diff --git a/sammy/src/io/CMakeLists.txt b/sammy/src/io/CMakeLists.txt
index da5aeef64f02b2825fd5fce7348142afc31d8ea1..7db5e2b7a7e35f6ae43cbd4f43d379828f29e079 100644
--- a/sammy/src/io/CMakeLists.txt
+++ b/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
diff --git a/sammy/src/io/hdf5IO.cpp b/sammy/src/io/hdf5IO.cpp
index 1244c43e875df2e8bb56ca40937836d385b0686d..6279eed432f9edaf7b2f1f60a36d3a871d705624 100644
--- a/sammy/src/io/hdf5IO.cpp
+++ b/sammy/src/io/hdf5IO.cpp
@@ -1,7 +1,4 @@
#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
diff --git a/sammy/src/io/hdf5IO.h b/sammy/src/io/hdf5IO.h
index 5ffe53355f78a2a6eb5f477e79b1693b191a3b79..eb8b666fe004354bfdc1aa91dfcdde03486805b0 100644
--- a/sammy/src/io/hdf5IO.h
+++ b/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[]);
};
}
diff --git a/sammy/src/io/odfIO.h b/sammy/src/io/odfIO.h
index 687637102290c95b7542e04f0c7c80f1682be871..8be74ec5413762f1758cac1e5723ed72bf3f3aa9 100644
--- a/sammy/src/io/odfIO.h
+++ b/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:
diff --git a/sammy/src/io/readodf.cpp b/sammy/src/io/readodf.cpp
index 34cdc50fbac8bb64e8eb4e349d4dccbba5625f64..1848814bd9086ac9112c757f4093b9aa869466c6 100644
--- a/sammy/src/io/readodf.cpp
+++ b/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