Merge pull request #56 from ornlneutronimaging/tof_imaging

Enable TOF imaging output
ornlneutronimaging · Aug 26, 2024 · bf23ec4 · bf23ec4
2 parents e6409a5 + d1e8bbc
commit bf23ec4
Show file tree

Hide file tree

Showing 27 changed files with 1,903 additions and 468 deletions.
diff --git a/sophiread/.clang-format b/sophiread/.clang-format
@@ -246,5 +246,3 @@ WhitespaceSensitiveMacros:
   - BOOST_PP_STRINGIZE
   - NS_SWIFT_NAME
   - CF_SWIFT_NAME
-...
-
diff --git a/sophiread/CMakeLists.txt b/sophiread/CMakeLists.txt
@@ -1,43 +1,65 @@
+# Sophiread CMakeLists.txt
 cmake_minimum_required(VERSION 3.20)
 
 execute_process(COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/scripts/version.sh -s print
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    OUTPUT_VARIABLE SOPHIREAD_VERSION)
+    OUTPUT_VARIABLE SOPHIREAD_VERSION
+    RESULT_VARIABLE VERSION_RESULT
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+if(NOT VERSION_RESULT EQUAL 0)
+  message(FATAL_ERROR "Failed to determine version")
+endif()
 
 project("Sophiread" VERSION ${SOPHIREAD_VERSION})
 
-# set(CMAKE_BUILD_TYPE DEBUG)
+# This is to avoid accidentally using Homebrew header/lib instead of the one from micromamba
+if(DEFINED ENV{CONDA_PREFIX})
+  set(CMAKE_PREFIX_PATH $ENV{CONDA_PREFIX} ${CMAKE_PREFIX_PATH})
+endif()
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+endif()
+
 set(CMAKE_CXX_STANDARD 20)
 # set(CMAKE_AUTOMOC ON)  # for meta object compiler, needed for Qt5
 
 # Dependencies
 find_package(Eigen3 REQUIRED)
-find_package(spdlog REQUIRED)
 find_package(HDF5 REQUIRED COMPONENTS CXX)
 find_package(GTest REQUIRED)
+find_package(nlohmann_json 3.2.0 REQUIRED)
+find_package(TBB REQUIRED)
+find_package(TIFF REQUIRED)
+find_package(spdlog 1.8.0 REQUIRED)
+find_package(fmt 7.0.0 REQUIRED)
 # find_package(Qt5 COMPONENTS Widgets REQUIRED)
 
-include_directories(${HDF5_INCLUDE_DIRS})
-
-link_directories(
-    $ENV{CONDA_PREFIX}/lib
-)
-
 # Testing setup
 enable_testing()
 include(GoogleTest)
-file(COPY ${CMAKE_SOURCE_DIR}/resources/data DESTINATION ${CMAKE_BINARY_DIR})
 
-# Add compiler flags
-add_compile_options(
-  -O3
-  -std=c++20
-  -march=native
-  -ffast-math
-  -pthread
-  -Wall
-  -Wextra
+# Copy resources
+add_custom_command(
+  OUTPUT ${CMAKE_BINARY_DIR}/data
+  COMMAND ${CMAKE_COMMAND} -E copy_directory
+          ${CMAKE_SOURCE_DIR}/resources/data
+          ${CMAKE_BINARY_DIR}/data
+  DEPENDS ${CMAKE_SOURCE_DIR}/resources/data
 )
+add_custom_target(copy_resources ALL DEPENDS ${CMAKE_BINARY_DIR}/data)
+
+# Add compiler flags
+if(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
+  add_compile_options(
+    -march=native
+    -ffast-math
+    -pthread
+    -Wall
+    -Wextra
+  )
+endif()
 
 # Add Sophiread library
 # NOTE: this will take care of the testing as well
@@ -65,6 +87,13 @@ if(DOXYGEN_FOUND)
   COMMENT "Generating API documentation with Doxygen"
   VERBATIM
   )
+  if(APPLE)
+    set(OPEN_COMMAND open)
+  elseif(UNIX)
+    set(OPEN_COMMAND xdg-open)
+  elseif(WIN32)
+    set(OPEN_COMMAND start)
+  endif()
   add_custom_command(TARGET docs POST_BUILD
     COMMAND ${CMAKE_COMMAND} -E chdir
         ${CMAKE_BINARY_DIR}/docs/html

diff --git a/sophiread/FastSophiread/CMakeLists.txt b/sophiread/FastSophiread/CMakeLists.txt
@@ -1,15 +1,4 @@
-# Config SophireadLib
-include_directories(
-    include
-    $ENV{CONDA_PREFIX}/include
-    ${EIGEN3_INCLUDE_DIR}
-    ${HDF5_INCLUDE_DIRS}
-)
-
-link_directories(
-    $ENV{CONDA_PREFIX}/lib
-)
-
+# Config FastSophireadLib
 set(SRC_FAST_FILES
     src/abs.cpp
     src/centroid.cpp
@@ -21,164 +10,78 @@ set(SRC_FAST_FILES
 
