hdf5/tools/lib/h5tools.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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.     *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*
 * Programmer:  Robb Matzke <matzke@llnl.gov>
 *              Thursday, July 23, 1998
 *
 * Purpose: A library for displaying the values of a dataset in a human
 *  readable format.
 */

#include <stdio.h>
#include <stdlib.h>

#include "h5tools.h"
#include "h5tools_ref.h"
#include "h5tools_str.h"
#include "h5tools_utils.h"
#include "H5private.h"

#define SANITY_CHECK

#define ALIGN(A,Z)  ((((A) + (Z) - 1) / (Z)) * (Z))

/* global variables */
int         compound_data;
FILE       *rawdatastream; /* should initialize to stdout but gcc moans about it */
int         bin_output;    /* binary output */
int         bin_form;      /* binary form */


/* local prototypes */
static int do_bin_output(FILE *stream, hsize_t nelmts, hid_t tid, void *_mem);
static int render_bin_output(FILE *stream, hid_t tid, void *_mem);

/* module-scoped variables */
static int  h5tools_init_g;     /* if h5tools lib has been initialized */
#ifdef H5_HAVE_PARALLEL
static int  h5tools_mpi_init_g; /* if MPI_Init() has been called */
#endif /* H5_HAVE_PARALLEL */

/* Names of VFDs */
static const char *drivernames[]={
    "sec2",
    "family",
    "split",
    "multi",
#ifdef H5_HAVE_STREAM
    "stream",
#endif /* H5_HAVE_STREAM */
#ifdef H5_HAVE_PARALLEL
    "mpio",
    "mpiposix"
#endif /* H5_HAVE_PARALLEL */
};

/* This enum should match the entries in the above drivers_list since they
 * are indexes into the drivers_list array. */
enum {
    SEC2_IDX = 0
   ,FAMILY_IDX
   ,SPLIT_IDX
   ,MULTI_IDX
#ifdef H5_HAVE_STREAM
   ,STREAM_IDX
#endif /* H5_HAVE_STREAM */
#ifdef H5_HAVE_PARALLEL
   ,MPIO_IDX
   ,MPIPOSIX_IDX
#endif /* H5_HAVE_PARALLEL */
} driver_idx;
#define NUM_DRIVERS     (sizeof(drivernames) / sizeof(drivernames[0]))

/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose:     Initialize the H5 Tools library
 * Description:
 *      This should be called before any other h5tools function is called.
 *      Effect of any h5tools function called before this has been called is
 *      undetermined.
 * Return:
 *      None
 * Programmer:
 *      Albert Cheng, 2000-10-31
 * Modifications:
 *-------------------------------------------------------------------------
 */
void
h5tools_init(void)
{
    if (!h5tools_init_g) {
    if (!rawdatastream)
        rawdatastream = stdout;

    h5tools_init_g++;
    }
}

/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose: Close the H5 Tools library
 * Description:
 *      Close or release resources such as files opened by the library. This
 *      should be called after all other h5tools functions have been called.
 *      Effect of any h5tools function called after this has been called is
 *      undetermined.
 * Return:
 *      None
 * Programmer:
 *      Albert Cheng, 2000-10-31
 * Modifications:
 *-------------------------------------------------------------------------
 */
void
h5tools_close(void)
{
    if (h5tools_init_g) {
        if (rawdatastream && rawdatastream != stdout) {
            if (fclose(rawdatastream))
            perror("closing rawdatastream");
            else
            rawdatastream = NULL;
        }

        /* Clean up the reference path table, if it's been used */
        term_ref_path_table();

        /* Shut down the library */
        H5close();

        h5tools_init_g = 0;
    }
}

/*-------------------------------------------------------------------------
 * Audience:    Private
 * Chapter:     H5Tools Library
 * Purpose: Get a FAPL for a driver
 * Description:
 *      Get a FAPL for a given VFL driver name.
 * Return:
 *      None
 * Programmer:
 *      Quincey Koziol, 2004-02-04
 * Modifications:
 *      Pedro Vicente Nunes, Thursday, July 27, 2006
 *   Added error return conditions for the H5Pset_fapl calls
 *-------------------------------------------------------------------------
 */
static hid_t
h5tools_get_fapl(hid_t fapl, const char *driver, unsigned *drivernum)
{
    hid_t new_fapl;     /* Copy of file access property list passed in, or new property list */

    /* Make a copy of the FAPL, for the file open call to use, eventually */
    if(fapl == H5P_DEFAULT) {
        if((new_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
            goto error;
    } /* end if */
    else {
        if((new_fapl = H5Pcopy(fapl)) < 0)
            goto error;
    } /* end else */

    /* Determine which driver the user wants to open the file with. Try
     * that driver. If it can't open it, then fail. */
    if(!strcmp(driver, drivernames[SEC2_IDX])) {
        /* SEC2 driver */
        if(H5Pset_fapl_sec2(new_fapl) < 0)
            goto error;

        if(drivernum)
            *drivernum = SEC2_IDX;
    } else if(!strcmp(driver, drivernames[FAMILY_IDX])) {
        /* FAMILY Driver */

        /* Set member size to be 0 to indicate the current first member size
         * is the member size.
         */
        if(H5Pset_fapl_family(new_fapl, (hsize_t)0, H5P_DEFAULT) < 0)
            goto error;

        if(drivernum)
            *drivernum = FAMILY_IDX;
    } else if(!strcmp(driver, drivernames[SPLIT_IDX])) {
        /* SPLIT Driver */
        if(H5Pset_fapl_split(new_fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0)
            goto error;

        if(drivernum)
            *drivernum = SPLIT_IDX;
    } else if(!strcmp(driver, drivernames[MULTI_IDX])) {
        /* MULTI Driver */
        if(H5Pset_fapl_multi(new_fapl, NULL, NULL, NULL, NULL, TRUE) < 0)
            goto error;

        if(drivernum)
            *drivernum = MULTI_IDX;
#ifdef H5_HAVE_STREAM
    } else if(!strcmp(driver, drivernames[STREAM_IDX])) {
        /* STREAM Driver */
        if(H5Pset_fapl_stream(new_fapl, NULL) < 0)
            goto error;

        if(drivernum)
            *drivernum = STREAM_IDX;
#endif /* H5_HAVE_STREAM */
#ifdef H5_HAVE_PARALLEL
    } else if(!strcmp(driver, drivernames[MPIO_IDX])) {
        /* MPI-I/O Driver */
    /* check if MPI has been initialized. */
    if(!h5tools_mpi_init_g)
        MPI_Initialized(&h5tools_mpi_init_g);
        if(h5tools_mpi_init_g) {
            if(H5Pset_fapl_mpio(new_fapl, MPI_COMM_WORLD, MPI_INFO_NULL) < 0)
        goto error;

            if(drivernum)
                *drivernum = MPIO_IDX;
        } /* end if */
    } else if (!strcmp(driver, drivernames[MPIPOSIX_IDX])) {
        /* MPI-I/O Driver */
    /* check if MPI has been initialized. */
    if(!h5tools_mpi_init_g)
        MPI_Initialized(&h5tools_mpi_init_g);
        if(h5tools_mpi_init_g) {
            if(H5Pset_fapl_mpiposix(new_fapl, MPI_COMM_WORLD, TRUE) < 0)
        goto error;

            if(drivernum)
                *drivernum = MPIPOSIX_IDX;
        } /* end if */
#endif /* H5_HAVE_PARALLEL */
    } else {
        goto error;
    }

    return(new_fapl);

error:
    if(new_fapl != H5P_DEFAULT)
        H5Pclose(new_fapl);
    return -1;
}

