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hdf5/tools/h5dump.c
Bill Wendling de25a136c3 [svn-r3437] Purpose: 
Feature Add
Description:
    This is the first phase of adding subsetting to the dumper. The
    command-line parsing should be pretty much set right now.

    NOTE: The revision before this one can be used to back port to the
    1.4 branch when the XML stuff is folded into that branch for
    release.
Platforms tested:
    Linux
2001-02-16 17:23:01 -05:00

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/*-------------------------------------------------------------------------
*
* Copyright (C) 1998 - 2001
* National Center for Supercomputing Applications
* All rights reserved.
*
*-------------------------------------------------------------------------
*/
#include <stdio.h>
#include <stdlib.h>
#include "h5dump.h"
#include "H5private.h"
#include "h5tools.h"
/* module-scoped variables */
static int display_oid = 0;
static int display_data = 1;
static int d_status = EXIT_SUCCESS;
static int unamedtype = 0; /* shared data type with no name */
static int prefix_len = 1024;
static table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL;
static char *prefix;
static const dump_header *dump_header_format;
/**
** Added for XML **
**/
/* fill_ref_path_table is called to inialize the object reference paths. */
static herr_t fill_ref_path_table(hid_t, const char *, void UNUSED *);
/* module-scoped variables for XML option */
#define DEFAULT_DTD "http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd"
static int doxml = 0;
static const char *xml_dtd_uri = NULL;
static hid_t thefile = -1;
/** end XML **/
/* internal functions */
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);
static char *lookup_ref_path(hobj_ref_t *);
static void check_compression(hid_t);
static struct ref_path_table_entry_t *ref_path_table_lookup(const char *);
/* external functions */
extern int print_data(hid_t, hid_t, 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 */
" %lu:%lu", /*obj_format */
1, /*dset_hidefileno */
"DATASET %lu:%lu ", /*dset_format */
"%s", /*dset_blockformat_pre */
"%s", /*dset_ptformat_pre */
"%s", /*dset_ptformat */
};
/**
** 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 */
" %lu:%lu", /*obj_format */
1, /*dset_hidefileno */
"DATASET %lu:%lu ", /*dset_format */
"%s", /*dset_blockformat_pre */
"%s", /*dset_ptformat_pre */
"%s", /*dset_ptformat */
};
/** XML **/
static const dump_header standardformat = {
"standardformat", /*name */
"HDF5", /*fileebgin */
"", /*fileend */
BOOT_BLOCK, /*bootblockbegin */
"", /*bootblockend */
GROUPNAME, /*groupbegin */
"", /*groupend */
DATASET, /*datasetbegin */
"", /*datasetend */
ATTRIBUTE, /*attributebegin */
"", /*attributeend */
DATATYPE, /*datatypebegin */
"", /*datatypeend */
DATASPACE, /*dataspacebegin */
"", /*dataspaceend */
DATA, /*databegin */
"", /*dataend */
SOFTLINK, /*softlinkbegin */
"", /*softlinkend */
"{", /*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 */
"", /*dataspacedescriptionbegin */
"", /*dataspacedescriptionend */
"(", /*dataspacedimbegin */
")", /*dataspacedimend */
};
/**
** Added for XML **
**/
/* The 'header' formats for XML -- mostly null
*
* XML output has values embedded in the 'headers', so
* all the XML headers are done on a case by case basis.
*/
static const dump_header xmlformat = {
"xml", /*name */
"", /*filebegin */
"</HDF5-File>", /*fileend */
"", /*bootblockbegin */
"", /*bootblockend */
"", /*groupbegin */
"</Group>", /*groupend */
"", /*datasetbegin */
"</Dataset>", /*datasetend */
"", /*attributebegin */
"</Attribute>", /*attributeend */
"<DataType>", /*datatypeend */
"</DataType>", /*datatypeend */
"<Dataspace>", /*dataspacebegin */
"</Dataspace>", /*dataspaceend */
"<Data>", /*databegin */
"</Data>", /*dataend */
"", /*softlinkbegin */
"", /*softlinkend */
"", /*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 */
"", /*dataspacedescriptionbegin */
"", /*dataspacedescriptionend */
"", /*dataspacedimbegin */
"", /*dataspacedimend */
};
/** XML **/
/**
** Added for XML **
**/
/* internal functions used by XML option */
static void xml_print_datatype(hid_t);
static void xml_print_enum(hid_t);
static int xml_print_refs(hid_t, int);
static int xml_print_strs(hid_t, int);
static hobj_ref_t *ref_path_table_put(hid_t, const char *);
static char *xml_escape_the_string(const char *, int);
static char *xml_escape_the_name(const char *);
/**
** 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_dataset(hid_t, const char *);
static void dump_data(hid_t, int);
static void dump_named_datatype(hid_t, const char *);
static void dump_dataspace(hid_t space);
static void dump_datatype(hid_t type);
static herr_t dump_attr(hid_t attr, const char *attr_name,
void UNUSED * op_data);
/* XML format: same interface, alternaive output */
static void xml_dump_group(hid_t, const char *);
static void xml_dump_dataset(hid_t ds, const char *dsname);
static void xml_dump_data(hid_t, int);
static void xml_dump_named_datatype(hid_t, const char *);
static void xml_dump_dataspace(hid_t space);
static void xml_dump_datatype(hid_t type);
static herr_t xml_dump_attr(hid_t attr, const char *attr_name,
void UNUSED * op_data);
/**
** 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 *);
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);
} 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;
/* a structure to hold the subsetting particulars for a dataset */
struct subset_t {
hsize_t *start;
hsize_t *stride;
hsize_t *count;
hsize_t *block;
};
/* a structure for handling the order command-line parameters come in */
struct handler_t {
void (*func)(hid_t, char *);
char *obj;
struct subset_t *subset_info;
};
/*
* Command-line options: The user can specify short or long-named
* parameters. The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
static const char *s_opts = "hBHvVa:d:g:l:t:w:xD:o:s:T:c:k:";
static struct long_options l_opts[] = {
{ "help", no_arg, 'h' },
{ "hel", no_arg, 'h' },
{ "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' },
{ "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, 'T' },
{ "strid", require_arg, 'T' },
{ "stri", require_arg, 'T' },
{ "str", require_arg, 'T' },
{ "width", require_arg, 'w' },
{ "widt", require_arg, 'w' },
{ "wid", require_arg, 'w' },
{ "wi", require_arg, 'w' },
{ "xml", no_arg, 'x' },
{ "xm", no_arg, 'x' },
{ "xml-dtd", require_arg, 'D' },
{ "xml-dt", require_arg, 'D' },
{ "xml-d", require_arg, 'D' },
{ NULL, 0, '\0' }
};
/*-------------------------------------------------------------------------
* Function: usage
*
* Purpose: Print the usage message about dumper
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
usage(const char *progname)
{
fflush(stdout);
fprintf(stderr, "\
usage: %s [OPTIONS] file\n\
OPTIONS\n\
-h, --help Print a usage message and exit\n\
-B, --bootblock Print the content of the boot block\n\
-H, --header Print the header only; no data is displayed\n\
-i, --object-ids Print the object ids\n\
-V, --version Print version number and exit\n\
-a P, --attribute=P Print the specified attribute\n\
-d P, --dataset=P Print the specified dataset\n\
-g P, --group=P Print the specified group and all members\n\
-l P, --soft-link=P Print the value(s) of the specified soft link\n\
-o F, --output=F Output raw data into file F\n\
-t T, --datatype=T Print the specified named data type\n\
-w #, --width=# Set the number of columns of output\n\
-x, --xml Output in XML\n\
-D U, --xml-dtd=U Use the DTD at U\n\
\n\
P - is the full path from the root group to the object.\n\
T - is the name of the data type.\n\
F - is a filename.\n\
# - is an integer greater than 1.\n\
U - is a URI reference (as defined in [IETF RFC 2396],\n\
updated by [IETF RFC 2732])\n\
\n\
Example:\n\
\n\
Attribute foo of the group /bar_none in file quux.h5\n\
\n\
h5dump -a /bar_none/foo quux.h5\n\
\n", progname);
}
/*-------------------------------------------------------------------------
* Function: print_datatype
*
* Purpose: print the data type.
