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hdf5/tools/h5tools.c
Bill Wendling ea7f4421f9 [svn-r2634] Purpose: 
Bug fix
Description:
	In the h5dump_fixtype function, when users created a COMPOUND
	datatype, the alignment would be off somewhat.
Solution:
	The alignment was being set after insertion. I changed this code:

	for (i = 0, offset = 0; i < nmembs; i++) {
	    H5Tinsert_array(m_type, name[i], offset, ndims[i], dims + i * 4,
			    NULL, memb[i]);

	    for (j = 0, nelmts = 1; j < ndims[i]; j++)
		    nelmts *= dims[i * 4 + j];

            offset = ALIGN(offset, H5Tget_size(memb[i])) +
	    			nelmts * H5Tget_size(memb[i]);
	}

	to:

	for (i = 0, offset = 0; i < nmembs; i++) {
            if (offset)
                offset = ALIGN(offset, H5Tget_size(memb[i]));

	    H5Tinsert_array(m_type, name[i], offset, ndims[i], dims + i * 4,
			    NULL, memb[i]);

	    for (j = 0, nelmts = 1; j < ndims[i]; j++)
		    nelmts *= dims[i * 4 + j];

	    offset += nelmts * H5Tget_size(memb[i]);
	}

	The alignment is now calculated before the insertion.
Platforms tested:
	Solaris, Linux
2000-10-05 11:56:30 -05:00

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/*
* Copyright © 1998 NCSA
* All rights reserved.
*
* Programmer: Robb Matzke <matzke@llnl.gov>
* Thursday, July 23, 1998
*
* Purpose: A library for displaying the values of a dataset in a human
* readable format.
*/
#include <assert.h>
#include <ctype.h>
#include <h5tools.h>
#include <hdf5.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <H5private.h>
#include <h5dump.h>
/* taken from h5dumputil.c */
int indent = 0;
int compound_data=0;
int nCols = 80;
FILE *rawdatastream = NULL; /* should be stdout but linux gcc moans about it*/
int print_data(hid_t oid, hid_t _p_type, int obj_data);
/*
* If REPEAT_VERBOSE is defined then character strings will be printed so
* that repeated character sequences like "AAAAAAAAAA" are displayed as
*
* 'A' repeates 9 times
*
* Otherwise the format is more Perl-like
*
* 'A'*10
*
*/
#define REPEAT_VERBOSE
/*
* The output functions need a temporary buffer to hold a piece of the
* dataset while it's being printed. This constant sets the limit on the
* size of that temporary buffer in bytes. For efficiency's sake, choose the
* largest value suitable for your machine (for testing use a small value).
*/
#if 1
#define H5DUMP_BUFSIZE (1024*1024)
#else
#define H5DUMP_BUFSIZE (1024)
#endif
#define OPT(X,S) ((X)?(X):(S))
#define ALIGN(A,Z) ((((A)+(Z)-1)/(Z))*(Z))
#define START_OF_DATA 0x0001
#define END_OF_DATA 0x0002
/* Special strings embedded in the output */
#define OPTIONAL_LINE_BREAK "\001"
/* Variable length string datatype */
#define STR_INIT_LEN 4096 /*initial length */
typedef struct h5dump_str_t {
char *s; /*allocate string */
size_t len; /*length of actual value */
size_t nalloc; /*allocated size of string */
} h5dump_str_t;
/* Output variables */
typedef struct h5dump_context_t {
size_t cur_column; /*current column for output */
size_t cur_elmt; /*current element/output line */
int need_prefix; /*is line prefix needed? */
int ndims; /*dimensionality */
hsize_t p_min_idx[H5S_MAX_RANK]; /*min selected index */
hsize_t p_max_idx[H5S_MAX_RANK]; /*max selected index */
int prev_multiline; /*was prev datum multiline? */
size_t prev_prefix_len;/*length of previous prefix */
int continuation; /*continuation of previous data?*/
int size_last_dim; /*the size of the last dimension,
*needed so we can break after each
*row */
int indent_level; /*the number of times we need some
*extra indentation */
int default_indent_level; /*this is used when the indent
*level gets changed */
} h5dump_context_t;
typedef herr_t (*H5G_operator_t)(hid_t, const char*, void*);
extern void init_prefix(char **temp, int length);
extern void init_table(table_t **table);
extern void free_table(table_t **table);
extern void dump_table(char *name, table_t* table);
extern herr_t find_objs(hid_t group, const char *name, void *op_data);
extern int search_obj (table_t *temp, unsigned long *);
extern int get_table_idx(table_t *table, unsigned long *);
extern int get_tableflag(table_t*, int);
extern int set_tableflag(table_t*, int);
extern char* get_objectname(table_t*, int);
/*-------------------------------------------------------------------------
* Function: h5dump_str_close
*
* Purpose: Closes a string by releasing it's memory and setting the size
* information to zero.
*
* Return: void
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
h5dump_str_close(h5dump_str_t *str)
{
if (str && str->nalloc) {
free(str->s);
memset(str, 0, sizeof(h5dump_str_t));
}
}
/*-------------------------------------------------------------------------
* Function: h5dump_str_len
*
* Purpose: Returns the length of the string, not counting the null
* terminator.
*
* Return: Success: Length of string
*
* Failure: 0
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
h5dump_str_len(h5dump_str_t *str)
{
return str->len;
}
/*-------------------------------------------------------------------------
* Function: h5dump_str_append
*
* Purpose: Formats variable arguments according to printf() format
* string and appends the result to variable length string STR.
*
* Return: Success: Pointer to buffer containing result.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_str_append(h5dump_str_t *str/*in,out*/, const char *fmt, ...)
{
va_list ap;
va_start(ap, fmt);
/* Make sure we have some memory into which to print */
if (!str->s || str->nalloc<=0) {
str->nalloc = STR_INIT_LEN;
str->s = malloc(str->nalloc);
assert(str->s);
str->s[0] = '\0';
str->len = 0;
}
while (1) {
size_t avail = str->nalloc - str->len;
size_t nchars = HDvsnprintf(str->s+str->len, avail, fmt, ap);
if (nchars<avail) {
/* success */
str->len += nchars;
break;
}
/* Try again with twice as much space */
str->nalloc *= 2;
str->s = realloc(str->s, str->nalloc);
assert(str->s);
}
va_end(ap);
return str->s;
}
/*-------------------------------------------------------------------------
* Function: h5dump_str_reset
*
* Purpose: Reset the string to the empty value. If no memory is
* allocated yet then initialize the h5dump_str_t struct.
*
* Return: Success: Ptr to the buffer which contains a null
* character as the first element.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_str_reset(h5dump_str_t *str/*in,out*/)
{
if (!str->s || str->nalloc<=0) {
str->nalloc = STR_INIT_LEN;
str->s = malloc(str->nalloc);
assert(str->s);
}
str->s[0] = '\0';
str->len = 0;
return str->s;
}
/*-------------------------------------------------------------------------
* Function: h5dump_str_trunc
*
* Purpose: Truncate a string to be at most SIZE characters.
*
* Return: Success: Pointer to the string
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_str_trunc(h5dump_str_t *str/*in,out*/, size_t size)
{
if (size<str->len) {
str->len = size;
str->s[size] = '\0';
}
return str->s;
}
/*-------------------------------------------------------------------------
* Function: h5dump_str_fmt
*
* Purpose: Reformat a string contents beginning at character START
* according to printf format FMT. FMT should contain no format
* specifiers except possibly the `%s' variety. For example, if
* the input string is `hello' and the format is "<<%s>>" then
* the output value will be "<<hello>>".