/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose:     Open a file with various VFL drivers.
 * Description:
 *      Loop through the various types of VFL drivers trying to open FNAME.
 *      If the HDF5 library is version 1.2 or less, then we have only the SEC2
 *      driver to try out. If the HDF5 library is greater than version 1.2,
 *      then we have the FAMILY, SPLIT, and MULTI drivers to play with (and
 *      the STREAM driver if H5_HAVE_STREAM is defined, that is).
 *
 *      If DRIVER is non-NULL, then it will try to open the file with that
 *      driver first. We assume that the user knows what they are doing so, if
 *      we fail, then we won't try other file drivers.
 * Return:
 *      On success, returns a file id for the opened file. If DRIVERNAME is
 *      non-null then the first DRIVERNAME_SIZE-1 characters of the driver
 *      name are copied into the DRIVERNAME array and null terminated.
 *
 *      Otherwise, the function returns FAIL. If DRIVERNAME is non-null then
 *      the first byte is set to the null terminator.
 * Programmer:
 *      Lost in the mists of time.
 * Modifications:
 *      Robb Matzke, 2000-06-23
 *      We only have to initialize driver[] on the first call, thereby
 *      preventing memory leaks from repeated calls to H5Pcreate().
 *
 *      Robb Matzke, 2000-06-23
 *      Added DRIVERNAME_SIZE arg to prevent overflows when writing to
 *      DRIVERNAME.
 *
 *      Robb Matzke, 2000-06-23
 *      Added test to prevent coredump when the file could not be opened by
 *      any driver.
 *
 *      Robb Matzke, 2000-06-23
 *      Changed name from H5ToolsFopen() so it jives better with the names we
 *      already have at the top of this source file.
 *
 *      Thomas Radke, 2000-09-12
 *      Added Stream VFD to the driver[] array.
 *
 *      Bill Wendling, 2001-01-10
 *      Changed macro behavior so that if we have a version other than 1.2.x
 *      (i.e., > 1.2), then we do the drivers check.
 *
 *      Bill Wendling, 2001-07-30
 *      Added DRIVER parameter so that the user can specify "try this driver"
 *      instead of the default behaviour. If it fails to open the file with
 *      that driver, this will fail completely (i.e., we won't try the other
 *      drivers). We're assuming the user knows what they're doing. How UNIX
 *      of us.
 *-------------------------------------------------------------------------
 */
hid_t
h5tools_fopen(const char *fname, unsigned flags, hid_t fapl, const char *driver,
    char *drivername, size_t drivername_size)
{
    unsigned    drivernum;
    hid_t       fid = FAIL;
    hid_t       my_fapl = H5P_DEFAULT;

    if(driver && *driver) {
        /* Get the correct FAPL for the given driver */
        if((my_fapl = h5tools_get_fapl(fapl, driver, &drivernum)) < 0)
            goto done;

        H5E_BEGIN_TRY {
            fid = H5Fopen(fname, flags, my_fapl);
        } H5E_END_TRY;

        if(fid == FAIL)
            goto done;

    } else {
        /* Try to open the file using each of the drivers */
        for(drivernum = 0; drivernum < NUM_DRIVERS; drivernum++) {
            /* Get the correct FAPL for the given driver */
            if((my_fapl = h5tools_get_fapl(fapl, drivernames[drivernum], NULL)) < 0)
                goto done;

            H5E_BEGIN_TRY {
                fid = H5Fopen(fname, flags, my_fapl);
            } H5E_END_TRY;

            if(fid != FAIL)
                break;
            else {
                /* Close the FAPL */
                H5Pclose(my_fapl);
                my_fapl = H5P_DEFAULT;
            } /* end else */
        }
    }

    /* Save the driver name */
    if(drivername && drivername_size) {
        if(fid != FAIL) {
            strncpy(drivername, drivernames[drivernum], drivername_size);
            drivername[drivername_size - 1] = '\0';
        } else {
            /*no file opened*/
            drivername[0] = '\0';
        }
    }

done:
    if(my_fapl != H5P_DEFAULT)
        H5Pclose(my_fapl);
    return fid;
}

/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose:     Count the number of columns in a string.
 * Description:
 *      Count the number of columns in a string. This is the number of
 *      characters in the string not counting line-control characters.
 * Return:
 *      On success, returns the width of the string. Otherwise this function
 *      returns 0.
 * Programmer:
 *       Robb Matzke, Tuesday, April 27, 1999
 * Modifications:
 *-------------------------------------------------------------------------
 */
static size_t
h5tools_ncols(const char *s)
{
    register size_t i;

    for (i = 0; *s; s++)
        if (*s >= ' ')
            i++;

    return i;
}

/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose:     Emit a simple prefix to STREAM.
 * Description:
 *      If /ctx->need_prefix/ is set then terminate the current line (if
 *      applicable), calculate the prefix string, and display it at the start
 *      of a line.
 * Return:
 *      None
 * Programmer:
 *      Robb Matzke, Monday, April 26, 1999
 * Modifications:
 *      Robb Matzke, 1999-09-29
 * If a new prefix is printed then the current element number is set back
 * to zero.
 *      pvn, 2004-07-08
 * Added support for printing array indices:
 *  the indentation is printed before the prefix (printed one indentation
 *  level before)
 *-------------------------------------------------------------------------
 */
static void
h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info,
                      h5tools_context_t *ctx, hsize_t elmtno, int secnum)
{
    h5tools_str_t prefix;
    h5tools_str_t str; /*temporary for indentation */
    size_t templength = 0;
    int i, indentlevel = 0;

    if (!ctx->need_prefix)
 return;

    memset(&prefix, 0, sizeof(h5tools_str_t));
    memset(&str, 0, sizeof(h5tools_str_t));

    /* Terminate previous line, if any */
    if (ctx->cur_column) {
     fputs(OPT(info->line_suf, ""), stream);
     putc('\n', stream);
     fputs(OPT(info->line_sep, ""), stream);
    }

    /* Calculate new prefix */
    h5tools_str_prefix(&prefix, info, elmtno, ctx->ndims, ctx->p_min_idx,
                       ctx->p_max_idx, ctx);

    /* Write new prefix to output */
    if (ctx->indent_level >= 0) {
        indentlevel = ctx->indent_level;
    } else {
        /*
         * This is because sometimes we don't print out all the header
         * info for the data (like the tattr-2.ddl example). If that happens
         * the ctx->indent_level is negative so we need to skip the above and
         * just print out the default indent levels.
         */
 indentlevel = ctx->default_indent_level;
    }

