Build fixes for C++17, Apple Silicon

.github/workflows/mac.yml

@@ -17,7 +17,7 @@ jobs:
         fetch-depth: 0
 
     - name: Install Qt
-      uses: jurplel/install-qt-action@v2.14.0
+      uses: jurplel/install-qt-action@v3
       env:
         ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
       with:
@@ -75,7 +75,7 @@ jobs:
         fetch-depth: 0
 
     - name: Install Qt
-      uses: jurplel/install-qt-action@v2.14.0
+      uses: jurplel/install-qt-action@v3
       env:
         ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
       with:
@@ -118,7 +118,7 @@ jobs:
         fetch-depth: 0
 
     - name: Install Qt
-      uses: jurplel/install-qt-action@v2.14.0
+      uses: jurplel/install-qt-action@v3
       env:
         ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
       with:

.github/workflows/windows.yml

@@ -45,7 +45,7 @@ jobs:
         fetch-depth: 0
 
     - name: Install Qt
-      uses: jurplel/install-qt-action@v2.14.0
+      uses: jurplel/install-qt-action@v3
       env:
         ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
       with:
@@ -93,7 +93,7 @@ jobs:
         fetch-depth: 0
 
     - name: Install Qt
-      uses: jurplel/install-qt-action@v2.14.0
+      uses: jurplel/install-qt-action@v3
       env:
         ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
       with:
@@ -149,7 +149,7 @@ jobs:
         fetch-depth: 0
 
     - name: Install Qt
-      uses: jurplel/install-qt-action@v2.14.0
+      uses: jurplel/install-qt-action@v3
       env:
         ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
       with:

Superbuild/EigenExternal.cmake

@@ -26,9 +26,8 @@
 
 SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
 
-# TODO: test on Windows
 ExternalProject_Add(Eigen_external
-  URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz"
+  URL "https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz"
   PATCH_COMMAND ""
   CONFIGURE_COMMAND ""
   BUILD_IN_SOURCE ON

Superbuild/SpdLogExternal.cmake

@@ -30,7 +30,7 @@ SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
 # git checkout -q will silence message about detached head (harmless).
 ExternalProject_Add(SpdLog_external
   GIT_REPOSITORY "https://github.com/gabime/spdlog"
-  GIT_TAG "v1.3.1"
+  GIT_TAG "v1.10.0"
   CONFIGURE_COMMAND ""
   BUILD_COMMAND ""
   INSTALL_COMMAND ""

src/Core/Algorithms/BrainStimulator/GenerateROIStatisticsAlgorithm.cc

@@ -199,7 +199,7 @@ boost::tuple<DenseMatrixHandle, VariableHandle> GenerateROIStatisticsAlgorithm::
   const double invalidDouble = std::numeric_limits<double>::quiet_NaN();
 
   /// efficient way to compute std dev. in just one loop over all mesh elements: sqrt ( 1/(n-1) (Sx^2 - avr Sx + n avr^2 )
-  for (VMesh::Elem::index_type j=0; j < number_of_atlas_materials; ++j)
+  for (auto j=0; j < number_of_atlas_materials; ++j)
   {
     double Sx=value_avr[j];
 

src/Core/Algorithms/BrainStimulator/SetupRHSforTDCSandTMSAlgorithm.cc

@@ -274,8 +274,10 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
   /// prepare LHS_KNOWNS which is the an input to addknownstolinearsystem (called x) besides the
   /// stiffness matrix
   lhs_knows = makeShared<DenseMatrix>(mesh_num_nodes, 1);
-  for (VMesh::Node::index_type idx = 0; idx < mesh_num_nodes; idx++)
-  { (*lhs_knows)(idx, 0) = std::numeric_limits<double>::quiet_NaN(); }
+  for (auto idx = 0; idx < mesh_num_nodes; idx++)
+  {
+    (*lhs_knows)(idx, 0) = std::numeric_limits<double>::quiet_NaN();
+  }
   (*lhs_knows)(refnode_number, 0) = 0;
 
   if (fi4.is_pointcloudmesh())
@@ -363,7 +365,7 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
   /// (Cleaver), this mapping is meant to map the GUI inputs to actual electrode geometry by having
   /// a lookup table
   int electrode_sponges = elc_sponge_location->nrows();
-  DenseMatrixHandle lookup(new DenseMatrix(electrode_sponges, 1));
+  std::vector<long> lookup(electrode_sponges);
   DenseMatrixHandle distances(new DenseMatrix(electrode_sponges, 1));
   VMesh::Node::index_type didx;
   double distance = 0;
@@ -388,7 +390,7 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
         found_index = j;
       }
     }
-    (*lookup)(i, 0) = found_index;
+    lookup[i] = found_index;
     (*distances)(i, 0) = min_dis;
   }
 
