Use std::string in rest of the code

cmd/connectome2tck.cpp

@@ -39,7 +39,7 @@ using namespace MR::DWI;
 using namespace MR::DWI::Tractography;
 using namespace MR::DWI::Tractography::Connectome;
 
-const char *file_outputs[] = {"per_edge", "per_node", "single", NULL};
+const std::vector<std::string> file_outputs = {"per_edge", "per_node", "single"};
 
 // clang-format off
 const OptionGroup TrackOutputOptions = OptionGroup ("Options for determining the content / format of output files")

cmd/connectomeedit.cpp

@@ -23,7 +23,8 @@ using namespace MR::Connectome;
 using namespace MR::Math;
 using namespace App;
 
-const char *operations[] = {"to_symmetric", "upper_triangular", "lower_triangular", "transpose", "zero_diagonal", NULL};
+const std::vector<std::string> operations = {
+    "to_symmetric", "upper_triangular", "lower_triangular", "transpose", "zero_diagonal"};
 
 // clang-format off
 void usage() {
@@ -73,4 +74,4 @@ void run() {
   }
 
   File::Matrix::save_matrix(connectome, output_path);
-}
+}

cmd/connectomestats.cpp

@@ -41,7 +41,7 @@ using Math::Stats::matrix_type;
 using Math::Stats::vector_type;
 using Stats::PermTest::count_matrix_type;
 
-const char *algorithms[] = {"nbs", "tfnbs", "none", nullptr};
+const std::vector<std::string> algorithms = {"nbs", "tfnbs", "none"};
 
 // TODO Eventually these will move to some kind of TFCE header
 #define TFCE_DH_DEFAULT 0.1

cmd/dwi2fod.cpp

@@ -29,7 +29,7 @@
 using namespace MR;
 using namespace App;
 
-const char *const algorithms[] = {"csd", "msmt_csd", NULL};
+const std::vector<std::string> algorithms = {"csd", "msmt_csd"};
 
 // clang-format off
 const OptionGroup CommonOptions = OptionGroup ("Options common to more than one algorithm")

cmd/dwidenoise.cpp

@@ -23,9 +23,8 @@
 using namespace MR;
 using namespace App;
 
-const char *const dtypes[] = {"float32", "float64", NULL};
-
-const char *const estimators[] = {"exp1", "exp2", NULL};
+const std::vector<std::string> dtypes = {"float32", "float64"};
+const std::vector<std::string> estimators = {"Exp1", "Exp2"};
 
 // clang-format off
 void usage() {

cmd/fixel2voxel.cpp

@@ -37,20 +37,19 @@ using namespace App;
 
 using Fixel::index_type;
 
-const char *operations[] = {"mean",
-                            "sum",
-                            "product",
-                            "min",
-                            "max",
-                            "absmax",
-                            "magmax",
-                            "count",
-                            "complexity",
-                            "sf",
-                            "dec_unit",
-                            "dec_scaled",
-                            "none",
-                            nullptr};
+const std::vector<std::string> operations = {"mean",
+                                             "sum",
+                                             "product",
+                                             "min",
+                                             "max",
+                                             "absmax",
+                                             "magmax",
+                                             "count",
+                                             "complexity",
+                                             "sf",
+                                             "dec_unit",
+                                             "dec_scaled",
+                                             "none"};
 
 // clang-format off
 

cmd/fixelfilter.cpp

@@ -33,7 +33,7 @@ using namespace MR;
 using namespace App;
 using namespace MR::Fixel;
 
-const char *const filters[] = {"connect", "smooth", nullptr};
+const std::vector<std::string> filters = {"connect", "smooth"};
 
 // clang-format off
 void usage() {

cmd/labelstats.cpp

@@ -28,7 +28,7 @@
 using namespace MR;
 using namespace App;
 
-const char *field_choices[] = {"mass", "centre", nullptr};
+const std::vector<std::string> field_choices = {"mass", "centre"};
 
 // clang-format off
 void usage() {

cmd/maskfilter.cpp

@@ -29,7 +29,7 @@ using namespace App;
 
 #define DEFAULT_CLEAN_SCALE 2
 
-const char *filters[] = {"clean", "connect", "dilate", "erode", "fill", "median", nullptr};
+const std::vector<std::string> filters = {"clean", "connect", "dilate", "erode", "fill", "median"};
 
 // clang-format off
 const OptionGroup CleanOption =

cmd/meshconvert.cpp

@@ -24,7 +24,7 @@ using namespace MR;
 using namespace App;
 using namespace MR::Surface;
 
-const char *transform_choices[] = {"first2real", "real2first", "voxel2real", "real2voxel", "fs2real", nullptr};
+const std::vector<std::string> transform_choices = {"first2real", "real2first", "voxel2real", "real2voxel", "fs2real"};
 
 // clang-format off
 void usage() {

cmd/meshfilter.cpp

@@ -27,7 +27,7 @@ using namespace MR;
 using namespace App;
 using namespace MR::Surface;
 
-const char *filters[] = {"smooth", NULL};
+const std::vector<std::string> filters = {"smooth"};
 
