Merge remote-tracking branch 'upstream/master'

Author: jessdtate

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

@@ -48,7 +48,7 @@ AlgorithmOutput FlipSurfaceNormalsAlgo::run(const AlgorithmInput& input) const
 {
 	auto input_field = input.get<Field>(Variables::InputField);
 
-	FieldHandle output_field = input_field;
+	FieldHandle output_field(input_field->deep_clone());
 	run(input_field,output_field);
 
 	AlgorithmOutput output;

src/Core/Algorithms/Legacy/Forward/BuildBEMatrixAlgo.cc

@@ -90,29 +90,31 @@ void BuildBEMatrixBase::getOmega(
   Vector Ny( y1.length() , y2.length() , y3.length() );
 
   Vector Nyij( y21.length() , y32.length() , y13.length() );
-
-
+  
   Vector gamma( 0 , 0 , 0 );
   double NomGamma , DenomGamma;
 
   NomGamma = Ny[0]*Nyij[0] + Dot(y1,y21);
   DenomGamma = Ny[1]*Nyij[0] + Dot(y2,y21);
-  if (fabs(DenomGamma-NomGamma) > epsilon && (DenomGamma != 0) && NomGamma != 0 )
+  if (fabs(DenomGamma-NomGamma) > epsilon && (DenomGamma != 0) && NomGamma != 0 ){
     gamma[0] = -1/Nyij[0] * log(NomGamma/DenomGamma);
-
+  }
   NomGamma = Ny[1]*Nyij[1] + Dot(y2,y32);
   DenomGamma = Ny[2]*Nyij[1] + Dot(y3,y32);
-  if (fabs(DenomGamma-NomGamma) > epsilon && (DenomGamma != 0) && NomGamma != 0 )
+  if (fabs(DenomGamma-NomGamma) > epsilon && (DenomGamma != 0) && NomGamma != 0 ){
     gamma[1] = -1/Nyij[1] * log(NomGamma/DenomGamma);
-
+  }
   NomGamma = Ny[2]*Nyij[2] + Dot(y3,y13);
   DenomGamma = Ny[0]*Nyij[2] + Dot(y1,y13);
-  if (fabs(DenomGamma-NomGamma) > epsilon && (DenomGamma != 0) && NomGamma != 0 )
+  if (fabs(DenomGamma-NomGamma) > epsilon && (DenomGamma != 0) && NomGamma != 0 ){
     gamma[2] = -1/Nyij[2] * log(NomGamma/DenomGamma);
+  }
 
   double d = Dot( y1, Cross(y2, y3) );
 
   Vector OmegaVec = (gamma[2]-gamma[0])*y1 + (gamma[0]-gamma[1])*y2 + (gamma[1]-gamma[2])*y3;
+  
+  
 
   /*
   In order to avoid problems with the arctan used in de Muncks paper
@@ -127,6 +129,7 @@ void BuildBEMatrixBase::getOmega(
 
   double Nn=0 , Omega=0 ;
   Nn = Ny[0]*Ny[1]*Ny[2] + Ny[0]*Dot(y2,y3) + Ny[2]*Dot(y1,y2) + Ny[1]*Dot(y3,y1);
+  
   if (Nn > 0)  Omega = 2 * atan( d / Nn );
   if (Nn < 0)  Omega = 2 * atan( d / Nn ) + 2*M_PI ;
   if (Nn == 0)
@@ -146,6 +149,7 @@ void BuildBEMatrixBase::getOmega(
   coef(0,0) = (1/A2) * ( Zn1*Omega + d * Dot(y32, OmegaVec) );
   coef(0,1) = (1/A2) * ( Zn2*Omega + d * Dot(y13, OmegaVec) );
   coef(0,2) = (1/A2) * ( Zn3*Omega + d * Dot(y21, OmegaVec) );
+  
 }
 
 void  BuildBEMatrixBase::get_cruse_weights(
@@ -737,6 +741,8 @@ template <class MatrixType>
 void BuildBEMatrixBaseCompute::make_auto_P_compute(VMesh* hsurf, MatrixType& auto_P, double in_cond, double out_cond, double op_cond)
 {
   auto nnodes = auto_P.rows();
+  
+  
 
