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
a2217d58c8
hdf5/tools/lib/h5tools.c
Pedro Vicente Nunes 1b313aa2f6 [svn-r10738] Purpose: 
bug fix 366

Description:
the printing of the array indices was done relatively to the stripmine data (data read
by hyperslabs when its memory requiremnts are too large)
this was causing an incorrect numbering of the array indices (the next read would initialize
the indices to zero)

Solution:
added a field to the print context that keeps track of the stripmine position
and pass to the rendering function the total element position

Platforms tested:
Linux

Misc. update:
2005-05-09 09:53:22 -05:00

1282 lines
41 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* 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_str.h"
#include "h5tools_utils.h"
#include "hdf5.h"
#include "H5private.h"
/*
* The output functions need a temporary buffer to hold a piece of the
* dataset while it's being printed. This constant sets the limit on the
* size of that temporary buffer in bytes. For efficiency's sake, choose the
* largest value suitable for your machine (for testing use a small value).
*/
#if 1
#define H5TOOLS_BUFSIZE (1024 * 1024)
#else
#define H5TOOLS_BUFSIZE (1024)
#endif /* 1 */
#define ALIGN(A,Z) ((((A) + (Z) - 1) / (Z)) * (Z))
/* global variables */
int indent;
int compound_data;
FILE *rawdatastream; /* should initialize to stdout but gcc moans about it */
/* module-scoped variables */
static int h5tools_init_g; /* if h5tools lib has been initialized */
#ifdef H5_HAVE_PARALLEL
static int h5tools_mpi_init_g; /* if MPI_Init() has been called */
#endif /* H5_HAVE_PARALLEL */
/* Names of VFDs */
static const char *drivernames[]={
"sec2",
"family",
"split",
"multi",
#ifdef H5_HAVE_STREAM
"stream",
#endif /* H5_HAVE_STREAM */
#ifdef H5_HAVE_PARALLEL
"mpio",
"mpiposix"
#endif /* H5_HAVE_PARALLEL */
};
/* This enum should match the entries in the above drivers_list since they
* are indexes into the drivers_list array. */
enum {
SEC2_IDX = 0
,FAMILY_IDX
,SPLIT_IDX
,MULTI_IDX
#ifdef H5_HAVE_STREAM
,STREAM_IDX
#endif /* H5_HAVE_STREAM */
#ifdef H5_HAVE_PARALLEL
,MPIO_IDX
,MPIPOSIX_IDX
#endif /* H5_HAVE_PARALLEL */
} driver_idx;
#define NUM_DRIVERS (sizeof(drivernames) / sizeof(drivernames[0]))
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Initialize the H5 Tools library
* Description:
* This should be called before any other h5tools function is called.
* Effect of any h5tools function called before this has been called is
* undetermined.
* Return:
* None
* Programmer:
* Albert Cheng, 2000-10-31
* Modifications:
*-------------------------------------------------------------------------
*/
void
h5tools_init(void)
{
if (!h5tools_init_g) {
if (!rawdatastream)
rawdatastream = stdout;
h5tools_init_g++;
}
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Close the H5 Tools library
* Description:
* Close or release resources such as files opened by the library. This
* should be called after all other h5tools functions have been called.
* Effect of any h5tools function called after this has been called is
* undetermined.
* Return:
* None
* Programmer:
* Albert Cheng, 2000-10-31
* Modifications:
*-------------------------------------------------------------------------
*/
void
h5tools_close(void)
{
if (h5tools_init_g) {
if (rawdatastream && rawdatastream != stdout) {
if (fclose(rawdatastream))
perror("closing rawdatastream");
else
rawdatastream = NULL;
}
/* Shut down the library */
H5close();
#ifdef H5_HAVE_PARALLEL
/* Check if we need to shut down MPI */
if(h5tools_mpi_init_g) {
MPI_Finalize();
h5tools_mpi_init_g=0;
} /* end if */
#endif
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:
*-------------------------------------------------------------------------
*/
static hid_t
h5tools_get_fapl(const char *driver, unsigned *drivernum,
#ifdef H5_HAVE_PARALLEL
int argc, const char *argv[]
#else /* H5_HAVE_PARALLEL */
int UNUSED argc, const char UNUSED *argv[]
#endif /* H5_HAVE_PARALLEL */
)
{
hid_t fapl = H5P_DEFAULT;
/* 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])) {
if(drivernum)
*drivernum = SEC2_IDX;
} else if (!strcmp(driver, drivernames[FAMILY_IDX])) {
/* FAMILY Driver */
if((fapl = H5Pcreate(H5P_FILE_ACCESS))>=0) {
/* Set member size to be 0 to indicate the current first member size
* is the member size.
