/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include "h5dump.h" #include "H5private.h" #include "h5tools.h" #include "h5tools_utils.h" /* module-scoped variables */ static const char *progname = "h5dump"; static int d_status = EXIT_SUCCESS; static int unamedtype = 0; /* shared data type with no name */ static size_t prefix_len = 1024; static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL; static char *prefix; static const char *driver = NULL; /* The driver to open the file with. */ static const dump_header *dump_header_format; /* things to display or which are set via command line parameters */ static int display_all = TRUE; static int display_bb = FALSE; static int display_oid = FALSE; static int display_data = TRUE; static int usingdasho = FALSE; /** ** Added for XML ** **/ /* fill_ref_path_table is called to inialize the object reference paths. */ static herr_t fill_ref_path_table(hid_t, const char *, void *); /* module-scoped variables for XML option */ #define DEFAULT_DTD "http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd" static int doxml = 0; static const char *xml_dtd_uri = NULL; static hid_t thefile = -1; /** end XML **/ /* internal functions */ static void dump_oid(hid_t oid); static void print_enum(hid_t type); static herr_t dump_all(hid_t group, const char *name, void *op_data); static char *lookup_ref_path(hobj_ref_t *); static void check_compression(hid_t); static struct ref_path_table_entry_t *ref_path_table_lookup(const char *); /* external functions */ 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 */ ",", /*vlen_sep */ "(", /*vlen_pre */ ")", /*vlen_suf */ "", /*vlen_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 */ }; /** ** Added for XML ** **/ /* * Alternative formating for data dumped to XML * In general, the numbers are the same, but separators * except spaces are not used. * * Some of these are not used, as some kinds of data are * dumped in completely new subroutines. * * Some of this formatting may yet need to change. * * This table only affects XML output. */ static h5dump_t xml_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 */ " ", /*cmpd_sep */ "", /*cmpd_pre */ "", /*cmpd_suf */ "", /*cmpd_end */ " ", /*vlen_sep */ " ", /*vlen_pre */ " ", /*vlen_suf */ "", /*vlen_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 */ }; /** XML **/ 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 */ SUBSET, /*subsettingbegin */ "", /*subsettingend */ START, /*startbegin */ "", /*startend */ STRIDE, /*stridebegin */ "", /*strideend */ COUNT, /*countbegin */ "", /*countend */ BLOCK, /*blockbegin */ "", /*blockend */ "{", /*fileblockbegin */ "}", /*fileblockend */ "{", /*bootblockblockbegin */ "}", /*bootblockblockend */ "{", /*groupblockbegin */ "}", /*groupblockend */ "{", /*datasetblockbegin */ "}", /*datasetblockend */ "{", /*attributeblockbegin */ "}", /*attributeblockend */ "", /*datatypeblockbegin */ "", /*datatypeblockend */ "", /*dataspaceblockbegin */ "", /*dataspaceblockend */ "{", /*datablockbegin */ "}", /*datablockend */ "{", /*softlinkblockbegin */ "}", /*softlinkblockend */ "{", /*strblockbegin */ "}", /*strblockend */ "{", /*enumblockbegin */ "}", /*enumblockend */ "{", /*structblockbegin */ "}", /*structblockend */ "{", /*vlenblockbegin */ "}", /*vlenblockend */ "{", /*subsettingblockbegin */ "}", /*subsettingblockend */ "(", /*startblockbegin */ ");", /*startblockend */ "(", /*strideblockbegin */ ");", /*strideblockend */ "(", /*countblockbegin */ ");", /*countblockend */ "(", /*blockblockbegin */ ");", /*blockblockend */ "", /*dataspacedescriptionbegin */ "", /*dataspacedescriptionend */ "(", /*dataspacedimbegin */ ")", /*dataspacedimend */ }; /** ** Added for XML ** **/ /* The 'header' formats for XML -- mostly null * * XML output has values embedded in the 'headers', so * all the XML headers are done on a case by case basis. */ 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 */ "", /*subsettingbegin */ "", /*subsettingend */ "", /*startbegin */ "", /*startend */ "", /*stridebegin */ "", /*strideend */ "", /*countbegin */ "", /*countend */ "", /*blockbegin */ "", /*blockend */ "", /*fileblockbegin */ "", /*fileblockend */ "", /*bootblockblockbegin */ "", /*bootblockblockend */ "", /*groupblockbegin */ "", /*groupblockend */ "", /*datasetblockbegin */ "", /*datasetblockend */ "", /*attributeblockbegin */ "", /*attributeblockend */ "", /*datatypeblockbegin */ "", /*datatypeblockend */ "", /*dataspaceblockbegin */ "", /*dataspaceblockend */ "", /*datablockbegin */ "", /*datablockend */ "", /*softlinkblockbegin */ "", /*softlinkblockend */ "", /*strblockbegin */ "", /*strblockend */ "", /*enumblockbegin */ "", /*enumblockend */ "", /*structblockbegin */ "", /*structblockend */ "", /*vlenblockbegin */ "", /*vlenblockend */ "", /*subsettingblockbegin */ "", /*subsettingblockend */ "", /*startblockbegin */ "", /*startblockend */ "", /*strideblockbegin */ "", /*strideblockend */ "", /*countblockbegin */ "", /*countblockend */ "", /*blockblockbegin */ "", /*blockblockend */ "", /*dataspacedescriptionbegin */ "", /*dataspacedescriptionend */ "", /*dataspacedimbegin */ "", /*dataspacedimend */ }; /** XML **/ /** ** Added for XML ** **/ /* internal functions used by XML option */ static void xml_print_datatype(hid_t); static void xml_print_enum(hid_t); static int xml_print_refs(hid_t, int); static int xml_print_strs(hid_t, int); static hobj_ref_t *ref_path_table_put(hid_t, const char *); static char *xml_escape_the_string(const char *, int); 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, char *, void *); char *obj; struct subset_t *subset_info; }; /* * Command-line options: The user can specify short or long-named * parameters. The long-named ones can be partially spelled. When * adding more, make sure that they don't clash with each other. */ #if 0 /* binary: not implemented yet */ static const char *s_opts = "hbBHiVa:d:f:g:l:t:w:xD:o:s:S:c:k:"; #else static const char *s_opts = "hBHiVa:d:f:g:l:t:w:xD:o:s:S:c:k:"; #endif /* 0 */ static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "hel", no_arg, 'h' }, #if 0 /* binary: not implemented yet */ { "binary", no_arg, 'b' }, { "binar", no_arg, 'b' }, { "bina", no_arg, 'b' }, { "bin", no_arg, 'b' }, { "bi", no_arg, 'b' }, #endif /* 0 */ { "boot-block", no_arg, 'B' }, { "boot-bloc", no_arg, 'B' }, { "boot-blo", no_arg, 'B' }, { "boot-bl", no_arg, 'B' }, { "boot-b", no_arg, 'B' }, { "boot", no_arg, 'B' }, { "boo", no_arg, 'B' }, { "bo", no_arg, 'B' }, { "header", no_arg, 'H' }, { "heade", no_arg, 'H' }, { "head", no_arg, 'H' }, { "hea", no_arg, 'H' }, { "object-ids", no_arg, 'i' }, { "object-id", no_arg, 'i' }, { "object-i", no_arg, 'i' }, { "object", no_arg, 'i' }, { "objec", no_arg, 'i' }, { "obje", no_arg, 'i' }, { "obj", no_arg, 'i' }, { "ob", no_arg, 'i' }, { "version", no_arg, 'V' }, { "versio", no_arg, 'V' }, { "versi", no_arg, 'V' }, { "vers", no_arg, 'V' }, { "ver", no_arg, 'V' }, { "ve", no_arg, 'V' }, { "attribute", require_arg, 'a' }, { "attribut", require_arg, 'a' }, { "attribu", require_arg, 'a' }, { "attrib", require_arg, 'a' }, { "attri", require_arg, 'a' }, { "attr", require_arg, 'a' }, { "att", require_arg, 'a' }, { "at", require_arg, 'a' }, { "block", require_arg, 'k' }, { "bloc", require_arg, 'k' }, { "blo", require_arg, 'k' }, { "bl", require_arg, 'k' }, { "count", require_arg, 'c' }, { "coun", require_arg, 'c' }, { "cou", require_arg, 'c' }, { "co", require_arg, 'c' }, { "dataset", require_arg, 'd' }, { "datase", require_arg, 'd' }, { "datas", require_arg, 'd' }, { "datatype", require_arg, 't' }, { "datatyp", require_arg, 't' }, { "dataty", require_arg, 't' }, { "datat", require_arg, 't' }, { "filedriver", require_arg, 'f' }, { "filedrive", require_arg, 'f' }, { "filedriv", require_arg, 'f' }, { "filedri", require_arg, 'f' }, { "filedr", require_arg, 'f' }, { "filed", require_arg, 'f' }, { "file", require_arg, 'f' }, { "fil", require_arg, 'f' }, { "fi", require_arg, 'f' }, { "group", require_arg, 'g' }, { "grou", require_arg, 'g' }, { "gro", require_arg, 'g' }, { "gr", require_arg, 'g' }, { "output", require_arg, 'o' }, { "outpu", require_arg, 'o' }, { "outp", require_arg, 'o' }, { "out", require_arg, 'o' }, { "ou", require_arg, 'o' }, { "soft-link", require_arg, 'l' }, { "soft-lin", require_arg, 'l' }, { "soft-li", require_arg, 'l' }, { "soft-l", require_arg, 'l' }, { "soft", require_arg, 'l' }, { "sof", require_arg, 'l' }, { "so", require_arg, 'l' }, { "start", require_arg, 's' }, { "star", require_arg, 's' }, { "sta", require_arg, 's' }, { "stride", require_arg, 'S' }, { "strid", require_arg, 'S' }, { "stri", require_arg, 'S' }, { "str", require_arg, 'S' }, { "width", require_arg, 'w' }, { "widt", require_arg, 'w' }, { "wid", require_arg, 'w' }, { "wi", require_arg, 'w' }, { "xml", no_arg, 'x' }, { "xm", no_arg, 'x' }, { "xml-dtd", require_arg, 'D' }, { "xml-dt", require_arg, 'D' }, { "xml-d", require_arg, 'D' }, { NULL, 0, '\0' } }; /** ** Change for XML ** ** ** The 'dump_xxx' functions have two versions, standard and XML. ** ** They are called indirectly through the 'dump_function_table'. ** e.g., dump_group(...) becomes dump_functions->dump_group(...); ** ** The standard functions are unchanged except for the way ** they are called **/ /* The dump functions of the dump_function_table */ /* standard format: no change */ static void dump_group(hid_t, const char *); static void dump_named_datatype(hid_t, const char *); static void dump_dataset(hid_t, const char *, struct subset_t *); static void dump_dataspace(hid_t space); static void dump_datatype(hid_t type); static herr_t dump_attr(hid_t, const char *, void *); static void dump_data(hid_t, int, struct subset_t *); /* XML format: same interface, alternative output */ static void xml_dump_group(hid_t, const char *); static void xml_dump_named_datatype(hid_t, const char *); static void xml_dump_dataset(hid_t, const char *, struct subset_t *); static void xml_dump_dataspace(hid_t space); static void xml_dump_datatype(hid_t type); static herr_t xml_dump_attr(hid_t, const char *, void *); static void xml_dump_data(hid_t, int, struct subset_t *); /** ** Added for XML ** ** ** This is the global dispatch table for the dump functions. **/ /* the table of dump functions */ typedef struct dump_functions_t { void (*dump_group_function) (hid_t, const char *); void (*dump_named_datatype_function) (hid_t, const char *); void (*dump_dataset_function) (hid_t, const char *, struct subset_t *); void (*dump_dataspace_function) (hid_t); void (*dump_datatype_function) (hid_t); herr_t (*dump_attribute_function) (hid_t, const char *, void *); void (*dump_data_function) (hid_t, int, struct subset_t *); } dump_functions; /* Standard