Merge remote-tracking branch 'SCIInstitute/master' into GetMeshQualityField_Convert

Author: allywarner

src/Core/Algorithms/Legacy/Fields/CMakeLists.txt

@@ -30,6 +30,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   ClipMesh/ClipMeshBySelection.h
   ClipMesh/ClipMeshByIsovalue.h
   ConvertMeshType/ConvertMeshToPointCloudMeshAlgo.h
+  ConvertMeshType/ConvertMeshToUnstructuredMesh.h
   DistanceField/CalculateSignedDistanceField.h
   DistanceField/CalculateDistanceField.h
   Mapping/ApplyMappingMatrix.h
@@ -113,7 +114,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
   ConvertMeshType/ConvertMeshToPointCloudMeshAlgo.cc
   ConvertMeshType/ConvertMeshToTetVolMesh.cc
   ConvertMeshType/ConvertMeshToTriSurfMeshAlgo.cc
-  #ConvertMeshType/ConvertMeshToUnstructuredMesh.cc
+  ConvertMeshType/ConvertMeshToUnstructuredMesh.cc
   ConvertMeshType/ConvertMeshToIrregularMesh.cc
   #ConvertMeshType/ConvertLatVolDataFromElemToNode.cc
   #ConvertMeshType/ConvertLatVolDataFromNodeToElem.cc

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToIrregularMesh.cc

@@ -42,7 +42,7 @@ using namespace SCIRun::Core::Algorithms;
 using namespace SCIRun::Core::Datatypes;
 
 bool 
-ConvertMeshToIrregularMeshAlgo::run(FieldHandle input, FieldHandle& output) const
+ConvertMeshToIrregularMeshAlgo::runImpl(FieldHandle input, FieldHandle& output) const
 {
   // Mark that we are starting the algorithm, but do not report progress
   ScopedAlgorithmStatusReporter asr(this, "ConvertMeshToIrregularMesh");
@@ -188,17 +188,15 @@ ConvertMeshToIrregularMeshAlgo::run(FieldHandle input, FieldHandle& output) cons
   return (true);
 }
 
-AlgorithmOutputName ConvertMeshToIrregularMeshAlgo::OutputField("OutputField");
-
 AlgorithmOutput ConvertMeshToIrregularMeshAlgo::run(const AlgorithmInput& input) const
 {
   auto ifield = input.get<Field>(Variables::InputField);
 
   FieldHandle ofield;
-  if (!run(ifield, ofield))
+  if (!runImpl(ifield, ofield))
     THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");
 
   AlgorithmOutput output;
-  output[OutputField] = ofield;
+  output[Variables::OutputField] = ofield;
   return output;
 }

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToIrregularMesh.h

@@ -31,8 +31,6 @@
 #define CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTTOIRREGULARMESH_H 1
 
 #include <Core/Algorithms/Base/AlgorithmBase.h>
-
-// for Windows support
 #include <Core/Algorithms/Legacy/Fields/share.h>
 
 namespace SCIRun {
@@ -47,11 +45,9 @@ class SCISHARE ConvertMeshToIrregularMeshAlgo : public AlgorithmBase
     {
     }
 
-    bool run(FieldHandle input, FieldHandle& output) const;
-
-    static AlgorithmOutputName OutputField;
+    bool runImpl(FieldHandle input, FieldHandle& output) const;
 
-    virtual AlgorithmOutput run(const AlgorithmInput& input) const; 
+    virtual AlgorithmOutput run(const AlgorithmInput& input) const override; 
 };
 
 }}}}

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToPointCloudMeshAlgo.h

@@ -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
@@ -24,7 +24,7 @@
    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
    DEALINGS IN THE SOFTWARE.
-*/
+   */
 
 
 #ifndef CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTTOPOINTCLOUDMESH_H
@@ -39,18 +39,21 @@ namespace SCIRun {
     namespace Algorithms {
       namespace Fields {
 
-class SCISHARE ConvertMeshToPointCloudMeshAlgo : public AlgorithmBase
-{
-  public:
-    ConvertMeshToPointCloudMeshAlgo();
+        class SCISHARE ConvertMeshToPointCloudMeshAlgo : public AlgorithmBase
+        {
+        public:
+          ConvertMeshToPointCloudMeshAlgo();
 
-    bool runImpl(FieldHandle input, FieldHandle& output) const;
-    virtual AlgorithmOutput run(const AlgorithmInput& input) const override;
+          bool runImpl(FieldHandle input, FieldHandle& output) const;
+          virtual AlgorithmOutput run(const AlgorithmInput& input) const override;
 
-    static AlgorithmParameterName Location;
-};
+          static AlgorithmParameterName Location;
+        };
 
