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hdf5/tools/h5jam/h5jam.c
Dana Robinson aa4fc58ac9 [svn-r28599] Normalization of tools with revise_chunks. 
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
           serial only, autotools and CMake (3.3.2)
2015-12-11 14:14:43 -05:00

559 lines
15 KiB
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "hdf5.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */
#define PROGRAMNAME "h5jam"
hsize_t write_pad (int, hsize_t);
hsize_t compute_user_block_size (hsize_t);
hsize_t copy_some_to_file (int, int, hsize_t, hsize_t, ssize_t);
void parse_command_line (int, const char *[]);
int do_clobber = FALSE;
char *output_file = NULL;
char *input_file = NULL;
char *ub_file = NULL;
/*
* Command-line options: The user can specify short or long-named
* parameters. The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
static const char *s_opts = "hi:u:o:c:V"; /* add more later ? */
static struct long_options l_opts[] = {
{"help", no_arg, 'h'},
{"hel", no_arg, 'h'},
{"i", require_arg, 'i'}, /* input file */
{"u", require_arg, 'u'}, /* user block file */
{"o", require_arg, 'o'}, /* output file */
{"clobber", no_arg, 'c'}, /* clobber existing UB */
{"clobbe", no_arg, 'c'},
{"clobb", no_arg, 'c'},
{"clob", no_arg, 'c'},
{"clo", no_arg, 'c'},
{"cl", no_arg, 'c'},
{NULL, 0, '\0'}
};
/*-------------------------------------------------------------------------
* Function: usage
*
* Purpose: Print the usage message
*
* Return: void
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
usage (const char *prog)
{
HDfflush (stdout);
HDfprintf (stdout,
"usage: %s -i <in_file.h5> -u <in_user_file> [-o <out_file.h5>] [--clobber]\n", prog);
HDfprintf (stdout, "\n");
HDfprintf (stdout,
"Adds user block to front of an HDF5 file and creates a new concatenated file.\n");
HDfprintf (stdout, "\n");
HDfprintf (stdout,
"OPTIONS\n");
HDfprintf (stdout,
" -i in_file.h5 Specifies the input HDF5 file.\n");
HDfprintf (stdout,
" -u in_user_file Specifies the file to be inserted into the user block.\n");
HDfprintf (stdout,
" Can be any file format except an HDF5 format.\n");
HDfprintf (stdout,
" -o out_file.h5 Specifies the output HDF5 file.\n");
HDfprintf (stdout,
" If not specified, the user block will be concatenated in\n");
HDfprintf (stdout,
" place to the input HDF5 file.\n");
HDfprintf (stdout,
" --clobber Wipes out any existing user block before concatenating\n");
HDfprintf (stdout,
" the given user block.\n");
HDfprintf (stdout,
" The size of the new user block will be the larger of;\n");
HDfprintf (stdout,
" - the size of existing user block in the input HDF5 file\n");
HDfprintf (stdout,
" - the size of user block required by new input user file\n");
HDfprintf (stdout,
" (size = 512 x 2N, N is positive integer.)\n");
HDfprintf (stdout, "\n");
HDfprintf (stdout,
" -h Prints a usage message and exits.\n");
HDfprintf (stdout,
" -V Prints the HDF5 library version and exits.\n");
HDfprintf (stdout, "\n");
HDfprintf (stdout,
"Exit Status:\n");
HDfprintf (stdout,
" 0 Succeeded.\n");
HDfprintf (stdout,
" >0 An error occurred.\n");
}
/*-------------------------------------------------------------------------
* Function: leave
*
* Purpose: Shutdown and call exit()
*
* Return: Does not return
*
*-------------------------------------------------------------------------
*/
static void
leave(int ret)
{
if (ub_file)
HDfree (ub_file);
if (input_file)
HDfree (input_file);
if (output_file)
HDfree (output_file);
h5tools_close();
HDexit(ret);
}
/*-------------------------------------------------------------------------
* Function: parse_command_line
*
* Purpose: Parse the command line for the h5dumper.
*
* Return: Success:
*
* Failure: Exits program with EXIT_FAILURE value.