DDL output */ static const dump_functions ddl_function_table = { dump_group, dump_named_datatype, dump_dataset, dump_dataspace, dump_datatype, dump_attr, dump_data }; /* XML output */ static const dump_functions xml_function_table = { xml_dump_group, xml_dump_named_datatype, xml_dump_dataset, xml_dump_dataspace, xml_dump_datatype, xml_dump_attr, xml_dump_data }; /* * The global table is set to either ddl_function_table or * xml_function_table in the initialization. */ static const dump_functions *dump_function_table; /*------------------------------------------------------------------------- * Function: usage * * Purpose: Print the usage message about dumper * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *------------------------------------------------------------------------- */ static void usage(const char *prog) { fflush(stdout); fprintf(stdout, "usage: %s [OPTIONS] file\n", prog); fprintf(stdout, " OPTIONS\n"); fprintf(stdout, " -h, --help Print a usage message and exit\n"); fprintf(stdout, " -B, --bootblock Print the content of the boot block\n"); fprintf(stdout, " -H, --header Print the header only; no data is displayed\n"); fprintf(stdout, " -i, --object-ids Print the object ids\n"); fprintf(stdout, " -V, --version Print version number and exit\n"); fprintf(stdout, " -a P, --attribute=P Print the specified attribute\n"); fprintf(stdout, " -d P, --dataset=P Print the specified dataset\n"); fprintf(stdout, " -f D, --filedriver=D Specify which driver to open the file with\n"); fprintf(stdout, " -g P, --group=P Print the specified group and all members\n"); fprintf(stdout, " -l P, --soft-link=P Print the value(s) of the specified soft link\n"); fprintf(stdout, " -o F, --output=F Output raw data into file F\n"); fprintf(stdout, " -t P, --datatype=P Print the specified named data type\n"); fprintf(stdout, " -w N, --width=N Set the number of columns of output\n"); fprintf(stdout, " -x, --xml Output in XML\n"); fprintf(stdout, " -D U, --xml-dtd=U Use the DTD at U\n"); fprintf(stdout, "\n"); fprintf(stdout, " Subsetting is available by using the following options with a dataset\n"); fprintf(stdout, " attribute. Subsetting is done by selecting a hyperslab from the data.\n"); fprintf(stdout, " Thus, the options mirror those for performing a hyperslab selection.\n"); fprintf(stdout, " The START and COUNT parameters are mandatory if you do subsetting.\n"); fprintf(stdout, " The STRIDE and BLOCK parameters are optional and will default to 1 in\n"); fprintf(stdout, " each dimension.\n"); fprintf(stdout, "\n"); fprintf(stdout, " -s L, --start=L Offset of start of subsetting selection\n"); fprintf(stdout, " -S L, --stride=L Hyperslab stride\n"); fprintf(stdout, " -c L, --count=L Number of blocks to include in selection\n"); fprintf(stdout, " -k L, --block=L Size of block in hyperslab\n"); fprintf(stdout, "\n"); fprintf(stdout, " D - is the file driver to use in opening the file. Acceptable values\n"); fprintf(stdout, " are \"sec2\", \"family\", \"split\", \"multi\", and \"stream\". Without\n"); fprintf(stdout, " the file driver flag, the file will be opened with each driver in\n"); fprintf(stdout, " turn and in the order specified above until one driver succeeds\n"); fprintf(stdout, " in opening the file.\n"); fprintf(stdout, " F - is a filename.\n"); fprintf(stdout, " P - is the full path from the root group to the object.\n"); fprintf(stdout, " N - is an integer greater than 1.\n"); fprintf(stdout, " L - is a list of integers the number of which are equal to the\n"); fprintf(stdout, " number of dimensions in the dataspace being queried\n"); fprintf(stdout, " U - is a URI reference (as defined in [IETF RFC 2396],\n"); fprintf(stdout, " updated by [IETF RFC 2732])\n"); fprintf(stdout, "\n"); fprintf(stdout, " Examples:\n"); fprintf(stdout, "\n"); fprintf(stdout, " 1) Attribute foo of the group /bar_none in file quux.h5\n"); fprintf(stdout, "\n"); fprintf(stdout, " h5dump -a /bar_none/foo quux.h5\n"); fprintf(stdout, "\n"); fprintf(stdout, " 2) Selecting a subset from dataset /foo in file quux.h5\n"); fprintf(stdout, "\n"); fprintf(stdout, " h5dump -d /foo -s \"0,1\" -S \"1,1\" -c \"2,3\" -k \"2,2\" quux.h5\n"); fprintf(stdout, "\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 size; hsize_t dims[H5DUMP_MAX_RANK]; 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 = EXIT_FAILURE; } 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 = EXIT_FAILURE; } 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); printf("H5T_STRING %s\n", dump_header_format->strblockbegin); indent += COL; indentation(indent + COL); printf("%s %d;\n", 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 = EXIT_FAILURE; } H5Tclose(str_type); } indent -= COL; 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 = EXIT_FAILURE; } 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); 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\"", type_table->objs[i].objname); } else { error_msg(progname, "unknown committed type.\n"); d_status = EXIT_FAILURE; } } else { nmembers = H5Tget_nmembers(type); printf("H5T_COMPOUND %s\n", dump_header_format->structblockbegin); for (i = 0; i < nmembers; i++) { fname = H5Tget_member_name(type, i); mtype = H5Tget_member_type(type, i); #ifdef WANT_H5_V1_2_COMPAT /* v1.2 returns the base type of an array field, work around this */ { hid_t new_mtype; /* datatype for array, if necessary */ int arrndims; /* Array rank for reading */ size_t dims[H5S_MAX_RANK]; /* Array dimensions for reading */ hsize_t arrdims[H5S_MAX_RANK]; /* Array dimensions for reading */ int k; /* Local index variable */ /* Get the array dimensions */ arrndims=H5Tget_member_dims(type,i,dims,NULL); /* Patch up array information */ if(arrndims>0) { for(k=0; kstructblockend); } break; case H5T_REFERENCE: printf("H5T_REFERENCE"); break; case H5T_ENUM: printf("H5T_ENUM %s\n", dump_header_format->enumblockbegin); indent += COL; indentation(indent + COL); super = H5Tget_super(type); print_datatype(super); printf(";\n"); print_enum(type); indent -= COL; indentation(indent + COL); printf("%s", dump_header_format->enumblockend); break; case H5T_VLEN: printf("H5T_VLEN %s ", dump_header_format->vlenblockbegin); super = H5Tget_super(type); print_datatype(super); H5Tclose(super); /* Print closing */ printf("%s", dump_header_format->vlenblockend); break; case H5T_ARRAY: /* Get array base type */ super = H5Tget_super(type); /* Print lead-in */ printf("H5T_ARRAY { "); /* Get array information */ ndims = H5Tget_array_ndims(type); H5Tget_array_dims(type, dims, perm); /* Print array dimensions */ for (j = 0; j < ndims; j++) printf("[%d]", (int) dims[j]); printf(" "); /* Print base type */ print_datatype(super); /* Close array base type */ H5Tclose(super); /* Print closing */ printf(" }"); break; default: printf("unknown data type"); d_status = EXIT_FAILURE; 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); printf("%s %s ", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); print_datatype(type); if (H5Tget_class(type) == H5T_COMPOUND || H5Tget_class(type) == H5T_STRING) indentation(indent); 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) { indentation(indent + COL); error_msg(progname, "unable to open attribute \"%s\"\n", attr_name); indentation(indent); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = EXIT_FAILURE; ret = FAIL; } else { 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, NULL); H5Tclose(type); H5Sclose(space); H5Aclose(attr_id); indentation(indent); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); } 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, const char *name) { int j; char *obj_name; const char *attr_name; hid_t oid, attr_id, type, space; H5G_stat_t statbuf; j = (int)strlen(name) - 1; obj_name = malloc((size_t)j + 2); /* find the last / */ while (name[j] != '/' && j >= 0) j--; /* object name */ if (j == -1) { strcpy(obj_name, "/"); } else { strncpy(obj_name, name, (size_t)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); error_msg(progname, "unable to open group \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = EXIT_FAILURE; return FAIL; } break; case H5G_DATASET: if ((oid = H5Dopen(loc_id, obj_name)) < 0) { indentation(COL); error_msg(progname, "unable to open dataset \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = EXIT_FAILURE; return FAIL; } break; case H5G_TYPE: if ((oid = H5Topen(loc_id, obj_name)) < 0) { indentation(COL); error_msg(progname, "unable to open datatype \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = EXIT_FAILURE; return FAIL; } break; default: indentation(COL); error_msg(progname, "unable to open unknown \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = EXIT_FAILURE; 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, NULL); H5Tclose(type); H5Sclose(space); H5Aclose(attr_id); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); } else { indentation(COL); error_msg(progname, "unable to open attribute \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); d_status = EXIT_FAILURE; } switch (statbuf.type) { case H5G_GROUP: if (H5Gclose(oid) < 0) { d_status = EXIT_FAILURE; return FAIL; } break; case H5G_DATASET: if (H5Dclose(oid) < 0) { d_status = EXIT_FAILURE; return FAIL; } break; case H5G_TYPE: if (H5Tclose(oid) < 0) { d_status = EXIT_FAILURE; return FAIL; } break; default: d_status = EXIT_FAILURE; 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: * RMcG, November 2000 * Added XML support. Also, optionally checks the op_data * argument. * *------------------------------------------------------------------------- */ static herr_t dump_all(hid_t group, const char *name, void * op_data) { hid_t obj; char *buf, *tmp = NULL; H5G_stat_t statbuf; int i; herr_t ret = SUCCEED; H5Gget_objinfo(group, name, FALSE, &statbuf); if (*(int *)op_data != H5G_UNKNOWN && statbuf.type != *(int *) op_data) goto done; tmp = malloc(strlen(prefix) + strlen(name) + 2); strcpy(tmp, prefix); switch (statbuf.type) { case H5G_LINK: indentation(indent); buf = malloc(statbuf.linklen); if (!doxml) { begin_obj(dump_header_format->softlinkbegin, name, dump_header_format->softlinkblockbegin); indentation(indent + COL); } if (H5Gget_linkval(group, name, statbuf.linklen, buf) < 0) { error_msg(progname, "unable to get link value\n"); d_status = EXIT_FAILURE; ret = FAIL; } else { /* print the value of a soft link */ if (!doxml) { /* Standard DDL: no modification */ printf("LINKTARGET \"%s\"\n", buf); } else { /* XML */ char *t_name = xml_escape_the_name(name); char *t_buf = xml_escape_the_name(buf); char *t_prefix = xml_escape_the_name(prefix); char *tmp2, *t_tmp2, *t_tmp; tmp2 = malloc(strlen(prefix) + statbuf.linklen + 1); strcpy(tmp2, prefix); if (buf && buf[0] == '/') strcat(tmp2, buf); else strcat(strcat(tmp2, "/"), buf); t_tmp = xml_escape_the_name(strcat(strcat(tmp, "/"), name)); t_tmp2 = xml_escape_the_name(tmp2); printf("\n", t_name, t_buf, t_tmp2, t_tmp, (strcmp(prefix, "") ? t_prefix : "root")); free(t_name); free(t_buf); free(t_prefix); free(t_tmp); free(t_tmp2); free(tmp2); } } if (!doxml) { indentation(indent); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); } free(buf); break; case H5G_GROUP: if ((obj = H5Gopen(group, name)) < 0) { error_msg(progname, "unable to dump group \"%s\"\n", name); d_status = EXIT_FAILURE; ret = FAIL; } else { size_t new_len = strlen(prefix) + strlen(name) + 2; if (prefix_len <= new_len) { prefix_len = new_len + 1; prefix = realloc(prefix, prefix_len); } strcat(strcat(prefix, "/"), name); dump_function_table->dump_group_function(obj, name); strcpy(prefix, tmp); H5Gclose(obj); } 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); error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); d_status = EXIT_FAILURE; ret = FAIL; H5Dclose(obj); goto done; } else if (dset_table->objs[i].displayed) { indentation(indent); if (!doxml) { 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); } else { /* the XML version */ char *t_name = xml_escape_the_name(name); char *t_tmp = xml_escape_the_name(strcat(strcat(tmp, "/"), name)); char *t_prefix = xml_escape_the_name(prefix); char *t_objname = xml_escape_the_name(dset_table->objs[i].objname); printf("\n", t_name, t_tmp, (strcmp(prefix, "") ? t_prefix : "root")); indentation(indent + COL); printf("\n", t_objname); indentation(indent); printf("%s\n", dump_header_format->datasetend); free(t_name); free(t_tmp); free(t_prefix); free(t_objname); } H5Dclose(obj); goto done; } else { dset_table->objs[i].displayed = 1; strcat(tmp, "/"); strcat(tmp, name); free(dset_table->objs[i].objname); dset_table->objs[i].objname = HDstrdup(tmp); } } dump_function_table->dump_dataset_function(obj, name, NULL); H5Dclose(obj); } else { error_msg(progname, "unable to dump dataset \"%s\"\n", name); d_status = EXIT_FAILURE; ret = FAIL; } break; case H5G_TYPE: if ((obj = H5Topen(group, name)) < 0) { error_msg(progname, "unable to dump data type \"%s\"\n", name); d_status = EXIT_FAILURE; ret = FAIL; } else { dump_function_table->dump_named_datatype_function(obj, name); H5Tclose(obj); } break; default: error_msg(progname, "unknown object \"%s\"\n", name); d_status = EXIT_FAILURE; ret = FAIL; } done: free(tmp); return ret; } /*------------------------------------------------------------------------- * 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) { indentation(indent); printf("%s \"%s\" %s", dump_header_format->datatypebegin, name, dump_header_format->datatypeblockbegin); if (H5Tget_class(type) == H5T_COMPOUND) { hid_t temp_type = H5Tcopy(type); print_datatype(temp_type); H5Tclose(temp_type); } 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: * * Call to dump_all -- add parameter to select everything. * *------------------------------------------------------------------------- */ static void dump_group(hid_t gid, const char *name) { H5G_stat_t statbuf; hid_t dset, type; char type_name[1024], *tmp, comment[50]; int i, xtype = H5G_UNKNOWN; /* dump all */ 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); comment[0] = '\0'; H5Gget_comment(gid, ".", sizeof(comment), comment); if (comment[0]) { indentation(indent); printf("COMMENT \"%s\"\n", comment); } 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(type_name, "#%lu:%lu", type_table->objs[i].objno[0], type_table->objs[i].objno[1]); dump_named_datatype(type, type_name); 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); error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); d_status = EXIT_FAILURE; } else if (group_table->objs[i].displayed) { indentation(indent); printf("%s \"%s\"\n", HARDLINK, group_table->objs[i].objname); } else { free(group_table->objs[i].objname); group_table->objs[i].objname = HDstrdup(prefix); group_table->objs[i].displayed = 1; H5Aiterate(gid, NULL, dump_attr, NULL); H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); } } else { H5Aiterate(gid, NULL, dump_attr, NULL); H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); } 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, struct subset_t *sset) { 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: case H5T_VLEN: case H5T_ARRAY: dump_data(did, DATASET_DATA, sset); 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); } /*------------------------------------------------------------------------- * Function: dump_tables * * Purpose: display the contents of tables for debugging purposes * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *------------------------------------------------------------------------- */ static void dump_tables(void) { #ifdef H5DUMP_DEBUG register int i; printf("group_table: # of entries = %d\n", group_table->nobjs); for (i = 0; i < group_table->nobjs; i++) printf("%lu %lu %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("%lu %lu %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("%lu %lu %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); #else return; #endif /* H5DUMP_DEBUG */ } /*------------------------------------------------------------------------- * Function: dump_dims * * Purpose: Dump the dimensions handed to it in a comma separated list * * Return: void * * Programmer: Bill Wendling * Tuesday, 27. February 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void dump_dims(hsize_t *s, int dims) { register int i; for (i = 0; i < dims; i++) { printf("%u", (unsigned int)s[i]); if (i + 1 != dims) printf(", "); } } /*------------------------------------------------------------------------- * Function: dump_subsetting_header * * Purpose: Dump the subsetting header like specified in the DDL. * * Return: void * * Programmer: Bill Wendling * Tuesday, 27. February 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void dump_subsetting_header(struct subset_t *sset, int dims) { indentation(indent); printf("%s %s\n", dump_header_format->subsettingbegin, dump_header_format->subsettingblockbegin); indent += COL; indentation(indent); printf("%s %s ", dump_header_format->startbegin, dump_header_format->startblockbegin); dump_dims((hsize_t *)sset->start, dims); printf("%s %s\n", dump_header_format->startend, dump_header_format->startblockend); indentation(indent); printf("%s %s ", dump_header_format->stridebegin, dump_header_format->strideblockbegin); dump_dims(sset->stride, dims); printf("%s %s\n", dump_header_format->strideend, dump_header_format->strideblockend); indentation(indent); printf("%s %s ", dump_header_format->countbegin, dump_header_format->countblockbegin); if (sset->count) dump_dims(sset->count, dims); else printf("DEFAULT"); printf("%s %s\n", dump_header_format->countend, dump_header_format->countblockend); indentation(indent); printf("%s %s ", dump_header_format->blockbegin, dump_header_format->blockblockbegin); if (sset->block) dump_dims(sset->block, dims); else printf("DEFAULT"); printf("%s %s\n", dump_header_format->blockend, dump_header_format->blockblockend); } /*------------------------------------------------------------------------- * 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, struct subset_t *sset) { h5dump_t *outputformat = &dataformat; int status = -1; void *buf; hid_t space, type, p_type; int ndims, i; hsize_t size[64], nelmts = 1, alloc_size; 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; if (sset && obj_data == DATASET_DATA) { hid_t f_space = H5Dget_space(obj_id); dump_subsetting_header(sset, H5Sget_simple_extent_ndims(f_space)); H5Sclose(f_space); /* recalculate the depth of the data */ depth = indent / stdindent + 1; } indentation(indent); begin_obj(dump_header_format->databegin, (const char *)NULL, dump_header_format->datablockbegin); /* Print all the values. */ if (obj_data == DATASET_DATA) { status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, sset, depth); } else { /* need to call h5tools_dump_mem for the attribute data */ type = H5Aget_type(obj_id); p_type = h5tools_fixtype(type); space = H5Aget_space(obj_id); ndims = H5Sget_simple_extent_dims(space, size, NULL); for (i = 0; i < ndims; i++) nelmts *= size[i]; alloc_size = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/ buf = malloc((size_t)alloc_size); assert(buf); if (H5Aread(obj_id, p_type, buf) >= 0) status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type, space, buf, depth); free(buf); H5Tclose(p_type); H5Sclose(space); H5Tclose(type); } if (status == FAIL) { indentation(indent + COL); error_msg(progname, "unable to print data\n"); d_status = EXIT_FAILURE; } indentation(indent); end_obj(dump_header_format->dataend, dump_header_format->datablockend); indent -= COL; if (sset && obj_data == DATASET_DATA) { indentation(indent); end_obj(dump_header_format->subsettingend, dump_header_format->subsettingblockend); indent -= COL; } } /*------------------------------------------------------------------------- * 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 %d %s\n", OBJID, BEGIN, oid, END); } /*------------------------------------------------------------------------- * 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: * *------------------------------------------------------------------------- */ static 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")) != NULL) { rawdatastream = f; return 0; } return -1; } /*------------------------------------------------------------------------- * Function: handle_attributes * * Purpose: Handle the attributes from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void handle_attributes(hid_t fid, char *attr, void * UNUSED data) { dump_selected_attr(fid, attr); } /*------------------------------------------------------------------------- * Function: parse_hsize_list * * Purpose: Parse a list of comma or space separated integers and return * them in a list. The string being passed into this function * should be at the start of the list you want to parse. You are * responsible for freeing the array returned from here. * * Lists in the so-called "terse" syntax are separated by * semicolons (;). The lists themselves can be separated by * either commas (,) or white spaces. * * Return: Success: hsize_t array. NULL is a valid return type if * there aren't any elements in the array. * * Programmer: Bill Wendling * Tuesday, 6. February 2001 * * Modifications: * *------------------------------------------------------------------------- */ static hsize_t * parse_hsize_list(const char *h_list) { hsize_t *p_list; const char *ptr; unsigned int size_count = 0, i = 0, last_digit = 0; if (!h_list || !