merge newest master

Author: benjaminlarson

src/CMakeLists.txt

@@ -143,7 +143,7 @@ IF(BUILD_TESTING)
     MESSAGE( WARNING "Test resource path does not exist. Please set it correctly to run all the unit and regression tests. Clone this github repo to get all the files: https://github.com/CIBC-Internal/SCIRunTestData" )
   ENDIF()
 
-  ADD_DEFINITIONS(-DTEST_RESOURCE_ROOT_DIR="${USER_UNIT_TEST_RESOURCE_DIR}" -DBUILD_TESTING)
+  ADD_DEFINITIONS(-DTEST_RESOURCE_ROOT_DIR="${SCIRUN_TEST_RESOURCE_DIR}" -DBUILD_TESTING)
 ENDIF()
 
 ########################################################################
@@ -675,6 +675,7 @@ SET_PROPERTY(TARGET Interface_Modules_Fields   PROPERTY FOLDER "Interface/Module
 SET_PROPERTY(TARGET Interface_Modules_Bundle   PROPERTY FOLDER "Interface/Modules")
 SET_PROPERTY(TARGET Interface_Modules_Matlab   PROPERTY FOLDER "Interface/Modules")
 SET_PROPERTY(TARGET Interface_Modules_Forward   PROPERTY FOLDER "Interface/Modules")
+SET_PROPERTY(TARGET Interface_Modules_Inverse   PROPERTY FOLDER "Interface/Modules")
 SET_PROPERTY(TARGET Interface_Modules_Factory   PROPERTY FOLDER "Interface/Modules")
 SET_PROPERTY(TARGET Interface_Application   PROPERTY FOLDER "Interface/Application")
 
@@ -692,6 +693,7 @@ SET_PROPERTY(TARGET Modules_BrainStimulator   PROPERTY FOLDER "Modules/Brain")
 SET_PROPERTY(TARGET Modules_Legacy_FiniteElements   PROPERTY FOLDER "Modules/FiniteElements")
 SET_PROPERTY(TARGET Modules_Legacy_Fields PROPERTY FOLDER "Modules/Fields")
 SET_PROPERTY(TARGET Modules_Legacy_Forward PROPERTY FOLDER "Modules/Forward")
+SET_PROPERTY(TARGET Modules_Legacy_Inverse PROPERTY FOLDER "Modules/Inverse")
 SET_PROPERTY(TARGET Modules_Legacy_Matlab_DataIO PROPERTY FOLDER "Modules/DataIO")
 SET_PROPERTY(TARGET Modules_Factory   PROPERTY FOLDER "Modules")
 

src/Core/Algorithms/Base/AlgorithmVariableNames.cc

@@ -47,6 +47,7 @@ PARAMETER(ColorMapName)
 PARAMETER(FileTypeList)
 PARAMETER(FileExtension)
 PARAMETER(FileTypeName)
+PARAMETER(FunctionString)
 
 INPUT(InputMatrix)
 INPUT(FirstMatrix)

src/Core/Algorithms/Base/AlgorithmVariableNames.h

@@ -52,6 +52,7 @@ class SCISHARE Variables
   static const AlgorithmParameterName FileTypeList;
   static const AlgorithmParameterName FileExtension;
   static const AlgorithmParameterName FileTypeName;
+	static const AlgorithmParameterName FunctionString; 
 
   static const AlgorithmInputName InputMatrix;
   static const AlgorithmInputName FirstMatrix;

src/Core/Algorithms/BrainStimulator/SetupRHSforTDCSandTMSAlgorithm.cc

@@ -26,7 +26,7 @@
    DEALINGS IN THE SOFTWARE.
 */
 
-///@file SetupRHSforTDCSandTMSAlgorithm
+///@file SetupTDCSAlgorithm
 ///@brief 
 /// This module sets up tDCS by providing the right hand side vector (parameterized by module GUI) and inputs for the modules: AddKnownsToLinearSystem, BuildTDCSMatrix.
 ///
@@ -37,8 +37,8 @@
 /// .
 /// 
 
-#ifndef ALGORITHMS_MATH_SETUPRHSFORTDCSANDTMSALGORITHM_H
-#define ALGORITHMS_MATH_SETUPRHSFORTDCSANDTMSALGORITHM_H
+#ifndef ALGORITHMS_MATH_SetupTDCSAlgorithm_H
+#define ALGORITHMS_MATH_SetupTDCSAlgorithm_H
 
