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first working prototype for string datasets [HDF5]

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q-posev 2021-05-31 16:42:11 +02:00
parent edfe8817d1
commit 753c767ce2
1 changed files with 33 additions and 20 deletions
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53
src/templates_hdf5/templator_hdf5.org
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@ -428,32 +428,24 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
const trexio_hdf5_t* f = (const trexio_hdf5_t*) file; const trexio_hdf5_t* f = (const trexio_hdf5_t*) file;
herr_t status; herr_t status;
int rrank;
// get the rank of the dataset in a file
status = H5LTget_dataset_ndims (f->$group$_group, $GROUP_DSET$_NAME, &rrank);
if (status < 0) return TREXIO_FAILURE;
if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
// open the dataset to get its dimensions // open the dataset to get its dimensions
hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT); hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
if (dset_id <= 0) return TREXIO_INVALID_ID; if (dset_id <= 0) return TREXIO_INVALID_ID;
hid_t dspace = H5Dget_space(dset_id);
int rrank;
// allocate space for the dimensions to be read // allocate space for the dimensions to be read
hsize_t* ddims = CALLOC( (int) rank, hsize_t); hsize_t* ddims = CALLOC( (int) rank, hsize_t);
if (ddims == NULL) return TREXIO_FAILURE; if (ddims == NULL) return TREXIO_FAILURE;
// read dimensions from the existing dataset // get the rank of the dataset in a file
status = H5LDget_dset_dims(dset_id, ddims); rrank = H5Sget_simple_extent_dims(dspace, ddims, NULL);
H5Dclose(dset_id); if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
if (status < 0) {
free(ddims);
return TREXIO_FAILURE;
}
for (uint32_t i=0; i<rank; ++i){ for (int i=0; i<rrank; i++){
if (ddims[i] != dims[i]) { if (ddims[i] != dims[i]) {
free(ddims); free(ddims);
return TREXIO_INVALID_ARG_4; return TREXIO_INVALID_ARG_4;
@ -461,12 +453,33 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
} }
free(ddims); free(ddims);
/* High-level H5LT API. No need to deal with dataspaces and datatypes */ hid_t memtype = H5Tcopy (H5T_C_S1);
status = H5LTread_dataset_string(f->$group$_group, status = H5Tset_size(memtype, H5T_VARIABLE);
$GROUP_DSET$_NAME,
$group_dset$);
if (status < 0) return TREXIO_FAILURE; if (status < 0) return TREXIO_FAILURE;
char** rdata = CALLOC(dims[0], char*);
if (rdata == NULL) return TREXIO_ALLOCATION_FAILED;
status = H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
if (status < 0) return TREXIO_FAILURE;
// copy contents of temporary rdata buffer into the group_dset otherwise they are lost
// when calling H5Treclaim or H5Dvlen_reclaim
for (uint64_t i=0; i<dims[0]; i++){
strcpy($group_dset$[i], rdata[i]);
}
// this function is introduced in HDF5 v.1.12.0
//status = H5Treclaim (memtype, dspace, H5P_DEFAULT, rdata);
// this function is introduced is deprecated but used in v.<1.12.0
status = H5Dvlen_reclaim (memtype, dspace, H5P_DEFAULT, rdata);
if (status < 0) return TREXIO_FAILURE;
if (rdata != NULL) FREE(rdata);
H5Dclose(dset_id);
H5Sclose(dspace);
H5Tclose(memtype);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
#+end_src #+end_src
@ -510,7 +523,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
H5S_ALL, H5S_ALL, H5P_DEFAULT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
$group_dset$); $group_dset$);
H5Dclose (dset_id) H5Dclose (dset_id);
H5Sclose (dspace); H5Sclose (dspace);
H5Tclose (filetype); H5Tclose (filetype);
H5Tclose (memtype); H5Tclose (memtype);