 -0.891007 0.45399 -1.45818e-17
 3 11 10 0
 3 11 0 1
 3 12 11 1
diff --git a/meshing/test/res/ITKConeMeshConvertedToVTK.ply b/meshing/test/res/ITKConeMeshConvertedToVTK.ply
index fc5d7f4c7..32f00a3eb 100644
--- a/meshing/test/res/ITKConeMeshConvertedToVTK.ply
+++ b/meshing/test/res/ITKConeMeshConvertedToVTK.ply
@@ -11,9 +11,9 @@ property float nz
 element face 96
 property list uchar int vertex_indices
 end_header
-0 0 0 -8.46545e-16 -3.46366e-16 -0.370705
+0 0 0 -8.39606e-16 -2.35922e-16 -0.370705
 0 0 5 0 0 1
-2 0 5 0.463381 -4.56232e-16 0.314648
+2 0 5 0.463381 -4.55365e-16 0.314648
 1.98289 0.261052 5 0.459417 0.0604834 0.314648
 1.93185 0.517638 5 0.447592 0.119932 0.314648
 1.84776 0.765367 5 0.428108 0.177328 0.314648
@@ -37,7 +37,7 @@ end_header
 -1.84776 0.765367 5 -0.428108 0.177328 0.314648
 -1.93185 0.517638 5 -0.447592 0.119932 0.314648
 -1.98289 0.261052 5 -0.459417 0.0604834 0.314648
--2 2.02129e-15 5 -0.463381 5.91541e-16 0.314648
+-2 2.02129e-15 5 -0.463381 5.88071e-16 0.314648
 -1.98289 -0.261052 5 -0.459417 -0.0604834 0.314648
 -1.93185 -0.517638 5 -0.447592 -0.119932 0.314648
 -1.84776 -0.765367 5 -0.428108 -0.177328 0.314648
@@ -49,7 +49,7 @@ end_header
 -0.765367 -1.84776 5 -0.177328 -0.428108 0.314648
 -0.517638 -1.93185 5 -0.119932 -0.447592 0.314648
 -0.261052 -1.98289 5 -0.0604834 -0.459417 0.314648
--5.69646e-15 -2 5 -1.38257e-15 -0.463381 0.314648
+-5.69646e-15 -2 5 -1.38171e-15 -0.463381 0.314648
 0.261052 -1.98289 5 0.0604834 -0.459417 0.314648
 0.517638 -1.93185 5 0.119932 -0.447592 0.314648
 0.765367 -1.84776 5 0.177328 -0.428108 0.314648
diff --git a/meshing/test/res/ITKCubeMeshConvertedToVTK.ply b/meshing/test/res/ITKCubeMeshConvertedToVTK.ply
index 14861774c..e085376fb 100644
--- a/meshing/test/res/ITKCubeMeshConvertedToVTK.ply
+++ b/meshing/test/res/ITKCubeMeshConvertedToVTK.ply
@@ -11,23 +11,23 @@ property float nz
 element face 12
 property list uchar int vertex_indices
 end_header
-0 0 0 0 -0.2 -0.4
-0 5 0 0.25 0 -0.25
-5 5 0 0 -0.2 -0.4
-5 0 0 -0.25 0 -0.25
-0 0 5 -0.25 0 -0.25
-0 5 5 0 0.2 -0.4
-5 5 5 0.25 0 -0.25
-5 0 5 0 0.2 -0.4
+0 0 0 -0.2 -0.4 -0.4
+0 5 0 -0.5 0.25 -0.25
+5 5 0 0.2 0.4 -0.4
+5 0 0 0.5 -0.25 -0.25
+0 0 5 -0.5 -0.25 0.25
+0 5 5 -0.2 0.4 0.4
+5 5 5 0.5 0.25 0.25
+5 0 5 0.2 -0.4 0.4
 3 0 1 2
-3 0 1 5
 3 0 2 3
-3 0 3 4
-3 0 4 5
-3 1 2 6
-3 1 5 6
-3 2 3 7
-3 2 6 7
-3 3 4 7
-3 4 5 7
-3 5 6 7
+3 3 2 6
+3 3 6 7
+3 7 6 5
+3 7 5 4
+3 4 5 1
+3 4 1 0
+3 0 3 7
+3 0 7 4
+3 5 6 2
+3 5 2 1
diff --git a/meshing/test/res/ITKSphereMeshConvertedToVTK.ply b/meshing/test/res/ITKSphereMeshConvertedToVTK.ply
index 63511ec26..3edf82ef9 100644
--- a/meshing/test/res/ITKSphereMeshConvertedToVTK.ply
+++ b/meshing/test/res/ITKSphereMeshConvertedToVTK.ply
@@ -11,35 +11,35 @@ property float nz
 element face 320
 property list uchar int vertex_indices
 end_header
--0.525731 0.850651 0 -0.518109 0.838317 0
-0.525731 0.850651 0 0.518109 0.838317 0
--0.525731 -0.850651 0 -0.518109 -0.838317 0
-0.525731 -0.850651 0 0.518109 -0.838317 0
+-0.525731 0.850651 0 -0.518109 0.838317 -8.60276e-18
+0.525731 0.850651 0 0.518109 0.838317 3.05164e-18
+-0.525731 -0.850651 0 -0.518109 -0.838317 6.93889e-18
+0.525731 -0.850651 0 0.518109 -0.838317 -8.60276e-18
 0 -0.525731 0.850651 0 -0.518109 0.838317
-0 0.525731 0.850651 0 0.518109 0.838317
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diff --git a/meshing/test/res/PlaneResamplePointCloudExample.pcd b/meshing/test/res/PlaneResamplePointCloudExample.pcd
deleted file mode 100644
index c66705de9..000000000
--- a/meshing/test/res/PlaneResamplePointCloudExample.pcd
+++ /dev/null
@@ -1,36 +0,0 @@
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diff --git a/meshing/test/res/ScaledArchMesh.obj b/meshing/test/res/ScaledArchMesh.obj
index 89b4bb8f3..d01cf5146 100644
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 v 12.1353 8.81678 21
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-vn 0.987688 0.156434 0
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 v 12.1353 8.81678 24
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 v 8.81678 12.1353 24
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 v 4.63525 14.2658 24
-vn 0.305212 0.939347 0
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 v 9.18485e-16 15 24
-vn 2.91434e-16 0.987688 0
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 v -4.63525 14.2658 24
-vn -0.305212 0.939347 0
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 v -8.81678 12.1353 24
-vn -0.580549 0.799057 0
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 v -12.1353 8.81678 24
-vn -0.799057 0.580549 0
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 v -14.2658 4.63525 24
-vn -0.891007 0.45399 0
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 v 15 0 27
-vn 0.987688 0.156434 0
+vn 0.987688 0.156434 -5.03317e-18
 v 14.2658 4.63525 27
-vn 0.955461 0.25562 0
+vn 0.955461 0.25562 -1.20476e-17
 v 12.1353 8.81678 27
-vn 0.829707 0.538363 0
+vn 0.829707 0.538363 6.82205e-18
 v 8.81678 12.1353 27
-vn 0.622735 0.768407 0
+vn 0.622735 0.768407 1.67673e-17
 v 4.63525 14.2658 27
-vn 0.354805 0.923234 0
+vn 0.354805 0.923234 -2.10236e-18
 v 9.18485e-16 15 27
-vn 0.0521448 0.987688 0
+vn 0.0521448 0.987688 3.29587e-18
 v -4.63525 14.2658 27
-vn -0.25562 0.955461 0
+vn -0.25562 0.955461 1.27304e-17
