Add logging of groom and optimize parameters to file log

Author: akenmorris

Libs/Analyze/MeshGenerator.cpp

@@ -165,6 +165,8 @@ MeshHandle MeshGenerator::build_mesh_from_file(std::string filename, float iso_v
     }
   } else if (is_image) {
     try {
+      ImageUtils::register_itk_factories();
+
       // read file using ITK
       using ReaderType = itk::ImageFileReader<ImageType>;
       ReaderType::Pointer reader = ReaderType::New();

Libs/Groom/GroomParameters.h

@@ -137,7 +137,6 @@ class GroomParameters {
   bool get_skip_grooming();
   void set_skip_grooming(bool skip);
 
-
   bool get_shared_boundary();
   void set_shared_boundary(bool shared_boundary);
 
@@ -152,6 +151,8 @@ class GroomParameters {
 
   void restore_defaults();
 
+  Parameters get_parameters() const { return params_; }
+
   // constants
   const static std::string GROOM_SMOOTH_VTK_LAPLACIAN_C;
   const static std::string GROOM_SMOOTH_VTK_WINDOWED_SINC_C;

Libs/Image/ImageUtils.cpp

@@ -2,6 +2,11 @@
 
 #include <itkPointSet.h>
 
+// ITK image factories
+#include <itkMetaImageIOFactory.h>
+#include <itkNiftiImageIOFactory.h>
+#include <itkNrrdImageIOFactory.h>
+
 namespace shapeworks {
 
 PhysicalRegion ImageUtils::boundingBox(const std::vector<std::string>& filenames, Image::PixelType isoValue) {
@@ -39,6 +44,18 @@ PhysicalRegion ImageUtils::boundingBox(const std::vector<std::reference_wrapper<
   return bbox;
 }
 
+void ImageUtils::register_itk_factories()
+{
+  static bool registered = false;
+  if (!registered) {
+    // register all the factories
+    itk::NrrdImageIOFactory::RegisterOneFactory();
+    itk::NiftiImageIOFactory::RegisterOneFactory();
+    itk::MetaImageIOFactory::RegisterOneFactory();
+    registered = true;
+  }
+}
+
 ImageUtils::TPSTransform::Pointer ImageUtils::createWarpTransform(const std::string& source_landmarks_file,
                                                                   const std::string& target_landmarks_file,
                                                                   const int stride) {

Libs/Image/ImageUtils.h

@@ -22,6 +22,9 @@ class ImageUtils {
   using TPSTransform = itk::ThinPlateSplineKernelTransform<double, 3>;
   static TPSTransform::Pointer createWarpTransform(const std::string& source_landmarks_file,
                                                    const std::string& target_landmarks_file, const int stride = 1);
+
+  static void register_itk_factories();
+
 };
 
 }  // namespace shapeworks

Libs/Optimize/OptimizeParameters.cpp

@@ -864,3 +864,6 @@ double OptimizeParameters::get_shared_boundary_weight() { return params_.get(Key
 
 //---------------------------------------------------------------------------
 void OptimizeParameters::set_shared_boundary_weight(double value) { params_.set(Keys::shared_boundary_weight, value); }
+
+//---------------------------------------------------------------------------
+Parameters OptimizeParameters::get_parameters() const { return params_; }

Libs/Optimize/OptimizeParameters.h

@@ -138,6 +138,8 @@ class OptimizeParameters {
   double get_shared_boundary_weight();
   void set_shared_boundary_weight(double value);
 
+  Parameters get_parameters() const;
+
  private:
   std::string get_output_prefix();
 

Studio/Groom/GroomTool.cpp

@@ -591,6 +591,18 @@ void GroomTool::on_run_groom_button_clicked() {
   timer_.start();
 
   SW_LOG("Please wait: running groom step...");
+
+  // log parameters
+  SW_LOG_ONLY("Grooming parameters:");
+
+  for (const auto& domain_name : session_->get_project()->get_domain_names()) {
+    auto params = GroomParameters(session_->get_project(), domain_name);
+    SW_LOG_ONLY("Domain: " + domain_name);
+    for (const auto& pair : params.get_parameters().get_map()) {
+      SW_LOG_ONLY(pair.first + ": " + pair.second);
+    }
+  }
+
   Q_EMIT progress(0);
 
   groom_ = QSharedPointer<Groom>(new Groom(session_->get_project()));