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
parse_command_line (int argc, const char *argv[])
{
int opt = FALSE;
/* parse command line options */
while ((opt = get_option (argc, argv, s_opts, l_opts)) != EOF)
{
switch ((char) opt)
{
case 'o':
output_file = HDstrdup (opt_arg);
break;
case 'i':
input_file = HDstrdup (opt_arg);
break;
case 'u':
ub_file = HDstrdup (opt_arg);
break;
case 'c':
do_clobber = TRUE;
break;
case 'h':
usage (h5tools_getprogname());
leave (EXIT_SUCCESS);
case 'V':
print_version (h5tools_getprogname());
leave (EXIT_SUCCESS);
case '?':
default:
usage (h5tools_getprogname());
leave (EXIT_FAILURE);
}
}
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: HDF5 user block jammer
*
* Return: Success: 0
* Failure: 1
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main (int argc, const char *argv[])
{
int ufid = -1;
int h5fid = -1;
int ofid = -1;
void *edata;
H5E_auto2_t func;
hid_t ifile = -1;
hid_t plist = -1;
herr_t status;
htri_t testval;
hsize_t usize;
hsize_t h5fsize;
hsize_t startub;
hsize_t where;
hsize_t newubsize;
off_t fsize;
h5_stat_t sbuf;
h5_stat_t sbuf2;
int res;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
parse_command_line (argc, argv);
if (ub_file == NULL) {
/* no user block */
error_msg("missing arguemnt for -u <user_file>.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
testval = H5Fis_hdf5 (ub_file);
if (testval > 0) {
error_msg("-u <user_file> cannot be HDF5 file, but it appears to be an HDF5 file.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
if (input_file == NULL) {
error_msg("missing arguemnt for -i <HDF5 file>.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
testval = H5Fis_hdf5 (input_file);
if (testval <= 0) {
error_msg("Input HDF5 file \"%s\" is not HDF5 format.\n", input_file);
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
ifile = H5Fopen (input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
if (ifile < 0) {
error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
leave (EXIT_FAILURE);
}
plist = H5Fget_create_plist (ifile);
if (plist < 0) {
error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
H5Fclose(ifile);
leave (EXIT_FAILURE);
}
status = H5Pget_userblock (plist, &usize);
if (status < 0) {
error_msg("Can't get user block for file \"%s\"\n", input_file);
H5Pclose(plist);
H5Fclose(ifile);
leave (EXIT_FAILURE);
}
H5Pclose(plist);
H5Fclose(ifile);
ufid = HDopen(ub_file, O_RDONLY, 0);
if(ufid < 0) {
error_msg("unable to open user block file \"%s\"\n", ub_file);
leave (EXIT_FAILURE);
}
res = HDfstat(ufid, &sbuf);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", ub_file);
HDclose (ufid);
leave (EXIT_FAILURE);
}
fsize = (off_t)sbuf.st_size;
h5fid = HDopen(input_file, O_RDONLY, 0);
if(h5fid < 0) {
error_msg("unable to open HDF5 file for read \"%s\"\n", input_file);
HDclose (ufid);
leave (EXIT_FAILURE);
}
res = HDfstat(h5fid, &sbuf2);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", input_file);
HDclose (h5fid);
HDclose (ufid);
leave (EXIT_FAILURE);
}
h5fsize = (hsize_t)sbuf2.st_size;
if (output_file == NULL) {
ofid = HDopen (input_file, O_WRONLY, 0);
if (ofid < 0) {
error_msg("unable to open output file \"%s\"\n", output_file);
HDclose (h5fid);
HDclose (ufid);
leave (EXIT_FAILURE);
}
}
else {
ofid = HDopen (output_file, O_WRONLY | O_CREAT | O_TRUNC, 0644);
if (ofid < 0) {
error_msg("unable to create output file \"%s\"\n", output_file);
HDclose (h5fid);
HDclose (ufid);
leave (EXIT_FAILURE);
}
}
newubsize = compute_user_block_size ((hsize_t) fsize);
startub = usize;
if (usize > 0) {
if (do_clobber == TRUE) {
/* where is max of the current size or the new UB */
if (usize > newubsize) {
newubsize = usize;
}
startub = 0; /*blast the old */
}
else {
/* add new ub to current ublock, pad to new offset */
newubsize += usize;
newubsize = compute_user_block_size ((hsize_t) newubsize);
}
}
/* copy the HDF5 from starting at usize to starting at newubsize:
* makes room at 'from' for new ub */
/* if no current ub, usize is 0 */
copy_some_to_file (h5fid, ofid, usize, newubsize, (ssize_t) (h5fsize - usize));
/* copy the old ub to the beginning of the new file */
if (!do_clobber) {
where = copy_some_to_file (h5fid, ofid, (hsize_t) 0, (hsize_t) 0, (ssize_t) usize);
}
/* copy the new ub to the end of the ub */
where = copy_some_to_file (ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1);
/* pad the ub */
where = write_pad (ofid, where);
if(ub_file)
HDfree (ub_file);
if(input_file)
HDfree (input_file);
if(output_file)
HDfree (output_file);
if(ufid >= 0)
HDclose (ufid);
if(h5fid >= 0)
HDclose (h5fid);
if(ofid >= 0)
HDclose (ofid);
return h5tools_getstatus();
}
/*-------------------------------------------------------------------------
* Function: copy_some_to_file
*
* Purpose: Copy part of the input file to output.
