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-rw-r--r--tools/h5repack/h5repack_copy.c2214
-rw-r--r--tools/h5repack/h5repack_refs.c241
-rw-r--r--tools/h5repack/h5repack_verify.c246
3 files changed, 1286 insertions, 1415 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 9c01b7e..547f61a 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -36,7 +36,7 @@
#define USERBLOCK_XFER_SIZE 512
/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
-#define CHECK_H5DRW_ERROR(_fun, _did, _mtid, _msid, _fsid, _pid, _buf) { \
+#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \
H5E_BEGIN_TRY { \
if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) { \
hid_t _err_num = 0; \
@@ -44,7 +44,7 @@
H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
- goto done; \
+ HGOTO_DONE(_fail) \
} \
} H5E_END_TRY; \
}
@@ -97,170 +97,166 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
*-------------------------------------------------------------------------
*/
-int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) {
+int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
+{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t fidin;
- hid_t fidout = -1;
- trav_table_t *travt = NULL;
- hsize_t ub_size = 0; /* size of user block */
- hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
- hid_t fapl = H5P_DEFAULT; /* file access property list ID */
-
- /*-------------------------------------------------------------------------
- * open input file
- *-------------------------------------------------------------------------
- */
- if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL,
- (size_t) 0)) < 0) {
- error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ hid_t fidout = -1;
+ trav_table_t *travt = NULL;
+ hsize_t ub_size = 0; /* size of user block */
+ hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
+ hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+
+ /*-------------------------------------------------------------------------
+ * open input file
+ *-------------------------------------------------------------------------
+ */
+ if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) {
+ error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- /* get user block size and file space strategy/threshold */
- {
- hid_t fcpl_in; /* file creation property list ID for input file */
+ /* get user block size and file space strategy/threshold */
+ {
+ hid_t fcpl_in; /* file creation property list ID for input file */
- if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
- error_msg("failed to retrieve file creation property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
+ error_msg("failed to retrieve file creation property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
- error_msg("failed to retrieve userblock size\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
+ error_msg("failed to retrieve userblock size\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- if (!options->fs_strategy) {
- if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
- error_msg("failed to retrieve file space strategy\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (!options->fs_strategy) {
+ if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
+ error_msg("failed to retrieve file space strategy\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- }
+ }
- if (!options->fs_threshold) {
- if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
- error_msg("failed to retrieve file space threshold\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (!options->fs_threshold) {
+ if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
+ error_msg("failed to retrieve file space threshold\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- }
+ }
- if (H5Pclose(fcpl_in) < 0) {
- error_msg("failed to close property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(fcpl_in) < 0) {
+ error_msg("failed to close property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- }
+ }
- /* Check if we need to create a non-default file creation property list */
- if (options->latest || ub_size > 0) {
- /* Create file creation property list */
- if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
- error_msg("fail to create a file creation property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /* Check if we need to create a non-default file creation property list */
+ if (options->latest || ub_size > 0) {
+ /* Create file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- if (ub_size > 0) {
- if (H5Pset_userblock(fcpl, ub_size) < 0) {
- error_msg("failed to set non-default userblock size\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (ub_size > 0) {
+ if (H5Pset_userblock(fcpl, ub_size) < 0) {
+ error_msg("failed to set non-default userblock size\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- }
+ }
- if (options->latest) {
- unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
+ if (options->latest) {
+ unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
- /* Adjust group creation parameters for root group */
- /* (So that it is created in "dense storage" form) */
- if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
- (unsigned) options->grp_indexed) < 0) {
- error_msg(
- "fail to adjust group creation parameters for root group\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /* Adjust group creation parameters for root group */
+ /* (So that it is created in "dense storage" form) */
+ if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
+ (unsigned) options->grp_indexed) < 0) {
+ error_msg("fail to adjust group creation parameters for root group\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- for (i = 0; i < 5; i++) {
- if (options->msg_size[i] > 0) {
- switch (i) {
- case 0:
- mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
- break;
-
- case 1:
- mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
- break;
-
- case 2:
- mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
- break;
-
- case 3:
- mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
- break;
-
- case 4:
- mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
- break;
- default:
- break;
- } /* end switch */
- min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
-
- nindex++;
- } /* end if */
- } /* end for */
-
- if (nindex > 0) {
- if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
- error_msg(
- "fail to set the number of shared object header message indexes\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ for (i = 0; i < 5; i++) {
+ if (options->msg_size[i] > 0) {
+ switch (i) {
+ case 0:
+ mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
+ break;
+
+ case 1:
+ mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
+ break;
+
+ case 2:
+ mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
+ break;
+
+ case 3:
+ mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
+ break;
+
+ case 4:
+ mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
+ break;
+
+ default:
+ break;
+ } /* end switch */
+ min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
+
+ nindex++;
+ } /* end if */
+ } /* end for */
+
+ if (nindex > 0) {
+ if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
+ error_msg("fail to set the number of shared object header message indexes\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
- for (i = 0; i < (nindex - 1); i++) {
- if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i],
- min_mesg_sizes[i]) < 0) {
- error_msg(
- "fail to configure the specified shared object header message index\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
+ for (i = 0; i < (nindex - 1); i++) {
+ if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
+ error_msg("fail to configure the specified shared object header message index\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
} /* end if */
- } /* end for */
- } /* if (nindex>0) */
+ } /* end for */
+ } /* if (nindex>0) */
- /* Create file access property list */
- if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
- error_msg("Could not create file access property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /* Create file access property list */
+ if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ error_msg("Could not create file access property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
} /* end if */
- if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
- error_msg(
- "Could not set property for using latest version of the format\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+ error_msg("Could not set property for using latest version of the format\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
} /* end if */
- } /* end if */
- } /* end if */
+ } /* end if */
+ } /* end if */
#if defined (H5REPACK_DEBUG_USER_BLOCK)
- print_user_block(fnamein, fidin);
+print_user_block(fnamein, fidin);
#endif
- /*-------------------------------------------------------------------------
- * set the new user userblock options in the FCPL (before H5Fcreate )
- *-------------------------------------------------------------------------
- */
- if (options->ublock_size > 0) {
- /* either use the FCPL already created or create a new one */
- if (fcpl == H5P_DEFAULT) {
- /* create a file creation property list */
- if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
- error_msg("fail to create a file creation property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /*-------------------------------------------------------------------------
+ * set the new user userblock options in the FCPL (before H5Fcreate )
+ *-------------------------------------------------------------------------
+ */
+ if (options->ublock_size > 0) {
+ /* either use the FCPL already created or create a new one */
+ if (fcpl == H5P_DEFAULT) {
+ /* create a file creation property list */
+ if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+ error_msg("fail to create a file creation property list\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- }
+ }
/* set user block size */
if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
error_msg("failed to set userblock size\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
@@ -274,13 +270,13 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* create a file access property list */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
error_msg("Could not create file access property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
error_msg("failed to set alignment\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
@@ -294,13 +290,13 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* create a file access property list */
if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
error_msg("Could not create file access property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
error_msg("failed to set metadata block size\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
@@ -314,14 +310,14 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* create a file creation property list */
if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
error_msg("fail to create a file creation property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
/* set file space strategy and free space threshold */
if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) {
error_msg("failed to set file space strategy & threshold \n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
/*-------------------------------------------------------------------------
@@ -333,7 +329,7 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
error_msg("<%s>: Could not create file\n", fnameout);
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
/*-------------------------------------------------------------------------
@@ -341,95 +337,91 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
*-------------------------------------------------------------------------
*/
if (options->ublock_size > 0) {
- if (copy_user_block(options->ublock_filename, fnameout,
- options->ublock_size) < 0) {
+ if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) {
error_msg("Could not copy user block. Exiting...\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
}
