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hdf5/tools/h5dump/h5dump.c
Quincey Koziol defe612ab2 [svn-r9370] Purpose: 
Refactor code

Description:
    Refactor common code for determining the native type for using in the
tools into separate routine.

    Also, reduce diffs between the two branches and bring back some fixes from
the development branch to the release branch.

Platforms tested:
    FreeBSD 4.10 (sleipnir)
    too minor to require h5committest
2004-10-06 11:11:18 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include "h5dump.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5tools_ref.h"
#include "h5trav.h"
/* module-scoped variables */
const char *progname = "h5dump";
/* 3 private values: can't be set, but can be read.
Note: these are defined in H5Zprivate, they are
duplicated here.
*/
#define H5_SZIP_LSB_OPTION_MASK 8
#define H5_SZIP_MSB_OPTION_MASK 16
#define H5_SZIP_RAW_OPTION_MASK 128
int d_status = EXIT_SUCCESS;
static int unamedtype = 0; /* shared data type with no name */
static size_t prefix_len = 1024;
static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL;
char *prefix;
static const char *driver = NULL; /* The driver to open the file with. */
static const dump_header *dump_header_format;
/* things to display or which are set via command line parameters */
static int display_all = TRUE;
static int display_oid = FALSE;
static int display_data = TRUE;
static int display_attr_data = TRUE;
static int display_char = FALSE; /*print 1-byte numbers as ASCII */
static int usingdasho = FALSE;
static int display_bb = FALSE; /*superblock */
static int display_dcpl = FALSE; /*dcpl */
static int display_fi = FALSE; /*file index */
static int display_ai = TRUE; /*array index */
static int display_escape = FALSE; /*escape non printable characters */
/**
** Added for XML **
**/
/* module-scoped variables for XML option */
#define DEFAULT_XSD "http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd"
#define DEFAULT_DTD "http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd"
static int doxml = 0;
static int useschema = 1;
static const char *xml_dtd_uri = NULL;
static const char *xmlnsprefix="hdf5:";
hid_t thefile = -1;
/** end XML **/
/* internal functions */
static hid_t h5_fileaccess(void);
static void dump_oid(hid_t oid);
static void print_enum(hid_t type);
static herr_t dump_all(hid_t group, const char *name, void *op_data);
#ifdef LATER
static void check_compression(hid_t);
#endif /* LATER */
static int xml_name_to_XID(const char *, char *, int , int );
static h5dump_t dataformat = {
0, /*raw */
"", /*fmt_raw */
"%d", /*fmt_int */
"%u", /*fmt_uint */
"%d", /*fmt_schar */
"%u", /*fmt_uchar */
"%d", /*fmt_short */
"%u", /*fmt_ushort */
"%ld", /*fmt_long */
"%lu", /*fmt_ulong */
NULL, /*fmt_llong */
NULL, /*fmt_ullong */
"%g", /*fmt_double */
"%g", /*fmt_float */
0, /*ascii */
0, /*str_locale */
0, /*str_repeat */
"[ ", /*arr_pre */
",", /*arr_sep */
" ]", /*arr_suf */
1, /*arr_linebreak */
"", /*cmpd_name */
",\n", /*cmpd_sep */
"{\n", /*cmpd_pre */
"}", /*cmpd_suf */
"\n", /*cmpd_end */
", ", /*vlen_sep */
"(", /*vlen_pre */
")", /*vlen_suf */
"", /*vlen_end */
"%s", /*elmt_fmt */
",", /*elmt_suf1 */
" ", /*elmt_suf2 */
"", /*idx_n_fmt */
"", /*idx_sep */
"", /*idx_fmt */
80, /*line_ncols *//*standard default columns */
0, /*line_per_line */
"", /*line_pre */
"%s", /*line_1st */
"%s", /*line_cont */
"", /*line_suf */
"", /*line_sep */
1, /*line_multi_new */
" ", /*line_indent */
1, /*skip_first */
1, /*obj_hidefileno */
" "H5_PRINTF_HADDR_FMT, /*obj_format */
1, /*dset_hidefileno */
"DATASET "H5_PRINTF_HADDR_FMT" ", /*dset_format */
"%s", /*dset_blockformat_pre */
"%s", /*dset_ptformat_pre */
"%s", /*dset_ptformat */
1, /*array indices */
1 /*escape non printable characters */
};
/**
** Added for XML **
**/
/*
* Alternative formating for data dumped to XML
* In general, the numbers are the same, but separators
* except spaces are not used.
*
* Some of these are not used, as some kinds of data are
* dumped in completely new subroutines.
*
* Some of this formatting may yet need to change.
*
* This table only affects XML output.
*/
static h5dump_t xml_dataformat = {
0, /*raw */
"", /*fmt_raw */
"%d", /*fmt_int */
"%u", /*fmt_uint */
"%d", /*fmt_schar */
"%u", /*fmt_uchar */
"%d", /*fmt_short */
"%u", /*fmt_ushort */
"%ld", /*fmt_long */
"%lu", /*fmt_ulong */
NULL, /*fmt_llong */
NULL, /*fmt_ullong */
"%g", /*fmt_double */
"%g", /*fmt_float */
0, /*ascii */
0, /*str_locale */
0, /*str_repeat */
" ", /*arr_pre */
"", /*arr_sep */
"", /*arr_suf */
1, /*arr_linebreak */
"", /*cmpd_name */
" ", /*cmpd_sep */
"", /*cmpd_pre */
"", /*cmpd_suf */
"", /*cmpd_end */
" ", /*vlen_sep */
" ", /*vlen_pre */
"", /*vlen_suf */
"", /*vlen_end */
"%s", /*elmt_fmt */
"", /*elmt_suf1 */
" ", /*elmt_suf2 */
"", /*idx_n_fmt */
"", /*idx_sep */
"", /*idx_fmt */
80, /*line_ncols *//*standard default columns */
0, /*line_per_line */
"", /*line_pre */
"%s", /*line_1st */
"%s", /*line_cont */
"", /*line_suf */
"", /*line_sep */
1, /*line_multi_new */
" ", /*line_indent */
1, /*skip_first */
1, /*obj_hidefileno */
" "H5_PRINTF_HADDR_FMT, /*obj_format */
1, /*dset_hidefileno */
"DATASET "H5_PRINTF_HADDR_FMT" ", /*dset_format */
"%s", /*dset_blockformat_pre */
"%s", /*dset_ptformat_pre */
"%s", /*dset_ptformat */
0, /*array indices */
0 /*escape non printable characters */
};
/** XML **/
static const dump_header standardformat = {
"standardformat", /*name */
"HDF5", /*fileebgin */
"", /*fileend */
SUPER_BLOCK, /*bootblockbegin */
"", /*bootblockend */
GROUPNAME, /*groupbegin */
"", /*groupend */
DATASET, /*datasetbegin */
"", /*datasetend */
ATTRIBUTE, /*attributebegin */
"", /*attributeend */
DATATYPE, /*datatypebegin */
"", /*datatypeend */
DATASPACE, /*dataspacebegin */
"", /*dataspaceend */
DATA, /*databegin */
"", /*dataend */
SOFTLINK, /*softlinkbegin */
"", /*softlinkend */
SUBSET, /*subsettingbegin */
"", /*subsettingend */
START, /*startbegin */
"", /*startend */
STRIDE, /*stridebegin */
"", /*strideend */
COUNT, /*countbegin */
"", /*countend */
BLOCK, /*blockbegin */
"", /*blockend */
"{", /*fileblockbegin */
"}", /*fileblockend */
"{", /*bootblockblockbegin */
"}", /*bootblockblockend */
"{", /*groupblockbegin */
"}", /*groupblockend */
"{", /*datasetblockbegin */
"}", /*datasetblockend */
"{", /*attributeblockbegin */
"}", /*attributeblockend */
"", /*datatypeblockbegin */
"", /*datatypeblockend */
"", /*dataspaceblockbegin */
"", /*dataspaceblockend */
"{", /*datablockbegin */
"}", /*datablockend */
"{", /*softlinkblockbegin */
"}", /*softlinkblockend */
"{", /*strblockbegin */
"}", /*strblockend */
"{", /*enumblockbegin */
"}", /*enumblockend */
"{", /*structblockbegin */
"}", /*structblockend */
"{", /*vlenblockbegin */
"}", /*vlenblockend */
"{", /*subsettingblockbegin */
"}", /*subsettingblockend */
"(", /*startblockbegin */
");", /*startblockend */
"(", /*strideblockbegin */
");", /*strideblockend */
"(", /*countblockbegin */
");", /*countblockend */
"(", /*blockblockbegin */
");", /*blockblockend */
"", /*dataspacedescriptionbegin */
"", /*dataspacedescriptionend */
"(", /*dataspacedimbegin */
")", /*dataspacedimend */
};
/**
** Added for XML **
**/
/* internal functions used by XML option */
static void xml_print_datatype(hid_t, unsigned);
static void xml_print_enum(hid_t);
static int xml_print_refs(hid_t, int);
static int xml_print_strs(hid_t, int);
static char *xml_escape_the_string(const char *, int);
static char *xml_escape_the_name(const char *);
/* a structure for handling the order command-line parameters come in */
struct handler_t {
void (*func)(hid_t, char *, void *);
char *obj;
struct subset_t *subset_info;
};
/*
* Command-line options: The user can specify short or long-named
* parameters. The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
static const char *s_opts = "hnpeyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o:s:S:A";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "hel", no_arg, 'h' },
{ "contents", no_arg, 'n' },
{ "properties", no_arg, 'p' },
{ "boot-block", no_arg, 'B' },
{ "boot-bloc", no_arg, 'B' },
{ "boot-blo", no_arg, 'B' },
{ "boot-bl", no_arg, 'B' },
{ "boot-b", no_arg, 'B' },
{ "boot", no_arg, 'B' },
{ "boo", no_arg, 'B' },
{ "bo", no_arg, 'B' },
{ "header", no_arg, 'H' },
{ "heade", no_arg, 'H' },
{ "head", no_arg, 'H' },
{ "hea", no_arg, 'H' },
{ "object-ids", no_arg, 'i' },
{ "object-id", no_arg, 'i' },
{ "object-i", no_arg, 'i' },
{ "object", no_arg, 'i' },
{ "objec", no_arg, 'i' },
{ "obje", no_arg, 'i' },
{ "obj", no_arg, 'i' },
{ "ob", no_arg, 'i' },
{ "version", no_arg, 'V' },
{ "versio", no_arg, 'V' },
{ "versi", no_arg, 'V' },
{ "vers", no_arg, 'V' },
{ "ver", no_arg, 'V' },
{ "ve", no_arg, 'V' },
{ "attribute", require_arg, 'a' },
{ "attribut", require_arg, 'a' },
{ "attribu", require_arg, 'a' },
{ "attrib", require_arg, 'a' },
{ "attri", require_arg, 'a' },
{ "attr", require_arg, 'a' },
{ "att", require_arg, 'a' },
{ "at", require_arg, 'a' },
{ "block", require_arg, 'k' },
{ "bloc", require_arg, 'k' },
{ "blo", require_arg, 'k' },
{ "bl", require_arg, 'k' },
{ "count", require_arg, 'c' },
{ "coun", require_arg, 'c' },
{ "cou", require_arg, 'c' },
{ "co", require_arg, 'c' },
{ "dataset", require_arg, 'd' },
{ "datase", require_arg, 'd' },
{ "datas", require_arg, 'd' },
{ "datatype", require_arg, 't' },
{ "datatyp", require_arg, 't' },
{ "dataty", require_arg, 't' },
{ "datat", require_arg, 't' },
{ "filedriver", require_arg, 'f' },
{ "filedrive", require_arg, 'f' },
{ "filedriv", require_arg, 'f' },
{ "filedri", require_arg, 'f' },
{ "filedr", require_arg, 'f' },
{ "filed", require_arg, 'f' },
{ "file", require_arg, 'f' },
{ "fil", require_arg, 'f' },
{ "fi", require_arg, 'f' },
{ "group", require_arg, 'g' },
{ "grou", require_arg, 'g' },
{ "gro", require_arg, 'g' },
{ "gr", require_arg, 'g' },
{ "output", require_arg, 'o' },
{ "outpu", require_arg, 'o' },
{ "outp", require_arg, 'o' },
{ "out", require_arg, 'o' },
{ "ou", require_arg, 'o' },
{ "soft-link", require_arg, 'l' },
{ "soft-lin", require_arg, 'l' },
{ "soft-li", require_arg, 'l' },
{ "soft-l", require_arg, 'l' },
{ "soft", require_arg, 'l' },
{ "sof", require_arg, 'l' },
{ "so", 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' },
{ NULL, 0, '\0' }
};
/**
** Change for XML **
**
** The 'dump_xxx' functions have two versions, standard and XML.
**
** They are called indirectly through the 'dump_function_table'.
** e.g., dump_group(...) becomes dump_functions->dump_group(...);
**
** The standard functions are unchanged except for the way
** they are called
**/
/* The dump functions of the dump_function_table */
/* standard format: no change */
static void dump_group(hid_t, const char *);
static void dump_named_datatype(hid_t, const char *);
static void dump_dataset(hid_t, const char *, struct subset_t *);
static void dump_dataspace(hid_t space);
static void dump_datatype(hid_t type);
static herr_t dump_attr(hid_t, const char *, void *);
static void dump_data(hid_t, int, struct subset_t *, int);
static void dump_dcpl(hid_t dcpl, hid_t type_id, hid_t obj_id);
static void dump_comment(hid_t obj_id);
static void dump_fcpl(hid_t fid);
static void dump_fcontents(hid_t fid);
/* XML format: same interface, alternative output */
static void xml_dump_group(hid_t, const char *);
static void xml_dump_named_datatype(hid_t, const char *);
static void xml_dump_dataset(hid_t, const char *, struct subset_t *);
static void xml_dump_dataspace(hid_t space);
static void xml_dump_datatype(hid_t type);
static herr_t xml_dump_attr(hid_t, const char *, void *);
static void xml_dump_data(hid_t, int, struct subset_t *, int);
/**
** Added for XML **
**
** This is the global dispatch table for the dump functions.
**/
/* the table of dump functions */
typedef struct dump_functions_t {
void (*dump_group_function) (hid_t, const char *);
void (*dump_named_datatype_function) (hid_t, const char *);
void (*dump_dataset_function) (hid_t, const char *, struct subset_t *);
void (*dump_dataspace_function) (hid_t);
void (*dump_datatype_function) (hid_t);
herr_t (*dump_attribute_function) (hid_t, const char *, void *);
void (*dump_data_function) (hid_t, int, struct subset_t *, int);
} dump_functions;
/* Standard DDL output */
static const dump_functions ddl_function_table = {
dump_group,
dump_named_datatype,
dump_dataset,
dump_dataspace,
dump_datatype,
dump_attr,
dump_data
};
/* XML output */
static const dump_functions xml_function_table = {
xml_dump_group,
xml_dump_named_datatype,
xml_dump_dataset,
xml_dump_dataspace,
xml_dump_datatype,
xml_dump_attr,
xml_dump_data
};
/*
* The global table is set to either ddl_function_table or
* xml_function_table in the initialization.
*/
static const dump_functions *dump_function_table;
/*-------------------------------------------------------------------------
* Function: leave
*
* Purpose: Shutdown MPI & HDF5 and call exit()
*
* Return: Does not return
*
* Programmer: Quincey Koziol
* Saturday, 31. January 2004
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
leave(int ret)
{
h5tools_close();
exit(ret);
}
/*-------------------------------------------------------------------------
* Function: usage
*
* Purpose: Print the usage message about dumper
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
usage(const char *prog)
{
fflush(stdout);
fprintf(stdout, "usage: %s [OPTIONS] file\n", prog);
fprintf(stdout, " OPTIONS\n");
fprintf(stdout, " -h, --help Print a usage message and exit\n");
fprintf(stdout, " -n, --contents Print a list of the file contents and exit\n");
fprintf(stdout, " -B, --bootblock Print the content of the boot block\n");
fprintf(stdout, " -H, --header Print the header only; no data is displayed\n");
fprintf(stdout, " -A Print the header and value of attributes; data of datasets is not displayed\n");
fprintf(stdout, " -i, --object-ids Print the object ids\n");
fprintf(stdout, " -r, --string Print 1-byte integer datasets as ASCII\n");
fprintf(stdout, " -e, Escape non printing characters\n");
fprintf(stdout, " -V, --version Print version number and exit\n");
fprintf(stdout, " -a P, --attribute=P Print the specified attribute\n");
fprintf(stdout, " -d P, --dataset=P Print the specified dataset\n");
fprintf(stdout, " -y Do not print array indices with the data\n");
fprintf(stdout, " -p, --properties Print dataset filters, storage layout and fill value\n");
fprintf(stdout, " -f D, --filedriver=D Specify which driver to open the file with\n");
fprintf(stdout, " -g P, --group=P Print the specified group and all members\n");
fprintf(stdout, " -l P, --soft-link=P Print the value(s) of the specified soft link\n");
fprintf(stdout, " -o F, --output=F Output raw data into file F\n");
fprintf(stdout, " -t P, --datatype=P Print the specified named data type\n");
fprintf(stdout, " -w N, --width=N Set the number of columns of output\n");
fprintf(stdout, " -x, --xml Output in XML using Schema\n");
fprintf(stdout, " -u, --use-dtd Output in XML using DTD\n");
fprintf(stdout, " -D U, --xml-dtd=U Use the DTD or schema at U\n");
fprintf(stdout, " -X S, --xml-ns=S (XML Schema) Use qualified names n the XML\n");
fprintf(stdout, " \":\": no namespace, default: \"hdf5:\"\n");
fprintf(stdout, " E.g., to dump a file called `-f', use h5dump -- -f\n");
fprintf(stdout, "\n");
fprintf(stdout, " Subsetting is available by using the following options with a dataset\n");
fprintf(stdout, " attribute. Subsetting is done by selecting a hyperslab from the data.\n");
fprintf(stdout, " Thus, the options mirror those for performing a hyperslab selection.\n");
fprintf(stdout, " The START and COUNT parameters are mandatory if you do subsetting.\n");
fprintf(stdout, " The STRIDE and BLOCK parameters are optional and will default to 1 in\n");
fprintf(stdout, " each dimension.\n");
fprintf(stdout, "\n");
fprintf(stdout, " -s L, --start=L Offset of start of subsetting selection\n");
fprintf(stdout, " -S L, --stride=L Hyperslab stride\n");
fprintf(stdout, " -c L, --count=L Number of blocks to include in selection\n");
fprintf(stdout, " -k L, --block=L Size of block in hyperslab\n");
fprintf(stdout, "\n");
fprintf(stdout, " D - is the file driver to use in opening the file. Acceptable values\n");
fprintf(stdout, " are \"sec2\", \"family\", \"split\", \"multi\", and \"stream\". Without\n");
fprintf(stdout, " the file driver flag, the file will be opened with each driver in\n");
fprintf(stdout, " turn and in the order specified above until one driver succeeds\n");
fprintf(stdout, " in opening the file.\n");
fprintf(stdout, " F - is a filename.\n");
fprintf(stdout, " P - is the full path from the root group to the object.\n");
fprintf(stdout, " N - is an integer greater than 1.\n");
fprintf(stdout, " L - is a list of integers the number of which are equal to the\n");
fprintf(stdout, " number of dimensions in the dataspace being queried\n");
fprintf(stdout, " U - is a URI reference (as defined in [IETF RFC 2396],\n");
fprintf(stdout, " updated by [IETF RFC 2732])\n");
fprintf(stdout, "\n");
fprintf(stdout, " Examples:\n");
fprintf(stdout, "\n");
fprintf(stdout, " 1) Attribute foo of the group /bar_none in file quux.h5\n");
fprintf(stdout, "\n");
fprintf(stdout, " h5dump -a /bar_none/foo quux.h5\n");
fprintf(stdout, "\n");
fprintf(stdout, " 2) Selecting a subset from dataset /foo in file quux.h5\n");
fprintf(stdout, "\n");
fprintf(stdout, " h5dump -d /foo -s \"0,1\" -S \"1,1\" -c \"2,3\" -k \"2,2\" quux.h5\n");
fprintf(stdout, "\n");
}
/*-------------------------------------------------------------------------
* Function: print_datatype
*
* Purpose: print the data type.
