Merge branch 'master' into sphere_scaling

Author: dcwhite

Superbuild/GLMExternal.cmake

@@ -1,21 +1,21 @@
 #  For more information, please see: http://software.sci.utah.edu
-# 
+#
 #  The MIT License
-# 
+#
 #  Copyright (c) 2015 Scientific Computing and Imaging Institute,
 #  University of Utah.
-# 
-#  
+#
+#
 #  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. 
-# 
+#  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

Superbuild/OsprayExternal.cmake

@@ -27,6 +27,9 @@
 SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
 SET(ospray_GIT_TAG "origin/scirun-build-2.4")
 
+set(ospray_DEPENDENCIES)
+LIST(APPEND ospray_DEPENDENCIES GLM_external)
+
 # If CMake ever allows overriding the checkout command or adding flags,
 # git checkout -q will silence message about detached head (harmless).
 ExternalProject_Add(Ospray_external
@@ -41,6 +44,7 @@ ExternalProject_Add(Ospray_external
     -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
     -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
     -DENABLE_OSPRAY_SUPERBUILD:BOOL=ON
+    -Dglm_DIR:PATH=${GLM_DIR}/cmake/glm
 )
 
 ExternalProject_Get_Property(Ospray_external BINARY_DIR)

src/CMakeLists.txt

@@ -558,9 +558,12 @@ MACRO(SCIRUN_ADD_LIBRARY library)
     # target_compile_options(${library} PRIVATE /W4 /WX)
   else()
     # TODO:
-    #target_compile_options(${library} PRIVATE -Wunused-parameter)
-        #eventually: -Wall -Wextra -pedantic -Werror)
-    # to fix: -Wunused-parameter
+    if(APPLE)
+      target_compile_options(${library} PRIVATE -Wall -Werror -Wunused-parameter -Winfinite-recursion)
+          #eventually: -Wall -Wextra -pedantic -Werror)
+    else()
+      target_compile_options(${library} PRIVATE -Wall -Wunused-parameter)
+    endif()
   endif()
 
   # Set up installer package (Release build only)

src/Core/Algorithms/BrainStimulator/ElectrodeCoilSetupAlgorithm.cc

@@ -220,7 +220,7 @@ VariableHandle ElectrodeCoilSetupAlgorithm::fill_table(FieldHandle, DenseMatrixH
 }
 
 
-DenseMatrixHandle ElectrodeCoilSetupAlgorithm::make_rotation_matrix(const double angle, const std::vector<double>& normal) const
+DenseMatrixHandle ElectrodeCoilSetupAlgorithm::make_rotation_matrix(const std::vector<double>& normal) const
 {
   DenseMatrixHandle result(new DenseMatrix(3, 3));
 
@@ -387,7 +387,7 @@ FieldHandle ElectrodeCoilSetupAlgorithm::make_tms(FieldHandle scalp, const std::
           coil_vector.push_back(coil_ny[i]);
           coil_vector.push_back(coil_nz[i]);
 
-          rotation_matrix1 = make_rotation_matrix(angle, coil_vector);
+          rotation_matrix1 = make_rotation_matrix(coil_vector);
 
           if (angle != 0) /// test it !
           {
@@ -609,7 +609,7 @@ boost::tuple<Variable::List, double, double, double> ElectrodeCoilSetupAlgorithm
 }
 
 
-boost::tuple<DenseMatrixHandle, FieldHandle, FieldHandle, VariableHandle> ElectrodeCoilSetupAlgorithm::make_tdcs_electrodes(FieldHandle scalp_mesh, const std::vector<FieldHandle>& elc_coil_proto, const std::vector<double>& elc_prototyp_map, const std::vector<double>& elc_x, const std::vector<double>& elc_y, const std::vector<double>& elc_z, const std::vector<double>& elc_angle_rotation, const std::vector<double>& elc_thickness, VariableHandle table) const
+boost::tuple<DenseMatrixHandle, FieldHandle, FieldHandle, VariableHandle> ElectrodeCoilSetupAlgorithm::make_tdcs_electrodes(FieldHandle scalp_mesh, const std::vector<FieldHandle>& elc_coil_proto, const std::vector<double>& elc_prototyp_map, const std::vector<double>& elc_x, const std::vector<double>& elc_y, const std::vector<double>& elc_z, const std::vector<double>& elc_angle_rotation, const std::vector<double>& elc_thickness) const
 {
   int nr_elc_sponge_triangles = 0, num_valid_electrode_definition = 0, nr_elc_sponge_triangles_on_scalp = 0;
   std::vector<double> field_values, field_values_elc_on_scalp;
@@ -688,8 +688,8 @@ boost::tuple<DenseMatrixHandle, FieldHandle, FieldHandle, VariableHandle> Electr
       axis.push_back(norm[2]);
       double angle = elc_angle_rotation[i];
       DenseMatrixHandle rotation_matrix, rotation_matrix1, rotation_matrix2;
-      rotation_matrix1 = make_rotation_matrix(angle, axis);
-      if (elc_angle_rotation[i] != 0)
+      rotation_matrix1 = make_rotation_matrix(axis);
+      if (angle != 0)
       {
         rotation_matrix2 = make_rotation_matrix_around_axis(angle, axis);
         rotation_matrix = boost::make_shared<DenseMatrix>((*rotation_matrix2) * (*rotation_matrix1));
@@ -1696,7 +1696,7 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
 
