mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2024-11-27 02:10:55 +08:00
Code Issues Packages Projects Releases Wiki Activity
c7590ca38e
hdf5/tools/lib/h5tools.c
Allen Byrne c7590ca38e [svn-r17450] Bring h5dump single subsetting selection and region reference changes from NPOESS 
Tested: local linux smirom
2009-09-04 09:50:13 -05:00

3605 lines
121 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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_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 */
int region_output; /* region output */
static h5tool_format_t h5tools_dataformat = {
0, /*raw */
"", /*fmt_raw */
"%d", /*fmt_int */
"%u", /*fmt_uint */
"%d", /*fmt_schar */
"%u", /*fmt_uchar */
"%d", /*fmt_short */
"%u", /*fmt_ushort */
"%ld", /*fmt_long */
"%lu", /*fmt_ulong */
NULL, /*fmt_llong */
NULL, /*fmt_ullong */
"%g", /*fmt_double */
"%g", /*fmt_float */
0, /*ascii */
0, /*str_locale */
0, /*str_repeat */
"[ ", /*arr_pre */
",", /*arr_sep */
" ]", /*arr_suf */
1, /*arr_linebreak */
"", /*cmpd_name */
",\n", /*cmpd_sep */
"{\n", /*cmpd_pre */
"}", /*cmpd_suf */
"\n", /*cmpd_end */
", ", /*vlen_sep */
"(", /*vlen_pre */
")", /*vlen_suf */
"", /*vlen_end */
"%s", /*elmt_fmt */
",", /*elmt_suf1 */
" ", /*elmt_suf2 */
"", /*idx_n_fmt */
"", /*idx_sep */
"", /*idx_fmt */
80, /*line_ncols *//*standard default columns */
0, /*line_per_line */
"", /*line_pre */
"%s", /*line_1st */
"%s", /*line_cont */
"", /*line_suf */
"", /*line_sep */
1, /*line_multi_new */
" ", /*line_indent */
1, /*skip_first */
1, /*obj_hidefileno */
" "H5_PRINTF_HADDR_FMT, /*obj_format */
1, /*dset_hidefileno */
"DATASET %s ", /*dset_format */
"%s", /*dset_blockformat_pre */
"%s", /*dset_ptformat_pre */
"%s", /*dset_ptformat */
1, /*array indices */
1 /*escape non printable characters */
};
static const h5tools_dump_header_t h5tools_standardformat = {
"standardformat", /*name */
"HDF5", /*fileebgin */
"", /*fileend */
SUPER_BLOCK, /*bootblockbegin */
"", /*bootblockend */
H5_TOOLS_GROUP, /*groupbegin */
"", /*groupend */
H5_TOOLS_DATASET, /*datasetbegin */
"", /*datasetend */
ATTRIBUTE, /*attributebegin */
"", /*attributeend */
H5_TOOLS_DATATYPE, /*datatypebegin */
"", /*datatypeend */
DATASPACE, /*dataspacebegin */
"", /*dataspaceend */
DATA, /*databegin */
"", /*dataend */
SOFTLINK, /*softlinkbegin */
"", /*softlinkend */
EXTLINK, /*extlinkbegin */
"", /*extlinkend */
UDLINK, /*udlinkbegin */
"", /*udlinkend */
SUBSET, /*subsettingbegin */
"", /*subsettingend */
START, /*startbegin */
"", /*startend */
STRIDE, /*stridebegin */
"", /*strideend */
COUNT, /*countbegin */
"", /*countend */
BLOCK, /*blockbegin */
"", /*blockend */
"{", /*fileblockbegin */
"}", /*fileblockend */
"{", /*bootblockblockbegin */
"}", /*bootblockblockend */
"{", /*groupblockbegin */
"}", /*groupblockend */
"{", /*datasetblockbegin */
"}", /*datasetblockend */
"{", /*attributeblockbegin */
"}", /*attributeblockend */
"", /*datatypeblockbegin */
"", /*datatypeblockend */
"", /*dataspaceblockbegin */
"", /*dataspaceblockend */
"{", /*datablockbegin */
"}", /*datablockend */
"{", /*softlinkblockbegin */
"}", /*softlinkblockend */
"{", /*extlinkblockbegin */
"}", /*extlinkblockend */
"{", /*udlinkblockbegin */
"}", /*udlinkblockend */
"{", /*strblockbegin */
"}", /*strblockend */
"{", /*enumblockbegin */
"}", /*enumblockend */
"{", /*structblockbegin */
"}", /*structblockend */
"{", /*vlenblockbegin */
"}", /*vlenblockend */
"{", /*subsettingblockbegin */
"}", /*subsettingblockend */
"(", /*startblockbegin */
");", /*startblockend */
"(", /*strideblockbegin */
");", /*strideblockend */
"(", /*countblockbegin */
");", /*countblockend */
"(", /*blockblockbegin */
");", /*blockblockend */
"", /*dataspacedescriptionbegin */
"", /*dataspacedescriptionend */
"(", /*dataspacedimbegin */
")", /*dataspacedimend */
};
static const h5tools_dump_header_t * h5tools_dump_header_format;
/* 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);
static hbool_t h5tools_is_zero(const void *_mem, size_t size);
int h5tools_render_element(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/,
h5tools_str_t *buffer/*string into which to render */,
hsize_t *curr_pos/*total data element position*/,
size_t ncols, hsize_t local_elmt_counter/*element counter*/,
hsize_t elmt_counter);
int h5tools_render_region_element(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/,
h5tools_str_t *buffer/*string into which to render */,
hsize_t *curr_pos/*total data element position*/,
size_t ncols, hsize_t *ptdata,
hsize_t local_elmt_counter/*element counter*/,
hsize_t elmt_counter);
int h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/,
h5tools_str_t *buffer/*string into which to render */,
hsize_t *curr_pos/*total data element position*/,
size_t ncols, hsize_t region_elmt_counter/*element counter*/,
hsize_t elmt_counter);
int h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/,
h5tools_str_t *buffer/*string into which to render */,
hsize_t *curr_pos/*total data element position*/,
size_t ncols, hsize_t region_elmt_counter/*element counter*/,
hsize_t elmt_counter);
/* 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_dump_header_format = &h5tools_standardformat;
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: 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
*-------------------------------------------------------------------------
*/
