Merge 2019-10-22 warning fixes back to 2018-05-15

src/2d/barrel/describe_scanner_cmd.cpp

@@ -40,6 +40,8 @@ int main(int argc, char* argv[]) {
     world = Gate::D2::build_new_full_scanner_volume<F>();
   } else if (cl.exist("ideal")) {
     world = Gate::D2::build_ideal_scanner_volume<F>();
+  } else {
+    throw("you need to select one of: big-barrel, full, new-module");
   }
 
   const int n_detectors = Gate::D2::count_cristals<F, S>(world);

src/2d/barrel/detector_set_test.cpp

@@ -29,7 +29,7 @@ TEST("Serialise") {
     std::ifstream in(name);
     auto scanner_copy = Builder::deserialize(in);
 
-    for (int d = 0; d < scanner.size(); d++) {
+    for (size_t d = 0; d < scanner.size(); d++) {
       REQUIRE(scanner[d].approx_equal_dihedral(scanner_copy[d], 1e-5));
     }
     in.close();
@@ -56,7 +56,7 @@ TEST("Serialise") {
         PET2D::Barrel::SymmetryDescriptor<S>::deserialize(in_s));
     in_s.close();
     std::remove(name_s.c_str());
-    for (int d = 0; d < scanner.size(); d++) {
+    for (size_t d = 0; d < scanner.size(); d++) {
       REQUIRE(scanner[d].approx_equal_dihedral(scanner_copy[d], 1e-5));
     }
     auto descriptor_copy = scanner_copy.symmetry_descriptor();

src/2d/barrel/matrix_cmd.cpp

@@ -209,7 +209,6 @@ static void run(cmdline::parser& cl, ModelArgs... args) {
 
   ModelClass model(args...);
 
-  auto n_detectors = scanner.size();
   auto& n_pixels = cl.get<int>("n-pixels");
   auto& m_pixel = cl.get<int>("m-pixel");
   auto& s_pixel = cl.get<double>("s-pixel");

src/2d/barrel/monte_carlo_test.cpp

@@ -30,6 +30,6 @@ F strip_length = 0.300;
 }
 
 TEST("2d/barrel/phantom_monte_carlo") {
-  auto scanner2d = PET2D::Barrel::ScannerBuilder<Scanner>::build_single_ring(
+  PET2D::Barrel::ScannerBuilder<Scanner>::build_single_ring(
       inner_radius, 32, strip_width, strip_height);
 }

src/2d/barrel/symmetry_descriptor_test.cpp

@@ -69,7 +69,7 @@ TEST("Find symmetry") {
   REQUIRE(symmetry_descriptor.symmetric_detector(6, 7) == 0);
 
   for (S s = 0; s < SymmetryDescriptor::EIGHT; s++) {
-    for (S d = 0; d < detector.size(); d++) {
+    for (size_t d = 0; d < detector.size(); d++) {
       INFO("s = " << s << " d =  " << d);
       REQUIRE(find_symmetric(detector, s, d, 1e-4) ==
               symmetry_descriptor.symmetric_detector(d, s));

src/2d/gate/gate_macros.h

@@ -10,7 +10,10 @@ namespace D2 {
 template <typename FType, typename SType> class GateMacrosInterpreter {
  public:
   using F = FType;
-  void interpret(const std::istream& macro){};
+  void interpret(const std::istream& macro) {
+    // FIXME: provide implementation
+    (void)macro;  // mark as used (for now)
+  }
   Gate::D2::Volume<F>* volume() { return new Gate::D2::Box<F>(2.0, 1.0); };
 };
 }

src/2d/gate/gate_volume.h

@@ -82,7 +82,7 @@ template <typename FType> class Volume {
   using VolumeList = std::list<Volume*>;
   using Transformation = PET2D::Transformation<F>;
 