 #include <Core/Algorithms/Base/AlgorithmBase.h>
 #include <Core/Algorithms/BrainStimulator/share.h>
@@ -49,6 +49,7 @@ namespace Algorithms {
 namespace BrainStimulator {
   ALGORITHM_PARAMETER_DECL(ImpedanceTableValues);
   ALGORITHM_PARAMETER_DECL(ElectrodeTableValues);
+  ALGORITHM_PARAMETER_DECL(SurfaceAreaValues);
   ALGORITHM_PARAMETER_DECL(ELECTRODE_VALUES);
   ALGORITHM_PARAMETER_DECL(IMPEDANCE_VALUES);
   ALGORITHM_PARAMETER_DECL(refnode);
@@ -62,7 +63,8 @@ namespace BrainStimulator {
     SetupTDCSAlgorithm();
     virtual AlgorithmOutput run_generic(const AlgorithmInput& input) const;
 
-    boost::tuple<Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, FieldHandle, Datatypes::DenseMatrixHandle> run(FieldHandle mesh, const std::vector<Variable>& elcs, const std::vector<Variable>& impelc,int num_of_elc, FieldHandle scalp_tri_surf, FieldHandle elc_tri_surf, SCIRun::Core::Datatypes::DenseMatrixHandle elc_sponge_location) const;
+    boost::tuple<Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle,
+    Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, FieldHandle, Datatypes::DenseMatrixHandle, std::vector<double>> run(FieldHandle mesh, const std::vector<Variable>& elcs, const std::vector<Variable>& impelc,int num_of_elc, FieldHandle scalp_tri_surf, FieldHandle elc_tri_surf, SCIRun::Core::Datatypes::DenseMatrixHandle elc_sponge_location) const;
 
     //static AlgorithmParameterName number_of_electrodes();
 
@@ -82,10 +84,11 @@ namespace BrainStimulator {
     static Core::Algorithms::AlgorithmParameterName ElectrodeParameterName(int i);
     static Core::Algorithms::AlgorithmParameterName ElectrodeImpedanceParameterName(int i);
   private:  
-    static const double special_label;
+    static const int special_label;
+    static const int max_number_of_electrodes;
     static const double electode_current_summation_bound;
     SCIRun::Core::Datatypes::DenseMatrixHandle create_rhs(FieldHandle mesh, const std::vector<Variable>& elcs, int num_of_elc) const;
-    boost::tuple<Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, FieldHandle> create_lhs(FieldHandle mesh, const std::vector<Variable>& impelc, FieldHandle scalp_tri_surf, FieldHandle elc_tri_surf, SCIRun::Core::Datatypes::DenseMatrixHandle elc_sponge_location) const;
+    boost::tuple<Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, Datatypes::DenseMatrixHandle, FieldHandle, std::vector<double>> create_lhs(FieldHandle mesh, const std::vector<Variable>& impelc, FieldHandle scalp_tri_surf, FieldHandle elc_tri_surf, SCIRun::Core::Datatypes::DenseMatrixHandle elc_sponge_location) const;
   };
 
 }}}}

src/Core/Algorithms/BrainStimulator/SetupRHSforTDCSandTMSAlgorithm.h

@@ -66,6 +66,7 @@ TARGET_LINK_LIBRARIES(Algorithms_Math
   Core_Datatypes
   Core_Thread
   Algorithms_Base
+  Core_Parser
   ${SCI_BOOST_LIBRARY}
 )
 

src/Core/Algorithms/Math/CMakeLists.txt

@@ -30,14 +30,18 @@
 #include <Core/Algorithms/Base/AlgorithmVariableNames.h>
 #include <Core/Algorithms/Math/EvaluateLinearAlgebraBinaryAlgo.h>
 #include <Core/Datatypes/DenseMatrix.h>
+#include <Core/Parser/ArrayMathEngine.h> 
+#include <Core/Datatypes/MatrixTypeConversions.h> 
 
 using namespace SCIRun::Core::Algorithms;
 using namespace SCIRun::Core::Datatypes;
 using namespace SCIRun::Core::Algorithms::Math;
+using namespace SCIRun;
 
 EvaluateLinearAlgebraBinaryAlgorithm::EvaluateLinearAlgebraBinaryAlgorithm()
 {
   addParameter(Variables::Operator, 0);
+	addParameter(Variables::FunctionString, "x+y"); 
 }
 