*
* Return: Success: A pointer to the resulting string.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_str_fmt(h5dump_str_t *str/*in,out*/, size_t start, const char *fmt)
{
char _temp[1024], *temp=_temp;
/* If the format string is simply "%s" then don't bother doing anything */
if (!strcmp(fmt, "%s")) return str->s;
/*
* Save the input value if there is a `%' anywhere in FMT. Otherwise
* don't bother because we don't need a temporary copy.
*/
if (strchr(fmt, '%')) {
if ((str->len-start)+1>sizeof _temp) {
temp = malloc((str->len-start)+1);
assert(temp);
}
strcpy(temp, str->s+start);
}
/* Reset the output string and append a formatted version */
h5dump_str_trunc(str, start);
h5dump_str_append(str, fmt, temp);
/* Free the temp buffer if we allocated one */
if (temp != _temp) free(temp);
return str->s;
}
/*-------------------------------------------------------------------------
* Function: h5dump_prefix
*
* Purpose: Renders the line prefix value into string STR.
*
* Return: Success: Pointer to the prefix.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_prefix(h5dump_str_t *str/*in,out*/, const h5dump_t *info,
hsize_t elmtno, int ndims, hsize_t min_idx[], hsize_t max_idx[])
{
hsize_t p_prod[H5S_MAX_RANK], p_idx[H5S_MAX_RANK];
hsize_t n, i=0;
h5dump_str_reset(str);
if (ndims>0) {
/*
* Calculate the number of elements represented by a unit change in a
* certain index position.
*/
for (i=ndims-1, p_prod[ndims-1]=1; i>0; --i) {
p_prod[i-1] = (max_idx[i]-min_idx[i]) * p_prod[i];
}
/*
* Calculate the index values from the element number.
*/
for (i=0, n=elmtno; i<(hsize_t)ndims; i++) {
p_idx[i] = n / p_prod[i] + min_idx[i];
n %= p_prod[i];
}
/*
* Print the index values.
*/
for (i=0; i<(hsize_t)ndims; i++) {
if (i) h5dump_str_append(str, "%s", OPT(info->idx_sep, ","));
h5dump_str_append(str, OPT(info->idx_n_fmt, "%lu"),
(unsigned long)p_idx[i]);
}
} else {
/* Scalar */
h5dump_str_append(str, OPT(info->idx_n_fmt, "%lu"), (unsigned long)0);
}
/*
* Add prefix and suffix to the index.
*/
return h5dump_str_fmt(str, 0, OPT(info->idx_fmt, "%s: "));
}
/*-------------------------------------------------------------------------
* Function: h5dump_escape
*
* Purpose: Changes all "funny" characters in S into standard C escape
* sequences. If ESCAPE_SPACES is non-zero then spaces are
* escaped by prepending a backslash.
*
* Return: Success: S
*
* Failure: NULL if the buffer would overflow. The
* buffer has as many left-to-right escapes as
* possible before overflow would have happened.
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_escape(char *s/*in,out*/, size_t size, int escape_spaces)
{
size_t n = strlen(s);
size_t i;
const char *escape;
char octal[8];
for (i=0; i<n; i++) {
switch (s[i]) {
case '"':
escape = "\\\"";
break;
case '\\':
escape = "\\\\";
break;
case '\b':
escape = "\\b";
break;
case '\f':
escape = "\\f";
break;
case '\n':
escape = "\\n";
break;
case '\r':
escape = "\\r";
break;
case '\t':
escape = "\\t";
break;
case ' ':
escape = escape_spaces ? "\\ " : NULL;
break;
default:
if (!isprint((int)*s)) {
sprintf(octal, "\\%03o", (unsigned char)(s[i]));
escape = octal;
} else {
escape = NULL;
}
break;
}
if (escape) {
size_t esc_size = strlen(escape);
if (n+esc_size+1>size) return NULL; /*would overflow*/
memmove(s+i+esc_size, s+i, (n-i)+1); /*make room*/
memcpy(s+i, escape, esc_size); /*insert*/
n += esc_size;
i += esc_size - 1;
}
}
return s;
}
/*-------------------------------------------------------------------------
* Function: h5dump_is_zero
*
* Purpose: Determines if memory is initialized to all zero bytes.
*
* Return: TRUE if all bytes are zero; FALSE otherwise
*
* Programmer: Robb Matzke
* Monday, June 7, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static hbool_t
h5dump_is_zero(const void *_mem, size_t size)
{
const unsigned char *mem = (const unsigned char*)_mem;
while (size-- > 0) {
if (mem[size]) return FALSE;
}
return TRUE;
}
/*-------------------------------------------------------------------------
* Function: h5dump_region
*
* Purpose: Prints information about a dataspace region by appending
* the information to the specified string.
*
* Return: Success: 0
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Monday, June 7, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
h5dump_region(hid_t region, h5dump_str_t *str/*in,out*/, const h5dump_t *info)
{
hssize_t nblocks, npoints, i;
hsize_t *ptdata;
int j;
int ndims = H5Sget_simple_extent_ndims(region);
/*
* These two functions fail if the region does not have blocks or points,
* respectively. They do not currently know how to translate from one to
* the other.
*/
H5E_BEGIN_TRY {
nblocks = H5Sget_select_hyper_nblocks(region);
npoints = H5Sget_select_elem_npoints(region);
} H5E_END_TRY;
h5dump_str_append(str, "{");
/* Print block information */
if (nblocks>0) {
ptdata = malloc(nblocks*ndims*2*sizeof(ptdata[0]));
H5Sget_select_hyper_blocklist(region, 0, nblocks, ptdata);
for (i=0; i<nblocks; i++) {
h5dump_str_append(str, info->dset_blockformat_pre,
i?","OPTIONAL_LINE_BREAK" ":"",
(unsigned long)i);
/* Start coordinates and opposite corner */
for (j=0; j<ndims; j++) {
h5dump_str_append(str, "%s%lu", j?",":"(",
(unsigned long)(ptdata[i*2*ndims+j]));
}
for (j=0; j<ndims; j++) {
h5dump_str_append(str, "%s%lu", j?",":")-(",
(unsigned long)(ptdata[i*2*ndims+j+ndims]));
}
h5dump_str_append(str, ")");
}
free(ptdata);
}
/* Print point information */
if (npoints>0) {
ptdata = malloc(npoints*ndims*sizeof(ptdata[0]));
H5Sget_select_elem_pointlist(region, 0, npoints, ptdata);
for (i=0; i<npoints; i++) {
h5dump_str_append(str, info->dset_ptformat_pre ,
i?","OPTIONAL_LINE_BREAK" ":"",
(unsigned long)i);
for (j=0; j<ndims; j++) {
h5dump_str_append(str, "%s%lu", j?",":"(",
(unsigned long)(ptdata[i*ndims+j]));
}
h5dump_str_append(str, ")");
}
free(ptdata);
}
h5dump_str_append(str, "}");
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5dump_sprint
*
* Purpose: Renders the value pointed to by VP of type TYPE into variable
* length string STR.
*
* Return: A pointer to memory containing the result or NULL on error.
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
* Robb Matzke, 1999-04-26
* Made this function safe from overflow problems by allowing it
* to reallocate the output string.
*
* Robb Matzke, 1999-06-04
* Added support for object references. The new `container'
* argument is the dataset where the reference came from.
*
* Robb Matzke, 1999-06-07
* Added support for printing raw data. If info->raw is non-zero
* then data is printed in hexadecimal format.
