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-rw-r--r--tools/h5dump.c758
-rw-r--r--tools/h5dump.h11
-rw-r--r--tools/h5dumputil.c50
-rwxr-xr-xtools/testh5dump.sh11
4 files changed, 699 insertions, 131 deletions
diff --git a/tools/h5dump.c b/tools/h5dump.c
index 9d77d63..d29696d 100644
--- a/tools/h5dump.c
+++ b/tools/h5dump.c
@@ -2,14 +2,33 @@
#include <stdio.h>
#include "H5private.h"
-static int indent = 0;
+int indent = 0;
+int ischar=0;
static int display_data = 1;
static int status = 0;
+static int unamedtype = 0; /* shared data type with no name */
+
+typedef struct shared_obj_t{
+unsigned long objno[2];
+char objname[1024];
+int displayed;
+} shared_obj_t;
+
+typedef struct table_t{
+int size;
+int nobjs;
+shared_obj_t *objs;
+} table_t;
+
+static int prefix_len = 1024;
+static char *prefix;
+static table_t group_table, dset_table, type_table;
static void dump_group (hid_t , const char* );
static void dump_dataset (hid_t, const char*);
static void dump_data (hid_t, int);
static void dump_named_datatype (hid_t , const char *);
+static int search_obj (table_t, unsigned long *);
/*-------------------------------------------------------------------------
* Function: usage
@@ -29,15 +48,17 @@ usage(void)
fprintf(stderr,
"\nUsage of HDF5 Dumper:\n\n \
h5dump [-h] [-bb] [-header] [-a <names>] [-d <names>] [-g <names>]\n \
- [-l <names>] <file>\n\n\
+ [-l <names>] [-t <names>] <file>\n\n\
-h Print information on this command.\n\
- -bb Display the conent of boot block. The default is not to display.\n\
- -header Display header only; that is, no data displayed.\n\
+ -bb Display the conent of the boot block. The default is not to display.\n\
+ -header Display header only; no data is displayed.\n\
-a <names> Display the specified attribute(s).\n\
-d <names> Display the specified dataset(s).\n\
- -g <names> Display all the objects within the specified group(s).\n\
- -l <names> Display the specified link value(s).\n\n");
-
+ -g <names> Display the specified group(s) and all the members.\n\
+ -l <names> Displays the value(s) of the specified soft link(s).\n\
+ -t <names> Display the specified named data type(s).\n\
+ \n\
+ <names> is one or more appropriate object names.\n\n");
}
@@ -55,18 +76,15 @@ h5dump [-h] [-bb] [-header] [-a <names>] [-d <names>] [-g <names>]\n \
*-----------------------------------------------------------------------*/
static void indentation(int x) {
- while (x>0) {
- printf(" ");
- x--;
- }
+ while (x>0) { printf(" "); x--; }
}
/*-------------------------------------------------------------------------
- * Function: datatype_name
+ * Function: print_datatype
*
- * Purpose: Prints the name of data type.
+ * Purpose: print the data type.
*
* Return: void
*
@@ -76,7 +94,13 @@ static void indentation(int x) {
*
*-----------------------------------------------------------------------*/
static void
-datatype_name(hid_t type) {
+print_datatype(hid_t type) {
+char *fname ;
+hid_t nmembers, mtype;
+int i, j, ndims, perm[H5DUMP_MAX_NDIMS];
+size_t dims[H5DUMP_MAX_NDIMS];
+
+H5G_stat_t statbuf;
switch (H5Tget_class(type)) {
@@ -134,7 +158,10 @@ datatype_name(hid_t type) {
printf( "H5T_NATIVE_LLONG");
else if (H5Tequal(type, H5T_NATIVE_ULLONG))
printf( "H5T_NATIVE_ULLONG");
- else printf( "unknown integer");
+ else {
+ printf( "undefined integer");
+ status = 1;
+ }
break;
case H5T_FLOAT:
@@ -152,11 +179,14 @@ datatype_name(hid_t type) {
printf( "H5T_NATIVE_DOUBLE");
else if (H5Tequal(type, H5T_NATIVE_LDOUBLE))
printf( "H5T_NATIVE_LDOUBLE");
- else printf( "unknown float");
+ else {
+ printf( "undefined float");
+ status = 1;
+ }
break;
case H5T_TIME:
- printf( "time: not yet implemented");
+ printf( "H5T_TIME: not yet implemented");
case H5T_STRING:
@@ -164,7 +194,10 @@ datatype_name(hid_t type) {
printf( "H5T_C_S1");
else if (H5Tequal(type,H5T_FORTRAN_S1))
printf( "H5T_FORTRAN_S1");
- else printf( "unknown string");
+ else {
+ printf( "undefined string");
+ status = 1;
+ }
break;
case H5T_BITFIELD:
@@ -185,20 +218,70 @@ datatype_name(hid_t type) {
printf( "H5T_STD_B64BE");
else if (H5Tequal(type, H5T_STD_B64LE))
printf( "H5T_STD_B64LE");
- else printf( "unknown bitfield");
+ else {
+ printf( "undefined bitfield");
+ status = 1;
+ }
break;
case H5T_OPAQUE:
- printf( "opaque: not yet implemented");
+ printf( "H5T_OPAQUE: not yet implemented");
break;
case H5T_COMPOUND:
- printf( "compound: not yet implemented");
+ if (H5Tcommitted(type) > 0) {
+ H5Gget_objinfo(type, ".", TRUE, &statbuf);
+
+ i = search_obj (type_table, statbuf.objno);
+
+ indentation (indent+col);
+ if (i >= 0) {
+ if (!type_table.objs[i].displayed) /* unamed data type */
+ printf("%s %s \"#%lu:%lu\" %s\n", HARDLINK, BEGIN,
+ type_table.objs[i].objno[0],
+ type_table.objs[i].objno[1], END);
+ else
+ printf("%s %s \"%s\" %s\n", HARDLINK, BEGIN,type_table.objs[i].objname, END);
+ } else {
+ printf("h5dump error: unknown committed type.\n");
+ status = 1;
+ }
+
+ } else {
+
+ nmembers = H5Tget_nmembers(type);
+
+ for (i = 0; i < nmembers; i++) {
+
+ fname = H5Tget_member_name(type, i);
+
+ mtype = H5Tget_member_type(type, i);
+
+ ndims = H5Tget_member_dims(type, i, dims, perm);
+
+ indentation (indent+col);
+
+ print_datatype(mtype);
+
+ printf (" %s", fname);
+
+ if (ndims != 1 || dims[0] != 1) {
+ for (j = 0; j < ndims; j++)
+ printf("[%d]",dims[j]);
+ }
+
+ printf (";\n");
+
+ free (fname);
+ }
+ }
+
break;
default:
printf( "unknown data type");
+ status = 1;
break;
}
@@ -229,7 +312,7 @@ dump_bb(void) {
* Function: dump_datatype
*
* Purpose: Dump the data type. Data type can be HDF5 predefined
- * atomic data type, named data type or compound data type.
