mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2024-12-09 07:32:32 +08:00
Code Issues Packages Projects Releases Wiki Activity
1b645ffd91
hdf5/tools/h5repack/h5repack.c
Pedro Vicente Nunes 1b645ffd91 [svn-r14299] new feature: add support for h5repack to handle several global filters 
usage is to repeat the -f option

tested: windows, linux, solaris
2007-11-28 15:30:43 -05:00

716 lines
21 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "H5private.h"
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
extern char *progname;
/*-------------------------------------------------------------------------
* File: h5repack.c
* Purpose: Public API functions
*-------------------------------------------------------------------------
*/
static int check_options(pack_opt_t *options);
static int check_objects(const char* fname, pack_opt_t *options);
static const char* get_sfilter (H5Z_filter_t filtn);
static int have_request(pack_opt_t *options);
/*-------------------------------------------------------------------------
* Function: h5repack
*
* Purpose: locate all high-level HDF5 objects in the file
* and compress/chunk them using options
*
* Algorythm: 2 traversals are made to the file; the 1st builds a list of
* the objects, the 2nd makes a copy of them, using the options;
* the reason for the 1st traversal is to check for invalid
* object name requests
*
* Return: 0, ok, -1, fail
*
* Programmer: pvn@ncsa.uiuc.edu
*
* Date: September, 22, 2003
*
*-------------------------------------------------------------------------
*/
int h5repack(const char* infile,
const char* outfile,
pack_opt_t *options)
{
/* check input */
if (check_options(options)<0)
return -1;
/* check for objects in input that are in the file */
if (check_objects(infile,options) < 0)
return -1;
/* copy the objects */
if (copy_objects(infile,outfile,options) < 0)
return -1;
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5repack_init
*
* Purpose: initialize options
*
* Return: 0, ok, -1, fail
*
*-------------------------------------------------------------------------
*/
int h5repack_init (pack_opt_t *options,
int verbose)
{
int k, n;
memset(options,0,sizeof(pack_opt_t));
options->threshold = 1024;
options->verbose = verbose;
for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
{
options->filter_g[n].filtn = -1;
for ( k = 0; k < CDVALUES; k++)
options->filter_g[n].cd_values[k] = -1;
}
return (options_table_init(&(options->op_tbl)));
}
/*-------------------------------------------------------------------------
* Function: h5repack_end
*
* Purpose: free options table
*
*-------------------------------------------------------------------------
*/
int h5repack_end (pack_opt_t *options)
{
return options_table_free(options->op_tbl);
}
/*-------------------------------------------------------------------------
* Function: h5repack_addfilter
*
* Purpose: add a compression -f option to table
* Example: -f dset:GZIP=6
*
* Return: 0, ok, -1, fail
*
*-------------------------------------------------------------------------
*/
int h5repack_addfilter(const char* str,
pack_opt_t *options)
{
obj_list_t *obj_list=NULL; /* one object list for the -f and -l option entry */
filter_info_t filter; /* filter info for the current -f option entry */
int n_objs; /* number of objects in the current -f or -l option entry */
int is_glb; /* is the filter global */
/* parse the -f option */
obj_list=parse_filter(str,&n_objs,&filter,options,&is_glb);
if (obj_list==NULL)
{
return -1;
}
/* if it applies to all objects */
if (is_glb)
{
int n;
n = options->n_filter_g++; /* increase # of global filters */
if (options->n_filter_g > H5_REPACK_MAX_NFILTERS)
{
error_msg(progname, "maximum number of filters exceeded for <%s>\n",str);
return -1;
}
options->filter_g[n] = filter;
}
else
options_add_filter(obj_list,n_objs,filter,options->op_tbl);
free(obj_list);
return 0;
}
/*-------------------------------------------------------------------------
