Merge remote-tracking branch 'origin/dev' into mrmath_memleak_fix

Conflicts:
	core/misc/voxel2vector.h

Resolves #2781 with #2764.

.github/workflows/checks.yml

@@ -54,10 +54,10 @@ jobs:
       run: cmake --build build
 
     - name: unit tests
-      run: cd build && ctest -R unit
+      run: cd build && ctest -R unit --output-on-failure
 
     - name: binary tests
-      run: cd build && ctest -R bin
+      run: cd build && ctest -R bin --output-on-failure
 
   linux-gcc-build:
 
@@ -103,10 +103,10 @@ jobs:
       run: cmake --build build
 
     - name: unit tests
-      run: cd build && ctest -R unit
+      run: cd build && ctest -R unit --output-on-failure
 
     - name: binary tests
-      run: cd build && ctest -R bin
+      run: cd build && ctest -R bin --output-on-failure
 
   macos-build:
 
@@ -154,10 +154,10 @@ jobs:
       run: cmake --build build
 
     - name: unit tests
-      run: cd build && ctest -R unit
+      run: cd build && ctest -R unit --output-on-failure
 
     - name: binary tests
-      run: cd build && ctest -R bin
+      run: cd build && ctest -R bin --output-on-failure
 
     - name: check command documentation
       run: ./docs/generate_user_docs.sh --build-dir ./build && git diff --exit-code docs/
@@ -224,10 +224,10 @@ jobs:
         run: cmake --build build
 
       - name: unit tests
-        run: cd build && ctest -R unit
+        run: cd build && ctest -R unit --output-on-failure
 
       - name: binary tests
-        run: cd build && ctest -R bin
+        run: cd build && ctest -R bin --output-on-failure
 
   secondary-checks:
     runs-on: ubuntu-latest

.github/workflows/clang-tidy.yml

@@ -8,11 +8,12 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - uses: ZedThree/clang-tidy-review@v0.14.0
+    - uses: ZedThree/clang-tidy-review@v0.17.0
       id: review
       with:
         apt_packages: g++,libqt5opengl5-dev,libqt5svg5-dev,libglvnd-dev,libeigen3-dev,zlib1g-dev,libfftw3-dev,ninja-build
         cmake_command: cmake . -DCMAKE_EXPORT_COMPILE_COMMANDS=on
+        config_file: ${{ github.workspace }}/.clang-tidy
 
-    - uses: ZedThree/clang-tidy-review/upload@v0.14.0
+    - uses: ZedThree/clang-tidy-review/upload@v0.17.0
       id: upload-review

check_syntax

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2008-2023 the MRtrix3 contributors.
+# Copyright (c) 2008-2024 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -64,20 +64,6 @@ for f in $(find cmd core src -type f -name '*.h' -o -name '*.cpp' | $grep -v '_m
 # remove quoted strings:
   cat .check_syntax2.tmp | perl -pe 's/(")(\\"|.)*?"//g' > .check_syntax.tmp
 
-# detect any instances of std::vector:
-  res="$res"$(
-    cat .check_syntax.tmp | \
-# match for the parts we're interested in and output just the bits that match:
-    $grep -Po '(?<!::)std::vector\b'
-  )
-
-
-# detect any instances of std::make_shared:
-  res="$res"$(
-    cat .check_syntax.tmp | \
-# match for the parts we're interested in and output just the bits that match:
-    $grep -Po '(?<!::)std::make_shared\b'
-  )
 
 # detect any instances of "using namespace std;":
   res="$res"$(
@@ -126,8 +112,6 @@ else
   echo "" >> $LOG
   echo "Please check the following syntax requirements:
   - Add MEMALIGN() or NOMEMALIGN macro to any class declarations identified above;
-  - Replace all occurrences of std::vector<> with MR::vector<> (or just vector<>);
-  - Avoid use of std::make_shared();
   - Replace all instances of std::abs() with MR::abs() (or just abs());
   - Replace all instances of %zu in print() calls with PRI_SIZET." >> $LOG
   exit 1

clang-format-all

@@ -1,6 +1,6 @@
 #!/usr/env/python3
 
-# Copyright (c) 2008-2023 the MRtrix3 contributors.
+# Copyright (c) 2008-2024 the MRtrix3 contributors.
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5tt2gmwmi.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5tt2vis.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5ttcheck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/5ttedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/afdconnectivity.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -215,7 +215,7 @@ value_type AFDConnectivity::get(const std::string &path) {
     if (all_fixels) {
 