 // clang-format off
 const OptionGroup smooth_option = OptionGroup ("Options for mesh smoothing filter")

cmd/mrcalc.cpp

@@ -480,13 +480,13 @@ class LoadedImage {
 
 class StackEntry {
 public:
-  StackEntry(const char *entry) : arg(entry), rng_gaussian(false), image_is_complex(false) {}
+  StackEntry(std::string entry) : arg(std::move(entry)), rng_gaussian(false), image_is_complex(false) {}
 
   StackEntry(Evaluator *evaluator_p)
       : arg(nullptr), evaluator(evaluator_p), rng_gaussian(false), image_is_complex(false) {}
 
   void load() {
-    if (!arg)
+    if (arg.empty())
       return;
     auto search = image_list.find(arg);
     if (search != image_list.end()) {
@@ -530,10 +530,9 @@ class StackEntry {
         }
       }
     }
-    arg = nullptr;
   }
 
-  const char *arg;
+  std::string arg;
   std::shared_ptr<Evaluator> evaluator;
   std::shared_ptr<Image<complex_type>> image;
   copy_ptr<Math::RNG> rng;
@@ -898,7 +897,7 @@ void run_operations(const std::vector<StackEntry> &stack) {
   if (stack.size() > 2)
     throw Exception("too many operands left on stack!");
 
-  if (!stack[1].arg)
+  if (stack[1].arg.empty())
     throw Exception("output image not specified");
 
   if (stack[0].is_complex()) {
@@ -984,15 +983,14 @@ class OpTernary : public OpBase {
 void run() {
   std::vector<StackEntry> stack;
 
-  for (int n = 1; n < App::argc; ++n) {
-
-    const Option *opt = match_option(App::argv[n]);
+  for (const auto &argument : App::raw_arguments_list) {
+    const Option *opt = match_option(argument);
     if (opt) {
 
       if (opt->is("datatype"))
-        ++n;
+        continue;
       else if (opt->is("nthreads"))
-        ++n;
+        continue;
       else if (opt->is("force") || opt->is("info") || opt->is("debug") || opt->is("quiet"))
         continue;
 
@@ -1003,7 +1001,7 @@ void run() {
         throw Exception(std::string("operation \"") + opt->id + "\" not yet implemented!");
 
     } else {
-      stack.push_back(App::argv[n]);
+      stack.push_back(argument);
     }
   }
 

cmd/mrcolour.cpp

@@ -30,21 +30,16 @@ using namespace MR;
 using namespace App;
 
 std::vector<std::string> colourmap_choices_std;
-std::vector<const char *> colourmap_choices_cstr;
 
 // clang-format off
 void usage() {
 
-  const ColourMap::Entry *entry = ColourMap::maps;
-  do {
-    if (strcmp(entry->name, "Complex"))
-      colourmap_choices_std.push_back(lowercase(entry->name));
-    ++entry;
-  } while(entry->name != nullptr);
-  colourmap_choices_cstr.reserve(colourmap_choices_std.size() + 1);
-  for (const auto& s : colourmap_choices_std)
-    colourmap_choices_cstr.push_back(s.c_str());
-  colourmap_choices_cstr.push_back(nullptr);
+  for(const auto& entry : ColourMap::maps) {
+    const bool is_complex = strcmp(entry.name, "Complex") == 0;
+    if(is_complex) {
+      colourmap_choices_std.push_back(entry.name);
+    }
+  }
 
   AUTHOR = "Robert E. Smith ([email protected])";
 
@@ -67,7 +62,7 @@ void usage() {
   ARGUMENTS
   + Argument ("input",  "the input image").type_image_in()
   + Argument ("map",    "the colourmap to apply;"
-                        " choices are: " + join(colourmap_choices_std, ",")).type_choice (colourmap_choices_cstr.data())
+                        " choices are: " + join(colourmap_choices_std, ",")).type_choice (colourmap_choices_std)
   + Argument ("output", "the output image").type_image_out();
 
   OPTIONS

cmd/mrdegibbs.cpp

@@ -23,7 +23,7 @@
 using namespace MR;
 using namespace App;
 
-const char *modes[] = {"2d", "3d", nullptr};
+const std::vector<std::string> modes = {"2d", "3d"};
 
 // clang-format off
 void usage() {

cmd/mrfilter.cpp

@@ -29,7 +29,7 @@
 using namespace MR;
 using namespace App;
 
-const char *filters[] = {"fft", "gradient", "median", "smooth", "normalise", "zclean", NULL};
+const std::vector<std::string> filters = {"fft", "gradient", "median", "smooth", "normalise", "zclean"};
 
 // clang-format off
 const OptionGroup FFTOption = OptionGroup ("Options for FFT filter")

cmd/mrgrid.cpp

@@ -30,9 +30,10 @@
 using namespace MR;
 using namespace App;
 
-const char *interp_choices[] = {"nearest", "linear", "cubic", "sinc", NULL};
+
 #define DEFAULT_INTERP 2 // cubic
-const char *operation_choices[] = {"regrid", "crop", "pad", NULL};
+const std::vector<std::string> interp_choices = {"nearest", "linear", "cubic", "sinc"};
+const std::vector<std::string> operation_choices = {"regrid", "crop", "pad"};
 