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
print_datatype(hid_t type,unsigned in_group)
{
char *fname;
hid_t mtype, str_type;
unsigned nmembers;
int perm[H5DUMP_MAX_RANK];
unsigned ndims;
unsigned i;
size_t size=0;
hsize_t dims[H5DUMP_MAX_RANK];
H5T_str_t str_pad;
H5T_cset_t cset;
H5G_stat_t statbuf;
hid_t super;
hid_t tmp_type;
htri_t is_vlstr=FALSE;
herr_t ret; /* Generic return value */
if (!in_group && H5Tcommitted(type) > 0) {
H5Gget_objinfo(type, ".", TRUE, &statbuf);
ret = search_obj(type_table, statbuf.objno);
if (ret >= 0) {
if (!type_table->objs[ret].recorded)
HDfprintf(stdout,"\"/#%a\"", type_table->objs[ret].objno);
else
printf("\"%s\"", type_table->objs[ret].objname);
} else {
error_msg(progname, "unknown committed type.\n");
d_status = EXIT_FAILURE;
}
} else {
switch (H5Tget_class(type)) {
case H5T_INTEGER:
if (H5Tequal(type, H5T_STD_I8BE)) {
printf("H5T_STD_I8BE");
} else if (H5Tequal(type, H5T_STD_I8LE)) {
printf("H5T_STD_I8LE");
} else if (H5Tequal(type, H5T_STD_I16BE)) {
printf("H5T_STD_I16BE");
} else if (H5Tequal(type, H5T_STD_I16LE)) {
printf("H5T_STD_I16LE");
} else if (H5Tequal(type, H5T_STD_I32BE)) {
printf("H5T_STD_I32BE");
} else if (H5Tequal(type, H5T_STD_I32LE)) {
printf("H5T_STD_I32LE");
} else if (H5Tequal(type, H5T_STD_I64BE)) {
printf("H5T_STD_I64BE");
} else if (H5Tequal(type, H5T_STD_I64LE)) {
printf("H5T_STD_I64LE");
} else if (H5Tequal(type, H5T_STD_U8BE)) {
printf("H5T_STD_U8BE");
} else if (H5Tequal(type, H5T_STD_U8LE)) {
printf("H5T_STD_U8LE");
} else if (H5Tequal(type, H5T_STD_U16BE)) {
printf("H5T_STD_U16BE");
} else if (H5Tequal(type, H5T_STD_U16LE)) {
printf("H5T_STD_U16LE");
} else if (H5Tequal(type, H5T_STD_U32BE)) {
printf("H5T_STD_U32BE");
} else if (H5Tequal(type, H5T_STD_U32LE)) {
printf("H5T_STD_U32LE");
} else if (H5Tequal(type, H5T_STD_U64BE)) {
printf("H5T_STD_U64BE");
} else if (H5Tequal(type, H5T_STD_U64LE)) {
printf("H5T_STD_U64LE");
} else if (H5Tequal(type, H5T_NATIVE_SCHAR)) {
printf("H5T_NATIVE_SCHAR");
} else if (H5Tequal(type, H5T_NATIVE_UCHAR)) {
printf("H5T_NATIVE_UCHAR");
} else if (H5Tequal(type, H5T_NATIVE_SHORT)) {
printf("H5T_NATIVE_SHORT");
} else if (H5Tequal(type, H5T_NATIVE_USHORT)) {
printf("H5T_NATIVE_USHORT");
} else if (H5Tequal(type, H5T_NATIVE_INT)) {
printf("H5T_NATIVE_INT");
} else if (H5Tequal(type, H5T_NATIVE_UINT)) {
printf("H5T_NATIVE_UINT");
} else if (H5Tequal(type, H5T_NATIVE_LONG)) {
printf("H5T_NATIVE_LONG");
} else if (H5Tequal(type, H5T_NATIVE_ULONG)) {
printf("H5T_NATIVE_ULONG");
} else if (H5Tequal(type, H5T_NATIVE_LLONG)) {
printf("H5T_NATIVE_LLONG");
} else if (H5Tequal(type, H5T_NATIVE_ULLONG)) {
printf("H5T_NATIVE_ULLONG");
} else {
printf("undefined integer");
d_status = EXIT_FAILURE;
}
break;
case H5T_FLOAT:
if (H5Tequal(type, H5T_IEEE_F32BE)) {
printf("H5T_IEEE_F32BE");
} else if (H5Tequal(type, H5T_IEEE_F32LE)) {
printf("H5T_IEEE_F32LE");
} else if (H5Tequal(type, H5T_IEEE_F64BE)) {
printf("H5T_IEEE_F64BE");
} else if (H5Tequal(type, H5T_IEEE_F64LE)) {
printf("H5T_IEEE_F64LE");
} else if (H5Tequal(type, H5T_NATIVE_FLOAT)) {
printf("H5T_NATIVE_FLOAT");
} else if (H5Tequal(type, H5T_NATIVE_DOUBLE)) {
printf("H5T_NATIVE_DOUBLE");
} else if (H5Tequal(type, H5T_NATIVE_LDOUBLE)) {
printf("H5T_NATIVE_LDOUBLE");
} else {
printf("undefined float");
d_status = EXIT_FAILURE;
}
break;
case H5T_TIME:
printf("H5T_TIME: not yet implemented");
break;
case H5T_STRING:
/* Make a copy of type in memory in case when TYPE is on disk, the size
* will be bigger than in memory. This makes it easier to compare
* types in memory. */
tmp_type = H5Tcopy(type);
size = H5Tget_size(tmp_type);
str_pad = H5Tget_strpad(tmp_type);
cset = H5Tget_cset(tmp_type);
is_vlstr = H5Tis_variable_str(tmp_type);
printf("H5T_STRING %s\n", dump_header_format->strblockbegin);
indent += COL;
indentation(indent + COL);
if(is_vlstr)
printf("%s H5T_VARIABLE;\n", STRSIZE);
else
printf("%s %d;\n", STRSIZE, (int) size);
indentation(indent + COL);
printf("%s ", STRPAD);
if (str_pad == H5T_STR_NULLTERM)
printf("H5T_STR_NULLTERM;\n");
else if (str_pad == H5T_STR_NULLPAD)
printf("H5T_STR_NULLPAD;\n");
else if (str_pad == H5T_STR_SPACEPAD)
printf("H5T_STR_SPACEPAD;\n");
else
printf("H5T_STR_ERROR;\n");
indentation(indent + COL);
printf("%s ", CSET);
if (cset == H5T_CSET_ASCII)
printf("H5T_CSET_ASCII;\n");
else
printf("unknown_cset;\n");
str_type = H5Tcopy(H5T_C_S1);
if(is_vlstr)
H5Tset_size(str_type, H5T_VARIABLE);
else
H5Tset_size(str_type, size);
H5Tset_cset(str_type, cset);
H5Tset_strpad(str_type, str_pad);
indentation(indent + COL);
printf("%s ", CTYPE);
if (H5Tequal(tmp_type, str_type)) {
printf("H5T_C_S1;\n");
H5Tclose(str_type);
} else {
H5Tclose(str_type);
str_type = H5Tcopy(H5T_FORTRAN_S1);
H5Tset_cset(str_type, cset);
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
if (H5Tequal(tmp_type, str_type)) {
printf("H5T_FORTRAN_S1;\n");
} else {
printf("unknown_one_character_type;\n ");
d_status = EXIT_FAILURE;
}
H5Tclose(str_type);
}
H5Tclose(tmp_type);
indent -= COL;
indentation(indent + COL);
printf("%s", dump_header_format->strblockend);
break;
case H5T_BITFIELD:
if (H5Tequal(type, H5T_STD_B8BE)) {
printf("H5T_STD_B8BE");
} else if (H5Tequal(type, H5T_STD_B8LE)) {
printf("H5T_STD_B8LE");
} else if (H5Tequal(type, H5T_STD_B16BE)) {
printf("H5T_STD_B16BE");
} else if (H5Tequal(type, H5T_STD_B16LE)) {
printf("H5T_STD_B16LE");
} else if (H5Tequal(type, H5T_STD_B32BE)) {
printf("H5T_STD_B32BE");
} else if (H5Tequal(type, H5T_STD_B32LE)) {
printf("H5T_STD_B32LE");
} else if (H5Tequal(type, H5T_STD_B64BE)) {
printf("H5T_STD_B64BE");
} else if (H5Tequal(type, H5T_STD_B64LE)) {
printf("H5T_STD_B64LE");
} else {
printf("undefined bitfield");
d_status = EXIT_FAILURE;
}
break;
case H5T_OPAQUE:
printf("\n");
indentation(indent + COL);
printf("H5T_OPAQUE;\n");
indentation(indent + COL);
printf("OPAQUE_TAG \"%s\";\n", H5Tget_tag(type));
indentation(indent);
break;
case H5T_COMPOUND:
nmembers = H5Tget_nmembers(type);
printf("H5T_COMPOUND %s\n", dump_header_format->structblockbegin);
for (i = 0; i < nmembers; i++) {
fname = H5Tget_member_name(type, i);
mtype = H5Tget_member_type(type, i);
indentation(indent + COL);
if (H5Tget_class(mtype) == H5T_COMPOUND)
indent += COL;
print_datatype(mtype,0);
if (H5Tget_class(mtype) == H5T_COMPOUND)
indent -= COL;
printf(" \"%s\";\n", fname);
free(fname);
}
indentation(indent);
printf("%s", dump_header_format->structblockend);
break;
case H5T_REFERENCE:
printf("H5T_REFERENCE");
break;
case H5T_ENUM:
printf("H5T_ENUM %s\n", dump_header_format->enumblockbegin);
indent += COL;
indentation(indent + COL);
super = H5Tget_super(type);
print_datatype(super,0);
printf(";\n");
print_enum(type);
indent -= COL;
indentation(indent + COL);
printf("%s", dump_header_format->enumblockend);
break;
case H5T_VLEN:
printf("H5T_VLEN %s ", dump_header_format->vlenblockbegin);
super = H5Tget_super(type);
print_datatype(super,0);
H5Tclose(super);
/* Print closing */
printf("%s", dump_header_format->vlenblockend);
break;
case H5T_ARRAY:
/* Get array base type */
super = H5Tget_super(type);
/* Print lead-in */
printf("H5T_ARRAY { ");
/* Get array information */
ndims = H5Tget_array_ndims(type);
H5Tget_array_dims(type, dims, perm);
/* Print array dimensions */
for (i = 0; i < ndims; i++)
printf("[%d]", (int) dims[i]);
printf(" ");
/* Print base type */
print_datatype(super,0);
/* Close array base type */
H5Tclose(super);
/* Print closing */
printf(" }");
break;
default:
printf("unknown data type");
d_status = EXIT_FAILURE;
break;
}
} /* end else */
}
/*-------------------------------------------------------------------------
* Function: dump_datatype
*
* Purpose: Dump the data type. Data type can be HDF5 predefined
* atomic data type or committed/transient data type.
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_datatype(hid_t type)
{
indent += COL;
indentation(indent);
printf("%s %s ", dump_header_format->datatypebegin,
dump_header_format->datatypeblockbegin);
print_datatype(type,0);
end_obj(dump_header_format->datatypeend,
dump_header_format->datatypeblockend);
indent -= COL;
}
/*-------------------------------------------------------------------------
* Function: dump_dataspace
*
* Purpose: Dump the data space. Data space can be named data space,
* array, or others.
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_dataspace(hid_t space)
{
hsize_t size[H5DUMP_MAX_RANK];
hsize_t maxsize[H5DUMP_MAX_RANK];
int ndims = H5Sget_simple_extent_dims(space, size, maxsize);
H5S_class_t space_type = H5Sget_simple_extent_type(space);
int i;
indentation(indent + COL);
printf("%s ", dump_header_format->dataspacebegin);
switch (space_type) {
case H5S_SCALAR:
/* scalar dataspace */
HDfprintf(stdout, "%s %s",
dump_header_format->dataspacedescriptionbegin, S_SCALAR);
break;
case H5S_SIMPLE:
/* simple dataspace */
HDfprintf(stdout, "%s %s { %s %Hu",
dump_header_format->dataspacedescriptionbegin, S_SIMPLE,
dump_header_format->dataspacedimbegin, size[0]);
for (i = 1; i < ndims; i++)
HDfprintf(stdout, ", %Hu", size[i]);
printf(" %s / ", dump_header_format->dataspacedimend);
if (maxsize[0] == H5S_UNLIMITED)
HDfprintf(stdout, "%s %s",
dump_header_format->dataspacedimbegin,
"H5S_UNLIMITED");
else
HDfprintf(stdout, "%s %Hu",
dump_header_format->dataspacedimbegin, maxsize[0]);
for (i = 1; i < ndims; i++)
if (maxsize[i] == H5S_UNLIMITED)
HDfprintf(stdout, ", %s", "H5S_UNLIMITED");
else
HDfprintf(stdout, ", %Hu", maxsize[i]);
printf(" %s }", dump_header_format->dataspacedimend);
break;
case H5S_NULL:
/* null dataspace */
HDfprintf(stdout, "%s %s",
dump_header_format->dataspacedescriptionbegin, S_NULL);
break;
case H5S_COMPLEX:
printf("%s not yet implemented %s\n", BEGIN, END);
break;
case H5S_NO_CLASS:
default:
printf("%s unknown dataspace %s\n", BEGIN, END);
}
end_obj(dump_header_format->dataspaceend,
dump_header_format->dataspaceblockend);
}
/*-------------------------------------------------------------------------
* Function: dump_attr
*
* Purpose: dump the attribute
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
dump_attr(hid_t attr, const char *attr_name, void UNUSED * op_data)
{
hid_t attr_id, type, space;
herr_t ret = SUCCEED;
indentation(indent);
begin_obj(dump_header_format->attributebegin, attr_name,
dump_header_format->attributeblockbegin);
if ((attr_id = H5Aopen_name(attr, attr_name)) < 0) {
indentation(indent + COL);
error_msg(progname, "unable to open attribute \"%s\"\n", attr_name);
indentation(indent);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
d_status = EXIT_FAILURE;
ret = FAIL;
} else {
type = H5Aget_type(attr_id);
space = H5Aget_space(attr_id);
dump_datatype(type);
dump_dataspace(space);
if (display_oid)
dump_oid(attr_id);
if (display_data || display_attr_data)
dump_data(attr_id, ATTRIBUTE_DATA, NULL, display_ai);
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
indentation(indent);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
}
return ret;
}
/*-------------------------------------------------------------------------
* Function: dump_selected_attr
*
* Purpose: dump the selected attribute
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
dump_selected_attr(hid_t loc_id, const char *name)
{
int j;
char *obj_name;
const char *attr_name;
hid_t oid, attr_id, type, space;
H5G_stat_t statbuf;
j = (int)strlen(name) - 1;
obj_name = malloc((size_t)j + 2);
/* find the last / */
while (name[j] != '/' && j >= 0)
j--;
/* object name */
if (j == -1) {
strcpy(obj_name, "/");
} else {
strncpy(obj_name, name, (size_t)j + 1);
obj_name[j + 1] = '\0';
}
attr_name = name + j + 1;
begin_obj(dump_header_format->attributebegin, name,
dump_header_format->attributeblockbegin);
H5Gget_objinfo(loc_id, obj_name, FALSE, &statbuf);
switch (statbuf.type) {
case H5G_GROUP:
if ((oid = H5Gopen(loc_id, obj_name)) < 0) {
indentation(COL);
error_msg(progname, "unable to open group \"%s\"\n", obj_name);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
d_status = EXIT_FAILURE;
return FAIL;
}
break;
case H5G_DATASET:
if ((oid = H5Dopen(loc_id, obj_name)) < 0) {
indentation(COL);
error_msg(progname, "unable to open dataset \"%s\"\n", obj_name);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
d_status = EXIT_FAILURE;
return FAIL;
}
break;
case H5G_TYPE:
if ((oid = H5Topen(loc_id, obj_name)) < 0) {
indentation(COL);
error_msg(progname, "unable to open datatype \"%s\"\n", obj_name);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
d_status = EXIT_FAILURE;
return FAIL;
}
break;
default:
indentation(COL);
error_msg(progname, "unable to open unknown \"%s\"\n", obj_name);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
d_status = EXIT_FAILURE;
return FAIL;
}
if ((attr_id = H5Aopen_name(oid, attr_name)) >= 0) {
type = H5Aget_type(attr_id);
space = H5Aget_space(attr_id);
dump_datatype(type);
dump_dataspace(space);
if (display_oid)
dump_oid(attr_id);
if (display_data || display_attr_data)
dump_data(attr_id, ATTRIBUTE_DATA, NULL, display_ai);
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
} else {
indentation(COL);
error_msg(progname, "unable to open attribute \"%s\"\n", obj_name);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
d_status = EXIT_FAILURE;
}
switch (statbuf.type) {
case H5G_GROUP:
if (H5Gclose(oid) < 0) {
d_status = EXIT_FAILURE;
return FAIL;
}
break;
case H5G_DATASET:
if (H5Dclose(oid) < 0) {
d_status = EXIT_FAILURE;
return FAIL;
}
break;
case H5G_TYPE:
if (H5Tclose(oid) < 0) {
d_status = EXIT_FAILURE;
return FAIL;
}
break;
default:
d_status = EXIT_FAILURE;
return FAIL;
}
free(obj_name);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: dump_all
*
* Purpose: Dump everything in the specified object
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
* RMcG, November 2000
* Added XML support. Also, optionally checks the op_data
* argument.