 v -8.81678 12.1353 27
-vn -0.538363 0.829707 0
+vn -0.538363 0.829707 2.78331e-17
 v -12.1353 8.81678 27
-vn -0.768407 0.622735 0
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 v -14.2658 4.63525 27
-vn -0.891007 0.45399 0
+vn -0.891007 0.45399 -1.45818e-17
 # Faces: 162
 f 12//12 11//11 1//1 
 f 12//12 1//1 2//2 
diff --git a/meshing/test/res/ScaledConeMesh.obj b/meshing/test/res/ScaledConeMesh.obj
index 99eccb712..3516b240e 100644
--- a/meshing/test/res/ScaledConeMesh.obj
+++ b/meshing/test/res/ScaledConeMesh.obj
@@ -2,11 +2,11 @@
 # VC OBJ Exporter v1.0
 # Vertices: 50
 v 0 0 0
-vn -8.46545e-16 -3.46366e-16 -0.370705
+vn -8.39606e-16 -2.35922e-16 -0.370705
 v 0 0 15
 vn 0 0 1
 v 6 0 15
-vn 0.463381 -4.56232e-16 0.314648
+vn 0.463381 -4.55365e-16 0.314648
 v 5.94867 0.783157 15
 vn 0.459417 0.0604834 0.314648
 v 5.79555 1.55291 15
@@ -54,7 +54,7 @@ vn -0.447592 0.119932 0.314648
 v -5.94867 0.783157 15
 vn -0.459417 0.0604834 0.314648
 v -6 6.06386e-15 15
-vn -0.463381 5.91541e-16 0.314648
+vn -0.463381 5.88071e-16 0.314648
 v -5.94867 -0.783157 15
 vn -0.459417 -0.0604834 0.314648
 v -5.79555 -1.55291 15
@@ -78,7 +78,7 @@ vn -0.119932 -0.447592 0.314648
 v -0.783157 -5.94867 15
 vn -0.0604834 -0.459417 0.314648
 v -1.70894e-14 -6 15
-vn -1.38257e-15 -0.463381 0.314648
+vn -1.38171e-15 -0.463381 0.314648
 v 0.783157 -5.94867 15
 vn 0.0604834 -0.459417 0.314648
 v 1.55291 -5.79555 15
diff --git a/meshing/test/res/ScaledCubeMesh.obj b/meshing/test/res/ScaledCubeMesh.obj
index 35890cfaf..a12617128 100644
--- a/meshing/test/res/ScaledCubeMesh.obj
+++ b/meshing/test/res/ScaledCubeMesh.obj
@@ -2,31 +2,31 @@
 # VC OBJ Exporter v1.0
 # Vertices: 8
 v 0 0 0
-vn 0 -0.2 -0.4
+vn -0.2 -0.4 -0.4
 v 0 15 0
-vn 0.25 0 -0.25
+vn -0.5 0.25 -0.25
 v 15 15 0
-vn 0 -0.2 -0.4
+vn 0.2 0.4 -0.4
 v 15 0 0
-vn -0.25 0 -0.25
+vn 0.5 -0.25 -0.25
 v 0 0 15
-vn -0.25 0 -0.25
+vn -0.5 -0.25 0.25
 v 0 15 15
-vn 0 0.2 -0.4
+vn -0.2 0.4 0.4
 v 15 15 15
-vn 0.25 0 -0.25
+vn 0.5 0.25 0.25
 v 15 0 15
-vn 0 0.2 -0.4
+vn 0.2 -0.4 0.4
 # Faces: 12
 f 1//1 2//2 3//3 
-f 1//1 2//2 6//6 
 f 1//1 3//3 4//4 
-f 1//1 4//4 5//5 
-f 1//1 5//5 6//6 
-f 2//2 3//3 7//7 
-f 2//2 6//6 7//7 
-f 3//3 4//4 8//8 
-f 3//3 7//7 8//8 
-f 4//4 5//5 8//8 
-f 5//5 6//6 8//8 
-f 6//6 7//7 8//8 
+f 4//4 3//3 7//7 
+f 4//4 7//7 8//8 
+f 8//8 7//7 6//6 
+f 8//8 6//6 5//5 
+f 5//5 6//6 2//2 
+f 5//5 2//2 1//1 
+f 1//1 4//4 8//8 
+f 1//1 8//8 5//5 
+f 6//6 7//7 3//3 
+f 6//6 3//3 2//2 
diff --git a/meshing/test/res/ScaledSphereMesh.obj b/meshing/test/res/ScaledSphereMesh.obj
index 03ac0676c..f842bd426 100644
--- a/meshing/test/res/ScaledSphereMesh.obj
+++ b/meshing/test/res/ScaledSphereMesh.obj
@@ -2,29 +2,29 @@
 # VC OBJ Exporter v1.0
 # Vertices: 162
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-vn -0.518109 0.838317 0
+vn -0.518109 0.838317 -8.60276e-18
 v 1.57719 2.55195 0
-vn 0.518109 0.838317 0
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-vn -0.518109 -0.838317 0
+vn -0.518109 -0.838317 6.93889e-18
 v 1.57719 -2.55195 0
-vn 0.518109 -0.838317 0
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 v 0 -1.57719 2.55195
 vn 0 -0.518109 0.838317
 v 0 1.57719 2.55195
-vn 0 0.518109 0.838317
+vn -6.93889e-18 0.518109 0.838317
 v 0 -1.57719 -2.55195
 vn 0 -0.518109 -0.838317
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-vn -2.77556e-18 0.518109 -0.838317
+vn 0 0.518109 -0.838317
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-vn 0.838317 0 -0.518109
+vn 0.838317 3.46945e-18 -0.518109
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-vn 0.838317 0 0.518109
+vn 0.838317 -3.46945e-18 0.518109
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-vn -0.838317 0 -0.518109
+vn -0.838317 6.93889e-18 -0.518109
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-vn -0.838317 0 0.518109
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 v -2.42705 1.5 0.927051
 vn -0.796697 0.492386 0.304311
 v -1.5 0.927051 2.42705
@@ -34,7 +34,7 @@ vn -0.304311 0.796697 0.492386
 v 0.927051 2.42705 1.5
 vn 0.304311 0.796697 0.492386
 v 0 3 0
-vn 0 0.984772 9.25186e-18
+vn 4.64705e-19 0.984772 0
 v 0.927051 2.42705 -1.5
 vn 0.304311 0.796697 -0.492386
 v -0.927051 2.42705 -1.5
@@ -44,7 +44,7 @@ vn -0.492386 0.304311 -0.796697
 v -2.42705 1.5 -0.927051
 vn -0.796697 0.492386 -0.304311
 v -3 0 0
-vn -0.984772 -4.62593e-18 0
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 v 1.5 0.927051 2.42705
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 v 2.42705 1.5 0.927051
@@ -52,13 +52,13 @@ vn 0.796697 0.492386 0.304311
 v -1.5 -0.927051 2.42705
 vn -0.492386 -0.304311 0.796697
 v 0 0 3
-vn 4.62593e-18 0 0.984772
+vn 0 -4.64705e-19 0.984772
 v -2.42705 -1.5 -0.927051
 vn -0.796697 -0.492386 -0.304311
 v -2.42705 -1.5 0.927051
 vn -0.796697 -0.492386 0.304311
 v 0 0 -3
-vn 4.62593e-18 0 -0.984772
+vn 0 4.64705e-19 -0.984772
 v -1.5 -0.927051 -2.42705
 vn -0.492386 -0.304311 -0.796697
 v 2.42705 1.5 -0.927051
@@ -74,7 +74,7 @@ vn 0.304311 -0.796697 0.492386
 v -0.927051 -2.42705 1.5
 vn -0.304311 -0.796697 0.492386
 v 0 -3 0
-vn 0 -0.984772 9.25186e-18
+vn -4.64705e-19 -0.984772 0
 v -0.927051 -2.42705 -1.5
 vn -0.304311 -0.796697 -0.492386
 v 0.927051 -2.42705 -1.5
@@ -84,7 +84,7 @@ vn 0.492386 -0.304311 -0.796697
 v 2.42705 -1.5 -0.927051
