diff --git a/sammy/src/io/CMakeLists.txt b/sammy/src/io/CMakeLists.txt
index 10a4c64a62e4391c5e12462b7ea0d045be93b911..99491c78fb4ca1d9a0d7e62536202331a21b5e66 100644
--- a/sammy/src/io/CMakeLists.txt
+++ b/sammy/src/io/CMakeLists.txt
@@ -2,15 +2,18 @@ INCLUDE(SammyPackageSetup)
TRIBITS_PACKAGE(io)
+find_package(HDF5 REQUIRED COMPONENTS C CXX HL)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/../sammy_conf.h.in sammy_conf.h @ONLY)
-INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
+INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}
+ ${HDF5_INCLUDE_DIR})
# Set headers
SET(HEADERS ExperimentalParametersIO.h
odfIO.h
+ hdf5IO.h
interface/cpp/ExperimentalParametersIOInterface.h
)
@@ -18,6 +21,7 @@ APPEND_SET(IO_SOURCES
ExperimentalParametersIO.cpp
odfIO.cpp
+ hdf5IO.cpp
interface/cpp/ExperimentalParametersIOInterface.cpp
interface/fortran/ExperimentalParametersIO_M.f90
interface/fortran/ExperimentalParametersIO_I.f90
@@ -36,3 +40,15 @@ INSTALL(FILES ${HEADERS} DESTINATION "src/io")
TRIBITS_ADD_TEST_DIRECTORIES(tests)
TRIBITS_PACKAGE_POSTPROCESS()
+
+
+# --------------------------------------------
+# Build separate executable to convert ODF
+# to HDF5 files, install to normal location
+# --------------------------------------------
+
+add_executable(readodf readodf.cpp)
+target_link_libraries(readodf PRIVATE HDF5::HDF5
+ SammyIOUtilsLib)
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/readodf DESTINATION "bin/")
+
diff --git a/sammy/src/io/hdf5IO.cpp b/sammy/src/io/hdf5IO.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..188df114fef65fb4f4c45af0cbd9e4edf5295028
--- /dev/null
+++ b/sammy/src/io/hdf5IO.cpp
@@ -0,0 +1,11 @@
+#include "hdf5IO.h"
+
+namespace sammy {
+
+ hdf5IO::hdf5IO() {}
+
+ void hdf5IO::writeODFtoHDF5(){
+ std::cout << "hello world" << std::endl;
+ }
+
+}
\ No newline at end of file
diff --git a/sammy/src/io/hdf5IO.h b/sammy/src/io/hdf5IO.h
new file mode 100644
index 0000000000000000000000000000000000000000..2113c59d325cf472a67fbb9f017003db935f9547
--- /dev/null
+++ b/sammy/src/io/hdf5IO.h
@@ -0,0 +1,25 @@
+#ifndef SAMMY_HDF5IO_H
+#define SAMMY_HDF5IO_H
+
+#include <vector>
+#include <fstream> // ifstream
+#include <iostream>
+#include "hdf5.h"
+
+namespace sammy{
+
+ class hdf5IO {
+
+ public:
+ hdf5IO();
+ virtual ~hdf5IO() {}
+
+ /****************************************
+ * Write data from ODF file into HDF5
+ ***************************************/
+ void writeODFtoHDF5();
+
+ };
+}
+
+#endif /* SAMMY_HDF5IO_H */
\ No newline at end of file
diff --git a/sammy/src/io/odfIO.cpp b/sammy/src/io/odfIO.cpp
index 885d94e04b15559e47fc02b5bf6e17f522453dc4..02b5b0b15c9baf426d222175c129699045e50497 100644
--- a/sammy/src/io/odfIO.cpp
+++ b/sammy/src/io/odfIO.cpp
@@ -16,7 +16,7 @@ namespace sammy{
fs.read( (char*)&tmp2, 1 );
fs.read( (char*)&tmp3, 1 );
fs.read( (char*)&tmp4, 1 );
- // std::cout << "1,2,3,4 = " << (int)tmp1<<","<< (int)tmp2<<","<< (int)tmp3<<","<< (int)tmp4<<","<<std::endl;
+ // to print: std::cout << "tmp1 = " << (int)tmp1 << std::endl;
if((tmp2 & 0x7f) == 0){
if(tmp1+tmp3+tmp4 != 0) {
tmp1=tmp2=tmp3=0;
@@ -39,8 +39,15 @@ namespace sammy{
return value;
}
+ int odfIO::readInteger(std::ifstream &fs){
+ size_t intsize = sizeof(int);
+ int val;
+ fs.read( (char*)&val, intsize );
+ return val;
+ }
+
std::vector<double> odfIO::getSection(int start, int readSize, int section,
- header &hd, std::ifstream &in){
+ odfHeader &hd, std::ifstream &in){
in.seekg(0,std::ios::beg);
std::vector<double> dataSec;
int block,skipped,channel,max;
