Fix bundle modules

Author: dcwhite

src/Dataflow/Network/Module.cc

@@ -35,6 +35,7 @@
 #include <boost/timer.hpp>
 #include <atomic>
 
+#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
 #include <Dataflow/Network/PortManager.h>
 #include <Dataflow/Network/ModuleStateInterface.h>
 #include <Dataflow/Network/Module.h>
@@ -278,6 +279,12 @@ bool Module::executeWithSignals() NOEXCEPT
     ostr << "Port not found, it may need initializing the module constructor. " << std::endl << "Message: " << e.what() << std::endl;
     error(ostr.str());
   }
+  catch (AlgorithmParameterNotFound& e)
+  {
+    std::ostringstream ostr;
+    ostr << "State key not found, it may need initializing in ModuleClass::setStateDefaults(). " << std::endl << "Message: " << e.what() << std::endl;
+    error(ostr.str());
+  }
   catch (Core::ExceptionBase& e)
   {
     /// @todo: this block is repetitive (logging-wise) if the macros are used to log AND throw an exception with the same message. Figure out a reasonable condition to enable it.

src/Modules/BrainStimulator/GenerateROIStatistics.cc

@@ -6,7 +6,7 @@
    Copyright (c) 2015 Scientific Computing and Imaging Institute,
    University of Utah.
 
-   
+
    Permission is hereby granted, free of charge, to any person obtaining a
    copy of this software and associated documentation files (the "Software"),
    to deal in the Software without restriction, including without limitation
@@ -52,7 +52,8 @@ GenerateROIStatisticsModule::GenerateROIStatisticsModule() : Module(ModuleLookup
 
 void GenerateROIStatisticsModule::setStateDefaults()
 {
-  setStateStringFromAlgoOption(Parameters::PhysicalUnitStr);  
+  setStateStringFromAlgoOption(Parameters::PhysicalUnitStr);
+  get_state()->setValue(Parameters::StatisticsTableValues, VariableList());
 }
 
 void GenerateROIStatisticsModule::execute()
@@ -63,29 +64,29 @@ void GenerateROIStatisticsModule::execute()
   auto atlasMeshLabels_ = getOptionalInput(AtlasMeshLabels);
   auto coordinateSpace_ = getOptionalInput(CoordinateSpace);
   auto coordinateSpaceLabel_ = getOptionalInput(CoordinateSpaceLabel);
-  
-  setAlgoListFromState(Parameters::StatisticsTableValues); /// to transfer data between algo and dialog use the state variable 
-  
+
+  setAlgoListFromState(Parameters::StatisticsTableValues); /// to transfer data between algo and dialog use the state variable
+
   auto roiSpec = transient_value_cast<DenseMatrixHandle>(get_state()->getTransientValue(GenerateROIStatisticsAlgorithm::SpecifyROI)); /// transfer the ROI specification from GUI dialog as additional input
   //algorithm input and run
   auto input = make_input((MeshDataOnElements, meshData_)(PhysicalUnit, optionalAlgoInput(physicalUnit_))(AtlasMesh, atlasMesh_)(AtlasMeshLabels,
   optionalAlgoInput(atlasMeshLabels_))(CoordinateSpace, optionalAlgoInput(coordinateSpace_))(CoordinateSpaceLabel,
   optionalAlgoInput(coordinateSpaceLabel_)));
-  
+
   if (roiSpec)
     input[GenerateROIStatisticsAlgorithm::SpecifyROI] = roiSpec;
-  
-  auto output = algo().run(input); /// call run generic 
 