 vn 0.796697 -0.492386 -0.304311
 v 3 0 0
-vn 0.984772 4.62593e-18 0
+vn 0.984772 6.93889e-18 9.78962e-19
 v -2.08134 2.10614 0.481866
 vn -0.676851 0.700156 0.150881
 v -1.76336 2.06457 1.27598
@@ -106,13 +106,13 @@ vn -0.244131 0.43272 0.851037
 v -0.48738 2.85317 0.788597
 vn -0.148877 0.935942 0.265487
 v -0.8198 2.88582 0
-vn -0.281839 0.944287 0
+vn -0.281839 0.944287 -6.93889e-18
 v 0.481866 2.08134 2.10614
 vn 0.150881 0.676851 0.700156
 v 0 2.55195 1.57719
-vn 0 0.843931 0.506376
+vn -3.04696e-18 0.843931 0.506376
 v 0.8198 2.88582 0
-vn 0.281839 0.944287 0
+vn 0.281839 0.944287 6.93889e-18
 v 0.48738 2.85317 0.788597
 vn 0.148877 0.935942 0.265487
 v 1.30167 2.58801 0.779676
@@ -128,7 +128,7 @@ vn 0.148877 0.935942 -0.265487
 v -0.481866 2.08134 -2.10614
 vn -0.150881 0.676851 -0.700156
 v 0 2.55195 -1.57719
-vn 0 0.843931 -0.506376
+vn 5.78241e-18 0.843931 -0.506376
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 vn 0.150881 0.676851 -0.700156
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@@ -146,15 +146,15 @@ vn -0.670456 0.429567 -0.578444
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 vn -0.700156 0.150881 -0.676851
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-vn -0.843931 0.506376 0
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-vn -0.944287 -4.62593e-18 -0.281839
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 vn -0.935942 0.265487 0.148877
 v -2.88582 0 0.8198
-vn -0.944287 9.25186e-18 0.281839
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 v 1.76336 2.06457 1.27598
 vn 0.578444 0.670456 0.429567
 v 2.08134 2.10614 0.481866
@@ -172,13 +172,13 @@ vn 0.700156 0.150881 0.676851
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 vn -0.265487 0.148877 0.935942
 v 0 0.8198 2.88582
-vn -9.25186e-18 0.281839 0.944287
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@@ -194,15 +194,15 @@ vn -0.935942 -0.265487 -0.148877
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 vn -0.676851 -0.700156 0.150881
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-vn -0.843931 -0.506376 0
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 vn -0.676851 -0.700156 -0.150881
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-vn 4.62593e-18 0.281839 -0.944287
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 vn -0.265487 0.148877 -0.935942
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@@ -210,7 +210,7 @@ vn -0.244131 -0.43272 -0.851037
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-vn -9.25186e-18 -0.281839 -0.944287
+vn 6.93889e-18 -0.281839 -0.944287
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 vn 0.429567 0.578444 -0.670456
 v 0.779676 1.30167 -2.58801
@@ -246,13 +246,13 @@ vn 0.244131 -0.43272 0.851037
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 vn 0.148877 -0.935942 0.265487
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-vn 0.281839 -0.944287 0
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 vn -0.150881 -0.676851 0.700156
 v 0 -2.55195 1.57719
-vn 0 -0.843931 0.506376
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@@ -268,7 +268,7 @@ vn -0.148877 -0.935942 -0.265487
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diff --git a/meshing/test/res/SphereResamplePointCloudExample.pcd b/meshing/test/res/SphereResamplePointCloudExample.pcd
deleted file mode 100644
index 5ed5dee5b..000000000
--- a/meshing/test/res/SphereResamplePointCloudExample.pcd
+++ /dev/null
@@ -1,27 +0,0 @@
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-VERSION 0.7
-FIELDS x y z normal_x normal_y normal_z curvature
-SIZE 4 4 4 4 4 4 4
-TYPE F F F F F F F
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-HEIGHT 1
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-POINTS 16
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diff --git a/meshing/test/res/SphereWithSmoothedNormals.obj b/meshing/test/res/SphereWithSmoothedNormals.obj
index 9afeaecf6..cf5e7468b 100644
--- a/meshing/test/res/SphereWithSmoothedNormals.obj
+++ b/meshing/test/res/SphereWithSmoothedNormals.obj
@@ -2,29 +2,29 @@
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diff --git a/meshing/test/res/VTKArchMeshConvertedToITK.obj b/meshing/test/res/VTKArchMeshConvertedToITK.obj
index 448268cd6..f077f557e 100644
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-vn 0.799057 0.580549 0
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-vn 0.580549 0.799057 0
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-vn 0.305212 0.939347 0
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-vn 2.91434e-16 0.987688 0
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 v -1.54508 4.75528 8
-vn -0.305212 0.939347 0
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-vn -0.580549 0.799057 0
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-vn -0.799057 0.580549 0
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 v -4.75528 1.54508 8
-vn -0.891007 0.45399 0
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 v 5 0 9
-vn 0.987688 0.156434 0
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 v 4.75528 1.54508 9
-vn 0.955461 0.25562 0
+vn 0.955461 0.25562 -1.20476e-17
 v 4.04508 2.93893 9
-vn 0.829707 0.538363 0
+vn 0.829707 0.538363 6.82205e-18
 v 2.93893 4.04508 9
-vn 0.622735 0.768407 0
+vn 0.622735 0.768407 1.67673e-17
