"IQuantVis" first draft

src/CMakeLists.txt

@@ -745,6 +745,7 @@ SET_PROPERTY(TARGET Modules_Legacy_Matlab_DataIO PROPERTY FOLDER "Modules/DataIO
 SET_PROPERTY(TARGET Modules_Legacy_Visualization   PROPERTY FOLDER "Modules/Visualization")
 SET_PROPERTY(TARGET Modules_Legacy_Teem_DataIO   PROPERTY FOLDER "Modules/Teem")
 SET_PROPERTY(TARGET Modules_Legacy_Teem_Misc   PROPERTY FOLDER "Modules/Teem")
+SET_PROPERTY(TARGET Modules_Legacy_Teem_Tend   PROPERTY FOLDER "Modules/Teem")
 SET_PROPERTY(TARGET Modules_Legacy_Teem_Converters   PROPERTY FOLDER "Modules/Teem")
 SET_PROPERTY(TARGET Modules_Factory   PROPERTY FOLDER "Modules")
 

src/Core/Algorithms/Base/AlgorithmData.h

@@ -75,7 +75,7 @@ namespace Algorithms {
     void setTransient(boost::any t) { transient_ = t; }
     boost::any getTransient() const { return transient_; }
 
-  private:
+  protected:
     Map data_;
     boost::any transient_;
   };
@@ -92,6 +92,15 @@ namespace Algorithms {
   public:
     VariableHandle additionalAlgoOutput() const { return additionalAlgoOutput_; }
     void setAdditionalAlgoOutput(VariableHandle var) { additionalAlgoOutput_ = var; }
+    Datatypes::DatatypeHandle at(size_t index) const
+    {
+      if (index >= size())
+        return nullptr;
+      auto iter = data_.begin();
+      std::advance(iter, index);
+      return iter->second[0];
+    }
+    size_t size() const { return data_.size(); }
   private:
     VariableHandle additionalAlgoOutput_;
   };

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

@@ -35,7 +35,7 @@ SET(Core_Algorithms_Legacy_Converter_SRCS
   FieldToNrrd.cc
   ConvertToNrrd.cc
   #MatricesToDipoleField.cc
-  #ConvertBundleToField.cc
+  ConvertBundleToField.cc
   ConvertMatrixToString.cc
 )
 
@@ -45,6 +45,7 @@ SET(Core_Algorithms_Legacy_Converter_HEADERS
   FieldToNrrd.h
   ConvertToNrrd.h
   ConvertMatrixToString.h
+  ConvertBundleToField.h
   share.h
 )
 
@@ -57,6 +58,7 @@ TARGET_LINK_LIBRARIES(Core_Algorithms_Legacy_Converter
   Core_Datatypes
   Core_Datatypes_Legacy_Field
   Core_Datatypes_Legacy_Nrrd
+  Core_Datatypes_Legacy_Bundle
 )
 
 IF(BUILD_SHARED_LIBS)

src/Core/Algorithms/Legacy/Converter/ConvertBundleToField.cc

@@ -29,71 +29,60 @@
 */
 
 
-#include <Core/Algorithms/Converter/ConvertBundleToField.h>
-#include <Core/Datatypes/MatrixTypeConverter.h>
-
-#include <Core/Datatypes/SparseRowMatrix.h>
-#include <Core/Algorithms/Fields/MergeFields/JoinFields.h>
-#include <Core/Datatypes/FieldInformation.h>
-#include <Core/Datatypes/Mesh.h>
-#include <Core/Containers/SearchGridT.h>
-#include <vector>
+#include <Core/Algorithms/Legacy/Converter/ConvertBundleToField.h>
+#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
+#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
+#include <Core/Datatypes/Legacy/Field/FieldInformation.h>
+#include <Core/Datatypes/Legacy/Field/Field.h>
+#include <Core/Datatypes/Legacy/Field/VField.h>
+#include <Core/Datatypes/Legacy/Field/VMesh.h>
+#include <Core/Datatypes/Legacy/Bundle/Bundle.h>
 
