Merge branch 'master' into regressionv2

Libs/Groom/Groom.cpp

@@ -513,6 +513,7 @@ bool Groom::run_alignment() {
 
   bool global_icp = false;
   bool global_landmarks = false;
+  bool any_alignment = false;
 
   int reference_index = -1;
   int subset_size = -1;
@@ -524,6 +525,9 @@ bool Groom::run_alignment() {
     }
 
     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;
@@ -594,16 +598,17 @@ bool Groom::run_alignment() {
         meshes.push_back(mesh);
       } else {
         // insert blank for each excluded shape
-        meshes.push_back(vtkSmartPointer<vtkPolyData>::New());
+        meshes.emplace_back(vtkSmartPointer<vtkPolyData>::New());
       }
     }
 
     if (global_icp) {
-      std::vector<Mesh> reference_meshes;
-
       Mesh reference_mesh = vtkSmartPointer<vtkPolyData>::New();
       if (reference_index < 0 || reference_index >= reference_meshes.size()) {
         reference_index = MeshUtils::findReferenceMesh(reference_meshes, subset_size);
+        if (reference_index < 0 || reference_index >= reference_meshes.size()) {
+          throw std::runtime_error("could not find reference mesh");
+        }
         reference_mesh = reference_meshes[reference_index];
       } else {
         reference_mesh = get_mesh(reference_index, 0, true);
@@ -623,12 +628,14 @@ bool Groom::run_alignment() {
       size_t domain = num_domains;  // end
       assign_transforms(transforms, domain, true /* global */);
 
-    } else {  // just center
+    } else {
       std::vector<std::vector<double>> transforms;
       for (size_t i = 0; i < subjects.size(); i++) {
         auto subject = subjects[i];
         auto transform = vtkSmartPointer<vtkTransform>::New();
-        Groom::add_center_transform(transform, meshes[i]);
+        if (any_alignment) {  // just center
+          Groom::add_center_transform(transform, meshes[i]);
+        }
         transforms.push_back(ProjectUtils::convert_transform(transform));
       }
       size_t domain = num_domains;  // end

Libs/Project/ProjectReader.cpp

@@ -68,16 +68,18 @@ void ProjectReader::load_subjects(StringMapList list) {
     if (contains(item, "excluded")) {
       subject->set_excluded(Variant(item["excluded"]));
     }
+
     if (contains(item, "explanatory_variable")) {
       subject->set_explanatory_variable(Variant(item["explanatory_variable"]));
     }
 
-    if (name == "") {
-      if (subject->get_original_filenames().size() != 0) {
+    if (name.empty()) {
+      if (!subject->get_original_filenames().empty()) {
+
         name = StringUtils::getBaseFilenameWithoutExtension(subject->get_original_filenames()[0]);
-      } else if (subject->get_groomed_filenames().size() != 0) {
+      } else if (!subject->get_groomed_filenames().empty()) {
         name = StringUtils::getBaseFilenameWithoutExtension(subject->get_groomed_filenames()[0]);
-      } else if (subject->get_local_particle_filenames().size() > 0) {
+      } else if (!subject->get_local_particle_filenames().empty()) {
         name = StringUtils::getBaseFilenameWithoutExtension(subject->get_local_particle_filenames()[0]);
       }
     }

Studio/Analysis/AnalysisTool.cpp

@@ -21,6 +21,9 @@
 #include <jkqtplotter/jkqtplotter.h>
 #include <ui_AnalysisTool.h>
 
+#include <QClipboard>
+#include <QMenu>
+
 #include "ParticleAreaPanel.h"
 #include "ShapeScalarPanel.h"
 
@@ -80,8 +83,6 @@ AnalysisTool::AnalysisTool(Preferences& prefs) : preferences_(prefs) {
   ui_->tabWidget->tabBar()->setElideMode(Qt::TextElideMode::ElideNone);
 #endif
 
-  stats_ready_ = false;
-
   connect(ui_->view_header, &QPushButton::clicked, ui_->view_open_button, &QPushButton::toggle);
   connect(ui_->metrics_header, &QPushButton::clicked, ui_->metrics_open_button, &QPushButton::toggle);
   connect(ui_->surface_header, &QPushButton::clicked, ui_->surface_open_button, &QPushButton::toggle);
@@ -179,6 +180,14 @@ AnalysisTool::AnalysisTool(Preferences& prefs) : preferences_(prefs) {
           &AnalysisTool::handle_samples_predicted_scalar_options);
   connect(ui_->show_absolute_difference, &QPushButton::clicked, this,
           &AnalysisTool::handle_samples_predicted_scalar_options);
+
+  // add a right click menu to the samples table allowing the user to copy the table to the clipboard
+  ui_->samples_table->setContextMenuPolicy(Qt::CustomContextMenu);
+  connect(ui_->samples_table, &QTableWidget::customContextMenuRequested, this,
+          &AnalysisTool::samples_table_context_menu);
+
+  // disable editing of the table
+  ui_->samples_table->setEditTriggers(QAbstractItemView::NoEditTriggers);
 }
 
