/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include "h5dump.h" #include "H5private.h" #include "h5tools.h" #include "h5tools_utils.h" #include "h5tools_ref.h" #include "h5trav.h" /* Name of tool */ #define PROGRAMNAME "h5dump" /* Macros for displaying objects */ #define begin_obj(obj,name,begin) \ do { \ if (name) \ printf("%s \"%s\" %s\n", (obj), (name), (begin)); \ else \ printf("%s %s\n", (obj), (begin)); \ } while(0); #define end_obj(obj,end) \ do { \ if(HDstrlen(end)) { \ printf("%s", end); \ if(HDstrlen(obj)) \ printf(" "); \ } \ if(HDstrlen(obj)) \ printf("%s", obj); \ printf("\n"); \ } while(0); /* 3 private values: can't be set, but can be read. Note: these are defined in H5Zprivate, they are duplicated here. */ #define H5_SZIP_LSB_OPTION_MASK 8 #define H5_SZIP_MSB_OPTION_MASK 16 #define H5_SZIP_RAW_OPTION_MASK 128 /* List of table structures. There is one table structure for each file */ typedef struct h5dump_table_list_t { size_t nalloc; size_t nused; struct { unsigned long fileno; /* File number that these tables refer to */ hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ table_t *group_table; /* Table of groups */ table_t *dset_table; /* Table of datasets */ table_t *type_table; /* Table of datatypes */ } *tables; } h5dump_table_list_t; static int unamedtype = 0; /* shared datatype with no name */ static h5dump_table_list_t table_list = {0, 0, NULL}; static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL; static hbool_t hit_elink = FALSE; /* whether we have traversed an external link */ static size_t prefix_len = 1024; static char *prefix; static const char *driver = NULL; /* The driver to open the file with. */ static const h5dump_header_t *dump_header_format; static const char *fp_format = NULL; const char *outfname=NULL; /* things to display or which are set via command line parameters */ static int display_all = TRUE; static int display_oid = FALSE; static int display_data = TRUE; static int display_attr_data = TRUE; static int display_char = FALSE; /*print 1-byte numbers as ASCII */ static int usingdasho = FALSE; static int display_bb = FALSE; /*superblock */ static int display_dcpl = FALSE; /*dcpl */ static int display_fi = FALSE; /*file index */ static int display_ai = TRUE; /*array index */ static int display_escape = FALSE; /*escape non printable characters */ static int display_region = FALSE; /*print region reference data */ static int enable_error_stack= FALSE; /* re-enable error stack */ #ifdef H5_HAVE_H5DUMP_PACKED_BITS static int display_packed_bits = FALSE; /*print 1-8 byte numbers as packed bits*/ #endif /* sort parameters */ static H5_index_t sort_by = H5_INDEX_NAME; /*sort_by [creation_order | name] */ static H5_iter_order_t sort_order = H5_ITER_INC; /*sort_order [ascending | descending] */ #ifdef H5_HAVE_H5DUMP_PACKED_BITS #define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */ #define PACKED_BITS_SIZE_MAX 8*sizeof(long long) /* Maximum bits size of integer types of packed-bits */ /* mask list for packed bits */ static unsigned long long packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */ /* packed bits display parameters */ static int packed_offset[PACKED_BITS_MAX]; static int packed_length[PACKED_BITS_MAX]; #endif /** ** Added for XML ** **/ /* module-scoped variables for XML option */ #define DEFAULT_XSD "http://www.hdfgroup.org/DTDs/HDF5-File.xsd" #define DEFAULT_DTD "http://www.hdfgroup.org/DTDs/HDF5-File.dtd" static int doxml = 0; static int useschema = 1; static const char *xml_dtd_uri = NULL; static const char *xmlnsprefix="hdf5:"; static int indent; /*how far in to indent the line */ /** end XML **/ /* internal functions */ static hid_t h5_fileaccess(void); static void dump_oid(hid_t oid); #ifdef H5_HAVE_H5DUMP_PACKED_BITS static void dump_packed_bits(unsigned int packed_index, hid_t type); #endif static void print_enum(hid_t type); static int xml_name_to_XID(const char *, char *, int , int ); static void init_prefix(char **prfx, size_t prfx_len); static void add_prefix(char **prfx, size_t *prfx_len, const char *name); /* callback function used by H5Literate() */ static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void *op_data); static int dump_extlink(hid_t group, const char *linkname, const char *objname); static h5tool_format_t dataformat = { 0, /*raw */ "", /*fmt_raw */ "%d", /*fmt_int */ "%u", /*fmt_uint */ "%hhd", /*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 */ " "H5_PRINTF_HADDR_FMT, /*obj_format */ 1, /*dset_hidefileno */ "DATASET %s ", /*dset_format */ "%s", /*dset_blockformat_pre */ "%s", /*dset_ptformat_pre */ "%s", /*dset_ptformat */ 1, /*array indices */ 1 /*escape non printable characters */ }; /** ** 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 h5tool_format_t xml_dataformat = { 0, /*raw */ "", /*fmt_raw */ "%d", /*fmt_int */ "%u", /*fmt_uint */ "%hhd", /*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 */ " "H5_PRINTF_HADDR_FMT, /*obj_format */ 1, /*dset_hidefileno */ "DATASET %s ", /*dset_format */ "%s", /*dset_blockformat_pre */ "%s", /*dset_ptformat_pre */ "%s", /*dset_ptformat */ 0, /*array indices */ 0 /*escape non printable characters */ }; /** XML **/ static const h5dump_header_t standardformat = { "standardformat", /*name */ "HDF5", /*fileebgin */ "", /*fileend */ SUPER_BLOCK, /*bootblockbegin */ "", /*bootblockend */ H5_TOOLS_GROUP, /*groupbegin */ "", /*groupend */ H5_TOOLS_DATASET, /*datasetbegin */ "", /*datasetend */ ATTRIBUTE, /*attributebegin */ "", /*attributeend */ H5_TOOLS_DATATYPE, /*datatypebegin */ "", /*datatypeend */ DATASPACE, /*dataspacebegin */ "", /*dataspaceend */ DATA, /*databegin */ "", /*dataend */ SOFTLINK, /*softlinkbegin */ "", /*softlinkend */ EXTLINK, /*extlinkbegin */ "", /*extlinkend */ UDLINK, /*udlinkbegin */ "", /*udlinkend */ 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 */ "{", /*extlinkblockbegin */ "}", /*extlinkblockend */ "{", /*udlinkblockbegin */ "}", /*udlinkblockend */ "{", /*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 ** **/ /* internal functions used by XML option */ static void xml_print_datatype(hid_t, unsigned); static void xml_print_enum(hid_t); static int xml_print_refs(hid_t, int); static int xml_print_strs(hid_t, int); 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, const char *, void *, int, const char *); 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. */ /* The following initialization makes use of C language cancatenating */ /* "xxx" "yyy" into "xxxyyy". */ static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:b*F:s:S:Aq:z:m:RE" #ifdef H5_HAVE_H5DUMP_PACKED_BITS "M:" #endif ; /* end of *s_opt initialization */ static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "hel", no_arg, 'h' }, { "contents", no_arg, 'n' }, { "properties", no_arg, 'p' }, { "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' }, { "start", require_arg, 's' }, { "star", require_arg, 's' }, { "sta", require_arg, 's' }, { "stride", require_arg, 'S' }, { "strid", require_arg, 'S' }, { "string", no_arg, 'r' }, { "strin", no_arg, 'r' }, { "use-dtd", no_arg, 'u' }, { "use-dt", no_arg, 'u' }, { "use-d", no_arg, 'u' }, { "use-", no_arg, 'u' }, { "use", no_arg, 'u' }, { "us", no_arg, 'u' }, { "u", no_arg, 'u' }, { "width", require_arg, 'w' }, { "widt", require_arg, 'w' }, { "wid", require_arg, 'w' }, { "wi", require_arg, 'w' }, { "xml-dtd", require_arg, 'D' }, { "xml-dt", require_arg, 'D' }, { "xml-d", require_arg, 'D' }, { "xml-ns", require_arg, 'X' }, { "xml-n", require_arg, 'X' }, { "xml", no_arg, 'x' }, { "xm", no_arg, 'x' }, { "onlyattr", no_arg, 'A' }, { "escape", no_arg, 'e' }, { "noindex", no_arg, 'y' }, { "binary", optional_arg, 'b' }, { "form", require_arg, 'F' }, { "sort_by", require_arg, 'q' }, { "sort_order", require_arg, 'z' }, { "format", require_arg, 'm' }, { "region", no_arg, 'R' }, { "enable-error-stack", no_arg, 'E' }, #ifdef H5_HAVE_H5DUMP_PACKED_BITS { "packed-bits", require_arg, 'M' }, #endif { 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 void dump_data(hid_t, int, struct subset_t *, int); static void dump_dcpl(hid_t dcpl, hid_t type_id, hid_t obj_id); static void dump_comment(hid_t obj_id); static void dump_fcpl(hid_t fid); static void dump_fcontents(hid_t fid); /* callback function used by H5Aiterate2() */ static herr_t dump_attr_cb(hid_t loc_id, const char *attr_name, const H5A_info_t *info, void *_op_data); /* 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 *, const H5A_info_t *, void *); static void xml_dump_data(hid_t, int, struct subset_t *, int); /** ** 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 *, const H5A_info_t *, void *); void (*dump_data_function) (hid_t, int, struct subset_t *, int); } 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_cb, 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: leave * * Purpose: Shutdown MPI & HDF5 and call exit() * * Return: Does not return * * Programmer: Quincey Koziol * Saturday, 31. January 2004 * * Modifications: * *------------------------------------------------------------------------- */ static void leave(int ret) { h5tools_close(); exit(ret); } /*------------------------------------------------------------------------- * Function: usage * * Purpose: Print the usage message about dumper * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * Pedro Vicente, October 5, 2007. Add -q and -z flags *------------------------------------------------------------------------- */ 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, " -n, --contents Print a list of the file contents and exit\n"); fprintf(stdout, " -B, --superblock Print the content of the super block\n"); fprintf(stdout, " -H, --header Print the header only; no data is displayed\n"); fprintf(stdout, " -A, --onlyattr Print the header and value of attributes\n"); fprintf(stdout, " -i, --object-ids Print the object ids\n"); fprintf(stdout, " -r, --string Print 1-byte integer datasets as ASCII\n"); fprintf(stdout, " -e, --escape Escape non printing characters\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, " -y, --noindex Do not print array indices with the data\n"); fprintf(stdout, " -p, --properties Print dataset filters, storage layout and fill value\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, " -b B, --binary=B Binary file output, of form B\n"); fprintf(stdout, " -t P, --datatype=P Print the specified named datatype\n"); fprintf(stdout, " -w N, --width=N Set the number of columns of output. A value of 0 (zero)\n"); fprintf(stdout, " sets the number of columns to the maximum (65535).\n"); fprintf(stdout, " Default width is 80 columns.\n"); fprintf(stdout, " -m T, --format=T Set the floating point output format\n"); fprintf(stdout, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); fprintf(stdout, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n"); #ifdef H5_HAVE_H5DUMP_PACKED_BITS fprintf(stdout, " -M L, --packedbits=L Print packed bits as unsigned integers, using mask\n" " format L for an integer dataset specified with\n" " option -d. L is a list of offset,length values,\n" " separated by commas. Offset is the beginning bit in\n" " the data value and length is the number of bits of\n" " the mask.\n" ); #endif fprintf(stdout, " -R, --region Print dataset pointed by region references\n"); fprintf(stdout, " -x, --xml Output in XML using Schema\n"); fprintf(stdout, " -u, --use-dtd Output in XML using DTD\n"); fprintf(stdout, " -D U, --xml-dtd=U Use the DTD or schema at U\n"); fprintf(stdout, " -X S, --xml-ns=S (XML Schema) Use qualified names n the XML\n"); fprintf(stdout, " \":\": no namespace, default: \"hdf5:\"\n"); fprintf(stdout, " E.g., to dump a file called `-f', use h5dump -- -f\n"); fprintf(stdout, " --enable-error-stack Prints messages from the HDF5 error stack as they\n"); fprintf(stdout, " occur.\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, " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n"); fprintf(stdout, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n"); fprintf(stdout, " each dimension. START is optional and will default to 0 in each dimension.\n"); fprintf(stdout, "\n"); fprintf(stdout, " -s START, --start=START Offset of start of subsetting selection\n"); fprintf(stdout, " -S STRIDE, --stride=STRIDE Hyperslab stride\n"); fprintf(stdout, " -c COUNT, --count=COUNT Number of blocks to include in selection\n"); fprintf(stdout, " -k BLOCK, --block=BLOCK Size of block in hyperslab\n"); fprintf(stdout, " START, COUNT, STRIDE, and BLOCK - 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, "\n"); fprintf(stdout, " D - is the file driver to use in opening the file. Acceptable values\n"); fprintf(stdout, " are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", 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, " T - is a string containing the floating point format, e.g '%%.3f'\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, " B - is the form of binary output: NATIVE for a memory type, FILE for the\n"); fprintf(stdout, " file type, LE or BE for pre-existing little or big endian types.\n"); fprintf(stdout, " Must be used with -o (output file) and it is recommended that\n"); fprintf(stdout, " -d (dataset) is used. B is an optional argument, defaults to NATIVE\n"); fprintf(stdout, " Q - is the sort index type. It can be \"creation_order\" or \"name\" (default)\n"); fprintf(stdout, " Z - is the sort order type. It can be \"descending\" or \"ascending\" (default)\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"); fprintf(stdout, " 3) Saving dataset 'dset' in file quux.h5 to binary file 'out.bin'\n"); fprintf(stdout, " using a little-endian type\n"); fprintf(stdout, "\n"); fprintf(stdout, " h5dump -d /dset -b LE -o out.bin quux.h5\n"); #ifdef H5_HAVE_H5DUMP_PACKED_BITS fprintf(stdout, "\n"); fprintf(stdout, " 4) Display two packed bits (bits 0-1 and bits 4-6) in the dataset /dset\n"); fprintf(stdout, "\n"); fprintf(stdout, " h5dump -d /dset -M 0,1,4,3 quux.h5\n"); #endif fprintf(stdout, "\n"); } /*------------------------------------------------------------------------- * Function: table_list_add * * Purpose: Add a new set of tables * * Return: index of added table on success, -1 on failure * * Programmer: Neil Fortner, nfortne2@hdfgroup.org * Adapted from trav_addr_add in h5trav.c by Quincey Koziol * * Date: October 13, 2008 * *------------------------------------------------------------------------- */ static ssize_t table_list_add(hid_t oid, unsigned long file_no) { size_t idx; /* Index of table to use */ find_objs_t info; /* Allocate space if necessary */ if(table_list.nused == table_list.nalloc) { void *tmp_ptr; table_list.nalloc = MAX(1, table_list.nalloc * 2); if(NULL == (tmp_ptr = HDrealloc(table_list.tables, table_list.nalloc * sizeof(table_list.tables[0])))) return -1; table_list.tables = tmp_ptr; } /* end if */ /* Append it */ idx = table_list.nused++; table_list.tables[idx].fileno = file_no; table_list.tables[idx].oid = oid; if(H5Iinc_ref(oid) < 0) { table_list.nused--; return -1; } if(init_objs(oid, &info, &table_list.tables[idx].group_table, &table_list.tables[idx].dset_table, &table_list.tables[idx].type_table) < 0) { H5Idec_ref(oid); table_list.nused--; return -1; } #ifdef H5DUMP_DEBUG dump_tables(&info); #endif /* H5DUMP_DEBUG */ return((ssize_t) idx); } /* end table_list_add() */ /*------------------------------------------------------------------------- * Function: table_list_visited * * Purpose: Check if a table already exists for the specified fileno * * Return: The index of the matching table, or -1 if no matches found * * Programmer: Neil Fortner, nfortne2@hdfgroup.org * Adapted from trav_addr_visited in h5trav.c by Quincey Koziol * * Date: October 13, 2008 * *------------------------------------------------------------------------- */ static ssize_t table_list_visited(unsigned long file_no) { size_t u; /* Local index variable */ /* Look for table */ for(u = 0; u < table_list.nused; u++) /* Check for fileno value already in array */ if(table_list.tables[u].fileno == file_no) return((ssize_t) u); /* Didn't find table */ return(-1); } /* end table_list_visited() */ /*------------------------------------------------------------------------- * Function: table_list_free * * Purpose: Frees the table list * * Return: void * * Programmer: Neil Fortner, nfortne2@hdfgroup.org * * Date: October 13, 2008 * *------------------------------------------------------------------------- */ static void table_list_free(void) { size_t u; /* Local index variable */ /* Iterate over tables */ for(u = 0; u < table_list.nused; u++) { /* Release object id */ if(H5Idec_ref(table_list.tables[u].oid) < 0) h5tools_setstatus(EXIT_FAILURE); /* Free each table */ free_table(table_list.tables[u].group_table); HDfree(table_list.tables[u].group_table); free_table(table_list.tables[u].dset_table); HDfree(table_list.tables[u].dset_table); free_table(table_list.tables[u].type_table); HDfree(table_list.tables[u].type_table); } /* Free the table list */ HDfree(table_list.tables); table_list.tables = NULL; table_list.nalloc = table_list.nused = 0; } /* end table_list_free() */ /*------------------------------------------------------------------------- * Function: print_datatype * * Purpose: print the datatype. