I am trying to write a c-struct (that describes a dummy "event") to HDF5 format. The struct contains 4 vectors of floats, that will have different length for each event (the events will be grouped together in the HDF5 file) and hence should be written to file using a variable length type. However, after writing the data using a "buffer-struct", only every other vector is written to the file (1 and 3 in the code below). The others are None. What am I doing wrong?
#include <iostream>
#include <vector>
#include <cstdlib>
#include <string>
#include "H5Cpp.h"
const char * FILE_NAME = "test.h5";
const double HI = 300.0;
const double LO = -20.0;
typedef struct
{
int ID;
float energy;
std::vector<float> v1, v2, v3, v4;
} event_struct;
typedef struct
{
int ID;
float energy;
hvl_t v1Handle, v2Handle, v3Handle, v4Handle;
} event_struct_buffer;
int main(void)
{
event_struct* event = new event_struct();
event_struct_buffer* event_buffer = new event_struct_buffer();
event->ID = 5;
event->energy = 23.45;
int n1 = 10;
int n2 = 8;
int n3 = 4;
int n4 = 2;
for( int i = 0; i < n1; ++i ){
float x = LO + static_cast <float> (rand()) /( static_cast <float> (RAND_MAX/(HI-LO)));
event->v1.push_back(x);
std::cout << x << ' ';
if( i < n2 ){
event->v2.push_back(x/2);
if( i < n3 ){
event->v3.push_back(x/3);
if( i < n4 ){
event->v4.push_back(x/5);
}
}
}
}// end for loop
std::cout << std::endl;
hid_t event_tid; /* File datatype identifier */
hid_t file, dataset, space, vlen_tid; /* Handles */
hsize_t dim[] = {1}; /* Dataspace dimensions */
int rank = sizeof(dim) / sizeof(hsize_t);
std::cout << "Rank = " << rank << std::endl;
space = H5Screate_simple(rank, dim, NULL);
file = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
vlen_tid = H5Tvlen_create(H5T_NATIVE_FLOAT);
event_tid = H5Tcreate( H5T_COMPOUND, sizeof(event_struct_buffer) );
H5Tinsert(event_tid, "Event_ID", HOFFSET(event_struct_buffer, ID), H5T_NATIVE_INT);
H5Tinsert(event_tid, "Energy", HOFFSET(event_struct_buffer, energy), H5T_NATIVE_FLOAT);
H5Tinsert(event_tid, "Image1", HOFFSET(event_struct_buffer, v1Handle), vlen_tid);
H5Tinsert(event_tid, "Image2", HOFFSET(event_struct_buffer, v2Handle), vlen_tid);
H5Tinsert(event_tid, "Image3", HOFFSET(event_struct_buffer, v3Handle), vlen_tid);
H5Tinsert(event_tid, "Image4", HOFFSET(event_struct_buffer, v4Handle), vlen_tid);
dataset = H5Dcreate(file, "/Events_List", event_tid, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
event_buffer->ID = event->ID;
event_buffer->energy = event->energy;
event_buffer->v1Handle.len = event->v1.size();
event_buffer->v1Handle.p = event->v1.data();
event_buffer->v2Handle.len = event->v2.size();
event_buffer->v2Handle.p = event->v2.data();
event_buffer->v3Handle.len = event->v3.size();
event_buffer->v3Handle.p = event->v3.data();
event_buffer->v4Handle.len = event->v4.size();
event_buffer->v4Handle.p = event->v4.data();
H5Dwrite(dataset, event_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, event_buffer);
H5Tclose(event_tid);
H5Tclose(vlen_tid);
H5Sclose(space);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
The pseudo-rand list of numbers is:
-19.9975 22.0921 221.794 126.768 150.486 50.0669 -4.94572 197.237 197.375 279.102
and the output I get when reading the HDF5 file with h5py is:
[ (5, 23.450000762939453, [-19.997495651245117, 22.09209442138672, 221.793701171875,
126.76803588867188, 150.4855194091797, 50.06694030761719, -4.945722579956055,
197.23670959472656, 197.37486267089844, 279.1017150878906],
[-6.665832042694092, 7.3640313148498535, 73.93123626708984, 42.256011962890625], None, None)]
Thanks for your help.
The problem was actually reading the h5 file with h5py (and also with tables).
When running h5dump test.h5
, the data structure and the values in all vectors and all events (I write eventually a vector of event_struct's with 4 variable length std::vector in each event) are filled in correctly.
I also use only one struct and added the hvl_t handles to the event_struct.