 v 1.54508 4.75528 9
-vn 0.354805 0.923234 0
+vn 0.354805 0.923234 -2.10236e-18
 v 3.06162e-16 5 9
-vn 0.0521448 0.987688 0
+vn 0.0521448 0.987688 3.29587e-18
 v -1.54508 4.75528 9
-vn -0.25562 0.955461 0
+vn -0.25562 0.955461 1.27304e-17
 v -2.93893 4.04508 9
-vn -0.538363 0.829707 0
+vn -0.538363 0.829707 2.78331e-17
 v -4.04508 2.93893 9
-vn -0.768407 0.622735 0
+vn -0.768407 0.622735 1.03551e-17
 v -4.75528 1.54508 9
-vn -0.891007 0.45399 0
+vn -0.891007 0.45399 -1.45818e-17
 # Faces: 162
 f 12//12 11//11 1//1 
 f 12//12 1//1 2//2 
diff --git a/meshing/test/res/VTKConeMeshConvertedToITK.obj b/meshing/test/res/VTKConeMeshConvertedToITK.obj
index 2cb9d0013..96e5352ce 100644
--- a/meshing/test/res/VTKConeMeshConvertedToITK.obj
+++ b/meshing/test/res/VTKConeMeshConvertedToITK.obj
@@ -2,11 +2,11 @@
 # VC OBJ Exporter v1.0
 # Vertices: 50
 v 0 0 0
-vn -8.46545e-16 -3.46366e-16 -0.370705
+vn -8.39606e-16 -2.35922e-16 -0.370705
 v 0 0 5
 vn 0 0 1
 v 2 0 5
-vn 0.463381 -4.56232e-16 0.314648
+vn 0.463381 -4.55365e-16 0.314648
 v 1.98289 0.261052 5
 vn 0.459417 0.0604834 0.314648
 v 1.93185 0.517638 5
@@ -54,7 +54,7 @@ vn -0.447592 0.119932 0.314648
 v -1.98289 0.261052 5
 vn -0.459417 0.0604834 0.314648
 v -2 2.02129e-15 5
-vn -0.463381 5.91541e-16 0.314648
+vn -0.463381 5.88071e-16 0.314648
 v -1.98289 -0.261052 5
 vn -0.459417 -0.0604834 0.314648
 v -1.93185 -0.517638 5
@@ -78,7 +78,7 @@ vn -0.119932 -0.447592 0.314648
 v -0.261052 -1.98289 5
 vn -0.0604834 -0.459417 0.314648
 v -5.69646e-15 -2 5
-vn -1.38257e-15 -0.463381 0.314648
+vn -1.38171e-15 -0.463381 0.314648
 v 0.261052 -1.98289 5
 vn 0.0604834 -0.459417 0.314648
 v 0.517638 -1.93185 5
diff --git a/meshing/test/res/VTKCubeMeshConvertedToITK.obj b/meshing/test/res/VTKCubeMeshConvertedToITK.obj
index 5a4d93bd9..ddd89a32e 100644
--- a/meshing/test/res/VTKCubeMeshConvertedToITK.obj
+++ b/meshing/test/res/VTKCubeMeshConvertedToITK.obj
@@ -2,31 +2,31 @@
 # VC OBJ Exporter v1.0
 # Vertices: 8
 v 0 0 0
-vn 0 -0.2 -0.4
+vn -0.2 -0.4 -0.4
 v 0 5 0
-vn 0.25 0 -0.25
+vn -0.5 0.25 -0.25
 v 5 5 0
-vn 0 -0.2 -0.4
+vn 0.2 0.4 -0.4
 v 5 0 0
-vn -0.25 0 -0.25
+vn 0.5 -0.25 -0.25
 v 0 0 5
-vn -0.25 0 -0.25
+vn -0.5 -0.25 0.25
 v 0 5 5
-vn 0 0.2 -0.4
+vn -0.2 0.4 0.4
 v 5 5 5
-vn 0.25 0 -0.25
+vn 0.5 0.25 0.25
 v 5 0 5
-vn 0 0.2 -0.4
+vn 0.2 -0.4 0.4
 # Faces: 12
 f 1//1 2//2 3//3 
-f 1//1 2//2 6//6 
 f 1//1 3//3 4//4 
-f 1//1 4//4 5//5 
-f 1//1 5//5 6//6 
-f 2//2 3//3 7//7 
-f 2//2 6//6 7//7 
-f 3//3 4//4 8//8 
-f 3//3 7//7 8//8 
-f 4//4 5//5 8//8 
-f 5//5 6//6 8//8 
-f 6//6 7//7 8//8 
+f 4//4 3//3 7//7 
+f 4//4 7//7 8//8 
+f 8//8 7//7 6//6 
+f 8//8 6//6 5//5 
+f 5//5 6//6 2//2 
+f 5//5 2//2 1//1 
+f 1//1 4//4 8//8 
+f 1//1 8//8 5//5 
+f 6//6 7//7 3//3 
+f 6//6 3//3 2//2 
diff --git a/meshing/test/res/VTKSphereMeshConvertedToITK.obj b/meshing/test/res/VTKSphereMeshConvertedToITK.obj
index 262764f92..c0b036017 100644
--- a/meshing/test/res/VTKSphereMeshConvertedToITK.obj
+++ b/meshing/test/res/VTKSphereMeshConvertedToITK.obj
@@ -2,29 +2,29 @@
 # VC OBJ Exporter v1.0
 # Vertices: 162
 v -0.525731 0.850651 0
-vn -0.518109 0.838317 0
+vn -0.518109 0.838317 -8.60276e-18
 v 0.525731 0.850651 0
-vn 0.518109 0.838317 0
+vn 0.518109 0.838317 3.05164e-18
 v -0.525731 -0.850651 0
-vn -0.518109 -0.838317 0
+vn -0.518109 -0.838317 6.93889e-18
 v 0.525731 -0.850651 0
-vn 0.518109 -0.838317 0
+vn 0.518109 -0.838317 -8.60276e-18
 v 0 -0.525731 0.850651
 vn 0 -0.518109 0.838317
 v 0 0.525731 0.850651
-vn 0 0.518109 0.838317
+vn -6.93889e-18 0.518109 0.838317
 v 0 -0.525731 -0.850651
 vn 0 -0.518109 -0.838317
 v 0 0.525731 -0.850651
-vn -2.77556e-18 0.518109 -0.838317
+vn 0 0.518109 -0.838317
 v 0.850651 0 -0.525731
-vn 0.838317 0 -0.518109
+vn 0.838317 3.46945e-18 -0.518109
 v 0.850651 0 0.525731
-vn 0.838317 0 0.518109
+vn 0.838317 -3.46945e-18 0.518109
 v -0.850651 0 -0.525731
-vn -0.838317 0 -0.518109
+vn -0.838317 6.93889e-18 -0.518109
 v -0.850651 0 0.525731
-vn -0.838317 0 0.518109
+vn -0.838317 1.38778e-17 0.518109
 v -0.809017 0.5 0.309017
 vn -0.796697 0.492386 0.304311
 v -0.5 0.309017 0.809017
@@ -34,7 +34,7 @@ vn -0.304311 0.796697 0.492386
 v 0.309017 0.809017 0.5
 vn 0.304311 0.796697 0.492386
 v 0 1 0
-vn 0 0.984772 9.25186e-18
+vn 4.64705e-19 0.984772 0
 v 0.309017 0.809017 -0.5
 vn 0.304311 0.796697 -0.492386
 v -0.309017 0.809017 -0.5
@@ -44,7 +44,7 @@ vn -0.492386 0.304311 -0.796697
 v -0.809017 0.5 -0.309017
 vn -0.796697 0.492386 -0.304311
 v -1 0 0
-vn -0.984772 -4.62593e-18 0
+vn -0.984772 -6.93889e-18 9.78962e-19
 v 0.5 0.309017 0.809017
 vn 0.492386 0.304311 0.796697
 v 0.809017 0.5 0.309017
@@ -52,13 +52,13 @@ vn 0.796697 0.492386 0.304311
 v -0.5 -0.309017 0.809017
 vn -0.492386 -0.304311 0.796697
 v 0 0 1
-vn 4.62593e-18 0 0.984772
+vn 0 -4.64705e-19 0.984772
 v -0.809017 -0.5 -0.309017
 vn -0.796697 -0.492386 -0.304311
 v -0.809017 -0.5 0.309017
 vn -0.796697 -0.492386 0.304311
 v 0 0 -1
-vn 4.62593e-18 0 -0.984772
+vn 0 4.64705e-19 -0.984772
 v -0.5 -0.309017 -0.809017
 vn -0.492386 -0.304311 -0.796697
 v 0.809017 0.5 -0.309017
@@ -74,7 +74,7 @@ vn 0.304311 -0.796697 0.492386
 v -0.309017 -0.809017 0.5
 vn -0.304311 -0.796697 0.492386
 v 0 -1 0
-vn 0 -0.984772 9.25186e-18
+vn -4.64705e-19 -0.984772 0
 v -0.309017 -0.809017 -0.5
 vn -0.304311 -0.796697 -0.492386