* Function: h5repack_addlayout
*
* Purpose: add a layout option
*
* Return: 0, ok, -1, fail
*
*-------------------------------------------------------------------------
*/
int h5repack_addlayout(const char* str,
pack_opt_t *options)
{
obj_list_t *obj_list=NULL; /*one object list for the -t and -c option entry */
int n_objs; /*number of objects in the current -t or -c option entry */
pack_info_t pack; /*info about layout to extract from parse */
int j;
init_packobject(&pack);
if (options->all_layout==1){
error_msg(progname, "invalid layout input: 'all' option \
is present with other objects <%s>\n",str);
return -1;
}
/* parse the layout option */
obj_list=parse_layout(str,&n_objs,&pack,options);
if (obj_list==NULL)
return -1;
/* set global layout option */
if (options->all_layout==1 )
{
options->layout_g=pack.layout;
if (pack.layout==H5D_CHUNKED)
{
/* -2 means the NONE option, remove chunking
and set the global layout to contiguous */
if (pack.chunk.rank==-2)
{
options->layout_g = H5D_CONTIGUOUS;
}
/* otherwise set the global chunking type */
else
{
options->chunk_g.rank=pack.chunk.rank;
for (j = 0; j < pack.chunk.rank; j++)
options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
}
}
}
if (options->all_layout==0)
options_add_layout(obj_list,
n_objs,
&pack,
options->op_tbl);
free(obj_list);
return 0;
}
/*-------------------------------------------------------------------------
* Function: check_options
*
* Purpose: print options, checks for invalid options
*
* Return: void, return -1 on error
*
* Programmer: pvn@ncsa.uiuc.edu
*
* Date: September, 22, 2003
*
* Modification:
* Peter Cao, July 9, 2007
* Add "-L, --latest" and other options to pack a file with the latest file format
*
*-------------------------------------------------------------------------
*/
static int check_options(pack_opt_t *options)
{
unsigned int i;
int k, j, has_cp=0, has_ck=0;
char slayout[30];
/*-------------------------------------------------------------------------
* objects to layout
*-------------------------------------------------------------------------
*/
if (options->verbose && have_request(options) /* only print if requested */)
{
printf("Objects to modify layout are...\n");
if (options->all_layout==1) {
switch (options->layout_g)
{
case H5D_COMPACT:
strcpy(slayout,"compact");
break;
case H5D_CONTIGUOUS:
strcpy(slayout,"contiguous");
break;
case H5D_CHUNKED:
strcpy(slayout,"chunked");
break;
default:
strcpy(slayout,"unknown");
break;
}
printf(" Apply %s layout to all\n", slayout);
if (H5D_CHUNKED==options->layout_g) {
printf("with dimension [");
for ( j = 0; j < options->chunk_g.rank; j++)
printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
printf("]\n");
}
}
}/* verbose */
for ( i = 0; i < options->op_tbl->nelems; i++)
{
char* name=options->op_tbl->objs[i].path;
if (options->op_tbl->objs[i].chunk.rank>0)
{
if (options->verbose){
printf(" <%s> with chunk size ",name);
for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
printf("\n");
}
has_ck=1;
}
else if (options->op_tbl->objs[i].chunk.rank==-2)
{
if (options->verbose)
printf(" <%s> %s\n",name,"NONE (contigous)");
has_ck=1;
}
}
if (options->all_layout==1 && has_ck){
error_msg(progname, "invalid chunking input: 'all' option\
is present with other objects\n");
return -1;
}
/*-------------------------------------------------------------------------
* objects to filter
*-------------------------------------------------------------------------
*/
if (options->verbose && have_request(options) /* only print if requested */)
{
printf("Objects to apply filter are...\n");
if (options->all_filter==1)
{
for (k = 0; k < options->n_filter_g; k++ )
{
H5Z_filter_t filtn=options->filter_g[k].filtn;
switch (filtn)
{
case H5Z_FILTER_NONE:
printf(" Uncompress all\n");
break;
case H5Z_FILTER_SHUFFLE:
case H5Z_FILTER_FLETCHER32:
printf(" All with %s\n",get_sfilter(filtn));
break;
