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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
 * access to either file, you may request a copy from help@hdfgroup.org.     *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*-------------------------------------------------------------------------
 *
 * Created:    H5system.c
 *      Aug 21 2006
 *      Quincey Koziol <koziol@hdfgroup.org>
 *
 * Purpose:    System call wrapper implementations.
 *
 *-------------------------------------------------------------------------
 */

/****************/
/* Module Setup */
/****************/


/***********/
/* Headers */
/***********/
#include "H5private.h"        /* Generic Functions            */
#include "H5Eprivate.h"        /* Error handling              */
#include "H5Fprivate.h"        /* File access                */
#include "H5MMprivate.h"    /* Memory management            */


/****************/
/* Local Macros */
/****************/


/******************/
/* Local Typedefs */
/******************/


/********************/
/* Package Typedefs */
/********************/


/********************/
/* Local Prototypes */
/********************/


/*********************/
/* Package Variables */
/*********************/


/*****************************/
/* Library Private Variables */
/*****************************/


/*******************/
/* Local Variables */
/*******************/

/* Track whether tzset routine was called */
static hbool_t H5_ntzset = FALSE;


/*-------------------------------------------------------------------------
 * Function:  HDfprintf
 *
 * Purpose:  Prints the optional arguments under the control of the format
 *    string FMT to the stream STREAM.  This function takes the
 *    same format as fprintf(3c) with a few added features:
 *
 *    The conversion modifier `H' refers to the size of an
 *    `hsize_t' or `hssize_t' type.  For instance, "0x%018Hx"
 *    prints an `hsize_t' value as a hex number right justified and
 *    zero filled in an 18-character field.
 *
 *    The conversion `a' refers to an `haddr_t' type.
 *
 * Return:  Success:  Number of characters printed
 *
 *    Failure:  -1
 *
 * Programmer:  Robb Matzke
 *              Thursday, April  9, 1998
 *
 * Modifications:
 *    Robb Matzke, 1999-07-27
 *    The `%a' format refers to an argument of `haddr_t' type
 *    instead of `haddr_t*' and the return value is correct.
 *-------------------------------------------------------------------------
 */
int
HDfprintf(FILE *stream, const char *fmt, ...)
{
    int    n=0, nout = 0;
    int    fwidth, prec;
    int    zerofill;
    int    leftjust;
    int    plussign;
    int    ldspace;
    int    prefix;
    char  modifier[8];
    int    conv;
    char  *rest, format_templ[128];
    int    len;
    const char  *s;
    va_list  ap;

    HDassert(stream);
    HDassert(fmt);

    va_start (ap, fmt);
    while (*fmt) {
        fwidth = prec = 0;
        zerofill = 0;
        leftjust = 0;
        plussign = 0;
        prefix = 0;
        ldspace = 0;
        modifier[0] = '\0';

        if ('%'==fmt[0] && '%'==fmt[1]) {
            HDputc ('%', stream);
            fmt += 2;
            nout++;
        } else if ('%'==fmt[0]) {
            s = fmt + 1;

            /* Flags */
            while(HDstrchr("-+ #", *s)) {
                switch(*s) {
                    case '-':
                        leftjust = 1;
                        break;

                    case '+':
                        plussign = 1;
                        break;

                    case ' ':
                        ldspace = 1;
                        break;

                    case '#':
                        prefix = 1;
                        break;

                    default:
                        HDassert(0 && "Unknown format flag");
                } /* end switch */ /*lint !e744 Switch statement doesn't _need_ default */
                s++;
            } /* end while */

            /* Field width */
            if(HDisdigit(*s)) {
                zerofill = ('0' == *s);
                fwidth = (int)HDstrtol (s, &rest, 10);
                s = rest;
            } /* end if */
            else if ('*'==*s) {
                fwidth = va_arg(ap, int);
                if(fwidth < 0) {
                    leftjust = 1;
                    fwidth = -fwidth;
                }
                s++;
            }

            /* Precision */
            if('.'==*s) {
                s++;
                if(HDisdigit(*s)) {
                    prec = (int)HDstrtol(s, &rest, 10);
                    s = rest;
                } else if('*'==*s) {
                    prec = va_arg(ap, int);
                    s++;
                }
                if(prec < 1)
                    prec = 1;
            }

            /* Extra type modifiers */
            if(HDstrchr("zZHhlqLI", *s)) {
                switch(*s) {
                    /*lint --e{506} Don't issue warnings about constant value booleans */
                    /*lint --e{774} Don't issue warnings boolean within 'if' always evaluates false/true */
                    case 'H':
                        if(sizeof(hsize_t) < sizeof(long))
                            modifier[0] = '\0';
                        else if(sizeof(hsize_t) == sizeof(long)) {
                            HDstrncpy(modifier, "l", sizeof(modifier));
                            modifier[sizeof(modifier) - 1] = '\0';
                        } /* end if */
                        else {
                            HDstrncpy(modifier, H5_PRINTF_LL_WIDTH, sizeof(modifier));
                            modifier[sizeof(modifier) - 1] = '\0';
                        } /* end else */
                        break;

                    case 'Z':
                    case 'z':
                        if(sizeof(size_t) < sizeof(long))
                            modifier[0] = '\0';
                        else if(sizeof(size_t) == sizeof(long)) {
                            HDstrncpy(modifier, "l", sizeof(modifier));
                            modifier[sizeof(modifier) - 1] = '\0';
                        } /* end if */
                        else {
                            HDstrncpy(modifier, H5_PRINTF_LL_WIDTH, sizeof(modifier));
                            modifier[sizeof(modifier) - 1] = '\0';
                        } /* end else */
                        break;

                    default:
                        /* Handle 'I64' modifier for Microsoft's "__int64" type */
                        if(*s=='I' && *(s+1)=='6' && *(s+2)=='4') {
                            modifier[0] = *s;
                            modifier[1] = *(s+1);
                            modifier[2] = *(s+2);
                            modifier[3] = '\0';
                            s += 2; /* Increment over 'I6', the '4' is taken care of below */
                        } /* end if */
                        else {
                            /* Handle 'll' for long long types */
                            if(*s=='l' && *(s+1)=='l') {
                                modifier[0] = *s;
                                modifier[1] = *s;
                                modifier[2] = '\0';
                                s++; /* Increment over first 'l', second is taken care of below */
                            } /* end if */
                            else {
                                modifier[0] = *s;
                                modifier[1] = '\0';
                            } /* end else */
                        } /* end else */
                        break;
                }
                s++;
            }

            /* Conversion */
            conv = *s++;

            /* Create the format template */
            len = 0;
            len += HDsnprintf(format_templ, (sizeof(format_templ) - (size_t)(len + 1)), "%%%s%s%s%s%s", (leftjust ? "-" : ""),
                    (plussign ? "+" : ""), (ldspace ? " " : ""),
                    (prefix ? "#" : ""), (zerofill ? "0" : ""));
            if(fwidth > 0)
                len += HDsnprintf(format_templ + len, (sizeof(format_templ) - (size_t)(len + 1)), "%d", fwidth);
            if(prec > 0)
                len += HDsnprintf(format_templ + len, (sizeof(format_templ) - (size_t)(len + 1)), ".%d", prec);
            if(*modifier)
                len += HDsnprintf(format_templ + len, (sizeof(format_templ) - (size_t)(len + 1)), "%s", modifier);
            HDsnprintf(format_templ + len, (sizeof(format_templ) - (size_t)(len + 1)), "%c", conv);

            /* Conversion */
            switch (conv) {
                case 'd':
                case 'i':
                    if(!HDstrcmp(modifier, "h")) {
                        short x = (short)va_arg(ap, int);
                        n = fprintf(stream, format_templ, x);
                    } else if(!*modifier) {
                        int x = va_arg(ap, int);
                        n = fprintf(stream, format_templ, x);
                    } else if(!HDstrcmp(modifier, "l")) {
                        long x = va_arg(ap, long);
                        n = fprintf(stream, format_templ, x);
                    } else {
                        int64_t x = va_arg(ap, int64_t);
                        n = fprintf(stream, format_templ, x);
                    }
                    break;

                case 'o':
                case 'u':
                case 'x':
                case 'X':
                    if(!HDstrcmp(modifier, "h")) {
                        unsigned short x = (unsigned short)va_arg(ap, unsigned int);
                        n = fprintf(stream, format_templ, x);
                    } else if(!*modifier) {
                        unsigned int x = va_arg(ap, unsigned int); /*lint !e732 Loss of sign not really occuring */
                        n = fprintf(stream, format_templ, x);
                    } else if(!HDstrcmp(modifier, "l")) {
                        unsigned long x = va_arg(ap, unsigned long); /*lint !e732 Loss of sign not really occuring */
                        n = fprintf(stream, format_templ, x);
                    } else {
                        uint64_t x = va_arg(ap, uint64_t); /*lint !e732 Loss of sign not really occuring */
                        n = fprintf(stream, format_templ, x);
                    }
                    break;

                case 'f':
                case 'e':
                case 'E':
                case 'g':
                case 'G':
                    if(!HDstrcmp(modifier, "h")) {
                        float x = (float)va_arg(ap, double);
                        n = fprintf(stream, format_templ, (double)x);
                    } else if(!*modifier || !HDstrcmp(modifier, "l")) {
                        double x = va_arg(ap, double);
                        n = fprintf(stream, format_templ, x);
                    } else {
                    /*
                    * Some compilers complain when `long double' and
                    * `double' are the same thing.
                    */
#if H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE
                        long double x = va_arg(ap, long double);
                        n = fprintf(stream, format_templ, x);
#else
                        double x = va_arg(ap, double);
                        n = fprintf(stream, format_templ, x);
#endif
                    }
                    break;

                case 'a':
                    {
                        haddr_t x = va_arg(ap, haddr_t); /*lint !e732 Loss of sign not really occuring */

                        if(H5F_addr_defined(x)) {
                            len = 0;
                            len += HDsnprintf(format_templ, (sizeof(format_templ) - (size_t)(len + 1)), "%%%s%s%s%s%s",
                                (leftjust ? "-" : ""), (plussign ? "+" : ""),
                                (ldspace ? " " : ""), (prefix ? "#" : ""),
                                (zerofill ? "0" : ""));
                            if(fwidth > 0)
                                len += HDsnprintf(format_templ + len, (sizeof(format_templ) - (size_t)(len + 1)), "%d", fwidth);

                            /*lint --e{506} Don't issue warnings about constant value booleans */
                            /*lint --e{774} Don't issue warnings boolean within 'if' always evaluates false/true */
                            if(sizeof(x) == H5_SIZEOF_INT) {
                                HDstrncat(format_templ, "u", (sizeof(format_templ) - (size_t)(len + 1)));
                                len++;
                            } /* end if */
                            else if(sizeof(x) == H5_SIZEOF_LONG) {
                                HDstrncat(format_templ, "lu", (sizeof(format_templ) - (size_t)(len + 1)));
                                len++;
                            } /* end if */
                            else if(sizeof(x) == H5_SIZEOF_LONG_LONG) {
                                HDstrncat(format_templ, H5_PRINTF_LL_WIDTH, (sizeof(format_templ) - (size_t)(len + 1)));
                                len += (int)sizeof(H5_PRINTF_LL_WIDTH);
                                HDstrncat(format_templ, "u", (sizeof(format_templ) - (size_t)(len + 1)));
                                len++;
                            }
                            n = fprintf(stream, format_templ, x);
                        } else {
                            len = 0;
                            HDstrncpy(format_templ, "%", (sizeof(format_templ) - (size_t)(len + 1)));
                            len++;
                            if(leftjust) {
                                HDstrncat(format_templ, "-", (sizeof(format_templ) - (size_t)(len + 1)));
                                len++;
                            } /* end if */
                            if(fwidth)
                                len += HDsnprintf(format_templ + len, (sizeof(format_templ) - (size_t)(len + 1)),  "%d", fwidth);
                            HDstrncat(format_templ, "s", (sizeof(format_templ) - (size_t)(len + 1)));
                            fprintf(stream, format_templ, "UNDEF");
                        }
                    }
                    break;

                case 'c':
                    {
                        char x = (char)va_arg(ap, int);
                        n = fprintf(stream, format_templ, x);
                    }
                    break;

                case 's':
                case 'p':
                    {
                        char *x = va_arg(ap, char*); /*lint !e64 Type mismatch not really occuring */
                        n = fprintf(stream, format_templ, x);
                    }
                    break;

                case 'n':
                    format_templ[HDstrlen(format_templ) - 1] = 'u';
                    n = fprintf(stream, format_templ, nout);
                    break;

                case 't':
                    {
                        htri_t tri_var = va_arg(ap, htri_t);