static 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 (!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_region_prefix(&prefix, info, elmtno, ptdata, 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, The HDF Group, 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 */
size_t size; /*size of each datum */
hid_t region_space;
hid_t region_id;
int dimension_break = 1;
size_t ncols = 80; /*available output width */
h5tools_str_t buffer; /*string into which to render */
hsize_t curr_pos; /* total data element position */
hsize_t 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);
} /* 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++) {
void* memref = mem + i * size;
if (region_output && H5Tequal(type, H5T_STD_REF_DSETREG)) {
char ref_name[1024];
/* region data */
region_id = H5Rdereference(container, H5R_DATASET_REGION, memref);
if (region_id >= 0) {
region_space = H5Rget_region(container, H5R_DATASET_REGION, memref);
if (region_space >= 0) {
if (h5tools_is_zero(memref, H5Tget_size(type))) {
h5tools_str_append(&buffer, "NULL");
}
else {
H5Rget_name(region_id, H5R_DATASET_REGION, memref, (char*) ref_name, 1024);
/* Render the region element begin */
h5tools_str_reset(&buffer);
h5tools_str_append(&buffer, info->dset_format, ref_name);
dimension_break = h5tools_render_element(stream, info,
ctx, &buffer, &curr_pos, ncols, i, elmt_counter);
/* Print block information */
dimension_break = h5tools_dump_region_data_blocks(
region_space, region_id, stream, info, ctx,
&buffer, &curr_pos, ncols, i, elmt_counter);
/* Print point information */
dimension_break = h5tools_dump_region_data_points(
region_space, region_id, stream, info, ctx,
&buffer, &curr_pos, ncols, i, elmt_counter);
/* Render the region element end */
} /* end else to if (h5tools_is_zero(... */
H5Sclose(region_space);
} /* end if (region_space >= 0) */
H5Dclose(region_id);
} /* if (region_id >= 0) */
ctx->need_prefix = TRUE;
} /* end if (region_output... */
else {
/* Render the data element begin*/
h5tools_str_reset(&buffer);
h5tools_str_sprint(&buffer, info, container, type, memref, ctx);
if (i + 1 < nelmts || (flags & END_OF_DATA) == 0)
h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));
dimension_break = h5tools_render_element(stream, info, ctx, &buffer,
&curr_pos, ncols, i, elmt_counter);
/* Render the data element end*/
}
if(dimension_break==0)
elmt_counter = 0;
} /* end for (i = 0; i < nelmts... */
h5tools_str_close(&buffer);
}/* else bin */
}
/*-------------------------------------------------------------------------
* 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
*-------------------------------------------------------------------------
*/
int
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)
{
int dimension_break = 1;
char *s;
char *section; /*a section of output */
int secnum; /*section sequence number */
int multiline; /*datum was multiline */
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 (elmt_counter == ctx->size_last_dim) {
ctx->need_prefix = TRUE;
dimension_break = 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.
*/
multiline = 0;
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 || local_elmt_counter) &&
(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 + local_elmt_counter;
h5tools_simple_prefix(stream, info, ctx, *curr_pos, secnum);
}
else if ((local_elmt_counter || 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;
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
*-------------------------------------------------------------------------
*/
int
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)
{
int dimension_break = 1;
char *s;
char *section; /*a section of output */
int secnum; /*section sequence number */
int multiline; /*datum was multiline */
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 (elmt_counter == ctx->size_last_dim) {
ctx->need_prefix = TRUE;
dimension_break = 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.
*/
multiline = 0;
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 || local_elmt_counter) &&
(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 + local_elmt_counter;
h5tools_region_simple_prefix(stream, info, ctx, local_elmt_counter, ptdata, secnum);
}
else if ((local_elmt_counter || 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;
return dimension_break;
}
/*-------------------------------------------------------------------------
* 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 the last dimension has been reached, otherwise True
*
* In/Out:
* h5tools_context_t *ctx
* 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 region_elmt_counter is the region element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
int
h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id,
FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx/*in,out*/,
h5tools_str_t *buffer/*string into which to render */,
hsize_t *curr_pos/*total data element position*/,
size_t ncols, hsize_t region_elmt_counter/*element counter*/,
hsize_t elmt_counter) {
int dimension_break = 1;
hssize_t nblocks;
hsize_t alloc_size;
hsize_t *ptdata;
hsize_t *dims1;
hsize_t *start;
hsize_t *count;
size_t numelem;
hsize_t region_total_size[H5S_MAX_RANK];
h5tools_context_t region_ctx; /* print context */
hsize_t region_elmtno; /* elemnt index */
int region_dimension_break = 1;
unsigned int region_flags; /* buffer extent flags */
hsize_t region_curr_pos;
int ndims;
int jndx;
int type_size;
hid_t mem_space;
hid_t dtype;
hid_t type_id;
void *region_buf;
herr_t status;
int i;
int blkndx;
hid_t sid1;
/*
* This function fails if the region does not have blocks.
