Resolution of merge of master to dev

Resolution of content merged to dev initially omitted from #3061.
- #2693 (completely omitted)
- #3005 (partial propagation / independent address of some common issues on both branches)
- #3001 (completely omitted)
- #2908 (completely omitted)
- #2955 (completely omitted)
- #2600 (completely omitted)
- #2962 (completely omitted)
- #2935 (completely omitted)
- #2923 (completely omitted)
- #2910 (completely omitted)
- #2638 (completely omitted)
- #2698 (completely omitted)
- #2721 (completely omitted)
- #2794 (completely omitted)
- #2768 (completely omitted; required modification to conform to other dev changes)
- #2713 (residual compilation errors following adf8fdd, including resolution against changes in #2437 on dev.

cpp/cmd/dwi2tensor.cpp

@@ -295,14 +295,14 @@ void run() {
   Header header(dwi);
   header.datatype() = DataType::Float32;
   header.ndim() = 4;
-  DWI::stash_DW_scheme(header, grad);
   PhaseEncoding::clear_scheme(header);
 
   Image<value_type> predict;
   opt = get_options("predicted_signal");
   if (!opt.empty())
     predict = Image<value_type>::create(opt[0][0], header);
 
+  DWI::stash_DW_scheme(header, grad);
   header.size(3) = 6;
   auto dt = Image<value_type>::create(argument[1], header);
 

cpp/cmd/mrcalc.cpp

@@ -992,6 +992,8 @@ void run() {
         ++n;
       else if (opt->is("force") || opt->is("info") || opt->is("debug") || opt->is("quiet"))
         continue;
+      else if (opt->is("config"))
+        n+=2;
 
 #define SECTION 3
 #include "mrcalc.cpp"

cpp/cmd/mrdegibbs.cpp

@@ -51,11 +51,19 @@ void usage() {
       " you should run denoising before this command to not alter the noise structure,"
       " which would impact on dwidenoise's performance."
 
+    + "For best results, any form of filtering performed by the scanner should be disabled,"
+      " whether performed in the image domain or k-space."
+      " This includes elliptic filtering and other filters "
+      " that are often applied to reduce Gibbs ringing artifacts."
+      " While this method can still safely be applied to such data,"
+      " some residual ringing artefacts may still be present in the output."
+
     + "Note that this method is designed to work on images acquired with full k-space coverage."
-      " Running this method on partial Fourier ('half-scan')"
-      " or filtered data may not remove all ringing artefacts."
-      " Users are encouraged to acquired full-Fourier data where possible,"
-      " and disable any form of filtering on the scanner.";
+      " If this method is executed on data acquired with partial Fourier (eg. \"half-scan\") acceleration,"
+      " it may not fully remove all ringing artifacts,"
+      " and you may observe residuals of the original artifact in the partial Fourier direction."
+      " Nonetheless, application of the method is still considered safe and worthwhile."
+      " Users are however encouraged to acquired full-Fourier data where possible.";
 
 
   ARGUMENTS

cpp/cmd/mrgrid.cpp

@@ -150,7 +150,7 @@ void usage() {
                     " to match the specified reference image grid."
                     " This operation ignores differences in image transformation"
                     " between input and reference image.")
-      + Argument ("reference image").type_image_in()
+      + Argument ("reference_image").type_image_in()
 
     + Option ("uniform", "pad or crop the input image"
                          " by a uniform number of voxels on all sides")

cpp/cmd/mrinfo.cpp

@@ -51,7 +51,7 @@ const OptionGroup FieldExportOptions = OptionGroup ("Options for exporting image
 
 void usage() {
 
-  AUTHOR = "J-Donald Tournier ([email protected])"
+  AUTHOR = "J-Donald Tournier ([email protected])"
            " and Robert E. Smith ([email protected])";
 
   SYNOPSIS = "Display image header information,"

cpp/core/adapter/reslice.h

@@ -42,11 +42,21 @@ typename std::enable_if<!std::is_same<value_type, bool>::value && std::is_integr
   return value_type(std::round(sum * norm));
 }
 
-template <typename value_type>
-typename std::enable_if<std::is_floating_point<value_type>::value, value_type>::type inline normalise(
-    const default_type sum, const default_type norm) {
-  return (sum * norm);
+// Standard implementation for floating point (either real or complex)
+template <typename value_type, typename summing_type>
+typename std::enable_if<!std::is_same<value_type, bool>::value && !std::is_integral<value_type>::value, value_type>::type
+inline normalise (const summing_type sum, const default_type norm) {
+  return value_type (sum * norm);
 }
+
+// If summing complex numbers, use double precision complex;
+//   otherwise, use double precision real
+template <typename value_type> struct summing_type {
+  using type = double;
+};
+template <typename value_type> struct summing_type<is_complex<value_type>> {
+  using type = std::complex<double>;
+};
 } // namespace
 
