Mods to support spectra file IO out of fortran

CMakeLists.txt

@@ -2,13 +2,15 @@ if(POLICY CMP0091)
   cmake_policy(SET CMP0091 NEW) # For CMake 3.15 and newer, enable use of CMAKE_MSVC_RUNTIME_LIBRARY, without requiring CMake 3.15
 endif()
 
-cmake_minimum_required(VERSION 3.1...3.22)
+cmake_minimum_required(VERSION 3.1...3.29)
 
 if(${CMAKE_VERSION} VERSION_LESS 3.12)
   cmake_policy(VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION})
 endif()
 
-project( SpecUtils )
+project( SpecUtils VERSION 1.0.0 )
+
+enable_testing()
 
 option( SpecUtils_ENABLE_D3_CHART "Enables exporting of the D3 chart format" ON )
 option( SpecUtils_D3_SUPPORT_FILE_STATIC "Compiles the JS and CSS files into memory, rather than reading files on disk; disable to allow changing JS/CSS without having to recompile" ON )
@@ -27,7 +29,6 @@ option( SpecUtils_USE_FROM_CHARS "Use c++17 std::from_chars for parsing floats/i
 option( SpecUtils_ENABLE_EQUALITY_CHECKS "Enables the equal_enough(...) functions for comparing two spectrum files." OFF )  #code size is only reason to default to off, I think
 option( PERFORM_DEVELOPER_CHECKS "Performs additional computationally expensive tests during execution" off )
 
-
 # If we are building this on Windows, not as a sub-project, lets enable selecting C++ runtime
 if( MSVC AND (SpecUtils_PYTHON_BINDINGS OR SpecUtils_BUILD_UNIT_TESTS) )
   get_directory_property(hasParent PARENT_DIRECTORY)
@@ -230,6 +231,11 @@ add_library( SpecUtils ${SpecUtils_LIB_TYPE} ${sources} ${headers} ${OTHER_SUPPO
 set_target_properties( SpecUtils PROPERTIES PREFIX "lib" OUTPUT_NAME "SpecUtils" )
 
 
+#For CMake 3.8+, could specify C++11 using the following so it will be propagated to down-line targets...
+#target_compile_features(SpecUtils PUBLIC cxx_std_11)
+#set_target_properties(SpecUtils PROPERTIES CXX_EXTENSIONS OFF)
+
+
 if( SpecUtils_USE_FROM_CHARS )
   if( NOT (MSVC AND (MSVC_VERSION GREATER_EQUAL 1920)) )
     # MSVC >=2019 supports floating point from_chars, while Xcode 14 still doesnt (havent checked Android Studio)
@@ -305,7 +311,7 @@ elseif( WIN32 )
   target_link_libraries( SpecUtils PUBLIC "Shlwapi.lib" )
 endif( MINGW )
 
-target_include_directories( SpecUtils PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ${Boost_INCLUDE_DIRS}
+target_include_directories( SpecUtils PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}> $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}> ${Boost_INCLUDE_DIRS}
                             PRIVATE ${THIRD_PARTY_DIR} ${PYTHON_INCLUDE_DIRS} )
 
 if( SpecUtils_BUILD_REGRESSION_TEST )
@@ -326,9 +332,52 @@ if( SpecUtils_BUILD_FUZZING_TESTS )
   add_subdirectory( fuzz_test )
 endif( SpecUtils_BUILD_FUZZING_TESTS )
 
+set_property( TARGET SpecUtils PROPERTY POSITION_INDEPENDENT_CODE ON )
+
+# Specify installation rules
+include(GNUInstallDirs)
+
+# Install the library
+install(TARGETS SpecUtils
+    EXPORT SpecUtilsTargets
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+    INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
+
+set( SpecUtils_config_OUT ${CMAKE_CURRENT_BINARY_DIR}/SpecUtils_config.h )
 configure_file(
     ${CMAKE_CURRENT_SOURCE_DIR}/SpecUtils/SpecUtils_config.h.in
-    ${CMAKE_CURRENT_BINARY_DIR}/SpecUtils_config.h
+    ${SpecUtils_config_OUT}
+)
+LIST(APPEND headers ${SpecUtils_config_OUT})
+# Install the headers
+install(FILES ${headers} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/SpecUtils)
+
+# Create and install the CMake package configuration files
+include(CMakePackageConfigHelpers)
+
+write_basic_package_version_file(
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfigVersion.cmake"
+    VERSION ${PROJECT_VERSION}
+    COMPATIBILITY AnyNewerVersion
 )
 
