astro-informatics · tkoskela · Nov 14, 2024 · Nov 14, 2024 · Nov 14, 2024 · Nov 14, 2024
diff --git a/cmake_files/LookUpONNXRT.cmake b/cmake_files/LookUpONNXRT.cmake
@@ -0,0 +1,54 @@
+
+find_package(onnxruntime QUIET)
+
+if(${onnxruntime_FOUND})
+  find_path(onnxruntime_INCLUDE_DIR NAMES onnxruntime_cxx_api.h
+      HINTS
+      ENV onnxruntime_ROOT
+      ENV onnxruntime_ROOT_DIR
+      ${CMAKE_INSTALL_PREFIX}/include
+      ${KDE4_INCLUDE_DIR}
+      PATH_SUFFIXES onnxruntime
+  )
+  include(FindPackageHandleStandardArgs)
+  find_package_handle_standard_args(onnxruntime DEFAULT_MSG onnxruntime_INCLUDE_DIR TRUE)
+  set(onnxruntime_LIBRARIES onnxruntime::onnxruntime)
+  get_filename_component(onnxruntime_INSTALL_PREFIX "${onnxruntime_INCLUDE_DIR}/../../" ABSOLUTE)
+  find_library(onnxruntime_LIBRARY onnxruntime PATHS "${onnxruntime_INSTALL_PREFIX}/lib")
+  set_target_properties(${onnxruntime_LIBRARIES} PROPERTIES IMPORTED_LOCATION "${onnxruntime_LIBRARY}")
+  set_target_properties(${onnxruntime_LIBRARIES} PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${onnxruntime_INCLUDE_DIR}")
+endif()
+
+if(NOT ${onnxruntime_FOUND})
+  message(STATUS "ONNXrt not found. Attempt to install...")
+  EXECUTE_PROCESS( COMMAND uname -m COMMAND tr -d '\n' OUTPUT_VARIABLE ARCH )
+  message( STATUS "Detected architecture: ${ARCH}" )
+  if ("${ARCH}" STREQUAL "x86_64")
+    set(ARCH "x64")
+  endif()
+  set(ORT_VERSION "1.16.3")
+  set(ORT_URL_BASE "https://github.com/microsoft/onnxruntime/releases/download")
+  set(ORT_TARNAME "onnxruntime-linux-${ARCH}-${ORT_VERSION}")
+  set(ORT_DEST "${CMAKE_CURRENT_BINARY_DIR}/external/${ORT_TARNAME}.tgz")
+  set(ORT_URL "${ORT_URL_BASE}/v${ORT_VERSION}/${ORT_TARNAME}.tgz")
+  # https://cmake.org/cmake/help/latest/policy/CMP0135.html
+  #
+  # CMP0135 is for solving re-building and re-downloading.
+  # The NEW policy suppresses warnings for some CMake versions.
+  if(POLICY CMP0135)
+    cmake_policy(SET CMP0135 NEW)
+  endif()
+  set(onnxruntime_DIR "${CMAKE_INSTALL_PREFIX}/external")
+  file(DOWNLOAD ${ORT_URL} ${ORT_DEST}
+       EXPECTED_HASH SHA256=b072f989d6315ac0e22dcb4771b083c5156d974a3496ac3504c77f4062eb248e
+  )
+  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${ORT_DEST})
+  execute_process(COMMAND ${CMAKE_COMMAND} -E copy_directory ${ORT_TARNAME} ${onnxruntime_DIR})
+  set(onnxruntime_INCLUDE_DIR "${onnxruntime_DIR}/include")
+  set(onnxruntime_LIBRARY_DIR "${onnxruntime_DIR}/lib")
+  set(onnxruntime_LIBRARIES onnxruntime::onnxruntime)
+  add_library(${onnxruntime_LIBRARIES} SHARED IMPORTED GLOBAL)
+  set_target_properties(${onnxruntime_LIBRARIES} PROPERTIES IMPORTED_LOCATION ${onnxruntime_LIBRARY_DIR}/libonnxruntime.so)
+  set(onnxruntime_FOUND TRUE)
+endif()
+
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
diff --git a/cpp/tests/algo_factory.cc b/cpp/tests/algo_factory.cc
@@ -22,15 +22,12 @@
 #include "purify/test_data.h"
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 TEST_CASE("padmm_factory") {
   const std::string &test_dir = "expected/padmm/";
-  const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-  const std::string &expected_solution_path =
-      notinstalled::data_filename(test_dir + "solution.fits");
-  const std::string &expected_residual_path =
-      notinstalled::data_filename(test_dir + "residual.fits");
+  const std::string &input_data_path = data_filename(test_dir + "input_data.vis");
+  const std::string &expected_solution_path = data_filename(test_dir + "solution.fits");
+  const std::string &expected_residual_path = data_filename(test_dir + "residual.fits");
 