@@ -62,7 +69,7 @@ namespace sammy{
int read = 0;
for(int i=0;i<max;i++){
if( hd.mode == 3 ) dataSec[read] = readFloat(in,hd.unix);
- else if( hd.mode == 1 ) dataSec[read] = readFloat(in,hd.unix); // needs to read integer not float
+ else if( hd.mode == 1 ) dataSec[read] = readInteger(in);
read++;
}
in.ignore(intsize*2); // skip over two ints in the block which contain no data
@@ -74,7 +81,7 @@ namespace sammy{
for( int i=0; i<125 && read<readSize; i++ ) {
if( hd.mode == 3) dataSec[read] = readFloat(in,hd.unix);
- else if(hd.mode == 1) dataSec[read] = readFloat(in,hd.unix); // needs to read integer not float
+ else if(hd.mode == 1) dataSec[read] = readInteger(in);
read++;
}
in.ignore(intsize*2); // skip over two ints in the block which contain no data
@@ -83,11 +90,31 @@ namespace sammy{
return dataSec;
}
- void odfIO::readHeader(std::ifstream &in, header &head){
+ std::vector<std::vector<double>> odfIO::getAllSections(odfHeader &head,
+ std::ifstream &in){
+ // --- go to start of file ---
+ in.seekg(0, std::ios::beg);
+
+ std::vector<std::vector<double>> data;
+ data.resize(head.numSection);
+
+ // --- grab each section ---
+ for( int section=1; section<=head.numSection; ++section ){
+ data[section-1].resize(head.numChan);
+ data[section-1] = getSection(0,head.numChan,section,head,in);
+ }
+
+ return data;
+ }
+
+ void odfIO::readHeader(std::ifstream &in, odfHeader &head){
size_t intsize = sizeof(int);
int bytes_per_block = 512;
int bytes_per_word = 4;
// comments based on OPRODF manual: Jack Craven, report no. ORNL/CSD/TM-45, 1978
+ // ** keep in mind that changes may have happened between that report and
+ // ** the writing of the files!!! For example it seems that 36 bit ints are no
+ // ** longer used.
in.read( (char*)&head.mode, intsize ); // 0,1,3 for 18-bit ints, 36-bit ints, floating-point vals
in.read( (char*)&head.source, intsize ); // 0,1,2 for SEL, CSISRS, or ENDF/B data
in.read( (char*)&head.irun, intsize ); // run number
@@ -142,7 +169,7 @@ namespace sammy{
int bytes_to_scalars = (head.nsblks) * bytes_per_block;
}
- void odfIO::printHeader(header &head){
+ void odfIO::printHeader(odfHeader &head){
std::cout << "mode = " << head.mode << std::endl
<< "source = " << head.source << std::endl
<< "irun = " << head.irun << std::endl
diff --git a/sammy/src/io/odfIO.h b/sammy/src/io/odfIO.h
index 34f24b874ad98f036153d9fbc86fb37cb9b834b3..687637102290c95b7542e04f0c7c80f1682be871 100644
--- a/sammy/src/io/odfIO.h
+++ b/sammy/src/io/odfIO.h
@@ -7,35 +7,43 @@
namespace sammy{
+ /****************************************
+ * Object for ODF header info
+ ***************************************/
+ struct odfHeader {
+ // variables explained in readHeader()
+ int mode, source, irun;
+ int ncblks, ncwrds, nsblks, nswrds, ncstrt, ncntrs, nxstrt, nxwrds;
+ int npblks, npwrds, ndtype, numSection, ifb, numChan;
+ int zan, awr, mat, mf, mt; // ENDF identifiers
+ int varswt,dctswt,strt,ndwend;
+ bool unix;
+ std::vector<int> ndtbl;
+ };
+
class odfIO {
public:
odfIO();
virtual ~odfIO() {}
- /****************************************
- * Object for ODF header info
- ***************************************/
- struct header {
- // variables explained in readHeader()
- int mode, source, irun;
- int ncblks, ncwrds, nsblks, nswrds, ncstrt, ncntrs, nxstrt, nxwrds;
- int npblks, npwrds, ndtype, numSection, ifb, numChan;
- int zan, awr, mat, mf, mt; // ENDF identifiers
- int varswt,dctswt,strt,ndwend;
- bool unix;
- std::vector<int> ndtbl;
- };
-
/****************************************