*h_list || *h_list == ';') return NULL; /* count how many integers do we have */ for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) if (isdigit(*ptr)) { if (!last_digit) /* the last read character wasn't a digit */ size_count++; last_digit = 1; } else { last_digit = 0; } if (size_count == 0) /* there aren't any integers to read */ return NULL; /* allocate an array for the integers in the list */ p_list = calloc(size_count, sizeof(hsize_t)); for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) if (isdigit(*ptr)) { /* we should have an integer now */ p_list[i++] = (hsize_t)atoi(ptr); while (isdigit(*ptr)) /* scroll to end of integer */ ptr++; } return p_list; } /*------------------------------------------------------------------------- * Function: parse_subset_params * * Purpose: Parse the so-called "terse" syntax for specifying subsetting * parameters. * * Return: Success: struct subset_t object * Failure: NULL * * Programmer: Bill Wendling * Tuesday, 6. February 2001 * * Modifications: * *------------------------------------------------------------------------- */ static struct subset_t * parse_subset_params(char *dset) { struct subset_t *s = NULL; register char *brace; if ((brace = strrchr(dset, '[')) != NULL) { char *slash = strrchr(dset, '/'); /* sanity check to make sure the [ isn't part of the dataset name */ if (brace > slash) { *brace++ = '\0'; s = calloc(1, sizeof(struct subset_t)); s->start = (hssize_t *)parse_hsize_list(brace); while (*brace && *brace != ';') brace++; if (*brace) brace++; s->stride = parse_hsize_list(brace); while (*brace && *brace != ';') brace++; if (*brace) brace++; s->count = parse_hsize_list(brace); while (*brace && *brace != ';') brace++; if (*brace) brace++; s->block = parse_hsize_list(brace); } } return s; } /*------------------------------------------------------------------------- * Function: handle_datasets * * Purpose: Handle the datasets from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void handle_datasets(hid_t fid, char *dset, void *data) { H5G_stat_t statbuf; hid_t dsetid; struct subset_t *sset = (struct subset_t *)data; if ((dsetid = H5Dopen(fid, dset)) < 0) { begin_obj(dump_header_format->datasetbegin, dset, dump_header_format->datasetblockbegin); indentation(COL); error_msg(progname, "unable to open dataset \"%s\"\n", dset); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); d_status = EXIT_FAILURE; return; } if (sset) { if (!sset->start || !sset->stride || !sset->count || !sset->block) { /* they didn't specify a ``stride'' or ``block''. default to 1 in all * dimensions */ hid_t sid = H5Dget_space(dsetid); unsigned int ndims = H5Sget_simple_extent_ndims(sid); if (!sset->start) /* default to (0, 0, ...) for the start coord */ sset->start = calloc(ndims, sizeof(hsize_t)); if (!sset->stride) { unsigned int i; sset->stride = calloc(ndims, sizeof(hsize_t)); for (i = 0; i < ndims; i++) sset->stride[i] = 1; } if (!sset->count) { hsize_t dims[H5S_MAX_RANK]; herr_t status = H5Sget_simple_extent_dims(sid, dims, NULL); unsigned int i; if (status == FAIL) { error_msg(progname, "unable to get dataset dimensions\n"); d_status = EXIT_FAILURE; H5Sclose(sid); return; } sset->count = calloc(ndims, sizeof(hsize_t)); for (i = 0; i < ndims; i++) sset->count[i] = dims[i] - sset->start[i]; } if (!sset->block) { unsigned int i; sset->block = calloc(ndims, sizeof(hsize_t)); for (i = 0; i < ndims; i++) sset->block[i] = 1; } H5Sclose(sid); } } H5Gget_objinfo(dsetid, ".", TRUE, &statbuf); if (statbuf.nlink > 1) { int idx = search_obj(dset_table, statbuf.objno); if (idx >= 0) { if (dset_table->objs[idx].displayed) { begin_obj(dump_header_format->datasetbegin, dset, dump_header_format->datasetblockbegin); indentation(indent + COL); printf("%s \"%s\"\n", HARDLINK, dset_table->objs[idx].objname); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); } else { free(dset_table->objs[idx].objname); dset_table->objs[idx].objname = HDstrdup(dset); dset_table->objs[idx].displayed = 1; dump_dataset(dsetid, dset, sset); } } else { d_status = EXIT_FAILURE; } } else { dump_dataset(dsetid, dset, sset); } if (H5Dclose(dsetid) < 1) d_status = EXIT_FAILURE; } /*------------------------------------------------------------------------- * Function: handle_groups * * Purpose: Handle the groups from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void handle_groups(hid_t fid, char *group, void * UNUSED data) { H5G_stat_t statbuf; hid_t gid; if ((gid = H5Gopen(fid, group)) < 0) { begin_obj(dump_header_format->groupbegin, group, dump_header_format->groupblockbegin); indentation(COL); error_msg(progname, "unable to open group \"%s\"\n", group); end_obj(dump_header_format->groupend, dump_header_format->groupblockend); d_status = EXIT_FAILURE; } else { size_t new_len = strlen(group) + 1; if (prefix_len <= new_len) { prefix_len = new_len; prefix = realloc(prefix, prefix_len); } H5Gget_objinfo(gid, ".", TRUE, &statbuf); strcpy(prefix, group); dump_group(gid, group); if (H5Gclose(gid) < 0) d_status = EXIT_FAILURE; } } /*------------------------------------------------------------------------- * Function: handle_links * * Purpose: Handle the links from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void handle_links(hid_t fid, char *links, void * UNUSED data) { H5G_stat_t statbuf; if (H5Gget_objinfo(fid, links, FALSE, &statbuf) < 0) { begin_obj(dump_header_format->softlinkbegin, links, dump_header_format->softlinkblockbegin); indentation(COL); error_msg(progname, "unable to get obj info from \"%s\"\n", links); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); d_status = EXIT_FAILURE; } else if (statbuf.type == H5G_LINK) { char *buf = malloc(statbuf.linklen); begin_obj(dump_header_format->softlinkbegin, links, dump_header_format->softlinkblockbegin); indentation(COL); if (H5Gget_linkval(fid, links, statbuf.linklen, buf) >= 0) { printf("LINKTARGET \"%s\"\n", buf); } else { error_msg(progname, "h5dump error: unable to get link value for \"%s\"\n", links); d_status = EXIT_FAILURE; } end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); free(buf); } else { begin_obj(dump_header_format->softlinkbegin, links, dump_header_format->softlinkblockbegin); indentation(COL); error_msg(progname, "\"%s\" is not a link\n", links); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); d_status = EXIT_FAILURE; } } /*------------------------------------------------------------------------- * Function: handle_datatypes * * Purpose: Handle the datatypes from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void handle_datatypes(hid_t fid, char *type, void * UNUSED data) { hid_t type_id; if ((type_id = H5Topen(fid, type)) < 0) { /* check if type is unamed data type */ int idx = 0; while (idx < type_table->nobjs ) { char name[128], name1[128]; if (!type_table->objs[idx].recorded) { /* unamed data type */ sprintf(name, "#%lu:%lu\n", type_table->objs[idx].objno[0], type_table->objs[idx].objno[1]); sprintf(name1, "/#%lu:%lu\n", type_table->objs[idx].objno[0], type_table->objs[idx].objno[1]); if (!strncmp(name, type, strlen(type)) || !strncmp(name1, type, strlen(type))) break; } idx++; } if (idx == type_table->nobjs) { /* unknown type */ begin_obj(dump_header_format->datatypebegin, type, dump_header_format->datatypeblockbegin); indentation(COL); error_msg(progname, "unable to open datatype \"%s\"\n", type); end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); d_status = EXIT_FAILURE; } else { hid_t dsetid = H5Dopen(fid, type_table->objs[idx].objname); type_id = H5Dget_type(dsetid); dump_named_datatype(type_id, type); H5Tclose(type_id); H5Dclose(dsetid); } } else { dump_named_datatype(type_id, type); if (H5Tclose(type_id) < 0) d_status = EXIT_FAILURE; } } /*------------------------------------------------------------------------- * Function: parse_command_line * * Purpose: Parse the command line for the h5dumper. * * Return: Success: A pointer to an array of handler_t structures. * These contain all the information needed to dump * the necessary object. * * Failure: Exits program with EXIT_FAILURE value. * * Programmer: Bill Wendling * Tuesday, 20. February 2001 * * Modifications: * *------------------------------------------------------------------------- */ static struct handler_t * parse_command_line(int argc, const char *argv[]) { struct handler_t *hand, *last_dset = NULL; int i, opt, last_was_dset = FALSE; if (argc < 2) { usage(progname); exit(EXIT_FAILURE); } /* this will be plenty big enough to hold the info */ hand = calloc((size_t)argc, sizeof(struct handler_t)); /* parse command line options */ while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { parse_start: switch ((char)opt) { #if 0 case 'b': /* binary output */ break; #endif /* 0 */ case 'B': display_bb = TRUE; last_was_dset = FALSE; break; case 'H': display_data = FALSE; last_was_dset = FALSE; break; case 'i': display_oid = TRUE; last_was_dset = FALSE; break; case 'V': print_version(progname); exit(EXIT_SUCCESS); break; case 'w': nCols = atoi(opt_arg); last_was_dset = FALSE; break; case 'a': display_all = 0; for (i = 0; i < argc; i++) if (!hand[i].func) { hand[i].func = handle_attributes; hand[i].obj = HDstrdup(opt_arg); break; } last_was_dset = FALSE; break; case 'd': display_all = 0; for (i = 0; i < argc; i++) if (!hand[i].func) { hand[i].func = handle_datasets; hand[i].obj = HDstrdup(opt_arg); hand[i].subset_info = parse_subset_params(hand[i].obj); last_dset = hand; break; } last_was_dset = TRUE; break; case 'f': driver = opt_arg; break; case 'g': display_all = 0; for (i = 0; i < argc; i++) if (!hand[i].func) { hand[i].func = handle_groups; hand[i].obj = HDstrdup(opt_arg); break; } last_was_dset = FALSE; break; case 'l': display_all = 0; for (i = 0; i < argc; i++) if (!hand[i].func) { hand[i].func = handle_links; hand[i].obj = HDstrdup(opt_arg); break; } last_was_dset = FALSE; break; case 't': display_all = 0; for (i = 0; i < argc; i++) if (!hand[i].func) { hand[i].func = handle_datatypes; hand[i].obj = HDstrdup(opt_arg); break; } last_was_dset = FALSE; break; case 'o': if (set_output_file(opt_arg) < 0){ /* failed to set output file */ usage(progname); exit(EXIT_FAILURE); } usingdasho = TRUE; last_was_dset = FALSE; break; /** begin XML parameters **/ case 'x': /* select XML output */ doxml = TRUE; dump_header_format = &xmlformat; dump_function_table = &xml_function_table; break; case 'D': /* specify alternative XML DTD */ xml_dtd_uri = opt_arg; break; /** end XML parameters **/ /** begin subsetting parameters **/ case 's': case 'S': case 'c': case 'k': { struct subset_t *s; if (!last_was_dset) { error_msg(progname, "option `-%c' can only be used after --dataset option\n", opt); exit(EXIT_FAILURE); } if (last_dset->subset_info) { /* * This overrides the "terse" syntax if they