Add feature to export clipped meshes (constraints clipped) for #2436

Libs/Analyze/Shape.cpp

@@ -915,6 +915,16 @@ Constraints& Shape::get_constraints(int domain_id) {
   return constraints_[domain_id];
 }
 
+//---------------------------------------------------------------------------
+bool Shape::has_constraints() {
+  for (int i = 0; i < constraints_.size(); i++) {
+    if (constraints_[i].hasConstraints()) {
+      return true;
+    }
+  }
+  return false;
+}
+
 //---------------------------------------------------------------------------
 bool Shape::has_planes() {
   for (int i = 0; i < constraints_.size(); i++) {

Libs/Analyze/Shape.h

@@ -185,6 +185,8 @@ class Shape {
 
   Constraints& get_constraints(int domain_id);
 
+  bool has_constraints();
+
   bool has_planes();
 
   std::vector<std::shared_ptr<Surface>> get_groomed_mesh_wrappers();

Studio/Data/ExportUtils.cpp

@@ -7,12 +7,14 @@
 #include <Shape.h>
 #include <StringUtils.h>
 #include <Utils/StudioUtils.h>
+#include <Visualization/Visualizer.h>
 #include <vtkPointData.h>
 #include <vtkPolyData.h>
 
 #include <QDir>
 #include <QFileDialog>
 #include <QFileInfo>
+#include <QObject>
 #include <QProgressDialog>
 
 namespace shapeworks {
@@ -225,4 +227,9 @@ bool ExportUtils::write_pca_scores(ShapeWorksStudioApp* app, ParticleShapeStatis
   return true;
 }
 
+//----------------------------------------------------------------------------
+QString ExportUtils::get_mesh_file_filter() {
+  return QObject::tr("VTK files (*.vtk);;PLY files (*.ply);;VTP files (*.vtp);;OBJ files (*.obj);;STL files (*.stl)");
+}
+
 }  // namespace shapeworks

Studio/Data/ExportUtils.h

@@ -23,6 +23,9 @@ class ExportUtils {
   static bool write_particle_scalars(ShapeWorksStudioApp* app, std::shared_ptr<Shape> shape, QString filename);
 
   static bool write_pca_scores(ShapeWorksStudioApp* app, ParticleShapeStatistics* stats, QString filename);
+
+  static QString get_mesh_file_filter();
+
 };
 
 }  // namespace shapeworks

Studio/Interface/ShapeWorksStudioApp.cpp

@@ -241,8 +241,17 @@ ShapeWorksStudioApp::ShapeWorksStudioApp() {
   connect(ui_->action_export_all_subjects_particle_scalars, &QAction::triggered, this,
           &ShapeWorksStudioApp::action_export_all_subjects_particle_scalars_triggered);
 
-  connect(ui_->action_export_current_mesh, &QAction::triggered, this,
-          &ShapeWorksStudioApp::action_export_current_mesh_triggered);
+  connect(ui_->action_export_current_mesh, &QAction::triggered, this, [&]() {
+    // get the first index of the visualizer (top left lightbox item)
+    int index = visualizer_->get_lightbox()->get_start_shape();
+    ShapeWorksStudioApp::action_export_current_mesh_triggered(index);
+  });
+
+  connect(ui_->action_export_current_mesh_clipped, &QAction::triggered, this, [&]() {
+    // get the first index of the visualizer (top left lightbox item)
+    int index = visualizer_->get_lightbox()->get_start_shape();
+    ShapeWorksStudioApp::action_export_current_mesh_triggered(index, true);
+  });
 
   connect(ui_->save_as_swproj, &QAction::triggered, this, &ShapeWorksStudioApp::save_as_swproj_clicked);
   connect(ui_->save_as_xlsx, &QAction::triggered, this, &ShapeWorksStudioApp::save_as_xlsx_clicked);
@@ -951,10 +960,15 @@ void ShapeWorksStudioApp::handle_lightbox_right_click(int index) {
   QMenu* menu = new QMenu(nullptr);
   menu->setAttribute(Qt::WA_DeleteOnClose);
   QAction* export_mesh_action = menu->addAction("Export Mesh");
+  QAction* export_clipped_mesh_action = nullptr;
   QAction* mark_excluded_action = nullptr;
   QAction* unmark_excluded_action = nullptr;
   QAction* mark_fixed_action = nullptr;
   QAction* unmark_fixed_action = nullptr;
+
+  if (shape->has_constraints()) {
+    export_clipped_mesh_action = menu->addAction("Export Clipped Mesh");
+  }
   if (shape->is_subject() && !shape->is_excluded()) {
     mark_excluded_action = menu->addAction("Mark as excluded");
   }
@@ -971,7 +985,9 @@ void ShapeWorksStudioApp::handle_lightbox_right_click(int index) {
   menu->popup(QCursor::pos());
   connect(menu, &QMenu::triggered, menu, [=](QAction* action) {
     if (action == export_mesh_action) {
-      action_export_current_mesh_triggered(index);
+      action_export_current_mesh_triggered(index, false);
+    } else if (action == export_clipped_mesh_action) {
+      action_export_current_mesh_triggered(index, true);
     } else if (action == mark_excluded_action) {
       shape->get_subject()->set_excluded(true);
     } else if (action == unmark_excluded_action) {
@@ -1617,19 +1633,20 @@ void ShapeWorksStudioApp::on_action_preferences_triggered() {
 }
 