*
*-------------------------------------------------------------------------
*/
static herr_t
dump_all(hid_t group, const char *name, void * op_data)
{
hid_t obj;
char *targbuf, *tmp = NULL;
H5G_stat_t statbuf;
int i;
herr_t ret = SUCCEED;
H5Gget_objinfo(group, name, FALSE, &statbuf);
if (*(int *)op_data != H5G_UNKNOWN && statbuf.type != *(int *) op_data)
goto done;
tmp = malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
switch (statbuf.type) {
case H5G_LINK:
indentation(indent);
targbuf = malloc(statbuf.linklen);
if (!doxml) {
begin_obj(dump_header_format->softlinkbegin, name,
dump_header_format->softlinkblockbegin);
indentation(indent + COL);
}
if (H5Gget_linkval(group, name, statbuf.linklen, targbuf) < 0) {
error_msg(progname, "unable to get link value\n");
d_status = EXIT_FAILURE;
ret = FAIL;
} else {
/* print the value of a soft link */
if (!doxml) {
/* Standard DDL: no modification */
printf("LINKTARGET \"%s\"\n", targbuf);
} else {
/* XML */
char *linkxid = malloc(100);
char *parentxid = malloc(100);
char *targetxid = malloc(100);
char *t_prefix = xml_escape_the_name(strcmp(prefix,"") ? prefix : "/");
char *t_name = xml_escape_the_name(name);
char *t_targbuf = xml_escape_the_name(targbuf);
char *tmp2, *t_tmp;
int res;
tmp2 = malloc(strlen(prefix) + statbuf.linklen + 1);
strcpy(tmp2, prefix);
if (targbuf && targbuf[0] == '/')
strcpy(tmp2, targbuf);
else
strcat(strcat(tmp2, "/"), targbuf);
t_tmp = xml_escape_the_name(strcat(strcat(tmp, "/"), name));
xml_name_to_XID(t_tmp,linkxid,100,1);
xml_name_to_XID(prefix,parentxid,100,1);
res = xml_name_to_XID(tmp2,targetxid,100,0);
if (res == 0) {
/* target obj found */
printf("<%sSoftLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetPath=\"%s\" TargetObj=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
xmlnsprefix,
t_name,
linkxid,
t_tmp,
t_targbuf, targetxid,
parentxid, t_prefix);
free(targetxid);
} else {
/* dangling link -- omit from xml attributes */
printf("<%sSoftLink LinkName=\"%s\" "
"OBJ-XID=\"%s\" "
"H5SourcePath=\"%s\" "
"TargetPath=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
xmlnsprefix,
t_name,
linkxid,
t_tmp,
t_targbuf,
parentxid, t_prefix);
}
free(t_name);
free(t_targbuf);
free(t_tmp);
free(tmp2);
free(linkxid);
free(parentxid);
}
}
if (!doxml) {
indentation(indent);
end_obj(dump_header_format->softlinkend,
dump_header_format->softlinkblockend);
}
free(targbuf);
break;
case H5G_GROUP:
if ((obj = H5Gopen(group, name)) < 0) {
error_msg(progname, "unable to dump group \"%s\"\n", name);
d_status = EXIT_FAILURE;
ret = FAIL;
} else {
size_t new_len = strlen(prefix) + strlen(name) + 2;
if (prefix_len <= new_len) {
prefix_len = new_len + 1;
prefix = realloc(prefix, prefix_len);
}
strcat(strcat(prefix, "/"), name);
dump_function_table->dump_group_function(obj, name);
strcpy(prefix, tmp);
H5Gclose(obj);
}
break;
case H5G_DATASET:
if ((obj = H5Dopen(group, name)) >= 0) {
/* hard link */
H5Gget_objinfo(obj, ".", TRUE, &statbuf);
if (statbuf.nlink > 1) {
i = search_obj(dset_table, statbuf.objno);
if (i < 0) {
indentation(indent);
begin_obj(dump_header_format->datasetbegin, name,
dump_header_format->datasetblockbegin);
indentation(indent + COL);
error_msg(progname,
"internal error (file %s:line %d)\n",
__FILE__, __LINE__);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
d_status = EXIT_FAILURE;
ret = FAIL;
H5Dclose(obj);
goto done;
} else if (dset_table->objs[i].displayed) {
indentation(indent);
if (!doxml) {
begin_obj(dump_header_format->datasetbegin, name,
dump_header_format->datasetblockbegin);
indentation(indent + COL);
printf("%s \"%s\"\n", HARDLINK,
dset_table->objs[i].objname);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
} else {
/* the XML version */
char *t_tmp;
char *t_prefix;
char *t_name;
char *dsetxid = malloc(100);
char *parentxid = malloc(100);
char *pointerxid = malloc(100);
char *tx_tmp = malloc(strlen(tmp)+strlen(name)+1);
strcpy(tx_tmp,tmp);
t_tmp = xml_escape_the_name(strcat(strcat(tx_tmp, "/"), name));
t_prefix = xml_escape_the_name(prefix);
t_name = xml_escape_the_name(name);
xml_name_to_XID( strcat(strcat(tmp,"/"),name), dsetxid,100,1);
xml_name_to_XID( prefix ,parentxid,100,1);
printf("<%sDataset Name=\"%s\" OBJ-XID=\"%s-%d\" "
"H5Path=\"%s\" Parents=\"%s\" "
"H5ParentPaths=\"%s\">\n",
xmlnsprefix,
t_name, dsetxid, get_next_xid(),
t_tmp, parentxid,
(strcmp(prefix, "") ? t_prefix : "/"));
indentation(indent + COL);
xml_name_to_XID(dset_table->objs[i].objname,pointerxid,100,1);
printf("<%sDatasetPtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n",
xmlnsprefix,
pointerxid,t_tmp);
indentation(indent);
printf("</%sDataset>\n", xmlnsprefix);
free(t_name);
free(dsetxid);
free(parentxid);
free(pointerxid);
free(t_tmp);
free(tx_tmp);
free(t_prefix);
}
H5Dclose(obj);
goto done;
} else {
dset_table->objs[i].displayed = 1;
}
}
dump_function_table->dump_dataset_function(obj, name, NULL);
H5Dclose(obj);
} else {
error_msg(progname, "unable to dump dataset \"%s\"\n", name);
d_status = EXIT_FAILURE;
ret = FAIL;
}
break;
case H5G_TYPE:
if ((obj = H5Topen(group, name)) < 0) {
error_msg(progname, "unable to dump data type \"%s\"\n", name);
d_status = EXIT_FAILURE;
ret = FAIL;
} else {
dump_function_table->dump_named_datatype_function(obj, name);
H5Tclose(obj);
}
break;
default:
error_msg(progname, "unknown object \"%s\"\n", name);
d_status = EXIT_FAILURE;
ret = FAIL;
}
done:
free(tmp);
return ret;
}
/*-------------------------------------------------------------------------
* Function: dump_named_datatype
*
* Purpose: Dump named data type
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications: Comments: not yet implemented.
*
*-------------------------------------------------------------------------
*/
static void
dump_named_datatype(hid_t type, const char *name)
{
indentation(indent);
printf("%s \"%s\" %s", dump_header_format->datatypebegin, name,
dump_header_format->datatypeblockbegin);
if (H5Tget_class(type) == H5T_COMPOUND) {
print_datatype(type,1);
} else {
indentation(indent + COL);
print_datatype(type,1);
printf(";\n");
}
end_obj(dump_header_format->datatypeend,
dump_header_format->datatypeblockend);
}
/*-------------------------------------------------------------------------
* Function: dump_group
*
* Purpose: Dump everything within the specified group
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
* Call to dump_all -- add parameter to select everything.
*
*-------------------------------------------------------------------------
*/
static void
dump_group(hid_t gid, const char *name)
{
H5G_stat_t statbuf;
hid_t dset, type;
char type_name[1024], *tmp;
int i, xtype = H5G_UNKNOWN; /* dump all */
tmp = malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
indentation(indent);
begin_obj(dump_header_format->groupbegin, name,
dump_header_format->groupblockbegin);
indent += COL;
if (display_oid)
dump_oid(gid);
dump_comment(gid);
if (!strcmp(name, "/") && unamedtype)
/* dump unamed type in root group */
for (i = 0; i < type_table->nobjs; i++)
if (!type_table->objs[i].recorded) {
dset = H5Dopen(gid, type_table->objs[i].objname);
type = H5Dget_type(dset);
sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[i].objno);
dump_named_datatype(type, type_name);
H5Tclose(type);
H5Dclose(dset);
}
H5Gget_objinfo(gid, ".", TRUE, &statbuf);
if (statbuf.nlink > 1) {
i = search_obj(group_table, statbuf.objno);
if (i < 0) {
indentation(indent);
error_msg(progname, "internal error (file %s:line %d)\n",
__FILE__, __LINE__);
d_status = EXIT_FAILURE;
} else if (group_table->objs[i].displayed) {
indentation(indent);
printf("%s \"%s\"\n", HARDLINK, group_table->objs[i].objname);
} else {
group_table->objs[i].displayed = 1;
H5Aiterate(gid, NULL, dump_attr, NULL);
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
}
} else {
H5Aiterate(gid, NULL, dump_attr, NULL);
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
}
indent -= COL;
indentation(indent);
end_obj(dump_header_format->groupend, dump_header_format->groupblockend);
free(tmp);
}
/*-------------------------------------------------------------------------
* Function: dump_dataset
*
* Purpose: Dump the specified data set
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications: pvn, 2004, added dcpl dump
*
*-------------------------------------------------------------------------
*/
static void
dump_dataset(hid_t did, const char *name, struct subset_t *sset)
{
hid_t type, space, dcpl_id;
indentation(indent);
begin_obj(dump_header_format->datasetbegin, name,
dump_header_format->datasetblockbegin);
type = H5Dget_type(did);
space = H5Dget_space(did);
dcpl_id = H5Dget_create_plist(did);
dump_comment(did);
dump_datatype(type);
dump_dataspace(space);
if (display_oid)
dump_oid(did);
if (display_dcpl)
dump_dcpl(dcpl_id, type, did);
if (display_data)
switch (H5Tget_class(type)) {
case H5T_TIME:
indentation(indent + COL);
printf("DATA{ not yet implemented.}\n");
break;
case H5T_INTEGER:
case H5T_FLOAT:
case H5T_STRING:
case H5T_BITFIELD:
case H5T_OPAQUE:
case H5T_COMPOUND:
case H5T_REFERENCE:
case H5T_ENUM:
case H5T_VLEN:
case H5T_ARRAY:
dump_data(did, DATASET_DATA, sset, display_ai);
break;
default:
break;
}
indent += COL;
H5Aiterate(did, NULL, dump_attr, NULL);
indent -= COL;
H5Tclose(type);
H5Sclose(space);
H5Pclose(dcpl_id);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
}
/*-------------------------------------------------------------------------
* Function: dump_tables
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_tables(void)
{
#ifdef H5DUMP_DEBUG
register int i;
printf("group_table: # of entries = %d\n", group_table->nobjs);
for (i = 0; i < group_table->nobjs; i++)
HDfprintf(stdout,"%a %s %d %d\n", group_table->objs[i].objno,
group_table->objs[i].objname,
group_table->objs[i].displayed, group_table->objs[i].recorded);
printf("\ndset_table: # of entries = %d\n", dset_table->nobjs);
for (i = 0; i < dset_table->nobjs; i++)
HDfprintf(stdout,"%a %s %d %d\n", dset_table->objs[i].objno,
dset_table->objs[i].objname,
dset_table->objs[i].displayed, dset_table->objs[i].recorded);
printf("\ntype_table: # of entries = %d\n", type_table->nobjs);
for (i = 0; i < type_table->nobjs; i++)
HDfprintf(stdout,"%a %s %d %d\n", type_table->objs[i].objno,
type_table->objs[i].objname,
type_table->objs[i].displayed, type_table->objs[i].recorded);
#else
return;
#endif /* H5DUMP_DEBUG */
}
/*-------------------------------------------------------------------------
* Function: dump_dims
*
* Purpose: Dump the dimensions handed to it in a comma separated list
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 27. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_dims(hsize_t *s, int dims)
{
register int i;
for (i = 0; i < dims; i++) {
printf("%u", (unsigned int)s[i]);
if (i + 1 != dims)
printf(", ");
}
}
/*-------------------------------------------------------------------------
* Function: dump_subsetting_header
*
* Purpose: Dump the subsetting header like specified in the DDL.
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 27. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_subsetting_header(struct subset_t *sset, int dims)
{
indentation(indent);
printf("%s %s\n", dump_header_format->subsettingbegin,
dump_header_format->subsettingblockbegin);
indent += COL;
indentation(indent);
printf("%s %s ", dump_header_format->startbegin,
dump_header_format->startblockbegin);
dump_dims((hsize_t *)sset->start, dims);
printf("%s %s\n", dump_header_format->startend,
dump_header_format->startblockend);
indentation(indent);
printf("%s %s ", dump_header_format->stridebegin,
dump_header_format->strideblockbegin);
dump_dims(sset->stride, dims);
printf("%s %s\n", dump_header_format->strideend,
dump_header_format->strideblockend);
indentation(indent);
printf("%s %s ", dump_header_format->countbegin,
dump_header_format->countblockbegin);
if (sset->count)
dump_dims(sset->count, dims);
else
printf("DEFAULT");
printf("%s %s\n", dump_header_format->countend,
dump_header_format->countblockend);
indentation(indent);
printf("%s %s ", dump_header_format->blockbegin,
dump_header_format->blockblockbegin);
if (sset->block)
dump_dims(sset->block, dims);
else
printf("DEFAULT");
printf("%s %s\n", dump_header_format->blockend,
dump_header_format->blockblockend);
}
/*-------------------------------------------------------------------------
* Function: dump_data
*
* Purpose: Dump attribute or dataset data
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications: pvn, print the matrix indices
*
*-------------------------------------------------------------------------
*/
static void
dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int pindex)
{
h5dump_t *outputformat = &dataformat;
int status = -1;
void *buf;
hid_t space, type, p_type;
H5S_class_t space_type;
int ndims, i;
hsize_t size[64], nelmts = 1, alloc_size;
int depth;
int stdindent = COL; /* should be 3 */
outputformat->line_ncols = nCols;
outputformat->do_escape=display_escape;
/* print the matrix indices */
outputformat->pindex=pindex;
if (outputformat->pindex)
{
outputformat->idx_fmt = "(%s): ";
outputformat->idx_n_fmt = "%lu";
outputformat->idx_sep = ",";
outputformat->line_pre = "%s";
}
indent += COL;
/*
* the depth will tell us how far we need to indent extra. we use to just
* use indent but with the merging of the tools lib we have to do
* something different for the lib funtions... the normal indentation is 6
* so when we don't need any extra indentation, depth will be 0.
*/
depth = indent / stdindent + 1;
if (sset && obj_data == DATASET_DATA) {
hid_t f_space = H5Dget_space(obj_id);
dump_subsetting_header(sset, H5Sget_simple_extent_ndims(f_space));
H5Sclose(f_space);
/* recalculate the depth of the data */
depth = indent / stdindent + 1;
}
indentation(indent);
begin_obj(dump_header_format->databegin, (const char *)NULL,
dump_header_format->datablockbegin);
/* Print all the values. */
if (obj_data == DATASET_DATA) {
hid_t f_type = H5Dget_type(obj_id);
char string_prefix[64];
h5dump_t string_dataformat;
if (display_char && H5Tget_size(f_type) == 1 && H5Tget_class(f_type) == H5T_INTEGER) {
/*
* Print 1-byte integer data as an ASCII character string
* instead of integers if the `-r' or `--string' command-line
* option was given.
*
* We don't want to modify the global dataformat, so make a
* copy of it instead.
*/
string_dataformat = *outputformat;
string_dataformat.idx_fmt = " ";
string_dataformat.line_multi_new = 1;
string_dataformat.line_1st = " %s\"";
string_dataformat.line_pre = " %s";
string_dataformat.line_cont = " %s";
string_dataformat.str_repeat = 8;
string_dataformat.ascii = TRUE;
string_dataformat.elmt_suf1 = "";
string_dataformat.elmt_suf2 = "";
string_dataformat.line_indent = "";
strcpy(string_prefix, string_dataformat.line_pre);
strcat(string_prefix, "\"");
string_dataformat.line_pre = string_prefix;
string_dataformat.line_suf = "\"";
outputformat = &string_dataformat;
}
status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, sset, depth);
H5Tclose(f_type);
} else {
/* need to call h5tools_dump_mem for the attribute data */
space = H5Aget_space(obj_id);
space_type = H5Sget_simple_extent_type(space);
if(space_type == H5S_NULL || space_type == H5S_NO_CLASS || space_type == H5S_COMPLEX) {
status = SUCCEED;
} else {
type = H5Aget_type(obj_id);
p_type = h5tools_get_native_type(type);
ndims = H5Sget_simple_extent_dims(space, size, NULL);
for (i = 0; i < ndims; i++)
nelmts *= size[i];
alloc_size = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type));
assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/
buf = malloc((size_t)alloc_size);
assert(buf);
if (H5Aread(obj_id, p_type, buf) >= 0)
status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type,
space, buf, depth);
free(buf);
H5Tclose(p_type);
H5Tclose(type);
}
H5Sclose(space);
}
if (status == FAIL) {
indentation(indent + COL);
error_msg(progname, "unable to print data\n");
d_status = EXIT_FAILURE;
}
indentation(indent);
end_obj(dump_header_format->dataend, dump_header_format->datablockend);
indent -= COL;
if (sset && obj_data == DATASET_DATA) {
indentation(indent);
end_obj(dump_header_format->subsettingend,
dump_header_format->subsettingblockend);
indent -= COL;
}
}
/*-------------------------------------------------------------------------
* Function: dump_oid
*
* Purpose: Prints the object ids
*
* Return: void
*
* Programmer: Patrick Lu
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_oid(hid_t oid)
{
indentation(indent + COL);
printf("%s %s %d %s\n", OBJID, BEGIN, oid, END);
}
/*-------------------------------------------------------------------------
* Function: dump_comment
*
* Purpose: prints the comment for the the object name
*
* Return: void
*
* Programmer: pvn
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void dump_comment(hid_t obj_id)
{
char comment[50];
comment[0] = '\0';
H5Gget_comment(obj_id, ".", sizeof(comment), comment);
if (comment[0]) {
indentation(indent);
printf("COMMENT \"%s\"\n", comment);
}
}
/*-------------------------------------------------------------------------
* Function: dump_fill_value
*
* Purpose: prints the fill value
*
* Return: void
*
* Programmer: pvn
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void dump_fill_value(hid_t dcpl,hid_t type_id, hid_t obj_id)
{
h5tools_context_t ctx; /*print context */
size_t size;
void *buf=NULL;
hsize_t nelmts=1;
h5dump_t *outputformat = &dataformat;
hid_t n_type;
memset(&ctx, 0, sizeof(ctx));
ctx.indent_level=2;
n_type = h5tools_get_native_type(type_id);
size = H5Tget_size(n_type);
buf = malloc(size);
H5Pget_fill_value(dcpl, n_type, buf);
h5tools_dump_simple_data(stdout, outputformat, obj_id, &ctx, START_OF_DATA | END_OF_DATA, nelmts, n_type, buf);
H5Tclose(n_type);
if (buf)
free (buf);
}
/*-------------------------------------------------------------------------
* Function: dump_dcpl
*
* Purpose: prints several dataset create property list properties
*
* Return: void
*
* Programmer: pvn
*
*-------------------------------------------------------------------------
*/
static void
dump_dcpl(hid_t dcpl_id,hid_t type_id, hid_t obj_id)
{
int nfilters; /* number of filters */
unsigned filt_flags; /* filter flags */
H5Z_filter_t filtn; /* filter identification number */
unsigned cd_values[20]; /* filter client data values */
size_t cd_nelmts; /* filter client number of values */
char f_name[256]; /* filter name */
unsigned szip_options_mask;
unsigned szip_pixels_per_block;
hsize_t chsize[64]; /* chunk size in elements */
int rank; /* rank */
char name[256]; /* external file name */
off_t offset; /* offset of external file */
hsize_t size; /* size of external file */
H5D_fill_value_t fvstatus;
H5D_alloc_time_t at;
H5D_fill_time_t ft;
hsize_t storage_size;
haddr_t ioffset;
int i, next;
unsigned j;
storage_size=H5Dget_storage_size(obj_id);
ioffset=H5Dget_offset(obj_id);
next=H5Pget_external_count(dcpl_id);
strcpy(f_name,"\0");
/*-------------------------------------------------------------------------
* STORAGE_LAYOUT
*-------------------------------------------------------------------------
*/
indentation(indent + COL);