actually mixed * the two. */ s = last_dset->subset_info; } else { last_dset->subset_info = s = calloc(1, sizeof(struct subset_t)); } /* * slightly convoluted, but...we are only interested in options * for subsetting: "--start", "--stride", "--count", and "--block" * which can come in any order. If we run out of parameters (EOF) * or run into one which isn't a subsetting parameter (NOT s, S, * c, or K), then we exit the do-while look, set the subset_info * to the structure we've been filling. If we've reached the end * of the options, we exit the parsing (goto parse_end) otherwise, * since we've "read" the next option, we need to parse it. So we * jump to the beginning of the switch statement (goto parse_start). */ do { switch ((char)opt) { case 's': free(s->start); s->start = (hssize_t *)parse_hsize_list(opt_arg); break; case 'S': free(s->stride); s->stride = parse_hsize_list(opt_arg); break; case 'c': free(s->count); s->count = parse_hsize_list(opt_arg); break; case 'k': free(s->block); s->block = parse_hsize_list(opt_arg); break; default: goto end_collect; } } while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF); end_collect: last_was_dset = FALSE; if (opt != EOF) goto parse_start; else goto parse_end; } /** end subsetting parameters **/ case 'h': usage(progname); exit(EXIT_SUCCESS); case '?': default: usage(progname); exit(EXIT_FAILURE); } } parse_end: return hand; } /*------------------------------------------------------------------------- * Function: free_handler * * Purpose: Convenience function to free the handler_t structures. Needs a * length variable (LEN) to know how many in the array it needs * to free * * Return: Nothing * * Programmer: Bill Wendling * Tuesday, 20. February 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void free_handler(struct handler_t *hand, int len) { register int i; for (i = 0; i < len; i++) { free(hand[i].obj); if (hand[i].subset_info) { free(hand[i].subset_info->start); free(hand[i].subset_info->stride); free(hand[i].subset_info->count); free(hand[i].subset_info->block); free(hand[i].subset_info); } } free(hand); } /*------------------------------------------------------------------------- * Function: main * * Purpose: HDF5 dumper * * Return: Success: 0 * Failure: 1 * * Programmer: Ruey-Hsia Li * * Modifications: * Albert Cheng * 30. September 2000 * Add the -o option--output file for datasets raw data * * REMcG * November 2000 * Changes to support XML. * * Bill Wendling * Wednesday, 10. January 2001 * Modified the way command line parameters are interpreted. They go * through one function call now (get_option). * * Bill Wendling * Tuesday, 20. February 2001 * Moved command line parsing to separate function. Made various * "display_*" flags global. * *------------------------------------------------------------------------- */ int main(int argc, const char *argv[]) { hid_t fid, gid; const char *fname = NULL; void *edata; hid_t (*func)(void*); find_objs_t info; struct handler_t *hand; int i; if (argc < 2) { usage(progname); exit(EXIT_FAILURE); } dump_header_format = &standardformat; dump_function_table = &ddl_function_table; /* Disable error reporting */ H5Eget_auto(&func, &edata); H5Eset_auto(NULL, NULL); /* Initialize h5tools lib */ h5tools_init(); hand = parse_command_line(argc, argv); /* Check for conflicting options */ if (doxml) { if (!display_all) { error_msg(progname, "option \"%s\" not available for XML\n", "to display selected objects"); exit(EXIT_FAILURE); } else if (display_bb) { error_msg(progname, "option \"%s\" not available for XML\n", "--boot-block"); exit(EXIT_FAILURE); } else if (!display_data) { error_msg(progname, "option \"%s\" not available for XML\n", "--header"); exit(EXIT_FAILURE); } else if (display_oid == 1) { error_msg(progname, "option \"%s\" not available for XML\n", "--object-ids"); exit(EXIT_FAILURE); } else if (usingdasho) { error_msg(progname, "option \"%s\" not available for XML\n", "--output"); exit(EXIT_FAILURE); } } else { if (xml_dtd_uri) { warn_msg(progname, "option \"%s\" only applies with XML: %s\n", "--xml-dtd", xml_dtd_uri); } } if (argv[opt_ind][0] == '\\') fname = &argv[opt_ind][1]; else fname = argv[opt_ind]; fid = h5tools_fopen(fname, driver, NULL, 0); if (fid < 0) { error_msg(progname, "unable to open file \"%s\"\n", fname); exit(EXIT_FAILURE); } /* 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 = prefix_len; info.prefix = calloc((size_t)info.prefix_len, 1); info.group_table = group_table; info.type_table = type_table; info.dset_table = dset_table; info.status = d_status; if (doxml) { /* initialize XML */ thefile = fid; /* find all objects that might be targets of a refernce */ if ((gid = H5Gopen(fid, "/")) < 0) { error_msg(progname, "unable to open root group\n"); d_status = EXIT_FAILURE; goto done; } ref_path_table_put(gid, "/"); H5Giterate(fid, "/", NULL, fill_ref_path_table, NULL); H5Gclose(gid); /* reset prefix! */ strcpy(prefix, ""); /* make sure the URI is initialized to something */ if (xml_dtd_uri == NULL) xml_dtd_uri = DEFAULT_DTD; } /* find all shared objects */ H5Giterate(fid, "/", NULL, find_objs, (void *)&info); /* does there exist unamed committed data type */ for (i = 0; i < type_table->nobjs; i++) if (type_table->objs[i].recorded == 0) unamedtype = 1; dump_tables(); if (info.status) { error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); d_status = EXIT_FAILURE; goto done; } /* start to dump */ if (!doxml) { begin_obj(dump_header_format->filebegin, fname, dump_header_format->fileblockbegin); } else { printf("\n"); printf("\n", xml_dtd_uri); printf("\n"); } if (display_bb) dump_bb(); if (display_all) { if ((gid = H5Gopen(fid, "/")) < 0) { error_msg(progname, "unable to open root group\n"); d_status = EXIT_FAILURE; } else { dump_function_table->dump_group_function(gid, "/"); } if (H5Gclose(gid) < 0) { error_msg(progname, "unable to close root group\n"); d_status = EXIT_FAILURE; } } else { if (doxml) { /* Note: this option is not supported for XML */ error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); d_status = EXIT_FAILURE; goto done; } for (i = 0; i < argc; i++) if (hand[i].func) hand[i].func(fid, hand[i].obj, hand[i].subset_info); } if (!doxml) { end_obj(dump_header_format->fileend, dump_header_format->fileblockend); } else { printf("%s\n", dump_header_format->fileend); } done: if (H5Fclose(fid) < 0) d_status = EXIT_FAILURE; free_handler(hand, argc); free(group_table->objs); free(dset_table->objs); free(type_table->objs); free(prefix); free(info.prefix); /* To Do: clean up XML table */ h5tools_close(); H5Eset_auto(func, edata); 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; 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 */ assert(nmembs>0); name = calloc((size_t)nmembs, sizeof(char *)); value = calloc((size_t)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, (hsize_t)nmembs, value, NULL, H5P_DEFAULT); /* * Sort members by increasing value * ***not implemented yet*** */ /* Print members */ for (i = 0; i < nmembs; i++) { indentation(indent + COL); nchars = printf("\"%s\"", name[i]); printf("%*s ", MAX(0, 16 - nchars), ""); if (native < 0) { size_t j; printf("0x"); for (j = 0; j < dst_size; j++) printf("%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "u", *((unsigned long_long *) ((void *) (value + i * dst_size)))); } else { HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "d", *((long_long *) ((void *) (value + i * dst_size)))); } printf(";\n"); } /* 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, ""); } /* * XML support */ /* * XML needs a table to look up a path name for an object * reference. * * This table stores mappings of reference -> path * for all objects in the file that may be the target of * an object reference. * * The 'path' is an absolute path by which the object * can be accessed. When an object has > 1 such path, * only one will be used in the table, with no particular * method of selecting which one. */ struct ref_path_table_entry_t { hsize_t obj; hobj_ref_t *obj_ref; char *apath; struct ref_path_table_entry_t *next; }; struct ref_path_table_entry_t *ref_path_table = NULL; /* the table */ int npte = 0; /* number of entries in the table */ /*------------------------------------------------------------------------- * Function: ref_path_table_lookup * * Purpose: Looks up a table entry given a path name. * Used during construction of the table. * * Return: The table entre (pte) or NULL if not in the * table. * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static struct ref_path_table_entry_t * ref_path_table_lookup(const char *thepath) { int i; hobj_ref_t *ref; herr_t status; struct ref_path_table_entry_t *pte = ref_path_table; if (ref_path_table == NULL) return NULL; ref = (hobj_ref_t *) malloc(sizeof(hobj_ref_t)); if (ref == NULL) { /* fatal error ? */ return NULL; } status = H5Rcreate(ref, thefile, thepath, H5R_OBJECT, -1); if (status < 0) { /* fatal error ? */ return NULL; } for (i = 0; i < npte; i++) { if (memcmp(ref, pte->obj_ref, sizeof(hobj_ref_t)) == 0) { return pte; } pte = pte->next; } return NULL; } /*------------------------------------------------------------------------- * Function: ref_path_table_put * * Purpose: Enter the 'obj' with 'path' in the table if * not already there. * Create an object reference, pte, and store them * in the table. * * Return: The object reference for the object. * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static hobj_ref_t * ref_path_table_put(hid_t obj, const char *path) { hobj_ref_t *ref; herr_t status; struct ref_path_table_entry_t *pte; /* look up 'obj'. If already in table, return */ pte = ref_path_table_lookup(path); if (pte != NULL) return pte->obj_ref; /* if not found, then make new entry */ pte = (struct ref_path_table_entry_t *) malloc(sizeof(struct ref_path_table_entry_t)); if (pte == NULL) { /* fatal error? */ return NULL; } pte->obj = obj; ref = (hobj_ref_t *) malloc(sizeof(hobj_ref_t)); if (ref == NULL) { /* fatal error? */ free(pte); return NULL; } status = H5Rcreate(ref, thefile, path, H5R_OBJECT, -1); if (status < 0) { /* fatal error? */ free(ref); free(pte); return NULL; } pte->obj_ref = ref; pte->apath = HDstrdup(path); pte->next = ref_path_table; ref_path_table = pte; npte++; return ref; } /*------------------------------------------------------------------------- * Function: lookup_ref_path * * Purpose: Lookup the path to the object with refernce 'ref'. * * Return: Return a path to the object, or NULL if not found. * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static char * lookup_ref_path(hobj_ref_t * ref) { int i; struct ref_path_table_entry_t *pte = NULL; if (ref_path_table == NULL) return NULL; pte = ref_path_table; if (pte == NULL) { /* fatal -- not initialized? */ return NULL; } for (i = 0; i < npte; i++) { if (memcmp(ref, pte->obj_ref, sizeof(hobj_ref_t)) == 0) { return pte->apath; } pte = pte->next; } return NULL; } /*------------------------------------------------------------------------- * Function: fill_ref_path_table * * Purpose: Called by interator to create references for * all objects and enter them in the table. * * Return: Error status. * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static herr_t fill_ref_path_table(hid_t group, const char *name, void * UNUSED op_data) { hid_t obj; char *tmp; H5G_stat_t statbuf; struct ref_path_table_entry_t *pte; char *thepath; H5Gget_objinfo(group, name, FALSE, &statbuf); tmp = (char *) malloc(strlen(prefix) + strlen(name) + 2); if (tmp == NULL) return FAIL; thepath = (char *) malloc(strlen(prefix) + strlen(name) + 2); if (thepath == NULL) { free(tmp); return FAIL; } strcpy(tmp, prefix); strcpy(thepath, prefix); strcat(thepath, "/"); strcat(thepath, name); switch (statbuf.type) { case H5G_DATASET: if ((obj = H5Dopen(group, name)) >= 0) { pte = ref_path_table_lookup(thepath); if (pte == NULL) { ref_path_table_put(obj, thepath); } H5Dclose(obj); } else { error_msg(progname, "unable to get dataset \"%s\"\n", name); d_status = EXIT_FAILURE; } break; case H5G_GROUP: if ((obj = H5Gopen(group, name)) >= 0) { strcat(strcat(prefix, "/"), name); pte = ref_path_table_lookup(thepath); if (pte == NULL) { ref_path_table_put(obj, thepath); H5Giterate(obj, ".", NULL, fill_ref_path_table, NULL); strcpy(prefix, tmp); } H5Gclose(obj); } else { error_msg(progname, "unable to dump group \"%s\"\n", name); d_status = EXIT_FAILURE; } break; case H5G_TYPE: if ((obj = H5Topen(group, name)) >= 0) { pte = ref_path_table_lookup(thepath); if (pte == NULL) { ref_path_table_put(obj, thepath); } H5Tclose(obj); } else { error_msg(progname, "unable to get dataset \"%s\"\n", name); d_status = EXIT_FAILURE; } break; default: break; } free(tmp); free(thepath); return 0; } static const char *quote = """; static const char *amp = "&"; static const char *lt = "<"; static const char *gt = ">"; static const char *apos = "'"; /*------------------------------------------------------------------------- * Function: xml_escape_the_name * * Purpose: Escape XML reserved chars in a name, so HDF5 strings * and paths can be correctly read back in XML element. * * Return: The revised string. * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static char * xml_escape_the_name(const char *str) { size_t extra; size_t len; size_t i; const char *cp; char *ncp; char *rcp; if (!str) return NULL; cp = str; len = strlen(str); extra = 0; for (i = 0; i < len; i++) { if (*cp == '\"') { extra += (strlen(quote) - 1); } else if (*cp == '\'') { extra += (strlen(apos) - 1); } else if (*cp == '<') { extra += (strlen(lt) - 1); } else if (*cp == '>') { extra += (strlen(gt) - 1); } else if (*cp == '&') { extra += (strlen(amp) - 1); } cp++; } if (extra == 0) return HDstrdup(str); cp = str; rcp = ncp = calloc((size_t)(len + extra + 1), sizeof(char)); if (!ncp) return NULL; /* ?? */ for (i = 0; i < len; i++) { if (*cp == '\'') { strncpy(ncp, apos, strlen(apos)); ncp += strlen(apos); cp++; } else if (*cp == '<') { strncpy(ncp, lt, strlen(lt)); ncp += strlen(lt); cp++; } else if (*cp == '>') { strncpy(ncp, gt, strlen(gt)); ncp += strlen(gt); cp++; } else if (*cp == '\"') { strncpy(ncp, quote, strlen(quote)); ncp += strlen(quote); cp++; } else if (*cp == '&') { strncpy(ncp, amp, strlen(amp)); ncp += strlen(amp); cp++; } else { *ncp++ = *cp++; } } *ncp = '\0'; return rcp; } /*------------------------------------------------------------------------- * Function: xml_escape_the_string * * Purpose: Escape XML reserved chars in a string, so HDF5 strings * and paths can be correctly read back in XML CDATA. * * Return: The revised string. * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static char * xml_escape_the_string(const char *str, int slen) { size_t extra; size_t len; size_t i; const char *cp; char *ncp; char *rcp; if (!str) return NULL; cp = str; if (slen < 0) len = strlen(str); else len = slen; extra = 0; for (i = 0; i < len; i++) { if (*cp == '\\') { extra++; } else if (*cp == '\"') { extra++; } else if (*cp == '\'') { extra += (strlen(apos) - 1); } else if (*cp == '<') { extra += (strlen(lt) - 1); } else if (*cp == '>') { extra += (strlen(gt) - 1); } else if (*cp == '&') { extra += (strlen(amp) - 1); } cp++; } cp = str; rcp = ncp = calloc((size_t)(len + extra + 1), sizeof(char)); if (ncp == NULL) return NULL; /* ?? */ for (i = 0; i < len; i++) { if (*cp == '\\') { *ncp++ = '\\'; *ncp++ = *cp++; } else if (*cp == '\"') { *ncp++ = '\\'; *ncp++ = *cp++; } else if (*cp == '\'') { strncpy(ncp, apos, strlen(apos)); ncp += strlen(apos); cp++; } else if (*cp == '<') { strncpy(ncp, lt, strlen(lt)); ncp += strlen(lt); cp++; } else if (*cp == '>') { strncpy(ncp, gt, strlen(gt)); ncp += strlen(gt); cp++; } else if (*cp == '&') { strncpy(ncp, amp, strlen(amp)); ncp += strlen(amp); cp++; } else { *ncp++ = *cp++; } } *ncp = '\0'; return rcp; } /** ** XML print functions--these replace some functions in the ** h5tools.c suite. **/ /*------------------------------------------------------------------------- * Function: xml_print_datatype * * Purpose: Print description of a datatype in XML. * Note: this is called inside a element. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_print_datatype(hid_t type) { char *fname; hid_t nmembers, mtype; int i, j, ndims, perm[H5DUMP_MAX_RANK]; size_t size; hsize_t dims[H5DUMP_MAX_RANK]; H5T_str_t str_pad; H5T_cset_t cset; H5G_stat_t statbuf; hid_t super; H5T_order_t ord; H5T_sign_t sgn; size_t sz; size_t spos; size_t epos; size_t esize; size_t mpos; size_t msize; int nmembs; switch (H5Tget_class(type)) { case H5T_INTEGER: indentation(indent); printf("\n"); indent += COL; /* */ ord = H5Tget_order(type); sgn = H5Tget_sign(type); indentation(indent); printf("\n"); indent -= COL; indentation(indent); printf("\n"); break; case H5T_FLOAT: /* */ ord = H5Tget_order(type); indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\n", (unsigned)msize, (unsigned)mpos); indent -= COL; indentation(indent); printf("\n"); break; case H5T_TIME: indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\n"); printf(""); indent -= COL; indentation(indent); printf("\n"); break; case H5T_STRING: /* */ size = H5Tget_size(type); str_pad = H5Tget_strpad(type); cset = H5Tget_cset(type); indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\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"); } indent -= COL; indentation(indent); printf("\n"); break; case H5T_BITFIELD: /* */ ord = H5Tget_order(type); indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\n", (unsigned)size); indent -= COL; indentation(indent); printf("\n"); break; case H5T_OPAQUE: /* */ indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\n", (unsigned)size); indent -= COL; indentation(indent); printf("\n"); break; case H5T_COMPOUND: /* recursively describe the components of a compound datatype */ if (H5Tcommitted(type) > 0) { /* detect a shared datatype, output only once */ H5Gget_objinfo(type, ".", TRUE, &statbuf); i = search_obj(type_table, statbuf.objno); if (i >= 0) { /* This should be defined somewhere else */ if (!type_table->objs[i].recorded) { /* 'anonymous' NDT. Use it's object num. as it's name. */ printf("\n", type_table->objs[i].objno[0], type_table->objs[i].objno[1]); } else { /* point to the NDT by name */ char *t_objname = xml_escape_the_name(type_table->objs[i].objname); printf("\n", t_objname); free(t_objname); } } else { printf("\n"); d_status = EXIT_FAILURE; } } else { /* type of a dataset */ nmembers = H5Tget_nmembers(type); indentation(indent); printf("\n"); /* List each member Field of the type */ /* */ /* */ indent += COL; for (i = 0; i < nmembers; i++) { char *t_fname; fname = H5Tget_member_name(type, i); mtype = H5Tget_member_type(type, i); #ifdef WANT_H5_V1_2_COMPAT /* v1.2 returns the base type of an array field, work around this */ { hid_t new_mtype; /* datatype for array, if necessary */ int arrndims; /* Array rank for reading */ size_t dims[H5S_MAX_RANK]; /* Array dimensions for reading */ hsize_t arrdims[H5S_MAX_RANK]; /* Array dimensions for reading */ int k; /* Local index variable */ /* Get the array dimensions */ arrndims=H5Tget_member_dims(type,i,dims,NULL); /* Patch up array information */ if(arrndims>0) { for(k=0; k\n", t_fname); free(fname); free(t_fname); indent += COL; indentation(indent); printf("\n"); indent += COL; xml_print_datatype(mtype); indent -= COL; indentation(indent); printf("%s\n", dump_header_format->datatypeend); indent -= COL; indentation(indent); printf("\n"); } indent -= COL; indentation(indent); printf("\n"); } break; case H5T_REFERENCE: indentation(indent); printf("\n"); indent += COL; indentation(indent); /* Only Object references supported at this time */ printf("\n"); indentation(indent + COL); printf("\n"); indentation(indent); printf("\n"); indent -= COL; indentation(indent); printf("\n"); break; case H5T_ENUM: /* list Name, values of enum */ nmembs = H5Tget_nmembers(type); indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\n", nmembs); xml_print_enum(type); indentation(indent); printf("\n"); indent -= COL; indentation(indent); printf("\n"); break; case H5T_VLEN: indentation(indent); printf("\n"); super = H5Tget_super(type); indent += COL; indentation(indent); printf("\n"); indent += COL; xml_print_datatype(super); indent -= COL; indentation(indent); printf("%s\n", dump_header_format->datatypeend); indent -= COL; indentation(indent); printf("\n"); H5Tclose(super); break; case H5T_ARRAY: /* Get array base type */ super = H5Tget_super(type); /* Print lead-in */ indentation(indent); printf("\n", ndims); /* Get array information */ H5Tget_array_dims(type, dims, perm); /* list of dimensions */ indent += COL; if (perm != NULL) { /* for each dimension, list */ for (j = 0; j < ndims; j++) { indentation(indent); printf("\n", (int) dims[j], (int) perm[j]); } } else { for (j = 0; j < ndims; j++) { indentation(indent); printf("\n", (int) dims[j]); } } indent -= COL; indent += COL; indentation(indent); printf("\n"); indent += COL; xml_print_datatype(super); indent -= COL; indentation(indent); printf("%s\n", dump_header_format->datatypeend); indent -= COL; indentation(indent); printf("\n"); /* Close array base type */ H5Tclose(super); break; default: printf(""); d_status = EXIT_FAILURE; break; } } /*------------------------------------------------------------------------- * Function: xml_dump_datatype * * Purpose: Dump description of a datatype in XML. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_dump_datatype(hid_t type) { int i; H5G_stat_t statbuf; indent += COL; indentation(indent); if (H5Tcommitted(type) > 0) { /* Data type is a shared or named data type */ H5Gget_objinfo(type, ".", TRUE, &statbuf); i = search_obj(type_table, statbuf.objno); if (i >= 0) { /* Shared data type, must be entered as an object */ if (!type_table->objs[i].recorded) { /* anonymous stored data type: following the dumper's current practice: use it's object ref as its name */ printf("\n", type_table->objs[i].objno[0], type_table->objs[i].objno[1]); } else { /* pointer to a named data type already in XML */ char *t_objname = xml_escape_the_name(type_table->objs[i].objname); printf("\n", t_objname); free(t_objname); } } else { printf("\n"); } indent -= COL; return; } printf("%s %s\n", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); indent += COL; xml_print_datatype(type); indent -= COL; indentation(indent); printf("%s\n", dump_header_format->datatypeend); indent -= COL; } /*------------------------------------------------------------------------- * Function: xml_dump_dataspace * * Purpose: Dump description of a dataspace in XML. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_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\n", dump_header_format->dataspacebegin); if (H5Sis_simple(space)) { indentation(indent + COL + COL); if (ndims == 0) { /* scalar dataspace (just a tag, no XML attrs. defined */ printf("\n"); } else { /* simple dataspace */ /* */ printf("\n", ndims); /* print the elements */ for (i = 0; i < ndims; i++) { indentation(indent + COL + COL + COL); if (maxsize[i] == H5S_UNLIMITED) { HDfprintf(stdout, "\n", size[i]); } else if (maxsize[i] == (hsize_t) 0) { HDfprintf(stdout, "\n", size[i], size[i]); } else { HDfprintf(stdout, "\n", size[i], maxsize[i]); } } indentation(indent + COL + COL); printf("\n"); } } else { printf("\n"); } indentation(indent + COL); printf("%s\n", dump_header_format->dataspaceend); } /*------------------------------------------------------------------------- * Function: xml_dump_data * * Purpose: Dump description of data in XML. * Note that this calls the h5dump_xxx calls in * the h5tools library. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_dump_data(hid_t obj_id, int obj_data, struct subset_t * UNUSED sset) { h5dump_t *outputformat = &xml_dataformat; int 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; /* Print all the values. */ indentation(indent); printf("%s\n", dump_header_format->databegin); indentation(indent + COL); printf("\n"); if (obj_data == DATASET_DATA) { type = H5Dget_type(obj_id); if (H5Tget_class(type) == H5T_REFERENCE) { status = xml_print_refs(obj_id, DATASET_DATA); } else if (H5Tget_class(type) == H5T_STRING) { status = xml_print_strs(obj_id, DATASET_DATA); } else { status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, NULL, depth); } } else { /* Attribute data */ type = H5Aget_type(obj_id); if (H5Tget_class(type) == H5T_REFERENCE) { /* references are done differently than the standard output: XML dumps a path to the object referenced. */ status = xml_print_refs(obj_id, ATTRIBUTE_DATA); H5Tclose(type); } else if (H5Tget_class(type) == H5T_STRING) { status = xml_print_strs(obj_id, ATTRIBUTE_DATA); } else { /* all other data */ p_type = h5tools_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((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)))); assert(buf); if (H5Aread(obj_id, p_type, buf) >= 0) status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type, space, buf, depth); free(buf); H5Tclose(p_type); H5Sclose(space); H5Tclose(type); } } if (status == FAIL) { indentation(indent + COL); printf("Unable to print data.\n"); status = 1; } indentation(indent + COL); printf("\n"); indentation(indent); printf("%s\n", dump_header_format->dataend); indent -= COL; } /*------------------------------------------------------------------------- * Function: xml_dump_attr * * Purpose: Dump a description of an HDF5 attribute in XML. * * Return: herr_t * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static herr_t xml_dump_attr(hid_t attr, const char *attr_name, void * UNUSED op_data) { hid_t attr_id, type, space; char *t_aname = xml_escape_the_name(attr_name); indentation(indent); printf("\n", t_aname); free(t_aname); if ((attr_id = H5Aopen_name(attr, attr_name)) >= 0) { type = H5Aget_type(attr_id); space = H5Aget_space(attr_id); dump_function_table->dump_dataspace_function(space); dump_function_table->dump_datatype_function(type); if (display_data) { switch (H5Tget_class(type)) { case H5T_INTEGER: case H5T_FLOAT: case H5T_STRING: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_ENUM: case H5T_ARRAY: dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL); break; case H5T_TIME: indent += COL; indentation(indent); printf("\n"); indentation(indent); printf("\n"); indentation(indent); printf("\n"); indentation(indent); printf("\n"); indent -= COL; break; case H5T_COMPOUND: indentation(indent); printf("\n"); dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL); break; case H5T_REFERENCE: indentation(indent); printf("\n"); indentation(indent); if (!H5Tequal(type, H5T_STD_REF_OBJ)) { printf("\n"); indentation(indent); printf("\n"); } else { printf("\n"); xml_print_refs(attr_id, ATTRIBUTE_DATA); indentation(indent); printf("\n"); } indentation(indent); printf("\n"); break; case H5T_VLEN: printf("\n"); dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL); break; default: indentation(indent); printf("\n"); indentation(indent); printf("\n", H5Tget_class(type)); indentation(indent); printf("\n"); indentation(indent); printf("\n"); break; } } else { /* The case of an attribute never yet written ?? */ indentation(indent); printf("\n"); indentation(indent + COL); printf("\n"); indentation(indent); printf("\n"); } H5Tclose(type); H5Sclose(space); H5Aclose(attr_id); indentation(indent); printf("%s\n", dump_header_format->attributeend); return SUCCEED; } else { /* ?? failed */ indentation(indent + COL); printf("\n"); indentation(indent); printf("%s\n", dump_header_format->attributeend); d_status = EXIT_FAILURE; return FAIL; } } /*------------------------------------------------------------------------- * Function: xml_dump_named_datatype * * Purpose: Dump a description of an HDF5 NDT in XML. * * Return: herr_t * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_dump_named_datatype(hid_t type, const char *name) { int nmembers = 1, x; hid_t mtype; char *fname; char *tmp; tmp = malloc(strlen(prefix) + strlen(name) + 2); strcpy(tmp, prefix); strcat(tmp, "/"); strcat(tmp, name); indentation(indent); if (strncmp(name, "#", 1) == 0) { /* Special: this is an 'anonymous' NDT, deleted but still in use. We follow the dumper's undocumented practice, and use its object id as its name. Exactly the same as normal, but a separate case in the event we want to do something else in the future. */ char *t_tmp = xml_escape_the_name(tmp); char *t_prefix = xml_escape_the_name(prefix); printf("\n", name, t_tmp, (strcmp(prefix, "") ? t_prefix : "root")); free(t_tmp); free(t_prefix); } else { char *t_name = xml_escape_the_name(name); char *t_prefix = xml_escape_the_name(prefix); char *t_tmp = xml_escape_the_name(tmp); printf("\n", t_name, t_tmp, (strcmp(prefix, "") ? t_prefix : "root")); free(t_name); free(t_prefix); free(t_tmp); } indent += COL; if (H5Tget_class(type) == H5T_COMPOUND) { /* Dump this here for sure. */ nmembers = H5Tget_nmembers(type); indentation(indent); printf("\n"); indentation(indent); printf("\n"); indent += COL; for (x = 0; x < nmembers; x++) { char *t_fname; fname = H5Tget_member_name(type, x); mtype = H5Tget_member_type(type, x); #ifdef WANT_H5_V1_2_COMPAT /* v1.2 returns the base type of an array field, work around this */ { hid_t new_mtype; /* datatype for array, if necessary */ int arrndims; /* Array rank for reading */ size_t dims[H5S_MAX_RANK]; /* Array dimensions for reading */ hsize_t arrdims[H5S_MAX_RANK]; /* Array dimensions for reading */ int k; /* Local index variable */ /* Get the array dimensions */ arrndims=H5Tget_member_dims(type,x,dims,NULL); /* Patch up array information */ if(arrndims>0) { for(k=0; k\n", t_fname); free(fname); free(t_fname); if ((H5Tget_class(mtype) == H5T_COMPOUND) || (H5Tget_class(mtype) == H5T_VLEN) || (H5Tget_class(mtype) == H5T_ARRAY)) { indent += COL; /* Nested compound type: recur */ indentation(indent); printf("%s %s\n", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); indent += COL; xml_print_datatype(mtype); indent -= COL; indentation(indent); printf("%s\n", dump_header_format->datatypeend); indent -= COL; } else { indent += COL; indentation(indent); printf("%s %s\n", dump_header_format->datatypebegin, dump_header_format->datatypeblockbegin); indent += COL; xml_print_datatype(mtype); indent -= COL; indentation(indent); printf("%s\n", dump_header_format->datatypeend); indent -= COL; } indentation(indent); printf("\n"); } indent -= COL; indentation(indent); printf("\n"); indentation(indent); printf("\n"); } else { /* Other data types: call print_datatype */ indentation(indent); printf("\n"); indent += COL; xml_print_datatype(type); indent -= COL; indentation(indent); printf("\n"); } indent -= COL; indentation(indent); printf("\n"); } /*------------------------------------------------------------------------- * Function: xml_dump_group * * Purpose: Dump a description of an HDF5 Group (and its members) in XML. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_dump_group(hid_t gid, const char *name) { H5G_stat_t statbuf; char *cp; hid_t dset, type; char type_name[1024], *tmp = NULL; char *par = NULL; int i; int isRoot = 0; int xtype; if (strcmp(name, "/") == 0) { isRoot = 1; } else { tmp = malloc(strlen(prefix) + strlen(name) + 2); strcpy(tmp, prefix); par = HDstrdup(tmp); cp = strrchr(par, '/'); if (cp != NULL) { if ((cp == par) && strlen(par) > 1) { *(cp + 1) = '\0'; } else { *cp = '\0'; } } } indentation(indent); if (isRoot) { printf("\n"); } else { char *t_name = xml_escape_the_name(name); char *t_tmp = xml_escape_the_name(tmp); char *t_par = xml_escape_the_name(par); printf("\n", t_name, t_tmp, (strcmp(prefix, "") ? t_par : "root")); free(t_name); free(t_tmp); free(t_par); } indent += COL; H5Gget_objinfo(gid, ".", TRUE, &statbuf); if (statbuf.nlink > 1) { /* Group with more than one link to it... */ i = search_obj(group_table, statbuf.objno); if (i < 0) { indentation(indent); error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__); d_status = EXIT_FAILURE; } else if (group_table->objs[i].displayed) { /* already seen: enter a groupptr */ char *t_objname = xml_escape_the_name(group_table->objs[i].objname); indentation(indent + COL); printf("\n", t_objname); free(t_objname); } else { /* first time this group has been seen -- describe it */ free(group_table->objs[i].objname); group_table->objs[i].objname = HDstrdup(prefix); group_table->objs[i].displayed = 1; /* 1. do all the attributes of the group */ H5Aiterate(gid, NULL, dump_function_table->dump_attribute_function, NULL); if (!strcmp(name, "/") && unamedtype) { /* Very special case: 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(type_name, "#%lu:%lu", type_table->objs[i].objno[0], type_table->objs[i].objno[1]); dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } } /* iterate through all the members */ xtype = H5G_TYPE; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); xtype = H5G_DATASET; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); xtype = H5G_GROUP; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); xtype = H5G_LINK; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); } } else { /* 1. do all the attributes of the group */ H5Aiterate(gid, NULL, dump_function_table->dump_attribute_function, NULL); if (!strcmp(name, "/") && unamedtype) { /* Very special case: 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(type_name, "#%lu:%lu", type_table->objs[i].objno[0], type_table->objs[i].objno[1]); dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } } /* iterate through all the members */ xtype = H5G_TYPE; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); xtype = H5G_DATASET; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); xtype = H5G_GROUP; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); xtype = H5G_LINK; H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype); } indent -= COL; indentation(indent); if (isRoot) { printf("\n"); } else { printf("%s\n", dump_header_format->groupend); } /* don't free this!!! free(tmp); */ } /*------------------------------------------------------------------------- * Function: xml_print_refs * * Purpose: Print a path to the objects referenced by HDF5 Referneces. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static int xml_print_refs(hid_t did, int source) { herr_t e; hid_t type, space; char *buf; hobj_ref_t *refbuf; char *path; hsize_t ssiz; hsize_t i; if (source == DATASET_DATA) { type = H5Dget_type(did); } else if (source == ATTRIBUTE_DATA) { type = H5Aget_type(did); } else { /* return an error */ return FAIL; } if (H5Tget_class(type) != H5T_REFERENCE) { /* return an error */ return FAIL; } if (!H5Tequal(type, H5T_STD_REF_OBJ)) { /* region ref not supported yet... */ /* return an error */ return FAIL; } if (source == DATASET_DATA) { space = H5Dget_space(did); ssiz = H5Sget_simple_extent_npoints(space); ssiz *= H5Tget_size(type); buf = calloc((size_t)ssiz, sizeof(char)); if (buf == NULL) { return FAIL; } e = H5Dread(did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); /* need to check result here */ if (e < 0) { free(buf); return FAIL; } } else if (source == ATTRIBUTE_DATA) { space = H5Aget_space(did); ssiz = H5Sget_simple_extent_npoints(space); ssiz *= H5Tget_size(type); buf = calloc((size_t)ssiz, sizeof(char)); if (buf == NULL) { free(buf); return FAIL; } e = H5Aread(did, H5T_STD_REF_OBJ, buf); /* need to check the result here */ } else { /* error */ return FAIL; } refbuf = (hobj_ref_t *) buf; ssiz = H5Sget_simple_extent_npoints(space); for (i = 0; i < ssiz; i++) { path = lookup_ref_path(refbuf); indentation(indent + COL); if (!path) { printf("\"%s\"\n", "NULL"); } else { char *t_path = xml_escape_the_string(path, -1); printf("\"%s\"\n", t_path); free(t_path); } refbuf++; } return SUCCEED; } /*------------------------------------------------------------------------- * Function: xml_print_strs * * Purpose: Print strings. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static int xml_print_strs(hid_t did, int source) { herr_t e; hid_t type, space; char *buf; char *bp; char *onestring; hsize_t ssiz; size_t tsiz; size_t i; if (source == DATASET_DATA) { type = H5Dget_type(did); } else if (source == ATTRIBUTE_DATA) { type = H5Aget_type(did); } else { /* return an error */ return FAIL; } if (H5Tget_class(type) != H5T_STRING) { /* return an error */ return FAIL; } if (source == DATASET_DATA) { space = H5Dget_space(did); ssiz = H5Sget_simple_extent_npoints(space); ssiz *= H5Tget_size(type); buf = calloc((size_t)ssiz, sizeof(char)); if (buf == NULL) { return FAIL; } e = H5Dread(did, type, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); if (e < 0) { free(buf); return FAIL; } } else if (source == ATTRIBUTE_DATA) { space = H5Aget_space(did); ssiz = H5Sget_simple_extent_npoints(space); ssiz *= H5Tget_size(type); buf = calloc((size_t)ssiz, sizeof(char)); if (buf == NULL) { return FAIL; } e = H5Aread(did, type, buf); if (e < 0) { free(buf); return FAIL; } } else { /* error */ return FAIL; } /* pull out each string... */ ssiz = H5Sget_simple_extent_npoints(space); tsiz = H5Tget_size(type); onestring = (char *) calloc((size_t)tsiz, sizeof(char)); bp = buf; for (i = 0; i < ssiz; i++) { strncpy(onestring, bp, tsiz); indentation(indent + COL); if (!onestring) { printf("\"%s\"\n", "NULL"); } else { char *t_onestring = xml_escape_the_string(onestring, (int)tsiz); printf("\"%s\"\n", xml_escape_the_string(onestring, (int)tsiz)); free(t_onestring); } bp += tsiz; } return SUCCEED; } /*------------------------------------------------------------------------- * Function: check_compression * * Purpose: private function to check for compression and * put a comment in the XML. (Not fully implemented.) * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void check_compression(hid_t dcpl) { int nfilt; int i; H5Z_filter_t filter; char namebuf[20]; size_t cd_nelmts = 1; unsigned int cd_values; unsigned int flags; /* not used yet: will need to do somehting more elaborate to handle future * compression methods. char *t1 = "H5Z_FILTER_DEFLATE"; */ nfilt = H5Pget_nfilters(dcpl); if (nfilt <= 0) return; for (i = 0; i < nfilt; i++) { filter = H5Pget_filter(dcpl, i, &flags, (size_t *) &cd_nelmts, &cd_values, 20, namebuf); if (filter == H5Z_FILTER_DEFLATE) { indentation(indent + COL); printf("\n"); indentation(indent + COL); printf("\n", cd_values); } } } /*------------------------------------------------------------------------- * Function: xml_dump_group * * Purpose: Dump a description of an HDF5 Group (and its members) in XML. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_dump_dataset(hid_t did, const char *name, struct subset_t * UNUSED sset) { hid_t type, space; hid_t dcpl; int maxdims; hsize_t *chsize; int ndims; int i; char *tmp; char *t_name, *t_tmp, *t_prefix; tmp = malloc(strlen(prefix) + strlen(name) + 2); strcpy(tmp, prefix); strcat(tmp, "/"); strcat(tmp, name); indentation(indent); t_name = xml_escape_the_name(name); t_tmp = xml_escape_the_name(tmp); t_prefix = xml_escape_the_name(prefix); printf("\n", t_name, t_tmp, (strcmp(prefix, "") ? t_prefix : "root")); free(t_name); free(t_tmp); free(t_prefix); dcpl = H5Dget_create_plist(did); type = H5Dget_type(did); space = H5Dget_space(did); /* Print information about chunked storage */ if (H5D_CHUNKED == H5Pget_layout(dcpl)) { maxdims = H5Sget_simple_extent_ndims(space); chsize = (hsize_t *) malloc(maxdims * sizeof(hsize_t)); indent += COL; indentation(indent); printf("\n"); indent += COL; indentation(indent); printf("\n", ndims); /* check for compression and tell about it... */ check_compression(dcpl); indent += COL; for (i = 0; i < ndims; i++) { indentation(indent); HDfprintf(stdout, "\n", chsize[i]); } indent -= COL; indentation(indent); printf("\n"); indent -= COL; indentation(indent); printf("\n"); indent -= COL; free(chsize); } /* and check for external.... */ dump_function_table->dump_dataspace_function(space); dump_function_table->dump_datatype_function(type); indent += COL; H5Aiterate(did, NULL, dump_function_table->dump_attribute_function, NULL); indent -= COL; i = (int)H5Dget_storage_size(did); if (display_data && (i > 0)) { switch (H5Tget_class(type)) { case H5T_INTEGER: case H5T_FLOAT: case H5T_STRING: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_ENUM: case H5T_ARRAY: dump_function_table->dump_data_function(did, DATASET_DATA, NULL); break; case H5T_TIME: indent += COL; indentation(indent); printf("\n"); indentation(indent); printf("\n"); indentation(indent); printf("\n"); indentation(indent); printf("\n"); indent -= COL; break; case H5T_COMPOUND: indentation(indent); printf("\n"); dump_function_table->dump_data_function(did, DATASET_DATA, NULL); break; case H5T_REFERENCE: indentation(indent); printf("\n"); indentation(indent); if (!H5Tequal(type, H5T_STD_REF_OBJ)) { printf("\n"); indentation(indent); printf("\n"); } else { printf("\n"); xml_print_refs(did, DATASET_DATA); indentation(indent); printf("\n"); } indentation(indent); printf("\n"); break; case H5T_VLEN: printf("\n"); dump_function_table->dump_data_function(did, DATASET_DATA, NULL); break; default: indentation(indent); printf("\n"); indentation(indent); printf("\n", H5Tget_class(type)); indentation(indent); printf("\n"); indentation(indent); printf("\n"); break; } } else { /* no data written */ indentation(indent); printf("\n"); indentation(indent); printf("\n"); indentation(indent); printf("\n"); } /* free(tmp); */ H5Tclose(type); H5Sclose(space); indentation(indent); printf("%s\n", dump_header_format->datasetend); } /*------------------------------------------------------------------------- * Function: xml_print_enum * * Purpose: Print the values of an HDF5 ENUM in XML. * Very similar to regular DDL output. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void xml_print_enum(hid_t type) { char **name = NULL; /*member names */ unsigned char *value = NULL; /*value array */ int nmembs; /*number of members */ 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((size_t)nmembs, sizeof(char *)); value = calloc((size_t)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, (hsize_t)nmembs, value, NULL, H5P_DEFAULT); /* Sort members by increasing value */ /*not implemented yet */ /* Print members */ indent += COL; for (i = 0; i < nmembs; i++) { char *t_name = xml_escape_the_name(name[i]); indentation(indent); printf("\n"); indentation(indent + COL); printf("%s\n", t_name); free(t_name); indentation(indent); printf("\n"); indentation(indent); printf("\n"); indentation(indent + COL); 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)) { HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "u", *((unsigned long_long *) ((void *) (value + i * dst_size)))); } else { HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "d", *((long_long *) ((void *) (value + i * dst_size)))); } printf("\n"); indentation(indent); printf("\n"); } indent -= COL; /* Release resources */ for (i = 0; i < nmembs; i++) free(name[i]); free(name); free(value); H5Tclose(super); }