-      }}}}
+      }
+    }
+  }
+}
 
 #endif 
 

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.cc

@@ -27,39 +27,30 @@
 */
 
 // Get all the class definitions. 
-#include <Core/Algorithms/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.h>
-#include <Core/Datatypes/FieldInformation.h>
-
-// As we already included DynamicAlgorithm.h in the header we do not need to
-// include it again here.
-
-namespace SCIRunAlgo {
+#include <Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.h>
+#include <Core/Datatypes/Legacy/Field/FieldInformation.h>
+#include <Core/Datatypes/Legacy/Field/VMesh.h>
+#include <Core/Datatypes/Legacy/Field/VField.h>
+#include <Core/Datatypes/PropertyManagerExtensions.h>
+#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
+#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
 
 using namespace SCIRun;
+using namespace SCIRun::Core::Algorithms::Fields;
+using namespace SCIRun::Core::Geometry;
+using namespace SCIRun::Core::Utility;
+using namespace SCIRun::Core::Algorithms;
+using namespace SCIRun::Core::Datatypes;
 
-// Implementation of the actual access point to the algorithm
-
-bool 
-ConvertMeshToUnstructuredMeshAlgo::
-run(FieldHandle input, FieldHandle& output)
+bool ConvertMeshToUnstructuredMeshAlgo::runImpl(FieldHandle input, FieldHandle& output) const
 {
-  // Mark that we are starting the algorithm, but do not report progress
-  algo_start("ConvertMeshToUnstructuredMesh");
-
-  // Step 0:
-  // Safety test:
-  // Test whether we received actually a field. A handle can point to no object.
-  // Using a null handle will cause the program to crash. Hence it is a good
-  // policy to check all incoming handles and to see whether they point to actual
-  // objects.
-  
-  // Handle: the function get_rep() returns the pointer contained in the handle
-  if (input.get_rep() == 0)
+  ScopedAlgorithmStatusReporter asr(this, "ConvertMeshToUnstructuredMesh");
+
+  // Null check
+  if (!input)
   {
-    // If we encounter a null pointer we return an error message and return to
-    // the program to deal with this error. 
     error("No input field");
-    algo_end(); return (false);
+    return (false);
   }
 
  // Step 1: determine the type of the input fields and determine what type the
@@ -91,7 +82,7 @@ run(FieldHandle input, FieldHandle& output)
    if (fi.is_nonlinear())
   {
     error("This function has not yet been defined for non-linear elements");
-    algo_end(); return (false);
+    return (false);
   }
 
   // If the mesh is already unstructured, we only need to copy the input to the
@@ -102,7 +93,7 @@ run(FieldHandle input, FieldHandle& output)
     remark("Mesh already is unstructured; copying input to output");
     // Copy input to output (output is a reference to the input)
     output = input;
-    algo_end(); return (true);
+    return (true);
   }
 
   // Define the output type of the data
@@ -121,19 +112,19 @@ run(FieldHandle input, FieldHandle& output)
   else
   {
     error("No unstructure method available for mesh: " + fi.get_mesh_type());
-    algo_end(); return (false);
+    return (false);
   }
 
   // Create a new output field
   output = CreateField(fo);
 
-  if (output.get_rep() == 0)
+  if (!output)
   { 
     // Error reporting:
     // we forward the specific message to the ProgressReporter and return a
     // false to indicate that an error has occured.
     error("Could not obtain input field");
-    algo_end(); return (false);
+    return (false);
   }  
 
   // Get the virtual interface of the objects
@@ -169,16 +160,23 @@ run(FieldHandle input, FieldHandle& output)
     omesh->add_elem(nodes);
   }
 
-  // Resize the data
-  // and copy the data
   ofield->resize_values();
   ofield->copy_values(ifield);
 
-  /// Copy properties of the property manager
-	output->copy_properties(input.get_rep());
+  CopyProperties(*input, *output);
 
-  // Success:
-  algo_end(); return (true);
+  return (true);
 }
 
-} // End namespace SCIRunAlgo
+AlgorithmOutput ConvertMeshToUnstructuredMeshAlgo::run(const AlgorithmInput& input) const
+{
+  auto ifield = input.get<Field>(Variables::InputField);
+
+  FieldHandle ofield;
+  if (!runImpl(ifield, ofield))
+    THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");
+
+  AlgorithmOutput output;
+  output[Variables::OutputField] = ofield;
+  return output;
+}

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.h

@@ -30,32 +30,29 @@
 #ifndef CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTMESHTOUNSTRUCTUREDMESH_H
 #define CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTMESHTOUNSTRUCTUREDMESH_H 1
 
-// Datatypes that the algorithm uses
-#include <Core/Datatypes/Mesh.h>
-#include <Core/Datatypes/Field.h>
+#include <Core/Algorithms/Base/AlgorithmBase.h>
+#include <Core/Algorithms/Legacy/Fields/share.h>
 
-// Base class for algorithm
-#include <Core/Algorithms/Util/AlgoBase.h>
+namespace SCIRun {
+  namespace Core {
+    namespace Algorithms {
+      namespace Fields {
 
-// for Windows support
-#include <Core/Algorithms/Fields/share.h>
+        class SCISHARE ConvertMeshToUnstructuredMeshAlgo : public AlgorithmBase
+        {
+        public:
+          ConvertMeshToUnstructuredMeshAlgo()
+          {
+          }
 