printf("%s %s\n", STORAGE_LAYOUT, BEGIN);
if (H5D_CHUNKED == H5Pget_layout(dcpl_id))
{
/*start indent */
indent += COL;
indentation(indent + COL);
printf("%s ", CHUNKED);
rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize);
HDfprintf(stdout,"%s %Hu", dump_header_format->dataspacedimbegin, chsize[0]);
for ( i=1; i<rank; i++)
HDfprintf(stdout, ", %Hu", chsize[i]);
printf(" %s\n", dump_header_format->dataspacedimend);
indentation(indent + COL);
HDfprintf(stdout, "SIZE %Hu\n ", storage_size);
/*end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
}
else if (H5D_COMPACT == H5Pget_layout(dcpl_id))
{
/*start indent */
indent += COL;
indentation(indent + COL);
printf("%s\n", COMPACT);
indentation(indent + COL);
HDfprintf(stdout, "SIZE %Hu\n", storage_size);
/*end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
}
else if (H5D_CONTIGUOUS == H5Pget_layout(dcpl_id))
{
/*-------------------------------------------------------------------------
* EXTERNAL_FILE
*-------------------------------------------------------------------------
*/
if (next)
{
/*start indent */
indent += COL;
indentation(indent + COL);
printf("%s\n", CONTIGUOUS);
indentation(indent + COL);
printf("%s %s\n", EXTERNAL, BEGIN);
/*start indent */
indent += COL;
for ( j=0; j<(unsigned)next; j++) {
H5Pget_external(dcpl_id,j,sizeof(name),name,&offset,&size);
indentation(indent + COL);
HDfprintf(stdout,"FILENAME %s SIZE %Hu OFFSET %ld\n",name,size,offset);
}
/*end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
/*end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
}
else
{
/*start indent */
indent += COL;
indentation(indent + COL);
printf("%s\n", CONTIGUOUS);
indentation(indent + COL);
HDfprintf(stdout,"SIZE %Hu\n", storage_size);
indentation(indent + COL);
HDfprintf(stdout,"OFFSET %Hu\n", ioffset);
/*end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
}
}
/*-------------------------------------------------------------------------
* FILTERS
*-------------------------------------------------------------------------
*/
nfilters = H5Pget_nfilters(dcpl_id);
indentation(indent + COL);
printf("%s %s\n", FILTERS, BEGIN);
indent += COL;
if (nfilters)
{
for (i=0; i<nfilters; i++)
{
cd_nelmts = NELMTS(cd_values);
#ifdef H5_WANT_H5_V1_6_COMPAT
filtn = H5Pget_filter(dcpl_id,
(unsigned)i,
&filt_flags,
&cd_nelmts,
cd_values,
sizeof(f_name),
f_name);
#else
filtn = H5Pget_filter(dcpl_id,
(unsigned)i,
&filt_flags,
&cd_nelmts,
cd_values,
sizeof(f_name),
f_name,
NULL);
#endif /* H5_WANT_H5_V1_6_COMPAT */
switch (filtn)
{
case H5Z_FILTER_DEFLATE:
indentation(indent + COL);
printf("%s %s %s %d %s\n", DEFLATE, BEGIN, DEFLATE_LEVEL, cd_values[0], END);
break;
case H5Z_FILTER_SHUFFLE:
indentation(indent + COL);
printf("%s\n", SHUFFLE);
break;
case H5Z_FILTER_FLETCHER32:
indentation(indent + COL);
printf("%s\n", FLETCHER32);
break;
case H5Z_FILTER_SZIP:
{
szip_options_mask=cd_values[0];;
szip_pixels_per_block=cd_values[1];
indentation(indent + COL);
printf("%s %s\n",SZIP, BEGIN);
/*start indent */
indent += COL;
indentation(indent + COL);
printf("PIXELS_PER_BLOCK %d\n", szip_pixels_per_block);
indentation(indent + COL);
if (szip_options_mask & H5_SZIP_CHIP_OPTION_MASK)
printf("MODE %s\n", "HARDWARE");
else if (szip_options_mask & H5_SZIP_ALLOW_K13_OPTION_MASK)
printf("MODE %s\n", "K13");
indentation(indent + COL);
if (szip_options_mask & H5_SZIP_EC_OPTION_MASK)
printf("CODING %s\n", "ENTROPY");
else if (szip_options_mask & H5_SZIP_NN_OPTION_MASK)
printf("CODING %s\n", "NEAREST NEIGHBOUR");
indentation(indent + COL);
if (szip_options_mask & H5_SZIP_LSB_OPTION_MASK)
printf("BYTE_ORDER %s\n", "LSB");
else if (szip_options_mask & H5_SZIP_MSB_OPTION_MASK)
printf("BYTE_ORDER %s\n", "MSB");
indentation(indent + COL);
if (szip_options_mask & H5_SZIP_RAW_OPTION_MASK)
printf("HEADER %s\n", "RAW");
/*end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
}
break;
default:
indentation(indent + COL);
if (H5Zfilter_avail(filtn))
printf("%s %s\n", "USER_REGISTERED_FILTER", BEGIN);
else
printf("%s %s\n", "UNKNOWN_FILTER", BEGIN);
/*start indent */
indent += COL;
indentation(indent + COL);
printf("FILTER_ID %d\n", filtn);
if (f_name[0]!='\0') {
indentation(indent + COL);
printf("COMMENT %s\n", f_name);
}
if (cd_nelmts) {
indentation(indent + COL);
printf("%s %s ","PARAMS", BEGIN);
for (j=0; j<cd_nelmts; j++) {
printf("%d ", cd_values[j]);
}
printf("%s\n", END);
}
break;
}/*switch*/
} /*i*/
}/*nfilters*/
else
{
indentation(indent + COL);
printf("NONE\n");
}
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
/*-------------------------------------------------------------------------
* FILLVALUE
*-------------------------------------------------------------------------
*/
indentation(indent + COL);
printf("%s %s\n", FILLVALUE, BEGIN);
/*start indent */
indent += COL;
indentation(indent + COL);
printf("FILL_TIME ");
H5Pget_fill_time(dcpl_id, &ft);
switch ( ft )
{
case H5D_FILL_TIME_ALLOC:
printf("%s", "H5D_FILL_TIME_ALLOC\n");
break;
case H5D_FILL_TIME_NEVER:
printf("%s", "H5D_FILL_TIME_NEVER\n");
break;
case H5D_FILL_TIME_IFSET:
printf("%s", "H5D_FILL_TIME_IFSET\n");
break;
default:
assert(0);
break;
}
indentation(indent + COL);
printf("%s ", "VALUE ");
H5Pfill_value_defined(dcpl_id, &fvstatus);
if (fvstatus == H5D_FILL_VALUE_UNDEFINED)
{
printf("%s\n", "H5D_FILL_VALUE_UNDEFINED");
}
else
{
dump_fill_value(dcpl_id,type_id,obj_id);
}
/* end indent */
indent -= COL;
indentation(indent + COL);
printf("\n");
indentation(indent + COL);
printf("%s\n",END);
/*-------------------------------------------------------------------------
* ALLOCATION_TIME
*-------------------------------------------------------------------------
*/
indentation(indent + COL);
printf("ALLOCATION_TIME %s\n",BEGIN);
/*start indent */
indent += COL;
indentation(indent + COL);
H5Pget_alloc_time(dcpl_id, &at);
switch (at)
{
case H5D_ALLOC_TIME_EARLY:
printf("%s", "H5D_ALLOC_TIME_EARLY\n");
break;
case H5D_ALLOC_TIME_INCR:
printf("%s", "H5D_ALLOC_TIME_INCR\n");
break;
case H5D_ALLOC_TIME_LATE:
printf("%s", "H5D_ALLOC_TIME_LATE\n");
break;
default:
assert(0);
break;
}
/* end indent */
indent -= COL;
indentation(indent + COL);
printf("%s\n",END);
}
/*-------------------------------------------------------------------------
* Function: dump_fcpl
*
* Purpose: prints file creation property list information
*
* Return: void
*
* Programmer: pvn
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_fcpl(hid_t fid)
{
hid_t fcpl; /* file creation property list ID */
hid_t fapl; /* file access property list ID */
hsize_t userblock; /* userblock size retrieved from FCPL */
size_t off_size; /* size of offsets in the file */
size_t len_size; /* size of lengths in the file */
#ifdef H5_WANT_H5_V1_6_COMPAT
int super; /* superblock version # */
int freelist; /* free list version # */
int stab; /* symbol table entry version # */
int shhdr; /* shared object header version # */
#else
unsigned super; /* superblock version # */
unsigned freelist; /* free list version # */
unsigned stab; /* symbol table entry version # */
unsigned shhdr; /* shared object header version # */
#endif
hid_t fdriver; /* file driver */
char dname[15]; /* buffer to store driver name */
unsigned sym_lk; /* symbol table B-tree leaf 'K' value */
#ifdef H5_WANT_H5_V1_6_COMPAT
int sym_ik; /* symbol table B-tree initial 'K' value */
int istore_ik; /* indexed storage B-tree initial 'K' value */
#else
unsigned sym_ik; /* symbol table B-tree initial 'K' value */
unsigned istore_ik; /* indexed storage B-tree initial 'K' value */
#endif
fcpl=H5Fget_create_plist(fid);
H5Pget_version(fcpl, &super, &freelist, &stab, &shhdr);
H5Pget_userblock(fcpl,&userblock);
H5Pget_sizes(fcpl,&off_size,&len_size);
H5Pget_sym_k(fcpl,&sym_ik,&sym_lk);
H5Pget_istore_k(fcpl,&istore_ik);
H5Pclose(fcpl);
fapl=h5_fileaccess();
fdriver=H5Pget_driver(fapl);
H5Pclose(fapl);
/*-------------------------------------------------------------------------
* SUPER_BLOCK
*-------------------------------------------------------------------------
*/
printf("%s %s\n",SUPER_BLOCK, BEGIN);
indentation(indent + COL);
printf("%s %d\n","SUPERBLOCK_VERSION", super);
indentation(indent + COL);
printf("%s %d\n","FREELIST_VERSION", freelist);
indentation(indent + COL);
printf("%s %d\n","SYMBOLTABLE_VERSION", stab);
indentation(indent + COL);
printf("%s %d\n","OBJECTHEADER_VERSION", (int)shhdr);
indentation(indent + COL);
HDfprintf(stdout,"%s %Hd\n","OFFSET_SIZE", (long_long)off_size);
indentation(indent + COL);
HDfprintf(stdout,"%s %Hd\n","LENGTH_SIZE", (long_long)len_size);
indentation(indent + COL);
printf("%s %d\n","BTREE_RANK", sym_ik);
indentation(indent + COL);
printf("%s %d\n","BTREE_LEAF", sym_lk);
if (H5FD_CORE==fdriver)
{
strcpy(dname,"H5FD_CORE");
}
else if (H5FD_FAMILY==fdriver)
{
strcpy(dname,"H5FD_FAMILY");
}
else if (H5FD_GASS==fdriver)
{
strcpy(dname,"H5FD_GASS");
}
else if (H5FD_LOG==fdriver)
{
strcpy(dname,"H5FD_LOG");
}
else if (H5FD_MPIO==fdriver)
{
strcpy(dname,"H5FD_MPIO");
}
else if (H5FD_MULTI==fdriver)
{
strcpy(dname,"H5FD_MULTI");
}
else if (H5FD_SEC2==fdriver)
{
strcpy(dname,"H5FD_SEC2");
}
else if (H5FD_STDIO==fdriver)
{
strcpy(dname,"H5FD_STDIO");
}
#ifdef H5_HAVE_STREAM
else if (H5FD_STREAM==fdriver)
{
strcpy(dname,"H5FD_STREAM");
}
#endif
indentation(indent + COL);
printf("%s %s\n","FILE_DRIVER", dname);
indentation(indent + COL);
printf("%s %d\n","ISTORE_K", istore_ik);
printf("%s\n",END);
/*-------------------------------------------------------------------------
* USER_BLOCK
*-------------------------------------------------------------------------
*/
printf("USER_BLOCK %s\n",BEGIN);
indentation(indent + COL);
HDfprintf(stdout,"%s %Hu\n","USERBLOCK_SIZE", userblock);
printf("%s\n",END);
}
/*-------------------------------------------------------------------------
* Function: dump_fcontents
*
* Purpose: prints all objects
*
* Return: void
*
* Programmer: pvn
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void dump_fcontents(hid_t fid)
{
hid_t did, tid, gid;
char type_name[1024];
int i;
printf("%s %s\n",FILE_CONTENTS, BEGIN);
/* special case of unamed types in root group */
if (unamedtype)
{
gid=H5Gopen(fid,"/");
for (i = 0; i < type_table->nobjs; i++)
if (!type_table->objs[i].recorded)
{
did = H5Dopen(gid, type_table->objs[i].objname);
tid = H5Dget_type(did);
sprintf(type_name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[i].objno);
H5Tclose(tid);
H5Dclose(did);
printf(" %-10s %s\n", "datatype", type_name );
}
H5Gclose(gid);
}
/* print objects in the files */
h5trav_getinfo(fid, NULL, 1);
printf(" %s\n",END);
}
/*-------------------------------------------------------------------------
* Function: set_output_file
*
* Purpose: Open fname as the output file for dataset raw data.
* Set rawdatastream as its file stream.
*
* Return: 0 -- succeeded
* negative -- failed
*
* Programmer: Albert Cheng, 2000/09/30
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
set_output_file(const char *fname)
{
FILE *f; /* temporary holding place for the stream pointer
* so that rawdatastream is changed only when succeeded */
if ((f = fopen(fname, "w")) != NULL) {
rawdatastream = f;
return 0;
}
return -1;
}
/*-------------------------------------------------------------------------
* Function: handle_attributes
*
* Purpose: Handle the attributes from the command.
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 9. January 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
handle_attributes(hid_t fid, char *attr, void UNUSED * data)
{
dump_selected_attr(fid, attr);
}
/*-------------------------------------------------------------------------
* Function: parse_hsize_list
*
* Purpose: Parse a list of comma or space separated integers and return
* them in a list. The string being passed into this function
* should be at the start of the list you want to parse. You are
* responsible for freeing the array returned from here.
*
* Lists in the so-called "terse" syntax are separated by
* semicolons (;). The lists themselves can be separated by
* either commas (,) or white spaces.
*
* Return: Success: hsize_t array. NULL is a valid return type if
* there aren't any elements in the array.
*
* Programmer: Bill Wendling
* Tuesday, 6. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static hsize_t *
parse_hsize_list(const char *h_list)
{
hsize_t *p_list;
const char *ptr;
unsigned int size_count = 0, i = 0, last_digit = 0;
if (!h_list || !*h_list || *h_list == ';')
return NULL;
/* count how many integers do we have */
for (ptr = h_list; ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if (isdigit(*ptr)) {
if (!last_digit)
/* the last read character wasn't a digit */
size_count++;
last_digit = 1;
} else {
last_digit = 0;
}
if (size_count == 0)
/* there aren't any integers to read */
return NULL;
/* allocate an array for the integers in the list */
p_list = calloc(size_count, sizeof(hsize_t));
for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++)
if (isdigit(*ptr)) {
/* we should have an integer now */
p_list[i++] = (hsize_t)atoi(ptr);
while (isdigit(*ptr))
/* scroll to end of integer */
ptr++;
}
return p_list;
}
/*-------------------------------------------------------------------------
* Function: parse_subset_params
*
* Purpose: Parse the so-called "terse" syntax for specifying subsetting
* parameters.
*
* Return: Success: struct subset_t object
* Failure: NULL
*
* Programmer: Bill Wendling
* Tuesday, 6. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static struct subset_t *
parse_subset_params(char *dset)
{
struct subset_t *s = NULL;
register char *brace;
if ((brace = strrchr(dset, '[')) != NULL) {
char *slash = strrchr(dset, '/');
/* sanity check to make sure the [ isn't part of the dataset name */
if (brace > slash) {
*brace++ = '\0';
s = calloc(1, sizeof(struct subset_t));
s->start = (hssize_t *)parse_hsize_list(brace);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
s->stride = parse_hsize_list(brace);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
s->count = parse_hsize_list(brace);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
s->block = parse_hsize_list(brace);
}
}
return s;
}
/*-------------------------------------------------------------------------
* Function: handle_datasets
*
* Purpose: Handle the datasets from the command.
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 9. January 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
handle_datasets(hid_t fid, char *dset, void *data)
{
H5G_stat_t statbuf;
hid_t dsetid;
struct subset_t *sset = (struct subset_t *)data;
if ((dsetid = H5Dopen(fid, dset)) < 0) {
begin_obj(dump_header_format->datasetbegin, dset,
dump_header_format->datasetblockbegin);
indentation(COL);
error_msg(progname, "unable to open dataset \"%s\"\n", dset);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
d_status = EXIT_FAILURE;
return;
}
if (sset) {
if (!sset->start || !sset->stride || !sset->count || !sset->block) {
/* they didn't specify a ``stride'' or ``block''. default to 1 in all
* dimensions */
hid_t sid = H5Dget_space(dsetid);
unsigned int ndims = H5Sget_simple_extent_ndims(sid);
if (!sset->start)
/* default to (0, 0, ...) for the start coord */
sset->start = calloc(ndims, sizeof(hsize_t));
if (!sset->stride) {
unsigned int i;
sset->stride = calloc(ndims, sizeof(hsize_t));
for (i = 0; i < ndims; i++)
sset->stride[i] = 1;
}
if (!sset->count) {
hsize_t dims[H5S_MAX_RANK];
herr_t status = H5Sget_simple_extent_dims(sid, dims, NULL);
unsigned int i;
if (status == FAIL) {
error_msg(progname, "unable to get dataset dimensions\n");
d_status = EXIT_FAILURE;
H5Sclose(sid);
return;
}
sset->count = calloc(ndims, sizeof(hsize_t));
for (i = 0; i < ndims; i++)
sset->count[i] = dims[i] - sset->start[i];
}
if (!sset->block) {
unsigned int i;
sset->block = calloc(ndims, sizeof(hsize_t));
for (i = 0; i < ndims; i++)
sset->block[i] = 1;
}
H5Sclose(sid);
}
}
H5Gget_objinfo(dsetid, ".", TRUE, &statbuf);
if (statbuf.nlink > 1) {
int idx = search_obj(dset_table, statbuf.objno);
if (idx >= 0) {
if (dset_table->objs[idx].displayed) {
begin_obj(dump_header_format->datasetbegin, dset,
dump_header_format->datasetblockbegin);
indentation(indent + COL);
printf("%s \"%s\"\n", HARDLINK,
dset_table->objs[idx].objname);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
} else {
dset_table->objs[idx].displayed = 1;
dump_dataset(dsetid, dset, sset);
}
} else {
d_status = EXIT_FAILURE;
}
} else {
dump_dataset(dsetid, dset, sset);
}
if (H5Dclose(dsetid) < 1)
d_status = EXIT_FAILURE;
}
/*-------------------------------------------------------------------------
* Function: handle_groups
*
* Purpose: Handle the groups from the command.
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 9. January 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
handle_groups(hid_t fid, char *group, void UNUSED * data)
{
H5G_stat_t statbuf;
hid_t gid;
if ((gid = H5Gopen(fid, group)) < 0) {
begin_obj(dump_header_format->groupbegin, group,
dump_header_format->groupblockbegin);
indentation(COL);
error_msg(progname, "unable to open group \"%s\"\n", group);
end_obj(dump_header_format->groupend,
dump_header_format->groupblockend);
d_status = EXIT_FAILURE;
} else {
size_t new_len = strlen(group) + 1;
if (prefix_len <= new_len) {
prefix_len = new_len;
prefix = realloc(prefix, prefix_len);
}
H5Gget_objinfo(gid, ".", TRUE, &statbuf);
strcpy(prefix, group);
dump_group(gid, group);
if (H5Gclose(gid) < 0)
d_status = EXIT_FAILURE;
}
}
/*-------------------------------------------------------------------------
* Function: handle_links
*
* Purpose: Handle the links from the command.
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 9. January 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
handle_links(hid_t fid, char *links, void UNUSED * data)
{
H5G_stat_t statbuf;
if (H5Gget_objinfo(fid, links, FALSE, &statbuf) < 0) {
begin_obj(dump_header_format->softlinkbegin, links,
dump_header_format->softlinkblockbegin);
indentation(COL);
error_msg(progname, "unable to get obj info from \"%s\"\n", links);
end_obj(dump_header_format->softlinkend,
dump_header_format->softlinkblockend);
d_status = EXIT_FAILURE;
} else if (statbuf.type == H5G_LINK) {
char *buf = malloc(statbuf.linklen);
begin_obj(dump_header_format->softlinkbegin, links,
dump_header_format->softlinkblockbegin);
indentation(COL);
if (H5Gget_linkval(fid, links, statbuf.linklen, buf) >= 0) {
printf("LINKTARGET \"%s\"\n", buf);
} else {
error_msg(progname, "h5dump error: unable to get link value for \"%s\"\n",
links);
d_status = EXIT_FAILURE;
}
end_obj(dump_header_format->softlinkend,
dump_header_format->softlinkblockend);
free(buf);
} else {
begin_obj(dump_header_format->softlinkbegin, links,
dump_header_format->softlinkblockbegin);
indentation(COL);
error_msg(progname, "\"%s\" is not a link\n", links);
end_obj(dump_header_format->softlinkend,
dump_header_format->softlinkblockend);
d_status = EXIT_FAILURE;
}
}
/*-------------------------------------------------------------------------
* Function: handle_datatypes
*
* Purpose: Handle the datatypes from the command.