   //const double mult = 1/(2*M_PI)*((out_cond - in_cond)/op_cond);  // op_cond=out_cond for all the surfaces but the outermost surface which in op_cond=in_cond
   const double mult = 1/(4*M_PI)*(out_cond - in_cond);
@@ -756,14 +762,15 @@ void BuildBEMatrixBaseCompute::make_auto_P_compute(VMesh* hsurf, MatrixType& aut
     Point pp = hsurf->get_point(ppi);
 
     hsurf->begin(fi); hsurf->end(fie);
+    
     for (; fi != fie; ++fi) { //! find contributions from every triangle
 
       hsurf->get_nodes(nodes, *fi);
       if (ppi!=nodes[0] && ppi!=nodes[1] && ppi!=nodes[2]){
         Vector v1 = hsurf->get_point(nodes[0]) - pp;
         Vector v2 = hsurf->get_point(nodes[1]) - pp;
         Vector v3 = hsurf->get_point(nodes[2]) - pp;
-
+        
         getOmega(v1, v2, v3, coef);
 
         for (i=0; i<3; ++i)
@@ -1099,7 +1106,7 @@ MatrixHandle SurfaceToSurface::compute(const bemfield_vector& fields) const
       else
       {
         auto block = EE.blockRef(i, j);
-        make_cross_P_compute(fields[i].field_->vmesh(), fields[j].field_->vmesh(), block, fields[i].insideconductivity, fields[i].outsideconductivity, op_cond);
+        make_cross_P_compute(fields[i].field_->vmesh(), fields[j].field_->vmesh(), block, fields[j].insideconductivity, fields[j].outsideconductivity, op_cond);
       }
     }
   }
@@ -1130,27 +1137,24 @@ MatrixHandle SurfaceToSurface::compute(const bemfield_vector& fields) const
       if (i == sourcefieldindices[j])
       {
         auto block = EJ.blockRef(i,j);
-        //std::cout << "EJ block auto " << i << "," << j << " is size " << block.rows() << " x " << block.cols() /*<< " starting at " << blockStartsEE[i] << "," << blockStartsEJ[j]*/ << std::endl;
-
         make_auto_G_compute(fields[i].field_->vmesh(), block, fields[i].insideconductivity, fields[i].outsideconductivity, op_cond, triangleareas);
       }
       else
       {
         auto block = EJ.blockRef(i,j);
-        //std::cout << "EJ block cross " << i << "," << j << " is size " << block.rows() << " x " << block.cols()/* << " starting at " << blockStartsEE[i] << "," << blockStartsEJ[j]*/ << std::endl;
-
-        make_cross_G_compute(fields[i].field_->vmesh(), fields[sourcefieldindices[j]].field_->vmesh(), block, fields[i].insideconductivity, fields[i].outsideconductivity, op_cond, triangleareas);
+        make_cross_G_compute(fields[i].field_->vmesh(), fields[sourcefieldindices[j]].field_->vmesh(), block, fields[j].insideconductivity, fields[j].outsideconductivity, op_cond, triangleareas);
       }
     }
   }
 
   printInfo(EJ.matrix(), "EJ");
 
+  // This needs to be checked.  It was taken out because the deflation was producing errors
+  // Jeroen's matlab code, which was the basis of this code, only does a defation in test cases.
+  
   // Perform deflation on EE matrix
-  const double deflationconstant = 1.0/EE.matrix().ncols();
-  EE.matrix() = EE.matrix().array() + deflationconstant;
-
-  printInfo(EE.matrix(), "EE after deflation");
+  //const double deflationconstant = 1.0/EE.matrix().ncols();
+  //EE.matrix() = EE.matrix().array() + deflationconstant;
 
   std::vector<int> measurementNodeSize(measurementfieldindices.size());
   auto measFields = fields | boost::adaptors::filtered([](const bemfield& f) { return f.measurement; });

src/Core/Datatypes/Color.h

@@ -81,6 +81,7 @@ namespace Datatypes {
   struct SCISHARE ViewSceneFeedback : ModuleFeedback
   {
     Geometry::Transform transform;
+    std::string selectionName;
   };
 
 }}}

src/Dataflow/Network/Module.cc

@@ -964,3 +964,10 @@ void Module::sendFeedbackUpstreamAlongIncomingConnections(const ModuleFeedback&
     }
   }
 }
+
+std::string Module::helpPageUrl() const
+{
+  auto url = "http://scirundocwiki.sci.utah.edu/SCIRunDocs/index.php/CIBC:Documentation:SCIRun:Reference:"
+    + legacyPackageName() + ":" + get_module_name();
+  return url;
+}

src/Dataflow/Network/Module.h

@@ -68,6 +68,8 @@ namespace Networks {
     std::string get_packagename() const { return info_.package_name_; }
     ModuleId get_id() const override { return id_; }
 