 EvaluateLinearAlgebraBinaryAlgorithm::Outputs EvaluateLinearAlgebraBinaryAlgorithm::run(const EvaluateLinearAlgebraBinaryAlgorithm::Inputs& inputs, const EvaluateLinearAlgebraBinaryAlgorithm::Parameters& params) const
@@ -48,8 +52,7 @@ EvaluateLinearAlgebraBinaryAlgorithm::Outputs EvaluateLinearAlgebraBinaryAlgorit
   ENSURE_ALGORITHM_INPUT_NOT_NULL(lhs, "lhs");
   ENSURE_ALGORITHM_INPUT_NOT_NULL(rhs, "rhs");
 
-  Operator oper = params;
-
+  Operator oper = params.get<0>();
   /// @todo: absolutely need matrix move semantics here!!!!!!!
   switch (oper)
   {
@@ -65,6 +68,31 @@ EvaluateLinearAlgebraBinaryAlgorithm::Outputs EvaluateLinearAlgebraBinaryAlgorit
     result.reset(lhs->clone());
     *result *= *rhs;
     break;
+	case FUNCTION:
+			{
+				NewArrayMathEngine engine; 
+				MatrixHandle lhsInput, rhsInput;
+				lhsInput.reset(lhs->clone());
+				rhsInput.reset(rhs->clone());
+			
+				if (!(engine.add_input_fullmatrix("x", lhsInput ) )) ;//return;
+				if (!(engine.add_input_fullmatrix("y", rhsInput ) )) ;//return;
+      
+				boost::optional<std::string> func = params.get<1>(); 
+				std::string function_string = func.get(); 
+
+				function_string = "RESULT="+function_string;
+				engine.add_expressions(function_string);
+
+				if(!(engine.add_output_fullmatrix("RESULT",lhsInput))) ;//return;
+        //if (!(engine.add_output_fullmatrix("RESULT", lhsInput))); 
+				// Actual engine call, which does the dynamic compilation, the creation of the
+				// code for all the objects, as well as inserting the function and looping 
+				// over every data point
+				if (!(engine.run())) ;//return;
+				result = matrix_cast::as_dense(lhsInput); 
+			}
+    break;   
   default:
     THROW_ALGORITHM_INPUT_ERROR("ERROR: unknown binary operation");
     break;
@@ -77,8 +105,9 @@ AlgorithmOutput EvaluateLinearAlgebraBinaryAlgorithm::run_generic(const Algorith
 {
   auto LHS = input.get<DenseMatrix>(Variables::LHS);
   auto RHS = input.get<DenseMatrix>(Variables::RHS);
+	auto func = boost::make_optional(get(Variables::FunctionString).toString()); 
 
-  auto result = run(boost::make_tuple(LHS, RHS), Operator(get(Variables::Operator).toInt()));
+  auto result = run(boost::make_tuple(LHS, RHS), boost::make_tuple(Operator(get(Variables::Operator).toInt()), func));
 
   AlgorithmOutput output;
   output[Variables::Result] = result;

src/Core/Algorithms/Math/EvaluateLinearAlgebraBinaryAlgo.cc

@@ -37,15 +37,15 @@ namespace SCIRun {
 namespace Core {
 namespace Algorithms {
 namespace Math {
-
   class SCISHARE EvaluateLinearAlgebraBinaryAlgorithm : public AlgorithmBase
   {
   public:
     enum Operator
     {
       ADD,
       SUBTRACT,
-      MULTIPLY
+      MULTIPLY,
+			FUNCTION
     };
 
     /// @todo: idea (type, name)
@@ -54,7 +54,7 @@ namespace Math {
 
     EvaluateLinearAlgebraBinaryAlgorithm();
     typedef boost::tuple<SCIRun::Core::Datatypes::DenseMatrixConstHandle, SCIRun::Core::Datatypes::DenseMatrixConstHandle> Inputs;
-    typedef Operator Parameters;
+    typedef boost::tuple<Operator, boost::optional<std::string> > Parameters;
     typedef SCIRun::Core::Datatypes::DenseMatrixHandle Outputs;
 