-namespace SCIRunAlgo {
+          bool runImpl(FieldHandle input, FieldHandle& output) const;
 
-using namespace SCIRun;
+          virtual AlgorithmOutput run(const AlgorithmInput& input) const override;
+        };
 
-class SCISHARE ConvertMeshToUnstructuredMeshAlgo : public AlgoBase
-{
-  public:
-    /// Set defaults
-    ConvertMeshToUnstructuredMeshAlgo()
-    {
+      }
     }
+  }
+}
 
-    /// run the algorithm
-    bool run(FieldHandle input, FieldHandle& output);};
-
-} // end namespace SCIRunAlgo
-
-#endif
-
+#endif 

src/Core/Algorithms/Legacy/Fields/MeshData/SetMeshNodes.cc

@@ -75,7 +75,7 @@ SetMeshNodesAlgo::run(FieldHandle input, DenseMatrixHandle matrix, FieldHandle&
     /// @todo: worth separating out into factory call for mocking purposes? probably not, just keep the concrete dependence
     ConvertMeshToIrregularMeshAlgo algo;
 
-    if (!algo.run(input,output))
+    if (!algo.runImpl(input,output))
       return (false);
   }
   else

src/Dataflow/Engine/Controller/NetworkEditorController.cc

@@ -147,7 +147,7 @@ namespace
           nec_.requestConnection(c.first, c.second);
       }
 
-      nec_.updateModulePositions(positions);
+      nec_.updateModulePositions(positions, true);
 
       return mods_.back();
     }
@@ -170,7 +170,6 @@ namespace
       if (!isSnippetName(label))
         return {};
 
-      //TODO: need a way to specify more than just linear connections.
       parseModules(label);
 
       if (mods_.size() < 2)
@@ -483,7 +482,7 @@ void NetworkEditorController::loadNetwork(const NetworkFileHandle& xml)
       }
       if (serializationManager_)
       {
-        serializationManager_->updateModulePositions(xml->modulePositions);
+        serializationManager_->updateModulePositions(xml->modulePositions, false);
         serializationManager_->updateModuleNotes(xml->moduleNotes);
         serializationManager_->updateConnectionNotes(xml->connectionNotes);
         serializationManager_->updateModuleTags(xml->moduleTags);
@@ -560,7 +559,7 @@ void NetworkEditorController::appendToNetwork(const NetworkFileHandle& xml)
       {
         xml->modulePositions.modulePositions = remapIdBasedContainer(xml->modulePositions.modulePositions, info.moduleIdMapping);
         shiftAppendedModules(xml->modulePositions.modulePositions);
-        serializationManager_->updateModulePositions(xml->modulePositions); // need to shift everything.
+        serializationManager_->updateModulePositions(xml->modulePositions, false); // need to shift everything.
         xml->moduleNotes.notes = remapIdBasedContainer(xml->moduleNotes.notes, info.moduleIdMapping);
         serializationManager_->updateModuleNotes(xml->moduleNotes);
         xml->connectionNotes.notes = remapIdBasedContainer(xml->connectionNotes.notes, info.moduleIdMapping);
@@ -688,11 +687,11 @@ const ModuleLookupInfoSet& NetworkEditorController::possibleReplacements(ModuleH
   return replacementFilter_->findReplacements(makeConnectedPortInfo(module));
 }
 
-void NetworkEditorController::updateModulePositions(const ModulePositions& modulePositions)
+void NetworkEditorController::updateModulePositions(const ModulePositions& modulePositions, bool selectAll)
 {
   if (serializationManager_)
   {
-    serializationManager_->updateModulePositions(modulePositions);
+    serializationManager_->updateModulePositions(modulePositions, selectAll);
   }
 }
 
@@ -726,5 +725,5 @@ void NetworkEditorController::cleanUpNetwork()
     }
   }
 
-  updateModulePositions(cleanedUp);
+  updateModulePositions(cleanedUp, false);
 }

src/Dataflow/Engine/Controller/NetworkEditorController.h

@@ -153,7 +153,7 @@ namespace Engine {
 
     const Networks::ReplacementImpl::ModuleLookupInfoSet& possibleReplacements(Networks::ModuleHandle module);
 
-    void updateModulePositions(const SCIRun::Dataflow::Networks::ModulePositions& modulePositions);
+    void updateModulePositions(const SCIRun::Dataflow::Networks::ModulePositions& modulePositions, bool selectAll);
 
     void cleanUpNetwork();
 

src/Dataflow/Serialization/Network/ModulePositionGetter.h

@@ -48,7 +48,7 @@ namespace Networks {
   public:
     virtual ~NetworkEditorSerializationManager() {}
     virtual ModulePositionsHandle dumpModulePositions(ModuleFilter filter) const = 0;
-    virtual void updateModulePositions(const ModulePositions& modulePositions) = 0;
+    virtual void updateModulePositions(const ModulePositions& modulePositions, bool selectAll) = 0;
 
     //TODO: refactor into dump/updateNotes, shouldn't need to distinguish parent.
     virtual ModuleNotesHandle dumpModuleNotes(ModuleFilter filter) const = 0;