*
*-------------------------------------------------------------------------
*/
static char *
h5dump_sprint(h5dump_str_t *str/*in,out*/, const h5dump_t *info,
hid_t container, hid_t type, void *vp, h5dump_context_t *ctx)
{
size_t i, n, offset, size, dims[H5S_MAX_RANK], nelmts, start;
char *name, quote='\0';
hid_t memb, obj, region;
int nmembs, x, j, k, ndims, otype;
static char fmt_llong[8], fmt_ullong[8];
H5T_str_t pad;
H5G_stat_t sb;
/*some tempvars to store the value before we append it to the string
to get rid of the memory alignment problem*/
float tempfloat;
double tempdouble;
int tempint;
unsigned int tempuint;
short tempshort;
unsigned short tempushort;
long templong;
unsigned long tempulong;
unsigned long_long tempullong;
long_long templlong;
/* Build default formats for long long types */
if (!fmt_llong[0]) {
sprintf(fmt_llong, "%%%sd", PRINTF_LL_WIDTH);
sprintf(fmt_ullong, "%%%su", PRINTF_LL_WIDTH);
}
/* Append value depending on data type */
start = h5dump_str_len(str);
if (info->raw) {
h5dump_str_append(str, "0x");
n = H5Tget_size(type);
for (i=0; i<n; i++) {
h5dump_str_append(str, OPT(info->fmt_raw, "%02x"),
((unsigned char*)vp)[i]);
}
} else if (H5Tequal(type, H5T_NATIVE_DOUBLE)) {
memcpy(&tempdouble,vp,sizeof(double));
h5dump_str_append(str, OPT(info->fmt_double, "%g"), tempdouble);
} else if (H5Tequal(type, H5T_NATIVE_FLOAT)) {
memcpy(&tempfloat,vp,sizeof(float));
h5dump_str_append(str, OPT(info->fmt_double, "%g"), tempfloat);
} else if (info->ascii &&
(H5Tequal(type, H5T_NATIVE_SCHAR) ||
H5Tequal(type, H5T_NATIVE_UCHAR))) {
if (ESCAPE_HTML==info->str_locale) {
if (*((char*)vp)<=' ' || *((char*)vp)>'~') {
h5dump_str_append(str, "%%%02X", *((unsigned char*)vp));
} else {
h5dump_str_append(str, "%c", *((char*)vp));
}
} else {
switch (*((char*)vp)) {
case '"':
h5dump_str_append(str, "\\\"");
break;
case '\\':
h5dump_str_append(str, "\\\\");
break;
case '\b':
h5dump_str_append(str, "\\b");
break;
case '\f':
h5dump_str_append(str, "\\f");
break;
case '\n':
h5dump_str_append(str, "\\n");
break;
case '\r':
h5dump_str_append(str, "\\r");
break;
case '\t':
h5dump_str_append(str, "\\t");
break;
default:
if (isprint(*((char*)vp))) {
h5dump_str_append(str, "%c", *((char*)vp));
} else {
h5dump_str_append(str, "\\%03o", *((unsigned char*)vp));
}
break;
}
}
} else if (H5T_STRING==H5Tget_class(type)) {
size = H5Tget_size(type);
quote = '\0';
pad = H5Tget_strpad(type);
for (i=0;
i<size && ((pad == H5T_STR_NULLPAD)?1:(((char*)vp)[i] != '\0'));
i++) {
/*
* Count how many times the next character repeats. If the
* threshold is zero then that means it can repeat any number
* of times.
*/
j=1;
if (info->str_repeat>0) {
while (i+j<size && ((char*)vp)[i]==((char*)vp)[i+j]) j++;
}
/*
* Print the opening quote. If the repeat count is high enough to
* warrant printing the number of repeats instead of enumerating
* the characters, then make sure the character to be repeated is
* in it's own quote.
*/
if (info->str_repeat>0 && j>info->str_repeat) {
if (quote) h5dump_str_append(str, "%c", quote);
quote = '\'';
h5dump_str_append(str, "%s%c", i?" ":"", quote);
} else if (!quote) {
quote = '"';
h5dump_str_append(str, "%s%c", i?" ":"", quote);
}
/* Print the character */
if (ESCAPE_HTML==info->str_locale) {
if (((char*)vp)[i]<=' ' || ((char*)vp)[i]>'~') {
h5dump_str_append(str, "%%%02X", ((unsigned char*)vp)[i]);
} else {
h5dump_str_append(str, "%c", ((char*)vp)[i]);
}
} else {
switch (((char*)vp)[i]) {
case '"':
h5dump_str_append(str, "\\\"");
break;
case '\\':
h5dump_str_append(str, "\\\\");
break;
case '\b':
h5dump_str_append(str, "\\b");
break;
case '\f':
h5dump_str_append(str, "\\f");
break;
case '\n':
h5dump_str_append(str, "\\n");
break;
case '\r':
h5dump_str_append(str, "\\r");
break;
case '\t':
h5dump_str_append(str, "\\t");
break;
default:
if (isprint(((char*)vp)[i])) {
h5dump_str_append(str, "%c", ((char*)vp)[i]);
} else {
h5dump_str_append(str, "\\%03o",
((unsigned char*)vp)[i]);
}
break;
}
}
/* Print the repeat count */
if (info->str_repeat && j>info->str_repeat) {
#ifdef REPEAT_VERBOSE
h5dump_str_append(str, "%c repeats %d times", quote, j-1);
#else
h5dump_str_append(str, "%c*%d", quote, j-1);
#endif
quote = '\0';
i += j-1;
}
}
if (quote) h5dump_str_append(str, "%c", quote);
if (0==i) {
h5dump_str_append(str, "\"\""); /*empty string*/
}
} else if (H5Tequal(type, H5T_NATIVE_INT)) {
memcpy(&tempint, vp, sizeof(int));
h5dump_str_append(str, OPT(info->fmt_int, "%d"),
tempint);
} else if (H5Tequal(type, H5T_NATIVE_UINT)) {
memcpy(&tempuint, vp, sizeof(unsigned int));
h5dump_str_append(str, OPT(info->fmt_uint, "%u"),
tempuint);
} else if (H5Tequal(type, H5T_NATIVE_SCHAR)) {
h5dump_str_append(str, OPT(info->fmt_schar, "%d"),
*((signed char*)vp));
} else if (H5Tequal(type, H5T_NATIVE_UCHAR)) {
h5dump_str_append(str, OPT(info->fmt_uchar, "%u"),
*((unsigned char*)vp));
} else if (H5Tequal(type, H5T_NATIVE_SHORT)) {
memcpy(&tempshort, vp, sizeof(short));
h5dump_str_append(str, OPT(info->fmt_short, "%d"),
tempshort);
} else if (H5Tequal(type, H5T_NATIVE_USHORT)) {
memcpy(&tempushort, vp, sizeof(unsigned short));
h5dump_str_append(str, OPT(info->fmt_ushort, "%u"),
tempushort);
} else if (H5Tequal(type, H5T_NATIVE_LONG)) {
memcpy(&templong, vp, sizeof(long));
h5dump_str_append(str, OPT(info->fmt_long, "%ld"),
templong);
} else if (H5Tequal(type, H5T_NATIVE_ULONG)) {
memcpy(&tempulong, vp, sizeof(unsigned long));
h5dump_str_append(str, OPT(info->fmt_ulong, "%lu"),
tempulong);
} else if (H5Tequal(type, H5T_NATIVE_LLONG)) {
memcpy(&templlong, vp, sizeof(long_long));
h5dump_str_append(str, OPT(info->fmt_llong, fmt_llong),
templlong);
} else if (H5Tequal(type, H5T_NATIVE_ULLONG)) {
memcpy(&tempullong, vp, sizeof(unsigned long_long));
h5dump_str_append(str, OPT(info->fmt_ullong, fmt_ullong),
tempullong);
} else if (H5Tequal(type, H5T_NATIVE_HSSIZE)) {
if (sizeof(hssize_t)==sizeof(int)) {
memcpy(&tempint, vp, sizeof(int));
