diff options
Diffstat (limited to 'tools/h5dump/h5dump.c')
| -rw-r--r-- | tools/h5dump/h5dump.c | 1802 |
1 files changed, 0 insertions, 1802 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c deleted file mode 100644 index 562cfd5..0000000 --- a/tools/h5dump/h5dump.c +++ /dev/null @@ -1,1802 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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 <stdio.h> -#include <stdlib.h> - -#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/DTD/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:A*q:z:m:RECM:O*N:vG:"; -static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "hel", no_arg, 'h' }, - { "contents", optional_arg, 'n' }, - { "properties", no_arg, 'p' }, - { "superblock", no_arg, 'B' }, - { "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", optional_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' }, - { "any_path", require_arg, 'N' }, - { "vds-view-first-missing", no_arg, 'v' }, - { "vds-gap-size", require_arg, 'G' }, - { 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 - *------------------------------------------------------------------------- - */ -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, " -V, --version Print version number and exit\n"); - PRINTVALSTREAM(rawoutstream, "--------------- File Options ---------------\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, " -f D, --filedriver=D Specify which driver to open the file with\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, " -O F, --ddl=F Output ddl text into file F\n"); - PRINTVALSTREAM(rawoutstream, " Use blank(empty) filename F to suppress ddl display\n"); - PRINTVALSTREAM(rawoutstream, "--------------- Object Options ---------------\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, " -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, " -t P, --datatype=P Print the specified named datatype\n"); - PRINTVALSTREAM(rawoutstream, " -N P, --any_path=P Print any attribute, dataset, group, datatype, or link that matches P\n"); - PRINTVALSTREAM(rawoutstream, " P can be the absolute path or just a relative path.\n"); - PRINTVALSTREAM(rawoutstream, " -A, --onlyattr Print the header and value of attributes\n"); - PRINTVALSTREAM(rawoutstream, " Optional value 0 suppresses printing attributes.\n"); - PRINTVALSTREAM(rawoutstream, " --vds-view-first-missing Set the VDS bounds to first missing mapped elements.\n"); - PRINTVALSTREAM(rawoutstream, " --vds-gap-size=N Set the missing file gap size, N=non-negative integers\n"); - PRINTVALSTREAM(rawoutstream, "--------------- Object Property Options ---------------\n"); - PRINTVALSTREAM(rawoutstream, " -i, --object-ids Print the object ids\n"); - PRINTVALSTREAM(rawoutstream, " -p, --properties Print dataset filters, storage layout and fill value\n"); - PRINTVALSTREAM(rawoutstream, " -M L, --packedbits=L Print packed bits as unsigned integers, using mask\n"); - PRINTVALSTREAM(rawoutstream, " format L for an integer dataset specified with\n"); - PRINTVALSTREAM(rawoutstream, " option -d. L is a list of offset,length values,\n"); - PRINTVALSTREAM(rawoutstream, " separated by commas. Offset is the beginning bit in\n"); - PRINTVALSTREAM(rawoutstream, " the data value and length is the number of bits of\n"); - PRINTVALSTREAM(rawoutstream, " the mask.\n"); - PRINTVALSTREAM(rawoutstream, " -R, --region Print dataset pointed by region references\n"); - PRINTVALSTREAM(rawoutstream, "--------------- Formatting Options ---------------\n"); - PRINTVALSTREAM(rawoutstream, " -e, --escape Escape non printing characters\n"); - PRINTVALSTREAM(rawoutstream, " -r, --string Print 1-byte integer datasets as ASCII\n"); - PRINTVALSTREAM(rawoutstream, " -y, --noindex Do not print array indices with the data\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, " --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, " -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, "--------------- XML Options ---------------\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, "\n"); - PRINTVALSTREAM(rawoutstream, "--------------- Subsetting Options ---------------\n"); - PRINTVALSTREAM(rawoutstream, " Subsetting is available by using the following options with a dataset\n"); - PRINTVALSTREAM(rawoutstream, " option. 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, "--------------- Option Argument Conventions ---------------\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, " See examples below for family, split, and multi driver special file name usage.\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"); - PRINTVALSTREAM(rawoutstream, " 7) Dataset foo in multi files mf-s.h5, mf-b.h5, mf-r.h5, mf-g.h5, mf-l.h5 and mf-o.h5\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -f multi mf\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " 8) Dataset foo in family files fam00000.h5 fam00001.h5 and fam00002.h5\n"); - PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " h5dump -d /foo -f family fam%%05d.h5\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) { - h5dump_table_items_t *tmp_ptr; - - table_list.nalloc = MAX(1, table_list.nalloc * 2); - if(NULL == (tmp_ptr = (h5dump_table_items_t *)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 - * - *------------------------------------------------------------------------- - */ -H5_ATTR_PURE 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_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: <none> - * - * 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)HDstrtoull(ptr, NULL, 0); - - while (HDisdigit(*ptr)) - /* scroll to end of integer */ - ptr++; - } - d->data = p_list; - d->len = size_count; -} - -/*------------------------------------------------------------------------- - * 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; - 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 soffset_value; - unsigned offset_value; - int slength_value; - unsigned 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; - } - soffset_value = HDatoi(ptr); - offset_value = (unsigned)soffset_value; - if (soffset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) { - error_msg("Packed Bit offset value(%d) must be between 0 and %u\n", - soffset_value, (unsigned)(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; - } - slength_value = HDatoi(ptr); - if (slength_value <= 0) { - error_msg("Packed Bit length value(%d) must be positive.\n", slength_value); - return FAIL; - } - length_value = (unsigned)slength_value; - if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX) { - error_msg("Packed Bit offset+length value(%u) too large. Max is %u\n", - offset_value+length_value, (unsigned)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 = ~0ULL; - if(length_value < (int)(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': - if ( opt_arg != NULL) { - if(0 == HDatoi(opt_arg)) include_attrs = FALSE; - } - else { - 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': - { - int sh5tools_nCols = HDatoi(opt_arg); - - if (sh5tools_nCols <= 0) - h5tools_nCols = 65535; - else - h5tools_nCols = (unsigned)sh5tools_nCols; - last_was_dset = FALSE; - } - break; - case 'N': - display_all = 0; - - for (i = 0; i < argc; i++) - if (!hand[i].func) { - hand[i].func = handle_paths; - hand[i].obj = HDstrdup(opt_arg); - break; - } - - 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 (h5tools_set_output_file(opt_arg, 0) < 0) { - usage(h5tools_getprogname()); - goto error; - } - break; - - case 'o': - if ( bin_output ) { - if (h5tools_set_data_output_file(opt_arg, 1) < 0) { - usage(h5tools_getprogname()); - goto error; - } - } - else { - if(display_attr_data && !display_data) { - if (h5tools_set_attr_output_file(opt_arg, 0) < 0) { - usage(h5tools_getprogname()); - goto error; - } - } - if(display_data || display_all) { - if (h5tools_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 (h5tools_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; - case 'v': - display_vds_first = TRUE; - break; - case 'G': - vds_gap_size = HDatoi(opt_arg); - if (vds_gap_size < 0) { - usage(h5tools_getprogname()); - goto error; - } - 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 <filename>\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, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); - - /* alternative first element, depending on schema or DTD. */ - if (useschema) { - if (HDstrcmp(xmlnsprefix,"") == 0) { - PRINTSTREAM(rawoutstream, "<HDF5-File xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"%s\">\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.xsd\" " - "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, "<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n", xml_dtd_uri); - PRINTVALSTREAM(rawoutstream, "<HDF5-File>\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, "</%sHDF5-File>\n", xmlnsprefix); - } - /* Free tables for objects */ - table_list_free(); - - if(fid >=0) - if (H5Fclose(fid) < 0) - h5tools_setstatus(EXIT_FAILURE); - - if(prefix) { - HDfree(prefix); - prefix = NULL; - } - if(fname) { - HDfree(fname); - fname = NULL; - } - } /* 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); - prefix = NULL; - } - if(fname) { - HDfree(fname); - fname = NULL; - } - - 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<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) { - memb_fapl[mt] = H5P_DEFAULT; - memb_map[mt] = mt; - sprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]); - memb_name[mt] = sv[mt]; - memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10); - } - - if (H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0) - return -1; - } - else if (!HDstrcmp(name, "family")) { - hsize_t fam_size = 100*1024*1024; /*100 MB*/ - - /* Family of files, each 1MB and using the default driver */ - if ((val=HDstrtok(NULL, " \t\n\r"))) - fam_size = (hsize_t)(HDstrtod(val, NULL) * 1024*1024); - if (H5Pset_fapl_family(fapl, fam_size, H5P_DEFAULT)<0) - return -1; - } - else if (!HDstrcmp(name, "log")) { - long log_flags = H5FD_LOG_LOC_IO; - - /* Log file access */ - if ((val = HDstrtok(NULL, " \t\n\r"))) - log_flags = HDstrtol(val, NULL, 0); - - if (H5Pset_fapl_log(fapl, NULL, (unsigned)log_flags, 0) < 0) - return -1; - } - else if (!HDstrcmp(name, "direct")) { - /* Substitute Direct I/O driver with sec2 driver temporarily because - * some output has sec2 driver as the standard. */ - if (H5Pset_fapl_sec2(fapl)<0) return -1; - } - else { - /* Unknown driver */ - return -1; - } - - return fapl; -} - - -/*------------------------------------------------------------------------- - * Function: init_prefix - * - * Purpose: allocate and initialize prefix - * - * Return: void - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static void -init_prefix(char **prfx, size_t prfx_len) -{ - HDassert(prfx_len > 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 */ - |