Merge pull request #2442 from SCIInstitute/mesh-isolate

akenmorris · web-flow · commit 67d3f2de0b62 · 2025-10-10T22:09:41.000-06:00
Add Mesh/Grooming isolate / extract largest component functionality
diff --git a/Applications/shapeworks/Commands.h b/Applications/shapeworks/Commands.h
@@ -82,6 +82,7 @@ COMMAND_DECLARE(FieldMean, MeshCommand);
 COMMAND_DECLARE(FieldStd, MeshCommand);
 COMMAND_DECLARE(FieldNames, MeshCommand);
 COMMAND_DECLARE(FixElement, MeshCommand);
+COMMAND_DECLARE(MeshLargestComponent, MeshCommand);
 COMMAND_DECLARE(ClipClosedSurface, MeshCommand);
 COMMAND_DECLARE(ClosestPoint, MeshCommand);
 COMMAND_DECLARE(GeodesicDistance, MeshCommand);
diff --git a/Applications/shapeworks/MeshCommands.cpp b/Applications/shapeworks/MeshCommands.cpp
@@ -765,6 +765,27 @@ bool FixElement::execute(const optparse::Values &options, SharedCommandData &sha
   return sharedData.validMesh();
 }
 
+///////////////////////////////////////////////////////////////////////////////
+// MeshLargestComponent
+///////////////////////////////////////////////////////////////////////////////
+void MeshLargestComponent::buildParser() {
+  const std::string prog = "mesh-largest-component";
+  const std::string desc = "extract the largest connected component from the mesh";
+  parser.prog(prog).description(desc);
+
+  Command::buildParser();
+}
+
+bool MeshLargestComponent::execute(const optparse::Values &options, SharedCommandData &sharedData) {
+  if (!sharedData.validMesh()) {
+    std::cerr << "No mesh to operate on\n";
+    return false;
+  }
+
+  sharedData.mesh->extractLargestComponent();
+  return sharedData.validMesh();
+}
+
 ///////////////////////////////////////////////////////////////////////////////
 // ClipClosedSurface
 ///////////////////////////////////////////////////////////////////////////////
diff --git a/Applications/shapeworks/shapeworks.cpp b/Applications/shapeworks/shapeworks.cpp
@@ -82,6 +82,7 @@ int main(int argc, char *argv[])
   shapeworks.addCommand(MeshBounds::getCommand());
   shapeworks.addCommand(Distance::getCommand());
   shapeworks.addCommand(FixElement::getCommand());
+  shapeworks.addCommand(MeshLargestComponent::getCommand());
   shapeworks.addCommand(ClipClosedSurface::getCommand());
   shapeworks.addCommand(ComputeNormals::getCommand());
   shapeworks.addCommand(ClosestPoint::getCommand());
diff --git a/Libs/Groom/Groom.cpp b/Libs/Groom/Groom.cpp
@@ -368,6 +368,12 @@ bool Groom::mesh_pipeline(std::shared_ptr<Subject> subject, size_t domain) {
 
 //---------------------------------------------------------------------------
 bool Groom::run_mesh_pipeline(Mesh& mesh, GroomParameters params) {
+  // Extract largest component (should be first)
+  if (params.get_mesh_largest_component()) {
+    mesh.extractLargestComponent();
+    increment_progress();
+  }
+
   if (params.get_fill_mesh_holes_tool()) {
     mesh.fillHoles();
     increment_progress();
@@ -505,6 +511,7 @@ int Groom::get_total_ops() {
                     (project_->get_original_domain_types()[i] == DomainType::Image && params.get_convert_to_mesh());
 
     if (run_mesh) {
+      num_tools += params.get_mesh_largest_component() ? 1 : 0;
       num_tools += params.get_fill_mesh_holes_tool() ? 1 : 0;
       num_tools += params.get_mesh_smooth() ? 1 : 0;
       num_tools += params.get_remesh() ? 1 : 0;
diff --git a/Libs/Groom/GroomParameters.cpp b/Libs/Groom/GroomParameters.cpp
@@ -23,6 +23,7 @@ const std::string ISO_SPACING = "iso_spacing";
 const std::string SPACING = "spacing";
 const std::string CONVERT_MESH = "convert_to_mesh";
 const std::string FILL_MESH_HOLES = "fill_mesh_holes";
+const std::string MESH_LARGEST_COMPONENT = "mesh_largest_component";
 const std::string FILL_HOLES = "fill_holes";
 const std::string ISOLATE = "isolate";
 const std::string PAD = "pad";
@@ -77,6 +78,7 @@ const std::vector<double> spacing{0, 0, 0};
 const bool convert_mesh = false;
 const bool fill_holes = true;
 const bool fill_holes_mesh = false;
+const bool mesh_largest_component = true;
 const bool isolate = true;
 const bool pad = true;
 const int pad_value = 10;
@@ -156,6 +158,7 @@ GroomParameters::GroomParameters(ProjectHandle project, std::string domain_name)
       Keys::SPACING,
       Keys::CONVERT_MESH,
       Keys::FILL_MESH_HOLES,
+      Keys::MESH_LARGEST_COMPONENT,
       Keys::FILL_HOLES,
       Keys::ISOLATE,
       Keys::PAD,
@@ -233,6 +236,14 @@ bool GroomParameters::get_fill_mesh_holes_tool() {
 //---------------------------------------------------------------------------
 void GroomParameters::set_fill_mesh_holes_tool(bool value) { params_.set(Keys::FILL_MESH_HOLES, value); }
 