 extern const transform_type NoTransform;
@@ -175,7 +185,7 @@ class Reslice : public ImageBase<Reslice<Interpolator, ImageType>, typename Imag
     using namespace Eigen;
     if (oversampling) {
       Vector3d d(x[0] + from[0], x[1] + from[1], x[2] + from[2]);
-      default_type sum(0.0);
+      typename summing_type<value_type>::type sum(0);
       Vector3d s;
       for (uint32_t z = 0; z < OS[2]; ++z) {
         s[2] = d[2] + z * inc[2];

cpp/core/app.cpp

@@ -187,6 +187,8 @@ std::string underline(const std::string &text, bool ignore_whitespace = false) {
 
 const char *argtype_description(ArgType type) {
   switch (type) {
+  case Boolean:
+    return ("boolean");
   case Integer:
     return ("integer");
   case Float:
@@ -450,6 +452,9 @@ std::string Argument::usage() const {
   case Undefined:
     assert(0);
     break;
+  case Boolean:
+    stream << "BOOL";
+    break;
   case Integer: {
     const auto int_range = std::get<IntRange>(limits);
     stream << "INT " << int_range.min << " " << int_range.max;

cpp/core/dwi/fmls.cpp

@@ -78,7 +78,7 @@ void load_fmls_thresholds(Segmenter &segmenter) {
     }
   }
 
-  opt = get_options("fmls_merge_ratio");
+  opt = get_options("fmls_lobe_merge_ratio");
   if (!opt.empty())
     segmenter.set_lobe_merge_ratio(default_type(opt[0][0]));
 }

cpp/core/file/dicom/select_cmdline.cpp

@@ -100,7 +100,7 @@ std::vector<std::shared_ptr<Series>> select_cmdline(const Tree &tree) {
       }
       std::cerr << "? ";
       std::cin >> buf;
-      if (buf[0] == 'q' || buf[0] == 'Q')
+      if (!std::cin || buf[0] == 'q' || buf[0] == 'Q')
         throw CancelException();
       if (isdigit(buf[0])) {
         int n = to<int>(buf) - 1;
@@ -138,7 +138,7 @@ std::vector<std::shared_ptr<Series>> select_cmdline(const Tree &tree) {
       }
       std::cerr << "? ";
       std::cin >> buf;
-      if (buf[0] == 'q' || buf[0] == 'Q')
+      if (!std::cin || buf[0] == 'q' || buf[0] == 'Q')
         throw CancelException();
       if (isdigit(buf[0])) {
         int n = to<int>(buf) - 1;
@@ -179,7 +179,7 @@ std::vector<std::shared_ptr<Series>> select_cmdline(const Tree &tree) {
       }
       std::cerr << "? ";
       std::cin >> buf;
-      if (buf[0] == 'q' || buf[0] == 'Q')
+      if (!std::cin || buf[0] == 'q' || buf[0] == 'Q')
         throw CancelException();
       if (isdigit(buf[0])) {
         std::vector<uint32_t> seq;

cpp/core/file/mmap.cpp

@@ -109,7 +109,8 @@ MMap::MMap(const Entry &entry, bool readwrite, bool preload, int64_t mapped_size
 
     if (fsbuf.f_type == 0xff534d42 /* CIFS */ || fsbuf.f_type == 0x6969 /* NFS */ ||
         fsbuf.f_type == 0x65735546 /* FUSE */ || fsbuf.f_type == 0x517b /* SMB */ ||
-        fsbuf.f_type == 0x47504653 /* GPFS */ || fsbuf.f_type == 0xbd00bd0 /* LUSTRE */
+        fsbuf.f_type == 0x47504653 /* GPFS */ || fsbuf.f_type == 0xbd00bd0 /* LUSTRE */ ||
+        fsbuf.f_type == 0x1021997 /* 9P (WSL) */
 
 #ifdef MRTRIX_MACOSX
         || fsbuf.f_type == 0x0017                                          /* OSXFUSE */

cpp/core/file/png.cpp

@@ -309,7 +309,6 @@ void Writer::save(uint8_t *data) {
       row_pointers[row] = to_write + row * row_bytes;
     png_write_image(png_ptr, row_pointers.get());
     png_write_end(png_ptr, info_ptr);
-    delete [] row_pointers;
   };
 
   if (data_type == DataType::UInt8 || data_type == DataType::UInt16BE) {

cpp/core/file/png.h

@@ -87,9 +87,11 @@ template <typename T>
 void Writer::fill(uint8_t *in_ptr, uint8_t *out_ptr, const DataType data_type, const size_t num_elements) {
   auto fetch_func = __set_fetch_function<default_type>(data_type);
   for (size_t i = 0; i != num_elements; ++i)
-    Raw::store_BE<T> (std::min (default_type(std::numeric_limits<T>::max()),                                //
-                                std::max (0.0, std::round(multiplier * fetch_func (in_ptr, i, 0.0, 1.0)))), //
-                      out_ptr, i);                                                                          //
+    Raw::store_BE<T> (std::min (default_type(std::numeric_limits<T>::max()),                      //
+                                std::max (0.0, std::round(multiplier * fetch_func (in_ptr, 0)))), //
+                      out_ptr, i);                                                                //
+    in_ptr += data_type.bytes();
+    out_ptr += sizeof(T);
 };
 