*
* Return: void
*
* Programmer: Bill Wendling
* Tuesday, 9. January 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
handle_datatypes(hid_t fid, char *type, void UNUSED * data)
{
hid_t type_id;
if ((type_id = H5Topen(fid, type)) < 0) {
/* check if type is unamed data type */
int idx = 0;
while (idx < type_table->nobjs ) {
char name[128], name1[128];
if (!type_table->objs[idx].recorded) {
/* unamed data type */
sprintf(name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno);
sprintf(name1,"/%s",name);
if (!strncmp(name, type, strlen(type)) || !strncmp(name1, type, strlen(type)))
break;
}
idx++;
}
if (idx == type_table->nobjs) {
/* unknown type */
begin_obj(dump_header_format->datatypebegin, type,
dump_header_format->datatypeblockbegin);
indentation(COL);
error_msg(progname, "unable to open datatype \"%s\"\n", type);
end_obj(dump_header_format->datatypeend,
dump_header_format->datatypeblockend);
d_status = EXIT_FAILURE;
} else {
hid_t dsetid = H5Dopen(fid, type_table->objs[idx].objname);
type_id = H5Dget_type(dsetid);
dump_named_datatype(type_id, type);
H5Tclose(type_id);
H5Dclose(dsetid);
}
} else {
dump_named_datatype(type_id, type);
if (H5Tclose(type_id) < 0)
d_status = EXIT_FAILURE;
}
}
/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: Parse the command line for the h5dumper.
*
* Return: Success: A pointer to an array of handler_t structures.
* These contain all the information needed to dump
* the necessary object.
*
* Failure: Exits program with EXIT_FAILURE value.
*
* Programmer: Bill Wendling
* Tuesday, 20. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static struct handler_t *
parse_command_line(int argc, const char *argv[])
{
struct handler_t *hand, *last_dset = NULL;
int i, opt, last_was_dset = FALSE;
/* this will be plenty big enough to hold the info */
hand = calloc((size_t)argc, sizeof(struct handler_t));
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
parse_start:
switch ((char)opt) {
case 'B':
display_bb = TRUE;
last_was_dset = FALSE;
break;
case 'n':
display_fi = TRUE;
last_was_dset = FALSE;
break;
case 'p':
display_dcpl = TRUE;
break;
case 'y':
display_ai = FALSE;
break;
case 'e':
display_escape = TRUE;
break;
case 'H':
display_data = FALSE;
display_attr_data = FALSE;
last_was_dset = FALSE;
break;
case 'A':
display_data = FALSE;
display_attr_data = TRUE;
last_was_dset = FALSE;
break;
case 'i':
display_oid = TRUE;
last_was_dset = FALSE;
break;
case 'r':
display_char = TRUE;
break;
case 'V':
print_version(progname);
leave(EXIT_SUCCESS);
break;
case 'w':
nCols = atoi(opt_arg);
last_was_dset = FALSE;
break;
case 'a':
display_all = 0;
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_attributes;
hand[i].obj = HDstrdup(opt_arg);
break;
}
last_was_dset = FALSE;
break;
case 'd':
display_all = 0;
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_datasets;
hand[i].obj = HDstrdup(opt_arg);
hand[i].subset_info = parse_subset_params(hand[i].obj);
last_dset = hand;
break;
}
last_was_dset = TRUE;
break;
case 'f':
driver = opt_arg;
break;
case 'g':
display_all = 0;
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_groups;
hand[i].obj = HDstrdup(opt_arg);
break;
}
last_was_dset = FALSE;
break;
case 'l':
display_all = 0;
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_links;
hand[i].obj = HDstrdup(opt_arg);
break;
}
last_was_dset = FALSE;
break;
case 't':
display_all = 0;
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_datatypes;
hand[i].obj = HDstrdup(opt_arg);
break;
}
last_was_dset = FALSE;
break;
case 'o':
if (set_output_file(opt_arg) < 0){
/* failed to set output file */
usage(progname);
leave(EXIT_FAILURE);
}
usingdasho = TRUE;
last_was_dset = FALSE;
break;
/** begin XML parameters **/
case 'x':
/* select XML output */
doxml = TRUE;
useschema = TRUE;
dump_header_format = NULL;
dump_function_table = &xml_function_table;
break;
case 'u':
doxml = TRUE;
useschema = FALSE;
xmlnsprefix = "";
dump_header_format = NULL;
dump_function_table = &xml_function_table;
break;
case 'D':
/* specify alternative XML DTD or schema */
/* To Do: check format of this value? */
xml_dtd_uri = opt_arg;
break;
case 'X':
/* specify XML namespace (default="hdf5:"), or none */
/* To Do: check format of this value? */
if (!useschema) {
usage(progname);
leave(EXIT_FAILURE);
}
if (strcmp(opt_arg,":") == 0) {
xmlnsprefix = "";
} else {
xmlnsprefix = opt_arg;
}
break;
/** end XML parameters **/
/** begin subsetting parameters **/
case 's':
case 'S':
case 'c':
case 'k': {
struct subset_t *s;
if (!last_was_dset) {
error_msg(progname,
"option `-%c' can only be used after --dataset option\n",
opt);
leave(EXIT_FAILURE);
}
if (last_dset->subset_info) {
/*
* This overrides the "terse" syntax if they actually mixed
* the two.
*/
s = last_dset->subset_info;
} else {
last_dset->subset_info = s = calloc(1, sizeof(struct subset_t));
}
/*
* slightly convoluted, but...we are only interested in options
* for subsetting: "--start", "--stride", "--count", and "--block"
* which can come in any order. If we run out of parameters (EOF)
* or run into one which isn't a subsetting parameter (NOT s, S,
* c, or K), then we exit the do-while look, set the subset_info
* to the structure we've been filling. If we've reached the end
* of the options, we exit the parsing (goto parse_end) otherwise,
* since we've "read" the next option, we need to parse it. So we
* jump to the beginning of the switch statement (goto parse_start).
*/
do {
switch ((char)opt) {
case 's': free(s->start); s->start = (hssize_t *)parse_hsize_list(opt_arg); break;
case 'S': free(s->stride); s->stride = parse_hsize_list(opt_arg); break;
case 'c': free(s->count); s->count = parse_hsize_list(opt_arg); break;
case 'k': free(s->block); s->block = parse_hsize_list(opt_arg); break;
default: goto end_collect;
}
} while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF);
end_collect:
last_was_dset = FALSE;
if (opt != EOF)
goto parse_start;
else
goto parse_end;
}
/** end subsetting parameters **/
case 'h':
usage(progname);
leave(EXIT_SUCCESS);
case '?':
default:
usage(progname);
leave(EXIT_FAILURE);
}
}
parse_end:
/* check for file name to be processed */
if (argc <= opt_ind) {
error_msg(progname, "missing file name\n");
usage(progname);
leave(EXIT_FAILURE);
}
return hand;
}
/*-------------------------------------------------------------------------
* Function: free_handler
*
* Purpose: Convenience function to free the handler_t structures. Needs a
* length variable (LEN) to know how many in the array it needs
* to free
*
* Return: Nothing
*
* Programmer: Bill Wendling
* Tuesday, 20. February 2001
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
free_handler(struct handler_t *hand, int len)
{
register int i;
for (i = 0; i < len; i++) {
free(hand[i].obj);
if (hand[i].subset_info) {
free(hand[i].subset_info->start);
free(hand[i].subset_info->stride);
free(hand[i].subset_info->count);
free(hand[i].subset_info->block);
free(hand[i].subset_info);
}
}
free(hand);
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: HDF5 dumper
*
* Return: Success: 0
* Failure: 1
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
* Albert Cheng
* 30. September 2000
* Add the -o option--output file for datasets raw data
*
* REMcG
* November 2000
* Changes to support XML.
*
* Bill Wendling
* Wednesday, 10. January 2001
* Modified the way command line parameters are interpreted. They go
* through one function call now (get_option).
*
* Bill Wendling
* Tuesday, 20. February 2001
* Moved command line parsing to separate function. Made various
* "display_*" flags global.
*
* REMcG
* August 2003
* Major upgrade to XML support.
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
hid_t fid, gid;
const char *fname = NULL;
void *edata;
H5E_auto_stack_t func;
find_objs_t info;
struct handler_t *hand;
int i;
dump_header_format = &standardformat;
dump_function_table = &ddl_function_table;
/* Disable error reporting */
H5Eget_auto_stack(H5E_DEFAULT, &func, &edata);
H5Eset_auto_stack(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
hand = parse_command_line(argc, argv);
/* Check for conflicting options */
if (doxml) {
if (!display_all) {
error_msg(progname, "option \"%s\" not available for XML\n",
"to display selected objects");
leave(EXIT_FAILURE);
} else if (display_bb) {
error_msg(progname, "option \"%s\" not available for XML\n",
"--boot-block");
leave(EXIT_FAILURE);
} else if (display_oid == 1) {
error_msg(progname, "option \"%s\" not available for XML\n",
"--object-ids");
leave(EXIT_FAILURE);
} else if (display_char == TRUE) {
error_msg(progname, "option \"%s\" not available for XML\n",
"--string");
leave(EXIT_FAILURE);
} else if (usingdasho) {
error_msg(progname, "option \"%s\" not available for XML\n",
"--output");
leave(EXIT_FAILURE);
}
} else {
if (xml_dtd_uri) {
warn_msg(progname, "option \"%s\" only applies with XML: %s\n",
"--xml-dtd", xml_dtd_uri);
}
}
if (argc <= opt_ind) {
error_msg(progname, "missing file name\n");
usage(progname);
leave(EXIT_FAILURE);
}
fname = argv[opt_ind];
fid = h5tools_fopen(fname, driver, NULL, 0, argc, argv);
if (fid < 0) {
error_msg(progname, "unable to open file \"%s\"\n", fname);
leave(EXIT_FAILURE);
}
/* allocate and initialize internal data structure */
init_table(&group_table);
init_table(&type_table);
init_table(&dset_table);
init_prefix(&prefix, prefix_len);
/* init the find_objs_t */
info.threshold = 0;
info.prefix_len = prefix_len;
info.prefix = calloc((size_t)info.prefix_len, 1);
info.group_table = group_table;
info.type_table = type_table;
info.dset_table = dset_table;
info.status = d_status;
thefile = fid;
/* find all objects that might be targets of a refernce */
if ((gid = H5Gopen(fid, "/")) < 0) {
error_msg(progname, "unable to open root group\n");
d_status = EXIT_FAILURE;
goto done;
}
ref_path_table_put(gid, "/");
H5Giterate(fid, "/", NULL, fill_ref_path_table, NULL);
H5Gclose(gid);
if (doxml) {
/* initialize XML */
/* reset prefix! */
strcpy(prefix, "");
/* make sure the URI is initialized to something */
if (xml_dtd_uri == NULL) {
if (useschema) {
xml_dtd_uri = DEFAULT_XSD;
} else {
xml_dtd_uri = DEFAULT_DTD;
xmlnsprefix = "";
}
} else {
if (useschema && strcmp(xmlnsprefix,"")) {
error_msg(progname, "Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n");
leave(EXIT_FAILURE);
}
}
}
/* find all shared objects */
H5Giterate(fid, "/", NULL, find_objs, (void *)&info);
/* does there exist unamed committed data type */
for (i = 0; i < type_table->nobjs; i++)
if (type_table->objs[i].recorded == 0)
unamedtype = 1;
dump_tables();
if (info.status) {
error_msg(progname, "internal error (file %s:line %d)\n",
__FILE__, __LINE__);
d_status = EXIT_FAILURE;
goto done;
}
/* start to dump */
if (!doxml) {
begin_obj(dump_header_format->filebegin, fname,
dump_header_format->fileblockbegin);
} else {
printf("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
/* alternative first element, depending on schema or DTD. */
if (useschema) {
if (strcmp(xmlnsprefix,"") == 0) {
printf("<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 = strdup(xmlnsprefix);
indx = strrchr(ns,(int)':');
if (indx) *indx = '\0';
printf("<%sHDF5-File xmlns:%s=\"http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File\" "
"xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" "
"xsi:schemaLocation=\"http://hdf.ncsa.uiuc.edu/DTDs/HDF5File "
"http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd\">\n",xmlnsprefix,ns);
}
} else {
printf("<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n",
xml_dtd_uri);
printf("<HDF5-File>\n");
}
}
if (!doxml)
{
if (display_fi)
{
dump_fcontents(fid);
end_obj(dump_header_format->fileend,dump_header_format->fileblockend);
goto done;
}
if (display_bb)
dump_fcpl(fid);
}
if (display_all) {
if ((gid = H5Gopen(fid, "/")) < 0) {
error_msg(progname, "unable to open root group\n");
d_status = EXIT_FAILURE;
} else {
dump_function_table->dump_group_function(gid, "/");
}
if (H5Gclose(gid) < 0) {
error_msg(progname, "unable to close root group\n");
d_status = EXIT_FAILURE;
}
} else {
if (doxml) {
/* Note: this option is not supported for XML */
error_msg(progname, "internal error (file %s:line %d)\n",
__FILE__, __LINE__);
d_status = EXIT_FAILURE;
goto done;
}
for (i = 0; i < argc; i++)
if (hand[i].func)
hand[i].func(fid, hand[i].obj, hand[i].subset_info);
}
if (!doxml) {
end_obj(dump_header_format->fileend,
dump_header_format->fileblockend);
} else {
printf("</%sHDF5-File>\n", xmlnsprefix);
}
done:
if (H5Fclose(fid) < 0)
d_status = EXIT_FAILURE;
free_handler(hand, argc);
for(i=0; i<info.group_table->nobjs; i++) {
if(info.group_table->objs[i].objname)
free(info.group_table->objs[i].objname);
}
free(group_table->objs);
for(i=0; i<info.dset_table->nobjs; i++) {
if(info.dset_table->objs[i].objname)
free(info.dset_table->objs[i].objname);
}
free(dset_table->objs);
for(i=0; i<info.type_table->nobjs; i++) {
if(info.type_table->objs[i].objname)
free(info.type_table->objs[i].objname);
}
free(type_table->objs);
free(prefix);
free(info.prefix);
/* To Do: clean up XML table */
H5Eset_auto_stack(H5E_DEFAULT, func, edata);
leave(d_status);
}
/*-------------------------------------------------------------------------
* Function: print_enum
*
* Purpose: prints the enum data
*
* Return: void
*
* Programmer: Patrick Lu
*
* Modifications:
*
* NOTE: this function was taken from h5ls. should be moved into the toolslib
*
*-----------------------------------------------------------------------*/
static void
print_enum(hid_t type)
{
char **name = NULL; /*member names */
unsigned char *value = NULL; /*value array */
unsigned nmembs; /*number of members */
int nchars; /*number of output characters */
hid_t super; /*enum base integer type */
hid_t native = -1; /*native integer data type */
size_t dst_size; /*destination value type size */
unsigned i;
nmembs = H5Tget_nmembers(type);
assert(nmembs>0);
super = H5Tget_super(type);
/*
* Determine what data type to use for the native values. To simplify
* things we entertain three possibilities:
* 1. long_long -- the largest native signed integer
* 2. unsigned long_long -- the largest native unsigned integer
* 3. raw format
*/
if (H5Tget_size(type) <= sizeof(long_long)) {
dst_size = sizeof(long_long);
if (H5T_SGN_NONE == H5Tget_sign(type)) {
native = H5T_NATIVE_ULLONG;
} else {
native = H5T_NATIVE_LLONG;
}
} else {
dst_size = H5Tget_size(type);
}
/* Get the names and raw values of all members */
name = calloc(nmembs, sizeof(char *));
value = calloc(nmembs, MAX(H5Tget_size(type), dst_size));
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
H5Tget_member_value(type, i, value + i * H5Tget_size(type));
}
/* Convert values to native data type */
if (native > 0)
H5Tconvert(super, native, nmembs, value, NULL, H5P_DEFAULT);
/*
* Sort members by increasing value
* ***not implemented yet***
*/
/* Print members */
for (i = 0; i < nmembs; i++) {
indentation(indent + COL);
nchars = printf("\"%s\"", name[i]);
printf("%*s ", MAX(0, 16 - nchars), "");
if (native < 0) {
size_t j;
printf("0x");
for (j = 0; j < dst_size; j++)
printf("%02x", value[i * dst_size + j]);
} else if (H5T_SGN_NONE == H5Tget_sign(native)) {
HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "u", *((unsigned long_long *)
((void *) (value + i * dst_size))));
} else {
HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "d",
*((long_long *) ((void *) (value + i * dst_size))));
}
printf(";\n");
}
/* Release resources */
for (i = 0; i < nmembs; i++)
free(name[i]);
free(name);
free(value);
H5Tclose(super);
if (0 == nmembs)
printf("\n%*s <empty>", indent + 4, "");
}
#if 0
/*
* XML support
*/
/*
* XML needs a table to look up a path name for an object
* reference.
*
* This table stores mappings of reference -> path
* for all objects in the file that may be the target of
* an object reference.
*
* The 'path' is an absolute path by which the object
* can be accessed. When an object has > 1 such path,
* only one will be used in the table, with no particular
* method of selecting which one.
*/
ref_path_table_entry_t *ref_path_table = NULL; /* the table */
/*-------------------------------------------------------------------------
* Function: ref_path_table_lookup
*
* Purpose: Looks up a table entry given a path name.
* Used during construction of the table.
*
* Return: The table entre (pte) or NULL if not in the
* table.
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static ref_path_table_entry_t *
ref_path_table_lookup(const char *thepath)
{
H5G_stat_t sb;
ref_path_table_entry_t *pte = ref_path_table;
if(H5Gget_objinfo(thefile, thepath, TRUE, &sb)<0) {
/* fatal error ? */
return NULL;
}
while(pte!=NULL) {
if (sb.objno==pte->statbuf.objno)
return pte;
pte = pte->next;
}
return NULL;
}
/*-------------------------------------------------------------------------
* Function: ref_path_table_put
*
* Purpose: Enter the 'obj' with 'path' in the table if
* not already there.
* Create an object reference, pte, and store them
* in the table.
*
* Return: The object reference for the object.
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static ref_path_table_entry_t *
ref_path_table_put(hid_t obj, const char *path)
{
ref_path_table_entry_t *pte;
/* look up 'obj'. If already in table, return */
pte = ref_path_table_lookup(path);
if (pte != NULL)
return pte;
/* if not found, then make new entry */
pte = (ref_path_table_entry_t *) malloc(sizeof(ref_path_table_entry_t));
if (pte == NULL) {
/* fatal error? */
return NULL;
}
pte->obj = obj;
pte->apath = HDstrdup(path);
if(H5Gget_objinfo(thefile, path, TRUE, &pte->statbuf)<0) {
/* fatal error? */
free(pte);
return NULL;
}
pte->next = ref_path_table;
ref_path_table = pte;
return pte;
}
/*
* counter used to disambiguate multiple instances of same object.
*/
static int xid = 1;
static int get_next_xid() {
return xid++;
}
/*
* This counter is used to create fake object ID's
* The idea is to set it to the largest possible offest, which
* minimizes the chance of collision with a real object id.