+//---------------------------------------------------------------------------
+bool GroomParameters::get_mesh_largest_component() {
+  return params_.get(Keys::MESH_LARGEST_COMPONENT, Defaults::mesh_largest_component);
+}
+
+//---------------------------------------------------------------------------
+void GroomParameters::set_mesh_largest_component(bool value) { params_.set(Keys::MESH_LARGEST_COMPONENT, value); }
+
 //---------------------------------------------------------------------------
 bool GroomParameters::get_auto_pad_tool() { return params_.get(Keys::PAD, Defaults::pad); }
 
diff --git a/Libs/Groom/GroomParameters.h b/Libs/Groom/GroomParameters.h
@@ -61,6 +61,9 @@ class GroomParameters {
   bool get_fill_mesh_holes_tool();
   void set_fill_mesh_holes_tool(bool value);
 
+  bool get_mesh_largest_component();
+  void set_mesh_largest_component(bool value);
+
   bool get_auto_pad_tool();
   void set_auto_pad_tool(bool value);
 
diff --git a/Libs/Mesh/Mesh.cpp b/Libs/Mesh/Mesh.cpp
@@ -597,6 +597,22 @@ Mesh& Mesh::fixNonManifold() {
   return *this;
 }
 
+Mesh& Mesh::extractLargestComponent() {
+  auto connectivityFilter = vtkSmartPointer<vtkPolyDataConnectivityFilter>::New();
+  connectivityFilter->SetExtractionModeToLargestRegion();
+  connectivityFilter->SetInputData(poly_data_);
+  connectivityFilter->Update();
+
+  // Clean to remove unused points from other components
+  auto cleanFilter = vtkSmartPointer<vtkCleanPolyData>::New();
+  cleanFilter->SetInputData(connectivityFilter->GetOutput());
+  cleanFilter->Update();
+  poly_data_ = cleanFilter->GetOutput();
+
+  this->invalidateLocators();
+  return *this;
+}
+
 bool Mesh::detectNonManifold() {
   auto features = vtkSmartPointer<vtkFeatureEdges>::New();
   features->SetInputData(this->poly_data_);
diff --git a/Libs/Mesh/Mesh.h b/Libs/Mesh/Mesh.h
@@ -128,6 +128,9 @@ class Mesh {
   /// Attempt to fix non-manifold edges
   Mesh& fixNonManifold();
 
+  /// Extract the largest connected component from the mesh
+  Mesh& extractLargestComponent();
+
   /// Detect if mesh contain non-manifold edges
   bool detectNonManifold();
 
diff --git a/Libs/Python/ShapeworksPython.cpp b/Libs/Python/ShapeworksPython.cpp
@@ -935,6 +935,8 @@ PYBIND11_MODULE(shapeworks_py, m) {
 
       .def("fixElement", &Mesh::fixElement, "fix element winding of mesh")
 
