/*------------------------------------------------------------------------- * * Copyright (C) 1998 National Center for Supercomputing Applications. * All rights reserved. * *------------------------------------------------------------------------- */ #include #include "h5dump.h" #include "H5private.h" #include "h5tools.h" static int display_oid = 0; static int display_data = 1; static int d_status = 0; static int unamedtype = 0; /* shared data type with no name */ static int prefix_len = 1024; static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL; static char *prefix; static const dump_header *dump_header_format; /* internal functions */ 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 void dump_oid(hid_t oid); static void print_enum(hid_t type); /* external functions */ extern void indentation(int); extern int print_data(hid_t, hid_t, int); static h5dump_t dataformat = { 0, /*raw*/ "", /*fmt_raw*/ "%d", /*fmt_int*/ "%u", /*fmt_uint*/ "%d", /*fmt_schar*/ "%u", /*fmt_uchar*/ "%d", /*fmt_short*/ "%u", /*fmt_ushort*/ "%ld", /*fmt_long*/ "%lu", /*fmt_ulong*/ NULL, /*fmt_llong*/ NULL, /*fmt_ullong*/ "%g", /*fmt_double*/ "%g", /*fmt_float*/ 0, /*ascii*/ 0, /*str_locale*/ 0, /*str_repeat*/ "[ ", /*arr_pre*/ ", ", /*arr_sep*/ " ]", /*arr_suf*/ 1, /*arr_linebreak*/ "", /*cmpd_name*/ ",\n", /*cmpd_sep*/ "{\n", /*cmpd_pre*/ "}", /*cmpd_suf*/ "\n", /*cmpd_end*/ "%s", /*elmt_fmt*/ ",", /*elmt_suf1*/ " ", /*elmt_suf2*/ "", /*idx_n_fmt*/ "", /*idx_sep*/ "", /*idx_fmt*/ 80, /*line_ncols*//*standard default columns*/ 0, /*line_per_line*/ "", /*line_pre*/ "%s", /*line_1st*/ "%s", /*line_cont*/ "", /*line_suf*/ "", /*line_sep*/ 1, /*line_multi_new*/ " ", /*line_indent*/ 1, /*skip_first*/ 1, /*obj_hidefileno*/ " %lu:%lu",/*obj_format*/ 1, /*dset_hidefileno*/ "DATASET %lu:%lu ",/*dset_format*/ "%s", /*dset_blockformat_pre*/ "%s", /*dset_ptformat_pre*/ "%s", /*dset_ptformat*/ }; static const dump_header standardformat = { "standardformat", /*name*/ "HDF5", /*fileebgin*/ "", /*fileend*/ BOOT_BLOCK, /*bootblockbegin*/ "", /*bootblockend*/ GROUPNAME, /*groupbegin*/ "", /*groupend*/ DATASET, /*datasetbegin*/ "", /*datasetend*/ ATTRIBUTE, /*attributebegin*/ "", /*attributeend*/ DATATYPE, /*datatypebegin*/ "", /*datatypeend*/ DATASPACE, /*dataspacebegin*/ "", /*dataspaceend*/ DATA, /*databegin*/ "", /*dataend*/ SOFTLINK, /*softlinkbegin*/ "", /*softlinkend*/ "{", /*fileblockbegin*/ "}", /*fileblockend*/ "{", /*bootblockblockbegin*/ "}", /*bootblockblockend*/ "{", /*groupblockbegin*/ "}", /*groupblockend*/ "{", /*datasetblockbegin*/ "}", /*datasetblockend*/ "{", /*attributeblockbegin*/ "}", /*attributeblockend*/ "{", /*datatypeblockbegin*/ "}", /*datatypeblockend*/ "{", /*dataspaceblockbegin*/ "}", /*dataspaceblockend*/ "{", /*datablockbegin*/ "}", /*datablockend*/ "{", /*softlinkblockbegin*/ "}", /*softlinkblockend*/ "{", /*strblockbegin*/ "}", /*strblockend*/ "{", /*enumblockbegin*/ "}", /*enumblockend*/ "{", /*dataspacedescriptionbegin*/ "}", /*dataspacedescriptionend*/ "(", /*dataspacedimbegin*/ ")", /*dataspacedimend*/ }; static const dump_header xmlformat = { "xml", /*name*/ "", /*filebegin*/ "", /*fileend*/ "", /*bootblockbegin*/ "", /*bootblockend*/ "", /*groupbegin*/ "", /*groupend*/ "", /*datasetbegin*/ "", /*datasetend*/ "", /*attributebegin*/ "", /*attributeend*/ "", /*datatypeend*/ "", /*datatypeend*/ "", /*dataspacebegin*/ "", /*dataspaceend*/ "", /*databegin*/ "", /*dataend*/ "", /*softlinkbegin*/ "", /*softlinkend*/ "", /*fileblockbegin*/ "", /*fileblockend*/ "", /*bootblockblockbegin*/ "", /*bootblockblockend*/ "", /*groupblockbegin*/ "", /*groupblockend*/ "", /*datasetblockbegin*/ "", /*datasetblockend*/ "", /*attributeblockbegin*/ "", /*attributeblockend*/ "", /*datatypeblockbegin*/ "", /*datatypeblockend*/ "", /*dataspaceblockbegin*/ "", /*dataspaceblockend*/ "", /*datablockbegin*/ "", /*datablockend*/ "", /*softlinkblockbegin*/ "", /*softlinkblockend*/ "", /*strblockbegin*/ "", /*strblockend*/ "", /*enumblockbegin*/ "", /*enumblockend*/ "", /*dataspacedescriptionbegin*/ "", /*dataspacedescriptionend*/ "(", /*dataspacedimbegin*/ ")", /*dataspacedimend*/ }; /*------------------------------------------------------------------------- * Function: usage * * Purpose: Print the usage message about dumper * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void usage(void) { fprintf(stderr, "\n\ Usage of HDF5 Dumper:\n\ \n\ h5dump [-h] [-bb] [-header] [-v] [-V] [-a ] [-d ] [-g ]\n\ [-l ] [-t ] [-w ] \n\ \n\ -h Print information on this command and exit.\n\ -bb Display the conent of the boot block. [Default: don't display]\n\ -header Display header only; no data is displayed.