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hdf5/tools/lib/h5tools.c
Quincey Koziol 2e4302818a [svn-r24864] Description: 
Remove all traces of MPI-POSIX VFD and GPFS detection/code.

    Remove remaining traces of stream VFD.

    Remove testpar/t_posix_compliant test (it's not actually verifying anything).

    Clean up H5D__mpio_opt_possible() further.

    Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).

    A few other small code cleanups.

Tested on:
    Mac OSX/64 10.9.2 (amazon) w/parallel & serial
2014-03-21 18:02:24 -05:00

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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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* 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_dump.h"
#include "h5tools_ref.h"
#include "h5tools_utils.h"
#include "H5private.h"
/* global variables */
hid_t H5tools_ERR_STACK_g = 0;
hid_t H5tools_ERR_CLS_g = -1;
hid_t H5E_tools_g = -1;
hid_t H5E_tools_min_id_g = -1;
int compound_data;
FILE *rawattrstream = NULL; /* should initialize to stdout but gcc moans about it */
FILE *rawdatastream = NULL; /* should initialize to stdout but gcc moans about it */
FILE *rawinstream = NULL; /* should initialize to stdin but gcc moans about it */
FILE *rawoutstream = NULL; /* should initialize to stdout but gcc moans about it */
FILE *rawerrorstream = NULL; /* should initialize to stderr but gcc moans about it */
int bin_output; /* binary output */
int bin_form; /* binary form */
int region_output; /* region output */
int oid_output; /* oid output */
int data_output; /* data output */
int attr_data_output; /* attribute data output */
int packed_bits_num; /* number of packed bits to display */
int packed_data_offset; /* offset of packed bits to display */
int packed_data_length; /* lengtht of packed bits to display */
unsigned long long packed_data_mask; /* mask in which packed bits to display */
/* 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_PARALLEL
"mpio",
#endif /* H5_HAVE_PARALLEL */
};
/* This enum should match the entries in the above drivers_list since they
* are indexes into the drivers_list array. */
typedef enum {
SEC2_IDX = 0
,FAMILY_IDX
,SPLIT_IDX
,MULTI_IDX
#ifdef H5_HAVE_PARALLEL
,MPIO_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)
{
char lib_str[256];
if (!h5tools_init_g) {
/* register the error class */
HDsnprintf(lib_str, sizeof(lib_str), "%d.%d.%d",H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE);
H5tools_ERR_STACK_g = H5Ecreate_stack();
H5TOOLS_INIT_ERROR()
if (!rawattrstream)
rawattrstream = stdout;
if (!rawdatastream)
rawdatastream = stdout;
if (!rawinstream)
rawinstream = stdin;
if (!rawoutstream)
rawoutstream = stdout;
if (!rawerrorstream)
rawerrorstream = stderr;
h5tools_dump_init();
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)
{
H5E_auto2_t tools_func;
void *tools_edata;
if (h5tools_init_g) {
/* special case where only data is output to stdout */
if((rawoutstream == NULL) && rawdatastream && (rawdatastream == stdout))
HDfprintf(rawdatastream, "\n");
H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata);
if(tools_func!=NULL)
H5Eprint2(H5tools_ERR_STACK_g, rawerrorstream);
if (rawattrstream && rawattrstream != stdout) {
if (fclose(rawattrstream))
perror("closing rawattrstream");
else
rawattrstream = NULL;
}
if (rawdatastream && rawdatastream != stdout) {
if (fclose(rawdatastream))
perror("closing rawdatastream");
else
rawdatastream = NULL;
}
if (rawinstream && rawinstream != stdin) {
if (fclose(rawinstream))
perror("closing rawinstream");
else
rawinstream = NULL;
}
if (rawoutstream && rawoutstream != stdout) {
if (fclose(rawoutstream))
perror("closing rawoutstream");
else
rawoutstream = NULL;
}
if (rawerrorstream && rawerrorstream != stderr) {
if (fclose(rawerrorstream))
perror("closing rawerrorstream");
else
rawerrorstream = NULL;
}
/* Clean up the reference path table, if it's been used */
term_ref_path_table();
H5TOOLS_CLOSE_ERROR()
H5Eclose_stack(H5tools_ERR_STACK_g);
/* Shut down the library */
H5close();
h5tools_init_g = 0;
}
}
/*-------------------------------------------------------------------------
* Function: h5tools_set_data_output_file
*
* Purpose: Open fname as the output file for dataset raw data.