*/
H5E_BEGIN_TRY {
nblocks = H5Sget_select_hyper_nblocks(region_space);
} H5E_END_TRY;
if (nblocks <= 0)
return dimension_break;
/* Print block information */
ndims = H5Sget_simple_extent_ndims(region_space);
/* Render the region { element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "{");
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region { element end */
/* Render the region datatype info and indices element begin */
h5tools_str_reset(buffer);
ctx->indent_level++;
ctx->need_prefix = TRUE;
h5tools_str_append(buffer, "REGION_TYPE BLOCK ");
alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]);
assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
ptdata = (hsize_t*) malloc((size_t) alloc_size);
H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t);
H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata);
for (i = 0; i < nblocks; i++) {
int j;
h5tools_str_append(buffer, info->dset_blockformat_pre,
i ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long) i);
/* Start coordinates and opposite corner */
for (j = 0; j < ndims; j++)
h5tools_str_append(buffer, "%s%lu", j ? "," : "(",
(unsigned long) ptdata[i * 2 * ndims + j]);
for (j = 0; j < ndims; j++)
h5tools_str_append(buffer, "%s%lu", j ? "," : ")-(",
(unsigned long) ptdata[i * 2 * ndims + j + ndims]);
h5tools_str_append(buffer, ")");
} /* end for (i = 0; i < nblocks; i++) */
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region datatype info and indices element end */
ctx->need_prefix = TRUE;
dtype = H5Dget_type(region_id);
type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT);
/* Render the datatype element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ",
h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
h5tools_print_datatype(buffer, info, ctx, dtype);
if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (HDstrlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, " ");
}
if (HDstrlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the datatype element end */
ctx->need_prefix = TRUE;
/* Render the dataspace element begin */
h5tools_str_reset(buffer);
ctx->need_prefix = TRUE;
h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin);
h5tools_print_dataspace(buffer, info, ctx, region_space);
if (HDstrlen(h5tools_dump_header_format->dataspaceblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
if (HDstrlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, " ");
}
if (HDstrlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the dataspace element end */
ctx->need_prefix = TRUE;
/* Render the databegin element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ",
h5tools_dump_header_format->databegin,
h5tools_dump_header_format->datablockbegin);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the databegin element end */
ctx->need_prefix = TRUE;
/* Get the dataspace of the dataset */
sid1 = H5Dget_space(region_id);
/* Allocate space for the dimension array */
dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims);
/* 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 */
mem_space = H5Screate_simple(ndims, dims1, NULL);
type_size = H5Tget_size(type_id);
region_buf = malloc(type_size * numelem);
/* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */
/* 1 2 n 1 2 n */
start = (hsize_t *) malloc(sizeof(hsize_t) * ndims);
count = (hsize_t *) malloc(sizeof(hsize_t) * ndims);
region_curr_pos = 0;
for (blkndx = 0; blkndx < nblocks; blkndx++) {
/* initialize context structure for the region loop */
memset(&region_ctx, 0, sizeof(region_ctx));
region_ctx.indent_level = ctx->indent_level;
region_ctx.ndims = ndims;
region_ctx.need_prefix = TRUE;
region_ctx.cur_column = ctx->cur_column;
region_ctx.cur_elmt = 0;
region_ctx.prev_multiline = ctx->prev_multiline;
region_ctx.prev_prefix_len = ctx->prev_prefix_len;
region_ctx.continuation = ctx->continuation;
region_ctx.default_indent_level = ctx->default_indent_level;
for (jndx = 0; jndx < ndims; jndx++) {
start[jndx] = ptdata[jndx + blkndx * ndims * 2];
count[jndx] = dims1[jndx];
}
status = H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL);
status = H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf);
region_ctx.indent_level++;
H5Sget_simple_extent_dims(mem_space, region_total_size, NULL);
/* assume entire data space to be printed */
for (jndx = 0; jndx < (size_t) region_ctx.ndims; jndx++)
region_ctx.p_min_idx[jndx] = start[jndx];
init_acc_pos(&region_ctx, region_total_size);
/* print the data */
region_flags = START_OF_DATA;
if (blkndx == nblocks - 1)
region_flags |= END_OF_DATA;
for (jndx = 0; jndx < region_ctx.ndims; jndx++)
region_ctx.p_max_idx[jndx] = dims1[jndx];
region_curr_pos = 0;
region_ctx.sm_pos = blkndx*2*ndims;
region_ctx.size_last_dim = dims1[ndims-1];
h5tools_region_simple_prefix(stream, info, &region_ctx, region_curr_pos, ptdata, 0);
region_elmtno = 0;
for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, region_ctx.cur_elmt++) {
/* Render the region data element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s", jndx ? OPTIONAL_LINE_BREAK "" : "");
h5tools_str_sprint(buffer, info, region_id, type_id,
((char*)region_buf + jndx * type_size), &region_ctx);
if (jndx + 1 < numelem || (region_flags & END_OF_DATA) == 0)
h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ","));
region_dimension_break = h5tools_render_region_element(stream, info, &region_ctx, buffer, &region_curr_pos,
ncols, ptdata, jndx, region_elmtno);
/* Render the region data element end */
if(region_dimension_break==0)
region_elmtno = 0;
} /* end for (jndx = 0; jndx < numelem; jndx++, region_elmtno++, region_ctx.cur_elmt++) */
region_ctx.indent_level--;
} /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */
free(start);
free(count);
free(region_buf);
free(ptdata);
free(dims1);
status = H5Tclose(dtype);
status = H5Sclose(mem_space);
status = H5Sclose(sid1);
ctx->need_prefix = TRUE;
/* Render the dataend element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ",
h5tools_dump_header_format->dataend,
h5tools_dump_header_format->datablockend);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos,
ncols, region_elmt_counter, elmt_counter);
/* Render the dataend element end */
ctx->indent_level--;
ctx->need_prefix = TRUE;
/* Render the region } element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "}");
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos,
ncols, region_elmt_counter, elmt_counter);
/* Render the region } element end */
return dimension_break;
}
/*-------------------------------------------------------------------------
* 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
*
* In/Out:
* h5tools_context_t *ctx
* 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 region_elmt_counter is the region element loop counter
* hsize_t elmt_count is the data element loop counter
*-------------------------------------------------------------------------
*/
int
h5tools_dump_region_data_points(hid_t region_space, hid_t region_id,
FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx,
h5tools_str_t *buffer, hsize_t *curr_pos, size_t ncols, hsize_t region_elmt_counter,
hsize_t elmt_counter) {
int dimension_break = 1;
hssize_t npoints;
hsize_t alloc_size;
hsize_t *ptdata;
hsize_t *dims1;
h5tools_context_t region_ctx; /* print context */
hsize_t region_elmtno; /* elemnt index */
int region_dimension_break = 1;
unsigned int region_flags; /* buffer extent flags */
hsize_t region_curr_pos;
int ndims;
int jndx;
int type_size;
hid_t mem_space;
hid_t dtype;
hid_t type_id;
void *region_buf;
herr_t status;
/*
* This function fails if the region does not have blocks.
