Merge branch 'development' of github.com:astro-informatics/purify int…

…o development
astro-informatics · Nov 21, 2024 · 24a812c · 24a812c
2 parents 9f0923b + ce03559
commit 24a812c
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Showing 48 changed files with 114 additions and 204 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -97,7 +97,7 @@ jobs:
     - name: Install Dependencies on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
       run: |
-        brew install open-mpi libomp yaml-cpp eigen cfitsio ccache
+        brew install open-mpi libomp yaml-cpp eigen cfitsio ccache onnxruntime
         echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV
         echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH
 
@@ -136,14 +136,14 @@ jobs:
         export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH
         mkdir -p ${{github.workspace}}/sopt/build
         cd ${{github.workspace}}/sopt/build
-        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=OFF -Dexamples=OFF
+        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Donnxrt=ON -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=OFF -Dexamples=OFF
         make -j$(nproc --ignore 1) install
 
     - name: Pack dependencies
       run: |
         cd ${{github.workspace}}
         tar cfv dependencies.tar local
-        
+
     - uses: actions/upload-artifact@v4
       with:
         name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }}
@@ -206,7 +206,7 @@ jobs:
     - name: Install Dependencies on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
       run: |
-        brew install open-mpi libomp eigen ccache cfitsio boost yaml-cpp
+        brew install open-mpi libomp eigen ccache cfitsio boost yaml-cpp onnxruntime
         echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV
         echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH
 
@@ -216,7 +216,7 @@ jobs:
         export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH
         mkdir -p ${{github.workspace}}/build
         cd ${{github.workspace}}/build
-        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Ddocasa=OFF -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=ON
+        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Donnxrt=ON -Ddocasa=OFF -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=ON
         make -j$(nproc --ignore 1) install
 
     - name: Test
@@ -267,7 +267,7 @@ jobs:
     - name: Install Dependencies on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
       run: |
-        brew install gcc libtiff eigen libyaml ccache cfitsio boost yaml-cpp
+        brew install gcc libtiff eigen libyaml ccache cfitsio boost yaml-cpp onnxruntime
         echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV
         echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH
 
@@ -276,7 +276,7 @@ jobs:
         export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH
         mkdir -p ${{github.workspace}}/build
         cd ${{github.workspace}}/build
-        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Ddompi=OFF -Dopenmp=OFF -Ddocs=ON
+        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Donnxrt=ON -Ddompi=OFF -Dopenmp=OFF -Ddocs=ON
         make -j$(nproc --ignore 1) install
 
     - name: Deploy to GH pages

diff --git a/cmake_files/dependencies.cmake b/cmake_files/dependencies.cmake
@@ -26,10 +26,6 @@ find_package(Boost COMPONENTS system filesystem REQUIRED)
 
 find_package(yaml-cpp REQUIRED)
 
-if (onnxrt)
-  find_package(onnxruntime REQUIRED)
-endif()
-
 find_package(sopt REQUIRED)
 set(PURIFY_ONNXRT FALSE)
 if (onnxrt)
@@ -38,6 +34,7 @@ if (onnxrt)
   else()
     message(FATAL_ERROR "SOPT built without ONNXrt support")
   endif()
+  install(DIRECTORY ${CMAKE_SOURCE_DIR}/models DESTINATION .)
 endif()
 
 find_package(Cubature QUIET)

diff --git a/cpp/benchmarks/measurement_operator_mpi.cc b/cpp/benchmarks/measurement_operator_mpi.cc
@@ -10,7 +10,6 @@
 #include <sopt/wavelets.h>
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 // ----------------- Degrid operator constructor fixture -----------------------//
 

diff --git a/cpp/benchmarks/measurement_operator_wproj.cc b/cpp/benchmarks/measurement_operator_wproj.cc
@@ -12,7 +12,6 @@
 #include <sopt/wavelets.h>
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 // ----------------- Degrid operator constructor fixture -----------------------//
 

diff --git a/cpp/benchmarks/utilities.cc b/cpp/benchmarks/utilities.cc
@@ -9,7 +9,6 @@
 #include <sopt/linear_transform.h>
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 namespace b_utilities {
 

diff --git a/cpp/example/casa.cc b/cpp/example/casa.cc
@@ -19,7 +19,7 @@
 int main(int, char **) {
   purify::logging::set_level(purify::default_logging_level());
   // Loads a measurement set
-  auto const ngc3256_filename = purify::notinstalled::ngc3256_ms();
+  auto const ngc3256_filename = purify::ngc3256_ms();
   auto const ngc3256 = purify::casa::MeasurementSet(ngc3256_filename);
 
   try {

diff --git a/cpp/example/compare_wprojection.cc b/cpp/example/compare_wprojection.cc
@@ -11,7 +11,6 @@
 #include <sopt/power_method.h>
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
 #define ARGS_MACRO(NAME, ARGN, VALUE, TYPE) \

diff --git a/cpp/example/generate_vis_data.cc b/cpp/example/generate_vis_data.cc
@@ -12,7 +12,6 @@
 
 int main(int nargs, char const **args) {
   using namespace purify;
-  using namespace purify::notinstalled;
   purify::logging::set_level(purify::default_logging_level());
 
   const std::string &pos_filename = mwa_filename("Phase1_config.txt");

diff --git a/cpp/example/histogram_equalisation.cc b/cpp/example/histogram_equalisation.cc
@@ -4,7 +4,6 @@
 #include "purify/directories.h"
 #include "purify/pfitsio.h"
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
   // up samples M31 example

diff --git a/cpp/example/image_wproj_chirp.cc b/cpp/example/image_wproj_chirp.cc
@@ -10,7 +10,6 @@
 #include <sopt/power_method.h>
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
 #define ARGS_MACRO(NAME, ARGN, VALUE, TYPE) \

