diff options
Diffstat (limited to 'tools/h5dump/h5dump.c')
| -rw-r--r-- | tools/h5dump/h5dump.c | 394 |
1 files changed, 328 insertions, 66 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c index 8ace682..979c2ff 100644 --- a/tools/h5dump/h5dump.c +++ b/tools/h5dump/h5dump.c @@ -55,9 +55,24 @@ const char *progname = "h5dump"; #define H5_SZIP_MSB_OPTION_MASK 16 #define H5_SZIP_RAW_OPTION_MASK 128 +/* List of table structures. There is one table structure for each file */ +typedef struct h5dump_table_list_t { + size_t nalloc; + size_t nused; + struct { + unsigned long fileno; /* File number that these tables refer to */ + hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ + table_t *group_table; /* Table of groups */ + table_t *dset_table; /* Table of datasets */ + table_t *type_table; /* Table of datatypes */ + } *tables; +} h5dump_table_list_t; + int d_status = EXIT_SUCCESS; static int unamedtype = 0; /* shared datatype with no name */ +static h5dump_table_list_t table_list = {0, 0, NULL}; static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL; +static hbool_t hit_elink = FALSE; /* whether we have traversed an external link */ static size_t prefix_len = 1024; static char *prefix; static const char *driver = NULL; /* The driver to open the file with. */ @@ -106,7 +121,7 @@ static void init_prefix(char **prfx, size_t prfx_len); static void add_prefix(char **prfx, size_t *prfx_len, const char *name); /* callback function used by H5Literate() */ static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void *op_data); -static int dump_extlink(const char *filename, const char *targname); +static int dump_extlink(hid_t group, const char *linkname, const char *objname); static h5tool_format_t dataformat = { @@ -359,7 +374,7 @@ static char *xml_escape_the_name(const char *); /* a structure for handling the order command-line parameters come in */ struct handler_t { - void (*func)(hid_t, const char *, void *, int); + void (*func)(hid_t, const char *, void *, int, const char *); char *obj; struct subset_t *subset_info; }; @@ -690,6 +705,126 @@ usage(const char *prog) fprintf(stdout, "\n"); } + +/*------------------------------------------------------------------------- + * Function: table_list_add + * + * Purpose: Add a new set of tables + * + * Return: index of added table on success, -1 on failure + * + * Programmer: Neil Fortner, nfortne2@hdfgroup.org + * Adapted from trav_addr_add in h5trav.c by Quincey Koziol + * + * Date: October 13, 2008 + * + *------------------------------------------------------------------------- + */ +static ssize_t +table_list_add(hid_t oid, unsigned long file_no) +{ + size_t idx; /* Index of table to use */ + find_objs_t info; + void *tmp_ptr; + + /* Allocate space if necessary */ + if(table_list.nused == table_list.nalloc) { + table_list.nalloc = MAX(1, table_list.nalloc * 2); + if(NULL == (tmp_ptr = HDrealloc(table_list.tables, table_list.nalloc * sizeof(table_list.tables[0])))) + return -1; + table_list.tables = tmp_ptr; + } /* end if */ + + /* Append it */ + idx = table_list.nused++; + table_list.tables[idx].fileno = file_no; + table_list.tables[idx].oid = oid; + if(H5Iinc_ref(oid) < 0) { + table_list.nused--; + return -1; + } + if(init_objs(oid, &info, &table_list.tables[idx].group_table, + &table_list.tables[idx].dset_table, &table_list.tables[idx].type_table) < 0) { + H5Idec_ref(oid); + table_list.nused--; + return -1; + } + +#ifdef H5DUMP_DEBUG + dump_tables(&info); +#endif /* H5DUMP_DEBUG */ + + return((ssize_t) idx); +} /* end table_list_add() */ + + +/*------------------------------------------------------------------------- + * Function: table_list_visited + * + * Purpose: Check if a table already exists for the specified fileno + * + * Return: The index of the matching table, or -1 if no matches found + * + * Programmer: Neil Fortner, nfortne2@hdfgroup.org + * Adapted from trav_addr_visited in h5trav.c by Quincey Koziol + * + * Date: October 13, 2008 + * + *------------------------------------------------------------------------- + */ +static ssize_t +table_list_visited(unsigned long file_no) +{ + size_t u; /* Local index variable */ + + /* Look for table */ + for(u = 0; u < table_list.nused; u++) + /* Check for fileno value already in array */ + if(table_list.tables[u].fileno == file_no) + return((ssize_t) u); + + /* Didn't find table */ + return(-1); +} /* end table_list_visited() */ + + +/*------------------------------------------------------------------------- + * Function: table_list_free + * + * Purpose: Frees the table list + * + * Return: void + * + * Programmer: Neil Fortner, nfortne2@hdfgroup.org + * + * Date: October 13, 2008 + * + *------------------------------------------------------------------------- + */ +static void +table_list_free(void) +{ + size_t u; /* Local index variable */ + + /* Iterate over tables */ + for(u = 0; u < table_list.nused; u++) { + /* Release object id */ + if(H5Idec_ref(table_list.tables[u].oid) < 0) + d_status = EXIT_FAILURE; + + /* Free each table */ + free_table(table_list.tables[u].group_table); + free_table(table_list.tables[u].dset_table); + free_table(table_list.tables[u].type_table); + } + + /* Free the table list */ + HDfree(table_list.tables); + table_list.tables = NULL; + table_list.nalloc = table_list.nused = 0; +} /* end table_list_free() */ + + /*------------------------------------------------------------------------- * Function: print_datatype * @@ -1443,7 +1578,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED case H5O_TYPE_DATASET: if((obj = H5Dopen2(group, name, H5P_DEFAULT)) >= 0) { - if(oinfo.rc > 1) { + if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(dset_table, oinfo.addr); @@ -1479,6 +1614,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED char *t_obj_path = xml_escape_the_name(obj_path); char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); char *t_name = xml_escape_the_name(name); + char *t_objname = xml_escape_the_name(found_obj->objname); char dsetxid[100]; char parentxid[100]; char pointerxid[100]; @@ -1501,13 +1637,14 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED xml_name_to_XID(found_obj->objname, pointerxid, sizeof(pointerxid), 1); printf("<%sDatasetPtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n", xmlnsprefix, - pointerxid,t_obj_path); + pointerxid,t_objname); indentation(indent); printf("</%sDataset>\n", xmlnsprefix); HDfree(t_name); HDfree(t_obj_path); HDfree(t_prefix); + HDfree(t_objname); } H5Dclose(obj); @@ -1672,7 +1809,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED /* dump the external link */ - dump_extlink(filename,targname); + dump_extlink(group, name, targname); } /* end if */ @@ -1786,7 +1923,7 @@ done: static void dump_named_datatype(hid_t tid, const char *name) { - + H5O_info_t oinfo; unsigned attr_crt_order_flags; hid_t tcpl_id; /* datatype creation property list ID */ @@ -1814,13 +1951,33 @@ dump_named_datatype(hid_t tid, const char *name) printf("%s \"%s\" %s", dump_header_format->datatypebegin, name, dump_header_format->datatypeblockbegin); - if(H5Tget_class(tid) == H5T_COMPOUND) - print_datatype(tid, 1); - else { - indentation(indent + COL); - print_datatype(tid, 1); + H5Oget_info(tid, &oinfo); + + /* Must check for uniqueness of all objects if we've traversed an elink, + * otherwise only check if the reference count > 1. + */ + if(oinfo.rc > 1 || hit_elink) { + obj_t *found_obj; /* Found object */ + + found_obj = search_obj(type_table, oinfo.addr); + + if (found_obj == NULL) { + error_msg(progname, "internal error (file %s:line %d)\n", + __FILE__, __LINE__); + d_status = EXIT_FAILURE; + goto done; + } + else if (found_obj->displayed) { + printf("%s \"%s\"\n", HARDLINK, found_obj->objname); + goto done; + } + else + found_obj->displayed = TRUE; + } /* end if */ + + print_datatype(tid, 1); + if(H5Tget_class(tid) != H5T_COMPOUND) printf(";\n"); - } /* end else */ /* print attributes */ indent += COL; @@ -1834,6 +1991,8 @@ dump_named_datatype(hid_t tid, const char *name) H5Aiterate2(tid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL); indent -= COL; + +done: end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); } @@ -1921,7 +2080,10 @@ dump_group(hid_t gid, const char *name) H5Oget_info(gid, &oinfo); - if(oinfo.rc > 1) { + /* Must check for uniqueness of all objects if