add headers for pipeline pass

sammy/src/io/hdf5IO.cpp

@@ -25,7 +25,9 @@ namespace sammy {
         char sect9[9][MAX_NAME_LEN] = {};
 
         // HDF5 accepts set-size double arrays for datasets: copy over
-        double dset_data[data.size()][data[0].size()];
+        const size_t ns = head.numSection;
+        const size_t nc = head.numChan;
+        double dset_data[ns][nc];
         for( size_t i=0;i<data.size();++i ){
             std::copy(data[i].begin(),data[i].end(), dset_data[i]);
         }

sammy/src/io/hdf5IO.h

@@ -4,6 +4,8 @@
 #include <vector>
 #include <fstream> // ifstream
 #include <iostream>
+#include <cstring>
+#include <stdexcept>
 #include "odfIO.h"
 #include "H5Cpp.h"