   const auto solution = pfitsio::read2d(expected_solution_path);
   const auto residual = pfitsio::read2d(expected_residual_path);
@@ -81,11 +78,9 @@ TEST_CASE("padmm_factory") {
 // See https://github.com/astro-informatics/purify/issues/317 for details.
 TEST_CASE("primal_dual_factory", "[!shouldfail]") {
   const std::string &test_dir = "expected/primal_dual/";
-  const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-  const std::string &expected_solution_path =
-      notinstalled::data_filename(test_dir + "solution.fits");
-  const std::string &expected_residual_path =
-      notinstalled::data_filename(test_dir + "residual.fits");
+  const std::string &input_data_path = data_filename(test_dir + "input_data.vis");
+  const std::string &expected_solution_path = data_filename(test_dir + "solution.fits");
+  const std::string &expected_residual_path = data_filename(test_dir + "residual.fits");
 
   const auto solution = pfitsio::read2d(expected_solution_path);
   const auto residual = pfitsio::read2d(expected_residual_path);
@@ -136,12 +131,10 @@ TEST_CASE("primal_dual_factory", "[!shouldfail]") {
 
 TEST_CASE("fb_factory") {
   const std::string &test_dir = "expected/fb/";
-  const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-  const std::string &expected_solution_path =
-      notinstalled::data_filename(test_dir + "solution.fits");
-  const std::string &expected_residual_path =
-      notinstalled::data_filename(test_dir + "residual.fits");
-  const std::string &result_path = notinstalled::data_filename(test_dir + "fb_result.fits");
+  const std::string &input_data_path = data_filename(test_dir + "input_data.vis");
+  const std::string &expected_solution_path = data_filename(test_dir + "solution.fits");
+  const std::string &expected_residual_path = data_filename(test_dir + "residual.fits");
+  const std::string &result_path = data_filename(test_dir + "fb_result.fits");
 
   const auto solution = pfitsio::read2d(expected_solution_path);
   const auto residual = pfitsio::read2d(expected_residual_path);
@@ -192,12 +185,10 @@ TEST_CASE("fb_factory") {
 #ifdef PURIFY_ONNXRT
 TEST_CASE("tf_fb_factory") {
   const std::string &test_dir = "expected/fb/";
-  const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-  const std::string &expected_solution_path =
-      notinstalled::data_filename(test_dir + "solution.fits");
-  const std::string &expected_residual_path =
-      notinstalled::data_filename(test_dir + "residual.fits");
-  const std::string &result_path = notinstalled::data_filename(test_dir + "tf_result.fits");
+  const std::string &input_data_path = data_filename(test_dir + "input_data.vis");
+  const std::string &expected_solution_path = data_filename(test_dir + "solution.fits");
+  const std::string &expected_residual_path = data_filename(test_dir + "residual.fits");
+  const std::string &result_path = data_filename(test_dir + "tf_result.fits");
 
   const auto solution = pfitsio::read2d(expected_solution_path);
   const auto residual = pfitsio::read2d(expected_residual_path);
@@ -227,8 +218,7 @@ TEST_CASE("tf_fb_factory") {
   t_real const beta = sigma * sigma;
   t_real const gamma = 0.0001;
 