- /*-------------------------------------------------------------------------
- * get list of objects
- *-------------------------------------------------------------------------
- */
+ /*-------------------------------------------------------------------------
+ * get list of objects
+ *-------------------------------------------------------------------------
+ */
- /* init table */
- trav_table_init(&travt);
+ /* init table */
+ trav_table_init(&travt);
- /* get the list of objects in the file */
- if (h5trav_gettable(fidin, travt) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fidin, travt) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
- if (do_copy_objects(fidin, fidout, travt, options) < 0) {
- error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_objects(fidin, fidout, travt, options) < 0) {
+ error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
} /* end if */
- /*-------------------------------------------------------------------------
- * do the copy of referenced objects
- * and create hard links
- *-------------------------------------------------------------------------
- */
- if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
- printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein,
- fnameout);
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /*-------------------------------------------------------------------------
+ * do the copy of referenced objects
+ * and create hard links
+ *-------------------------------------------------------------------------
+ */
+ if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
+ printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if (fapl > 0)
- H5Pclose(fapl);
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
- if (fcpl > 0)
- H5Pclose(fcpl);
+ if (fapl > 0)
+ H5Pclose(fapl);
- H5Fclose(fidin);
- H5Fclose(fidout);
+ if (fcpl > 0)
+ H5Pclose(fcpl);
- /* free table */
- trav_table_free(travt);
- travt = NULL;
+ H5Fclose(fidin);
+ H5Fclose(fidout);
- /*-------------------------------------------------------------------------
- * write only the input file user block if there is no user block file input
- *-------------------------------------------------------------------------
- */
+ /* free table */
+ trav_table_free(travt);
+ travt = NULL;
- if (ub_size > 0 && options->ublock_size == 0) {
- if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
- error_msg("Could not copy user block. Exiting...\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /*-------------------------------------------------------------------------
+ * write only the input file user block if there is no user block file input
+ *-------------------------------------------------------------------------
+ */
- }
- }
+ if (ub_size > 0 && options->ublock_size == 0) {
+ if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
+ error_msg("Could not copy user block. Exiting...\n");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
- return 0;
+ return 0;
- /*-------------------------------------------------------------------------
- * out
- *-------------------------------------------------------------------------
- */
+ /*-------------------------------------------------------------------------
+ * out
+ *-------------------------------------------------------------------------
+ */
done:
- H5E_BEGIN_TRY
- {
- H5Pclose(fapl);
- H5Pclose(fcpl);
- H5Fclose(fidin);
- H5Fclose(fidout);
- }H5E_END_TRY;
- if (travt)
- trav_table_free(travt);
-
- return -1;
+ H5E_BEGIN_TRY {
+ H5Pclose(fapl);
+ H5Pclose(fcpl);
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ } H5E_END_TRY;
+ if (travt)
+ trav_table_free(travt);
+
+ return ret_value;
}
/*-------------------------------------------------------------------------
@@ -470,133 +462,126 @@ done:
*-----------------------------------------*/
int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
- size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) {
+ size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
+{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- int status = 0;
- int k;
- H5D_layout_t dset_layout;
- int rank_chunk;
- hsize_t dims_chunk[H5S_MAX_RANK];
- hsize_t size_chunk = 1;
- hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
- hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
- hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
- hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
- hsize_t hslab_nbytes; /* size of hyperslab in byte */
-
- /* init to set as size of a data element */
- hslab_nbytes = size_datum;
-
- /* get layout of dataset */
- dset_layout = H5Pget_layout(dcpl_id);
-
- /* if dataset is chunked */
- if (dset_layout == H5D_CHUNKED) {
- /* get chunk dims */
- rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
- if (rank_chunk < 0) {
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ int k;
+ H5D_layout_t dset_layout;
+ int rank_chunk;
+ hsize_t dims_chunk[H5S_MAX_RANK];
+ hsize_t size_chunk = 1;
+ hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+ hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
+ hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
+ hsize_t hslab_nbytes; /* size of hyperslab in byte */
+
+ /* init to set as size of a data element */
+ hslab_nbytes = size_datum;
+
+ /* get layout of dataset */
+ dset_layout = H5Pget_layout(dcpl_id);
+
+ /* if dataset is chunked */
+ if (dset_layout == H5D_CHUNKED) {
+ /* get chunk dims */
+ rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
+ if (rank_chunk < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+ for (k = rank_dset; k > 0; --k)
+ size_chunk *= dims_chunk[k - 1];
+
+ /* figure out how many chunks can fit in the hyperslab buffer */
+ nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
+
+ /* 1. if a chunk fit in hyperslab buffer */
+ if (nchunk_fit >= 1) {
+ /* Calulate a hyperslab that contains as many chunks that can fit
+ * in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ * In the loop, used mapping from a datum to a chunk to figure out
+ * chunk based hyperslab.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ /* map dataset dimentions with a chunk dims */
+ chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
+
+ /* if reminder exist, increse by 1 to cover partial edge chunks */
+ if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
+ chunk_dims_map[k - 1]++;
+
+ /* get mapped hyperslab dims */
+ hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
+
+ /* prepare next round */
+ nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
+ /* if a chunk is bigger than the rest of buffer */
+ if (nchunk_fit == 0)
+ nchunk_fit = 1;
+
+ /* get hyperslab dimentions as unmapping to actual size */
+ dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+ }
}
-
- for (k = rank_dset; k > 0; --k)
- size_chunk *= dims_chunk[k - 1];
-
- /* figure out how many chunks can fit in the hyperslab buffer */
- nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
-
- /* 1. if a chunk fit in hyperslab buffer */
- if (nchunk_fit >= 1) {
- /* Calulate a hyperslab that contains as many chunks that can fit
- * in hyperslab buffer. Hyperslab will be increased starting from
- * the last dimention of the dataset (see h5dump's dims output).
- * The calculation boundary is dataset dims.
- * In the loop, used mapping from a datum to a chunk to figure out
- * chunk based hyperslab.
- */
- for (k = rank_dset; k > 0; --k) {
- /* map dataset dimentions with a chunk dims */
- chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
-
- /* if reminder exist, increse by 1 to cover partial edge chunks */
- if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
- chunk_dims_map[k - 1]++;
-
- /* get mapped hyperslab dims */
- hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
-
- /* prepare next round */
- nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
- /* if a chunk is bigger than the rest of buffer */
- if (nchunk_fit == 0)
- nchunk_fit = 1;
-
- /* get hyperslab dimentions as unmapping to actual size */
- dims_hslab[k - 1] =
- MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
- }
- }
- /* 2. if a chunk is bigger than hyperslab buffer */
- else {
- /* Calulate a hyperslab that contains as many data elements that
- * can fit in hyperslab buffer. Hyperslab will be increased
- * starting from the last dimention of the chunk (see h5dump's dims
- * output).
- * The calculation boundary is a chunk dims.
- */
- for (k = rank_dset; k > 0; --k) {
- ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
- /* if a datum is bigger than rest of buffer */
- if (ndatum_fit == 0)
- ndatum_fit = 1;
- /* get hyperslab dimentions within a chunk boundary */
- dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
-
- if (hslab_nbytes <= 0) {
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
- }
- }
- }
- }
- /* 3. if dataset is not chunked */
- else {
- /* Calulate a hyperslab that contains as many data elements that can
- * fit in hyperslab buffer. Hyperslab will be increased starting from
- * the last dimention of the dataset (see h5dump's dims output).
- * The calculation boundary is dataset dims.
- */
- for (k = rank_dset; k > 0; --k) {
- ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
- /* if a datum is bigger than rest of buffer */
- if (ndatum_fit == 0)
- ndatum_fit = 1;
- /* get hyperslab dimentions within dataset boundary */
- dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
-
- /* calculate total size for the hyperslab */
- hslab_nbytes *= dims_hslab[k - 1];
-
- if (hslab_nbytes <= 0) {
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ /* 2. if a chunk is bigger than hyperslab buffer */
+ else {
+ /* Calulate a hyperslab that contains as many data elements that
+ * can fit in hyperslab buffer. Hyperslab will be increased
+ * starting from the last dimention of the chunk (see h5dump's dims
+ * output).
+ * The calculation boundary is a chunk dims.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if (ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within a chunk boundary */
+ dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
}
- }
- }
+ }
+ }
+ /* 3. if dataset is not chunked */
+ else {
+ /* Calulate a hyperslab that contains as many data elements that can
+ * fit in hyperslab buffer. Hyperslab will be increased starting from
+ * the last dimention of the dataset (see h5dump's dims output).
+ * The calculation boundary is dataset dims.
+ */
+ for (k = rank_dset; k > 0; --k) {
+ ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+ /* if a datum is bigger than rest of buffer */
+ if (ndatum_fit == 0)
+ ndatum_fit = 1;
+ /* get hyperslab dimentions within dataset boundary */
+ dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
+
+ /* calculate total size for the hyperslab */
+ hslab_nbytes *= dims_hslab[k - 1];
+
+ if (hslab_nbytes <= 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ }
+ }
- /* pass out the hyperslab size*/
- *hslab_nbytes_p = hslab_nbytes;
+ /* pass out the hyperslab size*/
+ *hslab_nbytes_p = hslab_nbytes;
done:
- return status;
+ return ret_value;
}
/*-------------------------------------------------------------------------
@@ -698,709 +683,637 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
hid_t grp_in = -1; /* group ID */
- hid_t grp_out = -1; /* group ID */
- hid_t dset_in = -1; /* read dataset ID */
- hid_t dset_out = -1; /* write dataset ID */
- hid_t gcpl_in = -1; /* group creation property list */
- hid_t gcpl_out = -1; /* group creation property list */
- hid_t type_in = -1; /* named type ID */
- hid_t type_out = -1; /* named type ID */
- hid_t dcpl_in = -1; /* dataset creation property list ID */
- hid_t dcpl_out = -1; /* dataset creation property list ID */
- hid_t f_space_id = -1; /* file space ID */
- hid_t ftype_id = -1; /* file type ID */
- hid_t wtype_id = -1; /* read/write type ID */
- named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
- size_t msize; /* size of type */
- hsize_t nelmts; /* number of elements in dataset */
- H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
- int rank; /* rank of dataset */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- hsize_t dsize_in; /* input dataset size before filter */
- hsize_t dsize_out; /* output dataset size after filter */
