Fix parsing Lynx CSV files.

The "Energy Cali..." line was being mistaken for a column header.

Author: wcjohns

src/SpecFile_csv.cpp

@@ -1019,7 +1019,7 @@ void Measurement::set_info_from_txt_or_csv( std::istream& istr )
         }
 
         int channel = 0;
-        float energy = 0.0f, count = 0.0f; //, count2 = 0.0f;
+        float energy = 0.0f, count = 0.0f;
         for( size_t col = 0; col < fields.size(); ++col )
         {
           if( column_map.count(col) )
@@ -1029,7 +1029,6 @@ void Measurement::set_info_from_txt_or_csv( std::istream& istr )
               case kChannel:       channel = atoi(fields[col].c_str()); break;
               case kEnergy:        energy  = static_cast<float>(atof(fields[col].c_str())); break;
               case kCounts:        count   = static_cast<float>(atof(fields[col].c_str())); break;
-              //case kCounts + 1:    count2  = static_cast<float>(atof(fields[col].c_str())); break;
               default:
                 // \TODO: Ignoring past the first record...
                 assert( column_map[col] > kCounts );
@@ -1040,12 +1039,9 @@ void Measurement::set_info_from_txt_or_csv( std::istream& istr )
 
         if( IsNan(energy) || IsInf(energy) )
           continue;
-        if( IsNan(count) || IsInf(count) /*|| IsNan(count2) || IsInf(count2)*/ )
+        if( IsNan(count) || IsInf(count) )
           continue;
 
-        //        if( errno )
-        //          throw runtime_error( "Error converting to float" );
-        
         energy *= energy_units;
 
         if( (energies->size() && (energies->back() > energy) )
@@ -1062,11 +1058,11 @@ void Measurement::set_info_from_txt_or_csv( std::istream& istr )
       }while( SpecUtils::safe_get_line( istr, line, maxlen ) );
 
       if( counts->empty() )
-        throw runtime_error( "Didnt find and channel counts" );
+        throw runtime_error( "Didnt find any channel counts" );
 
       gamma_counts_ = counts;
 
-      if( (energies->size() >= counts->size()) && (energies->back()!=0.0f) )
+      if( (energies->size() >= counts->size()) && (energies->back() != 0.0f) )
       {
         try
         {
@@ -1082,12 +1078,20 @@ void Measurement::set_info_from_txt_or_csv( std::istream& istr )
 
       break;
     }else if( column_map.empty()
-             && (  istarts_with( fields[0], "channel" )
+             && (
+                 //Let counts header be "Channel", "Counts", "Ch", or similar non-English varients
+                 istarts_with( fields[0], "channel" )
                  || istarts_with( fields[0], "counts" )
-                 || istarts_with( fields[0], "data" )
-                 || istarts_with( fields[0], "energy" )
                  || istarts_with( fields[0], "Ch" )
                  || istarts_with( fields[0], "Канал" )
+                 //For a single column data
+                 || istarts_with( fields[0], "data" )
+                 //energy header can be like "Energy", "Energy (keV)", "En", or similar, but we dont
+                 //  want to mistake something like "Energy Calibration, ..." as a column header
+                 || istarts_with( fields[0], "energy (" )
+                 || iequals_ascii(fields[0], "energy" )
+                 || iequals_ascii(fields[0], "en" )
+                 || iequals_ascii(fields[0], "en (" )
                  || fields[0]=="##" ) )
     {
       ++nlines_used;
@@ -1345,21 +1349,53 @@ void Measurement::set_info_from_txt_or_csv( std::istream& istr )
 
       if( c > 0 || b > 0 )
         poly_calib_coeff = { d, c, b, a };
+    }else if( poly_calib_coeff.empty()
+             && starts_with( fields[0], "energy calibration" )
+             && (fields.size() >= 3)
+             && starts_with( fields[1], "offset:" )
+             && starts_with( fields[2], "slope:" ) )
+    {
+      // Canberra Lynx CSV files get here
+      //fields == {"energy calibration", "offset: -2.69", "slope: 0.37", "quadratic: -2.89e-7"}
+      //Note: because lower channel energies are also provided, this polynomial calibration we are
+      //      parsing out here, wont be used.
+      map<string,float> vals_map{ {"offset", 0.0f}, {"slope", 0.0f}, {"quadratic", 0.0f} };
+        
+      for( size_t i = 1; i < fields.size(); ++i )
+      {
+        float val;
+        vector<string> parts;
+        SpecUtils::split( parts, fields[i], ": \t" );
+        
+        if( (parts.size() >= 2) && SpecUtils::parse_float(parts[1].c_str(), parts[1].size(), val) )
+          vals_map[parts[0]] = val;
+      }
+        
+      poly_calib_coeff = vector<float>{ vals_map["offset"], vals_map["slope"], vals_map["quadratic"] };
+      while( !poly_calib_coeff.empty() && (poly_calib_coeff.back() == 0.0) )
+        poly_calib_coeff.resize( poly_calib_coeff.size() - 1 );
+    }else
+    {
+      // unidentified line
     }
-    
   }//while( getline( istr, line ) )
 
-  if( nlines_total < 10 || nlines_used < static_cast<size_t>( ceil(0.25*nlines_total) ))
+  if( (nlines_total < 10) || (nlines_used < static_cast<size_t>( ceil(0.25*nlines_total) )) )
   {
     reset();
     istr.seekg( orig_pos, ios::beg );
     istr.clear( ios::failbit );
     throw runtime_error( "Not enough (useful) lines in the file." );
   }//
 
+  // If we have polynomial energy calibration terms, we will only use them if we dont already
+  //  have another energy calibration - this includes when lower channel energies are specified
+  //  (perhaps we should check if polynomial and lower channel energies are about the same, and
+  //   if so, go with the polynomial)
   const size_t nchannel = gamma_counts_ ? gamma_counts_->size() : size_t(0);
-  if( nchannel>=2 && !poly_calib_coeff.empty()
-      && (energy_calibration_->type() == EnergyCalType::InvalidEquationType) )
+  if( (nchannel >= 2)
+     && (poly_calib_coeff.size() >= 2)
+     && (energy_calibration_->type() == EnergyCalType::InvalidEquationType) )
   {
     try
     {