 //---------------------------------------------------------------------------
-void ShapeWorksStudioApp::action_export_current_mesh_triggered(int index) {
+void ShapeWorksStudioApp::action_export_current_mesh_triggered(int index, bool clip_constraints) {
   bool single = StudioUtils::ask_multiple_domains_as_single(this, session_->get_project());
 
-  QString filename = ExportUtils::get_save_filename(this, tr("Export Mesh"), get_mesh_file_filter(), ".vtk");
+  QString filename =
+      ExportUtils::get_save_filename(this, tr("Export Mesh"), ExportUtils::get_mesh_file_filter(), ".vtk");
   if (filename.isEmpty()) {
     return;
   }
 
   if (single) {
-    StudioUtils::write_mesh(visualizer_->get_current_mesh(index), filename);
+    StudioUtils::write_mesh(visualizer_->get_current_mesh(index, clip_constraints), filename);
     SW_MESSAGE("Wrote: " + filename.toStdString());
   } else {
-    auto meshes = visualizer_->get_current_meshes_transformed(index);
+    auto meshes = visualizer_->get_current_meshes_transformed(index, clip_constraints);
     auto domain_names = session_->get_project()->get_domain_names();
 
     if (meshes.empty()) {
@@ -1756,7 +1773,7 @@ void ShapeWorksStudioApp::on_action_export_mesh_scalars_triggered() {
   }
 
   if (single) {
-    auto poly_data = visualizer_->get_current_mesh(0);
+    auto poly_data = visualizer_->get_current_mesh(0, false);
     write_scalars(poly_data, filename);
   } else {
     auto meshes = visualizer_->get_current_meshes_transformed(0);
@@ -2092,11 +2109,6 @@ bool ShapeWorksStudioApp::write_particle_file(std::string filename, Eigen::Vecto
   return true;
 }
 
-//---------------------------------------------------------------------------
-QString ShapeWorksStudioApp::get_mesh_file_filter() {
-  return tr("VTK files (*.vtk);;PLY files (*.ply);;VTP files (*.vtp);;OBJ files (*.obj);;STL files (*.stl)");
-}
-
 //---------------------------------------------------------------------------
 void ShapeWorksStudioApp::update_feature_map_selection(int index) {
   QString feature_map = ui_->features->itemText(index);

Studio/Interface/ShapeWorksStudioApp.h

@@ -27,7 +27,7 @@
 class Ui_ShapeWorksStudioApp;
 
 namespace monailabel {
-  class MonaiLabelTool;
+class MonaiLabelTool;
 }
 
 namespace shapeworks {
@@ -89,7 +89,7 @@ class ShapeWorksStudioApp : public QMainWindow {
   void on_actionExport_Eigenvectors_triggered();
   void on_actionExport_PCA_Mode_Points_triggered();
   void on_action_preferences_triggered();
-  void action_export_current_mesh_triggered(int index = 0);
+  void action_export_current_mesh_triggered(int index = 0, bool clip_constraints = false);
   void on_action_export_current_particles_triggered();
   void on_action_export_mesh_scalars_triggered();
   void on_action_export_pca_scores_triggered();
@@ -162,6 +162,8 @@ class ShapeWorksStudioApp : public QMainWindow {
   Preferences& prefs() { return preferences_; }
   QSharedPointer<Session> session() { return session_; }
 
+  QSharedPointer<Visualizer> get_visualizer() { return visualizer_; }
+
  protected:
   void dragEnterEvent(QDragEnterEvent* event) override;
   void dragLeaveEvent(QDragLeaveEvent* event) override;
@@ -180,8 +182,6 @@ class ShapeWorksStudioApp : public QMainWindow {
 
   static bool write_particle_file(std::string filename, Eigen::VectorXd particles);
 
-  static QString get_mesh_file_filter();
-
   static const std::string SETTING_ZOOM_C;
 
   void set_view_combo_item_enabled(int item, bool value);