@@ -580,11 +582,11 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
       double elc_thickness = 0;
       bool found = false;
 
-      for (long j = 0; j < lookup->nrows(); j++)
+      for (auto j = 0; j < lookup.size(); j++)
       {
-        if ((*lookup)(j, 0) == k)
+        if (lookup[j] == k)
         {
-          elc_thickness = (*elc_sponge_location)((*lookup)(j, 0), 3);
+          elc_thickness = (*elc_sponge_location)(k, 3);
           found = true;
         }
       }
@@ -816,7 +818,7 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
   double area = 0.0, prev_elc = 0, tmp_fld_val = 0;
   for (VMesh::Elem::index_type l = 0; l < elc_sponge_surf_vmesh->num_elems(); l++)
   {
-    (*elc_elem_typ)(l, 0) = 2;  // define triangles to incject currents in TDCS simulations
+    (*elc_elem_typ)(static_cast<std::uint64_t>(l), 0) = 2;  // define triangles to incject currents in TDCS simulations
     VMesh::Node::array_type onodes(3);
     elc_sponge_surf_vmesh->get_nodes(onodes, l);
     elc_sponge_surf_vmesh->get_center(p, onodes[0]);
@@ -828,7 +830,7 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
           "Reference node is part of electrode definition. Choose another reference node for given "
           "electrode surface mesh. ");
     }
-    (*elc_elem_def)(l, 0) = node_ind;
+    (*elc_elem_def)(static_cast<std::uint64_t>(l), 0) = node_ind;
     Point pos;
     mesh_vmesh->get_point(pos, node_ind);
     double x1 = pos.x(), y1 = pos.y(), z1 = pos.z();
@@ -842,7 +844,7 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
           "Reference node is part of electrode definition. Choose another reference node for given "
           "electrode surface mesh. ");
     }
-    (*elc_elem_def)(l, 1) = node_ind;
+    (*elc_elem_def)(static_cast<uint64_t>(l), 1) = node_ind;
     mesh_vmesh->get_point(pos, node_ind);
     double x2 = pos.x(), y2 = pos.y(), z2 = pos.z();
     elc_sponge_surf_vmesh->get_center(p, onodes[2]);
@@ -854,12 +856,12 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
           "Reference node is part of electrode definition. Choose another reference node for given "
           "electrode surface mesh. ");
     }
-    (*elc_elem_def)(l, 2) = node_ind;
+    (*elc_elem_def)(static_cast<uint64_t>(l), 2) = node_ind;
     mesh_vmesh->get_point(pos, node_ind);
     double x3 = pos.x(), y3 = pos.y(), z3 = pos.z();
 
-    (*elc_elem_def)(l, 3) = 0;
-    (*elc_elem)(l, 0) = field_values[l];
+    (*elc_elem_def)(static_cast<uint64_t>(l), 3) = 0;
+    (*elc_elem)(static_cast<uint64_t>(l), 0) = field_values[l];
 
     /// compute surface area of electrode/scalp interface
     double area_tmp = y1 * z2 + z1 * y3 + y2 * z3 - z2 * y3 - z1 * y2 - y1 * z3;
@@ -898,7 +900,7 @@ SetupTDCSAlgorithm::create_lhs(FieldHandle mesh, const std::vector<Variable>& im
           "Internal ERROR (should not happen): could not scale contact impedance by electrode "
           "surface area (index out of bound). ");
     }
-    (*elc_con_imp)(l, 0) = impedances[tmp_fld_val] * electrode_sponge_areas[tmp_fld_val];
+    (*elc_con_imp)(static_cast<uint64_t>(l), 0) = impedances[tmp_fld_val] * electrode_sponge_areas[tmp_fld_val];
   }
 