+ * atomic data type or committed/transient data type.
*
* Return: void
*
@@ -241,10 +324,19 @@ dump_bb(void) {
static void
dump_datatype (hid_t type) {
- indentation (indent+col);
- printf ("%s %s \"", DATATYPE, BEGIN);
- datatype_name(type);
- printf ("\" %s\n", END);
+ indent += col;
+ indentation (indent);
+ if (H5Tget_class(type) == H5T_COMPOUND) {
+ printf ("%s %s\n", DATATYPE, BEGIN);
+ print_datatype(type);
+ indentation (indent);
+ printf ("%s\n", END);
+ } else {
+ printf ("%s %s \"", DATATYPE, BEGIN);
+ print_datatype(type);
+ printf ("\" %s\n", END);
+ }
+ indent -= col;
}
@@ -264,8 +356,8 @@ dump_datatype (hid_t type) {
static void
dump_dataspace (hid_t space)
{
- hsize_t size[64];
- hsize_t maxsize[64]; /* check max dims size */
+ hsize_t size[H5DUMP_MAX_NDIMS];
+ hsize_t maxsize[H5DUMP_MAX_NDIMS];
int ndims = H5Sget_simple_extent_dims(space, size, maxsize);
int i;
@@ -275,26 +367,29 @@ dump_dataspace (hid_t space)
if (H5Sis_simple(space)) {
- HDfprintf (stdout, "%s %s ( %Hu",BEGIN, ARRAY, size[0]);
- for (i = 1; i < ndims; i++)
- HDfprintf (stdout, ", %Hu", size[i]);
- printf(" ) ");
+ if (ndims == 0) /* scalar space */
+ HDfprintf (stdout, "%s %s ( 0 ) ( 0 ) %s\n",BEGIN, ARRAY, END);
+ else {
+ HDfprintf (stdout, "%s %s ( %Hu",BEGIN, ARRAY, size[0]);
+ for (i = 1; i < ndims; i++)
+ HDfprintf (stdout, ", %Hu", size[i]);
+ printf(" ) ");
- if (maxsize[0]==H5S_UNLIMITED)
- HDfprintf (stdout, "( %s", "H5S_UNLIMITED");
- else
- HDfprintf (stdout, "( %Hu", maxsize[0]);
-
- for (i = 1; i < ndims; i++)
- if (maxsize[i]==H5S_UNLIMITED)
- HDfprintf (stdout, ", %s", "H5S_UNLIMITED");
- else
- HDfprintf (stdout, ", %Hu", maxsize[i]);
-
- printf(" ) %s\n", END);
+ if (maxsize[0]==H5S_UNLIMITED)
+ HDfprintf (stdout, "( %s", "H5S_UNLIMITED");
+ else
+ HDfprintf (stdout, "( %Hu", maxsize[0]);
+
+ for (i = 1; i < ndims; i++)
+ if (maxsize[i]==H5S_UNLIMITED)
+ HDfprintf (stdout, ", %s", "H5S_UNLIMITED");
+ else
+ HDfprintf (stdout, ", %Hu", maxsize[i]);
+
+ printf(" ) %s\n", END);
+ }
} else
-
printf("%s not yet implemented %s\n", BEGIN, END);
}
@@ -372,9 +467,9 @@ hid_t oid, attr_id, type, space;
H5G_stat_t statbuf;
-
j = strlen(name)-1;
obj_name = malloc ((j+2) * sizeof(char));
+
/* find the last / */
while (name[j] != '/' && j >=0) j--;
/* object name */
@@ -472,6 +567,7 @@ H5G_stat_t statbuf;
return SUCCEED;
}
+
/*-------------------------------------------------------------------------
* Function: dump all
*
@@ -489,14 +585,16 @@ H5G_stat_t statbuf;
static herr_t
dump_all (hid_t group, const char *name, void __unused__ *op_data)
{
- hid_t obj;
- char *buf;
- H5G_stat_t statbuf;
-
+hid_t obj;
+char *buf, *tmp;
+H5G_stat_t statbuf;
+int i;
H5Gget_objinfo(group, name, FALSE, &statbuf);
+ tmp = (char *) malloc ((strlen(prefix)+strlen(name)+2) * sizeof(char));
+ strcpy(tmp, prefix);
switch (statbuf.type) {
case H5G_LINK:
@@ -507,7 +605,7 @@ dump_all (hid_t group, const char *name, void __unused__ *op_data)
begin_obj(SOFTLINK, name);
indentation (indent+col);
if (H5Gget_linkval (group, name, statbuf.linklen, buf)>=0)
- printf ("linktarget \"%s\"\n", buf);
+ printf ("LINKTARGET \"%s\"\n", buf);
else {
printf ("h5dump error: unable to get link value.\n");
status = 1;
@@ -520,7 +618,9 @@ dump_all (hid_t group, const char *name, void __unused__ *op_data)
case H5G_GROUP:
if ((obj=H5Gopen (group, name))>=0) {
+ strcat(strcat(prefix,"/"), name);
dump_group (obj, name);
+ strcpy(prefix, tmp);
H5Gclose (obj);
} else {
printf ("h5dump error: unable to dump group %s\n",name);
@@ -532,6 +632,36 @@ dump_all (hid_t group, const char *name, void __unused__ *op_data)
case H5G_DATASET:
if ((obj=H5Dopen (group, name))>=0) {
+
+ /* hard link */
+ H5Gget_objinfo(obj, ".", TRUE, &statbuf);
+ if (statbuf.nlink > 1) {
+ i = search_obj (dset_table, statbuf.objno);
+ if (i < 0) {
+ indentation (indent);
+ begin_obj(DATASET, name);
+ indentation (indent+col);
