Apply suggestions from code review

Co-authored-by: Toby Searle <[email protected]>

Author: frld

src/mains/CMakeLists.txt

@@ -42,5 +42,5 @@ ecbuild_add_executable( TARGET  orcamodel_ErrorCovarianceToolbox.x
 
 oops_output_json_schema( "orcamodel_hofx.x" )
 oops_output_json_schema( "orcamodel_hofx3D.x" )
-#oops_output_json_schema( "orcamodel_3DVar.x" )
-#oops_output_json_schema( "orcamodel_ErrorCovarianceToolbox.x" )
+oops_output_json_schema( "orcamodel_3DVar.x" )
+oops_output_json_schema( "orcamodel_ErrorCovarianceToolbox.x" )

src/orca-jedi/increment/Increment.cc

@@ -558,11 +558,7 @@ void Increment::write(const OrcaIncrementParameters & params) const {
   oops::Log::debug() << "Increment::write to filename "
                      << nemo_field_path << std::endl;
 
-  for (size_t i=0; i < vars_.size(); ++i) {
-    auto gv_varname = vars_[i].name();
-// halo exchange update ghost points
-    geom_->functionSpace().haloExchange(incrementFields_[gv_varname]);
-  }
+incrementFields_.haloExchange();
 
   writeFieldsToFile(nemo_field_path, *geom_, time_, incrementFields_);
 }

src/orca-jedi/interpolator/Interpolator.cc

@@ -208,26 +208,9 @@ void Interpolator::apply(const oops::Variables& vars, const Increment& inc,
   for (size_t jvar=0; jvar < nvars; ++jvar) nvals += nlocs_ * varSizes[jvar];
   result.resize(nvals);
 
-  std::size_t out_idx = 0;
+  auto res_iter = result.begin();
   for (size_t jvar=0; jvar < nvars; ++jvar) {
-    auto gv_varname = vars[jvar].name();
-    atlas::Field tgt_field = atlasObsFuncSpace_.createField<double>(
-        atlas::option::name(gv_varname) |
-        atlas::option::levels(varSizes[jvar]));
-    interpolator_.execute(inc.incrementFields()[gv_varname], tgt_field);
-    auto field_view = atlas::array::make_view<double, 2>(tgt_field);
-    atlas::field::MissingValue mv(inc.incrementFields()[gv_varname]);
-    bool has_mv = static_cast<bool>(mv);
-    for (std::size_t klev=0; klev < varSizes[jvar]; ++klev) {
-      for (std::size_t iloc=0; iloc < nlocs_; iloc++) {
-        if (has_mv && mv(field_view(iloc, klev))) {
-          result[out_idx] = util::missingValue<double>();
-        } else {
-          result[out_idx] = field_view(iloc, klev);
-        }
-        ++out_idx;
-      }
-    }
+      executeInterpolation<double>(vars[jvar].name(), varSizes[jvar], state, mask, res_iter);
   }
 }
 

src/orca-jedi/state/State.cc

@@ -83,7 +83,7 @@ State::State(const Geometry & geom,
     readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background",
          stateFields_);
     nemo_file_name = params.errorFieldFile.value().value_or("");
-    if (nemo_file_name != "") {
+    if (params.errorFieldFile.value()) {
       readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background error standard deviation",
          stateFields_);
       readFieldsFromFile(nemo_file_name, *geom_, validTime(), "background error variance",

src/orca-jedi/variablechanges/LinearVariableChange.cc

@@ -19,7 +19,6 @@
 namespace orcamodel {
 
 // -----------------------------------------------------------------------------
-// LinearVariableChange::LinearVariableChange(const Parameters_ &, const Geometry &) {}
 LinearVariableChange::LinearVariableChange(const Geometry &, const Parameters_ &) {}
 LinearVariableChange::LinearVariableChange(const Geometry &, const eckit::Configuration &) {}
 // -----------------------------------------------------------------------------

src/orca-jedi/variablechanges/LinearVariableChange.h

@@ -28,7 +28,6 @@ namespace orcamodel {
 // -----------------------------------------------------------------------------
 
 class LinearVariableChange: public util::Printable {
-// private util::ObjectCounter<LinearVariableChange>
  public:
   typedef LinearVariableChangeParameters Parameters_;
   static const std::string classname() {