    /* when printing array indices, print the indentation before the prefix
       the prefix is printed one indentation level before */
    if (info->pindex) {
     for (i = 0; i < indentlevel-1; i++){
      fputs(h5tools_str_fmt(&str, 0, info->line_indent), stream);
     }
    }

    if (elmtno == 0 && secnum == 0 && info->line_1st)
        fputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
    else if (secnum && info->line_cont)
        fputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
    else
        fputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);

    templength = h5tools_str_len(&prefix);

    for (i = 0; i < indentlevel; i++){
        /*we already made the indent for the array indices case */
     if (!info->pindex) {
        fputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
        templength += h5tools_str_len(&prefix);
     }
     else {
      /*we cannot count the prefix for the array indices case */
      templength += h5tools_str_len(&str);
     }
    }

    ctx->cur_column = ctx->prev_prefix_len = templength;
    ctx->cur_elmt = 0;
    ctx->need_prefix = 0;

    /* Free string */
    h5tools_str_close(&prefix);
    h5tools_str_close(&str);
}

/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose:     Prints NELMTS data elements to output STREAM.
 * Description:
 *      Prints some (NELMTS) data elements to output STREAM. The elements are
 *      stored in _MEM as type TYPE and are printed according to the format
 *      described in INFO. The CTX struct contains context information shared
 *      between calls to this function. The FLAGS is a bit field that
 *      indicates whether the data supplied in this call falls at the
 *      beginning or end of the total data to be printed (START_OF_DATA and
 *      END_OF_DATA).
 * Return:
 *      None
 * Programmer:
 *      Robb Matzke, Monday, April 26, 1999
 * Modifications:
 *  Robb Matzke, 1999-06-04
 * The `container' argument is the optional dataset for reference types.
 *
 *  Robb Matzke, 1999-09-29
 * Understands the `per_line' property which indicates that every Nth
 * element should begin a new line.
 *
 *      Robb Matzke, LLNL, 2003-06-05
 *      Do not dereference the memory for a variable-length string here.
 *      Deref in h5tools_str_sprint() instead so recursive types are
 *      handled correctly.
 *
 *      Pedro Vicente Nunes, THG, 2005-10-19
 *        pass to the prefix in h5tools_simple_prefix the total position
 *        instead of the current stripmine position i; this is necessary
 *        to print the array indices
 *        new field sm_pos in h5tools_context_t, the current stripmine element position
 *-------------------------------------------------------------------------
 */
void
h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t container,
                         h5tools_context_t *ctx/*in,out*/, unsigned flags,
                         hsize_t nelmts, hid_t type, void *_mem)
{
    unsigned char *mem = (unsigned char*)_mem;
    hsize_t  i;  /*element counter  */
    char  *s, *section; /*a section of output  */
    int   secnum;  /*section sequence number */
    size_t  size;  /*size of each datum  */
    size_t  ncols = 80; /*available output width */
    h5tools_str_t buffer;  /*string into which to render */
    int   multiline; /*datum was multiline  */
    hsize_t  curr_pos;  /* total data element position   */
    int                 elmt_counter = 0;/*counts the # elements printed.
                                          *I (ptl?) needed something that
                                          *isn't going to get reset when a new
                                          *line is formed. I'm going to use
                                          *this var to count elements and
                                          *break after we see a number equal
                                          *to the ctx->size_last_dim.   */

     /* binary dump */
    if(bin_output) {
        do_bin_output(stream, nelmts, type, _mem);
        bin_output = 0;
    } /* end if */
    else {
        /* Setup */
        HDmemset(&buffer, 0, sizeof(h5tools_str_t));
        size = H5Tget_size(type);

        if(info->line_ncols > 0)
            ncols = info->line_ncols;


        /* pass to the prefix in h5tools_simple_prefix the total position
         * instead of the current stripmine position i; this is necessary
         * to print the array indices
         */
        curr_pos = ctx->sm_pos;

        h5tools_simple_prefix(stream, info, ctx, curr_pos, 0);

        for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) {
            /* Render the element */
            h5tools_str_reset(&buffer);
            h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx);

            if (i + 1 < nelmts || (flags & END_OF_DATA) == 0)
                h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));

            s = h5tools_str_fmt(&buffer, 0, "%s");

            /*
             * If the element would split on multiple lines if printed at our
             * current location...
             */
            if (info->line_multi_new == 1 &&
                    (ctx->cur_column + h5tools_ncols(s) +
                     strlen(OPT(info->elmt_suf2, " ")) +
                     strlen(OPT(info->line_suf, ""))) > ncols) {
                if (ctx->prev_multiline) {
                    /*
                     * ... and the previous element also occupied more than one
                     * line, then start this element at the beginning of a line.
                     */
                    ctx->need_prefix = TRUE;
                } else if ((ctx->prev_prefix_len + h5tools_ncols(s) +
                        strlen(OPT(info->elmt_suf2, " ")) +
                        strlen(OPT(info->line_suf, ""))) <= ncols) {
                    /*
                     * ...but *could* fit on one line otherwise, then we
                     * should end the current line and start this element on its
                     * own line.
                     */
                    ctx->need_prefix = TRUE;
                }
            }

            /*
             * We need to break after each row of a dimension---> we should
             * break at the end of the each last dimension well that is the
             * way the dumper did it before
             */
            if (info->arr_linebreak && ctx->cur_elmt) {
                if (ctx->size_last_dim && (ctx->cur_elmt % ctx->size_last_dim) == 0)
                    ctx->need_prefix = TRUE;

                if ((hsize_t)elmt_counter == ctx->size_last_dim) {
                    ctx->need_prefix = TRUE;
                    elmt_counter = 0;
                }
            }

            /*
             * If the previous element occupied multiple lines and this element
             * is too long to fit on a line then start this element at the
             * beginning of the line.
             */
            if (info->line_multi_new == 1 && ctx->prev_multiline &&
                    (ctx->cur_column + h5tools_ncols(s) +
                     strlen(OPT(info->elmt_suf2, " ")) +
                     strlen(OPT(info->line_suf, ""))) > ncols)
                ctx->need_prefix = TRUE;

            /*
             * If too many elements have already been printed then we need to
             * start a new line.
             */
            if (info->line_per_line > 0 && ctx->cur_elmt >= info->line_per_line)
                ctx->need_prefix = TRUE;

            /*
             * Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause
             * the data to split across multiple lines.  We display the sections
             * one-at a time.
             */
            for (secnum = 0, multiline = 0;
                     (section = strtok(secnum ? NULL : s, OPTIONAL_LINE_BREAK));
                     secnum++) {
                /*
                 * If the current section plus possible suffix and end-of-line
                 * information would cause the output to wrap then we need to
                 * start a new line.
                 */

