write header to h5 file as well

appended to group called meta

sammy/src/io/CMakeLists.txt

@@ -3,8 +3,6 @@ INCLUDE(SammyPackageSetup)
 TRIBITS_PACKAGE(io)
 
 find_package(HDF5 REQUIRED COMPONENTS C CXX HL)
-find_library( h5lib HDF5 )
-find_library( h5lib_CPP HDF5_CPP )
 
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/../sammy_conf.h.in sammy_conf.h @ONLY)
 
@@ -42,7 +40,7 @@ TRIBITS_ADD_TEST_DIRECTORIES(tests)
 
 TRIBITS_PACKAGE_POSTPROCESS()
 
-target_link_libraries(SammyIOUtilsLib ${h5lib} ${h5lib_CPP})
+target_link_libraries(SammyIOUtilsLib ${HDF5_LIBRARIES} ) # from find_package()
 
 # --------------------------------------------
 # Build separate executable to convert ODF

sammy/src/io/hdf5IO.cpp

 #include "hdf5IO.h"
-#include "H5Cpp.h"
-
-#define MAX_NAME_LEN 32
 
 namespace sammy {
     
@@ -17,7 +14,7 @@ namespace sammy {
             std::cerr << "Reading of ODF files with < 11 sections"
                       << "has not been implemented yet. " << std::endl;
             std::cerr << "---------------------------------------" << std::endl;
-            return;
+            throw std::runtime_error("Unrecognized ODF file.");
         }
         
         // HDF5 works best with set-size char arrays
@@ -31,13 +28,12 @@ namespace sammy {
             std::copy(data[i].begin(),data[i].end(), dset_data[i]);
         }
 
-        // write 2 datasets: data and data section names
+        // write 3 datasets: data, data section names, and header
 
         // data space
         hsize_t ddim[2];
         ddim[0] = head.numSection;
         ddim[1] = head.numChan;
-
         int drank = sizeof(ddim) / sizeof(hsize_t);
 
         std::string dataname("/data/sections");
@@ -45,28 +41,74 @@ namespace sammy {
         // section names space
         hsize_t sdim[1];
         sdim[0] = head.numSection;
-
         int srank = sizeof(sdim) / sizeof(hsize_t);
 
         std::string sectionnames("/data/sectnames");
 
+        // header
+        const int numMembers = 26;
+        sammy::odfMetaKey h5head[numMembers];
+        sammy::hdf5IO h5writer;
+        h5writer.fillHDF5header(head,h5head);
+
+        hsize_t mdim[1];
+        mdim[0] = sizeof(h5head) / sizeof(sammy::odfMetaKey);
+        int mrank = sizeof(mdim) / sizeof(hsize_t);
+
+        const std::string headername("/meta/header");
+        const std::string headKeyword("keyword");
+        const std::string headVal("val");
+
+        // define compound type for header struct
+        H5::CompType htype(sizeof(sammy::odfMetaKey));
+        htype.insertMember(headKeyword, HOFFSET(sammy::odfMetaKey, keyword),H5::StrType(H5::PredType::C_S1, MAX_NAME_LEN));
+        htype.insertMember(headVal,     HOFFSET(sammy::odfMetaKey, value  ),H5::PredType::NATIVE_INT);
+
         // open file and write
         H5::DataSpace dspace(drank,ddim);
         H5::DataSpace sspace(srank,sdim);
+        H5::DataSpace mspace(mrank,mdim);
         H5::H5File  *file = new H5::H5File(hdf5Filename,H5F_ACC_TRUNC);
         H5::Group   *group = new H5::Group( file->createGroup( "/data" ));
+        H5::Group   *metaGroup = new H5::Group( file->createGroup( "/meta" ));
 
         H5::DataSet *dataset = new H5::DataSet(file->createDataSet(dataname,H5::PredType::NATIVE_DOUBLE,dspace));
         H5::DataSet *nameset = new H5::DataSet(file->createDataSet(sectionnames,H5::StrType(H5::PredType::C_S1, MAX_NAME_LEN),sspace));
+        H5::DataSet *metaset = new H5::DataSet(file->createDataSet(headername,htype,mspace));
 
         dataset->write( dset_data, H5::PredType::NATIVE_DOUBLE );
         nameset->write( sect11,    H5::StrType(H5::PredType::C_S1, MAX_NAME_LEN) );
+        metaset->write( h5head,    htype );
 
         // sweep, sweep
         delete file;
         delete dataset;
         delete nameset;
+        delete metaset;
+    }
 
+    void hdf5IO::fillHDF5header(sammy::odfHeader &head,
+                                sammy::odfMetaKey h5head[]){
+
+        const int numMembers = 26;
+
+        char desc[numMembers][MAX_NAME_LEN] = {"mode","source","irun","ncblks",
+                        "ncwrds","nsblks","nswrds","ncstrt","ncntrs","nxstrt",
+                        "nxwrds","npblks","npwrds","ndtype","numSectio","ifb",
+                        "numChan","zan","awr","mat","mf","mt","varswt","dctswt",
+                        "strt","ndwend"};
+        int vals[numMembers] = {head.mode,head.source,head.irun,head.ncblks,
+                                head.ncwrds,head.nsblks,head.nswrds,head.ncstrt,
+                                head.ncntrs,head.nxstrt,head.nxwrds,head.npblks,
+                                head.npwrds,head.ndtype,head.numSection,head.ifb,
+                                head.numChan,head.zan,head.awr,head.mat,head.mf,
+                                head.mt,head.varswt,head.dctswt,head.strt,
+                                head.ndwend};
+
+        for( int i=0;i<numMembers;++i ){
+            std::strncpy(h5head[i].keyword, desc[i], MAX_NAME_LEN );
+            h5head[i].value = vals[i];
+        }
     }
 
 }
\ No newline at end of file

sammy/src/io/hdf5IO.h

@@ -22,6 +22,9 @@ namespace sammy{
                             std::vector<std::vector<double>> &data,
                             std::string hdf5Filename,
                             bool elevenSect);
+        
+        void fillHDF5header(sammy::odfHeader &head,
+                            sammy::odfMetaKey h5head[]);
     };
 }
 

sammy/src/io/odfIO.h

@@ -5,6 +5,8 @@
 #include <fstream> // ifstream
 #include <iostream>
 
+#define MAX_NAME_LEN 32
+
 namespace sammy{
 
     /****************************************
@@ -21,6 +23,11 @@ namespace sammy{
         std::vector<int> ndtbl;
     };
 
+    struct odfMetaKey{
+        char keyword[MAX_NAME_LEN];
+        int value;
+    };
+
     class odfIO {
     
     public:

sammy/src/io/readodf.cpp

@@ -53,5 +53,7 @@ int main(int argc, char const *argv[])
     sammy::hdf5IO h5writer;
     h5writer.writeODFtoHDF5(head,data,hdf5Filename,true);
 
+
+
     return 0;
 }
\ No newline at end of file