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-rw-r--r--tools/src/h5repack/h5repack.c63
-rw-r--r--tools/src/h5repack/h5repack_copy.c66
2 files changed, 68 insertions, 61 deletions
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index d49a16b..f12c3b4 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -382,7 +382,8 @@ copy_attr(
*/
for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
/* 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)
+ attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT);
+ if (attr_id < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
@@ -504,7 +505,7 @@ copy_attr(
} /*H5T_REFERENCE*/
if (options->verbose)
- printf(FORMAT_OBJ_ATTR, "attr", name);
+ HDprintf(FORMAT_OBJ_ATTR, "attr", name);
/*---------------------------------------------------------------------
* close
@@ -567,7 +568,7 @@ check_options(pack_opt_t *options)
*/
if (options->verbose && have_request(options)) {
if (options->all_layout == 1) {
- printf("All objects to modify layout are...\n");
+ HDprintf("All objects to modify layout are...\n");
switch (options->layout_g) {
case H5D_COMPACT:
strcpy(slayout, "compact");
@@ -588,17 +589,17 @@ check_options(pack_opt_t *options)
strcpy(slayout, "invalid layout\n");
HGOTO_DONE(FAIL);
}
- printf(" Apply %s layout to all", slayout);
+ HDprintf(" Apply %s layout to all", slayout);
if (H5D_CHUNKED == options->layout_g) {
- printf("with dimension [ ");
+ HDprintf("with dimension [ ");
for (j = 0; j < options->chunk_g.rank; j++)
- printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
- printf("]");
+ HDprintf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+ HDprintf("]");
}
- printf("\n");
+ HDprintf("\n");
}
else
- printf("No all objects to modify layout\n");
+ HDprintf("No all objects to modify layout\n");
} /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
@@ -606,16 +607,16 @@ check_options(pack_opt_t *options)
if (options->op_tbl->objs[i].chunk.rank > 0) {
if (options->verbose) {
- printf(" <%s> with chunk size ", name);
+ HDprintf(" <%s> with chunk size ", name);
for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
- printf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
- printf("\n");
+ HDprintf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+ HDprintf("\n");
}
has_ck = 1;
}
else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */
if (options->verbose)
- printf(" <%s> %s\n", name, "NONE (contiguous)");
+ HDprintf(" <%s> %s\n", name, "NONE (contiguous)");
has_ck = 1;
}
} /* end for each object in options */
@@ -631,35 +632,35 @@ check_options(pack_opt_t *options)
if (options->verbose && have_request(options)) {
if (options->all_filter == 1) {
- printf("All objects to apply filter are...\n");
+ HDprintf("All objects to apply filter are...\n");
for (k = 0; k < options->n_filter_g; k++) {
H5Z_filter_t filtn = options->filter_g[k].filtn;
if (filtn < 0) {
- printf(" Unknown\n");
+ HDprintf(" Unknown\n");
continue;
}
switch (filtn) {
case H5Z_FILTER_NONE:
- printf(" Uncompress all\n");
+ HDprintf(" Uncompress all\n");
break;
case H5Z_FILTER_SHUFFLE:
case H5Z_FILTER_FLETCHER32:
- printf(" All with %s\n", get_sfilter(filtn));
+ HDprintf(" All with %s\n", get_sfilter(filtn));
break;
case H5Z_FILTER_SZIP:
case H5Z_FILTER_DEFLATE:
- printf(" All with %s, parameter %d\n",
+ HDprintf(" All with %s, parameter %d\n",
get_sfilter(filtn),
options->filter_g[k].cd_values[0]);
break;
default:
- printf(" User Defined %d\n", filtn);
+ HDprintf(" User Defined %d\n", filtn);
break;
} /* end switch */
} /* end for each filter */
} /* end if options->all_filter == 1 (TODO: meaning) */
else
- printf("No all objects to apply filter\n");
+ HDprintf("No all objects to apply filter\n");
} /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
@@ -669,15 +670,16 @@ check_options(pack_opt_t *options)
for (j = 0; j < pack.nfilters; j++) {
if (options->verbose) {
if (pack.filter[j].filtn >= 0) {
- if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET)
- printf(" <%s> with %s filter %d\n",
- name,
+ if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) {
+ HDprintf(" <%s> with %s filter %d\n", name,
get_sfilter(pack.filter[j].filtn),
pack.filter[j].filtn);
- else
- printf(" <%s> with %s filter\n",
+ }
+ else {
+ HDprintf(" <%s> with %s filter\n",
name,
get_sfilter(pack.filter[j].filtn));
+ }
}
}
has_cp = 1;
@@ -714,7 +716,7 @@ check_options(pack_opt_t *options)
*/
if (options->ublock_filename != NULL && options->ublock_size == 0) {
if (options->verbose) {
- printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename);
+ HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename);
options->ublock_size = 1024;
}
}
@@ -787,15 +789,14 @@ check_objects(const char* fname, pack_opt_t *options)
*/
if (options->verbose)
- printf("Opening file. Searching %zu objects to modify ...\n",
- travt->nobjs);
+ HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs);
for (i = 0; i < options->op_tbl->nelems; i++) {
pack_info_t obj = options->op_tbl->objs[i];
char* name = obj.path;
if (options->verbose)
- printf(" <%s>", name);
+ HDprintf(" <%s>", name);
/* the input object names are present in the file and are valid */
if (h5trav_getindext(name, travt) < 0)
@@ -803,7 +804,7 @@ check_objects(const char* fname, pack_opt_t *options)
"%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose ? "\n" : ""), name, fname);
if (options->verbose)
- printf("...Found\n");
