Hello Pytablers,
In our readout software for a PET scanner, I write the data to an HDF5
array of compound datatypes (in C++).
When I want to read this table in ipython with pytables, I get the message:
In [11]: import tables
In [11]: f=tables.openFile("Events_0012.h5")
In [12]: f.root.dset
/usr/local/lib/python2.6/dist-packages/tables/path.py:102:
NaturalNameWarning: object name is not a valid Python identifier: 'ToT
'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you
will not be able to use natural naming to access this object; using
``getattr()`` will still work, though
NaturalNameWarning )
/usr/local/lib/python2.6/dist-packages/tables/group.py:1215:
UserWarning: problems loading leaf ``/dset``::
table ``/dset``, column ``hits``: data type not understood
The leaf will become an ``UnImplemented`` node.
% (self._g_join(childName), exc))
Out[12]:
/dset (UnImplemented(16384,)) ''
NOTE: <The UnImplemented object represents a PyTables unimplemented
dataset present in the 'Events_0012.h5' HDF5 file. If you
want to see this
kind of HDF5 dataset implemented in PyTables, please contact the
developers.>
I also attached the C++ code which writes the table.
Should I write the HDF5 file in a different way in order to read the
data with pytables?
Thanks a lot for your help!
Best regards,
Michael Rissi
--
Dr. Michael Rissi
room ø385A
Sem Sælandsvei 24
N-0316 Oslo
Universitetet i Oslo
NORWAY
#include <iostream>
#include <sys/prctl.h>
#include <unistd.h>
#include "hdf5.h"
#include "CWriteHDF5.h"
void CWriteHDF5::start()
{
m_Thread = boost::thread(&CWriteHDF5::WriteHDF5, this);
}
void CWriteHDF5::join()
{
m_Thread.join();
}
void CWriteHDF5::WriteHDF5()
{
//thread name:
char thr_name[] = "CREADOUT_WriteHDF5\0";
prctl(PR_SET_NAME, thr_name);
//set up the HDF5 stuff:
hid_t file_id, dataset_id,dataspace_id; /* identifiers */
herr_t status;
hsize_t dims[] = {NUMBEROFEVENTSPERFILE};
C5Event *c5event = new C5Event[NUMBEROFEVENTSPERFILE];
hsize_t dim[] = {MAXNUMHITSINSLOT};
hid_t hits_datatype = H5Tcreate (H5T_COMPOUND, sizeof (CHit));
H5Tinsert(hits_datatype, "ev_nr" , HOFFSET(C5Hit, ev_nr) , H5T_NATIVE_USHORT);
H5Tinsert(hits_datatype, "ch_nr" , HOFFSET(C5Hit, ch_nr) , H5T_NATIVE_USHORT);
H5Tinsert(hits_datatype, "rel_time", HOFFSET(C5Hit, rel_time), H5T_NATIVE_USHORT);
H5Tinsert(hits_datatype, "ToT ", HOFFSET(C5Hit, ToT) , H5T_NATIVE_USHORT);
hid_t array_tid = H5Tarray_create(hits_datatype, 1, dim, NULL);
//create the compound data type:
hid_t events_datatype = H5Tcreate (H5T_COMPOUND, sizeof(C5Event));
H5Tinsert(events_datatype, "numhits", HOFFSET(C5Event, numhits), H5T_NATIVE_INT);
H5Tinsert(events_datatype, "hits", HOFFSET(C5Event, hits), array_tid);
dataspace_id = H5Screate_simple(1, dims, NULL);
int evt = 0;
int filenumber = 0;
while(!m_exitflag)
{
CEvent event_tmp;
m_events->pop_back(&event_tmp);
usleep(100);
c5event[evt] = event_tmp.copy();
evt++;
if(evt == NUMBEROFEVENTSPERFILE)
{
evt = 0;
filenumber++;
char filename[128];
sprintf(filename, "Events_%04u.h5",filenumber);
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
dataset_id = H5Dcreate(file_id, "/dset", events_datatype, dataspace_id, H5P_DEFAULT);
std::cout<<"writing file "<<filename<<std::endl;
status = H5Dwrite(dataset_id, events_datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
c5event);
status = H5Dclose(dataset_id);
status = H5Fclose(file_id);
}
}
}
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