\n\ -v Display the object ids\n\ -V Display version information and exit.\n\ -a Display the specified attribute(s).\n\ -d Display the specified dataset(s).\n\ -g Display the specified group(s) and all the members.\n\ -l Display the value(s) of the specified soft link(s).\n\ -o Display the raw data of datasets to a separate Output file .\n\ -t Display the specified named data type(s).\n\ -w Display the information with the specified maximum number of columns.\n\ \n\ is one or more appropriate object names.\n\ is an integer greater than 1.\n\ \n"); } /*------------------------------------------------------------------------- * Function: print_datatype * * Purpose: print the data type. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void print_datatype(hid_t type) { char *fname ; hid_t nmembers, mtype, str_type; int i, j, ndims, perm[H5DUMP_MAX_RANK]; size_t dims[H5DUMP_MAX_RANK], size; H5T_str_t str_pad; H5T_cset_t cset; H5G_stat_t statbuf; hid_t super; switch (H5Tget_class(type)) { case H5T_INTEGER: if (H5Tequal(type, H5T_STD_I8BE)) { printf("H5T_STD_I8BE"); } else if (H5Tequal(type, H5T_STD_I8LE)) { printf("H5T_STD_I8LE"); } else if (H5Tequal(type, H5T_STD_I16BE)) { printf("H5T_STD_I16BE"); } else if (H5Tequal(type, H5T_STD_I16LE)) { printf("H5T_STD_I16LE"); } else if (H5Tequal(type, H5T_STD_I32BE)) { printf("H5T_STD_I32BE"); } else if (H5Tequal(type, H5T_STD_I32LE)) { printf("H5T_STD_I32LE"); } else if (H5Tequal(type, H5T_STD_I64BE)) { printf("H5T_STD_I64BE"); } else if (H5Tequal(type, H5T_STD_I64LE)) { printf("H5T_STD_I64LE"); } else if (H5Tequal(type, H5T_STD_U8BE)) { printf("H5T_STD_U8BE"); } else if (H5Tequal(type, H5T_STD_U8LE)) { printf("H5T_STD_U8LE"); } else if (H5Tequal(type, H5T_STD_U16BE)) { printf("H5T_STD_U16BE"); } else if (H5Tequal(type, H5T_STD_U16LE)) { printf("H5T_STD_U16LE"); } else if (H5Tequal(type, H5T_STD_U32BE)) { printf("H5T_STD_U32BE"); } else if (H5Tequal(type, H5T_STD_U32LE)) { printf("H5T_STD_U32LE"); } else if (H5Tequal(type, H5T_STD_U64BE)) { printf("H5T_STD_U64BE"); } else if (H5Tequal(type, H5T_STD_U64LE)) { printf("H5T_STD_U64LE"); } else if (H5Tequal(type, H5T_NATIVE_SCHAR)) { printf("H5T_NATIVE_SCHAR"); } else if (H5Tequal(type, H5T_NATIVE_UCHAR)) { printf("H5T_NATIVE_UCHAR"); } else if (H5Tequal(type, H5T_NATIVE_SHORT)) { printf("H5T_NATIVE_SHORT"); } else if (H5Tequal(type, H5T_NATIVE_USHORT)) { printf("H5T_NATIVE_USHORT"); } else if (H5Tequal(type, H5T_NATIVE_INT)) { printf("H5T_NATIVE_INT"); } else if (H5Tequal(type, H5T_NATIVE_UINT)) { printf("H5T_NATIVE_UINT"); } else if (H5Tequal(type, H5T_NATIVE_LONG)) { printf("H5T_NATIVE_LONG"); } else if (H5Tequal(type, H5T_NATIVE_ULONG)) { printf("H5T_NATIVE_ULONG"); } else if (H5Tequal(type, H5T_NATIVE_LLONG)) { printf("H5T_NATIVE_LLONG"); } else if (H5Tequal(type, H5T_NATIVE_ULLONG)) { printf("H5T_NATIVE_ULLONG"); } else { printf("undefined integer"); d_status = 1; } break; case H5T_FLOAT: if (H5Tequal(type, H5T_IEEE_F32BE)) { printf("H5T_IEEE_F32BE"); } else if (H5Tequal(type, H5T_IEEE_F32LE)) { printf("H5T_IEEE_F32LE"); } else if (H5Tequal(type, H5T_IEEE_F64BE)) { printf("H5T_IEEE_F64BE"); } else if (H5Tequal(type, H5T_IEEE_F64LE)) { printf("H5T_IEEE_F64LE"); } else if (H5Tequal(type, H5T_NATIVE_FLOAT)) { printf("H5T_NATIVE_FLOAT"); } else if (H5Tequal(type, H5T_NATIVE_DOUBLE)) { printf("H5T_NATIVE_DOUBLE"); } else if (H5Tequal(type, H5T_NATIVE_LDOUBLE)) { printf("H5T_NATIVE_LDOUBLE"); } else { printf("undefined float"); d_status = 1; } break; case H5T_TIME: printf("H5T_TIME: not yet implemented"); break; case H5T_STRING: size = H5Tget_size(type); str_pad = H5Tget_strpad(type); cset = H5Tget_cset(type); indentation (indent + COL); printf("%s %s %d;\n", dump_header_format->strblockbegin, STRSIZE, (int)size); indentation(indent + COL); printf(" %s ", STRPAD); if (str_pad == H5T_STR_NULLTERM ) printf("H5T_STR_NULLTERM;\n"); else if (str_pad == H5T_STR_NULLPAD ) printf("H5T_STR_NULLPAD;\n"); else if (str_pad == H5T_STR_SPACEPAD ) printf("H5T_STR_SPACEPAD;\n"); else printf("H5T_STR_ERROR;\n"); indentation(indent + COL); printf(" %s ", CSET); if (cset == H5T_CSET_ASCII) printf("H5T_CSET_ASCII;\n"); else printf("unknown_cset;\n"); str_type = H5Tcopy(H5T_C_S1); 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)) { printf("H5T_C_S1;\n"); H5Tclose(str_type); } else { H5Tclose(str_type); str_type = H5Tcopy(H5T_FORTRAN_S1); H5Tset_cset(str_type, cset ) ; H5Tset_size(str_type, size); H5Tset_strpad(str_type, str_pad ); if (H5Tequal(type,str_type)) { printf( "H5T_FORTRAN_S1;\n"); } else { printf("unknown_one_character_type;\n "); d_status = 1; } H5Tclose(str_type); } indentation(indent + COL); printf("%s", dump_header_format->strblockend); break; case H5T_BITFIELD: if (H5Tequal(type, H5T_STD_B8BE)) { printf("H5T_STD_B8BE"); } else if (H5Tequal(type, H5T_STD_B8LE)) { printf("H5T_STD_B8LE"); } else if (H5Tequal(type, H5T_STD_B16BE)) { printf("H5T_STD_B16BE"); } else if (H5Tequal(type, H5T_STD_B16LE)) { printf("H5T_STD_B16LE"); } else if (H5Tequal(type, H5T_STD_B32BE)) { printf("H5T_STD_B32BE"); } else if (H5Tequal(type, H5T_STD_B32LE)) { printf("H5T_STD_B32LE"); } else if (H5Tequal(type, H5T_STD_B64BE)) { printf("H5T_STD_B64BE"); } else if (H5Tequal(type, H5T_STD_B64LE)) { printf("H5T_STD_B64LE"); } else { printf("undefined bitfield"); d_status = 1; } break; case H5T_OPAQUE: printf("\n"); indentation(indent + COL); printf("H5T_OPAQUE;\n"); indentation(indent + COL); printf("OPAQUE_TAG \"%s\";\n", H5Tget_tag(type)); indentation(indent); break; case H5T_COMPOUND: 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].recorded) printf("\"/#%lu:%lu\"\n", type_table->objs[i].objno[0], type_table->objs[i].objno[1]); else printf("\"%s\"\n", type_table->objs[i].objname); } else { printf("h5dump error: unknown committed type.\n"); d_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); if (H5Tget_class(mtype) != H5T_STRING) indentation (indent + COL); if (H5Tget_class(mtype) == H5T_COMPOUND) { indent += COL; printf("{\n"); } print_datatype(mtype); if (H5Tget_class(mtype) == H5T_COMPOUND) { indent -= COL; indentation(indent + COL); printf("}"); } printf (" \"%s\"", fname); if (ndims != 1 || dims[0] != 1) for (j = 0; j < ndims; j++) printf("[%d]",(int)dims[j]); printf(";\n"); free(fname); } } break; case H5T_REFERENCE: printf("H5T_REFERENCE"); break; case H5T_ENUM: printf("H5T_ENUM\n"); indentation(indent + COL); printf("%s ", dump_header_format->enumblockbegin); super = H5Tget_super(type); print_datatype(super); printf(";"); print_enum(type); printf("\n"); indentation(indent + COL); printf("%s", dump_header_format->enumblockend); break; default: printf("unknown data type"); d_status = 1; break; } } /*------------------------------------------------------------------------- * Function: dump_bb * * Purpose: Dump the boot block * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void dump_bb(void) { printf("%s %s boot block not yet implemented %s\n", BOOT_BLOCK, BEGIN, END); } /*------------------------------------------------------------------------- * Function: dump_datatype * * Purpose: Dump the data type. Data type can be HDF5 predefined * atomic data type or committed/transient data type. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void dump_datatype(hid_t type) { indent += COL; indentation(indent); if (H5Tget_class(type) == H5T_COMPOUND) { printf("%s %s\n", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); print_datatype(type); indentation(indent); printf("%s %s\n", dump_header_format->datatypeblockend, dump_header_format->datatypeend); } else if (H5Tget_class(type) == H5T_STRING) { printf("%s %s\n", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); print_datatype(type); printf("\n"); indentation(indent); printf("%s %s\n", dump_header_format->datatypeblockend, dump_header_format->datatypeend); } else { printf("%s %s ", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); print_datatype(type); printf(" %s %s\n", dump_header_format->datatypeblockend, dump_header_format->datatypeend); } indent -= COL; } /*------------------------------------------------------------------------- * Function: dump_dataspace * * Purpose: Dump the data space. Data space can be named data space, * array, or others. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void dump_dataspace(hid_t space) { hsize_t size[H5DUMP_MAX_RANK]; hsize_t maxsize[H5DUMP_MAX_RANK]; int ndims = H5Sget_simple_extent_dims(space, size, maxsize); int i; indentation(indent + COL); printf("%s ", dump_header_format->dataspacebegin); if (H5Sis_simple(space)) { if (ndims == 0) { /* scalar dataspace */ HDfprintf(stdout, "%s %s ", dump_header_format->dataspacedescriptionbegin, SCALAR); } else { /* simple dataspace */ HDfprintf(stdout, "%s %s %s %Hu", dump_header_format->dataspacedescriptionbegin, SIMPLE, dump_header_format->dataspacedimbegin,size[0]); for (i = 1; i < ndims; i++) HDfprintf(stdout, ", %Hu", size[i]); printf(" %s / ", dump_header_format->dataspacedimend); if (maxsize[0] == H5S_UNLIMITED) HDfprintf(stdout, "%s %s", dump_header_format->dataspacedimbegin, "H5S_UNLIMITED"); else HDfprintf(stdout, "%s %Hu", dump_header_format->dataspacedimbegin, 