                        if(tri_var > 0)
                            fprintf(stream, "TRUE");
                        else if(!tri_var)
                            fprintf(stream, "FALSE");
                        else
                            fprintf(stream, "FAIL(%d)", (int)tri_var);
                    }
                    break;

                default:
                    HDfputs(format_templ, stream);
                    n = (int)HDstrlen(format_templ);
                    break;
            }
            nout += n;
            fmt = s;
        } else {
            HDputc(*fmt, stream);
            fmt++;
            nout++;
        }
    }
    va_end(ap);
    return nout;
} /* end HDfprintf() */


/*-------------------------------------------------------------------------
 * Function:  HDstrtoll
 *
 * Purpose:  Converts the string S to an int64_t value according to the
 *    given BASE, which must be between 2 and 36 inclusive, or be
 *    the special value zero.
 *
 *    The string must begin with an arbitrary amount of white space
 *    (as determined by isspace(3c)) followed by a single optional
 *              `+' or `-' sign.  If BASE is zero or 16 the string may then
 *    include a `0x' or `0X' prefix, and the number will be read in
 *    base 16; otherwise a zero BASE is taken as 10 (decimal)
 *    unless the next character is a `0', in which case it is taken
 *    as 8 (octal).
 *
 *    The remainder of the string is converted to an int64_t in the
 *    obvious manner, stopping at the first character which is not
 *    a valid digit in the given base.  (In bases above 10, the
 *    letter `A' in either upper or lower case represetns 10, `B'
 *    represents 11, and so forth, with `Z' representing 35.)
 *
 *    If REST is not null, the address of the first invalid
 *    character in S is stored in *REST.  If there were no digits
 *    at all, the original value of S is stored in *REST.  Thus, if
 *    *S is not `\0' but **REST is `\0' on return the entire string
 *    was valid.
 *
 * Return:  Success:  The result.
 *
 *    Failure:  If the input string does not contain any
 *        digits then zero is returned and REST points
 *        to the original value of S.  If an overflow
 *        or underflow occurs then the maximum or
 *        minimum possible value is returned and the
 *        global `errno' is set to ERANGE.  If BASE is
 *        incorrect then zero is returned.
 *
 * Programmer:  Robb Matzke
 *              Thursday, April  9, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
#ifndef HDstrtoll
int64_t
HDstrtoll(const char *s, const char **rest, int base)
{
    int64_t  sign=1, acc=0;
    hbool_t  overflow = FALSE;

    errno = 0;
    if (!s || (base && (base<2 || base>36))) {
        if (rest)
            *rest = s;
        return 0;
    }

    /* Skip white space */
    while (HDisspace (*s)) s++;

    /* Optional minus or plus sign */
    if ('+'==*s) {
        s++;
    } else if ('-'==*s) {
        sign = -1;
        s++;
    }

    /* Zero base prefix */
    if (0==base && '0'==*s && ('x'==s[1] || 'X'==s[1])) {
        base = 16;
        s += 2;
    } else if (0==base && '0'==*s) {
        base = 8;
        s++;
    } else if (0==base) {
        base = 10;
    }

    /* Digits */
    while ((base<=10 && *s>='0' && *s<'0'+base) ||
     (base>10 && ((*s>='0' && *s<='9') ||
      (*s>='a' && *s<'a'+base-10) ||
      (*s>='A' && *s<'A'+base-10)))) {
        if (!overflow) {
            int64_t digit = 0;

            if (*s>='0' && *s<='9')
                digit = *s - '0';
            else if (*s>='a' && *s<='z')
                digit = (*s-'a')+10;
            else
                digit = (*s-'A')+10;

            if (acc*base+digit < acc) {
                overflow = TRUE;
            } else {
                acc = acc*base + digit;
            }
        }
        s++;
    }

    /* Overflow */
    if (overflow) {
        if (sign>0) {
            acc = ((uint64_t)1<<(8*sizeof(int64_t)-1))-1;
        } else {
            acc = (int64_t)((uint64_t)1<<(8*sizeof(int64_t)-1));
        }
        errno = ERANGE;
    }

    /* Return values */
    acc *= sign;
    if (rest)
        *rest = s;
    return acc;
} /* end HDstrtoll() */
#endif

/*-------------------------------------------------------------------------
 * Function:  HDrand/HDsrand
 *
 * Purpose:  Wrapper function for rand.  If rand_r exists on this system,
 *     use it.
 *
 *     Wrapper function for srand.  If rand_r is available, it will keep
 *     track of the seed locally instead of using srand() which modifies
 *     global state and can break other programs.
 *
 * Return:  Success:  Random number from 0 to RAND_MAX
 *
 *    Failure:  Cannot fail.
 *
 * Programmer:  Leon Arber
 *              March 6, 2006.
 *
 *-------------------------------------------------------------------------
 */
#ifdef H5_HAVE_RAND_R

static unsigned int g_seed = 42;

int HDrand(void)
{
    return rand_r(&g_seed);
}

void HDsrand(unsigned int seed)
{
    g_seed = seed;
}
#endif /* H5_HAVE_RAND_R */



/*-------------------------------------------------------------------------
 * Function:    Pflock
 *
 * Purpose:     Wrapper function for POSIX systems where flock(2) is not
 *              available.
 *
 * Return:      Success:    0
 *              Failure:    -1
 *
 *-------------------------------------------------------------------------
 */
/* NOTE: Compile this all the time on POSIX systems, even when flock(2) is
 *       present so that it's less likely to become dead code.
 */
#ifdef H5_HAVE_FCNTL
int
Pflock(int fd, int operation) {

    struct flock    flk;

    /* Set the lock type */
    if(operation & LOCK_UN)
        flk.l_type = F_UNLCK;
    else if(operation & LOCK_SH)
        flk.l_type = F_RDLCK;
    else
        flk.l_type = F_WRLCK;

    /* Set the other flock struct values */
    flk.l_whence = SEEK_SET;
    flk.l_start = 0;
    flk.l_len = 0;              /* to EOF */
    flk.l_pid = 0;              /* not used with set */

    /* Lock or unlock */
    if(HDfcntl(fd, F_SETLK, flk) < 0)
        return -1;

    return 0;

} /* end Pflock() */
#endif /* H5_HAVE_FCNTL */


/*-------------------------------------------------------------------------
 * Function:    Nflock
 *
 * Purpose:     Wrapper function for systems where no file locking is
 *              available.
 *
 * Return:      Failure:    -1 (always fails)
 *
 *-------------------------------------------------------------------------
 */
int H5_ATTR_CONST
Nflock(int H5_ATTR_UNUSED fd, int H5_ATTR_UNUSED operation) {
    /* just fail */
    return -1;
} /* end Nflock() */


/*-------------------------------------------------------------------------
 * Function:    H5_make_time
 *
 * Purpose:    Portability routine to abstract converting a 'tm' struct into
 *        a time_t value.
 *
 * Note:    This is a little problematic because mktime() operates on
 *        local times.  We convert to local time and then figure out the
 *        adjustment based on the local time zone and daylight savings
 *        setting.
 *
 * Return:    Success:  The value of timezone
 *        Failure:  -1
 *
 * Programmer:  Quincey Koziol
 *              November 18, 2015
 *
 *-------------------------------------------------------------------------
 */
time_t
H5_make_time(struct tm *tm)
{
    time_t the_time;    /* The converted time */
#if defined(H5_HAVE_VISUAL_STUDIO) && (_MSC_VER >= 1900)  /* VS 2015 */
    /* In gcc and in Visual Studio prior to VS 2015 'timezone' is a global
     * variable declared in time.h. That variable was deprecated and in
     * VS 2015 is removed, with _get_timezone replacing it.
     */
    long timezone = 0;
#endif /* defined(H5_HAVE_VISUAL_STUDIO) && (_MSC_VER >= 1900) */
    time_t ret_value;   /* Return value */

    FUNC_ENTER_NOAPI_NOINIT

    /* Sanity check */
    HDassert(tm);

    /* Initialize timezone information */
    if(!H5_ntzset) {
        HDtzset();
        H5_ntzset = TRUE;
    } /* end if */

    /* Perform base conversion */
    if((time_t)-1 == (the_time = HDmktime(tm)))
        HGOTO_ERROR(H5E_INTERNAL, H5E_CANTCONVERT, FAIL, "badly formatted modification time message")

    /* Adjust for timezones */
#if defined(H5_HAVE_TM_GMTOFF)
    /* BSD-like systems */
    the_time += tm->tm_gmtoff;
#elif defined(H5_HAVE_TIMEZONE)
#if defined(H5_HAVE_VISUAL_STUDIO) && (_MSC_VER >= 1900)  /* VS 2015 */
    /* In gcc and in Visual Studio prior to VS 2015 'timezone' is a global
     * variable declared in time.h. That variable was deprecated and in
     * VS 2015 is removed, with _get_timezone replacing it.
     */
    _get_timezone(&timezone);
#endif /* defined(H5_HAVE_VISUAL_STUDIO) && (_MSC_VER >= 1900) */

    the_time -= timezone - (tm->tm_isdst ? 3600 : 0);
#else
    /*
     * The catch-all.  If we can't convert a character string universal
     * coordinated time to a time_t value reliably then we can't decode the
     * modification time message. This really isn't as bad as it sounds -- the
     * only way a user can get the modification time is from our internal
     * query routines, which can gracefully recover.
     */
    HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "unable to obtain local timezone information")
#endif

    /* Set return value */
    ret_value = the_time;

done:
    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5_make_time() */

#ifdef H5_HAVE_WIN32_API

/* Offset between 1/1/1601 and 1/1/1970 in 100 nanosecond units */
#define _W32_FT_OFFSET (116444736000000000ULL)


/*-------------------------------------------------------------------------
 * Function:  Wgettimeofday
 *
 * Purpose:  Wrapper function for gettimeofday on Windows systems
 *
 *     This function can get the time as well as a timezone
 *
 * Return:  0
 *
 *      This implementation is taken from the Cygwin source distribution at
 *          src/winsup/mingw/mingwex/gettimeofday.c
 *
 *      The original source code was contributed by
 *          Danny Smith <dannysmith@users.sourceforge.net>
 *      and released in the public domain.
 *
 * Programmer:  Scott Wegner
 *              May 19, 2009
 *
 *-------------------------------------------------------------------------
 */
int
Wgettimeofday(struct timeval *tv, struct timezone *tz)
{
  union {
    unsigned long long ns100; /*time since 1 Jan 1601 in 100ns units */
    FILETIME ft;
  }  _now;

    static int tzsetflag;

    if(tv) {
      GetSystemTimeAsFileTime (&_now.ft);
      tv->tv_usec=(long)((_now.ns100 / 10ULL) % 1000000ULL );
      tv->tv_sec= (long)((_now.ns100 - _W32_FT_OFFSET) / 10000000ULL);
    }

    if(tz) {
        if(!tzsetflag) {
            _tzset();
            tzsetflag = 1;
        }
        tz->tz_minuteswest = _timezone / 60;
        tz->tz_dsttime = _daylight;
    }

  /* Always return 0 as per Open Group Base Specifications Issue 6.
     Do not set errno on error.  */
  return 0;
} /* end Wgettimeofday() */


/*-------------------------------------------------------------------------
 * Function:    Wsetenv
 *
 * Purpose:     Wrapper function for setenv on Windows systems.
 *              Interestingly, getenv *is* available in the Windows
 *              POSIX layer, just not setenv.
 *
 * Return:      Success:    0
 *              Failure:    non-zero error code
 *
 * Programmer:  Dana Robinson
 *              February 2016
 *
 *-------------------------------------------------------------------------
 */
int
Wsetenv(const char *name, const char *value, int overwrite)
{
    size_t bufsize;
    errno_t err;

    /* If we're not overwriting, check if the environment variable exists.
     * If it does (i.e.: the required buffer size to store the variable's
     * value is non-zero), then return an error code.
     */
    if(!overwrite) {
        err = getenv_s(&bufsize, NULL, 0, name);
        if (err || bufsize)
            return (int)err;
    } /* end if */

    return (int)_putenv_s(name, value);
} /* end Wsetenv() */

#ifdef H5_HAVE_WINSOCK2_H
#pragma comment(lib, "advapi32.lib")
#endif

#define WloginBuffer_count 256
static char Wlogin_buffer[WloginBuffer_count];

char*
Wgetlogin()
{

#ifdef H5_HAVE_WINSOCK2_H
    long bufferCount = WloginBuffer_count;
    if (GetUserName(Wlogin_buffer, &bufferCount) == 0)
        return (Wlogin_buffer);
    else
#endif /* H5_HAVE_WINSOCK2_H */
        return NULL;
}

int c99_snprintf(char* str, size_t size, const char* format, ...)
{
    int count;
    va_list ap;

    va_start(ap, format);
    count = c99_vsnprintf(str, size, format, ap);
    va_end(ap);

    return count;
}

int c99_vsnprintf(char* str, size_t size, const char* format, va_list ap)
{
    int count = -1;

    if (size != 0)
        count = _vsnprintf_s(str, size, _TRUNCATE, format, ap);
    if (count == -1)
        count = _vscprintf(format, ap);

    return count;
}


/*-------------------------------------------------------------------------
 * Function:    Wflock
 *
 * Purpose:     Wrapper function for flock on Windows systems
 *
 * Return:      Success:    0
 *              Failure:    -1
 *
 *-------------------------------------------------------------------------
 */
int
Wflock(int H5_ATTR_UNUSED fd, int H5_ATTR_UNUSED operation) {