 using namespace SCIRun;
-
-namespace SCIRunAlgo {
+using namespace SCIRun::Core;
+using namespace SCIRun::Core::Algorithms;
+using namespace SCIRun::Core::Datatypes;
+using namespace SCIRun::Core::Utility;
+using namespace SCIRun::Core::Geometry;
+using namespace SCIRun::Core::Algorithms::Converters;
+
+ALGORITHM_PARAMETER_DEF(Converters, MergeNodes);
+ALGORITHM_PARAMETER_DEF(Converters, Tolerance);
+ALGORITHM_PARAMETER_DEF(Converters, MatchNodeValues);
+ALGORITHM_PARAMETER_DEF(Converters, MakeNoData);
 
 ConvertBundleToFieldAlgo::ConvertBundleToFieldAlgo()
 {
+  using namespace Parameters;
   //! Merge duplicate nodes?
-  add_bool("merge_nodes", true);
+  addParameter(Parameters::MergeNodes, true);
 
   //! Tolerance for merging duplicate nodes?
-  add_scalar("tolerance", 1e-6);
+  addParameter(Parameters::Tolerance, 1e-6);
 
   //! Only merge nodes whose value is the same
   //! in this module, this option always set false
-  add_bool("match_node_values", false);
+  addParameter(Parameters::MatchNodeValues, false);
 
   //! Create a field with no data
-  add_bool("make_no_data", false);
+  addParameter(Parameters::MakeNoData, false);
 }
 
-ConvertBundleToFieldAlgo::~ConvertBundleToFieldAlgo() {}
-
-bool
-ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
+bool ConvertBundleToFieldAlgo::runImpl(const BundleHandle& input, FieldHandle& output) const
 {
-  // Mark that we are starting the algorithm
-  algo_start("ConvertBundleToField");
-
-  std::vector<FieldHandle> inputs;
-  FieldHandle fhandle;
-  std::string fieldname;
-
-  int numFields = input->numFields();
-
-  //! deal with the empty field, if the field is empty, just return and do nothing
-  //if (numFields==0) return true;
-
-  for (int p = 0; p < numFields; p++)
-  {
-    fieldname=input->getFieldName(p);
-    fhandle = input->getField(fieldname);
-    inputs.push_back(fhandle);
-  }
+  ScopedAlgorithmStatusReporter asr(this, "ConvertBundleToField");
 
+  const auto inputs = input->getFields();
   if (inputs.empty())
   {
     error("Input bundle is empty");
-    algo_end();
     return false;
   }
 
-  bool match_node_values = get_bool("match_node_values");
-  bool make_no_data = get_bool("make_no_data");
-  bool merge_nodes = get_bool("merge_nodes");
-  double tol = get_scalar("tolerance");
+  const bool match_node_values = get(Parameters::MatchNodeValues).toBool();
+  const bool make_no_data = get(Parameters::MakeNoData).toBool();
+  const bool merge_nodes = get(Parameters::MergeNodes).toBool();
+  const double tol = get(Parameters::Tolerance).toDouble();
   const double tol2 = tol*tol;
 
   // Check whether mesh types are the same
@@ -108,14 +97,12 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
     if (fi.get_mesh_type() != first.get_mesh_type())
     {
       error("Mesh elements need to be equal in order to join multiple fields together");
-      algo_end();
       return false;
     }
 
     if (fi.mesh_basis_order() != first.mesh_basis_order())
     {
       error("Mesh elements need to be of the same order in for joining multiple fields together");
-      algo_end();
       return false;
     }
   }
@@ -132,7 +119,7 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
       if (fi.field_basis_order() != first.field_basis_order())
       {
         error("Fields need to have the same basis order");
-        algo_end();
+
         return false;
       }
 
@@ -146,7 +133,6 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
         else
         {
           error("Fields have different, possibly non-scalar, data types");
-          algo_end();
           return false;
         }
       }
@@ -161,7 +147,6 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
       if (! fi.is_scalar() )
       {
         error("Node values can only be matched for scalar values");
-        algo_end();
         return false;
       }
 