-  Volume() : is_sd_(false), transformation_(new Transformation()) {}
+  Volume() : transformation_(new Transformation()), is_sd_(false) {}
 
   bool is_sd() const { return is_sd_; }
 
@@ -130,7 +130,6 @@ template <typename FType> class Volume {
   std::unique_ptr<Repeater<F>> repeater_;
   // Material
   std::unique_ptr<Transformation> transformation_;
-
   bool is_sd_;
 };
 

src/2d/gate/gate_volume_test.cpp

@@ -349,7 +349,7 @@ TEST("old multi ring") {
                                                                   0.021);
 
     for (S s = 0; s < 8; s++) {
-      for (S d = 0; d < scanner.size(); d++) {
+      for (size_t d = 0; d < scanner.size(); d++) {
         REQUIRE(s_descriptor.symmetric_detector(d, s) ==
                 ref_scanner.symmetry_descriptor().symmetric_detector(d, s));
       }

src/2d/geometry/find_symmetry.h

@@ -9,6 +9,7 @@ PET2D::Transformation<F> symmetry_transformation(S symmetry) {
 
   using Vector = typename Transformation::Vector;
   switch (symmetry) {
+    default:
     case 0:
       return Transformation();
     case 1:
@@ -29,17 +30,16 @@ PET2D::Transformation<F> symmetry_transformation(S symmetry) {
 }
 
 template <typename Scanner>
-typename Scanner::S find_symmetric(Scanner scanner,
-                                   typename Scanner::S symmetry,
-                                   typename Scanner::S detector,
-                                   typename Scanner::F epsilon) {
+size_t find_symmetric(Scanner scanner,
+                      typename Scanner::S symmetry,
+                      typename Scanner::S detector,
+                      typename Scanner::F epsilon) {
   using F = typename Scanner::F;
-  using S = typename Scanner::S;
 
   auto t = symmetry_transformation<F>(symmetry);
   auto t_detector = scanner[detector].transformed(t);
 
-  for (S d = 0; d < scanner.size(); d++) {
+  for (size_t d = 0; d < scanner.size(); d++) {
     if (t_detector.approx_equal_dihedral(scanner[d], epsilon))
       return d;
   }
@@ -53,7 +53,7 @@ bool fill_symmetry_descriptor(
     typename Scanner::F epsilon) {
   using S = typename Scanner::S;
 
-  for (S d = 0; d < scanner.size(); d++) {
+  for (size_t d = 0; d < scanner.size(); d++) {
     for (S s = 0; s < descriptor.n_symmetries; s++) {
       auto symmetric = find_symmetric(scanner, s, d, epsilon);
       if (symmetric < 0)

src/2d/geometry/point_test.cpp

@@ -8,7 +8,6 @@ TEST("Transforming and comparing points") {
 
   using Point = PET2D::Point<F>;
   using Transformation = PET2D::Transformation<F>;
-  using Vector = typename Point::Vector;
 
   Point p(0, 1);
   Point q(0, 1);

src/2d/geometry/polygon.h

@@ -32,7 +32,7 @@ class Polygon : public util::array<NumPoints, Point<FType>> {
     return *this;
   }
 
-  Polygon& transformed(Transformation tr) {
+  Polygon transformed(Transformation tr) {
     Polygon tmp(*this);
     return tmp.transform(tr);
   }
@@ -148,7 +148,7 @@ class Polygon : public util::array<NumPoints, Point<FType>> {
 
   bool approx_equal_circular(const Polygon& rhs, F epsilon = 1e-5) {
     Polygon p(rhs);
-    for (int i = 0; i < rhs.size(); i++) {
+    for (size_t i = 0; i < rhs.size(); i++) {
       std::rotate(p.begin(), p.begin() + 1, p.end());
       if (approx_equal(p, epsilon))
         return true;

src/2d/strip/cuda/gpu_events_soa.h

@@ -20,7 +20,7 @@ template <typename FType> struct ResponsesSOA {
     F* cpu_dl = new F[n_responses];
 
     // fill CPU side SOA
-    for (int i = 0; i < n_responses; ++i) {
+    for (size_t i = 0; i < n_responses; ++i) {
       cpu_z_u[i] = source[i].z_u;
       cpu_z_d[i] = source[i].z_d;
       cpu_dl[i] = source[i].dl;

src/2d/strip/cuda/reconstruction.cu

@@ -115,8 +115,8 @@ void run(Scanner<F, S>& scanner,
 template <typename F>
 void fill_with_sensitivity(F* sensitivity, Scanner<F, S>& scanner) {
 