h5dump_str_append(str, OPT(info->fmt_int, "%d"),
tempint);
} else if (sizeof(hssize_t)==sizeof(long)) {
memcpy(&templong, vp, sizeof(long));
h5dump_str_append(str, OPT(info->fmt_long, "%ld"),
templong);
} else {
memcpy(&templlong, vp, sizeof(long_long));
h5dump_str_append(str, OPT(info->fmt_llong, fmt_llong),
templlong);
}
} else if (H5Tequal(type, H5T_NATIVE_HSIZE)) {
if (sizeof(hsize_t)==sizeof(int)) {
memcpy(&tempuint, vp, sizeof(unsigned int));
h5dump_str_append(str, OPT(info->fmt_uint, "%u"),
tempuint);
} else if (sizeof(hsize_t)==sizeof(long)) {
memcpy(&tempulong, vp, sizeof(long));
h5dump_str_append(str, OPT(info->fmt_ulong, "%lu"),
tempulong);
} else {
memcpy(&tempullong, vp, sizeof(unsigned long_long));
h5dump_str_append(str, OPT(info->fmt_ullong, fmt_ullong),
tempullong);
}
} else if (H5T_COMPOUND==H5Tget_class(type)) {
nmembs = H5Tget_nmembers(type);
h5dump_str_append(str, "%s", OPT(info->cmpd_pre, "{"));
for (j=0; j<nmembs; j++) {
if (j) h5dump_str_append(str, "%s",
OPT(info->cmpd_sep,
", " OPTIONAL_LINE_BREAK));
/*put code to indent compound type elemnts here*/
if (ctx->indent_level >= 0) {
h5dump_str_append(str, "%s", OPT(info->line_pre, ""));
}
for (x=0; x < ctx->indent_level + 1; x++){
h5dump_str_append(str,"%s",OPT(info->line_indent,""));
}
/* The name */
name = H5Tget_member_name(type, j);
h5dump_str_append(str, OPT(info->cmpd_name, ""), name);
free(name);
/* The value */
offset = H5Tget_member_offset(type, j);
memb = H5Tget_member_type(type, j);
size = H5Tget_size(memb);
ndims = H5Tget_member_dims(type, j, dims, NULL);
assert(ndims>=0 && ndims<=H5S_MAX_RANK);
for (k=0, nelmts=1; k<ndims; k++) nelmts *= dims[k];
if (nelmts>1) {
h5dump_str_append(str, "%s", OPT(info->arr_pre, "["));
}
for (i=0; i<nelmts; i++) {
if (i) {
h5dump_str_append(str, "%s",
OPT(info->arr_sep,
"," OPTIONAL_LINE_BREAK));
}
if (ndims>0 && info->arr_linebreak &&
i && 0==i%dims[ndims-1]) {
h5dump_str_append(str, "%s", "\n");
/*need to indent some more here*/
if (ctx->indent_level >= 0) {
h5dump_str_append(str, "%s", OPT(info->line_pre, ""));
}
for (x=0; x < ctx->indent_level+1; x++){
h5dump_str_append(str,"%s",OPT(info->line_indent,""));
}
}
ctx->indent_level++;
h5dump_sprint(str, info, container, memb,
(char*)vp+offset+i*size, ctx);
ctx->indent_level--;
}
if (nelmts>1) {
h5dump_str_append(str, "%s", OPT(info->arr_suf, "]"));
}
H5Tclose(memb);
}
h5dump_str_append(str, "%s", OPT(info->cmpd_end, ""));
/*put code to indent compound type elemnts here*/
if (ctx->indent_level >= 0) {
h5dump_str_append(str, "%s", OPT(info->line_pre, ""));
}
for (x=0; x < ctx->indent_level; x++){
h5dump_str_append(str,"%s",OPT(info->line_indent,""));
}
h5dump_str_append(str, "%s", OPT(info->cmpd_suf, "}"));
} else if (H5T_ENUM==H5Tget_class(type)) {
char enum_name[1024];
if (H5Tenum_nameof(type, vp, enum_name, sizeof enum_name)>=0) {
h5dump_str_append(str, h5dump_escape(enum_name, sizeof enum_name,
TRUE));
} else {
h5dump_str_append(str, "0x");
n = H5Tget_size(type);
for (i=0; i<n; i++) {
h5dump_str_append(str, "%02x", ((unsigned char*)vp)[i]);
}
}
} else if (H5Tequal(type, H5T_STD_REF_DSETREG)) {
/*
* Dataset region reference -- show the type and OID of the referenced
* object, but we are unable to show the region yet because there
* isn't enough support in the data space layer. - rpm 19990604
*/
if (h5dump_is_zero(vp, H5Tget_size(type))) {
h5dump_str_append(str, "NULL");
} else {
obj = H5Rdereference(container, H5R_DATASET_REGION, vp);
region = H5Rget_region(container, H5R_DATASET_REGION, vp);
H5Gget_objinfo(obj, ".", FALSE, &sb);
if (info->dset_hidefileno){
h5dump_str_append(str, info->dset_format,
sb.objno[1], sb.objno[0]);
} else {
h5dump_str_append(str, info->dset_format,
sb.fileno[1], sb.fileno[0],
sb.objno[1], sb.objno[0]);
}
h5dump_region(region, str, info);
H5Sclose(region);
H5Dclose(obj);
}
} else if (H5Tequal(type, H5T_STD_REF_OBJ)) {
/*
* Object references -- show the type and OID of the referenced
* object.
*/
if (h5dump_is_zero(vp, H5Tget_size(type))) {
h5dump_str_append(str, "NULL");
} else {
otype = H5Rget_object_type(container, vp);
obj = H5Rdereference(container, H5R_OBJECT, vp);
H5Gget_objinfo(obj, ".", FALSE, &sb);
/* Print object type and close object */
switch (otype) {
case H5G_GROUP:
h5dump_str_append(str, GROUPNAME);
H5Gclose(obj);
break;
case H5G_DATASET:
h5dump_str_append(str, DATASET);
H5Dclose(obj);
break;
case H5G_TYPE:
h5dump_str_append(str, DATATYPE);
H5Tclose(obj);
break;
default:
h5dump_str_append(str, "%u-", otype);
break;
}
/* Print OID */
if (info->obj_hidefileno){
h5dump_str_append(str, info->obj_format,
sb.objno[1], sb.objno[0]);
} else {
h5dump_str_append(str, info->obj_format,
sb.fileno[1], sb.fileno[0],
sb.objno[1], sb.objno[0]);
}
}
} else {
/* All other types get printed as hexadecimal */
h5dump_str_append(str, "0x");
n = H5Tget_size(type);
for (i=0; i<n; i++) {
h5dump_str_append(str, "%02x", ((unsigned char*)vp)[i]);
}
}
return h5dump_str_fmt(str, start, OPT(info->elmt_fmt, "%s"));
}
/*-------------------------------------------------------------------------
* Function: h5dump_ncols
*
* Purpose: Count the number of columns in a string. This is the number
* of characters in the string not counting line-control
* characters.
*
* Return: Success: Width of string.
*
* Failure: 0
*
* Programmer: Robb Matzke
* Tuesday, April 27, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
h5dump_ncols(const char *s)
{
size_t i;
for (i=0; *s; s++) if (*s>=' ') i++;
return i;
}
/*-------------------------------------------------------------------------
* Function: h5dump_simple_prefix
*
* Purpose: If ctx->need_prefix is set then terminate the current line
* (if applicable), calculate the prefix string, and display it
* at the start of a line.
*
* Return: void
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
* Robb Matzke, 1999-09-29
* If a new prefix is printed then the current element number is
* set back to zero.