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
print_datatype(hid_t type)
{
char *fname;
hid_t nmembers, mtype, str_type;
int i, j, ndims, perm[H5DUMP_MAX_RANK];
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;
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:
size = H5Tget_size(type);
str_pad = H5Tget_strpad(type);
cset = H5Tget_cset(type);
printf("H5T_STRING %s\n", dump_header_format->strblockbegin);
indent += COL;
indentation(indent + COL);
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);
H5Tset_cset(str_type, cset);
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
indentation(indent + COL);
printf("%s ", CTYPE);
if (H5Tequal(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(type, str_type)) {
printf("H5T_FORTRAN_S1;\n");
} else {
printf("unknown_one_character_type;\n ");
d_status = EXIT_FAILURE;
}
H5Tclose(str_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:
if (H5Tcommitted(type) > 0) {
H5Gget_objinfo(type, ".", TRUE, &statbuf);
i = search_obj(type_table, statbuf.objno);
if (i >= 0) {
if (!type_table->objs[i].recorded)
printf("\"/#%lu:%lu\"\n", type_table->objs[i].objno[0],
type_table->objs[i].objno[1]);
else
printf("\"%s\"", type_table->objs[i].objname);
} else {
fflush(stdout);
fprintf(stderr, "h5dump error: unknown committed type.\n");
d_status = EXIT_FAILURE;
}
} else {
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);
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);
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);
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 (j = 0; j < ndims; j++)
printf("[%d]", (int) dims[j]);
printf(" ");
/* Print base type */
print_datatype(super);
/* Close array base type */
H5Tclose(super);
/* Print closing */
printf(" }");
break;
default:
printf("unknown data type");
d_status = EXIT_FAILURE;
break;
}
}
/*-------------------------------------------------------------------------
* Function: dump_bb
*
* Purpose: Dump the boot block
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_bb(void)
{
printf("%s %s boot block not yet implemented %s\n",
BOOT_BLOCK, BEGIN, END);
}
/*-------------------------------------------------------------------------
* 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);
if (H5Tget_class(type) == H5T_COMPOUND || H5Tget_class(type) == H5T_STRING)
indentation(indent);
printf(" %s %s\n", dump_header_format->datatypeblockend,
dump_header_format->datatypeend);
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);
int i;
indentation(indent + COL);
printf("%s ", dump_header_format->dataspacebegin);
if (H5Sis_simple(space)) {
if (ndims == 0) {
/* scalar dataspace */
HDfprintf(stdout, "%s %s ",
dump_header_format->dataspacedescriptionbegin, SCALAR);
} else {
/* simple dataspace */
HDfprintf(stdout, "%s %s { %s %Hu",
dump_header_format->dataspacedescriptionbegin, 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);
}
} else {
printf("%s not yet implemented %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) {
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)
dump_data(attr_id, ATTRIBUTE_DATA);
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
indentation(indent);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
} else {
indentation(indent + COL);
fflush(stdout);
fprintf(stderr, "h5dump error: 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;
}
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);
fflush(stdout);
fprintf(stderr, "h5dump error: 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);
fflush(stdout);
fprintf(stderr, "h5dump error: 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);
fflush(stdout);
fprintf(stderr, "h5dump error: 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);
fflush(stdout);
fprintf(stderr, "h5dump error: 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)
dump_data(attr_id, ATTRIBUTE_DATA);
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
end_obj(dump_header_format->attributeend,
dump_header_format->attributeblockend);
} else {
indentation(COL);
fflush(stdout);
fprintf(stderr, "h5dump error: 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:
* 11/00 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 *buf, *tmp;
H5G_stat_t statbuf;
int i;
H5Gget_objinfo(group, name, FALSE, &statbuf);
if ((*(int *)op_data != H5G_UNKNOWN) &&
(statbuf.type != *(int *) op_data))
return SUCCEED;
tmp = (char *) malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
switch (statbuf.type) {
case H5G_LINK:
indentation(indent);
buf = 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, buf) >= 0) {
/* print the value of a soft link */
if (!doxml) {
/* Standard DDL: no modification */
printf("LINKTARGET \"%s\"\n", buf);
} else {
/* XML */
printf
("<SoftLink LinkName=\"%s\" Target=\"%s\" TargetObj=\"%s\" OBJ-XID=\"%s\" Source=\"%s\"/>\n",
xml_escape_the_name(name), xml_escape_the_name(buf),
xml_escape_the_name(buf), xml_escape_the_name(name),
(strcmp(prefix, "") ? xml_escape_the_name(prefix) : "root"));
}
} else {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to get link value\n");
d_status = EXIT_FAILURE;
}
if (!doxml) {
indentation(indent);
end_obj(dump_header_format->softlinkend,
dump_header_format->softlinkblockend);
}
free(buf);
break;
case H5G_GROUP:
if ((obj = H5Gopen(group, name)) >= 0) {
strcat(strcat(prefix, "/"), name);
dump_function_table->dump_group_function(obj, name);
strcpy(prefix, tmp);
H5Gclose(obj);
} else {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to dump group \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
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);
fflush(stdout);
fprintf(stderr, "h5dump error: internal error (line %d)\n", __LINE__);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
d_status = EXIT_FAILURE;
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 */
printf
("<Dataset Name=\"%s\" OBJ-XID=\"%s\" Parents=\"%s\">\n",
xml_escape_the_name(name),
xml_escape_the_name(tmp),
(strcmp(prefix, "") ? xml_escape_the_name(prefix)
: "root"));
indentation(indent + COL);
printf("<DatasetPtr OBJ-XID=\"%s\"/>\n",
xml_escape_the_name(dset_table->objs[i].objname));
indentation(indent);
printf("%s\n", dump_header_format->datasetend);
}
H5Dclose(obj);
goto done;
} else {
dset_table->objs[i].displayed = 1;
strcat(tmp, "/");
strcat(tmp, name);
strcpy(dset_table->objs[i].objname, tmp);
}
}
dump_function_table->dump_dataset_function(obj, name);
H5Dclose(obj);
} else {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to dump dataset \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
break;
case H5G_TYPE:
if ((obj = H5Topen(group, name)) >= 0) {
dump_function_table->dump_named_datatype_function(obj, name);
H5Tclose(obj);
} else {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to dump data type \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
break;
default:
fflush(stdout);
fprintf(stderr, "h5dump error: unknown object \"%s\"\n", name);
d_status = EXIT_FAILURE;
return FAIL;
}
done:
free(tmp);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* 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) {
hid_t temp_type = H5Tcopy(type);
print_datatype(temp_type);
H5Tclose(temp_type);
} else {
indentation(indent + COL);
print_datatype(type);
printf(";\n");
}
indentation(indent);
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 typename[1024], *tmp;
int i;
int 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);
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(typename, "#%lu:%lu",
type_table->objs[i].objno[0],
type_table->objs[i].objno[1]);
dump_named_datatype(type, typename);
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);
fflush(stdout);
fprintf(stderr, "h5dump error: internal error (line %d)\n", __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 {
strcpy(group_table->objs[i].objname, prefix);
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:
*
*-------------------------------------------------------------------------
*/
static void
dump_dataset(hid_t did, const char *name)
{
hid_t type, space;
indentation(indent);
begin_obj(dump_header_format->datasetbegin, name,
dump_header_format->datasetblockbegin);
type = H5Dget_type(did);
space = H5Dget_space(did);
dump_datatype(type);
dump_dataspace(space);
if (display_oid)
dump_oid(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);
break;
default:
break;
}
indent += COL;
H5Aiterate(did, NULL, dump_attr, NULL);
indent -= COL;
H5Tclose(type);
H5Sclose(space);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
}
#if H5DUMP_DEBUG
/*-------------------------------------------------------------------------
* Function: dump_tables
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_tables(void)
{
int i;
printf("group_table: # of entries = %d\n", group_table->nobjs);
for (i = 0; i < group_table->nobjs; i++)
printf("%lu %lu %s %d %d\n", group_table->objs[i].objno[0],
group_table->objs[i].objno[1],
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++)
printf("%lu %lu %s %d %d\n", dset_table->objs[i].objno[0],
dset_table->objs[i].objno[1],
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++)
printf("%lu %lu %s %d %d\n", type_table->objs[i].objno[0],
type_table->objs[i].objno[1],
type_table->objs[i].objname,
type_table->objs[i].displayed, type_table->objs[i].recorded);
}
#endif /* H5DUMP_DEBUG */
/*-------------------------------------------------------------------------
* Function: dump_data
*
* Purpose: Dump attribute or dataset data
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
dump_data(hid_t obj_id, int obj_data)
{
h5dump_t *outputformat = &dataformat;
int status = -1;
void *buf;
hid_t space, type, p_type;
int ndims, i;
hsize_t size[64], nelmts = 1, alloc_size;
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;
indentation(indent);
begin_obj(dump_header_format->databegin, (const char *) NULL,
dump_header_format->datablockbegin);
/* Print all the values. */
if (obj_data == DATASET_DATA) {
status = h5dump_dset(stdout, outputformat, obj_id, -1, depth);
} else {
/* need to call h5dump_mem for the attribute data */
type = H5Aget_type(obj_id);
p_type = h5dump_fixtype(type);
space = H5Aget_space(obj_id);
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 = h5dump_mem(stdout, outputformat, obj_id, p_type, space, buf, depth);
free(buf);
H5Tclose(p_type);
H5Sclose(space);
H5Tclose(type);
}
if (status < 0) {
indentation(indent + COL);
fflush(stdout);
fprintf(stderr, "h5dump error: unable to print data\n");
d_status = EXIT_FAILURE;
}
indentation(indent);
end_obj(dump_header_format->dataend, dump_header_format->datablockend);
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: 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)
{
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));
printf("start\n");
s->start = parse_hsize_list(brace);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
printf("stride\n");
s->stride = parse_hsize_list(brace);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
printf("count\n");
s->count = parse_hsize_list(brace);
while (*brace && *brace != ';')
brace++;
if (*brace)
brace++;
printf("block\n");
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)
{
H5G_stat_t statbuf;
hid_t dsetid;
if ((dsetid = H5Dopen(fid, dset)) < 0) {
begin_obj(dump_header_format->datasetbegin, dset,
dump_header_format->datasetblockbegin);
indentation(COL);
fflush(stdout);
fprintf(stderr, "h5dump error: unable to open dataset \"%s\"\n", dset);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
d_status = EXIT_FAILURE;
} else {
H5Gget_objinfo(dsetid, ".", TRUE, &statbuf);
if (statbuf.nlink > 1) {
int index = search_obj(dset_table, statbuf.objno);
if (index >= 0) {
if (dset_table->objs[index].displayed) {
begin_obj(dump_header_format->datasetbegin, dset,
dump_header_format->datasetblockbegin);
indentation(indent + COL);
printf("%s \"%s\"\n", HARDLINK,
dset_table->objs[index].objname);
indentation(indent);
end_obj(dump_header_format->datasetend,
dump_header_format->datasetblockend);
} else {
strcpy(dset_table->objs[index].objname, dset);
dset_table->objs[index].displayed = 1;
dump_dataset(dsetid, dset);
}
} else {
d_status = EXIT_FAILURE;
}
} else {
dump_dataset(dsetid, dset);
}
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)
{
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);
fflush(stdout);
fprintf(stderr, "h5dump error: unable to open group \"%s\"\n", group);
end_obj(dump_header_format->groupend,
dump_header_format->groupblockend);
d_status = EXIT_FAILURE;
} else {
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)
{
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);
fflush(stdout);
fprintf(stderr, "h5dump error: 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 {
fflush(stdout);
fprintf(stderr, "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);
fflush(stdout);
fprintf(stderr, "h5dump error: \"%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)
{
hid_t typeid;
if ((typeid = H5Topen(fid, type)) < 0) {
/* check if type is unamed data type */
int index = 0;
while (index < type_table->nobjs ) {
char name[128], name1[128];
if (!type_table->objs[index].recorded) {
/* unamed data type */
sprintf(name, "#%lu:%lu\n",
type_table->objs[index].objno[0],
type_table->objs[index].objno[1]);
sprintf(name1, "/#%lu:%lu\n",
type_table->objs[index].objno[0],
type_table->objs[index].objno[1]);
if (!strncmp(name, type, strlen(type)) ||
!strncmp(name1, type, strlen(type)))
break;
}
index++;
}
if (index == type_table->nobjs) {
/* unknown type */
begin_obj(dump_header_format->datatypebegin, type,
dump_header_format->datatypeblockbegin);
indentation(COL);
fflush(stdout);
fprintf(stderr, "h5dump error: 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[index].objname);
typeid = H5Dget_type(dsetid);
dump_named_datatype(typeid, type);
H5Tclose(typeid);
H5Dclose(dsetid);
}
} else {
dump_named_datatype(typeid, type);
if (H5Tclose(typeid) < 0)
d_status = EXIT_FAILURE;
}
}
/*-------------------------------------------------------------------------
* 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).