@@ -174,7 +159,7 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
   }
 
   BBox box;
-  Handle<SearchGridT<index_type> > node_grid;
+  std::unique_ptr<SearchGridT<index_type>> node_grid;
   size_type ni = 0, nj = 0, nk = 0;
 
   size_type tot_num_nodes = 0;
@@ -208,26 +193,25 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
     size_type sy = static_cast<size_type>(ceil(diag.y() / trace*s));
     size_type sz = static_cast<size_type>(ceil(diag.z() / trace*s));
 
-    node_grid = new SearchGridT<index_type>(sx, sy, sz, box.min(), box.max());
+    node_grid = std::make_unique<SearchGridT<index_type>>(sx, sy, sz, box.get_min(), box.get_max());
 
     ni = node_grid->get_ni() - 1;
     nj = node_grid->get_nj() - 1;
     nk = node_grid->get_nk() - 1;
   }
 
-  MeshHandle mesh = CreateMesh(first);
-  if (mesh.get_rep() == 0)
+  auto mesh = CreateMesh(first);
+  if (!mesh)
   {
     error("Could not create output mesh");
-    algo_end();
+
     return false;
   }
 
-  output = CreateField(first,mesh);
-  if (output.get_rep() == 0)
+  output = CreateField(first, mesh);
+  if (!output)
   {
     error("Could not create output field");
-    algo_end();
     return false;
   }
 
@@ -429,11 +413,25 @@ ConvertBundleToFieldAlgo::run(BundleHandle& input, FieldHandle& output)
     elems_offset += elems_count;
     nodes_offset += nodes_count;
 
-    update_progress(p+1, inputs.size());
+    update_progress_max(p+1, inputs.size());
   }
 
-  algo_end();
   return true;
 }
 
-} // end namespace SCIRunAlgo
+const AlgorithmInputName ConvertBundleToFieldAlgo::InputBundle("InputBundle");
+
+AlgorithmOutput ConvertBundleToFieldAlgo::run(const AlgorithmInput& input) const
+{
+  auto bundle = input.get<Bundle>(InputBundle);
+
+  FieldHandle outputField;
+
+  if (!runImpl(bundle, outputField))
+    THROW_ALGORITHM_PROCESSING_ERROR("False thrown on legacy run call");
+
+  AlgorithmOutput output;
+  output[Variables::OutputField] = outputField;
+
+  return output;
+}

src/Core/Algorithms/Legacy/Converter/ConvertBundleToField.h

@@ -32,30 +32,26 @@
 #ifndef CORE_ALGORITHMS_CONVERTER_CONVERTBUNDLETOFIELD_H
 #define CORE_ALGORITHMS_CONVERTER_CONVERTBUNDLETOFIELD_H 1
 
-//! Datatypes used
-#include <Core/Datatypes/Bundle.h>
-#include <Core/Datatypes/Field.h>
+#include <Core/Datatypes/DatatypeFwd.h>
+#include <Core/Algorithms/Base/AlgorithmBase.h>
+#include <Core/Algorithms/Legacy/Converter/share.h>
 
-//! Base for algorithm
-#include <Core/Algorithms/Util/AlgoBase.h>
-
-//! for Windows support
-#include <Core/Algorithms/Converter/share.h>
-
-namespace SCIRunAlgo {
+namespace SCIRun::Core::Algorithms::Converters
+{
+  ALGORITHM_PARAMETER_DECL(MergeNodes);
+  ALGORITHM_PARAMETER_DECL(Tolerance);
+  ALGORITHM_PARAMETER_DECL(MatchNodeValues);
+  ALGORITHM_PARAMETER_DECL(MakeNoData);
 