*-------------------------------------------------------------------------
*/
static void
h5dump_simple_prefix(FILE *stream, const h5dump_t *info,
h5dump_context_t *ctx, hsize_t elmtno, int secnum)
{
h5dump_str_t prefix;
size_t templength = 0;
int i, indentlevel = 0;
memset(&prefix, 0, sizeof(h5dump_str_t));
if (!ctx->need_prefix) return;
/* Terminate previous line, if any */
if (ctx->cur_column) {
fputs(OPT(info->line_suf, ""), stream);
#if 0 /*why?*/
if (info->line_ncols != ctx->cur_column) {
putc('\n', stream);
}
#endif
putc('\n',stream);
fputs(OPT(info->line_sep, ""), stream);
}
/* Calculate new prefix */
h5dump_prefix(&prefix, info, elmtno, ctx->ndims,
ctx->p_min_idx, ctx->p_max_idx);
/* Write new prefix to output */
if (ctx->indent_level >= 0) {
indentlevel = ctx->indent_level;
} else {
/* this is because sometimes we dont print out all the header
* info for the data(like the tattr-2.ddl example. if that happens
* the ctx->indent_level a negative so we need to skip the above
* and just print out the default indent levels. */
indentlevel = ctx->default_indent_level;
}
if (0==elmtno && 0==secnum && info->line_1st) {
fputs(h5dump_str_fmt(&prefix, 0, info->line_1st), stream);
} else if (secnum && info->line_cont) {
fputs(h5dump_str_fmt(&prefix, 0, info->line_cont),
stream);
} else {
fputs(h5dump_str_fmt(&prefix, 0, info->line_pre), stream);
}
templength = h5dump_str_len(&prefix);
for (i = 0; i < indentlevel; i++){
fputs(h5dump_str_fmt(&prefix, 0, info->line_indent), stream);
templength += h5dump_str_len(&prefix);
}
ctx->cur_column = ctx->prev_prefix_len = templength;
ctx->cur_elmt = 0;
ctx->need_prefix = 0;
/* Free string */
h5dump_str_close(&prefix);
}
/*-------------------------------------------------------------------------
* Function: h5dump_simple_data
*
* Purpose: Prints some (NELMTS) data elements to output STREAM. The
* elements are stored in _MEM as type TYPE and are printed
* according to the format described in INFO. The CTX struct
* contains context information shared between calls to this
* function. The FLAGS is a bit field that indicates whether
* the data supplied in this call falls at the beginning or end
* of the total data to be printed (START_OF_DATA and
* END_OF_DATA).
*
* Return: void
*
* Programmer: Robb Matzke
* Monday, April 26, 1999
*
* Modifications:
* Robb Matzke, 1999-06-04
* The `container' argument is the optional dataset for
* reference types.
*
* Robb Matzke, 1999-09-29
* Understands the `per_line' property which indicates that
* every Nth element should begin a new line.
*
*-------------------------------------------------------------------------
*/
static void
h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
h5dump_context_t *ctx/*in,out*/, unsigned flags,
hsize_t nelmts, hid_t type, void *_mem)
{
unsigned char *mem = (unsigned char*)_mem;
hsize_t i; /*element counter */
char *s, *section; /*a section of output */
int secnum; /*section sequence number */
size_t size; /*size of each datum */
size_t ncols=80; /*available output width */
h5dump_str_t buffer; /*string into which to render */
int multiline; /*datum was multiline */
int elmt_counter=0; /*counts the # elements printed.
* I (ptl?) needed something that
* isnt going to get reset when a new
* line is formed. I'm going to use
* this var to count elements and
* break after we see a number equal
* to the ctx->size_last_dim. */
/* Setup */
memset(&buffer, 0, sizeof(h5dump_str_t));
size = H5Tget_size(type);
if (info->line_ncols>0) ncols = info->line_ncols;
h5dump_simple_prefix(stream, info, ctx, 0, 0);
for (i=0; i<nelmts; i++, ctx->cur_elmt++, elmt_counter++){
/* Render the element */
h5dump_str_reset(&buffer);
h5dump_sprint(&buffer, info, container, type, mem+i*size, ctx);
if (i+1<nelmts || 0==(flags & END_OF_DATA)) {
h5dump_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));
}
s = h5dump_str_fmt(&buffer, 0, "%s");
/*
* If the element would split on multiple lines if printed at our
* current location...
*/
if (1==info->line_multi_new &&
(ctx->cur_column + h5dump_ncols(s) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) > ncols) {
if (ctx->prev_multiline) {
/*
* ... and the previous element also occupied more than one
* line, then start this element at the beginning of a line.
*/
ctx->need_prefix = TRUE;
} else if ((ctx->prev_prefix_len + h5dump_ncols(s) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) <= ncols) {
/*
* ...but *could* fit on one line otherwise, then we
* should end the current line and start this element on its
* own line.
*/
ctx->need_prefix = TRUE;
}
}
/* we need to break after each row of a dimension---> we should
* break at the end of the each last dimension well that is the
* way the dumper did it before */
if (info->arr_linebreak && ctx->cur_elmt){
if ((ctx->cur_elmt%ctx->size_last_dim) == 0){
ctx->need_prefix = TRUE;
}
if (elmt_counter==ctx->size_last_dim){
ctx->need_prefix = TRUE;
elmt_counter = 0;
}
}
/*
* If the previous element occupied multiple lines and this element
* is too long to fit on a line then start this element at the
* beginning of the line.
*/
if (1==info->line_multi_new &&
ctx->prev_multiline &&
(ctx->cur_column + h5dump_ncols(s) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) > ncols) {
ctx->need_prefix = TRUE;
}
/*
* If too many elements have already been printed then we need to
* start a new line.
*/
if (info->line_per_line>0 && ctx->cur_elmt>=info->line_per_line) {
ctx->need_prefix = TRUE;
}
/*
* Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause
* the data to split across multiple lines. We display the sections
* one-at a time.
*/
for (secnum=0, multiline=0;
(section=strtok(secnum?NULL:s, OPTIONAL_LINE_BREAK));
secnum++) {
/*
* If the current section plus possible suffix and end-of-line
* information would cause the output to wrap then we need to
* start a new line.
*/
/* added the info->skip_first because the dumper does not want
* this check to happen for the first line */
if ((!info->skip_first || i) &&
(ctx->cur_column + strlen(section) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) > ncols) {
ctx->need_prefix = 1;
}
/*
* Print the prefix or separate the beginning of this element
* from the previous element.
*/
if (ctx->need_prefix) {
if (secnum) multiline++;
h5dump_simple_prefix(stream, info, ctx, i, secnum);
} else if ((i || ctx->continuation) && 0==secnum) {
fputs(OPT(info->elmt_suf2, " "), stream);
ctx->cur_column += strlen(OPT(info->elmt_suf2, " "));
}
/* Print the section */
fputs(section, stream);
ctx->cur_column += strlen(section);
}
ctx->prev_multiline = multiline;
}
h5dump_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Function: h5dump_simple_dset
*
* Purpose: Print some values from a dataset with a simple data space.
* This is a special case of h5dump_dset(). This function only
* intended for dumping datasets -- it does strip mining and
* some other things which are unnecessary for smaller objects
* such as attributes (to print small objects like attributes
* simply read the attribute and call h5dump_simple_mem()).
