Merge 3.0.5 into dev

.github/workflows/package-linux-anaconda.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
 
     - name: install conda-build # and anaconda-client
-      run: $CONDA/bin/conda install -y conda-build #anaconda-client
+      run: $CONDA/bin/conda install -c conda-forge -y conda-build #anaconda-client
 
     - name: fetch recipe
       run: |
@@ -28,6 +28,6 @@ jobs:
     - name: Upload package to GitHub Release
       uses: AButler/[email protected]
       with:
-        files: '*.tar.bz2'
+        files: '*.conda*'
         repo-token: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/package-macos-anaconda.yml

@@ -6,33 +6,34 @@ on:
 
 jobs:
   package:
-
     runs-on: macos-latest
 
     steps:
-
-    - name: fetch MacOSX 10.11 SDK
-      run: curl -L https://github.com/phracker/MacOSX-SDKs/releases/download/MacOSX10.11.sdk/MacOSX10.11.sdk.tar.xz | sudo tar xf - -C /opt/
-
-    - name: install conda-build # and anaconda-client
-      run: sudo $CONDA/bin/conda install -y conda-build # anaconda-client
-
-    - name: fetch recipe
-      run: |
-        git clone https://github.com/MRtrix3/conda-build.git
-        mv conda-build/* .
-        { echo "CONDA_BUILD_SYSROOT:"; echo "  - /opt/MacOSX10.11.sdk        # [osx]"; } > conda_build_config.yaml
-
-    - name: build package
-      run: sudo CONDA="$CONDA" ./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%/*} conda-macos
-
-#    - name: upload package
-#      run: $CONDA/bin/anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u MRtrix3 $(sudo $CONDA/bin/conda build conda-build/ --output)
-
-    - name: Upload package to GitHub Release
-      uses: AButler/[email protected]
-      with:
-        files: '*.tar.bz2'
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-
-
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+
+      - name: Install conda-build
+        run: conda install -c conda-forge -y conda-build
+
+      - name: fetch MacOSX 10.11 SDK
+        run: curl -L https://github.com/phracker/MacOSX-SDKs/releases/download/MacOSX10.11.sdk/MacOSX10.11.sdk.tar.xz | sudo tar xf - -C /opt/
+
+      - name: fetch recipe
+        run: |
+          git clone https://github.com/MRtrix3/conda-build.git
+          mv conda-build/* .
+          { echo "CONDA_BUILD_SYSROOT:"; echo "  - /opt/MacOSX10.11.sdk        # [osx]"; } > conda_build_config.yaml
+
+      - name: build package
+        run: CONDA="$CONDA" ./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%/*} conda-macos
+
+      #    - name: upload package
+      #      run: $CONDA/bin/anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u MRtrix3 $(sudo $CONDA/bin/conda build conda-build/ --output)
+
+      - name: Upload package to GitHub Release
+        uses: AButler/[email protected]
+        with:
+          files: "*.conda*"
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/package-macos-native.yml

@@ -11,11 +11,16 @@ jobs:
 
     steps:
 
+    - name: Symlink Python3
+      run: |
+        mkdir -p python_dir
+        ln -s $(which python3) python_dir/python
+
     - name: fetch recipe
       run: git clone https://github.com/MRtrix3/macos-installer.git
 
     - name: build packages
-      run: ./build ${GITHUB_REF#refs/*/}
+      run: ./build ${GITHUB_REF#refs/*/} 5.15.16 ${{ github.workspace }}/python_dir
       working-directory: ./macos-installer
 
     - name: Upload package to GitHub Release

.github/workflows/package-windows-msys2.yml

@@ -4,37 +4,45 @@ on:
   release:
     types: [created]
 
-
 jobs:
   package:
-
     runs-on: windows-latest
+    defaults:
+      run:
+        shell: msys2 {0}
 
     env:
-      MSYSTEM: MINGW64
       MSYSCON: defterm
       CHERE_INVOKING: enabled_from_arguments
       MSYS2_NOSTART: yes
+      MINGW_PACKAGE_PREFIX: mingw-w64-x86_64
 
