Added NFSFT interface for Julia and Python

.github/workflows/c-cpp.yml

@@ -0,0 +1,33 @@
+name: C/C++ CI
+
+on:
+  push:
+    branches: [ develop, master, 'release/**', 'feature/**', 'bugfix/**' ]
+  pull_request:
+    branches: [ develop, master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install libraries
+      run: |
+        sudo apt-get update
+        sudo apt-get install libfftw3-dev libcunit1-dev liboctave-dev doxygen-latex graphviz
+    - name: bootstrap
+      run: ./bootstrap.sh
+    - name: configure
+      run: ./configure --enable-all --enable-openmp --with-octave=/usr
+    - name: make
+      run: make
+    - name: make check
+      run: make check
+    - name: run Octave testfiles
+      run: for DIR in matlab/nf*t matlab/fastsum; do cd $DIR; for NAME in simple_test*.m; do octave --eval="run('$NAME')"; done; cd ../..; done
+    - name: run Julia testfiles
+      run: for DIR in julia/nf*t julia/fastsum; do cd $DIR; for NAME in simple_test*.jl; do julia "$NAME"; done; cd ../..; done
+    - name: make dist
+      run: make dist

.gitignore

@@ -41,6 +41,7 @@
 *.asv
 
 # Other
+.autotools
 .cproject
 .project
 .settings
@@ -90,6 +91,8 @@ applications/fastsum/fastsum_test
 applications/fastsum/fastsum_test_threads
 applications/fastsumS2/fastsumS2
 applications/iterS2/iterS2
+applications/mri/mri2d/*.dat
+applications/mri/mri2d/pics_*
 applications/mri/mri2d/construct_data_2d
 applications/mri/mri2d/construct_data_inh_2d1d
 applications/mri/mri2d/construct_data_inh_3d
@@ -98,6 +101,8 @@ applications/mri/mri2d/reconstruct_data_gridding
 applications/mri/mri2d/reconstruct_data_inh_2d1d
 applications/mri/mri2d/reconstruct_data_inh_3d
 applications/mri/mri2d/reconstruct_data_inh_nnfft
+applications/mri/mri3d/*.dat
+applications/mri/mri3d/pics_*
 applications/mri/mri3d/construct_data_2d1d
 applications/mri/mri3d/construct_data_3d
 applications/mri/mri3d/reconstruct_data_2d1d
@@ -153,3 +158,4 @@ matlab/tests/check_*_matlab.output
 windows-build-dll*/*
 linux-build-mex/*
 nfft-3.*.tar.gz
+.vscode/*