/* This is a no-op while we implement a Win32 VFD */
#if 0
int
Wflock(int fd, int operation) {

    HANDLE          hFile;
    DWORD           dwFlags = LOCKFILE_FAIL_IMMEDIATELY;
    DWORD           dwReserved = 0;
                    /* MAXDWORD for entire file */
    DWORD           nNumberOfBytesToLockLow = MAXDWORD;
    DWORD           nNumberOfBytesToLockHigh = MAXDWORD;
                    /* Must initialize OVERLAPPED struct */
    OVERLAPPED      overlapped = {0};

    /* Get Windows HANDLE */
    hFile = _get_osfhandle(fd);

    /* Convert to Windows flags */
    if(operation & LOCK_EX)
        dwFlags |= LOCKFILE_EXCLUSIVE_LOCK;

    /* Lock or unlock */
    if(operation & LOCK_UN)
        if(0 == UnlockFileEx(hFile, dwReserved, nNumberOfBytesToLockLow,
                            nNumberOfBytesToLockHigh, &overlapped))
            return -1;
    else
        if(0 == LockFileEx(hFile, dwFlags, dwReserved, nNumberOfBytesToLockLow,
                            nNumberOfBytesToLockHigh, &overlapped))
            return -1;
#endif /* 0 */
    return 0;
} /* end Wflock() */


 /*--------------------------------------------------------------------------
  * Function:    Wnanosleep
  *
  * Purpose:     Sleep for a given # of nanoseconds (Windows version)
  *
  * Return:      SUCCEED/FAIL
  *
  * Programmer:  Dana Robinson
  *              Fall 2016
  *--------------------------------------------------------------------------
  */
int
Wnanosleep(const struct timespec *req, struct timespec *rem)
{
    /* XXX: Currently just a placeholder */
    return 0;

} /* end Wnanosleep() */


/*-------------------------------------------------------------------------
 * Function:    Wllround, Wllroundf, Wlround, Wlroundf, Wround, Wroundf
 *
 * Purpose:     Wrapper function for round functions for use with VS2012
 *              and earlier.
 *
 * Return:      The rounded value that was passed in.
 *
 * Programmer:  Dana Robinson
 *              December 2016
 *
 *-------------------------------------------------------------------------
 */
long long
Wllround(double arg)
{
    return (long long)(arg < 0.0 ? HDceil(arg - 0.5) : HDfloor(arg + 0.5));
}

long long
Wllroundf(float arg)
{
    return (long long)(arg < 0.0F ? HDceil(arg - 0.5F) : HDfloor(arg + 0.5F));
}

long
Wlround(double arg)
{
    return (long)(arg < 0.0 ? HDceil(arg - 0.5) : HDfloor(arg + 0.5));
}

long
Wlroundf(float arg)
{
    return (long)(arg < 0.0F ? HDceil(arg - 0.5F) : HDfloor(arg + 0.5F));
}

double
Wround(double arg)
{
    return arg < 0.0 ? HDceil(arg - 0.5) : HDfloor(arg + 0.5);
}

float
Wroundf(float arg)
{
    return arg < 0.0F ? HDceil(arg - 0.5F) : HDfloor(arg + 0.5F);
}

#endif /* H5_HAVE_WIN32_API */


/*-------------------------------------------------------------------------
 * Function:    H5_build_extpath
 *
 * Purpose:     To build the path for later searching of target file for external
 *              links and external files.  This path can be either:
 *                  1. The absolute path of NAME
 *                      or
 *                  2. The current working directory + relative path of NAME
 *
 * Return:      SUCCEED/FAIL
 *
 * Programmer:  Vailin Choi
 *              April 2, 2008
 *
 *-------------------------------------------------------------------------
 */
#define MAX_PATH_LEN     1024

herr_t
H5_build_extpath(const char *name, char **extpath /*out*/)
{
    char        *full_path = NULL;      /* Pointer to the full path, as built or passed in */
    char        *cwdpath = NULL;        /* Pointer to the current working directory path */
    char        *new_name = NULL;       /* Pointer to the name of the file */
    herr_t      ret_value = SUCCEED;    /* Return value */

    FUNC_ENTER_NOAPI_NOINIT

    /* Sanity check */
    HDassert(name);
    HDassert(extpath);

    /* Clear external path pointer to begin with */
    *extpath = NULL;

    /*
     * Unix: name[0] is a "/"
     * Windows: name[0-2] is "<drive letter>:\" or "<drive-letter>:/"
     */
    if(H5_CHECK_ABSOLUTE(name)) {
        if(NULL == (full_path = (char *)H5MM_strdup(name)))
            HGOTO_ERROR(H5E_INTERNAL, H5E_NOSPACE, FAIL, "memory allocation failed")
    } /* end if */
    else { /* relative pathname */
        char *retcwd;
        size_t name_len;
        int drive;

        if(NULL == (cwdpath = (char *)H5MM_malloc(MAX_PATH_LEN)))
            HGOTO_ERROR(H5E_INTERNAL, H5E_NOSPACE, FAIL, "memory allocation failed")
        name_len = HDstrlen(name) + 1;
        if(NULL == (new_name = (char *)H5MM_malloc(name_len)))
            HGOTO_ERROR(H5E_INTERNAL, H5E_NOSPACE, FAIL, "memory allocation failed")

        /*
         * Windows: name[0-1] is "<drive-letter>:"
         *   Get current working directory on the drive specified in NAME
         * Unix: does not apply
         */
        if(H5_CHECK_ABS_DRIVE(name)) {
            drive = name[0] - 'A' + 1;
            retcwd = HDgetdcwd(drive, cwdpath, MAX_PATH_LEN);
            HDstrncpy(new_name, &name[2], name_len);
        } /* end if */
       /*
        * Windows: name[0] is a '/' or '\'
        *  Get current drive
        * Unix: does not apply
        */
        else if(H5_CHECK_ABS_PATH(name) && (0 != (drive = HDgetdrive()))) {
            HDsnprintf(cwdpath, MAX_PATH_LEN, "%c:%c", (drive + 'A' - 1), name[0]);
            retcwd = cwdpath;
            HDstrncpy(new_name, &name[1], name_len);
        }
        /* totally relative for Unix and Windows: get current working directory  */
        else {
            retcwd = HDgetcwd(cwdpath, MAX_PATH_LEN);
            HDstrncpy(new_name, name, name_len);
        } /* end if */

        if(retcwd != NULL) {
            size_t cwdlen;
            size_t path_len;

            HDassert(cwdpath);
            cwdlen = HDstrlen(cwdpath);
            HDassert(cwdlen);
            HDassert(new_name);
            path_len = cwdlen + HDstrlen(new_name) + 2;
            if(NULL == (full_path = (char *)H5MM_malloc(path_len)))
                HGOTO_ERROR(H5E_INTERNAL, H5E_NOSPACE, FAIL, "memory allocation failed")

            HDstrncpy(full_path, cwdpath, cwdlen + 1);
            if(!H5_CHECK_DELIMITER(cwdpath[cwdlen - 1]))
                HDstrncat(full_path, H5_DIR_SEPS, HDstrlen(H5_DIR_SEPS));
            HDstrncat(full_path, new_name, HDstrlen(new_name));
        } /* end if */
    } /* end else */

    /* strip out the last component (the file name itself) from the path */
    if(full_path) {
        char *ptr = NULL;

        H5_GET_LAST_DELIMITER(full_path, ptr)
        HDassert(ptr);
        *++ptr = '\0';
        *extpath = full_path;
    } /* end if */

done:
    /* Release resources */
    if(cwdpath)
        H5MM_xfree(cwdpath);
    if(new_name)
        H5MM_xfree(new_name);

    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5_build_extpath() */


/*--------------------------------------------------------------------------
 * Function:    H5_combine_path
 *
 * Purpose:     If path2 is relative, interpret path2 as relative to path1
 *              and store the result in full_name. Otherwise store path2
 *              in full_name.
 *
 * Return:      SUCCEED/FAIL
 *
 * Programmer:  Steffen Kiess
 *              June 22, 2015
 *--------------------------------------------------------------------------
 */
herr_t
H5_combine_path(const char* path1, const char* path2, char **full_name /*out*/)
{
    size_t      path1_len;            /* length of path1 */
    size_t      path2_len;            /* length of path2 */
    herr_t      ret_value = SUCCEED;  /* Return value */

    FUNC_ENTER_NOAPI_NOINIT

    HDassert(path1);
    HDassert(path2);

    path1_len = HDstrlen(path1);
    path2_len = HDstrlen(path2);

    if(*path1 == '\0' || H5_CHECK_ABSOLUTE(path2)) {

        /* If path1 is empty or path2 is absolute, simply use path2 */
        if(NULL == (*full_name = (char *)H5MM_strdup(path2)))
            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")

    } /* end if */
    else if(H5_CHECK_ABS_PATH(path2)) {

        /* On windows path2 is a path absolute name */
        if (H5_CHECK_ABSOLUTE(path1) || H5_CHECK_ABS_DRIVE(path1)) {
            /* path1 is absolute or drive absolute and path2 is path absolute.
             * Use the drive letter of path1 + path2
             */
            if(NULL == (*full_name = (char *)H5MM_malloc(path2_len + 3)))
                HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate path2 buffer")
            HDsnprintf(*full_name, (path2_len + 3), "%c:%s", path1[0], path2);
        } /* end if */
        else {
            /* On windows path2 is path absolute name ("\foo\bar"),
             * path1 does not have a drive letter (i.e. is "a\b" or "\a\b").
             * Use path2.
             */
            if(NULL == (*full_name = (char *)H5MM_strdup(path2)))
                HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
        } /* end else */

    } /* end else if */
    else {

        /* Relative path2:
         * Allocate a buffer to hold path1 + path2 + possibly the delimiter
         *      + terminating null byte
         */
        if(NULL == (*full_name = (char *)H5MM_malloc(path1_len + path2_len + 2)))
            HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate filename buffer")

        /* Compose the full file name */
        HDsnprintf(*full_name, (path1_len + path2_len + 2), "%s%s%s", path1,
                   (H5_CHECK_DELIMITER(path1[path1_len - 1]) ? "" : H5_DIR_SEPS), path2);
    } /* end else */

done:
    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5_combine_path() */


/*--------------------------------------------------------------------------
 * Function:    H5_nanosleep
 *
 * Purpose:     Sleep for a given # of nanoseconds
 *
 * Return:      SUCCEED/FAIL
 *
 * Programmer:  Quincey Koziol
 *              October 01, 2016
 *--------------------------------------------------------------------------
 */
void
H5_nanosleep(uint64_t nanosec)
{
    struct timespec sleeptime;  /* Struct to hold time to sleep */

    FUNC_ENTER_NOAPI_NOINIT_NOERR

    /* Set up time to sleep */
    sleeptime.tv_sec = 0;
    sleeptime.tv_nsec = (long)nanosec;

    HDnanosleep(&sleeptime, NULL);

    FUNC_LEAVE_NOAPI_VOID
} /* end H5_nanosleep() */


/*--------------------------------------------------------------------------
 * Function:    H5_get_time
 *
 * Purpose:     Get the current time, as the time of seconds after the UNIX epoch
 *
 * Return:      SUCCEED/FAIL
 *
 * Programmer:  Quincey Koziol
 *              October 05, 2016
 *--------------------------------------------------------------------------
 */
double
H5_get_time(void)
{
#ifdef H5_HAVE_GETTIMEOFDAY
    struct timeval curr_time;
#endif /* H5_HAVE_GETTIMEOFDAY */
    double ret_value = (double)0.0f;

    FUNC_ENTER_NOAPI_NOINIT_NOERR

#ifdef H5_HAVE_GETTIMEOFDAY
    HDgettimeofday(&curr_time, NULL);

    ret_value = (double)curr_time.tv_sec + ((double)curr_time.tv_usec / (double)1000000.0f);
#endif /* H5_HAVE_GETTIMEOFDAY */

