for droplet analysis

tix209 · Nov 9, 2014 · 5678f66 · 5678f66
1 parent 07e49c2
commit 5678f66
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Showing 8 changed files with 232 additions and 90 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -42,8 +42,6 @@ set(gui_srcs
 
 set(common_srcs
   global.h
-#  multisnake.h
-#  multisnake.cc
   snake.h
   snake.cc
   solver_bank.h
@@ -68,17 +66,15 @@ set(moc_gui_srcs
 
 set(rcc_srcs icons.qrc)
 
-# add_definitions(-Wall)
-
 qt4_wrap_cpp(multisnake_moc multisnake.h)
 qt4_wrap_cpp(mocs ${moc_gui_srcs})
 qt4_add_resources(rccs ${rcc_srcs})
 
 add_executable(soax soax.cc ${common_srcs} ${gui_srcs} ${mocs}
   ${rccs} ${multisnake_moc} multisnake.cc multisnake.h)
 
-# add_executable(batch_soax batch_soax.cc ${common_srcs}
-#   ${multisnake_moc} multisnake.cc multisnake.h)
+add_executable(batch_soax batch_soax.cc ${common_srcs}
+  ${multisnake_moc} multisnake.cc multisnake.h)
 # # add_executable(eval_gt evaluate_gt.cc ${common_srcs})
 # # add_executable(eval_f evaluate_f.cc ${common_srcs})
 # add_executable(best_snake best_snake.cc ${common_srcs}
@@ -97,13 +93,13 @@ target_link_libraries(soax
   ${Boost_PROGRAM_OPTIONS_LIBRARY}
   )
 
-# target_link_libraries(batch_soax
-#   ${QT_LIBRARIES}
-#   ${ITK_LIBRARIES}
-#   ${Boost_PROGRAM_OPTIONS_LIBRARY}
-#   ${Boost_FILESYSTEM_LIBRARY}
-#   ${Boost_SYSTEM_LIBRARY}
-#   )
+target_link_libraries(batch_soax
+  ${QT_LIBRARIES}
+  ${ITK_LIBRARIES}
+  ${Boost_PROGRAM_OPTIONS_LIBRARY}
+  ${Boost_FILESYSTEM_LIBRARY}
+  ${Boost_SYSTEM_LIBRARY}
+  )
 
 # target_link_libraries(eval_gt
 #   ${ITK_LIBRARIES}

diff --git a/main_window.cc b/main_window.cc
@@ -292,6 +292,9 @@ void MainWindow::CreateProcessMenuActions() {
   group_snakes_ = new QAction(tr("Group Snakes"), this);
   group_snakes_->setIcon(QIcon(":/icon/Favorites.png"));
   connect(group_snakes_, SIGNAL(triggered()), this, SLOT(GroupSnakes()));
+
+  find_correspondence_ = new QAction(tr("Find Correspondence for Sequence"), this);
+  connect(find_correspondence_, SIGNAL(triggered()), this, SLOT(FindCorrespondence()));
 }
 
 void MainWindow::CreateAnalysisMenuActions() {
@@ -397,16 +400,9 @@ void MainWindow::CreateMenus() {
   process_->addAction(deform_snakes_for_sequence_);
   process_->addAction(cut_snakes_);
   process_->addAction(group_snakes_);
+  process_->addAction(find_correspondence_);
 
   analysis_ = menuBar()->addMenu(tr("&Analysis"));
-  // actin_cable_submenu_ = analysis_->addMenu(tr("Actin Cable"));
-  // contractile_ring_submenu_ = analysis_->addMenu(tr("Contractile Ring"));
-  // fibrin_submenu_ = analysis_->addMenu(tr("Fibrin Network"));
-  // fibrin_submenu_->addAction(compute_spherical_orientation_);
-  // droplet_submenu_ = analysis_->addMenu(tr("Actin Droplet"));
-  // droplet_submenu_->addAction(compute_radial_orientation_);
-  // droplet_submenu_->addAction(compute_point_density_);
-  // droplet_submenu_->addAction(compute_curvature_);
   analysis_->addAction(compute_spherical_orientation_);
   analysis_->addAction(compute_radial_orientation_);
   analysis_->addAction(compute_point_density_);
@@ -507,6 +503,7 @@ void MainWindow::ResetActions() {
   deform_snakes_for_sequence_->setEnabled(false);
   cut_snakes_->setEnabled(false);
   group_snakes_->setEnabled(false);
+  find_correspondence_->setEnabled(false);
 