*/
H5E_BEGIN_TRY {
npoints = H5Sget_select_elem_npoints(region_space);
} H5E_END_TRY;
if (npoints > 0) {
int indx;
/* Render the region { element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "{");
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region { element end */
/* Render the region datatype info and indices element begin */
h5tools_str_reset(buffer);
ctx->indent_level++;
ctx->need_prefix = TRUE;
h5tools_str_append(buffer, "REGION_TYPE POINT ");
/* Allocate space for the dimension array */
ndims = H5Sget_simple_extent_ndims(region_space);
alloc_size = npoints * ndims * sizeof(ptdata[0]);
assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/
ptdata = malloc((size_t) alloc_size);
H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t);
H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata);
for (indx = 0; indx < npoints; indx++) {
int loop_indx;
h5tools_str_append(buffer, info->dset_ptformat_pre,
indx ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long) indx);
for (loop_indx = 0; loop_indx < ndims; loop_indx++)
h5tools_str_append(buffer, "%s%lu", loop_indx ? "," : "(",
(unsigned long) (ptdata[indx * ndims + loop_indx]));
h5tools_str_append(buffer, ")");
} /* end for (indx = 0; indx < npoints; indx++) */
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the region datatype info and indices element end */
ctx->need_prefix = TRUE;
dtype = H5Dget_type(region_id);
type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT);
/* Render the datatype element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ",
h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
h5tools_print_datatype(buffer, info, ctx, dtype);
if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (HDstrlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, " ");
}
if (HDstrlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the datatype element end */
ctx->need_prefix = TRUE;
/* Render the dataspace element begin */
h5tools_str_reset(buffer);
ctx->need_prefix = TRUE;
h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin);
h5tools_print_dataspace(buffer, info, ctx, region_space);
if (HDstrlen(h5tools_dump_header_format->dataspaceblockend)) {
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
if (HDstrlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, " ");
}
if (HDstrlen(h5tools_dump_header_format->dataspaceend))
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the dataspace element end */
ctx->need_prefix = TRUE;
/* Render the databegin element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ",
h5tools_dump_header_format->databegin,
h5tools_dump_header_format->datablockbegin);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter);
/* Render the databegin element end */
ctx->need_prefix = TRUE;
type_size = H5Tget_size(type_id);
region_buf = malloc(type_size * npoints);
/* Allocate space for the dimension array */
dims1 = (hsize_t *) malloc(sizeof(hsize_t) * ndims);
dims1[0] = npoints;
mem_space = H5Screate_simple(1, dims1, NULL);
status = H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf);
region_elmtno = 0;
region_curr_pos = 0;
for (jndx = 0; jndx < npoints; jndx++, region_elmtno++) {
/* initialize context structure for the region loop */
memset(&region_ctx, 0, sizeof(region_ctx));
region_ctx.indent_level = ctx->indent_level;
region_ctx.ndims = ndims;
region_ctx.need_prefix = TRUE;
region_ctx.cur_column = ctx->cur_column;
region_ctx.cur_elmt = 0; /* points are always 0 */
region_ctx.prev_multiline = ctx->prev_multiline;
region_ctx.prev_prefix_len = ctx->prev_prefix_len;
region_ctx.continuation = ctx->continuation;
region_ctx.default_indent_level = ctx->default_indent_level;
/* Render the point element begin */
h5tools_str_reset(buffer);
region_ctx.indent_level++;
/* assume entire data space to be printed */
for (indx = 0; indx < (size_t) region_ctx.ndims; indx++)
region_ctx.p_min_idx[indx] = 0;
H5Sget_simple_extent_dims(region_space, region_ctx.p_max_idx, NULL);
if (region_ctx.ndims > 0) {
region_ctx.size_last_dim = (int) (region_ctx.p_max_idx[region_ctx.ndims - 1]);
}
else
region_ctx.size_last_dim = 0;
if (region_ctx.ndims > 0)
init_acc_pos(&region_ctx, region_ctx.p_max_idx);
/* print the data */
region_flags = START_OF_DATA;
if (jndx == npoints - 1)
region_flags |= END_OF_DATA;
region_curr_pos = 0; /* points requires constant 0 */
region_ctx.sm_pos = jndx * ndims;
h5tools_region_simple_prefix(stream, info, &region_ctx, region_curr_pos, ptdata, 0);
h5tools_str_sprint(buffer, info, region_id, type_id,
((char*)region_buf + jndx * type_size), &region_ctx);
if (jndx + 1 < npoints || (region_flags & END_OF_DATA) == 0)
h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ","));
region_dimension_break =
h5tools_render_region_element(stream, info, &region_ctx, buffer, &region_curr_pos,
ncols, ptdata, 0, region_elmtno);
/* Render the point element end */
region_ctx.indent_level--;
if(region_dimension_break == 0)
region_elmtno = 0;
} /* end for (jndx = 0; jndx < npoints; jndx++, region_elmtno++) */
free(region_buf);
free(ptdata);
free(dims1);
status = H5Tclose(dtype);
status = H5Sclose(mem_space);
ctx->need_prefix = TRUE;
/* Render the dataend element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "%s %s ",
h5tools_dump_header_format->dataend,
h5tools_dump_header_format->datablockend);
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos,
ncols, region_elmt_counter, elmt_counter);
/* Render the dataend element end*/
ctx->indent_level--;
ctx->need_prefix = TRUE;
/* Render the region } element begin */
h5tools_str_reset(buffer);
h5tools_str_append(buffer, "}");
dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos,
ncols, region_elmt_counter, elmt_counter);
/* Render the region } element end */
} /* end if (npoints > 0) */
return dimension_break;
}
/*-------------------------------------------------------------------------
* 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.
*
* Hyperslabs select "count" blocks of size "block", spaced "stride" elements
* from each other, starting at coordinate "start".
*
* Return:
* On success, return SUCCEED. Otherwise, the function returns FAIL.
