/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 "h5dump_ddl.h" #include "h5dump_xml.h" /* Name of tool */ #define PROGRAMNAME "h5dump" static const char *driver = NULL; /* The driver to open the file with. */ const char *outfname=NULL; static int doxml = 0; static int useschema = 1; static const char *xml_dtd_uri = NULL; /* module-scoped variables for XML option */ #define DEFAULT_XSD "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd" #define DEFAULT_DTD "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.dtd" /* 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 }; /* internal functions */ static void init_prefix(char **prfx, size_t prfx_len); /* 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 = "hn*peyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o*b*F:s:S:Aq:z:m:RECM:O*"; static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "hel", no_arg, 'h' }, { "contents", optional_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", optional_arg, 'o' }, { "outpu", optional_arg, 'o' }, { "outp", optional_arg, 'o' }, { "out", optional_arg, 'o' }, { "ou", optional_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' }, { "packed-bits", require_arg, 'M' }, { "no-compact-subset", no_arg, 'C' }, { "ddl", optional_arg, 'O' }, { NULL, 0, '\0' } }; /*------------------------------------------------------------------------- * 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(); HDexit(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) { FLUSHSTREAM(rawoutstream); PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] files\n", prog); PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); PRINTVALSTREAM(rawoutstream, " -n, --contents Print a list of the file contents and exit\n"); PRINTVALSTREAM(rawoutstream, " Optional value 1 also prints attributes.\n"); PRINTVALSTREAM(rawoutstream, " -B, --superblock Print the content of the super block\n"); PRINTVALSTREAM(rawoutstream, " -H, --header Print the header only; no data is displayed\n"); PRINTVALSTREAM(rawoutstream, " -A, --onlyattr Print the header and value of attributes\n"); PRINTVALSTREAM(rawoutstream, " -i, --object-ids Print the object ids\n"); PRINTVALSTREAM(rawoutstream, " -r, --string Print 1-byte integer datasets as ASCII\n"); PRINTVALSTREAM(rawoutstream, " -e, --escape Escape non printing characters\n"); PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); PRINTVALSTREAM(rawoutstream, " -a P, --attribute=P Print the specified attribute\n"); PRINTVALSTREAM(rawoutstream, " If an attribute name contains a slash (/), escape the\n"); PRINTVALSTREAM(rawoutstream, " slash with a preceding backslash (\\).\n"); PRINTVALSTREAM(rawoutstream, " (See example section below.)\n"); PRINTVALSTREAM(rawoutstream, " -d P, --dataset=P Print the specified dataset\n"); PRINTVALSTREAM(rawoutstream, " -y, --noindex Do not print array indices with the data\n"); PRINTVALSTREAM(rawoutstream, " -p, --properties Print dataset filters, storage layout and fill value\n"); PRINTVALSTREAM(rawoutstream, " -f D, --filedriver=D Specify which driver to open the file with\n"); PRINTVALSTREAM(rawoutstream, " -g P, --group=P Print the specified group and all members\n"); PRINTVALSTREAM(rawoutstream, " -l P, --soft-link=P Print the value(s) of the specified soft link\n"); PRINTVALSTREAM(rawoutstream, " -o F, --output=F Output raw data into file F\n"); PRINTVALSTREAM(rawoutstream, " -b B, --binary=B Binary file output, of form B\n"); PRINTVALSTREAM(rawoutstream, " -t P, --datatype=P Print the specified named datatype\n"); PRINTVALSTREAM(rawoutstream, " -w N, --width=N Set the number of columns of output. A value of 0 (zero)\n"); PRINTVALSTREAM(rawoutstream, " sets the number of columns to the maximum (65535).\n"); PRINTVALSTREAM(rawoutstream, " Default width is 80 columns.