intermediate commit - module structure done

Author: moritzdannhauer

src/Core/Algorithms/Factory/HardCodedAlgorithmFactory.cc

@@ -65,6 +65,7 @@
 #include <Core/Algorithms/DataIO/ReadMatrix.h>
 #include <Core/Algorithms/DataIO/WriteMatrix.h>
 #include <Core/Algorithms/Legacy/FiniteElements/BuildMatrix/BuildFEMatrix.h>
+#include <Core/Algorithms/Legacy/FiniteElements/BuildRHS/BuildFEVolRHS.h>
 #include <Core/Algorithms/BrainStimulator/ElectrodeCoilSetupAlgorithm.h>
 #include <Core/Algorithms/BrainStimulator/SetConductivitiesToTetMeshAlgorithm.h>
 #include <Core/Algorithms/BrainStimulator/GenerateROIStatisticsAlgorithm.h>
@@ -145,6 +146,7 @@ void HardCodedAlgorithmFactory::addToMakerMap()
       ADD_MODULE_ALGORITHM(MapFieldDataOntoElems, MapFieldDataOntoElemsAlgo)
       ADD_MODULE_ALGORITHM(ClipFieldByFunction, ClipMeshBySelectionAlgo)
       ADD_MODULE_ALGORITHM(MapFieldDataFromSourceToDestination, MapFieldDataFromSourceToDestinationAlgo)
+      ADD_MODULE_ALGORITHM(BuildFEVolRHS, BuildFEVolRHSAlgo)
     ;
   }
 }

src/Core/Algorithms/Legacy/FiniteElements/BuildRHS/BuildFEVolRHS.cc

@@ -29,6 +29,10 @@
 
 #include <Core/Algorithms/Legacy/FiniteElements/BuildRHS/BuildFEVolRHS.h>
 #include <Core/Datatypes/DenseMatrix.h>
+#include <Core/Datatypes/Legacy/Field/Mesh.h>
+#include <Core/Datatypes/Legacy/Field/VMesh.h>
+#include <Core/Datatypes/Legacy/Field/Field.h>
+#include <Core/Datatypes/Legacy/Field/VField.h>
 #include <Core/Datatypes/SparseRowMatrix.h>
 #include <Core/Thread/Barrier.h>
 #include <Core/Thread/Parallel.h>
@@ -48,24 +52,32 @@ AlgorithmInputName BuildFEVolRHSAlgo::Mesh("Mesh");
 AlgorithmInputName BuildFEVolRHSAlgo::Vector_Table("Vector_Table");
 AlgorithmOutputName BuildFEVolRHSAlgo::RHS("RHS");
 
+BuildFEVolRHSAlgo::BuildFEVolRHSAlgo() 
+{
+
+}
 
-FieldHandle BuildFEVolRHSAlgo::run(FieldHandle input, DenseMatrixHandle ctable) const
+
+DenseMatrixHandle BuildFEVolRHSAlgo::run(FieldHandle input, DenseMatrixHandle ctable) const
 {
- FieldHandle a;
+ DenseMatrixHandle a;
+ 
+ 
+ 
+ 
+ 
  return a;
 }
 
 AlgorithmOutput BuildFEVolRHSAlgo::run_generic(const AlgorithmInput& input) const
 {
-/*  auto field = input.get<Field>(Variables::InputField);
-  auto ctable = input.get<DenseMatrix>(Conductivity_Table);
-
-  SparseRowMatrixHandle stiffness;
-  if (!run(field, ctable, stiffness))
-    THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");*/
+  auto mesh = input.get<Field>(Mesh);
+  auto ctable = input.get<DenseMatrix>(Vector_Table);
 
+  DenseMatrixHandle volrhs = run(mesh, ctable);
+  
   AlgorithmOutput output;
- // output[Stiffness_Matrix] = stiffness;
+  output[RHS] = volrhs;
   return output;
 }
 

src/Core/Algorithms/Legacy/FiniteElements/BuildRHS/BuildFEVolRHS.h

@@ -42,12 +42,12 @@ namespace SCIRun {
 class SCISHARE BuildFEVolRHSAlgo : public AlgorithmBase
 {
   public:
-
+    BuildFEVolRHSAlgo();
     static AlgorithmInputName Mesh;
     static AlgorithmInputName Vector_Table;
     static AlgorithmOutputName RHS;
 