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: pvn, March 28, 2006 * print information about type when a native match is not possible * *------------------------------------------------------------------------- */ static void print_datatype(hid_t type,unsigned in_group) { char *mname; hid_t mtype, str_type; unsigned nmembers; unsigned ndims; unsigned i; size_t size=0; hsize_t dims[H5DUMP_MAX_RANK]; H5T_str_t str_pad; H5T_cset_t cset; H5T_order_t order; hid_t super; hid_t tmp_type; htri_t is_vlstr=FALSE; const char *order_s=NULL; /* byte order string */ H5T_sign_t sign; /* sign scheme value */ const char *sign_s=NULL; /* sign scheme string */ if (!in_group && H5Tcommitted(type) > 0) { H5O_info_t oinfo; obj_t *obj; /* Found object */ H5Oget_info(type, &oinfo); obj = search_obj(type_table, oinfo.addr); if(obj) { if(!obj->recorded) HDfprintf(stdout,"\"/#%a\"", obj->objno); else printf("\"%s\"", obj->objname); } else { error_msg("unknown committed type.\n"); h5tools_setstatus(EXIT_FAILURE); } } else { switch(H5Tget_class(type)) { case H5T_INTEGER: if(H5Tequal(type, H5T_STD_I8BE) == TRUE) { printf("H5T_STD_I8BE"); } else if(H5Tequal(type, H5T_STD_I8LE) == TRUE) { printf("H5T_STD_I8LE"); } else if(H5Tequal(type, H5T_STD_I16BE) == TRUE) { printf("H5T_STD_I16BE"); } else if(H5Tequal(type, H5T_STD_I16LE) == TRUE) { printf("H5T_STD_I16LE"); } else if(H5Tequal(type, H5T_STD_I32BE) == TRUE) { printf("H5T_STD_I32BE"); } else if(H5Tequal(type, H5T_STD_I32LE) == TRUE) { printf("H5T_STD_I32LE"); } else if(H5Tequal(type, H5T_STD_I64BE) == TRUE) { printf("H5T_STD_I64BE"); } else if(H5Tequal(type, H5T_STD_I64LE) == TRUE) { printf("H5T_STD_I64LE"); } else if(H5Tequal(type, H5T_STD_U8BE) == TRUE) { printf("H5T_STD_U8BE"); } else if(H5Tequal(type, H5T_STD_U8LE) == TRUE) { printf("H5T_STD_U8LE"); } else if(H5Tequal(type, H5T_STD_U16BE) == TRUE) { printf("H5T_STD_U16BE"); } else if(H5Tequal(type, H5T_STD_U16LE) == TRUE) { printf("H5T_STD_U16LE"); } else if(H5Tequal(type, H5T_STD_U32BE) == TRUE) { printf("H5T_STD_U32BE"); } else if(H5Tequal(type, H5T_STD_U32LE) == TRUE) { printf("H5T_STD_U32LE"); } else if(H5Tequal(type, H5T_STD_U64BE) == TRUE) { printf("H5T_STD_U64BE"); } else if(H5Tequal(type, H5T_STD_U64LE) == TRUE) { printf("H5T_STD_U64LE"); } else if(H5Tequal(type, H5T_NATIVE_SCHAR) == TRUE) { printf("H5T_NATIVE_SCHAR"); } else if(H5Tequal(type, H5T_NATIVE_UCHAR) == TRUE) { printf("H5T_NATIVE_UCHAR"); } else if(H5Tequal(type, H5T_NATIVE_SHORT) == TRUE) { printf("H5T_NATIVE_SHORT"); } else if(H5Tequal(type, H5T_NATIVE_USHORT) == TRUE) { printf("H5T_NATIVE_USHORT"); } else if(H5Tequal(type, H5T_NATIVE_INT) == TRUE) { printf("H5T_NATIVE_INT"); } else if(H5Tequal(type, H5T_NATIVE_UINT) == TRUE) { printf("H5T_NATIVE_UINT"); } else if(H5Tequal(type, H5T_NATIVE_LONG) == TRUE) { printf("H5T_NATIVE_LONG"); } else if(H5Tequal(type, H5T_NATIVE_ULONG) == TRUE) { printf("H5T_NATIVE_ULONG"); } else if(H5Tequal(type, H5T_NATIVE_LLONG) == TRUE) { printf("H5T_NATIVE_LLONG"); } else if(H5Tequal(type, H5T_NATIVE_ULLONG) == TRUE) { printf("H5T_NATIVE_ULLONG"); } else { /* byte order */ if(H5Tget_size(type)>1) { order = H5Tget_order(type); if (H5T_ORDER_LE == order) { order_s = " little-endian"; } else if (H5T_ORDER_BE == order) { order_s = " big-endian"; } else if (H5T_ORDER_VAX == order) { order_s = " mixed-endian"; } else { order_s = " unknown-byte-order"; } } else { order_s = ""; } /* sign */ if ((sign=H5Tget_sign(type))>=0) { if (H5T_SGN_NONE == sign) { sign_s = " unsigned"; } else if (H5T_SGN_2 == sign) { sign_s = ""; } else { sign_s = " unknown-sign"; } } else { sign_s = " unknown-sign"; } /* print size, order, and sign */ printf("%lu-bit%s%s integer", (unsigned long)(8*H5Tget_size(type)), order_s, sign_s); } break; case H5T_FLOAT: if(H5Tequal(type, H5T_IEEE_F32BE) == TRUE) { printf("H5T_IEEE_F32BE"); } else if(H5Tequal(type, H5T_IEEE_F32LE) == TRUE) { printf("H5T_IEEE_F32LE"); } else if(H5Tequal(type, H5T_IEEE_F64BE) == TRUE) { printf("H5T_IEEE_F64BE"); } else if(H5Tequal(type, H5T_IEEE_F64LE) == TRUE) { printf("H5T_IEEE_F64LE"); } else if(H5Tequal(type, H5T_VAX_F32) == TRUE) { printf("H5T_VAX_F32"); } else if(H5Tequal(type, H5T_VAX_F64) == TRUE) { printf("H5T_VAX_F64"); } else if(H5Tequal(type, H5T_NATIVE_FLOAT) == TRUE) { printf("H5T_NATIVE_FLOAT"); } else if(H5Tequal(type, H5T_NATIVE_DOUBLE) == TRUE) { printf("H5T_NATIVE_DOUBLE"); #if H5_SIZEOF_LONG_DOUBLE !=0 } else if(H5Tequal(type, H5T_NATIVE_LDOUBLE) == TRUE) { printf("H5T_NATIVE_LDOUBLE"); #endif } else { /* byte order */ if(H5Tget_size(type)>1) { order = H5Tget_order(type); if (H5T_ORDER_LE == order) { order_s = " little-endian"; } else if (H5T_ORDER_BE == order) { order_s = " big-endian"; } else if (H5T_ORDER_VAX == order) { order_s = " mixed-endian"; } else { order_s = " unknown-byte-order"; } } else { order_s = ""; } /* print size and byte order */ printf("%lu-bit%s floating-point", (unsigned long)(8*H5Tget_size(type)), order_s); } break; case H5T_TIME: printf("H5T_TIME: not yet implemented"); break; case H5T_STRING: /* Make a copy of type in memory in case when TYPE is on disk, the size * will be bigger than in memory. This makes it easier to compare * types in memory. */ tmp_type = H5Tcopy(type); size = H5Tget_size(tmp_type); str_pad = H5Tget_strpad(tmp_type); cset = H5Tget_cset(tmp_type); is_vlstr = H5Tis_variable_str(tmp_type); printf("H5T_STRING %s\n", dump_header_format->strblockbegin); indent += COL; indentation(indent + COL); if(is_vlstr) printf("%s H5T_VARIABLE;\n", STRSIZE); else 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); if(is_vlstr) H5Tset_size(str_type, H5T_VARIABLE); else H5Tset_size(str_type, size); H5Tset_cset(str_type, cset); H5Tset_strpad(str_type, str_pad); indentation(indent + COL); printf("%s ", CTYPE); /* Check C variable-length string first. Are the two types equal? */ if (H5Tequal(tmp_type, str_type)) { printf("H5T_C_S1;\n"); goto done; } /* Change the endianness and see if they're equal. */ order = H5Tget_order(tmp_type); if(order==H5T_ORDER_LE) H5Tset_order(str_type, H5T_ORDER_LE); else if(order==H5T_ORDER_BE) H5Tset_order(str_type, H5T_ORDER_BE); if (H5Tequal(tmp_type, str_type)) { printf("H5T_C_S1;\n"); goto done; } /* If not equal to C variable-length string, check Fortran type. */ 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); /* Are the two types equal? */ if (H5Tequal(tmp_type, str_type)) { printf("H5T_FORTRAN_S1;\n"); goto done; } /* Change the endianness and see if they're equal. */ order = H5Tget_order(tmp_type); if(order==H5T_ORDER_LE) H5Tset_order(str_type, H5T_ORDER_LE); else if(order==H5T_ORDER_BE) H5Tset_order(str_type, H5T_ORDER_BE); if (H5Tequal(tmp_type, str_type)) { printf("H5T_FORTRAN_S1;\n"); goto done; } /* Type doesn't match any of above. */ printf("unknown_one_character_type;\n "); h5tools_setstatus(EXIT_FAILURE); done: H5Tclose(str_type); H5Tclose(tmp_type); indent -= COL; indentation(indent + COL); printf("%s", dump_header_format->strblockend); break; case H5T_BITFIELD: if (H5Tequal(type, H5T_STD_B8BE)==TRUE) { printf("H5T_STD_B8BE"); } else if (H5Tequal(type, H5T_STD_B8LE)==TRUE) { printf("H5T_STD_B8LE"); } else if (H5Tequal(type, H5T_STD_B16BE)==TRUE) { printf("H5T_STD_B16BE"); } else if (H5Tequal(type, H5T_STD_B16LE)==TRUE) { printf("H5T_STD_B16LE"); } else if (H5Tequal(type, H5T_STD_B32BE)==TRUE) { printf("H5T_STD_B32BE"); } else if (H5Tequal(type, H5T_STD_B32LE)==TRUE) { printf("H5T_STD_B32LE"); } else if (H5Tequal(type, H5T_STD_B64BE)==TRUE) { printf("H5T_STD_B64BE"); } else if (H5Tequal(type, H5T_STD_B64LE)==TRUE) { printf("H5T_STD_B64LE"); } else { printf("undefined bitfield"); h5tools_setstatus(EXIT_FAILURE); } break; case H5T_OPAQUE: printf("\n"); indentation(indent + COL); printf("H5T_OPAQUE;\n"); indentation(indent + COL); mname = H5Tget_tag(type); printf("OPAQUE_TAG \"%s\";\n", mname); free(mname); indentation(indent); break; case H5T_COMPOUND: nmembers = H5Tget_nmembers(type); printf("H5T_COMPOUND %s\n", dump_header_format->structblockbegin); for (i = 0; i < nmembers; i++) { mname = H5Tget_member_name(type, i); mtype = H5Tget_member_type(type, i); indentation(indent + COL); if (H5Tget_class(mtype) == H5T_COMPOUND) indent += COL; print_datatype(mtype,0); if (H5Tget_class(mtype) == H5T_COMPOUND) indent -= COL; printf(" \"%s\";\n", mname); free(mname); } indentation(indent); printf("%s", dump_header_format->structblockend); break; case H5T_REFERENCE: printf("H5T_REFERENCE"); /* The BNF document states that the type of reference should be * displayed after "H5T_REFERENCE". */ if (H5Tequal(type, H5T_STD_REF_DSETREG)==TRUE) { printf(" { H5T_STD_REF_DSETREG }"); } else { printf(" { H5T_STD_REF_OBJECT }"); } 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,0); 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,0); 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_dims2(type, dims); /* Print array dimensions */ for (i = 0; i < ndims; i++) printf("[%d]", (int) dims[i]); printf(" "); /* Print base type */ print_datatype(super,0); /* Close array base type */ H5Tclose(super); /* Print closing */ printf(" }"); break; default: printf("unknown datatype"); h5tools_setstatus(EXIT_FAILURE); break; } } /* end else */ } /*------------------------------------------------------------------------- * Function: dump_datatype * * Purpose: Dump the datatype. Datatype can be HDF5 predefined * atomic datatype or committed/transient datatype. * * 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,0); end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); indent -= COL; } /*------------------------------------------------------------------------- * Function: dump_dataspace * * Purpose: Dump the dataspace. Dataspace can be named dataspace, * 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); H5S_class_t space_type = H5Sget_simple_extent_type(space); int i; indentation(indent + COL); printf("%s ", dump_header_format->dataspacebegin); switch(space_type) { case H5S_SCALAR: /* scalar dataspace */ HDfprintf(stdout, "%s %s", dump_header_format->dataspacedescriptionbegin, S_SCALAR); break; case H5S_SIMPLE: /* simple dataspace */ HDfprintf(stdout, "%s %s { %s %Hu", dump_header_format->dataspacedescriptionbegin, S_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); break; case H5S_NULL: /* null dataspace */ HDfprintf(stdout, "%s %s", dump_header_format->dataspacedescriptionbegin, S_NULL); break; case H5S_NO_CLASS: default: printf("%s unknown dataspace %s\n", BEGIN, END); break; } /* end switch */ end_obj(dump_header_format->dataspaceend, dump_header_format->dataspaceblockend); } /*------------------------------------------------------------------------- * Function: dump_attr_cb * * Purpose: attribute function callback called by H5Aiterate2, displays the attribute * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: Pedro Vicente, October 4, 2007 * Added H5A_info_t parameter to conform with H5Aiterate2 * *------------------------------------------------------------------------- */ static herr_t dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t UNUSED *info, void UNUSED *_op_data) { hid_t attr_id; herr_t ret = SUCCEED; indentation(indent); begin_obj(dump_header_format->attributebegin, attr_name, dump_header_format->attributeblockbegin); if((attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT)) < 0) { indentation(indent + COL); error_msg("unable to open attribute \"%s\"\n", attr_name); indentation(indent); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { hid_t type, space; 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 || display_attr_data) dump_data(attr_id, ATTRIBUTE_DATA, NULL, display_ai); 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) { hid_t oid = -1; hid_t attr_id = -1; char *obj_name; const char *attr_name; int j; j = (int)HDstrlen(name) - 1; obj_name = (char *)HDmalloc((size_t)j + 2); if(obj_name == NULL) goto error; /* find the last / */ while(j >= 0) { if (name[j] == '/') break; j--; } /* object name */ if(j == -1) HDstrcpy(obj_name, "/"); else { HDstrncpy(obj_name, name, (size_t)j + 1); obj_name[j + 1] = '\0'; } /* end else */ attr_name = name + j + 1; begin_obj(dump_header_format->attributebegin, name, dump_header_format->attributeblockbegin); /* Open the object with the attribute */ if((oid = H5Oopen(loc_id, obj_name, H5P_DEFAULT)) < 0) { indentation(COL); error_msg("unable to open object \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); goto error; } /* end if */ if((attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT)) >= 0) { hid_t type, space; 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 || display_attr_data) dump_data(attr_id, ATTRIBUTE_DATA, NULL, display_ai); H5Tclose(type); H5Sclose(space); H5Aclose(attr_id); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); } else { indentation(COL); error_msg("unable to open attribute \"%s\"\n", obj_name); end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend); goto error; } /* Close object */ if(H5Oclose(oid) < 0) { goto error; } /* end if */ HDfree(obj_name); return SUCCEED; error: h5tools_setstatus(EXIT_FAILURE); if(obj_name) HDfree(obj_name); H5E_BEGIN_TRY { H5Oclose(oid); H5Aclose(attr_id); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * Function: dump_all_cb * * Purpose: function callback called by H5Literate, * displays 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 * * PVN, May 2008 * Dump external links * *------------------------------------------------------------------------- */ static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED *op_data) { hid_t obj; char *obj_path = NULL; /* Full path of object */ herr_t ret = SUCCEED; /* Build the object's path name */ obj_path = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); if(!obj_path) { ret = FAIL; goto done; } HDstrcpy(obj_path, prefix); HDstrcat(obj_path, "/"); HDstrcat(obj_path, name); if(linfo->type == H5L_TYPE_HARD) { H5O_info_t oinfo; /* Stat the object */ if(H5Oget_info_by_name(group, name, &oinfo, H5P_DEFAULT) < 0) { error_msg("unable to get object information for \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; goto done; } /* end if */ switch(oinfo.type) { case H5O_TYPE_GROUP: if((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) { error_msg("unable to dump group \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { char *old_prefix; /* Pointer to previous prefix */ /* Keep copy of prefix before iterating into group */ old_prefix = HDstrdup(prefix); HDassert(old_prefix); /* Append group name to prefix */ add_prefix(&prefix, &prefix_len, name); /* Iterate into group */ dump_function_table->dump_group_function(obj, name); /* Restore old prefix name */ HDstrcpy(prefix, old_prefix); HDfree(old_prefix); /* Close group */ H5Gclose(obj); } break; case H5O_TYPE_DATASET: if((obj = H5Dopen2(group, name, H5P_DEFAULT)) >= 0) { if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(dset_table, oinfo.addr); if(found_obj == NULL) { indentation(indent); begin_obj(dump_header_format->datasetbegin, name, dump_header_format->datasetblockbegin); indentation(indent + COL); error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; H5Dclose(obj); goto done; } else if(found_obj->displayed) { indentation(indent); if(!doxml) { begin_obj(dump_header_format->datasetbegin, name, dump_header_format->datasetblockbegin); indentation(indent + COL); printf("%s \"%s\"\n", HARDLINK, found_obj->objname); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); } else { /* the XML version */ char *t_obj_path = xml_escape_the_name(obj_path); char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); char *t_name = xml_escape_the_name(name); char *t_objname = xml_escape_the_name(found_obj->objname); char dsetxid[100]; char parentxid[100]; char pointerxid[100]; /* Create OBJ-XIDs for the parent and object */ xml_name_to_XID(obj_path, dsetxid, sizeof(dsetxid), 1); xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1); printf("<%sDataset Name=\"%s\" OBJ-XID=\"%s-%d\" " "H5Path=\"%s\" Parents=\"%s\" " "H5ParentPaths=\"%s\">\n", xmlnsprefix, t_name, /* Dataset Name */ dsetxid, get_next_xid(), /* OBJ-XID */ t_obj_path, /* H5Path */ parentxid, /* Parents */ t_prefix); /* H5ParentPaths */ indentation(indent + COL); xml_name_to_XID(found_obj->objname, pointerxid, sizeof(pointerxid), 1); printf("<%sDatasetPtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n", xmlnsprefix, pointerxid,t_objname); indentation(indent); printf("\n", xmlnsprefix); HDfree(t_name); HDfree(t_obj_path); HDfree(t_prefix); HDfree(t_objname); } H5Dclose(obj); goto done; } else { found_obj->displayed = TRUE; } } /* end if */ dump_function_table->dump_dataset_function(obj, name, NULL); H5Dclose(obj); } else { error_msg("unable to dump dataset \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } break; case H5O_TYPE_NAMED_DATATYPE: if((obj = H5Topen2(group, name, H5P_DEFAULT)) < 0) { error_msg("unable to dump datatype \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { dump_function_table->dump_named_datatype_function(obj, name); H5Tclose(obj); } break; default: error_msg("unknown object \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } } /* end if */ else { char *targbuf; switch(linfo->type) { case H5L_TYPE_SOFT: indentation(indent); targbuf = (char *)HDmalloc(linfo->u.val_size); HDassert(targbuf); if(!doxml) { begin_obj(dump_header_format->softlinkbegin, name, dump_header_format->softlinkblockbegin); indentation(indent + COL); } if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { error_msg("unable to get link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { /* print the value of a soft link */ if (!doxml) { /* Standard DDL: no modification */ printf("LINKTARGET \"%s\"\n", targbuf); } else { /* XML */ char linkxid[100]; char parentxid[100]; char targetxid[100]; char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); char *t_name = xml_escape_the_name(name); char *t_targbuf = xml_escape_the_name(targbuf); char *t_obj_path = xml_escape_the_name(obj_path); char *t_link_path; int res; t_link_path = (char *)HDmalloc(HDstrlen(prefix) + linfo->u.val_size + 1); if(targbuf[0] == '/') HDstrcpy(t_link_path, targbuf); else { HDstrcpy(t_link_path, prefix); HDstrcat(HDstrcat(t_link_path, "/"), targbuf); } /* end else */ /* Create OBJ-XIDs for the parent and object */ xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1); xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1); /* Try to create an OBJ-XID for the object pointed to */ res = xml_name_to_XID(t_link_path, targetxid, sizeof(targetxid), 0); if (res == 0) { /* target obj found */ printf("<%sSoftLink LinkName=\"%s\" " "OBJ-XID=\"%s\" " "H5SourcePath=\"%s\" " "TargetPath=\"%s\" TargetObj=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" />\n", xmlnsprefix, t_name, /* LinkName */ linkxid, /* OBJ-XID */ t_obj_path, /* H5SourcePath */ t_targbuf, /* TargetPath */ targetxid, /* TargetObj */ parentxid, /* Parents */ t_prefix); /* H5ParentPaths */ } else { /* dangling link -- omit from xml attributes */ printf("<%sSoftLink LinkName=\"%s\" " "OBJ-XID=\"%s\" " "H5SourcePath=\"%s\" " "TargetPath=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" />\n", xmlnsprefix, t_name, /* LinkName */ linkxid, /* OBJ-XID */ t_obj_path, /* H5SourcePath */ t_targbuf, /* TargetPath */ parentxid, /* Parents */ t_prefix); /* H5ParentPaths */ } HDfree(t_prefix); HDfree(t_name); HDfree(t_targbuf); HDfree(t_obj_path); HDfree(t_link_path); } } if (!doxml) { indentation(indent); end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); } HDfree(targbuf); break; case H5L_TYPE_EXTERNAL: targbuf = (char *)HDmalloc(linfo->u.val_size); HDassert(targbuf); indentation(indent); if(!doxml) begin_obj(dump_header_format->extlinkbegin, name, dump_header_format->extlinkblockbegin); if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { error_msg("unable to get external link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } /* end if */ else { const char *filename; const char *targname; if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) { error_msg("unable to unpack external link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } /* end if */ else { if(!doxml) { indentation(indent + COL); printf("TARGETFILE \"%s\"\n", filename); indentation(indent + COL); printf("TARGETPATH \"%s\"\n", targname); /* dump the external link */ dump_extlink(group, name, targname); } /* end if */ /* XML */ else { char linkxid[100]; char parentxid[100]; char *t_name = xml_escape_the_name(name); char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); char *t_obj_path = xml_escape_the_name(obj_path); char *t_filename = xml_escape_the_name(filename); char *t_targname = xml_escape_the_name(targname); /* Create OBJ-XIDs for the parent and object */ xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1); xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1); printf("<%sExternalLink LinkName=\"%s\" " "OBJ-XID=\"%s\" " "H5SourcePath=\"%s\" " "TargetFilename=\"%s\" " "TargetPath=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" />\n", xmlnsprefix, t_name, /* LinkName */ linkxid, /* OBJ-XID */ t_obj_path, /* H5SourcePath */ filename, /* TargetFilename */ targname, /* TargetPath*/ parentxid, /* Parents */ t_prefix); /* H5ParentPaths */ HDfree(t_prefix); HDfree(t_name); HDfree(t_filename); HDfree(t_targname); HDfree(t_obj_path); } /* end else */ } /* end else */ } /* end else */ if(!doxml) { indentation(indent); end_obj(dump_header_format->extlinkend, dump_header_format->extlinkblockend); } /* end if */ HDfree(targbuf); break; default: indentation(indent); if(!doxml) { begin_obj(dump_header_format->udlinkbegin, name, dump_header_format->udlinkblockbegin); indentation(indent + COL); printf("LINKCLASS %d\n", linfo->type); indentation(indent); end_obj(dump_header_format->udlinkend, dump_header_format->udlinkblockend); } /* end if */ /* XML */ else { char linkxid[100]; char parentxid[100]; char *t_name = xml_escape_the_name(name); char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/"); char *t_obj_path = xml_escape_the_name(obj_path); /* Create OBJ-XIDs for the parent and object */ xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1); xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1); printf("<%sUserDefined LinkName=\"%s\" " "OBJ-XID=\"%s\" " "H5SourcePath=\"%s\" " "LinkClass=\"%d\" " "Parents=\"%s\" H5ParentPaths=\"%s\" />\n", xmlnsprefix, t_name, /* LinkName */ linkxid, /* OBJ-XID */ t_obj_path, /* H5SourcePath */ linfo->type, /* LinkClass */ parentxid, /* Parents */ t_prefix); /* H5ParentPaths */ HDfree(t_prefix); HDfree(t_name); HDfree(t_obj_path); } /* end else */ break; } /* end switch */ } /* end else */ done: if(obj_path) HDfree(obj_path); return ret; } /*------------------------------------------------------------------------- * Function: dump_named_datatype * * Purpose: Dump named datatype * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * Pedro Vicente, March 27, 2006 * added display of attributes * Pedro Vicente, October 4, 2007, added parameters to H5Aiterate2() to allow for * other iteration orders * *------------------------------------------------------------------------- */ static void dump_named_datatype(hid_t tid, const char *name) { H5O_info_t oinfo; unsigned attr_crt_order_flags; hid_t tcpl_id; /* datatype creation property list ID */ if ((tcpl_id = H5Tget_create_plist(tid)) < 0) { error_msg("error in getting creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the creation properties for attributes */ if (H5Pget_attr_creation_order(tcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } if(H5Pclose(tcpl_id) < 0) { error_msg("error in closing creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } indentation(indent); printf("%s \"%s\" %s", dump_header_format->datatypebegin, name, dump_header_format->datatypeblockbegin); H5Oget_info(tid, &oinfo); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. */ if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(type_table, oinfo.addr); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } else if (found_obj->displayed) { printf("%s \"%s\"\n", HARDLINK, found_obj->objname); goto done; } else found_obj->displayed = TRUE; } /* end if */ print_datatype(tid, 1); if(H5Tget_class(tid) != H5T_COMPOUND) printf(";\n"); /* print attributes */ indent += COL; /* attribute iteration: if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the datatype's create property list for attributes, then, sort by creation order, otherwise by name */ if( (sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(tid, sort_by, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(tid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ indent -= COL; done: 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_cb -- add parameter to select everything. * * Pedro Vicente, October 1, 2007 * handle several iteration orders for attributes and groups * *------------------------------------------------------------------------- */ static void dump_group(hid_t gid, const char *name) { H5O_info_t oinfo; hid_t dset, type; char type_name[1024], *tmp; unsigned crt_order_flags; unsigned attr_crt_order_flags; hid_t gcpl_id; if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties for attributes */ if (H5Pget_attr_creation_order(gcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties */ if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } if(H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); HDstrcpy(tmp, prefix); indentation(indent); begin_obj(dump_header_format->groupbegin, name, dump_header_format->groupblockbegin); indent += COL; if(display_oid) dump_oid(gid); dump_comment(gid); if(!HDstrcmp(name, "/") && unamedtype) { unsigned u; /* Local index variable */ /* dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) if(!type_table->objs[u].recorded) { dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } /* end if */ H5Oget_info(gid, &oinfo); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. */ if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(group_table, oinfo.addr); if (found_obj == NULL) { indentation(indent); error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); } else if (found_obj->displayed) { indentation(indent); printf("%s \"%s\"\n", HARDLINK, found_obj->objname); } else { found_obj->displayed = TRUE; /* attribute iteration: if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group for attributes, then, sort by creation order, otherwise by name */ if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ /* if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group, then, sort by creation order, otherwise by name */ if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } } else { /* attribute iteration: if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group for attributes, then, sort by creation order, otherwise by name */ if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ /* if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group, then, sort by creation order, otherwise by name */ if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } indent -= COL; indentation(indent); end_obj(dump_header_format->groupend, dump_header_format->groupblockend); free(tmp); } /*------------------------------------------------------------------------- * Function: dump_dataset * * Purpose: Dump the specified data set * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * Pedro Vicente, 2004, added dataset creation property list display * Pedro Vicente, October 4, 2007, added parameters to H5Aiterate2() to allow for * other iteration orders * *------------------------------------------------------------------------- */ static void dump_dataset(hid_t did, const char *name, struct subset_t *sset) { hid_t type, space; unsigned attr_crt_order_flags; hid_t dcpl_id; /* dataset creation property list ID */ if ((dcpl_id = H5Dget_create_plist(did)) < 0) { error_msg("error in getting creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the creation properties for attributes */ if (H5Pget_attr_creation_order(dcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } indentation(indent); begin_obj(dump_header_format->datasetbegin, name, dump_header_format->datasetblockbegin); type = H5Dget_type(did); space = H5Dget_space(did); dump_comment(did); dump_datatype(type); dump_dataspace(space); if(display_oid) dump_oid(did); if(display_dcpl) dump_dcpl(dcpl_id, type, did); if(display_data) { #ifdef H5_HAVE_H5DUMP_PACKED_BITS int data_loop = 1; int i; if(display_packed_bits) data_loop = packed_bits_num; for(i=0;idatasetend,dump_header_format->datasetblockend); } /*------------------------------------------------------------------------- * 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) { int i; for (i = 0; i < dims; i++) { printf(HSIZE_T_FORMAT, 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(sset->start.data, 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.data, 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.data) dump_dims(sset->count.data, 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.data) dump_dims(sset->block.data, 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: pvn, print the matrix indices * Albert Cheng, 2004/11/18 * Add --string printing for attributes too. * *------------------------------------------------------------------------- */ static void dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index) { h5tool_format_t *outputformat = &dataformat; int status = -1; void *buf = NULL; hid_t space, type, p_type; H5S_class_t space_type; int ndims, i; hsize_t size[64], nelmts = 1, alloc_size; int depth; int stdindent = COL; /* should be 3 */ if (fp_format) { outputformat->fmt_double = fp_format; outputformat->fmt_float = fp_format; } if (nCols==0) { outputformat->line_ncols = 65535; outputformat->line_per_line = 1; } else outputformat->line_ncols = nCols; outputformat->do_escape=display_escape; /* print the matrix indices */ outputformat->pindex=display_index; /* do not print indices for regions */ if(obj_data == DATASET_DATA) { hid_t f_type = H5Dget_type(obj_id); if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) { /* For the region option, correct the display of indices */ if (display_region) { if (display_index) { outputformat->pindex = 1; outputformat->idx_fmt = "(%s): "; outputformat->idx_n_fmt = HSIZE_T_FORMAT; outputformat->idx_sep = ","; outputformat->line_pre = "%s"; } else { outputformat->pindex = 0; outputformat->idx_fmt = ""; outputformat->idx_n_fmt = ""; outputformat->idx_sep = ""; outputformat->line_pre = ""; } } else outputformat->pindex = 0; } H5Tclose(f_type); } if (outputformat->pindex) { outputformat->idx_fmt = "(%s): "; outputformat->idx_n_fmt = HSIZE_T_FORMAT; outputformat->idx_sep = ","; outputformat->line_pre = "%s"; } 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) { hid_t f_type = H5Dget_type(obj_id); char string_prefix[64]; h5tool_format_t string_dataformat; if(display_char && H5Tget_size(f_type) == 1 && H5Tget_class(f_type) == H5T_INTEGER) { /* * Print 1-byte integer data as an ASCII character string * instead of integers if the `-r' or `--string' command-line * option was given. * * We don't want to modify the global dataformat, so make a * copy of it instead. */ string_dataformat = *outputformat; string_dataformat.idx_fmt = " "; string_dataformat.line_multi_new = 1; string_dataformat.line_1st = " %s\""; string_dataformat.line_pre = " %s"; string_dataformat.line_cont = " %s"; string_dataformat.str_repeat = 8; string_dataformat.ascii = TRUE; string_dataformat.elmt_suf1 = ""; string_dataformat.elmt_suf2 = ""; string_dataformat.line_indent = ""; strcpy(string_prefix, string_dataformat.line_pre); strcat(string_prefix, "\""); string_dataformat.line_pre = string_prefix; string_dataformat.line_suf = "\""; outputformat = &string_dataformat; } status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, sset, depth); H5Tclose(f_type); } else { /* need to call h5tools_dump_mem for the attribute data */ space = H5Aget_space(obj_id); space_type = H5Sget_simple_extent_type(space); if(space_type == H5S_NULL || space_type == H5S_NO_CLASS) { status = SUCCEED; } else { char string_prefix[64]; h5tool_format_t string_dataformat; /* VL data special information */ unsigned int vl_data = 0; /* contains VL datatypes */ type = H5Aget_type(obj_id); p_type = h5tools_get_native_type(type); ndims = H5Sget_simple_extent_dims(space, size, NULL); /* Check if we have VL data in the dataset's datatype */ if (h5tools_detect_vlen(p_type) == TRUE) vl_data = TRUE; 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*/ if(alloc_size) { buf = malloc((size_t)alloc_size); assert(buf); if (H5Aread(obj_id, p_type, buf) >= 0) if (display_char && H5Tget_size(type) == 1 && H5Tget_class(type) == H5T_INTEGER) { /* * Print 1-byte integer data as an ASCII character string * instead of integers if the `-r' or `--string' command-line * option was given. * * We don't want to modify the global dataformat, so make a * copy of it instead. */ string_dataformat = *outputformat; string_dataformat.idx_fmt = " "; string_dataformat.line_multi_new = 1; string_dataformat.line_1st = " %s\""; string_dataformat.line_pre = " %s"; string_dataformat.line_cont = " %s"; string_dataformat.str_repeat = 8; string_dataformat.ascii = TRUE; string_dataformat.elmt_suf1 = ""; string_dataformat.elmt_suf2 = ""; string_dataformat.line_indent = ""; strcpy(string_prefix, string_dataformat.line_pre); strcat(string_prefix, "\""); string_dataformat.line_pre = string_prefix; string_dataformat.line_suf = "\""; outputformat = &string_dataformat; } status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type, space, buf, depth); /* Reclaim any VL memory, if necessary */ if (vl_data) H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); free(buf); } else status = SUCCEED; H5Tclose(p_type); H5Tclose(type); } H5Sclose(space); } if (status == FAIL) { indentation(indent + COL); error_msg("unable to print data\n"); h5tools_setstatus(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); } #ifdef H5_HAVE_H5DUMP_PACKED_BITS /*------------------------------------------------------------------------- * Function: dump_packed_bits * * Purpose: Prints the packed bits offset and length * * Return: void * *------------------------------------------------------------------------- */ static void dump_packed_bits(unsigned int packed_index, hid_t type) { int packed_bits_size = 0; hid_t n_type = h5tools_get_native_type(type); if(H5Tget_class(n_type)==H5T_INTEGER) { if(H5Tequal(n_type, H5T_NATIVE_SCHAR) == TRUE) { packed_bits_size = 8 * sizeof(char); } else if(H5Tequal(n_type, H5T_NATIVE_UCHAR) == TRUE) { packed_bits_size = 8 * sizeof(unsigned char); } else if(H5Tequal(n_type, H5T_NATIVE_SHORT) == TRUE) { packed_bits_size = 8 * sizeof(short); } else if(H5Tequal(n_type, H5T_NATIVE_USHORT) == TRUE) { packed_bits_size = 8 * sizeof(unsigned short); } else if(H5Tequal(n_type, H5T_NATIVE_INT) == TRUE) { packed_bits_size = 8 * sizeof(int); } else if(H5Tequal(n_type, H5T_NATIVE_UINT) == TRUE) { packed_bits_size = 8 * sizeof(unsigned int); } else if(H5Tequal(n_type, H5T_NATIVE_LONG) == TRUE) { packed_bits_size = 8 * sizeof(long); } else if(H5Tequal(n_type, H5T_NATIVE_ULONG) == TRUE) { packed_bits_size = 8 * sizeof(unsigned long); } else if(H5Tequal(n_type, H5T_NATIVE_LLONG) == TRUE) { packed_bits_size = 8 * sizeof(long long); } else if(H5Tequal(n_type, H5T_NATIVE_ULLONG) == TRUE) { packed_bits_size = 8 * sizeof(unsigned long long); } else error_msg("Packed Bit not valid for this datatype"); } indentation(indent + COL); if ((packed_bits_size>0) && (packed_offset[packed_index] + packed_length[packed_index]) > packed_bits_size) { error_msg("Packed Bit offset+length value(%d) too large. Max is %d\n", packed_offset[packed_index]+packed_length[packed_index], packed_bits_size); packed_mask[packed_index] = 0; }; printf("%s %s=%d %s=%d\n", PACKED_BITS, PACKED_OFFSET, packed_offset[packed_index], PACKED_LENGTH, packed_length[packed_index]); } #endif /*------------------------------------------------------------------------- * Function: dump_comment * * Purpose: prints the comment for the the object name * * Return: void * * Programmer: pvn * * Modifications: * *------------------------------------------------------------------------- */ static void dump_comment(hid_t obj_id) { size_t buf_size = 0; char* comment = NULL; ssize_t cmt_bufsize = -1; cmt_bufsize = H5Oget_comment(obj_id, comment, buf_size); /* call H5Oget_comment again with the correct value. * If the call to H5Oget_comment returned an error, skip this block */ if (cmt_bufsize > 0) { comment = (char *)HDmalloc((size_t)(cmt_bufsize+1)); /* new_size including null terminator */ if(comment) { cmt_bufsize = H5Oget_comment(obj_id, comment, cmt_bufsize); if(cmt_bufsize > 0) { comment[cmt_bufsize] = '\0'; /* necessary because null char is not returned */ indentation(indent); printf("COMMENT \"%s\"\n", comment); } /* end if */ HDfree(comment); } } } /* end dump_comment() */ /*------------------------------------------------------------------------- * Function: dump_fill_value * * Purpose: prints the fill value * * Return: void * * Programmer: pvn * * Modifications: * *------------------------------------------------------------------------- */ static void dump_fill_value(hid_t dcpl,hid_t type_id, hid_t obj_id) { h5tools_context_t ctx; /*print context */ size_t size; void *buf=NULL; hsize_t nelmts=1; h5tool_format_t *outputformat = &dataformat; hid_t n_type; memset(&ctx, 0, sizeof(ctx)); ctx.indent_level=2; n_type = h5tools_get_native_type(type_id); size = H5Tget_size(n_type); buf = malloc(size); H5Pget_fill_value(dcpl, n_type, buf); h5tools_dump_simple_data(stdout, outputformat, obj_id, &ctx, START_OF_DATA | END_OF_DATA, nelmts, n_type, buf); H5Tclose(n_type); if (buf) free (buf); } /*------------------------------------------------------------------------- * Function: dump_dcpl * * Purpose: prints several dataset create property list properties * * Return: void * * Programmer: pvn * * Modifications: pvn, March 28, 2008 * Add a COMPRESSION ratio information for cases when filters are present * *------------------------------------------------------------------------- */ static void dump_dcpl(hid_t dcpl_id,hid_t type_id, hid_t obj_id) { int nfilters; /* number of filters */ unsigned filt_flags; /* filter flags */ H5Z_filter_t filtn; /* filter identification number */ unsigned cd_values[20]; /* filter client data values */ size_t cd_nelmts; /* filter client number of values */ char f_name[256]; /* filter name */ unsigned szip_options_mask; unsigned szip_pixels_per_block; hsize_t chsize[64]; /* chunk size in elements */ int rank; /* rank */ char name[256]; /* external file name */ off_t offset; /* offset of external file */ hsize_t size; /* size of external file */ H5D_fill_value_t fvstatus; H5D_alloc_time_t at; H5D_fill_time_t ft; hsize_t storage_size; haddr_t ioffset; int i; unsigned j; storage_size = H5Dget_storage_size(obj_id); nfilters = H5Pget_nfilters(dcpl_id); ioffset = H5Dget_offset(obj_id); HDstrcpy(f_name,"\0"); /*------------------------------------------------------------------------- * STORAGE_LAYOUT *------------------------------------------------------------------------- */ indentation(indent + COL); printf("%s %s\n", STORAGE_LAYOUT, BEGIN); if (H5D_CHUNKED == H5Pget_layout(dcpl_id)) { /*start indent */ indent += COL; indentation(indent + COL); printf("%s ", CHUNKED); rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize); HDfprintf(stdout,"%s %Hu", dump_header_format->dataspacedimbegin, chsize[0]); for ( i=1; idataspacedimend); indentation(indent + COL); /* if there are filters, print a compression ratio */ if ( nfilters ) { hid_t sid = H5Dget_space( obj_id ); hid_t tid = H5Dget_type( obj_id ); size_t datum_size = H5Tget_size( tid ); hsize_t dims[H5S_MAX_RANK]; int ndims = H5Sget_simple_extent_dims( sid, dims, NULL); hsize_t nelmts = 1; double ratio = 0; int ok = 0; /* only print the compression ratio for these filters */ for ( i = 0; i < nfilters; i++) { cd_nelmts = NELMTS(cd_values); filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, sizeof(f_name), f_name, NULL); switch (filtn) { case H5Z_FILTER_DEFLATE: case H5Z_FILTER_SZIP: case H5Z_FILTER_NBIT: case H5Z_FILTER_SCALEOFFSET: ok = 1; break; } } if (ndims && ok ) { hsize_t uncomp_size; for (i = 0; i < ndims; i++) { nelmts *= dims[i]; } uncomp_size = nelmts * datum_size; /* compression ratio = uncompressed size / compressed size */ if (storage_size != 0) ratio = (double) uncomp_size / (double) storage_size; HDfprintf(stdout, "SIZE %Hu (%.3f:1 COMPRESSION)\n ", storage_size, ratio); } else HDfprintf(stdout, "SIZE %Hu\n ", storage_size); H5Sclose(sid); H5Tclose(tid); } else { HDfprintf(stdout, "SIZE %Hu\n ", storage_size); } /*end indent */ indent -= COL; indentation(indent + COL); printf("%s\n",END); } else if (H5D_COMPACT == H5Pget_layout(dcpl_id)) { /*start indent */ indent += COL; indentation(indent + COL); printf("%s\n", COMPACT); indentation(indent + COL); HDfprintf(stdout, "SIZE %Hu\n", storage_size); /*end indent */ indent -= COL; indentation(indent + COL); printf("%s\n",END); } else if (H5D_CONTIGUOUS == H5Pget_layout(dcpl_id)) { int next; next = H5Pget_external_count(dcpl_id); /*------------------------------------------------------------------------- * EXTERNAL_FILE *------------------------------------------------------------------------- */ if (next) { /*start indent */ indent += COL; indentation(indent + COL); printf("%s\n", CONTIGUOUS); indentation(indent + COL); printf("%s %s\n", EXTERNAL, BEGIN); /*start indent */ indent += COL; for ( j=0; j<(unsigned)next; j++) { H5Pget_external(dcpl_id,j,sizeof(name),name,&offset,&size); indentation(indent + COL); HDfprintf(stdout,"FILENAME %s SIZE %Hu OFFSET %ld\n",name,size,offset); } /*end indent */ indent -= COL; indentation(indent + COL); printf("%s\n",END); /*end indent */ indent -= COL; indentation(indent + COL); printf("%s\n",END); } else { /*start indent */ indent += COL; indentation(indent + COL); printf("%s\n", CONTIGUOUS); indentation(indent + COL); HDfprintf(stdout,"SIZE %Hu\n", storage_size); indentation(indent + COL); HDfprintf(stdout,"OFFSET %Hu\n", ioffset); /*end indent */ indent -= COL; indentation(indent + COL); printf("%s\n",END); } } /*------------------------------------------------------------------------- * FILTERS *------------------------------------------------------------------------- */ indentation(indent + COL); printf("%s %s\n", FILTERS, BEGIN); indent += COL; if (nfilters) { for (i=0; inobjs; u++) { if (!type_table->objs[u].recorded) printf(" %-10s /#"H5_PRINTF_HADDR_FMT"\n", "datatype", type_table->objs[u].objno); } } /* print objects in the files */ h5trav_print(fid); printf(" %s\n",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: * pvn June, 1, 2006. Add a switch for binary output * *------------------------------------------------------------------------- */ static int set_output_file(const char *fname, int is_bin) { FILE *f; /* temporary holding place for the stream pointer * so that rawdatastream is changed only when succeeded */ if (rawdatastream && rawdatastream != stdout) { if (fclose(rawdatastream)) perror("closing rawdatastream"); else rawdatastream = NULL; } /* binary output */ if (is_bin) { if ((f = fopen(fname, "wb")) != NULL) { rawdatastream = f; return 0; } } else { if ((f = fopen(fname, "w")) != NULL) { rawdatastream = f; return 0; } } return -1; } /*------------------------------------------------------------------------- * Function: set_binary_form * * Purpose: set the binary form of output by translating from a string input * parameter to a integer return value * * Return: integer form of binary output or -1 if none found * * Programmer: Pedro Vicente Nunes * June 28, 2006 * * Modifications: * *------------------------------------------------------------------------- */ static int set_binary_form(const char *form) { int bform=-1; if (strcmp(form,"NATIVE")==0 || strcmp(form,"MEMORY")==0) {/* native form */ bform = 0; } else if (strcmp(form,"FILE")==0) /* file type form */ bform = 1; else if (strcmp(form,"LE")==0) /* convert to little endian */ bform = 2; else if (strcmp(form,"BE")==0) /* convert to big endian */ bform = 3; return bform; } /*------------------------------------------------------------------------- * Function: set_sort_by * * Purpose: set the "by" form of sorting by translating from a string input * parameter to a H5_index_t return value * current sort values are [creation_order | name] * * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found * * Programmer: Pedro Vicente Nunes * October 1, 2007 * * Modifications: * *------------------------------------------------------------------------- */ static H5_index_t set_sort_by(const char *form) { H5_index_t idx_type = H5_INDEX_UNKNOWN; if (strcmp(form,"name")==0) /* H5_INDEX_NAME */ idx_type = H5_INDEX_NAME; else if (strcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */ idx_type = H5_INDEX_CRT_ORDER; return idx_type; } /*------------------------------------------------------------------------- * Function: set_sort_order * * Purpose: set the order of sorting by translating from a string input * parameter to a H5_iter_order_t return value * current order values are [ascending | descending ] * * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found * * Programmer: Pedro Vicente Nunes * October 1, 2007 * * Modifications: * *------------------------------------------------------------------------- */ static H5_iter_order_t set_sort_order(const char *form) { H5_iter_order_t iter_order = H5_ITER_UNKNOWN; if (strcmp(form,"ascending")==0) /* H5_ITER_INC */ iter_order = H5_ITER_INC; else if (strcmp(form,"descending")==0) /* H5_ITER_DEC */ iter_order = H5_ITER_DEC; return iter_order; } /*------------------------------------------------------------------------- * Function: handle_attributes * * Purpose: Handle the attributes from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * * PVN, May 2008 * add an extra parameter PE, to allow printing/not printing of error messages * *------------------------------------------------------------------------- */ static void handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { 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: * * Programmer: Bill Wendling * Tuesday, 6. February 2001 * *------------------------------------------------------------------------- */ static void parse_hsize_list(const char *h_list, subset_d *d) { 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; /* 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; /* allocate an array for the integers in the list */ p_list = (hsize_t *)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)atof(ptr); while (isdigit(*ptr)) /* scroll to end of integer */ ptr++; } d->data = p_list; d->len = size_count; return; } /*------------------------------------------------------------------------- * 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 = (struct subset_t *)calloc(1, sizeof(struct subset_t)); parse_hsize_list(brace, &s->start); while (*brace && *brace != ';') brace++; if (*brace) brace++; parse_hsize_list(brace, &s->stride); while (*brace && *brace != ';') brace++; if (*brace) brace++; parse_hsize_list(brace, &s->count); while (*brace && *brace != ';') brace++; if (*brace) brace++; parse_hsize_list(brace, &s->block); } } return s; } #ifdef H5_HAVE_H5DUMP_PACKED_BITS /*------------------------------------------------------------------------- * Function: parse_mask_list * * Purpose: Parse a list of comma or space separated integers and fill * the packed_bits list and counter. The string being passed into this function * should be at the start of the list you want to parse. * * Return: Success: SUCCEED * * Failure: FAIL * * *------------------------------------------------------------------------- */ static int parse_mask_list(const char *h_list) { const char *ptr; int offset_value, length_value; unsigned long long temp_mask; /* sanity check */ HDassert(h_list); HDmemset(packed_mask,0,sizeof(packed_mask)); packed_bits_num = 0; /* scan in pair of offset,length separated by commas. */ ptr = h_list; while (*ptr) { /* scan for an offset which is an unsigned int */ if (!HDisdigit(*ptr)){ error_msg("Bad mask list(%s)\n", h_list); return FAIL; } offset_value = HDatoi(ptr); if (offset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX){ error_msg("Packed Bit offset value(%d) must be between 0 and %d\n", offset_value, PACKED_BITS_SIZE_MAX - 1); return FAIL; } /* skip to end of integer */ while (HDisdigit(*++ptr)) ; /* Look for the common separator */ if (*ptr++ != ',') { error_msg("Bad mask list(%s), missing expected comma separator.