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authorRaymond Lu <songyulu@hdfgroup.org>2002-11-18 16:38:11 (GMT)
committerRaymond Lu <songyulu@hdfgroup.org>2002-11-18 16:38:11 (GMT)
commit0105a3b97cabccd3463c82c22da7e3f4d23c2b05 (patch)
tree9b0002e531446227f62b929adba84b9bfbcacc8a /tools/h5dump
parent02fe47462b798e7f212f09fe65f022965ce4b365 (diff)
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[svn-r6099]
Purpose: bug fix. Description: h5dump cannot dump data and datatype for VL string. Platforms tested: eirene, arabica Misc. update: MANIFEST, RELEASE.txt
Diffstat (limited to 'tools/h5dump')
-rw-r--r--tools/h5dump/h5dump.c92
-rw-r--r--tools/h5dump/h5dumpgentest.c54
-rwxr-xr-xtools/h5dump/testh5dump.sh4
3 files changed, 126 insertions, 24 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index d751d25..36250d3 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -677,12 +677,14 @@ print_datatype(hid_t type)
char *fname;
hid_t nmembers, mtype, str_type;
int i, j, ndims, perm[H5DUMP_MAX_RANK];
- size_t size;
+ size_t size=0;
hsize_t dims[H5DUMP_MAX_RANK];
H5T_str_t str_pad;
H5T_cset_t cset;
H5G_stat_t statbuf;
hid_t super;
+ hid_t tmp_type;
+ htri_t is_vlstr=FALSE;
switch (H5Tget_class(type)) {
case H5T_INTEGER:
@@ -770,15 +772,23 @@ print_datatype(hid_t type)
break;
case H5T_STRING:
- size = H5Tget_size(type);
- str_pad = H5Tget_strpad(type);
- cset = H5Tget_cset(type);
+ /* Make a copy of type in memory in case when TYPE is on disk, the size
+ * will be bigger than in memory. This makes it easier to compare
+ * types in memory. */
+ tmp_type = H5Tcopy(type);
+ size = H5Tget_size(tmp_type);
+ str_pad = H5Tget_strpad(tmp_type);
+ cset = H5Tget_cset(tmp_type);
+ is_vlstr = H5Tis_variable_str(tmp_type);
printf("H5T_STRING %s\n", dump_header_format->strblockbegin);
indent += COL;
indentation(indent + COL);
- printf("%s %d;\n", STRSIZE, (int) size);
+ if(is_vlstr)
+ printf("%s H5T_VARIABLE;\n", STRSIZE);
+ else
+ printf("%s %d;\n", STRSIZE, (int) size);
indentation(indent + COL);
printf("%s ", STRPAD);
@@ -800,14 +810,17 @@ print_datatype(hid_t type)
printf("unknown_cset;\n");
str_type = H5Tcopy(H5T_C_S1);
+ if(is_vlstr)
+ H5Tset_size(str_type, H5T_VARIABLE);
+ else
+ H5Tset_size(str_type, size);
H5Tset_cset(str_type, cset);
- H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
indentation(indent + COL);
printf("%s ", CTYPE);
- if (H5Tequal(type, str_type)) {
+ if (H5Tequal(tmp_type, str_type)) {
printf("H5T_C_S1;\n");
H5Tclose(str_type);
} else {
@@ -817,7 +830,7 @@ print_datatype(hid_t type)
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
- if (H5Tequal(type, str_type)) {
+ if (H5Tequal(tmp_type, str_type)) {
printf("H5T_FORTRAN_S1;\n");
} else {
printf("unknown_one_character_type;\n ");
@@ -827,6 +840,8 @@ print_datatype(hid_t type)
H5Tclose(str_type);
}
+ H5Tclose(tmp_type);
+
indent -= COL;
indentation(indent + COL);
printf("%s", dump_header_format->strblockend);
@@ -1887,13 +1902,14 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset)
alloc_size = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type));
assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
+
buf = malloc((size_t)alloc_size);
assert(buf);
if (H5Aread(obj_id, p_type, buf) >= 0)
status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type,
- space, buf, depth);
-
+ space, buf, depth);
+
free(buf);
H5Tclose(p_type);
H5Sclose(space);
@@ -2857,10 +2873,25 @@ done:
d_status = EXIT_FAILURE;
free_handler(hand, argc);
