Merge branch 'master' into dependabot/pip/jinja2-3.1.6

Author: akenmorris

Examples/Python/ellipsoid_multiple_domain_mesh.py

@@ -38,9 +38,7 @@ def Run_Pipeline(args):
     else:
         dataset_name = "ellipsoid_multiple_domain_mesh"
         sw.download_dataset(dataset_name, output_directory)
-        dataset_name = "ellipsoid_joint_rotation"
-        mesh_files = sorted(glob.glob(output_directory +
-                                     dataset_name + "/meshes/*.vtk"))
+        mesh_files = sorted(glob.glob(output_directory + "/meshes/*.vtk"))
 
         if args.use_subsample:
             inputMeshes =[sw.Mesh(filename) for filename in mesh_files]

Libs/Analyze/Shape.cpp

@@ -118,7 +118,7 @@ void Shape::recompute_original_surface() {
   }
   auto meshes = original_meshes_.meshes();
   Image copy = *seg;
-  copy.binarize(0, 1);
+  copy.binarize(0, 2);
   Mesh mesh = copy.toMesh(0.001);
   MeshHandle mesh_handle = std::make_shared<StudioMesh>();
   mesh_handle->set_poly_data(mesh.getVTKMesh());

Libs/Groom/Groom.cpp

@@ -529,58 +529,9 @@ bool Groom::run_alignment() {
 
   // per-domain alignment
   for (size_t domain = 0; domain < num_domains; domain++) {
-    if (abort_) {
-      return false;
-    }
-
     auto params = GroomParameters(project_, project_->get_domain_names()[domain]);
-    if (params.get_alignment_enabled()) {
-      any_alignment = true;
-    }
-
     if (params.get_use_icp()) {
       global_icp = true;
-      std::vector<Mesh> reference_meshes;
-      std::vector<Mesh> meshes;
-      for (size_t i = 0; i < subjects.size(); i++) {
-        if (!subjects[i]->is_excluded()) {
-          Mesh mesh = get_mesh(i, domain, true);
-          // if fixed subjects are present, only add the fixed subjects
-          if (subjects[i]->is_fixed() || !project_->get_fixed_subjects_present()) {
-            reference_meshes.push_back(mesh);
-          }
-          meshes.push_back(mesh);
-        }
-      }
-
-      reference_index = params.get_alignment_reference();
-      subset_size = params.get_alignment_subset_size();
-
-      Mesh reference_mesh = vtkSmartPointer<vtkPolyData>::New();
-      if (reference_index < 0 || reference_index >= subjects.size()) {
-        reference_index = MeshUtils::findReferenceMesh(reference_meshes, subset_size);
-        reference_index = reference_meshes[reference_index].get_id();
-      }
-      reference_mesh = get_mesh(reference_index, domain, true);
-
-      params.set_alignment_reference_chosen(reference_index);
-      params.save_to_project();
-
-      auto transforms = Groom::get_icp_transforms(meshes, reference_mesh);
-      assign_transforms(transforms, domain);
-    } else if (params.get_use_landmarks()) {
-      global_landmarks = true;
-      std::vector<vtkSmartPointer<vtkPoints>> landmarks;
-      for (size_t i = 0; i < subjects.size(); i++) {
-        landmarks.push_back(get_landmarks(i, domain));
-      }
-
-      int reference_index = Groom::find_reference_landmarks(landmarks);
-      params.set_alignment_reference_chosen(reference_index);
-      params.save_to_project();
-
-      auto transforms = Groom::get_landmark_transforms(landmarks, reference_index);
-      assign_transforms(transforms, domain);
     }
   }
 