+ printf("h5dump error: internal error\n");
+ indentation (indent);
+ end_obj();
+ status = 1;
+ goto done;
+ } else if (dset_table.objs[i].displayed) {
+ indentation (indent);
+ begin_obj(DATASET, name);
+ indentation (indent+col);
+ printf("%s %s \"%s\" %s\n",HARDLINK, BEGIN,
+ dset_table.objs[i].objname,END);
+ indentation (indent);
+ end_obj();
+ goto done;
+ } else {
+ dset_table.objs[i].displayed = 1;
+ strcat(tmp,"/");
+ strcat(tmp,name);
+ strcpy(dset_table.objs[i].objname, tmp);
+ }
+ }
dump_dataset (obj, name);
H5Dclose (obj);
} else {
@@ -542,20 +672,24 @@ dump_all (hid_t group, const char *name, void __unused__ *op_data)
break;
case H5G_TYPE:
- dump_named_datatype (obj, name);
- H5Tclose(obj);
+ if ((obj=H5Topen (group, name)) >= 0) {
+ dump_named_datatype (obj, name);
+ H5Tclose(obj);
+ } else {
+ printf ("h5dump error: unable to dump data type %s\n",name);
+ status = 1;
+ }
break;
default:
- printf ("Unknown Object %s\n", name);
+ printf ("h5dump error: unknown object %s\n", name);
status = 1;
return FAIL;
- break;
}
-
-
+done:
+ free(tmp);
return SUCCEED;
}
@@ -574,25 +708,43 @@ dump_all (hid_t group, const char *name, void __unused__ *op_data)
*
*-----------------------------------------------------------------------*/
static void
-dump_named_datatype (hid_t type_id, const char *name) {
-hid_t id;
-/*
+dump_named_datatype (hid_t type, const char *name) {
char *fname ;
hid_t nmembers, mtype;
-int i, ndims, perm[512];
-*/
-
-id = type_id; /*doesn't like warning message */
+int i, j, ndims, perm[H5DUMP_MAX_NDIMS];
+size_t dims[H5DUMP_MAX_NDIMS];
indentation (indent);
begin_obj(DATATYPE, name);
- indentation(indent+col);
- printf("named data type: not yet implemented.\n");
+ nmembers = H5Tget_nmembers(type);
+
+ for (i = 0; i < nmembers; i++) {
+
+ fname = H5Tget_member_name(type, i);
+
+ mtype = H5Tget_member_type(type, i);
+
+ ndims = H5Tget_member_dims(type, i, dims, perm);
+
+ indentation (indent+col);
+
+ print_datatype(mtype);
+
+ printf (" %s", fname);
+
+ if (ndims != 1 || dims[0] != 1) {
+ for (j = 0; j < ndims; j++)
+ printf("[%d]",dims[j]);
+ }
+ printf (";\n");
+
+ free (fname);
+ }
+
indentation (indent);
end_obj();
-
}
@@ -611,25 +763,67 @@ id = type_id; /*doesn't like warning message */
static void
dump_group (hid_t gid, const char *name) {
H5G_stat_t statbuf;
+hid_t dset, type;
+char typename[1024], *tmp;
+int i;
+
+ tmp = (char *) malloc ((strlen(prefix)+strlen(name)+2) * sizeof(char));
+ strcpy(tmp, prefix);
+
indentation (indent);
begin_obj(GROUP, name);
indent += col;
- /* hard link */
+ if (!strcmp(name,"/") && unamedtype) { /* dump unamed type in root group */
+ for (i = 0; i < type_table.nobjs; i++)
+ if (!type_table.objs[i].displayed) {
+ dset = H5Dopen (gid, type_table.objs[i].objname);
+ type = H5Dget_type (dset);
+ sprintf(typename,"#%lu:%lu", type_table.objs[i].objno[0],
+ type_table.objs[i].objno[1]);
+ dump_named_datatype (type, typename);
+ H5Tclose(type);
+ H5Dclose(dset);
+ }
+ }
+
H5Gget_objinfo(gid, ".", TRUE, &statbuf);
if (statbuf.nlink > 1) {
- indentation (indent);
- printf("%s %s (%s %u) (%s %lu %lu) (%s %lu %lu ) %s\n",
- HARDLINK, BEGIN, NLINK, statbuf.nlink, FILENO, statbuf.fileno[0],
- statbuf.fileno[1], OBJNO, statbuf.objno[0], statbuf.objno[1], END);
+
+ i = search_obj (group_table, statbuf.objno);
+ if (i < 0) {
+
+ indentation (indent);
+ printf("h5dump error: internal error\n");
+ status = 1;
+
+ } else if (group_table.objs[i].displayed) {
+
+ indentation (indent);
+ printf("%s %s \"%s\" %s\n",HARDLINK, BEGIN, group_table.objs[i].objname,END);
+
+ } else {
+
+ strcpy(group_table.objs[i].objname, prefix);
+ group_table.objs[i].displayed=1;
+ H5Aiterate (gid, NULL, dump_attr, NULL);
+ H5Giterate (gid, ".", NULL, dump_all, NULL);
+
+ }
+
+ } else {
+
+ H5Aiterate (gid, NULL, dump_attr, NULL);
+ H5Giterate (gid, ".", NULL, dump_all, NULL);
+
}
- H5Aiterate (gid, NULL, dump_attr, NULL);
- H5Giterate (gid, ".", NULL, dump_all, NULL);