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
hid_t fid, gid;
const char *progname = "h5dump";
const char *fname = NULL;
int i, display_bb = 0, display_all = 1, newwidth = 0;
void *edata;
hid_t (*func)(void*);
find_objs_t info;
int opt;
struct handler_t *hand, *last_dset;
int usingdasho = FALSE, last_was_dset = FALSE;
if (argc < 2) {
usage(progname);
exit(EXIT_FAILURE);
}
dump_header_format = &standardformat;
dump_function_table = &ddl_function_table;
/* Disable error reporting */
H5Eget_auto(&func, &edata);
H5Eset_auto(NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
/* 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 'H':
display_data = FALSE;
last_was_dset = FALSE;
break;
case 'v':
display_oid = TRUE;
last_was_dset = FALSE;
break;
case 'V':
print_version(progname);
exit(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 = strdup(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 = strdup(opt_arg);
hand[i].subset_info = parse_subset_params(hand[i].obj);
last_dset = hand;
break;
}
last_was_dset = TRUE;
break;
case 'g':
display_all = 0;
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_groups;
hand[i].obj = strdup(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 = strdup(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 = strdup(opt_arg);
break;
}
last_was_dset = FALSE;
break;
case 'o':
if (set_output_file(opt_arg) < 0){
/* failed to set output file */
usage(progname);
exit(EXIT_FAILURE);
}
usingdasho = TRUE;
last_was_dset = FALSE;
break;
/** XML parameters **/
case 'x':
/* select XML output */
doxml = TRUE;
dump_header_format = &xmlformat;
dump_function_table = &xml_function_table;
break;
case 'D':
/* specify alternative XML DTD */
xml_dtd_uri = opt_arg;
break;
/** end XML parameters **/
/** subsetting parameters **/
case 's':
case 'T':
case 'c':
case 'k': {
struct subset_t *s;
if (!last_was_dset) {
fprintf(stderr, "%s error: option `-%c' can only be used after --dataset option\n",
progname, opt);
exit(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, T,
* c, or K), then we exit the do-while look, set hte 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
* just to the beginning of the switch statement (goto parse_start).
*/
do {
switch ((char)opt) {
case 's': free(s->start); s->start = parse_hsize_list(opt_arg); break;
case 'T': 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);
exit(EXIT_SUCCESS);
case '?':
default:
usage(progname);
exit(EXIT_FAILURE);
}
}
parse_end:
/* check for conflicting options */
if (doxml) {
if (!display_all) {
fflush(stdout);
fprintf(stderr, "h5dump error: option \"%s\" not available for XML\n",
"to display selected objects");
exit(EXIT_FAILURE);
} else if (display_bb) {
fflush(stdout);
fprintf(stderr, "h5dump error: option \"%s\" not available for XML\n",
"--boot-block");
exit(EXIT_FAILURE);
} else if (!display_data) {
fflush(stdout);
fprintf(stderr, "h5dump error: option \"%s\" not available for XML\n",
"--header");
exit(EXIT_FAILURE);
} else if (display_oid == 1) {
fflush(stdout);
fprintf(stderr, "h5dump error: option \"%s\" not available for XML\n",
"--object-ids");
exit(EXIT_FAILURE);
} else if (usingdasho) {
fflush(stdout);
fprintf(stderr, "h5dump error: option \"%s\" not available for XML\n",
"--output");
exit(EXIT_FAILURE);
}
} else {
if (xml_dtd_uri != NULL) {
fflush(stdout);
fprintf(stderr,
"h5dump warning: option \"%s\" only applies with XML: %s\n",
"--xml-dtd", xml_dtd_uri);
}
}
if (argv[argc - 1][0] == '\\')
fname = &argv[opt_ind][1];
else
fname = argv[opt_ind];
fid = h5dump_fopen(fname, NULL, 0);
if (fid < 0) {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to open file \"%s\"\n", fname);
exit(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;
if (doxml) {
/* initialize XML */
thefile = fid;
/* find all objects that might be targets of a refernce */
if ((gid = H5Gopen(fid, "/")) < 0) {
fflush(stdout);
fprintf(stderr, "h5dump error: 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);
/* reset prefix! */
strcpy(prefix, "");
/* make sure the URI is initialized to something */
if (xml_dtd_uri == NULL)
xml_dtd_uri = DEFAULT_DTD;
}
/* 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;
#ifdef H5DUMP_DEBUG
dump_tables();
#endif /* H5DUMP_DEBUG */
if (info.status) {
fflush(stdout);
fprintf(stderr, "h5dump error: internal error (line %d)\n", __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");
printf("<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n",
xml_dtd_uri);
printf("<HDF5-File>\n");
}
if (display_bb)
dump_bb();
if (newwidth)
sscanf(argv[newwidth + 1], "%d", &nCols);
if (display_all) {
if ((gid = H5Gopen (fid, "/")) < 0 ) {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to open root group\n");
d_status = EXIT_FAILURE;
} else {
dump_function_table->dump_group_function(gid, "/");
}
if (H5Gclose (gid) < 0) {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to close root group\n");
d_status = EXIT_FAILURE;
}
} else {
if (doxml) {
/* Note: this option is not supported for XML */
fflush(stdout);
fprintf(stderr, "h5dump error: internal error (line %d)\n", __LINE__);
d_status = EXIT_FAILURE;
goto done;
}
for (i = 0; i < argc; i++)
if (hand[i].func)
hand[i].func(fid, hand[i].obj);
}
if (!doxml) {
end_obj(dump_header_format->fileend,
dump_header_format->fileblockend);
} else {
printf("%s\n", dump_header_format->fileend);
}
done:
if (H5Fclose(fid) < 0)
d_status = EXIT_FAILURE;
for (i = 0; i < argc; 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);
free(group_table->objs);
free(dset_table->objs);
free(type_table->objs);
free(prefix);
free(info.prefix);
/* To Do: clean up XML table */
h5tools_close();
H5Eset_auto(func, edata);
return 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 */
int 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 */
int i;
nmembs = H5Tget_nmembers(type);
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 */
assert(nmembs>0);
name = calloc((size_t)nmembs, sizeof(char *));
value = calloc((size_t)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, (hsize_t)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)) {
printf("%" PRINTF_LL_WIDTH "u", *((unsigned long_long *)
((void *) (value + i * dst_size))));
} else {
printf("%" 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, "");
}
/*
* 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.