case H5Z_FILTER_SZIP:
case H5Z_FILTER_DEFLATE:
printf(" All with %s, parameter %d\n",
get_sfilter(filtn),
options->filter_g[k].cd_values[0]);
break;
} /* k */
};
}
} /* verbose */
for ( i = 0; i < options->op_tbl->nelems; i++)
{
pack_info_t pack = options->op_tbl->objs[i];
char* name = pack.path;
for ( j=0; j<pack.nfilters; j++)
{
if (options->verbose)
{
printf(" <%s> with %s filter\n",
name,
get_sfilter(pack.filter[j].filtn));
}
has_cp=1;
} /* j */
} /* i */
if (options->all_filter==1 && has_cp){
error_msg(progname, "invalid compression input: 'all' option\
is present with other objects\n");
return -1;
}
/* check options for the latest format */
if (options->grp_compact < 0) {
error_msg(progname, "invalid maximum number of links to store as header messages\n");
return -1;
}
if (options->grp_indexed < 0) {
error_msg(progname, "invalid minimum number of links to store in the indexed format\n");
return -1;
}
if (options->grp_indexed > options->grp_compact) {
error_msg(progname, "minimum indexed size is greater than the maximum compact size\n");
return -1;
}
for (i=0; i<8; i++) {
if (options->msg_size[i]<0) {
error_msg(progname, "invalid shared message size\n");
return -1;
}
}
return 0;
}
/*-------------------------------------------------------------------------
* Function: check_objects
*
* Purpose: locate all HDF5 objects in the file and compare with user
* supplied list
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: September, 23, 2003
*
*-------------------------------------------------------------------------
*/
static int check_objects(const char* fname,
pack_opt_t *options)
{
hid_t fid;
unsigned int i;
trav_table_t *travt = NULL;
/* nothing to do */
if(options->op_tbl->nelems == 0)
return 0;
/*-------------------------------------------------------------------------
* open the file
*-------------------------------------------------------------------------
*/
if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0){
printf("<%s>: %s\n", fname, H5FOPENERROR );
return -1;
}
/*-------------------------------------------------------------------------
* get the list of objects in the file
*-------------------------------------------------------------------------
*/
/* init table */
trav_table_init(&travt);
/* get the list of objects in the file */
if(h5trav_gettable(fid, travt) < 0)
goto out;
/*-------------------------------------------------------------------------
* compare with user supplied list
*-------------------------------------------------------------------------
*/
if(options->verbose)
printf("Opening file <%s>. Searching for objects to modify...\n", fname);
for(i = 0; i < options->op_tbl->nelems; i++) {
char* name=options->op_tbl->objs[i].path;
if(options->verbose)
printf(" <%s>",name);
/* the input object names are present in the file and are valid */
if(h5trav_getindext(name, travt) < 0) {
error_msg(progname, "%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose?"\n":""),name,fname);
goto out;
}
if(options->verbose)
printf("...Found\n");
/* check for extra filter conditions */
switch(options->op_tbl->objs[i].filter->filtn) {
/* chunk size must be smaller than pixels per block */
case H5Z_FILTER_SZIP:
{
int j;
int csize = 1;
int ppb = options->op_tbl->objs[i].filter->cd_values[0];
hsize_t dims[H5S_MAX_RANK];
int rank;
hid_t did;
hid_t sid;
if(options->op_tbl->objs[i].chunk.rank > 0) {
rank = options->op_tbl->objs[i].chunk.rank;
for(j = 0; j < rank; j++)
csize *= (int)options->op_tbl->objs[i].chunk.chunk_lengths[j];
}
else {
if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
goto out;
if((sid = H5Dget_space(did)) < 0)
goto out;
if((rank = H5Sget_simple_extent_ndims(sid)) < 0)
goto out;
HDmemset(dims, 0, sizeof dims);
if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
goto out;
for(j = 0; j < rank; j++)
csize *= (int)dims[j];
if(H5Sclose(sid) < 0)
goto out;
if(H5Dclose(did) < 0)
goto out;
}
if (csize < ppb ) {