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
hid_t p_type, int indentlevel)
{
hid_t f_space; /*file data space */
hsize_t elmtno, i; /*counters */
int carry; /*counter carry value */
hssize_t zero[8]; /*vector of zeros */
unsigned flags; /*buffer extent flags */
hsize_t total_size[H5S_MAX_RANK];/*total size of dataset*/
/* Print info */
h5dump_context_t ctx; /*print context */
size_t p_type_nbytes; /*size of memory type */
hsize_t p_nelmts; /*total selected elmts */
/* Stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
hsize_t sm_nelmts; /*elements per stripmine*/
unsigned char *sm_buf=NULL; /*buffer for raw data */
hid_t sm_space; /*stripmine data space */
/* Hyperslab info */
hssize_t hs_offset[H5S_MAX_RANK];/*starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
hsize_t hs_nelmts; /*elements in request */
#if 0
hsize_t dim_n_size;
#endif
/*
* Check that everything looks okay. The dimensionality must not be too
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
memset(&ctx, 0, sizeof ctx);
ctx.indent_level = indentlevel;
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
f_space = H5Dget_space(dset);
ctx.ndims = H5Sget_simple_extent_ndims(f_space);
if ((size_t)(ctx.ndims)>NELMTS(sm_size)) return -1;
/* Assume entire data space to be printed */
for (i=0; i<(hsize_t)(ctx.ndims); i++) ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(f_space, total_size, NULL);
for (i=0, p_nelmts=1; i<(hsize_t)(ctx.ndims); i++) {
p_nelmts *= total_size[i];
}
if (0==p_nelmts) return 0; /*nothing to print*/
ctx.size_last_dim = total_size[ctx.ndims-1];
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
p_type_nbytes = H5Tget_size(p_type);
for (i=ctx.ndims, sm_nbytes=p_type_nbytes; i>0; --i) {
sm_size[i-1] = MIN (total_size[i-1], H5DUMP_BUFSIZE/sm_nbytes);
sm_nbytes *= sm_size[i-1];
assert(sm_nbytes>0);
}
sm_buf = malloc(sm_nbytes);
sm_nelmts = sm_nbytes/p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
/* The stripmine loop */
memset(hs_offset, 0, sizeof hs_offset);
memset(zero, 0, sizeof zero);
for (elmtno=0; elmtno<p_nelmts; elmtno+=hs_nelmts) {
/* Calculate the hyperslab size */
if (ctx.ndims>0) {
for (i=0, hs_nelmts=1; i<(hsize_t)(ctx.ndims); i++) {
hs_size[i] = MIN(total_size[i]-hs_offset[i], sm_size[i]);
ctx.p_max_idx[i] = ctx.p_min_idx[i] + hs_size[i];
hs_nelmts *= hs_size[i];
}
H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL,
hs_size, NULL);
H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL,
&hs_nelmts, NULL);
#if 0
dim_n_size = total_size[ctx.ndims-1];
#endif
} else {
H5Sselect_all(f_space);
H5Sselect_all(sm_space);
hs_nelmts = 1;
#if 0
dim_n_size = 1;
#endif
}
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf)<0) {
return -1;
}
/* Print the data */
flags = ((0==elmtno ? START_OF_DATA : 0) |
(elmtno+hs_nelmts>=p_nelmts ? END_OF_DATA : 0));
h5dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts,
p_type, sm_buf);
/* Calculate the next hyperslab offset */
for (i=ctx.ndims, carry=1; i>0 && carry; --i) {
ctx.p_min_idx[i-1] = ctx.p_max_idx[i-1];
hs_offset[i-1] += hs_size[i-1];
if (hs_offset[i-1]==(hssize_t)(total_size[i-1])) {
hs_offset[i-1] = 0;
} else {
carry = 0;
}
}
ctx.continuation++;
}
/* Terminate the output */
if (ctx.cur_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
}
H5Sclose(sm_space);
H5Sclose(f_space);
if (sm_buf) free(sm_buf);
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5dump_simple_mem
*
* Purpose: Print some values from memory with a simple data space.
* This is a special case of h5dump_mem().
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
h5dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t type,
hid_t space, void *mem, int indentlevel)
{
hsize_t i; /*counters */
hsize_t nelmts; /*total selected elmts */
h5dump_context_t ctx; /*printing context */
/*
* Check that everything looks okay. The dimensionality must not be too
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
memset(&ctx, 0, sizeof ctx);
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
ctx.ndims = H5Sget_simple_extent_ndims(space);
if ((size_t)(ctx.ndims)>NELMTS(ctx.p_min_idx)) return -1;
/* Assume entire data space to be printed */
for (i=0; i<(hsize_t)(ctx.ndims); i++) ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(space, ctx.p_max_idx, NULL);
for (i=0, nelmts=1; (ctx.ndims != 0) && (i<(hsize_t)(ctx.ndims)); i++) {
nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i];
}
if (0==nelmts) return 0; /*nothing to print*/
ctx.size_last_dim = ctx.p_max_idx[ctx.ndims-1];
ctx.indent_level = indentlevel;
/* Print it */
h5dump_simple_data(stream, info, -1/*no dataset*/, &ctx,
START_OF_DATA|END_OF_DATA, nelmts, type, mem);
/* Terminate the output */
if (ctx.cur_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
}
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5dump_fixtype
*
* Purpose: Given a file data type choose a memory data type which is
* appropriate for printing the data.
*
* Return: Success: Memory data type
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
* Robb Matzke, 1999-06-04
* Added support for references.
*
*-------------------------------------------------------------------------
*/
hid_t
h5dump_fixtype(hid_t f_type)
{
hid_t m_type = FAIL, f_memb;
hid_t *memb = NULL;
char **name = NULL;
int nmembs = 0, i, j, *ndims = NULL;
size_t size, offset, *dims = NULL, nelmts;
/* H5T_str_t strpad; */
size = H5Tget_size(f_type);
switch (H5Tget_class(f_type)) {
case H5T_INTEGER:
/*
* Use the smallest native integer type of the same sign as the file
* such that the memory type is at least as large as the file type.
* If there is no memory type large enough then use the largest
* memory type available.
*/
if (size <= sizeof(char)) {
m_type = H5Tcopy(H5T_NATIVE_SCHAR);
} else if (size <= sizeof(short)) {
m_type = H5Tcopy(H5T_NATIVE_SHORT);
} else if (size <= sizeof(int)) {
m_type = H5Tcopy(H5T_NATIVE_INT);
} else if (size <= sizeof(long)) {
m_type = H5Tcopy(H5T_NATIVE_LONG);
} else {
m_type = H5Tcopy(H5T_NATIVE_LLONG);
}
H5Tset_sign(m_type, H5Tget_sign(f_type));
break;
case H5T_FLOAT:
/*
* Use the smallest native floating point type available such that
* its size is at least as large as the file type. If there is not
* native type large enough then use the largest native type.
*/
if (size <= sizeof(float)) {
m_type = H5Tcopy(H5T_NATIVE_FLOAT);
} else if (size <= sizeof(double)) {
m_type = H5Tcopy(H5T_NATIVE_DOUBLE);
} else {
m_type = H5Tcopy(H5T_NATIVE_LDOUBLE);
}
break;
case H5T_STRING:
/*
* This is needed because the function in dumputil.c is the case where
* strDUAction == TRUE. if it is false we will do the original action
* here.
*/
m_type = H5Tcopy(f_type);
H5Tset_cset(m_type, H5T_CSET_ASCII);
break;
case H5T_COMPOUND:
/*
* We have to do this in two steps. The first step scans the file
* type and converts the members to native types and remembers all
* their names and sizes, computing the size of the memory compound
* type at the same time. Then we create the memory compound type
* and add the members.
*/
nmembs = H5Tget_nmembers(f_type);
memb = calloc(nmembs, sizeof(hid_t));
name = calloc(nmembs, sizeof(char *));
ndims = calloc(nmembs, sizeof(int));
dims = calloc(nmembs*4, sizeof(size_t));
for (i = 0, size = 0; i < nmembs; i++) {
/* Get the member type and fix it */
f_memb = H5Tget_member_type(f_type, i);
memb[i] = h5dump_fixtype(f_memb);
H5Tclose(f_memb);
if (memb[i] < 0)
goto done;
/* Get the member dimensions */
ndims[i] = H5Tget_member_dims(f_type, i, dims + i * 4, NULL);
assert(ndims[i] >= 0 && ndims[i] <= 4);
for (j = 0, nelmts = 1; j < ndims[i]; j++)
nelmts *= dims[i * 4 + j];
/* Get the member name */
name[i] = H5Tget_member_name(f_type, i);
if (NULL == name[i])
goto done;
/*
* Compute the new offset so each member is aligned on a byte
* boundary which is the same as the member size.