   compute_spherical_orientation_->setEnabled(false);
   compute_radial_orientation_->setEnabled(false);
@@ -780,6 +777,7 @@ void MainWindow::LoadSnakesSequence() {
   viewer_->set_snake_filename(snake_filename_);
   viewer_->SetupUpperRightCornerText();
   toggle_corner_text_->setChecked(true);
+  find_correspondence_->setEnabled(true);
   // save_jfilament_snakes_->setEnabled(true);
   // compare_snakes_->setEnabled(true);
   // toggle_delete_snake_->setEnabled(true);
@@ -962,12 +960,19 @@ void MainWindow::CloseSession() {
   viewer_->Reset();
   viewer_->Render();
   multisnake_->Reset();
-  disconnect(scroll_bar_, SIGNAL(valueChanged(int)),
-             viewer_, SLOT(UpdateSnakesJunctions(int)));
+  disconnect(multisnake_, SIGNAL(ExtractionCompleteForFrame(int)),
+             progress_bar_, SLOT(setValue(int)));
+  disconnect(multisnake_, SIGNAL(ExtractionCompleteForFrame(int)),
+             progress_bar_, SLOT(setValue(int)));
+
   disconnect(scroll_bar_, SIGNAL(valueChanged(int)), viewer_, SLOT(UpdateFrame(int)));
   disconnect(scroll_bar_, SIGNAL(valueChanged(int)), this, SLOT(ShowFrameNumber(int)));
   disconnect(scroll_bar_, SIGNAL(valueChanged(int)),
              viewer_, SLOT(UpdateLeftCornerText(int)));
+  disconnect(scroll_bar_, SIGNAL(valueChanged(int)),
+             viewer_, SLOT(UpdateSnakesJunctions(int)));
+  disconnect(scroll_bar_, SIGNAL(valueChanged(int)),
+             viewer_, SLOT(HighlightCorrespondingSnake(int)));
 
   this->ResetActions();
   open_image_->setEnabled(true);
@@ -1204,6 +1209,7 @@ void MainWindow::DeformSnakesForSequence() {
   this->ViewSnakesSequence();
   initialize_snakes_for_sequence_->setEnabled(false);
   save_snakes_sequence_->setEnabled(true);
+  find_correspondence_->setEnabled(true);
   // deform_snakes_->setEnabled(false);
   // save_snakes_->setEnabled(true);
   // save_jfilament_snakes_->setEnabled(true);
@@ -1227,6 +1233,12 @@ void MainWindow::DeformSnakesForSequence() {
   // show_analysis_options_->setEnabled(true);
 }
 
+void MainWindow::FindCorrespondence() {
+  viewer_->SolveCorrespondence();
+  connect(scroll_bar_, SIGNAL(valueChanged(int)),
+          viewer_, SLOT(HighlightCorrespondingSnake(int)));
+}
+
 void MainWindow::ViewSnakesSequence() {
   connect(scroll_bar_, SIGNAL(valueChanged(int)),
           viewer_, SLOT(UpdateSnakesJunctions(int)));
@@ -1289,33 +1301,57 @@ void MainWindow::ComputeSphericalOrientation() {
       this, tr("Save spherical orientation"), "..",
       tr("Text files(*.txt)"));
   if (filename.isEmpty()) return;
-  multisnake_->ComputeSphericalOrientation(filename.toStdString());
+
+  std::ofstream outfile;
+  outfile.open(filename.toStdString().c_str());
+  if (!outfile.is_open()) {
+    QMessageBox msg_box;
+    msg_box.setText("Opening file failed.");
+    msg_box.setIcon(QMessageBox::Critical);
+    msg_box.exec();
+    return;
+  }
+
+  multisnake_->ComputeSphericalOrientation(outfile);
   statusBar()->showMessage(tr("Spherical orientation file saved."));
+  outfile.close();
 }
 
 void MainWindow::ComputeRadialOrientation() {
   QString filename = QFileDialog::getSaveFileName(
-      this, tr("Save radial orientation file"), "..",
+      this, tr("Save radial orientation"), "..",
       tr("Text files(*.txt)"));
   if (filename.isEmpty()) return;
 