*/
H5Pset_fapl_family(fapl, (hsize_t)0, H5P_DEFAULT);
if(drivernum)
*drivernum = FAMILY_IDX;
} /* end if */
} else if (!strcmp(driver, drivernames[SPLIT_IDX])) {
/* SPLIT Driver */
if((fapl = H5Pcreate(H5P_FILE_ACCESS))>=0) {
H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT);
if(drivernum)
*drivernum = SPLIT_IDX;
} /* end if */
} else if (!strcmp(driver, drivernames[MULTI_IDX])) {
/* MULTI Driver */
if((fapl = H5Pcreate(H5P_FILE_ACCESS))>=0) {
H5Pset_fapl_multi(fapl, NULL, NULL, NULL, NULL, TRUE);
if(drivernum)
*drivernum = MULTI_IDX;
} /* end if */
#ifdef H5_HAVE_STREAM
} else if (!strcmp(driver, drivernames[STREAM_IDX])) {
/* STREAM Driver */
if((fapl = H5Pcreate(H5P_FILE_ACCESS))>=0) {
H5Pset_fapl_stream(fapl, NULL);
if(drivernum)
*drivernum = STREAM_IDX;
} /* end if */
#endif /* H5_HAVE_STREAM */
#ifdef H5_HAVE_PARALLEL
} else if (!strcmp(driver, drivernames[MPIO_IDX])) {
/* MPI-I/O Driver */
if((fapl = H5Pcreate(H5P_FILE_ACCESS))>=0) {
H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
/* Initialize the MPI library, if it wasn't already */
if(!h5tools_mpi_init_g) {
MPI_Init(&argc, (char ***)&argv);
h5tools_mpi_init_g=1;
} /* end if */
if(drivernum)
*drivernum = MPIO_IDX;
} /* end if */
} else if (!strcmp(driver, drivernames[MPIPOSIX_IDX])) {
/* MPI-I/O Driver */
if((fapl = H5Pcreate(H5P_FILE_ACCESS))>=0) {
H5Pset_fapl_mpiposix(fapl, MPI_COMM_WORLD, TRUE);
/* Initialize the MPI library, if it wasn't already */
if(!h5tools_mpi_init_g) {
MPI_Init(&argc, (char ***)&argv);
h5tools_mpi_init_g=1;
} /* end if */
if(drivernum)
*drivernum = MPIPOSIX_IDX;
} /* end if */
#endif /* H5_HAVE_PARALLEL */
} else {
fapl=(-1);
}
return(fapl);
}
/*-------------------------------------------------------------------------
* 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, const char *driver, char *drivername,
size_t drivername_size, int argc, const char *argv[])
{
unsigned drivernum;
hid_t fid = FAIL;
hid_t fapl = H5P_DEFAULT;
if (driver && *driver) {
/* Get the correct FAPL for the given driver */
if((fapl=h5tools_get_fapl(driver,&drivernum,argc,argv))<0)
goto done;
H5E_BEGIN_TRY {
fid = H5Fopen(fname, H5F_ACC_RDONLY, 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((fapl=h5tools_get_fapl(drivernames[drivernum],NULL,argc,argv))<0)
goto done;
H5E_BEGIN_TRY {
fid = H5Fopen(fname, H5F_ACC_RDONLY, fapl);
} H5E_END_TRY;
if (fid != FAIL)
break;
else {
/* Close the FAPL */
H5Pclose(fapl);
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(fapl!=H5P_DEFAULT)
H5Pclose(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 h5dump_t *info,
h5tools_context_t *ctx, hsize_t elmtno, int secnum)
{
h5tools_str_t prefix;
h5tools_str_t str; /*temporary for indentation */
size_t templength = 0;
int i, indentlevel = 0;
if (!ctx->need_prefix)
return;
memset(&prefix, 0, sizeof(h5tools_str_t));
memset(&str, 0, sizeof(h5tools_str_t));
/* Terminate previous line, if any */
if (ctx->cur_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
}
/* Calculate new prefix */
h5tools_str_prefix(&prefix, info, elmtno, ctx->ndims, ctx->p_min_idx,
ctx->p_max_idx, ctx);
/* Write new prefix to output */
if (ctx->indent_level >= 0) {
indentlevel = ctx->indent_level;
} else {
/*
* This is because sometimes we don't print out all the header
* info for the data (like the tattr-2.ddl example). If that happens
* the ctx->indent_level is negative so we need to skip the above and
* just print out the default indent levels.