                /*
                 * Added the info->skip_first because the dumper does not want
                 * this check to happen for the first line
                 */
                if ((!info->skip_first || i) &&
                        (ctx->cur_column + strlen(section) +
                         strlen(OPT(info->elmt_suf2, " ")) +
                         strlen(OPT(info->line_suf, ""))) > ncols)
                    ctx->need_prefix = 1;

                /*
                 * Print the prefix or separate the beginning of this element
                 * from the previous element.
                 */
                if (ctx->need_prefix) {
                    if (secnum)
                        multiline++;

                    /* pass to the prefix in h5tools_simple_prefix the total
                     * position instead of the current stripmine position i;
                     * this is necessary to print the array indices
                     */
                    curr_pos = ctx->sm_pos + i;

                    h5tools_simple_prefix(stream, info, ctx, curr_pos, secnum);
                } else if ((i || ctx->continuation) && secnum == 0) {
                    fputs(OPT(info->elmt_suf2, " "), stream);
                    ctx->cur_column += strlen(OPT(info->elmt_suf2, " "));
                }

                /* Print the section */
                fputs(section, stream);
                ctx->cur_column += strlen(section);
            }

            ctx->prev_multiline = multiline;
        }

        h5tools_str_close(&buffer);
    }/* else bin */
}


/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose:     Dump out a subset of a dataset.
 * Description:
 *      Select a hyperslab from the dataset DSET using the parameters
 *      specified in SSET. Dump this out to STREAM.
 * Return:
 *      On success, return SUCCEED. Otherwise, the function returns FAIL.
 * Programmer:
 *      Bill Wendling, Wednesday, 07. March 2001
 * Modifications:
 *      Pedro Vicente, 12 December 2006
 *       Add information to print array indices from the element position
 *       The algorythm used is 
 *       Given an index I(z,y,x) its position from the beginning of an array 
 *       of sizes A(size_z, size_y,size_x) is given by
 *       Position of I(z,y,x) = index_z * size_y * size_x 
 *                             + index_y * size_x
 *                             + index_x
 *
 *      Pedro Vicente, Quincey Koziol, 4 January 2007
 *       Introduced an outer loop for cases where dimensionality is greater 
 *       than 2D. In each iteration a 2D block is displayed by rows in a inner
 *       loop. The remainning slower dimensions above the first 2 are incremented 
 *       one at a time in the outer loop
 *      
 *-------------------------------------------------------------------------
 */
static herr_t
h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset,
                           hid_t p_type, struct subset_t *sset,
                           int indentlevel)
{
    herr_t            ret;                     /* the value to return */
    hid_t             f_space;                 /* file data space */
    size_t            i;                       /* counters  */
    size_t            j;                       /* counters  */
    hsize_t           n;                       /* counters  */
    hsize_t           zero = 0;                /* vector of zeros */
    unsigned int      flags;                   /* buffer extent flags */
    hsize_t           total_size[H5S_MAX_RANK];/* total size of dataset*/
    hsize_t           elmtno;                  /* elemnt index  */
    hsize_t           low[H5S_MAX_RANK];       /* low bound of hyperslab */
    hsize_t           high[H5S_MAX_RANK];      /* higher bound of hyperslab */
    h5tools_context_t ctx;                     /* print context  */
    size_t            p_type_nbytes;           /* size of memory type */
    hsize_t           sm_size[H5S_MAX_RANK];   /* stripmine size */
    hsize_t           sm_nbytes;               /* bytes per stripmine */
    hsize_t           sm_nelmts;               /* elements per stripmine*/
    unsigned char     *sm_buf = NULL;          /* buffer for raw data */
    hid_t             sm_space;                /* stripmine data space */
    hsize_t           count;                   /* hyperslab count */
    hsize_t           outer_count;             /* offset count */
    unsigned int      row_dim;                 /* index of row dimension */
    int               current_outer_dim;       /* dimension for start */
    hsize_t           temp_start[H5S_MAX_RANK];/* temporary start inside offset count loop */
    hsize_t           max_start[H5S_MAX_RANK]; /* maximum start inside offset count loop */
    hsize_t           temp_count[H5S_MAX_RANK];/* temporary count inside offset count loop  */
    hsize_t           temp_block[H5S_MAX_RANK];/* temporary block size used in loop  */
    int               reset_dim;

#if defined (SANITY_CHECK)
    hsize_t total_points = 1; /* to print */
    hsize_t printed_points = 0; /* printed */
#endif
    

    ret = FAIL;     /* be pessimistic */
    f_space = H5Dget_space(dset);
    
    if (f_space == FAIL)
        goto done;
    
    /*
     * check that everything looks okay. the dimensionality must not be too
     * great and the dimensionality of the items selected for printing must
     * match the dimensionality of the dataset.
     */
    memset(&ctx, 0, sizeof(ctx));
    ctx.indent_level = indentlevel;
    ctx.need_prefix = 1;
    ctx.ndims = H5Sget_simple_extent_ndims(f_space);

    if ((size_t)ctx.ndims > NELMTS(sm_size))
        goto done_close;

    /* assume entire data space to be printed */
    if (ctx.ndims > 0)
        for (i = 0; i < (size_t)ctx.ndims; i++)
            ctx.p_min_idx[i] = 0;

    H5Sget_simple_extent_dims(f_space, total_size, NULL);
    ctx.size_last_dim = total_size[ctx.ndims - 1];

    if (ctx.ndims == 1)
        row_dim = 0;
    else
        row_dim = ctx.ndims - 2;

    /* get the offset count */
    outer_count = 1;
    if (ctx.ndims > 2)
        for (i = 0; i < (size_t)ctx.ndims - 2; i++)
            outer_count *= sset->count[ i ];

    if(ctx.ndims>0)
        init_acc_pos(&ctx,total_size);

    /* calculate total number of points to print */
#if defined (SANITY_CHECK)
    for (i = 0; i < (size_t)ctx.ndims; i++)
    {
        total_points *= sset->count[ i ] * sset->block[ i ];;
    }
#endif
    


    /* initialize temporary start, count and maximum start */
    for (i = 0; i < (size_t)ctx.ndims; i++)
    {
        temp_start[ i ] = sset->start[ i ];
        temp_count[ i ] = sset->count[ i ];
        temp_block[ i ] = 1; /* block size is considered in temp_count later */
        max_start[ i ] = 0;

    }
    if (ctx.ndims > 2)
    {
        for (i = 0; i < (size_t)ctx.ndims - 2; i++)
        {
            max_start[ i ] = temp_start[ i ] + sset->count[ i ];
            temp_count[ i ] = 1;
            
        }
    }

      
    /* offset loop */
    for (n = 0; n < outer_count; n++)
    {

        /* number of read iterations in inner loop, read by rows, to match 2D display */
        if (ctx.ndims > 1)
        {

#if 0
            count = sset->count[ row_dim ];
            temp_count[ row_dim ] = 1; 
#else

