Some small cleanups.

Fix SpecUtils Threadpool not going serial execution on macOS, when selected for in CMake.
Fixed some warnings, and some small cleanup.

Author: wcjohns

SpecUtils/SpecUtilsAsync.h

@@ -33,17 +33,16 @@
 #include <functional>
 #include <condition_variable>
 
-
-#if( __APPLE__ && __clang__ )
+#if( SpecUtils_USING_NO_THREADING )
+  #define ThreadPool_USING_SERIAL 1
+#elif( SpecUtils_USE_WT_THREADPOOL )
+  #define ThreadPool_USING_WT 1
+#elif( __APPLE__ && __clang__ )
   //On apple systems, when we use Apples compilers, we can use Grand Central
   //  Dispatch (GCD) to power the queue.
   //  ToDo: Would !defined(__GNUC__) be better than __clang__ ?
   #include <dispatch/dispatch.h>
   #define ThreadPool_USING_GCD 1
-#elif( SpecUtils_USE_WT_THREADPOOL )
-  #define ThreadPool_USING_WT 1
-#elif( SpecUtils_USING_NO_THREADING )
-  #define ThreadPool_USING_SERIAL 1
 #else
   #define ThreadPool_USING_THREADS 1
   #if( __APPLE__ )

src/ParseUtils.cpp

@@ -147,6 +147,9 @@ void expand_counted_zeros( const vector<float> &data, vector<float> &return_answ
       if( (*iter) <= 0.5f )
         throw runtime_error( "Invalid counted zeros: less than one number of zeros" );
 
+      if( (*iter) > 65537.0f )
+        throw runtime_error( "Invalid counted zeros: too large number of zeros" );
+      
       const size_t nZeroes = ((iter==data.end()) ? 0u : static_cast<size_t>(floor(*iter + 0.5f)) );
 
       if( (answer.size() + nZeroes) > 131072 )

src/SerialToDetectorModel.cpp

@@ -262,7 +262,10 @@ namespace SerialToDetectorModel
       uint32_t val = 0;
       try
       {
-        val = stoul( strval, nullptr, 10 );
+        unsigned long tmp_val = stoul( strval, nullptr, 10 );
+        //I guess we'll truncate, although we shouldnt actually get this, given the known
+        //  length of these serial numbers
+        val = static_cast<uint32_t>( tmp_val );
         if( strval.size() >= 2 && val < 100 )
           continue;
       }catch(...)

src/SpecFile_cnf.cpp

@@ -170,7 +170,7 @@ namespace
             //duration in years is larger than an int32, divide by a million years
             if ( (duration / 31557600.0) > static_cast<double>(INT32_MAX) )
             {
-                int32_t y_duration = static_cast<int32_t>(t_duration / 1e6);
+                int32_t y_duration = SpecUtils::float_to_integral<int32_t>(t_duration / 1e6);
                 const auto y_bytes = to_bytes(y_duration);
                 std::copy(begin(y_bytes), end(y_bytes), begin(bytes));
                 //set the flags
@@ -884,7 +884,7 @@ bool SpecFile::write_cnf( std::ostream &output, std::set<int> sample_nums,
         }
 
  //TODO: implement converted shape calibration information into CNF files 
-        //shape calibration, just use the defualt values for NaI detectors if the type cotains any NaI, if not use Ge defaults
+        //shape calibration, just use the default values for NaI detectors if the type cotains any NaI, if not use Ge defaults
         const string& detector_type = summed->detector_type();
         enter_CAM_value("SQRT", cnf_file, acqp_loc + 0x464, cam_type::cam_string);
         if(detector_type.find("NaI") == 0 || detector_type.find("nai") == 0 || detector_type.find("NAI") == 0)

src/SpecFile_gr135.cpp

@@ -817,7 +817,7 @@ bool SpecFile::write_binary_exploranium_gr130v0( std::ostream &output ) const
 