printf(" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
goto out;
}
}
break;
}
} /* i */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
H5Fclose(fid);
trav_table_free(travt);
return 0;
out:
H5Fclose(fid);
trav_table_free(travt);
return -1;
}
/*-------------------------------------------------------------------------
* Function: read_info
*
* Purpose: read comp and chunk options from file
*
* Return: void, exit on error
*
* Programmer: pvn@ncsa.uiuc.edu
*
* Date: September, 22, 2003
*
*-------------------------------------------------------------------------
*/
void read_info(const char *filename,
pack_opt_t *options)
{
char stype[10];
char comp_info[1024];
FILE *fp;
char c;
int i, rc=1;
char *srcdir = getenv("srcdir"); /* the source directory */
char data_file[512]=""; /* buffer to hold name of existing file */
/* compose the name of the file to open, using the srcdir, if appropriate */
if (srcdir){
strcpy(data_file,srcdir);
strcat(data_file,"/");
}
strcat(data_file,filename);
if ((fp = fopen(data_file, "r")) == (FILE *)NULL) {
error_msg(progname, "cannot open options file %s\n", filename);
exit(1);
}
/* cycle until end of file reached */
while( 1 )
{
rc=fscanf(fp, "%s", stype);
if (rc==-1)
break;
/*-------------------------------------------------------------------------
* filter
*-------------------------------------------------------------------------
*/
if (strcmp(stype,"-f") == 0) {
/* find begining of info */
i=0; c='0';
while( c!=' ' )
{
fscanf(fp, "%c", &c);
if (feof(fp)) break;
}
c='0';
/* go until end */
while( c!=' ' )
{
fscanf(fp, "%c", &c);
comp_info[i]=c;
i++;
if (feof(fp)) break;
if (c==10 /*eol*/) break;
}
comp_info[i-1]='\0'; /*cut the last " */
if (h5repack_addfilter(comp_info,options)==-1){
error_msg(progname, "could not add compression option\n");
exit(1);
}
}
/*-------------------------------------------------------------------------
* layout
*-------------------------------------------------------------------------
*/
else if (strcmp(stype,"-l") == 0) {
/* find begining of info */
i=0; c='0';
while( c!=' ' )
{
fscanf(fp, "%c", &c);
if (feof(fp)) break;
}
c='0';
/* go until end */
while( c!=' ' )
{
fscanf(fp, "%c", &c);
comp_info[i]=c;
i++;
if (feof(fp)) break;
if (c==10 /*eol*/) break;
}
comp_info[i-1]='\0'; /*cut the last " */
if (h5repack_addlayout(comp_info,options)==-1){
error_msg(progname, "could not add chunck option\n");
exit(1);
}
}
/*-------------------------------------------------------------------------
* not valid
*-------------------------------------------------------------------------
*/
else {
error_msg(progname, "bad file format for %s", filename);
exit(1);
}
}
fclose(fp);
return;
}
/*-------------------------------------------------------------------------
* Function: have_request
*
* Purpose: check if a filter or layout was requested
*
* Return: 1 yes, 0 no
*
* Date: May, 24, 2007
*
*-------------------------------------------------------------------------
*/
static int have_request(pack_opt_t *options)
{
if (options->all_filter || options->all_layout || options->op_tbl->nelems)
return 1;
return 0;
}
/*-------------------------------------------------------------------------
* Function: get_sfilter
*
* Purpose: return the filter as a string name
*
* Return: name of filter, exit on error
*
*-------------------------------------------------------------------------
*/
static const char* get_sfilter(H5Z_filter_t filtn)
{
if (filtn==H5Z_FILTER_NONE)
return "NONE";
else if (filtn==H5Z_FILTER_DEFLATE)
return "GZIP";
else if (filtn==H5Z_FILTER_SZIP)
return "SZIP";
else if (filtn==H5Z_FILTER_SHUFFLE)
return "SHUFFLE";
else if (filtn==H5Z_FILTER_FLETCHER32)
return "FLETCHER32";
else if (filtn==H5Z_FILTER_NBIT)
return "NBIT";
else if (filtn==H5Z_FILTER_SCALEOFFSET)
return "SOFF";
else {
error_msg(progname, "input error in filter type\n");
exit(1);
}
return NULL;
}
Reference in New Issue View Git Blame Copy Permalink