Merge branch 'master' into dependabot/pip/requests-2.33.0

Author: akenmorris

.github/workflows/build-mac-arm64.yml

@@ -95,6 +95,18 @@ jobs:
       shell: bash -l {0}
       run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
 
+    - name: Print crash reports
+      if: failure()
+      run: |
+        echo "=== Crash Reports ==="
+        for f in ~/Library/Logs/DiagnosticReports/*.crash ~/Library/Logs/DiagnosticReports/*.ips; do
+          if [ -f "$f" ]; then
+            echo "--- $f ---"
+            cat "$f"
+            echo ""
+          fi
+        done
+
     - uses: actions/upload-artifact@v4
       with:
         name: artifact-${{github.sha}}-mac-arm64

.github/workflows/build-mac.yml

@@ -95,6 +95,18 @@ jobs:
       shell: bash -l {0}
       run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
 
+    - name: Print crash reports
+      if: failure()
+      run: |
+        echo "=== Crash Reports ==="
+        for f in ~/Library/Logs/DiagnosticReports/*.crash ~/Library/Logs/DiagnosticReports/*.ips; do
+          if [ -f "$f" ]; then
+            echo "--- $f ---"
+            cat "$f"
+            echo ""
+          fi
+        done
+
     - uses: actions/upload-artifact@v4
       with:
         name: artifact-${{github.sha}}-mac

Applications/shapeworks/Command.cpp

@@ -1,4 +1,5 @@
 #include "Command.h"
+#include <Profiling.h>
 #include <sstream>
 
 namespace shapeworks {
@@ -22,6 +23,7 @@ std::vector<std::string> Command::parse_args(const std::vector<std::string> &arg
 ///////////////////////////////////////////////////////////////////////////////
 int Command::run(SharedCommandData &sharedData)
 {
+  TIME_SCOPE(QString::fromStdString(name()));
   const optparse::Values &options = parser.get_parsed_options();
 
   return this->execute(options, sharedData) ? EXIT_SUCCESS : EXIT_FAILURE;

Libs/Alignment/Procrustes3D.cpp

@@ -1,5 +1,6 @@
 #include "Procrustes3D.h"
 
+#include <Profiling.h>
 #include <vnl/algo/vnl_svd.h>
 
 #include <iostream>
@@ -44,6 +45,7 @@ void Procrustes3D::RemoveTranslation(SimilarityTransformListType& transforms, Sh
 
 //---------------------------------------------------------------------------
 void Procrustes3D::AlignShapes(SimilarityTransformListType& transforms, ShapeListType& shapes) {
+  TIME_SCOPE("Procrustes3D::AlignShapes");
   const RealType SOS_EPSILON = 1.0e-8;
 
   PointType center;

Libs/Analyze/Analyze.cpp

@@ -2,6 +2,7 @@
 
 #include <Groom/GroomParameters.h>
 #include <Logging.h>
+#include <Profiling.h>
 #include <MeshWarper.h>
 #include <Particles/ParticleNormalEvaluation.h>
 #include <StringUtils.h>
@@ -167,6 +168,7 @@ Analyze::Analyze(ProjectHandle project) : project_(project), mesh_manager_(new M
 
 //---------------------------------------------------------------------------
 void Analyze::run_offline_analysis(std::string outfile, float range, float steps) {
+  TIME_SCOPE("Analyze::run_offline_analysis");
   SW_LOG("ShapeWorks Offline Analysis");
   if (!project_->get_particles_present()) {
     throw std::runtime_error("Project has not been optimized, please run optimize first");
@@ -478,6 +480,7 @@ bool Analyze::update_shapes() {
 
 //---------------------------------------------------------------------------
 bool Analyze::compute_stats() {
+  TIME_SCOPE("Analyze::compute_stats");
   if (stats_ready_) {
     return true;
   }

Libs/Analyze/Reconstruction.cpp

@@ -23,6 +23,7 @@
 #include "itkNrrdImageIOFactory.h"
 #include "itkMetaImageIOFactory.h"
 #include "Reconstruction.h"
+#include <Profiling.h>
 
 #include <vtkLoopSubdivisionFilter.h>
 #include <vtkButterflySubdivisionFilter.h>
@@ -67,6 +68,7 @@ vtkSmartPointer<vtkPolyData> Reconstruction<TTransformType,TInterpolatorType, TC
         std::vector< PointArrayType > local_pts,
         std::vector< PointArrayType > global_pts,
         std::vector<std::string> distance_transform) {
+    TIME_SCOPE("Reconstruction::getDenseMean");
     if (!this->denseDone_ || !local_pts.empty() ||
             !distance_transform.empty() || !global_pts.empty()) {
         this->denseDone_ = false;
@@ -439,6 +441,7 @@ void Reconstruction<TTransformType,TInterpolatorType, TCoordRep, PixelType, Imag
         std::vector< PointArrayType > local_pts,
         std::vector< PointArrayType > global_pts,
         std::vector<std::string> distance_transform) {
+    TIME_SCOPE("Reconstruction::computeDenseMean");
     try {
         //turn the sets of global points to one sparse global mean.
         float init[] = { 0.f,0.f,0.f };