* Set rawdatastream as its file stream.
*
* Return: 0 -- succeeded
* negative -- failed
*
* Programmer: Albert Cheng, 2000/09/30
*
* Modifications:
* pvn June, 1, 2006. Add a switch for binary output
*
*-------------------------------------------------------------------------
*/
int
h5tools_set_data_output_file(const char *fname, int is_bin)
{
int retvalue = FAIL;
FILE *f; /* temporary holding place for the stream pointer
* so that rawdatastream is changed only when succeeded */
if (rawdatastream && rawdatastream != stdout) {
if (HDfclose(rawdatastream))
HDperror("closing rawdatastream");
else
rawdatastream = NULL;
}
/* First check if filename is string "NULL" */
if (fname != NULL) {
/* binary output */
if (is_bin) {
if ((f = HDfopen(fname, "wb")) != NULL) {
rawdatastream = f;
retvalue = SUCCEED;
}
}
else {
if ((f = HDfopen(fname, "w")) != NULL) {
rawdatastream = f;
retvalue = SUCCEED;
}
}
}
else {
rawdatastream = NULL;
retvalue = SUCCEED;
}
return retvalue;
}
/*-------------------------------------------------------------------------
* Function: h5tools_set_attr_output_file
*
* Purpose: Open fname as the output file for attribute raw data.
* Set rawattrstream as its file stream.
*
* Return: 0 -- succeeded
* negative -- failed
*
*-------------------------------------------------------------------------
*/
int
h5tools_set_attr_output_file(const char *fname, int is_bin)
{
int retvalue = FAIL;
FILE *f; /* temporary holding place for the stream pointer
* so that rawattrstream is changed only when succeeded */
if (rawattrstream && rawattrstream != stdout) {
if (HDfclose(rawattrstream))
HDperror("closing rawattrstream");
else
rawattrstream = NULL;
}
/* First check if filename is string "NULL" */
if (fname != NULL) {
/* binary output */
if (is_bin) {
if ((f = HDfopen(fname, "wb")) != NULL) {
rawattrstream = f;
retvalue = SUCCEED;
}
}
else {
if ((f = HDfopen(fname, "w")) != NULL) {
rawattrstream = f;
retvalue = SUCCEED;
}
}
}
else {
rawattrstream = NULL;
retvalue = SUCCEED;
}
return retvalue;
}
/*-------------------------------------------------------------------------
* Function: h5tools_set_input_file
*
* Purpose: Open fname as the input file for raw input.
* Set rawinstream as its file stream.
*
* Return: 0 -- succeeded
* negative -- failed
*
*-------------------------------------------------------------------------
*/
int
h5tools_set_input_file(const char *fname, int is_bin)
{
int retvalue = FAIL;
FILE *f; /* temporary holding place for the stream pointer
* so that rawinstream is changed only when succeeded */
if (rawinstream && rawinstream != stdin) {
if (HDfclose(rawinstream))
HDperror("closing rawinstream");
else
rawinstream = NULL;
}
/* First check if filename is string "NULL" */
if (fname != NULL) {
/* binary output */
if (is_bin) {
if ((f = HDfopen(fname, "rb")) != NULL) {
rawinstream = f;
retvalue = SUCCEED;
}
}
else {
if ((f = HDfopen(fname, "r")) != NULL) {
rawinstream = f;
retvalue = SUCCEED;
}
}
}
else {
rawinstream = NULL;
retvalue = SUCCEED;
}
return retvalue;
}
/*-------------------------------------------------------------------------
* Function: h5tools_set_output_file
*
* Purpose: Open fname as the output file for raw output.
* Set rawoutstream as its file stream.
*
* Return: 0 -- succeeded
* negative -- failed
*
*-------------------------------------------------------------------------
*/
int
h5tools_set_output_file(const char *fname, int is_bin)
{
int retvalue = FAIL;
FILE *f; /* temporary holding place for the stream pointer
* so that rawoutstream is changed only when succeeded */
if (rawoutstream && rawoutstream != stdout) {
if (HDfclose(rawoutstream))
HDperror("closing rawoutstream");
else
rawoutstream = NULL;
}
/* First check if filename is string "NULL" */
if (fname != NULL) {
/* binary output */
if (is_bin) {
if ((f = HDfopen(fname, "wb")) != NULL) {
rawoutstream = f;
retvalue = SUCCEED;
}
}
else {
if ((f = HDfopen(fname, "w")) != NULL) {
rawoutstream = f;
retvalue = SUCCEED;
}
}
}
else {
rawoutstream = NULL;
retvalue = SUCCEED;
}
return retvalue;
}
/*-------------------------------------------------------------------------
* Function: h5tools_set_error_file
*
* Purpose: Open fname as the error output file for dataset raw error.
