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Commit 8b3f1b30 authored by Brown's avatar Brown
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move hdf5 data writing to hdf5 class

parent 7db2e07a
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sammy/src/io/CMakeLists.txt
+ 5
− 4
View file @ 8b3f1b30
......@@ -3,12 +3,13 @@ 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(${CMAKE_CURRENT_SOURCE_DIR}/../sammy_conf.h.in sammy_conf.h @ONLY)
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}
${HDF5_INCLUDE_DIR})
${HDF5_INCLUDE_DIRS}) # from find_package()
# Set headers
SET(HEADERS ExperimentalParametersIO.h
......@@ -41,6 +42,7 @@ TRIBITS_ADD_TEST_DIRECTORIES(tests)
TRIBITS_PACKAGE_POSTPROCESS()
target_link_libraries(SammyIOUtilsLib ${h5lib} ${h5lib_CPP})
# --------------------------------------------
# Build separate executable to convert ODF
......@@ -48,7 +50,6 @@ TRIBITS_PACKAGE_POSTPROCESS()
# --------------------------------------------
add_executable(readodf readodf.cpp)
target_link_libraries(readodf PRIVATE HDF5::HDF5
SammyIOUtilsLib)
target_link_libraries(readodf SammyIOUtilsLib)
install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/readodf DESTINATION "bin/")
sammy/src/io/hdf5IO.cpp
+ 63
− 2
View file @ 8b3f1b30
#include "hdf5IO.h"
#include "H5Cpp.h"
#define MAX_NAME_LEN 32
namespace sammy {
hdf5IO::hdf5IO() {}
void hdf5IO::writeODFtoHDF5(){
std::cout << "hello world" << std::endl;
void hdf5IO::writeODFtoHDF5(odfHeader &head,
std::vector<std::vector<double>> &data,
std::string hdf5Filename,
bool elevenSect){
if( !elevenSect ){
std::cerr << "---------------------------------------" << std::endl;
std::cerr << "Reading of ODF files with < 11 sections"
<< "has not been implemented yet. " << std::endl;
std::cerr << "---------------------------------------" << std::endl;
return;
}
// HDF5 works best with set-size char arrays
char sect11[11][MAX_NAME_LEN] = {"energy","trans","dtrans",
"cro","dcro","cs","zero","co","zero","idk","dcs"};
char sect9[9][MAX_NAME_LEN] = {};
// HDF5 accepts set-size double arrays for datasets: copy over
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( sect11, H5::StrType(H5::PredType::C_S1, MAX_NAME_LEN) );
// sweep, sweep
delete file;
delete dataset;
delete nameset;
}
}
\ No newline at end of file
sammy/src/io/hdf5IO.h
+ 6
− 3
View file @ 8b3f1b30
......@@ -4,7 +4,8 @@
#include <vector>
#include <fstream> // ifstream
#include <iostream>
#include "hdf5.h"
#include "odfIO.h"
#include "H5Cpp.h"
namespace sammy{
......@@ -17,8 +18,10 @@ namespace sammy{
/****************************************
* Write data from ODF file into HDF5
***************************************/
void writeODFtoHDF5();
void writeODFtoHDF5(sammy::odfHeader &head,
std::vector<std::vector<double>> &data,
std::string hdf5Filename,
bool elevenSect);
};
}
......
sammy/src/io/odfIO.cpp
+ 2
− 1
View file @ 8b3f1b30
......@@ -142,7 +142,6 @@ namespace sammy{
in.read( (char*)&head.strt, intsize ); // starting word number of each dataset in data section (mode 0 only)
in.read( (char*)&head.ndwend, intsize ); // ending word number of last word written in block NDBEND
/* the following doesn't work properly yet */
// ------------------------------------
// --- Read crunch table
......@@ -159,6 +158,8 @@ namespace sammy{
comments.resize( bytes_in_comments );
in.seekg(bytes_to_comments,std::ios::beg);
in.ignore(bytes_per_word);
for( int i=0;i<bytes_in_comments;++i ){
in.read( (char*)&comments[i], 1 );
comments[i] = comments[i];
......
sammy/src/io/readodf.cpp
+ 3
− 109
View file @ 8b3f1b30
......@@ -2,6 +2,7 @@
// #include "hdf5.h"
#include "H5Cpp.h"
#include "odfIO.h"
#include "hdf5IO.h"
#define MAX_NAME_LEN 32
......@@ -48,116 +49,9 @@ int main(int argc, char const *argv[])
// -------------------------------------------------------------------------
// --- 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);
*/
sammy::hdf5IO h5writer;
h5writer.writeODFtoHDF5(head,data,hdf5Filename,true);
return 0;
}
\ No newline at end of file
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