          
            /* count is the number of iterations to display all the rows 
               consider how many blocks */
            count = sset->count[ row_dim ] * sset->block[ row_dim ];

            temp_count[ row_dim ] = 1; /* always 1 row at a time */ 
            /* but consider the block size in temp_count */
            temp_count[ row_dim + 1 ] = sset->count[ row_dim + 1 ] 
                                        * sset->block[ row_dim + 1 ]; 


#endif
        }
        /* for the 1D case */
        else
        {
            count = 1;
        }

        
        /* display loop */
        for (; count > 0; temp_start[ row_dim ] += sset->stride[ row_dim ],
            count--) 
        {
            /* calculate the potential number of elements we're going to print */
            H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
                temp_start,
                sset->stride,
                temp_count,
                /*sset->block);*/
                temp_block);
            sm_nelmts = H5Sget_select_npoints(f_space);
             
            if (sm_nelmts == 0) {
                /* nothing to print */
                ret = SUCCEED;
                goto done_close;
            }
            
            /*
            * determine the strip mine size and allocate a buffer. the strip mine is
            * a hyperslab whose size is manageable.
            */
            sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
            
            if (ctx.ndims > 0)
                for (i = ctx.ndims; i > 0; --i) {
                    sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
                    sm_nbytes *= sm_size[i - 1];
                    assert(sm_nbytes > 0);
                }
                
                assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
                sm_buf = malloc((size_t)sm_nelmts * p_type_nbytes);
                sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
                
                H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL);
                
                /* read the data */
                if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
                    H5Sclose(f_space);
                    H5Sclose(sm_space);
                    free(sm_buf);
                    return FAIL;
                }
                
                /* print the data */
                flags = START_OF_DATA;
                
                if (count == 1)
                    flags |= END_OF_DATA;
                
                for (i = 0; i < ctx.ndims; i++)
                    ctx.p_max_idx[i] = ctx.p_min_idx[i] + MIN(total_size[i], sm_size[i]);
                
                /* print array indices. get the lower bound of the hyperslab and calulate
                the element position at the start of hyperslab */
                H5Sget_select_bounds(f_space,low,high);
                elmtno=0;
                for (i = 0; i < (size_t)ctx.ndims-1; i++) 
                {
                    hsize_t offset = 1; /* accumulation of the previous dimensions */
                    for (j = i+1; j < (size_t)ctx.ndims; j++) 
                        offset *= total_size[j];
                    elmtno+= low[i] * offset;
                }
                elmtno+= low[ctx.ndims - 1];
                
                /* initialize the current stripmine position; this is necessary to print the array
                indices */
                ctx.sm_pos = elmtno;
                
                h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts,
                    p_type, sm_buf);
                free(sm_buf);
                
                /* we need to jump to next line and update the index */
                ctx.need_prefix = 1;
                
                ctx.continuation++;
                
                
#if defined (SANITY_CHECK)
                printed_points += sm_nelmts;
#endif


        } /* count */

        if (ctx.ndims > 2)
        {
            /* dimension for start */
            current_outer_dim = (ctx.ndims - 2) -1;
            
            /* set start to original from current_outer_dim up */
            for (i = current_outer_dim + 1; i < ctx.ndims; i++)
            {
                temp_start[ i ] = sset->start[ i ]; 
            }
            
            /* increment start dimension */
            do
            {
                reset_dim = 0;
                temp_start[ current_outer_dim ]++;
                if (temp_start[ current_outer_dim ] >= max_start[ current_outer_dim ])
                {
                    temp_start[ current_outer_dim ] = sset->start[ current_outer_dim ];
                    current_outer_dim--;
                    reset_dim = 1;
                }
            }
            while (current_outer_dim >= 0 && reset_dim);
            
        } /* ctx.ndims > 1 */
        
    } /* outer_count */

#if defined (SANITY_CHECK)
    assert( printed_points == total_points );
#endif


    /* Terminate the output */
    if (ctx.cur_column) {
        fputs(OPT(info->line_suf, ""), stream);
        putc('\n', stream);
        fputs(OPT(info->line_sep, ""), stream);
    }
    
    ret = SUCCEED;
    
done_close:
    H5Sclose(f_space);
done:
    return ret;
}



/*-------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     H5Tools Library
 * Purpose: Print some values from a dataset with a simple data space.
 * Description:
 *      This is a special case of h5tools_dump_dset(). This function only
 *      intended for dumping datasets -- it does strip mining and some other
 *      things which are unnecessary for smaller objects such as attributes
 *      (to print small objects like attributes simply read the attribute and
 *      call h5tools_dump_simple_mem()).
 * Return:
 *      On success, the function returns SUCCEED. Otherwise, the function
 *      returns FAIL.
 * Programmer:
 *      Robb Matzke, Thursday, July 23, 1998
 * Modifications:
 *-------------------------------------------------------------------------
 */
static int
h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, hid_t dset,
                         hid_t p_type, int indentlevel)
{
    hid_t               f_space;                  /* file data space */
    hsize_t             elmtno;                   /* counter  */
    size_t             i;                        /* counter  */
    int                 carry;                    /* counter carry value */
    hsize_t             zero[8];                  /* vector of zeros */
    unsigned int        flags;                    /* buffer extent flags */
    hsize_t             total_size[H5S_MAX_RANK]; /* total size of dataset*/

    /* Print info */
    h5tools_context_t   ctx;                      /* print context  */
    size_t              p_type_nbytes;            /* size of memory type */
    hsize_t             p_nelmts;                 /* total selected elmts */

    /* Stripmine info */
    hsize_t             sm_size[H5S_MAX_RANK];    /* stripmine size */
    hsize_t             sm_nbytes;                /* bytes per stripmine */
    hsize_t             sm_nelmts;                /* elements per stripmine*/
    unsigned char       *sm_buf = NULL;           /* buffer for raw data */
    hid_t               sm_space;                 /* stripmine data space */

    /* Hyperslab info */
    hsize_t            hs_offset[H5S_MAX_RANK];   /* starting offset */
    hsize_t            hs_size[H5S_MAX_RANK];     /* size this pass */
    hsize_t            hs_nelmts;                 /* elements in request */

    /* VL data special information */
    unsigned int       vl_data = 0;               /* contains VL datatypes */

    f_space = H5Dget_space(dset);

    if (f_space == FAIL)
        return FAIL;

    /*
     * Check that everything looks okay. The dimensionality must not be too
     * great and the dimensionality of the items selected for printing must
     * match the dimensionality of the dataset.
     */
    memset(&ctx, 0, sizeof(ctx));
    ctx.indent_level = indentlevel;
    ctx.need_prefix = 1;
    ctx.ndims = H5Sget_simple_extent_ndims(f_space);
    
    if ((size_t)ctx.ndims > NELMTS(sm_size)) {
        H5Sclose(f_space);
        return FAIL;
    }

    /* Assume entire data space to be printed */
    if (ctx.ndims > 0)
        for (i = 0; i < (size_t)ctx.ndims; i++)
            ctx.p_min_idx[i] = 0;

    H5Sget_simple_extent_dims(f_space, total_size, NULL);