indent -= col;
indentation (indent);
end_obj();
+
+ free(tmp);
}
@@ -649,20 +843,10 @@ H5G_stat_t statbuf;
static void
dump_dataset (hid_t did, const char *name) {
hid_t type, space;
-H5G_stat_t statbuf;
indentation (indent);
begin_obj(DATASET, name);
- /* hard link */
- H5Gget_objinfo(did, ".", TRUE, &statbuf);
- if (statbuf.nlink > 1) {
- indentation (indent+col);
- printf("%s %s (%s %u) (%s %lu %lu) (%s %lu %lu ) %s\n",
- HARDLINK, BEGIN, NLINK, statbuf.nlink, FILENO, statbuf.fileno[0],
- statbuf.fileno[1], OBJNO, statbuf.objno[0], statbuf.objno[1], END);
- }
-
type = H5Dget_type (did);
space = H5Dget_space (did);
dump_datatype(type);
@@ -701,10 +885,7 @@ H5G_stat_t statbuf;
printf("DATA{ not yet implemented.}\n");
break;
case H5T_COMPOUND:
- indent += col;
- indentation (indent);
- indent -= col;
- printf("DATA{ not yet implemented.}\n");
+ dump_data(did, DATASET_DATA);
break;
default: break;
}
@@ -715,6 +896,7 @@ H5G_stat_t statbuf;
H5Tclose(type);
H5Sclose(space);
+
indentation (indent);
end_obj();
@@ -722,6 +904,256 @@ H5G_stat_t statbuf;
/*-------------------------------------------------------------------------
+ * Function: init_table
+ *
+ * Purpose: allocate and initialize tables for shared groups, datasets,
+ * and committed types
+ *
+ * Return: void
+ *
+ * Programmer: Ruey-Hsia Li
+ *
+ * Modifications:
+ *
+ *-----------------------------------------------------------------------*/
+static void
+init_table (void){
+int i;
+
+ group_table.size = dset_table.size = type_table.size = 20;
+ group_table.nobjs = dset_table.nobjs = type_table.nobjs = 0;
+
+ group_table.objs = (shared_obj_t*) malloc(group_table.size*sizeof(shared_obj_t));
+ dset_table.objs = (shared_obj_t*) malloc(dset_table.size*sizeof(shared_obj_t));
+ type_table.objs = (shared_obj_t*) malloc(type_table.size*sizeof(shared_obj_t));
+
+ for (i = 0; i < group_table.size; i++) {
+ group_table.objs[i].objno[0] = group_table.objs[i].objno[1] = 0;
+ group_table.objs[i].displayed = 0;
+ }
+
+ for (i = 0; i < dset_table.size; i++) {
+ dset_table.objs[i].objno[0] = dset_table.objs[i].objno[1] = 0;
+ dset_table.objs[i].displayed = 0;
+ }
+
+ for (i = 0; i < type_table.size; i++) {
+ dset_table.objs[i].objno[0] = dset_table.objs[i].objno[1] = 0;
+ dset_table.objs[i].displayed = 0;
+ }
+
+ prefix = (char *) malloc(prefix_len * sizeof (char));
+ strcpy(prefix, "");
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: search_obj
+ *
+ * Purpose: search the object specified by objno in the table
+ *
+ * Return: an integer, the location of the object
+ * -1 if object is not found
+ *
+ *
+ * Programmer: Ruey-Hsia Li
+ *
+ * Modifications:
+ *
+ *-----------------------------------------------------------------------*/
+static int
+search_obj (table_t table, unsigned long *objno) {
+int i=0, found=0;
+
+ while (i < table.nobjs && !found)
+ if (table.objs[i].objno[0] == *(objno) &&
+ table.objs[i].objno[1] == *(objno+1) ) found = 1;
+ else i++;
+
+ if (!found) return -1;
+ else return i;
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: add_obj
+ *
+ * Purpose: add a shared object to the table
+ * realloc the table if necessary
+ *
+ * Return: void
+ *
+ * Programmer: Ruey-Hsia Li
+ *
+ * Modifications:
+ *
+ *-----------------------------------------------------------------------*/
+static void
+add_obj (table_t *table, unsigned long *objno, char *objname) {
+int i;
+
+ if (table->nobjs == table->size) {
+ table->size *= 2;
+ table->objs = realloc (table->objs, table->size*sizeof(shared_obj_t));
+ for (i = table->nobjs; i < table->size; i++) {
+ table->objs[i].objno[0] = table->objs[i].objno[1] = 0;
+ table->objs[i].displayed = 0;
+ }
+ }
+
+ i = table->nobjs++;
+ table->objs[i].objno[0] = *objno;
+ table->objs[i].objno[1] = *(objno+1);
+ strcpy (table->objs[i].objname, objname);
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: dump_tables
+ *