-
+
+ for(i=0; i<info.group_table->nobjs; i++) {
+ if(info.group_table->objs[i].objname)
+ free(info.group_table->objs[i].objname);
+ }
free(group_table->objs);
+
+ for(i=0; i<info.dset_table->nobjs; i++) {
+ if(info.dset_table->objs[i].objname)
+ free(info.dset_table->objs[i].objname);
+ }
free(dset_table->objs);
+
+ for(i=0; i<info.type_table->nobjs; i++) {
+ if(info.type_table->objs[i].objname)
+ free(info.type_table->objs[i].objname);
+ }
free(type_table->objs);
+
free(prefix);
free(info.prefix);
@@ -4557,12 +4588,14 @@ xml_print_strs(hid_t did, int source)
{
herr_t e;
hid_t type, space;
- char *buf;
+ void *buf;
char *bp;
char *onestring;
hsize_t ssiz;
- size_t tsiz;
+ size_t tsiz, str_size;
size_t i;
+ htri_t is_vlstr;
+
if (source == DATASET_DATA) {
type = H5Dget_type(did);
} else if (source == ATTRIBUTE_DATA) {
@@ -4575,12 +4608,14 @@ xml_print_strs(hid_t did, int source)
/* return an error */
return FAIL;
}
+ is_vlstr = H5Tis_variable_str(type);
+
if (source == DATASET_DATA) {
space = H5Dget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
- buf = calloc((size_t)ssiz, sizeof(char));
+ buf = malloc((size_t)ssiz);
if (buf == NULL) {
return FAIL;
@@ -4596,11 +4631,12 @@ xml_print_strs(hid_t did, int source)
space = H5Aget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
-
- buf = calloc((size_t)ssiz, sizeof(char));
+
+ buf = malloc((size_t)ssiz);
if (buf == NULL) {
return FAIL;
}
+
e = H5Aread(did, type, buf);
if (e < 0) {
free(buf);
@@ -4611,28 +4647,36 @@ xml_print_strs(hid_t did, int source)
return FAIL;
}
-/* pull out each string... */
+ /* pull out each string... */
ssiz = H5Sget_simple_extent_npoints(space);
tsiz = H5Tget_size(type);
- onestring = (char *) calloc((size_t)tsiz, sizeof(char));
- bp = buf;
+ bp = (char*)buf;
+ if(!is_vlstr)
+ onestring = (char *) calloc(tsiz, sizeof(char));
for (i = 0; i < ssiz; i++) {
- strncpy(onestring, bp, tsiz);
+ if(is_vlstr) {
+ onestring = *(char **)bp;
+ str_size = (size_t)strlen(onestring);
+ } else {
+ strncpy(onestring, bp, tsiz);
+ str_size = tsiz;
+ }
indentation(indent + COL);
if (!onestring) {
printf("\"%s\"\n", "NULL");
} else {
- char *t_onestring = xml_escape_the_string(onestring, (int)tsiz);
+ char *t_onestring = xml_escape_the_string(onestring, (int)str_size);
- printf("\"%s\"\n", xml_escape_the_string(onestring, (int)tsiz));
+ printf("\"%s\"\n", t_onestring);
free(t_onestring);
}
-
- bp += tsiz;
+
+ bp += tsiz;
}
+
return SUCCEED;
}
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c
index 8f6e3bc..f0e9515 100644
--- a/tools/h5dump/h5dumpgentest.c
+++ b/tools/h5dump/h5dumpgentest.c
@@ -63,6 +63,7 @@
#define FILE35 "tfamily%05d.h5"
#define FILE36 "tmulti"
#define FILE37 "tlarge_objname.h5"
+#define FILE38 "tvlstr.h5"
#define LENSTR 50
#define LENSTR2 11
@@ -108,6 +109,9 @@ typedef struct s1_t {
#define ARRAY3_DIM1 6
#define ARRAY3_DIM2 3
+/* VL string datatype name */
+#define VLSTR_TYPE "vl_string_type"
+
static void gent_group(void)
{
hid_t fid, group;
@@ -2838,6 +2842,55 @@ static void gent_large_objname(void)
H5Fclose(fid);
}
+static void gent_vlstr(void)
+{
+ const char *wdata[SPACE1_DIM1]= {
+ "Four score and seven years ago our forefathers brought forth on this continent a new nation,",
+ "conceived in liberty and dedicated to the proposition that all men are created equal.",
+ "Now we are engaged in a great civil war,",
+ "testing whether that nation or any nation so conceived and so dedicated can long endure."