*/
indentlevel = ctx->default_indent_level;
}
/* when printing array indices, print the indentation before the prefix
the prefix is printed one indentation level before */
if (info->pindex) {
for (i = 0; i < indentlevel-1; i++){
fputs(h5tools_str_fmt(&str, 0, info->line_indent), stream);
}
}
if (elmtno == 0 && secnum == 0 && info->line_1st)
fputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream);
else if (secnum && info->line_cont)
fputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream);
else
fputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream);
templength = h5tools_str_len(&prefix);
for (i = 0; i < indentlevel; i++){
/*we already made the indent for the array indices case */
if (!info->pindex) {
fputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream);
templength += h5tools_str_len(&prefix);
}
else {
/*we cannot count the prefix for the array indices case */
templength += h5tools_str_len(&str);
}
}
ctx->cur_column = ctx->prev_prefix_len = templength;
ctx->cur_elmt = 0;
ctx->need_prefix = 0;
/* Free string */
h5tools_str_close(&prefix);
h5tools_str_close(&str);
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Prints NELMTS data elements to output STREAM.
* Description:
* Prints some (NELMTS) data elements to output STREAM. The elements are
* stored in _MEM as type TYPE and are printed according to the format
* described in INFO. The CTX struct contains context information shared
* between calls to this function. The FLAGS is a bit field that
* indicates whether the data supplied in this call falls at the
* beginning or end of the total data to be printed (START_OF_DATA and
* END_OF_DATA).
* Return:
* None
* Programmer:
* Robb Matzke, Monday, April 26, 1999
* Modifications:
* Robb Matzke, 1999-06-04
* The `container' argument is the optional dataset for reference types.
*
* Robb Matzke, 1999-09-29
* Understands the `per_line' property which indicates that every Nth
* element should begin a new line.
*
* Robb Matzke, LLNL, 2003-06-05
* Do not dereference the memory for a variable-length string here.
* Deref in h5tools_str_sprint() instead so recursive types are
* handled correctly.
*-------------------------------------------------------------------------
*/
void
h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container,
h5tools_context_t *ctx/*in,out*/, unsigned flags,
hsize_t nelmts, hid_t type, void *_mem)
{
unsigned char *mem = (unsigned char*)_mem;
hsize_t i; /*element counter */
char *s, *section; /*a section of output */
int secnum; /*section sequence number */
size_t size; /*size of each datum */
size_t ncols = 80; /*available output width */
h5tools_str_t buffer; /*string into which to render */
int multiline; /*datum was multiline */
hsize_t curr_pos; /* total data element position */
int elmt_counter = 0;/*counts the # elements printed.
*I (ptl?) needed something that
*isn't going to get reset when a new
*line is formed. I'm going to use
*this var to count elements and
*break after we see a number equal
*to the ctx->size_last_dim. */
/* Setup */
memset(&buffer, 0, sizeof(h5tools_str_t));
size = H5Tget_size(type);
if (info->line_ncols > 0)
ncols = info->line_ncols;
h5tools_simple_prefix(stream, info, ctx, (hsize_t)0, 0);
for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) {
/* Render the element */
h5tools_str_reset(&buffer);
h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx);
if (i + 1 < nelmts || (flags & END_OF_DATA) == 0)
h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ","));
s = h5tools_str_fmt(&buffer, 0, "%s");
/*
* If the element would split on multiple lines if printed at our
* current location...