-  std::string tf_model_path =
-      purify::notinstalled::models_directory() + "/snr_15_model_dynamic.onnx";
+  std::string tf_model_path = purify::models_directory() + "/snr_15_model_dynamic.onnx";
 
   auto const fb = factory::fb_factory<sopt::algorithm::ImagingForwardBackward<t_complex>>(
       factory::algo_distribution::serial, measurements_transform, wavelets, uv_data, sigma, beta,
@@ -252,12 +242,10 @@ TEST_CASE("tf_fb_factory") {
 
 TEST_CASE("onnx_fb_factory") {
   const std::string &test_dir = "expected/fb/";
-  const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-  const std::string &expected_solution_path =
-      notinstalled::data_filename(test_dir + "solution.fits");
-  const std::string &expected_residual_path =
-      notinstalled::data_filename(test_dir + "residual.fits");
-  const std::string &result_path = notinstalled::data_filename(test_dir + "onnx_result.fits");
+  const std::string &input_data_path = data_filename(test_dir + "input_data.vis");
+  const std::string &expected_solution_path = data_filename(test_dir + "solution.fits");
+  const std::string &expected_residual_path = data_filename(test_dir + "residual.fits");
+  const std::string &result_path = data_filename(test_dir + "onnx_result.fits");
   const auto solution = pfitsio::read2d(expected_solution_path);
   const auto residual = pfitsio::read2d(expected_residual_path);
 
@@ -287,9 +275,9 @@ TEST_CASE("onnx_fb_factory") {
   t_real const gamma = 0.0001;
 
   std::string const prior_path =
-      purify::notinstalled::models_directory() + "/example_cost_dynamic_CRR_sigma_5_t_5.onnx";
+      purify::models_directory() + "/example_cost_dynamic_CRR_sigma_5_t_5.onnx";
   std::string const prior_gradient_path =
-      purify::notinstalled::models_directory() + "/example_grad_dynamic_CRR_sigma_5_t_5.onnx";
+      purify::models_directory() + "/example_grad_dynamic_CRR_sigma_5_t_5.onnx";
   std::shared_ptr<sopt::ONNXDifferentiableFunc<t_complex>> diff_function =
       std::make_shared<sopt::ONNXDifferentiableFunc<t_complex>>(
           prior_path, prior_gradient_path, sigma, 20, 5e4, *measurements_transform);
@@ -317,11 +305,9 @@ TEST_CASE("onnx_fb_factory") {
 
 TEST_CASE("joint_map_factory") {
   const std::string &test_dir = "expected/joint_map/";
-  const std::string &input_data_path = notinstalled::data_filename(test_dir + "input_data.vis");
-  const std::string &expected_solution_path =
-      notinstalled::data_filename(test_dir + "solution.fits");
-  const std::string &expected_residual_path =
-      notinstalled::data_filename(test_dir + "residual.fits");
+  const std::string &input_data_path = data_filename(test_dir + "input_data.vis");
+  const std::string &expected_solution_path = data_filename(test_dir + "solution.fits");
+  const std::string &expected_residual_path = data_filename(test_dir + "residual.fits");
 
   const auto solution = pfitsio::read2d(expected_solution_path);
   const auto residual = pfitsio::read2d(expected_residual_path);

diff --git a/cpp/tests/casacore.cc b/cpp/tests/casacore.cc
@@ -17,7 +17,6 @@
 #include "catch2/catch_all.hpp"
 namespace casa = casacore;
 
-using namespace purify::notinstalled;
 TEST_CASE("Casacore") {
   // create the table descriptor
   casa::TableDesc simpleDesc = casa::MS::requiredTableDesc();

diff --git a/cpp/tests/convolution.cc b/cpp/tests/convolution.cc
@@ -8,7 +8,6 @@
 #include "purify/convolution.h"
 
 using namespace purify;
-using namespace purify::notinstalled;
 
 TEST_CASE("1d_zeropad") {
   const Vector<t_int> signal = Vector<t_int>::Random(3);