.travis.yml

@@ -1,54 +1,128 @@
 language: c
 compiler:
 - gcc
-- clang
+before_cache:
+- |-
+  case $TRAVIS_OS_NAME in
+    osx)
+      brew cleanup;;
+    windows)
+      # https://unix.stackexchange.com/a/137322/107554
+      $msys2 pacman --sync --clean --noconfirm;
+      rm -f C:\tools\msys64\update.log;
+      rm -rf C:\tools\msys64\var\log;;
+  esac
 os: linux
-dist: xenial
-sudo: false
+dist: bionic
 addons:
   apt:
     packages:
     - libfftw3-dev
     - libcunit1-dev
 env:
 - WINDOW=kaiserbessel PRECISION=
-- WINDOW=gaussian PRECISION=
-- WINDOW=bspline PRECISION=
-- WINDOW=sinc PRECISION=
 - WINDOW=kaiserbessel PRECISION=--enable-float
-- WINDOW=gaussian PRECISION=--enable-float
-- WINDOW=bspline PRECISION=--enable-float
-- WINDOW=sinc PRECISION=--enable-float
 - WINDOW=kaiserbessel PRECISION=--enable-long-double
-- WINDOW=gaussian PRECISION=--enable-long-double
-- WINDOW=bspline PRECISION=--enable-long-double
-- WINDOW=sinc PRECISION=--enable-long-double
-matrix:
+jobs:
   include:
-    - compiler: gcc
-      sudo: required
-      env: WINDOW=kaiserbessel PRECISION= BUILD_OCTAVE=1
-    - compiler: clang
-      sudo: required
-      env: WINDOW=kaiserbessel PRECISION= BUILD_OCTAVE=1
-    - compiler: gcc
+    - os: osx
+      osx_image: xcode12u
+      env: WINDOW=kaiserbessel PRECISION= BUILD_OCTAVE=1 BUILD_JULIA=1
+      addons: { homebrew: { packages: ["fftw", "cunit", "gcc@9", "octave"], casks: ["julia"] } }
+      cache: { directories: ["$HOME/Library/Caches/Homebrew"] }
+    - os: windows
+      compiler: gcc
       env: WINDOW=kaiserbessel PRECISION= BUILD_JULIA=1
-      addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev"] } }
-    - compiler: clang
+      cache: { directories: ["$HOME/AppData/Local/Temp/chocolatey", "/C/tools/msys64"] }
+      git: { autocrlf: input, symlinks: true }
+    - os: windows
+      compiler: clang
       env: WINDOW=kaiserbessel PRECISION= BUILD_JULIA=1
-      addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev"] } }
+      cache: { directories: ["$HOME/AppData/Local/Temp/chocolatey", "/C/tools/msys64"] }
+      git: { autocrlf: input, symlinks: true }
+    - dist: focal
+      compiler: gcc
+      env: WINDOW=kaiserbessel PRECISION= BUILD_OCTAVE=1 BUILD_JULIA=1
+      addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev", "liboctave-dev", "julia"] } }
+    - dist: bionic
+      compiler: clang
+      env: WINDOW=kaiserbessel PRECISION= BUILD_OCTAVE=1 BUILD_JULIA=1
+      addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev", "liboctave-dev"] } }
     - compiler: gcc
-      env: WINDOW=kaiserbessel PRECISION= DIST=dist
+      env: WINDOW=kaiserbessel PRECISION= DIST=distcheck
       addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev", "doxygen", "doxygen-latex", "graphviz"] } }
     - compiler: clang
-      env: WINDOW=kaiserbessel PRECISION= DIST=dist
+      env: WINDOW=kaiserbessel PRECISION= DIST=distcheck
       addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev", "doxygen", "doxygen-latex", "graphviz"] } }
+    - dist: focal
+      compiler: gcc
+      env: WINDOW=kaiserbessel PRECISION=--enable-float BUILD_OCTAVE=1 
+      addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev", "liboctave-dev"] } }
+    - compiler: clang
+      env: WINDOW=kaiserbessel PRECISION=--enable-float BUILD_OCTAVE=1
+      addons: { apt: { packages: ["libfftw3-dev", "libcunit1-dev", "liboctave-dev"] } }
+    - compiler: clang
+      env: WINDOW=kaiserbessel PRECISION=--enable-long-double
+    - env: WINDOW=gaussian PRECISION=
+    - env: WINDOW=bspline PRECISION=
+    - env: WINDOW=sinc PRECISION=
+    - env: WINDOW=gaussian PRECISION=--enable-long-double
+    - env: WINDOW=bspline PRECISION=--enable-long-double
+    - env: WINDOW=sinc PRECISION=--enable-long-double
+    - env: WINDOW=gaussian PRECISION=--enable-float
+    - env: WINDOW=bspline PRECISION=--enable-float
+    - env: WINDOW=sinc PRECISION=--enable-float
+before_install:
+- |-
+  case $TRAVIS_OS_NAME in
+  windows)
+    [[ ! -f C:/tools/msys64/msys2_shell.cmd ]] && rm -rf C:/tools/msys64
+    choco uninstall -y mingw
+    choco upgrade --no-progress -y msys2 julia
+    export msys2='cmd //C RefreshEnv.cmd '
+    export msys2+='& set MSYS=winsymlinks:nativestrict '
+    export msys2+='& C:\\tools\\msys64\\msys2_shell.cmd -defterm -no-start'
+    export mingw64="$msys2 -mingw64 -full-path -here -c "\"\$@"\" --"
+    export msys2+=" -msys2 -c "\"\$@"\" --"
+    $msys2 pacman --sync --noconfirm --needed mingw-w64-x86_64-gcc mingw-w64-x86_64-make mingw-w64-x86_64-fftw mingw-w64-x86_64-cunit autoconf perl libtool automake make 
+    if [ "$CC" == "clang" ]; then $msys2 pacman --sync --noconfirm --needed mingw-w64-x86_64-clang mingw-w64-x86_64-openmp; fi