-  auto table = output.additionalAlgoOutput(); /// get the two outputs, the upper table (as DenseMatrix) and the container that establishes data transfer between GUI/Algo via state  
+  auto output = algo().run(input); /// call run generic
+
+  auto table = output.additionalAlgoOutput(); /// get the two outputs, the upper table (as DenseMatrix) and the container that establishes data transfer between GUI/Algo via state
   get_state()->setTransientValue(Parameters::StatisticsTableValues, table);
-  
+
   if (physicalUnit_ && *physicalUnit_) /// set physicalUnit string immediately to state, and then to dialog
      get_state()->setTransientValue(Parameters::PhysicalUnitStr,(*physicalUnit_)->value());
-  
+
   if (coordinateSpaceLabel_ && *coordinateSpaceLabel_)/// set coordinateSpaceLabel string immediately to state, and then to dialog
-     get_state()->setTransientValue(Parameters::CoordinateSpaceLabelStr,(*coordinateSpaceLabel_)->value()); 
-  
+     get_state()->setTransientValue(Parameters::CoordinateSpaceLabelStr,(*coordinateSpaceLabel_)->value());
+
   //algorithm output
   sendOutputFromAlgorithm(StatisticalResults, output); /// set the upper table (DenseMatrix) as only output of the module
 }

src/Modules/Legacy/Bundle/InsertFieldsIntoBundle.cc

@@ -6,7 +6,7 @@
    Copyright (c) 2015 Scientific Computing and Imaging Institute,
    University of Utah.
 
-   
+
    Permission is hereby granted, free of charge, to any person obtaining a
    copy of this software and associated documentation files (the "Software"),
    to deal in the Software without restriction, including without limitation
@@ -51,18 +51,18 @@ InsertFieldsIntoBundle::InsertFieldsIntoBundle() : Module(staticInfo_)
 
 void InsertFieldsIntoBundle::setStateDefaults()
 {
-
+  get_state()->setValue(FieldReplace, VariableList());
 }
 
 void InsertFieldsIntoBundle::execute()
 {
   auto bundleOption = getOptionalInput(InputBundle);
   auto fields = getRequiredDynamicInputs(InputFields);
 
-  //if (inputs_changed_ || guifield1name_.changed() || 
+  //if (inputs_changed_ || guifield1name_.changed() ||
   //  guifield2name_.changed() || guifield3name_.changed() ||
   //  guifield4name_.changed() || guifield5name_.changed() ||
-  //  guifield6name_.changed() || 
+  //  guifield6name_.changed() ||
   //  guireplace1_.changed() || guireplace2_.changed() ||
   //  guireplace3_.changed() || guireplace4_.changed() ||
   //  guireplace5_.changed() || guireplace6_.changed() ||
@@ -126,9 +126,9 @@ void InsertFieldsIntoBundle::execute()
 
 private:
   GuiString     guifield6name_;
-  
+
   GuiInt        guireplace6_;
-  
+
   GuiString     guibundlename_;
 };
 
@@ -151,4 +151,4 @@ void InsertFieldsIntoBundle::execute()
 {
 }
 
-#endif
+#endif

src/Modules/Legacy/Bundle/InsertMatricesIntoBundle.cc

@@ -52,7 +52,7 @@ InsertMatricesIntoBundle::InsertMatricesIntoBundle() : Module(staticInfo_)
 
 void InsertMatricesIntoBundle::setStateDefaults()
 {
-
+  get_state()->setValue(MatrixReplace, VariableList());
 }
 
 void InsertMatricesIntoBundle::execute()

src/Modules/Legacy/Bundle/InsertStringsIntoBundle.cc

@@ -6,7 +6,7 @@
    Copyright (c) 2015 Scientific Computing and Imaging Institute,
    University of Utah.
 
-   
+
    Permission is hereby granted, free of charge, to any person obtaining a
    copy of this software and associated documentation files (the "Software"),
    to deal in the Software without restriction, including without limitation
@@ -52,7 +52,7 @@ InsertStringsIntoBundle::InsertStringsIntoBundle() : Module(staticInfo_)
 
 void InsertStringsIntoBundle::setStateDefaults()
 {
-
+  get_state()->setValue(StringReplace, VariableList());
 }
 
 void InsertStringsIntoBundle::execute()