Merge pull request #2468 from SCIInstitute/groom_issues

Fix Groom issues #2467, #2466

Author: akenmorris

Libs/Analyze/MeshGenerator.cpp

@@ -135,7 +135,6 @@ MeshHandle MeshGenerator::build_mesh_from_image(ImageType::Pointer image, float
 
 //---------------------------------------------------------------------------
 MeshHandle MeshGenerator::build_mesh_from_file(std::string filename, float iso_value) {
-  // std::cerr << "build_mesh from " << filename << "\n";
   MeshHandle mesh(new StudioMesh);
 
   if (!QFileInfo(QString::fromStdString(filename)).exists()) {

Libs/Mesh/Mesh.cpp

@@ -298,6 +298,12 @@ Mesh& Mesh::smoothSinc(int iterations, double passband) {
   iterations = std::max<int>(iterations, 2);
   smoother->SetNumberOfIterations(iterations);
   smoother->SetPassBand(passband);
+
+  smoother->BoundarySmoothingOff();
+  smoother->FeatureEdgeSmoothingOff();
+  smoother->NonManifoldSmoothingOn();
+  smoother->NormalizeCoordinatesOn();
+
   smoother->Update();
   this->poly_data_ = smoother->GetOutput();
 
@@ -722,6 +728,10 @@ Mesh& Mesh::clipClosedSurface(const Plane plane) {
 }
 
 Mesh& Mesh::computeNormals() {
+  // Remove existing normals first
+  poly_data_->GetPointData()->SetNormals(nullptr);
+  poly_data_->GetCellData()->SetNormals(nullptr);
+
   auto normal = vtkSmartPointer<vtkPolyDataNormals>::New();
 
   normal->SetInputData(this->poly_data_);

Studio/Interface/ShapeWorksStudioApp.cpp

@@ -1335,15 +1335,17 @@ void ShapeWorksStudioApp::handle_groom_start() {
 void ShapeWorksStudioApp::handle_groom_complete() {
   update_view_combo();
 
+  // Clear cache BEFORE setting display mode, because set_display_mode triggers
+  // update_view_mode() which calls update_display() and would use stale cached meshes
+  session_->handle_clear_cache();
+
   if (!session_->groomed_present()) {
     // grooming may have failed, if so, we don't want to switch to groomed that don't exist
     session_->set_display_mode(DisplayMode::Original);
   } else {
     session_->set_display_mode(DisplayMode::Groomed);
   }
 
-  session_->handle_clear_cache();
-
   update_display(true);
   visualizer_->reset_camera();
   enable_possible_actions();

Testing/data/reconstruct_mean_surface.nrrd

@@ -1,3 +1,3 @@
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-oid sha256:c82102f0aaa408c3e2ba3503219575a218a952fe159dd692a9f712e8fa7d4f6d
-size 388356
+oid sha256:a007e47aa5c7b3c30cfae9055aa73d6cc009f8fd0e972c2806a062df54843744
+size 385579

Testing/data/reconstruct_mean_surface.vtk

@@ -1,3 +1,3 @@
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-oid sha256:5e7fb2d2dae972c9ba2070a8498af279269d9780af0cc238b5968993b778bcd4
-size 246231
+oid sha256:50faf83cc9d39e44a1932c3f1de5b8392e30b4715512fbd1492a6eecaa9f43cf
+size 432903

Testing/data/shapeworksTests/analyze/analysis_baseline.json

@@ -1288,70 +1288,70 @@
     "groups": [],
     "good_bad_angles": [
         [
-            9.84,
+            9.82,
             4.17,
-            4.07,
-            10.96,
-            6.45,
-            7.3,
-            9.21,
-            8.39,
-            4.97,
-            10.62,
-            6.31,
-            4.74,
-            9.99,
-            7.71,
-            7.57,
-            8.0,
+            4.05,
+            10.88,
+            6.44,
+            7.45,
+            9.12,
+            8.36,
+            4.92,
+            10.55,
+            6.25,
+            4.64,
+            9.74,
+            7.68,
+            7.55,
+            7.95,
+            8.99,
+            3.93,
+            13.49,
             9.03,
-            4.13,
-            13.58,
-            9.14,
             3.43,
-            9.26,
+            8.82,
             5.16,
-            9.76,
-            4.21,
-            8.78,
+            9.64,
+            4.23,
+            8.75,
             4.56,
-            9.1,
-            7.51,
-            6.63,
-            9.97,
-            7.11,
-            11.15,
-            9.11,
-            7.6,
-            9.48,
+            9.06,
+            7.46,
+            6.54,
+            9.9,
+            7.1,
+            11.12,
+            8.98,
+            7.54,
+            9.38,
             5.1,
-            17.11,
-            9.64,
-            5.94,
-            8.06,
-            7.9,
-            12.86,
-            7.06,
-            9.07,
-            3.91,
-            12.09,
-            5.81,
-            11.3,
             12.96,
-            15.91,
-            12.14,
-            6.36,
-            12.83,
-            5.32,
-            11.5,
-            5.84,
-            6.2,
-            8.91,
-            6.27,
-            6.43,
-            4.98,
-            9.04,
-            8.81
+            9.62,
+            5.93,
+            8.02,
+            7.88,
+            12.76,
+            6.93,
+            9.02,
+            3.93,
+            11.97,
+            5.77,
+            11.3,
+            12.89,
+            15.77,
+            12.05,
+            6.33,
+            12.58,
+            5.36,
+            11.36,
+            5.86,
+            6.08,
+            8.86,
+            6.23,
+            6.26,
+            4.86,
+            8.64,
+            8.76
         ]
     ]
 }

Testing/data/shapeworksTests/analyze/mean_shape_0.baseline.vtk

@@ -1,3 +1,3 @@
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-size 33002
+oid sha256:7b3a4c5cd0e617e9a86d5edfe8e6358b81eb7d584cfde178bef6ba9b4d93db5c
+size 49228

Testing/data/shapeworksTests/analyze/pca_mode_1_domain_0_minus_0.3.baseline.vtk

@@ -1,3 +1,3 @@
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-oid sha256:1a3e79ac29fe8720e7fa6f983ed14e55c417d92e501c02b9ac5ac9df96d58abb
-size 33002
+oid sha256:03791ed5d2528d3d54da0b0e6fba76b4eb0413558d3a6ca20bdf63b371909480
+size 49209

Testing/data/smoothsinc.vtp

@@ -1,3 +1,3 @@
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-oid sha256:ca7aa53ca7ee84b523ff66bdd5b89827254279026070a95e36ec4edd473a0ad2
-size 7299939
+oid sha256:11dff539015f11fc545839df9eb89ba61d3e3ee531638a0de4e1307d0244abd4
+size 7873251