*
*/
haddr_t fake_xid = HADDR_MAX;
static haddr_t
get_fake_xid () {
return (fake_xid--);
}
/*
* for an object that does not have an object id (e.g., soft link),
* create a table entry with a fake object id as the key.
*/
static ref_path_table_entry_t *
ref_path_table_gen_fake(const char *path)
{
ref_path_table_entry_t *pte;
/* look up 'obj'. If already in table, return */
pte = ref_path_table_lookup(path);
if (pte != NULL) {
return pte;
}
/* if not found, then make new entry */
pte = (ref_path_table_entry_t *) malloc(sizeof(ref_path_table_entry_t));
if (pte == NULL) {
/* fatal error? */
return NULL;
}
pte->obj = (hid_t)-1;
memset(&pte->statbuf,0,sizeof(H5G_stat_t));
pte->statbuf.objno = get_fake_xid();
pte->apath = HDstrdup(path);
pte->next = ref_path_table;
ref_path_table = pte;
return pte;
}
/*-------------------------------------------------------------------------
* Function: lookup_ref_path
*
* Purpose: Lookup the path to the object with refernce 'ref'.
*
* Return: Return a path to the object, or NULL if not found.
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
char *
lookup_ref_path(hobj_ref_t ref)
{
ref_path_table_entry_t *pte = ref_path_table;
while(pte!=NULL) {
if (ref==pte->statbuf.objno)
return pte->apath;
pte = pte->next;
}
return NULL;
}
/*-------------------------------------------------------------------------
* Function: fill_ref_path_table
*
* Purpose: Called by interator to create references for
* all objects and enter them in the table.
*
* Return: Error status.
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
fill_ref_path_table(hid_t group, const char *name, void UNUSED * op_data)
{
hid_t obj;
char *tmp;
H5G_stat_t statbuf;
ref_path_table_entry_t *pte;
char *thepath;
H5Gget_objinfo(group, name, FALSE, &statbuf);
tmp = (char *) malloc(strlen(prefix) + strlen(name) + 2);
if (tmp == NULL)
return FAIL;
thepath = (char *) malloc(strlen(prefix) + strlen(name) + 2);
if (thepath == NULL) {
free(tmp);
return FAIL;
}
strcpy(tmp, prefix);
strcpy(thepath, prefix);
strcat(thepath, "/");
strcat(thepath, name);
switch (statbuf.type) {
case H5G_DATASET:
if ((obj = H5Dopen(group, name)) >= 0) {
pte = ref_path_table_lookup(thepath);
if (pte == NULL) {
ref_path_table_put(obj, thepath);
}
H5Dclose(obj);
} else {
error_msg(progname, "unable to get dataset \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
break;
case H5G_GROUP:
if ((obj = H5Gopen(group, name)) >= 0) {
strcat(strcat(prefix, "/"), name);
pte = ref_path_table_lookup(thepath);
if (pte == NULL) {
ref_path_table_put(obj, thepath);
H5Giterate(obj, ".", NULL, fill_ref_path_table, NULL);
strcpy(prefix, tmp);
}
H5Gclose(obj);
} else {
error_msg(progname, "unable to dump group \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
break;
case H5G_TYPE:
if ((obj = H5Topen(group, name)) >= 0) {
pte = ref_path_table_lookup(thepath);
if (pte == NULL) {
ref_path_table_put(obj, thepath);
}
H5Tclose(obj);
} else {
error_msg(progname, "unable to get dataset \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
break;
default:
break;
}
free(tmp);
free(thepath);
return 0;
}
#endif
/*
* create a string suitable for and XML NCNAME. Uses the
* object reference to create the string.
*
* 'gen'; 0 - return null if not found
* 1 - generate a fake entry and return fake id.
*/
int
xml_name_to_XID(const char *str , char *outstr, int outlen, int gen)
{
ref_path_table_entry_t *r;
char *os;
if (outlen < 22) return 1;
os = outstr;
r = ref_path_table_lookup(str);
if (r == NULL) {
if (strlen(str) == 0) {
r = ref_path_table_lookup("/");
if (r == NULL) {
if (gen) {
sprintf(os," "); /* ?? */
r = ref_path_table_gen_fake(str);
sprintf(os, "xid_"H5_PRINTF_HADDR_FMT, r->statbuf.objno);
return 0;
} else {
return 1;
}
}
} else {
if (gen) {
sprintf(os," "); /* ?? */
r = ref_path_table_gen_fake(str);
sprintf(os, "xid_"H5_PRINTF_HADDR_FMT, r->statbuf.objno);
return 0;
} else {
return 1;
}
}
}
sprintf(os, "xid_"H5_PRINTF_HADDR_FMT, r->statbuf.objno);
return(0);
}
static const char *quote = "&quot;";
static const char *amp = "&amp;";
static const char *lt = "&lt;";
static const char *gt = "&gt;";
static const char *apos = "&apos;";
/*-------------------------------------------------------------------------
* Function: xml_escape_the_name
*
* Purpose: Escape XML reserved chars in a name, so HDF5 strings
* and paths can be correctly read back in XML element.
*
* Return: The revised string.
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
xml_escape_the_name(const char *str)
{
size_t extra;
size_t len;
size_t i;
const char *cp;
char *ncp;
char *rcp;
if (!str)
return NULL;
cp = str;
len = strlen(str);
extra = 0;
for (i = 0; i < len; i++) {
if (*cp == '\"') {
extra += (strlen(quote) - 1);
} else if (*cp == '\'') {
extra += (strlen(apos) - 1);
} else if (*cp == '<') {
extra += (strlen(lt) - 1);
} else if (*cp == '>') {
extra += (strlen(gt) - 1);
} else if (*cp == '&') {
extra += (strlen(amp) - 1);
}
cp++;
}
if (extra == 0)
return HDstrdup(str);
cp = str;
rcp = ncp = calloc((size_t)(len + extra + 1), sizeof(char));
if (!ncp)
return NULL; /* ?? */
for (i = 0; i < len; i++) {
if (*cp == '\'') {
strncpy(ncp, apos, strlen(apos));
ncp += strlen(apos);
cp++;
} else if (*cp == '<') {
strncpy(ncp, lt, strlen(lt));
ncp += strlen(lt);
cp++;
} else if (*cp == '>') {
strncpy(ncp, gt, strlen(gt));
ncp += strlen(gt);
cp++;
} else if (*cp == '\"') {
strncpy(ncp, quote, strlen(quote));
ncp += strlen(quote);
cp++;
} else if (*cp == '&') {
strncpy(ncp, amp, strlen(amp));
ncp += strlen(amp);
cp++;
} else {
*ncp++ = *cp++;
}
}
*ncp = '\0';
return rcp;
}
/*-------------------------------------------------------------------------
* Function: xml_escape_the_string
*
* Purpose: Escape XML reserved chars in a string, so HDF5 strings
* and paths can be correctly read back in XML CDATA.
*
* Return: The revised string.
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
xml_escape_the_string(const char *str, int slen)
{
size_t extra;
size_t len;
size_t i;
const char *cp;
char *ncp;
char *rcp;
if (!str)
return NULL;
cp = str;
if (slen < 0)
len = strlen(str);
else
len = slen;
extra = 0;
for (i = 0; i < len; i++) {
if (*cp == '\\') {
extra++;
} else if (*cp == '\"') {
extra++;
} else if (*cp == '\'') {
extra += (strlen(apos) - 1);
} else if (*cp == '<') {
extra += (strlen(lt) - 1);
} else if (*cp == '>') {
extra += (strlen(gt) - 1);
} else if (*cp == '&') {
extra += (strlen(amp) - 1);
}
cp++;
}
cp = str;
rcp = ncp = calloc((len + extra + 1), sizeof(char));
if (ncp == NULL)
return NULL; /* ?? */
for (i = 0; i < len; i++) {
if (*cp == '\\') {
*ncp++ = '\\';
*ncp++ = *cp++;
} else if (*cp == '\"') {
*ncp++ = '\\';
*ncp++ = *cp++;
} else if (*cp == '\'') {
strncpy(ncp, apos, strlen(apos));
ncp += strlen(apos);
cp++;
} else if (*cp == '<') {
strncpy(ncp, lt, strlen(lt));
ncp += strlen(lt);
cp++;
} else if (*cp == '>') {
strncpy(ncp, gt, strlen(gt));
ncp += strlen(gt);
cp++;
} else if (*cp == '&') {
strncpy(ncp, amp, strlen(amp));
ncp += strlen(amp);
cp++;
} else {
*ncp++ = *cp++;
}
}
*ncp = '\0';
return rcp;
}
/**
** XML print functions--these replace some functions in the
** h5tools.c suite.
**/
/*-------------------------------------------------------------------------
* Function: xml_print_datatype
*
* Purpose: Print description of a datatype in XML.
* Note: this is called inside a <DataType> element.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_print_datatype(hid_t type, unsigned in_group)
{
char *fname;
hid_t mtype;
unsigned nmembers;
int perm[H5DUMP_MAX_RANK];
unsigned ndims;
unsigned i;
size_t size;
hsize_t dims[H5DUMP_MAX_RANK];
H5T_str_t str_pad;
H5T_cset_t cset;
H5G_stat_t statbuf;
hid_t super;
H5T_order_t ord;
H5T_sign_t sgn;
size_t sz;
size_t spos;
size_t epos;
size_t esize;
size_t mpos;
size_t msize;
int nmembs;
htri_t is_vlstr=FALSE;
herr_t ret;
if (!in_group && H5Tcommitted(type) > 0) {
/* detect a shared datatype, output only once */
H5Gget_objinfo(type, ".", TRUE, &statbuf);
ret = search_obj(type_table, statbuf.objno);
if (ret >= 0) {
/* This should be defined somewhere else */
/* These 2 cases are handled the same right now, but
probably will have something different eventually */
char * dtxid = malloc(100);
xml_name_to_XID(type_table->objs[ret].objname,dtxid,100,1);
if (!type_table->objs[ret].recorded) {
/* 'anonymous' NDT. Use it's object num.
as it's name. */
printf("<%sNamedDataTypePtr OBJ-XID=\"/%s\"/>\n",
xmlnsprefix,
dtxid);
} else {
/* point to the NDT by name */
char *t_objname = xml_escape_the_name(type_table->objs[ret].objname);
printf("<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\"/>\n",
xmlnsprefix,
dtxid,t_objname);
free(t_objname);
}
free(dtxid);
} else {
printf("<!-- h5dump error: unknown committed type. -->\n");
d_status = EXIT_FAILURE;
}
} else {
switch (H5Tget_class(type)) {
case H5T_INTEGER:
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
/* <hdf5:IntegerType ByteOrder="bo" Sign="torf" Size="bytes"/> */
ord = H5Tget_order(type);
sgn = H5Tget_sign(type);
indentation(indent);
printf("<%sIntegerType ByteOrder=\"",xmlnsprefix);
switch (ord) {
case H5T_ORDER_LE:
printf("LE");
break;
case H5T_ORDER_BE:
printf("BE");
break;
case H5T_ORDER_VAX:
default:
printf("ERROR_UNKNOWN");
}
printf("\" Sign=\"");
switch (sgn) {
case H5T_SGN_NONE:
printf("false");
break;
case H5T_SGN_2:
printf("true");
break;
default:
printf("ERROR_UNKNOWN");
}
printf("\" Size=\"");
sz = H5Tget_size(type);
printf("%lu", (unsigned long)sz);
printf("\" />\n");
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_FLOAT:
/* <hdf5:FloatType ByteOrder="bo" Size="bytes"
SignBitLocation="bytes"
ExponentBits="eb" ExponentLocation="el"
MantissaBits="mb" MantissaLocation="ml" /> */
ord = H5Tget_order(type);
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sFloatType ByteOrder=\"",xmlnsprefix);
switch (ord) {
case H5T_ORDER_LE:
printf("LE");
break;
case H5T_ORDER_BE:
printf("BE");
break;
case H5T_ORDER_VAX:
default:
printf("ERROR_UNKNOWN");
}
printf("\" Size=\"");
sz = H5Tget_size(type);
printf("%lu", (unsigned long)sz);
H5Tget_fields(type, &spos, &epos, &esize, &mpos, &msize);
printf("\" SignBitLocation=\"%lu\" ", (unsigned long)spos);
printf("ExponentBits=\"%lu\" ExponentLocation=\"%lu\" ", (unsigned long)esize, (unsigned long)epos);
printf("MantissaBits=\"%lu\" MantissaLocation=\"%lu\" />\n",
(unsigned long)msize, (unsigned long)mpos);
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_TIME:
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sTimeType />\n",xmlnsprefix);
printf("<!-- H5T_TIME: not yet implemented -->");
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_STRING:
/* <hdf5:StringType Cset="cs" StrSize="chars" StrPad="pad" /> */
size = H5Tget_size(type);
str_pad = H5Tget_strpad(type);
cset = H5Tget_cset(type);
is_vlstr = H5Tis_variable_str(type);
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sStringType Cset=\"",xmlnsprefix);
if (cset == H5T_CSET_ASCII) {
printf("H5T_CSET_ASCII\" ");
} else {
printf("unknown_cset\" ");
}
if(is_vlstr)
printf("StrSize=\"H5T_VARIABLE\" StrPad=\"");
else
printf("StrSize=\"%d\" StrPad=\"", (int) size);
if (str_pad == H5T_STR_NULLTERM) {
printf("H5T_STR_NULLTERM\"/>\n");
} else if (str_pad == H5T_STR_NULLPAD) {
printf("H5T_STR_NULLPAD\"/>\n");
} else if (str_pad == H5T_STR_SPACEPAD) {
printf("H5T_STR_SPACEPAD\"/>\n");
} else {
printf("H5T_STR_ERROR\"/>\n");
}
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_BITFIELD:
/* <hdf5:BitfieldType ByteOrder="bo" Size="bytes"/> */
ord = H5Tget_order(type);
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sBitfieldType ByteOrder=\"",xmlnsprefix);
switch (ord) {
case H5T_ORDER_LE:
printf("LE");
break;
case H5T_ORDER_BE:
printf("BE");
break;
case H5T_ORDER_VAX:
default:
printf("ERROR_UNKNOWN");
}
size = H5Tget_size(type);
printf("\" Size=\"%lu\"/>\n", (unsigned long)size);
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_OPAQUE:
/* <hdf5:OpaqueType Tag="tag" Size="bytes" /> */
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sOpaqueType Tag=\"%s\" ",xmlnsprefix, H5Tget_tag(type));
size = H5Tget_size(type);
printf("Size=\"%lu\"/>\n", (unsigned long)size);
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_COMPOUND:
/* recursively describe the components of a compound datatype */
/* type of a dataset */
nmembers = H5Tget_nmembers(type);
indentation(indent);
printf("<%sCompoundType>\n",xmlnsprefix);
/* List each member Field of the type */
/* <hdf5:Field FieldName="name" > */
/* <hdf5:DataType > */
indent += COL;
for (i = 0; i < nmembers; i++) {
char *t_fname;
fname = H5Tget_member_name(type, i);
mtype = H5Tget_member_type(type, i);
indentation(indent);
t_fname = xml_escape_the_name(fname);
printf("<%sField FieldName=\"%s\">\n",xmlnsprefix, t_fname);
free(fname);
free(t_fname);
indent += COL;
indentation(indent);
printf("<%sDataType>\n",xmlnsprefix);
indent += COL;
xml_print_datatype(mtype,0);
indent -= COL;
indentation(indent);
printf("</%sDataType>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sField>\n",xmlnsprefix);
}
indent -= COL;
indentation(indent);
printf("</%sCompoundType>\n",xmlnsprefix);
break;
case H5T_REFERENCE:
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
/* Only Object references supported at this time */
printf("<%sReferenceType>\n",xmlnsprefix);
indentation(indent + COL);
printf("<%sObjectReferenceType />\n",xmlnsprefix);
indentation(indent);
printf("</%sReferenceType>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_ENUM:
/* <hdf5:EnumType Nelems="ne" >
list Name, values of enum
*/
nmembs = H5Tget_nmembers(type);
indentation(indent);
printf("<%sAtomicType>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sEnumType Nelems=\"%d\">\n",xmlnsprefix, nmembs);
xml_print_enum(type);
indentation(indent);
printf("</%sEnumType>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sAtomicType>\n",xmlnsprefix);
break;
case H5T_VLEN:
indentation(indent);
printf("<%sVLType>\n",xmlnsprefix);
super = H5Tget_super(type);
indent += COL;
indentation(indent);
printf("<%sDataType>\n",xmlnsprefix);
indent += COL;
xml_print_datatype(super,0);
indent -= COL;
indentation(indent);
printf("</%sDataType>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sVLType>\n",xmlnsprefix);
H5Tclose(super);
break;
case H5T_ARRAY:
/* Get array base type */
super = H5Tget_super(type);
/* Print lead-in */
indentation(indent);
printf("<%sArrayType Ndims=\"",xmlnsprefix);
ndims = H5Tget_array_ndims(type);
printf("%u\">\n", ndims);
/* Get array information */
H5Tget_array_dims(type, dims, perm);
/* list of dimensions */
indent += COL;
if (perm != NULL) {
/* for each dimension, list */
for (i = 0; i < ndims; i++) {
indentation(indent);
printf("<%sArrayDimension DimSize=\"%u\" DimPerm=\"%u\"/>\n",
xmlnsprefix,(int) dims[i], (int) perm[i]);
}
} else {
for (i = 0; i < ndims; i++) {
indentation(indent);
printf("<%sArrayDimension DimSize=\"%u\" DimPerm=\"0\"/>\n",
xmlnsprefix,
(int) dims[i]);
}
}
indent -= COL;
indent += COL;
indentation(indent);
printf("<%sDataType>\n",xmlnsprefix);
indent += COL;
xml_print_datatype(super,0);
indent -= COL;
indentation(indent);
printf("</%sDataType>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sArrayType>\n",xmlnsprefix);
/* Close array base type */
H5Tclose(super);
break;
default:
printf("<!-- unknown data type -->");
d_status = EXIT_FAILURE;
break;
}
} /* end else */
}
/*-------------------------------------------------------------------------
* Function: xml_dump_datatype
*
* Purpose: Dump description of a datatype in XML.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_dump_datatype(hid_t type)
{
int i;
H5G_stat_t statbuf;
indent += COL;
indentation(indent);
if (H5Tcommitted(type) > 0) {
/* Data type is a shared or named data type */
H5Gget_objinfo(type, ".", TRUE, &statbuf);
i = search_obj(type_table, statbuf.objno);
if (i >= 0) {
/* Shared data type, must be entered as an object */
/* These 2 cases are the same now, but may change */
char * dtxid = malloc(100);
xml_name_to_XID(type_table->objs[i].objname,dtxid,100,1);
if (!type_table->objs[i].recorded) {
/* anonymous stored data type:
following the dumper's current
practice:
use it's object ref as its name
*/
printf("<%sNamedDataTypePtr OBJ-XID=\"%s\"/>\n",
xmlnsprefix,
dtxid);
} else {
/* pointer to a named data type already in XML */
char *t_objname = xml_escape_the_name(type_table->objs[i].objname);
printf("<%sNamedDataTypePtr OBJ-XID=\"%s\" H5Path=\"%s\" />\n",
xmlnsprefix,
dtxid,t_objname);
free(t_objname);
}
free(dtxid);
} else {
printf("<!-- h5dump error: unknown committed type. -->\n");
}
indent -= COL;
return;
}
printf("<%sDataType>\n",xmlnsprefix);
indent += COL;
xml_print_datatype(type,0);
indent -= COL;
indentation(indent);
printf("</%sDataType>\n",xmlnsprefix);
indent -= COL;
}
/*-------------------------------------------------------------------------
* Function: xml_dump_dataspace
*
* Purpose: Dump description of a dataspace in XML.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_dump_dataspace(hid_t space)
{
hsize_t size[H5DUMP_MAX_RANK];
hsize_t maxsize[H5DUMP_MAX_RANK];
int ndims =
H5Sget_simple_extent_dims(space, size, maxsize);
H5S_class_t space_type = H5Sget_simple_extent_type(space);
int i;
indentation(indent + COL);
printf("<%sDataspace>\n", xmlnsprefix);
indentation(indent + COL + COL);
switch (space_type) {
case H5S_SCALAR:
/* scalar dataspace (just a tag, no XML attrs. defined */
printf("<%sScalarDataspace />\n",xmlnsprefix);
break;
case H5S_SIMPLE:
/* simple dataspace */
/* <hdf5:SimpleDataspace Ndims="nd"> */
printf("<%sSimpleDataspace Ndims=\"%d\">\n",xmlnsprefix, ndims);
/* print the <hdf5:Dimension> elements */
for (i = 0; i < ndims; i++) {
indentation(indent + COL + COL + COL);
if (maxsize[i] == H5S_UNLIMITED) {
HDfprintf(stdout,
"<%sDimension DimSize=\"%Hu\" MaxDimSize=\"UNLIMITED\"/>\n",
xmlnsprefix,size[i]);
} else if (maxsize[i] == (hsize_t) 0) {
HDfprintf(stdout,
"<%sDimension DimSize=\"%Hu\" MaxDimSize=\"%Hu\"/>\n",
xmlnsprefix,size[i], size[i]);
} else {
HDfprintf(stdout,
"<%sDimension DimSize=\"%Hu\" MaxDimSize=\"%Hu\"/>\n",
xmlnsprefix, size[i], maxsize[i]);
}
}
indentation(indent + COL + COL);
printf("</%sSimpleDataspace>\n", xmlnsprefix );
break;
#ifdef TMP
/* Commented out: wait until the schema is updated first */
case H5S_NULL:
/* null dataspace (just a tag, no XML attrs. defined */
printf("<%sNullDataspace />\n",xmlnsprefix);
break;
#endif /* TMP */
case H5S_COMPLEX:
printf("<!-- not yet implemented -->\n");
break;
case H5S_NO_CLASS:
default:
printf("<!-- unknown dataspace -->\n");
}
indentation(indent + COL);
printf("</%sDataspace>\n", xmlnsprefix);
}
/*-------------------------------------------------------------------------
* Function: xml_dump_data
*
* Purpose: Dump description of data in XML.