+ * Purpose: display the contents of tables for debugging purposes
+ *
+ * Return: void
+ *
+ * Programmer: Ruey-Hsia Li
+ *
+ * Modifications:
+ *
+ *-----------------------------------------------------------------------*/
+/*
+static void
+dump_tables(void) {
+int i;
+
+ printf("group_table: # of entries = %d\n", group_table.nobjs);
+ for ( i = 0; i < group_table.nobjs; i++)
+ printf ("%ul %ul %s\n %d", group_table.objs[i].objno[0],
+ group_table.objs[i].objno[1],
+ group_table.objs[i].objname,
+ group_table.objs[i].displayed);
+
+ printf("\ndset_table: # of entries = %d\n", dset_table.nobjs);
+ for ( i = 0; i < dset_table.nobjs; i++)
+ printf ("%ul %ul %s %d\n", dset_table.objs[i].objno[0],
+ dset_table.objs[i].objno[1],
+ dset_table.objs[i].objname,
+ dset_table.objs[i].displayed);
+
+ printf("\ntype_table: # of entries = %d\n", type_table.nobjs);
+ for ( i = 0; i < type_table.nobjs; i++)
+ printf ("%ul %ul %s %d\n", type_table.objs[i].objno[0],
+ type_table.objs[i].objno[1],
+ type_table.objs[i].objname,
+ type_table.objs[i].displayed);
+}
+*/
+
+
+/*-------------------------------------------------------------------------
+ * Function: Find_shared_objs
+ *
+ * Purpose: Find shared objects, committed types and store them in tables
+ *
+ * Return: Success: SUCCEED
+ *
+ * Failure: FAIL
+ *
+ * Programmer: Ruey-Hsia Li
+ *
+ * Modifications:
+ *
+ *-----------------------------------------------------------------------*/
+static herr_t
+find_shared_objs(hid_t group, const char *name, void __unused__ *op_data)
+{
+hid_t obj, type;
+H5G_stat_t statbuf;
+char *tmp;
+int i;
+
+ H5Gget_objinfo(group, name, TRUE, &statbuf);
+
+ tmp = (char *) malloc ((strlen(prefix)+strlen(name)+2) * sizeof(char));
+
+ strcpy(tmp, prefix);
+
+ switch (statbuf.type) {
+
+ case H5G_GROUP:
+ if ((obj=H5Gopen (group, name))>=0) {
+
+ if (prefix_len < (int)(strlen(prefix) + strlen(name) + 2)) {
+ prefix_len *= 2;
+ prefix = realloc (prefix, prefix_len * sizeof(char));
+ }
+ strcat(strcat(prefix,"/"), name);
+
+ if (statbuf.nlink > 1) {
+ if (search_obj (group_table, statbuf.objno) < 0) {
+ add_obj (&group_table, statbuf.objno, prefix);
+ H5Giterate (obj, ".", NULL, find_shared_objs, NULL);
+ }
+ } else
+ H5Giterate (obj, ".", NULL, find_shared_objs, NULL);
+
+ strcpy(prefix, tmp);
+ H5Gclose (obj);
+
+ } else
+ status = 1;
+
+ break;
+
+ case H5G_DATASET:
+
+ strcat(tmp,"/");
+ strcat(tmp,name); /* absolute name of the data set */
+ if (statbuf.nlink > 1 &&
+ search_obj (dset_table, statbuf.objno) < 0)
+ add_obj (&dset_table, statbuf.objno, tmp);
+
+ if ((obj=H5Dopen (group, name))>=0) {
+ type = H5Dget_type (obj);
+ if (H5Tcommitted(type) > 0 ) {
+ H5Gget_objinfo(type, ".", TRUE, &statbuf);
+ if (search_obj (type_table, statbuf.objno) < 0) {
+ add_obj (&type_table, statbuf.objno, tmp) ;
+ type_table.objs[type_table.nobjs-1].displayed = 0;
+ }
+ }
+ H5Tclose(type);
+ H5Dclose (obj);
+ } else
+ status = 1;
+
+ break;
+
+ case H5G_TYPE:
+ strcat(tmp,"/");
+ strcat(tmp,name); /* absolute name of the type */
+ i = search_obj (type_table, statbuf.objno);
+ if (i < 0) {
+ add_obj (&type_table, statbuf.objno, tmp) ;
+ type_table.objs[type_table.nobjs-1].displayed = 1; /* named data type */
+ } else {
+ strcpy (type_table.objs[i].objname, tmp);
+ type_table.objs[i].displayed = 1; /* named data type */
+ }
+ break;
+
+ default:
+ break;
+ }
+
+ free (tmp);
+
+ return SUCCEED;
+}
+
+
+/*-------------------------------------------------------------------------
* Function: dump_data
*
* Purpose: Dump attribute or dataset data
@@ -742,7 +1174,7 @@ dump_data (hid_t obj_id, int obj_data) {
indent += col;
indentation (indent);
- printf("%s %s", DATA, BEGIN);
+ printf("%s %s\n", DATA, BEGIN);
if (obj_data == DATASET_DATA)
f_type = H5Dget_type(obj_id);
@@ -754,7 +1186,7 @@ dump_data (hid_t obj_id, int obj_data) {
/* Set to all default values and then override */
memset(&info, 0, sizeof info);
info.idx_fmt = " (%s) ";