*
* Original programmer:
* Bill Wendling, Wednesday, March 07, 2001
*
* Rewritten with modified algorithm by:
* Pedro Vicente, Wednesday, January 16, 2008, contributions from Quincey Koziol
*
* Algorithm
*
* In a inner loop, the parameters from SSET are translated into temporary
* variables so that 1 row is printed at a time (getting the coordinate indices
* at each row).
* We define the stride, count and block to be 1 in the row dimension to achieve
* this and advance until all points are printed.
* An outer loop for cases where dimensionality is greater than 2D is made.
* In each iteration, the 2D block is displayed in the inner loop. The remaining
* slower dimensions above the first 2 are incremented one at a time in the outer loop
*
* The element position is obtained from the matrix according to:
* 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
*
*-------------------------------------------------------------------------
*/
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_counter 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 */
hsize_t temp_stride[H5S_MAX_RANK];/* temporary stride size used in loop */
int reset_dim;
hsize_t size_row_block; /* size for blocks along rows */
#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++) {
/* consider block size */
outer_count = outer_count * sset->count[i] * sset->block[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] = sset->block[i];
temp_stride[i] = sset->stride[i];
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++) {
hsize_t row_counter = 0;
/* number of read iterations in inner loop, read by rows, to match 2D display */
if (ctx.ndims > 1) {
/* count is the number of iterations to display all the rows,
the block size count times */
count = sset->count[row_dim] * sset->block[row_dim];
/* always 1 row_counter at a time, that is a block of size 1, 1 time */
temp_count[row_dim] = 1;
temp_block[row_dim] = 1;
/* advance 1 row_counter at a time */
if (sset->block[row_dim] > 1)
temp_stride[row_dim] = 1;
}
/* for the 1D case */
else {
count = 1;
}
size_row_block = sset->block[row_dim];
/* display loop */
for (; count > 0; temp_start[row_dim] += temp_stride[row_dim], count--) {
/* jump rows if size of block exceeded
cases where block > 1 only and stride > block */
if (size_row_block > 1
&& row_counter == size_row_block
&& sset->stride[row_dim] > sset->block[row_dim]) {
hsize_t increase_rows = sset->stride[row_dim] - sset->block[row_dim];
temp_start[row_dim] += increase_rows;
row_counter = 0;
}
row_counter++;
/* calculate the potential number of elements we're going to print */
H5Sselect_hyperslab(f_space, H5S_SELECT_SET, temp_start, temp_stride, temp_count, 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) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(total_size[i - 1], size);
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];
/* consider block */
if (sset->block[current_outer_dim] > 1)
temp_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.
*-------------------------------------------------------------------------
*/
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.ndims = H5Sget_simple_extent_ndims(f_space);
if ((size_t)ctx.ndims > NELMTS(sm_size)) {
H5Sclose(f_space);
return FAIL;
}
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
/* 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) {
hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
size = 1;
sm_size[i - 1] = MIN(total_size[i - 1], size);
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
*
*-------------------------------------------------------------------------
*/
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
*
* 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
*
*-------------------------------------------------------------------------
*/
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: print_datatype
*
* Purpose: print the datatype.
*
* Return: void
*
* In/Out: h5tools_str_t *buffer
* h5tools_context_t *ctx
*
*-------------------------------------------------------------------------
*/
void
h5tools_print_datatype(h5tools_str_t *buffer, const h5tool_format_t *info,
h5tools_context_t *ctx, hid_t type)
{
char *mname;
hid_t mtype, str_type;
unsigned nmembers;
unsigned ndims;
unsigned i;
size_t size = 0;
hsize_t dims[H5TOOLS_DUMP_MAX_RANK];
H5T_str_t str_pad;
H5T_cset_t cset;
H5T_order_t order;
hid_t super;
hid_t tmp_type;
htri_t is_vlstr = FALSE;
const char *order_s = NULL; /* byte order string */
H5T_sign_t sign; /* sign scheme value */
const char *sign_s = NULL; /* sign scheme string */
switch (H5Tget_class(type)) {
case H5T_INTEGER:
if (H5Tequal(type, H5T_STD_I8BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I8BE");
}
else if (H5Tequal(type, H5T_STD_I8LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I8LE");
}
else if (H5Tequal(type, H5T_STD_I16BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I16BE");
}
else if (H5Tequal(type, H5T_STD_I16LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I16LE");
}
else if (H5Tequal(type, H5T_STD_I32BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I32BE");
}
else if (H5Tequal(type, H5T_STD_I32LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I32LE");