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 ", dump_header_format->dataspacedimend); } } else { printf("%s not yet implemented %s\n", BEGIN, END); } end_obj(dump_header_format->dataspaceend, dump_header_format->dataspaceblockend); } /*------------------------------------------------------------------------- * Function: dump_attr * * Purpose: dump the attribute * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static herr_t dump_attr(hid_t attr, const char *attr_name, void UNUSED *op_data) { hid_t attr_id, type, space; herr_t ret = SUCCEED; indentation(indent); begin_obj(dump_header_format->attributebegin, attr_name, dump_header_format->attributeblockbegin); if ((attr_id = H5Aopen_name (attr, attr_name)) >= 0) { type = H5Aget_type(attr_id); space = H5Aget_space(attr_id); dump_datatype(type); dump_dataspace(space); if (display_oid) dump_oid(attr_id); if (display_data) dump_data(attr_id, ATTRIBUTE_DATA); H5Tclose(type); H5Sclose(space); H5Aclose (attr_id); indentation (indent); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); } else { indentation(indent + COL); printf("h5dump error: unable to open attribute.\n"); indentation(indent); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = 1; ret = FAIL; } return ret; } /*------------------------------------------------------------------------- * Function: dump_selected_attr * * Purpose: dump the selected attribute * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static herr_t dump_selected_attr(hid_t loc_id, char *name) { int j; char *obj_name, *attr_name; hid_t oid, attr_id, type, space; H5G_stat_t statbuf; j = (int)strlen(name) - 1; obj_name = malloc(j + 2); /* find the last / */ while (name[j] != '/' && j >=0) j--; /* object name */ if (j == -1) { strcpy(obj_name, "/"); } else { strncpy(obj_name, name, j+1); obj_name[j+1] = '\0'; } attr_name = name + j + 1; begin_obj(dump_header_format->attributebegin, name, dump_header_format->attributeblockbegin); H5Gget_objinfo(loc_id, obj_name, FALSE , &statbuf); switch (statbuf.type) { case H5G_GROUP: if ((oid = H5Gopen(loc_id, obj_name)) < 0) { indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = 1; return FAIL; } break; case H5G_DATASET: if ((oid = H5Dopen(loc_id, obj_name)) < 0) { indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = 1; return FAIL; } break; case H5G_TYPE: if ((oid = H5Topen(loc_id, obj_name)) < 0 ) { indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = 1; return FAIL; } break; default: indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = 1; return FAIL; } if ((attr_id = H5Aopen_name (oid, attr_name)) >= 0) { type = H5Aget_type(attr_id); space = H5Aget_space(attr_id); dump_datatype(type); dump_dataspace(space); if (display_oid) dump_oid(attr_id); if (display_data) dump_data(attr_id, ATTRIBUTE_DATA); H5Tclose(type); H5Sclose(space); H5Aclose (attr_id); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); } else { indentation(COL); printf("h5dump error: unable to open attribute.\n"); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = 1; } switch (statbuf.type) { case H5G_GROUP: if (H5Gclose (oid) < 0) { d_status = 1; return FAIL; } break; case H5G_DATASET: if (H5Dclose (oid) < 0 ) { d_status = 1; return FAIL; } break; case H5G_TYPE: if (H5Tclose(oid) < 0 ) { d_status = 1; return FAIL; } break; default: d_status = 1; return FAIL; } free(obj_name); return SUCCEED; } /*------------------------------------------------------------------------- * Function: dump all * * Purpose: Dump everything in the specified object * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static herr_t dump_all(hid_t group, const char *name, void UNUSED *op_data) { 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); strcpy(tmp, prefix); switch (statbuf.type) { case H5G_LINK: indentation(indent); buf = malloc(statbuf.linklen); begin_obj(dump_header_format->softlinkbegin, name, dump_header_format->softlinkblockbegin); indentation(indent + COL); if (H5Gget_linkval(group, name, statbuf.linklen, buf) >= 0) { printf("LINKTARGET \"%s\"\n", buf); } else { printf("h5dump error: unable to get link value.