mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2025-01-06 14:56:51 +08:00
Code Issues Packages Projects Releases Wiki Activity
357424423c
hdf5/tools/h5repack/h5repack.c
Jonathan Kim 50e3990f2a [svn-r22805] Purpose: 
HDFFV-8012 - h5repack changes max dims and cause failure if only "-f none" is used without changing layout for chunked dataset when a chunk dim is bigger than a dataset dim

Description:
    "h5repack -f <obj>:NONE <file.h5> out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than a dataset dim. 
    Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim. 
    These issue occurred when dataset size is smaller than 64k (compact size limit)
    Fixed them.

Tested: 
    jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE),  Windows (32-LE cmake), cmake (jam)
2012-09-24 18:13:57 -05:00

1015 lines
31 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"
/*-------------------------------------------------------------------------
* 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
*
* Algorithm: 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, H5F_file_space_type_t strategy,
hsize_t threshold)
{
int k, n;
HDmemset(options, 0, sizeof(pack_opt_t));
options->min_comp = 1024;
options->verbose = verbose;
options->layout_g = H5D_LAYOUT_ERROR;
for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
{
options->filter_g[n].filtn = -1;
options->filter_g[n].cd_nelmts = 0;
for ( k = 0; k < CD_VALUES; k++)
options->filter_g[n].cd_values[k] = 0;
}
options->fs_strategy = strategy;
options->fs_threshold = threshold;
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 */
if(NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
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("maximum number of filters exceeded for <%s>\n", str);
HDfree(obj_list);
return -1;
}
options->filter_g[n] = filter;
}
else
options_add_filter(obj_list, n_objs, filter, options->op_tbl);
HDfree(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("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 layout option */
options->layout_g = pack.layout;
/* no individual dataset specified */
if (options->all_layout==1 )
{
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];
}
}
}
/* individual dataset specified */
if (options->all_layout==0)
options_add_layout(obj_list,
n_objs,
&pack,
options->op_tbl);
HDfree(obj_list);
return 0;
}
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
* were located in h5repack_copy.c as static prior to bugfix1726.
* Made shared functions as copy_attr() was needed in h5repack_refs.c.
* However copy_attr() may be obsoleted when H5Acopy is available and put back
* others to static in h5repack_copy.c.
*/
/*-------------------------------------------------------------------------
* Function: copy_named_datatype
*
* Purpose: Copies the specified datatype anonymously, and returns an open
* id for that datatype in the output file. The first time this
* is called it scans every named datatype in travt into a
* private stack, afterwards it simply scans that stack. The id
* returned must be closed after it is no longer needed.
* named_datatype_free must be called before the program exits
* to free the stack.
*
* Programmer: Neil Fortner
*
* Date: April 14, 2009
*
*-------------------------------------------------------------------------
*/
hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info_t oinfo; /* Object info of input dtype */
hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
if(H5Oget_info(type_in, &oinfo) < 0)
goto error;
if(*named_dt_head_p)
{
/* Stack already exists, search for the datatype */
while(dt && dt->addr_in != oinfo.addr)
dt = dt->next;
dt_ret = dt;
}
else
{
/* Create the stack */
size_t i;
for(i=0; i<travt->nobjs; i++)
if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
{
/* Push onto the stack */
if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
goto error;
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
/* Update the address and id */
dt->addr_in = travt->objs[i].objno;
dt->id_out = -1;
/* Check if this type is the one requested */
if(oinfo.addr == dt->addr_in)
{
HDassert(!dt_ret);
dt_ret = dt;
} /* end if */
} /* end if */
} /* end else */
/* Handle the case that the requested datatype was not found. This is
* possible if the datatype was committed anonymously in the input file. */
if(!dt_ret)
{
/* Push the new datatype onto the stack */
if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
goto error;
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
/* Update the address and id */
dt_ret->addr_in = oinfo.addr;
dt_ret->id_out = -1;
} /* end if */
/* If the requested datatype does not yet exist in the output file, copy it
* anonymously */
if(dt_ret->id_out < 0)
{
if (options->use_native==1)
dt_ret->id_out = h5tools_get_native_type(type_in);
else
dt_ret->id_out = H5Tcopy(type_in);
if(dt_ret->id_out < 0)
goto error;
if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
} /* end if */
/* Set return value */
ret_value = dt_ret->id_out;
/* Increment the ref count on id_out, because the calling function will try
* to close it */
if(H5Iinc_ref(ret_value) < 0)
goto error;
return(ret_value);
error:
return(-1);
} /* end copy_named_datatype */
/*-------------------------------------------------------------------------
* Function: named_datatype_free
*
* Purpose: Frees the stack of named datatypes.
*
* Programmer: Neil Fortner
*
* Date: April 14, 2009
*
*-------------------------------------------------------------------------
*/
int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
{
named_dt_t *dt = *named_dt_head_p;
while(dt)
{
/* Pop the datatype off the stack and free it */
if(H5Tclose(dt->id_out) < 0 && !ignore_err)
goto error;
dt = dt->next;
HDfree(*named_dt_head_p);
*named_dt_head_p = dt;
} /* end while */
return 0;
error:
return -1;
} /* end named_datatype_free */
/*-------------------------------------------------------------------------
* Function: copy_attr
*
* Purpose: copy attributes located in LOC_IN, which is obtained either from
* loc_id = H5Gopen2( fid, name);
* loc_id = H5Dopen2( fid, name);