- int apply_s; /* flag for apply filter to small dataset sizes */
- int apply_f; /* flag for apply filter to return error on H5Dcreate */
- void *buf = NULL; /* buffer for raw data */
- void *hslab_buf = NULL; /* hyperslab buffer for raw data */
- int has_filter; /* current object has a filter */
- int req_filter; /* there was a request for a filter */
- int req_obj_layout = 0; /* request layout to current object */
- unsigned crt_order_flags; /* group creation order flag */
- unsigned i;
- unsigned u;
- int is_ref = 0;
- htri_t is_named;
- hbool_t limit_maxdims;
- hsize_t size_dset;
-
- /*-------------------------------------------------------------------------
- * copy the suppplied object list
- *-------------------------------------------------------------------------
- */
-
- if (options->verbose) {
- printf("-----------------------------------------\n");
- printf(" Type Filter (Compression) Name\n");
- printf("-----------------------------------------\n");
- }
-
- for (i = 0; i < travt->nobjs; i++) {
- /* init variables per obj */
- buf = NULL;
- limit_maxdims = FALSE;
-
- switch (travt->objs[i].type) {
-
- case H5TRAV_TYPE_UNKNOWN:
- HDassert(0);
- break;
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_GROUP
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_GROUP:
-
- if (options->verbose) {
- printf(FORMAT_OBJ, "group", travt->objs[i].name);
- }
-
- /* open input group */
- if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
- < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gopen2 failed");
-
- /* get input group creation property list */
- if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gget_create_plist failed");
-
- /* query and set the group creation properties */
- if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
-
- /* set up group creation property list */
- if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pcreate failed");
-
- if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
-
- /*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(travt->objs[i].name, "/") == 0) {
- if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gopen2 failed");
- }
- else {
-
- if (options->grp_compact > 0 || options->grp_indexed > 0) {
- if (H5Pset_link_phase_change(gcpl_out,
- (unsigned) options->grp_compact,
- (unsigned) options->grp_indexed) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
- }
-
- if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name,
- H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gcreate2 failed");
-
- }
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_attr failed");
-
- if (H5Pclose(gcpl_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
- if (H5Pclose(gcpl_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
- if (H5Gclose(grp_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gclose failed");
- if (H5Gclose(grp_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gclose failed");
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_DATASET
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_DATASET:
-
- has_filter = 0;
- req_filter = 0;
-
- /* check if global filters were requested */
- if (options->n_filter_g)
- req_filter = 1;
-
- /* check if filters were requested for individual objects */
- for (u = 0; u < options->op_tbl->nelems; u++) {
-
- if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
- if (options->op_tbl->objs[u].filter->filtn > 0) {
- req_filter = 1;
- }
- }
- }
-
- /* check if layout change requested individual object */
- if (options->layout_g != H5D_LAYOUT_ERROR) {
- pack_info_t *pckinfo;
- /* any dataset is specified */
- if (options->op_tbl->nelems > 0) {
- /* check if object exist */
- pckinfo = options_get_object(travt->objs[i].name,
- options->op_tbl);
- if (pckinfo) {
- req_obj_layout = 1;
- }
- }
- }
-
- /* early detection of references */
- if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
- < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
- if ((ftype_id = H5Dget_type(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_type failed");
- if (H5T_REFERENCE == H5Tget_class(ftype_id))
- is_ref = 1;
-
- /* Check if the datatype is committed */
- if ((is_named = H5Tcommitted(ftype_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tcommitted failed");
- if (is_named)
- if ((wtype_id = copy_named_datatype(ftype_id, fidout,
- &named_dt_head, travt, options)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_named_datatype failed");
-
- if (H5Tclose(ftype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
- if (H5Dclose(dset_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
-
- /*-------------------------------------------------------------------------
- * check if we should use H5Ocopy or not
- * if there is a request for filters/layout, we read/write the object
- * otherwise we do a copy using H5Ocopy
- *-------------------------------------------------------------------------
- */
- if (options->op_tbl->nelems || options->all_filter == 1
- || options->all_layout == 1 || is_ref || is_named) {
-
- int j;
-
- if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
- if ((f_space_id = H5Dget_space(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_space failed");
- if ((ftype_id = H5Dget_type(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_type failed");
- if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_create_plist failed");
- if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pcopy failed");
- if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
- HDmemset(dims, 0, sizeof dims);
- if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
-
- if (H5Dget_space_status(dset_in, &space_status) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_space_status failed");
-
- nelmts = 1;
- for (j = 0; j < rank; j++)
- nelmts *= dims[j];
-
- /* wtype_id will have already been set if using a named dtype */
- if (!is_named) {
- if (options->use_native == 1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
- } /* end if */
-
- if ((msize = H5Tget_size(wtype_id)) == 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_size failed");
-
- /* size of current dset */
- size_dset = nelmts * msize;
-
- /*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
- if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
- apply_s = 1;
- apply_f = 1;
-
- /*-------------------------------------------------------------------------
- * references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- * in a second traversal of the output file
- *-------------------------------------------------------------------------
- */
- if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
- /* get the storage size of the input dataset */
- dsize_in = H5Dget_storage_size(dset_in);
-
- /* check for small size datasets (less than 1k) except
- * changing to COMPACT. For the reference, COMPACT is limited
- * by size 64K by library.
- */
- if (options->layout_g != H5D_COMPACT) {
- if (size_dset < options->min_comp)
- apply_s = 0;
- }
-
- /* apply the filter */
- if (apply_s) {
- if (apply_filters(travt->objs[i].name, rank, dims,
- msize, dcpl_out, options, &has_filter) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "apply_filters failed");
- }
-
- /* only if layout change requested for entire file or
- * individual obj */
- if (options->all_layout > 0 || req_obj_layout == 1)
- /*-------------------------------------------------
- * Unset the unlimited max dims if convert to other
- * than chunk layouts, because unlimited max dims
- * only can be applied to chunk layout.
- * Also perform only for targeted dataset
- * Also check for size limit to convert to compact
- *-------------------------------------------------*/
- if (options->layout_g != H5D_CHUNKED) {
- /* any dataset is specified */
- if (options->op_tbl->nelems > 0) {
- /* if current obj match specified obj */
- if (options_get_object(travt->objs[i].name,
- options->op_tbl))
- limit_maxdims = TRUE;
- }
- else { /* no dataset is specified */
- limit_maxdims = TRUE;
- }
-
- /* if convert to COMPACT */
- if (options->layout_g == H5D_COMPACT) {
- /* should be smaller than 64K */
- if (size_dset > MAX_COMPACT_DSIZE)
- limit_maxdims = FALSE;
- }
-
- /* unset unlimited max dims */
- if (limit_maxdims)
- H5Sset_extent_simple(f_space_id, rank, dims,
- NULL);
- }
-
- /*-------------------------------------------------------------------------
- * create the output dataset;
- * disable error checking in case the dataset cannot be created with the
- * modified dcpl; in that case use the original instead
- *-------------------------------------------------------------------------
- */
- dset_out = H5Dcreate2(fidout,
- travt->objs[i].name, wtype_id,
- f_space_id, H5P_DEFAULT, dcpl_out,
- H5P_DEFAULT);
-
- if (dset_out == FAIL) {
- HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
- if (options->verbose)
- printf(
- " warning: could not create dataset <%s>. Applying original settings\n",
- travt->objs[i].name);
-
- if ((dset_out = H5Dcreate2(fidout,
- travt->objs[i].name, wtype_id, f_space_id,
- H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
- apply_f = 0;
- }
-
- /*-------------------------------------------------------------------------
- * read/write
- *-------------------------------------------------------------------------
- */
- if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
- size_t need = (size_t)(nelmts * msize); /* bytes needed */
-
- /* have to read the whole dataset if there is only one element in the dataset */
- if (need < H5TOOLS_MALLOCSIZE)
- buf = HDmalloc(need);
-
- if (buf != NULL) {
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id,
- H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id,
- H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-
- /* Check if we have VL data in the dataset's
- * datatype that must be reclaimed */
- if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
- if (H5Dvlen_reclaim(wtype_id, f_space_id,
- H5P_DEFAULT, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
- }
- else { /* possibly not enough memory, read/write by hyperslabs */
- size_t p_type_nbytes = msize; /*size of memory type */
- hsize_t p_nelmts = nelmts; /*total elements */
- hsize_t elmtno; /*counter */
- int carry; /*counter carry value */
- unsigned int vl_data = 0; /*contains VL datatypes */
-
- /* hyperslab info */
- hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
- hsize_t hslab_nbytes; /*bytes per hyperslab */
- hsize_t hslab_nelmts; /*elements per hyperslab*/
- hid_t hslab_space; /*hyperslab data space */
-
- /* hyperslab selection info */
- hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
- hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
- hsize_t hs_select_nelmts; /* selected elements */
- hsize_t zero[8]; /*vector of zeros */
- int k;
- H5D_layout_t dset_layout;
- hid_t dcpl_tmp = -1; /* dataset creation property list ID */
-
- /* check if we have VL data in the dataset's datatype */
- if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
- vl_data = TRUE;
-
- /* check first if writing dataset is chunked,
- * if so use its chunk layout for better performance. */
- dset_layout = H5Pget_layout(dcpl_out);
- if (dset_layout == H5D_CHUNKED)
- dcpl_tmp = dcpl_out; /* writing dataset */
- else { /* if reading dataset is chunked */
- dset_layout = H5Pget_layout(dcpl_in);
- if (dset_layout == H5D_CHUNKED)
- dcpl_tmp = dcpl_in; /* reading dataset */
- }
-
- /* get hyperslab dims and size in byte */
- if (Get_hyperslab(dcpl_tmp, rank, dims,
- p_type_nbytes, hslab_dims,
- &hslab_nbytes) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "Get_hyperslab failed");
-
- hslab_buf = HDmalloc((size_t)hslab_nbytes);
-
- hslab_nelmts = hslab_nbytes / p_type_nbytes;
- hslab_space = H5Screate_simple(1, &hslab_nelmts,
- NULL);
-
- /* the hyperslab selection loop */
- HDmemset(hs_sel_offset, 0,
- sizeof hs_sel_offset);
- HDmemset(zero, 0, sizeof zero);
-
- for (elmtno = 0; elmtno < p_nelmts; elmtno +=
- hs_select_nelmts) {
- if (rank > 0) {
- /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
- */
- for (k = 0, hs_select_nelmts = 1;
- k < rank; k++) {
- /* MIN() is used to get the remaining edge portion if exist.
- * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
- hs_sel_count[k] =
- MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
- hs_select_nelmts *= hs_sel_count[k];
- }
-
- if (H5Sselect_hyperslab(f_space_id,
- H5S_SELECT_SET, hs_sel_offset,
- NULL, hs_sel_count, NULL) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
- if (H5Sselect_hyperslab(hslab_space,
- H5S_SELECT_SET, zero, NULL,
- &hs_select_nelmts, NULL) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
- }
- else {
- H5Sselect_all(f_space_id);
- H5Sselect_all(hslab_space);
- hs_select_nelmts = 1;
- } /* rank */
-
- /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
- CHECK_H5DRW_ERROR(H5Dread, dset_in,
- wtype_id, hslab_space, f_space_id,
- H5P_DEFAULT, hslab_buf);
- CHECK_H5DRW_ERROR(H5Dwrite, dset_out,
- wtype_id, hslab_space, f_space_id,
- H5P_DEFAULT, hslab_buf);
-
- /* reclaim any VL memory, if necessary */
- if (vl_data)
- H5Dvlen_reclaim(wtype_id, hslab_space,
- H5P_DEFAULT, hslab_buf);
-
- /* calculate the next hyperslab offset */
- for (k = rank, carry = 1; k > 0 && carry;
- --k) {
- hs_sel_offset[k - 1] += hs_sel_count[k
- - 1];
- /* if reached the end of a dim */
- if (hs_sel_offset[k - 1] == dims[k - 1])
- hs_sel_offset[k - 1] = 0;
- else
- carry = 0;
- } /* k */
- } /* elmtno */
-
- H5Sclose(hslab_space);
- /* free */
- if (hslab_buf != NULL) {
- HDfree(hslab_buf);
- hslab_buf = NULL;
- }
- } /* hyperslab read */
- } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
-
- /*-------------------------------------------------------------------------
- * amount of compression used
- *-------------------------------------------------------------------------
- */
- if (options->verbose) {
- double ratio = 0;
-
- /* only print the compression ration if there was a filter request */
- if (apply_s && apply_f && req_filter) {
- /* get the storage size of the output dataset */
- dsize_out = H5Dget_storage_size(dset_out);
-
- /* compression ratio = uncompressed size / compressed size */
- if (dsize_out != 0)
- ratio = (double) dsize_in
- / (double) dsize_out;
-
- print_dataset_info(dcpl_out,
- travt->objs[i].name, ratio, 1);
- }
- else
- print_dataset_info(dcpl_in, travt->objs[i].name,
- ratio, 0);
-
- /* print a message that the filter was not applied
- (in case there was a filter)
- */
- if (has_filter && apply_s == 0)
- printf(
- " <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
- travt->objs[i].name,
- (int) options->min_comp);
-
- if (has_filter && apply_f == 0)
- printf(
- " <warning: could not apply the filter to %s>\n",
- travt->objs[i].name);
-
- } /* verbose */
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if (copy_attr(dset_in, dset_out, &named_dt_head, travt,
- options) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_attr failed");
- /*close */
- if (H5Dclose(dset_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
-
- }/*!H5T_REFERENCE*/
- }/*h5tools_canreadf*/
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
- if (H5Tclose(ftype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
- if (H5Tclose(wtype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
- if (H5Pclose(dcpl_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
- if (H5Pclose(dcpl_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
- if (H5Sclose(f_space_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
- if (H5Dclose(dset_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
-
- }
- /*-------------------------------------------------------------------------
- * we do not have request for filter/chunking use H5Ocopy instead
- *-------------------------------------------------------------------------
- */
- else {
- hid_t pid;
-
- /* create property to pass copy options */
- if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pcreate failed");
-
- /* set options for object copy */
- if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pset_copy_object failed");
-
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
-
- if (H5Ocopy(fidin, /* Source file or group identifier */
- travt->objs[i].name, /* Name of the source object to be copied */
- fidout, /* Destination file or group identifier */
- travt->objs[i].name, /* Name of the destination object */
- pid, /* Properties which apply to the copy */
- H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Ocopy failed");
-
- /* close property */
- if (H5Pclose(pid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
-
- /*-------------------------------------------------------------------------
- * copy attrs manually
- *-------------------------------------------------------------------------
- */
- if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
- < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
- if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
- if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_attr failed");
- if (H5Dclose(dset_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
- if (H5Dclose(dset_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
-
- if (options->verbose)
- printf(FORMAT_OBJ, "dset", travt->objs[i].name);
-
- } /* end do we have request for filter/chunking */
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_NAMED_DATATYPE
- *-------------------------------------------------------------------------
- */
- case H5TRAV_TYPE_NAMED_DATATYPE:
-
- if (options->verbose)
- printf(FORMAT_OBJ, "type", travt->objs[i].name);
-
- if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Topen2 failed");
+ hid_t grp_out = -1; /* group ID */
+ hid_t dset_in = -1; /* read dataset ID */
+ hid_t dset_out = -1; /* write dataset ID */
+ hid_t gcpl_in = -1; /* group creation property list */
+ hid_t gcpl_out = -1; /* group creation property list */
+ hid_t type_in = -1; /* named type ID */
+ hid_t type_out = -1; /* named type ID */
+ hid_t dcpl_in = -1; /* dataset creation property list ID */
+ hid_t dcpl_out = -1; /* dataset creation property list ID */
+ hid_t f_space_id = -1; /* file space ID */
+ hid_t ftype_id = -1; /* file type ID */
+ hid_t wtype_id = -1; /* read/write type ID */
+ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
+ size_t msize; /* size of type */
+ hsize_t nelmts; /* number of elements in dataset */
+ H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ hsize_t dsize_in; /* input dataset size before filter */
+ hsize_t dsize_out; /* output dataset size after filter */
+ int apply_s; /* flag for apply filter to small dataset sizes */
+ int apply_f; /* flag for apply filter to return error on H5Dcreate */
+ void *buf = NULL; /* buffer for raw data */
+ void *hslab_buf = NULL; /* hyperslab buffer for raw data */
+ int has_filter; /* current object has a filter */
+ int req_filter; /* there was a request for a filter */
+ int req_obj_layout = 0; /* request layout to current object */
+ unsigned crt_order_flags; /* group creation order flag */
+ unsigned i;
+ unsigned u;
+ int is_ref = 0;
+ htri_t is_named;
+ hbool_t limit_maxdims;
+ hsize_t size_dset;
- /* Copy the datatype anonymously */
- if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
- travt, options)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_named_datatype failed");
-
- /* Link in to group structure */
- if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
- H5P_DEFAULT, H5P_DEFAULT) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Lcreate_hard failed");
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_attr failed");
-
- if (H5Tclose(type_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
- if (H5Tclose(type_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ /*-------------------------------------------------------------------------
+ * copy the suppplied object list
+ *-------------------------------------------------------------------------
+ */
- break;
+ if (options->verbose) {
+ printf("-----------------------------------------\n");
+ printf(" Type Filter (Compression) Name\n");
+ printf("-----------------------------------------\n");
+ }
- /*-------------------------------------------------------------------------
- * H5TRAV_TYPE_LINK
- * H5TRAV_TYPE_UDLINK
- *
- * Only handles external links; H5Lcopy will fail for other UD link types
- * since we don't have creation or copy callbacks for them.
- *-------------------------------------------------------------------------
- */
+ for (i = 0; i < travt->nobjs; i++) {
+ /* init variables per obj */
+ buf = NULL;
+ limit_maxdims = FALSE;
+
+ switch (travt->objs[i].type) {
+ case H5TRAV_TYPE_UNKNOWN:
+ HDassert(0);
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_GROUP:
+ if (options->verbose)
+ printf(FORMAT_OBJ, "group", travt->objs[i].name);
+
+ /* open input group */
+ if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+
+ /* get input group creation property list */
+ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+
+ /* query and set the group creation properties */
+ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+
+ /* set up group creation property list */
+ if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+
+ if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
+
+ /*-------------------------------------------------------------------------
+ * the root is a special case, we get an ID for the root group
+ * and copy its attributes using that ID
+ *-------------------------------------------------------------------------
+ */
+ if (HDstrcmp(travt->objs[i].name, "/") == 0) {
+ if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+ }
+ else {
+ if (options->grp_compact > 0 || options->grp_indexed > 0)
+ if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
- case H5TRAV_TYPE_LINK:
- case H5TRAV_TYPE_UDLINK: {
+ if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed");
+ }
- if (options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+
+ if (H5Pclose(gcpl_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(gcpl_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Gclose(grp_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+ if (H5Gclose(grp_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_DATASET
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_DATASET:
+ has_filter = 0;
+ req_filter = 0;
+
+ /* check if global filters were requested */
+ if (options->n_filter_g)
+ req_filter = 1;
+
+ /* check if filters were requested for individual objects */
+ for (u = 0; u < options->op_tbl->nelems; u++)
+ if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
+ if (options->op_tbl->objs[u].filter->filtn > 0)
+ req_filter = 1;
+
+ /* check if layout change requested individual object */
+ if (options->layout_g != H5D_LAYOUT_ERROR) {
+ pack_info_t *pckinfo;
+
+ /* any dataset is specified */
+ if (options->op_tbl->nelems > 0) {
+ /* check if object exist */
+ pckinfo = options_get_object(travt->objs[i].name, options->op_tbl);
+ if (pckinfo)
+ req_obj_layout = 1;
+ }
+ }
- if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
- H5P_DEFAULT, H5P_DEFAULT) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Lcopy failed");
+ /* early detection of references */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+ if (H5T_REFERENCE == H5Tget_class(ftype_id))
+ is_ref = 1;
+
+ /* Check if the datatype is committed */
+ if ((is_named = H5Tcommitted(ftype_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
+ if (is_named)
+ if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
+
+ if (H5Tclose(ftype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+
+ /*-------------------------------------------------------------------------
+ * check if we should use H5Ocopy or not
+ * if there is a request for filters/layout, we read/write the object
+ * otherwise we do a copy using H5Ocopy
+ *-------------------------------------------------------------------------
+ */
+ if (options->op_tbl->nelems || options->all_filter == 1
+ || options->all_layout == 1 || is_ref || is_named) {
+
+ int j;
+
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if ((f_space_id = H5Dget_space(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
+ if ((ftype_id = H5Dget_type(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
+ if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+ if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ HDmemset(dims, 0, sizeof dims);
+ if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ if (H5Dget_space_status(dset_in, &space_status) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");
+
+ nelmts = 1;
+ for (j = 0; j < rank; j++)
+ nelmts *= dims[j];
+
+ /* wtype_id will have already been set if using a named dtype */
+ if (!is_named) {
+ if (options->use_native == 1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
+ } /* end if */
- if (options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ if ((msize = H5Tget_size(wtype_id)) == 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+
+ /* size of current dset */
+ size_dset = nelmts * msize;
+
+ /*-------------------------------------------------------------------------
+ * check if the dataset creation property list has filters that
+ * are not registered in the current configuration
+ * 1) the external filters GZIP and SZIP might not be available
+ * 2) the internal filters might be turned off
+ *-------------------------------------------------------------------------
+ */
+ if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
+ apply_s = 1;
+ apply_f = 1;
+
+ /*-------------------------------------------------------------------------
+ * references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ * in a second traversal of the output file
+ *-------------------------------------------------------------------------
+ */
+ if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
+ /* get the storage size of the input dataset */
+ dsize_in = H5Dget_storage_size(dset_in);
+
+ /* check for small size datasets (less than 1k) except
+ * changing to COMPACT. For the reference, COMPACT is limited
+ * by size 64K by library.