-   FieldHandle run(FieldHandle input, Datatypes::DenseMatrixHandle ctable) const;  
+   Datatypes::DenseMatrixHandle run(FieldHandle input, Datatypes::DenseMatrixHandle ctable) const;  
    virtual AlgorithmOutput run_generic(const AlgorithmInput &) const;
 private:
 

src/Interface/Modules/Factory/ModuleDialogFactoryAdditional.cc

@@ -28,11 +28,11 @@
 
 #include <Interface/Modules/Factory/ModuleDialogFactory.h>
 #include <Interface/Modules/FiniteElements/TDCSSimulatorDialog.h>
+#include <Interface/Modules/FiniteElements/BuildFEVolRHSDialog.h>
 #include <Interface/Modules/BrainStimulator/SetConductivitiesToTetMeshDialog.h>
 #include <Interface/Modules/BrainStimulator/ElectrodeCoilSetupDialog.h>
 #include <Interface/Modules/BrainStimulator/GenerateROIStatisticsDialog.h>
 #include <Interface/Modules/BrainStimulator/SetupRHSforTDCSandTMSDialog.h>
-
 #include <boost/assign.hpp>
 #include <boost/functional/factory.hpp>
 
@@ -47,6 +47,7 @@ void ModuleDialogFactory::addDialogsToMakerMap2()
     ADD_MODULE_DIALOG(ElectrodeCoilSetup, ElectrodeCoilSetupDialog)
     ADD_MODULE_DIALOG(SetConductivitiesToTetMesh, SetConductivitiesToTetMeshDialog)
     ADD_MODULE_DIALOG(GenerateROIStatistics, GenerateROIStatisticsDialog)
-    ADD_MODULE_DIALOG(SetupRHSforTDCSandTMS, SetupRHSforTDCSandTMSDialog)      
+    ADD_MODULE_DIALOG(SetupRHSforTDCSandTMS, SetupRHSforTDCSandTMSDialog)
+    ADD_MODULE_DIALOG(BuildFEVolRHS, BuildFEVolRHSDialog)     
   ;
 }

src/Interface/Modules/FiniteElements/BuildFEVolRHS.ui

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>BuildFEVolRHS</class>
+ <widget class="QWidget" name="BuildFEVolRHS">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>233</width>
+    <height>37</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Dialog</string>
+  </property>
+  <layout class="QGridLayout" name="gridLayout">
+   <item row="0" column="0">
+    <widget class="QCheckBox" name="vectorTableBasisMatrices">
+     <property name="text">
+      <string>Use Vector TableBasis Matrices</string>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

src/Interface/Modules/FiniteElements/BuildFEVolRHSDialog.cc

@@ -0,0 +1,53 @@
+/*
+   For more information, please see: http://software.sci.utah.edu
+
+   The MIT License
+
+   Copyright (c) 2012 Scientific Computing and Imaging Institute,
+   University of Utah.
+
+   License for the specific language governing rights and limitations under
+   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
+   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+   and/or sell copies of the Software, and to permit persons to whom the
+   Software is furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included
+   in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+   OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   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.
+*/
+
+#include <Interface/Modules/FiniteElements/BuildFEVolRHSDialog.h>
+#include <Core/Algorithms/Legacy/FiniteElements/BuildRHS/BuildFEVolRHS.h>
+#include <Dataflow/Network/ModuleStateInterface.h> 
+#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
+
+using namespace SCIRun::Gui;
+using namespace SCIRun::Dataflow::Networks;
+using namespace SCIRun::Core::Algorithms;
+using namespace SCIRun::Core::Algorithms::FiniteElements;
+
+
+BuildFEVolRHSDialog::BuildFEVolRHSDialog(const std::string& name, ModuleStateHandle state,
+  QWidget* parent /* = 0 */)
+  : ModuleDialogGeneric(state, parent)
+{
+  setupUi(this);
+  setWindowTitle(QString::fromStdString(name));
+  fixSize();
+}
+
+void BuildFEVolRHSDialog::pull()
+{
+  //TODO
+}
+

src/Interface/Modules/FiniteElements/BuildFEVolRHSDialog.h

@@ -0,0 +1,54 @@
+/*
+   For more information, please see: http://software.sci.utah.edu
+
+   The MIT License
+
+   Copyright (c) 2012 Scientific Computing and Imaging Institute,
+   University of Utah.
+
+   License for the specific language governing rights and limitations under
+   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
+   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+   and/or sell copies of the Software, and to permit persons to whom the
+   Software is furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included
+   in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+   OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   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 INTERFACE_MODULES_BuildFEVolRHSDialog_H
+#define INTERFACE_MODULES_BuildFEVolRHSDialog_H
+
+#include "Interface/Modules/FiniteElements/ui_BuildFEVolRHS.h"
+#include <Interface/Modules/Base/ModuleDialogGeneric.h>
+#include <Interface/Modules/FiniteElements/share.h>
+
+namespace SCIRun {
+namespace Gui {
+  
+class SCISHARE BuildFEVolRHSDialog : public ModuleDialogGeneric, 
+  public Ui::BuildFEVolRHS
+{
+	Q_OBJECT
+	
+public:
+  BuildFEVolRHSDialog(const std::string& name, 
+    SCIRun::Dataflow::Networks::ModuleStateHandle state,
+    QWidget* parent = 0);
+  virtual void pull();
+};
+
+}
+}
+
+#endif

src/Interface/Modules/FiniteElements/CMakeLists.txt

@@ -29,15 +29,18 @@
 
 SET(Interface_Modules_FiniteElements_FORMS
  TDCSSimulatorDialog.ui
+ BuildFEVolRHS.ui
 )
 