+      .def("extractLargestComponent", &Mesh::extractLargestComponent, "extract the largest connected component from the mesh")
+
       .def(
           "distance",
           [](Mesh& mesh, const Mesh& target, const Mesh::DistanceMethod method) -> decltype(auto) {
diff --git a/Studio/Groom/GroomTool.cpp b/Studio/Groom/GroomTool.cpp
@@ -489,6 +489,7 @@ void GroomTool::set_ui_from_params(GroomParameters params) {
   ui_->blur_checkbox->setChecked(params.get_blur_tool());
   ui_->isolate_checkbox->setChecked(params.get_isolate_tool());
   ui_->fill_holes_checkbox->setChecked(params.get_fill_holes_tool());
+  ui_->mesh_largest_component->setChecked(params.get_mesh_largest_component());
   ui_->mesh_fill_holes->setChecked(params.get_fill_mesh_holes_tool());
   ui_->antialias_iterations->setValue(params.get_antialias_iterations());
   ui_->blur_sigma->setValue(params.get_blur_amount());
@@ -586,6 +587,7 @@ void GroomTool::store_params() {
   params.set_blur_amount(ui_->blur_sigma->value());
   params.set_isolate_tool(ui_->isolate_checkbox->isChecked());
   params.set_fill_holes_tool(ui_->fill_holes_checkbox->isChecked());
+  params.set_mesh_largest_component(ui_->mesh_largest_component->isChecked());
   params.set_fill_mesh_holes_tool(ui_->mesh_fill_holes->isChecked());
   params.set_antialias_iterations(ui_->antialias_iterations->value());
   params.set_groom_output_prefix(preferences_.get_groom_file_template().toStdString());
diff --git a/Studio/Groom/GroomTool.ui b/Studio/Groom/GroomTool.ui
@@ -1397,6 +1397,50 @@ QWidget#domain_panel {
             <property name="bottomMargin">
              <number>0</number>
             </property>
+            <item>
+             <widget class="QWidget" name="mesh_largest_component_widget" native="true">
+              <property name="minimumSize">
+               <size>
+                <width>0</width>
+                <height>30</height>
+               </size>
+              </property>
+              <layout class="QGridLayout" name="gridLayout_22">
+               <property name="leftMargin">
+                <number>0</number>
+               </property>
+               <property name="topMargin">
+                <number>6</number>
+               </property>
+               <property name="rightMargin">
+                <number>0</number>
+               </property>
+               <property name="bottomMargin">
+                <number>6</number>
+               </property>
+               <property name="spacing">
+                <number>0</number>
+               </property>
+               <item row="0" column="0">
+                <widget class="QCheckBox" name="mesh_largest_component">
+                 <property name="text">
+                  <string>Extract Largest Component</string>
+                 </property>
+                 <property name="checked">
+                  <bool>true</bool>
+                 </property>
+                </widget>
+               </item>
+              </layout>
+             </widget>
+            </item>
+            <item>
+             <widget class="Line" name="line_11">
+              <property name="orientation">
+               <enum>Qt::Horizontal</enum>
+              </property>
+             </widget>
+            </item>
             <item>
              <widget class="QWidget" name="fill_holes_mesh_widget" native="true">
               <property name="minimumSize">
diff --git a/Testing/MeshTests/MeshTests.cpp b/Testing/MeshTests/MeshTests.cpp
@@ -844,3 +844,36 @@ TEST(MeshTests, interpolateFieldAtPoint) {
   ASSERT_DOUBLE_EQ(mesh.interpolateFieldAtPoint(fieldName, Point3({0, 0, 50})), 0);
 }
 
+TEST(MeshTests, extractLargestComponentTest) {
+  // Test extractLargestComponent on two_spheres.vtk which has two disconnected spheres
+  // Created with VTK: large sphere (82 points) + small sphere (12 points) = 94 points total
+  Mesh multi_component(std::string(TEST_DATA_DIR) + "/two_spheres.vtk");
+
+  // Verify initial state: should have both spheres
+  ASSERT_EQ(multi_component.numPoints(), 94);
+  ASSERT_EQ(multi_component.numFaces(), 180);
+
+  // Extract the largest component (should keep the larger sphere with 82 points)
+  multi_component.extractLargestComponent();
+
+  // Compare with baseline
+  Mesh baseline(std::string(TEST_DATA_DIR) + "/two_spheres_largest.vtk");
+  ASSERT_TRUE(multi_component == baseline);
+}
+
+TEST(MeshTests, extractLargestComponentSingleComponentTest) {
+  // Test that extracting from a mesh with only one component preserves count
+  Mesh femur(std::string(TEST_DATA_DIR) + "/femur.vtk");
+
+  int original_points = femur.numPoints();
+  int original_faces = femur.numFaces();
+
+  // Extract largest component from a mesh that's already a single component
+  femur.extractLargestComponent();
+
+  // Should have the same number of points and faces
+  // (even though VTK may reorder vertices internally)
+  ASSERT_EQ(femur.numPoints(), original_points);
+  ASSERT_EQ(femur.numFaces(), original_faces);
+}
+
diff --git a/Testing/data/two_spheres.vtk b/Testing/data/two_spheres.vtk
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f7b36e586f74669c9eaa1246409e00afaa86508fcdbe54d9f6d80ebd787358c6
+size 7257
diff --git a/Testing/data/two_spheres_largest.vtk b/Testing/data/two_spheres_largest.vtk
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7e90f299659474a1958e394357907e8c476bb7696ed8f89ad0043d5aa5874351
+size 6530
diff --git a/Testing/shapeworksTests/meshlargestcomponent.sh b/Testing/shapeworksTests/meshlargestcomponent.sh
@@ -0,0 +1,3 @@
+#! /bin/bash
+
+shapeworks readmesh --name $DATA/two_spheres.vtk mesh-largest-component comparemesh --name $DATA/two_spheres_largest.vtk
diff --git a/Testing/shapeworksTests/shapeworksTests.cpp b/Testing/shapeworksTests/shapeworksTests.cpp
@@ -154,3 +154,5 @@ TEST(shapeworksTests, isolateTest) { run_test("isolate.sh"); }
 TEST(shapeworksTests, analyzeTest) { run_sandboxed_test("analyze"); }
 
 TEST(shapeworksTests, thicknessTest) { run_test("thickness.sh"); }
+
+TEST(shapeworksTests, meshlargestcomponentTest) { run_test("meshlargestcomponent.sh"); }