* loc_id = H5Topen2( fid, name);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
int copy_attr(hid_t loc_in,
hid_t loc_out,
named_dt_t **named_dt_head_p,
trav_table_t *travt,
pack_opt_t *options)
{
hid_t attr_id=-1; /* attr ID */
hid_t attr_out=-1; /* attr ID */
hid_t space_id=-1; /* space ID */
hid_t ftype_id=-1; /* file type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
void *buf = NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
htri_t is_named; /* Whether the datatype is named */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* object info */
int j;
unsigned u;
hbool_t is_ref=0;
H5T_class_t type_class = -1;
if(H5Oget_info(loc_in, &oinfo) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy all attributes
*-------------------------------------------------------------------------
*/
for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr_id, (size_t)255, name) < 0)
goto error;
/* get the file datatype */
if((ftype_id = H5Aget_type(attr_id)) < 0 )
goto error;
/* Check if the datatype is committed */
if((is_named = H5Tcommitted(ftype_id)) < 0)
goto error;
if(is_named && travt) {
hid_t fidout;
/* Create out file id */
if((fidout = H5Iget_file_id(loc_out)) < 0)
goto error;
/* Copy named dt */
if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
travt, options)) < 0)
{
H5Fclose(fidout);
goto error;
} /* end if */
if(H5Fclose(fidout) < 0)
goto error;
} /* end if */
else {
if(options->use_native == 1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
} /* end else */
/* get the dataspace handle */
if((space_id = H5Aget_space(attr_id)) < 0)
goto error;
/* get dimensions */
if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
goto error;
nelmts = 1;
for(j = 0; j < rank; j++)
nelmts *= dims[j];
if((msize = H5Tget_size(wtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case. We cannot just copy the buffers,
* but instead we recreate the reference.
* This is done on a second sweep of the file that just copies the referenced
* objects at copy_refs_attr()
*-------------------------------------------------------------------------
*/
type_class = H5Tget_class(wtype_id);
is_ref = (type_class == H5T_REFERENCE);
if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
H5Tclose(base_type);
}
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(wtype_id) ;
for (j=0; j<nmembers; j++) {
hid_t mtid = H5Tget_member_type( wtype_id, (unsigned) j );
H5T_class_t mtclass = H5Tget_class(mtid);
H5Tclose(mtid);
if (mtclass==H5T_REFERENCE) {
is_ref = 1;
break;
}
} /* for (j=0; i<nmembers; j++) */
} /* if (type_class == H5T_COMPOUND) */
if(is_ref) {
; /* handled by copy_refs_attr() */
}
else {
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
if(buf == NULL) {
error_msg("h5repack", "cannot read into memory\n" );
goto error;
} /* end if */
if(H5Aread(attr_id, wtype_id, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(H5Awrite(attr_out, wtype_id, buf) < 0)
goto error;
/*close*/
if(H5Aclose(attr_out) < 0)
goto error;
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
HDfree(buf);
buf = NULL;
} /*H5T_REFERENCE*/
if(options->verbose)
printf(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if(H5Tclose(ftype_id) < 0)
goto error;
if(H5Tclose(wtype_id) < 0)
goto error;
if(H5Sclose(space_id) < 0)
goto error;
if(H5Aclose(attr_id) < 0)
goto error;
} /* u */
return 0;
error:
H5E_BEGIN_TRY {
if(buf) {
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
/* Free buf */
HDfree(buf);
} /* end if */
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
} H5E_END_TRY;
return -1;
} /* end copy_attr() */
/*-------------------------------------------------------------------------
* 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;
case H5D_LAYOUT_ERROR:
case H5D_NLAYOUTS:
error_msg("invalid layout\n");
return -1;
default:
strcpy(slayout,"invalid layout\n");
return -1;
}
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("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;
default:
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("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("invalid maximum number of links to store as header messages\n");
return -1;
}
if (options->grp_indexed < 0)
{
error_msg("invalid minimum number of links to store in the indexed format\n");
return -1;
}
if (options->grp_indexed > options->grp_compact)
{
error_msg("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("invalid shared message size\n");
return -1;
}
}
/*--------------------------------------------------------------------------------
* verify new user userblock options; file name must be present
*---------------------------------------------------------------------------------
*/
if ( options->ublock_filename != NULL && options->ublock_size == 0 )
{
if ( options->verbose )
{
printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
options->ublock_filename);
options->ublock_size = 1024;
}
}
if ( options->ublock_filename == NULL && options->ublock_size != 0 )
{
error_msg("file name missing for user block\n",
options->ublock_filename);
return -1;
}
/*--------------------------------------------------------------------------------
* verify alignment options; threshold is zero default but alignment not
*---------------------------------------------------------------------------------
*/
if ( options->alignment == 0 && options->threshold != 0 )
{
error_msg("alignment for H5Pset_alignment missing\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("%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;
hsize_t csize = 1;
unsigned 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 *= 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 *= 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;
default:
break;
}
} /* i */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
H5Fclose(fid);
trav_table_free(travt);
return 0;
out:
H5Fclose(fid);
trav_table_free(travt);
return -1;
}
/*-------------------------------------------------------------------------
* 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("input error in filter type\n");
HDexit(EXIT_FAILURE);
}
}
Reference in New Issue View Git Blame Copy Permalink