* Set rawerrorstream as its file stream.
*
* Return: 0 -- succeeded
* negative -- failed
*
*-------------------------------------------------------------------------
*/
int
h5tools_set_error_file(const char *fname, int is_bin)
{
int retvalue = FAIL;
FILE *f; /* temporary holding place for the stream pointer
* so that rawerrorstream is changed only when succeeded */
if (rawerrorstream && rawerrorstream != stderr) {
if (HDfclose(rawerrorstream))
HDperror("closing rawerrorstream");
else
rawerrorstream = NULL;
}
/* First check if filename is string "NULL" */
if (fname != NULL) {
/* binary output */
if (is_bin) {
if ((f = HDfopen(fname, "wb")) != NULL) {
rawerrorstream = f;
retvalue = SUCCEED;
}
}
else {
if ((f = HDfopen(fname, "w")) != NULL) {
rawerrorstream = f;
retvalue = SUCCEED;
}
}
}
else {
rawerrorstream = NULL;
retvalue = SUCCEED;
}
return retvalue;
}
/*-------------------------------------------------------------------------
* 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 (!HDstrcmp(driver, drivernames[SEC2_IDX])) {
/* SEC2 driver */
if (H5Pset_fapl_sec2(new_fapl) < 0)
goto error;
if (drivernum)
*drivernum = SEC2_IDX;
}
else if (!HDstrcmp(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 (!HDstrcmp(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 (!HDstrcmp(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_PARALLEL
else if(!HDstrcmp(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 */
}
#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.
*
* 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) {
HDstrncpy(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_count_ncols(const char *s)
{
register size_t i;
for (i = 0; *s; s++)
if (*s >= ' ')
i++;
return i;
}
/*-------------------------------------------------------------------------
* Function: h5tools_detect_vlen
*
* Purpose: Recursive check for any variable length data in given type.
*
* Return:
* TRUE : type conatains any variable length data
* FALSE : type doesn't contain any variable length data
* Negative value: error occur
*
* Programmer: Jonathan Kim March 18, 2011
*-------------------------------------------------------------------------
*/
htri_t
h5tools_detect_vlen(hid_t tid)
{
htri_t ret;
/* recursive detect any vlen data values in type (compound, array ...) */
ret = H5Tdetect_class(tid, H5T_VLEN);
if((ret == TRUE) || (ret < 0))
goto done;
/* recursive detect any vlen string in type (compound, array ...) */
ret = h5tools_detect_vlen_str(tid);
if((ret == TRUE) || (ret < 0))
goto done;
done:
return ret;
}
/*-------------------------------------------------------------------------
* Function: h5tools_detect_vlen_str
*
* Purpose: Recursive check for variable length string of a datatype.
*
* Return:
* TRUE : type conatains any variable length string
* FALSE : type doesn't contain any variable length string
* Negative value: error occur
*
*-------------------------------------------------------------------------
*/
htri_t
h5tools_detect_vlen_str(hid_t tid)
{
H5T_class_t tclass = -1;
htri_t ret = FALSE;
ret = H5Tis_variable_str(tid);
if((ret == TRUE) || (ret < 0))
goto done;
tclass = H5Tget_class(tid);
if(tclass == H5T_ARRAY || tclass == H5T_VLEN) {
hid_t btid = H5Tget_super(tid);
if(btid < 0) {
ret = (htri_t)btid;
goto done;
}
ret = h5tools_detect_vlen_str(btid);
if((ret == TRUE) || (ret < 0)) {
H5Tclose(btid);
goto done;
}
}
else if(tclass == H5T_COMPOUND) {
unsigned nmembs;
int snmembs = H5Tget_nmembers(tid);
unsigned u;
if(snmembs < 0) {
ret = FAIL;
goto done;
}
nmembs = (unsigned)snmembs;
for(u = 0; u < nmembs; u++) {
hid_t mtid = H5Tget_member_type(tid, u);
ret = h5tools_detect_vlen_str(mtid);
if((ret == TRUE) || (ret < 0)) {
H5Tclose(mtid);
goto done;
}
H5Tclose(mtid);
}
}
done:
return ret;
}
/*-------------------------------------------------------------------------
* 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)
*-------------------------------------------------------------------------
*/
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 (stream == NULL)
return;
if (!ctx->need_prefix)
return;
HDmemset(&prefix, 0, sizeof(h5tools_str_t));
HDmemset(&str, 0, sizeof(h5tools_str_t));
/* Terminate previous line, if any */
if (ctx->cur_column) {
PUTSTREAM(OPT(info->line_suf, ""), stream);
HDputc('\n', stream);
PUTSTREAM(OPT(info->line_sep, ""), stream);
}
/* Calculate new prefix */
h5tools_str_prefix(&prefix, info, elmtno, ctx->ndims, 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++) {
PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream);
}
}
if (elmtno == 0 && secnum == 0 && info->line_1st) {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream);
}
else if (secnum && info->line_cont) {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream);
}
else {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)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) {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)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: 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. Calls region specific function.