       // All fixels contribute to the result
-      for (vector<AFDConnFixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i) {
+      for (std::vector<AFDConnFixel>::const_iterator i = fixels.begin(); i != fixels.end(); ++i) {
         if (i->is_selected())
           sum_volumes += i->get_FOD();
       }

cmd/amp2response.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -101,8 +101,8 @@ Eigen::Matrix<default_type, 3, 3> gen_rotation_matrix(const Eigen::Vector3d &dir
   return R;
 }
 
-vector<size_t> all_volumes(const size_t num) {
-  vector<size_t> result(num);
+std::vector<size_t> all_volumes(const size_t num) {
+  std::vector<size_t> result(num);
   for (size_t i = 0; i != num; ++i)
     result[i] = i;
   return result;
@@ -112,7 +112,7 @@ class Accumulator {
 public:
   class Shared {
   public:
-    Shared(int lmax, const vector<size_t> &volumes, const Eigen::MatrixXd &dirs)
+    Shared(int lmax, const std::vector<size_t> &volumes, const Eigen::MatrixXd &dirs)
         : lmax(lmax),
           dirs(dirs),
           volumes(volumes),
@@ -122,7 +122,7 @@ class Accumulator {
 
     const int lmax;
     const Eigen::MatrixXd &dirs;
-    const vector<size_t> &volumes;
+    const std::vector<size_t> &volumes;
     Eigen::MatrixXd M;
     Eigen::VectorXd b;
     size_t count;
@@ -196,8 +196,8 @@ void run() {
   auto header = Header::open(argument[0]);
 
   // May be dealing with multiple shells
-  vector<Eigen::MatrixXd> dirs_azel;
-  vector<vector<size_t>> volumes;
+  std::vector<Eigen::MatrixXd> dirs_azel;
+  std::vector<std::vector<size_t>> volumes;
   std::unique_ptr<DWI::Shells> shells;
 
   auto opt = get_options("directions");
@@ -207,7 +207,7 @@ void run() {
   } else {
     auto hit = header.keyval().find("directions");
     if (hit != header.keyval().end()) {
-      vector<default_type> dir_vector;
+      std::vector<default_type> dir_vector;
       for (auto line : split_lines(hit->second)) {
         auto v = parse_floats(line);
         dir_vector.insert(dir_vector.end(), v.begin(), v.end());
@@ -230,7 +230,7 @@ void run() {
     }
   }
 
-  vector<uint32_t> lmax;
+  std::vector<uint32_t> lmax;
   uint32_t max_lmax = 0;
   opt = get_options("lmax");
   if (get_options("isotropic").size()) {

cmd/amp2sh.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -81,14 +81,14 @@ class Amp2SHCommon {
 public:
   template <class MatrixType>
   Amp2SHCommon(const MatrixType &sh2amp,
-               const vector<size_t> &bzeros,
-               const vector<size_t> &dwis,
+               const std::vector<size_t> &bzeros,
+               const std::vector<size_t> &dwis,
                bool normalise_to_bzero)
       : sh2amp(sh2amp), amp2sh(Math::pinv(sh2amp)), bzeros(bzeros), dwis(dwis), normalise(normalise_to_bzero) {}
 
   Eigen::MatrixXd sh2amp, amp2sh;
-  const vector<size_t> &bzeros;
-  const vector<size_t> &dwis;
+  const std::vector<size_t> &bzeros;
+  const std::vector<size_t> &dwis;
   bool normalise;
 };
 
@@ -175,7 +175,7 @@ void run() {
   auto amp = Image<value_type>::open(argument[0]).with_direct_io(3);
   Header header(amp);
 
-  vector<size_t> bzeros, dwis;
+  std::vector<size_t> bzeros, dwis;
   Eigen::MatrixXd dirs;
   auto opt = get_options("directions");
   if (opt.size()) {
@@ -185,7 +185,7 @@ void run() {
   } else {
     auto hit = header.keyval().find("directions");
     if (hit != header.keyval().end()) {
-      vector<default_type> dir_vector;
+      std::vector<default_type> dir_vector;
       for (auto line : split_lines(hit->second)) {
         auto v = parse_floats(line);
         dir_vector.insert(dir_vector.end(), v.begin(), v.end());

cmd/connectome2tck.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -158,9 +158,9 @@ void run() {
   Tractography::Properties properties;
   Tractography::Reader<float> reader(argument[0], properties);
 
-  vector<vector<node_t>> assignments_lists;
+  std::vector<std::vector<node_t>> assignments_lists;
   assignments_lists.reserve(to<size_t>(properties["count"]));
-  vector<NodePair> assignments_pairs;
+  std::vector<NodePair> assignments_pairs;
   bool nonpair_found = false;
   node_t max_node_index = 0;
   {
@@ -172,7 +172,7 @@ void run() {
       if (line.empty())
         continue;
       std::stringstream line_stream(line);
-      vector<node_t> nodes;
+      std::vector<node_t> nodes;
       while (1) {
         node_t n;
         line_stream >> n;
@@ -216,7 +216,7 @@ void run() {
   const bool keep_self = get_options("keep_self").size();
 