+ */
+ if (options->layout_g != H5D_COMPACT)
+ if (size_dset < options->min_comp)
+ apply_s = 0;
+
+ /* apply the filter */
+ if (apply_s)
+ if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");
+
+ /* only if layout change requested for entire file or
+ * individual obj */
+ if (options->all_layout > 0 || req_obj_layout == 1)
+ /*-------------------------------------------------
+ * Unset the unlimited max dims if convert to other
+ * than chunk layouts, because unlimited max dims
+ * only can be applied to chunk layout.
+ * Also perform only for targeted dataset
+ * Also check for size limit to convert to compact
+ *-------------------------------------------------*/
+ if (options->layout_g != H5D_CHUNKED) {
+ /* any dataset is specified */
+ if (options->op_tbl->nelems > 0) {
+ /* if current obj match specified obj */
+ if (options_get_object(travt->objs[i].name, options->op_tbl))
+ limit_maxdims = TRUE;
+ }
+ else /* no dataset is specified */
+ limit_maxdims = TRUE;
+
+ /* if convert to COMPACT */
+ if (options->layout_g == H5D_COMPACT)
+ /* should be smaller than 64K */
+ if (size_dset > MAX_COMPACT_DSIZE)
+ limit_maxdims = FALSE;
+
+ /* unset unlimited max dims */
+ if (limit_maxdims)
+ H5Sset_extent_simple(f_space_id, rank, dims, NULL);
+ }
+
+ /*-------------------------------------------------------------------------
+ * create the output dataset;
+ * disable error checking in case the dataset cannot be created with the
+ * modified dcpl; in that case use the original instead
+ *-------------------------------------------------------------------------
+ */
+ dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
+ if (dset_out == FAIL) {
+ H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ if (options->verbose)
+ printf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);
+
+ if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ apply_f = 0;
+ }
- }
- break;
+ /*-------------------------------------------------------------------------
+ * read/write
+ *-------------------------------------------------------------------------
+ */
+ if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
+ size_t need = (size_t)(nelmts * msize); /* bytes needed */
+
+ /* have to read the whole dataset if there is only one element in the dataset */
+ if (need < H5TOOLS_MALLOCSIZE)
+ buf = HDmalloc(need);
+
+ if (buf != NULL) {
+ /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+ CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+ /* Check if we have VL data in the dataset's
+ * datatype that must be reclaimed */
+ if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+ if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
+ }
+ else { /* possibly not enough memory, read/write by hyperslabs */
+ size_t p_type_nbytes = msize; /*size of memory type */
+ hsize_t p_nelmts = nelmts; /*total elements */
+ hsize_t elmtno; /*counter */
+ int carry; /*counter carry value */
+ unsigned int vl_data = 0; /*contains VL datatypes */
+
+ /* hyperslab info */
+ hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
+ hsize_t hslab_nbytes; /*bytes per hyperslab */
+ hsize_t hslab_nelmts; /*elements per hyperslab*/
+ hid_t hslab_space; /*hyperslab data space */
+
+ /* hyperslab selection info */
+ hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
+ hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
+ hsize_t hs_select_nelmts; /* selected elements */
+ hsize_t zero[8]; /*vector of zeros */
+ int k;
+ H5D_layout_t dset_layout;
+ hid_t dcpl_tmp = -1; /* dataset creation property list ID */
+
+ /* check if we have VL data in the dataset's datatype */
+ if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+ vl_data = TRUE;
+
+ /* check first if writing dataset is chunked,
+ * if so use its chunk layout for better performance. */
+ dset_layout = H5Pget_layout(dcpl_out);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_out; /* writing dataset */
+ else { /* if reading dataset is chunked */
+ dset_layout = H5Pget_layout(dcpl_in);
+ if (dset_layout == H5D_CHUNKED)
+ dcpl_tmp = dcpl_in; /* reading dataset */
+ }
- default:
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "Object type not found");
+ /* get hyperslab dims and size in byte */
+ if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");
+
+ hslab_buf = HDmalloc((size_t)hslab_nbytes);
+
+ hslab_nelmts = hslab_nbytes / p_type_nbytes;
+ hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
+
+ /* the hyperslab selection loop */
+ HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
+ HDmemset(zero, 0, sizeof zero);
+
+ for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) {
+ if (rank > 0) {
+ /* calculate the hyperslab selections.
+ * The selection would be same as the hyperslab
+ * except for remaining edge portion of the dataset
+ * which is smaller then the hyperslab.
+ */
+ for (k = 0, hs_select_nelmts = 1; k < rank; k++) {
+ /* MIN() is used to get the remaining edge portion if exist.
+ * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+ hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
+ hs_select_nelmts *= hs_sel_count[k];
+ }
+
+ if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
+ if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
+ }
+ else {
+ H5Sselect_all(f_space_id);
+ H5Sselect_all(hslab_space);
+ hs_select_nelmts = 1;
+ } /* rank */
+
+ /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+ CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
+ CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
+
+ /* reclaim any VL memory, if necessary */
+ if (vl_data)
+ H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
+
+ /* calculate the next hyperslab offset */
+ for (k = rank, carry = 1; k > 0 && carry; --k) {
+ hs_sel_offset[k - 1] += hs_sel_count[k - 1];
+ /* if reached the end of a dim */
+ if (hs_sel_offset[k - 1] == dims[k - 1])
+ hs_sel_offset[k - 1] = 0;
+ else
+ carry = 0;
+ } /* k */
+ } /* elmtno */
+
+ H5Sclose(hslab_space);
+ /* free */
+ if (hslab_buf != NULL) {
+ HDfree(hslab_buf);
+ hslab_buf = NULL;
+ }
+ } /* hyperslab read */
+ } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+
+ /*-------------------------------------------------------------------------
+ * amount of compression used
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose) {
+ double ratio = 0;
+
+ /* only print the compression ration if there was a filter request */
+ if (apply_s && apply_f && req_filter) {
+ /* get the storage size of the output dataset */
+ dsize_out = H5Dget_storage_size(dset_out);
+
+ /* compression ratio = uncompressed size / compressed size */
+ if (dsize_out != 0)
+ ratio = (double) dsize_in / (double) dsize_out;
+ print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1);
+ }
+ else
+ print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0);
+
+ /* print a message that the filter was not applied
+ (in case there was a filter)
+ */
+ if (has_filter && apply_s == 0)
+ printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);
+
+ if (has_filter && apply_f == 0)
+ printf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
+ } /* verbose */
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+
+ /*close */
+ if (H5Dclose(dset_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ }/*!H5T_REFERENCE*/
+ }/*h5tools_canreadf*/
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tclose(ftype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Tclose(wtype_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Pclose(dcpl_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Pclose(dcpl_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+ if (H5Sclose(f_space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+ if (H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ }
+ /*-------------------------------------------------------------------------
+ * we do not have request for filter/chunking use H5Ocopy instead
+ *-------------------------------------------------------------------------
+ */
+ else {
+ hid_t pid;
+
+ /* create property to pass copy options */
+ if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+
+ /* set options for object copy */
+ if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");
+
+ /*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Ocopy(fidin, /* Source file or group identifier */
+ travt->objs[i].name, /* Name of the source object to be copied */
+ fidout, /* Destination file or group identifier */
+ travt->objs[i].name, /* Name of the destination object */
+ pid, /* Properties which apply to the copy */
+ H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");
+
+ /* close property */
+ if (H5Pclose(pid) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+
+ /*-------------------------------------------------------------------------
+ * copy attrs manually
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
+ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+ if (H5Dclose(dset_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+ if (H5Dclose(dset_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+
+ } /* end do we have request for filter/chunking */
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_NAMED_DATATYPE
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_NAMED_DATATYPE:
+ if (options->verbose)
+ printf(FORMAT_OBJ, "type", travt->objs[i].name);
+
+ if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
+
+ /* Copy the datatype anonymously */
+ if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
+
+ /* Link in to group structure */
+ if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed");
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
+
+ if (H5Tclose(type_in) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+ if (H5Tclose(type_out) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5TRAV_TYPE_LINK
+ * H5TRAV_TYPE_UDLINK
+ *
+ * Only handles external links; H5Lcopy will fail for other UD link types
+ * since we don't have creation or copy callbacks for them.