* Return:
* None
*-------------------------------------------------------------------------
*/
void
h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, hsize_t elmtno, hsize_t *ptdata, int secnum)
{
h5tools_str_t prefix;
h5tools_str_t str; /*temporary for indentation */
size_t templength = 0;
int i, indentlevel = 0;
if (stream == NULL)
return;
if (!ctx->need_prefix)
return;
HDmemset(&prefix, 0, sizeof(h5tools_str_t));
HDmemset(&str, 0, sizeof(h5tools_str_t));
/* Terminate previous line, if any */
if (ctx->cur_column) {
PUTSTREAM(OPT(info->line_suf, ""), stream);
HDputc('\n', stream);
PUTSTREAM(OPT(info->line_sep, ""), stream);
}
/* Calculate new prefix */
h5tools_str_region_prefix(&prefix, info, elmtno, ptdata, ctx->ndims, 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++) {
PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream);
}
if (elmtno == 0 && secnum == 0 && info->line_1st) {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream);
} else if (secnum && info->line_cont) {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream);
} else
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)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) {
PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)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: Render an element to output STREAM.
* Description:
* Prints the string buffer to the output STREAM. The string is
* printed according to the format described in INFO. The CTX struct
* contains context information shared between calls to this function.
*
* Return:
* False if a dimension end is reached, otherwise true
*
* In/Out:
* h5tools_context_t *ctx
* h5tools_str_t *buffer
* hsize_t *curr_pos
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* hsize_t curr_pos is the total data element position
* size_t ncols
* hsize_t local_elmt_counter is the local element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
hbool_t
h5tools_render_element(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, h5tools_str_t *buffer, hsize_t *curr_pos,
size_t ncols, hsize_t local_elmt_counter, hsize_t elmt_counter)
{
hbool_t dimension_break = TRUE;
char *s;
char *section; /*a section of output */
int secnum; /*section sequence number */
int multiline; /*datum was multiline */
if (stream == NULL)
return dimension_break;
s = h5tools_str_fmt(buffer, (size_t)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_count_ncols(s) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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_count_ncols(s) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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 (elmt_counter == ctx->size_last_dim) {
ctx->need_prefix = TRUE;
dimension_break = FALSE;
}
}
/*
* 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_count_ncols(s) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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.
*/
multiline = 0;
for (secnum = 0, multiline = 0;
(section = HDstrtok(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.
*/
/*
* check for displaying prefix for each section
*/
if ( (ctx->cur_column + HDstrlen(section) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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 + local_elmt_counter;
h5tools_simple_prefix(stream, info, ctx, *curr_pos, secnum);
}
else if ((local_elmt_counter || ctx->continuation) && secnum == 0) {
PUTSTREAM(OPT(info->elmt_suf2, " "), stream);
ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " "));
}
/* Print the section */
PUTSTREAM(section, stream);
ctx->cur_column += HDstrlen(section);
}
ctx->prev_multiline = multiline;
return dimension_break;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Render a region element to output STREAM.
* Description:
* Prints the string buffer to the output STREAM. The string is
* printed according to the format described in INFO. The CTX struct
* contains context information shared between calls to this function.