 // clang-format off
 void usage() {

cmd/mrhistmatch.cpp

@@ -29,7 +29,7 @@
 using namespace MR;
 using namespace App;
 
-const char *choices[] = {"scale", "linear", "nonlinear", nullptr};
+const std::vector<std::string> choices = {"scale", "linear", "nonlinear"};
 
 // clang-format off
 void usage() {

cmd/mrmath.cpp

@@ -33,19 +33,20 @@
 using namespace MR;
 using namespace App;
 
-const char *operations[] = {"mean",
-                            "median",
-                            "sum",
-                            "product",
-                            "rms",
-                            "norm",
-                            "var",
-                            "std",
-                            "min",
-                            "max",
-                            "absmax", // Maximum of absolute values
-                            "magmax", // Value for which the magnitude is the maximum (i.e. preserves signed-ness)
-                            NULL};
+const std::vector<std::string> operations = {
+    "mean",
+    "median",
+    "sum",
+    "product",
+    "rms",
+    "norm",
+    "var",
+    "std",
+    "min",
+    "max",
+    "absmax", // Maximum of absolute values
+    "magmax"  // Value for which the magnitude is the maximum (i.e. preserves signed-ness)
+};
 
 // clang-format off
 void usage() {

cmd/mrmetric.cpp

@@ -37,10 +37,11 @@
 using namespace MR;
 using namespace App;
 
-const char *interp_choices[] = {"nearest", "linear", "cubic", "sinc", NULL};
 #define DEFAULT_INTERP 1 // linear
-const char *space_choices[] = {"voxel", "image1", "image2", "average", NULL};
 #define DEFAULT_SPACE 0 // voxel
+const std::vector<std::string> interp_choices = {"nearest", "linear", "cubic", "sinc"};
+const std::vector<std::string> space_choices = {"voxel", "image1", "image2", "average"};
+
 
 template <class ValueType>
 inline void
@@ -169,7 +170,7 @@ void evaluate_voxelwise_msq(InType1 &in1,
 }
 
 enum MetricType { MeanSquared, CrossCorrelation };
-const char *metric_choices[] = {"diff", "cc", NULL};
+const std::vector<std::string> metric_choices = {"diff", "cc"};
 
 // clang-format off
 void usage() {

cmd/mrregister.cpp

@@ -39,15 +39,9 @@
 using namespace MR;
 using namespace App;
 
-const char *transformation_choices[] = {"rigid",
-                                        "affine",
-                                        "nonlinear",
-                                        "rigid_affine",
-                                        "rigid_nonlinear",
-                                        "affine_nonlinear",
-                                        "rigid_affine_nonlinear",
-                                        nullptr};
 #define DEFAULT_TRANSFORMATION_TYPE 5 // affine_nonlinear
+const std::vector<std::string> transformation_choices = {
+    "rigid", "affine", "nonlinear", "rigid_affine", "rigid_nonlinear", "affine_nonlinear", "rigid_affine_nonlinear"};
 
 // clang-format off
 const OptionGroup multiContrastOptions =

cmd/mrthreshold.cpp

@@ -28,7 +28,7 @@ using namespace MR;
 using namespace App;
 
 enum class operator_type { LT, LE, GE, GT, UNDEFINED };
-const char *const operator_list[] = {"lt", "le", "ge", "gt", nullptr};
+const std::vector<std::string> operator_list = {"lt", "le", "ge", "gt"};
 
 // clang-format off
 void usage() {

cmd/mrtransform.cpp

@@ -42,9 +42,9 @@
 using namespace MR;
 using namespace App;
 
-const char *interp_choices[] = {"nearest", "linear", "cubic", "sinc", nullptr};
 #define DEFAULT_INTERP 2 // cubic
-const char *modulation_choices[] = {"fod", "jac", nullptr};
+const std::vector<std::string> interp_choices = {"nearest", "linear", "cubic", "sinc"};
+const std::vector<std::string> modulation_choices = {"fod", "jac"};
 
 // clang-format off
 void usage() {

cmd/mtnormalise.cpp

@@ -30,7 +30,7 @@ using namespace App;
 #define DEFAULT_BALANCE_MAXITER_VALUE 7
 #define DEFAULT_POLY_ORDER 3
 
-const char *poly_order_choices[] = {"0", "1", "2", "3", nullptr};
+const std::vector<std::string> poly_order_choices = {"0", "1", "2", "3"};
 
 // clang-format off
 void usage() {

cmd/shbasis.cpp

@@ -30,7 +30,7 @@
 using namespace MR;
 using namespace App;
 
-const char *conversions[] = {"old", "new", "force_oldtonew", "force_newtoold", nullptr};
+const std::vector<std::string> conversions = {"old", "new", "force_oldtonew", "force_newtoold"};
 enum conv_t { NONE, OLD, NEW, FORCE_OLDTONEW, FORCE_NEWTOOLD };
 
 // clang-format off