    /* calculate the number of elements we're going to print */
    p_nelmts = 1;

    if (ctx.ndims > 0) {
        for (i = 0; i < ctx.ndims; i++)
            p_nelmts *= total_size[i];
        ctx.size_last_dim = (total_size[ctx.ndims - 1]);
    } /* end if */
    else
        ctx.size_last_dim = 0;

    if (p_nelmts == 0) {
        /* nothing to print */
        H5Sclose(f_space);
        return SUCCEED;
    }

    /* Check if we have VL data in the dataset's datatype */
    if (H5Tdetect_class(p_type, H5T_VLEN) == TRUE)
        vl_data = TRUE;

    /*
     * Determine the strip mine size and allocate a buffer. The strip mine is
     * a hyperslab whose size is manageable.
     */
    sm_nbytes = p_type_nbytes = H5Tget_size(p_type);

    if (ctx.ndims > 0) {
        for (i = ctx.ndims; i > 0; --i) {
            sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
            sm_nbytes *= sm_size[i - 1];
            assert(sm_nbytes > 0);
        }
    }

    assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
    sm_buf = malloc((size_t)sm_nbytes);

    sm_nelmts = sm_nbytes / p_type_nbytes;
    sm_space = H5Screate_simple(1, &sm_nelmts, NULL);

    if(ctx.ndims>0)
     init_acc_pos(&ctx,total_size);

    /* The stripmine loop */
    memset(hs_offset, 0, sizeof hs_offset);
    memset(zero, 0, sizeof zero);

    for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
        /* Calculate the hyperslab size */
        if (ctx.ndims > 0) {
            for (i = 0, hs_nelmts = 1; i < ctx.ndims; i++) {
                hs_size[i] = MIN(total_size[i] - hs_offset[i], sm_size[i]);
                ctx.p_max_idx[i] = ctx.p_min_idx[i] + hs_size[i];
                hs_nelmts *= hs_size[i];
            }

            H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL,
                                hs_size, NULL);
            H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL,
                                &hs_nelmts, NULL);
        } else {
            H5Sselect_all(f_space);
            H5Sselect_all(sm_space);
            hs_nelmts = 1;
        }

        /* Read the data */
        if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
            H5Sclose(f_space);
            H5Sclose(sm_space);
            free(sm_buf);
            return FAIL;
        }

        /* Print the data */
        flags = (elmtno == 0) ? START_OF_DATA : 0;
        flags |= ((elmtno + hs_nelmts) >= p_nelmts) ? END_OF_DATA : 0;

        /* initialize the current stripmine position; this is necessary to print the array
           indices */
        ctx.sm_pos = elmtno;

        h5tools_dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts,
                             p_type, sm_buf);

        /* Reclaim any VL memory, if necessary */
        if(vl_data)
            H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);

        /* Calculate the next hyperslab offset */
        for (i = ctx.ndims, carry = 1; i > 0 && carry; --i) {
            ctx.p_min_idx[i - 1] = ctx.p_max_idx[i - 1];
            hs_offset[i - 1] += hs_size[i - 1];

            if (hs_offset[i - 1] == total_size[i - 1])
                hs_offset[i - 1] = 0;
            else
                carry = 0;
        }

        ctx.continuation++;
    }

    /* Terminate the output */
    if (ctx.cur_column) {
        fputs(OPT(info->line_suf, ""), stream);
        putc('\n', stream);
        fputs(OPT(info->line_sep, ""), stream);
    }

    H5Sclose(sm_space);
    H5Sclose(f_space);

    free(sm_buf);

    return SUCCEED;
}

/*-------------------------------------------------------------------------
 * Function: h5tools_dump_simple_mem
 *
 * Purpose: Print some values from memory with a simple data space.
 *  This is a special case of h5tools_dump_mem().
 *
 * Return: Success:    SUCCEED
 *
 *  Failure:    FAIL
 *
 * Programmer: Robb Matzke
 *              Thursday, July 23, 1998
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static int
h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, hid_t obj_id,
                        hid_t type, hid_t space, void *mem, int indentlevel)
{
    int   i;   /*counters  */
    hsize_t  nelmts;   /*total selected elmts */
    h5tools_context_t ctx;   /*printing context */

    /*
     * Check that everything looks okay.  The dimensionality must not be too
     * great and the dimensionality of the items selected for printing must
     * match the dimensionality of the dataset.
     */
    memset(&ctx, 0, sizeof(ctx));
    ctx.ndims = H5Sget_simple_extent_ndims(space);

    if ((size_t)ctx.ndims > NELMTS(ctx.p_min_idx))
        return FAIL;

    ctx.indent_level = indentlevel;
    ctx.need_prefix = 1;

    /* Assume entire data space to be printed */
    for (i = 0; i < ctx.ndims; i++)
        ctx.p_min_idx[i] = 0;

    H5Sget_simple_extent_dims(space, ctx.p_max_idx, NULL);

    for (i = 0, nelmts = 1; ctx.ndims != 0 && i < ctx.ndims; i++)
        nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i];

    if (nelmts == 0)
        return SUCCEED; /*nothing to print*/
    if(ctx.ndims>0) {
        assert(ctx.p_max_idx[ctx.ndims - 1]==(hsize_t)((int)ctx.p_max_idx[ctx.ndims - 1]));
        ctx.size_last_dim = (int)(ctx.p_max_idx[ctx.ndims - 1]);
    } /* end if */
    else
        ctx.size_last_dim = 0;

    if(ctx.ndims>0)
     init_acc_pos(&ctx,ctx.p_max_idx);

    /* Print it */
    h5tools_dump_simple_data(stream, info, obj_id, &ctx,
                             START_OF_DATA | END_OF_DATA, nelmts, type, mem);

    /* Terminate the output */
    if (ctx.cur_column) {
        fputs(OPT(info->line_suf, ""), stream);
        putc('\n', stream);
        fputs(OPT(info->line_sep, ""), stream);
    }

    return SUCCEED;
}

/*-------------------------------------------------------------------------
 * Function: h5tools_dump_dset
 *
 * Purpose: Print some values from a dataset DSET to the file STREAM
 *  after converting all types to P_TYPE (which should be a
 *  native type).  If P_TYPE is a negative value then it will be
 *  computed from the dataset type using only native types.
 *
 * Note: This function is intended only for datasets since it does
 *  some things like strip mining which are unnecessary for
 *  smaller objects such as attributes. The easiest way to print
 *  small objects is to read the object into memory and call
 *  h5tools_dump_mem().
 *
 * Return: Success:    SUCCEED
 *
 *  Failure:    FAIL
 *
 * Programmer: Robb Matzke
 *              Thursday, July 23, 1998
 *
 * Modifications:
 *   Robb Matzke, 1999-06-07
 *  If info->raw is set then the memory datatype will be the same
 *  as the file datatype.
 *
 *  Bill Wendling, 2001-02-27
 *  Renamed to ``h5tools_dump_dset'' and added the subsetting
 *  parameter.
 *
 *-------------------------------------------------------------------------
 */
int
h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, hid_t dset, hid_t _p_type,
                  struct subset_t *sset, int indentlevel)
{
    hid_t     f_space;
    hid_t     p_type = _p_type;
    hid_t     f_type;
    H5S_class_t space_type;
    int       status = FAIL;
    h5tool_format_t  info_dflt;