+ }; /* Information to write */
+ char *string_att= "This is the string for the attribute";
+ hid_t fid1; /* HDF5 File IDs */
+ hid_t dataset, root; /* Dataset ID */
+ hid_t sid1, dataspace;/* Dataspace ID */
+ hid_t tid1, att; /* Datatype ID */
+ hsize_t dims1[] = {SPACE1_DIM1};
+
+ /* Create file */
+ fid1 = H5Fcreate(FILE38, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
+
+ /* Create a VL string datatype to refer to */
+ tid1 = H5Tcopy (H5T_C_S1);
+ H5Tset_size (tid1,H5T_VARIABLE);
+
+ /* Create a dataset and write VL string to it. */
+ dataset=H5Dcreate(fid1,"Dataset1",tid1,sid1,H5P_DEFAULT);
+ H5Dwrite(dataset,tid1,H5S_ALL,H5S_ALL,H5P_DEFAULT,wdata);
+ H5Dclose(dataset);
+
+ /* Create a named VL string type. Change padding of datatype */
+ H5Tset_strpad(tid1, H5T_STR_NULLPAD);
+ H5Tcommit(fid1, "vl_string_type", tid1);
+
+ /* Create an group attribute of VL string type */
+ root = H5Gopen(fid1, "/");
+ dataspace = H5Screate(H5S_SCALAR);
+
+ att = H5Acreate(root, "test_scalar", tid1, dataspace, H5P_DEFAULT);
+ H5Awrite(att, tid1, &string_att);
+
+ /* Close */
+ H5Tclose(tid1);
+ H5Sclose(sid1);
+ H5Sclose(dataspace);
+ H5Aclose(att);
+ H5Gclose(root);
+ H5Fclose(fid1);
+}
+
int main(void)
{
gent_group();
@@ -2888,6 +2941,7 @@ int main(void)
gent_multi();
gent_large_objname();
+ gent_vlstr();
return 0;
}
diff --git a/tools/h5dump/testh5dump.sh b/tools/h5dump/testh5dump.sh
index ec22362..99c1a89 100755
--- a/tools/h5dump/testh5dump.sh
+++ b/tools/h5dump/testh5dump.sh
@@ -144,6 +144,9 @@ TOOLTEST tvldtypes2.ddl tvldtypes2.h5
TOOLTEST tvldtypes3.ddl tvldtypes3.h5
TOOLTEST tvldtypes4.ddl tvldtypes4.h5
+#test for file with variable length string data
+TOOLTEST tvlstr.ddl tvlstr.h5
+
# test for files with array data
TOOLTEST tarray1.ddl tarray1.h5
TOOLTEST tarray2.ddl tarray2.h5
@@ -218,6 +221,7 @@ TOOLTEST tarray7.h5.xml --xml tarray7.h5
TOOLTEST tvldtypes1.h5.xml --xml tvldtypes1.h5
TOOLTEST tvldtypes2.h5.xml --xml tvldtypes2.h5
TOOLTEST tvldtypes3.h5.xml --xml tvldtypes3.h5
+TOOLTEST tvlstr.h5.xml --xml tvlstr.h5
TOOLTEST tsaf.h5.xml --xml tsaf.h5
TOOLTEST tempty.h5.xml --xml tempty.h5