*/
if (info->line_multi_new == 1 &&
(ctx->cur_column + h5tools_ncols(s) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) > ncols) {
if (ctx->prev_multiline) {
/*
* ... and the previous element also occupied more than one
* line, then start this element at the beginning of a line.
*/
ctx->need_prefix = TRUE;
} else if ((ctx->prev_prefix_len + h5tools_ncols(s) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) <= ncols) {
/*
* ...but *could* fit on one line otherwise, then we
* should end the current line and start this element on its
* own line.
*/
ctx->need_prefix = TRUE;
}
}
/*
* We need to break after each row of a dimension---> we should
* break at the end of the each last dimension well that is the
* way the dumper did it before
*/
if (info->arr_linebreak && ctx->cur_elmt) {
if (ctx->size_last_dim && (ctx->cur_elmt % ctx->size_last_dim) == 0)
ctx->need_prefix = TRUE;
if ((hsize_t)elmt_counter == ctx->size_last_dim) {
ctx->need_prefix = TRUE;
elmt_counter = 0;
}
}
/*
* If the previous element occupied multiple lines and this element
* is too long to fit on a line then start this element at the
* beginning of the line.
*/
if (info->line_multi_new == 1 && ctx->prev_multiline &&
(ctx->cur_column + h5tools_ncols(s) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) > ncols)
ctx->need_prefix = TRUE;
/*
* If too many elements have already been printed then we need to
* start a new line.
*/
if (info->line_per_line > 0 && ctx->cur_elmt >= info->line_per_line)
ctx->need_prefix = TRUE;
/*
* Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause
* the data to split across multiple lines. We display the sections
* one-at a time.
*/
for (secnum = 0, multiline = 0;
(section = strtok(secnum ? NULL : s, OPTIONAL_LINE_BREAK));
secnum++) {
/*
* If the current section plus possible suffix and end-of-line
* information would cause the output to wrap then we need to
* start a new line.
*/
/*
* Added the info->skip_first because the dumper does not want
* this check to happen for the first line
*/
if ((!info->skip_first || i) &&
(ctx->cur_column + strlen(section) +
strlen(OPT(info->elmt_suf2, " ")) +
strlen(OPT(info->line_suf, ""))) > ncols)
ctx->need_prefix = 1;
/*
* Print the prefix or separate the beginning of this element
* from the previous element.
*/
if (ctx->need_prefix) {
if (secnum)
multiline++;
/* pass to the prefix the total position instead of the current
stripmine position i; this is necessary to print the array
indices */
curr_pos = ctx->sm_pos + i;
h5tools_simple_prefix(stream, info, ctx, curr_pos, secnum);
} else if ((i || ctx->continuation) && secnum == 0) {
fputs(OPT(info->elmt_suf2, " "), stream);
ctx->cur_column += strlen(OPT(info->elmt_suf2, " "));
}
/* Print the section */
fputs(section, stream);
ctx->cur_column += strlen(section);
}
ctx->prev_multiline = multiline;
}
h5tools_str_close(&buffer);
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Dump out a subset of a dataset.
* Description:
* Select a hyperslab from the dataset DSET using the parameters
* specified in SSET. Dump this out to STREAM.
* Return:
* On success, return SUCCEED. Otherwise, the function returns FAIL.
* Programmer:
* Bill Wendling, Wednesday, 07. March 2001
* Modifications:
*-------------------------------------------------------------------------
*/
static herr_t
h5tools_dump_simple_subset(FILE *stream, const h5dump_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 */
int i; /*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*/
/* Print info */
h5tools_context_t ctx; /*print context */
size_t p_type_nbytes; /*size of memory type */
/* 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 */
hsize_t count;
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 < ctx.ndims; i++)
ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(f_space, total_size, NULL);
assert(total_size[ctx.ndims - 1]==(hsize_t)((int)(total_size[ctx.ndims - 1])));
ctx.size_last_dim = (int)(total_size[ctx.ndims - 1]);
count = sset->count[ctx.ndims - 1];
sset->count[ctx.ndims - 1] = 1;
if(ctx.ndims>0)
init_acc_pos(&ctx,total_size);
for (; count > 0; sset->start[ctx.ndims - 1] += sset->stride[ctx.ndims - 1],
count--) {
/* calculate the potential number of elements we're going to print */
H5Sselect_hyperslab(f_space, H5S_SELECT_SET,
sset->start,
sset->stride,
sset->count,
sset->block);
sm_nelmts = H5Sget_select_npoints(f_space);
/*
* start (0, 0)
* block (2, 2)
* stride (15, 5)
* count (4, 3)
*
* make:
*
* for up to "count" times.