+ *-------------------------------------------------------------------------
+ */
+ case H5TRAV_TYPE_LINK:
+ case H5TRAV_TYPE_UDLINK:
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+ if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed");
+
+ if (options->verbose)
+ printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ break;
+
+ default:
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
} /* switch */
- /* free */
- if (buf != NULL) {
- HDfree(buf);
- buf = NULL;
- }
+ /* free */
+ if (buf != NULL) {
+ HDfree(buf);
+ buf = NULL;
+ }
+ } /* i */
- } /* i */
+ /* Finalize (link) the stack of named datatypes (if any) */
+ named_datatype_free(&named_dt_head, 0);
- /* Finalize (link) the stack of named datatypes (if any) */
- named_datatype_free(&named_dt_head, 0);
-
- return 0;
+ return ret_value;
done:
- H5E_BEGIN_TRY
- {
- H5Gclose(grp_in);
- H5Gclose(grp_out);
- H5Pclose(dcpl_in);
- H5Pclose(gcpl_in);
- H5Pclose(gcpl_out);
- H5Sclose(f_space_id);
- H5Dclose(dset_in);
- H5Dclose(dset_out);
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Tclose(type_in);
- H5Tclose(type_out);
- named_datatype_free(&named_dt_head, 1);
- }H5E_END_TRY;
- /* free */
- if (buf != NULL)
- HDfree(buf);
- if (hslab_buf != NULL)
- HDfree(hslab_buf);
- return -1;
+ H5E_BEGIN_TRY
+ {
+ H5Gclose(grp_in);
+ H5Gclose(grp_out);
+ H5Pclose(dcpl_in);
+ H5Pclose(gcpl_in);
+ H5Pclose(gcpl_out);
+ H5Sclose(f_space_id);
+ H5Dclose(dset_in);
+ H5Dclose(dset_out);
+ H5Tclose(ftype_id);
+ H5Tclose(wtype_id);
+ H5Tclose(type_in);
+ H5Tclose(type_out);
+ named_datatype_free(&named_dt_head, 1);
+ }H5E_END_TRY;
+
+ /* free */
+ if (buf != NULL)
+ HDfree(buf);
+ if (hslab_buf != NULL)
+ HDfree(hslab_buf);
+
+ return ret_value;
}
/*-------------------------------------------------------------------------
@@ -1411,101 +1324,102 @@ done:
*-------------------------------------------------------------------------
*/
static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
- int pr) {
- char strfilter[255];
+ int pr)
+{
+ char strfilter[255];
#if defined (PRINT_DEBUG )
- char temp[255];
+ char temp[255];
#endif
- int nfilters; /* number of filters */
- unsigned filt_flags; /* filter flags */
- H5Z_filter_t filtn; /* filter identification number */
- unsigned cd_values[20]; /* filter client data values */
- size_t cd_nelmts; /* filter client number of values */
- char f_objname[256]; /* filter objname */
- int i;
-
- HDstrcpy(strfilter, "\0");
+ int nfilters; /* number of filters */
+ unsigned filt_flags; /* filter flags */
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[20]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+ char f_objname[256]; /* filter objname */
+ int i;
- /* get information about input filters */
- if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
- return;
+ HDstrcpy(strfilter, "\0");
- for (i = 0; i < nfilters; i++) {
- cd_nelmts = NELMTS(cd_values);
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
+ return;
- filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
- cd_values, sizeof(f_objname), f_objname, NULL);
+ for (i = 0; i < nfilters; i++) {
+ cd_nelmts = NELMTS(cd_values);
- switch (filtn) {
+ filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+ cd_values, sizeof(f_objname), f_objname, NULL);
- case H5Z_FILTER_NONE:
- HDstrcat(strfilter, "NONE ");
- break;
+ switch (filtn) {
+ case H5Z_FILTER_NONE:
+ HDstrcat(strfilter, "NONE ");
+ break;
- case H5Z_FILTER_DEFLATE:
- HDstrcat(strfilter, "GZIP ");
+ case H5Z_FILTER_DEFLATE:
+ HDstrcat(strfilter, "GZIP ");
#if defined (PRINT_DEBUG)
- {
- unsigned level=cd_values[0];
- sprintf(temp,"(%d)",level);
- HDstrcat(strfilter,temp);
- }
+ {
+ unsigned level = cd_values[0];
+
+ sprintf(temp,"(%d)", level);
+ HDstrcat(strfilter, temp);
+ }
#endif
- break;
+ break;
- case H5Z_FILTER_SZIP:
- HDstrcat(strfilter, "SZIP ");
+ case H5Z_FILTER_SZIP:
+ HDstrcat(strfilter, "SZIP ");
#if defined (PRINT_DEBUG)
- {
- unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
- unsigned ppb=cd_values[1];
- sprintf(temp,"(%d,",ppb);
- HDstrcat(strfilter,temp);
- if (options_mask & H5_SZIP_EC_OPTION_MASK)
- HDstrcpy(temp,"EC) ");
- else if (options_mask & H5_SZIP_NN_OPTION_MASK)
- HDstrcpy(temp,"NN) ");
- }
- HDstrcat(strfilter,temp);
-
+ {
+ unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/
+ unsigned ppb = cd_values[1];
+
+ sprintf(temp,"(%d,", ppb);
+ HDstrcat(strfilter, temp);
+ if (options_mask & H5_SZIP_EC_OPTION_MASK)
+ HDstrcpy(temp, "EC) ");
+ else if (options_mask & H5_SZIP_NN_OPTION_MASK)
+ HDstrcpy(temp, "NN) ");
+ }
+ HDstrcat(strfilter, temp);
#endif
+ break;
- break;
-
- case H5Z_FILTER_SHUFFLE:
- HDstrcat(strfilter, "SHUF ");
- break;
-
- case H5Z_FILTER_FLETCHER32:
- HDstrcat(strfilter, "FLET ");
- break;
-
- case H5Z_FILTER_NBIT:
- HDstrcat(strfilter, "NBIT ");
- break;
-
- case H5Z_FILTER_SCALEOFFSET:
- HDstrcat(strfilter, "SCALEOFFSET ");
- break;
-
- default:
- HDstrcat(strfilter, "UD ");
- break;
- } /* switch */
- }/*i*/
-
- if (!pr)
- printf(FORMAT_OBJ, "dset", objname);
- else {
- char str[255], temp[28];
- HDstrcpy(str, "dset ");
- HDstrcat(str, strfilter);
- sprintf(temp, " (%.3f:1)", ratio);
- HDstrcat(str, temp);
- printf(FORMAT_OBJ, str, objname);
- }
+ case H5Z_FILTER_SHUFFLE:
+ HDstrcat(strfilter, "SHUF ");
+ break;
+
+ case H5Z_FILTER_FLETCHER32:
+ HDstrcat(strfilter, "FLET ");
+ break;
+
+ case H5Z_FILTER_NBIT:
+ HDstrcat(strfilter, "NBIT ");
+ break;
+
+ case H5Z_FILTER_SCALEOFFSET:
+ HDstrcat(strfilter, "SCALEOFFSET ");
+ break;
+
+ default:
+ HDstrcat(strfilter, "UD ");
+ break;
+ } /* switch */
+ }/*i*/
+
+ if (!pr)
+ printf(FORMAT_OBJ, "dset", objname);
+ else {
+ char str[255], temp[28];
+
+ HDstrcpy(str, "dset ");
+ HDstrcat(str, strfilter);
+ sprintf(temp, " (%.3f:1)", ratio);
+ HDstrcat(str, temp);
+ printf(FORMAT_OBJ, str, objname);
+ }
}
/*-------------------------------------------------------------------------
@@ -1522,74 +1436,66 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
*-------------------------------------------------------------------------
*/
static int copy_user_block(const char *infile, const char *outfile,
- hsize_t size) {
+ hsize_t size)
+{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
int infid = -1, outfid = -1; /* File descriptors */
- int status = 0; /* Return value */
-
- /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
- HDassert(size > 0);
-
- /* Open files */
- if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
- }
- if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
- }
-
- /* Copy the userblock from the input file to the output file */
- while (size > 0) {
- ssize_t nread, nbytes; /* # of bytes transfered, etc. */
- char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
- const char *wbuf; /* Pointer into buffer, for writing */
-
- /* Read buffer from source file */
- if (size > USERBLOCK_XFER_SIZE)
- nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
- else
- nread = HDread(infid, rbuf, (size_t)size);
- if (nread < 0) {
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDread failed");
- } /* end if */
-
- /* Write buffer to destination file */
- /* (compensating for interrupted writes & checking for errors, etc.) */
- nbytes = nread;
- wbuf = rbuf;
- while (nbytes > 0) {
- ssize_t nwritten; /* # of bytes written */
-
- do {
- nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
- } while (-1 == nwritten && EINTR == errno);
- if (-1 == nwritten) { /* error */
- status = -1;
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDwrite failed");
- } /* end if */
- HDassert(nwritten > 0);
- HDassert(nwritten <= nbytes);
-
- /* Update # of bytes left & offset in buffer */
- nbytes -= nwritten;
- wbuf += nwritten;
- HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
- } /* end while */
- /* Update size of userblock left to transfer */
- size = size - (hsize_t) nread;
- } /* end while */
+ /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
+ HDassert(size > 0);
+
+ /* Open files */
+ if ((infid = HDopen(infile, O_RDONLY, 0)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+ if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
+
+ /* Copy the userblock from the input file to the output file */
+ while (size > 0) {
+ ssize_t nread, nbytes; /* # of bytes transfered, etc. */
+ char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
+ const char *wbuf; /* Pointer into buffer, for writing */
+
+ /* Read buffer from source file */
+ if (size > USERBLOCK_XFER_SIZE)
+ nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+ else
+ nread = HDread(infid, rbuf, (size_t)size);
+ if (nread < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed");
+
+ /* Write buffer to destination file */
+ /* (compensating for interrupted writes & checking for errors, etc.) */
+ nbytes = nread;
+ wbuf = rbuf;
+ while (nbytes > 0) {
+ ssize_t nwritten; /* # of bytes written */
+
+ do {
+ nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
+ } while (-1 == nwritten && EINTR == errno);
+ if (-1 == nwritten) /* error */
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed");
+ HDassert(nwritten > 0);
+ HDassert(nwritten <= nbytes);
+
+ /* Update # of bytes left & offset in buffer */
+ nbytes -= nwritten;
+ wbuf += nwritten;
+ HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
+ } /* end while */
+
+ /* Update size of userblock left to transfer */
+ size = size - (hsize_t) nread;
+ } /* end while */
done:
- if (infid > 0)
- HDclose(infid);
- if (outfid > 0)
- HDclose(outfid);
+ if (infid > 0)
+ HDclose(infid);
+ if (outfid > 0)
+ HDclose(outfid);
- return status;
+ return ret_value;
}
/*-------------------------------------------------------------------------
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index b2755c2..f0f32c3 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -1,4 +1,3 @@
-
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
@@ -86,18 +85,18 @@ int do_copy_refobjs(hid_t fidin,
*-------------------------------------------------------------------------
*/
if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_refs_attr failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
if(H5Gclose(grp_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
if(H5Gclose(grp_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
/*-------------------------------------------------------------------------
* check for hard links
@@ -114,26 +113,26 @@ int do_copy_refobjs(hid_t fidin,
*/
case H5TRAV_TYPE_DATASET:
if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if((space_id = H5Dget_space(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
if((ftype_id = H5Dget_type(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_type failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
if((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
nelmts = 1;
for(k = 0; k < rank; k++)
nelmts *= dims[k];
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
if((msize = H5Tget_size(mtype_id)) == 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_size failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
@@ -169,15 +168,15 @@ int do_copy_refobjs(hid_t fidin,
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
printf("cannot read into memory\n" );
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDmalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL){
printf("cannot allocate memory\n" );
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDcalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
@@ -191,7 +190,7 @@ int do_copy_refobjs(hid_t fidin,
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
/* create the reference, -1 parameter for objects */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rcreate failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
@@ -209,10 +208,10 @@ int do_copy_refobjs(hid_t fidin,
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dwrite failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
if(buf)
HDfree(buf);
@@ -223,7 +222,7 @@ int do_copy_refobjs(hid_t fidin,
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_attr failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
@@ -246,10 +245,10 @@ int do_copy_refobjs(hid_t fidin,
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDmalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/*-------------------------------------------------------------------------
* create output
@@ -258,7 +257,7 @@ int do_copy_refobjs(hid_t fidin,
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf("cannot allocate memory\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDcalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