- info.line_ncols = 80;
+ info.line_ncols = 70 - indent;
/*
* If the dataset is a 1-byte integer type then format it as an ASCI
@@ -764,8 +1196,11 @@ dump_data (hid_t obj_id, int obj_data) {
info.elmt_suf1 = "";
info.elmt_suf2 = "";
info.idx_fmt = " (%s) \"";
+/*
info.line_suf = "\"";
- printf("\"");
+*/
+ info.line_suf = "";
+ ischar = 1;
}
@@ -774,12 +1209,14 @@ dump_data (hid_t obj_id, int obj_data) {
*/
if (h5dump1(stdout, &info, obj_id, -1, obj_data)<0) {
- printf("Unable to print data.");
+ indentation(indent+col);
+ printf("Unable to print data.\n");
}
if (1==size && H5T_INTEGER==H5Tget_class(f_type))
- printf("\"");
+ ischar = 0;
+ indentation(indent);
printf("%s\n", END);
indent -= col;
@@ -789,7 +1226,7 @@ dump_data (hid_t obj_id, int obj_data) {
/*-------------------------------------------------------------------------
- * Function:
+ * Function: main
*
* Purpose: HDF5 dumper
*
@@ -803,19 +1240,20 @@ dump_data (hid_t obj_id, int obj_data) {
*-----------------------------------------------------------------------*/
int
main(int argc, char *argv[]) {
-hid_t fid, gid, dsetid;
+hid_t fid, gid, dsetid, typeid;
hid_t plist=H5P_DEFAULT;
const char *fname = NULL;
-int i, curr_arg, display_bb=0, display_all=1;
+int i, index, curr_arg, display_bb=0, display_all=1;
int nopts=0, *opts;
-char *buf;
+char *buf, name[128], name1[128];
H5G_stat_t statbuf;
void __unused__ *op_data;
- hid_t (*func)(void*);
- void *edata;
- /* Disable error reporting */
- H5Eget_auto (&func, &edata);
- H5Eset_auto (NULL, NULL);
+void *edata;
+hid_t (*func)(void*);
+
+/* Disable error reporting */
+H5Eget_auto (&func, &edata);
+H5Eset_auto (NULL, NULL);
if (argc < 2 ) {
usage();
@@ -832,8 +1270,8 @@ void __unused__ *op_data;
opts[nopts++] = curr_arg;
if (!strcmp(argv[curr_arg],"-h")) {
-
usage();
+ free(opts);
exit(0);
} else if (!strcmp(argv[curr_arg],"-bb"))
@@ -847,11 +1285,13 @@ void __unused__ *op_data;
else if (strcmp(argv[curr_arg],"-a") &&
strcmp(argv[curr_arg],"-d") &&
strcmp(argv[curr_arg],"-g") &&
- strcmp(argv[curr_arg],"-l")) {
+ strcmp(argv[curr_arg],"-l") &&
+ strcmp(argv[curr_arg],"-t")) {
fprintf(stderr, "h5dump error: illegal option %s \n",
argv[curr_arg]);
usage();
+ free(opts);
exit(1);
} else display_all = 0;
}
@@ -861,6 +1301,7 @@ void __unused__ *op_data;
if (opts[0] == 1) { /* argv[1] is an option */
fprintf(stderr, "h5dump error: no <names> or no <file>\n");
usage();
+ free(opts);
exit(1);
}
} else {
@@ -871,6 +1312,7 @@ void __unused__ *op_data;
fprintf(stderr,"h5dump error: no <names> after option %s\n",
argv[opts[i]]);
usage();
+ free(opts);
exit(1);
}
}
@@ -878,6 +1320,7 @@ void __unused__ *op_data;
if (argc - opts[nopts-1] == 1) {
fprintf(stderr,"h5dump error: no <file>\n");
usage();
+ free(opts);
exit(1);
}
if (argc - opts[nopts-1] == 2) {
@@ -885,6 +1328,7 @@ void __unused__ *op_data;
strcmp(argv[opts[i]], "-header") ) {
fprintf (stderr, "h5dump error: no <file> or no <names> after option %s\n", argv[opts[i]]);
usage();
+ free(opts);
exit(1);
}
}
@@ -896,9 +1340,32 @@ void __unused__ *op_data;
if ((fid = H5Fopen (fname, H5F_ACC_RDONLY, plist)) < 0) {
fprintf (stderr, "h5dump error: unable to open file %s \n", fname);
+ free(opts);
exit(1);
}
+ /* allocate and initialize internal data structure */
+ init_table();
+
+ /* find all shared objects */
+ H5Giterate (fid, "/", NULL, find_shared_objs, NULL);
+ strcpy(prefix, "");
+
+ /* assign names to unamed shared data type */
+ for ( i = 0; i < type_table.nobjs; i++)
+ if (type_table.objs[i].displayed == 0) unamedtype = 1;
+
+/*
+ #ifdef H5DUMP_DEBUG
+ dump_tables();
+ #endif
+*/
+
+ if (status) {
+ printf("internal error! \n");
+ goto done;
+ }
+
begin_obj("HDF5", fname);
if (display_bb) dump_bb();
@@ -908,7 +1375,7 @@ void __unused__ *op_data;
if ((gid = H5Gopen (fid, "/")) < 0 ) {
fprintf(stdout, "h5dump error: unable to open root group\n");
status = 1;
- } else
+ } else
dump_group(gid, "/");
