Merge branch 'master' into feature/showNonForePeaks

Author: wcjohns

bindings/python/CMakeLists.txt

@@ -6,13 +6,19 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 set( SpecUtils_ENABLE_D3_CHART ON CACHE BOOL "" )
 set( SpecUtils_D3_SUPPORT_FILE_STATIC ON CACHE BOOL "" )
-set( SpecUtils_ENABLE_URI_SPECTRA OFF CACHE BOOL "" )  #Lets not worry about linking to zlib right now
 set( SpecUtils_PYTHON_BINDINGS ON CACHE BOOL "Build the python bindings" )
 set( SpecUtils_ENABLE_EQUALITY_CHECKS OFF CACHE BOOL "" )
 set( PERFORM_DEVELOPER_CHECKS OFF CACHE BOOL "" )
 set( SpecUtils_SHARED_LIB OFF CACHE BOOL "" )  #we'll statically link SpecUtils into the lib we create here
 set( SpecUtils_FLT_PARSE_METHOD "strtod" CACHE STRING "Float parsing method" )
 
+# Enable URI spectra for macOS and Linux (since we are already linking to zlib), but not Windows
+if(WIN32)
+  set( SpecUtils_ENABLE_URI_SPECTRA OFF CACHE BOOL "" )
+else()
+  set( SpecUtils_ENABLE_URI_SPECTRA ON CACHE BOOL "" )
+endif()
+
 add_subdirectory( ${CMAKE_CURRENT_SOURCE_DIR}/../.. ${CMAKE_CURRENT_BINARY_DIR}/LibSpecUtils )
 
 if (NOT SKBUILD)

bindings/python/SpecFile_py.cpp

@@ -1354,6 +1354,9 @@ NB_MODULE(SpecUtils, m) {
   .value("ScanDataXml", SpecUtils::ParserType::ScanDataXml)
   .value("Json", SpecUtils::ParserType::Json)
   .value("CaenHexagonGXml", SpecUtils::ParserType::CaenHexagonGXml)
+  #if( SpecUtils_ENABLE_URI_SPECTRA )
+  .value("Uri", SpecUtils::ParserType::Uri)
+#endif
   .value("Auto", SpecUtils::ParserType::Auto);
 
 
@@ -2051,8 +2054,33 @@ m.def("polynomialCoefToFullRangeFraction",
         "Changes the name of a given detector.\n"
         "Throws exception if 'OriginalName' did not exist." )
 
-//size_t combine_gamma_channels( const size_t ncombine, const size_t nchannels );
-//size_t truncate_gamma_channels( ...)
+  .def( "truncateGammaChannels", 
+        static_cast<size_t (SpecUtils::SpecFile::*)(const size_t, const size_t, const size_t, const bool)>(&SpecUtils::SpecFile::truncate_gamma_channels),
+        "KeepFirstChannel"_a, "KeepLastChannel"_a, "NChannels"_a, "KeepUnderOverFlow"_a,
+        "Removes all channels below 'KeepFirstChannel' and above 'KeepLastChannel', "
+        "for every measurement that has 'NChannels' channels.\n"
+        "If 'KeepUnderOverFlow' is true, then removed channel counts will be added to the first/last channel.\n"
+        "Returns the number of modified measurements.\n"
+        "Throws exception if KeepLastChannel>=NChannels, or if KeepFirstChannel>=KeepLastChannel." )
+  .def( "truncateGammaChannels", 
+        static_cast<void (SpecUtils::SpecFile::*)(const size_t, const size_t, const bool, const std::shared_ptr<const SpecUtils::Measurement> &)>(&SpecUtils::SpecFile::truncate_gamma_channels),
+        "KeepFirstChannel"_a, "KeepLastChannel"_a, "KeepUnderOverFlow"_a, "Measurement"_a,
+        "Removes all channels below 'KeepFirstChannel' and above 'KeepLastChannel' for the specified measurement.\n"
+        "If 'KeepUnderOverFlow' is true, then removed channel counts will be added to the first/last channel.\n"
+        "Throws exception if invalid Measurement, or if KeepLastChannel>=measurement.num_gamma_channels(), "
+        "or if KeepFirstChannel>=KeepLastChannel." )
+  .def( "combineGammaChannels", 
+        static_cast<size_t (SpecUtils::SpecFile::*)(const size_t, const size_t)>(&SpecUtils::SpecFile::combine_gamma_channels),
+        "NCombine"_a, "NChannels"_a,
+        "Combines every 'NCombine' adjacent channels into a single channel for every measurement "
+        "that has 'NChannels' channels.\n"
+        "Returns the number of modified measurements.\n"
+        "Throws exception if (NChannels % NCombine) != 0." )
+  .def( "combineGammaChannels", 
+        static_cast<void (SpecUtils::SpecFile::*)(const size_t, const std::shared_ptr<const SpecUtils::Measurement> &)>(&SpecUtils::SpecFile::combine_gamma_channels),
+        "NCombine"_a, "Measurement"_a,
+        "Combines every 'NCombine' adjacent channels into a single channel for the specified measurement.\n"
+        "Throws exception if measurement is not owned by this SpecFile." )
 
   // Begin functions that set Measurement quantities, through thier SpecFile owner
   .def( "setLiveTime", &SpecUtils::SpecFile::set_live_time, 

bindings/python/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "SandiaSpecUtils"
-version = "0.0.6"
+version = "0.0.9"
 description = "Python bindings for SpecUtils using nanobind and scikit-build"
 readme = "README.md"
 requires-python = ">=3.9"

d3_resources/SpectrumChartD3.css

@@ -197,7 +197,7 @@ svg.SpectrumChartD3 {
 .mouseInfoBox{ fill: white; fill-opacity: 0.85; }
 
 .refLineCandidatesText {
-  font-size: 0.8em;
+  font-size: 1.2em;
   /* Not setting fill, so defaults to black - should be same behaviour as legend. */
   /* fill: var(--d3spec-text-color, black); */
 }

d3_resources/SpectrumChartD3.js

@@ -4121,7 +4121,6 @@ SpectrumChartD3.prototype.setKineticReferenceLines = function( data ) {
       } );  
     } );
   }//if( data )
-  //console.log( "setKineticReferenceLines:", data );
 
   this.kineticRefLines = data;
 
@@ -4138,6 +4137,7 @@ SpectrumChartD3.prototype.handleUpdateKineticRefLineUpdate = function(){
       this.currentKineticRefLineIndex = 0;
       this.stopKineticRefLineCycling();
       this.drawRefGammaLines();
+      this.updateKineticRefLineCandidateDisplay();
     }
     return;
   }//if( we dont need to draw the lines )
@@ -4266,10 +4266,12 @@ SpectrumChartD3.prototype.startKineticRefLineCycling = function(){
   const self = this;
 
   this.stopKineticRefLineCycling();
-  
-  if( this.candidateKineticRefLines.length <= 1 ) {
+  if( this.candidateKineticRefLines.length <= 1 )
     return;
-  }
+  
+  // If an element has active focus, then the arrow keys may not get through
+  if (document.activeElement instanceof HTMLElement)
+    document.activeElement.blur();
 
   this.kineticRefLineCycleTimer = setInterval(function(){
     if( self.kineticRefLineCycleTimer && self.candidateKineticRefLines.length > 1 ) {