Correct errors in clang-format disabling for CLI code

.git-blame-ignore-revs

@@ -103,8 +103,9 @@ aad44d847ac48d02bb7f8badf801dbfaa0ccdac0
 #Date:   Thu, 17 Aug 2023 15:36:14 +0100
 #    Apply formatting for C++ using clang-format
 
-0cec87a0e59749d4e14ebf55c288067d29f868f1
-#Author: Robert Smith <robert.smith@florey.edu.au>
-#Date:   Thu Feb 22 01:43:21 2024 +1100
+de4de955cd82065135d15383a639dd7f7373d834
+#Author: MRtrixBot <gitbot@mrtrix.org>
+#Date:   Mon Feb 26 13:38:02 2024 +1100
 #    Disable clang-format for CLI-related code
 #    When clang-format, introduced in #2652, applied its changes to MRtrix3 code relating to the command-line interface (particularly the way that options and their arguments are concatenated through the addition operator), the resulting code was often quite ugly. This commit replaces code relating to CLI configuration (both the usage() function in cmd/*.cpp, and in definitions of options and option groups utilised by multiple commands) with manually formatted code, and includes comment fields to disable further manipulation of that code by clang-format.
+#    This commit is a refactor of 0cec87a0e59749d4e14ebf55c288067d29f868f1 generated as part of #2815, with the changes being to omit other modifications to the command documentation that are not directly related to clang-format (those changes are in the parent commit to this commit: 15e253cf6a0af83a9a0f4f9369a256d01cf90ad8), and to change authorship of the commit.

cmd/dirorder.cpp

@@ -49,6 +49,7 @@ void usage() {
                          " instead of [az el].");
 
 }
+// clang-format on
 
 using value_type = double;
 

cmd/dirstat.cpp

@@ -27,7 +27,7 @@
 using namespace MR;
 using namespace App;
 
-//clang-format off
+// clang-format off
 void usage() {
 
   AUTHOR = "J-Donald Tournier (jdtournier@gmail.com)";

cmd/fixel2peaks.cpp

@@ -42,7 +42,7 @@ void usage() {
     " then the 3-vectors in the output image will be scaled based on the data in that file."
     " If the input is instead the fixel directory,"
     " or the index or directions file,"
-    " then all output 3-vectors will possess unit norm.";
+    " then all output 3-vectors will possess unit norm."
 
   + Fixel::format_description;
 

cmd/fixelcorrespondence.cpp

@@ -28,7 +28,7 @@ using Fixel::index_type;
 
 #define DEFAULT_ANGLE_THRESHOLD 45.0
 
-// clang-format on
+// clang-format off
 void usage() {
 
   AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";

cmd/fixelcrop.cpp

@@ -50,6 +50,7 @@ void usage() {
   + Argument ("output_fixel_directory", "the output directory to store the cropped directions"
                                         " and data files").type_directory_out();
 }
+// clang-format on
 
 void run() {
   const auto in_directory = argument[0];

cmd/fod2fixel.cpp

@@ -38,7 +38,7 @@ using namespace App;
 
 using Fixel::index_type;
 
-//clang-format off
+// clang-format off
 const OptionGroup OutputOptions = OptionGroup ("Metric values for fixel-based sparse output images")
 
   + Option ("afd",

cmd/label2mesh.cpp

@@ -51,8 +51,7 @@ void usage() {
                       " rather than the default Marching Cubes approach");
 
 }
-// coang-format on
-
+// clang-format on
 
 void run() {
 

cmd/mrgrid.cpp

@@ -33,7 +33,7 @@ using namespace App;
 const char *interp_choices[] = {"nearest", "linear", "cubic", "sinc", NULL};
 const char *operation_choices[] = {"regrid", "crop", "pad", NULL};
 
-//clang-format off
+// clang-format off
 void usage() {
 
   AUTHOR = "Max Pietsch (maximilian.pietsch@kcl.ac.uk)"

cmd/peaks2fixel.cpp

@@ -23,7 +23,7 @@
 using namespace MR;
 using namespace App;
 
-// clang-format on
+// clang-format off
 void usage() {
 
   AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
@@ -45,7 +45,7 @@ void usage() {
     + Argument ("path").type_text();
 
