Merge pull request #2178 from SCIInstitute/2177-display-thickness

Resolve #2177 by adding the new feature to display the thickness as an inner surface on slices

Author: akenmorris

Libs/Mesh/MeshComputeThickness.cpp

@@ -174,6 +174,7 @@ static double get_distance_to_opposite_side(Mesh& mesh, int point_id) {
   return distance;
 }
 
+//---------------------------------------------------------------------------
 double compute_thickness_from_signal(const std::vector<double>& intensities_input, double step_size) {
   auto smoothed = median_smooth_signal_intensities(intensities_input);
   for (int k = 0; k < 10; k++) {
@@ -518,4 +519,49 @@ void compute_thickness(Mesh& mesh, Image& image, Image* dt, double max_dist, dou
     d_mesh.write(distance_mesh);
   }
 }
+
+//---------------------------------------------------------------------------
+Mesh compute_inner_mesh(const Mesh& mesh, std::string array_name) {
+  // create a copy
+  Mesh new_mesh = mesh;
+
+  auto poly_data = new_mesh.getVTKMesh();
+
+  // check if it has this array
+  if (!poly_data->GetPointData()->HasArray(array_name.c_str())) {
+    SW_ERROR("Mesh does not have array {}", array_name);
+  }
+
+  // check if it has normals, if not, compute them
+  if (!poly_data->GetPointData()->GetNormals()) {
+    new_mesh.computeNormals();
+  }
+
+  auto values = vtkDoubleArray::SafeDownCast(poly_data->GetPointData()->GetArray(array_name.c_str()));
+  if (!values) {
+    return new_mesh;
+  }
+
+  // for each vertex, move the particle the distance scalar
+  for (int i = 0; i < mesh.numPoints(); i++) {
+    Point3 point;
+    poly_data->GetPoint(i, point.GetDataPointer());
+
+    double value = values->GetValue(i);
+
+    // get the normal
+    double normal[3];
+    poly_data->GetPointData()->GetNormals()->GetTuple(i, normal);
+
+    // move the point in the opposite direction of the normal by the value
+    for (int j = 0; j < 3; j++) {
+      point[j] -= normal[j] * value;
+    }
+
+    // modify the point position in the poly_data
+    poly_data->GetPoints()->SetPoint(i, point.GetDataPointer());
+  }
+  return new_mesh;
+}
+
 }  // namespace shapeworks::mesh

Libs/Mesh/MeshComputeThickness.h

@@ -9,4 +9,6 @@ namespace shapeworks::mesh {
 void compute_thickness(Mesh &mesh, Image &image, Image *dt, double max_dist, double median_radius,
                        std::string distance_mesh);
 
+Mesh compute_inner_mesh(const Mesh &mesh, std::string array_name);
+
 }  // namespace shapeworks::mesh

Studio/Data/Session.cpp

@@ -1102,6 +1102,28 @@ void Session::set_image_sync_slice(bool enabled) {
 //---------------------------------------------------------------------------
 bool Session::get_image_sync_slice() { return params_.get("image_sync_slice", true); }
 
+//---------------------------------------------------------------------------
+void Session::set_image_thickness_feature(bool enabled) {
+  if (enabled == get_image_thickness_feature() || is_loading()) {
+    return;
+  }
+  params_.set("image_thickness_feature", enabled);
+  Q_EMIT image_slice_settings_changed();
+}
+
+//---------------------------------------------------------------------------
+bool Session::get_image_thickness_feature() { return params_.get("image_thickness_feature", false); }
+
+//---------------------------------------------------------------------------
+void Session::set_feature_map(std::string feature_map) {
+  if (feature_map != get_feature_map() || is_loading()) {
+    params_.set("feature_map", feature_map);
+  }
+}
+
+//---------------------------------------------------------------------------
+std::string Session::get_feature_map() { return params_.get("feature_map", ""); }
+
 //---------------------------------------------------------------------------
 bool Session::has_constraints() {
   for (auto& shape : shapes_) {

Studio/Data/Session.h

@@ -202,6 +202,13 @@ class Session : public QObject, public QEnableSharedFromThis<Session> {
   void set_image_sync_slice(bool enabled);
   bool get_image_sync_slice();
 
+  // 3D image, thickness feature
+  void set_image_thickness_feature(bool enabled);
+  bool get_image_thickness_feature();
+
+  void set_feature_map(std::string feature_map);
+  std::string get_feature_map();
+
   bool has_constraints();
 
   void set_loading(bool loading);

Studio/Interface/ShapeWorksStudioApp.cpp

@@ -978,6 +978,7 @@ void ShapeWorksStudioApp::new_session() {
   connect(ui_->image_share_window_and_level_, &QCheckBox::clicked, session_.data(),
           &Session::set_image_share_window_and_level);
   connect(ui_->image_sync_slices, &QCheckBox::clicked, session_.data(), &Session::set_image_sync_slice);
+  connect(ui_->image_thickness_feature, &QCheckBox::clicked, session_.data(), &Session::set_image_thickness_feature);
 
   connect(ui_->planes_visible_button_, &QToolButton::toggled, session_.data(), &Session::set_show_planes);
   connect(ui_->landmarks_visible_button, &QToolButton::clicked, session_.data(), &Session::set_show_landmarks);
@@ -2050,9 +2051,7 @@ void ShapeWorksStudioApp::image_combo_changed(int index) {
 //---------------------------------------------------------------------------
 bool ShapeWorksStudioApp::set_feature_map(std::string feature_map) {
   if (feature_map != get_feature_map()) {
-    if (!session_->is_loading()) {
-      session_->parameters().set("feature_map", feature_map);
-    }
+    session_->set_feature_map(feature_map);
     update_view_mode();
     return true;
   }
@@ -2061,7 +2060,7 @@ bool ShapeWorksStudioApp::set_feature_map(std::string feature_map) {
 
 //---------------------------------------------------------------------------
 std::string ShapeWorksStudioApp::get_feature_map() {
-  std::string feature_map = session_->parameters().get("feature_map", "");
+  std::string feature_map = session_->get_feature_map();
 
   // confirm that this is a valid feature map
   auto feature_maps = session_->get_project()->get_feature_names();