*/
struct ref_path_table_entry_t {
hsize_t obj;
hobj_ref_t *obj_ref;
char *apath;
struct ref_path_table_entry_t *next;
};
struct ref_path_table_entry_t *ref_path_table = NULL; /* the table */
int npte = 0; /* number of entries in 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 struct ref_path_table_entry_t *
ref_path_table_lookup(const char *thepath)
{
int i;
hobj_ref_t *ref;
herr_t status;
struct ref_path_table_entry_t *pte = ref_path_table;
if (ref_path_table == NULL)
return NULL;
ref = (hobj_ref_t *) malloc(sizeof(hobj_ref_t));
if (ref == NULL) {
/* fatal error ? */
return NULL;
}
status = H5Rcreate(ref, thefile, thepath, H5R_OBJECT, -1);
if (status < 0) {
/* fatal error ? */
return NULL;
}
for (i = 0; i < npte; i++) {
if (memcmp(ref, pte->obj_ref, sizeof(hobj_ref_t)) == 0) {
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 hobj_ref_t *
ref_path_table_put(hid_t obj, const char *path)
{
hobj_ref_t *ref;
herr_t status;
struct 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->obj_ref;
/* if not found, then make new entry */
pte = (struct ref_path_table_entry_t *)
malloc(sizeof(struct ref_path_table_entry_t));
if (pte == NULL) {
/* fatal error? */
return NULL;
}
pte->obj = obj;
ref = (hobj_ref_t *) malloc(sizeof(hobj_ref_t));
if (ref == NULL) {
/* fatal error? */
free(pte);
return NULL;
}
status = H5Rcreate(ref, thefile, path, H5R_OBJECT, -1);
if (status < 0) {
/* fatal error? */
free(ref);
free(pte);
return NULL;
}
pte->obj_ref = ref;
pte->apath = strdup(path);
pte->next = ref_path_table;
ref_path_table = pte;
npte++;
return ref;
}
/*-------------------------------------------------------------------------
* 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:
*
*-------------------------------------------------------------------------
*/
static char *
lookup_ref_path(hobj_ref_t * ref)
{
int i;
struct ref_path_table_entry_t *pte = NULL;
if (ref_path_table == NULL)
return NULL;
pte = ref_path_table;
if (pte == NULL) {
/* fatal -- not initialized? */
return NULL;
}
for (i = 0; i < npte; i++) {
if (memcmp(ref, pte->obj_ref, sizeof(hobj_ref_t)) == 0) {
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;
struct 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 {
fflush(stdout);
fprintf(stderr, "h5dump error: 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 {
fflush(stdout);
fprintf(stderr, "h5dump error: 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 {
fflush(stdout);
fprintf(stderr, "h5dump error: unable to get dataset \"%s\"\n", name);
d_status = EXIT_FAILURE;
}
break;
default:;
}
free(tmp);
free(thepath);
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)
{
int extra;
int len;
int i;
const char *cp;
char *ncp;
char *rcp;
if (str == NULL)
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 (char *) str;
} else {
cp = str;
rcp = ncp = calloc((size_t)(len + extra + 1), sizeof(char));
if (ncp == NULL)
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)
{
int extra;
int len;
int i;
const char *cp;
char *ncp;
char *rcp;
if (str == NULL)
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((size_t)(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)
{
char *fname;
hid_t nmembers, mtype;
int i, j, ndims, perm[H5DUMP_MAX_RANK];
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;
switch (H5Tget_class(type)) {
case H5T_INTEGER:
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
/* <IntegerType ByteOrder="bo" Sign="torf" Size="bytes"/> */
ord = H5Tget_order(type);
sgn = H5Tget_sign(type);
indentation(indent);
printf("<IntegerType ByteOrder=\"");
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("%d", sz);
printf("\" />\n");
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_FLOAT:
/* <FloatType ByteOrder="bo" Size="bytes"
SignBitLocation="bytes"
ExponentBits="eb" ExponentLocation="el"
MatissaBits="mb" MatissaLocation="ml" /> */
ord = H5Tget_order(type);
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
printf("<FloatType ByteOrder=\"");
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("%d", sz);
H5Tget_fields(type, &spos, &epos, &esize, &mpos, &msize);
printf("\" SignBitLocation=\"%d\" ", spos);
printf("ExponentBits=\"%d\" ExponentLocation=\"%d\" ", esize, epos);
printf("MantissaBits=\"%d\" MantissaLocation=\"%d\" />\n",
msize, mpos);
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_TIME:
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
printf("<TimeType />\n");
printf("<!-- H5T_TIME: not yet implemented -->");
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_STRING:
/* <StringType Cset="cs" StrSize="chars" StrPad="pad" /> */
size = H5Tget_size(type);
str_pad = H5Tget_strpad(type);
cset = H5Tget_cset(type);
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
printf("<StringType Cset=\"");
if (cset == H5T_CSET_ASCII) {
printf("H5T_CSET_ASCII\" ");
} else {
printf("unknown_cset\" ");
}
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("</AtomicType>\n");
break;
case H5T_BITFIELD:
/* <BitfieldType ByteOrder="bo" Size="bytes"/> */
ord = H5Tget_order(type);
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
printf("<BitfieldType ByteOrder=\"");
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=\"%d\"/>\n", size);
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_OPAQUE:
/* <OpaqueType Tag="tag" Size="bytes" /> */
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
printf("<OpaqueType Tag=\"%s\" ", H5Tget_tag(type));
size = H5Tget_size(type);
printf("Size=\"%d\"/>\n", size);
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_COMPOUND:
/* recursively describe the components of a compound datatype */
if (H5Tcommitted(type) > 0) {
/* detect a shared datatype, output only once */
H5Gget_objinfo(type, ".", TRUE, &statbuf);
i = search_obj(type_table, statbuf.objno);
if (i >= 0) {
/* This should be defined somewhere else */
if (!type_table->objs[i].recorded) {
/* 'anonymous' NDT. Use it's object num.