*/
size = ALIGN(size, H5Tget_size(memb[i])) +
nelmts * H5Tget_size(memb[i]);
}
m_type = H5Tcreate(H5T_COMPOUND, size);
for (i = 0, offset = 0; i < nmembs; i++) {
if (offset)
offset = ALIGN(offset, H5Tget_size(memb[i]));
H5Tinsert_array(m_type, name[i], offset, ndims[i], dims + i * 4,
NULL, memb[i]);
for (j = 0, nelmts = 1; j < ndims[i]; j++)
nelmts *= dims[i * 4 + j];
offset += nelmts * H5Tget_size(memb[i]);
}
break;
case H5T_ENUM:
case H5T_REFERENCE:
case H5T_OPAQUE:
/* Same as file type */
m_type = H5Tcopy(f_type);
break;
case H5T_BITFIELD:
/*
* Same as the file except the offset is set to zero and the byte
* order is set to little endian.
*/
m_type = H5Tcopy(f_type);
H5Tset_offset(m_type, 0);
H5Tset_order(m_type, H5T_ORDER_LE);
break;
case H5T_TIME:
/*
* These type classes are not implemented yet.
*/
break;
default:
/* What the heck? */
break;
}
done:
/* Clean up temp buffers */
if (memb && name && ndims && dims) {
for (i=0; i<nmembs; i++) {
if (memb[i]>=0) H5Tclose(memb[i]);
if (name[i]) free(name[i]);
}
free(memb);
free(name);
free(ndims);
free(dims);
}
return m_type;
}
/*-------------------------------------------------------------------------
* Function: h5dump_dset
*
* Purpose: Print some values from a dataset DSET to the file STREAM
* after converting all types to P_TYPE (which should be a
* native type). If P_TYPE is a negative value then it will be
* computed from the dataset type using only native types.
*
* Note: This function is intended only for datasets since it does
* some things like strip mining which are unnecessary for
* smaller objects such as attributes. The easiest way to print
* small objects is to read the object into memory and call
* h5dump_mem().
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
* Robb Matzke, 1999-06-07
* If info->raw is set then the memory datatype will be the same
* as the file datatype.
*
*-------------------------------------------------------------------------
*/
int
h5dump_dset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t _p_type,
int indentlevel)
{
hid_t f_space;
hid_t p_type = _p_type;
hid_t f_type;
int status;
h5dump_t info_dflt;
/* Use default values */
if (!stream) stream = stdout;
if (!info) {
memset(&info_dflt, 0, sizeof info_dflt);
info = &info_dflt;
}
if (p_type<0) {
f_type = H5Dget_type(dset);
if (info->raw) {
p_type = H5Tcopy(f_type);
} else {
p_type = h5dump_fixtype(f_type);
}
H5Tclose(f_type);
if (p_type<0) return -1;
}
/* Check the data space */
f_space = H5Dget_space(dset);
if (H5Sis_simple(f_space)<=0) return -1;
H5Sclose(f_space);
/* Print the data */
/* a kludge because linux gcc does not accept the initialization with sdtout */
if (!rawdatastream)
rawdatastream=stdout;
status = h5dump_simple_dset(rawdatastream, info, dset, p_type, indentlevel);
if (p_type!=_p_type) H5Tclose(p_type);
return status;
}
/*-------------------------------------------------------------------------
* Function: h5dump_mem
*
* Purpose: Displays the data contained in MEM. MEM must have the
* specified data TYPE and SPACE. Currently only simple data
* spaces are allowed and only the `all' selection.
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Robb Matzke
* Wednesday, January 20, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
h5dump_mem(FILE *stream, const h5dump_t *info, hid_t type, hid_t space,
void *mem,int indentlevel)
{
h5dump_t info_dflt;
/* Use default values */
if (!stream) stream = stdout;
if (!info) {
memset(&info_dflt, 0, sizeof info_dflt);
info = &info_dflt;
}
/* Check the data space */
if (H5Sis_simple(space)<=0) return -1;
return h5dump_simple_mem(stream, info, type, space, mem, indentlevel);
}
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*from h5dumputil.c*/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*************************************************************************/
/*-------------------------------------------------------------------------
* Function: indentation
*
* Purpose: Print spaces for indentation
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-----------------------------------------------------------------------*/
void indentation(int x) {
if(x < nCols) {
while (x>0) { printf(" "); x--; }
}
else {
printf("The indentation exceeds the number of cols. Exiting....\n");
exit(1);
}
}
/* Print the program name and the version information which is */
/* defined the same as the HDF5 library version. */
void
print_version(const char *program_name)
{
printf("%s: Version %u.%u.%u%s%s\n",
program_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE,
H5_VERS_SUBRELEASE[0]?"-":"", H5_VERS_SUBRELEASE);
}
/*
THE FUNCTIONS BELOW ARE FROM THE H5FINSHD.C FILE
*/
/*-------------------------------------------------------------------------
* Function: init_table
*
* Purpose: allocate and initialize tables for shared groups, datasets,
* and committed types
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-----------------------------------------------------------------------*/
void
init_table (table_t** temp)
{
int i;
table_t *table = malloc(sizeof(table_t));
table->size = 20;
table->nobjs = 0;
table->objs = (obj_t*) malloc(table->size*sizeof(obj_t));
for (i = 0; i < table->size; i++) {
table->objs[i].objno[0] = table->objs[i].objno[1] = 0;
table->objs[i].displayed = 0;
table->objs[i].recorded = 0;
table->objs[i].objflag = 0;
}
*temp = table;
}
/*-------------------------------------------------------------------------
* Function: init_prefix
*
* Purpose: allocate and initialize prefix
*
* Return: void
*
* Modifications:
*
*-----------------------------------------------------------------------*/
void
init_prefix(char **prefix, int prefix_len)
{
char *temp;
temp = (char *) malloc(prefix_len * sizeof (char));
*temp = '\0';
*prefix = temp;
}
/*-------------------------------------------------------------------------
* Function: free_table
*
* Purpose: free tables for shared groups, datasets,
* and committed types
*
* Return: void
*
* Programmer: Paul Harten
*
* Modifications:
*
*-----------------------------------------------------------------------*/
void
free_table (table_t **table)
{
table_t *temp = *table;
if (temp->objs != NULL) {
HDfree(temp->objs);
}
*table = temp;
}
/*-------------------------------------------------------------------------
* Function: search_obj
*
* Purpose: search the object specified by objno in the table
*
* Return: an integer, the location of the object
* -1 if object is not found
*
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-----------------------------------------------------------------------*/
int
search_obj (table_t *table, unsigned long *objno)
{
int i=0, found=0;
while (i < table->nobjs && !found)
if (table->objs[i].objno[0] == *(objno) &&
table->objs[i].objno[1] == *(objno+1) ) found = 1;
else i++;
if (!found) return -1;
else return i;
}
/*-------------------------------------------------------------------------
* Function: add_obj
*
* Purpose: add a shared object to the table
* realloc the table if necessary
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-----------------------------------------------------------------------*/
static void
add_obj (table_t *table, unsigned long *objno, char *objname)
{
int i;
if (table->nobjs == table->size) {
table->size *= 2;
table->objs = realloc (table->objs, table->size*sizeof(obj_t));
for (i = table->nobjs; i < table->size; i++) {
table->objs[i].objno[0] = table->objs[i].objno[1] = 0;
table->objs[i].displayed = 0;
table->objs[i].recorded = 0;
table->objs[i].objflag = 0;
}
}
i = table->nobjs++;
table->objs[i].objno[0] = *objno;
table->objs[i].objno[1] = *(objno+1);
strcpy (table->objs[i].objname, objname);
}