-  size_t width = scanner.n_z_pixels;
-  size_t height = scanner.n_y_pixels;
+  const int width = scanner.n_z_pixels;
+  const int height = scanner.n_y_pixels;
 
   for (int y = 0; y < height; ++y) {
     for (int x = 0; x < width; ++x) {

src/3d/full/scanner.h

@@ -83,7 +83,7 @@ template <typename F, typename S, int MAX_VOLUMES = 2 << 9> class Scanner {
     util::array<MAX_VOLUMES, intersection_t> intersected_volumes_;
     int hits = 0;
 
-    for (int i = 0; i < volumes_.size(); i++) {
+    for (size_t i = 0; i < volumes_.size(); i++) {
       auto v = volumes_[i];
       auto hit = v->intersects_with(ray);
       if (hit.intersected) {

src/3d/hybrid/reconstruction_cmd.cpp

@@ -115,10 +115,8 @@ using Pixel = PET2D::Pixel<S>;
 using LOR = PET2D::Barrel::LOR<S>;
 using Matrix = PET2D::Barrel::SparseMatrix<Pixel, LOR, Hit>;
 
-static void run_with_geometry(cmdline::parser& cl,
-                              int argc,
-                              Geometry& geometry);
-static void run_with_matrix(cmdline::parser& cl, int argc, Matrix& matrix);
+static void run_with_geometry(cmdline::parser& cl, Geometry& geometry);
+static void run_with_matrix(cmdline::parser& cl, Matrix& matrix);
 static void run_reconstruction(cmdline::parser& cl,
                                Reconstruction::Scanner& scanner,
                                Reconstruction::Grid& grid,
@@ -245,7 +243,7 @@ int main(int argc, char* argv[]) {
     util::ibstream in_geometry(cl.get<std::string>("geometry"));
     ENSURE_IS_OPEN(in_geometry, "geometry", cl.get<std::string>("geometry"));
     Geometry geometry(in_geometry);
-    run_with_geometry(cl, argc, geometry);
+    run_with_geometry(cl, geometry);
   }
   // 3D reconstruction using system matrix only
   else if (cl.exist("system")) {
@@ -260,7 +258,7 @@ int main(int argc, char* argv[]) {
       matrix_cfg.close();
       cmdline::load(cl, matrix_name, matrix_base_name + ".cfg");
     }
-    run_with_matrix(cl, argc, matrix);
+    run_with_matrix(cl, matrix);
   }
   // bail out if no geometry or system matrix is given
   else {
@@ -278,9 +276,7 @@ int main(int argc, char* argv[]) {
   CMDLINE_CATCH
 }
 
-static void run_with_geometry(cmdline::parser& cl,
-                              int argc,
-                              Geometry& geometry) {
+static void run_with_geometry(cmdline::parser& cl, Geometry& geometry) {
   // FIXME: this is very very stupid way to set argument manually, so cmdline
   // thinks it was provided via command line, but in fact we load it from
   // geometry file
@@ -363,7 +359,7 @@ static void run_with_geometry(cmdline::parser& cl,
   run_reconstruction(cl, scanner, grid, geometry_soa);
 }
 
-static void run_with_matrix(cmdline::parser& cl, int argc, Matrix& matrix) {
+static void run_with_matrix(cmdline::parser& cl, Matrix& matrix) {
   if (matrix.triangular()) {
     throw(
         "matrix must be in full form, "

src/util/gate_parser.h

@@ -46,13 +46,11 @@ class Parser {
     }
 
     start++;
-    bool another_command = true;
     while (1) {
       auto next_backslash = input.find_first_of("/ \t\n", start);
       if (next_backslash == std::string::npos) {
         fprintf(stderr, "`%s' is not a gate command ", input.c_str());
         chain.is_valid_ = false;
-        another_command = false;
         return std::string::npos;
       }
       auto command = input.substr(start, next_backslash - start);