if (H5Gclose (gid) < 0) {
@@ -940,12 +1407,32 @@ void __unused__ *op_data;
end_obj();
status = 1;
} else {
- dump_dataset(dsetid, argv[curr_arg]);
+ H5Gget_objinfo(dsetid, ".", TRUE, &statbuf);
+ if (statbuf.nlink > 1) {
+ index = search_obj (dset_table, statbuf.objno);
+ if (index >= 0) {
+ if (dset_table.objs[index].displayed) {
+ begin_obj(DATASET, argv[curr_arg]);
+ indentation (indent+col);
+ printf("%s %s \"%s\" %s\n",HARDLINK, BEGIN,
+ dset_table.objs[index].objname,END);
+ indentation (indent);
+ end_obj();
+ } else {
+ strcpy(dset_table.objs[index].objname, argv[curr_arg]);
+ dset_table.objs[index].displayed = 1;
+ dump_dataset(dsetid, argv[curr_arg]);
+ }
+ } else status = 1;
+ } else
+ dump_dataset(dsetid, argv[curr_arg]);
if (H5Dclose(dsetid)<1) status = 1;
}
}
+
+
} else if (!strcmp(argv[opts[i]],"-g")) {
for (curr_arg = opts[i]+1;
@@ -959,6 +1446,8 @@ void __unused__ *op_data;
end_obj();
status = 1;
} else {
+ H5Gget_objinfo(gid, ".", TRUE, &statbuf);
+ strcpy(prefix, argv[curr_arg]);
dump_group(gid, argv[curr_arg]);
if (H5Gclose (gid) < 0) status = 1;
}
@@ -984,7 +1473,7 @@ void __unused__ *op_data;
begin_obj(SOFTLINK, argv[curr_arg]);
indentation (col);
if (H5Gget_linkval (fid, argv[curr_arg], statbuf.linklen, buf)>=0)
- printf ("linktarget \"%s\"\n", buf);
+ printf ("LINKTARGET \"%s\"\n", buf);
else {
fprintf (stdout, "h5dump error: unable to get link value\n");
status = 1;
@@ -1002,16 +1491,65 @@ void __unused__ *op_data;
}
+ } else if (!strcmp(argv[opts[i]],"-t")) {
+
+
+ for (curr_arg = opts[i]+1;
+ curr_arg < ((i+1)==nopts?(argc-1):opts[i+1]);
+ curr_arg++) {
+
+ if ((typeid=H5Topen (fid, argv[curr_arg])) < 0) {
+
+ /* check if argv[curr_arg] is unamed data type */
+ index = 0;
+ while (index < type_table.nobjs ) {
+ if (!type_table.objs[index].displayed) { /* unamed data type */
+ sprintf(name,"#%lu:%lu\n", type_table.objs[index].objno[0],
+ type_table.objs[index].objno[1]);
+ sprintf(name1,"/#%lu:%lu\n", type_table.objs[index].objno[0],
+ type_table.objs[index].objno[1]);
+ if (!strncmp(name, argv[curr_arg], strlen(argv[curr_arg])) ||
+ !strncmp(name1, argv[curr_arg], strlen(argv[curr_arg]))) {
+ break;
+ }
+ }
+ index++;
+ }
+ if (index == type_table.nobjs) { /* unknown type */
+ begin_obj (DATATYPE, argv[curr_arg]);
+ indentation (col);
+ fprintf (stdout, "h5dump error: unable to open %s\n",
+ argv[curr_arg]);
+ end_obj();
+ status = 1;
+ } else {
+ dsetid = H5Dopen (fid, type_table.objs[index].objname) ;
+ typeid = H5Dget_type (dsetid);
+ dump_named_datatype (typeid, argv[curr_arg]);
+ H5Tclose(typeid);
+ H5Dclose(dsetid);
+ }
+
+ } else {
+ dump_named_datatype (typeid, argv[curr_arg]);
+ if (H5Tclose(typeid) < 0) status = 1;
+ }
+ }
}
}
end_obj();
- free(opts);
+done:
- /* Restore error reporting */
H5Eset_auto (func, edata);
- if (H5Fclose (fid) < 0) exit(1);
+ free(opts);
+ if (H5Fclose (fid) < 0) status = 1;
+
+ free (group_table.objs);
+ free (dset_table.objs);
+ free (type_table.objs);
+ free (prefix);
return status;
diff --git a/tools/h5dump.h b/tools/h5dump.h
index aa1d296..2af2d04 100644
--- a/tools/h5dump.h
+++ b/tools/h5dump.h
@@ -27,22 +27,13 @@
#define ATTRIBUTE_DATA 0
#define DATASET_DATA 1
+#define H5DUMP_MAX_NDIMS 64
#define begin_obj(obj,name) printf("%s \"%s\" %s\n", obj, name, BEGIN)
#define end_obj() printf("%s\n", END);
#define col 3
-
-/*
-typedef enum
- {
- h, bb, header, a, d, g, l
- }
-command_t;
-*/
-
-
#endif
diff --git a/tools/h5dumputil.c b/tools/h5dumputil.c
index 63e1f71..b23251b 100644
--- a/tools/h5dumputil.c
+++ b/tools/h5dumputil.c
@@ -33,6 +33,8 @@
#define NELMTS(X) (sizeof(X)/sizeof(*X))
#define ALIGN(A,Z) ((((A)+(Z)-1)/(Z))*(Z))
+extern int indent;
+extern int ischar;
/*-------------------------------------------------------------------------
@@ -231,7 +233,7 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int
hsize_t elmtno, i; /*counters */
int carry; /*counter carry value */