*
* start (0, += stride[last_dim])
* block (2, 2)
* stride (15, 5)
* count (4, 1)
*/
if (sm_nelmts == 0) {
/* nothing to print */
ret = SUCCEED;
goto done_close;
}
/*
* determine the strip mine size and allocate a buffer. the strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
if (ctx.ndims > 0)
for (i = ctx.ndims; i > 0; --i) {
sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
sm_nbytes *= sm_size[i - 1];
assert(sm_nbytes > 0);
}
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
sm_buf = malloc((size_t)sm_nelmts * p_type_nbytes);
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL);
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
H5Sclose(f_space);
H5Sclose(sm_space);
free(sm_buf);
return FAIL;
}
/* Print the data */
flags = START_OF_DATA;
if (count == 1)
flags |= END_OF_DATA;
for (i = 0; i < ctx.ndims; i++) {
ctx.p_max_idx[i] = ctx.p_min_idx[i] + MIN(total_size[i], sm_size[i]);
}
h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts,
p_type, sm_buf);
free(sm_buf);
ctx.continuation++;
}
/* Terminate the output */
if (ctx.cur_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
}
ret = SUCCEED;
done_close:
H5Sclose(f_space);
done:
return ret;
}
/*-------------------------------------------------------------------------
* Audience: Public
* Chapter: H5Tools Library
* Purpose: Print some values from a dataset with a simple data space.
* Description:
* This is a special case of h5tools_dump_dset(). This function only
* intended for dumping datasets -- it does strip mining and some other
* things which are unnecessary for smaller objects such as attributes
* (to print small objects like attributes simply read the attribute and
* call h5tools_dump_simple_mem()).
* Return:
* On success, the function returns SUCCEED. Otherwise, the function
* returns FAIL.
* Programmer:
* Robb Matzke, Thursday, July 23, 1998
* Modifications:
*-------------------------------------------------------------------------
*/
static int
h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset,
hid_t p_type, int indentlevel)
{
hid_t f_space; /*file data space */
hsize_t elmtno; /*counter */
int i; /*counter */
int carry; /*counter carry value */
hsize_t zero[8]; /*vector of zeros */
unsigned int flags; /*buffer extent flags */
hsize_t total_size[H5S_MAX_RANK];/*total size of dataset*/
/* Print info */
h5tools_context_t ctx; /*print context */
size_t p_type_nbytes; /*size of memory type */
hsize_t p_nelmts; /*total selected elmts */
/* Stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
hsize_t sm_nelmts; /*elements per stripmine*/
unsigned char *sm_buf = NULL; /*buffer for raw data */
hid_t sm_space; /*stripmine data space */
/* Hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
hsize_t hs_nelmts; /*elements in request */
/* VL data special information */
unsigned int vl_data = 0; /*contains VL datatypes */
f_space = H5Dget_space(dset);
if (f_space == FAIL)
return FAIL;
/*
* Check that everything looks okay. The dimensionality must not be too
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
memset(&ctx, 0, sizeof(ctx));
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
ctx.ndims = H5Sget_simple_extent_ndims(f_space);
if ((size_t)ctx.ndims > NELMTS(sm_size)) {
H5Sclose(f_space);
return FAIL;
}
/* Assume entire data space to be printed */
if (ctx.ndims > 0)
for (i = 0; i < ctx.ndims; i++)
ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(f_space, total_size, NULL);
/* calculate the number of elements we're going to print */
p_nelmts = 1;
if (ctx.ndims > 0) {
for (i = 0; i < ctx.ndims; i++)
p_nelmts *= total_size[i];
ctx.size_last_dim = (total_size[ctx.ndims - 1]);
} /* end if */
else
ctx.size_last_dim = 0;
if (p_nelmts == 0) {
/* nothing to print */
H5Sclose(f_space);
return SUCCEED;
}
/* Check if we have VL data in the dataset's datatype */
if (H5Tdetect_class(p_type, H5T_VLEN) == TRUE)
vl_data = TRUE;
/*
* Determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = p_type_nbytes = H5Tget_size(p_type);