    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5_get_time() */


s="hl opt">,field_sizes,tid))<0) goto out; /* Get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* Get records */ if ( H5Sget_simple_extent_dims( sid, dims, NULL) < 0 ) goto out; if ( start + nrecords > dims[0] ) goto out; /* Define a hyperslab in the dataset of the size of the records */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ( H5Dwrite( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0 ) goto out; /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( sid ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( tid ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( mem_type_id ) < 0 ) return -1; /* End access to the dataset */ if ( H5Dclose( did ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Tclose(mem_type_id); H5Tclose(tid); H5Sclose(mem_space_id); H5Sclose(sid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBwrite_fields_name * * Purpose: Writes fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 21, 2001 * * Comments: * * Modifications: April 1, 2004 * the DST_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBwrite_fields_name( hid_t loc_id, const char *dset_name, const char *field_names, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, const void *data ) { hid_t did; hid_t tid=-1; hid_t write_type_id=-1; hid_t member_type_id; hid_t nmtype_id; hsize_t count[1]; hsize_t offset[1]; hid_t mem_space_id=-1; hid_t file_space_id=-1; char *member_name; hssize_t nfields; hssize_t i, j; hid_t PRESERVE; size_t size_native; /* Create xfer properties to preserve initialized data */ if ((PRESERVE = H5Pcreate (H5P_DATASET_XFER))<0) return -1; if (H5Pset_preserve (PRESERVE, 1)<0) return -1; /* Open the dataset. */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) goto out; /* Get the datatype */ if ( (tid = H5Dget_type( did )) < 0 ) goto out; /* Get the number of fields */ if ( ( nfields = H5Tget_nmembers( tid )) < 0 ) goto out; /* Create a write id */ if ( ( write_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0 ) goto out; j = 0; /* Iterate tru the members */ for ( i = 0; i < nfields; i++) { /* Get the member name */ member_name = H5Tget_member_name( tid, (unsigned)i ); if ( H5TB_find_field( member_name, field_names ) > 0 ) { /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( tid,(unsigned) i )) < 0 ) goto out; /* Convert to native type */ if ((nmtype_id=H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT))<0) goto out; size_native=H5Tget_size(nmtype_id); /* Adjust, if necessary */ if (field_sizes[j]!=size_native) { if (H5Tset_size(nmtype_id, field_sizes[j])<0) goto out; } /* The field in the file is found by its name */ if ( field_offset ) { if ( H5Tinsert( write_type_id, member_name, field_offset[j], nmtype_id ) < 0 ) goto out; } /* Only one field */ else { if ( H5Tinsert( write_type_id, member_name, (size_t)0, nmtype_id ) < 0 ) goto out; } j++; /* Close */ if ( H5Tclose( member_type_id ) < 0 ) goto out; if ( H5Tclose( nmtype_id ) < 0 ) goto out; } free( member_name ); } /* Get the dataspace handle */ if ( (file_space_id = H5Dget_space( did )) < 0 ) goto out; if ( (mem_space_id = H5Screate_simple(1, &nrecords, NULL)) < 0 ) goto out; /* Define a hyperslab in the dataset */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( file_space_id, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Write */ if ( H5Dwrite( did, write_type_id, mem_space_id, file_space_id, PRESERVE, data ) < 0 ) goto out; /* close */ if ( H5Tclose( write_type_id ) ) goto out; if ( H5Tclose( tid ) < 0 ) return -1; if ( H5Dclose( did ) < 0 ) return -1; if ( H5Pclose( PRESERVE ) < 0 ) return -1; if ( H5Sclose( file_space_id ) < 0 ) return -1; if ( H5Sclose( mem_space_id ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Pclose(PRESERVE); H5Dclose(did); H5Sclose(file_space_id); H5Sclose(mem_space_id); H5Tclose(write_type_id); H5Tclose(tid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBwrite_fields_index * * Purpose: Writes fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 21, 2001 * * Comments: Uses memory offsets * * Modifications: April 1, 2004 * the DST_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBwrite_fields_index( hid_t loc_id, const char *dset_name, hsize_t nfields, const int *field_index, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, const void *data ) { hid_t did; hid_t tid=-1; hid_t write_type_id=-1; hid_t member_type_id; hid_t nmtype_id; hsize_t count[1]; hsize_t offset[1]; hid_t mem_space_id=-1; hid_t file_space_id=-1; char *member_name; hsize_t i, j; hid_t PRESERVE; size_t size_native; /* Create xfer properties to preserve initialized data */ if ((PRESERVE = H5Pcreate (H5P_DATASET_XFER))<0) return -1; if (H5Pset_preserve (PRESERVE, 1)<0) return -1; /* Open the dataset. */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) goto out; /* Get the datatype */ if ( (tid = H5Dget_type( did )) < 0 ) goto out; /* Create a write id */ if ( ( write_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0 ) goto out; /* Iterate tru the members */ for ( i = 0; i < nfields; i++) { j = field_index[i]; /* Get the member name */ member_name = H5Tget_member_name( tid, (unsigned) j ); /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( tid, (unsigned) j )) < 0 ) goto out; /* Convert to native type */ if ((nmtype_id=H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT))<0) goto out; size_native=H5Tget_size(nmtype_id); if (field_sizes[i]!=size_native) { if (H5Tset_size(nmtype_id, field_sizes[i])<0) goto out; } /* The field in the file is found by its name */ if ( field_offset ) { if ( H5Tinsert( write_type_id, member_name, field_offset[ i ], nmtype_id ) < 0 ) goto out; } /* Only one field */ else { if ( H5Tinsert( write_type_id, member_name, (size_t)0, nmtype_id ) < 0 ) goto out; } /* Close */ if ( H5Tclose( member_type_id ) < 0 ) goto out; if ( H5Tclose( nmtype_id ) < 0 ) goto out; free( member_name ); } /* Get the dataspace handles */ if ( (file_space_id = H5Dget_space( did )) < 0 ) goto out; if ( (mem_space_id = H5Screate_simple(1, &nrecords, NULL)) < 0 ) goto out; /* Define a hyperslab in the dataset */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( file_space_id, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Write */ if ( H5Dwrite( did, write_type_id, mem_space_id, file_space_id, PRESERVE, data ) < 0 ) goto out; /* close */ if ( H5Tclose( write_type_id ) ) goto out; if ( H5Tclose( tid ) < 0 ) return -1; if ( H5Dclose( did ) < 0 ) return -1; if ( H5Pclose( PRESERVE ) < 0 ) return -1; if ( H5Sclose( file_space_id ) < 0 ) return -1; if ( H5Sclose( mem_space_id ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Pclose(PRESERVE); H5Dclose(did); H5Sclose(file_space_id); H5Sclose(mem_space_id); H5Tclose(write_type_id); H5Tclose(tid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * * Read functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBread_table * * Purpose: Reads a table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 20, 2001 * * Comments: * * Modifications: April 1, 2004 * used a memory type ID returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBread_table( hid_t loc_id, const char *dset_name, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *dst_buf ) { hid_t did; hid_t ftype_id=-1; hid_t mem_type_id=-1; hid_t sid; hsize_t dims[1]; /* open the dataset. */ if ((did=H5Dopen(loc_id,dset_name))<0) return -1; /* get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* get dimensions */ if ( H5Sget_simple_extent_dims( sid, dims, NULL) < 0 ) goto out; /* get the datatypes */ if ((ftype_id=H5Dget_type (did))<0) goto out; if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,ftype_id))<0) goto out; /* read */ if ( H5Dread( did, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, dst_buf) < 0 ) goto out; /* close */ if ( H5Tclose( ftype_id ) < 0 ) goto out; if ( H5Tclose( mem_type_id ) < 0 ) goto out; if ( H5Sclose( sid ) < 0 ) goto out; if ( H5Dclose( did ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Tclose(mem_type_id); H5Tclose(ftype_id); H5Sclose(sid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBread_records * * Purpose: Reads records * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * * Modifications: April 1, 2004 * the DST_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBread_records( hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *data ) { hid_t did; hid_t ftype_id; hid_t mem_type_id=-1; hsize_t count[1]; hsize_t offset[1]; hid_t sid=-1; hsize_t dims[1]; hid_t mem_space_id=-1; hsize_t mem_size[1]; hsize_t nrecords_orig; hsize_t nfields; /* get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords_orig ) < 0 ) return -1; /* open the dataset */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* get the datatypes */ if ( (ftype_id = H5Dget_type( did )) < 0 ) goto out; if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,ftype_id))<0) goto out; /* Read the records */ if ((H5TB_common_read_records(did, mem_type_id, start, (size_t)nrecords, nrecords_orig, data)) < 0) goto out; /* get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* get records */ if ( H5Sget_simple_extent_dims( sid, dims, NULL) < 0 ) goto out; if ( start + nrecords > dims[0] ) goto out; /* define a hyperslab in the dataset of the size of the records */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; /* read */ if ( H5Dread( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0 ) goto out; /* close */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; if ( H5Sclose( sid ) < 0 ) goto out; if ( H5Tclose( ftype_id ) < 0 ) return -1; if ( H5Tclose( mem_type_id ) < 0 ) return -1; if ( H5Dclose( did ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Tclose(mem_type_id); H5Tclose(ftype_id); H5Sclose(mem_space_id); H5Sclose(sid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBread_fields_name * * Purpose: Reads fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * * Modifications: April 1, 2004 * the DST_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBread_fields_name( hid_t loc_id, const char *dset_name, const char *field_names, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *data ) { hid_t did; hid_t ftype_id=-1; hid_t mem_type_id=-1; hid_t mtype_id; hid_t nmtype_id; char *member_name; hssize_t nfields; hsize_t count[1]; hsize_t offset[1]; hid_t sid=-1; hid_t mem_space_id=-1; hsize_t mem_size[1]; size_t size_native; hssize_t i, j; /* open the dataset */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) goto out; /* get the datatype */ if ( (ftype_id = H5Dget_type( did )) < 0 ) goto out; /* get the number of fields */ if ( ( nfields = H5Tget_nmembers( ftype_id )) < 0 ) goto out; /* create a memory read id */ if ( ( mem_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0 ) goto out; /* iterate tru the members */ for ( i=0,j=0; i<nfields; i++) { /* get the member name */ member_name = H5Tget_member_name( ftype_id, (unsigned)i ); if ( H5TB_find_field( member_name, field_names ) > 0 ) { /* get the member type */ if ( ( mtype_id = H5Tget_member_type( ftype_id, (unsigned) i )) < 0 ) goto out; /* convert to native type */ if ((nmtype_id=H5Tget_native_type(mtype_id,H5T_DIR_DEFAULT))<0) goto out; size_native=H5Tget_size(nmtype_id); if (field_sizes[j]!=size_native) { if (H5Tset_size(nmtype_id, field_sizes[j])<0) goto out; } /* the field in the file is found by its name */ if ( field_offset ) { if ( H5Tinsert( mem_type_id, member_name, field_offset[j], nmtype_id ) < 0 ) goto out; } else { if ( H5Tinsert( mem_type_id, member_name, (size_t)0, nmtype_id ) < 0 ) goto out; } /* close */ if ( H5Tclose( mtype_id ) < 0 ) goto out; if ( H5Tclose( nmtype_id ) < 0 ) goto out; j++; } free( member_name ); } /* get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* define a hyperslab in the dataset */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; /* read */ if ( H5Dread( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0 ) goto out; /* close */ if ( H5Tclose( mem_type_id ) ) goto out; if ( H5Tclose( ftype_id ) < 0 ) return -1; if ( H5Sclose( sid ) < 0 ) goto out; if ( H5Sclose( mem_space_id ) < 0 ) goto out; if ( H5Dclose( did ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Tclose(mem_type_id); H5Tclose(ftype_id); H5Sclose(mem_space_id); H5Sclose(sid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBread_fields_index * * Purpose: Reads fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * * Modifications: April 1, 2004 * the DST_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBread_fields_index( hid_t loc_id, const char *dset_name, hsize_t nfields, const int *field_index, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *data ) { hid_t did; hid_t tid=-1; hid_t read_type_id=-1; hid_t member_type_id; hid_t nmtype_id; char *member_name; hsize_t count[1]; hsize_t offset[1]; hid_t sid=-1; hid_t mem_space_id=-1; hsize_t mem_size[1]; size_t size_native; hsize_t i, j; /* Open the dataset. */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) goto out; /* Get the datatype */ if ( (tid = H5Dget_type( did )) < 0 ) goto out; /* Create a read id */ if ( ( read_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0 ) goto out; /* Iterate tru the members */ for ( i = 0; i < nfields; i++) { j = field_index[i]; /* Get the member name */ member_name = H5Tget_member_name( tid, (unsigned) j ); /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( tid, (unsigned) j )) < 0 ) goto out; /* Get the member size */ if ( H5Tget_size( member_type_id ) == 0 ) goto out; /* Convert to native type */ if ((nmtype_id=H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT))<0) goto out; size_native=H5Tget_size(nmtype_id); if (field_sizes[i]!