as it's name. */
printf("<NamedDataTypePtr OBJ-XID=\"");
printf("/#%lu:%lu",
type_table->objs[i].objno[0],
type_table->objs[i].objno[1]);
printf("\"/>\n");
} else {
/* point to the NDT by name */
printf("<NamedDataTypePtr OBJ-XID=\"");
printf("%s",
xml_escape_the_name(type_table->objs[i].objname));
printf("\"/>\n");
}
} else {
printf("<!-- h5dump error: unknown committed type. -->\n");
d_status = EXIT_FAILURE;
}
} else {
/* type of a dataset */
nmembers = H5Tget_nmembers(type);
indentation(indent);
printf("<CompoundType>\n");
/* List each member Field of the type */
/* <Field FieldName="name" > */
/* <DataType > */
indent += COL;
for (i = 0; i < nmembers; i++) {
fname = H5Tget_member_name(type, i);
mtype = H5Tget_member_type(type, i);
indentation(indent);
printf("<Field FieldName=\"%s\">\n",
xml_escape_the_name(fname));
free(fname);
indent += COL;
indentation(indent);
printf("<DataType>\n");
indent += COL;
xml_print_datatype(mtype);
indent -= COL;
indentation(indent);
printf("%s\n", dump_header_format->datatypeend);
indent -= COL;
indentation(indent);
printf("</Field>\n");
}
indent -= COL;
indentation(indent);
printf("</CompoundType>\n");
}
break;
case H5T_REFERENCE:
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
/* Only Object references supported at this time */
printf("<ReferenceType>\n");
indentation(indent + COL);
printf("<ObjectReferenceType />\n");
indentation(indent);
printf("</ReferenceType>\n");
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_ENUM:
/* <EnumType Nelems="ne" >
list Name, values of enum
*/
nmembs = H5Tget_nmembers(type);
indentation(indent);
printf("<AtomicType>\n");
indent += COL;
indentation(indent);
printf("<EnumType Nelems=\"%d\">\n", nmembs);
xml_print_enum(type);
indentation(indent);
printf("</EnumType>\n");
indent -= COL;
indentation(indent);
printf("</AtomicType>\n");
break;
case H5T_VLEN:
indentation(indent);
printf("<VLType>\n");
super = H5Tget_super(type);
indent += COL;
indentation(indent);
printf("<DataType>\n");
indent += COL;
xml_print_datatype(super);
indent -= COL;
indentation(indent);
printf("%s\n", dump_header_format->datatypeend);
indent -= COL;
indentation(indent);
printf("</VLType>\n");
H5Tclose(super);
break;
case H5T_ARRAY:
/* Get array base type */
super = H5Tget_super(type);
/* Print lead-in */
indentation(indent);
printf("<ArrayType Ndims=\"");
ndims = H5Tget_array_ndims(type);
printf("%d\">\n", ndims);
/* Get array information */
H5Tget_array_dims(type, dims, perm);
/* list of dimensions */
indent += COL;
if (perm != NULL) {
/* for each dimension, list */
for (j = 0; j < ndims; j++) {
indentation(indent);
printf("<ArrayDimension DimSize=\"%u\" DimPerm=\"%u\"/>\n",
(int) dims[j], (int) perm[j]);
}
} else {
for (j = 0; j < ndims; j++) {
indentation(indent);
printf("<ArrayDimension DimSize=\"%u\" DimPerm=\"0\"/>\n",
(int) dims[j]);
}
}
indent -= COL;
indent += COL;
indentation(indent);
printf("<DataType>\n");
indent += COL;
xml_print_datatype(super);
indent -= COL;
indentation(indent);
printf("%s\n", dump_header_format->datatypeend);
indent -= COL;
indentation(indent);
printf("</ArrayType>\n");
/* Close array base type */
H5Tclose(super);
break;
default:
printf("<!-- unknown data type -->");
d_status = EXIT_FAILURE;
break;
}
}
/*-------------------------------------------------------------------------
* 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 */
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("<NamedDataTypePtr OBJ-XID=\"");
printf("/#%lu:%lu",
type_table->objs[i].objno[0],
type_table->objs[i].objno[1]);
printf("\"/>\n");
} else {
/* pointer to a named data type already in XML */
printf("<NamedDataTypePtr OBJ-XID=\"");
printf("%s",
xml_escape_the_name(type_table->objs[i].objname));
printf("\"/>\n");
}
} else {
printf("<!-- h5dump error: unknown committed type. -->\n");
}
indent -= COL;
return;
}
printf("%s %s\n", dump_header_format->datatypebegin,
dump_header_format->datatypeblockbegin);
indent += COL;
xml_print_datatype(type);
indent -= COL;
indentation(indent);
printf("%s\n", dump_header_format->datatypeend);
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);
int i;
indentation(indent + COL);
printf("%s\n", dump_header_format->dataspacebegin);
if (H5Sis_simple(space)) {
indentation(indent + COL + COL);
if (ndims == 0) {
/* scalar dataspace (just a tag, no XML attrs. defined */
printf("<ScalarDataspace />\n");
} else {
/* simple dataspace */
/* <SimpleDataspace Ndims="nd"> */
printf("<SimpleDataspace Ndims=\"%d\">\n", ndims);
/* print the <Dimension> elements */
for (i = 0; i < ndims; i++) {
indentation(indent + COL + COL + COL);
if (maxsize[i] == H5S_UNLIMITED) {
HDfprintf(stdout,
"<Dimension DimSize=\"%Hu\" MaxDimSize=\"UNLIMITED\"/>\n",
size[i]);
} else if (maxsize[i] == (hsize_t) 0) {
HDfprintf(stdout,
"<Dimension DimSize=\"%Hu\" MaxDimSize=\"%Hu\"/>\n",
size[i], size[i]);
} else {
HDfprintf(stdout,
"<Dimension DimSize=\"%Hu\" MaxDimSize=\"%Hu\"/>\n",
size[i], maxsize[i]);
}
}
indentation(indent + COL + COL);
printf("</SimpleDataspace>\n");
}
} else {
printf("<!-- not yet implemented -->\n");
}
indentation(indent + COL);
printf("%s\n", dump_header_format->dataspaceend);
}
/*-------------------------------------------------------------------------
* 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)
{
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("%s\n", dump_header_format->databegin);
indentation(indent + COL);
printf("<DataFromFile>\n");
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 = h5dump_dset(stdout, outputformat, obj_id, -1, 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 = h5dump_fixtype(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 =
h5dump_mem(stdout, outputformat, obj_id, p_type, space,
buf, depth);
}
free(buf);
H5Tclose(p_type);
H5Sclose(space);
H5Tclose(type);
}
}
if (status < 0) {
indentation(indent + COL);
printf("Unable to print data.\n");
status = 1;
}
indentation(indent + COL);
printf("</DataFromFile>\n");