if (ctx.ndims > 0) {
for (i = ctx.ndims; i > 0; --i) {
sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
sm_nbytes *= sm_size[i - 1];
assert(sm_nbytes > 0);
}
}
assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/
sm_buf = malloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
if(ctx.ndims>0)
init_acc_pos(&ctx,total_size);
/* The stripmine loop */
memset(hs_offset, 0, sizeof hs_offset);
memset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) {
/* Calculate the hyperslab size */
if (ctx.ndims > 0) {
for (i = 0, hs_nelmts = 1; i < ctx.ndims; i++) {
hs_size[i] = MIN(total_size[i] - hs_offset[i], sm_size[i]);
ctx.p_max_idx[i] = ctx.p_min_idx[i] + hs_size[i];
hs_nelmts *= hs_size[i];
}
H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL,
hs_size, NULL);
H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL,
&hs_nelmts, NULL);
} else {
H5Sselect_all(f_space);
H5Sselect_all(sm_space);
hs_nelmts = 1;
}
/* Read the data */
if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) {
H5Sclose(f_space);
H5Sclose(sm_space);
free(sm_buf);
return FAIL;
}
/* Print the data */
flags = (elmtno == 0) ? START_OF_DATA : 0;
flags |= ((elmtno + hs_nelmts) >= p_nelmts) ? END_OF_DATA : 0;
/* initialize the current stripmine position i; this is necessary to print the array
indices */
ctx.sm_pos = elmtno;
h5tools_dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts,
p_type, sm_buf);
/* Reclaim any VL memory, if necessary */
if(vl_data)
H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf);
/* Calculate the next hyperslab offset */
for (i = ctx.ndims, carry = 1; i > 0 && carry; --i) {
ctx.p_min_idx[i - 1] = ctx.p_max_idx[i - 1];
hs_offset[i - 1] += hs_size[i - 1];
if (hs_offset[i - 1] == total_size[i - 1])
hs_offset[i - 1] = 0;
else
carry = 0;
}
ctx.continuation++;
}
/* Terminate the output */
if (ctx.cur_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
}
H5Sclose(sm_space);
H5Sclose(f_space);
free(sm_buf);
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: h5tools_dump_simple_mem
*
* Purpose: Print some values from memory with a simple data space.
* This is a special case of h5tools_dump_mem().
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id,
hid_t type, hid_t space, void *mem, int indentlevel)
{
int i; /*counters */
hsize_t nelmts; /*total selected elmts */
h5tools_context_t ctx; /*printing context */
/*
* Check that everything looks okay. The dimensionality must not be too
* great and the dimensionality of the items selected for printing must
* match the dimensionality of the dataset.
*/
memset(&ctx, 0, sizeof(ctx));
ctx.ndims = H5Sget_simple_extent_ndims(space);
if ((size_t)ctx.ndims > NELMTS(ctx.p_min_idx))
return FAIL;
ctx.indent_level = indentlevel;
ctx.need_prefix = 1;
/* Assume entire data space to be printed */
for (i = 0; i < ctx.ndims; i++)
ctx.p_min_idx[i] = 0;
H5Sget_simple_extent_dims(space, ctx.p_max_idx, NULL);
for (i = 0, nelmts = 1; ctx.ndims != 0 && i < ctx.ndims; i++)
nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i];
if (nelmts == 0)
return SUCCEED; /*nothing to print*/
if(ctx.ndims>0) {
assert(ctx.p_max_idx[ctx.ndims - 1]==(hsize_t)((int)ctx.p_max_idx[ctx.ndims - 1]));
ctx.size_last_dim = (int)(ctx.p_max_idx[ctx.ndims - 1]);
} /* end if */
else
ctx.size_last_dim = 0;
if(ctx.ndims>0)
init_acc_pos(&ctx,ctx.p_max_idx);
/* Print it */
h5tools_dump_simple_data(stream, info, obj_id, &ctx,
START_OF_DATA | END_OF_DATA, nelmts, type, mem);
/* Terminate the output */
if (ctx.cur_column) {
fputs(OPT(info->line_suf, ""), stream);
putc('\n', stream);
fputs(OPT(info->line_sep, ""), stream);
}
return SUCCEED;
}
/*-------------------------------------------------------------------------
* Function: h5tools_dump_dset
*
* Purpose: Print some values from a dataset DSET to the file STREAM
* after converting all types to P_TYPE (which should be a
* native type). If P_TYPE is a negative value then it will be
* computed from the dataset type using only native types.