   PointType center;
   analysis_options_dialog_->GetImageCenter(center);
-  std::cout << "Image center: " << center << std::endl;
-  multisnake_->ComputeRadialOrientation(center, filename.toStdString());
+  double pixel_size = analysis_options_dialog_->GetPixelSize();
+
+  std::ofstream outfile;
+  outfile.open(filename.toStdString().c_str());
+  if (!outfile.is_open()) {
+    QMessageBox msg_box;
+    msg_box.setText("Opening file failed.");
+    msg_box.setIcon(QMessageBox::Critical);
+    msg_box.exec();
+    return;
+  }
+
+  multisnake_->ComputeRadialOrientation(center, pixel_size, outfile);
   statusBar()->showMessage(tr("Radial orientation file saved."));
+  outfile.close();
 }
 
 void MainWindow::ComputePointDensity() {
   QString filename = QFileDialog::getSaveFileName(
-      this, tr("Save SOAC point density/intensity file"), "..",
+      this, tr("Save SOAC point density/intensity"), "..",
       tr("Text files(*.txt)"));
   if (filename.isEmpty()) return;
+
   PointType center;
   analysis_options_dialog_->GetImageCenter(center);
   unsigned max_radius = analysis_options_dialog_->GetRadius();
   double pixel_size = analysis_options_dialog_->GetPixelSize();
-  std::cout << "pixel size: " << pixel_size << std::endl;
 
   std::ofstream outfile;
   outfile.open(filename.toStdString().c_str());
@@ -1329,19 +1365,28 @@ void MainWindow::ComputePointDensity() {
 
   multisnake_->ComputePointDensityAndIntensity(center, max_radius,
                                                pixel_size, outfile);
+  statusBar()->showMessage(tr("SOAC point density/intensity file saved."));
   outfile.close();
-  statusBar()->showMessage(
-      tr("SOAC point density/intensity written successfully."));
 }
 
 void MainWindow::ComputeCurvature() {
   QString filename = QFileDialog::getSaveFileName(
-      this, tr("Save curvature file"), "..", tr("Text files(*.txt)"));
+      this, tr("Save curvature"), "..", tr("Text files(*.txt)"));
   if (filename.isEmpty()) return;
   int coarse_graining = analysis_options_dialog_->GetCoarseGraining();
-  std::cout << coarse_graining << std::endl;
-  multisnake_->ComputeCurvature(coarse_graining, filename.toStdString());
+
+  std::ofstream outfile;
+  outfile.open(filename.toStdString().c_str());
+  if (!outfile.is_open()) {
+    QMessageBox msg_box;
+    msg_box.setText("Opening file failed.");
+    msg_box.setIcon(QMessageBox::Critical);
+    msg_box.exec();
+    return;
+  }
+  multisnake_->ComputeCurvature(coarse_graining, outfile);
   statusBar()->showMessage(tr("Curvature file saved."));
+  outfile.close();
 }
 
 void MainWindow::ShowAnalysisOptions() {

diff --git a/main_window.h b/main_window.h
@@ -59,6 +59,7 @@ class MainWindow : public QMainWindow {
   void DeformSnakesForSequence();
   void CutSnakes();
   void GroupSnakes();
+  void FindCorrespondence();
 
   void ComputeSphericalOrientation();
   void ComputeRadialOrientation();
@@ -152,6 +153,7 @@ class MainWindow : public QMainWindow {
   QAction *deform_snakes_for_sequence_;
   QAction *cut_snakes_;
   QAction *group_snakes_;
+  QAction *find_correspondence_;
 
   // Actions in Analysis menu
   QAction *compute_spherical_orientation_;

diff --git a/multisnake.cc b/multisnake.cc
@@ -1457,37 +1457,26 @@ void Multisnake::PrintGroundTruthLocalSNRValues(int radial_near,
 
 
 void Multisnake::ComputeRadialOrientation(const PointType &center,
-                                          const std::string &filename) const {
+                                          double pixel_size,
+                                          std::ostream & os) const {
   if (converged_snakes_.empty()) return;
 
-  std::ofstream outfile;
-  outfile.open(filename.c_str());
-  if (!outfile.is_open()) {
-    std::cerr << "Cannot open file for radial orientation results."
-              << std::endl;
-    return;
-  }
-
-  const unsigned width = 15;
-  outfile << "Image file\t" << image_filename_ << "\n"
+  const unsigned width = 16;
+  os << "Image file\t" << image_filename_ << "\n"
           << "Image center\t" << center << "\n"
           << std::setw(width) << "radius (um)"
           << std::setw(width) << "theta" << std::endl;
 
-  const double spacing = 0.166; // droplet image
-
   for (SnakeConstIterator it = converged_snakes_.begin();
        it != converged_snakes_.end(); ++it) {
     for (unsigned i = 0; i < (*it)->GetSize() - 1; ++i) {
       double r, theta;
       this->ComputeRTheta((*it)->GetPoint(i), (*it)->GetPoint(i+1),
                           center, r, theta);
-      outfile << std::setw(width) << r * spacing
+      os << std::setw(width) << r * pixel_size
               << std::setw(width) << theta << std::endl;
     }
   }
-
-  outfile.close();
 }
 
 void Multisnake::ComputeRTheta(const PointType &point1,
@@ -1572,17 +1561,8 @@ void Multisnake::ComputePointDensityAndIntensity(const PointType &center,
   }
 }
 