=size_native) { if (H5Tset_size(nmtype_id, field_sizes[i])<0) goto out; } /* The field in the file is found by its name */ if ( field_offset ) { if ( H5Tinsert( read_type_id, member_name, field_offset[i], nmtype_id ) < 0 ) goto out; } else { if ( H5Tinsert( read_type_id, member_name, (size_t)0, nmtype_id ) < 0 ) goto out; } /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; if ( H5Tclose( nmtype_id ) < 0 ) goto out; free( member_name ); } /* Get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* Define a hyperslab in the dataset */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; /* Read */ if ( H5Dread( did, read_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( sid ) < 0 ) goto out; /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; /* End access to the read id */ if ( H5Tclose( read_type_id ) ) goto out; /* Release the datatype. */ if ( H5Tclose( tid ) < 0 ) return -1; /* End access to the dataset */ if ( H5Dclose( did ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Tclose(read_type_id); H5Tclose(tid); H5Sclose(mem_space_id); H5Sclose(sid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * * Manipulation functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBdelete_record * * Purpose: Delete records from middle of table ("pulling up" all the records after it) * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 26, 2001 * * Modifications: April 29, 2003 * * *------------------------------------------------------------------------- */ herr_t H5TBdelete_record( hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords ) { hsize_t nfields; hsize_t ntotal_records; hsize_t read_start; hsize_t read_nrecords; hid_t did; hid_t tid; hsize_t count[1]; hsize_t offset[1]; hid_t sid; hid_t mem_space_id; hsize_t mem_size[1]; unsigned char *tmp_buf; size_t src_size; size_t *src_offset; size_t *src_sizes; hsize_t nrows; #if defined (SHRINK) hsize_t dims[1]; #endif /*------------------------------------------------------------------------- * First we get information about type size and offsets on disk *------------------------------------------------------------------------- */ /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &ntotal_records ) < 0 ) return -1; src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t)); src_sizes = (size_t *)malloc((size_t)nfields * sizeof(size_t)); if ( src_offset == NULL ) return -1; /* Get field info */ if ( H5TBget_field_info( loc_id, dset_name, NULL, src_sizes, src_offset, &src_size ) < 0 ) return -1; /*------------------------------------------------------------------------- * Read the records after the deleted one(s) *------------------------------------------------------------------------- */ read_start = start + nrecords; read_nrecords = ntotal_records - read_start; tmp_buf = (unsigned char *)calloc((size_t) read_nrecords, src_size ); if ( tmp_buf == NULL ) return -1; /* Read the records after the deleted one(s) */ if ( H5TBread_records( loc_id, dset_name, read_start, read_nrecords, src_size, src_offset, src_sizes, tmp_buf ) < 0 ) return -1; /*------------------------------------------------------------------------- * Write the records in another position *------------------------------------------------------------------------- */ /* Open the dataset. */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* Get the datatype */ if ( (tid = H5Dget_type( did )) < 0 ) goto out; /* Get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* Define a hyperslab in the dataset of the size of the records */ offset[0] = start; count[0] = read_nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ( H5Dwrite( did, tid, mem_space_id, sid, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( sid ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( tid ) < 0 ) goto out; /*------------------------------------------------------------------------- * Change the table dimension *------------------------------------------------------------------------- */ #if defined (SHRINK) dims[0] = ntotal_records - nrecords; if ( H5Dset_extent( did, dims ) < 0 ) goto out; #endif /* End access to the dataset */ if ( H5Dclose( did ) < 0 ) return -1; free( tmp_buf ); free( src_offset ); free( src_sizes ); /*------------------------------------------------------------------------- * Store the new dimension as an attribute *------------------------------------------------------------------------- */ nrows = ntotal_records - nrecords; /* Set the attribute */ if (H5LT_set_attribute_numerical(loc_id,dset_name,"NROWS",(size_t)1, H5T_NATIVE_LLONG,&nrows)<0) return -1; return 0; out: H5Dclose( did ); return -1; } /*------------------------------------------------------------------------- * Function: H5TBinsert_record * * Purpose: Inserts records into middle of table ("pushing down" all the records after it) * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 26, 2001 * * Comments: Uses memory offsets * * Modifications: April 1, 2004 * the DST_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- */ herr_t H5TBinsert_record( hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *data ) { hsize_t nfields; hsize_t ntotal_records; hsize_t read_nrecords; hid_t did; hid_t tid=-1; hid_t mem_type_id=-1; hsize_t count[1]; hsize_t offset[1]; hid_t sid=-1; hid_t mem_space_id=-1; hsize_t dims[1]; hsize_t mem_dims[1]; unsigned char *tmp_buf; /*------------------------------------------------------------------------- * Read the records after the inserted one(s) *------------------------------------------------------------------------- */ /* Get the dimensions */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &ntotal_records ) < 0 ) return -1; /* Open the dataset. */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) goto out; /* Get the datatype */ if ( (tid = H5Dget_type( did )) < 0 ) goto out; /* Create the memory data type. */ if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,tid))<0) goto out; read_nrecords = ntotal_records - start; tmp_buf = (unsigned char *)calloc((size_t) read_nrecords, type_size ); /* Read the records after the inserted one(s) */ if ( H5TBread_records( loc_id, dset_name, start, read_nrecords, type_size, field_offset, field_sizes, tmp_buf ) < 0 ) return -1; /* Extend the dataset */ dims[0] = ntotal_records + nrecords; if ( H5Dextend ( did, dims ) < 0 ) goto out; /*------------------------------------------------------------------------- * Write the inserted records *------------------------------------------------------------------------- */ /* Create a simple memory data space */ mem_dims[0]=nrecords; if ( (mem_space_id = H5Screate_simple( 1, mem_dims, NULL )) < 0 ) return -1; /* Get the file data space */ if ( (sid = H5Dget_space( did )) < 0 ) return -1; /* Define a hyperslab in the dataset to write the new data */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; if ( H5Dwrite( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; if ( H5Sclose( sid ) < 0 ) goto out; /*------------------------------------------------------------------------- * Write the "pushed down" records *------------------------------------------------------------------------- */ /* Create a simple memory data space */ mem_dims[0]=read_nrecords; if ( (mem_space_id = H5Screate_simple( 1, mem_dims, NULL )) < 0 ) return -1; /* Get the file data space */ if ( (sid = H5Dget_space( did )) < 0 ) return -1; /* Define a hyperslab in the dataset to write the new data */ offset[0] = start + nrecords; count[0] = read_nrecords; if ( H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; if ( H5Dwrite( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; if ( H5Sclose( sid ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( tid ) < 0 ) return -1; /* Release the datatype. */ if ( H5Tclose( mem_type_id ) < 0 ) return -1; /* End access to the dataset */ if ( H5Dclose( did ) < 0 ) return -1; free( tmp_buf ); return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Sclose(sid); H5Sclose(mem_space_id); H5Tclose(mem_type_id); H5Tclose(tid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBadd_records_from * * Purpose: Add records from first table to second table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December 5, 2001 * * Comments: * * Modifications: * * *------------------------------------------------------------------------- */ herr_t H5TBadd_records_from( hid_t loc_id, const char *dset_name1, hsize_t start1, hsize_t nrecords, const char *dset_name2, hsize_t start2 ) { /* Identifiers for the 1st dataset. */ hid_t dataset_id1; hid_t type_id1; hid_t space_id1=-1; hid_t mem_space_id1=-1; size_t type_size1; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hsize_t nfields; hsize_t ntotal_records; unsigned char *tmp_buf; size_t src_size; size_t *src_offset; size_t *src_sizes; /*------------------------------------------------------------------------- * First we get information about type size and offsets on disk *------------------------------------------------------------------------- */ /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name1, &nfields, &ntotal_records ) < 0 ) return -1; src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t)); src_sizes = (size_t *)malloc((size_t)nfields * sizeof(size_t)); if ( src_offset == NULL ) return -1; /* Get field info */ if ( H5TBget_field_info( loc_id, dset_name1, NULL, src_sizes, src_offset, &src_size ) < 0 ) return -1; /*------------------------------------------------------------------------- * Get information about the first table and read it *------------------------------------------------------------------------- */ /* Open the 1st dataset. */ if ( (dataset_id1 = H5Dopen( loc_id, dset_name1 )) < 0 ) return -1; /* Get the datatype */ if ( (type_id1 = H5Dget_type( dataset_id1 )) < 0 ) goto out; /* Get the dataspace handle */ if ( (space_id1 = H5Dget_space( dataset_id1 )) < 0 ) goto out; /* Get the size of the datatype */ if ( ( type_size1 = H5Tget_size( type_id1 )) == 0 ) goto out; tmp_buf = (unsigned char *)calloc((size_t)nrecords, type_size1 ); /* Define a hyperslab in the dataset of the size of the records */ offset[0] = start1; count[0] = nrecords; if ( H5Sselect_hyperslab( space_id1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id1 = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ( H5Dread( dataset_id1, type_id1, mem_space_id1, space_id1, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Add to the second table *------------------------------------------------------------------------- */ if ( H5TBinsert_record(loc_id,dset_name2,start2,nrecords,src_size,src_offset,src_sizes,tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Close resources for table 1 *------------------------------------------------------------------------- */ /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id1 ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( space_id1 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id1 ) < 0 ) return -1; /* End access to the dataset */ if ( H5Dclose( dataset_id1 ) < 0 ) return -1; free( tmp_buf ); free( src_offset ); free( src_sizes ); return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(dataset_id1); H5Sclose(space_id1); H5Sclose(mem_space_id1); H5Tclose(type_id1); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBcombine_tables * * Purpose: Combine records from two tables into a third * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December 10, 2001 * * Comments: * * Modifications: * * *------------------------------------------------------------------------- */ herr_t H5TBcombine_tables( hid_t loc_id1, const char *dset_name1, hid_t loc_id2, const char *dset_name2, const char *dset_name3 ) { /* Identifiers for the 1st dataset. */ hid_t dataset_id1; hid_t type_id1; hid_t space_id1; hid_t plist_id1; /* Identifiers for the 2nd dataset. */ hid_t dataset_id2; hid_t type_id2; hid_t space_id2; hid_t plist_id2; /* Identifiers for the 3rd dataset. */ hid_t dataset_id3; hid_t type_id3; hid_t space_id3; hid_t plist_id3; hsize_t count[1]; hsize_t offset[1]; hid_t mem_space_id; hsize_t mem_size[1]; hsize_t nfields; hsize_t nrecords; hsize_t dims[1]; hsize_t maxdims[1] = { H5S_UNLIMITED }; size_t type_size; hid_t sid; hid_t member_type_id; size_t member_offset; char attr_name[255]; hid_t attr_id; char aux[255]; unsigned char *tmp_buf; unsigned char *tmp_fill_buf; hsize_t i; size_t src_size; size_t *src_offset; size_t *src_sizes; int has_fill=0; /*------------------------------------------------------------------------- * First we get information about type size and offsets on disk *------------------------------------------------------------------------- */ /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id1, dset_name1, &nfields, &nrecords ) < 0 ) return -1; src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t)); src_sizes = (size_t *)malloc((size_t)nfields * sizeof(size_t)); if ( src_offset == NULL ) return -1; /* Get field info */ if ( H5TBget_field_info( loc_id1, dset_name1, NULL, src_sizes, src_offset, &src_size ) < 0 ) return -1; /*------------------------------------------------------------------------- * Get information about the first table *------------------------------------------------------------------------- */ /* Open the 1st dataset. */ if ( (dataset_id1 = H5Dopen( loc_id1, dset_name1 )) < 0 ) goto out; /* Get the datatype */ if ( (type_id1 = H5Dget_type( dataset_id1 )) < 0 ) goto out; /* Get the dataspace handle */ if ( (space_id1 = H5Dget_space( dataset_id1 )) < 0 ) goto out; /* Get creation properties list */ if ( (plist_id1 = H5Dget_create_plist( dataset_id1 )) < 0 ) goto out; /* Get the dimensions */ if ( H5TBget_table_info ( loc_id1, dset_name1, &nfields, &nrecords ) < 0 ) return -1; /*------------------------------------------------------------------------- * Make the merged table with no data originally *------------------------------------------------------------------------- */ /* Clone the property list */ if ( ( plist_id3 = H5Pcopy( plist_id1 )) < 0 ) goto out; /* Clone the type id */ if ( ( type_id3 = H5Tcopy( type_id1 )) < 0 ) goto out; /*------------------------------------------------------------------------- * Here we do not clone the file space from the 1st dataset, because we want to create * an empty table. Instead we create a new dataspace with zero records and expandable. *------------------------------------------------------------------------- */ dims[0] = 0; /* Create a simple data space with unlimited size */ if ( (space_id3 = H5Screate_simple( 1, dims, maxdims )) < 0 ) return -1; /* Create the dataset */ if ( (dataset_id3 = H5Dcreate( loc_id1, dset_name3, type_id3, space_id3, plist_id3 )) < 0 ) goto out; /*------------------------------------------------------------------------- * Attach the conforming table attributes *------------------------------------------------------------------------- */ if ( H5TB_attach_attributes( "Merge table", loc_id1, dset_name3, nfields, type_id3 ) < 0 ) goto out; /*------------------------------------------------------------------------- * Get attributes *------------------------------------------------------------------------- */ type_size = H5Tget_size( type_id3 ); /* alloc fill value attribute buffer */ tmp_fill_buf = (unsigned char *)malloc((size_t) type_size ); /* Get the fill value attributes */ has_fill=H5TBAget_fill( loc_id1, dset_name1, dataset_id1, tmp_fill_buf ); /*------------------------------------------------------------------------- * Attach the fill attributes from previous table *------------------------------------------------------------------------- */ if ( has_fill == 1 ) { if (( sid = H5Screate(H5S_SCALAR)) < 0 ) goto out; for ( i = 0; i < nfields; i++) { /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id3, (unsigned) i )) < 0 ) goto out; /* Get the member offset */ member_offset = H5Tget_member_offset( type_id3, (unsigned) i ); strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d", (int) i ); strcat( attr_name, aux ); sprintf( aux, "%s", "_FILL" ); strcat( attr_name, aux ); if ( (attr_id = H5Acreate( dataset_id3, attr_name, member_type_id, sid, H5P_DEFAULT )) < 0 ) goto out; if ( H5Awrite( attr_id, member_type_id, tmp_fill_buf+member_offset ) < 0 ) goto out; if ( H5Aclose( attr_id ) < 0 ) goto out; if ( H5Tclose( member_type_id ) < 0 ) goto out; } /* Close data space. */ if ( H5Sclose( sid ) < 0 ) goto out; } /*------------------------------------------------------------------------- * Read data from 1st table *------------------------------------------------------------------------- */ tmp_buf = (unsigned char *)calloc((size_t) nrecords, type_size ); /* Define a hyperslab in the dataset of the size of the records */ offset[0] = 0; count[0] = nrecords; if ( H5Sselect_hyperslab( space_id1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ( H5Dread( dataset_id1, type_id1, mem_space_id, space_id1, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Save data from 1st table into new table *------------------------------------------------------------------------- */ /* Append the records to the new table */ if ( H5TBappend_records( loc_id1, dset_name3, nrecords, src_size, src_offset, src_sizes, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Release resources from 1st table *------------------------------------------------------------------------- */ /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( space_id1 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id1 ) < 0 ) goto out; /* Terminate access to a property list */ if ( H5Pclose( plist_id1 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id1 ) < 0 ) goto out; /* Release resources. */ free( tmp_buf ); /*------------------------------------------------------------------------- * Get information about the 2nd table *------------------------------------------------------------------------- */ /* Open the dataset. */ if ( (dataset_id2 = H5Dopen( loc_id2, dset_name2 )) < 0 ) goto out; /* Get the datatype */ if ( (type_id2 = H5Dget_type( dataset_id2 )) < 0 ) goto out; /* Get the dataspace handle */ if ( (space_id2 = H5Dget_space( dataset_id2 )) < 0 ) goto out; /* Get the property list handle */ if ( (plist_id2 = H5Dget_create_plist( dataset_id2 )) < 0 ) goto out; /* Get the dimensions */ if ( H5TBget_table_info ( loc_id2, dset_name2, &nfields, &nrecords ) < 0 ) return -1; /*------------------------------------------------------------------------- * Read data from 2nd table *------------------------------------------------------------------------- */ tmp_buf = (unsigned char *)calloc((size_t) nrecords, type_size ); /* Define a hyperslab in the dataset of the size of the records */ offset[0] = 0; count[0] = nrecords; if ( H5Sselect_hyperslab( space_id2, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ( H5Dread( dataset_id2, type_id2, mem_space_id, space_id2, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Save data from 2nd table into new table *------------------------------------------------------------------------- */ /* append the records to the new table */ if ( H5TBappend_records( loc_id1, dset_name3, nrecords, src_size, src_offset, src_sizes, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Release resources from 2nd table *------------------------------------------------------------------------- */ /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( space_id2 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id2 ) < 0 ) return -1; /* Terminate access to a property list */ if ( H5Pclose( plist_id2 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id2 ) < 0 ) return -1; /*------------------------------------------------------------------------- * Release resources from 3rd table *------------------------------------------------------------------------- */ /* Terminate access to the dataspace */ if ( H5Sclose( space_id3 ) < 0 ) return -1; /* Release the datatype. */ if ( H5Tclose( type_id3 ) < 0 ) return -1; /* Terminate access to a property list */ if ( H5Pclose( plist_id3 ) < 0 ) return -1; /* End access to the dataset */ if ( H5Dclose( dataset_id3 ) < 0 ) return -1; /* Release resources. */ free( tmp_buf ); free( tmp_fill_buf ); free( src_offset ); free( src_sizes ); return 0; out: H5Dclose( dataset_id1 ); return -1; } /*------------------------------------------------------------------------- * Function: H5TBinsert_field * * Purpose: Inserts a field * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2002 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5TBinsert_field( hid_t loc_id, const char *dset_name, const char *field_name, hid_t field_type, hsize_t position, const void *fill_data, const void *data ) { /* Identifiers for the 1st, original dataset */ hid_t dataset_id1; hid_t type_id1; hid_t space_id1; hid_t plist_id1; hid_t mem_space_id1; /* Identifiers for the 2nd, new dataset */ hid_t dataset_id2; hid_t type_id2; hid_t space_id2; hid_t plist_id2; hid_t mem_space_id2; hid_t member_type_id; size_t member_size; size_t new_member_size = 0; char *member_name; size_t total_size; hsize_t nfields; hsize_t nrecords; hsize_t dims_chunk[1]; hsize_t dims[1]; hsize_t maxdims[1] = { H5S_UNLIMITED }; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hid_t write_type_id; hid_t PRESERVE; size_t curr_offset; int inserted; hsize_t idx; char table_title[255]; size_t member_offset; char attr_name[255]; hid_t attr_id; char aux[255]; unsigned char *tmp_buf; unsigned char *tmp_fill_buf; hsize_t i; /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0 ) return -1; /*------------------------------------------------------------------------- * Get information about the old data type *------------------------------------------------------------------------- */ /* Open the dataset. */ if ( (dataset_id1 = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* Get creation properties list */ if ( (plist_id1 = H5Dget_create_plist( dataset_id1 )) < 0 ) goto out; /* Get the datatype */ if ( (type_id1 = H5Dget_type( dataset_id1 )) < 0 ) goto out; /* Get the size of the datatype */ if ( ( total_size = H5Tget_size( type_id1 )) == 0 ) goto out; /* Get the dataspace handle */ if ( (space_id1 = H5Dget_space( dataset_id1 )) < 0 ) goto out; /* Get dimension */ if ( H5Sget_simple_extent_dims( space_id1, dims, NULL) < 0 ) goto out; /*------------------------------------------------------------------------- * Get attributes *------------------------------------------------------------------------- */ /* Get the table title */ if ( (H5TBAget_title( dataset_id1, table_title )) < 0 ) goto out; /* alloc fill value attribute buffer */ tmp_fill_buf = (unsigned char *)malloc(total_size ); /* Get the fill value attributes */ if ( (H5TBAget_fill( loc_id, dset_name, dataset_id1, tmp_fill_buf )) < 0 ) goto out; /*------------------------------------------------------------------------- * Create a new data type *------------------------------------------------------------------------- */ /* Get the new member size */ member_size = H5Tget_size( field_type ); /* Create the data type. */ if (( type_id2 = H5Tcreate (H5T_COMPOUND,(size_t)(total_size + member_size) )) < 0 ) goto out; curr_offset = 0; inserted = 0; /* Insert the old fields, counting with the new one */ for ( i = 0; i < nfields + 1; i++) { idx = i; if ( inserted ) idx = i - 1; if ( i == position ) { /* Get the new member size */ new_member_size = H5Tget_size( field_type ); /* Insert the new field type */ if ( H5Tinsert( type_id2, field_name, curr_offset, field_type ) < 0 ) goto out; curr_offset += new_member_size; inserted = 1; continue; } /* Get the member name */ member_name = H5Tget_member_name( type_id1, (unsigned)idx ); /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1,(unsigned)idx )) < 0 ) goto out; /* Get the member size */ member_size = H5Tget_size( member_type_id ); /* Insert it into the new type */ if ( H5Tinsert( type_id2, member_name, curr_offset, member_type_id ) < 0 ) goto out; curr_offset += member_size; free( member_name ); /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; } /* i */ /*------------------------------------------------------------------------- * Create a new temporary dataset *------------------------------------------------------------------------- */ /* Retrieve the size of chunk */ if ( H5Pget_chunk( plist_id1, 1, dims_chunk ) < 0 ) goto out; /* Create a new simple data space with unlimited size, using the dimension */ if ( ( space_id2 = H5Screate_simple( 1, dims, maxdims )) < 0 ) return -1; /* Modify dataset creation properties, i.e. enable chunking */ plist_id2 = H5Pcreate (H5P_DATASET_CREATE); if ( H5Pset_chunk ( plist_id2, 1, dims_chunk ) < 0 ) return -1; /* Create the dataset. */ if ( ( dataset_id2 = H5Dcreate( loc_id, "new", type_id2, space_id2, plist_id2 )) < 0 ) goto out; /*------------------------------------------------------------------------- * Read data from 1st table *------------------------------------------------------------------------- */ tmp_buf = (unsigned char *)calloc((size_t) nrecords, (size_t)total_size ); /* Define a hyperslab in the dataset of the size of the records */ offset[0] = 0; count[0] = nrecords; if ( H5Sselect_hyperslab( space_id1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ( (mem_space_id1 = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ( H5Dread( dataset_id1, type_id1, mem_space_id1, H5S_ALL, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Save data from 1st table into new table, using the 1st type id *------------------------------------------------------------------------- */ /* Write */ if ( H5Dwrite( dataset_id2, type_id1, mem_space_id1, H5S_ALL, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /*------------------------------------------------------------------------- * Save the function supplied data of the new field *------------------------------------------------------------------------- */ /* Create a write id */ if ( ( write_type_id = H5Tcreate( H5T_COMPOUND, (size_t)new_member_size )) < 0 ) goto out; /* The field in the file is found by its name */ if ( H5Tinsert( write_type_id, field_name, (size_t)0, field_type ) < 0 ) goto out; /* Create xfer properties to preserve initialized data */ if ((PRESERVE = H5Pcreate (H5P_DATASET_XFER))<0) goto out; if (H5Pset_preserve (PRESERVE, 1)<0) goto out; /* Only write if there is something to write */ if ( data ) { /* Create a memory dataspace handle */ if ( (mem_space_id2 = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; /* Write */ if ( H5Dwrite( dataset_id2, write_type_id, mem_space_id2, space_id2, PRESERVE, data ) < 0 ) goto out; /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id2 ) < 0 ) goto out; } /* End access to the property list */ if ( H5Pclose( PRESERVE ) < 0 ) goto out; /*------------------------------------------------------------------------- * Release resources from 1st table *------------------------------------------------------------------------- */ /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id1 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id1 ) < 0 ) goto out; /* Terminate access to a property list */ if ( H5Pclose( plist_id1 ) < 0 ) goto out; /* Terminate access to the data space */ if ( H5Sclose( space_id1 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id1 ) < 0 ) goto out; /*------------------------------------------------------------------------- * Release resources from 2nd table *------------------------------------------------------------------------- */ /* Terminate access to the dataspace */ if ( H5Sclose( space_id2 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id2 ) < 0 ) return -1; /* Terminate access to a property list */ if ( H5Pclose( plist_id2 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id2 ) < 0 ) return -1; /*------------------------------------------------------------------------- * Delete 1st table *------------------------------------------------------------------------- */ if ( H5Gunlink( loc_id, dset_name ) < 0 ) return -1; /*------------------------------------------------------------------------- * Rename 2nd table *------------------------------------------------------------------------- */ if ( H5Lmove( loc_id, "new", H5L_SAME_LOC, dset_name, H5P_DEFAULT, H5P_DEFAULT ) < 0 ) return -1; /*------------------------------------------------------------------------- * Attach the conforming table attributes *------------------------------------------------------------------------- */ /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0 ) return -1; /* Open the dataset. */ if ( (dataset_id1 = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* Get the datatype */ if ( (type_id1 = H5Dget_type( dataset_id1 )) < 0 ) goto out; /* Set the attributes */ if ( H5TB_attach_attributes( table_title, loc_id, dset_name,(hsize_t) nfields, type_id1 ) < 0 ) return -1; /*------------------------------------------------------------------------- * Attach the fill attributes from previous table *------------------------------------------------------------------------- */ if (( space_id1 = H5Screate(H5S_SCALAR)) < 0 ) goto out; for ( i = 0; i < nfields-1; i++) { /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1, (unsigned) i )) < 0 ) goto out; /* Get the member offset */ member_offset = H5Tget_member_offset( type_id1, (unsigned) i ); strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d", (int)i ); strcat( attr_name, aux ); sprintf( aux, "%s", "_FILL" ); strcat( attr_name, aux ); if ( (attr_id = H5Acreate( dataset_id1, attr_name, member_type_id, space_id1, H5P_DEFAULT )) < 0 ) goto out; if ( H5Awrite( attr_id, member_type_id, tmp_fill_buf+member_offset ) < 0 ) goto out; if ( H5Aclose( attr_id ) < 0 ) goto out; /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; } /*------------------------------------------------------------------------- * Attach the fill attribute from the new field, if present *------------------------------------------------------------------------- */ if ( fill_data ) { strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d",(int)( nfields-1) ); strcat( attr_name, aux ); sprintf( aux, "%s", "_FILL" ); strcat( attr_name, aux ); /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1, (unsigned)nfields-1 )) < 0 ) goto out; if ( (attr_id = H5Acreate( dataset_id1, attr_name, member_type_id, space_id1, H5P_DEFAULT )) < 0 ) goto out; if ( H5Awrite( attr_id, member_type_id, fill_data ) < 0 ) goto out; if ( H5Aclose( attr_id ) < 0 ) goto out; if ( H5Tclose( member_type_id ) < 0 ) goto out; } /* Close data space. */ if ( H5Sclose( space_id1 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id1 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id1 ) < 0 ) goto out; /* Release resources. */ free ( tmp_buf ); free ( tmp_fill_buf ); return 0; out: H5Dclose( dataset_id1 ); return -1; } /*------------------------------------------------------------------------- * Function: H5TBdelete_field * * Purpose: Deletes a field * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2002 * * Comments: * * Modifications: * * *------------------------------------------------------------------------- */ herr_t H5TBdelete_field( hid_t loc_id, const char *dset_name, const char *field_name ) { /* Identifiers for the 1st original dataset */ hid_t dataset_id1; hid_t type_id1; hid_t space_id1; hid_t plist_id1; /* Identifiers for the 2nd new dataset */ hid_t dataset_id2; hid_t type_id2; hid_t space_id2; hid_t plist_id2; hid_t member_type_id; size_t member_size; char *member_name; size_t type_size1; size_t type_size2; hsize_t nfields; hsize_t nrecords; hsize_t dims_chunk[1]; hsize_t dims[1]; hsize_t maxdims[1] = { H5S_UNLIMITED }; hid_t PRESERVE; size_t curr_offset; size_t delete_member_size = 0; hid_t read_type_id; hid_t write_type_id; unsigned char *tmp_buf; unsigned char *tmp_fill_buf; char attr_name[255]; char aux[255]; char table_title[255]; size_t member_offset; hid_t attr_id; hsize_t i; int has_fill=0; /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0 ) return -1; /*------------------------------------------------------------------------- * Get information about the old data type *------------------------------------------------------------------------- */ /* Open the dataset. */ if ( (dataset_id1 = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* Get creation properties list */ if ( (plist_id1 = H5Dget_create_plist( dataset_id1 )) < 0 ) goto out; /* Get the datatype */ if ( (type_id1 = H5Dget_type( dataset_id1 )) < 0 ) goto out; /* Get the size of the datatype */ type_size1 = H5Tget_size( type_id1 ); /* Get the dataspace handle */ if ( (space_id1 = H5Dget_space( dataset_id1 )) < 0 ) goto out; /* Get dimension */ if ( H5Sget_simple_extent_dims( space_id1, dims, NULL) < 0 ) goto out; /*------------------------------------------------------------------------- * Create a new data type; first we find the size of the datatype to delete *------------------------------------------------------------------------- */ /* Check out the field */ for ( i = 0; i < nfields; i++) { /* Get the member name */ member_name = H5Tget_member_name( type_id1,(unsigned) i ); /* We want to find the field to delete */ if ( H5TB_find_field( member_name, field_name ) > 0 ) { /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1,(unsigned) i )) < 0 ) goto out; /* Get the member size */ delete_member_size = H5Tget_size( member_type_id ); /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; free( member_name ); break; } free( member_name ); } /* i */ /* No field to delete was found */ if ( delete_member_size == 0 ) goto out; /*------------------------------------------------------------------------- * Create a new data type; we now insert all the fields into the new type *------------------------------------------------------------------------- */ type_size2 = type_size1 - delete_member_size; /* Create the data type. */ if (( type_id2 = H5Tcreate (H5T_COMPOUND, type_size2 )) < 0 ) goto out; curr_offset = 0; /* alloc fill value attribute buffer */ tmp_fill_buf = (unsigned char *)malloc((size_t) type_size2 ); /*------------------------------------------------------------------------- * Get attributes from previous table in the process *------------------------------------------------------------------------- */ /* Get the table title */ if ( (H5TBAget_title( dataset_id1, table_title )) < 0 ) goto out; /* Insert the old fields except the one to delete */ for ( i = 0; i < nfields; i++) { /* Get the member name */ member_name = H5Tget_member_name( type_id1, (unsigned) i ); /* We want to skip the field to delete */ if ( H5TB_find_field( member_name, field_name ) > 0 ) { free( member_name ); continue; } /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1, (unsigned)i )) < 0 ) goto out; /* Get the member size */ member_size = H5Tget_size( member_type_id ); /* Insert it into the new type */ if ( H5Tinsert( type_id2, member_name, curr_offset, member_type_id ) < 0 ) goto out; /*------------------------------------------------------------------------- * Get the fill value information *------------------------------------------------------------------------- */ strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d", (int)i ); strcat( attr_name, aux ); sprintf( aux, "%s", "_FILL" ); strcat( attr_name, aux ); /* Check if we have the _FILL attribute */ has_fill = H5LT_find_attribute( dataset_id1, attr_name ); /* Get it */ if ( has_fill == 1 ) { if ( H5LT_get_attribute_disk( dataset_id1, attr_name, tmp_fill_buf+curr_offset ) < 0 ) goto out; } curr_offset += member_size; free( member_name ); /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; } /* i */ /*------------------------------------------------------------------------- * Create a new temporary dataset *------------------------------------------------------------------------- */ /* Retrieve the size of chunk */ if ( H5Pget_chunk( plist_id1, 1, dims_chunk ) < 0 ) goto out; /* Create a new simple data space with unlimited size, using the dimension */ if ( ( space_id2 = H5Screate_simple( 1, dims, maxdims )) < 0 ) return -1; /* Modify dataset creation properties, i.e. enable chunking */ plist_id2 = H5Pcreate (H5P_DATASET_CREATE); if ( H5Pset_chunk ( plist_id2, 1, dims_chunk ) < 0 ) return -1; /* Create the dataset. */ if ( ( dataset_id2 = H5Dcreate( loc_id, "new", type_id2, space_id2, plist_id2 )) < 0 ) goto out; /*------------------------------------------------------------------------- * We have to read field by field of the old dataset and save it into the new one *------------------------------------------------------------------------- */ for ( i = 0; i < nfields; i++) { /* Get the member name */ member_name = H5Tget_member_name( type_id1,(unsigned) i ); /* Skip the field to delete */ if ( H5TB_find_field( member_name, field_name ) > 0 ) { free( member_name ); continue; } /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1, (unsigned)i )) < 0 ) goto out; /* Get the member size */ member_size = H5Tget_size( member_type_id ); /* Create a read id */ if ( ( read_type_id = H5Tcreate( H5T_COMPOUND, member_size )) < 0 ) goto out; /* Insert it into the new type */ if ( H5Tinsert( read_type_id, member_name, (size_t)0, member_type_id ) < 0 ) goto out; tmp_buf = (unsigned char *)calloc((size_t) nrecords, member_size ); /* Read */ if ( H5Dread( dataset_id1, read_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, tmp_buf ) < 0 ) goto out; /* Create a write id */ if ( ( write_type_id = H5Tcreate( H5T_COMPOUND, member_size )) < 0 ) goto out; /* The field in the file is found by its name */ if ( H5Tinsert( write_type_id, member_name, (size_t)0, member_type_id ) < 0 ) goto out; /* Create xfer properties to preserve initialized data */ if ((PRESERVE = H5Pcreate (H5P_DATASET_XFER))<0) goto out; if (H5Pset_preserve (PRESERVE, 1)<0) goto out; /* Write */ if ( H5Dwrite( dataset_id2, write_type_id, H5S_ALL, H5S_ALL, PRESERVE, tmp_buf ) < 0 ) goto out; /* End access to the property list */ if ( H5Pclose( PRESERVE ) < 0 ) goto out; /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; /* Close the read type */ if ( H5Tclose( read_type_id ) < 0 ) goto out; /* Close the write type */ if ( H5Tclose( write_type_id ) < 0 ) goto out; /* Release resources. */ free( member_name ); free ( tmp_buf ); } /* i */ /*------------------------------------------------------------------------- * Release resources from 1st table *------------------------------------------------------------------------- */ /* Release the datatype. */ if ( H5Tclose( type_id1 ) < 0 ) goto out; /* Terminate access to a property list */ if ( H5Pclose( plist_id1 ) < 0 ) goto out; /* Terminate access to the data space */ if ( H5Sclose( space_id1 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id1 ) < 0 ) goto out; /*------------------------------------------------------------------------- * Release resources from 2nd table *------------------------------------------------------------------------- */ /* Terminate access to the dataspace */ if ( H5Sclose( space_id2 ) < 0 ) goto out; /* Release the datatype. */ if ( H5Tclose( type_id2 ) < 0 ) return -1; /* Terminate access to a property list */ if ( H5Pclose( plist_id2 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id2 ) < 0 ) return -1; /*------------------------------------------------------------------------- * Delete 1st table *------------------------------------------------------------------------- */ if ( H5Gunlink( loc_id, dset_name ) < 0 ) return -1; /*------------------------------------------------------------------------- * Rename 2nd table *------------------------------------------------------------------------- */ if ( H5Lmove( loc_id, "new", H5L_SAME_LOC, dset_name, H5P_DEFAULT, H5P_DEFAULT ) < 0 ) return -1; /*------------------------------------------------------------------------- * Attach the conforming table attributes *------------------------------------------------------------------------- */ /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0 ) return -1; /* Open the dataset. */ if ( (dataset_id1 = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* Get the datatype */ if ( (type_id1 = H5Dget_type( dataset_id1 )) < 0 ) goto out; /* Set the attributes */ if ( H5TB_attach_attributes( table_title, loc_id, dset_name, nfields, type_id1 ) < 0 ) return -1; /*------------------------------------------------------------------------- * Attach the fill attributes from previous table *------------------------------------------------------------------------- */ if ( has_fill == 1 ) { if (( space_id1 = H5Screate(H5S_SCALAR)) < 0 ) goto out; for ( i = 0; i < nfields; i++) { /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( type_id1, (unsigned)i )) < 0 ) goto out; /* Get the member offset */ member_offset = H5Tget_member_offset( type_id1, (unsigned)i ); strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d", (int)i ); strcat( attr_name, aux ); sprintf( aux, "%s", "_FILL" ); strcat( attr_name, aux ); if ( (attr_id = H5Acreate( dataset_id1, attr_name, member_type_id, space_id1, H5P_DEFAULT )) < 0 ) goto out; if ( H5Awrite( attr_id, member_type_id, tmp_fill_buf+member_offset ) < 0 ) goto out; if ( H5Aclose( attr_id ) < 0 ) goto out; /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; } /* Close data space. */ if ( H5Sclose( space_id1 ) < 0 ) goto out; } /*has_fill*/ /* Release the datatype. */ if ( H5Tclose( type_id1 ) < 0 ) goto out; /* End access to the dataset */ if ( H5Dclose( dataset_id1 ) < 0 ) goto out; /* Release resources. */ free ( tmp_fill_buf ); return 0; out: H5Dclose( dataset_id1 ); return -1; } /*------------------------------------------------------------------------- * * Table attribute functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBAget_title * * Purpose: Read the table title * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2001 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5TBAget_title( hid_t loc_id, char *table_title ) { /* Get the TITLE attribute */ if ( H5LT_get_attribute_disk( loc_id, "TITLE", table_title ) < 0 ) return -1; return 0; } /*------------------------------------------------------------------------- * Function: H5TBAget_fill * * Purpose: Read the table attribute fill values * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2002 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5TBAget_fill( hid_t loc_id, const char *dset_name, hid_t dset_id, unsigned char *dst_buf ) { hsize_t nfields; hsize_t nrecords; char attr_name[255]; char aux[255]; hsize_t i; size_t *src_offset; int has_fill=0; /* Get the number of records and fields */ if ( H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0 ) return -1; src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t)); if (src_offset == NULL ) return -1; /* Get field info */ if ( H5TBget_field_info( loc_id, dset_name, NULL, NULL, src_offset, NULL ) < 0 ) goto out; for ( i = 0; i < nfields; i++) { strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d", (int)i ); strcat( attr_name, aux ); sprintf( aux, "%s", "_FILL" ); strcat( attr_name, aux ); /* Check if we have the _FILL attribute */ has_fill = H5LT_find_attribute( dset_id, attr_name ); /* Get it */ if ( has_fill == 1 ) { if ( H5LT_get_attribute_disk( dset_id, attr_name, dst_buf+src_offset[i] ) < 0 ) goto out; } } free( src_offset ); return has_fill; out: free( src_offset ); return -1; } /*------------------------------------------------------------------------- * * Inquiry functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBget_table_info * * Purpose: Gets the number of records and fields of a table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * * Modifications: May 08, 2003 * In version 2.0 of Table, the number of records is stored as an * attribute "NROWS" * * *------------------------------------------------------------------------- */ herr_t H5TBget_table_info ( hid_t loc_id, const char *dset_name, hsize_t *nfields, hsize_t *nrecords ) { hid_t tid; hid_t sid=-1; hid_t did; int num_members; hsize_t dims[1]; int has_attr; hsize_t n[1]; /* Open the dataset. */ if ( (did = H5Dopen( loc_id, dset_name )) < 0 ) return -1; /* Get the datatype */ if ( (tid = H5Dget_type( did )) < 0 ) goto out; /* Get the number of members */ if ( (num_members = H5Tget_nmembers( tid )) < 0 ) goto out; if (nfields) *nfields = num_members; /*------------------------------------------------------------------------- * Get number of records *------------------------------------------------------------------------- */ if (nrecords) { /* Try to find the attribute "NROWS" */ has_attr = H5LT_find_attribute( did, "NROWS" ); /* It exists, get it */ if ( has_attr == 1 ) { /* Get the attribute */ if ( H5LTget_attribute(loc_id,dset_name,"NROWS",H5T_NATIVE_LLONG,n)<0) return -1; /**nrecords = *n;*/ *nrecords = n[0]; } else { /* Get the dataspace handle */ if ( (sid = H5Dget_space( did )) < 0 ) goto out; /* Get records */ if ( H5Sget_simple_extent_dims( sid, dims, NULL) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( sid ) < 0 ) goto out; *nrecords = dims[0]; } }/*nrecords*/ /* close */ if ( H5Tclose( tid ) < 0 ) goto out; if ( H5Dclose( did ) < 0 ) return -1; return 0; /* error zone, gracefully close */ out: H5E_BEGIN_TRY { H5Dclose(did); H5Sclose(sid); H5Tclose(tid); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: H5TBget_field_info * * Purpose: Get information about fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * * Modifications: * * *------------------------------------------------------------------------- */ herr_t H5TBget_field_info( hid_t loc_id, const char *dset_name, char *field_names[], size_t *field_sizes, size_t *field_offsets, size_t *type_size ) { hid_t did; hid_t ftype_id; hid_t native_type_id; hssize_t nfields; char *member_name; hid_t member_type_id; hid_t nativem_type_id; size_t member_size; size_t member_offset; size_t size; hssize_t i; /* Open the dataset. */ if ( ( did = H5Dopen( loc_id, dset_name )) < 0 ) goto out; /* Get the datatype */ if ( ( ftype_id = H5Dget_type( did )) < 0 ) goto out; if ((native_type_id = H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<0) goto out; /* Get the type size */ size = H5Tget_size( native_type_id ); if ( type_size ) *type_size = size; /* Get the number of members */ if ( ( nfields = H5Tget_nmembers( ftype_id )) < 0 ) goto out; /* Iterate tru the members */ for ( i = 0; i < nfields; i++) { /* Get the member name */ member_name = H5Tget_member_name( ftype_id, (unsigned)i ); if ( field_names ) strcpy( field_names[i], member_name ); /* Get the member type */ if ( ( member_type_id = H5Tget_member_type( ftype_id,(unsigned) i )) < 0 ) goto out; if ((nativem_type_id = H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT))<0) goto out; /* Get the member size */ member_size = H5Tget_size( nativem_type_id ); if ( field_sizes ) field_sizes[i] = member_size; /* Get the member offset */ member_offset = H5Tget_member_offset( native_type_id,(unsigned) i ); if ( field_offsets ) field_offsets[i] = member_offset; /* Close the member type */ if ( H5Tclose( member_type_id ) < 0 ) goto out; if ( H5Tclose( nativem_type_id ) < 0 ) goto out; free( member_name ); } /* i */ /* Release the datatype. */ if ( H5Tclose( ftype_id ) < 0 ) return -1; if ( H5Tclose( native_type_id ) < 0 ) return -1; /* End access to the dataset */ if ( H5Dclose( did ) < 0 ) return -1; return 0; out: H5Dclose( did ); return -1; } /*------------------------------------------------------------------------- * * internal functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TB_find_field * * Purpose: Find a string field * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * *------------------------------------------------------------------------- */ static int H5TB_find_field( const char *field, const char *field_list ) { const char *start = field_list; const char *end; while ( (end = strstr( start, "," )) != 0 ) { size_t count = end - start; if ( strncmp(start, field, count) == 0 && count == strlen(field) ) return 1; start = end + 1; } if ( strcmp( start, field ) == 0 ) return 1; return -1; } /*------------------------------------------------------------------------- * Function: H5TB_attach_attributes * * Purpose: Private function that creates the conforming table attributes; * Used by H5TBcombine_tables; not used by H5TBmake_table, which does not read * the fill value attributes from an existing table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December 6, 2001 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5TB_attach_attributes( const char *table_title, hid_t loc_id, const char *dset_name, hsize_t nfields, hid_t tid ) { char attr_name[255]; char *member_name; char aux[255]; hsize_t i; /* Attach the CLASS attribute */ if ( H5LTset_attribute_string( loc_id, dset_name, "CLASS", TABLE_CLASS ) < 0 ) goto out; /* Attach the VERSION attribute */ if ( H5LTset_attribute_string( loc_id, dset_name, "VERSION", "2.0" ) < 0 ) goto out; /* Attach the TITLE attribute */ if ( H5LTset_attribute_string( loc_id, dset_name, "TITLE", table_title ) < 0 ) goto out; /* Attach the FIELD_ name attribute */ for ( i = 0; i < nfields; i++) { /* Get the member name */ member_name = H5Tget_member_name( tid, (unsigned)i ); strcpy( attr_name, "FIELD_" ); sprintf( aux, "%d", (int)i ); strcat( attr_name, aux ); sprintf( aux, "%s", "_NAME" ); strcat( attr_name, aux ); /* Attach the attribute */ if ( H5LTset_attribute_string( loc_id, dset_name, attr_name, member_name ) < 0 ) goto out; free( member_name ); } return 0; out: return -1; } /*------------------------------------------------------------------------- * Function: H5TB_create_type * * Purpose: Private function that creates a memory type ID * * Return: Success: the memory type ID, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: March 31, 2004 * * Comments: * * Modifications: * *------------------------------------------------------------------------- */ static hid_t H5TB_create_type(hid_t loc_id, const char *dset_name, size_t type_size, const size_t *field_offset, const size_t *field_sizes, hid_t ftype_id) { hid_t mem_type_id; hid_t mtype_id=-1; hid_t nmtype_id=-1; size_t size_native; hsize_t nfields; char **fnames; unsigned i; /* get the number of fields */ if (H5TBget_table_info(loc_id,dset_name,&nfields,NULL)<0) return -1; if ((fnames=malloc(sizeof(char*)*(size_t)nfields))==NULL) return -1; for ( i=0; i<nfields; i++) { if ((fnames[i]=malloc(sizeof(char)*HLTB_MAX_FIELD_LEN))==NULL) { free(fnames); return -1; } } /* get field info */ if ( H5TBget_field_info(loc_id,dset_name,fnames,NULL,NULL,NULL)<0) goto out; /* create the memory data type */ if ((mem_type_id=H5Tcreate(H5T_COMPOUND,type_size))<0) goto out; /* get each field ID and adjust its size, if necessary */ for ( i=0; i<nfields; i++) { if ((mtype_id=H5Tget_member_type(ftype_id,i))<0) goto out; if ((nmtype_id=H5Tget_native_type(mtype_id,H5T_DIR_DEFAULT))<0) goto out; size_native=H5Tget_size(nmtype_id); if (field_sizes[i]!=size_native) { if (H5Tset_size(nmtype_id,field_sizes[i])<0) goto out; } if (H5Tinsert(mem_type_id,fnames[i],field_offset[i],nmtype_id) < 0 ) goto out; if (H5Tclose(mtype_id)<0) goto out; if (H5Tclose(nmtype_id)<0) goto out; } for ( i=0; i<nfields; i++) { free (fnames[i]); } free (fnames); return mem_type_id; /* error zone, gracefully close and free */ out: H5E_BEGIN_TRY { H5Tclose(mtype_id); H5Tclose(nmtype_id); } H5E_END_TRY; for ( i=0; i<nfields; i++) { if (fnames[i]) free (fnames[i]); } if (fnames) free (fnames); return -1; } /*------------------------------------------------------------------------- * * Functions shared between H5TB and H5PT * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TB_common_append_records * * Purpose: Common code for reading records shared between H5PT and H5TB * * Return: Success: 0, Failure: -1 * * Programmer: Nat Furrer, nfurrer@ncsa.uiuc.edu * James Laird, jlaird@ncsa.uiuc.edu * * Date: March 8, 2004 * * Comments: Called by H5TBappend_records and H5PTappend_records * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5TB_common_append_records( hid_t dataset_id, hid_t mem_type_id, size_t nrecords, hsize_t orig_table_size, const void * data) { hsize_t count[1]; hsize_t offset[1]; hid_t space_id = H5I_BADID; hid_t mem_space_id = H5I_BADID; hsize_t dims[1]; hsize_t mem_dims[1]; /* Extend the dataset */ dims[0] = nrecords + orig_table_size; if ( H5Dextend ( dataset_id, dims ) < 0 ) goto out; /* Create a simple memory data space */ mem_dims[0]=nrecords; if ( (mem_space_id = H5Screate_simple( 1, mem_dims, NULL )) < 0 ) goto out; /* Get a copy of the new file data space for writing */ if ( (space_id = H5Dget_space( dataset_id )) < 0 ) goto out; /* Define a hyperslab in the dataset */ offset[0] = orig_table_size; count[0] = nrecords; if ( H5Sselect_hyperslab( space_id, H5S_SELECT_SET, offset, NULL, count, NULL)<0) goto out; /* Write the records */ if ( H5Dwrite( dataset_id, mem_type_id, mem_space_id, space_id, H5P_DEFAULT, data )<0) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; if ( H5Sclose( space_id ) < 0 ) goto out; return 0; out: H5E_BEGIN_TRY H5Sclose(mem_space_id); H5Sclose(space_id); H5E_END_TRY return -1; } /*------------------------------------------------------------------------- * Function: H5TB_common_read_records * * Purpose: Common code for reading records shared between H5PT and H5TB * * Return: Success: 0, Failure: -1 * * Programmer: Nat Furrer, nfurrer@ncsa.uiuc.edu * James Laird, jlaird@ncsa.uiuc.edu * * Date: March 8, 2004 * * Comments: Called by H5TBread_records and H5PTread_records * * Modifications: * * *------------------------------------------------------------------------- */ herr_t H5TB_common_read_records( hid_t dataset_id, hid_t mem_type_id, hsize_t start, size_t nrecords, hsize_t table_size, void *data) { hsize_t count[1]; hsize_t offset[1]; hid_t space_id = H5I_BADID; hid_t mem_space_id = H5I_BADID; hsize_t mem_size[1]; /* Make sure the read request is in bounds */ if ( start + nrecords > table_size ) goto out; /* Get the dataspace handle */ if ( (space_id = H5Dget_space( dataset_id )) < 0 ) goto out; /* Define a hyperslab in the dataset of the size of the records */ offset[0] = start; count[0] = nrecords; if ( H5Sselect_hyperslab( space_id, H5S_SELECT_SET, offset, NULL, count, NULL) < 0 ) goto out; /* Create a memory dataspace handle */ mem_size[0] = count[0]; if ((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0 ) goto out; if ((H5Dread( dataset_id, mem_type_id, mem_space_id, space_id, H5P_DEFAULT, data))<0) goto out; /* Terminate access to the memory dataspace */ if ( H5Sclose( mem_space_id ) < 0 ) goto out; /* Terminate access to the dataspace */ if ( H5Sclose( space_id ) < 0 ) goto out; return 0; out: H5E_BEGIN_TRY H5Sclose(space_id); H5Sclose(mem_space_id); H5E_END_TRY return -1; }