diff --git a/cpp/example/mem_w_algos.cc b/cpp/example/mem_w_algos.cc
@@ -7,7 +7,6 @@
 #include "purify/utilities.h"
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
   auto const session = sopt::mpi::init(nargs, args);

diff --git a/cpp/example/padmm_mpi_random_coverage.cc b/cpp/example/padmm_mpi_random_coverage.cc
@@ -30,7 +30,6 @@
 #endif
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 std::tuple<utilities::vis_params, t_real> dirty_visibilities(
     Image<t_complex> const &ground_truth_image, t_uint number_of_vis, t_real snr,

diff --git a/cpp/example/padmm_mpi_real_data.cc b/cpp/example/padmm_mpi_real_data.cc
@@ -31,7 +31,6 @@
 #endif
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 utilities::vis_params dirty_visibilities(const std::vector<std::string> &names) {
   return utilities::read_visibility(names, true);

diff --git a/cpp/example/padmm_random_coverage.cc b/cpp/example/padmm_random_coverage.cc
@@ -21,7 +21,6 @@
 #include "purify/pfitsio.h"
 #include "purify/utilities.h"
 using namespace purify;
-using namespace purify::notinstalled;
 
 void padmm(const std::string &name, const Image<t_complex> &M31, const std::string &kernel,
            const t_int J, const utilities::vis_params &uv_data, const t_real sigma,
@@ -182,13 +181,5 @@ int main(int, char **) {
   // adding noise to visibilities
   uv_data.vis = utilities::add_noise(y0, 0., sigma);
   padmm(name + "30", M31, kernel, 4, uv_data, sigma, std::make_tuple(w_term, cellsize));
-  /*
-    const std::string &test_dir = "expected/padmm_serial/";
-    const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-    auto uv_data = utilities::read_visibility(input_data_path, false);
-    uv_data.units = utilities::vis_units::radians;
-    t_real const sigma = 0.02378738741225;
-    padmm(name + "10", M31, kernel, 4, uv_data, sigma, std::make_tuple(w_term, cellsize));
-    */
   return 0;
 }
diff --git a/cpp/example/padmm_real_data.cc b/cpp/example/padmm_real_data.cc
@@ -21,7 +21,6 @@
 #include "purify/uvfits.h"
 #include "purify/wproj_utilities.h"
 using namespace purify;
-using namespace purify::notinstalled;
 
 void padmm(const std::string &name, const t_uint &imsizex, const t_uint &imsizey,
            const std::string &kernel, const t_int J, const utilities::vis_params &uv_data,

diff --git a/cpp/example/padmm_reweighted_simulation.cc b/cpp/example/padmm_reweighted_simulation.cc
@@ -26,7 +26,6 @@ int main(int nargs, char const **args) {
   }
 
   using namespace purify;
-  using namespace purify::notinstalled;
   sopt::logging::set_level("debug");
 
   std::string const kernel = args[1];

diff --git a/cpp/example/padmm_simulation.cc b/cpp/example/padmm_simulation.cc
@@ -24,7 +24,6 @@ int main(int nargs, char const **args) {
   }
 
   using namespace purify;
-  using namespace purify::notinstalled;
   sopt::logging::set_level("debug");
   purify::logging::set_level("debug");
 

diff --git a/cpp/example/plot_wkernel.cc b/cpp/example/plot_wkernel.cc
@@ -15,7 +15,6 @@
 #include "purify/wkernel_integration.h"
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 using namespace purify;
 

diff --git a/cpp/example/sara_padmm_random_coverage.cc b/cpp/example/sara_padmm_random_coverage.cc
@@ -19,7 +19,6 @@
 
 int main(int, char **) {
   using namespace purify;
-  using namespace purify::notinstalled;
   sopt::logging::set_level("info");
 
   std::string const fitsfile = image_filename("M31.fits");

diff --git a/cpp/example/sdmm_m31_simulation.cc b/cpp/example/sdmm_m31_simulation.cc
@@ -19,7 +19,6 @@
 
 int main(int nargs, char const **args) {
   using namespace purify;
-  using namespace purify::notinstalled;
 
   if (nargs != 6) {
     PURIFY_CRITICAL(" Wrong number of arguments!");

diff --git a/cpp/example/show_image.cc b/cpp/example/show_image.cc
@@ -4,7 +4,6 @@
 #include "purify/directories.h"
 #include "purify/pfitsio.h"
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
   // up samples M31 example

diff --git a/cpp/example/time_w_algos.cc b/cpp/example/time_w_algos.cc
@@ -7,7 +7,6 @@
 #include "purify/utilities.h"
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
   auto const session = sopt::mpi::init(nargs, args);

diff --git a/cpp/example/wavelet_decomposition.cc b/cpp/example/wavelet_decomposition.cc
@@ -7,7 +7,6 @@
 #include "purify/wavelet_operator_factory.h"
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 int main(int nargs, char const **args) {
   purify::logging::set_level("debug");

diff --git a/cpp/purify/config.in.h b/cpp/purify/config.in.h
@@ -28,9 +28,9 @@
 //! Whether PURIFY is using (and SOPT was built with) onnxrt support
 #cmakedefine PURIFY_ONNXRT
 
+#include <cstdint>
 #include <string>
 #include <tuple>
-#include <cstdint>
 
 namespace purify {
 //! Returns library version
@@ -46,6 +46,6 @@ inline std::tuple<uint8_t, uint8_t, uint8_t> version_tuple() {
 inline std::string gitref() { return "@Purify_GITREF@"; }
 //! Default logging level
 inline std::string default_logging_level() { return "@PURIFY_TEST_LOG_LEVEL@"; }
-} // namespace purify
+}  // namespace purify
 
 #endif