   // Get the list of nodes of interest
-  vector<node_t> nodes;
+  std::vector<node_t> nodes;
   opt = get_options("nodes");
   bool manual_node_list = false;
   if (opt.size()) {
@@ -256,8 +256,8 @@ void run() {
     // Load the node image, get the centres of mass
     // Generate exemplars - these can _only_ be done per edge, and requires a mutex per edge to multi-thread
     auto image = Image<node_t>::open(opt[0][0]);
-    vector<Eigen::Vector3f> COMs(max_node_index + 1, Eigen::Vector3f(0.0f, 0.0f, 0.0f));
-    vector<size_t> volumes(max_node_index + 1, 0);
+    std::vector<Eigen::Vector3f> COMs(max_node_index + 1, Eigen::Vector3f(0.0f, 0.0f, 0.0f));
+    std::vector<size_t> volumes(max_node_index + 1, 0);
     for (auto i = Loop()(image); i; ++i) {
       const node_t index = image.value();
       if (index) {
@@ -344,7 +344,7 @@ void run() {
       } else {
         // For each node in the list, write one file for an exemplar to every other node
         ProgressBar progress("writing exemplars to files", nodes.size() * COMs.size());
-        for (vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
+        for (std::vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
           for (size_t i = first_node; i != COMs.size(); ++i) {
             generator.write(*n,
                             i,
@@ -356,7 +356,7 @@ void run() {
       }
     } else if (file_format == 1) { // One file per node
       ProgressBar progress("writing exemplars to files", nodes.size());
-      for (vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
+      for (std::vector<node_t>::const_iterator n = nodes.begin(); n != nodes.end(); ++n) {
         generator.write(
             *n, prefix + str(*n) + ".tck", weights_prefix.size() ? (weights_prefix + str(*n) + ".csv") : "");
         ++progress;
@@ -399,7 +399,7 @@ void run() {
       INFO("A total of " + str(writer.file_count()) + " output track files will be generated (one for each edge)");
       break;
     case 1: // One file per node
-      for (vector<node_t>::const_iterator i = nodes.begin(); i != nodes.end(); ++i)
+      for (std::vector<node_t>::const_iterator i = nodes.begin(); i != nodes.end(); ++i)
         writer.add(*i, prefix + str(*i) + ".tck", weights_prefix.size() ? (weights_prefix + str(*i) + ".csv") : "");
       INFO("A total of " + str(writer.file_count()) + " output track files will be generated (one for each node)");
       break;

cmd/connectomeedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this

cmd/connectomestats.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -210,7 +210,7 @@ void run() {
 
   // Before validating the contrast matrix, we first need to see if there are any
   //   additional design matrix columns coming from edge-wise subject data
-  vector<CohortDataImport> extra_columns;
+  std::vector<CohortDataImport> extra_columns;
   bool nans_in_columns = false;
   auto opt = get_options("column");
   for (size_t i = 0; i != opt.size(); ++i) {
@@ -236,7 +236,7 @@ void run() {
     CONSOLE("Number of variance groups: " + str(num_vgs));
 
   // Load hypotheses
-  const vector<Hypothesis> hypotheses = Math::Stats::GLM::load_hypotheses(argument[3]);
+  const std::vector<Hypothesis> hypotheses = Math::Stats::GLM::load_hypotheses(argument[3]);
   const index_type num_hypotheses = hypotheses.size();
   if (hypotheses[0].cols() != num_factors)
     throw Exception(

cmd/dcmedit.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -82,8 +82,8 @@ inline uint16_t read_hex(const std::string &m) {
 }
 
 void run() {
-  vector<Tag> tags;
-  vector<uint16_t> VRs;
+  std::vector<Tag> tags;
+  std::vector<uint16_t> VRs;
 
   auto opt = get_options("anonymise");
   if (opt.size()) {

cmd/dcminfo.cpp

@@ -1,4 +1,4 @@
-/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -62,7 +62,7 @@ void run() {
   if (opt.size()) {
     std::istringstream hex;
 
-    vector<Tag> tags(opt.size());
+    std::vector<Tag> tags(opt.size());
     for (size_t n = 0; n < opt.size(); ++n) {
       tags[n].group = read_hex(opt[n][0]);
       tags[n].element = read_hex(opt[n][1]);