   DenseMatrixHandle selectmatrixind(
@@ -939,7 +941,7 @@ DenseMatrixHandle SetupTDCSAlgorithm::create_rhs(FieldHandle mesh, FieldHandle e
     auto mesh_elc_tri_surf = elc_tri_surf->vmesh();
     mesh_elc_tri_surf->synchronize(Mesh::NODE_LOCATE_E);
     vmesh->synchronize(Mesh::NODE_LOCATE_E);
-    for (VMesh::Node::index_type l = 0; l < vmesh->num_nodes(); l++) { (*output)(l, 0) = 0; }
+    for (auto l = 0; l < vmesh->num_nodes(); l++) { (*output)(l, 0) = 0; }
     double min_dis = get(Parameters::pointdistancebound).toDouble();
     for (VMesh::Node::index_type l = 0; l < mesh_elc_tri_surf->num_nodes(); l++)
     {
@@ -948,14 +950,10 @@ DenseMatrixHandle SetupTDCSAlgorithm::create_rhs(FieldHandle mesh, FieldHandle e
       double distance = -1;
       VMesh::Node::index_type ind;
       vmesh->find_closest_node(distance, q, ind, p);
-      (*output)(ind, 0) = elcs_wanted[l].toDouble() / 1000.0;
+      (*output)(static_cast<uint64_t>(ind), 0) = elcs_wanted[l].toDouble() / 1000.0;
       if (min_dis < distance)
       {
-        std::ostringstream ostr4;
-        ostr4 << " The electrode locations (4th module input) are further away from them mesh as "
-                 "provided by the GUI (min. distance bound). "
-              << std::endl;
-        remark(ostr4.str());
+        remark("The electrode locations (4th module input) are further away from them mesh as provided by the GUI (min. distance bound).\n");
       }
     }
 

src/Core/Algorithms/Field/Tests/MapFieldDataFromElemToNodeAlgoTests.cc

@@ -124,12 +124,12 @@ TEST(MapFieldDataFromElemToNode, TetMeshTestInterpolateWithFile)
 
  DenseMatrixHandle output(new DenseMatrix(8, 1));
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    result->vfield()->get_value((*output)(idx, 0),idx);
  }
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp = 0;
    expected_result->vfield()->get_value(tmp,idx);
@@ -151,14 +151,14 @@ TEST(MapFieldDataFromElemToNode, TetMeshTestMin)
 
  DenseMatrixHandle output(new DenseMatrix(8, 1));
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    result->vfield()->get_value((*output)(idx, 0),idx);
  }
 
  DenseMatrixHandle expected_result_min = test_mapfielddatafromelemtonodeFLD_Min();
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp = (*expected_result_min)(idx,0);
    EXPECT_NEAR( tmp,(*output)(idx, 0), 1e-16);
@@ -179,14 +179,14 @@ TEST(MapFieldDataFromElemToNode, TetMeshTestMax)
 
  DenseMatrixHandle output(new DenseMatrix(8, 1));
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    result->vfield()->get_value((*output)(idx, 0),idx);
  }
 
  DenseMatrixHandle expected_result_max = test_mapfielddatafromelemtonodeFLD_Max();
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp = (*expected_result_max)(idx,0);
    EXPECT_NEAR( tmp,(*output)(idx, 0), 1e-16);
@@ -207,14 +207,14 @@ TEST(MapFieldDataFromElemToNode, TetMeshTestSum)
 
  DenseMatrixHandle output(new DenseMatrix(8, 1));
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    result->vfield()->get_value((*output)(idx, 0),idx);
  }
 
  DenseMatrixHandle expected_result_sum = test_mapfielddatafromelemtonodeFLD_Sum();
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp = (*expected_result_sum)(idx,0);
    EXPECT_NEAR( tmp,(*output)(idx, 0), 1e-16);
@@ -236,14 +236,14 @@ TEST(MapFieldDataFromElemToNode, TetMeshTestMed)
 
  DenseMatrixHandle output(new DenseMatrix(8, 1));
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    result->vfield()->get_value((*output)(idx, 0),idx);
  }
 