 } // namespace MR::File::PNG

cpp/core/formats/pipe.cpp

@@ -54,7 +54,8 @@ bool Pipe::check(Header &H, size_t num_axes) const {
     return false;
 
   if (isatty(STDOUT_FILENO))
-    throw Exception("attempt to pipe image to standard output (this will leave temporary files behind)");
+    throw Exception ("cannot create output piped image: "                                //
+                     "no command connected at other end of pipe to receive that image"); //
 
   H.name() = File::create_tempfile(0, "mif");
 

cpp/core/formats/png.cpp

@@ -160,7 +160,6 @@ bool PNG::check(Header &H, size_t num_axes) const {
       axis_to_zero = 1;
     } else if (H.size(0) == 1) {
       axis_to_zero = 0;
-      width_axis = 1;
     } else {
       // If image is 3D, and all three axes have size greater than one, and we
       //   haven't used the square-bracket notation, we can't export genuine 3D data
@@ -184,8 +183,6 @@ bool PNG::check(Header &H, size_t num_axes) const {
     if (axis < 0)
       throw Exception("Cannot export 4D image to PNG format if all three spatial axes have size greater than 1 and "
                       "square-bracket notation is not used");
-    if (!axis_to_zero)
-      width_axis = 1;
     break;
   default:
     throw Exception("Cannot generate PNG file(s) from image with more than 4 axes");

cpp/core/progressbar.cpp

@@ -155,7 +155,7 @@ bool ProgressBar::set_update_method() {
     // unable to determine nature of stderr; assuming socket
     stderr_to_file = false;
   else
-    stderr_to_file = S_ISREG(buf.st_mode);
+    stderr_to_file = S_ISREG(buf.st_mode) || S_ISFIFO(buf.st_mode);
 
   if (stderr_to_file) {
     ProgressBar::display_func = display_func_redirect;

docs/reference/commands/dirrotate.rst

@@ -60,7 +60,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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

docs/reference/commands/dwi2mask.rst

@@ -185,7 +185,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Ricardo Rios ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -276,7 +276,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -390,7 +390,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -485,7 +485,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -584,7 +584,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Warda Syeda ([email protected]) and Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -675,7 +675,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -761,7 +761,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -852,7 +852,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Warda Syeda ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -960,7 +960,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected]) and Arshiya Sangchooli ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -1064,7 +1064,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Ruobing Chen ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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
@@ -1162,7 +1162,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Warda Syeda ([email protected]) and Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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

docs/reference/commands/dwibiascorrect.rst

@@ -392,7 +392,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected]) and Arshiya Sangchooli ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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

docs/reference/commands/dwibiasnormmask.rst

@@ -115,7 +115,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected]) and Arshiya Sangchooli ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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

docs/reference/commands/dwinormalise.rst

@@ -354,7 +354,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Robert E. Smith ([email protected]) and Arshiya Sangchooli ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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

docs/reference/commands/mask2glass.rst

@@ -73,7 +73,7 @@ Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch
 
 **Author:** Remika Mito ([email protected]) and Robert E. Smith ([email protected])
 
-**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+**Copyright:** Copyright (c) 2008-2025 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

docs/reference/commands/mrdegibbs.rst

@@ -27,7 +27,7 @@ By default, the original 2D slice-wise version is used. If the -mode 3d option i
 
 This command is designed to run on data directly after it has been reconstructed by the scanner, before any interpolation of any kind has taken place. You should not run this command after any form of motion correction (e.g. not after dwifslpreproc). Similarly, if you intend running dwidenoise, you should run denoising before this command to not alter the noise structure, which would impact on dwidenoise's performance.
 
-For best results, any form of filtering performed by the scanner should be disabled, whether performed in the image domain or k-space. This includes elliptic filtering and other filters that are often applied to reduce Gibbs ringing artifacts. While this method can still safely be applied to such data, some residual ringing artefacts may still be present in the output.
+For best results, any form of filtering performed by the scanner should be disabled, whether performed in the image domain or k-space. This includes elliptic filtering and other filters  that are often applied to reduce Gibbs ringing artifacts. While this method can still safely be applied to such data, some residual ringing artefacts may still be present in the output.
 
 Note that this method is designed to work on images acquired with full k-space coverage. If this method is executed on data acquired with partial Fourier (eg. "half-scan") acceleration, it may not fully remove all ringing artifacts, and you may observe residuals of the original artifact in the partial Fourier direction. Nonetheless, application of the method is still considered safe and worthwhile. Users are however encouraged to acquired full-Fourier data where possible.