}
else if (H5Tequal(type, H5T_STD_I64BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I64BE");
}
else if (H5Tequal(type, H5T_STD_I64LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_I64LE");
}
else if (H5Tequal(type, H5T_STD_U8BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U8BE");
}
else if (H5Tequal(type, H5T_STD_U8LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U8LE");
}
else if (H5Tequal(type, H5T_STD_U16BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U16BE");
}
else if (H5Tequal(type, H5T_STD_U16LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U16LE");
}
else if (H5Tequal(type, H5T_STD_U32BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U32BE");
}
else if (H5Tequal(type, H5T_STD_U32LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U32LE");
}
else if (H5Tequal(type, H5T_STD_U64BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U64BE");
}
else if (H5Tequal(type, H5T_STD_U64LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_U64LE");
}
else if (H5Tequal(type, H5T_NATIVE_SCHAR) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_SCHAR");
}
else if (H5Tequal(type, H5T_NATIVE_UCHAR) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_UCHAR");
}
else if (H5Tequal(type, H5T_NATIVE_SHORT) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_SHORT");
}
else if (H5Tequal(type, H5T_NATIVE_USHORT) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_USHORT");
}
else if (H5Tequal(type, H5T_NATIVE_INT) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_INT");
}
else if (H5Tequal(type, H5T_NATIVE_UINT) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_UINT");
}
else if (H5Tequal(type, H5T_NATIVE_LONG) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_LONG");
}
else if (H5Tequal(type, H5T_NATIVE_ULONG) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_ULONG");
}
else if (H5Tequal(type, H5T_NATIVE_LLONG) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_LLONG");
}
else if (H5Tequal(type, H5T_NATIVE_ULLONG) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_ULLONG");
}
else {
/* byte order */
if (H5Tget_size(type) > 1) {
order = H5Tget_order(type);
if (H5T_ORDER_LE == order) {
order_s = " little-endian";
}
else if (H5T_ORDER_BE == order) {
order_s = " big-endian";
}
else if (H5T_ORDER_VAX == order) {
order_s = " mixed-endian";
}
else {
order_s = " unknown-byte-order";
}
}
else {
order_s = "";
}
/* sign */
if ((sign = H5Tget_sign(type)) >= 0) {
if (H5T_SGN_NONE == sign) {
sign_s = " unsigned";
}
else if (H5T_SGN_2 == sign) {
sign_s = "";
}
else {
sign_s = " unknown-sign";
}
}
else {
sign_s = " unknown-sign";
}
/* print size, order, and sign */
h5tools_str_append(buffer, "%lu-bit%s%s integer",
(unsigned long) (8 * H5Tget_size(type)), order_s, sign_s);
}
break;
case H5T_FLOAT:
if (H5Tequal(type, H5T_IEEE_F32BE) == TRUE) {
h5tools_str_append(buffer, "H5T_IEEE_F32BE");
}
else if (H5Tequal(type, H5T_IEEE_F32LE) == TRUE) {
h5tools_str_append(buffer, "H5T_IEEE_F32LE");
}
else if (H5Tequal(type, H5T_IEEE_F64BE) == TRUE) {
h5tools_str_append(buffer, "H5T_IEEE_F64BE");
}
else if (H5Tequal(type, H5T_IEEE_F64LE) == TRUE) {
h5tools_str_append(buffer, "H5T_IEEE_F64LE");
}
else if (H5Tequal(type, H5T_VAX_F32) == TRUE) {
h5tools_str_append(buffer, "H5T_VAX_F32");
}
else if (H5Tequal(type, H5T_VAX_F64) == TRUE) {
h5tools_str_append(buffer, "H5T_VAX_F64");
}
else if (H5Tequal(type, H5T_NATIVE_FLOAT) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_FLOAT");
}
else if (H5Tequal(type, H5T_NATIVE_DOUBLE) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_DOUBLE");
#if H5_SIZEOF_LONG_DOUBLE !=0
}
else if (H5Tequal(type, H5T_NATIVE_LDOUBLE) == TRUE) {
h5tools_str_append(buffer, "H5T_NATIVE_LDOUBLE");
#endif
}
else {
/* byte order */
if (H5Tget_size(type) > 1) {
order = H5Tget_order(type);
if (H5T_ORDER_LE == order) {
order_s = " little-endian";
}
else if (H5T_ORDER_BE == order) {
order_s = " big-endian";
}
else if (H5T_ORDER_VAX == order) {
order_s = " mixed-endian";
}
else {
order_s = " unknown-byte-order";
}
}
else {
order_s = "";
}
/* print size and byte order */
h5tools_str_append(buffer, "%lu-bit%s floating-point",
(unsigned long) (8 * H5Tget_size(type)), order_s);
}
break;
case H5T_TIME:
h5tools_str_append(buffer, "H5T_TIME: not yet implemented");
break;
case H5T_STRING:
/* Make a copy of type in memory in case when TYPE is on disk, the size
* will be bigger than in memory. This makes it easier to compare
* types in memory. */
tmp_type = H5Tcopy(type);
size = H5Tget_size(tmp_type);
str_pad = H5Tget_strpad(tmp_type);
cset = H5Tget_cset(tmp_type);
is_vlstr = H5Tis_variable_str(tmp_type);
h5tools_str_append(buffer, "H5T_STRING %s\n", h5tools_dump_header_format->strblockbegin);
ctx->indent_level++;
if (is_vlstr)
h5tools_str_append(buffer, "%s H5T_VARIABLE;\n", STRSIZE);
else
h5tools_str_append(buffer, "%s %d;\n", STRSIZE, (int) size);
h5tools_str_append(buffer, "%s ", STRPAD);
if (str_pad == H5T_STR_NULLTERM)
h5tools_str_append(buffer, "H5T_STR_NULLTERM;\n");
else if (str_pad == H5T_STR_NULLPAD)
h5tools_str_append(buffer, "H5T_STR_NULLPAD;\n");
else if (str_pad == H5T_STR_SPACEPAD)