  DenseMatrixHandle expected_result_med = test_mapfielddatafromelemtonodeFLD_Med();
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp = (*expected_result_med)(idx,0);
    EXPECT_NEAR( tmp,(*output)(idx, 0), 1e-16);

src/Core/Algorithms/Field/Tests/MapFieldDataFromNodeToElemAlgoTests.cc

@@ -125,7 +125,7 @@ TEST(MapFieldDataFromNodeToElemAlgoTests,TestInterpolationAverage)
 
  ASSERT_TRUE(result->vfield()->num_values() == 6);
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp=0;
    result->vfield()->get_value(tmp,idx);
@@ -140,7 +140,7 @@ TEST(MapFieldDataFromNodeToElemAlgoTests,TestInterpolationAverage)
 
  ASSERT_TRUE(result2->vfield()->num_values() == 6);
 
- for (VMesh::Elem::index_type idx = 0; idx < result2->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result2->vfield()->num_values(); idx++)
  {
    double tmp=0;
    result2->vfield()->get_value(tmp,idx);
@@ -181,7 +181,7 @@ TEST(MapFieldDataFromNodeToElemAlgoTests, TestMin)
 
  ASSERT_TRUE(result->vfield()->num_values() == 6);
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp=0;
    result->vfield()->get_value(tmp,idx);
@@ -206,7 +206,7 @@ TEST(MapFieldDataFromNodeToElemAlgoTests, TestMax)
 
  ASSERT_TRUE(result->vfield()->num_values() == 6);
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp=0;
    result->vfield()->get_value(tmp,idx);
@@ -231,7 +231,7 @@ TEST(MapFieldDataFromNodeToElemAlgoTests, TestSum)
 
  ASSERT_TRUE(result->vfield()->num_values() == 6);
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp=0;
    result->vfield()->get_value(tmp,idx);
@@ -256,7 +256,7 @@ TEST(MapFieldDataFromNodeToElemAlgoTests, TestMedian)
 
  ASSERT_TRUE(result->vfield()->num_values() == 6);
 
- for (VMesh::Elem::index_type idx = 0; idx < result->vfield()->num_values(); idx++)
+ for (auto idx = 0; idx < result->vfield()->num_values(); idx++)
  {
    double tmp=0;
    result->vfield()->get_value(tmp,idx);

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

@@ -221,7 +221,6 @@ bool ConvertBundleToFieldAlgo::runImpl(const BundleHandle& input, FieldHandle& o
   omesh->node_reserve(tot_num_nodes);
   omesh->elem_reserve(tot_num_elems);
 
-  size_type nodes_offset = 0;
   size_type elems_offset = 0;
   size_type nodes_count = 0;
   size_type elems_count = 0;
@@ -411,7 +410,6 @@ bool ConvertBundleToFieldAlgo::runImpl(const BundleHandle& input, FieldHandle& o
     }
 
     elems_offset += elems_count;
-    nodes_offset += nodes_count;
 
     update_progress_max(p+1, inputs.size());
   }

src/Core/Algorithms/Legacy/Fields/DistanceField/CalculateIsInsideField.cc

@@ -101,8 +101,6 @@ CalculateIsInsideFieldAlgo::runImpl(FieldHandle input, FieldHandle objfield, Fie
   if (fo.is_tensor()) fo.make_double();
   fo.make_constantdata();
 
-  bool clean_field = false;
-
   if (!output)
   {
     output = CreateField(fo,input->mesh());
@@ -112,7 +110,6 @@ CalculateIsInsideFieldAlgo::runImpl(FieldHandle input, FieldHandle objfield, Fie
       error("Could not create output field");
       return(false);
     }
-    clean_field = true;
   }
 
   // For the moment we calculate everything in doubles

src/Core/Algorithms/Legacy/Fields/FieldData/BuildMatrixOfSurfaceNormalsAlgo.cc

@@ -74,7 +74,7 @@ bool BuildMatrixOfSurfaceNormalsAlgo::runImpl(FieldHandle input, DenseMatrixHand
     return (false);
   }
 
-	VMesh::Node::index_type k = 0;
+	int k = 0;
   int cnt = 0;
   Vector norm;
   for (VMesh::Node::index_type i=0; i<num_nodes; ++i)