     steps:
-
-    - name: fetch and install MSYS2
-      run: bash -c 'curl -sL https://github.com/MRtrix3/MinGW/releases/download/1.0/msys2.tar.{0,1} | tar xf -'
-
-    - name: run qtbinpatcher
-      shell: cmd
-      run: msys64\msys2_shell.cmd -c "qtbinpatcher --qt-dir=$(dirname $(which qmake))"
-
-    - name: fetch PKGBUILD
-      shell: cmd
-      run: msys64\msys2_shell.cmd -c "git clone https://github.com/MRtrix3/MinGW.git && mv MinGW/* ."
-
-    - name: run makepkg
-      shell: cmd
-      run: msys64\msys2_shell.cmd -c "./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%%/*}"
-
-    - name: Upload package to GitHub Release
-      uses: AButler/[email protected]
-      with:
-        files: '*.tar.xz'
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: msys2/setup-msys2@v2
+        with:
+          msystem: MINGW64
+          install: |
+            git
+            pkg-config
+            python
+            ${{env.MINGW_PACKAGE_PREFIX}}-bc
+            ${{env.MINGW_PACKAGE_PREFIX}}-diffutils
+            ${{env.MINGW_PACKAGE_PREFIX}}-eigen3
+            ${{env.MINGW_PACKAGE_PREFIX}}-fftw
+            ${{env.MINGW_PACKAGE_PREFIX}}-gcc
+            ${{env.MINGW_PACKAGE_PREFIX}}-libtiff
+            ${{env.MINGW_PACKAGE_PREFIX}}-qt5-base
+            ${{env.MINGW_PACKAGE_PREFIX}}-qt5-svg
+            ${{env.MINGW_PACKAGE_PREFIX}}-zlib
+
+      - name: fetch PKGBUILD
+        run: git clone https://github.com/MRtrix3/MinGW.git && mv MinGW/* .
+
+      - name: run makepkg
+        run: LINKFLAGS=-lopengl32 ./run.sh ${GITHUB_REF#refs/*/} ${GITHUB_REPOSITORY%%/*}
+
+      - name: Upload package to GitHub Release
+        uses: AButler/[email protected]
+        with:
+          files: "*.tar.zst"
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 
 set(CMAKE_OSX_DEPLOYMENT_TARGET 11.00 CACHE STRING "")
-project(mrtrix3 LANGUAGES CXX VERSION 3.0.4)
+project(mrtrix3 LANGUAGES CXX VERSION 3.0.5)
 
 if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
     message(WARNING "It is recommended to use the Ninja generator to build MRtrix3. "

Dockerfile

@@ -22,6 +22,7 @@ RUN apt-get -qq update \
         libqt5opengl5-dev \
         libqt5svg5-dev \
         libtiff5-dev \
+        python3 \
         qtbase5-dev \
         zlib1g-dev \
     && rm -rf /var/lib/apt/lists/*

cpp/cmd/amp2sh.cpp

@@ -21,7 +21,7 @@
 #include "file/matrix.h"
 #include "image.h"
 #include "math/SH.h"
-#include "phase_encoding.h"
+#include "metadata/phase_encoding.h"
 #include "progressbar.h"
 
 using namespace MR;
@@ -183,8 +183,9 @@ class Amp2SH {
 };
 
 void run() {
-  auto amp = Image<value_type>::open(argument[0]).with_direct_io(3);
-  Header header(amp);
+  Header header_in(Header::open(argument[0]));
+  Header header_out(header_in);
+  header_out.datatype() = DataType::Float32;
 
   std::vector<size_t> bzeros, dwis;
   Eigen::MatrixXd dirs;
@@ -194,8 +195,8 @@ void run() {
     if (dirs.cols() == 3)
       dirs = Math::Sphere::cartesian2spherical(dirs);
   } else {
-    auto hit = header.keyval().find("directions");
-    if (hit != header.keyval().end()) {
+    auto hit = header_in.keyval().find("directions");
+    if (hit != header_in.keyval().end()) {
       std::vector<default_type> dir_vector;
       for (auto line : split_lines(hit->second)) {
         auto v = parse_floats(line);
@@ -206,32 +207,33 @@ void run() {
         dirs(i / 2, 0) = dir_vector[i];
         dirs(i / 2, 1) = dir_vector[i + 1];
       }
-      header.keyval()["basis_directions"] = hit->second;
-      header.keyval().erase(hit);
+      header_out.keyval()["basis_directions"] = hit->second;
+      header_out.keyval().erase(hit);
     } else {
-      auto grad = DWI::get_DW_scheme(amp);
+      auto grad = DWI::get_DW_scheme(header_in);
       DWI::Shells shells(grad);
       shells.select_shells(true, false, false);
       if (shells.smallest().is_bzero())
         bzeros = shells.smallest().get_volumes();
       dwis = shells.largest().get_volumes();
       dirs = DWI::gen_direction_matrix(grad, dwis);
-      DWI::stash_DW_scheme(header, grad);
+      DWI::stash_DW_scheme(header_out, grad);
     }
   }
-  PhaseEncoding::clear_scheme(header);
+  Metadata::PhaseEncoding::clear_scheme(header_out.keyval());
 
   auto sh2amp = DWI::compute_SH2amp_mapping(dirs, true, 8);
 
   const bool normalise = !get_options("normalise").empty();
   if (normalise && bzeros.empty())
     throw Exception("the normalise option is only available if the input data contains b=0 images.");
 