*
* Return:
* False if a dimension end is reached, otherwise true
*
* In/Out:
* h5tools_context_t *ctx
* h5tools_str_t *buffer
* hsize_t *curr_pos
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* hsize_t curr_pos is the total data element position
* size_t ncols
* hsize_t *ptdata
* hsize_t local_elmt_counter is the local element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
hbool_t
h5tools_render_region_element(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, h5tools_str_t *buffer, hsize_t *curr_pos,
size_t ncols, hsize_t *ptdata, hsize_t local_elmt_counter, hsize_t elmt_counter)
{
hbool_t dimension_break = TRUE;
char *s;
char *section; /*a section of output */
int secnum; /*section sequence number */
int multiline; /*datum was multiline */
s = h5tools_str_fmt(buffer, (size_t)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_count_ncols(s) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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_count_ncols(s) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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 (elmt_counter == ctx->size_last_dim) {
ctx->need_prefix = TRUE;
dimension_break = FALSE;
}
}
/*
* 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_count_ncols(s) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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.
*/
multiline = 0;
for (secnum = 0, multiline = 0; (section = HDstrtok(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 || local_elmt_counter) &&
(ctx->cur_column +
HDstrlen(section) +
HDstrlen(OPT(info->elmt_suf2, " ")) +
HDstrlen(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 + local_elmt_counter;
h5tools_region_simple_prefix(stream, info, ctx, local_elmt_counter, ptdata, secnum);
}
else if ((local_elmt_counter || ctx->continuation) && secnum == 0) {
PUTSTREAM(OPT(info->elmt_suf2, " "), stream);
ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " "));
}
/* Print the section */
PUTSTREAM(section, stream);
ctx->cur_column += HDstrlen(section);
}
ctx->prev_multiline = multiline;
return dimension_break;
}
/*-------------------------------------------------------------------------
* Function: init_acc_pos
*
* Purpose: initialize accumulator and matrix position
*
* Return: void
*-------------------------------------------------------------------------
*/
void
init_acc_pos(h5tools_context_t *ctx, hsize_t *dims)
{
int i;
unsigned j;
HDassert(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 (j = 0; j < ctx->ndims; j++)
ctx->pos[j] = 0;
}
/*-------------------------------------------------------------------------
* Function: render_bin_output
*
* Purpose: Write one element of memory buffer to a binary file stream
*
* Return: Success: SUCCEED
* Failure: FAIL
*-------------------------------------------------------------------------
*/
int
render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts)
{
HERR_INIT(int, SUCCEED)
unsigned char *mem = (unsigned char*)_mem;
size_t size; /* datum size */
hsize_t block_index;
H5T_class_t type_class;
if((size = H5Tget_size(tid)) == 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if((type_class = H5Tget_class(tid)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed");
switch (type_class) {
case H5T_INTEGER:
case H5T_FLOAT:
case H5T_ENUM:
block_index = block_nelmts * size;
while(block_index > 0) {
size_t bytes_in = 0; /* # of bytes to write */
size_t bytes_wrote = 0; /* # of bytes written */
if(block_index > sizeof(size_t))
bytes_in = sizeof(size_t);
else
bytes_in = (size_t)block_index;
bytes_wrote = HDfwrite(mem, 1, bytes_in, stream);
if(bytes_wrote != bytes_in || (0 == bytes_wrote && HDferror(stream)))
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
block_index -= (hsize_t)bytes_wrote;
mem = mem + bytes_wrote;
}
break;
case H5T_STRING:
{
unsigned int i;
H5T_str_t pad;
char *s;
unsigned char tempuchar;
pad = H5Tget_strpad(tid);
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
if (H5Tis_variable_str(tid)) {
s = *(char**) mem;
if (s != NULL)
size = HDstrlen(s);
else
H5E_THROW(FAIL, H5E_tools_min_id_g, "NULL string");
}
else {
s = (char *) mem;
}
for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) {
HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char));
if (1 != HDfwrite(&tempuchar, sizeof(unsigned char), 1, stream))
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
} /* i */
} /* for (block_index = 0; block_index < block_nelmts; block_index++) */
}
break;
case H5T_COMPOUND:
{
int snmembs;
unsigned nmembs;
if((snmembs = H5Tget_nmembers(tid)) < 0)
H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed");
nmembs = (unsigned)snmembs;
for (block_index = 0; block_index < block_nelmts; block_index++) {
unsigned j;
mem = ((unsigned char*)_mem) + block_index * size;
for (j = 0; j < nmembs; j++) {
hid_t memb;
size_t offset;
