Merge pull request #2141 from SCIInstitute/studio_fixed_domains

Studio fixed domains

Examples/Python/deep_ssm.py

@@ -107,7 +107,7 @@ def Run_Pipeline(args):
     The required grooming steps are:
     1. Load mesh
     2. Apply clipping with planes for finding alignment transform
-    3. Find reflection tansfrom
+    3. Find reflection transfrom
     4. Select reference mesh
     5. Find rigid alignment transform
     For more information on grooming see docs/workflow/groom.md
@@ -479,7 +479,8 @@ def Run_Pipeline(args):
         transform = [ train_transforms[i].flatten() ]
         subject.set_groomed_transforms(transform)
         subject.set_constraints_filenames(rel_plane_files)
-        subject.set_landmarks_filenames([train_local_particles[i]])
+        subject.set_local_particle_filenames([train_local_particles[i]])
+        subject.set_world_particle_filenames([train_local_particles[i]])
         subject.set_extra_values({"fixed": "yes"})
         subjects.append(subject)
     # Add new validation shapes
@@ -500,7 +501,8 @@ def Run_Pipeline(args):
         transform = [ val_transforms[i].flatten() ]
         subject.set_groomed_transforms(transform)
         subject.set_constraints_filenames(rel_plane_files)
-        subject.set_landmarks_filenames(rel_particle_files)
+        subject.set_local_particle_filenames(rel_particle_files)
+        subject.set_world_particle_filenames(rel_particle_files)
         subject.set_extra_values({"fixed": "no"})
         subjects.append(subject)
     project = sw.Project()
@@ -512,11 +514,7 @@ def Run_Pipeline(args):
     parameter_dictionary["procrustes"] = 0
     parameter_dictionary["procrustes_interval"] = 0
     parameter_dictionary["procrustes_scaling"] = 0
-    parameter_dictionary["use_landmarks"] = 1
-    parameter_dictionary["use_fixed_subjects"] = 1
     parameter_dictionary["narrow_band"] = 1e10
-    parameter_dictionary["fixed_subjects_column"] = "fixed"
-    parameter_dictionary["fixed_subjects_choice"] = "yes"
     for key in parameter_dictionary:
         parameters.set(key, sw.Variant(parameter_dictionary[key]))
     project.set_parameters("optimize", parameters)

Examples/Python/ellipsoid_fd.py

@@ -123,7 +123,8 @@ def Run_Pipeline(args):
         rel_particle_files = sw.utils.get_relative_paths([os.getcwd() + "/" + fixed_local_particles[i]],  project_location)
         subject.set_original_filenames(original_groom_files)
         subject.set_groomed_filenames(rel_groom_files)
-        subject.set_landmarks_filenames(rel_particle_files)
+        subject.set_local_particle_filenames(rel_particle_files)
+        subject.set_world_particle_filenames(rel_particle_files)
         subject.set_extra_values({"fixed": "yes"})
         subjects.append(subject)
 
@@ -135,7 +136,8 @@ def Run_Pipeline(args):
         rel_particle_files = sw.utils.get_relative_paths([os.getcwd() + "/" + mean_shape_path], project_location)
         subject.set_original_filenames(original_groom_files)
         subject.set_groomed_filenames(rel_groom_files)
-        subject.set_landmarks_filenames(rel_particle_files)
+        subject.set_local_particle_filenames(rel_particle_files)
+        subject.set_world_particle_filenames(rel_particle_files)
         subject.set_extra_values({"fixed": "no"})
         subjects.append(subject)
 
@@ -160,11 +162,7 @@ def Run_Pipeline(args):
         "procrustes_scaling": 0,
         "save_init_splits": 0,
         "verbosity": 0,
-        "use_landmarks": 1,
-        "use_fixed_subjects": 1,
         "narrow_band": 1e10,
-        "fixed_subjects_column": "fixed",
-        "fixed_subjects_choice": "yes"
     }
 
     for key in parameter_dictionary:
@@ -186,6 +184,7 @@ def Run_Pipeline(args):
 
     # Run optimization
     optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
+    print(optimize_cmd)
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Libs/Analyze/Shape.cpp

@@ -146,8 +146,10 @@ void Shape::clear_reconstructed_mesh() { reconstructed_meshes_ = MeshGroup(subje
 bool Shape::import_global_point_files(std::vector<std::string> filenames) {
   for (int i = 0; i < filenames.size(); i++) {
     Eigen::VectorXd points;
-    if (!Shape::import_point_file(filenames[i], points)) {
-      throw std::invalid_argument("Unable to import point file: " + filenames[i]);
+    if (filenames[i] != "") {
+      if (!Shape::import_point_file(filenames[i], points)) {
+        throw std::invalid_argument("Unable to import point file: " + filenames[i]);
+      }
     }
     global_point_filenames_.push_back(filenames[i]);
     particles_.set_world_particles(i, points);
@@ -160,8 +162,10 @@ bool Shape::import_global_point_files(std::vector<std::string> filenames) {
 bool Shape::import_local_point_files(std::vector<std::string> filenames) {
   for (int i = 0; i < filenames.size(); i++) {
     Eigen::VectorXd points;
-    if (!Shape::import_point_file(filenames[i], points)) {
-      throw std::invalid_argument("Unable to import point file: " + filenames[i]);
+    if (filenames[i] != "") {
+      if (!Shape::import_point_file(filenames[i], points)) {
+        throw std::invalid_argument("Unable to import point file: " + filenames[i]);
+      }
     }
     local_point_filenames_.push_back(filenames[i]);
     particles_.set_local_particles(i, points);
@@ -307,9 +311,7 @@ bool Shape::store_constraints() {
 Eigen::VectorXd Shape::get_global_correspondence_points() { return particles_.get_combined_global_particles(); }
 
 //---------------------------------------------------------------------------
-Eigen::VectorXd Shape::get_local_correspondence_points() {
-  return particles_.get_combined_local_particles();
-}
+Eigen::VectorXd Shape::get_local_correspondence_points() { return particles_.get_combined_local_particles(); }
 
 //---------------------------------------------------------------------------
 int Shape::get_id() { return id_; }
@@ -699,9 +701,7 @@ void Shape::set_particle_transform(vtkSmartPointer<vtkTransform> transform) {
 }
 
 //---------------------------------------------------------------------------
-void Shape::set_alignment_type(int alignment) {
-  particles_.set_alignment_type(alignment);
-}
+void Shape::set_alignment_type(int alignment) { particles_.set_alignment_type(alignment); }
 
 //---------------------------------------------------------------------------
 vtkSmartPointer<vtkTransform> Shape::get_reconstruction_transform(int domain) {