   if (t1 == t2 && t1 == t3 && t1 == t4 && t1 == t5 && t14 > 0 && t1 > 0)
   {
-    boost::tie(elc_sponge_locations, electrodes_field, final_electrodes_field, table_output) = make_tdcs_electrodes(scalp, elc_coil_proto, elc_prototyp_map, elc_x, elc_y, elc_z, elc_angle_rotation, elc_thickness, table_output);
+    boost::tie(elc_sponge_locations, electrodes_field, final_electrodes_field, table_output) = make_tdcs_electrodes(scalp, elc_coil_proto, elc_prototyp_map, elc_x, elc_y, elc_z, elc_angle_rotation, elc_thickness);
     valid_tdcs = true;
   }
 

src/Core/Algorithms/BrainStimulator/ElectrodeCoilSetupAlgorithm.h

@@ -91,9 +91,9 @@ namespace BrainStimulator {
     static const int TMS_stim_type; /// third  ...
 
     Datatypes::DenseMatrixHandle make_rotation_matrix_around_axis(double angle, std::vector<double>& axis_vector) const;
-    Datatypes::DenseMatrixHandle make_rotation_matrix(const double angle, const std::vector<double>& normal) const;
+    Datatypes::DenseMatrixHandle make_rotation_matrix(const std::vector<double>& normal) const;
     boost::tuple<Datatypes::DenseMatrixHandle, FieldHandle, FieldHandle, VariableHandle> make_tdcs_electrodes(FieldHandle scalp, const std::vector<FieldHandle>& elc_coil_proto,
-    const std::vector<double>& elc_prototyp_map, const std::vector<double>& elc_x, const std::vector<double>& elc_y, const std::vector<double>& elc_z, const std::vector<double>& elc_angle_rotation, const std::vector<double>& elc_thickness, VariableHandle table) const;
+    const std::vector<double>& elc_prototyp_map, const std::vector<double>& elc_x, const std::vector<double>& elc_y, const std::vector<double>& elc_z, const std::vector<double>& elc_angle_rotation, const std::vector<double>& elc_thickness) const;
     FieldHandle make_tms(FieldHandle scalp, const std::vector<FieldHandle>& elc_coil_proto, const std::vector<double>& coil_prototyp_map, const std::vector<double>& coil_x, const std::vector<double>& coil_y, const std::vector<double>& coil_z, const std::vector<double>& coil_angle_rotation, std::vector<double>& coil_nx, std::vector<double>& coil_ny, std::vector<double>& coil_nz) const;
     VariableHandle fill_table(FieldHandle scalp, Datatypes::DenseMatrixHandle locations, const std::vector<FieldHandle>& input) const;
     boost::tuple<Variable::List, double, double, double> make_table_row(int i,double x, double y, double z, double nx, double ny, double nz) const;

src/Core/Algorithms/BrainStimulator/ModelGenericCoilAlgorithm.cc

@@ -752,7 +752,7 @@ std::unique_ptr<BaseCoilgen> AlgoSelector(int idx,const AlgorithmBase* scirunAlg
 }
 
 
-AlgorithmOutput ModelTMSCoilAlgorithm::run(const AlgorithmInput& input) const
+AlgorithmOutput ModelTMSCoilAlgorithm::run(const AlgorithmInput&) const
 {
 	ModelTMSCoilAlgorithm::Args algoArgs;
 	algoArgs.current = static_cast<double>(get(Parameters::Current).toDouble())*1e6; ///MD: here is the unit scaling, wire current module input is in [megaA/s]

src/Core/Algorithms/DataIO/ReadMatrix.cc

@@ -96,7 +96,7 @@ ReadMatrixAlgorithm::Outputs ReadMatrixAlgorithm::run(const ReadMatrixAlgorithm:
   THROW_ALGORITHM_INPUT_ERROR("Unknown matrix file format");
 }
 
-AlgorithmOutput ReadMatrixAlgorithm::run(const AlgorithmInput& input) const
+AlgorithmOutput ReadMatrixAlgorithm::run(const AlgorithmInput&) const
 {
   auto filename = get(Variables::Filename).toFilename().string();
   auto file = run(filename);

src/Core/Algorithms/DataIO/TextToTriSurfField.cc

@@ -457,7 +457,7 @@ MeshHandle TextToTriSurfFieldAlgorithm::run(const std::string& filename)
   return MeshHandle();
 }
 
-AlgorithmOutput TextToTriSurfFieldAlgorithm::run(const AlgorithmInput& input) const
+AlgorithmOutput TextToTriSurfFieldAlgorithm::run(const AlgorithmInput&) const
 {
   throw 2;
 }

src/Core/Algorithms/Describe/DescribeDatatype.h

@@ -41,8 +41,7 @@ namespace General {
   {
   public:
     std::string describe(const Datatypes::DatatypeHandle& data) const;
-
-    AlgorithmOutput run(const AlgorithmInput& input) const override { return AlgorithmOutput(); }
+    AlgorithmOutput run(const AlgorithmInput&) const override { return AlgorithmOutput(); }
   };
 
 }}}}

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

@@ -790,7 +790,7 @@ bool ConverterAlgo::MatrixToString(Datatypes::MatrixHandle input, Datatypes::Str
 }
 
 
-AlgorithmOutput ConverterAlgo::run(const AlgorithmInput& input) const
+AlgorithmOutput ConverterAlgo::run(const AlgorithmInput&) const
 {
   throw "not implemented";
 }