* Note that this calls the h5dump_xxx calls in
* the h5tools library.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_dump_data(hid_t obj_id, int obj_data, struct subset_t UNUSED * sset, int UNUSED pindex)
{
h5dump_t *outputformat = &xml_dataformat;
int status = -1;
void *buf;
hid_t space, type, p_type;
int ndims, i;
hsize_t size[64], nelmts = 1;
int depth;
int stdindent = COL; /* should be 3 */
outputformat->line_ncols = nCols;
indent += COL;
/*
* the depth will tell us how far we need to indent extra. we use to just
* use indent but with the merging of the tools lib we have to do
* something different for the lib funtions... the normal indentation is 6
* so when we don't need any extra indentation, depth will be 0.
*/
depth = indent / stdindent + 1;
/* Print all the values. */
indentation(indent);
printf("<%sData>\n", xmlnsprefix);
indentation(indent + COL);
printf("<%sDataFromFile>\n",xmlnsprefix);
if (obj_data == DATASET_DATA) {
type = H5Dget_type(obj_id);
if (H5Tget_class(type) == H5T_REFERENCE) {
status = xml_print_refs(obj_id, DATASET_DATA);
} else if (H5Tget_class(type) == H5T_STRING) {
status = xml_print_strs(obj_id, DATASET_DATA);
} else {
status = h5tools_dump_dset(stdout, outputformat, obj_id, -1, NULL, depth);
}
} else {
/* Attribute data */
type = H5Aget_type(obj_id);
if (H5Tget_class(type) == H5T_REFERENCE) {
/* references are done differently than
the standard output:
XML dumps a path to the object
referenced.
*/
status = xml_print_refs(obj_id, ATTRIBUTE_DATA);
H5Tclose(type);
} else if (H5Tget_class(type) == H5T_STRING) {
status = xml_print_strs(obj_id, ATTRIBUTE_DATA);
} else {
/* all other data */
p_type = h5tools_get_native_type(type);
H5Tclose(type);
space = H5Aget_space(obj_id);
ndims = H5Sget_simple_extent_dims(space, size, NULL);
for (i = 0; i < ndims; i++)
nelmts *= size[i];
buf =
malloc((size_t)(nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type))));
assert(buf);
if (H5Aread(obj_id, p_type, buf) >= 0)
status = h5tools_dump_mem(stdout, outputformat, obj_id,
p_type, space, buf, depth);
free(buf);
H5Tclose(p_type);
H5Sclose(space);
H5Tclose(type);
}
}
if (status == FAIL) {
indentation(indent + COL);
printf("Unable to print data.\n");
status = 1;
}
indentation(indent + COL);
printf("</%sDataFromFile>\n",xmlnsprefix);
indentation(indent);
printf("</%sData>\n", xmlnsprefix);
indent -= COL;
}
/*-------------------------------------------------------------------------
* Function: xml_dump_attr
*
* Purpose: Dump a description of an HDF5 attribute in XML.
*
* Return: herr_t
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
xml_dump_attr(hid_t attr, const char *attr_name, void UNUSED * op_data)
{
hid_t attr_id, type, space;
H5S_class_t space_type;
char *t_aname = xml_escape_the_name(attr_name);
indentation(indent);
printf("<%sAttribute Name=\"%s\">\n",xmlnsprefix, t_aname);
free(t_aname);
if ((attr_id = H5Aopen_name(attr, attr_name)) >= 0) {
type = H5Aget_type(attr_id);
space = H5Aget_space(attr_id);
space_type = H5Sget_simple_extent_type(space);
dump_function_table->dump_dataspace_function(space);
dump_function_table->dump_datatype_function(type);
if (display_attr_data && space_type!=H5S_NULL) {
switch (H5Tget_class(type)) {
case H5T_INTEGER:
case H5T_FLOAT:
case H5T_STRING:
case H5T_BITFIELD:
case H5T_OPAQUE:
case H5T_ENUM:
case H5T_ARRAY:
dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0);
break;
case H5T_TIME:
indent += COL;
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indentation(indent);
printf("<!-- Time data not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData/>\n",xmlnsprefix);
indentation(indent);
printf("<hdf5:Data>\n");
printf("</%sData>\n",xmlnsprefix);
indent -= COL;
break;
case H5T_COMPOUND:
indentation(indent);
printf("<!-- Note: format of compound data not specified -->\n");
dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0);
break;
case H5T_REFERENCE:
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indentation(indent);
if (!H5Tequal(type, H5T_STD_REF_OBJ)) {
printf("<!-- Note: Region references not supported -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
} else {
printf("<%sDataFromFile>\n",xmlnsprefix);
xml_print_refs(attr_id, ATTRIBUTE_DATA);
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
}
indentation(indent);
printf("</%sData>\n",xmlnsprefix);
break;
case H5T_VLEN:
printf("<!-- Note: format of VL data not specified -->\n");
dump_function_table->dump_data_function(attr_id, ATTRIBUTE_DATA, NULL, 0);
break;
default:
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indentation(indent);
printf("<!-- Unknown datatype: %d -->\n", H5Tget_class(type));
indentation(indent);
printf("<%sNoData/>\n",xmlnsprefix);
indentation(indent);
printf("</%sData>\n",xmlnsprefix);
break;
}
} else {
/* The case of an attribute never yet written ??
* Or dataspace is H5S_NULL. */
indentation(indent + COL);
printf("<%sData>\n",xmlnsprefix);
indentation(indent + COL + COL);
printf("<%sNoData/>\n",xmlnsprefix);
indentation(indent + COL);
printf("</%sData>\n",xmlnsprefix);
}
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
indentation(indent);
printf("</%sAttribute>\n", xmlnsprefix );
return SUCCEED;
} else {
/* ?? failed */
indentation(indent + COL);
printf("<!-- h5dump error: unable to open attribute. -->\n");
indentation(indent);
printf("</%sAttribute>\n", xmlnsprefix );
d_status = EXIT_FAILURE;
return FAIL;
}
}
/*-------------------------------------------------------------------------
* Function: xml_dump_named_datatype
*
* Purpose: Dump a description of an HDF5 NDT in XML.
*
* Return: herr_t
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_dump_named_datatype(hid_t type, const char *name)
{
char *tmp;
char * dtxid;
char * parentxid;
char *t_tmp;
char *t_prefix;
char *t_name;
tmp = malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
strcat(tmp, "/");
strcat(tmp, name);
indentation(indent);
/*char **/ dtxid = malloc(100);
/*char **/ parentxid = malloc(100);
/*char **/t_tmp = xml_escape_the_name(tmp);
/*char **/t_prefix = xml_escape_the_name(prefix);
/*char **/t_name = xml_escape_the_name(name);
xml_name_to_XID(tmp,dtxid,100,1);
xml_name_to_XID(prefix,parentxid,100,1);
if (strncmp(name, "#", 1) == 0) {
/* Special: this is an 'anonymous' NDT, deleted but
still in use.
We follow the dumper's undocumented practice, and
use its object id as its name.
Exactly the same as normal, but a separate case
in the event we want to do something else in
the future.
*/
printf("<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\">\n",
xmlnsprefix,
name, dtxid,
parentxid,(strcmp(prefix, "") ? t_prefix : "/"));
} else {
printf("<%sNamedDataType Name=\"%s\" OBJ-XID=\"%s\" "
"H5Path=\"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">\n",
xmlnsprefix,
t_name, dtxid,
t_tmp, parentxid, (strcmp(prefix, "") ? t_prefix : "/"));
}
free(dtxid);
free(parentxid);
free(t_tmp);
free(t_prefix);
free(t_name);
free(tmp);
indent += COL;
indentation(indent);
printf("<%sDataType>\n",xmlnsprefix);
indent += COL;
xml_print_datatype(type,1);
indent -= COL;
indentation(indent);
printf("</%sDataType>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sNamedDataType>\n",xmlnsprefix);
}
/*-------------------------------------------------------------------------
* Function: xml_dump_group
*
* Purpose: Dump a description of an HDF5 Group (and its members) in XML.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_dump_group(hid_t gid, const char *name)
{
H5G_stat_t statbuf;
char *cp;
hid_t dset, type;
char type_name[1024], *tmp = NULL;
char *par = NULL;
int i;
int isRoot = 0;
int xtype;
char *ptrstr;
char *t_objname;
char *par_name;
if (strcmp(name, "/") == 0) {
isRoot = 1;
tmp = malloc(2);
strcpy(tmp, "/");
} else {
tmp = malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
par = HDstrdup(tmp);
cp = strrchr(par, '/');
if (cp != NULL) {
if ((cp == par) && strlen(par) > 1) {
*(cp + 1) = '\0';
} else {
*cp = '\0';
}
}
}
indentation(indent);
indent += COL;
H5Gget_objinfo(gid, ".", TRUE, &statbuf);
if (statbuf.nlink > 1) {
/* Group with more than one link to it... */
i = search_obj(group_table, statbuf.objno);
if (i < 0) {
indentation(indent);
error_msg(progname, "internal error (file %s:line %d)\n",
__FILE__, __LINE__);
d_status = EXIT_FAILURE;
} else if (group_table->objs[i].displayed) {
/* already seen: enter a groupptr */
char *t_name = xml_escape_the_name(name);
char *grpxid = malloc(100);
char *parentxid = malloc(100);
if (isRoot) {
/* probably can't happen! */
xml_name_to_XID("/",grpxid,100,1);
printf("<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">\n",
xmlnsprefix,grpxid,"/");
} else {
t_objname = xml_escape_the_name(group_table->objs[i].objname);
par_name = xml_escape_the_name(par);
xml_name_to_XID(tmp,grpxid,100,1);
xml_name_to_XID(par,parentxid,100,1);
printf("<%sGroup Name=\"%s\" OBJ-XID=\"%s-%d\" H5Path=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\">\n",
xmlnsprefix,t_name, grpxid, get_next_xid(),
t_objname, parentxid, par_name);
free(t_objname);
free(par_name);
}
free(t_name);
free(grpxid);
indentation(indent + COL);
ptrstr = malloc(100);
t_objname = xml_escape_the_name(group_table->objs[i].objname);
par_name = xml_escape_the_name(par);
xml_name_to_XID(par,parentxid,100,1);
xml_name_to_XID(group_table->objs[i].objname,ptrstr,100,1);
printf("<%sGroupPtr OBJ-XID=\"%s\" H5Path=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
xmlnsprefix,
ptrstr, t_objname, parentxid, par_name);
free(t_objname);
free(parentxid);
} else {
/* first time this group has been seen -- describe it */
char *t_name = xml_escape_the_name(name);
char *grpxid = malloc(100);
char *parentxid = malloc(100);
if (isRoot) {
xml_name_to_XID("/",grpxid,100,1);
printf("<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">\n",
xmlnsprefix,grpxid,"/");
} else {
char *t_tmp = xml_escape_the_name(tmp);
par_name = xml_escape_the_name(par);
xml_name_to_XID(tmp,grpxid,100,1);
xml_name_to_XID(par,parentxid,100,1);
printf("<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" >\n",
xmlnsprefix,t_name, grpxid, t_tmp, parentxid, par_name);
free(t_tmp);
free(par_name);
}
free(t_name);
free(grpxid);
free(parentxid);
group_table->objs[i].objname = HDstrdup(prefix);
group_table->objs[i].displayed = 1;
/* 1. do all the attributes of the group */
H5Aiterate(gid, NULL,
dump_function_table->dump_attribute_function, NULL);
if (!strcmp(name, "/") && unamedtype) {
/* Very special case: dump unamed type in root group */
for (i = 0; i < type_table->nobjs; i++) {
if (!type_table->objs[i].recorded) {
dset = H5Dopen(gid, type_table->objs[i].objname);
type = H5Dget_type(dset);
sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[i].objno);
dump_function_table->dump_named_datatype_function(type, type_name);
H5Tclose(type);
H5Dclose(dset);
}
}
}
/* iterate through all the members */
xtype = H5G_TYPE;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_DATASET;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_GROUP;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_LINK;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
}
} else {
/* only link -- must be first time! */
char *t_name = xml_escape_the_name(name);
char *grpxid = malloc(100);
char *parentxid = malloc(100);
if (isRoot) {
xml_name_to_XID("/",grpxid,100,1);
printf("<%sRootGroup OBJ-XID=\"%s\" H5Path=\"%s\">\n",
xmlnsprefix,grpxid,"/");
} else {
char *t_tmp = xml_escape_the_name(tmp);
par_name = xml_escape_the_name(par);
xml_name_to_XID(tmp,grpxid,100,1);
xml_name_to_XID(par,parentxid,100,1);
printf("<%sGroup Name=\"%s\" OBJ-XID=\"%s\" H5Path=\"%s\" "
"Parents=\"%s\" H5ParentPaths=\"%s\" >\n",
xmlnsprefix,t_name, grpxid, t_tmp,
parentxid, par_name);
free(t_tmp);
free(par_name);
}
free(t_name);
free(grpxid);
free(parentxid);
/* 1. do all the attributes of the group */
H5Aiterate(gid, NULL, dump_function_table->dump_attribute_function, NULL);
if (!strcmp(name, "/") && unamedtype) {
/* Very special case: dump unamed type in root group */
for (i = 0; i < type_table->nobjs; i++) {
if (!type_table->objs[i].recorded) {
dset = H5Dopen(gid, type_table->objs[i].objname);
type = H5Dget_type(dset);
sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[i].objno);
dump_function_table->dump_named_datatype_function(type, type_name);
H5Tclose(type);
H5Dclose(dset);
}
}
}
/* iterate through all the members */
xtype = H5G_TYPE;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_DATASET;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_GROUP;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_LINK;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
}
indent -= COL;
indentation(indent);
if (isRoot) {
printf("</%sRootGroup>\n",xmlnsprefix);
} else {
printf("</%sGroup>\n" ,xmlnsprefix);
}
free(tmp);
}
/*-------------------------------------------------------------------------
* Function: xml_print_refs
*
* Purpose: Print a path to the objects referenced by HDF5 Referneces.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
xml_print_refs(hid_t did, int source)
{
herr_t e;
hid_t type, space;
char *buf;
hobj_ref_t *refbuf;
char *path;
hsize_t ssiz;
hsize_t i;
if (source == DATASET_DATA) {
type = H5Dget_type(did);
} else if (source == ATTRIBUTE_DATA) {
type = H5Aget_type(did);
} else {
/* return an error */
return FAIL;
}
if (H5Tget_class(type) != H5T_REFERENCE) {
/* return an error */
return FAIL;
}
if (!H5Tequal(type, H5T_STD_REF_OBJ)) {
/* region ref not supported yet... */
/* return an error */
return FAIL;
}
if (source == DATASET_DATA) {
space = H5Dget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
buf = calloc((size_t)ssiz, sizeof(char));
if (buf == NULL) {
return FAIL;
}
e = H5Dread(did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
/* need to check result here */
if (e < 0) {
free(buf);
return FAIL;
}
} else if (source == ATTRIBUTE_DATA) {
space = H5Aget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
buf = calloc((size_t)ssiz, sizeof(char));
if (buf == NULL) {
free(buf);
return FAIL;
}
e = H5Aread(did, H5T_STD_REF_OBJ, buf);
/* need to check the result here */
} else {
/* error */
return FAIL;
}
refbuf = (hobj_ref_t *) buf;
ssiz = H5Sget_simple_extent_npoints(space);
for (i = 0; i < ssiz; i++) {
path = lookup_ref_path(*refbuf);
indentation(indent + COL);
if (!path) {
printf("\"%s\"\n", "NULL");
} else {
char *t_path = xml_escape_the_string(path, -1);
printf("\"%s\"\n", t_path);
free(t_path);
}
refbuf++;
}
free(buf);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: xml_print_strs
*
* Purpose: Print strings.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
xml_print_strs(hid_t did, int source)
{
herr_t e;
hid_t type, space;
void *buf;
char *bp;
char *onestring=NULL;
hsize_t ssiz;
size_t tsiz, str_size=0;
size_t i;
htri_t is_vlstr;
if (source == DATASET_DATA) {
type = H5Dget_type(did);
} else if (source == ATTRIBUTE_DATA) {
type = H5Aget_type(did);
} else {
/* return an error */
return FAIL;
}
if (H5Tget_class(type) != H5T_STRING) {
/* return an error */
return FAIL;
}
is_vlstr = H5Tis_variable_str(type);
if (source == DATASET_DATA) {
space = H5Dget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
buf = malloc((size_t)ssiz);
if (buf == NULL) {
return FAIL;
}
e = H5Dread(did, type, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
if (e < 0) {
free(buf);
return FAIL;
}
} else if (source == ATTRIBUTE_DATA) {
space = H5Aget_space(did);
ssiz = H5Sget_simple_extent_npoints(space);
ssiz *= H5Tget_size(type);
buf = malloc((size_t)ssiz);
if (buf == NULL) {
return FAIL;
}
e = H5Aread(did, type, buf);
if (e < 0) {
free(buf);
return FAIL;
}
} else {
/* error */
return FAIL;
}
/* pull out each string... */
ssiz = H5Sget_simple_extent_npoints(space);
tsiz = H5Tget_size(type);
bp = (char*)buf;
if(!is_vlstr)
onestring = (char *) calloc(tsiz, sizeof(char));
for (i = 0; i < ssiz; i++) {
if(is_vlstr) {
onestring = *(char **)bp;
if(onestring)
str_size = (size_t)HDstrlen(onestring);
} else {
HDstrncpy(onestring, bp, tsiz);
str_size = tsiz;
}
indentation(indent + COL);
if (!onestring) {
printf("NULL\n");
} else {
char *t_onestring = xml_escape_the_string(onestring, (int)str_size);
printf("\"%s\"\n", t_onestring);
free(t_onestring);
}
bp += tsiz;
}
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: check_compression
*
* Purpose: private function to check for compression and
* put a comment in the XML. (Not fully implemented.)