 v 0.309017 -0.809017 -0.5
@@ -84,7 +84,7 @@ vn 0.492386 -0.304311 -0.796697
 v 0.809017 -0.5 -0.309017
 vn 0.796697 -0.492386 -0.304311
 v 1 0 0
-vn 0.984772 4.62593e-18 0
+vn 0.984772 6.93889e-18 9.78962e-19
 v -0.69378 0.702046 0.160622
 vn -0.676851 0.700156 0.150881
 v -0.587785 0.688191 0.425325
@@ -106,13 +106,13 @@ vn -0.244131 0.43272 0.851037
 v -0.16246 0.951057 0.262866
 vn -0.148877 0.935942 0.265487
 v -0.273267 0.961938 0
-vn -0.281839 0.944287 0
+vn -0.281839 0.944287 -6.93889e-18
 v 0.160622 0.69378 0.702046
 vn 0.150881 0.676851 0.700156
 v 0 0.850651 0.525731
-vn 0 0.843931 0.506376
+vn -3.04696e-18 0.843931 0.506376
 v 0.273267 0.961938 0
-vn 0.281839 0.944287 0
+vn 0.281839 0.944287 6.93889e-18
 v 0.16246 0.951057 0.262866
 vn 0.148877 0.935942 0.265487
 v 0.433889 0.862668 0.259892
@@ -128,7 +128,7 @@ vn 0.148877 0.935942 -0.265487
 v -0.160622 0.69378 -0.702046
 vn -0.150881 0.676851 -0.700156
 v 0 0.850651 -0.525731
-vn 0 0.843931 -0.506376
+vn 5.78241e-18 0.843931 -0.506376
 v 0.160622 0.69378 -0.702046
 vn 0.150881 0.676851 -0.700156
 v -0.587785 0.688191 -0.425325
@@ -146,15 +146,15 @@ vn -0.670456 0.429567 -0.578444
 v -0.702046 0.160622 -0.69378
 vn -0.700156 0.150881 -0.676851
 v -0.850651 0.525731 0
-vn -0.843931 0.506376 0
+vn -0.843931 0.506376 1.73472e-17
 v -0.961938 0 -0.273267
-vn -0.944287 -4.62593e-18 -0.281839
+vn -0.944287 0 -0.281839
 v -0.951057 0.262866 -0.16246
 vn -0.935942 0.265487 -0.148877
 v -0.951057 0.262866 0.16246
 vn -0.935942 0.265487 0.148877
 v -0.961938 0 0.273267
-vn -0.944287 9.25186e-18 0.281839
+vn -0.944287 6.93889e-18 0.281839
 v 0.587785 0.688191 0.425325
 vn 0.578444 0.670456 0.429567
 v 0.69378 0.702046 0.160622
@@ -172,13 +172,13 @@ vn 0.700156 0.150881 0.676851
 v -0.262866 0.16246 0.951057
 vn -0.265487 0.148877 0.935942
 v 0 0.273267 0.961938
-vn -9.25186e-18 0.281839 0.944287
+vn 6.93889e-18 0.281839 0.944287
 v -0.702046 -0.160622 0.69378
 vn -0.700156 -0.150881 0.676851
 v -0.525731 0 0.850651
-vn -0.506376 0 0.843931
+vn -0.506376 3.04696e-18 0.843931
 v 0 -0.273267 0.961938
-vn 4.62593e-18 -0.281839 0.944287
+vn 6.93889e-18 -0.281839 0.944287
 v -0.262866 -0.16246 0.951057
 vn -0.265487 -0.148877 0.935942
 v -0.259892 -0.433889 0.862668
@@ -194,15 +194,15 @@ vn -0.935942 -0.265487 -0.148877
 v -0.69378 -0.702046 0.160622
 vn -0.676851 -0.700156 0.150881
 v -0.850651 -0.525731 0
-vn -0.843931 -0.506376 0
+vn -0.843931 -0.506376 -1.15648e-17
 v -0.69378 -0.702046 -0.160622
 vn -0.676851 -0.700156 -0.150881
 v -0.525731 0 -0.850651
-vn -0.506376 0 -0.843931
+vn -0.506376 -5.78241e-18 -0.843931
 v -0.702046 -0.160622 -0.69378
 vn -0.700156 -0.150881 -0.676851
 v 0 0.273267 -0.961938
-vn 4.62593e-18 0.281839 -0.944287
+vn 6.93889e-18 0.281839 -0.944287
 v -0.262866 0.16246 -0.951057
 vn -0.265487 0.148877 -0.935942
 v -0.259892 -0.433889 -0.862668
@@ -210,7 +210,7 @@ vn -0.244131 -0.43272 -0.851037
 v -0.262866 -0.16246 -0.951057
 vn -0.265487 -0.148877 -0.935942
 v 0 -0.273267 -0.961938
-vn -9.25186e-18 -0.281839 -0.944287
+vn 6.93889e-18 -0.281839 -0.944287
 v 0.425325 0.587785 -0.688191
 vn 0.429567 0.578444 -0.670456
 v 0.259892 0.433889 -0.862668
@@ -246,13 +246,13 @@ vn 0.244131 -0.43272 0.851037
 v 0.16246 -0.951057 0.262866
 vn 0.148877 -0.935942 0.265487
 v 0.273267 -0.961938 0
-vn 0.281839 -0.944287 0
+vn 0.281839 -0.944287 -6.93889e-18
 v -0.160622 -0.69378 0.702046
 vn -0.150881 -0.676851 0.700156
 v 0 -0.850651 0.525731
-vn 0 -0.843931 0.506376
+vn 3.04696e-18 -0.843931 0.506376
 v -0.273267 -0.961938 0
-vn -0.281839 -0.944287 0
+vn -0.281839 -0.944287 6.93889e-18
 v -0.16246 -0.951057 0.262866
 vn -0.148877 -0.935942 0.265487
 v -0.433889 -0.862668 0.259892
@@ -268,7 +268,7 @@ vn -0.148877 -0.935942 -0.265487
 v 0.160622 -0.69378 -0.702046
 vn 0.150881 -0.676851 -0.700156
 v 0 -0.850651 -0.525731
-vn 0 -0.843931 -0.506376
+vn -5.78241e-18 -0.843931 -0.506376
 v -0.160622 -0.69378 -0.702046
 vn -0.150881 -0.676851 -0.700156
 v 0.587785 -0.688191 -0.425325
@@ -286,19 +286,19 @@ vn 0.670456 -0.429567 -0.578444
 v 0.702046 -0.160622 -0.69378
 vn 0.700156 -0.150881 -0.676851
 v 0.850651 -0.525731 0
-vn 0.843931 -0.506376 0
+vn 0.843931 -0.506376 1.73472e-17
 v 0.961938 0 -0.273267
-vn 0.944287 4.62593e-18 -0.281839
+vn 0.944287 0 -0.281839
 v 0.951057 -0.262866 -0.16246
 vn 0.935942 -0.265487 -0.148877
 v 0.951057 -0.262866 0.16246
 vn 0.935942 -0.265487 0.148877
 v 0.961938 0 0.273267
-vn 0.944287 -9.25186e-18 0.281839
+vn 0.944287 -6.93889e-18 0.281839
 v 0.262866 -0.16246 0.951057
 vn 0.265487 -0.148877 0.935942
 v 0.525731 0 0.850651
-vn 0.506376 0 0.843931
+vn 0.506376 -3.04696e-18 0.843931
 v 0.262866 0.16246 0.951057
 vn 0.265487 0.148877 0.935942
 v -0.587785 -0.688191 0.425325
@@ -314,7 +314,7 @@ vn -0.578444 -0.670456 -0.429567
 v -0.688191 -0.425325 -0.587785
 vn -0.670456 -0.429567 -0.578444
 v 0.525731 0 -0.850651
-vn 0.506376 0 -0.843931
+vn 0.506376 5.78241e-18 -0.843931
 v 0.262866 -0.16246 -0.951057
 vn 0.265487 -0.148877 -0.935942
 v 0.262866 0.16246 -0.951057
@@ -324,7 +324,7 @@ vn 0.935942 0.265487 0.148877
 v 0.951057 0.262866 -0.16246
 vn 0.935942 0.265487 -0.148877
 v 0.850651 0.525731 0
-vn 0.843931 0.506376 0
+vn 0.843931 0.506376 -1.15648e-17
 # Faces: 320
 f 1//1 43//43 45//45 
 f 13//13 44//44 43//43 