\n"); d_status = 1; } indentation(indent); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); free(buf); break; 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); d_status = 1; } break; 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(dump_header_format->datasetbegin, name, dump_header_format->datasetblockbegin); indentation(indent + COL); printf("h5dump error: internal error\n"); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); d_status = 1; goto done; } else if (dset_table->objs[i].displayed) { indentation(indent); begin_obj(dump_header_format->datasetbegin, name, dump_header_format->datasetblockbegin); indentation(indent + COL); printf("%s \"%s\"\n", HARDLINK, dset_table->objs[i].objname); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); 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 { printf("h5dump error: unable to dump dataset %s\n", name); d_status = 1; } break; case H5G_TYPE: 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); d_status = 1; } break; default: printf ("h5dump error: unknown object %s\n", name); d_status = 1; return FAIL; } done: free(tmp); return SUCCEED; } /*------------------------------------------------------------------------- * Function: dump_named_datatype * * Purpose: Dump named data type * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: Comments: not yet implemented. * *-----------------------------------------------------------------------*/ static void dump_named_datatype(hid_t type, const char *name) { int nmembers = 1, x,j; hid_t comptype; char *compname; int ndims, perm[H5DUMP_MAX_RANK]; size_t dims[H5DUMP_MAX_RANK]; indentation(indent); begin_obj(dump_header_format->datatypebegin, name, dump_header_format->datatypeblockbegin); if (H5Tget_class(type) == H5T_COMPOUND) { nmembers = H5Tget_nmembers(type); for (x = 0; x < nmembers; x++) { comptype = H5Tget_member_type(type,x); compname = H5Tget_member_name(type,x); ndims = H5Tget_member_dims(type, x, dims, perm); indentation(indent + COL); print_datatype(comptype); printf(" \"%s\"", compname); if (ndims != 1 || dims[0] != 1) for (j = 0; j < ndims; j++) printf("[%d]",(int)dims[j]); printf(";\n"); } } else { indentation(indent + COL); print_datatype(type); printf(";\n"); } indentation(indent); end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); } /*------------------------------------------------------------------------- * Function: dump_group * * Purpose: Dump everything within the specified group * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ 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 = malloc(strlen(prefix) + strlen(name) + 2); strcpy(tmp, prefix); indentation(indent); begin_obj(dump_header_format->groupbegin, name, dump_header_format->groupblockbegin); indent += COL; if (display_oid) dump_oid(gid); if (!strcmp(name, "/") && unamedtype) /* dump unamed type in root group */ for (i = 0; i < type_table->nobjs; i++) if (!type_table->objs[i].recorded) { 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) { i = search_obj (group_table, statbuf.objno); if (i < 0) { indentation(indent); printf("h5dump error: internal error\n"); d_status = 1; } else if (group_table->objs[i].displayed) { indentation(indent); printf("%s \"%s\"\n", HARDLINK, group_table->objs[i].objname); } 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); } indent -= COL; indentation(indent); end_obj(dump_header_format->groupend, dump_header_format->groupblockend); free(tmp); } /*------------------------------------------------------------------------- * Function: dump_dataset * * Purpose: Dump the specified data set * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void dump_dataset(hid_t did, const char *name) { hid_t type, space; indentation (indent); begin_obj(dump_header_format->datasetbegin, name, dump_header_format->datasetblockbegin); type = H5Dget_type(did); space = H5Dget_space(did); dump_datatype(type); dump_dataspace(space); if (display_oid) dump_oid(did); if (display_data) switch (H5Tget_class(type)) { case H5T_TIME: indentation(indent + COL); printf("DATA{ not yet implemented.}\n"); break; case H5T_INTEGER: case H5T_FLOAT: case H5T_STRING: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_COMPOUND: case H5T_REFERENCE: case H5T_ENUM: dump_data(did,DATASET_DATA); break; default: break; } indent += COL; H5Aiterate(did, NULL, dump_attr, NULL); indent -= COL; H5Tclose(type); H5Sclose(space); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); } #if H5DUMP_DEBUG /*------------------------------------------------------------------------- * 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 %d %d\n", group_table->objs[i].objno[0], group_table->objs[i].objno[1], group_table->objs[i].objname, group_table->objs[i].displayed, group_table->objs[i].recorded); printf("\ndset_table: # of entries = %d\n", dset_table->nobjs); for ( i = 0; i < dset_table->nobjs; i++) printf("%ul %ul %s %d %d\n", dset_table->objs[i].objno[0], dset_table->objs[i].objno[1], dset_table->objs[i].objname, dset_table->objs[i].displayed, dset_table->objs[i].recorded); printf("\ntype_table: # of entries = %d\n", type_table->nobjs); for ( i = 0; i < type_table->nobjs; i++) printf("%ul %ul %s %d %d\n", type_table->objs[i].objno[0], type_table->objs[i].objno[1], type_table->objs[i].objname, type_table->objs[i].displayed, type_table->objs[i].recorded); } #endif /* H5DUMP_DEBUG */ /*------------------------------------------------------------------------- * Function: dump_data * * Purpose: Dump attribute or dataset data * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *----------------------------------------------------------------------- */ static void dump_data(hid_t obj_id, int obj_data) { h5dump_t *outputformat = &dataformat; int d_status = -1; void *buf; hid_t space, type, p_type; int ndims, i; hsize_t size[64], nelmts = 1; int depth; int stdindent = COL; /* should be 3*/ outputformat->line_ncols = nCols; indent += COL; /* * the depth will tell us how far we need to indent extra. we use to just * use indent but with the merging of the tools lib we have to do * something different for the lib funtions... the normal indentation is 6 * so when we don't need any extra indentation, depth will be 0. */ depth = indent / stdindent + 1; indentation(indent); begin_obj(dump_header_format->databegin, NULL, dump_header_format->datablockbegin); /* Print all the values. */ if (obj_data == DATASET_DATA) { d_status = h5dump_dset(stdout, outputformat, obj_id, -1,depth); } else { /* need to call h5dump_mem for the attribute data */ type = H5Aget_type(obj_id); p_type = h5dump_fixtype(type); H5Tclose(type); space = H5Aget_space(obj_id); ndims = H5Sget_simple_extent_dims(space, size, NULL); for (i = 0; i < ndims; i++) nelmts *= size[i]; buf = malloc(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))); assert(buf); if (H5Aread(obj_id, p_type, buf) >= 0) d_status = h5dump_mem(stdout, outputformat, p_type, space, buf, depth); free(buf); H5Tclose(p_type); H5Sclose(space); H5Tclose(type); } if (d_status < 0) { indentation(indent+COL); printf("Unable to print data.\n"); d_status = 1; } indentation(indent); end_obj(dump_header_format->dataend, dump_header_format->datablockend); indent -= COL; } /*------------------------------------------------------------------------- * Function: set_output_file * * Purpose: Open fname as the output file for dataset raw data. * Set rawdatastream as its file stream. * * Return: 0 -- succeeded * negative -- failed * * Programmer: Albert Cheng, 2000/09/30 * * Modifications: * *----------------------------------------------------------------------- */ int set_output_file(const char *fname) { FILE *f; /* temporary holding place for the stream pointer */ /* so that rawdatastream is changed only when succeeded */ if (f = fopen(fname, "w")){ rawdatastream = f; return 0; } return -1; } /*------------------------------------------------------------------------- * Function: main * * Purpose: HDF5 dumper * * Return: Success: 0 * Failure: 1 * * Programmer: Ruey-Hsia Li * * Modifications: * Albert Cheng, 2000/09/30 * Add the -o option--output file for datasets raw data * *-----------------------------------------------------------------------*/ int main(int argc, char *argv[]) { hid_t fid, gid, dsetid, typeid; char *fname = NULL; int i, index, curr_arg, display_bb=0, display_all=1, newwidth= 0; int nopts=0, *opts; char *buf, name[128], name1[128]; H5G_stat_t statbuf; void *edata; hid_t (*func)(void*); find_objs_t *info = malloc(sizeof(find_objs_t)); if (argc < 2) { usage(); exit(1); } dump_header_format = &standardformat; /* Disable error reporting */ H5Eget_auto(&func, &edata); H5Eset_auto(NULL, NULL); opts = malloc((argc / 2) * sizeof(int)); opts[0] = -1; /* parse command line options */ for (curr_arg = 1; curr_arg < argc; curr_arg++) { if (argv[curr_arg][0] == '-') { opts[nopts++] = curr_arg; if (!strcmp(argv[curr_arg],"-h")) { usage(); free(opts); exit(0); } else if (!strcmp(argv[curr_arg],"-V")) { print_version("h5dump"); free(opts); exit(0); } else if (!strcmp(argv[curr_arg],"-bb")) { display_bb = 1; } else if (!strcmp(argv[curr_arg],"-header")) { display_data=0; } else if (!strcmp(argv[curr_arg],"-v")) { display_oid = 1; } else if (!strcmp(argv[curr_arg],"-w")) { /* * this way we know which arg was the -w we know it won't be 0 * since curr_arg starts at 1 */ newwidth = curr_arg; } else if (!strcmp(argv[curr_arg], "-o")) { /* a separate output file for dataset raw data */ if (argc == curr_arg){ /* missing */ usage(); free(opts); exit(1); } if (set_output_file(argv[curr_arg+1]) < 0){ /* failed to set output file */ usage(); free(opts); exit(1); } } else if (!strcmp(argv[curr_arg], "-xml")) { dump_header_format = &xmlformat; } 