Merge branch 'f71tocsv-normlized' into 'master'

F71togapi normalized

See merge request !126

.gitlab-ci.yml

@@ -108,12 +108,38 @@ linux_gcc_testing:
         -Dradix_ENABLE_TESTS=ON
         -DENABLE_PYTHON_WRAPPERS=ON
         -Dradix_ENABLE_SECONDARY_TESTED_CODE=ON
-        -Dradix_ENABLE_TESTS=ON -DTPL_ENABLE_VTK=ON
+        -DTPL_ENABLE_VTK=ON
         -Dradix_ENABLE_radixplot=OFF
         -Dradix_ENABLE_radixwidgets=OFF ..
     - cmake --build .
     - ctest --output-junit ctest-results.xml
 
+linux_deployment:
+  tags:
+    - linux
+  artifacts:
+    name: ${CI_JOB_NAME}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_SHA}-linux-deployment
+    paths:
+      - bin/
+  script:
+    - which git
+    - git --version
+    - mkdir build
+    - cd build
+    - module load cmake/3.21.0
+    - which cmake
+    - cmake
+        -DBUILD_SHARED_LIBS=OFF
+        -DCMAKE_BUILD_TYPE=Release
+        -Dradix_ENABLE_TESTS=OFF
+        -DENABLE_PYTHON_WRAPPERS=OFF
+        -Dradix_ENABLE_ALL_PACKAGES=OFF
+        -Dradix_ENABLE_radixplot=OFF
+        -Dradix_ENABLE_radixwidgets=OFF
+        -Dradix_ENABLE_radixio=ON
+        -DCMAKE_INSTALL_PREFIX=${CI_PROJECT_DIR} ..
+    - cmake --build . --target bundle_install
+
 linux_analysis:
   stage: analysis
   tags:
@@ -184,6 +210,15 @@ windows_msvc_testing:
     - nsmwin10
   script:
     - ci\windows_msvc_testing.bat
+windows_msvc_deployment:
+  tags:
+    - nsmwin10
+  artifacts:
+    name: ${CI_JOB_NAME}-${CI_COMMIT_REF_NAME}-${CI_COMMIT_SHA}-windows-deployment
+    paths:
+      - bin/
+  script:
+    - ci\windows_msvc_deployment.bat
 
 windows_intel_shared_testing:
   tags:

CMakeLists.txt

@@ -71,7 +71,11 @@ IF (NOT TRIBITS_PROCESSING_PACKAGE)
       SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/cmake_runtime_output" CACHE STRING "")
     ENDIF()
   ENDIF()
-
+  IF(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Bundle/CMakeLists.txt")
+    ADD_SUBDIRECTORY(cmake/Bundle)
+  ELSE()
+    MESSAGE(STATUS "Bundling not supported.")
+  ENDIF()
   TRIBITS_PROJECT_ENABLE_ALL()
 ELSE()
   # This CMakeLists.txt file is being processed as the TriBITS package file.

ci/windows_msvc_deployment.bat

+set PATH=c:\Qt\5.9.1\msvc2013_64\bin;%PATH%;c:\Program Files (x86)\NSIS\Bin
+call "c:/Program Files (x86)/Microsoft Visual Studio 12.0/VC/vcvarsall.bat" amd64
+where git
+git --version
+where qmake
+qmake -version
+where cmake
+cmake --version
+mkdir build
+cd build
+SET radix_ENABLE_Fortran=OFF
+cmake ^
+-DBUILD_SHARED_LIBS=OFF ^
+-DCMAKE_BUILD_TYPE=RELEASE ^
+-Dradix_ENABLE_TESTS=OFF ^
+-Dradix_ENABLE_ALL_PACKAGES=OFF ^
+-Dradix_ENABLE_radixplot=OFF ^
+-Dradix_ENABLE_radixwidgets=OFF ^
+-Dradix_ENABLE_radixglls=OFF ^
+-Dradix_ENABLE_radixio=ON ^
+-DCMAKE_INSTALL_PREFIX=%CI_PROJECT_DIR% ^
+-G "NMake Makefiles" ..
+cmake --build . --target bundle_install
\ No newline at end of file

cmake/Bundle/CMakeLists.txt

+IF("${CMAKE_SYSTEM_NAME}" STREQUAL "Windows")
+   SET(FIXUP_FILE_PATTERN "${CMAKE_INSTALL_PREFIX}/bin/*.exe")
+ELSE()
+   SET(FIXUP_FILE_PATTERN "${CMAKE_INSTALL_PREFIX}/bin/*")
+ENDIF()
+#
+#
+SET(APP_PLUGINS_DIR "")
+CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/fixup_script.cmake.in
+      ${CMAKE_CURRENT_BINARY_DIR}/fixup_script.cmake
+      @ONLY)
+
+ADD_CUSTOM_TARGET(bundle_install
+  COMMAND ${CMAKE_MAKE_PROGRAM} install
+  COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/fixup_script.cmake
+  WORKING_DIRECTORY ${${PROJECT_NAME}_BINARY_DIR}
+  COMMENT "Bundling the installation..."
+  VERBATIM
+)