 # ------------- SophireadLibFast -------------- #
 add_library(FastSophiread ${SRC_FAST_FILES})
-
-# ----------------- TESTS ----------------- #
-# DiskIO Tests
-add_executable(
-    SophireadTests_diskio
-    tests/test_disk_io.cpp
-)
-target_link_libraries(
-    SophireadTests_diskio
-    FastSophiread
-    tbb
-    spdlog::spdlog
-    GTest::GTest
-    GTest::Main
-    ${HDF5_LIBRARIES}
-)
-gtest_discover_tests(SophireadTests_diskio)
-# Hit Test
-add_executable(
-    SophireadTests_hit
-    tests/test_hit.cpp
-)
-target_link_libraries(
-    SophireadTests_hit
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    GTest::GTest
-    GTest::Main
-)
-gtest_discover_tests(SophireadTests_hit)
-# TPX3 Test
-add_executable(
-    SophireadTests_tpx3
-    tests/test_tpx3.cpp
-)
-target_link_libraries(
-    SophireadTests_tpx3
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    GTest::GTest
-    GTest::Main
-    ${HDF5_LIBRARIES}
-)
-gtest_discover_tests(SophireadTests_tpx3)
-# ABS Test
-add_executable(
-    SophireadTests_abs
-    tests/test_abs.cpp
-)
-target_link_libraries(
-    SophireadTests_abs
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    GTest::GTest
-    GTest::Main
-)
-gtest_discover_tests(SophireadTests_abs)
-# Centroid Test
-add_executable(
-    SophireadTests_centroid
-    tests/test_centroid.cpp
-)
-target_link_libraries(
-    SophireadTests_centroid
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    GTest::GTest
-    GTest::Main
-)
-gtest_discover_tests(SophireadTests_centroid)
-# Fast Gaussian Test
-add_executable(
-    SophireadTests_fastgaussian
-    tests/test_fastgaussian.cpp
+target_include_directories(FastSophiread
+  PUBLIC
+    ${CMAKE_CURRENT_SOURCE_DIR}/include
+    $ENV{CONDA_PREFIX}/include
+    ${EIGEN3_INCLUDE_DIR}
+    ${HDF5_INCLUDE_DIRS}
 )
-target_link_libraries(
-    SophireadTests_fastgaussian
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    GTest::GTest
-    GTest::Main
+target_link_directories(FastSophiread
+  PRIVATE
+    $ENV{CONDA_PREFIX}/lib
 )
-gtest_discover_tests(SophireadTests_fastgaussian)
+
+# ----------------- TESTS ----------------- #
+function(add_sophiread_test test_name)
+  add_executable(${test_name} tests/test_${test_name}.cpp)
+  target_link_libraries(${test_name}
+    PRIVATE
+      FastSophiread
+      pthread
+      TBB::tbb
+      spdlog::spdlog
+      GTest::GTest
+      GTest::Main
+      ${ARGN}
+  )
+  gtest_discover_tests(${test_name})
+endfunction()
+# Add tests
+add_sophiread_test(disk_io ${HDF5_LIBRARIES})
+add_sophiread_test(hit)
+add_sophiread_test(tpx3  ${HDF5_LIBRARIES})
+add_sophiread_test(abs)
+add_sophiread_test(centroid)
+add_sophiread_test(fastgaussian)
+
 