h5tools_str_append(buffer, "H5T_STR_SPACEPAD;\n");
else
h5tools_str_append(buffer, "H5T_STR_ERROR;\n");
h5tools_str_append(buffer, "%s ", CSET);
if (cset == H5T_CSET_ASCII)
h5tools_str_append(buffer, "H5T_CSET_ASCII;\n");
else
h5tools_str_append(buffer, "unknown_cset;\n");
str_type = H5Tcopy(H5T_C_S1);
if (is_vlstr)
H5Tset_size(str_type, H5T_VARIABLE);
else
H5Tset_size(str_type, size);
H5Tset_cset(str_type, cset);
H5Tset_strpad(str_type, str_pad);
h5tools_str_append(buffer, "%s ", CTYPE);
/* Check C variable-length string first. Are the two types equal? */
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_C_S1;\n");
goto done;
}
/* Change the endianness and see if they're equal. */
order = H5Tget_order(tmp_type);
if (order == H5T_ORDER_LE)
H5Tset_order(str_type, H5T_ORDER_LE);
else if (order == H5T_ORDER_BE)
H5Tset_order(str_type, H5T_ORDER_BE);
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_C_S1;\n");
goto done;
}
/* If not equal to C variable-length string, check Fortran type. */
H5Tclose(str_type);
str_type = H5Tcopy(H5T_FORTRAN_S1);
H5Tset_cset(str_type, cset);
H5Tset_size(str_type, size);
H5Tset_strpad(str_type, str_pad);
/* Are the two types equal? */
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_FORTRAN_S1;\n");
goto done;
}
/* Change the endianness and see if they're equal. */
order = H5Tget_order(tmp_type);
if (order == H5T_ORDER_LE)
H5Tset_order(str_type, H5T_ORDER_LE);
else if (order == H5T_ORDER_BE)
H5Tset_order(str_type, H5T_ORDER_BE);
if (H5Tequal(tmp_type, str_type)) {
h5tools_str_append(buffer, "H5T_FORTRAN_S1;\n");
goto done;
}
/* Type doesn't match any of above. */
h5tools_str_append(buffer, "unknown_one_character_type;\n ");
done: H5Tclose(str_type);
H5Tclose(tmp_type);
ctx->indent_level--;
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->strblockend);
break;
case H5T_BITFIELD:
if (H5Tequal(type, H5T_STD_B8BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B8BE");
}
else if (H5Tequal(type, H5T_STD_B8LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B8LE");
}
else if (H5Tequal(type, H5T_STD_B16BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B16BE");
}
else if (H5Tequal(type, H5T_STD_B16LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B16LE");
}
else if (H5Tequal(type, H5T_STD_B32BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B32BE");
}
else if (H5Tequal(type, H5T_STD_B32LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B32LE");
}
else if (H5Tequal(type, H5T_STD_B64BE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B64BE");
}
else if (H5Tequal(type, H5T_STD_B64LE) == TRUE) {
h5tools_str_append(buffer, "H5T_STD_B64LE");
}
else {
h5tools_str_append(buffer, "undefined bitfield");
}
break;
case H5T_OPAQUE:
h5tools_str_append(buffer, "\n");
h5tools_str_append(buffer, "H5T_OPAQUE;\n");
h5tools_str_append(buffer, "OPAQUE_TAG \"%s\";\n", H5Tget_tag(type));
break;
case H5T_COMPOUND:
nmembers = H5Tget_nmembers(type);
h5tools_str_append(buffer, "H5T_COMPOUND %s\n", h5tools_dump_header_format->structblockbegin);
for (i = 0; i < nmembers; i++) {
mname = H5Tget_member_name(type, i);
mtype = H5Tget_member_type(type, i);
if (H5Tget_class(mtype) == H5T_COMPOUND)
ctx->indent_level++;
h5tools_print_datatype(buffer, info, ctx, mtype);
if (H5Tget_class(mtype) == H5T_COMPOUND)
ctx->indent_level--;
h5tools_str_append(buffer, " \"%s\";\n", mname);
free(mname);
}
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->structblockend);
break;
case H5T_REFERENCE:
h5tools_str_append(buffer, "H5T_REFERENCE");
if(region_output) {
if (H5Tequal(type, H5T_STD_REF_DSETREG) == TRUE) {
h5tools_str_append(buffer, " { H5T_STD_REF_DSETREG }");
}
else {
h5tools_str_append(buffer, " { H5T_STD_REF_OBJECT }");
}
}
break;
case H5T_ENUM:
h5tools_str_append(buffer, "H5T_ENUM %s\n", h5tools_dump_header_format->enumblockbegin);
ctx->indent_level++;
super = H5Tget_super(type);
h5tools_print_datatype(buffer, info, ctx, super);
h5tools_str_append(buffer, ";\n");
h5tools_print_enum(buffer, info, ctx, type);
ctx->indent_level--;
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->enumblockend);
break;
case H5T_VLEN:
h5tools_str_append(buffer, "H5T_VLEN %s ", h5tools_dump_header_format->vlenblockbegin);
super = H5Tget_super(type);
h5tools_print_datatype(buffer, info, ctx, super);
H5Tclose(super);
/* Print closing */
h5tools_str_append(buffer, "%s", h5tools_dump_header_format->vlenblockend);
break;
case H5T_ARRAY:
/* Get array base type */
super = H5Tget_super(type);
/* Print lead-in */
h5tools_str_append(buffer, "H5T_ARRAY { ");
/* Get array information */
ndims = H5Tget_array_ndims(type);
H5Tget_array_dims2(type, dims);
/* Print array dimensions */
for (i = 0; i < ndims; i++)
h5tools_str_append(buffer, "[%d]", (int) dims[i]);
h5tools_str_append(buffer, " ");
/* Print base type */
h5tools_print_datatype(buffer, info, ctx, super);
/* Close array base type */
H5Tclose(super);
/* Print closing */
h5tools_str_append(buffer, " }");
break;
default:
h5tools_str_append(buffer, "unknown datatype");
break;
}
}
/*-------------------------------------------------------------------------
* Function: print_dataspace
*
* Purpose: print the dataspace.