+configure_package_config_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/SpecUtilsConfig.cmake.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfig.cmake"
+    INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SpecUtils
+)
+
+install(FILES
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfig.cmake"
+    "${CMAKE_CURRENT_BINARY_DIR}/SpecUtilsConfigVersion.cmake"
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SpecUtils
+)
 
+install(EXPORT SpecUtilsTargets
+    FILE SpecUtilsTargets.cmake
+    NAMESPACE SpecUtils::
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/SpecUtils
+)

SpecUtils/ParseUtils.h

@@ -31,6 +31,8 @@
 #include <istream>
 #include <ostream>
 
+#include "SpecUtils/StringAlgo.h"
+
 /** Some functions and definitions that help to parse and write spectrum files,
  but maybe dont fit in other sections of code.
  */
@@ -290,6 +292,41 @@ Integral float_to_integral( float d )
     static constexpr Integral max_int_val = std::numeric_limits<Integral>::max();
     return std::signbit(d) ? min_int_val : max_int_val;
   }//float_to_integral
+
+  template<class StringVec>
+  inline std::string get_source(const StringVec & vec)
+  {
+    auto retVal = std::string();
+    auto sourceStringOffset = 8U;
+    for(auto str : vec)
+    {
+      if(SpecUtils::istarts_with(str, "Source:"))
+      {
+        retVal = str.substr(sourceStringOffset);
+        trim(retVal);
+        break;
+      }    
+    }
+    return retVal;
+  }
+
+  template<class StringVec>
+  inline std::string get_description(const StringVec & vec)
+  {
+    auto retVal = std::string();
+    auto descrOffset = 12U;
+    for(auto str : vec)
+    {
+      if(SpecUtils::istarts_with(str, "Description:"))
+      {
+        retVal = str.substr(descrOffset);
+        trim(retVal);
+        break;
+      }    
+    }
+    return retVal;
+  }
+
 }//namespace SpecUtils
 
 #endif //SpecUtils_ParseUtils_h

SpecUtils/SpecFile.h

@@ -38,7 +38,6 @@
 Shortcommings that wcjohns should address:
  - Many of the N24 fields possible are not checked for
     - comments for multiple different tags, ...
- - Neutron measurements should have their own live and real time
  - Neutron counts are typically merged into a gamma detectors Measurement if a
    reasonable pairing can be made. When and if this is done needs to be clearly
    specified, and either stopped of facilities added to keep neutron det. info.
@@ -513,12 +512,8 @@ double gamma_integral( const std::shared_ptr<const Measurement> &hist,
 //  InterSpec is using to represent detector response functions on disk.
 const std::string &detectorTypeToString( const DetectorType type );
 
-
-
-
-
-
-
+using FloatVec = std::vector<float>;
+using FloatVecPtr = std::shared_ptr<FloatVec>;    
 
 class Measurement
 {
@@ -538,9 +533,19 @@ class Measurement
 
   //live_time(): returned in units of seconds.  Will be 0 if not known.
   float live_time() const;
+
+  void set_live_time(float time)
+  {
+    live_time_ = time;
+  }
 
   //real_time(): returned in units of seconds.  Will be 0 if not known.
   float real_time() const;
+
+  void set_real_time(float time)
+  {
+    real_time_ = time;
+  }
 
   //contained_neutron(): returns whether or not the measurement is thought to
   //  contain the possibility to detect neutrons (e.g. if a neutron detector was
@@ -793,7 +798,15 @@ class Measurement
    */
   void set_gamma_counts( std::shared_ptr<const std::vector<float>> counts,
                                 const float livetime, const float realtime );
-
+
+  void set_gamma_counts( std::shared_ptr<const std::vector<float>> counts );
+
+  void set_gamma_counts(const FloatVec& spectrum)
+  {
+    auto counts = std::make_shared<FloatVec>(spectrum);
+
+    set_gamma_counts(counts, 0.0F, 0.0F);
+  }
   /** Sets the neutron counts, and also updates
    #Measurement::neutron_counts_sum_ and #Measurement::contained_neutron_ .
 