 }
-// clang-format off
+// clang-format on
 
 std::vector<Eigen::Vector3d> get(Image<float> &data) {
   data.index(3) = 0;

cmd/shbasis.cpp

@@ -73,7 +73,6 @@ void usage() {
 }
 // clang-format on
 
-
 // Perform a linear regression on the power ratio in each order
 // Omit l=2 - tends to be abnormally small due to non-isotropic brain-wide fibre distribution
 std::pair<float, float> get_regression(const std::vector<float> &ratios) {

cmd/shview.cpp

@@ -48,7 +48,7 @@ void usage() {
   REQUIRES_AT_LEAST_ONE_ARGUMENT = false;
 
 }
-
+// clang-format on
 
 void run() {
   GUI::DWI::Window window(get_options("response").size());

cmd/tckdfc.cpp

@@ -142,7 +142,6 @@ void usage () {
 }
 // clang-format on
 
-
 // This class is similar to Mapping::MapWriter, but doesn't write to a HDD file on close
 // Instead, the one timepoint volume generated during this iteration is written
 //   into the one large buffer that contains the entire TW-dFC time series

cmd/tckgen.cpp

@@ -231,7 +231,7 @@ void usage() {
   + DWI::GradImportOptions();
 
 }
-// clang-format off
+// clang-format on
 
 void run() {
 

cmd/tcksift2.cpp

@@ -139,7 +139,7 @@ void usage() {
   + SIFT2AlgorithmOption;
 
 }
-// clang-format off
+// clang-format on
 
 void run() {
 

cmd/voxel2fixel.cpp

@@ -28,7 +28,7 @@ using namespace App;
 
 using Fixel::index_type;
 
-// clang-format on
+// clang-format off
 void usage() {
 
   AUTHOR = "David Raffelt (david.raffelt@florey.edu.au)";

core/math/stats/glm.cpp

@@ -46,7 +46,7 @@ const char *const column_ones_description =
 
 App::OptionGroup glm_options(const std::string &element_name) {
   using namespace App;
-// clang-format off
+  // clang-format off
   OptionGroup result =
       OptionGroup("Options related to the General Linear Model (GLM)")
       + Option("variance",
@@ -69,7 +69,7 @@ App::OptionGroup glm_options(const std::string &element_name) {
                " (note that the contrast matrix must include an additional column for each use of this option);"
                " the text file provided via this option should contain a file name for each subject").allow_multiple()
         + Argument("path").type_file_in();
-// clang-format on
+  // clang-format on
   return result;
 }
 

core/math/stats/shuffle.cpp

@@ -32,7 +32,7 @@ const char *error_types[] = {"ee", "ise", "both", nullptr};
 App::OptionGroup shuffle_options(const bool include_nonstationarity, const default_type default_skew) {
   using namespace App;
 
-// clang-format off
+  // clang-format off
   OptionGroup result =
       OptionGroup("Options relating to shuffling of data for nonparametric statistical inference")
       + Option("notest",
@@ -90,7 +90,7 @@ App::OptionGroup shuffle_options(const bool include_nonstationarity, const defau
                     " Overrides the -nshuffles_nonstationarity option.")
              + Argument("file").type_file_in();
   }
-// clang-format off
+  // clang-format on
   return result;
 }
 

docs/reference/commands/fixel2peaks.rst

@@ -23,6 +23,9 @@ Description
 
 If a fixel data file is provided as input, then the 3-vectors in the output image will be scaled based on the data in that file. If the input is instead the fixel directory, or the index or directions file, then all output 3-vectors will possess unit norm.
 
+Fixel data are stored utilising the fixel directory format described in the main documentation, which can be found at the following link:  |br|
+https://mrtrix.readthedocs.io/en/3.0.4/fixel_based_analysis/fixel_directory_format.html
+
 Options
 -------
 

src/gui/mrview/tool/connectome/connectome.cpp

@@ -858,6 +858,7 @@ void Connectome::add_commandline_options(MR::App::OptionList &options) {
         + Argument("image").type_image_in()
       + Option("connectome.load", "Load a matrix file into the connectome tool.").allow_multiple()
         + Argument("path").type_file_in();
+  // clang-format on
 }
 
 bool Connectome::process_commandline_option(const MR::App::ParsedOption &opt) {

testing/tools/testing_diff_header.cpp

@@ -34,6 +34,7 @@ void usage() {
   + Option ("keyval", "also test the contents of the key-value entries in the header");
 
 }
+// clang-format on
 
 void run() {
   auto in1 = Header::open(argument[0]);