*
* Return: void
*
* In/Out: h5tools_str_t *buffer
* h5tools_context_t *ctx
*
*-------------------------------------------------------------------------
*/
void
h5tools_print_dataspace(h5tools_str_t *buffer, const h5tool_format_t *info,
h5tools_context_t *ctx, hid_t space)
{
hsize_t size[H5TOOLS_DUMP_MAX_RANK];
hsize_t maxsize[H5TOOLS_DUMP_MAX_RANK];
int ndims = H5Sget_simple_extent_dims(space, size, maxsize);
H5S_class_t space_type = H5Sget_simple_extent_type(space);
int i;
switch(space_type) {
case H5S_SCALAR:
/* scalar dataspace */
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedescriptionbegin, S_SCALAR);
break;
case H5S_SIMPLE:
/* simple dataspace */
h5tools_str_append(buffer, "%s %s { %s %" H5_PRINTF_LL_WIDTH "u",
h5tools_dump_header_format->dataspacedescriptionbegin, S_SIMPLE,
h5tools_dump_header_format->dataspacedimbegin, size[0]);
for(i = 1; i < ndims; i++)
h5tools_str_append(buffer, ", %" H5_PRINTF_LL_WIDTH "u", size[i]);
h5tools_str_append(buffer, " %s / ", h5tools_dump_header_format->dataspacedimend);
if(maxsize[0] == H5S_UNLIMITED)
h5tools_str_append(buffer, "%s %s",
h5tools_dump_header_format->dataspacedimbegin, "H5S_UNLIMITED");
else
h5tools_str_append(buffer, "%s %" H5_PRINTF_LL_WIDTH "u",
h5tools_dump_header_format->dataspacedimbegin, maxsize[0]);
for(i = 1; i < ndims; i++)
if(maxsize[i] == H5S_UNLIMITED)
h5tools_str_append(buffer, ", %s", "H5S_UNLIMITED");
else
h5tools_str_append(buffer, ", %" H5_PRINTF_LL_WIDTH "u", maxsize[i]);
h5tools_str_append(buffer, " %s }", h5tools_dump_header_format->dataspacedimend);
break;
case H5S_NULL:
/* null dataspace */
h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedescriptionbegin, S_NULL);
break;
case H5S_NO_CLASS:
default:
h5tools_str_append(buffer, "%s unknown dataspace %s\n", BEGIN, END);
break;
} /* end switch */
}
/*-------------------------------------------------------------------------
* Function: print_enum
*
* Purpose: prints the enum data
*
* Return: void
*
* In/Out: h5tools_str_t *buffer
* h5tools_context_t *ctx
*
*-----------------------------------------------------------------------*/
void
h5tools_print_enum(h5tools_str_t *buffer, const h5tool_format_t *info,
h5tools_context_t *ctx, hid_t type)
{
char **name = NULL; /*member names */
unsigned char *value = NULL; /*value array */
unsigned char *copy = NULL; /*a pointer to value array */
unsigned nmembs; /*number of members */
int nchars; /*number of output characters */
hid_t super; /*enum base integer type */
hid_t native = -1; /*native integer datatype */
size_t dst_size; /*destination value type size */
unsigned i;
nmembs = H5Tget_nmembers(type);
assert(nmembs > 0);
super = H5Tget_super(type);
/*
* Determine what datatype to use for the native values. To simplify
* things we entertain three possibilities:
* 1. long long -- the largest native signed integer
* 2. unsigned long long -- the largest native unsigned integer
* 3. raw format
*/
if (H5Tget_size(type) <= sizeof(long long)) {
dst_size = sizeof(long long);
if (H5T_SGN_NONE == H5Tget_sign(type)) {
native = H5T_NATIVE_ULLONG;
}
else {
native = H5T_NATIVE_LLONG;
}
}
else {
dst_size = H5Tget_size(type);
}
/* Get the names and raw values of all members */
name = calloc(nmembs, sizeof(char *));
value = calloc(nmembs, MAX(H5Tget_size(type), dst_size));
for (i = 0; i < nmembs; i++) {
name[i] = H5Tget_member_name(type, i);
H5Tget_member_value(type, i, value + i * H5Tget_size(type));
}
/* Convert values to native datatype */
if (native > 0)
H5Tconvert(super, native, nmembs, value, NULL, H5P_DEFAULT);
/*
* Sort members by increasing value
* ***not implemented yet***
*/
/* Print members */
for (i = 0; i < nmembs; i++) {
h5tools_str_append(buffer, "\"%s\"", name[i]);
nchars = strlen(name[i]);
h5tools_str_append(buffer, "%*s ", MAX(0, 16 - nchars), "");
if (native < 0) {
size_t j;
h5tools_str_append(buffer, "0x");
for (j = 0; j < dst_size; j++)
h5tools_str_append(buffer, "%02x", value[i * dst_size + j]);
}
else if (H5T_SGN_NONE == H5Tget_sign(native)) {
/*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size"
*strangely, unless use another pointer "copy".*/
copy = value + i * dst_size;
h5tools_str_append(buffer, "%" H5_PRINTF_LL_WIDTH "u", *((unsigned long long *) ((void *) copy)));
}
else {
/*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size"
*strangely, unless use another pointer "copy".*/
copy = value + i * dst_size;
h5tools_str_append(buffer, "%" H5_PRINTF_LL_WIDTH "d", *((long long *) ((void *) copy)));
}
h5tools_str_append(buffer, ";\n");
}
/* Release resources */
for (i = 0; i < nmembs; i++)
free(name[i]);
free(name);
free(value);
H5Tclose(super);
if (0 == nmembs)
h5tools_str_append(buffer, "\n<empty>");
}
/*-------------------------------------------------------------------------
* Function: dump_datatype
*
* Purpose: Dump the datatype. Datatype can be HDF5 predefined
* atomic datatype or committed/transient datatype.
*
* Return: void
*
* In/Out: h5tools_context_t *ctx
*-------------------------------------------------------------------------
*/
void
h5tools_dump_datatype(FILE *stream, const h5tool_format_t *info,
h5tools_context_t *ctx, hid_t type)
{
size_t ncols = 80; /* available output width */
h5tools_str_t buffer; /* string into which to render */
hsize_t curr_pos; /* total data element position */
hsize_t elmt_counter = 0;/* counts the # elements printed.*/
/* setup */
HDmemset(&buffer, 0, sizeof(h5tools_str_t));
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);
/* Render the element */
h5tools_str_reset(&buffer);
ctx->indent_level++;
h5tools_str_append(&buffer, "%s %s ",
h5tools_dump_header_format->datatypebegin,
h5tools_dump_header_format->datatypeblockbegin);
h5tools_print_datatype(&buffer, info, ctx, type);
if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) {
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeblockend);
if (HDstrlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(&buffer, " ");
}
if (HDstrlen(h5tools_dump_header_format->datatypeend))
h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeend);
h5tools_str_append(&buffer, "\n");
curr_pos = h5tools_render_element(stream, info, ctx, &buffer, curr_pos,
ncols, &elmt_counter, 0);
ctx->need_prefix = TRUE;
ctx->indent_level--;
}
/*-------------------------------------------------------------------------
* 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;
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
*-------------------------------------------------------------------------
*/
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
*-------------------------------------------------------------------------
*/
static int
render_bin_output(FILE *stream, hid_t tid, void *_mem)
{
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;
}
/*-------------------------------------------------------------------------
* Function: h5tools_is_zero
*
* Purpose: Determines if memory is initialized to all zero bytes.
*
* Return: TRUE if all bytes are zero; FALSE otherwise
*-------------------------------------------------------------------------
*/
static
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;
}
Reference in New Issue View Git Blame Copy Permalink