    /* Use default values */
    if (!stream)
        stream = stdout;

    if (!info) {
        memset(&info_dflt, 0, sizeof info_dflt);
        info = &info_dflt;
    }

    if (p_type < 0) {
        f_type = H5Dget_type(dset);

        if (info->raw || bin_form == 1 )
            p_type = H5Tcopy(f_type);
        else if (bin_form == 2 )
            p_type = h5tools_get_little_endian_type(f_type);
        else if (bin_form == 3 )
            p_type = h5tools_get_big_endian_type(f_type);
        else
            p_type = h5tools_get_native_type(f_type);

        H5Tclose(f_type);

        if (p_type < 0)
            goto done;
    }

    /* Check the data space */
    f_space = H5Dget_space(dset);

    space_type = H5Sget_simple_extent_type(f_space);

    /* Print the data */
    if (space_type == H5S_SIMPLE || space_type == H5S_SCALAR) {
        if (!sset)
            status = h5tools_dump_simple_dset(rawdatastream, info, dset, p_type,
                                              indentlevel);
        else
            status = h5tools_dump_simple_subset(rawdatastream, info, dset, p_type,
                                                sset, indentlevel);
    } else /* space is H5S_NULL */
        status = SUCCEED;

    /* Close the dataspace */
    H5Sclose(f_space);

done:
    if (p_type != _p_type)
        H5Tclose(p_type);

    return status;
}

/*-------------------------------------------------------------------------
 * Function: h5tools_dump_mem
 *
 * Purpose: Displays the data contained in MEM. MEM must have the
 *  specified data TYPE and SPACE.  Currently only simple data
 *  spaces are allowed and only the `all' selection.
 *
 * Return: Success:    SUCCEED
 *
 *  Failure:    FAIL
 *
 * Programmer: Robb Matzke
 *              Wednesday, January 20, 1999
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
int
h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, hid_t obj_id, hid_t type,
                 hid_t space, void *mem, int indentlevel)
{
    h5tool_format_t    info_dflt;

    /* Use default values */
    if (!stream)
 stream = stdout;

    if (!info) {
 memset(&info_dflt, 0, sizeof(info_dflt));
 info = &info_dflt;
    }

    /* Check the data space */
    if (H5Sis_simple(space) <= 0)
 return -1;

    return h5tools_dump_simple_mem(stream, info, obj_id, type, space, mem,
                                   indentlevel);
}

/*-------------------------------------------------------------------------
 * Function:    init_acc_pos
 *
 * Purpose:     initialize accumulator and matrix position
 *
 * Return:      void
 *
 * Programmer:  pvn
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
void init_acc_pos(h5tools_context_t *ctx, hsize_t *dims)
{
 int i;

 assert(ctx->ndims);

 ctx->acc[ctx->ndims-1]=1;
 for(i=(ctx->ndims-2); i>=0; i--)
 {
  ctx->acc[i]=ctx->acc[i+1] * dims[i+1];
 }
 for ( i = 0; i < ctx->ndims; i++)
  ctx->pos[i]=0;
}


/*-------------------------------------------------------------------------
 * Function: do_bin_output
 *
 * Purpose: Dump memory buffer to a binary file stream
 *
 * Return: Success:    SUCCEED
 *         Failure:    FAIL
 *
 * Programmer: Pedro Vicente Nunes
 *             Friday, June 2, 2006
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static
int do_bin_output(FILE *stream, hsize_t nelmts, hid_t tid, void *_mem)
{
 unsigned char *mem  = (unsigned char*)_mem;
 size_t         size; /* datum size */
 hsize_t        i;    /* element counter  */

 size = H5Tget_size(tid);

 for (i = 0; i < nelmts; i++)
 {
  if (render_bin_output(stream,tid,mem + i * size)<0)
  {
   printf("\nError in writing binary stream\n");
   return FAIL;
  }
 }

 return SUCCEED;
}


/*-------------------------------------------------------------------------
 * Function: render_bin_output
 *
 * Purpose: Write one element of memory buffer to a binary file stream
 *
 * Return: Success:    SUCCEED
 *         Failure:    FAIL
 *
 * Programmer: Pedro Vicente Nunes
 *             Friday, June 2, 2006
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static
int render_bin_output(FILE *stream, hid_t tid, void *_mem)
{
#if 0
 #define DEBUG_H5DUMP_BIN 1
#endif
 unsigned char     *mem  = (unsigned char*)_mem;
 size_t             size;   /* datum size */
 float              tempfloat;
 double             tempdouble;
 unsigned long_long tempullong;
 long_long          templlong;
 unsigned long      tempulong;
 long               templong;
 unsigned int       tempuint;
 int                tempint;
 unsigned short     tempushort;
 short              tempshort;
 unsigned char      tempuchar;
 char               tempschar;
#if H5_SIZEOF_LONG_DOUBLE !=0
 long double        templdouble;
#endif
#ifdef DEBUG_H5DUMP_BIN
 static char        fmt_llong[8], fmt_ullong[8];
 if (!fmt_llong[0]) {
  sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH);
  sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH);
 }
#endif

 size = H5Tget_size(tid);

 if (H5Tequal(tid, H5T_NATIVE_FLOAT))
 {
  memcpy(&tempfloat, mem, sizeof(float));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%g ", tempfloat);
#else
  if (1 != fwrite(&tempfloat, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_DOUBLE))
 {
  memcpy(&tempdouble, mem, sizeof(double));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%g ", tempdouble);
#else
  if (1 != fwrite(&tempdouble, size, 1, stream))
   return FAIL;
#endif
 }
#if H5_SIZEOF_LONG_DOUBLE !=0
 else if (H5Tequal(tid, H5T_NATIVE_LDOUBLE))
 {
  memcpy(&templdouble, mem, sizeof(long double));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%Lf ", templdouble);
#else
  if (1 != fwrite(&templdouble, size, 1, stream))
   return FAIL;
#endif
 }
#endif
 else if (H5T_STRING == H5Tget_class(tid))
 {
  unsigned int i;
  H5T_str_t    pad;
  char        *s;

  pad = H5Tget_strpad(tid);

