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hdf5/tools/h5dump/h5dump.c

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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
*
*-------------------------------------------------------------------------
*/
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)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':
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':
h5tools_nCols = HDatoi(opt_arg);
if (h5tools_nCols <= 0) {
h5tools_nCols = 65535;
}
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] = 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 */
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