\n", h_list); return FAIL; } /* scan for a length which is a positive int */ if (!HDisdigit(*ptr)){ error_msg("Bad mask list(%s)\n", h_list); return FAIL; } length_value = HDatoi(ptr); if (length_value <= 0){ error_msg("Packed Bit length value(%d) must be positive.\n", length_value); return FAIL; }; if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX){ error_msg("Packed Bit offset+length value(%d) too large. Max is %d\n", offset_value+length_value, PACKED_BITS_SIZE_MAX); return FAIL; }; /* skip to end of int */ while (HDisdigit(*++ptr)) ; /* store the offset,length pair */ if (packed_bits_num >= PACKED_BITS_MAX){ /* too many requests */ error_msg("Too many masks requested (max. %d). Mask list(%s)\n", PACKED_BITS_MAX, h_list); return FAIL; } packed_offset[packed_bits_num] = offset_value; packed_length[packed_bits_num] = length_value; /* create the bit mask by left shift 1's by length, then negate it. */ /* After packed_mask is calculated, packed_length is not needed but */ /* keep it for debug purpose. */ temp_mask = ~0L; if(length_value<8*sizeof(unsigned long long)) { temp_mask = temp_mask << length_value; packed_mask[packed_bits_num] = ~temp_mask; } else packed_mask[packed_bits_num] = temp_mask; packed_bits_num++; /* skip a possible comma separator */ if (*ptr == ','){ if (!(*++ptr)){ /* unexpected end of string */ error_msg("Bad mask list(%s), unexpected end of string.\n", h_list); return FAIL; } } } HDassert(packed_bits_num <= PACKED_BITS_MAX); if (packed_bits_num == 0){ /* got no masks! */ error_msg("Bad mask list(%s)\n", h_list); return FAIL; } return SUCCEED; } #endif /*------------------------------------------------------------------------- * Function: handle_datasets * * Purpose: Handle the datasets from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * Pedro Vicente, Tuesday, January 15, 2008 * check for block overlap\ * * Pedro Vicente, May 8, 2008 * added a flag PE that prints/not prints error messages * added for cases of external links not found, to avoid printing of * objects not found, since external links are dumped on a trial error basis * *------------------------------------------------------------------------- */ static void handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name) { H5O_info_t oinfo; hid_t dsetid; struct subset_t *sset = (struct subset_t *)data; const char *real_name = display_name ? display_name : dset; if((dsetid = H5Dopen2(fid, dset, H5P_DEFAULT)) < 0) { if (pe) { begin_obj(dump_header_format->datasetbegin, real_name, dump_header_format->datasetblockbegin); indentation(COL); error_msg("unable to open dataset \"%s\"\n", real_name); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); h5tools_setstatus(EXIT_FAILURE); } return; } /* end if */ if(sset) { unsigned int i; hid_t sid = H5Dget_space(dsetid); int ndims = H5Sget_simple_extent_ndims(sid); H5Sclose(sid); if(ndims < 0) { error_msg("H5Sget_simple_extent_ndims failed\n"); h5tools_setstatus(EXIT_FAILURE); return; } if(!sset->start.data || !sset->stride.data || !sset->count.data || !sset->block.data) { /* they didn't specify a ``stride'' or ``block''. default to 1 in all * dimensions */ if(!sset->start.data) { /* default to (0, 0, ...) for the start coord */ sset->start.data = (hsize_t *)calloc((size_t)ndims, sizeof(hsize_t)); sset->start.len = ndims; } if(!sset->stride.data) { sset->stride.data = (hsize_t *)calloc((size_t)ndims, sizeof(hsize_t)); sset->stride.len = ndims; for (i = 0; i < ndims; i++) sset->stride.data[i] = 1; } if(!sset->count.data) { sset->count.data = (hsize_t *)calloc((size_t)ndims, sizeof(hsize_t)); sset->count.len = ndims; for (i = 0; i < ndims; i++) sset->count.data[i] = 1; } if(!sset->block.data) { sset->block.data = (hsize_t *)calloc((size_t)ndims, sizeof(hsize_t)); sset->block.len = ndims; for (i = 0; i < ndims; i++) sset->block.data[i] = 1; } } /*------------------------------------------------------------------------- * check for dimension overflow *------------------------------------------------------------------------- */ if(sset->start.len > ndims) { error_msg("number of start dims (%u) exceed dataset dims (%u)\n", sset->start.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } if(sset->stride.len > ndims) { error_msg("number of stride dims (%u) exceed dataset dims (%u)\n", sset->stride.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } if(sset->count.len > ndims) { error_msg("number of count dims (%u) exceed dataset dims (%u)\n", sset->count.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } if(sset->block.len > ndims) { error_msg("number of block dims (%u) exceed dataset dims (%u)\n", sset->block.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } /*------------------------------------------------------------------------- * check for block overlap *------------------------------------------------------------------------- */ for(i = 0; i < ndims; i++) { if(sset->count.data[i] > 1) { if(sset->stride.data[i] < sset->block.data[i]) { error_msg("wrong subset selection; blocks overlap\n"); h5tools_setstatus(EXIT_FAILURE); return; } /* end if */ } /* end if */ } /* end for */ } /* end if */ H5Oget_info(dsetid, &oinfo); if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(dset_table, oinfo.addr); if(found_obj) { if (found_obj->displayed) { indentation(indent); begin_obj(dump_header_format->datasetbegin, real_name, dump_header_format->datasetblockbegin); indentation(indent + COL); printf("%s \"%s\"\n", HARDLINK, found_obj->objname); indentation(indent); end_obj(dump_header_format->datasetend, dump_header_format->datasetblockend); } else { found_obj->displayed = TRUE; dump_dataset(dsetid, real_name, sset); } } else h5tools_setstatus(EXIT_FAILURE); } else dump_dataset(dsetid, real_name, sset); if(H5Dclose(dsetid) < 0) h5tools_setstatus(EXIT_FAILURE); } /*------------------------------------------------------------------------- * Function: handle_groups * * Purpose: Handle the groups from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: Pedro Vicente, September 26, 2007 * handle creation order * * Pedro Vicente, May 8, 2008 * added a flag PE that prints/not prints error messages * added for cases of external links not found, to avoid printing of * objects not found, since external links are dumped on a trial error basis * *------------------------------------------------------------------------- */ static void handle_groups(hid_t fid, const char *group, void UNUSED * data, int pe, const char * display_name) { hid_t gid; const char *real_name = display_name ? display_name : group; if((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0) { if ( pe ) { begin_obj(dump_header_format->groupbegin, real_name, dump_header_format->groupblockbegin); indentation(COL); error_msg("unable to open group \"%s\"\n", real_name); end_obj(dump_header_format->groupend, dump_header_format->groupblockend); h5tools_setstatus(EXIT_FAILURE); } } else { size_t new_len = HDstrlen(group) + 1; if(prefix_len <= new_len) { prefix_len = new_len; prefix = (char *)HDrealloc(prefix, prefix_len); } /* end if */ HDstrcpy(prefix, group); dump_group(gid, real_name); if(H5Gclose(gid) < 0) h5tools_setstatus(EXIT_FAILURE); } /* end else */ } /* end handle_groups() */ /*------------------------------------------------------------------------- * Function: handle_links * * Purpose: Handle soft or UD links from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ static void handle_links(hid_t fid, const char *links, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { H5L_info_t linfo; if(H5Lget_info(fid, links, &linfo, H5P_DEFAULT) < 0) { error_msg("unable to get link info from \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } else if(linfo.type == H5L_TYPE_HARD) { error_msg("\"%s\" is a hard link\n", links); h5tools_setstatus(EXIT_FAILURE); } else { char *buf = (char *)HDmalloc(linfo.u.val_size); switch(linfo.type) { case H5L_TYPE_SOFT: /* Soft link */ begin_obj(dump_header_format->softlinkbegin, links, dump_header_format->softlinkblockbegin); indentation(COL); if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) printf("LINKTARGET \"%s\"\n", buf); else { error_msg("h5dump error: unable to get link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } end_obj(dump_header_format->softlinkend, dump_header_format->softlinkblockend); break; case H5L_TYPE_EXTERNAL: begin_obj(dump_header_format->udlinkbegin, links, dump_header_format->udlinkblockbegin); indentation(COL); begin_obj(dump_header_format->extlinkbegin, links, dump_header_format->extlinkblockbegin); if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) { const char *elink_file; const char *elink_path; if(H5Lunpack_elink_val(buf, linfo.u.val_size, NULL, &elink_file, &elink_path)>=0) { indentation(COL); printf("LINKCLASS %d\n", linfo.type); indentation(COL); printf("TARGETFILE \"%s\"\n", elink_file); indentation(COL); printf("TARGETPATH \"%s\"\n", elink_path); } else { error_msg("h5dump error: unable to unpack external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } } else { error_msg("h5dump error: unable to get external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } end_obj(dump_header_format->extlinkend, dump_header_format->extlinkblockend); break; default: begin_obj(dump_header_format->udlinkbegin, links, dump_header_format->udlinkblockbegin); indentation(COL); begin_obj(dump_header_format->udlinkbegin, links, dump_header_format->udlinkblockbegin); indentation(COL); printf("LINKCLASS %d\n", linfo.type); end_obj(dump_header_format->udlinkend, dump_header_format->udlinkblockend); break; } /* end switch */ HDfree(buf); } /* end else */ } /*------------------------------------------------------------------------- * Function: handle_datatypes * * Purpose: Handle the datatypes from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * * Pedro Vicente, May 8, 2008 * added a flag PE that prints/not prints error messages * added for cases of external links not found, to avoid printing of * objects not found, since external links are dumped on a trial error basis * *------------------------------------------------------------------------- */ static void handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe, const char *display_name) { hid_t type_id; const char *real_name = display_name ? display_name : type; if((type_id = H5Topen2(fid, type, H5P_DEFAULT)) < 0) { /* check if type is unamed datatype */ unsigned idx = 0; while(idx < type_table->nobjs ) { char name[128]; if(!type_table->objs[idx].recorded) { /* unamed datatype */ sprintf(name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno); if(!HDstrcmp(name, real_name)) break; } /* end if */ idx++; } /* end while */ if(idx == type_table->nobjs) { if ( pe ) { /* unknown type */ begin_obj(dump_header_format->datatypebegin, real_name, dump_header_format->datatypeblockbegin); indentation(COL); error_msg("unable to open datatype \"%s\"\n", real_name); end_obj(dump_header_format->datatypeend, dump_header_format->datatypeblockend); h5tools_setstatus(EXIT_FAILURE); } } else { hid_t dsetid = H5Dopen2(fid, type_table->objs[idx].objname, H5P_DEFAULT); type_id = H5Dget_type(dsetid); dump_named_datatype(type_id, real_name); H5Tclose(type_id); H5Dclose(dsetid); } } else { dump_named_datatype(type_id, real_name); if(H5Tclose(type_id) < 0) h5tools_setstatus(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: * pvn June, 1, 2006. Add a switch for binary output * *------------------------------------------------------------------------- */ 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; /* no arguments */ if (argc == 1) { usage(h5tools_getprogname()); leave(EXIT_FAILURE); } /* this will be plenty big enough to hold the info */ hand = (struct handler_t *)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) { case 'R': display_region = TRUE; region_output = TRUE; break; case 'B': display_bb = TRUE; last_was_dset = FALSE; break; case 'n': display_fi = TRUE; last_was_dset = FALSE; break; case 'p': display_dcpl = TRUE; break; case 'y': display_ai = FALSE; break; case 'e': display_escape = TRUE; break; case 'H': display_data = FALSE; display_attr_data = FALSE; last_was_dset = FALSE; break; case 'A': display_data = FALSE; display_attr_data = TRUE; last_was_dset = FALSE; break; case 'i': display_oid = TRUE; last_was_dset = FALSE; break; case 'r': display_char = TRUE; break; case 'V': print_version(h5tools_getprogname()); leave(EXIT_SUCCESS); break; case 'w': nCols = HDatoi(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[i]; 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 ( bin_output ) { if (set_output_file(opt_arg, 1) < 0) { usage(h5tools_getprogname()); leave(EXIT_FAILURE); } } else { if (set_output_file(opt_arg, 0) < 0) { usage(h5tools_getprogname()); leave(EXIT_FAILURE); } } usingdasho = TRUE; last_was_dset = FALSE; outfname = opt_arg; break; case 'b': if ( opt_arg != NULL) { if ( ( bin_form = set_binary_form(opt_arg)) < 0) { /* failed to set binary form */ usage(h5tools_getprogname()); leave(EXIT_FAILURE); } } bin_output = TRUE; if (outfname!