cmake/Bundle/fixup_script.cmake.in

+SET(CMAKE_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+IF("@CMAKE_SYSTEM_NAME@" STREQUAL "Windows")
+ELSEIF("@CMAKE_SYSTEM_NAME@" STREQUAL "Darwin")
+   FUNCTION(gp_item_default_embedded_path_override item path)
+     # This is required to change the Mac Bundle standard to conform to a linux form
+     SET(${path} "@executable_path/../lib" PARENT_SCOPE)
+   ENDFUNCTION()
+ELSE()
+   FUNCTION(gp_item_default_embedded_path_override item path)
+     SET(${path} "@executable_path/../lib/" PARENT_SCOPE)
+   ENDFUNCTION()
+   FUNCTION(gp_resolved_file_type_override item type_var)
+      GET_FILENAME_COMPONENT(item_dir "${item}" DIRECTORY)
+      STRING(REPLACE "bin/../lib" "lib/" item_dir "${item_dir}")
+      GET_FILENAME_COMPONENT(item_dir "${item_dir}" DIRECTORY)
+      IF("${item_dir}" STREQUAL "${CMAKE_INSTALL_PREFIX}")
+        SET(${type_var} "local" PARENT_SCOPE)
+      ENDIF()
+   ENDFUNCTION ()
+ENDIF()
+#
+# CMake code snippet for stand alone bundle
+#
+FILE(GLOB APPS @FIXUP_FILE_PATTERN@)
+MESSAGE("FIXUP_BUNDLE for: '${APPS}'")
+INCLUDE(BundleUtilities)
+FOREACH(APP ${APPS})
+  # don't process a directory
+  IF(NOT IS_DIRECTORY ${APP})
+     # get the file extension
+     GET_FILENAME_COMPONENT(FILE_EXT ${APP} EXT)
+     # only check no extension files or 'exe' extension files
+     IF("${FILE_EXT}" STREQUAL "" OR "${FILE_EXT}" STREQUAL ".exe")
+        FIXUP_BUNDLE("${APP}" "" "")
+     ENDIF()
+  ENDIF()
+ENDFOREACH()

radixio/f71togapi.cc

@@ -7,7 +7,7 @@ namespace radix
 {
 void F71toGapi::to_gapi_json(const F71Case& fcase, float detector_height,
                              float detector_distance, float live_time,
-                             DataObject& obj, float threshold)
+                             DataObject& obj, bool normalize, float threshold)
 {
   //
   //
@@ -65,6 +65,7 @@ void F71toGapi::to_gapi_json(const F71Case& fcase, float detector_height,
   }
   DecayDb decaydb;
   std::vector<std::pair<int, float>> isotope_activity;
+  float total_activity = 0.f;
   for (const auto& it : master)
   {
     int zaid        = it.first;
@@ -76,7 +77,20 @@ void F71toGapi::to_gapi_json(const F71Case& fcase, float detector_height,
     radix_line("Calculated activity(" << activity << ") for " << zaid << "["
                                       << light_abs << ", " << ac_abs << ", "
                                       << fp_abs << "]");
-    if (threshold < activity) isotope_activity.push_back({zaid, activity});
+    if (threshold < activity)
+    {
+      total_activity += activity;
+      isotope_activity.push_back({zaid, activity});
+    }
+  }
+  //
+  // Normalize by activity
+  if (normalize)
+  {
+    for (auto& isotope : isotope_activity)
+    {
+      isotope.second = isotope.second / total_activity;
+    }
   }
   //
   // Begin DataObject creation

radixio/f71togapi.hh

@@ -19,11 +19,13 @@ class RADIX_PUBLIC F71toGapi
    * @param detector_distance distance in cm to source
    * @param live_time measurement time in seconds
    * @param obj DataObject to construct
+   * @param normalize by total activity
    * @param threshold in curies
    */
   static void to_gapi_json(const F71Case& fcase, float detector_height,
                            float detector_distance, float live_time,
-                           DataObject& obj, float threshold = 1e-6);
+                           DataObject& obj, bool normalize = false,
+                           float threshold = 1e-6);
 };
 }  // namespace radix
 

radixio/f71togapi_main.cc

@@ -16,6 +16,7 @@ int main(int argc, char** argv)
   commandline.addOption("d", "Detector distance (cm)", true);
   commandline.addOption("l", "Live time (seconds)", true);
   commandline.addOption("i", "F71 case index. Defaults to 0");
+  commandline.addOption("n", "Normalize by total activity.");
 
   {
     std::vector<std::string> errors;
@@ -35,6 +36,7 @@ int main(int argc, char** argv)
   float detector_distance = commandline.get<float>("d");
   float live_time         = commandline.get<float>("l");
   int index               = commandline.get<int>("i", 0);
+  bool normalize          = commandline.get<bool>("n", false);
   if (output_file.empty())
   {
     output_file = to_native_path(dirname(f71file) + "/" +
@@ -65,7 +67,7 @@ int main(int argc, char** argv)
     if (result && findex == index)
     {
       F71toGapi::to_gapi_json(single_case, detector_height, detector_distance,
-                              live_time, obj);
+                              live_time, obj, normalize);
       std::ofstream ofs(output_file);
       obj.pack_json(ofs);
       ofs.close();