/*-------------------------------------------------------------------------
* Function: Find_objs
*
* Purpose: Find objects, committed types and store them in tables
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-----------------------------------------------------------------------*/
herr_t
find_objs(hid_t group, const char *name, void *op_data)
{
hid_t obj, type;
H5G_stat_t statbuf;
char *tmp;
int i;
find_objs_t *info = (find_objs_t*)op_data;
if (info->threshold > 1) {
/*will get an infinite loop if greater than 1*/
return(FAIL);
}
H5Gget_objinfo(group, name, TRUE, &statbuf);
tmp = (char *) malloc((strlen(info->prefix)+strlen(name)+2)*sizeof(char));
strcpy(tmp, info->prefix);
switch (statbuf.type) {
case H5G_GROUP:
if ((obj=H5Gopen (group, name))>=0) {
if (info->prefix_len<(int)(strlen(info->prefix)+strlen(name)+2)) {
info->prefix_len *= 2;
info->prefix = realloc(info->prefix,
info->prefix_len * sizeof(char));
}
strcat(strcat(info->prefix,"/"), name);
if (statbuf.nlink > info->threshold) {
if (search_obj (info->group_table, statbuf.objno) < 0) {
add_obj (info->group_table, statbuf.objno, info->prefix);
H5Giterate (obj, ".", NULL, find_objs, (void*)info);
}
} else
H5Giterate (obj, ".", NULL, find_objs, (void*)info);
strcpy(info->prefix, tmp);
H5Gclose (obj);
} else
info->status = 1;
break;
case H5G_DATASET:
strcat(tmp,"/");
strcat(tmp,name); /* absolute name of the data set */
if (statbuf.nlink > info->threshold &&
search_obj (info->dset_table, statbuf.objno) < 0)
add_obj (info->dset_table, statbuf.objno, tmp);
if ((obj=H5Dopen (group, name))>=0) {
type = H5Dget_type (obj);
if (H5Tcommitted(type) > 0 ) {
H5Gget_objinfo(type, ".", TRUE, &statbuf);
if (search_obj (info->type_table, statbuf.objno) < 0) {
add_obj (info->type_table, statbuf.objno, tmp) ;
info->type_table->objs[info->type_table->nobjs - 1].objflag = 0;
}
}
H5Tclose(type);
H5Dclose (obj);
} else
info->status = 1;
break;
case H5G_TYPE:
strcat(tmp,"/");
strcat(tmp,name); /* absolute name of the type */
i = search_obj (info->type_table, statbuf.objno);
if (i < 0) {
add_obj (info->type_table, statbuf.objno, tmp) ;
/* named data type */
info->type_table->objs[info->type_table->nobjs-1].recorded = 1;
/* named data type */
info->type_table->objs[info->type_table->nobjs-1].objflag = 1;
} else {
strcpy (info->type_table->objs[i].objname, tmp);
info->type_table->objs[i].recorded = 1;
/* named data type */
info->type_table->objs[info->type_table->nobjs-1].objflag = 1;
}
break;
default:
break;
}
free (tmp);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: dump_tables
*
* Purpose: display the contents of tables for debugging purposes
*
* Return: void
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-----------------------------------------------------------------------*/
void
dump_table(char* tablename, table_t *table)
{
int i;
printf("%s: # of entries = %d\n", tablename,table->nobjs);
for ( i = 0; i < table->nobjs; i++)
printf ("%lu %lu %s %d\n", table->objs[i].objno[0],
table->objs[i].objno[1],
table->objs[i].objname,
table->objs[i].objflag);
}
/*-------------------------------------------------------------------------
* Function: get_table_idx
*
* Purpose: Determine if objects are in a link loop
*
* Return: Success: table index of object detected to be in loop
*
* Failure: FAIL
*
* Programmer: Paul Harten
*
*-----------------------------------------------------------------------*/
int
get_table_idx(table_t *table, unsigned long *objno)
{
int idx = -1;
idx = search_obj(table, objno);
return idx;
}
/*-------------------------------------------------------------------------
* Function: Get table flag setting
*
* Purpose: Keep the structures and variables used private to
* this file.
*
* Return: Success: Boolean setting of the i'th element of the
* object table flag
*
* Failure: FAIL
*
* Programmer: Paul Harten
*
*-----------------------------------------------------------------------*/
int
get_tableflag(table_t *table, int idx)
{
return(table->objs[idx].objflag);
}
/*-------------------------------------------------------------------------
* Function: Set table flag setting
*
* Purpose: Keep the structures and variables used private to
* this file.
*
* Return: Success: Boolean setting of the i'th element of the
* object table flag
*
* Failure: FAIL
*
* Programmer: Paul Harten
*
*-----------------------------------------------------------------------*/
int
set_tableflag(table_t *table, int idx)
{
table->objs[idx].objflag = TRUE;
return(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: Get name of i'th object in table
*
* Purpose:
*
* Return: Success: strdup() of object name character string
*
* Failure: NULL
*
* Programmer: Paul Harten
*
*-----------------------------------------------------------------------*/
char *
get_objectname(table_t* table, int idx)
{
return(strdup(table->objs[idx].objname));
}
/*-------------------------------------------------------------------------
* Function: opens a file using the list of drivers
*
* Purpose: Attempts to open a file with various VFL drivers.
*
* Return: Success: a file id for the opened file. If
* DRIVERNAME is non-null then the first
* DRIVERNAME_SIZE-1 characters of the driver
* name are copied into the DRIVERNAME array
* and null terminated.
*
* Failure: -1. If DRIVERNAME is non-null then the
* first byte is set to the null terminator.
*
* Modifications:
* Robb Matzke, 2000-06-23
* We only have to initialize driver[] on the first call,
* thereby preventing memory leaks from repeated calls to
* H5Pcreate().
*
* Robb Matzke, 2000-06-23
* Added DRIVERNAME_SIZE arg to prevent overflows when
* writing to DRIVERNAME.
*
* Robb Matzke, 2000-06-23
* Added test to prevent coredump when the file could not be
* opened by any driver.
*
* Robb Matzke, 2000-06-23
* Changed name from H5ToolsFopen() so it jives better with
* the names we already have at the top of this source file.
*
* Thomas Radke, 2000-09-12
* Added Stream VFD to the driver[] array.
*-----------------------------------------------------------------------*/
hid_t
h5dump_fopen(const char *fname, char *drivername, size_t drivername_size)
{
static struct {
const char *name;
hid_t fapl;
} driver[16];
static int ndrivers = 0;
hid_t fid, fapl = H5P_DEFAULT;
int drivernum;
if (!ndrivers) {
/* Build a list of file access property lists which we should try
* when opening the file. Eventually we'd like some way for the
* user to augment/replace this list interactively. */
driver[ndrivers].name = "sec2";
driver[ndrivers].fapl = H5P_DEFAULT;
ndrivers++;
#if defined VERSION13
driver[ndrivers].name = "family";
driver[ndrivers].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_family(fapl, 0, H5P_DEFAULT);
ndrivers++;
driver[ndrivers].name = "split";
driver[ndrivers].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT);
ndrivers++;
driver[ndrivers].name = "multi";
driver[ndrivers].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_multi(fapl, NULL, NULL, NULL, NULL, TRUE);
ndrivers++;
#ifdef H5_HAVE_STREAM
driver[ndrivers].name = "stream";
driver[ndrivers].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_stream(fapl, NULL);
ndrivers++;
#endif
#endif
}
/* Try to open the file using each of the drivers */
for (drivernum=0; drivernum<ndrivers; drivernum++) {
H5E_BEGIN_TRY {
fid = H5Fopen(fname, H5F_ACC_RDONLY, driver[drivernum].fapl);
} H5E_END_TRY;
if (fid >= 0) break;
}
/* Save the driver name */
if (drivername && drivername_size){
if (fid>=0) {
strncpy(drivername, driver[drivernum].name, drivername_size);
drivername[drivername_size-1] = '\0';
} else {
drivername[0] = '\0'; /*no file opened*/
}
}
return (fid);
}
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