  if(H5Tis_variable_str(tid))
  {
   s = *(char**)mem;
   if(s!=NULL)
    size = HDstrlen(s);
  }
  else
  {
   s = (char *)mem;
   size = H5Tget_size(tid);
  }
  for (i=0; i<size && (s[i] || pad!=H5T_STR_NULLTERM); i++)
  {
   memcpy(&tempuchar, &s[i], sizeof(unsigned char));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "%d", tempuchar);
#else
   if (1 != fwrite(&tempuchar, size, 1, stream))
    return FAIL;
#endif
  } /* i */
 }
 else if (H5Tequal(tid, H5T_NATIVE_INT))
 {
  memcpy(&tempint, mem, sizeof(int));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%d ", tempint);
#else
  if (1 != fwrite(&tempint, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_UINT))
 {
  memcpy(&tempuint, mem, sizeof(unsigned int));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%u ", tempuint);
#else
  if (1 != fwrite(&tempuint, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_SCHAR))
 {
  memcpy(&tempschar, mem, sizeof(char));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%d ", tempschar);
#else
  if (1 != fwrite(&tempschar, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_UCHAR))
 {
  memcpy(&tempuchar, mem, sizeof(unsigned char));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%u ", tempuchar);
#else
  if (1 != fwrite(&tempuchar, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_SHORT))
 {
  memcpy(&tempshort, mem, sizeof(short));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%d ", tempshort);
#else
  if (1 != fwrite(&tempshort, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_USHORT))
 {
  memcpy(&tempushort, mem, sizeof(unsigned short));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%u ", tempushort);
#else
  if (1 != fwrite(&tempushort, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_LONG))
 {
  memcpy(&templong, mem, sizeof(long));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%ld ", templong);
#else
  if (1 != fwrite(&templong, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_ULONG))
 {
  memcpy(&tempulong, mem, sizeof(unsigned long));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, "%lu ", tempulong);
#else
  if (1 != fwrite(&tempulong, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_LLONG))
 {
  memcpy(&templlong, mem, sizeof(long_long));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, fmt_llong, templlong);
#else
  if (1 != fwrite(&templlong, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_ULLONG))
 {
  memcpy(&tempullong, mem, sizeof(unsigned long_long));
#ifdef DEBUG_H5DUMP_BIN
  fprintf(stream, fmt_ullong, tempullong);
#else
  if (1 != fwrite(&tempullong, size, 1, stream))
   return FAIL;
#endif
 }
 else if (H5Tequal(tid, H5T_NATIVE_HSSIZE))
 {
  if (sizeof(hssize_t) == sizeof(int))
  {
   memcpy(&tempint, mem, sizeof(int));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "%d ", tempint);
#else
   if (1 != fwrite(&tempint, size, 1, stream))
    return FAIL;
#endif
  }
  else if (sizeof(hssize_t) == sizeof(long))
  {
   memcpy(&templong, mem, sizeof(long));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "%ld ", templong);
#else
   if (1 != fwrite(&templong, size, 1, stream))
    return FAIL;
#endif
  }
  else
  {
   memcpy(&templlong, mem, sizeof(long_long));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, fmt_llong, templlong);
#else
   if (1 != fwrite(&templlong, size, 1, stream))
    return FAIL;
#endif
  }
 }
 else if (H5Tequal(tid, H5T_NATIVE_HSIZE))
 {
  if (sizeof(hsize_t) == sizeof(int))
  {
   memcpy(&tempuint, mem, sizeof(unsigned int));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "%u ", tempuint);
#else
   if (1 != fwrite(&tempuint, size, 1, stream))
    return FAIL;
#endif
  }
  else if (sizeof(hsize_t) == sizeof(long))
  {
   memcpy(&tempulong, mem, sizeof(unsigned long));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "%lu ", tempulong);
#else
   if (1 != fwrite(&tempulong, size, 1, stream))
    return FAIL;
#endif
  }
  else
  {
   memcpy(&tempullong, mem, sizeof(unsigned long_long));
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, fmt_ullong, tempullong);
#else
   if (1 != fwrite(&tempullong, size, 1, stream))
    return FAIL;
#endif
  }
 }
 else if (H5Tget_class(tid) == H5T_COMPOUND)
 {
  unsigned j;
  hid_t    memb;
  unsigned nmembs;
  size_t   offset;

  nmembs = H5Tget_nmembers(tid);

  for (j = 0; j < nmembs; j++)
  {
   offset = H5Tget_member_offset(tid, j);
   memb   = H5Tget_member_type(tid, j);

   if (render_bin_output(stream,memb,mem + offset)<0)
    return FAIL;

   H5Tclose(memb);
  }
 }
 else if (H5Tget_class(tid) == H5T_ENUM)
 {
  unsigned int i;
  if (1==size)
  {
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "0x%02x", mem[0]);
#else
   if (1 != fwrite(&mem[0], size, 1, stream))
    return FAIL;
#endif
  }
  else
  {
   for (i = 0; i < size; i++)
   {
#ifdef DEBUG_H5DUMP_BIN
    fprintf(stream, "%s%02x", i?":":"", mem[i]);
#else
    if (1 != fwrite(&mem[i], sizeof(char), 1, stream))
     return FAIL;
#endif
   } /*i*/
  }/*else 1 */
 }
 else if (H5Tget_class(tid) == H5T_ARRAY)
 {
  int     k, ndims;
  hsize_t i, dims[H5S_MAX_RANK], temp_nelmts, nelmts;
  hid_t   memb;

  /* get the array's base datatype for each element */
  memb = H5Tget_super(tid);
  size = H5Tget_size(memb);
  ndims = H5Tget_array_ndims(tid);
  H5Tget_array_dims2(tid, dims);
  assert(ndims >= 1 && ndims <= H5S_MAX_RANK);

  /* calculate the number of array elements */
  for (k = 0, nelmts = 1; k < ndims; k++)
  {
   temp_nelmts = nelmts;
   temp_nelmts *= dims[k];
   nelmts = (size_t)temp_nelmts;
  }

  /* dump the array element */
  for (i = 0; i < nelmts; i++)
  {
   if (render_bin_output(stream,memb,mem + i * size)<0)
    return FAIL;
  }

  H5Tclose(memb);
 }
 else if (H5Tget_class(tid) == H5T_VLEN)
 {
  unsigned int i;
  hsize_t nelmts;
  hid_t   memb;

  /* get the VL sequences's base datatype for each element */
  memb = H5Tget_super(tid);
  size = H5Tget_size(memb);

  /* Get the number of sequence elements */
  nelmts = ((hvl_t *)mem)->len;

  for (i = 0; i < nelmts; i++)
  {
   /* dump the array element */
   if (render_bin_output(stream,memb,((char *)(((hvl_t *)mem)->p)) + i * size)<0)
    return FAIL;
  }
  H5Tclose(memb);
 }
 else
 {
  size_t i;
  if (1==size)
  {
#ifdef DEBUG_H5DUMP_BIN
   fprintf(stream, "0x%02x", mem[0]);
#else
   if (1 != fwrite(&mem[0], size, 1, stream))
    return FAIL;
#endif
  }
  else
  {
   for (i = 0; i < size; i++)
   {
#ifdef DEBUG_H5DUMP_BIN
    fprintf(stream, "%s%02x", i?":":"", mem[i]);
#else
    if (1 != fwrite(&mem[i], sizeof(char), 1, stream))
     return FAIL;
#endif
   } /*i*/
  }/*else 1 */
 }


 return SUCCEED;
}