-class SCISHARE ConvertBundleToFieldAlgo : public AlgoBase
+class SCISHARE ConvertBundleToFieldAlgo : public AlgorithmBase
 {
-  public:
-    // Algorithm defaults
-    ConvertBundleToFieldAlgo();
-    ~ConvertBundleToFieldAlgo();
-
-  public:
-    // Algorithm Functions
-    bool run(SCIRun::BundleHandle& input, SCIRun::FieldHandle& output);
+public:
+  ConvertBundleToFieldAlgo();
+  static const AlgorithmInputName InputBundle;
+  bool runImpl(const SCIRun::Core::Datatypes::BundleHandle& input, SCIRun::FieldHandle& output) const;
+  AlgorithmOutput run(const AlgorithmInput& input) const override;
 };
 
-} // namespace SCIRunAlgo
+}
 
 #endif

src/Core/Algorithms/Legacy/Converter/ConvertMatrixToString.cc

@@ -61,4 +61,4 @@ AlgorithmOutput ConvertMatrixToStringAlgo::run(const AlgorithmInput& input) cons
 	return output;
 }
 
-AlgorithmOutputName ConvertMatrixToStringAlgo::ResultString("ResultString");
+const AlgorithmOutputName ConvertMatrixToStringAlgo::ResultString("ResultString");

src/Core/Algorithms/Legacy/Converter/ConvertMatrixToString.h

@@ -42,10 +42,10 @@ namespace SCIRun {
 		class SCISHARE ConvertMatrixToStringAlgo : public AlgorithmBase
 		{
 			public:
-				static AlgorithmOutputName ResultString;
+				static const AlgorithmOutputName ResultString;
 				ConvertMatrixToStringAlgo() {}
 				bool run(Datatypes::MatrixHandle input, Datatypes::StringHandle& output) const;
-                                AlgorithmOutput run(const AlgorithmInput& input) const override;
+        AlgorithmOutput run(const AlgorithmInput& input) const override;
 		};
 }}}}
 

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

@@ -36,7 +36,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   Mapping/ApplyMappingMatrix.h
   FieldData/BuildMatrixOfSurfaceNormalsAlgo.h
   #Mapping/ApplyMappingMatrix.h
-  #FieldData/CalculateFieldDataMetric.h
+  FieldData/CalculateFieldDataMetric.h
   FieldData/ConvertIndicesToFieldDataAlgo.h
   FieldData/CalculateGradientsAlgo.h
   FieldData/CalculateVectorMagnitudesAlgo.h
@@ -108,6 +108,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   Cleanup/ReorderNormalCoherentlyAlgo.h
   MeshDerivatives/CalculateMeshCenterAlgo.h
   MeshDerivatives/GetCentroids.h
+  MeshDerivatives/CalculateBundleDifference.h
   )
 
 SET(Core_Algorithms_Legacy_Fields_SRCS
@@ -142,7 +143,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
   FieldData/CalculateGradientsAlgo.cc
   #FieldData/CalculateLatVolGradientsAtNodes.cc
   FieldData/CalculateVectorMagnitudesAlgo.cc
-  #FieldData/CalculateFieldDataMetric.cc
+  FieldData/CalculateFieldDataMetric.cc
   FieldData/ConvertFieldDataType.cc
   FieldData/ConvertFieldBasisType.cc
   FieldData/SwapFieldDataWithMatrixEntriesAlgo.cc
@@ -197,6 +198,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
   #MeshDerivatives/GetBoundingBox.cc
   MeshDerivatives/SplitByConnectedRegion.cc
   MeshDerivatives/ExtractSimpleIsosurfaceAlgo.cc
+  MeshDerivatives/CalculateBundleDifference.cc
   RefineMesh/RefineMesh.cc
   RefineMesh/RefineMeshCurveAlgoV.cc
   RefineMesh/RefineMeshHexVolAlgoV.cc
@@ -231,6 +233,7 @@ TARGET_LINK_LIBRARIES(Core_Algorithms_Legacy_Fields
   Core_Datatypes
   Core_Datatypes_Legacy_Field
   Core_Datatypes_Legacy_Nrrd
+  Core_Datatypes_Legacy_Bundle
   Algorithms_Base
   Core_Exceptions_Legacy
   Core_Thread