Studio/Interface/ShapeWorksStudioApp.ui

@@ -6,7 +6,7 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>1243</width>
+    <width>1310</width>
     <height>705</height>
    </rect>
   </property>
@@ -714,7 +714,7 @@ QToolBar QToolButton::checked {
     <rect>
      <x>0</x>
      <y>0</y>
-     <width>1243</width>
+     <width>1310</width>
      <height>33</height>
     </rect>
    </property>
@@ -727,6 +727,7 @@ QToolBar QToolButton::checked {
       <string>Export...</string>
      </property>
      <addaction name="action_export_current_mesh"/>
+     <addaction name="action_export_current_mesh_clipped"/>
      <addaction name="action_export_current_particles"/>
      <addaction name="action_export_particle_scalars"/>
      <addaction name="action_export_mesh_scalars"/>
@@ -1171,16 +1172,16 @@ QToolBar QToolButton::checked {
    </property>
   </action>
   <action name="action_monai_mode">
-    <property name="checkable">
-     <bool>true</bool>
-    </property>
-    <property name="icon">
-     <iconset resource="../Resources/ShapeWorksStudio.qrc">
-      <normaloff>:/Studio/Images/MONAI-Label.png</normaloff>:/Studio/Images/MONAI-Label.png</iconset>
-    </property>
-    <property name="text">
-     <string>MONAI</string>
-    </property>
+   <property name="checkable">
+    <bool>true</bool>
+   </property>
+   <property name="icon">
+    <iconset resource="../Resources/ShapeWorksStudio.qrc">
+     <normaloff>:/Studio/Images/MONAI-Label.png</normaloff>:/Studio/Images/MONAI-Label.png</iconset>
+   </property>
+   <property name="text">
+    <string>MONAI</string>
+   </property>
   </action>
   <action name="action_export_pca_montage">
    <property name="text">
@@ -1220,6 +1221,11 @@ QToolBar QToolButton::checked {
     <enum>QAction::ApplicationSpecificRole</enum>
    </property>
   </action>
+  <action name="action_export_current_mesh_clipped">
+   <property name="text">
+    <string>Export Current Mesh Clipped...</string>
+   </property>
+  </action>
  </widget>
  <customwidgets>
   <customwidget>

Studio/Visualization/Lightbox.h

@@ -94,6 +94,8 @@ class Lightbox : public QObject {
 
   vtkRenderWindow* get_render_window();
 
+  int get_start_shape();
+
  public Q_SLOTS:
   void handle_timer_callback();
 
@@ -109,8 +111,6 @@ class Lightbox : public QObject {
 
   void insert_shape_into_viewer(std::shared_ptr<Shape> shape, int position);
 
-  int get_start_shape();
-
   vtkSmartPointer<vtkRenderer> renderer_;
 
   ShapeList shapes_;

Studio/Visualization/Visualizer.cpp

@@ -152,8 +152,8 @@ void Visualizer::handle_new_mesh() {
 }
 
 //-----------------------------------------------------------------------------
-vtkSmartPointer<vtkPolyData> Visualizer::get_current_mesh(int index) {
-  auto meshes = get_current_meshes_transformed(index);
+vtkSmartPointer<vtkPolyData> Visualizer::get_current_mesh(int index, bool clip_constraints) {
+  auto meshes = get_current_meshes_transformed(index, clip_constraints);
   if (meshes.empty()) {
     return nullptr;
   }
@@ -167,7 +167,7 @@ vtkSmartPointer<vtkPolyData> Visualizer::get_current_mesh(int index) {
 }
 
 //-----------------------------------------------------------------------------
-std::vector<vtkSmartPointer<vtkPolyData>> Visualizer::get_current_meshes_transformed(int index) {
+std::vector<vtkSmartPointer<vtkPolyData>> Visualizer::get_current_meshes_transformed(int index, bool clip_constraints) {
   std::vector<vtkSmartPointer<vtkPolyData>> list;
   auto shapes = lightbox_->get_shapes();
   if (shapes.size() > index) {
@@ -178,10 +178,17 @@ std::vector<vtkSmartPointer<vtkPolyData>> Visualizer::get_current_meshes_transfo
         if (!meshes[domain]->get_poly_data()) {
           return list;
         }
+
+        Mesh mesh(meshes[domain]->get_poly_data());
+        if (clip_constraints) {
+          auto constraint = shapes[index]->get_constraints(domain);
+          constraint.clipMesh(mesh);
+        }
+
         // we have to transform each domain to its location in order to export an appended mesh
         auto filter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
         filter->SetTransform(get_transform(shapes[index], get_alignment_domain(), domain));
-        filter->SetInputData(meshes[domain]->get_poly_data());
+        filter->SetInputData(mesh.getVTKMesh());
         filter->Update();
         list.push_back(filter->GetOutput());
       }

Studio/Visualization/Visualizer.h

@@ -80,8 +80,8 @@ class Visualizer : public QObject {
   vtkSmartPointer<vtkPolyData> get_current_particle_poly_data();
 
   void handle_new_mesh();
-  vtkSmartPointer<vtkPolyData> get_current_mesh(int index);
-  std::vector<vtkSmartPointer<vtkPolyData>> get_current_meshes_transformed(int index);
+  vtkSmartPointer<vtkPolyData> get_current_mesh(int index, bool clip_constraints);
+  std::vector<vtkSmartPointer<vtkPolyData>> get_current_meshes_transformed(int index, bool clip_constraints = false);
 
   //! Get the currently selected feature map
   const std::string& get_feature_map() const;