size_t CompoundType::memberOffset (size_t i) const {
ASSERT (i <= std::numeric_limits<unsigned>::max ());
unsigned i2 = static_cast<unsigned> (i);
size_t result = H5Tget_member_offset (handle (), i2);
if (result == 0) {
// Check for errors, H5Tget_member_offset fails only if H5Tget_member_name also fails
// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetMemberOffset
memberName (i);
}
return result;
}
/*-------------------------------------------------------------------------
* Function: H5LD_construct_info()
*
* Purpose: Get the remaining info for a field:
* 1) Get the type id of the last member in the field
* 2) Get the total offset of all the members in the field
* 3) Get the type size of the last member in the field
*
* Return: Success: 0
* Failure: negative
*
* Programmer: Vailin Choi; Aug 2010
*
*-------------------------------------------------------------------------
*/
static herr_t
H5LD_construct_info(H5LD_memb_t *memb, hid_t par_tid)
{
hid_t tmp_tid = -1; /* Dataset type id */
unsigned i; /* Local index variable */
herr_t ret_value = FAIL; /* Return value */
/* Make a copy of the incoming datatype */
tmp_tid = H5Tcopy(par_tid);
/* Validate all the members in a field */
for(i = 0; memb->names[i] != NULL; i++) {
hid_t memb_tid; /* Type id for a member in a field */
int idx; /* Index # of a member in a compound datatype */
/* Get the member index and member type id */
if((idx = H5Tget_member_index(tmp_tid, memb->names[i])) < 0)
goto done;
if((memb_tid = H5Tget_member_type(tmp_tid, (unsigned)idx)) < 0)
goto done;
/* Sum up the offset of all the members in the field */
memb->tot_offset += H5Tget_member_offset(tmp_tid, (unsigned)idx);
if(H5Tclose(tmp_tid) < 0)
goto done;
tmp_tid = memb_tid;
} /* end for */
/* Get the type size of the last member in the field */
memb->last_tsize = H5Tget_size(tmp_tid);
/* Save the type id of the last member in the field */
memb->last_tid = H5Tcopy(tmp_tid);
/* Indicate success */
ret_value = SUCCEED;
done:
H5E_BEGIN_TRY
H5Tclose(tmp_tid);
H5E_END_TRY
return(ret_value);
} /* H5LD_construct_info() */
H5CompoundData::H5CompoundData(H5Object & _parent, const hsize_t _totalSize, const hsize_t _dataSize, const hsize_t _ndims, const hsize_t * _dims, char * _data, hid_t compoundType, const hsize_t _stride, const size_t _offset, const bool _dataOwner) : H5BasicData<char>(_parent, _totalSize, _dataSize, _ndims, _dims, _data, _stride, _offset, _dataOwner), type(compoundType), cumprod(H5Object::getCumProd(_ndims, dims))
{
nfields = (unsigned int)H5Tget_nmembers(compoundType);
infos = new std::map<std::string, FieldInfo *>();
fieldinfos = new FieldInfo *[nfields];
for (unsigned int i = 0; i < nfields; i++)
{
hid_t mtype = H5Tget_member_type(compoundType, i);
hsize_t size = H5Tget_size(mtype);
char * mname = H5Tget_member_name(compoundType, i);
size_t offs = H5Tget_member_offset(compoundType, i);
FieldInfo * info = 0;
if (H5Tget_class(type) == H5T_STRING && !H5Tis_variable_str(type))
{
// We have a C-string so it is null terminated
size++;
}
info = new FieldInfo(mtype, size, offs, std::string(mname));
(*infos)[std::string(mname)] = info;
fieldinfos[i] = info;
free(mname);
}
}
int main(void)
{
hid_t fil,spc,set;
hid_t cs6, cmp, fix;
hid_t cmp1, cmp2, cmp3;
hid_t plist;
hid_t array_dt;
hsize_t dim[2];
hsize_t cdim[4];
char string5[5];
float fok[2] = {1234., 2341.};
float fnok[2] = {5678., 6785.};
float *fptr;
char *data;
char *mname;
int result = 0;
printf("%-70s", "Testing alignment in compound datatypes");
strcpy(string5, "Hi!");
HDunlink(fname);
fil = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (fil < 0) {
puts("*FAILED*");
return 1;
}
H5E_BEGIN_TRY {
H5Ldelete(fil, setname, H5P_DEFAULT);
} H5E_END_TRY;
cs6 = H5Tcopy(H5T_C_S1);
H5Tset_size(cs6, sizeof(string5));
