#include "h5dump.h" #include #include "H5private.h" static int indent = 0; static int display_data = 1; static int status = 0; 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 *); /*------------------------------------------------------------------------- * Function: usage * * Purpose: Print the usage message about dumper * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void usage(void) { fprintf(stderr, "\nUsage of HDF5 Dumper:\n\n \ h5dump [-h] [-bb] [-header] [-a ] [-d ] [-g ]\n \ [-l ] \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\ -a Display the specified attribute(s).\n\ -d Display the specified dataset(s).\n\ -g Display all the objects within the specified group(s).\n\ -l Display the specified link value(s).\n\n"); } /*------------------------------------------------------------------------- * Function: indentation * * Purpose: Print spaces for indentation * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void indentation(int x) { while (x>0) { printf(" "); x--; } } /*------------------------------------------------------------------------- * Function: datatype_name * * Purpose: Prints the name of data type. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void datatype_name(hid_t type) { 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_CHAR)) printf( "H5T_NATIVE_CHAR"); 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( "unknown integer"); 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( "unknown float"); break; case H5T_TIME: printf( "time: not yet implemented"); case H5T_STRING: if (H5Tequal(type,H5T_C_S1)) printf( "H5T_C_S1"); else if (H5Tequal(type,H5T_FORTRAN_S1)) printf( "H5T_FORTRAN_S1"); else printf( "unknown string"); 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( "unknown bitfield"); break; case H5T_OPAQUE: printf( "opaque: not yet implemented"); break; case H5T_COMPOUND: printf( "compound: not yet implemented"); break; default: printf( "unknown data type"); 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, named data type or compound data type. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ static void dump_datatype (hid_t type) { indentation (indent+col); printf ("%s %s \"", DATATYPE, BEGIN); datatype_name(type); printf ("\" %s\n", END); } /*------------------------------------------------------------------------- * 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[64]; hsize_t maxsize[64]; /* check max dims size */ int ndims = H5Sget_simple_extent_dims(space, size, maxsize); int i; indentation (indent+col); printf("%s ", DATASPACE); 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 (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); } /*------------------------------------------------------------------------- * 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; indentation(indent); begin_obj (ATTRIBUTE, attr_name); 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_data) dump_data(attr_id, ATTRIBUTE_DATA); H5Tclose(type); H5Sclose(space); H5Aclose (attr_id); indentation (indent); end_obj(); } else { indentation (indent+col); printf("h5dump error: unable to open attribute.\n"); indentation (indent); end_obj(); status = 1; return FAIL; } return SUCCEED; } /*------------------------------------------------------------------------- * 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 = strlen(name)-1; obj_name = malloc ((j+2) * sizeof(char)); /* find the last / */ while (name[j] != '/' && j >=0) j--; /* object name */ if (j == -1) strcpy(obj_name, "/"); else strncpy(obj_name, name, j+1); attr_name = name+j+1; begin_obj (ATTRIBUTE, name); 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(); 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(); 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(); status = 1; return FAIL; } break; default: indentation (col); fprintf (stdout, "h5dump error: unable to open %s\n", obj_name); end_obj(); 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_data) dump_data(attr_id, ATTRIBUTE_DATA); H5Tclose(type); H5Sclose(space); H5Aclose (attr_id); end_obj(); } else { indentation (col); printf("h5dump error: unable to open attribute.\n"); end_obj(); status = 1; return FAIL; } switch (statbuf.type) { case H5G_GROUP: if (H5Gclose (oid) < 0) { status = 1; return FAIL; } break; case H5G_DATASET: if (H5Dclose (oid) < 0 ) { status = 1; return FAIL; } break; case H5G_TYPE: if (H5Tclose(oid) < 0 ) { status = 1; return FAIL; } break; default: 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; H5G_stat_t statbuf; H5Gget_objinfo(group, name, FALSE, &statbuf); switch (statbuf.type) { case H5G_LINK: indentation (indent); buf = malloc (statbuf.linklen*sizeof(char)); begin_obj(SOFTLINK, name); 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"); status = 1; } indentation (indent); end_obj(); free (buf); break; case H5G_GROUP: if ((obj=H5Gopen (group, name))>=0) { dump_group (obj, name); H5Gclose (obj); } else { printf ("h5dump error: unable to dump group %s\n",name); status = 1; } break; case H5G_DATASET: if ((obj=H5Dopen (group, name))>=0) { dump_dataset (obj, name); H5Dclose (obj); } else { printf ("h5dump error: unable to dump dataset %s\n",name); status = 1; } break; case H5G_TYPE: dump_named_datatype (obj, name); H5Tclose(obj); break; default: printf ("Unknown Object %s\n", name); status = 1; return FAIL; break; } 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_id, const char *name) { hid_t id; /* char *fname ; hid_t nmembers, mtype; int i, ndims, perm[512]; */ id = type_id; /*doesn't like warning message */ indentation (indent); begin_obj(DATATYPE, name); indentation(indent+col); printf("named data type: not yet implemented.