@@ -652,6 +603,63 @@ bool Groom::run_alignment() {
     }
   }
 
+  // per-domain alignment
+  for (size_t domain = 0; domain < num_domains; domain++) {
+    if (abort_) {
+      return false;
+    }
+
+    auto params = GroomParameters(project_, project_->get_domain_names()[domain]);
+    if (params.get_alignment_enabled()) {
+      any_alignment = true;
+    }
+
+    if (params.get_use_icp()) {
+      global_icp = true;
+      std::vector<Mesh> reference_meshes;
+      std::vector<Mesh> meshes;
+      for (size_t i = 0; i < subjects.size(); i++) {
+        if (!subjects[i]->is_excluded()) {
+          Mesh mesh = get_mesh(i, domain, true);
+          // if fixed subjects are present, only add the fixed subjects
+          if (subjects[i]->is_fixed() || !project_->get_fixed_subjects_present()) {
+            reference_meshes.push_back(mesh);
+          }
+          meshes.push_back(mesh);
+        }
+      }
+
+      reference_index = params.get_alignment_reference();
+      subset_size = params.get_alignment_subset_size();
+
+      Mesh reference_mesh = vtkSmartPointer<vtkPolyData>::New();
+      if (reference_index < 0 || reference_index >= subjects.size()) {
+        reference_index = MeshUtils::findReferenceMesh(reference_meshes, subset_size);
+        reference_index = reference_meshes[reference_index].get_id();
+      }
+      reference_mesh = get_mesh(reference_index, domain, true);
+
+      params.set_alignment_reference_chosen(reference_index);
+      params.save_to_project();
+
+      auto transforms = Groom::get_icp_transforms(meshes, reference_mesh);
+      assign_transforms(transforms, domain);
+    } else if (params.get_use_landmarks()) {
+      global_landmarks = true;
+      std::vector<vtkSmartPointer<vtkPoints>> landmarks;
+      for (size_t i = 0; i < subjects.size(); i++) {
+        landmarks.push_back(get_landmarks(i, domain));
+      }
+
+      int reference_index = Groom::find_reference_landmarks(landmarks);
+      params.set_alignment_reference_chosen(reference_index);
+      params.save_to_project();
+
+      auto transforms = Groom::get_landmark_transforms(landmarks, reference_index);
+      assign_transforms(transforms, domain);
+    }
+  }
+
   return true;
 }
 

Libs/Particles/ParticleShapeStatistics.cpp

@@ -212,12 +212,13 @@ void ParticleShapeStatistics::compute_multi_level_analysis_statistics(std::vecto
     m += (this->num_particles_array_[idx]);
   }
   super_matrix_.resize(m, n);
+
   for (unsigned int i = 0; i < points.size(); i++) {
     unsigned int p = super_matrix_.rows();
     for (unsigned int j = 0; j < p; j++) {
-      super_matrix_(j, i * values_per_particle_) = points[i][j * values_per_particle_];
-      super_matrix_(j, i * values_per_particle_ + 1) = points[i][j * values_per_particle_ + 1];
-      super_matrix_(j, i * values_per_particle_ + 2) = points[i][j * values_per_particle_ + 2];
+      for (int k = 0; k < values_per_particle_; k++) {
+        super_matrix_(j, i * values_per_particle_ + k) = points[i][j * values_per_particle_ + k];
+      }
     }
   }
 
@@ -263,9 +264,9 @@ void ParticleShapeStatistics::compute_multi_level_analysis_statistics(std::vecto
   for (unsigned int i = 0; i < num_samples_; i++) {
     unsigned int p = m;
     for (unsigned int j = 0; j < p; j++) {
-      z_shape_dev_objective(j * values_per_particle_, i) = z_shape_dev_centered(j, i * values_per_particle_);
-      z_shape_dev_objective(j * values_per_particle_ + 1, i) = z_shape_dev_centered(j, i * values_per_particle_ + 1);
-      z_shape_dev_objective(j * values_per_particle_ + 2, i) = z_shape_dev_centered(j, i * values_per_particle_ + 2);
+      for (int k = 0; k < values_per_particle_; k++) {
+        z_shape_dev_objective(j * values_per_particle_ + k, i) = z_shape_dev_centered(j, i * values_per_particle_ + k);
+      }
     }
   }
   points_minus_mean_shape_dev_.resize(M, num_samples_);
@@ -277,9 +278,9 @@ void ParticleShapeStatistics::compute_multi_level_analysis_statistics(std::vecto
   z_rel_pose_objective.resize(domains_per_shape_ * values_per_particle_, num_samples_);
   for (unsigned int k = 0; k < domains_per_shape_; k++) {
     for (unsigned int i = 0; i < num_samples_; i++) {
-      z_rel_pose_objective(k * values_per_particle_, i) = z_rel_pose_centered(k, i * values_per_particle_);
-      z_rel_pose_objective(k * values_per_particle_ + 1, i) = z_rel_pose_centered(k, i * values_per_particle_ + 1);
-      z_rel_pose_objective(k * values_per_particle_ + 2, i) = z_rel_pose_centered(k, i * values_per_particle_ + 2);
+      for (int j = 0; j < values_per_particle_; j++) {
+        z_rel_pose_objective(k * values_per_particle_ + j, i) = z_rel_pose_centered(k, i * values_per_particle_ + j);
+      }
     }
   }
   points_minus_mean_rel_pose_.resize(domains_per_shape_ * values_per_particle_, num_samples_);

