Hi,
I’m trying to read/write compound datatype that contains std::string instead of char * using C hdf5.
Using the example from hdf5 I slightly modified it on the following way:
#include <string> // ADDED BY ME
#include "hdf5.h"
#include <stdio.h>
#include <stdlib.h>
#define FILE "h5ex_t_cmpd.h5"
#define DATASET "DS1"
#define DIM0 4
typedef struct {
int serial_no;
std::string location; // CHANGED FROM char* to std::string BY ME
double temperature;
double pressure;
} sensor_t; /* Compound type */
int
main (void)
{
hid_t file, filetype, memtype, strtype, space, dset;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0};
sensor_t wdata[DIM0], /* Write buffer */
rdata[DIM0]; /* Read buffer */
int ndims,
i;
/*
* Initialize data.
*/
wdata[0].serial_no = 1153;
wdata[0].location = "Exterior (static)";
wdata[0].temperature = 53.23;
wdata[0].pressure = 24.57;
wdata[1].serial_no = 1184;
wdata[1].location = "Intake";
wdata[1].temperature = 55.12;
wdata[1].pressure = 22.95;
wdata[2].serial_no = 1027;
wdata[2].location = "Intake manifold";
wdata[2].temperature = 103.55;
wdata[2].pressure = 31.23;
wdata[3].serial_no = 1313;
wdata[3].location = "Exhaust manifold";
wdata[3].temperature = 1252.89;
wdata[3].pressure = 84.11;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create variable-length string datatype.
*/
strtype = H5Tcopy (H5T_C_S1);
status = H5Tset_size (strtype, H5T_VARIABLE);
/*
* Create the compound datatype for memory.
*/
memtype = H5Tcreate (H5T_COMPOUND, sizeof (sensor_t));
status = H5Tinsert (memtype, "Serial number",
HOFFSET (sensor_t, serial_no), H5T_NATIVE_INT);
status = H5Tinsert (memtype, "Location", HOFFSET (sensor_t, location),
strtype);
status = H5Tinsert (memtype, "Temperature (F)",
HOFFSET (sensor_t, temperature), H5T_NATIVE_DOUBLE);
status = H5Tinsert (memtype, "Pressure (inHg)",
HOFFSET (sensor_t, pressure), H5T_NATIVE_DOUBLE);
/*
* Create the compound datatype for the file. Because the standard
* types we are using for the file may have different sizes than
* the corresponding native types, we must manually calculate the
* offset of each member.
*/
filetype = H5Tcreate (H5T_COMPOUND, 8 + sizeof (hvl_t) + 8 + 8);
status = H5Tinsert (filetype, "Serial number", 0, H5T_STD_I64BE);
status = H5Tinsert (filetype, "Location", 8, strtype);
status = H5Tinsert (filetype, "Temperature (F)", 8 + sizeof (hvl_t),
H5T_IEEE_F64BE);
status = H5Tinsert (filetype, "Pressure (inHg)", 8 + sizeof (hvl_t) + 8,
H5T_IEEE_F64BE);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the dataset and write the compound data to it.
*/
dset = H5Dcreate (file, DATASET, filetype, space, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Dwrite (dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
/*
* Close and release resources.
*/
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (filetype);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the dataset has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc(). For simplicity, we do not rebuild memtype.
*/
/*
* Open file and dataset.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET, H5P_DEFAULT);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Dget_space (dset);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
// rdata = (sensor_t *) malloc (dims[0] * sizeof (sensor_t)); // COMMENTED BY ME (I explicitely set the array size in the beginning)
/*
* Read the data.
*/
status = H5Dread (dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n", DATASET, i);
printf ("Serial number : %d\n", rdata[i].serial_no);
printf ("Location : %s\n", rdata[i].location);
printf ("Temperature (F) : %f\n", rdata[i].temperature);
printf ("Pressure (inHg) : %f\n\n", rdata[i].pressure);
}
/*
* Close and release resources. H5Dvlen_reclaim will automatically
* traverse the structure and free any vlen data (strings in this
* case).
*/
status = H5Dvlen_reclaim (memtype, space, H5P_DEFAULT, rdata);
free (rdata);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Tclose (memtype);
status = H5Tclose (strtype);
status = H5Fclose (file);
return 0;
}
After build and run the code I can see that everything was correctly written to the file (even location member variable) using HDFViewer.
But when I read the dataset I can see that location member variable is empty.
Is there a way to overcome this and read the data directly to the string?