H5Tset_strpad(cs6, H5T_STR_NULLPAD);
cmp = H5Tcreate(H5T_COMPOUND, sizeof(fok) + sizeof(string5) + sizeof(fnok));
H5Tinsert(cmp, "Awkward length", 0, cs6);
cdim[0] = sizeof(fok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp, "Ok", sizeof(string5), array_dt);
H5Tclose(array_dt);
cdim[0] = sizeof(fnok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp, "Not Ok", sizeof(fok) + sizeof(string5), array_dt);
H5Tclose(array_dt);
fix=h5tools_get_native_type(cmp);
cmp1 = H5Tcreate(H5T_COMPOUND, sizeof(fok));
cdim[0] = sizeof(fok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp1, "Ok", 0, array_dt);
H5Tclose(array_dt);
cmp2 = H5Tcreate(H5T_COMPOUND, sizeof(string5));
H5Tinsert(cmp2, "Awkward length", 0, cs6);
cmp3 = H5Tcreate(H5T_COMPOUND, sizeof(fnok));
cdim[0] = sizeof(fnok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp3, "Not Ok", 0, array_dt);
H5Tclose(array_dt);
plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_preserve(plist, 1);
/*
* Create a small dataset, and write data into it we write each field
* in turn so that we are avoid alignment issues at this point
*/
dim[0] = 1;
spc = H5Screate_simple(1, dim, NULL);
set = H5Dcreate2(fil, setname, cmp, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(set, cmp1, spc, H5S_ALL, plist, fok);
H5Dwrite(set, cmp2, spc, H5S_ALL, plist, string5);
H5Dwrite(set, cmp3, spc, H5S_ALL, plist, fnok);
H5Dclose(set);
/* Now open the set, and read it back in */
data = malloc(H5Tget_size(fix));
if(!data) {
perror("malloc() failed");
abort();
}
set = H5Dopen2(fil, setname, H5P_DEFAULT);
H5Dread(set, fix, spc, H5S_ALL, H5P_DEFAULT, data);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
if(fok[0] != fptr[0] || fok[1] != fptr[1]
|| fnok[0] != fptr[2] || fnok[1] != fptr[3]) {
result = 1;
printf("%14s (%2d) %6s = %s\n",
mname = H5Tget_member_name(fix, 0), (int)H5Tget_member_offset(fix,0),
string5, (char *)(data + H5Tget_member_offset(fix, 0)));
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
printf("Data comparison:\n"
"%14s (%2d) %6f = %f\n"
" %6f = %f\n",
mname = H5Tget_member_name(fix, 1), (int)H5Tget_member_offset(fix,1),
fok[0], fptr[0],
fok[1], fptr[1]);
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 2));
printf("%14s (%2d) %6f = %f\n"
" %6f = %6f\n",
mname = H5Tget_member_name(fix, 2), (int)H5Tget_member_offset(fix,2),
fnok[0], fptr[0],
fnok[1], fptr[1]);
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
printf("\n"
"Short circuit\n"
" %6f = %f\n"
" %6f = %f\n"
" %6f = %f\n"
" %6f = %f\n",
fok[0], fptr[0],
fok[1], fptr[1],
fnok[0], fptr[2],
fnok[1], fptr[3]);
puts("*FAILED*");
} else {
puts(" PASSED");
}
free(data);
H5Sclose(spc);
H5Tclose(cmp);
H5Tclose(cmp1);
H5Tclose(cmp2);
H5Tclose(cmp3);
H5Pclose(plist);
H5Fclose(fil);
HDunlink(fname);
fflush(stdout);
return result;
}
size_t DataType::member_offset(unsigned int index) const {
return H5Tget_member_offset(hid, index);
}
//--------------------------------------------------------------------------
// Function: CompType::getMemberOffset
///\brief Returns the byte offset of the beginning of a member with
/// respect to the beginning of the compound data type datum.
///\param member_num - IN: Zero-based index of the member
///\return Byte offset
///\exception H5::DataTypeIException
// Programmer Binh-Minh Ribler - 2000
// Description
/// Members are stored in no particular order with numbers 0
/// through N-1, where N is the value returned by the member
/// function \c CompType::getNmembers.
//
// Note that byte offset being returned as 0 doesn't indicate
// a failure. (According to Quincey)
//--------------------------------------------------------------------------
size_t CompType::getMemberOffset( unsigned member_num ) const
{
size_t offset = H5Tget_member_offset( id, member_num );
return( offset );
}