=NULL) { if (set_output_file(outfname, 1) < 0) { /* failed to set output file */ usage(h5tools_getprogname()); leave(EXIT_FAILURE); } last_was_dset = FALSE; } break; case 'q': if ( ( sort_by = set_sort_by(opt_arg)) < 0) { /* failed to set "sort by" form */ usage(h5tools_getprogname()); leave(EXIT_FAILURE); } break; case 'z': if ( ( sort_order = set_sort_order(opt_arg)) < 0) { /* failed to set "sort order" form */ usage(h5tools_getprogname()); leave(EXIT_FAILURE); } break; #ifdef H5_HAVE_H5DUMP_PACKED_BITS case 'M': if (!last_was_dset) { error_msg("option `-%c' can only be used after --dataset option\n", opt); leave(EXIT_FAILURE); } if (parse_mask_list(opt_arg) != SUCCEED){ usage(h5tools_getprogname()); leave(EXIT_FAILURE); } display_packed_bits = TRUE; break; #endif /** begin XML parameters **/ case 'x': /* select XML output */ doxml = TRUE; useschema = TRUE; dump_header_format = NULL; dump_function_table = &xml_function_table; break; case 'u': doxml = TRUE; useschema = FALSE; xmlnsprefix = ""; dump_header_format = NULL; dump_function_table = &xml_function_table; break; case 'D': /* specify alternative XML DTD or schema */ /* To Do: check format of this value? */ xml_dtd_uri = opt_arg; break; case 'm': /* specify alternative floating point printing format */ fp_format = opt_arg; break; case 'X': /* specify XML namespace (default="hdf5:"), or none */ /* To Do: check format of this value? */ if (!useschema) { usage(h5tools_getprogname()); leave(EXIT_FAILURE); } if (strcmp(opt_arg,":") == 0) { xmlnsprefix = ""; } else { xmlnsprefix = 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("option `-%c' can only be used after --dataset option\n", opt); leave(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 = (struct subset_t *)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': if(s->start.data) free(s->start.data); parse_hsize_list(opt_arg, &s->start); break; case 'S': if(s->stride.data) free(s->stride.data); parse_hsize_list(opt_arg, &s->stride); break; case 'c': if(s->count.data) free(s->count.data); parse_hsize_list(opt_arg, &s->count); break; case 'k': if(s->block.data) free(s->block.data); parse_hsize_list(opt_arg, &s->block); 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 'E': enable_error_stack = TRUE; break; case 'h': usage(h5tools_getprogname()); leave(EXIT_SUCCESS); case '?': default: usage(h5tools_getprogname()); leave(EXIT_FAILURE); } } parse_end: /* check for file name to be processed */ if (argc <= opt_ind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); leave(EXIT_FAILURE); } 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.data); free(hand[i].subset_info->stride.data); free(hand[i].subset_info->count.data); free(hand[i].subset_info->block.data); 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. * * REMcG * August 2003 * Major upgrade to XML support. * * Pedro Vicente * September 2007 * list objects in requested order (creation order or alphabetically) * *------------------------------------------------------------------------- */ int main(int argc, const char *argv[]) { hid_t fid, gid; char *fname = NULL; void *edata; H5E_auto2_t func; H5O_info_t oi; struct handler_t *hand; int i; unsigned u; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); dump_header_format = &standardformat; dump_function_table = &ddl_function_table; /* Disable error reporting */ H5Eget_auto2(H5E_DEFAULT, &func, &edata); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); /* Initialize h5tools lib */ h5tools_init(); hand = parse_command_line(argc, argv); if (bin_output && outfname == NULL) { error_msg("binary output requires a file name, use -o \n"); leave(EXIT_FAILURE); } if (enable_error_stack) H5Eset_auto2(H5E_DEFAULT, func, edata); /* Check for conflicting options */ if (doxml) { if (!display_all) { error_msg("option \"%s\" not available for XML\n", "to display selected objects"); leave(EXIT_FAILURE); } else if (display_bb) { error_msg("option \"%s\" not available for XML\n", "--boot-block"); leave(EXIT_FAILURE); } else if (display_oid == 1) { error_msg("option \"%s\" not available for XML\n", "--object-ids"); leave(EXIT_FAILURE); } else if (display_char == TRUE) { error_msg("option \"%s\" not available for XML\n", "--string"); leave(EXIT_FAILURE); } else if (usingdasho) { error_msg("option \"%s\" not available for XML\n", "--output"); leave(EXIT_FAILURE); } } else { if (xml_dtd_uri) { warn_msg("option \"%s\" only applies with XML: %s\n", "--xml-dtd", xml_dtd_uri); } } if (argc <= opt_ind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); leave(EXIT_FAILURE); } fname = HDstrdup(argv[opt_ind]); fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, driver, NULL, 0); if (fid < 0) { error_msg("unable to open file \"%s\"\n", fname); leave(EXIT_FAILURE); } /* allocate and initialize internal data structure */ init_prefix(&prefix, prefix_len); /* Prepare to find objects that might be targets of a reference */ fill_ref_path_table(fid); if(doxml) { /* initialize XML */ /* reset prefix! */ HDstrcpy(prefix, ""); /* make sure the URI is initialized to something */ if (xml_dtd_uri == NULL) { if (useschema) { xml_dtd_uri = DEFAULT_XSD; } else { xml_dtd_uri = DEFAULT_DTD; xmlnsprefix = ""; } } else { if (useschema && strcmp(xmlnsprefix,"")) { error_msg("Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n"); leave(EXIT_FAILURE); } } } /* Get object info for root group */ if(H5Oget_info_by_name(fid, "/", &oi, H5P_DEFAULT) < 0) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } /* Initialize object tables */ if(table_list_add(fid, oi.fileno) < 0) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } group_table = table_list.tables[0].group_table; dset_table = table_list.tables[0].dset_table; type_table = table_list.tables[0].type_table; /* does there exist unamed committed datatype */ for (u = 0; u < type_table->nobjs; u++) if (!type_table->objs[u].recorded) { unamedtype = 1; break; } /* end if */ /* start to dump - display file header information */ if (!doxml) { begin_obj(dump_header_format->filebegin, fname, dump_header_format->fileblockbegin); } else { printf("\n"); /* alternative first element, depending on schema or DTD. */ if (useschema) { if (strcmp(xmlnsprefix,"") == 0) { printf("\n", xml_dtd_uri); } else { /* TO DO: make -url option work in this case (may need new option) */ char * ns; char *indx; ns = HDstrdup(xmlnsprefix); indx = strrchr(ns,(int)':'); if (indx) *indx = '\0'; printf("<%sHDF5-File xmlns:%s=\"http://hdfgroup.org/DTDs/HDF5-File\" " "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " "xsi:schemaLocation=\"http://hdfgroup.org/DTDs/HDF5-File " "http://www.hdfgroup.org/DTDs/HDF5-File.xsd\">\n",xmlnsprefix,ns); HDfree(ns); } } else { printf("\n", xml_dtd_uri); printf("\n"); } } if (!doxml) { if (display_fi) { dump_fcontents(fid); end_obj(dump_header_format->fileend,dump_header_format->fileblockend); goto done; } if (display_bb) dump_fcpl(fid); } if(display_all) { if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) { error_msg("unable to open root group\n"); h5tools_setstatus(EXIT_FAILURE); } else { dump_function_table->dump_group_function(gid, "/" ); } if(H5Gclose(gid) < 0) { error_msg("unable to close root group\n"); h5tools_setstatus(EXIT_FAILURE); } } else { /* Note: this option is not supported for XML */ if(doxml) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } /* end if */ for(i = 0; i < argc; i++) if(hand[i].func) hand[i].func(fid, hand[i].obj, hand[i].subset_info, 1, NULL); } if (!doxml) { end_obj(dump_header_format->fileend, dump_header_format->fileblockend); } else { printf("\n", xmlnsprefix); } done: /* Free tables for objects */ table_list_free(); if (H5Fclose(fid) < 0) h5tools_setstatus(EXIT_FAILURE); free_handler(hand, argc); HDfree(prefix); HDfree(fname); /* To Do: clean up XML table */ H5Eset_auto2(H5E_DEFAULT, func, edata); leave(h5tools_getstatus()); } /*------------------------------------------------------------------------- * 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 */ unsigned char *copy = NULL; /*a pointer to value array */ unsigned nmembs; /*number of members */ int nchars; /*number of output characters */ hid_t super; /*enum base integer type */ hid_t native = -1; /*native integer datatype */ size_t dst_size; /*destination value type size */ unsigned i; nmembs = (unsigned)H5Tget_nmembers(type); super = H5Tget_super(type); /* * Determine what datatype 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; } /* end if */ else dst_size = H5Tget_size(type); /* Get the names and raw values of all members */ name = (char **)calloc(nmembs, sizeof(char *)); value = (unsigned char *)calloc(nmembs, MAX(H5Tget_size(type), dst_size)); for (i = 0; i < nmembs; i++) { name[i] = H5Tget_member_name(type, i); H5Tget_member_value(type, i, value + i * H5Tget_size(type)); } /* Convert values to native datatype */ if (native > 0) H5Tconvert(super, native, nmembs, value, NULL, H5P_DEFAULT); /* * Sort members by increasing value * ***not implemented yet*** */ /* Print members */ for (i = 0; i < nmembs; i++) { 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)) { /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" *strangely, unless use another pointer "copy".*/ copy = value+i*dst_size; HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "u", *((unsigned long long *) ((void *)copy))); } else { /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" *strangely, unless use another pointer "copy".*/ copy = value+i*dst_size; HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "d", *((long long *) ((void *)copy))); } 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, ""); } /* * create a string suitable for and XML NCNAME. Uses the * object reference to create the string. * * 'gen'; 0 - return null if not found * 1 - generate a fake entry and return fake id. */ int xml_name_to_XID(const char *str , char *outstr, int outlen, int gen) { haddr_t objno; /* Object ID for object at path */ if (outlen < 22) return 1; objno = ref_path_table_lookup(str); if (objno == HADDR_UNDEF) { if (HDstrlen(str) == 0) { objno = ref_path_table_lookup("/"); if (objno == HADDR_UNDEF) { if (gen) { objno = ref_path_table_gen_fake(str); sprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); return 0; } else { return 1; } } } else { if (gen) { objno = ref_path_table_gen_fake(str); sprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); return 0; } else { return 1; } } } sprintf(outstr, "xid_"H5_PRINTF_HADDR_FMT, objno); 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 = (char *)HDmalloc(len + extra + 1); 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 = (char *)calloc((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, unsigned in_group) { char *mname; hid_t mtype; unsigned nmembers; unsigned ndims; unsigned i; size_t size; hsize_t dims[H5DUMP_MAX_RANK]; H5T_str_t str_pad; H5T_cset_t cset; 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; htri_t is_vlstr=FALSE; if(!in_group && H5Tcommitted(type) > 0) { H5O_info_t oinfo; obj_t *found_obj; /* Found object */ /* detect a shared datatype, output only once */ H5Oget_info(type, &oinfo); found_obj = search_obj(type_table, oinfo.addr); if(found_obj) { /* This should be defined somewhere else */ /* These 2 cases are handled the same right now, but probably will have something different eventually */ char * dtxid = (char *)malloc(100); xml_name_to_XID(found_obj->objname, dtxid, 100, 1); if (!found_obj->recorded) { /* 'anonymous' NDT. Use it's object num. as it's name. */ printf("<%sNamedDataTypePtr OBJ-XID=\"/%s\"/>\n", xmlnsprefix, dtxid); } else { /* point to the NDT by name */ char *t_objname = xml_escape_the_name(found_obj->objname); printf("<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n", xmlnsprefix, dtxid, t_objname); free(t_objname); } free(dtxid); } else { printf("\n"); h5tools_setstatus(EXIT_FAILURE); } } else { switch (H5Tget_class(type)) { case H5T_INTEGER: indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; /* */ ord = H5Tget_order(type); sgn = H5Tget_sign(type); indentation(indent); printf("<%sIntegerType ByteOrder=\"",xmlnsprefix); switch (ord) { case H5T_ORDER_LE: printf("LE"); break; case H5T_ORDER_BE: printf("BE"); break; case H5T_ORDER_VAX: default: printf("ERROR_UNKNOWN"); } printf("\" Sign=\""); switch (sgn) { case H5T_SGN_NONE: printf("false"); break; case H5T_SGN_2: printf("true"); break; default: printf("ERROR_UNKNOWN"); } printf("\" Size=\""); sz = H5Tget_size(type); printf("%lu", (unsigned long)sz); printf("\" />\n"); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_FLOAT: /* */ ord = H5Tget_order(type); indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sFloatType ByteOrder=\"",xmlnsprefix); switch (ord) { case H5T_ORDER_LE: printf("LE"); break; case H5T_ORDER_BE: printf("BE"); break; case H5T_ORDER_VAX: printf("VAX"); break; default: printf("ERROR_UNKNOWN"); } printf("\" Size=\""); sz = H5Tget_size(type); printf("%lu", (unsigned long)sz); H5Tget_fields(type, &spos, &epos, &esize, &mpos, &msize); printf("\" SignBitLocation=\"%lu\" ", (unsigned long)spos); printf("ExponentBits=\"%lu\" ExponentLocation=\"%lu\" ", (unsigned long)esize, (unsigned long)epos); printf("MantissaBits=\"%lu\" MantissaLocation=\"%lu\" />\n", (unsigned long)msize, (unsigned long)mpos); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_TIME: indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sTimeType />\n",xmlnsprefix); printf(""); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_STRING: /* */ size = H5Tget_size(type); str_pad = H5Tget_strpad(type); cset = H5Tget_cset(type); is_vlstr = H5Tis_variable_str(type); indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sStringType Cset=\"",xmlnsprefix); if (cset == H5T_CSET_ASCII) { printf("H5T_CSET_ASCII\" "); } else { printf("unknown_cset\" "); } if(is_vlstr) printf("StrSize=\"H5T_VARIABLE\" StrPad=\""); else printf("StrSize=\"%d\" StrPad=\"", (int) size); 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"); } indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_BITFIELD: /* */ ord = H5Tget_order(type); indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sBitfieldType ByteOrder=\"",xmlnsprefix); switch (ord) { case H5T_ORDER_LE: printf("LE"); break; case H5T_ORDER_BE: printf("BE"); break; case H5T_ORDER_VAX: default: printf("ERROR_UNKNOWN"); } size = H5Tget_size(type); printf("\" Size=\"%lu\"/>\n", (unsigned long)size); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_OPAQUE: /* */ indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); mname = H5Tget_tag(type); printf("<%sOpaqueType Tag=\"%s\" ",xmlnsprefix, mname); free(mname); size = H5Tget_size(type); printf("Size=\"%lu\"/>\n", (unsigned long)size); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_COMPOUND: /* recursively describe the components of a compound datatype */ /* type of a dataset */ nmembers = H5Tget_nmembers(type); indentation(indent); printf("<%sCompoundType>\n",xmlnsprefix); /* List each member Field of the type */ /* */ /* */ indent += COL; for (i = 0; i < nmembers; i++) { char *t_fname; mname = H5Tget_member_name(type, i); mtype = H5Tget_member_type(type, i); indentation(indent); t_fname = xml_escape_the_name(mname); printf("<%sField FieldName=\"%s\">\n",xmlnsprefix, t_fname); free(mname); free(t_fname); indent += COL; indentation(indent); printf("<%sDataType>\n",xmlnsprefix); indent += COL; xml_print_datatype(mtype,0); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); } indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_REFERENCE: indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); /* Only Object references supported at this time */ printf("<%sReferenceType>\n",xmlnsprefix); indentation(indent + COL); printf("<%sObjectReferenceType />\n",xmlnsprefix); indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_ENUM: /* list Name, values of enum */ nmembs = H5Tget_nmembers(type); indentation(indent); printf("<%sAtomicType>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sEnumType Nelems=\"%d\">\n",xmlnsprefix, nmembs); xml_print_enum(type); indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); break; case H5T_VLEN: indentation(indent); printf("<%sVLType>\n",xmlnsprefix); super = H5Tget_super(type); indent += COL; indentation(indent); printf("<%sDataType>\n",xmlnsprefix); indent += COL; xml_print_datatype(super,0); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); H5Tclose(super); break; case H5T_ARRAY: /* Get array base type */ super = H5Tget_super(type); /* Print lead-in */ indentation(indent); printf("<%sArrayType Ndims=\"",xmlnsprefix); ndims = H5Tget_array_ndims(type); printf("%u\">\n", ndims); /* Get array information */ H5Tget_array_dims2(type, dims); /* list of dimensions */ indent += COL; for (i = 0; i < ndims; i++) { indentation(indent); printf("<%sArrayDimension DimSize=\"%u\"/>\n", xmlnsprefix, (int) dims[i]); } indent -= COL; indent += COL; indentation(indent); printf("<%sDataType>\n",xmlnsprefix); indent += COL; xml_print_datatype(super,0); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); /* Close array base type */ H5Tclose(super); break; default: printf(""); h5tools_setstatus(EXIT_FAILURE); break; } } /* end else */ } /*------------------------------------------------------------------------- * 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) { indent += COL; indentation(indent); if(H5Tcommitted(type) > 0) { H5O_info_t oinfo; obj_t *found_obj; /* Found object */ /* Datatype is a shared or named datatype */ H5Oget_info(type, &oinfo); found_obj = search_obj(type_table, oinfo.addr); if(found_obj) { /* Shared datatype, must be entered as an object */ /* These 2 cases are the same now, but may change */ char * dtxid = (char *)malloc(100); xml_name_to_XID(found_obj->objname, dtxid, 100, 1); if (!found_obj->recorded) { /* anonymous stored datatype: following the dumper's current practice: use it's object ref as its name */ printf("<%sNamedDataTypePtr OBJ-XID=\"%s\"/>\n", xmlnsprefix, dtxid); } else { /* pointer to a named