*
* Note: This function is intended only for datasets since it does
* some things like strip mining which are unnecessary for
* smaller objects such as attributes. The easiest way to print
* small objects is to read the object into memory and call
* h5tools_dump_mem().
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, July 23, 1998
*
* Modifications:
* Robb Matzke, 1999-06-07
* If info->raw is set then the memory datatype will be the same
* as the file datatype.
*
* Bill Wendling, 2001-02-27
* Renamed to ``h5tools_dump_dset'' and added the subsetting
* parameter.
*
*-------------------------------------------------------------------------
*/
int
h5tools_dump_dset(FILE *stream, const h5dump_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;
h5dump_t info_dflt;
/* Use default values */
if (!stream)
stream = stdout;
if (!info) {
memset(&info_dflt, 0, sizeof info_dflt);
info = &info_dflt;
}
if (p_type < 0) {
f_type = H5Dget_type(dset);
if (info->raw)
p_type = H5Tcopy(f_type);
else
p_type = h5tools_get_native_type(f_type);
H5Tclose(f_type);
if (p_type < 0)
goto done;
}
/* Check the data space */
f_space = H5Dget_space(dset);
space_type = H5Sget_simple_extent_type(f_space);
/* Print the data */
if (space_type == H5S_SIMPLE || space_type == H5S_SCALAR) {
if (!sset)
status = h5tools_dump_simple_dset(rawdatastream, info, dset, p_type,
indentlevel);
else
status = h5tools_dump_simple_subset(rawdatastream, info, dset, p_type,
sset, indentlevel);
} else /* space is H5S_NULL */
status = SUCCEED;
/* Close the dataspace */
H5Sclose(f_space);
done:
if (p_type != _p_type)
H5Tclose(p_type);
return status;
}
/*-------------------------------------------------------------------------
* Function: h5tools_dump_mem
*
* Purpose: Displays the data contained in MEM. MEM must have the
* specified data TYPE and SPACE. Currently only simple data
* spaces are allowed and only the `all' selection.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, January 20, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
h5tools_dump_mem(FILE *stream, const h5dump_t *info, hid_t obj_id, hid_t type,
hid_t space, void *mem, int indentlevel)
{
h5dump_t info_dflt;
/* Use default values */
if (!stream)
stream = stdout;
if (!info) {
memset(&info_dflt, 0, sizeof(info_dflt));
info = &info_dflt;
}
/* Check the data space */
if (H5Sis_simple(space) <= 0)
return -1;
return h5tools_dump_simple_mem(stream, info, obj_id, type, space, mem,
indentlevel);
}
/*-------------------------------------------------------------------------
* Function: init_acc_pos
*
* Purpose: initialize accumulator and matrix position
*
* Return: void
*
* Programmer: pvn
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void init_acc_pos(h5tools_context_t *ctx, hsize_t *dims)
{
int i;
assert(ctx->ndims);
ctx->acc[ctx->ndims-1]=1;
for(i=(ctx->ndims-2); i>=0; i--)
{
ctx->acc[i]=ctx->acc[i+1] * dims[i+1];
}
for ( i = 0; i < ctx->ndims; i++)
ctx->pos[i]=0;
}
Reference in New Issue View Git Blame Copy Permalink