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
#ifdef LATER
static void
check_compression(hid_t dcpl)
{
int nfilt;
int i;
H5Z_filter_t filter;
char namebuf[20];
size_t cd_nelmts = 1;
unsigned int cd_values;
unsigned int flags;
/* not used yet: will need to do somehting more elaborate to handle future
* compression methods.
char *t1 = "H5Z_FILTER_DEFLATE";
*/
nfilt = H5Pget_nfilters(dcpl);
if (nfilt <= 0)
return;
for (i = 0; i < nfilt; i++) {
#ifdef H5_WANT_H5_V1_6_COMPAT
filter = H5Pget_filter(dcpl, i, &flags,
(size_t *) &cd_nelmts,
&cd_values, 20, namebuf);
#else
filter = H5Pget_filter(dcpl, i, &flags,
(size_t *) &cd_nelmts,
&cd_values, 20, namebuf, NULL);
#endif /* H5_WANT_H5_V1_6_COMPAT */
if (filter == H5Z_FILTER_DEFLATE) {
indentation(indent + COL);
printf("<%sCompression />\n",xmlnsprefix);
indentation(indent + COL);
printf("<!-- Compression parameter %d -->\n", cd_values);
}
}
}
#endif /* LATER */
/*-------------------------------------------------------------------------
* Function: check_filters
*
* Purpose: private function to check for the filters and
* put tags in the XML.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
check_filters(hid_t dcpl)
{
int nfilt;
int i;
H5Z_filter_t filter;
char namebuf[120];
size_t cd_nelmts = 20;
unsigned int cd_values[20];
unsigned int flags;
nfilt = H5Pget_nfilters(dcpl);
if (nfilt <= 0)
return;
for (i = 0; i < nfilt; i++) {
#ifdef H5_WANT_H5_V1_6_COMPAT
filter = H5Pget_filter(dcpl, (unsigned)i, &flags,
(size_t *) &cd_nelmts,
cd_values, 120, namebuf);
#else
filter = H5Pget_filter(dcpl, (unsigned)i, &flags,
(size_t *) &cd_nelmts,
cd_values, 120, namebuf, NULL);
#endif /* H5_WANT_H5_V1_6_COMPAT */
if (filter == H5Z_FILTER_DEFLATE) {
indentation(indent + COL);
printf("<%sDeflate Level=\"",xmlnsprefix);
if (cd_nelmts < 1) {
/* not sure what this means? */
printf("6");
} else {
printf("%d",cd_values[0]);
}
printf("\"/>\n");
} else if (filter == H5Z_FILTER_FLETCHER32) {
indentation(indent + COL);
printf("<%sFletcher32 />",xmlnsprefix);
} else if (filter == H5Z_FILTER_SHUFFLE) {
indentation(indent + COL);
printf("<%sShuffle />",xmlnsprefix);
} else if (filter == H5Z_FILTER_SZIP) {
indentation(indent + COL);
printf("<%sSZIP ",xmlnsprefix);
if (cd_nelmts < 2) {
/* no pixels ? */
printf("Pixels_per_block=\"-1\" ");
} else {
printf("Pixels_per_block=\"%d\" ",cd_values[1]);
}
/* analyse the options mask */
if (cd_values[0] & H5_SZIP_CHIP_OPTION_MASK) {
printf("Mode =\"Hardware\" ");
} else if (cd_values[0] & H5_SZIP_ALLOW_K13_OPTION_MASK) {
printf("Mode =\"K13\" ");
}
printf("Coding=\"");
if (cd_values[0] & H5_SZIP_EC_OPTION_MASK) {
printf("Entropy");
} else if (cd_values[0] & H5_SZIP_NN_OPTION_MASK) {
printf("NN");
}
printf("\" ");
printf("ByteOrder=\"");
if (cd_values[0] & H5_SZIP_LSB_OPTION_MASK) {
printf("LSB");
} else if (cd_values[0] & H5_SZIP_MSB_OPTION_MASK) {
printf("MSB");
}
printf("\" ");
if (cd_values[0] & H5_SZIP_RAW_OPTION_MASK) {
printf("Header=\"Raw\"");
}
printf("/>\n");
} else {
/* unknown option */
}
}
}
static void xml_dump_fill_value(hid_t dcpl, hid_t type)
{
size_t sz;
size_t i;
hsize_t space;
void * buf;
char * path;
char * name;
indent += COL;
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indent += COL;
space = H5Tget_size(type);
buf = malloc((size_t)space);
H5Pget_fill_value(dcpl, type, buf);
if (H5Tget_class(type) == H5T_REFERENCE) {
path = lookup_ref_path(*(hobj_ref_t *)buf);
indentation(indent);
printf("<%sDataFromFile>\n",xmlnsprefix);
if (!path) {
printf("\"%s\"\n", "NULL");
} else {
char *t_path = xml_escape_the_string(path, -1);
printf("\"%s\"\n", t_path);
free(t_path);
}
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
} else if (H5Tget_class(type) == H5T_STRING) {
/* ????? */
indentation(indent);
printf("<!-- String fill values not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
} else {
/* all other data */
switch (H5Tget_class(type)) {
case H5T_INTEGER:
indentation(indent);
printf("<%sDataFromFile>\n",xmlnsprefix);
indentation(indent);
printf("\"%d\"\n",*(int *)buf);
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
break;
case H5T_FLOAT:
indentation(indent);
printf("<%sDataFromFile>\n",xmlnsprefix);
indentation(indent);
printf("\"%f\"\n",*(float *)buf);
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
break;
case H5T_BITFIELD:
case H5T_OPAQUE:
indentation(indent);
printf("<%sDataFromFile>\n",xmlnsprefix);
sz = H5Tget_size(type);
indentation(indent);
printf("\"");
for (i = 0; i < sz; i++) {
printf("%x ",*(unsigned int *)buf);
buf = (char *)buf + sizeof(unsigned int);
}
printf("\"\n");
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
break;
case H5T_ENUM:
indentation(indent);
printf("<%sDataFromFile>\n",xmlnsprefix);
name = H5Tget_member_name(type, *(unsigned *)buf);
indentation(indent);
printf("\"%s\"\n",name);
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
break;
case H5T_ARRAY:
indentation(indent);
printf("<!-- Array fill values not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
break;
case H5T_TIME:
indentation(indent);
printf("<!-- Time fill not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
break;
case H5T_COMPOUND:
indentation(indent);
printf("<!-- Compound fill not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
break;
case H5T_VLEN:
indentation(indent);
printf("<!-- VL fill not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
break;
default:
indentation(indent);
printf("<!-- Unknown fill datatype: %d -->\n", H5Tget_class(type));
indentation(indent);
printf("<%sNoData/>\n",xmlnsprefix);
break;
}
}
free(buf);
indent -= COL;
indentation(indent);
printf("</%sData>\n",xmlnsprefix);
indent -= COL;
}
/*-------------------------------------------------------------------------
* Function: xml_dump_group
*
* Purpose: Dump a description of an HDF5 Group (and its members) in XML.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_dump_dataset(hid_t did, const char *name, struct subset_t UNUSED * sset)
{
hid_t type, space;
hid_t dcpl;
H5D_fill_value_t fvstatus;
int maxdims;
hsize_t *chsize;
int ndims;
int i;
H5D_alloc_time_t at;
H5D_fill_time_t ft;
hsize_t tempi;
char *tmp;
char *t_name, *t_tmp, *t_prefix;
char *rstr = malloc(100);
char *pstr = malloc(100);
tmp = malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
strcat(tmp, "/");
strcat(tmp, name);
indentation(indent);
t_name = xml_escape_the_name(name);
t_tmp = xml_escape_the_name(tmp);
t_prefix = xml_escape_the_name(prefix);
xml_name_to_XID(tmp, rstr, 100, 1);
xml_name_to_XID(prefix, pstr, 100, 1);
printf("<%sDataset Name=\"%s\" OBJ-XID=\"%s\" H5Path= \"%s\" Parents=\"%s\" H5ParentPaths=\"%s\">\n",xmlnsprefix,
t_name, rstr, t_tmp, pstr, strcmp(prefix, "") ? t_prefix : "/");
free(t_name);
free(t_tmp);
free(t_prefix);
free(rstr);
free(pstr);
free(tmp);
dcpl = H5Dget_create_plist(did);
type = H5Dget_type(did);
space = H5Dget_space(did);
/* Print information about storage layout */
if (H5D_CHUNKED == H5Pget_layout(dcpl)) {
maxdims = H5Sget_simple_extent_ndims(space);
chsize = (hsize_t *) malloc(maxdims * sizeof(hsize_t));
indent += COL;
indentation(indent);
printf("<%sStorageLayout>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sChunkedLayout ",xmlnsprefix);
ndims = H5Pget_chunk(dcpl, maxdims, chsize);
printf("Ndims=\"%d\">\n", ndims);
indent += COL;
for (i = 0; i < ndims; i++) {
indentation(indent);
HDfprintf(stdout, "<%sChunkDimension DimSize=\"%Hu\" />\n",
xmlnsprefix, chsize[i]);
}
indentation(indent);
printf("<%sRequiredFilter>\n",xmlnsprefix);
indent += COL;
check_filters(dcpl);
indent -= COL;
indentation(indent);
printf("</%sRequiredFilter>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sChunkedLayout>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sStorageLayout>\n",xmlnsprefix);
indent -= COL;
free(chsize);
} else if (H5D_CONTIGUOUS == H5Pget_layout(dcpl)) {
indent += COL;
indentation(indent);
printf("<%sStorageLayout>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sContiguousLayout/>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sStorageLayout>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
} else if (H5D_COMPACT == H5Pget_layout(dcpl)) {
indent += COL;
indentation(indent);
printf("<%sStorageLayout>\n",xmlnsprefix);
indent += COL;
indentation(indent);
printf("<%sCompactLayout/>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sStorageLayout>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
}
/* and check for external.... ?? */
/* fill value */
indent += COL;
indentation(indent);
printf("<%sFillValueInfo ",xmlnsprefix);
H5Pget_fill_time(dcpl, &ft);
printf("FillTime=\"");
switch ( ft ) {
case H5D_FILL_TIME_ALLOC:
printf("FillOnAlloc");
break;
case H5D_FILL_TIME_NEVER:
printf("FillNever");
break;
case H5D_FILL_TIME_IFSET:
printf("FillIfSet");
break;
default:
printf("?");
break;
}
printf("\" ");
H5Pget_alloc_time(dcpl, &at);
printf("AllocationTime=\"");
switch ( at ) {
case H5D_ALLOC_TIME_EARLY:
printf("Early");
break;
case H5D_ALLOC_TIME_INCR:
printf("Incremental");
break;
case H5D_ALLOC_TIME_LATE:
printf("Late");
break;
case H5D_ALLOC_TIME_DEFAULT:
default:
printf("?");
break;
}
printf("\"");
printf(">\n");
indent += COL;
indentation(indent);
printf("<%sFillValue>\n",xmlnsprefix);
indent += COL;
H5Pfill_value_defined(dcpl, &fvstatus);
if (fvstatus == H5D_FILL_VALUE_UNDEFINED ||
(fvstatus==H5D_FILL_VALUE_DEFAULT && ft==H5D_FILL_TIME_IFSET)) {
indentation(indent + COL);
printf("<%sNoFill/>\n",xmlnsprefix);
} else {
xml_dump_fill_value(dcpl,type);
}
indent -= COL;
indentation(indent);
printf("</%sFillValue>\n",xmlnsprefix);
indent -= COL;
indentation(indent);
printf("</%sFillValueInfo>\n",xmlnsprefix);
indent -= COL;
dump_function_table->dump_dataspace_function(space);
dump_function_table->dump_datatype_function(type);
indent += COL;
H5Aiterate(did, NULL, dump_function_table->dump_attribute_function, NULL);
indent -= COL;
tempi = H5Dget_storage_size(did);
if (display_data && (tempi > 0)) {
switch (H5Tget_class(type)) {
case H5T_INTEGER:
case H5T_FLOAT:
case H5T_STRING:
case H5T_BITFIELD:
case H5T_OPAQUE:
case H5T_ENUM:
case H5T_ARRAY:
dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0);
break;
case H5T_TIME:
indent += COL;
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indentation(indent);
printf("<!-- Time data not yet implemented. -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indent -= COL;
break;
case H5T_COMPOUND:
indentation(indent);
printf("<!-- Note: format of compound data not specified -->\n");
dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0);
break;
case H5T_REFERENCE:
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indentation(indent);
if (!H5Tequal(type, H5T_STD_REF_OBJ)) {
printf("<!-- Note: Region references not supported -->\n");
indentation(indent);
printf("<%sNoData />\n",xmlnsprefix);
} else {
printf("<%sDataFromFile>\n",xmlnsprefix);
xml_print_refs(did, DATASET_DATA);
indentation(indent);
printf("</%sDataFromFile>\n",xmlnsprefix);
}
indentation(indent);
printf("</%sData>\n",xmlnsprefix);
break;
case H5T_VLEN:
printf("<!-- Note: format of VL data not specified -->\n");
dump_function_table->dump_data_function(did, DATASET_DATA, NULL, 0);
break;
default:
indentation(indent);
printf("<%sData>\n",xmlnsprefix);
indentation(indent);
printf("<!-- Unknown datatype: %d -->\n", H5Tget_class(type));
indentation(indent);
printf("<%sNoData/>\n",xmlnsprefix);
indentation(indent);
printf("</%sData>\n",xmlnsprefix);
break;
}
} else {
/* no data written */
indentation(indent + COL);
printf("<%sData>\n",xmlnsprefix);
indentation(indent + COL + COL);
printf("<%sNoData/>\n",xmlnsprefix);
indentation(indent + COL);
printf("</%sData>\n",xmlnsprefix);
}
H5Tclose(type);
H5Sclose(space);
H5Pclose(dcpl);
indentation(indent);
printf("</%sDataset>\n", xmlnsprefix);
}
/*-------------------------------------------------------------------------
* Function: xml_print_enum
*
* Purpose: Print the values of an HDF5 ENUM in XML.
* Very similar to regular DDL output.
*
* Return: void
*
* Programmer: REMcG
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
xml_print_enum(hid_t type)
{
char **name = NULL; /*member names */
unsigned char *value = NULL; /*value array */
unsigned nmembs; /*number of members */
hid_t super; /*enum base integer type */
hid_t native = -1; /*native integer data type */
size_t dst_size; /*destination value type size */
unsigned i; /*miscellaneous counters */
size_t j;
nmembs = H5Tget_nmembers(type);
super = H5Tget_super(type);
indentation(indent);
printf("<%sDataType>\n",xmlnsprefix);
xml_print_datatype(super,0);
indentation(indent);
printf("</%sDataType>\n",xmlnsprefix);
/*
* Determine what data type to use for the native values. To simplify
* things we entertain three possibilities:
* 1. long_long -- the largest native signed integer
* 2. unsigned long_long -- the largest native unsigned integer
* 3. raw format
*/
if (H5Tget_size(type) <= sizeof(long_long)) {
dst_size = sizeof(long_long);
if (H5T_SGN_NONE == H5Tget_sign(type)) {
native = H5T_NATIVE_ULLONG;
} else {
native = H5T_NATIVE_LLONG;
}
} else {
dst_size = H5Tget_size(type);
}
/* Get the names and raw values of all members */
name = calloc(nmembs, sizeof(char *));
value = calloc(nmembs, MAX(H5Tget_size(type), dst_size));
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
H5Tget_member_value(type, i, value + i * H5Tget_size(type));
}
/* Convert values to native data type */
if (native > 0)
H5Tconvert(super, native, nmembs, value, NULL, H5P_DEFAULT);
/* Sort members by increasing value */
/*not implemented yet */
/* Print members */
indent += COL;
for (i = 0; i < nmembs; i++) {
char *t_name = xml_escape_the_name(name[i]);
indentation(indent);
printf("<%sEnumElement>\n",xmlnsprefix);
indentation(indent + COL);
printf("%s\n", t_name);
free(t_name);
indentation(indent);
printf("</%sEnumElement>\n",xmlnsprefix);
indentation(indent);
printf("<%sEnumValue>\n",xmlnsprefix);
indentation(indent + COL);
if (native < 0) {
printf("0x");
for (j = 0; j < dst_size; j++)
printf("%02x", value[i * dst_size + j]);
} else if (H5T_SGN_NONE == H5Tget_sign(native)) {
HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "u", *((unsigned long_long *)
((void *) (value + i * dst_size))));
} else {
HDfprintf(stdout,"%" H5_PRINTF_LL_WIDTH "d",
*((long_long *) ((void *) (value + i * dst_size))));
}
printf("\n");
indentation(indent);
printf("</%sEnumValue>\n",xmlnsprefix);
}
indent -= COL;
/* Release resources */
for (i = 0; i < nmembs; i++)
free(name[i]);
free(name);
free(value);
H5Tclose(super);
}
/*-------------------------------------------------------------------------
* Function: h5_fileaccess
*
* Purpose: Returns a file access template which is the default template
* but with a file driver set according to the constant or
* environment variable HDF5_DRIVER
*
* Return: Success: A file access property list
*
* Failure: -1
*
* Programmer: Robb Matzke
* Thursday, November 19, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static hid_t
h5_fileaccess(void)
{
static const char *multi_letters = "msbrglo";
const char *val = NULL;
const char *name;
char s[1024];
hid_t fapl = -1;
/* First use the environment variable, then the constant */
val = HDgetenv("HDF5_DRIVER");
#ifdef HDF5_DRIVER
if (!val) val = HDF5_DRIVER;
#endif
if ((fapl=H5Pcreate(H5P_FILE_ACCESS))<0) return -1;
if (!val || !*val) return fapl; /*use default*/
HDstrncpy(s, val, sizeof s);
s[sizeof(s)-1] = '\0';
if (NULL==(name=HDstrtok(s, " \t\n\r"))) return fapl;
if (!HDstrcmp(name, "sec2")) {
/* Unix read() and write() system calls */
if (H5Pset_fapl_sec2(fapl)<0) return -1;
} else if (!HDstrcmp(name, "stdio")) {
/* Standard C fread() and fwrite() system calls */
if (H5Pset_fapl_stdio(fapl)<0) return -1;
} else if (!HDstrcmp(name, "core")) {
/* In-core temporary file with 1MB increment */
if (H5Pset_fapl_core(fapl, 1024*1024, FALSE)<0) return -1;
} else if (!HDstrcmp(name, "split")) {
/* Split meta data and raw data each using default driver */
if (H5Pset_fapl_split(fapl,
"-m.h5", H5P_DEFAULT,
"-r.h5", H5P_DEFAULT)<0)
return -1;
} else if (!HDstrcmp(name, "multi")) {
/* Multi-file driver, general case of the split driver */
H5FD_mem_t memb_map[H5FD_MEM_NTYPES];
hid_t memb_fapl[H5FD_MEM_NTYPES];
const char *memb_name[H5FD_MEM_NTYPES];
char sv[H5FD_MEM_NTYPES][1024];
haddr_t memb_addr[H5FD_MEM_NTYPES];
H5FD_mem_t mt;
HDmemset(memb_map, 0, sizeof memb_map);
HDmemset(memb_fapl, 0, sizeof memb_fapl);
HDmemset(memb_name, 0, sizeof memb_name);
HDmemset(memb_addr, 0, sizeof memb_addr);
assert(HDstrlen(multi_letters)==H5FD_MEM_NTYPES);
for (mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
memb_fapl[mt] = H5P_DEFAULT;
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 {
/* Unknown driver */
return -1;
}
return fapl;
}
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