* Read a single floating point value, based on whether it is in
* VAX-VMS format (?) or unix, from an ODF file
*
* @param fs a reference to the ODF file stream
* @param unix whether or not the format is unix-style
+ * @return val the stored value
***************************************/
double readFloat(std::ifstream &fs, bool unix);
+ /****************************************
+ * Read a single integer
+ * @param fs a reference to the ODF file stream
+ * @return val the stored value
+ ***************************************/
+ int readInteger(std::ifstream &fs);
+
/****************************************
* Read one section of data. Sections are typcially energy, transmission,
* cross section, etc.
@@ -43,9 +51,23 @@ namespace sammy{
* @param start what channel to start in
* @param readSize how many channels to read
* @param section which section to read from
+ * @param head a struct containing the header info
+ * @param in the input data file stream
+ * @return dataSec all requested channels of requested section
***************************************/
std::vector<double> getSection(int start, int readSize, int section,
- header &hd, std::ifstream &in);
+ odfHeader &head, std::ifstream &in);
+
+ /****************************************
+ * Read all sections of data into double-vector, grabbing all info.
+ * This calls getSection() for all sections and channels
+ *
+ * @param head a struct containing the header info
+ * @param in the input data file stream
+ * @return data all channels and all sections of data
+ ***************************************/
+ std::vector<std::vector<double>> getAllSections(odfHeader &head,
+ std::ifstream &in);
/****************************************
* Read the ODF header
@@ -53,14 +75,14 @@ namespace sammy{
* @param fs a reference to the ODF file stream
* @param head an ODF-header struct
***************************************/
- void readHeader(std::ifstream &in, header &head);
+ void readHeader(std::ifstream &in, odfHeader &head);
/****************************************
* Print the ODF header
*
* @param head an ODF-header struct
***************************************/
- void printHeader(header &head);
+ void printHeader(odfHeader &head);
};
}
diff --git a/sammy/src/io/readodf.cpp b/sammy/src/io/readodf.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..81fae8410b9202f17f36a5316fbb5ccfa70921b7
--- /dev/null
+++ b/sammy/src/io/readodf.cpp
@@ -0,0 +1,163 @@
+#include <iostream>
+// #include "hdf5.h"
+#include "H5Cpp.h"
+#include "odfIO.h"
+
+#define MAX_NAME_LEN 32
+
+int main(int argc, char const *argv[])
+{
+ // -------------------------------------------------------------------------
+ // --- Grabbing the input args
+ // -------------------------------------------------------------------------
+ if( argc < 3 ){
+ std::cerr << "Wrong number of arguments given." << std::endl
+ << "Specify input ODF file and output HDF5 file." << std::endl;
+ return -1;
+ }
+
+ std::string odfFilename = argv[1];
+ std::string hdf5Filename = argv[2];
+
+ std::cout << "Reading from file: " << odfFilename << std::endl;
+ std::cout << "Writing to file: " << hdf5Filename << std::endl;
+
+ // -------------------------------------------------------------------------
+ // --- Read ODF file
+ // -------------------------------------------------------------------------
+ sammy::odfIO odf;
+ sammy::odfHeader head;
+ std::vector<std::vector<double>> data;
+
+ // --- Open file ---
+ std::ifstream in( odfFilename, std::ios::in | std::ios::binary );
+ // --- kill bad open ---