 //---------------------------------------------------------------------------
@@ -1890,6 +1899,41 @@ void AnalysisTool::handle_samples_predicted_scalar_options() {
   Q_EMIT update_view();
 }
 
+//---------------------------------------------------------------------------
+void AnalysisTool::samples_table_context_menu() {
+  QMenu menu;
+  QAction* action = menu.addAction("Copy to Clipboard");
+  connect(action, &QAction::triggered, this, &AnalysisTool::samples_table_copy_to_clipboard);
+  menu.exec(QCursor::pos());
+}
+
+//---------------------------------------------------------------------------
+void AnalysisTool::samples_table_copy_to_clipboard() {
+  QTableWidget* table = ui_->samples_table;
+  QString text;
+  // start with headers
+  for (int i = 0; i < table->columnCount(); i++) {
+    text += table->horizontalHeaderItem(i)->text();
+    if (i < table->columnCount() - 1) {
+      text += ",";
+    }
+  }
+  text += "\n";
+  for (int i = 0; i < table->rowCount(); i++) {
+    for (int j = 0; j < table->columnCount(); j++) {
+      auto item = table->item(i, j);
+      if (item) {
+        text += item->text();
+      }
+      if (j < table->columnCount() - 1) {
+        text += ",";
+      }
+    }
+    text += "\n";
+  }
+  QApplication::clipboard()->setText(text);
+}
+
 //---------------------------------------------------------------------------
 void AnalysisTool::reconstruction_method_changed() {
   ui_->reconstruction_options->setVisible(ui_->distance_transform_radio_button->isChecked());

Studio/Analysis/AnalysisTool.h

@@ -199,6 +199,9 @@ class AnalysisTool : public QWidget {
 
   void handle_samples_predicted_scalar_options();
 
+  void samples_table_context_menu();
+  void samples_table_copy_to_clipboard();
+
  Q_SIGNALS:
 
   void update_view();

Studio/Data/DataTool.cpp

@@ -656,19 +656,32 @@ void DataTool::table_data_edited() {
   }
 
   bool change = false;
+
+  // find name and notes columns
+  int name_column = -1;
+  int notes_column = -1;
+  for (int i = 0; i < ui_->table->columnCount(); i++) {
+    if (ui_->table->horizontalHeaderItem(i)->text() == "name") {
+      name_column = i;
+    } else if (ui_->table->horizontalHeaderItem(i)->text() == "notes") {
+      notes_column = i;
+    }
+  }
+
   // iterate over all rows, not just selected
   for (int row = 0; row < ui_->table->rowCount(); row++) {
     auto shape = session_->get_shapes()[row];
     auto old_name = shape->get_subject()->get_display_name();
     auto old_notes = shape->get_subject()->get_notes();
-    if (ui_->table->item(row, 0) == nullptr) {
-      continue;
+
+    std::string new_name;
+    if (name_column != -1) {
+      new_name = ui_->table->item(row, name_column)->text().toStdString();
     }
-    auto new_name = ui_->table->item(row, 0)->text().toStdString();
-    if (ui_->table->item(row, 1) == nullptr) {
-      continue;
+    std::string new_notes;
+    if (notes_column != -1) {
+      new_notes = ui_->table->item(row, notes_column)->text().toStdString();
     }
-    auto new_notes = ui_->table->item(row, 1)->text().toStdString();
     if (old_name != new_name) {
       shape->get_subject()->set_display_name(new_name);
       shape->update_annotations();

Studio/Groom/GroomTool.cpp

@@ -605,6 +605,7 @@ void GroomTool::skip_grooming_toggled() {
     groom_ = QSharedPointer<Groom>(new Groom(session_->get_project()));
     groom_->run();
     SW_MESSAGE("Skipped Grooming");
+    SW_PROGRESS(100, "Grooming Skipped");
     Q_EMIT groom_complete();
   }
 }

python_requirements.txt

@@ -65,7 +65,7 @@ itk-segmentation==5.3.0
 itkwidgets==0.32.1
 itsdangerous==2.1.2
 jedi==0.18.2
-Jinja2==3.1.3
+Jinja2==3.1.4
 joblib==1.3.1
 jsonpointer==2.4
 jsonschema==4.18.0
@@ -172,7 +172,7 @@ threadpoolctl==3.1.0
 tinycss2==1.2.1
 toml==0.10.2
 tornado==6.3.3
-tqdm==4.65.0
+tqdm==4.66.3
 traitlets==5.9.0
 traittypes==0.2.1
 trimesh==3.12.6
@@ -187,7 +187,7 @@ wcwidth==0.2.6
 webcolors==1.13
 webencodings==0.5.1
 websocket-client==1.6.1
-Werkzeug==3.0.1
+Werkzeug==3.0.3
 widgetsnbextension==3.6.4
 zipp==3.15.0
 zstandard==0.21.0