 SET(Interface_Modules_FiniteElements_HEADERS
   TDCSSimulatorDialog.h
-  share.h
+  BuildFEVolRHSDialog.h 
+ share.h
 )
 
 SET(Interface_Modules_FiniteElements_SOURCES 
   TDCSSimulatorDialog.cc
+  BuildFEVolRHSDialog.cc
 )
 
 QT4_WRAP_UI(Interface_Modules_FiniteElements_FORMS_HEADERS ${Interface_Modules_FiniteElements_FORMS})

src/Modules/Factory/ModuleFactoryImpl2.cc

@@ -45,6 +45,7 @@ DEALINGS IN THE SOFTWARE.
 #include <Modules/BrainStimulator/GenerateROIStatistics.h>
 #include <Modules/Legacy/Math/AddKnownsToLinearSystem.h>
 #include <Modules/Legacy/FiniteElements/BuildTDCSMatrix.h>
+#include <Modules/Legacy/FiniteElements/BuildFEVolRHS.h>
 
 using namespace SCIRun::Dataflow::Networks;
 using namespace SCIRun::Modules;
@@ -77,4 +78,5 @@ void ModuleDescriptionLookup::addMoreModules()
   addModuleDesc<ConvertMatrixTypeModule>("ConvertMatrixType", "Math", "SCIRun", "Real ported module", "...");
   addModuleDesc<MapFieldDataFromNodeToElemModule>("MapFieldDataFromNodeToElem", "ChangeFieldData", "SCIRun", "Real ported module", "...");
   addModuleDesc<SplitFieldByConnectedRegion>("SplitFieldByConnectedRegion", "NewField", "SCIRun", "Real ported module", "...");
+  addModuleDesc<BuildFEVolRHS>("BuildFEVolRHS", "FiniteElements", "SCIRun", "Real ported module", "...");
 }

src/Modules/Legacy/FiniteElements/BuildFEVolRHS.cc

@@ -26,7 +26,7 @@
    DEALINGS IN THE SOFTWARE.
 */
 /// @todo Documentation Modules/Legacy/FiniteElements/BuildFEVolRHS.cc
-
+/*
 #ifdef SCIRUN4_ESSENTIAL_CODE_TO_BE_PORTED
  #include <Core/Datatypes/SparseRowMatrix.h>
  #include <Core/Datatypes/DenseMatrix.h>
@@ -39,28 +39,42 @@
  #include <Dataflow/GuiInterface/GuiVar.h>
  #include <Dataflow/Network/Module.h>
 #endif
-
-//#include <Core/Algorithms/FiniteElements/BuildRHS/BuildFEVolRHS.h>
-#include <Core/Datatypes/Legacy/Field/Field.h>
+*/
 #include <Modules/Legacy/FiniteElements/BuildFEVolRHS.h>
-
+#include <Core/Algorithms/Legacy/FiniteElements/BuildRHS/BuildFEVolRHS.h>
+#include <Core/Datatypes/Matrix.h>
+#include <Core/Datatypes/DenseMatrix.h>
+#include <Core/Datatypes/Legacy/Field/Field.h>
 
 using namespace SCIRun::Modules::FiniteElements;
 using namespace SCIRun::Dataflow::Networks;
-//using namespace SCIRun::Core::Datatypes;
-//using namespace SCIRun::Core::Algorithms;
+using namespace SCIRun::Core::Datatypes;
 using namespace SCIRun;
 
-BuildFEVolRHSModule::BuildFEVolRHSModule()
-  : Module(ModuleLookupInfo("BuildFEVolRHSModule", "FiniteElements", "SCIRun"), false)
+BuildFEVolRHS::BuildFEVolRHS()
+  : Module(ModuleLookupInfo("BuildFEVolRHS", "FiniteElements", "SCIRun"))
 {
   INITIALIZE_PORT(Mesh);
   INITIALIZE_PORT(Vector_Table);
   INITIALIZE_PORT(RHS);
 }
 
-void BuildFEVolRHSModule::execute()
+void BuildFEVolRHS::setStateDefaults()
 {
+// setStateBoolFromAlgo(SetFieldDataAlgo::keepTypeCheckBox);
+}
+
+void BuildFEVolRHS::execute()
+{
+  auto mesh = getRequiredInput(Mesh);
+  auto vtable = getRequiredInput(Vector_Table);
+
+  if (needToExecute())
+  {
+    auto output = algo().run_generic(make_input((Mesh, mesh)(Vector_Table, vtable)));
+    sendOutputFromAlgorithm(RHS, output);
+  }
+ 
  /* 
 #ifdef SCIRUN4_ESSENTIAL_CODE_TO_BE_PORTED  
   FieldHandle Field;