offset = H5Tget_member_offset(tid, j);
memb = H5Tget_member_type(tid, j);
if (render_bin_output(stream, container, memb, mem + offset, 1) < 0) {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output of compound member failed");
}
H5Tclose(memb);
}
}
}
break;
case H5T_ARRAY:
{
int k, ndims;
hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
hid_t memb;
/* get the array's base datatype for each element */
memb = H5Tget_super(tid);
ndims = H5Tget_array_ndims(tid);
H5Tget_array_dims2(tid, dims);
HDassert(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;
}
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
/* dump the array element */
if (render_bin_output(stream, container, memb, mem, nelmts) < 0) {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
}
}
H5Tclose(memb);
}
break;
case H5T_VLEN:
{
hsize_t nelmts;
hid_t memb;
/* get the VL sequences's base datatype for each element */
memb = H5Tget_super(tid);
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
/* Get the number of sequence elements */
nelmts = ((hvl_t *) mem)->len;
/* dump the array element */
if (render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)), nelmts) < 0) {
H5Tclose(memb);
H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
}
}
H5Tclose(memb);
}
break;
case H5T_REFERENCE:
{
if (size == H5R_DSET_REG_REF_BUF_SIZE) {
/* if (H5Tequal(tid, H5T_STD_REF_DSETREG)) */
if (region_output) {
/* region data */
hid_t region_id, region_space;
H5S_sel_type region_type;
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
region_id = H5Rdereference2(container, H5P_DEFAULT, H5R_DATASET_REGION, mem);
if (region_id >= 0) {
region_space = H5Rget_region(container, H5R_DATASET_REGION, mem);
if (region_space >= 0) {
region_type = H5Sget_select_type(region_space);
if(region_type == H5S_SEL_POINTS)
render_bin_output_region_points(region_space, region_id, stream, container);
else
render_bin_output_region_blocks(region_space, region_id, stream, container);
H5Sclose(region_space);
} /* end if (region_space >= 0) */
H5Dclose(region_id);
} /* end if (region_id >= 0) */
}
} /* end if (region_output... */
}
else if (size == H5R_OBJ_REF_BUF_SIZE) {
/* if (H5Tequal(tid, H5T_STD_REF_OBJ)) */
;
}
}
break;
default:
for (block_index = 0; block_index < block_nelmts; block_index++) {
mem = ((unsigned char*)_mem) + block_index * size;
if (size != HDfwrite(mem, sizeof(char), size, stream))
H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
}
break;
}
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print the data values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type blocks.
*
* Return:
* The function returns FAIL if there was an error, otherwise SUCEED
*
*-------------------------------------------------------------------------
*/
int
render_bin_output_region_data_blocks(hid_t region_id, FILE *stream,
hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata)
{
hsize_t *dims1 = NULL;
hsize_t *start = NULL;
hsize_t *count = NULL;
hsize_t numelem;
hsize_t total_size[H5S_MAX_RANK];
int jndx;
size_t type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
int blkndx;
hid_t sid1 = -1;
int ret_value = SUCCEED;
/* Get the dataspace of the dataset */
if((sid1 = H5Dget_space(region_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims");
/* find the dimensions of each data space from the block coordinates */
numelem = 1;
for (jndx = 0; jndx < ndims; jndx++) {
dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1;
numelem = dims1[jndx] * numelem;
}
/* Create dataspace for reading buffer */
if((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed");
if((type_size = H5Tget_size(type_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if((region_buf = HDmalloc(type_size * (size_t)numelem)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate region buffer");
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
if((start = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for start");
if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for count");
for (blkndx = 0; blkndx < nblocks; blkndx++) {
for (jndx = 0; jndx < ndims; jndx++) {
start[jndx] = ptdata[jndx + blkndx * ndims * 2];
count[jndx] = dims1[jndx];
}
if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
if(render_bin_output(stream, container, type_id, (char*)region_buf, numelem) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "render_bin_output of data region failed");
/* Render the region data element end */
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
done:
HDfree(start);
HDfree(count);
HDfree(region_buf);
HDfree(dims1);
if(H5Sclose(mem_space) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
if(H5Sclose(sid1) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from a dataset referenced by region blocks.
*
* Description:
* This is a special case subfunction to dump a region reference using blocks.