From 40e8a77c5fbccbbb05978e7040369041c08f8f1a Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 15:01:57 -0400
Subject: [PATCH 09/12] (meshing) Add OrientNormals tests

---
 apps/src/GeneratePPM.cpp             |  2 +-
 core/CMakeLists.txt                  |  1 -
 core/include/vc/core/shapes/Cube.hpp |  2 +-
 meshing/CMakeLists.txt               |  1 +
 meshing/test/ITK2VTKTest.cpp         |  4 +-
 meshing/test/OrientNormalsTest.cpp   | 77 ++++++++++++++++++++++++++++
 6 files changed, 82 insertions(+), 5 deletions(-)
 create mode 100644 meshing/test/OrientNormalsTest.cpp

diff --git a/apps/src/GeneratePPM.cpp b/apps/src/GeneratePPM.cpp
index 393ff4059..0dc5f39f9 100644
--- a/apps/src/GeneratePPM.cpp
+++ b/apps/src/GeneratePPM.cpp
@@ -5,9 +5,9 @@
 #include "vc/core/io/MeshIO.hpp"
 #include "vc/core/types/PerPixelMap.hpp"
 #include "vc/core/util/Logging.hpp"
+#include "vc/meshing/OrientNormals.hpp"
 #include "vc/texturing/AngleBasedFlattening.hpp"
 #include "vc/texturing/PPMGenerator.hpp"
-#include "vc/meshing/OrientNormals.hpp"
 