 # ------------------ Benchmarks ------------------ #
-# Raw2Hits Benchmark
-add_executable(
-    SophireadBenchmarks_raw2hits
-    benchmarks/benchmark_raw2hits.cpp
-)
-target_link_libraries(
-    SophireadBenchmarks_raw2hits
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    ${HDF5_LIBRARIES}
-)
-add_custom_command(TARGET SophireadBenchmarks_raw2hits POST_BUILD
-    COMMAND ${CMAKE_COMMAND} -E create_symlink 
-    ${PROJECT_BINARY_DIR}/FastSophiread/SophireadBenchmarks_raw2hits
-    ${PROJECT_BINARY_DIR}/FastSophireadBenchmarks_raw2hits.app
-)
-# Hits2Events Benchmark
-add_executable(
-    SophireadBenchmarks_hits2events
-    benchmarks/benchmark_hits2events.cpp
-)
-target_link_libraries(
-    SophireadBenchmarks_hits2events
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-)
-add_custom_command(TARGET SophireadBenchmarks_hits2events POST_BUILD
-    COMMAND ${CMAKE_COMMAND} -E create_symlink 
-    ${PROJECT_BINARY_DIR}/FastSophiread/SophireadBenchmarks_hits2events
-    ${PROJECT_BINARY_DIR}/FastSophireadBenchmarks_hits2events.app
-)
-# Raw2Events Benchmark
-add_executable(
-    SophireadBenchmarks_raw2events
-    benchmarks/benchmark_raw2events.cpp
-)
-target_link_libraries(
-    SophireadBenchmarks_raw2events
-    FastSophiread
-    pthread
-    tbb
-    spdlog::spdlog
-    ${HDF5_LIBRARIES}
-)
-add_custom_command(TARGET SophireadBenchmarks_raw2events POST_BUILD
-    COMMAND ${CMAKE_COMMAND} -E create_symlink 
-    ${PROJECT_BINARY_DIR}/FastSophiread/SophireadBenchmarks_raw2events
-    ${PROJECT_BINARY_DIR}/FastSophireadBenchmarks_raw2events.app
-)
-# CLI
-add_executable(
-    FastSophireadBenchmarksCLI
+# Define a function to add benchmark targets
+function(add_sophiread_benchmark NAME)
+    set(TARGET_NAME SophireadBenchmarks_${NAME})
+    add_executable(${TARGET_NAME} benchmarks/benchmark_${NAME}.cpp)
+
+    target_link_libraries(${TARGET_NAME}
+        PRIVATE
+            FastSophiread
+            pthread
+            TBB::tbb
+            spdlog::spdlog
+            ${ARGN}  # Additional libraries passed as arguments
+    )
+
+    add_custom_command(TARGET ${TARGET_NAME} POST_BUILD
+        COMMAND ${CMAKE_COMMAND} -E create_symlink
+        ${PROJECT_BINARY_DIR}/FastSophiread/${TARGET_NAME}
+        ${PROJECT_BINARY_DIR}/FastSophireadBenchmarks_${NAME}.app
+    )
+endfunction()
+
+# Add benchmarks
+add_sophiread_benchmark(raw2hits ${HDF5_LIBRARIES})
+add_sophiread_benchmark(hits2events)
+add_sophiread_benchmark(raw2events ${HDF5_LIBRARIES})
+
+# ----------------- CLI ----------------- #
+add_executable(FastSophireadBenchmarksCLI
     benchmarks/benchmark_mmap.cpp
 )
-target_link_libraries(
-    FastSophireadBenchmarksCLI
+target_link_libraries(FastSophireadBenchmarksCLI
+  PRIVATE
     FastSophiread
     pthread
-    tbb
+    TBB::tbb
     spdlog::spdlog
     ${HDF5_LIBRARIES}
 )

diff --git a/sophiread/FastSophiread/benchmarks/benchmark_mmap.cpp b/sophiread/FastSophiread/benchmarks/benchmark_mmap.cpp
@@ -75,19 +75,19 @@ void saveEventsToHDF5(const std::string out_file_name, const std::vector<Neutron
   y_dataset.write(y.data(), float_type);
   // -- write TOF_ns
   std::vector<double> tof_ns(events.size());
-  std::transform(events.begin(), events.end(), tof_ns.begin(),
+  std::transform(events.cbegin(), events.cend(), tof_ns.begin(),
                  [](const Neutron &event) { return event.getTOF_ns(); });
   H5::DataSet tof_ns_dataset = group.createDataSet("tof", float_type, dataspace);
   tof_ns_dataset.write(tof_ns.data(), float_type);
   // -- write Nhits
   std::vector<int> nhits(events.size());
-  std::transform(events.begin(), events.end(), nhits.begin(),
+  std::transform(events.cbegin(), events.cend(), nhits.begin(),
                  [](const Neutron &event) { return event.getNHits(); });
   H5::DataSet nhits_dataset = group.createDataSet("nHits", int_type, dataspace);
   nhits_dataset.write(nhits.data(), int_type);
   // -- write TOT
   std::vector<double> tot(events.size());
-  std::transform(events.begin(), events.end(), tot.begin(), [](const Neutron &event) { return event.getTOT(); });
+  std::transform(events.cbegin(), events.cend(), tot.begin(), [](const Neutron &event) { return event.getTOT(); });
   H5::DataSet tot_dataset = group.createDataSet("tot", float_type, dataspace);
   tot_dataset.write(tot.data(), float_type);
   // -- close file
@@ -260,7 +260,7 @@ int main(int argc, char* argv[])
 
   spdlog::debug("@{:p}, {}", raw_data.map, raw_data.max);
 
-  if ( raw_data.map == NULL )
+  if ( raw_data.map == nullptr )
   {
     spdlog::error("Insufficient memory: {}", in_tpx3);
     exit(EXIT_FAILURE);