Merge branch 'master' into compositionTikhonov

merging with the latest updates from sciinsitute

Author: jcollfont

.gitignore

@@ -28,5 +28,4 @@ cmake_install.cmake
 install_manifest.txt
 CTestTestfile.cmake
 DartConfiguration.tcl
-bin*
 cmake

src/Core/Algorithms/BrainStimulator/ElectrodeCoilSetupAlgorithm.cc

@@ -51,8 +51,6 @@ using namespace SCIRun::Core::Datatypes;
 using namespace SCIRun::Core::Algorithms::BrainStimulator;
 using namespace SCIRun::Core::Algorithms;
 using namespace SCIRun::TestUtils;
-using namespace boost;
-using namespace boost::assign;
 
 namespace
 {
@@ -97,8 +95,7 @@ TEST(ElectrodeCoilSetupAlgorithmTests, AlgoCorrect)
   var8=makeVariable("NY", boost::str(boost::format("%s") % "???"));
   var9=makeVariable("NZ", boost::str(boost::format("%s") % "???"));
   var10=makeVariable("thickness",boost::str(boost::format("%s") % "2"));
-  Variable::List tmp;
-  tmp += var1,var2,var3,var4,var5,var6,var7,var8,var9,var10;
+  Variable::List tmp{ var1, var2, var3, var4, var5, var6, var7, var8, var9, var10 };
   table.push_back(makeVariable("row" + boost::lexical_cast<std::string>(0), tmp)); 
   VariableHandle output(new Variable(Name("Table"), table));
   ///@Dan: I dont know how to set the table to the GUI so that the module can executed properly.

src/Core/Algorithms/BrainStimulator/Tests/ElectrodeCoilSetupAlgorithmTests.cc

@@ -63,7 +63,7 @@ namespace impl
     }
     virtual void visit(DenseColumnMatrixGeneric<double>& column) override
     {
-      column.transposeInPlace();
+      column = column.transpose();
     }
   };
 }
@@ -105,7 +105,7 @@ EvaluateLinearAlgebraUnaryAlgorithm::Outputs EvaluateLinearAlgebraUnaryAlgorithm
   break;
   case FUNCTION:
   {
-    // BUG FIX: the ArrayMathEngine is not well designed for use with sparse matrices, especially allocating proper space for the result. 
+    // BUG FIX: the ArrayMathEngine is not well designed for use with sparse matrices, especially allocating proper space for the result.
     // There's no way to know ahead of time, so I'll just throw an error here and require the user to do this type of math elsewhere.
     if (matrixIs::sparse(matrix) && (matrix->nrows() * matrix->ncols() > 10000))
     {

src/Core/Algorithms/Math/EvaluateLinearAlgebraUnaryAlgo.cc

@@ -90,7 +90,7 @@ boost::tuple<MatrixHandle, int> GetMatrixSliceAlgo::runImpl(MatrixHandle matrix,
       if (sparse)
       {
         //TODO: makes a copy of the transpose. Not good. Should test out manually copying elements, trade speed for memory.
-        return boost::make_tuple(boost::make_shared<SparseRowMatrix>(std::move(sparse->getColumn(index))), max);
+        return boost::make_tuple(boost::make_shared<SparseRowMatrix>(sparse->getColumn(index)), max);
       }
       return boost::make_tuple(nullptr, 0);
     }