indentation(indent);
printf("%s\n", dump_header_format->dataend);
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;
indentation(indent);
printf("<Attribute Name=\"%s\">\n", xml_escape_the_name(attr_name));
if ((attr_id = H5Aopen_name(attr, attr_name)) >= 0) {
type = H5Aget_type(attr_id);
space = H5Aget_space(attr_id);
dump_function_table->dump_dataspace_function(space);
dump_function_table->dump_datatype_function(type);
if (display_data) {
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);
break;
case H5T_TIME:
indent += COL;
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<!-- Time data not yet implemented. -->\n");
indentation(indent);
printf("<NoData />\n");
indentation(indent);
printf("<Data>\n");
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);
break;
case H5T_REFERENCE:
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<DataFromFile>\n");
xml_print_refs(attr_id, ATTRIBUTE_DATA);
indentation(indent);
printf("</DataFromFile>\n");
indentation(indent);
printf("</Data>\n");
break;
case H5T_VLEN:
printf("<!-- Note: format of VL data not specified -->\n");
dump_function_table->dump_data_function(attr_id,
ATTRIBUTE_DATA);
break;
default:
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<!-- Unknown datatype: %d -->\n", H5Tget_class(type));
indentation(indent);
printf("<NoData/>\n");
indentation(indent);
printf("</Data>\n");
break;
}
} else {
/* The case of an attribute never yet written ?? */
indentation(indent);
printf("<Data>\n");
indentation(indent + COL);
printf("<NoData/>\n");
indentation(indent);
printf("</Data>\n");
}
H5Tclose(type);
H5Sclose(space);
H5Aclose(attr_id);
indentation(indent);
printf("%s\n", dump_header_format->attributeend);
return SUCCEED;
} else {
/* ?? failed */
indentation(indent + COL);
printf("<!-- h5dump error: unable to open attribute. -->\n");
indentation(indent);
printf("%s\n", dump_header_format->attributeend);
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)
{
int nmembers = 1, x;
hid_t mtype;
char *fname;
char *tmp;
tmp = (char *) malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
strcat(tmp, "/");
strcat(tmp, name);
indentation(indent);
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("<NamedDataType Name=\"%s\" OBJ-XID=\"%s\" Parents=\"%s\">\n",
name, tmp, name);
} else {
printf("<NamedDataType Name=\"%s\" OBJ-XID=\"%s\" Parents=\"%s\">\n",
xml_escape_the_name(name),
xml_escape_the_name(tmp),
(strcmp(prefix, "") ? xml_escape_the_name(name) : "root"));
}
indent += COL;
if (H5Tget_class(type) == H5T_COMPOUND) {
/* Dump this here for sure. */
nmembers = H5Tget_nmembers(type);
indentation(indent);
printf("<CompoundType>\n");
indent += COL;
for (x = 0; x < nmembers; x++) {
fname = H5Tget_member_name(type, x);
mtype = H5Tget_member_type(type, x);
indentation(indent);
printf("<Field FieldName=\"%s\">\n", xml_escape_the_name(fname));
free(fname);
if ((H5Tget_class(mtype) == H5T_COMPOUND)
|| (H5Tget_class(mtype) == H5T_VLEN)
|| (H5Tget_class(mtype) == H5T_ARRAY)) {
indent += COL;
/* Nested compound type: recur */
indentation(indent);
printf("%s %s\n", dump_header_format->datatypebegin,
dump_header_format->datatypeblockbegin);
indent += COL;
xml_print_datatype(mtype);
indent -= COL;
indentation(indent);
printf("%s\n", dump_header_format->datatypeend);
indent -= COL;
} else {
indent += COL;
indentation(indent);
printf("%s %s\n", dump_header_format->datatypebegin,
dump_header_format->datatypeblockbegin);
indent += COL;
xml_print_datatype(mtype);
indent -= COL;
indentation(indent);
printf("%s\n", dump_header_format->datatypeend);
indent -= COL;
}
indentation(indent);
printf("</Field>\n");
}
indent -= COL;
indentation(indent);
printf("</CompoundType>\n");
} else {
/* Other data types: call print_datatype */
indent += COL;
xml_print_datatype(type);
indent -= COL;
}
indent -= COL;
indentation(indent);
printf("</NamedDataType>\n");
}
/*-------------------------------------------------------------------------
* 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 typename[1024], *tmp;
char *par;
int i;
int isRoot = 0;
int xtype;
if (strcmp(name, "/") == 0) {
isRoot = 1;
} else {
tmp = malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
par = strdup(tmp);
cp = strrchr(par, '/');
if (cp != NULL) {
if ((cp == par) && strlen(par) > 1) {
*(cp + 1) = '\0';
} else {
*cp = '\0';
}
}
}
indentation(indent);
if (isRoot) {
printf("<RootGroup OBJ-XID=\"root\">\n");
} else {
printf("<Group Name=\"%s\" OBJ-XID=\"%s\" Parents=\"%s\" >\n",
xml_escape_the_name(name),
xml_escape_the_name(tmp), xml_escape_the_name(par));
}
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);
fprintf(stderr, "h5dump error: internal error (line %d)\n", __LINE__);
d_status = EXIT_FAILURE;
} else if (group_table->objs[i].displayed) {
/* already seen: enter a groupptr */
indentation(indent + COL);
printf("<GroupPtr OBJ-XID=\"%s\"/>\n",
xml_escape_the_name(group_table->objs[i].objname));
} else {
/* first time this group has been seen -- describe it */
strcpy(group_table->objs[i].objname, 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(typename, "#%lu:%lu",
type_table->objs[i].objno[0],
type_table->objs[i].objno[1]);
dump_function_table->dump_named_datatype_function
(type, typename);
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_LINK;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_GROUP;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
}
} else {
/* 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(typename, "#%lu:%lu",
type_table->objs[i].objno[0],
type_table->objs[i].objno[1]);
dump_function_table->dump_named_datatype_function(type,
typename);
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_LINK;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
xtype = H5G_GROUP;
H5Giterate(gid, ".", NULL, dump_all, (void *) &xtype);
}
indent -= COL;
indentation(indent);
if (isRoot) {
printf("</RootGroup>\n");
} else {
printf("%s\n", dump_header_format->groupend);
}
/* don't free this!!!