for(u = 0; u < nelmts; u++) {
@@ -274,18 +273,15 @@ int do_copy_refobjs(hid_t fidin,
hid_t region_id; /* region id of the referenced dataset */
if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_region failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed");
/* create the reference, we need the space_id */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rcreate failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
if(H5Sclose(region_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(options->verbose)
{
-
-
-
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
@@ -301,10 +297,10 @@ int do_copy_refobjs(hid_t fidin,
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dwrite failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
if(buf)
HDfree(buf);
@@ -315,7 +311,7 @@ int do_copy_refobjs(hid_t fidin,
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_attr failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
@@ -323,7 +319,7 @@ int do_copy_refobjs(hid_t fidin,
*/
else {
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
} /* end else */
HDassert(dset_out != FAIL);
@@ -333,7 +329,7 @@ int do_copy_refobjs(hid_t fidin,
*-------------------------------------------------------------------------
*/
if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "copy_refs_attr failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
/*-------------------------------------------------------------------------
* check for hard links
@@ -344,7 +340,7 @@ int do_copy_refobjs(hid_t fidin,
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
if(H5Dclose(dset_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
} /*can_read*/
/*-------------------------------------------------------------------------
@@ -352,15 +348,15 @@ int do_copy_refobjs(hid_t fidin,
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(mtype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Pclose(dcpl_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if(H5Sclose(space_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(H5Dclose(dset_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
break;
/*-------------------------------------------------------------------------
@@ -369,9 +365,9 @@ int do_copy_refobjs(hid_t fidin,
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Topen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
if(H5Tclose(type_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
break;
/*-------------------------------------------------------------------------
@@ -384,7 +380,7 @@ int do_copy_refobjs(hid_t fidin,
case H5TRAV_TYPE_UNKNOWN:
case H5TRAV_TYPE_UDLINK:
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5TRAV invalid type");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5TRAV invalid type");
default:
break;
@@ -397,7 +393,7 @@ int do_copy_refobjs(hid_t fidin,
*/
named_datatype_free(&named_dt_head, 0);
- return 0;
+ return ret_value;
done:
H5E_BEGIN_TRY {
@@ -413,7 +409,7 @@ done:
named_datatype_free(&named_dt_head, 0);
} H5E_END_TRY;
- return -1;
+ return ret_value;
}
@@ -469,32 +465,32 @@ static int copy_refs_attr(hid_t loc_in,
void *refbuf = NULL;
void *buf = NULL;
const char* refname = NULL;
- int *ref_comp_index = NULL;
+ unsigned *ref_comp_index = NULL;
size_t *ref_comp_size = NULL;
int ref_comp_field_n = 0;
if(H5Oget_info(loc_in, &oinfo) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Oget_info failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
/* get the file datatype */
if((ftype_id = H5Aget_type(attr_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aget_type failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
type_class = H5Tget_class(ftype_id);
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
if((msize = H5Tget_size(mtype_id)) == 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_size failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
is_ref = (type_class == H5T_REFERENCE);
@@ -518,10 +514,10 @@ static int copy_refs_attr(hid_t loc_in,
int nmembers = H5Tget_nmembers(ftype_id) ;
if (nmembers < 1)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_nmembers failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed");
- ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int));
- ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size));
+ ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned));
+ ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size));
ref_comp_field_n = 0;
for (i=0; i<(unsigned)nmembers; i++) {
@@ -562,15 +558,15 @@ static int copy_refs_attr(hid_t loc_in,
/* get name */
if(H5Aget_name(attr_id, 255, name) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aget_name failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_name failed");
/* get the dataspace handle */
if((space_id = H5Aget_space(attr_id)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aget_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed");
/* get dimensions */
if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
/*-------------------------------------------------------------------------
@@ -582,8 +578,8 @@ static int copy_refs_attr(hid_t loc_in,
nelmts *= dims[j];
if (is_ref_array) {
- unsigned array_rank = 0;
- hsize_t array_size = 1;
+ unsigned array_rank = 0;
+ hsize_t array_size = 1;
hsize_t array_dims[H5S_MAX_RANK];
hid_t base_type;
@@ -591,7 +587,7 @@ static int copy_refs_attr(hid_t loc_in,
msize = H5Tget_size(base_type);
H5Tclose(base_type);
- array_rank = H5Tget_array_ndims(mtype_id);
+ array_rank = (unsigned)H5Tget_array_ndims(mtype_id);
H5Tget_array_dims2(mtype_id, array_dims);
for(j = 0; j <array_rank; j++)
array_size *= array_dims[j];
@@ -599,7 +595,7 @@ static int copy_refs_attr(hid_t loc_in,
}
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Acreate2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed");
if (nelmts>0) {
/* handle object references */
@@ -607,15 +603,15 @@ static int copy_refs_attr(hid_t loc_in,
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDmalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL) {
printf("cannot allocate memory\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDcalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
for(i = 0; i < (unsigned)nelmts; i++) {
@@ -631,10 +627,10 @@ static int copy_refs_attr(hid_t loc_in,
if(buf == NULL) {
printf( "cannot read into memory\n" );
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDmalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
/*-------------------------------------------------------------------------
* create output
@@ -643,7 +639,7 @@ static int copy_refs_attr(hid_t loc_in,
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf( "cannot allocate memory\n" );
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDcalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
for(i = 0; i < (unsigned)nelmts; i++) {
@@ -661,11 +657,11 @@ static int copy_refs_attr(hid_t loc_in,
if(buf == NULL) {
printf( "cannot read into memory\n" );
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDmalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
if (H5R_OBJ_REF_BUF_SIZE==msize) {
hobj_ref_t ref_out;
@@ -702,41 +698,43 @@ static int copy_refs_attr(hid_t loc_in,
if(buf == NULL)
{
printf( "cannot read into memory\n" );
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDmalloc failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aread failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
for (i=0; i<(unsigned)nelmts; i++) {
- for (j=0; j<(unsigned)ref_comp_field_n; j++) {
- if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
- int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
- hobj_ref_t ref_out;
- if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
- continue;
- HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
- } /* if */
- else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
- int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
- hdset_reg_ref_t ref_out;
- if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
- continue;
- HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
- } /* else if */
- } /* j */
+ for (j=0; j<(unsigned)ref_comp_field_n; j++) {
+ if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
+ size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
+ hobj_ref_t ref_out;
+
+ if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+ continue;
+ HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+ } /* if */
+ else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
+ size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
+ hdset_reg_ref_t ref_out;
+
+ if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+ continue;
+ HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+ } /* else if */
+ } /* j */
} /* i */
} /* else if (is_ref_comp) */
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Awrite failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
if (is_ref_vlen && buf)
H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
} /* if (nelmts) */
if (refbuf == buf)
- refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
+ refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
if(buf) {
HDfree(buf);
@@ -749,39 +747,39 @@ static int copy_refs_attr(hid_t loc_in,
}
if (ref_comp_index) {
- HDfree(ref_comp_index);
- ref_comp_index = NULL;
+ HDfree(ref_comp_index);
+ ref_comp_index = NULL;
}
if (ref_comp_size) {
- HDfree(ref_comp_size);
- ref_comp_size = NULL;
+ HDfree(ref_comp_size);
+ ref_comp_size = NULL;
}
if(H5Aclose(attr_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(mtype_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Sclose(space_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(H5Aclose(attr_id) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
} /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
- return 0;
+ return ret_value;
done:
- if(refbuf)
- HDfree(refbuf);
- if(buf)
- HDfree(buf);
+ if(refbuf)
+ HDfree(refbuf);
+ if(buf)
+ HDfree(buf);
if (ref_comp_index)
HDfree(ref_comp_index);
@@ -797,7 +795,7 @@ done:
H5Aclose(attr_out);
} H5E_END_TRY;
- return -1;
+ return ret_value;
}
/*-------------------------------------------------------------------------
@@ -848,30 +846,25 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt)
{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- herr_t ret = -1;
- const char* ref_obj_name;
- hid_t space_id=-1, ref_obj_id=-1;
+ const char* ref_obj_name;
+ hid_t space_id=-1, ref_obj_id=-1;
ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
- if (ref_obj_id<0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdereference2 failed");
+ if (ref_obj_id < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rdereference2 failed");
- ref_obj_name = MapIdToName(ref_obj_id, travt);
- if (ref_obj_name == NULL)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "MapIdToName failed");
+ ref_obj_name = MapIdToName(ref_obj_id, travt);
+ if (ref_obj_name == NULL)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "MapIdToName failed");
- if (ref_type == H5R_DATASET_REGION) {
- space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
- if (space_id < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_region failed");
+ if (ref_type == H5R_DATASET_REGION) {
+ space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
+ if (space_id < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed");
}
- ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id);
-
- if (ret < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rcreate failed");
-
- ret = 0;
+ if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
done:
H5E_BEGIN_TRY {
@@ -879,6 +872,6 @@ done:
H5Oclose(ref_obj_id);
} H5E_END_TRY;
- return ret;
+ return ret_value;
}
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 9565ce3..6765c49 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -80,20 +80,20 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*-------------------------------------------------------------------------
*/
if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if((sid = H5Dget_space(did)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
if((pid = H5Dget_create_plist(did)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
if((tid = H5Dget_type(did)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_type failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
/*-------------------------------------------------------------------------
* filter check
*-------------------------------------------------------------------------
*/
if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0)
- ok = 0;
+ ok = 0;
/*-------------------------------------------------------------------------