       //Lets write to a buffer before writing to the stream to make things a
       //  little easier in terms of keeping track of position.
-      char buffer[561];
+      uint8_t buffer[561];
       memset( buffer, 0, sizeof(buffer) );
 
       memcpy( buffer + 0, "ZZZZ", 4 );
@@ -841,9 +841,9 @@ bool SpecFile::write_binary_exploranium_gr130v0( std::ostream &output ) const
           const date::hh_mm_ss<time_point_t::duration> time_of_day = date::make_time(t - t_as_days);
           const unsigned day = static_cast<unsigned>( t_ymd.day() );
           const unsigned month = static_cast<unsigned>( t_ymd.month() );
-          const int hour = time_of_day.hours().count();
-          const int mins = time_of_day.minutes().count();
-          const int secs = time_of_day.seconds().count();
+          const int hour = static_cast<int>( time_of_day.hours().count() );
+          const int mins = static_cast<int>( time_of_day.minutes().count() );
+          const int secs = static_cast<int>( time_of_day.seconds().count() );
 
           buffer[7] = static_cast<uint8_t>(year);
           buffer[8] = static_cast<uint8_t>(month);
@@ -914,7 +914,7 @@ bool SpecFile::write_binary_exploranium_gr130v0( std::ostream &output ) const
 
       buffer[559] = 0; //CHSUM    check sum
 
-      output.write( buffer, 560 );
+      output.write( (const char *)buffer, 560 );
 
       ++nwrote;
     }//for( size_t measn = 0; measn < nmeas; ++measn )
@@ -975,7 +975,7 @@ bool SpecFile::write_binary_exploranium_gr135v2( std::ostream &output ) const
 
       //Lets write to a buffer before writing to the stream to make things a
       //  little easier in terms of keeping track of position.
-      char buffer[76+2*noutchannel] = { '\0' };
+      uint8_t buffer[76+2*noutchannel] = { '\0' };
       memset( buffer, 0, sizeof(buffer) );
 
       memcpy( buffer + 0, "ZZZZ", 4 );
@@ -1002,9 +1002,9 @@ bool SpecFile::write_binary_exploranium_gr135v2( std::ostream &output ) const
           const date::hh_mm_ss<time_point_t::duration> time_of_day = date::make_time(t - t_as_days);
           const unsigned day = static_cast<unsigned>( t_ymd.day() );
           const unsigned month = static_cast<unsigned>( t_ymd.month() );
-          const int hour = time_of_day.hours().count();
-          const int mins = time_of_day.minutes().count();
-          const int secs = time_of_day.seconds().count();
+          const int hour = static_cast<int>( time_of_day.hours().count() );
+          const int mins = static_cast<int>( time_of_day.minutes().count() );
+          const int secs = static_cast<int>( time_of_day.seconds().count() );
 
           buffer[13] = static_cast<uint8_t>(year - 2000);
           buffer[14] = static_cast<uint8_t>(month);
@@ -1104,7 +1104,7 @@ bool SpecFile::write_binary_exploranium_gr135v2( std::ostream &output ) const
 
       //2*nch+76  unsigned char    CHSUM    check sum
 
-      output.write( buffer, 76+2*noutchannel );
+      output.write( (const char *)buffer, 76+2*noutchannel );
 
       ++nwrote;
     }//for( size_t measn = 0; measn < nmeas; ++measn )

src/SpecFile_n42.cpp

@@ -940,12 +940,12 @@ namespace
   //add_spectra_to_measurement_node_in_2012_N42_xml(...): Adds the given
     //  spectra to the specified RadMeasurementNode.  All measurements should
     //  have the sample sample number, and the entries in calibid should
-    //  coorespond one to one to the entries in measurements.
+    //  correspond one to one to the entries in measurements.
     //  If something drastically goes wrong, and an exception is thrown somewhere
     //  this function will not throw, it will print an error to stderror and not
     //  insert itself into the DOM; this is so this function is safe to call in
     //  its own thread with no error handling.  I expect this to never happen, so
-    //  I'm not bothing with any better error handling.
+    //  I'm not bothering with any better error handling.
 
 void add_spectra_to_measurement_node_in_2012_N42_xml( ::rapidxml::xml_node<char> *RadMeasurement,
                   const std::vector< std::shared_ptr<const SpecUtils::Measurement> > measurements,
@@ -1089,8 +1089,11 @@ void add_spectra_to_measurement_node_in_2012_N42_xml( ::rapidxml::xml_node<char>
 
     for( size_t i = 0; i < measurements.size(); ++i )
     {
+      assert( i < calibids.size() );
+      
       const size_t calibid = calibids[i];
-      const std::shared_ptr<const Measurement> m = measurements[i];
+      const shared_ptr<const Measurement> m = measurements[i];
+      assert( m );
 
       char livetime[32], calibstr[32], spec_id_cstr[48];
 