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 == NULL) {
printf("\"%s\"\n", "NULL");
} else {
printf("\"%s\"\n", xml_escape_the_string(path, -1));
}
refbuf++;
}
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;
char *buf;
char *bp;
char *onestring;
hsize_t ssiz;
size_t tsiz;
size_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_STRING) {
/* 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, 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 = calloc((size_t)ssiz, sizeof(char));
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);
onestring = (char *) calloc((size_t)tsiz, sizeof(char));
bp = buf;
for (i = 0; i < ssiz; i++) {
strncpy(onestring, bp, tsiz);
indentation(indent + COL);
if (onestring == NULL) {
printf("\"%s\"\n", "NULL");
} else {
printf("\"%s\"\n", xml_escape_the_string(onestring, (int)tsiz));
}
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:
*
*-------------------------------------------------------------------------
*/
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++) {
filter = H5Pget_filter(dcpl, i, &flags,
(size_t *) &cd_nelmts,
&cd_values, 20, namebuf);
if (filter == H5Z_FILTER_DEFLATE) {
indentation(indent + COL);
printf("<Compression />\n");
indentation(indent + COL);
printf("<!-- Compression parameter %d -->\n", cd_values);
}
}
}
/*-------------------------------------------------------------------------
* 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)
{
hid_t type, space;
hid_t dcpl;
int maxdims;
hsize_t *chsize;
int ndims;
int i;
char *tmp;
tmp = (char *) malloc(strlen(prefix) + strlen(name) + 2);
strcpy(tmp, prefix);
strcat(tmp, "/");
strcat(tmp, name);
indentation(indent);
printf("<Dataset Name=\"%s\" OBJ-XID=\"%s\" Parents=\"%s\">\n",
xml_escape_the_name(name), xml_escape_the_name(tmp),
(strcmp(prefix, "") ? xml_escape_the_name(prefix) : "root"));
dcpl = H5Dget_create_plist(did);
type = H5Dget_type(did);
space = H5Dget_space(did);
/* Print information about chunked storage */
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("<StorageLayout>\n");
indent += COL;
indentation(indent);
printf("<ChunkedLayout ");
ndims = H5Pget_chunk(dcpl, maxdims, chsize);
printf("Ndims=\"%d\">\n", ndims);
/* check for compression and tell about it... */
check_compression(dcpl);
indent += COL;
for (i = 0; i < ndims; i++) {
indentation(indent);
HDfprintf(stdout,"<ChunkDimension DimSize=\"%Hu\" />\n", chsize[i]);
}
indent -= COL;
indentation(indent);
printf("</ChunkedLayout>\n");
indent -= COL;
indentation(indent);
printf("</StorageLayout>\n");
indent -= COL;
free(chsize);
}
/* and check for external.... */
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;
i = H5Dget_storage_size(did);
if (display_data && (i > 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);
break;
case H5T_TIME:
indent += COL;
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<!-- Time data not yet implemented. -->\n");
indentation(indent);
printf("<NoData />\n");
indentation(indent);
printf("<Data>\n");
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);
break;
case H5T_REFERENCE:
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<DataFromFile>\n");
xml_print_refs(did, DATASET_DATA);
indentation(indent);
printf("</DataFromFile>\n");
indentation(indent);
printf("</Data>\n");
break;
case H5T_VLEN:
printf("<!-- Note: format of VL data not specified -->\n");
dump_function_table->dump_data_function(did, DATASET_DATA);
break;
default:
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<!-- Unknown datatype: %d -->\n", H5Tget_class(type));
indentation(indent);
printf("<NoData/>\n");
indentation(indent);
printf("</Data>\n");
break;
}
} else {
/* no data written */
indentation(indent);
printf("<Data>\n");
indentation(indent);
printf("<NoData/>\n");
indentation(indent);
printf("</Data>\n");
}
/*
free(tmp);
*/
H5Tclose(type);
H5Sclose(space);
indentation(indent);
printf("%s\n", dump_header_format->datasetend);
}
/*-------------------------------------------------------------------------
* 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 */
int 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 */
int i; /*miscellaneous counters */
size_t j;
nmembs = H5Tget_nmembers(type);
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((size_t)nmembs, sizeof(char *));
value = calloc((size_t)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, (hsize_t)nmembs, value, NULL, H5P_DEFAULT);
/* Sort members by increasing value */
/*not implemented yet */
/* Print members */
indent += COL;
for (i = 0; i < nmembs; i++) {
indentation(indent);
printf("<EnumElement>\n");
indentation(indent + COL);
printf("%s\n", xml_escape_the_name(name[i]));
indentation(indent);
printf("</EnumElement>\n");
indentation(indent);
printf("<EnumValue>\n");
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)) {
printf("%" PRINTF_LL_WIDTH "u", *((unsigned long_long *)
((void *) (value + i * dst_size))));
} else {
printf("%" PRINTF_LL_WIDTH "d",
*((long_long *) ((void *) (value + i * dst_size))));
}
printf("\n");
indentation(indent);
printf("</EnumValue>\n");
}
indent -= COL;
/* Release resources */
for (i = 0; i < nmembs; i++)
free(name[i]);
free(name);
free(value);
H5Tclose(super);
}
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