@@ -809,7 +822,7 @@ class Measurement
 
    If `neutron_live_time` is less than or equal to zero, the gamma real time will be used.
    */
-  void set_neutron_counts( const std::vector<float> &counts, const float neutron_live_time );
+  void set_neutron_counts( const std::vector<float> &counts, const float neutron_live_time=-1.0F );
 
   //To set real and live times, see SpecFile::set_live_time(...)
 
@@ -1157,7 +1170,7 @@ class Measurement
   std::shared_ptr<const SpecUtils::LocationState> location_;
 
   friend class ::SpecMeas;
-  friend class SpecFile;
+  friend class SpecFile; // bruh...
   friend struct N42DecodeHelper2006;
   friend struct N42DecodeHelper2012;
   friend struct GrossCountNodeDecodeWorker;
@@ -1470,7 +1483,7 @@ class SpecFile
   //  number available if that detector does not already have that one or else
   //  its assigned to be one larger sample number - this by no means captures
   //  all use cases, but good enough for now.
-  void add_measurement( std::shared_ptr<Measurement> meas, const bool doCleanup );
+  void add_measurement( std::shared_ptr<Measurement> meas, const bool doCleanup=true );
 
   //remove_measurement(...): removes the measurement from this SpecFile
   //  object and if 'doCleanup' is specified, then all sums will be

SpecUtils/StringAlgo.h

@@ -413,6 +413,8 @@ namespace  SpecUtils
   unsigned int levenshtein_distance( const std::string &source,
                                     const std::string &target,
                                     const size_t max_str_len = 128 );
+
+
 
 }//namespace SpecUtils
 

SpecUtilsConfig.cmake.in

@@ -0,0 +1,11 @@
+@PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+
+# Add any dependencies here, e.g.,
+# find_dependency(SomeOtherLibrary)
+
+include("${CMAKE_CURRENT_LIST_DIR}/SpecUtilsTargets.cmake")
+
+set(SpecUtils_INCLUDE_DIRS "@PACKAGE_INCLUDE_INSTALL_DIR@")
+set(SpecUtils_LIBRARIES SpecUtils)

bindings/swig/fortran/SpecUtilsFortran.i

@@ -0,0 +1,69 @@
+%module SpecUtilsWrap
+
+%{
+#include <SpecUtils/SpecFile.h>
+#include <SpecUtils/ParseUtils.h>
+%}
+
+
+%include "stl.i"
+//%include "std_vector.i"
+/* instantiate the required template specializations */
+namespace std {
+    %template(IntVector)    vector<int>;
+    %template(DoubleVector) vector<double>;
+    %template(FloatVector)  vector<float>;
+    %template(MeasurementVector)  vector<SpecUtils::Measurement>;
+
+}
+
+
+%include "std_shared_ptr.i"
+%shared_ptr(vector<SpecUtils::Measurement>)
+%shared_ptr(SpecUtils::Measurement)
+%shared_ptr(std::vector<float>)
+
+%include "std_string.i"
+%apply std::string { std::string& }
+//%include "std_wstring.i"
+%include "wchar.i"
+
+%ignore combine_gamma_channels;
+%ignore truncate_gamma_channels; 
+%ignore set_energy_calibration;
+%ignore descriptionText;
+%ignore operator=;
+
+%include "SpecUtils/SpecFile.h"
+
+%extend SpecUtils::Measurement
+{
+    /// Return the count at a given index.
+    /// @param index is 1-based 
+    float gamma_count_at(int index) 
+    {
+        return $self->gamma_counts()->at(index-1);
+    }
+
+    std::string get_description()
+    {
+        auto &remarks = $self->remarks();
+        return SpecUtils::get_description(remarks);
+    }
+
+    std::string get_source()
+    {
+        auto &remarks = $self->remarks();
+        return SpecUtils::get_source(remarks);
+    }
+}
+
+%extend SpecUtils::SpecFile
+{
+    /// Return the measurement at a given index.
+    /// @param index is 1-based 
+    std::shared_ptr<const SpecUtils::Measurement> measurement_at(int index)
+    {
+        return $self->measurement(static_cast<size_t>(index-1));
+    }
+}