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],"-t")) { fprintf(stderr, "h5dump error: illegal option %s \n", argv[curr_arg]); usage(); free(opts); exit(1); } else { display_all = 0; } } } /* check names */ if (argc == 2) { if (opts[0] == 1) { /* argv[1] is an option */ fprintf(stderr, "h5dump error: no or no \n"); usage(); free(opts); exit(1); } } else { for (i = 0; i < nopts-1; i++) { if (opts[i + 1] - opts[i] == 1) { if (strcmp(argv[opts[i]], "-bb") && strcmp(argv[opts[i]], "-header") && strcmp(argv[opts[i]], "-xml") && strcmp(argv[opts[i]], "-v")) { fprintf(stderr, "h5dump error: no after option %s\n", argv[opts[i]]); usage(); free(opts); exit(1); } } } if (argc - opts[nopts - 1] == 1) { fprintf(stderr,"h5dump error: no \n"); usage(); free(opts); exit(1); } if (argc - opts[nopts - 1] == 2) { if (strcmp(argv[opts[i]], "-bb") && strcmp(argv[opts[i]], "-header") && strcmp(argv[opts[i]], "-xml") && strcmp(argv[opts[i]], "-v")) { fprintf(stderr, "h5dump error: no or no " "or no after option %s\n", argv[opts[i]]); usage(); free(opts); exit(1); } } } if (argv[argc - 1][0] == '\\') fname = &argv[argc - 1][1]; else fname = argv[argc - 1]; fid = h5dump_fopen(fname, NULL, 0); if (fid < 0) { fprintf(stderr, "h5dump error: unable to open file %s \n", fname); free(opts); exit(1); } /* allocate and initialize internal data structure */ init_table(&group_table); init_table(&type_table); init_table(&dset_table); init_prefix(&prefix, prefix_len); /* init the find_objs_t */ info->threshold = 0; info->prefix_len = 1024; info->prefix = malloc(info->prefix_len); info->prefix[0] = '\0'; info->group_table = group_table; info->type_table = type_table; info->dset_table = dset_table; info->status = d_status; /* find all shared objects */ H5Giterate(fid, "/", NULL, find_objs, (void*)info); strcpy(prefix, ""); /* does there exist unamed committed data type */ for ( i = 0; i < type_table->nobjs; i++) if (type_table->objs[i].recorded == 0) unamedtype = 1; #ifdef H5DUMP_DEBUG dump_tables(); #endif if (info->status) { printf("internal error! \n"); goto done; } /* start to dump */ begin_obj(dump_header_format->filebegin, fname, dump_header_format->fileblockbegin); if (display_bb) dump_bb(); if (newwidth) sscanf(argv[newwidth + 1], "%d", &nCols); if (display_all) { if ((gid = H5Gopen (fid, "/")) < 0 ) { fprintf(stdout, "h5dump error: unable to open root group\n"); d_status = 1; } else { dump_group(gid, "/"); } if (H5Gclose (gid) < 0) { fprintf(stdout, "h5dump error: unable to close root group\n"); d_status = 1; } } else { for (i = 0; i < nopts; i++) { if (!strcmp(argv[opts[i]],"-a")) { for (curr_arg = opts[i] + 1; curr_arg < ((i + 1) == nopts ? (argc - 1) : opts[i + 1]); curr_arg++) dump_selected_attr (fid, argv[curr_arg]); } else if (!strcmp(argv[opts[i]],"-d")) { for (curr_arg = opts[i] + 1; curr_arg < ((i + 1) == nopts ? (argc - 1) : opts[i + 1]); curr_arg++) { if ((dsetid = H5Dopen (fid, argv[curr_arg]))<0) { begin_obj(dump_header_format->datasetbegin, argv[curr_arg], dump_header_format->datasetblockbegin); indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", argv[curr_arg]); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); d_status = 1; } else { 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(dump_header_format->datasetbegin, argv[curr_arg], dump_header_format->datasetblockbegin); indentation(indent + COL); printf("%s \"%s\"\n", HARDLINK, dset_table->objs[index].objname); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); } else { strcpy(dset_table->objs[index].objname, argv[curr_arg]); dset_table->objs[index].displayed = 1; dump_dataset(dsetid, argv[curr_arg]); } } else { d_status = 1; } } else { dump_dataset(dsetid, argv[curr_arg]); } if (H5Dclose(dsetid) < 1) d_status = 1; } } } else if (!strcmp(argv[opts[i]],"-g")) { for (curr_arg = opts[i] + 1; curr_arg < ((i + 1) == nopts ? (argc - 1) : opts[i + 1]); curr_arg++) { if ((gid = H5Gopen(fid, argv[curr_arg])) < 0) { begin_obj(dump_header_format->groupbegin, argv[curr_arg], dump_header_format->groupblockbegin); indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", argv[curr_arg]); end_obj(dump_header_format->groupend, dump_header_format->groupblockend); d_status = 1; } else { H5Gget_objinfo(gid, ".", TRUE, &statbuf); strcpy(prefix, argv[curr_arg]); dump_group(gid, argv[curr_arg]); if (H5Gclose(gid) < 0) d_status = 1; } } } else if (!strcmp(argv[opts[i]],"-l")) { for (curr_arg = opts[i] + 1; curr_arg < ((i + 1) == nopts ? (argc - 1) : opts[i + 1]); curr_arg++) { if (H5Gget_objinfo(fid, argv[curr_arg], FALSE, &statbuf) < 