@@ -108,13 +108,13 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*-------------------------------------------------------------------------
*/
if(H5Pclose(pid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Sclose(sid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if (H5Dclose(did) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
if (H5Tclose(tid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
}
@@ -132,7 +132,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
/* get the list of objects in the file */
if(h5trav_gettable(fidout, travt) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "h5trav_gettable failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
for(i = 0; i < travt->nobjs; i++)
{
@@ -146,13 +146,13 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*-------------------------------------------------------------------------
*/
if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if((sid = H5Dget_space(did)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
if((pid = H5Dget_create_plist(did)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
if((tid = H5Dget_type(did)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_type failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
/*-------------------------------------------------------------------------
* filter check
@@ -160,7 +160,6 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*/
if(options->all_filter == 1)
{
-
if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0)
ok = 0;
}
@@ -172,6 +171,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
if(options->all_layout == 1)
{
pack_info_t pack;
+
init_packobject(&pack);
pack.layout = options->layout_g;
pack.chunk = options->chunk_g;
@@ -185,13 +185,13 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*-------------------------------------------------------------------------
*/
if (H5Pclose(pid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Sclose(sid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if (H5Dclose(did) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
if (H5Tclose(tid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
} /* if */
} /* i */
@@ -208,31 +208,31 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
/* open the input file */
if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fopen failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed");
/* Get file creation property list for input file */
if((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
error_msg("failed to retrieve file creation property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed");
}
/* Get file space management info for input file */
if(H5Pget_file_space(fcpl_in, &in_strat, &in_thresh) < 0) {
error_msg("failed to retrieve file space strategy & threshold\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_file_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space failed");
}
/* Output file is already opened */
/* Get file creation property list for output file */
if((fcpl_out = H5Fget_create_plist(fidout)) < 0) {
error_msg("failed to retrieve file creation property list\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed");
}
/* Get file space management info for output file */
if(H5Pget_file_space(fcpl_out, &out_strat, &out_thresh) < 0) {
error_msg("failed to retrieve file space strategy & threshold\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_file_space failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space failed");
}
/*
@@ -245,12 +245,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*/
if(!options->fs_strategy && out_strat != in_strat) {
error_msg("file space strategy not set as unexpected\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "file space strategy not set as unexpected");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
}
else if(options->fs_strategy && out_strat!= options->fs_strategy) {
error_msg("file space strategy not set as unexpected\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "file space strategy not set as unexpected");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
}
/*
@@ -263,22 +263,22 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
*/
if(!options->fs_threshold && out_thresh != in_thresh) {
error_msg("free space threshold not set as unexpected\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "free space threshold not set as unexpected");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free space threshold not set as unexpected");
}
else if(options->fs_threshold && out_thresh != options->fs_threshold) {
error_msg("free space threshold not set as unexpected\n");
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "free space threshold not set as unexpected");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free space threshold not set as unexpected");
}
/* Closing */
if (H5Pclose(fcpl_in) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Pclose(fcpl_out) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Fclose(fidin) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
if (H5Fclose(fidout) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
return ok;
@@ -294,7 +294,8 @@ done:
if (travt)
trav_table_free(travt);
} H5E_END_TRY;
- return -1;
+
+ return ret_value;
} /* h5repack_verify() */
@@ -397,12 +398,12 @@ int h5repack_cmp_pl(const char *fname1,
{
/* Open the files */
- if ((fid1=H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 )
+ if ((fid1 = H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 )
{
error_msg("<%s>: %s\n", fname1, H5FOPENERROR );
return -1;
}
- if ((fid2=H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 )
+ if ((fid2 = H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 )
{
error_msg("<%s>: %s\n", fname2, H5FOPENERROR );
H5Fclose(fid1);
@@ -417,7 +418,7 @@ int h5repack_cmp_pl(const char *fname1,
*/
trav_table_init(&trav);
if(h5trav_gettable(fid1, trav) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "h5trav_gettable failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
/*-------------------------------------------------------------------------
* traverse the suppplied object list
@@ -430,30 +431,30 @@ int h5repack_cmp_pl(const char *fname1,
{
if ((gid = H5Gopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
if ((gcplid = H5Gget_create_plist(gid)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
if (H5Pget_link_creation_order(gcplid, &crt_order_flag1) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
if (H5Pclose(gcplid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Gclose(gid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
if ((gid = H5Gopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
if ((gcplid = H5Gget_create_plist(gid)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
if (H5Pget_link_creation_order(gcplid, &crt_order_flag2) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
if (H5Pclose(gcplid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if (H5Gclose(gid) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Gclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
if (crt_order_flag1 != crt_order_flag2) {
error_msg("property lists for <%s> are different\n",trav->objs[i].name);
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "property lists failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed");
}
}
@@ -463,24 +464,24 @@ int h5repack_cmp_pl(const char *fname1,
else if(trav->objs[i].type == H5TRAV_TYPE_DATASET)
{
if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dopen2 failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
if((dcpl1 = H5Dget_create_plist(dset1)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
if((dcpl2 = H5Dget_create_plist(dset2)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dget_create_plist failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
/*-------------------------------------------------------------------------
* compare the property lists
*-------------------------------------------------------------------------
*/
if((ret = H5Pequal(dcpl1, dcpl2)) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pequal failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed");
if(ret == 0) {
error_msg("property lists for <%s> are different\n",trav->objs[i].name);
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "property lists failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed");
}
/*-------------------------------------------------------------------------
@@ -488,13 +489,13 @@ int h5repack_cmp_pl(const char *fname1,
*-------------------------------------------------------------------------
*/
if(H5Pclose(dcpl1) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if(H5Pclose(dcpl2) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
if(H5Dclose(dset1) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
if(H5Dclose(dset2) < 0)
- HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed");
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
} /*if*/
} /*i*/
@@ -512,13 +513,13 @@ int h5repack_cmp_pl(const char *fname1,
H5Fclose(fid1);
H5Fclose(fid2);
- return ret;
- /*-------------------------------------------------------------------------
- * error
- *-------------------------------------------------------------------------
- */
+ return ret;
+/*-------------------------------------------------------------------------
+* error
+*-------------------------------------------------------------------------
+*/
done:
H5E_BEGIN_TRY
{
@@ -532,8 +533,8 @@ done:
H5Gclose(gid);
trav_table_free(trav);
} H5E_END_TRY;
- return -1;
+ return ret_value;
}
@@ -602,100 +603,71 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
switch (filtn)
{
- case H5Z_FILTER_NONE:
+ case H5Z_FILTER_NONE:
break;
- case H5Z_FILTER_SHUFFLE:
-
- /* 1 private client value is returned by DCPL */
- if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS )
- return 0;
-
- /* get dataset's type size */
- if((size = H5Tget_size(tid)) <= 0)
- return -1;
-
- /* the private client value holds the dataset's type size */
- if ( size != cd_values[0] )
- return 0;
-
-
- break;
-
- case H5Z_FILTER_SZIP:
-
- /* 4 private client values are returned by DCPL */
- if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS )
- return 0;
-
- /* "User" parameter for pixels-per-block (index 1) */
- if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] )
- return 0;
-
-
- break;
-
- case H5Z_FILTER_NBIT:
-
- /* only client data values number of values checked */
- if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts)
- return 0;
-
-
-
- break;
+ case H5Z_FILTER_SHUFFLE:
+ /* 1 private client value is returned by DCPL */
+ if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS )
+ return 0;
- case H5Z_FILTER_SCALEOFFSET:
+ /* get dataset's type size */
+ if((size = H5Tget_size(tid)) <= 0)
+ return -1;
- /* only client data values checked */
- for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++)
- {
- if (cd_values[j] != filter[i].cd_values[j])
- {
+ /* the private client value holds the dataset's type size */
+ if ( size != cd_values[0] )
return 0;
- }
- }
+ break;
+ case H5Z_FILTER_SZIP:
+ /* 4 private client values are returned by DCPL */
+ if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS )
+ return 0;
- break;
-
- /* for these filters values must match, no local values set in DCPL */
- case H5Z_FILTER_FLETCHER32:
- case H5Z_FILTER_DEFLATE:
+ /* "User" parameter for pixels-per-block (index 1) */
+ if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] )
+ return 0;
- if ( cd_nelmts != filter[i].cd_nelmts)
- return 0;
+ break;
- for( j = 0; j < cd_nelmts; j++)
- {
- if (cd_values[j] != filter[i].cd_values[j])
- {
+ case H5Z_FILTER_NBIT:
+ /* only client data values number of values checked */
+ if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts)
return 0;
- }
+ break;
- }
+ case H5Z_FILTER_SCALEOFFSET:
+ /* only client data values checked */
+ for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++)
+ if (cd_values[j] != filter[i].cd_values[j])
+ return 0;
+ break;
+ /* for these filters values must match, no local values set in DCPL */
+ case H5Z_FILTER_FLETCHER32:
+ case H5Z_FILTER_DEFLATE:
+ if ( cd_nelmts != filter[i].cd_nelmts)
+ return 0;
- break;
+ for( j = 0; j < cd_nelmts; j++)
+ if (cd_values[j] != filter[i].cd_values[j])
+ return 0;
- default:
- if ( cd_nelmts != filter[i].cd_nelmts)
- return 0;
+ break;
- for( j = 0; j < cd_nelmts; j++)
- {
- if (cd_values[j] != filter[i].cd_values[j])
- {
- return 0;
- }
+ default:
+ if ( cd_nelmts != filter[i].cd_nelmts)
+ return 0;
- }
- break;
+ for( j = 0; j < cd_nelmts; j++)
+ if (cd_values[j] != filter[i].cd_values[j])
+ return 0;
+ break;
} /* switch */
-
}
return 1;