-void Multisnake::ComputeCurvature(int coarse_graining,
-                                  const std::string &filename) const {
-  std::ofstream outfile;
-  outfile.open(filename.c_str());
-  if (!outfile.is_open()) {
-    std::cerr << "Cannot open file for snake point density results."
-              << std::endl;
-    return;
-  }
-
-  outfile << "Image file\t" << image_filename_ << "\n"
+void Multisnake::ComputeCurvature(int coarse_graining, std::ostream &os) const {
+  os << "Image file\t" << image_filename_ << "\n"
           << "Coarse graining\t" << coarse_graining << std::endl;
 
   for (SnakeConstIterator it = converged_snakes_.begin();
@@ -1598,24 +1578,14 @@ void Multisnake::ComputeCurvature(int coarse_graining,
       vec2.Normalize();
       double length = coarse_graining * (*it)->spacing();
       double curvature = (vec1 - vec2).GetNorm() / length;
-      outfile << curvature << std::endl;
+      os << curvature << std::endl;
     }
   }
-  outfile.close();
 }
 
-void Multisnake::ComputeSphericalOrientation(
-    const std::string &filename) const {
-  std::ofstream outfile;
-  outfile.open(filename.c_str());
-  if (!outfile.is_open()) {
-    std::cerr << "Cannot open file for snake point density results."
-              << std::endl;
-    return;
-  }
-
-  const unsigned width = 15;
-  outfile << "Image file\t" << image_filename_ << "\n"
+void Multisnake::ComputeSphericalOrientation(std::ostream &os) const {
+  const unsigned width = 16;
+  os << "Image file\t" << image_filename_ << "\n"
           << std::setw(width) << "theta"
           << std::setw(width) << "phi" << std::endl;
   for (SnakeConstIterator it = converged_snakes_.begin();
@@ -1624,11 +1594,10 @@ void Multisnake::ComputeSphericalOrientation(
       VectorType vector = (*it)->GetPoint(i) - (*it)->GetPoint(i+1);
       double theta, phi;
       this->ComputeThetaPhi(vector, theta, phi);
-      outfile << std::setw(width) << theta
-              << std::setw(width) << phi << std::endl;
+      os << std::setw(width) << theta
+         << std::setw(width) << phi << std::endl;
     }
   }
-  outfile.close();
 }
 
 void Multisnake::ComputeThetaPhi(VectorType vector,

diff --git a/multisnake.h b/multisnake.h
@@ -185,15 +185,15 @@ class Multisnake : public QObject {
   void PrintGroundTruthLocalSNRValues(int radial_near, int radial_far) const;
 
   void ComputeRadialOrientation(const PointType &center,
-                                const std::string &filename) const;
+                                double pixel_size,
+                                std::ostream & os) const;
 
   void ComputePointDensityAndIntensity(const PointType &center,
                                        unsigned max_r, double pixel_size,
                                        std::ostream & os) const;
 
-  void ComputeCurvature(int coarse_graining,
-                        const std::string &filename) const;
-  void ComputeSphericalOrientation(const std::string &filename) const;
+  void ComputeCurvature(int coarse_graining, std::ostream &os) const;
+  void ComputeSphericalOrientation(std::ostream &os) const;
 
   void DeleteSnakes(const SnakeSet &snakes);
 

diff --git a/snake.cc b/snake.cc
@@ -543,15 +543,17 @@ double Snake::ComputeBackgroundMeanIntensity(bool is_head) const {
       this->ComputeSamplePoint(sample_point, vertex, radial, normal, d, s);
       if (this->IsInsideImage(sample_point)) {
         double intensity = interpolator_->Evaluate(sample_point);
-        bgs.push_back(intensity);
+        if (intensity > background_)
+          bgs.push_back(intensity);
       }
     }
   }
 
-  int number_of_samples = number_of_sectors_ * (radial_far_ - radial_near_);
-  unsigned threshold = static_cast<unsigned>(number_of_samples * 0.5);
-  // std::cout << threshold << std::endl;
-  if (bgs.size() < threshold)  {
+  // int number_of_samples = number_of_sectors_ * (radial_far_ - radial_near_);
+  // unsigned threshold = static_cast<unsigned>(number_of_samples * 0.5);
+
+  // if (bgs.size() < threshold)  {
+  if (bgs.empty()) {
     return -1.0; // return a negative value intentionally
   } else {
     return Mean(bgs);