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