 namespace vc = volcart;
 namespace vcm = volcart::meshing;
diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
index 5f49a83ae..1f211f9e5 100644
--- a/core/CMakeLists.txt
+++ b/core/CMakeLists.txt
@@ -61,7 +61,6 @@ set(util_srcs
 
 set(logging_srcs
     src/Logging.cpp
-        include/vc/core/util/Json.hpp
 )
 
 configure_file(src/Version.cpp.in Version.cpp)
diff --git a/core/include/vc/core/shapes/Cube.hpp b/core/include/vc/core/shapes/Cube.hpp
index 14c2863db..483b0ae40 100644
--- a/core/include/vc/core/shapes/Cube.hpp
+++ b/core/include/vc/core/shapes/Cube.hpp
@@ -43,7 +43,7 @@ class Cube : public ShapePrimitive
         addCell_(0, 1, 2);
         addCell_(0, 2, 3);
         addCell_(3, 2, 6);
-        addCell_(3,6,7);
+        addCell_(3, 6, 7);
         addCell_(7, 6, 5);
         addCell_(7, 5, 4);
         addCell_(4, 5, 1);
diff --git a/meshing/CMakeLists.txt b/meshing/CMakeLists.txt
index 813681bb9..95be48e88 100644
--- a/meshing/CMakeLists.txt
+++ b/meshing/CMakeLists.txt
@@ -71,6 +71,7 @@ set(test_srcs
     test/ScaleMeshTest.cpp
     test/SmoothNormalsTest.cpp
     test/OrderedPointSetMesherTest.cpp
+    test/OrientNormalsTest.cpp
 )
 
 # Add a test executable for each src
diff --git a/meshing/test/ITK2VTKTest.cpp b/meshing/test/ITK2VTKTest.cpp
index 85dc542d8..a47b1b07b 100644
--- a/meshing/test/ITK2VTKTest.cpp
+++ b/meshing/test/ITK2VTKTest.cpp
@@ -15,8 +15,8 @@ using namespace volcart;
 /*
  * The following five fixture build test inputs for the ITK2VTK tests
  *
- * Comments are included in the Plane Fixture only...the remainder of the fixture
- * copy the same ideas
+ * Comments are included in the Plane Fixture only...the remainder of the
+ * fixture copy the same ideas
  */
 
 class ITK2VTKPlaneFixture : public ::testing::Test
diff --git a/meshing/test/OrientNormalsTest.cpp b/meshing/test/OrientNormalsTest.cpp
new file mode 100644
index 000000000..de0b41d36
--- /dev/null
+++ b/meshing/test/OrientNormalsTest.cpp
@@ -0,0 +1,77 @@
+#include <gtest/gtest.h>
+
+#include "vc/core/shapes/Cube.hpp"
+#include "vc/core/shapes/Plane.hpp"
+#include "vc/meshing/OrientNormals.hpp"
+
+using namespace volcart;
+using namespace volcart::shapes;
+using namespace volcart::meshing;
+
+inline void ExpectNormalEq(
+    const ITKMesh::Pointer& result, const ITKMesh::Pointer& expected)
+{
+    for (auto it = result->GetPoints()->Begin();
+         it != result->GetPoints()->End(); ++it) {
+        ITKPixel resultN;
+        ITKPixel expectedN;
+        result->GetPointData(it.Index(), &resultN);
+        expected->GetPointData(it.Index(), &expectedN);
+
+        EXPECT_DOUBLE_EQ(resultN[0], expectedN[0]);
+        EXPECT_DOUBLE_EQ(resultN[1], expectedN[1]);
+        EXPECT_DOUBLE_EQ(resultN[2], expectedN[2]);
+    }
+}
+
+inline void ExpectNormalInverse(
+    const ITKMesh::Pointer& result, const ITKMesh::Pointer& expected)
+{
+    for (auto it = result->GetPoints()->Begin();
+         it != result->GetPoints()->End(); ++it) {
+        ITKPixel resultN;
+        ITKPixel expectedN;
+        result->GetPointData(it.Index(), &resultN);
+        expected->GetPointData(it.Index(), &expectedN);
+
+        EXPECT_DOUBLE_EQ(resultN[0], -expectedN[0]);
+        EXPECT_DOUBLE_EQ(resultN[1], -expectedN[1]);
+        EXPECT_DOUBLE_EQ(resultN[2], -expectedN[2]);
+    }
+}
+
+TEST(OrientNormals, Centroid)
+{
+    auto input = Cube().itkMesh();
+
+    OrientNormals orient;
+    orient.setReferenceMode(OrientNormals::ReferenceMode::Centroid);
+    orient.setMesh(input);
+    auto output = orient.compute();
+
+    ExpectNormalInverse(output, input);
+}
+
+TEST(OrientNormals, ManualPositive)
+{
+    auto input = Plane().itkMesh();
+
+    OrientNormals orient;
+    orient.setReferencePoint({0, 1, 0});
+    orient.setMesh(input);
+    auto output = orient.compute();
+
+    ExpectNormalEq(output, input);
+}
+
+TEST(OrientNormals, ManualNegative)
+{
+    auto input = Plane().itkMesh();
+
+    OrientNormals orient;
+    orient.setReferencePoint({0, -1, 0});
+    orient.setMesh(input);
+    auto output = orient.compute();
+
+    ExpectNormalInverse(output, input);
+}
\ No newline at end of file

From 2e4eda339366fed5f687dce9ff704c3b377499eb Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 21:23:07 -0400
Subject: [PATCH 10/12] Fix bug where we were passing the tests by changing the
 input mesh

---
 apps/src/Render.cpp                | 16 ++++++++--------
 meshing/src/OrientNormals.cpp      |  8 ++++----
 meshing/test/OrientNormalsTest.cpp |  9 +++++++++
 3 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/apps/src/Render.cpp b/apps/src/Render.cpp
index 0be602a07..afef94b2a 100644
--- a/apps/src/Render.cpp
+++ b/apps/src/Render.cpp
@@ -480,14 +480,6 @@ auto main(int argc, char* argv[]) -> int
             smooth->input = *results["mesh"];
             results["mesh"] = &smooth->output;
         }
-
-        // Save the intermediate mesh
-        if (parsed.count("intermediate-mesh") > 0) {
-            fs::path meshPath = parsed["intermediate-mesh"].as<std::string>();
-            auto writer = graph->insertNode<WriteMeshNode>();
-            writer->path = meshPath;
-            writer->mesh = *results["mesh"];
-        }
     }
 
     ///// Reorient the mesh normals /////
@@ -498,6 +490,14 @@ auto main(int argc, char* argv[]) -> int
         results["mesh"] = &orient->output;
     }
 
+    ///// Save the intermediate mesh /////
+    if (parsed.count("intermediate-mesh") > 0) {
+        fs::path meshPath = parsed["intermediate-mesh"].as<std::string>();
+        auto writer = graph->insertNode<WriteMeshNode>();
+        writer->path = meshPath;
+        writer->mesh = *results["mesh"];
+    }
+
     ///// Flattening /////
     if (needResample and results.count("uvMap") > 0) {
         Logger()->warn(
diff --git a/meshing/src/OrientNormals.cpp b/meshing/src/OrientNormals.cpp
index 2da44a1fc..564e81ff6 100644
--- a/meshing/src/OrientNormals.cpp
+++ b/meshing/src/OrientNormals.cpp
@@ -91,13 +91,13 @@ auto OrientNormals::compute() -> ITKMesh::Pointer
 