-  header.size(3) = sh2amp.cols();
-  Stride::set_from_command_line(header);
-  auto SH = Image<value_type>::create(argument[1], header);
+  header_out.size(3) = sh2amp.cols();
+  Stride::set_from_command_line(header_out);
 
   Amp2SHCommon common(sh2amp, bzeros, dwis, normalise);
+  auto amp = header_in.get_image<value_type>().with_direct_io(3);
+  auto SH = Image<value_type>::create(argument[1], header_out);
 
   opt = get_options("rician");
   if (!opt.empty()) {

cpp/cmd/dwi2adc.cpp

@@ -19,7 +19,7 @@
 #include "dwi/gradient.h"
 #include "image.h"
 #include "math/least_squares.h"
-#include "phase_encoding.h"
+#include "metadata/phase_encoding.h"
 #include "progressbar.h"
 
 using namespace MR;
@@ -44,7 +44,7 @@ void usage ()
     "adopts a 2-stage fitting strategy, in which the ADC is first estimated based on "
     "the DWI data with b > cutoff, and the other parameters are estimated subsequently. "
     "The output consists of 4 volumes, respectively S(0), D, f, and D'."
-    
+
   + "Note that this command ignores the gradient orientation entirely. This approach is "
     "therefore only suited for mean DWI (trace-weighted) images or for DWI data collected "
     "with isotropically-distributed gradient directions.";
@@ -60,12 +60,12 @@ void usage ()
     +   Argument ("bval").type_integer (0, 1000)
 
     + DWI::GradImportOptions();
-  
+
   REFERENCES
   + "Le Bihan, D.; Breton, E.; Lallemand, D.; Aubin, M.L.; Vignaud, J.; Laval-Jeantet, M. "
     "Separation of diffusion and perfusion in intravoxel incoherent motion MR imaging. "
     "Radiology, 1988, 168, 497–505."
-    
+
   + "Jalnefjord, O.; Andersson, M.; Montelius; M.; Starck, G.; Elf, A.; Johanson, V.; Svensson, J.; Ljungberg, M. "
     "Comparison of methods for estimation of the intravoxel incoherent motion (IVIM) "
     "diffusion coefficient (D) and perfusion fraction (f). "
@@ -144,26 +144,27 @@ class DWI2ADC {
 };
 
 void run() {
-  auto dwi = Header::open(argument[0]).get_image<value_type>();
-  auto grad = DWI::get_DW_scheme(dwi);
+  auto header_in = Header::open(argument[0]);
+  auto grad = DWI::get_DW_scheme(header_in);
 
   size_t dwi_axis = 3;
-  while (dwi.size(dwi_axis) < 2)
+  while (header_in.size(dwi_axis) < 2)
     ++dwi_axis;
   INFO("assuming DW images are stored along axis " + str(dwi_axis));
 
   auto opt = get_options("ivim");
   bool ivim = opt.size();
   int bmin = get_option_value("cutoff", 120);
 
-  Header header(dwi);
-  header.datatype() = DataType::Float32;
-  DWI::stash_DW_scheme(header, grad);
-  PhaseEncoding::clear_scheme(header);
-  header.ndim() = 4;
-  header.size(3) = ivim ? 4 : 2;
+  Header header_out(header_in);
+  header_out.datatype() = DataType::Float32;
+  DWI::stash_DW_scheme(header_out, grad);
+  Metadata::PhaseEncoding::clear_scheme(header_out.keyval());
+  header_out.ndim() = 4;
+  header_out.size(3) = ivim ? 4 : 2;
 
-  auto adc = Image<value_type>::create(argument[1], header);
+  auto dwi = header_in.get_image<value_type>();
+  auto adc = Image<value_type>::create(argument[1], header_out);
 
   ThreadedLoop("computing ADC values", dwi, 0, 3).run(DWI2ADC(grad.col(3), dwi_axis, ivim, bmin), dwi, adc);
 }

cpp/cmd/dwi2fod.cpp

@@ -21,7 +21,7 @@
 #include "header.h"
 #include "image.h"
 #include "math/SH.h"
-#include "phase_encoding.h"
+#include "metadata/phase_encoding.h"
 
 #include "dwi/sdeconv/csd.h"
 #include "dwi/sdeconv/msmt_csd.h"
@@ -258,7 +258,7 @@ void run() {
     shared.init();
 
     DWI::stash_DW_scheme(header_out, shared.grad);
-    PhaseEncoding::clear_scheme(header_out);
+    Metadata::PhaseEncoding::clear_scheme(header_out.keyval());
 
     header_out.size(3) = shared.nSH();
     auto fod = Image<float>::create(argument[3], header_out);