@@ -1114,8 +1117,7 @@ void add_spectra_to_measurement_node_in_2012_N42_xml( ::rapidxml::xml_node<char>
         //Probably shouldnt ever make it here.
         snprintf( spec_id_cstr, sizeof(spec_id_cstr), "Sample%iDet%iSpectrum", m->sample_number(), m->detector_number() );
       }
-      
-      spec_id_cstr[sizeof(spec_id_cstr) - 1] = '0'; //jic
+      spec_id_cstr[sizeof(spec_id_cstr) - 1] = '\0'; //jic
       string spec_idstr = spec_id_cstr;
 
       // If this is a derived data Measurement, we will append derived data properties to the "id"

src/SpecFile_spc.cpp

@@ -1083,7 +1083,7 @@ bool SpecFile::write_ascii_spc( std::ostream &output,
         //  other file formats to SPC, but such is life
         if(!res.nuclide_.empty() && !res.nuclide_type_.empty())
         {
-          const string postfix = string("") + char('0' + i);
+          const string postfix = std::to_string(i);
           output << pad_iaea_prefix( "Nuclide" + postfix ) << res.nuclide_ << "\r\n";
           if( SpecUtils::istarts_with(res.remark_, "Strength ") )
             output << pad_iaea_prefix( "Strength" + postfix ) << res.nuclide_ << "\r\n";
@@ -1093,7 +1093,7 @@ bool SpecFile::write_ascii_spc( std::ostream &output,
           output << pad_iaea_prefix( "Confidence" + postfix ) << res.id_confidence_ << "\r\n";
         }else if(!res.nuclide_.empty())
         {
-          const string postfix = string("") + char('1' + i);
+          const string postfix = std::to_string(i + 1);
           output << pad_iaea_prefix( "NuclideID" + postfix ) << res.nuclide_ << "\r\n";
         }
       }//
@@ -1392,6 +1392,7 @@ bool SpecFile::write_binary_spc( std::ostream &output,
     case DetectorType::VerifinderNaI:
     case DetectorType::VerifinderLaBr:
     case DetectorType::KromekD3S:
+    case DetectorType::RadiaCode:
     case DetectorType::Unknown:
       defaultname = "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
       break;

src/SpecFile_spe.cpp

@@ -808,7 +808,13 @@ bool SpecFile::load_from_iaea( std::istream& istr )
               vector<float> parts;
               SpecUtils::split_to_floats( line.c_str(), line.size(), parts );
               if( parts.size() == 2 )
-                bin_to_energy.push_back( make_pair(static_cast<int>(parts[0]),parts[1]) );
+              {
+                // Only add this point if the channel and energy are reasonable.
+                const int bin = float_to_integral<int>(parts[0]);
+                const float energy = parts[1];
+                if( (bin >= 0) && (bin < 131072) && (energy >= 0.0f) && (energy < 3000000.0f) )
+                  bin_to_energy.emplace_back( bin, parts[1] );
+              }
             }
           }//while( SpecUtils::safe_get_line( istr, line ) )
         }//if( file says how many entries to expect )
@@ -1058,10 +1064,10 @@ bool SpecFile::load_from_iaea( std::istream& istr )
           continue;
 
         int numresults = 0;
-        if( !toInt(analines[0], numresults) || numresults <= 0 )
+        if( !toInt(analines[0], numresults) || (numresults <= 0) )
           continue;
 
-        if( (analines.size()-1) != numresults*4 )
+        if( (analines.size()-1) != (4*static_cast<size_t>(numresults)) )
         {
           string remark;
           for( size_t i = 0; i < analines.size(); ++i )

src/StringAlgo.cpp

@@ -1621,6 +1621,9 @@ std::wstring convert_from_utf8_to_utf16( const std::string &input )
 
   std::string sequencesToBriefString( const std::set<int> &sample_numbers )
   {
+    if( sample_numbers.empty() )
+      return "";
+      
     stringstream editVal;
 
     int added = 0;