\n"); indentation (indent); end_obj(); } /*------------------------------------------------------------------------- * 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; indentation (indent); begin_obj(GROUP, name); indent += col; /* hard link */ 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); } H5Aiterate (gid, NULL, dump_attr, NULL); H5Giterate (gid, ".", NULL, dump_all, NULL); indent -= col; indentation (indent); end_obj(); } /*------------------------------------------------------------------------- * 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; 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); dump_dataspace(space); if (display_data) switch (H5Tget_class(type)) { case H5T_INTEGER: dump_data(did, DATASET_DATA); break; case H5T_FLOAT: dump_data(did, DATASET_DATA); break; case H5T_TIME: indent += col; indentation (indent); indent -= col; printf("DATA{ not yet implemented.}\n"); break; case H5T_STRING: indent += col; indentation (indent); indent -= col; printf("DATA{ not yet implemented.}\n"); break; case H5T_BITFIELD: indent += col; indentation (indent); indent -= col; printf("DATA{ not yet implemented.}\n"); break; case H5T_OPAQUE: indent += col; indentation (indent); indent -= col; printf("DATA{ not yet implemented.}\n"); break; case H5T_COMPOUND: indent += col; indentation (indent); indent -= col; printf("DATA{ not yet implemented.}\n"); break; default: break; } indent += col; H5Aiterate (did, NULL, dump_attr, NULL); indent -= col; H5Tclose(type); H5Sclose(space); indentation (indent); end_obj(); } /*------------------------------------------------------------------------- * 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) { hid_t f_type ; size_t size ; h5dump_t info; indent += col; indentation (indent); printf("%s %s", DATA, BEGIN); if (obj_data == DATASET_DATA) f_type = H5Dget_type(obj_id); else f_type = H5Aget_type(obj_id); size = H5Tget_size(f_type); /* Set to all default values and then override */ memset(&info, 0, sizeof info); info.idx_fmt = " (%s) "; info.line_ncols = 80; /* * If the dataset is a 1-byte integer type then format it as an ASCI * character string instead of integers. */ if (1==size && H5T_INTEGER==H5Tget_class(f_type)) { info.elmt_suf1 = ""; info.elmt_suf2 = ""; info.idx_fmt = " (%s) \""; info.line_suf = "\""; printf("\""); } /* * Print all the values. */ if (h5dump1(stdout, &info, obj_id, -1, obj_data)<0) { printf("Unable to print data."); } if (1==size && H5T_INTEGER==H5Tget_class(f_type)) printf("\""); printf("%s\n", END); indent -= col; H5Tclose(f_type); } /*------------------------------------------------------------------------- * Function: * * Purpose: HDF5 dumper * * Return: Success: 0 * Failure: 1 * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ int main(int argc, char *argv[]) { hid_t fid, gid, dsetid; hid_t plist=H5P_DEFAULT; const char *fname = NULL; int i, curr_arg, display_bb=0, display_all=1; int nopts=0, *opts; char *buf; 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); if (argc < 2 ) { usage(); exit(1); } 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(); 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],"-a") && strcmp(argv[curr_arg],"-d") && strcmp(argv[curr_arg],"-g") && strcmp(argv[curr_arg],"-l")) { fprintf(stderr, "h5dump error: illegal option %s \n", argv[curr_arg]); usage(); 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(); 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") ) { fprintf(stderr,"h5dump error: no after option %s\n", argv[opts[i]]); usage(); exit(1); } } } if (argc - opts[nopts-1] == 1) { fprintf(stderr,"h5dump error: no \n"); usage(); exit(1); } if (argc - opts[nopts-1] == 2) { if (strcmp(argv[opts[i]], "-bb") && strcmp(argv[opts[i]], "-header") ) { fprintf (stderr, "h5dump error: no or no after option %s\n", argv[opts[i]]); usage(); exit(1); } } } if (argv[argc-1][0] == '\\') fname = &argv[argc-1][1]; else fname = argv[argc-1]; if ((fid = H5Fopen (fname, H5F_ACC_RDONLY, plist)) < 0) { fprintf (stderr, "h5dump error: unable to open file %s \n", fname); exit(1); } begin_obj("HDF5", fname); if (display_bb) dump_bb(); if (display_all) { if ((gid = H5Gopen (fid, "/")) < 0 ) { fprintf(stdout, "h5dump error: unable to open root group\n"); status = 1; } else dump_group(gid, "/"); if (H5Gclose (gid) < 0) { fprintf(stdout, "h5dump error: unable to close root group\n"); 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 (DATASET, argv[curr_arg]); indentation (col); fprintf (stdout, "h5dump error: unable to open %s\n", argv[curr_arg]); end_obj(); 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; curr_arg < ((i+1)==nopts?(argc-1):opts[i+1]); curr_arg++) { if ((gid = H5Gopen (fid, argv[curr_arg])) < 0) { begin_obj (GROUP, argv[curr_arg]); indentation (col); fprintf (stdout, "h5dump error: unable to open %s\n", argv[curr_arg]); end_obj(); status = 1; } else { dump_group(gid, argv[curr_arg]); if (H5Gclose (gid) < 0) 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(SOFTLINK, argv[curr_arg]); indentation (col); fprintf(stdout, "h5dump error: unable to get obj info from %s\n", argv[curr_arg]); end_obj(); status = 1; } else if (statbuf.type == H5G_LINK) { buf = malloc(statbuf.linklen*sizeof(char)); begin_obj(SOFTLINK, argv[curr_arg]); 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"); status = 1; } end_obj(); free(buf); } else { begin_obj(SOFTLINK, argv[curr_arg]); indentation (col); fprintf(stdout, "h5dump error: %s is not a link\n", argv[curr_arg]); end_obj(); status = 1; } } } } end_obj(); free(opts); /* Restore error reporting */ H5Eset_auto (func, edata); if (H5Fclose (fid) < 0) exit(1); return status; }