+ HDprintf("...Found\n");
for (ifil = 0; ifil < obj.nfilters; ifil++) {
if (obj.filter[ifil].filtn < 0)
@@ -849,7 +850,7 @@ check_objects(const char* fname, pack_opt_t *options)
} /* end else (chunk rank is 0) */
if (csize < ppb) {
- printf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
+ HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
HGOTO_DONE(0);
}
} /* end case SZIP */
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 5939df4..07defa5 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -296,7 +296,7 @@ print_user_block(fnamein, fidin);
*-------------------------------------------------------------------------
*/
if (options->verbose)
- printf("Making new file ...\n");
+ HDprintf("Making new file ...\n");
if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout);
@@ -625,9 +625,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
if (options->verbose) {
- printf("-----------------------------------------\n");
- printf(" Type Filter (Compression) Name\n");
- printf("-----------------------------------------\n");
+ HDprintf("-----------------------------------------\n");
+ HDprintf(" Type Filter (Compression) Name\n");
+ HDprintf("-----------------------------------------\n");
}
if (travt->objs) {
@@ -646,7 +646,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
case H5TRAV_TYPE_GROUP:
if (options->verbose)
- printf(FORMAT_OBJ, "group", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "group", travt->objs[i].name);
/* open input group */
if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
@@ -782,17 +782,6 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
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 the input dataset has external storage, it must be contiguous.
- * Accordingly, there would be no filter or chunk properties to preserve.
- */
- if (H5Pget_external_count(dcpl_in)) {
- if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
- }
- else {
- 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);
@@ -801,6 +790,20 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Dget_space_status(dset_in, &space_status) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");
+ /* If the input dataset has external storage, it must be contiguous.
+ * Accordingly, there would be no filter or chunk properties to preserve,
+ * so create a new DCPL.
+ * Otherwise, copy dcpl_in.
+ */
+ if (H5Pget_external_count(dcpl_in)) {
+ if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+ }
+ else
+ if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) {
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+ }
+
nelmts = 1;
for (j = 0; j < rank; j++)
nelmts *= dims[j];
@@ -844,12 +847,14 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* 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)
+ if (options->layout_g != H5D_COMPACT) {
+ if (size_dset < options->min_comp) {
apply_s = 0;
+ }
+ }
/* apply the filter */
- if (apply_s)
+ if (apply_s) {
if (apply_filters(
travt->objs[i].name,
rank,
@@ -860,6 +865,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
&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 */
@@ -916,7 +922,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
H5E_tools_min_id_g,
"H5Dcreate2 failed");
if (options->verbose)
- printf(" warning: could not create dataset <%s>. Applying original settings\n",
+ HDprintf(" warning: could not create dataset <%s>. Applying original settings\n",
travt->objs[i].name);
dset_out = H5Dcreate2(fidout,
travt->objs[i].name,
@@ -1122,12 +1128,12 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* (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",
+ HDprintf(" <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);
+ HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
} /* end if verbose (print compression) */
/*-------------------------------------------------------------------------
@@ -1201,7 +1207,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
if (options->verbose)
- printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
} /* end whether we have request for filter/chunking */
break;
@@ -1212,7 +1218,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if (options->verbose)
- printf(FORMAT_OBJ, "type", travt->objs[i].name);
+ HDprintf(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");
@@ -1251,13 +1257,13 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
case H5TRAV_TYPE_LINK:
case H5TRAV_TYPE_UDLINK:
if (options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ HDprintf(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);
+ HDprintf(FORMAT_OBJ, "link", travt->objs[i].name);
break;
default:
@@ -1400,7 +1406,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
} /* end for each filter */
if (!pr)
- printf(FORMAT_OBJ, "dset", objname);
+ HDprintf(FORMAT_OBJ, "dset", objname);
else {
char str[512], temp[512];
@@ -1408,7 +1414,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
HDstrcat(str, strfilter);
sprintf(temp, " (%.3f:1)", ratio);
HDstrcat(str, temp);
- printf(FORMAT_OBJ, str, objname);
+ HDprintf(FORMAT_OBJ, str, objname);
}
} /* end print_dataset_info() */
@@ -1535,10 +1541,10 @@ print_user_block(const char *filename, hid_t fid)
for (i = 0; i < nread; i++) {
- printf("%c ", rbuf[i]);
+ HDprintf("%c ", rbuf[i]);
}
- printf("\n");
+ HDprintf("\n");
if (nread < 0) {
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
generated by cgit v0.12 at 2024-11-08 02:13:58 (GMT)