\n"); PRINTVALSTREAM(rawoutstream, " -m T, --format=T Set the floating point output format\n"); PRINTVALSTREAM(rawoutstream, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n"); PRINTVALSTREAM(rawoutstream, " -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" ); PRINTVALSTREAM(rawoutstream, " -R, --region Print dataset pointed by region references\n"); PRINTVALSTREAM(rawoutstream, " -x, --xml Output in XML using Schema\n"); PRINTVALSTREAM(rawoutstream, " -u, --use-dtd Output in XML using DTD\n"); PRINTVALSTREAM(rawoutstream, " -D U, --xml-dtd=U Use the DTD or schema at U\n"); PRINTVALSTREAM(rawoutstream, " -X S, --xml-ns=S (XML Schema) Use qualified names n the XML\n"); PRINTVALSTREAM(rawoutstream, " \":\": no namespace, default: \"hdf5:\"\n"); PRINTVALSTREAM(rawoutstream, " E.g., to dump a file called `-f', use h5dump -- -f\n"); PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n"); PRINTVALSTREAM(rawoutstream, " occur.\n"); PRINTVALSTREAM(rawoutstream, " --no-compact-subset Disable compact form of subsetting and allow the use\n"); PRINTVALSTREAM(rawoutstream, " of \"[\" in dataset names.\n"); PRINTVALSTREAM(rawoutstream, " -O F, --ddl=F Output ddl text into file F\n"); PRINTVALSTREAM(rawoutstream, " Do not use filename F to suppress ddl display\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Subsetting is available by using the following options with a dataset\n"); PRINTVALSTREAM(rawoutstream, " attribute. Subsetting is done by selecting a hyperslab from the data.\n"); PRINTVALSTREAM(rawoutstream, " Thus, the options mirror those for performing a hyperslab selection.\n"); PRINTVALSTREAM(rawoutstream, " One of the START, COUNT, STRIDE, or BLOCK parameters are mandatory if you do subsetting.\n"); PRINTVALSTREAM(rawoutstream, " The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n"); PRINTVALSTREAM(rawoutstream, " each dimension. START is optional and will default to 0 in each dimension.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " -s START, --start=START Offset of start of subsetting selection\n"); PRINTVALSTREAM(rawoutstream, " -S STRIDE, --stride=STRIDE Hyperslab stride\n"); PRINTVALSTREAM(rawoutstream, " -c COUNT, --count=COUNT Number of blocks to include in selection\n"); PRINTVALSTREAM(rawoutstream, " -k BLOCK, --block=BLOCK Size of block in hyperslab\n"); PRINTVALSTREAM(rawoutstream, " START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n"); PRINTVALSTREAM(rawoutstream, " number of dimensions in the dataspace being queried\n"); PRINTVALSTREAM(rawoutstream, " (Alternate compact form of subsetting is described in the Reference Manual)\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " D - is the file driver to use in opening the file. Acceptable values\n"); PRINTVALSTREAM(rawoutstream, " are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n"); PRINTVALSTREAM(rawoutstream, " the file driver flag, the file will be opened with each driver in\n"); PRINTVALSTREAM(rawoutstream, " turn and in the order specified above until one driver succeeds\n"); PRINTVALSTREAM(rawoutstream, " in opening the file.\n"); PRINTVALSTREAM(rawoutstream, " These are the letters that are appended to the file name(without .h5) when opening\n"); PRINTVALSTREAM(rawoutstream, " names for the split(m,r) and multi(s,b,r,g,l,o) drivers. They are:\n"); PRINTVALSTREAM(rawoutstream, " m: All meta data when using the split driver.\n"); PRINTVALSTREAM(rawoutstream, " s: The userblock, superblock, and driver info block\n"); PRINTVALSTREAM(rawoutstream, " b: B-tree nodes\n"); PRINTVALSTREAM(rawoutstream, " r: Dataset raw data\n"); PRINTVALSTREAM(rawoutstream, " g: Global heap\n"); PRINTVALSTREAM(rawoutstream, " l: local heap (object names)\n"); PRINTVALSTREAM(rawoutstream, " o: object headers\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " F - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " P - is the full path from the root group to the object.\n"); PRINTVALSTREAM(rawoutstream, " N - is an integer greater than 1.\n"); PRINTVALSTREAM(rawoutstream, " T - is a string containing the floating point format, e.g '%%.3f'\n"); PRINTVALSTREAM(rawoutstream, " U - is a URI reference (as defined in [IETF RFC 2396],\n"); PRINTVALSTREAM(rawoutstream, " updated by [IETF RFC 2732])\n"); PRINTVALSTREAM(rawoutstream, " B - is the form of binary output: NATIVE for a memory type, FILE for the\n"); PRINTVALSTREAM(rawoutstream, " file type, LE or BE for pre-existing little or big endian types.