Restore compilation following merging master to dev ##3255

In particular this includes resolving #3215 and #2755.

Author: Lestropie

cpp/core/algo/threaded_loop.h

@@ -337,7 +337,10 @@ template <class OuterLoopType> struct ThreadedLoopRunOuter {
     };
 
     MutexProtected<Shared> shared = {iterator, outer_loop(iterator)};
-
+    auto get_iterator = [](MutexProtected<Shared> &shared) {
+      auto guard = shared.lock();
+      return guard->iterator;
+    };
     struct PerThread {
       MutexProtected<Shared> &shared;
       Iterator pos;
@@ -351,7 +354,7 @@ template <class OuterLoopType> struct ThreadedLoopRunOuter {
         while (shared.lock()->next(pos))
           func(pos);
       }
-    } loop_thread = {shared, shared.iterator, functor};
+    } loop_thread = {shared, get_iterator(shared), functor};
 
     auto threads = Thread::run(Thread::multi(loop_thread), "loop threads");
 

cpp/core/dwi/tractography/SIFT/output.h

@@ -16,6 +16,8 @@
 
 #pragma once
 
+#include <vector>
+
 #include "header.h"
 #include "image.h"
 
@@ -204,7 +206,7 @@ template <class Fixel> void ModelBase<Fixel>::output_scatterplot(std::string_vie
   out << "# " << App::command_history_string << "\n";
   const default_type current_mu = mu();
   out << "#Fibre density,Track density (unscaled),Track density (scaled),Weight,\n";
-  typename vector<Fixel>::const_iterator i = fixels.begin(); // Skip first null fixel in DWI::Fixel_map<>
+  typename std::vector<Fixel>::const_iterator i = fixels.begin(); // Skip first null fixel in DWI::Fixel_map<>
   for (++i; i != fixels.end(); ++i)
     out << str(i->get_FOD()) << "," << str(i->get_TD()) << "," << str(i->get_TD() * current_mu) << ","
         << str(i->get_weight()) << ",\n";

cpp/core/dwi/tractography/SIFT2/tckfactor.cpp

@@ -14,6 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
+#include <vector>
+
 #include "header.h"
 #include "image.h"
 
@@ -58,7 +60,7 @@ void TckFactor::remove_excluded_fixels(const float min_td_frac) {
   const double cf = calc_cost_function();
   SIFT::track_t excluded_count = 0, zero_TD_count = 0;
   double zero_TD_cf_sum = 0.0, excluded_cf_sum = 0.0;
-  vector<Fixel>::iterator i = fixels.begin(); // SKip first fixel, which is an intentional null in DWI::Fixel_map<>
+  std::vector<Fixel>::iterator i = fixels.begin(); // SKip first fixel, which is an intentional null in DWI::Fixel_map<>
   for (++i; i != fixels.end(); ++i) {
     if (!i->get_orig_TD()) {
       ++zero_TD_count;

cpp/gui/mrview/mode/slice.cpp

@@ -16,6 +16,7 @@
 
 #include "mrview/mode/slice.h"
 
+#include "mrview/tool/roi_editor/item.h"
 #include "opengl/transformation.h"
 
 namespace MR::GUI::MRView::Mode {

cpp/gui/mrview/tool/fixel/base_fixel.h

@@ -18,6 +18,7 @@
 
 #include <cstdint>
 #include <unordered_map>
+#include <vector>
 
 #include "header.h"
 #include "image.h"
@@ -264,15 +265,14 @@ class BaseFixel : public Displayable {
   GL::VertexBuffer regular_grid_threshold_buffer;
 
   // Index buffer for rendering slabs
-  vector<uint32_t> element_indices;
+  std::vector<uint32_t> element_indices;
 
   float voxel_size_length_multipler;
   float user_line_length_multiplier;
   float line_thickness;
 };
 
 // Wrapper to generically store fixel data
-
 template <typename ImageType> class FixelType : public BaseFixel {
 public:
   FixelType(std::string_view filename, Fixel &fixel_tool)
@@ -289,4 +289,5 @@ template <typename ImageType> class FixelType : public BaseFixel {
 
 using FixelImage4DType = MR::Image<float>;
 using FixelIndexImageType = MR::Image<uint32_t>;
+
 } // namespace MR::GUI::MRView::Tool

cpp/gui/mrview/tool/tractography/tractogram.cpp

@@ -909,7 +909,7 @@ void Tractogram::load_tracks_onto_GPU(std::vector<Eigen::Vector3f> &buffer,
   num_tracks_per_buffer.push_back(tck_count);
 
   // Build an index buffer for this chunk of tracks
-  vector<uint32_t> chunk_indices;
+  std::vector<uint32_t> chunk_indices;
   for (size_t t = 0; t < sizes.size(); ++t) {
     const GLint start = starts[t];
     const GLint n = sizes[t];

cpp/gui/mrview/tool/tractography/tractogram.h

@@ -16,6 +16,8 @@
 
 #pragma once
 
+#include <vector>
+
 #include "dwi/tractography/properties.h"
 #include "mrview/displayable.h"
 #include "mrview/tool/tractography/tractography.h"
@@ -141,8 +143,8 @@ class Tractogram : public Displayable {
   std::vector<size_t> num_tracks_per_buffer;
 
   // EBOs and indices for chunks of tracks
-  vector<GLuint> element_buffers;
-  vector<GLsizei> element_counts;
+  std::vector<GLuint> element_buffers;
+  std::vector<GLsizei> element_counts;
 
   GLint sample_stride;
   bool vao_dirty;