Libs/Application/Job/Job.cpp

@@ -1,4 +1,5 @@
 #include <Job/Job.h>
+#include <Profiling.h>
 namespace shapeworks {
 
 //---------------------------------------------------------------------------
@@ -19,6 +20,12 @@ QString Job::get_abort_message() {
   return name() + " aborted.  Duration: " + duration + " seconds";
 }
 
+//---------------------------------------------------------------------------
+void Job::execute() {
+  TIME_SCOPE(name());
+  run();
+}
+
 //---------------------------------------------------------------------------
 void Job::start_timer() { this->timer_.start(); }
 

Libs/Application/Job/Job.h

@@ -15,6 +15,9 @@ class Job : public QObject {
   //! run the job
   virtual void run() = 0;
 
+  //! execute the job with profiling instrumentation
+  void execute();
+
   //! get the name of the job
   virtual QString name() = 0;
 

Libs/Application/Job/PythonWorker.cpp

@@ -104,7 +104,7 @@ void PythonWorker::start_job(QSharedPointer<Job> job) {
       }
       Q_EMIT job->progress(0);
       current_job_ = job;
-      current_job_->run();
+      current_job_->execute();
       current_job_->set_complete(true);
       if (!job->get_quiet_mode()) {
         SW_LOG(current_job_->get_completion_message().toStdString());

Libs/Groom/Groom.cpp

@@ -2,6 +2,7 @@
 #include <GroomParameters.h>
 #include <Image/Image.h>
 #include <Logging.h>
+#include <Profiling.h>
 #include <Mesh/Mesh.h>
 #include <Mesh/MeshUtils.h>
 #include <Optimize/Constraints/Constraints.h>
@@ -32,6 +33,7 @@ Groom::Groom(ProjectHandle project) : project_{project} {}
 
 //---------------------------------------------------------------------------
 bool Groom::run() {
+  TIME_SCOPE("Groom::run");
   ShapeWorksUtils::setup_threads();
 
   used_names_.clear();
@@ -124,6 +126,7 @@ bool Groom::run() {
 
 //---------------------------------------------------------------------------
 bool Groom::image_pipeline(std::shared_ptr<Subject> subject, size_t domain) {
+  TIME_SCOPE("Groom::image_pipeline");
   // grab parameters
   auto params = GroomParameters(project_, project_->get_domain_names()[domain]);
 
@@ -321,6 +324,7 @@ bool Groom::run_image_pipeline(Image& image, GroomParameters params) {
 
 //---------------------------------------------------------------------------
 bool Groom::mesh_pipeline(std::shared_ptr<Subject> subject, size_t domain) {
+  TIME_SCOPE("Groom::mesh_pipeline");
   // grab parameters
   auto params = GroomParameters(project_, project_->get_domain_names()[domain]);
 
@@ -381,8 +385,10 @@ bool Groom::mesh_pipeline(std::shared_ptr<Subject> subject, size_t domain) {
 
 //---------------------------------------------------------------------------
 bool Groom::run_mesh_pipeline(Mesh& mesh, GroomParameters params, const std::string& filename) {
-  // Repair mesh: triangulate, extract largest component, clean, fix non-manifold, remove zero-area triangles
-  mesh = Mesh(MeshUtils::repair_mesh(mesh.getVTKMesh()));
+  // Repair mesh: triangulate, clean, fix non-manifold, remove zero-area triangles
+  // Skip extract-largest-component for shared boundary domains to avoid removing fragments at the cut surface
+  bool extract_largest = !params.is_shared_boundary_domain();
+  mesh = Mesh(MeshUtils::repair_mesh(mesh.getVTKMesh(), extract_largest));
 
   if (params.get_fill_mesh_holes_tool()) {
     mesh.fillHoles();
@@ -557,6 +563,7 @@ bool Groom::get_aborted() { return abort_; }
 
 //---------------------------------------------------------------------------
 bool Groom::run_alignment() {
+  TIME_SCOPE("Groom::run_alignment");
   size_t num_domains = project_->get_number_of_domains_per_subject();
   SW_DEBUG("Running alignment, number of domains = {}", num_domains);
   auto subjects = project_->get_subjects();