+ if( !in.is_open() ){
+ std::cerr << "Error opening file: " << odfFilename << std::endl;
+ return 1;
+ }
+
+ // --- read header ---
+ odf.readHeader(in, head);
+
+ // --- read data sections ---
+ data = odf.getAllSections(head, in);
+
+ in.close();
+
+ // -------------------------------------------------------------------------
+ // --- Output HDF5 file
+ // -------------------------------------------------------------------------
+
+ char sectnames[11][MAX_NAME_LEN] = {"energy","trans","dtrans",
+ "cro","dcro","cs","zero","co","zero","idk","dcs"};
+
+ // make dataset
+ double dset_data[data.size()][data[0].size()];
+ for( size_t i=0;i<data.size();++i ){
+ std::copy(data[i].begin(),data[i].end(), dset_data[i]);
+ }
+
+ // write 2 datasets: data and data section names
+
+ // 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");
+
+ // section names space
+ hsize_t sdim[1];
+ sdim[0] = head.numSection;
+
+ int srank = sizeof(sdim) / sizeof(hsize_t);
+
+ std::string sectionnames("/data/sectnames");
+
+
+ // open file and write
+ H5::DataSpace dspace(drank,ddim);
+ H5::DataSpace sspace(srank,sdim);
+ H5::H5File *file = new H5::H5File(hdf5Filename,H5F_ACC_TRUNC);
+ H5::Group *group = new H5::Group( file->createGroup( "/data" ));
+
+ 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));
+
+ dataset->write(dset_data,H5::PredType::NATIVE_DOUBLE);
+ nameset->write(sectnames,H5::StrType(H5::PredType::C_S1, MAX_NAME_LEN));
+
+ delete file;
+ delete dataset;
+ delete nameset;
+
+
+ /* old
+
+ // --- setup with HDF types ---
+ hid_t file_id, dataspace_id, dataset_id, group_id, name_dataspace_id;
+ hid_t name_dataset_id;
+ herr_t status;
+ hsize_t dims[2];
+
+ //energy,trans,dtrans,cro,dcro,cs,zero,co,zero,idk,dcs
+
+ dims[0] = data.size();
+ dims[1] = data[0].size();
+ dataspace_id = H5Screate_simple(2, dims, NULL);
+
+ // --- open file ---
+ file_id = H5Fcreate(hdf5Filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ // --- make a dataset group ---
+ group_id = H5Gcreate2(file_id,"data",H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
+
+ // --- create dataset ---
+ // H5T_IEEE_F64LE is an HDF5 predefined datatype for 64 bit floating point,
+ // little endian. Might replace with H5T_NATIVE_DOUBLE
+ dataset_id = H5Dcreate2(file_id, "/data/sections", H5T_IEEE_F64LE, dataspace_id,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ double dset_data[data.size()][data[0].size()];
+ for( size_t i=0;i<data.size();++i ){
+ std::copy(data[i].begin(),data[i].end(), dset_data[i]);
+ }
+
+ // --- Write the dataset to file ---
+ status = H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ dset_data);
+
+
+ // --- write column names for dataset ---
+ std::vector<std::string> colnames;
+ colnames.resize(11);
+ colnames = {"energy","trans","dtrans","cro","dcro","cs",
+ "zero","co","zero","idk","dcs"};
+ std::string name = "energy";
+ const char* cname = name.c_str();
+
+ hid_t datatype = H5Tcopy (H5T_C_S1);
+ size_t MAX_NAME_LENGTH = 32;
+ H5Tset_size (datatype, H5T_VARIABLE);
+ hsize_t name_dims[1];
+ name_dims[0] = 1;
+ name_dataspace_id = H5Screate_simple(1, name_dims, NULL);
+ name_dataset_id = H5Dcreate2(file_id, "/data/colnames", datatype,
+ name_dataspace_id, H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ for( auto name : colnames ){
+ const char* cname = name.c_str();
+ status = H5Dwrite(name_dataset_id, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ &cname);
+ }
+
+
+ status = H5Fclose(file_id);
+
+ */
+
+ return 0;
+}
\ No newline at end of file