datatype already in XML */ char *t_objname = xml_escape_the_name(found_obj->objname); printf("<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\" />\n", xmlnsprefix, dtxid, t_objname); free(t_objname); } free(dtxid); } else { printf("\n"); } indent -= COL; } else { printf("<%sDataType>\n", xmlnsprefix); indent += COL; xml_print_datatype(type, 0); indent -= COL; indentation(indent); printf("\n", xmlnsprefix); 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); H5S_class_t space_type = H5Sget_simple_extent_type(space); int i; indentation(indent + COL); printf("<%sDataspace>\n", xmlnsprefix); indentation(indent + COL + COL); switch (space_type) { case H5S_SCALAR: /* scalar dataspace (just a tag, no XML attrs. defined */ printf("<%sScalarDataspace />\n",xmlnsprefix); break; case H5S_SIMPLE: /* simple dataspace */ /* */ printf("<%sSimpleDataspace Ndims=\"%d\">\n",xmlnsprefix, ndims); /* print the elements */ for (i = 0; i < ndims; i++) { indentation(indent + COL + COL + COL); if (maxsize[i] == H5S_UNLIMITED) { HDfprintf(stdout, "<%sDimension DimSize=\"%Hu\" MaxDimSize=\"UNLIMITED\"/>\n", xmlnsprefix,size[i]); } else if (maxsize[i] == (hsize_t) 0) { HDfprintf(stdout, "<%sDimension DimSize=\"%Hu\" MaxDimSize=\"%Hu\"/>\n", xmlnsprefix,size[i], size[i]); } else { HDfprintf(stdout, "<%sDimension DimSize=\"%Hu\" MaxDimSize=\"%Hu\"/>\n", xmlnsprefix, size[i], maxsize[i]); } } indentation(indent + COL + COL); printf("\n", xmlnsprefix ); break; #ifdef TMP /* Commented out: wait until the schema is updated first */ case H5S_NULL: /* null dataspace (just a tag, no XML attrs. defined */ printf("<%sNullDataspace />\n",xmlnsprefix); break; #endif /* TMP */ case H5S_NO_CLASS: default: printf("\n"); } indentation(indent + COL); printf("\n", xmlnsprefix); } /*------------------------------------------------------------------------- * 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, int UNUSED pindex) { h5tool_format_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 */ if (fp_format) { outputformat->fmt_double = fp_format; outputformat->fmt_float = fp_format; } if (nCols==0) { outputformat->line_ncols = 65535; outputformat->line_per_line = 1; } else 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("<%sData>\n", xmlnsprefix); indentation(indent + COL); printf("<%sDataFromFile>\n",xmlnsprefix); 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 */ /* VL data special information */ unsigned int vl_data = 0; /* contains VL datatypes */ p_type = h5tools_get_native_type(type); /* Check if we have VL data in the dataset's datatype */ if (h5tools_detect_vlen(p_type) == TRUE) vl_data = TRUE; 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); /* Reclaim any VL memory, if necessary */ if (vl_data) H5Dvlen_reclaim(p_type, space, H5P_DEFAULT, buf); 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",xmlnsprefix); indentation(indent); printf("\n", xmlnsprefix); 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, const H5A_info_t UNUSED *info, void UNUSED * op_data) { hid_t attr_id, type, space; H5S_class_t space_type; char *t_aname = xml_escape_the_name(attr_name); indentation(indent); printf("<%sAttribute Name=\"%s\">\n",xmlnsprefix, t_aname); free(t_aname); if ((attr_id = H5Aopen(attr, attr_name, H5P_DEFAULT)) >= 0) { type = H5Aget_type(attr_id); space = H5Aget_space(attr_id); space_type = H5Sget_simple_extent_type(space); dump_function_table->dump_dataspace_function(space); dump_function_table->dump_datatype_function(type); if (display_attr_data && space_type!=H5S_NULL) { 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, 0); break; case H5T_TIME: indent += COL; indentation(indent); printf("<%sData>\n",xmlnsprefix); indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData/>\n",xmlnsprefix); indentation(indent); printf("\n"); printf("\n",xmlnsprefix); indent -= COL; break; case H5T_COMPOUND: indentation(indent); printf("\n"); dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); break; case H5T_REFERENCE: indentation(indent); printf("<%sData>\n",xmlnsprefix); indentation(indent); if (!H5Tequal(type, H5T_STD_REF_OBJ)) { printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); } else { printf("<%sDataFromFile>\n",xmlnsprefix); xml_print_refs(attr_id, ATTRIBUTE_DATA); indentation(indent); printf("\n",xmlnsprefix); } indentation(indent); printf("\n",xmlnsprefix); break; case H5T_VLEN: printf("\n"); dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0); break; default: indentation(indent); printf("<%sData>\n",xmlnsprefix); indentation(indent); printf("\n", H5Tget_class(type)); indentation(indent); printf("<%sNoData/>\n",xmlnsprefix); indentation(indent); printf("\n",xmlnsprefix); break; } } else { /* The case of an attribute never yet written ?? * Or dataspace is H5S_NULL. */ indentation(indent + COL); printf("<%sData>\n",xmlnsprefix); indentation(indent + COL + COL); printf("<%sNoData/>\n",xmlnsprefix); indentation(indent + COL); printf("\n",xmlnsprefix); } H5Tclose(type); H5Sclose(space); H5Aclose(attr_id); indentation(indent); printf("\n", xmlnsprefix ); return SUCCEED; } else { /* ?? failed */ indentation(indent + COL); printf("\n"); indentation(indent); printf("\n", xmlnsprefix ); h5tools_setstatus(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) { char *tmp; char * dtxid; char * parentxid; char *t_tmp; char *t_prefix; char *t_name; tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); HDstrcpy(tmp, prefix); HDstrcat(tmp, "/"); HDstrcat(tmp, name); indentation(indent); dtxid = (char *)HDmalloc(100); parentxid = (char *)HDmalloc(100); t_tmp = xml_escape_the_name(tmp); t_prefix = xml_escape_the_name(prefix); t_name = xml_escape_the_name(name); xml_name_to_XID(tmp, dtxid, 100, 1); xml_name_to_XID(prefix, parentxid, 100, 1); if(HDstrncmp(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. */ printf("<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\">\n", xmlnsprefix, name, dtxid, parentxid, HDstrcmp(prefix,"") ? t_prefix : "/"); } else { H5O_info_t oinfo; /* Object info */ printf("<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" " "H5Path=\"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">\n", xmlnsprefix, t_name, dtxid, t_tmp, parentxid, (HDstrcmp(prefix, "") ? t_prefix : "/")); /* Check uniqueness of named datatype */ H5Oget_info(type, &oinfo); if(oinfo.rc > 1) { obj_t *found_obj; /* Found object */ /* Group with more than one link to it... */ found_obj = search_obj(type_table, oinfo.addr); if (found_obj == NULL) { indentation(indent); error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } else if(found_obj->displayed) { /* We have already printed this named datatype, print it as a * NamedDatatypePtr */ char pointerxid[100]; char *t_objname = xml_escape_the_name(found_obj->objname); indentation(indent + COL); xml_name_to_XID(found_obj->objname, pointerxid, sizeof(pointerxid), 1); printf("<%sNamedDatatypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n", xmlnsprefix, pointerxid, t_objname); indentation(indent); printf("\n", xmlnsprefix); HDfree(t_objname); goto done; } else found_obj->displayed = TRUE; } } indent += COL; indentation(indent); printf("<%sDataType>\n",xmlnsprefix); indent += COL; xml_print_datatype(type,1); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); done: HDfree(dtxid); HDfree(parentxid); HDfree(t_tmp); HDfree(t_prefix); HDfree(t_name); HDfree(tmp); } /*------------------------------------------------------------------------- * Function: xml_dump_group * * Purpose: Dump a description of an HDF5 Group (and its members) in XML. * * Return: void * * Programmer: REMcG * * Modifications: * Pedro Vicente, October 9, 2007 * added parameters to H5A(L)iterate to allow for other iteration orders * *------------------------------------------------------------------------- */ static void xml_dump_group(hid_t gid, const char *name) { H5O_info_t oinfo; char *cp; hid_t dset, type; char type_name[1024], *tmp = NULL; char *par = NULL; int isRoot = 0; char *t_objname; char *par_name; unsigned crt_order_flags; unsigned attr_crt_order_flags; hid_t gcpl_id; if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties for attributes */ if (H5Pget_attr_creation_order(gcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties */ if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } if(H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } if(HDstrcmp(name, "/") == 0) { isRoot = 1; tmp = HDstrdup("/"); } else { tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); HDstrcpy(tmp, prefix); par = HDstrdup(tmp); cp = HDstrrchr(par, '/'); if(cp) { if((cp == par) && HDstrlen(par) > 1) *(cp + 1) = '\0'; else *cp = '\0'; } } indentation(indent); indent += COL; H5Oget_info(gid, &oinfo); if(oinfo.rc > 1) { obj_t *found_obj; /* Found object */ /* Group with more than one link to it... */ found_obj = search_obj(group_table, oinfo.addr); if (found_obj == NULL) { indentation(indent); error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); } else { char *t_name = xml_escape_the_name(name); char *grpxid = (char *)malloc(100); char *parentxid = (char *)malloc(100); if(found_obj->displayed) { char *ptrstr = (char *)malloc(100); /* already seen: enter a groupptr */ if(isRoot) { /* probably can't happen! */ xml_name_to_XID("/", grpxid, 100, 1); printf("<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">\n", xmlnsprefix, grpxid, "/"); } else { t_objname = xml_escape_the_name(found_obj->objname); par_name = xml_escape_the_name(par); xml_name_to_XID(tmp, grpxid, 100, 1); xml_name_to_XID(par, parentxid, 100, 1); printf("<%sGroup Name=\"%s\" OBJ-XID=\"%s-%d\" H5Path=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\">\n", xmlnsprefix,t_name, grpxid, get_next_xid(), t_objname, parentxid, par_name); free(t_objname); free(par_name); indentation(indent + COL); t_objname = xml_escape_the_name(found_obj->objname);/* point to the NDT by name */ par_name = xml_escape_the_name(par); xml_name_to_XID(found_obj->objname, ptrstr, 100, 1); xml_name_to_XID(par, parentxid, 100, 1); printf("<%sGroupPtr OBJ-XID=\"%s\" H5Path=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" />\n", xmlnsprefix, ptrstr, t_objname, parentxid, par_name); free(t_objname); free(par_name); } free(ptrstr); } else { /* first time this group has been seen -- describe it */ if(isRoot) { xml_name_to_XID("/", grpxid, 100, 1); printf("<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">\n", xmlnsprefix, grpxid, "/"); } else { char *t_tmp = xml_escape_the_name(tmp); par_name = xml_escape_the_name(par); xml_name_to_XID(tmp, grpxid, 100, 1); xml_name_to_XID(par, parentxid, 100, 1); printf("<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" >\n", xmlnsprefix,t_name, grpxid, t_tmp, parentxid, par_name); free(t_tmp); free(par_name); } found_obj->displayed = TRUE; /* 1. do all the attributes of the group */ if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ if(isRoot && unamedtype) { unsigned u; /* Very special case: dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) { if(!type_table->objs[u].recorded) { dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } } /* iterate through all the links */ if( (sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } free(t_name); free(grpxid); free(parentxid); } } else { /* only link -- must be first time! */ char *t_name = xml_escape_the_name(name); char *grpxid = (char *)malloc(100); char *parentxid = (char *)malloc(100); if(isRoot) { xml_name_to_XID("/", grpxid, 100, 1); printf("<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">\n", xmlnsprefix, grpxid, "/"); } else { char *t_tmp = xml_escape_the_name(tmp); par_name = xml_escape_the_name(par); xml_name_to_XID(tmp, grpxid, 100, 1); xml_name_to_XID(par, parentxid, 100, 1); printf("<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" " "Parents=\"%s\" H5ParentPaths=\"%s\" >\n", xmlnsprefix, t_name, grpxid, t_tmp, parentxid, par_name); free(t_tmp); free(par_name); } free(t_name); free(grpxid); free(parentxid); /* 1. do all the attributes of the group */ if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ if(isRoot && unamedtype) { unsigned u; /* Very special case: dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) { if(!type_table->objs[u].recorded) { dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } } /* iterate through all the links */ if( (sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } indent -= COL; indentation(indent); if(isRoot) printf("\n", xmlnsprefix); else printf("\n" , xmlnsprefix); 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 = NULL; hobj_ref_t *refbuf = NULL; hssize_t ssiz; hsize_t i; size_t tsiz; 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 */ goto error; } if (!H5Tequal(type, H5T_STD_REF_OBJ)) { /* region ref not supported yet... */ /* return an error */ goto error; } if (source == DATASET_DATA) { space = H5Dget_space(did); if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; if ((tsiz = H5Tget_size(type)) == 0) goto error; buf = (char *) calloc((size_t)(ssiz * tsiz), sizeof(char)); if (buf == NULL) goto error; e = H5Dread(did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); /* need to check result here */ if (e < 0) { goto error; } } else if (source == ATTRIBUTE_DATA) { space = H5Aget_space(did); if ((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; if ((tsiz = H5Tget_size(type)) == 0) goto error; buf = (char *) calloc((size_t)(ssiz * tsiz), sizeof(char)); if (buf == NULL) { goto error; } e = H5Aread(did, H5T_STD_REF_OBJ, buf); /* need to check the result here */ if (e < 0) { goto error; } } refbuf = (hobj_ref_t *) buf; for (i = 0; i < ssiz; i++) { const char *path; 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++; } free(buf); H5Tclose(type); H5Sclose(space); return SUCCEED; error: if(buf) free(buf); H5E_BEGIN_TRY { H5Tclose(type); H5Sclose(space); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * 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; void *buf = NULL; char *bp; char *onestring = NULL; hssize_t ssiz; size_t tsiz; size_t str_size = 0; size_t i; htri_t is_vlstr; 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 */ goto error; } /* Check if we have VL data in the dataset's datatype */ is_vlstr = (TRUE == H5Tis_variable_str(type)); if (source == DATASET_DATA) { space = H5Dget_space(did); if((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; if((tsiz = H5Tget_size(type)) == 0) goto error; buf = malloc((size_t)(ssiz * tsiz)); if (buf == NULL) goto error; e = H5Dread(did, type, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); if (e < 0) { goto error; } } else if (source == ATTRIBUTE_DATA) { space = H5Aget_space(did); if((ssiz = H5Sget_simple_extent_npoints(space)) < 0) goto error; if((tsiz = H5Tget_size(type)) == 0) goto error; buf = malloc((size_t)(ssiz * tsiz)); if (buf == NULL) goto error; e = H5Aread(did, type, buf); if (e < 0) { goto error; } } bp = (char*) buf; if (!is_vlstr) onestring = (char *) calloc(tsiz, sizeof(char)); for (i = 0; i < ssiz; i++) { if (is_vlstr) { onestring = *(char **) bp; if (onestring) str_size = (size_t) HDstrlen(onestring); } else { HDstrncpy(onestring, bp, tsiz); str_size = tsiz; } indentation(indent + COL); if (!onestring) { printf("NULL\n"); } else { char *t_onestring = xml_escape_the_string(onestring, (int) str_size); if (t_onestring) { printf("\"%s\"\n", t_onestring); free(t_onestring); } } bp += tsiz; } /* Reclaim any VL memory, if necessary */ if (!is_vlstr) if (onestring) free(onestring); if (buf) { if (is_vlstr) H5Dvlen_reclaim(type, space, H5P_DEFAULT, buf); free(buf); } H5Tclose(type); H5Sclose(space); return SUCCEED; error: if(buf) free(buf); H5E_BEGIN_TRY { H5Tclose(type); H5Sclose(space); } H5E_END_TRY; return FAIL; } /*------------------------------------------------------------------------- * Function: check_filters * * Purpose: private function to check for the filters and * put tags in the XML. * * Return: void * * Programmer: REMcG * * Modifications: * *------------------------------------------------------------------------- */ static void check_filters(hid_t dcpl) { int nfilt; int i; H5Z_filter_t filter; char namebuf[120]; size_t cd_nelmts = 20; unsigned int cd_values[20]; unsigned