we've traversed an elink, + * otherwise only check if the reference count > 1. + */ + if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(group_table, oinfo.addr); @@ -3149,7 +3311,7 @@ set_sort_order(const char *form) *------------------------------------------------------------------------- */ static void -handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int pe) +handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { dump_selected_attr(fid, attr); } @@ -3301,20 +3463,21 @@ parse_subset_params(char *dset) *------------------------------------------------------------------------- */ static void -handle_datasets(hid_t fid, const char *dset, void *data, int pe) +handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name) { H5O_info_t oinfo; hid_t dsetid; struct subset_t *sset = (struct subset_t *)data; + const char *real_name = display_name ? display_name : dset; if((dsetid = H5Dopen2(fid, dset, H5P_DEFAULT)) < 0) { if (pe) { - begin_obj(dump_header_format->datasetbegin, dset, + begin_obj(dump_header_format->datasetbegin, real_name, dump_header_format->datasetblockbegin); indentation(COL); - error_msg(progname, "unable to open dataset \"%s\"\n", dset); + error_msg(progname, "unable to open dataset \"%s\"\n", real_name); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); d_status = EXIT_FAILURE; @@ -3407,14 +3570,15 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe) } H5Oget_info(dsetid, &oinfo); - if(oinfo.rc > 1) { + if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(dset_table, oinfo.addr); if(found_obj) { if (found_obj->displayed) { - begin_obj(dump_header_format->datasetbegin, dset, + indentation(indent); + begin_obj(dump_header_format->datasetbegin, real_name, dump_header_format->datasetblockbegin); indentation(indent + COL); printf("%s \"%s\"\n", HARDLINK, found_obj->objname); @@ -3423,14 +3587,14 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe) dump_header_format->datasetblockend); } else { found_obj->displayed = TRUE; - dump_dataset(dsetid, dset, sset); + dump_dataset(dsetid, real_name, sset); } } else d_status = EXIT_FAILURE; } else - dump_dataset(dsetid, dset, sset); + dump_dataset(dsetid, real_name, sset); if(H5Dclose(dsetid) < 0) d_status = EXIT_FAILURE; @@ -3459,18 +3623,19 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe) *------------------------------------------------------------------------- */ static void -handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe) +handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe, const char * display_name) { - hid_t gid; + hid_t gid; + const char *real_name = display_name ? display_name : group; if((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0) { if ( pe ) { - begin_obj(dump_header_format->groupbegin, group, dump_header_format->groupblockbegin); + begin_obj(dump_header_format->groupbegin, real_name, dump_header_format->groupblockbegin); indentation(COL); - error_msg(progname, "unable to open group \"%s\"\n", group); + error_msg(progname, "unable to open group \"%s\"\n", real_name); end_obj(dump_header_format->groupend, dump_header_format->groupblockend); d_status = EXIT_FAILURE; } @@ -3488,7 +3653,7 @@ handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe) HDstrcpy(prefix, group); - dump_group(gid, group); + dump_group(gid, real_name); if(H5Gclose(gid) < 0) d_status = EXIT_FAILURE; @@ -3510,7 +3675,7 @@ handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe) *------------------------------------------------------------------------- */ static void -handle_links(hid_t fid, const char *links, void UNUSED * data, int pe) +handle_links(hid_t fid, const char *links, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { H5L_info_t linfo; @@ -3602,9 +3767,10 @@ handle_links(hid_t fid, const char *links, void UNUSED * data, int pe) *------------------------------------------------------------------------- */ static void -handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe) +handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe, const char *display_name) { hid_t type_id; + const char *real_name = display_name ? display_name : type; if((type_id = H5Topen2(fid, type, H5P_DEFAULT)) < 0) { @@ -3619,7 +3785,7 @@ handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe) /* unamed datatype */ sprintf(name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno); - if(!HDstrcmp(name, type)) + if(!HDstrcmp(name, real_name)) break; } /* end if */ @@ -3631,10 +3797,10 @@ handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe) if ( pe ) { /* unknown type */ - begin_obj(dump_header_format->datatypebegin, type, + begin_obj(dump_header_format->datatypebegin, real_name, dump_header_format->datatypeblockbegin); indentation(COL); - error_msg(progname, "unable to open datatype \"%s\"\n", type); + error_msg(progname, "unable to open datatype \"%s\"\n", real_name); end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); d_status = EXIT_FAILURE; @@ -3645,14 +3811,14 @@ handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe) { hid_t dsetid = H5Dopen2(fid, type_table->objs[idx].objname, H5P_DEFAULT); type_id = H5Dget_type(dsetid); - dump_named_datatype(type_id, type); + dump_named_datatype(type_id, real_name); H5Tclose(type_id); H5Dclose(dsetid); } } else { - dump_named_datatype(type_id, type); + dump_named_datatype(type_id, real_name); if(H5Tclose(type_id) < 0) d_status = EXIT_FAILURE; @@ -4073,7 +4239,7 @@ main(int argc, const char *argv[]) char *fname = NULL; void *edata; H5E_auto2_t func; - find_objs_t info; + H5O_info_t oi; struct handler_t *hand; int i; unsigned u; @@ -4162,12 +4328,22 @@ main(int argc, const char *argv[]) } - /* find all shared objects */ - if(init_objs(fid, &info, &group_table, &dset_table, &type_table) < 0) { + /* Get object info for root group */ + if(H5Oget_info_by_name(fid, "/", &oi, H5P_DEFAULT) < 0) { error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); d_status = EXIT_FAILURE; goto done; } + + /* Initialize object tables */ + if(table_list_add(fid, oi.fileno) < 0) { + error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); + d_status = EXIT_FAILURE; + goto done; + } + group_table = table_list.tables[0].group_table; + dset_table = table_list.tables[0].dset_table; + type_table = table_list.tables[0].type_table; /* does there exist unamed committed datatype */ for (u = 0; u < type_table->nobjs; u++) @@ -4176,10 +4352,6 @@ main(int argc, const char *argv[]) break; } /* end if */ -#ifdef H5DUMP_DEBUG - dump_tables(&info); -#endif /* H5DUMP_DEBUG */ - /* start to dump - display file header information */ if (!doxml) { begin_obj(dump_header_format->filebegin, fname, @@ -4257,7 +4429,7 @@ main(int argc, const char *argv[]) for(i = 0; i < argc; i++) if(hand[i].func) - hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1); + hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1, NULL); } if (!doxml) { @@ -4267,16 +4439,14 @@ main(int argc, const char *argv[]) } done: + /* Free tables for objects */ + table_list_free(); + if (H5Fclose(fid) < 0) d_status = EXIT_FAILURE; free_handler(hand, argc); - /* Free tables for objects */ - free_table(group_table); - free_table(dset_table); - free_table(type_table); - HDfree(prefix); HDfree(fname); @@ -5435,20 +5605,49 @@ xml_dump_named_datatype(hid_t type, const char *name) "Parents=\"%s\" H5ParentPaths=\"%s\">\n", xmlnsprefix, name, dtxid, - parentxid,(HDstrcmp(prefix, "") ? t_prefix : "/")); + parentxid, HDstrcmp(prefix,"") ? t_prefix : "/"); } else { + H5O_info_t oinfo; /* Object info */ + printf("<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " "H5Path=\"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">\n", xmlnsprefix, t_name, dtxid, t_tmp, parentxid, (HDstrcmp(prefix, "") ? t_prefix : "/")); + + /* Check uniqueness of named datatype */ + H5Oget_info(type, &oinfo); + if(oinfo.rc > 1) { + obj_t *found_obj; /* Found object */ + + /* Group with more than one link to it... */ + found_obj = search_obj(type_table, oinfo.addr); + + if (found_obj == NULL) { + indentation(indent); + error_msg(progname, "internal error (file %s:line %d)\n", + __FILE__, __LINE__); + d_status = EXIT_FAILURE; + goto done; + } else if(found_obj->displayed) { + /* We have already printed this named datatype, print it as a + * NamedDatatypePtr + */ + char pointerxid[100]; + char *t_objname = xml_escape_the_name(found_obj->objname); + + indentation(indent + COL); + xml_name_to_XID(found_obj->objname, pointerxid, sizeof(pointerxid), 1); + printf("<%sNamedDatatypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n", + xmlnsprefix, pointerxid, t_objname); + indentation(indent); + printf("</%sNamedDataType>\n", xmlnsprefix); + HDfree(t_objname); + goto done; + } else + found_obj->displayed = TRUE; + } } - HDfree(dtxid); - HDfree(parentxid); - HDfree(t_tmp); - HDfree(t_prefix); - HDfree(t_name); - HDfree(tmp); indent += COL; indentation(indent); @@ -5464,6 +5663,14 @@ xml_dump_named_datatype(hid_t type, const char *name) indent -= COL; indentation(indent); printf("</%sNamedDataType>\n",xmlnsprefix); + +done: + HDfree(dtxid); + HDfree(parentxid); + HDfree(t_tmp); + HDfree(t_prefix); + HDfree(t_name); + HDfree(tmp); } /*------------------------------------------------------------------------- @@ -5581,7 +5788,7 @@ xml_dump_group(hid_t gid, const char *name) indentation(indent + COL); ptrstr = malloc(100); - t_objname = xml_escape_the_name(found_obj->objname); + t_objname = xml_escape_the_name(found_obj->objname);/* point to the NDT by name */ par_name = xml_escape_the_name(par); xml_name_to_XID(found_obj->objname, ptrstr, 100, 1); xml_name_to_XID(par, parentxid, 100, 1); @@ -6704,32 +6911,87 @@ add_prefix(char **prfx, size_t *prfx_len, const char *name) * basis, attempting to dump as a dataset, as a group and as a named datatype * Error messages are supressed * + * Modifications: + * Neil Fortner + * 13 October 2008 + * Function basically rewritten. No longer directly opens the target file, + * now initializes a new set of tables for the external file. No longer + * dumps on a trial and error basis, but errors are still suppressed. + * *------------------------------------------------------------------------- */ -static int dump_extlink(const char *filename, const char *targname) +static int dump_extlink(hid_t group, const char *linkname, const char *objname) { - hid_t fid; + hid_t oid; + H5O_info_t oi; + table_t *old_group_table = group_table; + table_t *old_dset_table = dset_table; + table_t *old_type_table = type_table; + hbool_t old_hit_elink; + ssize_t idx; - fid = h5tools_fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT, driver, NULL, 0); + /* Open target object */ + if ((oid = H5Oopen(group, linkname, H5P_DEFAULT)) < 0) + goto fail; - if (fid < 0) - { + /* Get object info */ + if (H5Oget_info(oid, &oi) < 0) { + H5Oclose(oid); goto fail; } - /* add some indentation to distinguish that these objects are external */ - indent += 2*COL; + /* Check if we have visited this file already */ + if ((idx = table_list_visited(oi.fileno)) < 0) { + /* We have not visited this file, build object tables */ + if ((idx = table_list_add(oid, oi.fileno)) < 0) { + H5Oclose(oid); + goto fail; + } + } - handle_datasets(fid, targname, NULL, 0); - handle_groups(fid, targname, NULL, 0); - handle_datatypes(fid, targname, NULL, 0); + /* Do not recurse through an external link into the original file (idx=0) */ + if (idx) { + /* Update table pointers */ + group_table = table_list.tables[idx].group_table; + dset_table = table_list.tables[idx].dset_table; + type_table = table_list.tables[idx].type_table; - indent -= 2*COL; + /* We will now traverse the external link, set this global to indicate this */ + old_hit_elink = hit_elink; + hit_elink = TRUE; + /* add some indentation to distinguish that these objects are external */ + indent += 2*COL; - if (H5Fclose(fid) < 0) + /* Recurse into the external file */ + switch (oi.type) { + case H5O_TYPE_GROUP: + handle_groups(group, linkname, NULL, 0, objname); + break; + case H5O_TYPE_DATASET: + handle_datasets(group, linkname, NULL, 0, objname); + break; + case H5O_TYPE_NAMED_DATATYPE: + handle_datatypes(group, linkname, NULL, 0, objname); + break; + default: + d_status = EXIT_FAILURE; + } + + indent -= 2*COL; + + /* Reset table pointers */ + group_table = old_group_table; + dset_table = old_dset_table; + type_table = old_type_table; + + /* Reset hit_elink */ + hit_elink = old_hit_elink; + } /* end if */ + + if (H5Idec_ref(oid) < 0) d_status = EXIT_FAILURE; |