+    virtual std::string helpPageUrl() const override;
+
     //for serialization
     virtual const ModuleLookupInfo& get_info() const override final { return info_; }
     virtual void set_id(const std::string& id) override final;
@@ -110,6 +112,10 @@ namespace Networks {
     virtual std::vector<Core::Datatypes::DatatypeHandleOption> get_dynamic_input_handles(const PortId& id) override final;
   protected:
     virtual void send_output_handle(const PortId& id, Core::Datatypes::DatatypeHandle data) override final;
+
+    // override this for modules that changed packages, to point to correct wiki page
+    virtual std::string legacyPackageName() const { return get_packagename(); }
+
   public:
     virtual void setLogger(Core::Logging::LoggerHandle log) override final;
     virtual Core::Logging::LoggerHandle getLogger() const override final;
@@ -1010,6 +1016,8 @@ namespace Modules
       return ModuleType::outputPortDescription(ModuleType::outputPort0Name(), ModuleType::outputPort1Name(), ModuleType::outputPort2Name(), ModuleType::outputPort3Name(), ModuleType::outputPort4Name(), ModuleType::outputPort5Name(), ModuleType::outputPort6Name(), ModuleType::outputPort7Name(), ModuleType::outputPort8Name());
     }
   };
+
+  #define LEGACY_BIOPSE_MODULE protected: virtual std::string legacyPackageName() const override { return "BioPSE"; }
 }
 }
 

src/Dataflow/Network/ModuleInterface.h

@@ -78,6 +78,8 @@ namespace Networks {
     virtual bool has_ui() const = 0;
     virtual const ModuleLookupInfo& get_info() const = 0;
     virtual bool hasDynamicPorts() const = 0;
+
+    virtual std::string helpPageUrl() const = 0;
   };
 
   class SCISHARE ModuleDisplayInterface

src/Dataflow/Network/PortManager.h

@@ -122,18 +122,16 @@ PortManager<T>::add(const T& item)
           portPair.second->incrementIndex();
       }
 
-      for (const auto& portPair : ports_)
-      {
-        DYNAMIC_PORT_LOG(std::cout << "\t id " << portPair.second->id().toString() << " index after setting " << portPair.second->getIndex() << std::endl);
-      }
+
+      DYNAMIC_PORT_LOG(for (const auto& portPair : ports_) std::cout << "\t id " << portPair.second->id().toString() << " index after setting " << portPair.second->getIndex() << std::endl;);
 
       return newPortIndex;
     }
   }
-  if (item->isDynamic())
-  {
-    DYNAMIC_PORT_LOG(std::cout << "original port: " << item->id().toString() << " newIndex: " << size() - 1 << std::endl);
-  }
+
+
+  DYNAMIC_PORT_LOG(if (item->isDynamic()) std::cout << "original port: " << item->id().toString() << " newIndex: " << size() - 1 << std::endl;);
+
   return size() - 1;
 }
 
@@ -147,10 +145,7 @@ PortManager<T>::lastIndexByName(const std::string& name) const
     return -1;
 
   DYNAMIC_PORT_LOG(std::cout << name << "  Input port object indexes:\n");
-  for (const auto& input : matches)
-  {
-    DYNAMIC_PORT_LOG(std::cout << input->id() << " " << input->id().name << " " << input->getIndex() << std::endl);
-  }
+  DYNAMIC_PORT_LOG(for (const auto& input : matches) std::cout << input->id() << " " << input->id().name << " " << input->getIndex() << std::endl;);
 
   return static_cast<int>((*std::max_element(matches.begin(), matches.end(), [](const T& port1, const T& port2) { return port1->getIndex() < port2->getIndex(); }))->getIndex());
 }

src/Dataflow/Network/Tests/MockModule.h

@@ -67,6 +67,7 @@ namespace SCIRun {
           MOCK_CONST_METHOD0(has_ui, bool());
           MOCK_CONST_METHOD0(hasDynamicPorts, bool());
           MOCK_CONST_METHOD0(metadata, const MetadataMap&());
+          MOCK_CONST_METHOD0(helpPageUrl, std::string());
           MOCK_METHOD1(setUiVisible, void(bool));
           MOCK_METHOD1(set_id, void(const std::string&));
           MOCK_CONST_METHOD0(get_info, const ModuleLookupInfo&());