* infid: fd of file to read
* outfid: fd of file to write
* startin: offset of where to read from infid
* startout: offset of where to write to outfid
* limit: bytes to read/write
*
* If limit is < 0, the entire input file is copied.
*
* Note: this routine can be used to copy within
* the same file, i.e., infid and outfid can be the
* same file.
*
* Return: Success: last byte written in the output.
* Failure: Exits program with EXIT_FAILURE value.
*
*-------------------------------------------------------------------------
*/
hsize_t
copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
ssize_t limit)
{
char buf[1024];
h5_stat_t sbuf;
int res;
ssize_t tot = 0;
ssize_t howmuch = 0;
ssize_t nchars = -1;
ssize_t to;
ssize_t from;
ssize_t toend;
ssize_t fromend;
if(startin > startout) {
/* this case is prohibited */
error_msg("copy_some_to_file: panic: startin > startout?\n");
exit (EXIT_FAILURE);
} /* end if */
if(limit < 0) {
res = HDfstat(infid, &sbuf);
if(res < 0) {
error_msg("Can't stat file \n");
HDexit(EXIT_FAILURE);
} /* end if */
howmuch = (ssize_t)sbuf.st_size;
} else {
howmuch = limit;
} /* end if */
if(0 == howmuch)
return 0;
toend = (ssize_t) startout + howmuch;
fromend = (ssize_t) startin + howmuch;
if (howmuch > 512) {
to = toend - 512;
from = fromend - 512;
} else {
to = toend - howmuch;
from = fromend - howmuch;
} /* end if */
while (howmuch > 0) {
HDlseek(outfid, (off_t) to, SEEK_SET);
HDlseek(infid, (off_t) from, SEEK_SET);
if (howmuch > 512) {
nchars = HDread(infid, buf, (unsigned) 512);
} else {
nchars = HDread(infid, buf, (unsigned)howmuch);
} /* end if */
if (nchars <= 0) {
error_msg("Read error \n");
HDexit(EXIT_FAILURE);
} /* end if */
if(HDwrite (outfid, buf, (unsigned) nchars) < 0) {
error_msg("Write error \n");
HDexit(EXIT_FAILURE);
}
tot += nchars;
howmuch -= nchars;
if(howmuch > 512) {
to -= nchars;
from -= nchars;
} else {
to -= howmuch;
from -= howmuch;
} /* end if */
} /* end while */
return (hsize_t)tot + (hsize_t)startout;
} /* end copy_some_to_file() */
/*-------------------------------------------------------------------------
* Function: compute_user_block_size
*
* Purpose: Find the offset of the HDF5 header after the user block:
* align at 0, 512, 1024, etc.
* ublock_size: the size of the user block (bytes).
*
* Return: Success: the location of the header == the size of the
* padded user block.
* Failure: none
*
* Return: Success: last byte written in the output.
* Failure: Exits program with EXIT_FAILURE value.
*-------------------------------------------------------------------------
*/
H5_ATTR_CONST hsize_t
compute_user_block_size(hsize_t ublock_size)
{
hsize_t where = 512;
if(0 == ublock_size)
return 0;
while(where < ublock_size)
where *= 2;
return where;
} /* end compute_user_block_size() */
/*
* Write zeroes to fill the file from 'where' to 512, 1024, etc. bytes.
*
* Returns the size of the padded file.
*/
hsize_t
write_pad(int ofile, hsize_t where)
{
unsigned int i;
char buf[1];
hsize_t psize;
buf[0] = '\0';
HDlseek(ofile, (off_t) where, SEEK_SET);
psize = compute_user_block_size (where);
psize -= where;
for(i = 0; i < psize; i++)
HDwrite (ofile, buf, 1);
return(where + psize); /* the new size of the file. */
}
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