\n"); PRINTVALSTREAM(rawoutstream, " Must be used with -o (output file) and it is recommended that\n"); PRINTVALSTREAM(rawoutstream, " -d (dataset) is used. B is an optional argument, defaults to NATIVE\n"); PRINTVALSTREAM(rawoutstream, " Q - is the sort index type. It can be \"creation_order\" or \"name\" (default)\n"); PRINTVALSTREAM(rawoutstream, " Z - is the sort order type. It can be \"descending\" or \"ascending\" (default)\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Examples:\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 1) Attribute foo of the group /bar_none in file quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -a /bar_none/foo quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Attribute \"high/low\" of the group /bar_none in the file quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -a \"/bar_none/high\\/low\" quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 2) Selecting a subset from dataset /foo in file quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -s \"0,1\" -S \"1,1\" -c \"2,3\" -k \"2,2\" quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 3) Saving dataset 'dset' in file quux.h5 to binary file 'out.bin'\n"); PRINTVALSTREAM(rawoutstream, " using a little-endian type\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /dset -b LE -o out.bin quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 4) Display two packed bits (bits 0-1 and bits 4-6) in the dataset /dset\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /dset -M 0,1,4,3 quux.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 5) Dataset foo in files file1.h5 file2.h5 file3.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /foo file1.h5 file2.h5 file3.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 6) Dataset foo in split files splitfile-m.h5 splitfile-r.h5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -f split splitfile\n"); PRINTVALSTREAM(rawoutstream, "\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 * *------------------------------------------------------------------------- */ 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 * *------------------------------------------------------------------------- */ 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: set_data_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_data_output_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawdatastream is changed only when succeeded */ if (rawdatastream && rawdatastream != stdout) { if (HDfclose(rawdatastream)) HDperror("closing rawdatastream"); else rawdatastream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { /* binary output */ if (is_bin) { if ((f = HDfopen(fname, "wb")) != NULL) { rawdatastream = f; retvalue = SUCCEED; } } else { if ((f = HDfopen(fname, "w")) != NULL) { rawdatastream = f; retvalue = SUCCEED; } } } else { rawdatastream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: set_attr_output_file * * Purpose: Open fname as the output file for attribute raw data. * Set rawattrstream as its file stream. * * Return: 0 -- succeeded * negative -- failed * *------------------------------------------------------------------------- */ static int set_attr_output_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawattrstream is changed only when succeeded */ if (rawattrstream && rawattrstream != stdout) { if (HDfclose(rawattrstream)) HDperror("closing rawattrstream"); else rawattrstream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { if ((f = HDfopen(fname, "w")) != NULL) { rawattrstream = f; retvalue = SUCCEED; } } else { rawattrstream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: set_output_file * * Purpose: Open fname as the output file for raw output. * Set rawoutstream as its file stream. * * Return: 0 -- succeeded * negative -- failed * *------------------------------------------------------------------------- */ static int set_output_file(const char *fname) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawoutstream is changed only when succeeded */ if (rawoutstream && rawoutstream != stdout) { if (HDfclose(rawoutstream)) HDperror("closing rawoutstream"); else rawoutstream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { if ((f = HDfopen(fname, "w")) != NULL) { rawoutstream = f; retvalue = SUCCEED; } } else { rawoutstream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: set_error_file * * Purpose: Open fname as the error output file for dataset raw error. * Set rawerrorstream as its file stream. * * Return: 0 -- succeeded * negative -- failed * *------------------------------------------------------------------------- */ static int set_error_file(const char *fname) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawerrorstream is changed only when succeeded */ if (rawerrorstream && rawerrorstream != stderr) { if (HDfclose(rawerrorstream)) HDperror("closing rawerrorstream"); else rawerrorstream = NULL; } if ((f = HDfopen(fname, "w")) != NULL) { rawerrorstream = f; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * 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 (HDstrcmp(form,"NATIVE") == 0 || HDstrcmp(form,"MEMORY") == 0) { /* native form */ bform = 0; } else if (HDstrcmp(form,"FILE") == 0) /* file type form */ bform = 1; else if (HDstrcmp(form,"LE") == 0) /* convert to little endian */ bform = 2; else if (HDstrcmp(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 (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */ idx_type = H5_INDEX_NAME; else if (HDstrcmp(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 (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */ iter_order = H5_ITER_INC; else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */ iter_order = H5_ITER_DEC; return iter_order; } /*------------------------------------------------------------------------- * 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; unsigned int i = 0; unsigned int 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 (HDisdigit(*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 *)HDcalloc(size_count, sizeof(hsize_t)); for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) if(HDisdigit(*ptr)) { /* we should have an integer now */ p_list[i++] = (hsize_t)HDatof(ptr); while (HDisdigit(*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 (!disable_compact_subset && ((brace = HDstrrchr(dset, '[')) != NULL)) { *brace++ = '\0'; s = (struct subset_t *)HDcalloc(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; } /*------------------------------------------------------------------------- * 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) { int offset_value; int length_value; unsigned long long temp_mask; const char *ptr = NULL; /* 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; } /*------------------------------------------------------------------------- * 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) { int i; if(hand) { for (i = 0; i < len; i++) { if(hand[i].obj) { HDfree(hand[i].obj); hand[i].obj=NULL; } if (hand[i].subset_info) { if(hand[i].subset_info->start.data) HDfree(hand[i].subset_info->start.data); if(hand[i].subset_info->stride.data) HDfree(hand[i].subset_info->stride.data); if(hand[i].subset_info->count.data) HDfree(hand[i].subset_info->count.data); if(hand[i].subset_info->block.data) HDfree(hand[i].subset_info->block.data); HDfree(hand[i].subset_info); hand[i].subset_info=NULL; } } HDfree(hand); } } /*------------------------------------------------------------------------- * 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 = NULL; struct handler_t *last_dset = NULL; int i; int opt; int last_was_dset = FALSE; /* no arguments */ if (argc == 1) { usage(h5tools_getprogname()); goto error; } /* this will be plenty big enough to hold the info */ if((hand = (struct handler_t *)HDcalloc((size_t)argc, sizeof(struct handler_t)))==NULL) { goto error; } /* 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; if ( opt_arg != NULL) { h5trav_set_verbose(HDatoi(opt_arg)); } 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()); free_handler(hand, argc); hand = NULL; h5tools_setstatus(EXIT_SUCCESS); goto done; break; case 'w': h5tools_nCols = HDatoi(opt_arg); if (h5tools_nCols <= 0) { h5tools_nCols = 65535; } 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 (set_output_file(opt_arg) < 0) { usage(h5tools_getprogname()); goto error; } break; case 'o': if ( bin_output ) { if (set_data_output_file(opt_arg, 1) < 0) { usage(h5tools_getprogname()); goto error; } } else { if(display_attr_data && !display_data) { if (set_attr_output_file(opt_arg, 0) < 0) { usage(h5tools_getprogname()); goto error; } } if(display_data || display_all) { if (set_data_output_file(opt_arg, 0) < 0) { usage(h5tools_getprogname()); goto error; } } } 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()); goto error; } } bin_output = TRUE; if (outfname!=NULL) { if (set_data_output_file(outfname, 1) < 0) { /* failed to set output file */ usage(h5tools_getprogname()); goto error; } 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()); goto error; } break; case 'z': if ( ( sort_order = set_sort_order(opt_arg)) < 0) { /* failed to set "sort order" form */ usage(h5tools_getprogname()); goto error; } break; case 'M': if (!last_was_dset) { error_msg("option `-%c' can only be used after --dataset option\n", opt); goto error; } if (parse_mask_list(opt_arg) != SUCCEED){ usage(h5tools_getprogname()); goto error; } display_packed_bits = TRUE; break; /** begin XML parameters **/ case 'x': /* select XML output */ doxml = TRUE; useschema = TRUE; h5tools_dump_header_format = NULL; dump_function_table = &xml_function_table; h5tools_nCols = 0; break; case 'u': doxml = TRUE; useschema = FALSE; xmlnsprefix = ""; h5tools_dump_header_format = NULL; dump_function_table = &xml_function_table; h5tools_nCols = 0; break; case 'D': /* specify alternative XML DTD or schema */ /* To Do: check format of this value? */ xml_dtd_uri = opt_arg; h5tools_nCols = 0; break; case 'm': /* specify alternative floating point printing format */ fp_format = opt_arg; h5tools_nCols = 0; break; case 'X': /* specify XML namespace (default="hdf5:"), or none */ /* To Do: check format of this value? */ if (!useschema) { usage(h5tools_getprogname()); goto error; } if (HDstrcmp(opt_arg,":") == 0) { xmlnsprefix = ""; } else { xmlnsprefix = opt_arg; } h5tools_nCols = 0; 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); goto error; } 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 *)HDcalloc(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) { HDfree(s->start.data); s->start.data = NULL; } parse_hsize_list(opt_arg, &s->start); break; case 'S': if (s->stride.data) { HDfree(s->stride.data); s->stride.data = NULL; } parse_hsize_list(opt_arg, &s->stride); break; case 'c': if (s->count.data) { HDfree(s->count.data); s->count.data = NULL; } parse_hsize_list(opt_arg, &s->count); break; case 'k': if (s->block.data) { HDfree(s->block.data); s->block.data = NULL; } 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 'C': disable_compact_subset = TRUE; break; case 'h': usage(h5tools_getprogname()); free_handler(hand, argc); hand = NULL; h5tools_setstatus(EXIT_SUCCESS); goto done; case '?': default: usage(h5tools_getprogname()); goto error; } } parse_end: /* check for file name to be processed */ if (argc <= opt_ind) { error_msg("missing file name\n"); usage(h5tools_getprogname()); goto error; } done: return hand; error: if (hand) { free_handler(hand, argc); hand = NULL; } h5tools_setstatus(EXIT_FAILURE); return 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 = -1; hid_t gid = -1; H5E_auto2_t func; H5E_auto2_t tools_func; H5O_info_t oi; struct handler_t *hand = NULL; int i; unsigned u; void *edata; void *tools_edata; char *fname = NULL; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); h5tools_dump_header_format = &h5tools_standardformat; dump_function_table = &ddl_function_table; dump_indent = 0; /* Disable error reporting */ H5Eget_auto2(H5E_DEFAULT, &func, &edata); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); /* Initialize h5tools lib */ h5tools_init(); /* Disable tools error reporting */ H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); if((hand = parse_command_line(argc, argv))==NULL) { goto done; } if (bin_output && outfname == NULL) { error_msg("binary