*
* Return:
* The function returns False if ERROR, otherwise True
*
*-------------------------------------------------------------------------
*/
hbool_t
render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container)
{
HERR_INIT(hbool_t, TRUE)
hssize_t snblocks;
hsize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata;
int ndims;
hid_t dtype;
hid_t type_id;
if((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
nblocks = (hsize_t)snblocks;
/* Print block information */
if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]);
HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
if((ptdata = (hsize_t*) HDmalloc((size_t) alloc_size)) == NULL)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata");
H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t);
if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Rget_select_hyper_blocklist failed");
if((dtype = H5Dget_type(region_id)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed");
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed");
render_bin_output_region_data_blocks(region_id, stream, container, ndims,
type_id, nblocks, ptdata);
done:
HDfree(ptdata);
if(H5Tclose(type_id) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(dtype) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
H5_LEAVE(TRUE)
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print the data values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to print the data in a region reference of type points.
*
* Return:
* The function returns FAIL on error, otherwise SUCCEED
*
* Parameters Description:
* h5tools_str_t *buffer is the string into which to render
* size_t ncols
* int ndims is the number of dimensions of the region element
* hssize_t npoints is the number of points in the region
*-------------------------------------------------------------------------
*/
int
render_bin_output_region_data_points(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container,
int ndims, hid_t type_id, hssize_t npoints)
{
hsize_t *dims1 = NULL;
int type_size;
hid_t mem_space = -1;
void *region_buf = NULL;
int ret_value = SUCCEED;
if((type_size = H5Tget_size(type_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
if((region_buf = HDmalloc(type_size * (size_t)npoints)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for region");
/* Allocate space for the dimension array */
if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims");
dims1[0] = npoints;
if((mem_space = H5Screate_simple(1, dims1, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed");
if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
if(H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
if(render_bin_output(stream, container, type_id, (char*)region_buf, npoints) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "render_bin_output of data points failed");
done:
HDfree(region_buf);
HDfree(dims1);
if(H5Sclose(mem_space) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed");
return ret_value;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from a dataset referenced by region points.
*
* Description:
* This is a special case subfunction to dump a region reference using points.
*
* Return:
* The function returns False if the last dimension has been reached, otherwise True
*
*-------------------------------------------------------------------------
*/
hbool_t
render_bin_output_region_points(hid_t region_space, hid_t region_id,
FILE *stream, hid_t container)
{
HERR_INIT(hbool_t, TRUE)
hssize_t npoints;
int ndims;
hid_t dtype;
hid_t type_id;
if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed");
/* Allocate space for the dimension array */
if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0)
H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
if((dtype = H5Dget_type(region_id)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed");
if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0)
HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed");
render_bin_output_region_data_points(region_space, region_id,
stream, container, ndims, type_id, npoints);
done:
if(H5Tclose(type_id) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(dtype) < 0)
HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed");
H5_LEAVE(ret_value)
CATCH
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: h5tools_is_zero
*
* Purpose: Determines if memory is initialized to all zero bytes.
*
* Return: TRUE if all bytes are zero; FALSE otherwise
*-------------------------------------------------------------------------
*/
hbool_t
h5tools_is_zero(const void *_mem, size_t size)
{
const unsigned char *mem = (const unsigned char *) _mem;
while (size-- > 0)
if (mem[size])
return FALSE;
return TRUE;
}
/*-------------------------------------------------------------------------
* Function: h5tools_is_obj_same
*
* Purpose: Check if two given object IDs or link names point to the same object.
*
* Parameters:
* hid_t loc_id1: location of the first object
* char *name1: link name of the first object.
* Use "." or NULL if loc_id1 is the object to be compared.
* hid_t loc_id2: location of the second object
* char *name1: link name of the first object.
* Use "." or NULL if loc_id2 is the object to be compared.
*
* Return: TRUE if it is the same object; FALSE otherwise.
*
* Programmer: Peter Cao
* 4/27/2011
*
*-------------------------------------------------------------------------
*/
hbool_t
h5tools_is_obj_same(hid_t loc_id1, const char *name1,
hid_t loc_id2, const char *name2)
{
H5O_info_t oinfo1, oinfo2;
hbool_t ret_val = 0;
if ( name1 && HDstrcmp(name1, "."))
H5Oget_info_by_name(loc_id1, name1, &oinfo1, H5P_DEFAULT);
else
H5Oget_info(loc_id1, &oinfo1);
if ( name2 && HDstrcmp(name2, "."))
H5Oget_info_by_name(loc_id2, name2, &oinfo2, H5P_DEFAULT);
else
H5Oget_info(loc_id2, &oinfo2);
if (oinfo1.fileno == oinfo2.fileno && oinfo1.addr==oinfo2.addr)
ret_val = 1;
return ret_val;
}
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