I want to create a HDF5 file in C++ and dynamically add data to a dataset contained in that file. I have been having some trouble getting this work however, with this minimal example as my current best attempt (based mainly on an answer by SOG):
#include <stdio.h>
#include <HDFql.hpp>
int main (int argc, const char * argv[]) {
char script[1024];
//Create HDF5 file
HDFql::execute("CREATE TRUNCATE FILE /tmp/test.h5");
HDFql::execute("USE FILE /tmp/test.h5");
//Generate some arbitrary data
int data_size = 10;
int data[data_size];
for (int i=0; i<data_size; i++) {data[i]=i+data_size;}
//Create a dataset "dset"
HDFql::execute("CREATE CHUNKED DATASET dset AS INT(UNLIMITED)");
//In the loop, add one element to dset on each iteration
for(int i=0; i<10; i++)
{
HDFql::execute("ALTER DIMENSION dset TO (+1)");
sprintf(script, "INSERT INTO dset(-1:1:1:1) VALUES(%d)", i);
HDFql::execute(script);
}
//Add an array of values to dset
sprintf(script, "ALTER DIMENSION dset TO (%d)", data_size);
HDFql::execute(script);
sprintf(script, "INSERT INTO dset(-1:1:1:1) VALUES(%d)", data_size);
HDFql::execute(script);
//Read all values in dset and print to console
HDFql::execute("SELECT FROM dset");
int cnt=0;
while(HDFql::cursorNext(NULL) == HDFQL_SUCCESS)
{
printf("Value at %d: %d\n", cnt, *HDFql::cursorGetInt(NULL));
cnt++;
}
HDFql::execute("CLOSE FILE");
}
I would expect the output of the console to be:
Value at 0: 0
Value at 1: 1
Value at 2: 2
...
Value at 19: 19
Instead the output is:
Value at 0: 10
And indeed, inspecting the HDF5 file shows that it contains only one value, 10. So what is wrong with my code and why? Also, a short explanation of the hyperslab (which I am using quite blindly here) or a link to documentation explaining it would be very appreciated.
Many thanks!
Here is a working code example based on the answer by @SOG:
#include <stdio.h>
#include <HDFql.hpp>
int main (int argc, const char * argv[]) {
char script[1024];
HDFql::execute("CREATE TRUNCATE FILE /tmp/test.h5");
HDFql::execute("USE FILE /tmp/test.h5");
int data_size = 10;
int data[data_size];
for (int i=0; i<data_size; i++) {data[i]=i+data_size;}
HDFql::execute("CREATE CHUNKED DATASET dset AS INT(UNLIMITED)");
for(int i=0; i<10; i++)
{
if(i>0) {HDFql::execute("ALTER DIMENSION dset TO +1");}
sprintf(script, "INSERT INTO dset(-1:1:1:1) VALUES(%d)", i);
HDFql::execute(script);
}
sprintf(script, "ALTER DIMENSION dset TO +%d", data_size);
HDFql::execute(script);
sprintf(script, "INSERT INTO dset(-%d:1:1:%d) VALUES FROM MEMORY %d",
data_size, data_size, HDFql::variableTransientRegister(data));
HDFql::execute(script);
int cnt=0;
HDFql::execute("SELECT FROM dset");
while(HDFql::cursorNext(NULL) == HDFQL_SUCCESS)
{
printf("Value at %d: %d\n", cnt, *HDFql::cursorGetInt(NULL));
cnt++;
}
HDFql::execute("CLOSE FILE");
}
According to HDFql release notes, operation ALTER DIMENSION
has changed syntax in version 2.1.0 (i.e. the operation does not require parenthesis to surround dimensions anymore).
Therefore, change your code to:
HDFql::execute("ALTER DIMENSION dset TO +1");
Additional information about this operation as well as hyperslabs can be found in HDFql reference manual.