     Outputs run(const Inputs& inputs, const Parameters& params) const;

src/Core/Algorithms/Math/EvaluateLinearAlgebraBinaryAlgo.h

@@ -32,6 +32,9 @@
 #include <Core/Datatypes/DenseMatrix.h>
 #include <stdexcept>
 
+#include <Core/Parser/ArrayMathEngine.h> 
+#include <Core/Datatypes/MatrixTypeConversions.h> 
+
 using namespace SCIRun::Core::Datatypes;
 using namespace SCIRun::Core::Algorithms::Math;
 using namespace SCIRun::Core::Algorithms;
@@ -40,6 +43,7 @@ EvaluateLinearAlgebraUnaryAlgorithm::EvaluateLinearAlgebraUnaryAlgorithm()
 {
   addParameter(Variables::Operator, 0);
   addParameter(Variables::ScalarValue, 0);
+	addParameter(Variables::FunctionString, "x+10"); 
 }
 
 EvaluateLinearAlgebraUnaryAlgorithm::Outputs EvaluateLinearAlgebraUnaryAlgorithm::run(const EvaluateLinearAlgebraUnaryAlgorithm::Inputs& matrix, const EvaluateLinearAlgebraUnaryAlgorithm::Parameters& params) const
@@ -50,7 +54,7 @@ EvaluateLinearAlgebraUnaryAlgorithm::Outputs EvaluateLinearAlgebraUnaryAlgorithm
   Operator oper = params.get<0>();
 
   /// @todo: absolutely need matrix move semantics here!!!!!!!
-  switch (oper)
+  switch (oper) 
   {
   case NEGATE:
     result.reset(matrix->clone());
@@ -70,6 +74,28 @@ EvaluateLinearAlgebraUnaryAlgorithm::Outputs EvaluateLinearAlgebraUnaryAlgorithm
       (*result) *= scalar;
     }
     break;
+	case FUNCTION:
+		{
+				NewArrayMathEngine engine;
+				MatrixHandle matrixInput;
+				matrixInput.reset(matrix->clone());
+			
+				if (!(engine.add_input_fullmatrix("x", matrixInput ) )) ;
+      
+				boost::optional<std::string> func = params.get<2>(); 
+				std::string function_string = func.get(); 
+
+				function_string = "RESULT="+function_string;
+				engine.add_expressions(function_string);
+
+				if(!(engine.add_output_fullmatrix("RESULT",matrixInput))) ;
+				// Actual engine call, which does the dynamic compilation, the creation of the
+				// code for all the objects, as well as inserting the function and looping 
+				// over every data point
+				if (!(engine.run())) ;
+				result = matrix_cast::as_dense(matrixInput);
+		}
+		break;
   default:
     THROW_ALGORITHM_INPUT_ERROR("Unknown operand");
   }
@@ -82,7 +108,9 @@ AlgorithmOutput EvaluateLinearAlgebraUnaryAlgorithm::run_generic(const Algorithm
   auto matrix = input.get<DenseMatrix>(Variables::InputMatrix);
 
   auto scalar = boost::make_optional(get(Variables::ScalarValue).toDouble());
-  auto result = run(matrix, boost::make_tuple(Operator(get(Variables::Operator).toInt()), scalar));
+	auto function = boost::make_optional(get(Variables::FunctionString).toString()); 
+
+  auto result = run(matrix, boost::make_tuple(Operator(get(Variables::Operator).toInt()), scalar, function));
 
   AlgorithmOutput output;
   output[Variables::Result] = result;

src/Core/Algorithms/Math/EvaluateLinearAlgebraUnaryAlgo.cc

@@ -31,7 +31,7 @@
 
 #include <Core/Algorithms/Base/AlgorithmBase.h>
 #include <Core/Datatypes/MatrixFwd.h>
-#include <boost/optional.hpp>
+//#include <boost/optional.hpp>
 #include <Core/Algorithms/Math/share.h>
 
 /// \addtogroup Algorithms_Math
@@ -85,11 +85,12 @@ namespace Math {
     {
       NEGATE,
       TRANSPOSE,
-      SCALAR_MULTIPLY
+      SCALAR_MULTIPLY,
+			FUNCTION
     };
 
     typedef SCIRun::Core::Datatypes::DenseMatrixConstHandle Inputs;
-    typedef boost::tuple<Operator, boost::optional<double> > Parameters;
+    typedef boost::tuple<Operator, boost::optional<double>, boost::optional<std::string> > Parameters;
     typedef SCIRun::Core::Datatypes::DenseMatrixHandle Outputs;
 
     EvaluateLinearAlgebraUnaryAlgorithm();