0) { begin_obj(dump_header_format->softlinkbegin, argv[curr_arg], dump_header_format->softlinkblockbegin); indentation(COL); fprintf(stdout, "h5dump error: unable to get obj info from %s\n", argv[curr_arg]); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); d_status = 1; } else if (statbuf.type == H5G_LINK) { buf = malloc(statbuf.linklen*sizeof(char)); begin_obj(dump_header_format->softlinkbegin, argv[curr_arg], dump_header_format->softlinkblockbegin); indentation(COL); if (H5Gget_linkval(fid, argv[curr_arg], statbuf.linklen, buf) >= 0) { printf("LINKTARGET \"%s\"\n", buf); } else { fprintf(stdout, "h5dump error: unable to get link value\n"); d_status = 1; } end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); free(buf); } else { begin_obj(dump_header_format->softlinkbegin, argv[curr_arg], dump_header_format->softlinkblockbegin); indentation(COL); fprintf(stdout, "h5dump error: %s is not a link\n", argv[curr_arg]); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); d_status = 1; } } } 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].recorded) { /* 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(dump_header_format->datatypebegin, argv[curr_arg], dump_header_format->datatypeblockbegin); indentation(COL); fprintf(stdout, "h5dump error: unable to open %s\n", argv[curr_arg]); end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); d_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) d_status = 1; } } } } } end_obj(dump_header_format->fileend, dump_header_format->fileblockend); done: H5Eset_auto(func, edata); free(opts); if (H5Fclose(fid) < 0) d_status = 1; if (rawdatastream && rawdatastream != stdout) if (fclose(rawdatastream)) perror("fclose"); free(group_table->objs); free(dset_table->objs); free(type_table->objs); free(prefix); free(info->prefix); free(info); return d_status; } /*------------------------------------------------------------------------- * Function: print_enum * * Purpose: prints the enum data - * * Return: void * * Programmer: Patrick Lu * * Modifications: * * NOTE: this function was taken from h5ls. should be moved into the toolslib * *-----------------------------------------------------------------------*/ static void print_enum(hid_t type) { char **name = NULL; /*member names */ unsigned char *value = NULL; /*value array */ int nmembs; /*number of members */ int nchars; /*number of output characters */ hid_t super; /*enum base integer type */ hid_t native = -1; /*native integer data type */ size_t dst_size; /*destination value type size */ int i; /*miscellaneous counters */ size_t j; nmembs = H5Tget_nmembers(type); super = H5Tget_super(type); /* * Determine what data type to use for the native values. To simplify * things we entertain three possibilities: * 1. long_long -- the largest native signed integer * 2. unsigned long_long -- the largest native unsigned integer * 3. raw format */ if (H5Tget_size(type)<=sizeof(long_long)) { dst_size = sizeof(long_long); if (H5T_SGN_NONE==H5Tget_sign(type)) { native = H5T_NATIVE_ULLONG; } else { native = H5T_NATIVE_LLONG; } } else { dst_size = H5Tget_size(type); } /* Get the names and raw values of all members */ name = calloc(nmembs, sizeof(char *)); value = calloc(nmembs, MAX(H5Tget_size(type), dst_size)); for (i = 0; i < nmembs; i++) { name[i] = H5Tget_member_name(type, i); H5Tget_member_value(type, i, value + i * H5Tget_size(type)); } /* Convert values to native data type */ if (native > 0) H5Tconvert(super, native, nmembs, value, NULL, H5P_DEFAULT); /* Sort members by increasing value */ /*not implemented yet*/ /* Print members */ for (i = 0; i < nmembs; i++) { printf("\n%*s", indent + 4, ""); nchars = printf("\"%s\"", name[i]);/*display_string(stdout, name[i], TRUE);*/ printf("%*s ", MAX(0, 16 - nchars), ""); if (native < 0) { printf("0x"); for (j = 0; j < dst_size; j++) printf("%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { printf("%" PRINTF_LL_WIDTH "u", *((unsigned long_long *)((void *)(value + i * dst_size)))); } else { printf("%" PRINTF_LL_WIDTH "d", *((long_long *)((void *)(value + i * dst_size)))); } printf(";"); } /* Release resources */ for (i = 0; i < nmembs; i++) free(name[i]); free(name); free(value); H5Tclose(super); if (0 == nmembs) printf("\n%*s ", indent+4, ""); } /*------------------------------------------------------------------------- * Function: dump_oid * * Purpose: Prints the object ids * * Return: void * * Programmer: Patrick Lu * * Modifications: * *-----------------------------------------------------------------------*/ static void dump_oid(hid_t oid) { indentation(indent + COL); printf("%s %s ", OBJID, BEGIN); printf("%d", oid); printf(" %s\n", END); }