int flags; nfilt = H5Pget_nfilters(dcpl); if (nfilt <= 0) return; for (i = 0; i < nfilt; i++) { filter = H5Pget_filter2(dcpl, (unsigned)i, &flags, (size_t *) &cd_nelmts, cd_values, 120, namebuf, NULL); if (filter == H5Z_FILTER_DEFLATE) { indentation(indent + COL); printf("<%sDeflate Level=\"",xmlnsprefix); if (cd_nelmts < 1) { /* not sure what this means? */ printf("6"); } else { printf("%d",cd_values[0]); } printf("\"/>\n"); } else if (filter == H5Z_FILTER_FLETCHER32) { indentation(indent + COL); printf("<%sFletcher32 />",xmlnsprefix); } else if (filter == H5Z_FILTER_SHUFFLE) { indentation(indent + COL); printf("<%sShuffle />",xmlnsprefix); } else if (filter == H5Z_FILTER_SZIP) { indentation(indent + COL); printf("<%sSZIP ",xmlnsprefix); if (cd_nelmts < 2) { /* no pixels ? */ printf("Pixels_per_block=\"-1\" "); } else { printf("Pixels_per_block=\"%d\" ",cd_values[1]); } /* analyse the options mask */ if (cd_values[0] & H5_SZIP_CHIP_OPTION_MASK) { printf("Mode =\"Hardware\" "); } else if (cd_values[0] & H5_SZIP_ALLOW_K13_OPTION_MASK) { printf("Mode =\"K13\" "); } printf("Coding=\""); if (cd_values[0] & H5_SZIP_EC_OPTION_MASK) { printf("Entropy"); } else if (cd_values[0] & H5_SZIP_NN_OPTION_MASK) { printf("NN"); } printf("\" "); printf("ByteOrder=\""); if (cd_values[0] & H5_SZIP_LSB_OPTION_MASK) { printf("LSB"); } else if (cd_values[0] & H5_SZIP_MSB_OPTION_MASK) { printf("MSB"); } printf("\" "); if (cd_values[0] & H5_SZIP_RAW_OPTION_MASK) { printf("Header=\"Raw\""); } printf("/>\n"); } else { /* unknown option */ } } } static void xml_dump_fill_value(hid_t dcpl, hid_t type) { size_t sz; size_t i; hsize_t space; void * buf; char * name; indent += COL; indentation(indent); printf("<%sData>\n",xmlnsprefix); indent += COL; space = H5Tget_size(type); buf = malloc((size_t)space); H5Pget_fill_value(dcpl, type, buf); if (H5Tget_class(type) == H5T_REFERENCE) { const char * path; path = lookup_ref_path(*(hobj_ref_t *)buf); indentation(indent); printf("<%sDataFromFile>\n",xmlnsprefix); if (!path) { printf("\"%s\"\n", "NULL"); } else { char *t_path = xml_escape_the_string(path, -1); printf("\"%s\"\n", t_path); free(t_path); } indentation(indent); printf("\n",xmlnsprefix); } else if (H5Tget_class(type) == H5T_STRING) { /* ????? */ indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); } else { /* all other data */ switch (H5Tget_class(type)) { case H5T_INTEGER: indentation(indent); printf("<%sDataFromFile>\n",xmlnsprefix); indentation(indent); printf("\"%d\"\n",*(int *)buf); indentation(indent); printf("\n",xmlnsprefix); break; case H5T_FLOAT: indentation(indent); printf("<%sDataFromFile>\n",xmlnsprefix); indentation(indent); printf("\"%f\"\n",*(float *)buf); indentation(indent); printf("\n",xmlnsprefix); break; case H5T_BITFIELD: case H5T_OPAQUE: indentation(indent); printf("<%sDataFromFile>\n",xmlnsprefix); sz = H5Tget_size(type); indentation(indent); printf("\""); for (i = 0; i < sz; i++) { printf("%x ",*(unsigned int *)buf); buf = (char *)buf + sizeof(unsigned int); } printf("\"\n"); indentation(indent); printf("\n",xmlnsprefix); break; case H5T_ENUM: indentation(indent); printf("<%sDataFromFile>\n",xmlnsprefix); name = H5Tget_member_name(type, *(unsigned *)buf); indentation(indent); printf("\"%s\"\n",name); indentation(indent); printf("\n",xmlnsprefix); break; case H5T_ARRAY: indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); break; case H5T_TIME: indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); break; case H5T_COMPOUND: indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); break; case H5T_VLEN: indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); break; default: indentation(indent); printf("\n", H5Tget_class(type)); indentation(indent); printf("<%sNoData/>\n",xmlnsprefix); break; } } free(buf); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; } /*------------------------------------------------------------------------- * Function: xml_dump_dataset * * Purpose: Dump a description of an HDF5 dataset in XML. * * Return: void * * Programmer: REMcG * * Modifications: * Pedro Vicente, October 9, 2007 * added parameters to H5Aiterate2 to allow for other iteration orders * *------------------------------------------------------------------------- */ static void xml_dump_dataset(hid_t did, const char *name, struct subset_t UNUSED * sset) { hid_t type, space; hid_t dcpl; H5D_fill_value_t fvstatus; int maxdims; hsize_t *chsize; int ndims; int i; H5D_alloc_time_t at; H5D_fill_time_t ft; hsize_t tempi; char *tmp; char *t_name, *t_tmp, *t_prefix; unsigned attr_crt_order_flags; char *rstr = (char *)HDmalloc(100); char *pstr = (char *)HDmalloc(100); tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); HDstrcpy(tmp, prefix); HDstrcat(tmp, "/"); HDstrcat(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); xml_name_to_XID(tmp, rstr, 100, 1); xml_name_to_XID(prefix, pstr, 100, 1); printf("<%sDataset Name=\"%s\" OBJ-XID=\"%s\" H5Path= \"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">\n",xmlnsprefix, t_name, rstr, t_tmp, pstr, strcmp(prefix, "") ? t_prefix : "/"); HDfree(t_name); HDfree(t_tmp); HDfree(t_prefix); HDfree(rstr); HDfree(pstr); HDfree(tmp); dcpl = H5Dget_create_plist(did); type = H5Dget_type(did); space = H5Dget_space(did); /* query the creation properties for attributes */ H5Pget_attr_creation_order(dcpl, &attr_crt_order_flags); /* Print information about storage layout */ 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("<%sStorageLayout>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sChunkedLayout ",xmlnsprefix); ndims = H5Pget_chunk(dcpl, maxdims, chsize); printf("Ndims=\"%d\">\n", ndims); indent += COL; for (i = 0; i < ndims; i++) { indentation(indent); HDfprintf(stdout, "<%sChunkDimension DimSize=\"%Hu\" />\n", xmlnsprefix, chsize[i]); } indentation(indent); printf("<%sRequiredFilter>\n",xmlnsprefix); indent += COL; check_filters(dcpl); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; free(chsize); } else if (H5D_CONTIGUOUS == H5Pget_layout(dcpl)) { indent += COL; indentation(indent); printf("<%sStorageLayout>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sContiguousLayout/>\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); } else if (H5D_COMPACT == H5Pget_layout(dcpl)) { indent += COL; indentation(indent); printf("<%sStorageLayout>\n",xmlnsprefix); indent += COL; indentation(indent); printf("<%sCompactLayout/>\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); } /* and check for external.... ?? */ /* fill value */ indent += COL; indentation(indent); printf("<%sFillValueInfo ",xmlnsprefix); H5Pget_fill_time(dcpl, &ft); printf("FillTime=\""); switch ( ft ) { case H5D_FILL_TIME_ALLOC: printf("FillOnAlloc"); break; case H5D_FILL_TIME_NEVER: printf("FillNever"); break; case H5D_FILL_TIME_IFSET: printf("FillIfSet"); break; default: printf("?"); break; } printf("\" "); H5Pget_alloc_time(dcpl, &at); printf("AllocationTime=\""); switch ( at ) { case H5D_ALLOC_TIME_EARLY: printf("Early"); break; case H5D_ALLOC_TIME_INCR: printf("Incremental"); break; case H5D_ALLOC_TIME_LATE: printf("Late"); break; case H5D_ALLOC_TIME_DEFAULT: default: printf("?"); break; } printf("\""); printf(">\n"); indent += COL; indentation(indent); printf("<%sFillValue>\n",xmlnsprefix); indent += COL; H5Pfill_value_defined(dcpl, &fvstatus); if (fvstatus == H5D_FILL_VALUE_UNDEFINED || (fvstatus==H5D_FILL_VALUE_DEFAULT && ft==H5D_FILL_TIME_IFSET)) { indentation(indent + COL); printf("<%sNoFill/>\n",xmlnsprefix); } else { xml_dump_fill_value(dcpl,type); } indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; indentation(indent); printf("\n",xmlnsprefix); indent -= COL; dump_function_table->dump_dataspace_function(space); dump_function_table->dump_datatype_function(type); indent += COL; if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(did, sort_by, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(did, H5_INDEX_NAME, sort_order, NULL, dump_function_table->dump_attribute_function, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ indent -= COL; tempi = H5Dget_storage_size(did); if (display_data && (tempi > 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, 0); break; case H5T_TIME: indent += COL; indentation(indent); printf("<%sData>\n",xmlnsprefix); indentation(indent); printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); indentation(indent); printf("<%sData>\n",xmlnsprefix); indent -= COL; break; case H5T_COMPOUND: indentation(indent); printf("\n"); dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); break; case H5T_REFERENCE: indentation(indent); printf("<%sData>\n",xmlnsprefix); indentation(indent); if (!H5Tequal(type, H5T_STD_REF_OBJ)) { printf("\n"); indentation(indent); printf("<%sNoData />\n",xmlnsprefix); } else { printf("<%sDataFromFile>\n",xmlnsprefix); xml_print_refs(did, DATASET_DATA); indentation(indent); printf("\n",xmlnsprefix); } indentation(indent); printf("\n",xmlnsprefix); break; case H5T_VLEN: printf("\n"); dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0); break; default: indentation(indent); printf("<%sData>\n",xmlnsprefix); indentation(indent); printf("\n", H5Tget_class(type)); indentation(indent); printf("<%sNoData/>\n",xmlnsprefix); indentation(indent); printf("\n",xmlnsprefix); break; } } else { /* no data written */ indentation(indent + COL); printf("<%sData>\n",xmlnsprefix); indentation(indent + COL + COL); printf("<%sNoData/>\n",xmlnsprefix); indentation(indent + COL); printf("\n",xmlnsprefix); } H5Tclose(type); H5Sclose(space); H5Pclose(dcpl); indentation(indent); printf("\n", xmlnsprefix); } /*------------------------------------------------------------------------- * 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 */ unsigned nmembs; /*number of members */ hid_t super; /*enum base integer type */ hid_t native = -1; /*native integer datatype */ size_t dst_size; /*destination value type size */ unsigned i; /*miscellaneous counters */ size_t j; nmembs = (unsigned)H5Tget_nmembers(type); super = H5Tget_super(type); indentation(indent); printf("<%sDataType>\n",xmlnsprefix); xml_print_datatype(super,0); indentation(indent); printf("\n",xmlnsprefix); /* * Determine what datatype 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 = (char **)calloc(nmembs, sizeof(char *)); value = (unsigned char *)calloc(nmembs, MAX(H5Tget_size(type), dst_size)); for (i = 0; i < nmembs; i++) { name[i] = H5Tget_member_name(type, i); H5Tget_member_value(type, i, value + i * H5Tget_size(type)); } /* Convert values to native datatype */ if (native > 0) H5Tconvert(super, native, 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("<%sEnumElement>\n",xmlnsprefix); indentation(indent + COL); printf("%s\n", t_name); free(t_name); indentation(indent); printf("\n",xmlnsprefix); indentation(indent); printf("<%sEnumValue>\n",xmlnsprefix); 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",xmlnsprefix); } indent -= COL; /* Release resources */ for (i = 0; i < nmembs; i++) free(name[i]); free(name); free(value); H5Tclose(super); } /*------------------------------------------------------------------------- * Function: h5_fileaccess * * Purpose: Returns a file access template which is the default template * but with a file driver set according to the constant or * environment variable HDF5_DRIVER * * Return: Success: A file access property list * * Failure: -1 * * Programmer: Robb Matzke * Thursday, November 19, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static hid_t h5_fileaccess(void) { static const char *multi_letters = "msbrglo"; const char *val = NULL; const char *name; char s[1024]; hid_t fapl = -1; /* First use the environment variable, then the constant */ val = HDgetenv("HDF5_DRIVER"); #ifdef HDF5_DRIVER if (!val) val = HDF5_DRIVER; #endif if ((fapl=H5Pcreate(H5P_FILE_ACCESS))<0) return -1; if (!val || !*val) return fapl; /*use default*/ HDstrncpy(s, val, sizeof s); s[sizeof(s)-1] = '\0'; if (NULL==(name=HDstrtok(s, " \t\n\r"))) return fapl; if (!HDstrcmp(name, "sec2")) { /* Unix read() and write() system calls */ if (H5Pset_fapl_sec2(fapl)<0) return -1; } else if (!HDstrcmp(name, "stdio")) { /* Standard C fread() and fwrite() system calls */ if (H5Pset_fapl_stdio(fapl)<0) return -1; } else if (!HDstrcmp(name, "core")) { /* In-core temporary file with 1MB increment */ if (H5Pset_fapl_core(fapl, 1024*1024, FALSE)<0) return -1; } else if (!HDstrcmp(name, "split")) { /* Split meta data and raw data each using default driver */ if (H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT)<0) return -1; } else if (!HDstrcmp(name, "multi")) { /* Multi-file driver, general case of the split driver */ H5FD_mem_t memb_map[H5FD_MEM_NTYPES]; hid_t memb_fapl[H5FD_MEM_NTYPES]; const char *memb_name[H5FD_MEM_NTYPES]; char sv[H5FD_MEM_NTYPES][1024]; haddr_t memb_addr[H5FD_MEM_NTYPES]; H5FD_mem_t mt; HDmemset(memb_map, 0, sizeof memb_map); HDmemset(memb_fapl, 0, sizeof memb_fapl); HDmemset(memb_name, 0, sizeof memb_name); HDmemset(memb_addr, 0, sizeof memb_addr); assert(HDstrlen(multi_letters)==H5FD_MEM_NTYPES); for (mt=H5FD_MEM_DEFAULT; mt 0); *prfx = (char *)HDcalloc(prfx_len, 1); } /*------------------------------------------------------------------------- * Function: add_prefix * * Purpose: Add object to prefix * * Return: void * *------------------------------------------------------------------------- */ static void add_prefix(char **prfx, size_t *prfx_len, const char *name) { size_t new_len = HDstrlen(*prfx) + HDstrlen(name) + 2; /* Check if we need more space */ if(*prfx_len <= new_len) { *prfx_len = new_len + 1; *prfx = (char *)HDrealloc(*prfx, *prfx_len); } /* Append object name to prefix */ HDstrcat(HDstrcat(*prfx, "/"), name); } /* end add_prefix */ /*------------------------------------------------------------------------- * Function: dump_extlink * * made by: PVN * * Purpose: Dump an external link * Since external links are soft links, they are dumped on a trial error * basis, attempting to dump as a dataset, as a group and as a named datatype * Error messages are supressed * * Modifications: * Neil Fortner * 13 October 2008 * Function basically rewritten. No longer directly opens the target file, * now initializes a new set of tables for the external file. No longer * dumps on a trial and error basis, but errors are still suppressed. * *------------------------------------------------------------------------- */ static int dump_extlink(hid_t group, const char *linkname, const char *objname) { hid_t oid; H5O_info_t oi; table_t *old_group_table = group_table; table_t *old_dset_table = dset_table; table_t *old_type_table = type_table; hbool_t old_hit_elink; ssize_t idx; /* Open target object */ if ((oid = H5Oopen(group, linkname, H5P_DEFAULT)) < 0) goto fail; /* Get object info */ if (H5Oget_info(oid, &oi) < 0) { H5Oclose(oid); goto fail; } /* Check if we have visited this file already */ if ((idx = table_list_visited(oi.fileno)) < 0) { /* We have not visited this file, build object tables */ if ((idx = table_list_add(oid, oi.fileno)) < 0) { H5Oclose(oid); goto fail; } } /* Do not recurse through an external link into the original file (idx=0) */ if (idx) { /* Update table pointers */ group_table = table_list.tables[idx].group_table; dset_table = table_list.tables[idx].dset_table; type_table = table_list.tables[idx].type_table; /* We will now traverse the external link, set this global to indicate this */ old_hit_elink = hit_elink; hit_elink = TRUE; /* add some indentation to distinguish that these objects are external */ indent += 2*COL; /* Recurse into the external file */ switch (oi.type) { case H5O_TYPE_GROUP: handle_groups(group, linkname, NULL, 0, objname); break; case H5O_TYPE_DATASET: handle_datasets(group, linkname, NULL, 0, objname); break; case H5O_TYPE_NAMED_DATATYPE: handle_datatypes(group, linkname, NULL, 0, objname); break; default: h5tools_setstatus(EXIT_FAILURE); } indent -= 2*COL; /* Reset table pointers */ group_table = old_group_table; dset_table = old_dset_table; type_table = old_type_table; /* Reset hit_elink */ hit_elink = old_hit_elink; } /* end if */ if (H5Idec_ref(oid) < 0) h5tools_setstatus(EXIT_FAILURE); return SUCCEED; fail: return FAIL; }