added function to replace NaN/Inf with low values near zero

Author: Arthur Glowacki

src/data_struct/spectra.h

@@ -164,6 +164,18 @@ class Spectra : public ArrayTr<_T>
         }
     }
 
+    void set_nan_to_near_zero()
+    {
+        for(Eigen::Index i = 0; i < this->size(); i++)
+        {
+            if( false == std::isfinite((*this)[i]) )
+            {
+                (*this)[i] = default_time_and_io_counts;
+            }
+        }
+       // this = this.unaryExpr([](double v) { return std::isfinite(v) ? v : default_time_and_io_counts; });
+    }
+
     void add(const Spectra<_T>& spectra)
     {
         *this += (ArrayTr<_T>)spectra;

src/data_struct/spectra_line.cpp

@@ -136,6 +136,16 @@ void Spectra_Line<T_real>::recalc_elapsed_livetime()
         _data_line[i].recalc_elapsed_livetime();
     }
 }
+// ----------------------------------------------------------------------------
+
+template<typename T_real>
+void Spectra_Line<T_real>::set_nan_to_near_zero()
+{
+    for(size_t i=0; i<_data_line.size(); i++)
+    {
+        _data_line[i].set_nan_to_near_zero();
+    }
+}
 
 // ----------------------------------------------------------------------------
 // ----------------------------------------------------------------------------

src/data_struct/spectra_line.h

@@ -83,6 +83,8 @@ class DLL_EXPORT Spectra_Line
 
     size_t samples_size() const { if (_data_line.size() > 0) return _data_line[0].size(); else return 0; }
 
+    void set_nan_to_near_zero();
+    
 private:
 
 

src/data_struct/spectra_volume.cpp

@@ -212,6 +212,17 @@ void Spectra_Volume<T_real>::recalc_elapsed_livetime()
 
 // ----------------------------------------------------------------------------
 
+template<typename T_real>
+void Spectra_Volume<T_real>::set_nan_to_near_zero()
+{
+    for(size_t i=0; i<_data_vol.size(); i++)
+    {
+        _data_vol[i].set_nan_to_near_zero();
+    }
+}
+
+// ----------------------------------------------------------------------------
+
 template<typename T_real>
 void Spectra_Volume<T_real>::generate_scaler_maps(std::map<std::string, Scaler_Map<T_real>> *scaler_maps)
 {

src/data_struct/spectra_volume.h

@@ -92,6 +92,7 @@ class DLL_EXPORT Spectra_Volume
 
     int rank() { return 3; }
 
+    void set_nan_to_near_zero();
 private:
 
     std::vector<Spectra_Line<T_real> > _data_vol;