Studio/CMakeLists.txt

@@ -228,6 +228,7 @@ SET(STUDIO_VISUALIZATION_SRCS
   Visualization/ParticleColors.cpp
   Visualization/StudioInteractorStyle.cpp
   Visualization/StudioSliceInteractorStyle.cpp
+  Visualization/StudioImageActorPointPlacer.cpp
   Visualization/SliceView.cpp
   Visualization/MeshSlice.cpp
   Visualization/Viewer.cpp

Studio/Data/SegmentationToolPanel.cpp

@@ -40,6 +40,10 @@ SegmentationToolPanel::SegmentationToolPanel(QWidget* parent) : QWidget(parent),
   connect(ui_->recompute_surface_, &QPushButton::clicked, this, &SegmentationToolPanel::recompute_surface);
   ui_->header_label->setAttribute(Qt::WA_TransparentForMouseEvents);
   ui_->open_button->setChecked(false);
+
+  // for 6.6 release we don't have include/exclude
+  ui_->included_mode_->hide();
+  ui_->excluded_mode_->hide();
 }
 
 //---------------------------------------------------------------------------

Studio/Visualization/PaintWidget.cpp

@@ -2,6 +2,7 @@
 #include "PaintWidget.h"
 
 #include <Logging.h>
+#include <Visualization/StudioImageActorPointPlacer.h>
 
 #include <QCursor>
 
@@ -10,7 +11,6 @@
 #include "vtkCommand.h"
 #include "vtkEvent.h"
 #include "vtkImageActor.h"
-#include "vtkImageActorPointPlacer.h"
 #include "vtkObjectFactory.h"
 #include "vtkOrientedGlyphContourRepresentation.h"
 #include "vtkPointPlacer.h"
@@ -255,10 +255,13 @@ bool PaintWidget::use_point_placer(double displayPos[2], int newState) {
 
   if (WidgetState == PaintWidget::Paint || WidgetState == PaintWidget::Erase) {
     if (WidgetState == PaintWidget::Paint) {
+      if (circle_mode_) {
+        // we have to transform the point back to the image space in case there is alignment
+        auto transform = viewer_->get_inverse_image_transform();
+        transform->TransformPoint(worldPos, worldPos);
+      }
+
       viewer_->handle_paint(displayPos, worldPos);
-      ////paint_position( this, worldPos );
-    } else if (WidgetState == PaintWidget::Erase) {
-      ////erase_position( this, worldPos );
     }
 
     EventCallbackCommand->SetAbortFlag(1);

Studio/Visualization/SliceView.cpp

@@ -3,7 +3,7 @@
 #include <vtkCellData.h>
 #include <vtkCutter.h>
 #include <vtkImageActor.h>
-#include <vtkImageActorPointPlacer.h>
+#include <Visualization/StudioImageActorPointPlacer.h>
 #include <vtkImageProperty.h>
 #include <vtkImageSliceMapper.h>
 #include <vtkLookupTable.h>
@@ -62,7 +62,7 @@ SliceView::SliceView(Viewer *viewer) : viewer_(viewer) {
   mask_slice_ = vtkSmartPointer<vtkImageActor>::New();
   slice_mapper_ = vtkSmartPointer<vtkImageSliceMapper>::New();
   mask_mapper_ = vtkSmartPointer<vtkImageSliceMapper>::New();
-  placer_ = vtkSmartPointer<vtkImageActorPointPlacer>::New();
+  placer_ = vtkSmartPointer<StudioImageActorPointPlacer>::New();
   placer_->SetImageActor(image_slice_);
 }