hssize_t zero[8]; /*vector of zeros */
- /* int need_prefix=1;*/ /*indices need printing */
+ int need_prefix=1; /*indices need printing */
/* Print info */
hsize_t p_min_idx[8]; /*min selected index */
@@ -239,9 +241,9 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int
size_t p_type_nbytes; /*size of memory type */
hsize_t p_nelmts; /*total selected elmts */
char p_buf[256]; /*output string */
- /* size_t p_column=0;*/ /*output column */
+ size_t p_column=0; /*output column */
size_t p_ncolumns=80; /*default num columns */
- /* char p_prefix[1024];*/ /*line prefix string */
+ char p_prefix[1024]; /*line prefix string */
/* Stripmine info */
hsize_t sm_size[8]; /*stripmine size */
@@ -254,7 +256,7 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int
hssize_t hs_offset[8]; /*starting offset */
hsize_t hs_size[8]; /*size this pass */
hsize_t hs_nelmts; /*elements in request */
-
+int j, print_once=1;
/*
* Check that everything looks okay. The dimensionality must not be too
* great and the dimensionality of the items selected for printing must
@@ -331,7 +333,6 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int
}
/* Print the prefix */
-/*
if ((p_column +
strlen(p_buf) +
strlen(OPT(info->elmt_suf2, " ")) +
@@ -339,26 +340,34 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int
need_prefix = 1;
}
if (need_prefix) {
+/*
h5dump_prefix(p_prefix, info, elmtno+i, ndims,
p_min_idx, p_max_idx);
+*/
+
if (p_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
+
}
+ for (j=0;j<indent+col;j++) putc(' ', stream);
+ if (ischar && print_once) {
+ putc('"', stream);
+ print_once=0;
+ }
+/*
fputs(p_prefix, stream);
+*/
p_column = strlen(p_prefix);
need_prefix = 0;
} else {
fputs(OPT(info->elmt_suf2, " "), stream);
p_column += strlen(OPT(info->elmt_suf2, " "));
}
-*/
fputs(p_buf, stream);
-/*
p_column += strlen(p_buf);
-*/
}
@@ -373,13 +382,17 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int
}
}
-/*
if (p_column) {
+/*
fputs(OPT(info->line_suf, ""), stream);
+*/
+ if (ischar)
+ putc('"',stream);
putc('\n', stream);
+/*
fputs(OPT(info->line_sep, ""), stream);
- }
*/
+ }
H5Sclose(sm_space);
H5Sclose(f_space);
return 0;
@@ -559,6 +572,9 @@ h5dump1(FILE *stream, const h5dump_t *info, hid_t dset, hid_t _p_type, int data_
int status;
h5dump_t info_dflt;
+ char p_buf[256], sm_buf[256]; /*tmp for scala */
+ int j;
+
/* Use default values */
if (!stream) stream = stdout;
if (!info) {
@@ -584,10 +600,24 @@ h5dump1(FILE *stream, const h5dump_t *info, hid_t dset, hid_t _p_type, int data_
f_space = H5Aget_space(dset);
if (H5Sis_simple(f_space)<=0) return -1;
+
+
+ if ( H5Sget_simple_extent_ndims(f_space) == 0){
+ if (data_flag == ATTRIBUTE_DATA) {
+ if (H5Aread(dset, p_type, sm_buf) < 0)
+ return -1;
+ } else return -1;
+ h5dump_sprint(p_buf, info, p_type, sm_buf);
+ for (j=0;j<indent+col;j++) putc(' ', stream);
+ fputs(p_buf, stream);
+ putc('\n', stream);
+ H5Sclose(f_space);
+ } else {
H5Sclose(f_space);
/* Print the data */
status = h5dump_simple(stream, info, dset, p_type, data_flag);
+ }
if (p_type!=_p_type) H5Tclose(p_type);
return status;
}
diff --git a/tools/testh5dump.sh b/tools/testh5dump.sh
index b55bafb..ea607d9 100755
--- a/tools/testh5dump.sh
+++ b/tools/testh5dump.sh
@@ -190,7 +190,16 @@ TEST tattr-4.ddl -a attr4 tattr.h5
TEST tslink-1.ddl tslink.h5
TEST tslink-2.ddl -l slink2 tslink.h5
-#TEST thlink-1.ddl thlink.h5
+TEST thlink-1.ddl thlink.h5
+TEST thlink-2.ddl -d /g1/link2 /dset /g1/link1/link3 thlink.h5
+TEST thlink-3.ddl -d /dset /g1/link1/link3 /g1/link2 thlink.h5
+TEST thlink-4.ddl -g /g1 thlink.h5
+TEST thlink-5.ddl -d /dset -g /g2 -d /g1/link2 thlink.h5
+
+TEST tcomp-1.ddl tcompound.h5
+TEST tcomp-2.ddl -t /type1 /type2 /group1/type3 tcompound.h5
+TEST tcomp-3.ddl -d /group2/dset5 -g /group1 tcompound.h5
+TEST tcomp-4.ddl -t /#3432:0 -g /group2 tcompound.h5
TEST tall-1.ddl tall.h5
TEST tall-2.ddl -header -g /g1/g1.1 -a attr2 tall.h5