output requires a file name, use -o \n"); h5tools_setstatus(EXIT_FAILURE); goto done; } if (enable_error_stack) { H5Eset_auto2(H5E_DEFAULT, func, edata); H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); } /* Check for conflicting options */ if (doxml) { if (!display_all) { error_msg("option \"%s\" not available for XML\n", "to display selected objects"); h5tools_setstatus(EXIT_FAILURE); goto done; } else if (display_bb) { error_msg("option \"%s\" not available for XML\n", "--boot-block"); h5tools_setstatus(EXIT_FAILURE); goto done; } else if (display_oid == 1) { error_msg("option \"%s\" not available for XML\n", "--object-ids"); h5tools_setstatus(EXIT_FAILURE); goto done; } else if (display_char == TRUE) { error_msg("option \"%s\" not available for XML\n", "--string"); h5tools_setstatus(EXIT_FAILURE); goto done; } else if (usingdasho) { error_msg("option \"%s\" not available for XML\n", "--output"); h5tools_setstatus(EXIT_FAILURE); goto done; } } 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()); h5tools_setstatus(EXIT_FAILURE); goto done; } /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); while(opt_ind < argc) { 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); h5tools_setstatus(EXIT_FAILURE); goto done; } /* 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 && HDstrcmp(xmlnsprefix,"")) { error_msg("Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n"); h5tools_setstatus(EXIT_FAILURE); goto done; } } } /* 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(h5tools_dump_header_format->filebegin, fname, h5tools_dump_header_format->fileblockbegin); } else { PRINTVALSTREAM(rawoutstream, "\n"); /* alternative first element, depending on schema or DTD. */ if (useschema) { if (HDstrcmp(xmlnsprefix,"") == 0) { PRINTSTREAM(rawoutstream, "\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 = HDstrrchr(ns,(int)':'); if (indx) *indx = '\0'; PRINTSTREAM(rawoutstream, "<%sHDF5-File xmlns:%s=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File\" " "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" " "xsi:schemaLocation=\"http://hdfgroup.org/HDF5/XML/schema/HDF5-File " "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\">\n",xmlnsprefix,ns); HDfree(ns); } } else { PRINTSTREAM(rawoutstream, "\n", xml_dtd_uri); PRINTVALSTREAM(rawoutstream, "\n"); } } if (!doxml) { if (display_fi) { PRINTVALSTREAM(rawoutstream, "\n"); dump_fcontents(fid); end_obj(h5tools_dump_header_format->fileend,h5tools_dump_header_format->fileblockend); PRINTVALSTREAM(rawoutstream, "\n"); 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 { if (!doxml) dump_indent += COL; dump_function_table->dump_group_function(gid, "/" ); if (!doxml) dump_indent -= COL; PRINTVALSTREAM(rawoutstream, "\n"); } 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); } } PRINTVALSTREAM(rawoutstream, "\n"); } if (!doxml) { end_obj(h5tools_dump_header_format->fileend, h5tools_dump_header_format->fileblockend); PRINTVALSTREAM(rawoutstream, "\n"); } else { PRINTSTREAM(rawoutstream, "\n", xmlnsprefix); } /* Free tables for objects */ table_list_free(); if(fid >=0) if (H5Fclose(fid) < 0) h5tools_setstatus(EXIT_FAILURE); if(prefix) HDfree(prefix); if(fname) HDfree(fname); } /* end while */ if(hand) free_handler(hand, argc); /* To Do: clean up XML table */ leave(h5tools_getstatus()); done: /* Free tables for objects */ table_list_free(); if(fid >=0) if (H5Fclose(fid) < 0) h5tools_setstatus(EXIT_FAILURE); if(prefix) HDfree(prefix); if(fname) HDfree(fname); if(hand) free_handler(hand, argc); /* To Do: clean up XML table */ H5Eset_auto2(H5E_DEFAULT, func, edata); leave(h5tools_getstatus()); } /*------------------------------------------------------------------------- * 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: * *------------------------------------------------------------------------- */ 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); HDassert(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 * *------------------------------------------------------------------------- */ 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 */