+    ## Install more MSYS2 packages from https://packages.msys2.org/base here
+    taskkill //IM gpg-agent.exe //F  # https://travis-ci.community/t/4967
+    export PATH=/C/tools/msys64/mingw64/bin:$PATH
+    export MAKE=mingw32-make  # so that Autotools can find it
+    ;;
+  *)
+    export mingw64=
+    ;;
+  esac
 before_script:
-  if [ "$BUILD_OCTAVE" = "1" ]; then
-    sudo add-apt-repository -y ppa:octave/stable;
-    sudo apt-get update --option Acquire::Retries=10 --option Acquire::http::Timeout="30";
-    sudo apt-get install -y libfftw3-dev libcunit1-dev liboctave-dev;
-  fi;
+  cat /proc/cpuinfo; 
+  case $TRAVIS_OS_NAME in
+  linux)
+    if [ "$CC" == "clang" ]; then export LD_LIBRARY_PATH='/usr/local/clang/lib'; fi;
+    if [ "$BUILD_OCTAVE" = "1" ]; then
+      export OCTAVEDIR=/usr;
+      export OCTAVE=octave;
+    fi; 
+    if [ "$BUILD_JULIA" = "1" ] && [ "$TRAVIS_DIST" = "bionic" ]; then
+      wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.3/julia-1.3.1-linux-x86_64.tar.gz && tar -xf julia-*-linux-x86_64.tar.gz; 
+      export julia=$(pwd)/julia-1.3.1/bin/julia;
+    fi;;
+  windows)
+    if [ "$CC" == "clang" ]; then export OPENMP_CFLAGS=-fopenmp=libomp; export LDFLAGS=-lomp; fi;
+    if [ "$BUILD_OCTAVE" = "1" ]; then
+      wget -q https://ftp.gnu.org/gnu/octave/windows/octave-5.2.0-w64.7z && 7z x octave-*.7z;
+      export OCTAVEDIR=$(pwd)/octave-5.2.0-w64;
+      rm $OCTAVEDIR/lib/octave/5.2.0/lib*.la;
+      export OCTAVE=$OCTAVEDIR/bin/octave-cli.exe;
+    fi;;
+  osx)
+    export CC=gcc-9;
+    export CPPFLAGS=-I/usr/local/include;
+    export LDFLAGS=-L/usr/local/lib;
+    export OCTAVEDIR=/usr/local;
+    export OCTAVE=octave-cli;;
+  esac;
   if [ "x$TRAVIS_TAG" != "x" ]; then
     NFFT_TRAVIS_TAG=$(sed -e 's/\([0-9]*\.[0-9]*\.[0-9]*\)\(.*\)/\1.\2/' <<< "$TRAVIS_TAG");
     a=( ${NFFT_TRAVIS_TAG//./ } );
@@ -57,13 +131,15 @@ before_script:
       mv configure.ac.modified configure.ac;
     fi;
   fi;
-script: cat /proc/cpuinfo; ./bootstrap.sh && ./configure --with-window=$WINDOW $PRECISION --enable-all
-  $(if test "$CC" = "clang"; then echo ""; else echo "--enable-openmp"; fi)
-  $(if test "$BUILD_OCTAVE" = "1"; then echo "--with-octave=/usr"; else echo ""; fi)
-  $(if test "$BUILD_JULIA" = "1"; then echo "--enable-julia"; else echo ""; fi)
-  && make
-  && make check && make $DIST
-  && if test "$BUILD_JULIA" = "1"; then wget https://julialang-s3.julialang.org/bin/linux/x64/1.1/julia-1.1.1-linux-x86_64.tar.gz && tar -xf julia-1.1.1-linux-x86_64.tar.gz && for DIR in nfft nfct; do cd julia/$DIR; for NAME in simple_test*.jl; do ./../../julia-1.1.1/bin/julia "$NAME"; done; cd ../..; done; fi;
+
+script: $mingw64 ./bootstrap.sh
+  && $mingw64 ./configure --with-window=$WINDOW $PRECISION --enable-all --enable-openmp
+  $(if [ "$BUILD_OCTAVE" = "1" ]; then echo "--with-octave=$OCTAVEDIR"; else echo ""; fi)
+  $(if [ "$BUILD_JULIA" = "1" ]; then echo "--enable-julia"; else echo ""; fi)
+  && $mingw64 make
+  && $mingw64 make check && $mingw64 make $DIST
+  && if test "$BUILD_JULIA" = "1"; then for DIR in julia/nf*t julia/fastsum; do cd $DIR; for NAME in simple_test*.jl; do julia "$NAME"; done; cd ../..; done; fi
+  && if test "$BUILD_OCTAVE" = "1"; then for DIR in matlab/nf*t matlab/fastsum; do cd $DIR; for NAME in simple_test*.m; do $OCTAVE --eval="run('$NAME')"; done; cd ../..; done; fi
 after_failure: cat config.log && cat tests/test-suite.log && if test "$BUILD_OCTAVE" = "1"; then cat matlab/tests/test-suite.log; fi
 notifications:
   email: false
@@ -79,6 +155,6 @@ deploy:
   file: ${NFFT_DISTRO}
   skip_cleanup: true
   on:
-    condition: $DIST = dist && $CC = clang
+    condition: $DIST = distcheck && $CC = clang
     tags: true
     repo: NFFT/nfft

3rdparty/README

@@ -7,3 +7,5 @@ package. Currently, the following packages are included:
 CSTRIPACK - A C-version of Robert J. Renka's the STRIPACK Fortran package to 
   compute Delaunay triangulations and Voronoi partitions on the unit sphere.
 
+This package is currently not contained in make dist, since it is only used by 
+iterS2.

AUTHORS

@@ -39,8 +39,21 @@ Dr. Tobias Knopp
 Dr. Antje Vollrath <[email protected]>
  - transforms on the rotation group SO(3) (/kernel/nfsoft)
 
-Toni Volkmer
+Dr. Toni Volkmer
  - OpenMP parallelization of nfft (/kernel/nfft)
  - OpenMP parallelization of nfsft (/kernel/nfsft)
  - OpenMP parallelization of fast summation (/applications/fastsum)
 
+Dr. Michael Quellmalz
+ - OpenMP parallelization of nfsoft (/kernel/nfsoft)
+ - Matlab mex interface for nfsoft (/matlab/nfsoft)
+
+Felix Bartel
+ - Matlab mex interface for fpt (/matlab/fpt)
+
+Melanie Kircheis
+ - inverse nfft in 1D (/matlab/infft1d)
+
+Michael Schmischke
+ - Julia interface (/julia)
+