     // Flip the normals as required
     if (flip) {
-        for (auto it = input_->GetPoints()->Begin();
-             it != input_->GetPoints()->End(); ++it) {
+        for (auto it = output_->GetPoints()->Begin();
+             it != output_->GetPoints()->End(); ++it) {
             // Convert point data to cv::Vec3d
             ITKPixel normal;
-            input_->GetPointData(it.Index(), &normal);
+            output_->GetPointData(it.Index(), &normal);
             normal *= -1;
-            input_->SetPointData(it.Index(), normal);
+            output_->SetPointData(it.Index(), normal);
         }
     }
 
diff --git a/meshing/test/OrientNormalsTest.cpp b/meshing/test/OrientNormalsTest.cpp
index de0b41d36..a6bbe309c 100644
--- a/meshing/test/OrientNormalsTest.cpp
+++ b/meshing/test/OrientNormalsTest.cpp
@@ -49,7 +49,10 @@ TEST(OrientNormals, Centroid)
     orient.setMesh(input);
     auto output = orient.compute();
 
+    // Check the output has changed
     ExpectNormalInverse(output, input);
+    // Check that the input hasn't changed
+    ExpectNormalEq(input, Cube().itkMesh());
 }
 
 TEST(OrientNormals, ManualPositive)
@@ -61,7 +64,10 @@ TEST(OrientNormals, ManualPositive)
     orient.setMesh(input);
     auto output = orient.compute();
 
+    // Check the output hasn't changed
     ExpectNormalEq(output, input);
+    // Check that the input hasn't changed
+    ExpectNormalEq(input, Plane().itkMesh());
 }
 
 TEST(OrientNormals, ManualNegative)
@@ -73,5 +79,8 @@ TEST(OrientNormals, ManualNegative)
     orient.setMesh(input);
     auto output = orient.compute();
 
+    // Check the output has changed
     ExpectNormalInverse(output, input);
+    // Check that the input hasn't changed
+    ExpectNormalEq(input, Plane().itkMesh());
 }
\ No newline at end of file

From be8fcbdba94109a3bf55fb7f577308e826afbd46 Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 21:29:46 -0400
Subject: [PATCH 11/12] Revert other node changes. Will come back in a diff PR

---
 graph/src/meshing.cpp | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/graph/src/meshing.cpp b/graph/src/meshing.cpp
index 063b59a6d..f08f5fcec 100644
--- a/graph/src/meshing.cpp
+++ b/graph/src/meshing.cpp
@@ -33,7 +33,7 @@ MeshingNode::MeshingNode()
 {
     registerInputPort("points", points);
     registerOutputPort("mesh", mesh);
-    compute = [this]() { mesh_ = mesher_.compute(); };
+    compute = [=]() { mesh_ = mesher_.compute(); };
 }
 
 auto MeshingNode::serialize_(bool useCache, const fs::path& cacheDir)
@@ -63,7 +63,7 @@ ScaleMeshNode::ScaleMeshNode()
     registerInputPort("scaleFactor", scaleFactor);
     registerOutputPort("output", output);
 
-    compute = [this]() {
+    compute = [=]() {
         if (input_) {
             output_ = ScaleMesh(input_, scaleFactor_);
         }
@@ -102,7 +102,7 @@ CalculateNumVertsNode::CalculateNumVertsNode()
     registerInputPort("density", density);
     registerOutputPort("numVerts", numVerts);
 
-    compute = [this]() {
+    compute = [=]() {
         using meshmath::SurfaceArea;
         static constexpr double UM_TO_MM{0.000001};
         static constexpr std::size_t MIN_NUM{100};
@@ -134,7 +134,7 @@ LaplacianSmoothMeshNode::LaplacianSmoothMeshNode()
 {
     registerInputPort("input", input);
     registerOutputPort("output", output);
-    compute = [this]() { mesh_ = smoother_.compute(); };
+    compute = [=]() { mesh_ = smoother_.compute(); };
 }
 
 auto LaplacianSmoothMeshNode::serialize_(
@@ -187,7 +187,7 @@ ResampleMeshNode::ResampleMeshNode()
     registerInputPort("subsampleThreshold", subsampleThreshold);
     registerInputPort("quadricsOptimizationLevel", quadricsOptimizationLevel);
     registerOutputPort("output", output);
-    compute = [this]() { mesh_ = acvd_.compute(); };
+    compute = [=]() { mesh_ = acvd_.compute(); };
 }
 
 auto ResampleMeshNode::serialize_(bool useCache, const fs::path& cacheDir)
@@ -234,7 +234,7 @@ UVMapToMeshNode::UVMapToMeshNode()
     registerInputPort("scaleToUVDimensions", scaleToUVDimensions);
     registerOutputPort("outputMesh", outputMesh);
 
-    compute = [this]() {
+    compute = [=]() {
         mesher_.setScaleToUVDimensions(scaleDims_);
         output_ = mesher_.compute();
     };
@@ -272,7 +272,7 @@ OrientNormalsNode::OrientNormalsNode()
     registerInputPort("referenceMode", referenceMode);
     registerInputPort("referencePoint", referencePoint);
     registerOutputPort("output", output);
-    compute = [this]() { output_ = orientNormals_.compute(); };
+    compute = [&]() { output_ = orientNormals_.compute(); };
 }
 
 auto OrientNormalsNode::serialize_(bool useCache, const fs::path& cacheDir)

From 332fac37285d2e4b446c45bede6fb64e18803b4d Mon Sep 17 00:00:00 2001
From: Seth Parker <csparker247@gmail.com>
Date: Thu, 2 Nov 2023 21:49:42 -0400
Subject: [PATCH 12/12] Small docs change

---
 meshing/include/vc/meshing/OrientNormals.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/meshing/include/vc/meshing/OrientNormals.hpp b/meshing/include/vc/meshing/OrientNormals.hpp
index add06200b..e4f6f5d36 100644
--- a/meshing/include/vc/meshing/OrientNormals.hpp
+++ b/meshing/include/vc/meshing/OrientNormals.hpp
@@ -19,8 +19,8 @@ class OrientNormals
 public:
     /** @brief Reference point mode */
     enum class ReferenceMode {
-        Centroid, /** Mesh centroid reference point for convex meshes. */
-        Manual    /** Point provided by setReferencePoint(). */
+        Centroid,  ///< Mesh centroid reference point for convex meshes.
+        Manual     ///< Point provided by setReferencePoint().
     };
 
     /** @brief Default constructor */